Functions for point and interval estimation in
	     error-in-variables models via total least squares or
	     generalized total least squares method. See Golub and Van
	     Loan (1980) <doi:10.1137/0717073>, Gleser (1981)
	     <https://www.jstor.org/stable/2240867>, Ivan Markovsky
	     and Huffel (2007) <doi:10.1016/j.sigpro.2007.04.004> for
	     more information.
An implementation of the blocking algorithm transitive locality-sensitive hashing (TLSH) in Steorts, Ventura, Sadinle, Fienberg (2014) <DOI:10.1007/978-3-319-11257-2_20>, which is a k-means variant of locality sensitive hashing. The method is illustrated with examples and a vignette.
A framework for text mining applications within R.
This package provides a tm Source to create corpora from
  a corpus prepared in the format used by the Alceste application (i.e.
  a single text file with inline meta-data). It is able to import both
  text contents and meta-data (starred) variables.
A plug-in for the text mining framework tm to support text mining 
             in a distributed way. The package provides a convenient interface for
             handling distributed corpus objects based on distributed list objects.
Provides a 'tm' Source to create corpora from
  articles exported from the 'Europresse' content provider as
  HTML files. It is able to read both text content and meta-data
  information (including source, date, title, author and pages).
Provides a 'tm' Source to create corpora from
  articles exported from the Dow Jones 'Factiva' content provider as
  XML or HTML files. It is able to read both text content and meta-data
  information (including source, date, title, author, subject,
  geographical coverage, company, industry, and various
  provider-specific fields).
Enhances 'koRpus' text object classes and methods to also support large
          corpora. Hierarchical ordering of corpus texts into arbitrary categories will
          be preserved. Provided classes and methods also improve the ability of using
          the 'koRpus' package together with the 'tm' package. To ask for help, report
          bugs, suggest feature improvements, or discuss the global development of the
          package, please subscribe to the koRpus-dev mailing list
          (<https://korpusml.reaktanz.de>).
Provides a 'tm' Source to create corpora from
  articles exported from the 'LexisNexis' content provider as
  HTML files. It is able to read both text content and meta-data
  information (including source, date, title, author and pages).
  Note that the file format is highly unstable: there is no warranty
  that this package will work for your corpus, and you may have
  to adjust the code to adapt it to your particular format.
A plug-in for the tm text mining framework providing mail handling
  functionality.
Facilitate text retrieval from feed
    formats like XML (RSS, ATOM) and JSON. Also direct retrieval from
    HTML is supported. As most (news) feeds only incorporate small
    fractions of the original text tm.plugin.webmining even retrieves
    and extracts the text of the original text source.
Useful functions to connect to 'TM1' <https://www.ibm.com/uk-en/products/planning-and-analytics> instance from R via REST API. With the functions in the package, data can be imported from 'TM1' via mdx view or native view, data can be sent to 'TM1', processes and chores can be executed, and cube and dimension metadata information can be taken.
Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.
Set of tools for reading and processing spatial data. The aim is to supply the workflow to create thematic maps. This package also facilitates 'tmap', the package for visualizing thematic maps.
With this tool, a user should be able to quickly implement
    complex random effect models through simple C++ templates. The package combines
    'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector
    library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain
    an efficient implementation of the applied Laplace approximation with exact
    derivatives. Key features are: Automatic sparseness detection, parallelism
    through 'BLAS' and parallel user templates.
Enables all 'rstan' functionality for a 'TMB' model object, in particular MCMC sampling and chain visualization. Sampling can be performed with or without Laplace approximation for the random effects.
A Text mining toolkit for Chinese, which includes facilities for 
    Chinese string processing, Chinese NLP supporting, encoding detecting and 
    converting. Moreover, it provides some functions to support 'tm' package 
    in Chinese.
Provides an R-interface to the TMDb API (see TMDb API on <https://developers.themoviedb.org/3/getting-started/introduction>). The Movie Database (TMDb) is a popular user editable database for movies and TV shows (see <https://www.themoviedb.org>).
Random number generation of truncated multivariate Gaussian distributions using Hamiltonian Monte Carlo. The truncation is defined using linear and/or quadratic polynomials.
Predicting the topology of membrane proteins is part of
    the field of computational biology.
    'TMHMM' is a program to predict transmembrane helices in proteins. 
    'TMHMM' can be called from a website and/or locally using Bash. 
    This package allows to install and call TMHMM from R and parse its results.
Miscellaneous utility functions for data manipulation,
    data tidying, and working with gene expression data.
Targeted maximum likelihood estimation of point treatment effects (Targeted Maximum Likelihood Learning, The International Journal of Biostatistics, 2(1), 2006.  This version automatically estimates the additive treatment effect among the treated (ATT) and among the controls (ATC).  The tmle() function calculates the adjusted marginal difference in mean outcome associated with a binary point treatment, for continuous or binary outcomes.  Relative risk and odds ratio estimates are also reported for binary outcomes. Missingness in the outcome is allowed, but not in treatment assignment or baseline covariate values.  The population mean is calculated when there is missingness, and no variation in the treatment assignment. The tmleMSM() function estimates the parameters of a marginal structural model for a binary point treatment effect. Effect estimation stratified by a binary mediating variable is also available. An ID argument can be used to identify repeated measures. Default settings call 'SuperLearner' to estimate the Q and g portions of the likelihood, unless values or a user-supplied regression function are passed in as arguments.
Targeted minimum loss estimation (TMLE) of a non-parametric variable importance measure of a continuous exposure 'X' on an outcome 'Y', taking baseline covariates 'W' into account.
Methods and feature set definitions for feature or gene set
  enrichment analysis in transcriptional and metabolic profiling data.
  Package includes tests for enrichment based on ranked lists of features,
  functions for visualisation and multivariate functional analysis.
Trauma Mortality prediction for ICD-9, ICD-10, and AIS lexicons in
    long or wide format based on Dr. Alan Cook's tmpm mortality model.
Provides conditional maximum likelihood (CML) estimation of item parameters in multistage designs (Zwitser & Maris, 2013, <doi:10.1007/s11336-013-9369-6>) and CML estimation for conventional designs. Additional features are the likelihood ratio test (Andersen, 1973, <doi:10.1007/BF02291180>) and simulation of multistage designs.
Create, control, and capture 'tmux' sessions, windows, and panes
    using a pipeable API.
Efficient sampling of truncated multivariate (scale) mixtures of normals under linear inequality constraints is nontrivial due to the analytically intractable normalizing constant. Meanwhile, traditional methods may subject to numerical issues, especially when the dimension is high and dependence is strong.    Algorithms proposed by Li and Ghosh (2015) <doi: 10.1080/15598608.2014.996690> are adopted for overcoming difficulties in simulating truncated distributions. Efficient rejection sampling for simulating truncated univariate normal distribution is included in the package, which shows superiority in terms of acceptance rate and numerical stability compared to existing methods and R packages. An efficient function for sampling from truncated multivariate normal distribution subject to convex polytope restriction regions based on Gibbs sampler for conditional truncated univariate distribution is provided. By extending the sampling method, a function for sampling truncated multivariate Student's t distribution is also developed.     Moreover, the proposed method and computation remain valid for high dimensional and strong dependence scenarios. Empirical results in Li and Ghosh (2015) <doi: 10.1080/15598608.2014.996690> illustrated the superior performance in terms of various criteria (e.g. mixing and integrated auto-correlation time).
Importance sampling from the truncated multivariate normal using the GHK (Geweke-Hajivassiliou-Keane) simulator.
  Unlike Gibbs sampling which can get stuck in one truncation sub-region depending on initial values, this package allows 
  truncation based on disjoint regions that are created by truncation of absolute values. The GHK algorithm uses simple Cholesky
  transformation followed by recursive simulation of univariate truncated normals hence there are also no convergence issues. 
  Importance sample is returned along with sampling weights, based on which, one can calculate integrals over truncated regions
  for multivariate normals.
Random number generation for the truncated multivariate normal and Student t distribution. 
  Computes probabilities, quantiles and densities, 
  including one-dimensional and bivariate marginal densities. Computes first and second moments (i.e. mean and covariance matrix) for the double-truncated multinormal case.
Node centrality measures for temporal networks. Available measures are temporal degree centrality, temporal closeness centrality and temporal betweenness centrality defined by Kim and Anderson (2012) <doi:10.1103/PhysRevE.85.026107>. Applying the REN algorithm by Hanke and Foraita (2017) <doi:10.1186/s12859-017-1677-x> when calculating the centrality measures keeps the computational running time linear in the number of graph snapshots. Further, all methods can run in parallel up to the number of nodes in the network.
Binary ties limit the richness of network analyses as relations are unique. The two-mode structure contains a number of features lost when projection it to a one-mode network. Longitudinal datasets allow for an understanding of the causal relationship among ties, which is not the case in cross-sectional datasets as ties are dependent upon each other.
Construction of the Total Operating Characteristic (TOC) Curve and the Receiver (aka Relative) Operating Characteristic (ROC) Curve for spatial and non-spatial data. The TOC method is a modification of the ROC method which measures the ability of an index variable to diagnose either presence or absence of a characteristic. The diagnosis depends on whether the value of an index variable is above a threshold. Each threshold generates a two-by-two contingency table, which contains four entries: hits (H), misses (M), false alarms (FA), and correct rejections (CR). While ROC shows for each threshold only two ratios, H/(H + M) and FA/(FA + CR), TOC reveals the size of every entry in the contingency table for each threshold (Pontius Jr., R.G., Si, K. 2014. <doi:10.1080/13658816.2013.862623>).
This is a simple addin to 'RStudio' that finds all 'TODO', 'FIX ME', 'CHANGED' etc. comments in your project and shows them as a markers list.
Use the <http://toggl.com> time tracker api through R.
Approximations of global p-values when testing hypothesis in presence of non-identifiable nuisance parameters. The method relies on the Euler characteristic heuristic and the expected Euler characteristic is efficiently computed by  in Algeri and van Dyk (2018) <arXiv:1803.03858>.
Create browsers for reading full texts from a token list format.
    Information obtained from text analyses (e.g., topic modeling, word scaling)
    can be used to annotate the texts.
Convert natural language text into tokens. Includes tokenizers for
    shingled n-grams, skip n-grams, words, word stems, sentences, paragraphs,
    characters, shingled characters, lines, tweets, Penn Treebank, regular
    expressions, as well as functions for counting characters, words, and sentences,
    and a function for splitting longer texts into separate documents, each with
    the same number of words.  The tokenizers have a consistent interface, and
    the package is built on the 'stringi' and 'Rcpp' packages for  fast
    yet correct tokenization in 'UTF-8'.
Unsupervised text tokenizer focused on computational efficiency. Wraps the 'YouTokenToMe' library <https://github.com/VKCOM/YouTokenToMe> which is an implementation of fast Byte Pair Encoding (BPE) <https://www.aclweb.org/anthology/P16-1162>.
Statistical tolerance limits provide the limits between which we can expect to find a specified proportion of a sampled population with a given level of confidence.  This package provides functions for estimating tolerance limits (intervals) for various univariate distributions (binomial, Cauchy, discrete Pareto, exponential, two-parameter exponential, extreme value, hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric, normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot), Bayesian normal tolerance limits, multivariate normal tolerance regions, nonparametric tolerance intervals, tolerance bands for regression settings (linear regression, nonlinear regression, nonparametric regression, and multivariate regression), and analysis of variance tolerance intervals.  Visualizations are also available for most of these settings.
Several functions to allow comparisons of data across different geographies, in particular for Canadian census data from different censuses.
Implements two tests for same-source of toolmarks. The chumbley_non_random() test follows the paper "An Improved Version of a Tool Mark Comparison Algorithm" by Hadler and Morris (2017) <doi:10.1111/1556-4029.13640>. This is an extension of the Chumbley score as previously described in "Validation of Tool Mark Comparisons Obtained Using a Quantitative, Comparative, Statistical Algorithm" by Chumbley et al (2010) <doi:10.1111/j.1556-4029.2010.01424.x>. fixed_width_no_modeling() is based on correlation measures in a diamond shaped area of the toolmark as described in Hadler (2017).
Uplift modeling aims at predicting the causal effect of an action such as a marketing campaign on a particular individual. In order to simplify the task for practitioners in uplift modeling, we propose a combination of tools that can be separated into the following ingredients: i) quantization, ii) visualization, iii) variable selection, iv) parameters estimation and, v) model validation. For more details, see <https://dms.umontreal.ca/~murua/research/UpliftRegression.pdf>.
Provides functions for multivariate analysis with compositional data. Includes a function for doing compositional canonical correlation analysis.  This analysis requires two data matrices of compositions, which can be adequately transformed and used as entries in a specialized program for canonical correlation analysis, that is able to deal with singular covariance matrices. The methodology is described in Graffelman et al. (2017) <doi:10.1101/144584>. A function for log-ratio principal component analysis with condition number computations has been added to the package.
An R wrapper for using 'TooManyCells', a command line program for clustering, visualizing, and quantifying cell clade relationships. See <https://gregoryschwartz.github.io/too-many-cells/> for more details.
Language specific cardinal to ordinal number conversion.
Calculates topic-specific diagnostics (e.g. mean token length, exclusivity) for 
    Latent Dirichlet Allocation and Correlated Topic Models fit using the 'topicmodels' package.
    For more details, see Chapter 12 in Airoldi et al. (2014, ISBN:9781466504080), 
    pp 262-272 Mimno et al. (2011, ISBN:9781937284114), and Bischof et al. (2014) <arXiv:1206.4631v1>.
Provides an interface to the C code for Latent Dirichlet
	     Allocation (LDA) models and Correlated Topics Models
	     (CTM) by David M. Blei and co-authors and the C++ code
	     for fitting LDA models using Gibbs sampling by Xuan-Hieu
	     Phan and co-authors.
Provides implementation of the "Topic SCORE" algorithm that is
	     proposed by Tracy Ke and Minzhe Wang. The singular value decomposition
	     step is optimized through the usage of svds() function in 'RSpectra'
	     package, on a 'dgRMatrix' sparse matrix. Also provides a column-wise
	     error measure in the word-topic matrix A, and an algorithm for
	     recovering the topic-document matrix W given A and D based on
	     quadratic programming.
		The details about the techniques are explained in the paper "A new SVD approach to optimal topic estimation" by Tracy Ke and Minzhe Wang (2017) <arXiv:1704.07016>.
For multiple ranked input lists (full or partial) representing the same set of N objects, the package TopKLists offers (1) statistical inference on the lengths of informative top-k lists, (2) stochastic aggregation of full or partial lists, and (3) graphical tools for the statistical exploration of input lists, and for the visualization of aggregation results.
Set of hydrological functions including an R
        implementation of the hydrological model TOPMODEL, which is
        based on the 1995 FORTRAN version by Keith Beven. From version
        0.7.0, the package is put into maintenance mode.
A toolkit for calculating topographic distances and identifying and plotting topographic paths. Topographic distances can be calculated along shortest topographic paths (Wang (2009) <doi:10.1111/j.1365-294X.2009.04338.x>), weighted topographic paths (Zhan et al. (1993) <doi:10.1007/3-540-57207-4_29>), and topographic least cost paths (Wang and Summers (2010) <doi:10.1111/j.1365-294X.2009.04465.x>). Functions can map topographic paths on colored or hill shade maps and plot topographic cross sections (elevation profiles) for the paths.
Using Gaussian graphical models we propose a novel approach to
             perform pathway analysis using gene expression. Given the
             structure of a graph (a pathway) we introduce two statistical
             tests to compare the mean and the concentration matrices between
             two groups. Specifically, these tests can be performed on the
             graph and on its connected components (cliques).
Estimate geometric sensitivity indices reconstructing the embedding manifold of the data. The reconstruction is done via a Vietoris Rips with a fixed radius. With the homology of order 2 we estimate symmetric reflections of the those manifold to determine a sensitivity index on of the input model. Detailed information of the methods can be found in <https://www.dropbox.com/s/0kcrjhhkl7899n1/article-symmetric-reflection.pdf> (WIP preprint).
Evaluation of alternatives based on multiple criteria using TOPSIS method.
The goal of tor (to-R) is to help you to import
    multiple files from a single directory at once, and to do so as
    quickly, flexibly, and simply as possible.
Provides functionality to define and train neural networks similar to 
    'PyTorch' by Paszke et al (2019) <arXiv:1912.01703> but written entirely in R 
    using the 'libtorch' library. Also supports low-level tensor operations and 
    'GPU' acceleration.
Provides access to datasets, models and preprocessing
    facilities for deep learning in audio.
Provides datasets in a format that can be easily consumed by torch 'dataloaders'.
  Handles data downloading from multiple sources, caching and pre-processing so
  users can focus only on their model implementations.
Provides access to datasets, models and preprocessing
    facilities for deep learning with images. Integrates seamlessly
    with the 'torch' package and it's 'API' borrows heavily from 
    'PyTorch' vision package.
A framework for statistical analysis in content analysis. In addition to a pipeline for preprocessing text corpora and linking to the latent Dirichlet allocation from the 'lda' package, plots are offered for the descriptive analysis of text corpora and topic models. In addition, an implementation of Chang's intruder words and intruder topics is provided.
Fit an Instrumental Variables Two Stage Least Squares model
Two one-sided tests (TOST) procedure to test equivalence for t-tests, correlations, differences between proportions, and meta-analyses, including power analysis for t-tests and correlations. Allows you to specify equivalence bounds in raw scale units or in terms of effect sizes. See: Lakens (2017) <doi:10.1177/1948550617697177>.
Download summary files from Census Bureau <https://www2.census.gov/> 
    and extract data, in particular high resolution data at 
    block, block group, and tract level, from decennial census and 
    American Community Survey 1-year and 5-year estimates.
For a given phylogenetic tree, calculates the Total Cophenetic Index.
  Reference: A. Mir, F. Rossello, L. A. Rotger (2013).
  A new balance index for phylogenetic trees.
  Math. Biosci. 241, 125-136 <doi:10.1016/j.mbs.2012.10.005>.
R implementation of the software tools developed in the H-CUP
    (Healthcare Cost and Utilization Project) <https://www.hcup-us.ahrq.gov>
    and AHRQ (Agency for Healthcare Research and Quality)
    <https://www.ahrq.gov>.  It currently contains functions for mapping ICD-9
    codes to the AHRQ comorbidity measures and translating ICD-9
    (resp. ICD-10) codes to ICD-10 (resp. ICD-9) codes based on GEM (General
    Equivalence Mappings) from CMS (Centers for Medicare and Medicaid
    Services).
Tools for analyzing count data with the Touchard model (Matsushita et al., 2018, Comm Stat Th Meth <doi:10.1080/03610926.2018.1444177>). It includes univariate estimation (ML and MM) and regression tools developed by Andrade et al. (submitted).
Contains two functions related to sports competitions. One to create league tables and one to create a match schedule.
Implements geodesic interpolation and basis
    generation functions that allow you to create new tour
    methods from R.
Data analysis package for estimating potential biological effects from chemical concentrations in environmental samples. Included are a set of functions to analyze, visualize, and organize measured concentration data as it relates to user-selected chemical-biological interaction benchmark data such as water quality criteria. The intent of these analyses is to develop a better understanding of the potential biological relevance of environmental chemistry data. Results can be used to prioritize which chemicals at which sites may be of greatest concern. These methods are meant to be used as a screening technique to predict potential for biological influence from chemicals that ultimately need to be validated with direct biological assays. A description of the analysis can be found in Blackwell et al. (2017) <doi:10.1021/acs.est.7b01613>.
Calculates sample size and dose allocation for binary toxicity 
 tests, using the Fish Embryo Toxicity Test as example. 
 An optimal test design is obtained by running 
 (i) spoD (calculate the number of individuals to test under control 
 conditions), (ii) setD (estimate the minimal sample size per treatment
 given the users precision requirements) and (iii) doseD (construct 
 an individual dose scheme).
Estimation of transition probabilities for the illness-death model. Both the Aalen-Johansen estimator for a Markov model and a novel non-Markovian estimator by de Una-Alvarez and Meira-Machado (2015) <doi:10.1111/biom.12288>, see also Balboa and de Una-Alvarez (2018) <doi:10.18637/jss.v083.i10>, are included.
Tools for estimating and inferring two-way partial area under receiver operating characteristic curves (two-way pAUC), partial area under receiver operating characteristic curves (pAUC), and partial area under ordinal dominance curves (pODC). Methods includes Mann-Whitney statistic and Jackknife, etc.
Tools to calculate trait probability density functions (TPD) at
    any scale (e.g. populations, species, communities). TPD functions are used to compute
    several indices of functional diversity, as well as its partition across scales.
    These indices constitute a unified framework that incorporates the underlying
    probabilistic nature of trait distributions into uni- or multidimensional
    functional trait-based studies. See Carmona et al. (2016) <doi:10.1016/j.tree.2016.02.003> for
    further information.
This package implements the greedy approximation for tree
        preserving embedding.
We described a novel Topology-based pathway enrichment analysis, which integrated the global position of the nodes and the topological property of the pathways in  Kyoto Encyclopedia of Genes and Genomes Database.
             We also provide some functions to obtain the latest information about pathways to finish pathway enrichment analysis using this method.
A bioinformatics tool for the estimation of the tumor purity from sequencing data. 
    It uses the set of putative clonal somatic single nucleotide variants within copy number neutral
    segments to call tumor cellularity.
Uses thresholded partial least squares algorithm to create a regression or classification model.
A tool created to simplify the data manipulation necessary to create clinical reports.
Estimation of transition probabilities for the
        illness-death model and or the three-state progressive model.
Regression models for temporal process responses with
        time-varying coefficient.
Plant ecologists often need to collect "traits" data
    about plant species which are often scattered among various
    databases: TR8 contains a set of tools which take care of
    automatically retrieving some of those functional traits data
    for plant species from publicly available databases (Biolflor,
    The Ecological Flora of the British Isles, LEDA traitbase, Ellenberg
    values for Italian Flora, Mycorrhizal intensity databases, Catminat, BROT,
    PLANTS, Jepson Flora Project).
    The TR8 name, inspired by "car plates" jokes, was chosen since
    it both reminds of the main object of the package and is
    extremely short to type.
Better looking call stacks after an error.
'BEAST2' (<https://www.beast2.org>) is a widely used
  Bayesian phylogenetic tool, that uses DNA/RNA/protein data
  and many model priors to create a posterior of jointly estimated 
  phylogenies and parameters.
  'Tracer' (<http://tree.bio.ed.ac.uk/software/tracer/>) is a GUI tool 
  to parse and analyze the files generated by 'BEAST2'.
  This package provides a way to parse and analyze 'BEAST2' input
  files without active user input, but using
  R function calls instead.
Contains functions to standardize tracheid profiles
    using the traditional method (Vaganov) and a new method to standardize
    tracheidograms based on the relative position of tracheids within tree rings.
Automatically stores objects in files on disk
  so that files are rewritten when objects are changed, and
  so that objects are accessible but do not occupy memory
  until they are accessed. Keeps track of times when objects
  are created and modified, and caches some basic
  characteristics of objects to allow for fast summaries of
  objects.  Also provides a command history mechanism that
  saves the last command to a history file after each
  command completes.
Obtain population density and body size structure, using video material or image sequences as input. Functions assist in the creation of image sequences from videos, background detection and subtraction, particle identification and tracking. An artificial neural network can be trained for noise filtering. The goal is to supply accurate estimates of population size, structure and/or individual behavior, for use in  evolutionary and ecological studies.
Data frame class for storing collective movement data (e.g. fish
    schools, ungulate herds, baboon troops) collected from GPS trackers or
    computer vision tracking software.
Provides infrastructure for handling running, cycling and swimming data from GPS-enabled tracking devices within R. The package provides methods to extract, clean and organise workout and competition data into session-based and unit-aware data objects of class 'trackeRdata' (S3 class). The information can then be visualised, summarised, and analysed through flexible and extensible methods. Frick and Kosmidis (2017) <doi: 10.18637/jss.v082.i07>, which is updated and maintained as one of the vignettes, provides detailed descriptions of the package and its methods, and real-data demonstrations of the package functionality.
Provides an integrated user interface and workflow for
             the analysis of running, cycling and swimming data from GPS-enabled
             tracking devices through the 'trackeR' <https://CRAN.R-project.org/package=trackeR> R package.
Automatically annotates R-based artifacts
	     with relevant descriptive and provenance-related
    	     and provides a backend-agnostic storage and
	     discoverability system for organizing, retrieving, and
	     interrogating such artifacts.
Reconstructs animal tracks from magnetometer, accelerometer, depth and optional speed data.  Designed primarily using data from Wildlife Computers Daily Diary tags deployed on northern fur seals.
Functions for working with magnetic resonance images. Reading and
    writing of popular file formats (DICOM, Analyze, NIfTI-1, NIfTI-2, MGH);
    interactive and non-interactive visualisation; flexible image manipulation;
    metadata and sparse image handling.
A collection of tools for trade practitioners, including the ability to calibrate different consumer demand systems and simulate the effects of tariffs and quotas under different competitive regimes. These tools are derived from Anderson et al. (2001) <doi:10.1016/S0047-2727(00)00085-2> and Froeb et al. (2003) <doi:10.1016/S0304-4076(02)00166-5>.
Tree Ring Analysis of Disturbance Events in R (TRADER) package provides only one way for disturbance reconstruction from tree-ring data.
Access 'Open Trade Statistics' API from R to download international trade data.
Contains performance analysis metrics of track records including entropy-based
            correlation and dynamic beta based on the Kalman filter. The normalized sample entropy method
            has been implemented which produces accurate entropy estimation even on smaller datasets while for
            the dynamic beta calculation the Kalman filter methodology has been utilized.
            On a separate stream, trades from the five major assets classes and also
            functionality to use pricing curves, rating tables, CSAs and add-on tables. The
            implementation follows an object oriented logic whereby each trade inherits from
            more abstract classes while also the curves/tables are objects. There is a lot
            of functionality focusing on the counterparty credit risk calculations however
            the package can be used for trading applications in general.
Estimate and return either the traffic speed or the car entries in the city of Thessaloniki using historical traffic data. It's used in transport pilot <http://trafficstatusprediction.imet.gr/> of the 'BigDataEurope' project <https://www.big-data-europe.eu/>. There are functions for processing these data, training a neural network, select the most appropriate model and predict the traffic speed or the car entries for a selected time date.
Estimation, selection and comparison of several families of
 transformations. The families of transformations included in the package are 
 the following: Bickel-Doksum (Bickel and Doksum 1981 <doi:10.2307/2287831>), 
 Box-Cox, Dual (Yang 2006 <doi:10.1016/j.econlet.2006.01.011>), 
 Glog (Durbin et al. 2002 <doi:10.1093/bioinformatics/18.suppl_1.S105>), 
 gpower (Kelmansky et al. 2013 <doi:10.1515/sagmb-2012-0030>), 
 Log, Log-shift opt (Feng et al. 2016 <doi:10.1002/sta4.104>),
 Manly, modulus (John and Draper 1980 <doi:10.2307/2986305>), 
 Neglog (Whittaker et al. 2005 <doi:10.1111/j.1467-9876.2005.00520.x>), 
 Reciprocal and Yeo-Johnson. The package simplifies to 
 compare linear models with untransformed and transformed dependent variable 
 as well as linear models where the dependent variable is transformed with 
 different transformations. Furthermore, the package employs maximum likelihood 
 approaches, moments optimization and divergence minimization to estimate the optimal 
 transformation parameter.
Methods to unify the different ways of creating predictive models and their different predictive formats. It includes 
       methods such as K-Nearest Neighbors, Decision Trees, ADA Boosting, Extreme Gradient Boosting, Random Forest, Neural Networks, Deep Learning,
       Support Vector Machines and Bayesian Methods.
The goal of 'trainR' is to provide a simple interface to the 
    National Rail Enquiries (NRE) systems. There are few data feeds 
    available, the simplest of them is Darwin, which provides real-time 
    arrival and departure predictions, platform numbers, delay estimates, 
    schedule changes and cancellations. Other data feeds provide historical 
    data, Historic Service Performance (HSP), and much more. 'trainR' 
    simplifies the data retrieval, so that the users can focus on their 
    analyses. For more details visit 
    <https://www.nationalrail.co.uk/46391.aspx>.
A collection of commonly used tools for animal movement and other tracking 
 data. Variously distance, angle, bearing, distance-to, bearing-to and speed are 
 provided for geographic data that can be used directly or within 'tidyverse' 
 syntax. Distances and bearings are calculated using modern geodesic methods as 
 provided by Charles F. F. Karney (2013) <doi:10.1007/s00190-012-0578-z> 
 via the 'geodist' and 'geosphere' packages.
Assistance for handling ecological trait data and applying the 
    Ecological Trait-Data Standard terminology (Schneider et al. 2019
    <doi:10.1111/2041-210X.13288>). There are two major use cases: (1) preparation of
    own trait datasets for upload into public data bases, and (2) harmonizing
    trait datasets from different sources by re-formatting them into a unified
    format. See 'traitdataform' website for full documentation.
Species trait data from many different sources, including
    sequence data from 'NCBI' (<https://www.ncbi.nlm.nih.gov/>),
    plant trait data from 'BETYdb', data from 'EOL' 'Traitbank',
    'Birdlife' International, and more.
Functions for analysis of bulk data generated from experiments in Randomized block design as per Panse and Sukhatme (1954) <https://books.google.co.in/books?id=Efo9AAAAYAAJ>. Computes analysis of variance; Descriptive statistics parameter like Mean, Minimum, Maximum, CV, Standard error of mean, Standard Error of deviation, CD; Genetic parameter statistics Genotypic Coefficient of Variation, Phenotypic Coefficient of Variation, Heritability in broad sense, Genetic Advance and Genetic Advance per cent mean; Variance and Co-variance matrix of genotypic, phenotypic and environmental; Correlation of genotypic, phenotypic and environmental. Further includes directly publication ready tables.
Implements the three-step procedure proposed by Leffondree et al. (2004) to identify clusters of individual longitudinal trajectories. The procedure involves (1) calculating 24 measures describing the features of the trajectories; (2) using factor analysis to select a subset of the 24 measures and (3) using cluster analysis to identify clusters of trajectories, and classify each individual trajectory in one of the clusters.
Contains a set of methods for trajectory data preparation, such as filtering, compressing and clustering, and for trajectory pattern discovery.
Classes and methods for trajectory data, with support for nesting individual Track objects in track sets (Tracks) and track sets for different entities in collections of Tracks. Methods include selection, generalization, aggregation, intersection, simulation, and plotting.
A toolbox to assist with statistical analysis of 2-dimensional animal trajectories.
    It provides simple access to algorithms for calculating and assessing a variety of 
    characteristics such as speed and acceleration, as well as multiple measures of 
    straightness or tortuosity. McLean & Skowron Volponi (2018) <doi:10.1111/eth.12739>.
Formula-based user-interfaces to specific transformation models
  implemented in package 'mlt'. Available models include Cox models, some parametric 
  survival models (Weibull, etc.), models for ordered categorical variables,
  normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
  (Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
  is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
  transformation models for clustered data is provided (Hothorn, 2019, <arxiv:1910.09219>).
  Multivariate conditional transformation models (<arxiv:1906.03151>) can be fitted as well.
Toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Collection of ancillary functions and utilities to be used in conjunction with the 'TraMineR' package for sequence data exploration. Most of the functions are in test phase, lack systematic consistency check of the arguments and are subject to changes. Once fully checked, some of the functions of this collection could be included in a next release of 'TraMineR'.
Likelihood-based estimation of mixed-effects transformation models using the Template
  Model Builder (TMB). The technical details of transformation models are given in Hothorn et al. (2018)
  <doi:10.1111/sjos.12291>. The random effects are assumed to be normally distributed on the scale of the
  transformation function, the marginal likelihood is evaluated using the Laplace approximation,
  and the gradients are calculated with automatic differentiation (AD).
Partially penalized versions of specific transformation models
    implemented in package 'mlt'. Available models include a fully parametric version
    of the Cox model, other parametric survival models (Weibull, etc.), models for
    binary and ordered categorical variables, normal and transformed-normal (Box-Cox type)
    linear models, and continuous outcome logistic regression. Hyperparameter tuning
    is facilitated through model-based optimization functionalities from package 'mlrMBO'.
    The accompanying vignette describes the methodology used in 'tramnet' in detail.
    Transformation models and model-based optimization are described in
    Hothorn et al. (2019) <doi:10.1111/sjos.12291> and
    Bischl et al. (2016) <arxiv:1703.03373>, respectively.
Matching terminal restriction fragment length
        polymorphism ('TRFLP') profiles between unknown samples and a
        database of known samples.  'TRAMPR' facilitates analysis of
        many unknown profiles at once, and provides tools for working
        directly with electrophoresis output through to generating
        summaries suitable for community analyses with R's rich set of
        statistical functions.  'TRAMPR' also resolves the issues of
        multiple 'TRFLP' profiles within a species, and shared 'TRFLP'
        profiles across species.
Transcribes audio to text with the HP IDOL API. Includes functions to upload files, 
	     retrieve transcriptions, and monitor jobs.
Implementation of the transformation of the Mean Opinion Scores (MOS) to be used before applying the rank based statistical techniques. The method and its necessity is described in: Babak Naderi, Sebastian Möller (2020) <arXiv:2004.11490>.
In order to smoothly animate the transformation of polygons and 
    paths, many aspects needs to be taken into account, such as differing number 
    of control points, changing center of rotation, etc. The 'transformr' 
    package provides an extensive framework for manipulating the shapes of 
    polygons and paths and can be seen as the spatial brother to the 'tweenr' 
    package.
Bindings for the Google Translate API v2
translateR provides easy access to the Google and Microsoft APIs. The package is easy to use with the related R package "stm" for the estimation of multilingual topic models.
R  version 2.1.0 and later support Korean translations of program messages.  The continuous efforts have been made by <http://developer.r-project.org/TranslationTeams.html>   The R Documentation files are licensed under the General Public License, version 2 or 3.   This means that the pilot project to translate them into Korean has permission to reproduce them and translate them.  This work is done with GNU 'gettext' utilities.  The portable object template is updated a weekly basis or whenever changes are necessary.  Comments and corrections via email to the maintainer is of course most welcome.   In order to voluntarily participate in or offer your help with this translation, please contact the maintainer.   To check the change and progress of Korean translation, please visit <http://www.openstatistics.net>.
Treatment and visualization of membrane (selective) transport 
    data. Transport profiles involving up to three species are produced as
    publication-ready plots and several membrane performance parameters 
    (e.g. separation factors as defined in Koros et al. (1996) 
    <doi:10.1351/pac199668071479> and non-linear regression parameters
    for the equations described in Rodriguez de San Miguel et al. (2014)
    <doi:10.1016/j.jhazmat.2014.03.052>) can be obtained. Many widely used 
    experimental setups (e.g. membrane physical aging) can be easily studied
    through the package's graphical representations.
A unified estimation procedure for the analysis of right censored data using linear transformation models.
Implementation of two transportation problem algorithms. 
             1. North West Corner Method 
             2. Minimum Cost Method or Least cost method.
             For more technical details about the algorithms please refer below URLs.
             <http://www.universalteacherpublications.com/univ/ebooks/or/Ch5/nw.htm>.
             <http://personal.maths.surrey.ac.uk/st/J.F/chapter7.pdf>.
Inference of transmission tree from a dated phylogeny. 
    Includes methods to simulate and analyse outbreaks.
    The methodology is described in
    Didelot et al. (2014) <doi:10.1093/molbev/msu121>,
    Didelot et al. (2017) <doi:10.1093/molbev/msw275>.
A set of vectorised functions to calculate medical equations used in transplantation, 
    focused mainly on transplantation of abdominal organs. These functions include donor and recipient
    risk indices as used by NHS Blood & Transplant, OPTN/UNOS and Eurotransplant, tools for 
    quantifying HLA mismatches, functions for calculating estimated glomerular filtration rate (eGFR), 
    a function to calculate the APRI (AST to platelet ratio) score used in initial screening of suitability to receive a 
    transplant from a hepatitis C seropositive donor and some biochemical unit converter functions. 
    All functions are designed to work with either US or international units.
    References for the equations are provided in the vignettes and function documentation.
Solve optimal transport problems. Compute Wasserstein distances (a.k.a. Kantorovitch, Fortet--Mourier, Mallows, Earth Mover's, or minimal L_p distances), return the corresponding transference plans, and display them graphically. Objects that can be compared include grey-scale images, (weighted) point patterns, and mass vectors.
A latent, quasi-independent truncation time is assumed to be linked with the observed dependent truncation time, the event time, and an unknown transformation parameter via a structural transformation model. The transformation parameter is chosen to minimize the conditional Kendall's tau (Martin and Betensky, 2005) <doi:10.1198/016214504000001538> or the regression coefficient estimates (Jones and Crowley, 1992) <doi:10.2307/2336782>. The marginal distribution for the truncation time and the event time are completely left unspecified. The methodology is applied to survival curve estimation and regression analysis.
Univariate time series operations that follow an opinionated design. 
    The main principle of 'transx' is to keep the number of observations the same. 
    Operations that reduce this number have to fill the observations gap.
The trapezoid package provides dtrapezoid, ptrapezoid,
        qtrapezoid, and rtrapezoid functions for the trapezoidal
        distribution.
Transmission Ratio Distortion (TRD) is a genetic phenomenon where the two alleles from either parent are not transmitted to the offspring at the expected 1:1 ratio under Mendelian inheritance, leading to spurious signals in genetic association studies. Functions in this package are developed to account for this phenomenon using loglinear model and Transmission Disequilibrium Test (TDT). Some population information can also be calculated.
A suite of descriptive and inferential methods designed to evaluate one or more biomarkers for their ability to guide patient treatment recommendations.  Package includes functions to assess the calibration of risk models; and plot, evaluate, and compare markers. Please see the reference Janes H, Brown MD, Huang Y, et al. (2014) <doi:10.1515/ijb-2012-0052> for further details.
An R re-implementation of the 'treeinterpreter' package on PyPI
        <https://pypi.org/project/treeinterpreter/>. Each prediction can be
        decomposed as 'prediction = bias + feature_1_contribution + ... +
        feature_n_contribution'. This decomposition is then used to calculate
        the Mean Decrease Impurity (MDI) and Mean Decrease Impurity using
        out-of-bag samples (MDI-oob) feature importance measures based on the
        work of Li et al. (2019) <arXiv:1906.10845>.
Interface to the API for 'TreeBASE' <http://treebase.org>
    from 'R.' 'TreeBASE' is a repository of user-submitted phylogenetic
    trees (of species, population, or genes) and the data used to create
    them.
User-friendly analysis of hierarchical multinomial processing tree (MPT) 
    models that are often used in cognitive psychology. Implements the latent-trait 
    MPT approach (Klauer, 2010) <DOI:10.1007/s11336-009-9141-0> and the beta-MPT 
    approach (Smith & Batchelder, 2010) <DOI:10.1016/j.jmp.2009.06.007> to model 
    heterogeneity of participants. MPT models are conveniently specified by an
    .eqn-file as used by other MPT software and data are provided by a .csv-file 
    or directly in R. Models are either fitted by calling JAGS or by an MPT-tailored 
    Gibbs sampler in C++ (only for nonhierarchical and beta MPT models). Provides 
    tests of heterogeneity and MPT-tailored summaries and plotting functions.
    A detailed documentation is available in Heck, Arnold, & Arnold (2018) 
    <DOI:10.3758/s13428-017-0869-7>.
Bootstrapped response and correlation functions,
    seasonal correlations and evaluation of reconstruction
    skills for use in dendroclimatology and dendroecology,
    see Zang and Biondi (2015) <doi:10.1111/ecog.01335>.
Create a measure of inter-point dissimilarity useful 
 for clustering mixed data, and, optionally, perform the clustering.
The centre of mass is a crucial data for arborists in order to
    consolidate a tree using steel or dynamic cables. Given field-recorded data
    on branchiness of a tree, the package: (i) computes and plots the centre of
    mass of the tree itself, (ii) computes branches slenderness coefficient in
    order to aid the arborist identify potentially dangerous branches, and
    (iii) computes the force acting on a ground plinth and its best position
    relating to the tree centre of mass, should the tree need to be stabilized
    by a steel cable.
Performs sparse discriminant analysis on a combination of
    node and leaf predictors when the predictor variables are
    structured according to a tree, as described in Fukuyama et
    al. (2017) <doi:10.1371/journal.pcbi.1005706>.
An implementation that combines trait data and a phylogenetic tree (or trees) into a 
    single object of class treedata.table. The resulting object can be easily 
    manipulated to simultaneously change the trait- and tree-level sampling.
    Currently implemented functions allow users to use a 'data.table' syntax when
    performing operations on the trait dataset within the treedata.table object.
Functions for estimating times of common ancestry and molecular clock rates of evolution using a variety of evolutionary models, parametric and nonparametric bootstrap confidence intervals, methods for detecting outlier lineages, root-to-tip regression, and a statistical test for selecting molecular clock models. The methods are described in Volz, E.M. and S.D.W. Frost (2017) <doi:10.1093/ve/vex025>.
The model estimates air pollution removal by dry deposition on trees. It also estimates or uses hourly values for aerodynamic resistance, boundary layer resistance, canopy resistance, stomatal resistance, cuticular resistance, mesophyll resistance, soil resistance, friction velocity and deposition velocity. It also allows plotting graphical results for a specific time period. The pollutants are nitrogen dioxide, ozone, sulphur dioxide, carbon monoxide and particulate matter. Baldocchi D (1994) <doi:10.1093/treephys/14.7-8-9.1069>. Farquhar GD, von Caemmerer S, Berry JA (1980) Planta 149: 78-90. Hirabayashi S, Kroll CN, Nowak DJ (2015) i-Tree Eco Dry Deposition Model. Nowak DJ, Crane DE, Stevens JC (2006) <doi:10.1016/j.ufug.2006.01.007>. US EPA (1999) PCRAMMET User's Guide. EPA-454/B-96-001. Weiss A, Norman JM (1985) Agricultural and Forest Meteorology 34: 205—213.
Visualizing cuts for either axis-align or non axis-align tree methods (e.g. decision tree, random tessellation process).
Implements measures of tree similarity, including 
  information-based generalized Robinson-Foulds distances
  (Phylogenetic Information Distance, Clustering Information Distance,
  Matching Split Information Distance; Smith, 2020)
  <doi:10.1093/bioinformatics/btaa614>; 
  Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
  <doi:10.1007/978-3-642-40453-5_13>, 
  including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
  the Matching Split Distance (Bogdanowicz & Giaro 2012)
  <doi:10.1109/TCBB.2011.48>;
  Maximum Agreement Subtree distances;
  the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
  Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. 
  (1996) <doi:10.1007/3-540-61332-3_168>.
  Includes tools for visualizing the landscape of a tree space, and for
  calculating the median of a set of trees under any distance metric.
Simulates nested phylogenetic trees (gene trees in species tree, 
    symbiont trees in host trees) using birth-death processes and transfers
    between lineages. Simulations of gene trees within species trees are performed
    using a three-tree model with species trees, locus trees, and gene trees.
    The cophylogenetic birth-death process is used to simulate sets of host and
    symbiont trees with extant associations between tips.  
    For more information about the three-tree model see:
    Mallo et al. (2015) <doi:10.1093/sysbio/syv082>, 
    Rasmussen and Kellis (2012) <doi:10.1101/gr.123901.111>.
Perform two types of analysis: 1) checking the
    goodness-of-fit of tree models to your single-cell gene expression
    data; and 2) deciding which tree best fits your data.
Creates interpretable decision tree visualizations 
    with the data represented as a heatmap at the tree's leaf nodes.
    'treeheatr' utilizes the customizable 'ggparty' package for 
    drawing decision trees.
Treelets provides a novel construction of multi-scale bases that extends
        wavelets to non-smooth signals. It returns a multi-scale orthonormal 
	basis, where the final computed basis functions are supported 
	on nested clusters in a hierarchical tree.  Both the tree and
	the basis, which are constructed simultaneously, reflect the 
	internal structure of the data.
High performance algorithms for manipulation of terrestrial 'LiDAR' (but not only) point clouds for use in research and forest monitoring applications, being fully compatible with the 'LAS' infrastructure of 'lidR'. For in depth descriptions of stem denoising and segmentation algorithms refer to Conto et al. (2017) <doi:10.1016/j.compag.2017.10.019>.
S4 class and methods for intuitive and efficient phylogenetic tree manipulation.
A treemap is a space-filling visualization of hierarchical
    structures. This package offers great flexibility to draw treemaps.
Provides 'ggplot2' geoms for drawing treemaps.
Provides functionality for creation and comparison of polynomials that uniquely
  describe trees as introduced in Liu (2019, <arXiv:1904.03332>). The core method
  converts rooted unlabeled phylo objects from 'ape' to the tree defining polynomials 
  described with coefficient matrices. Additionally, a conversion for rooted binary trees 
  with binary trait labels is also provided. Once the polynomials of trees are calculated 
  there are functions to calculate distances, distance matrices and plot different distance 
  trees from a target tree. Manipulation and conversion to the tree defining polynomials is 
  implemented in C++ with 'Rcpp' and 'RcppArmadillo'. Furthermore, parallel programming with 
  'RcppThread' is used to improve performance converting to polynomials and calculating distances.
(i) For a given species phylogeny on present day data which is calibrated to calendar-time, a method for estimating maximum likelihood speciation and extinction processes is provided. The method allows for non-constant rates. Rates may change (1) as a function of time, i.e. rate shifts at specified times or mass extinction events (likelihood implemented as LikShifts, optimization as bd.shifts.optim and visualized as bd.shifts.plot) or (2) as a function of the number of species, i.e. density-dependence (likelihood implemented as LikDD and optimization as bd.densdep.optim) or (3) extinction rate may be a function of species age (likelihood implemented as LikAge and optimization as bd.age.optim.matlab). Note that the methods take into account the whole phylogeny, in particular it accounts for the "pull of the present" effect. (1-3) can take into account incomplete species sampling, as long as each species has the same probability of being sampled. For a given phylogeny on higher taxa (i.e. all but one species per taxa are missing), where the number of species is known within each higher taxa, speciation and extinction rates can be estimated under model (1) (implemented within LikShifts and bd.shifts.optim with groups !=0). (ii) For a given phylogeny with sequentially sampled tips, e.g. a virus phylogeny, rates can be estimated under a model where rates vary across time using bdsky.stt.optim based on likelihood LikShiftsSTT (extending LikShifts and bd.shifts.optim). Furthermore, rates may vary as a function of host types using LikTypesSTT (multitype branching process extending functions in R package diversitree). This function can furthermore calculate the likelihood under an epidemiological model where infected individuals are first exposed and then infectious.
An implementation of permutation tests in R, supporting both exact and asymptotic K sample test of data locations. The p value of exact tests is found using tree algorithms. Tree algorithms treat permutations of input data as tree nodes and perform constraint depth-first searches for permutations that fall into the critical region of a test systematically. Pruning of tree search and optimisations at C level enable exact tests for certain large data sets.
Matches phylogenetic trees and trait data, and
    allows simultaneous manipulation of the tree and data using 'dplyr'.
Searches for phylogenetic trees that are optimal using a 
  user-defined criterion. 
  Handles inapplicable data using the algorithm of 
  Brazeau, Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083>.
  Implements Profile Parsimony (Faith and Trueman, 2001) 
  <doi:10.1080/10635150118627>, and Successive Approximations (Farris, 1969) 
  <doi:10.2307/2412182>.
Simulation methods for phylogenetic trees where (i) all tips are sampled at one time point or (ii) tips are sampled sequentially through time. (i) For sampling at one time point, simulations are performed under a constant rate birth-death process, conditioned on having a fixed number of final tips (sim.bd.taxa()), or a fixed age (sim.bd.age()), or a fixed age and number of tips (sim.bd.taxa.age()). When conditioning on the number of final tips, the method allows for shifts in rates and mass extinction events during the birth-death process (sim.rateshift.taxa()). The function sim.bd.age() (and sim.rateshift.taxa() without extinction) allow the speciation rate to change in a density-dependent way. The LTT plots of the simulations can be displayed using LTT.plot(), LTT.plot.gen() and LTT.average.root(). TreeSim further samples trees with n final tips from a set of trees generated by the common sampling algorithm stopping when a fixed number m>>n of tips is first reached (sim.gsa.taxa()). This latter method is appropriate for m-tip trees generated under a big class of models (details in the sim.gsa.taxa() man page). For incomplete phylogeny, the missing speciation events can be added through simulations (corsim()). (ii) sim.rateshifts.taxa() is generalized to sim.bdsky.stt() for serially sampled trees, where the trees are conditioned on either the number of sampled tips or the age. Furthermore, for a multitype-branching process with sequential sampling, trees on a fixed number of tips can be simulated using sim.bdtypes.stt.taxa(). This function further allows to simulate under epidemiological models with an exposed class. The function sim.genespeciestree() simulates coalescent gene trees within birth-death species trees, and sim.genetree() simulates coalescent gene trees.
Provides a flexible simulation tool for phylogenetic trees under a general model for speciation and extinction. Trees with a user-specified number of extant tips, or a user-specified stem age are simulated. It is possible to assume any probability distribution for the waiting time until speciation and extinction. Furthermore, the waiting times to speciation / extinction may be scaled in different parts of the tree, meaning we can simulate trees with clade-dependent diversification processes. At a speciation event, one species splits into two. We allow for two different modes at these splits: (i) symmetric, where for every speciation event new waiting times until speciation and extinction are drawn for both daughter lineages; and (ii) asymmetric, where a speciation event results in one species with new waiting times, and another that carries the extinction time and age of its ancestor. The symmetric mode can be seen as an vicariant or allopatric process where divided populations suffer equal evolutionary forces while the asymmetric mode could be seen as a peripatric speciation where a mother lineage continues to exist.  Reference: O. Hagen and T. Stadler (2017). TreeSimGM: Simulating phylogenetic trees under general Bellman Harris models with lineage-specific shifts of speciation and extinction in R. Methods in Ecology and Evolution. <doi:10.1111/2041-210X.12917>.
Tools for the exploration of distributions of phylogenetic trees.
    This package includes a 'shiny' interface which can be started from R using
    treespaceServer(). 
    For further details see Jombart et al. (2017) <DOI:10.1111/1755-0998.12676>.
Combine a list of taxa with a phylogeny to generate a starting tree for use in
    total evidence dating analyses.
Algorithms for detecting population structure from the history of coalescent events recorded in phylogenetic trees. This method classifies each tip and internal node of a tree into disjoint sets characterized by similar coalescent patterns. The methods are described in Volz, E., Wiuf, C., Grad, Y., Frost, S., Dennis, A., & Didelot, X. (2020) <doi:10.1093/sysbio/syaa009>.
Efficient implementations of functions for the creation, 
  modification and analysis of phylogenetic trees.
  Applications include:
  generation of trees with specified shapes;
  analysis of tree shape;
  rooting of trees and extraction of subtrees;
  calculation and depiction of node support;
  calculation of ancestor-descendant relationships;
  import and export of trees from Newick, Nexus (Maddison et al. 1997)
  <doi:10.1093/sysbio/46.4.590>,
  and TNT <http://www.lillo.org.ar/phylogeny/tnt/> formats;
  and analysis of splits and cladistic information.
Provides a dataset of predefined color palettes based on the Star Trek science fiction series, associated color palette functions, 
    and additional functions for generating customized palettes that are on theme. The package also offers functions for applying 
    the palettes to plots made using the 'ggplot2' package.
Provides a collection of true type and open type Star Trek-themed fonts.
Trelliscope is a scalable, flexible, interactive approach to visualizing data (Hafen, 2013 <doi:10.1109/LDAV.2013.6675164>). This package provides methods that make it easy to create a Trelliscope display specification for TrelliscopeJS. High-level functions are provided for creating displays from within 'tidyverse' or 'ggplot2' workflows. Low-level functions are also provided for creating new interfaces.
Provides access to Trello API (<https://developers.trello.com/>).
    A family of GET functions make it easy to retrieve cards, labels, members,
    teams and other data from both public and private boards. Server responses
    are formatted upon retrieval. Automated paging allows for large requests
    that exceed server limit. See <https://github.com/jchrom/trelloR> for more
    information.
The analysis of environmental data often requires
	     the detection of trends and change-points. 
	     This package includes tests for trend detection
	     (Cox-Stuart Trend Test, Mann-Kendall Trend Test, 
	     (correlated) Hirsch-Slack Test,
             partial Mann-Kendall Trend Test, multivariate (multisite)
	     Mann-Kendall Trend Test, (Seasonal) Sen's slope, 
	     partial Pearson and Spearman correlation trend test),
             change-point detection (Lanzante's test procedures, 
	     Pettitt's test, Buishand Range Test,
	     Buishand U Test, Standard Normal Homogeinity Test),
	     detection of non-randomness (Wallis-Moore Phase Frequency Test,
	     Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test)
	     and the two sample Robust Rank-Order Distributional Test.
Innovative Trend Analysis is a graphical method to examine the trends in time series data. Sequential Mann-Kendall test uses the intersection of prograde and retrograde series to indicate the possible change point in time series data. Distribution free cumulative sum charts indicate location and significance of the change point in time series.
  Zekai, S. (2011). <doi:10.1061/(ASCE)HE.1943-5584.0000556>.
  Grayson, R. B. et al. (1996). Hydrological Recipes: Estimation Techniques in Australian Hydrology. Cooperative Research Centre for Catchment Hydrology, Australia, p. 125. 
  Sneyers, S. (1990). On the statistical analysis of series of observations. Technical note no 5 143, WMO No 725 415. Secretariat of the World Meteorological Organization, Geneva, 192 pp.
Provides a coherent interface for evaluating models fit with the
  trending package.  This package is part of the RECON
  (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Provides a coherent interface to multiple modelling tools for
  fitting trends along with a standardised approach for generating confidence
  and prediction intervals.
Estimation of causal odds ratio and power calculation given trends in exposure prevalence    and outcome frequencies of stratified data.
Performs the detection of point anomalies and linear trend changes 
    for univariate time series by implementing the bottom-up unbalanced wavelet transformation 
    proposed by H. Maeng and P. Fryzlewicz (2019) <http://personal.lse.ac.uk/maengh/>. 
    The estimated number and locations of the change-points are returned with the 
    piecewise-linear estimator for signal.
Analysis of annual average ocean water level time series, providing
    improved estimates of trend (mean sea level) and associated real-time velocities and
    accelerations. Improved trend estimates are based on singular spectrum analysis
    methods. Various gap-filling options are included to accommodate incomplete time
    series records. The package also includes a range of diagnostic tools to inspect
    the components comprising the original time series which enables expert
    interpretation and selection of likely trend components. A wide range of
    screen and plot to file options are available in the package.
Access Google Trends information. This package provides a tidy wrapper to the 'gtrendsR' package.
    Use four spaces when indenting paragraphs within the Description.
Provides three estimators for tensor response regression (TRR) and tensor predictor regression (TPR) models with tensor envelope structure. The three types of estimation approaches are generic and can be applied to any envelope estimation problems. The full Grassmannian (FG) optimization is often associated with likelihood-based estimation but requires heavy computation and good initialization; the one-directional optimization approaches (1D and ECD algorithms) are faster, stable and does not require carefully chosen initial values; the SIMPLS-type is motivated by the partial least squares regression and is computationally the least expensive. For details of TRR, see Li L, Zhang X (2017) <doi:10.1080/01621459.2016.1193022>. For details of TPR, see Zhang X, Li L (2017) <doi:10.1080/00401706.2016.1272495>. For details of 1D algorithm, see Cook RD, Zhang X (2016) <doi:10.1080/10618600.2015.1029577>. For details of ECD algorithm, see Cook RD, Zhang X (2018) <doi:10.5705/ss.202016.0037>.
Simulate genotypes for case-parent triads, case-control, and quantitative trait samples with realistic linkage diequilibrium structure and allele frequency distribution. For studies of epistasis one can simulate models that involve specific SNPs at specific sets of loci, which we will refer to as "pathways". TriadSim generates genotype data by resampling triad genotypes from existing data. The details of the method is described in the manuscript under preparation "Simulating Autosomal Genotypes with Realistic Linkage Disequilibrium and a Spiked in Genetic Effect" Shi, M., Umbach, D.M., Wise A.S., Weinberg, C.R.
A collection of clinical trial designs and methods, implemented in 
    'rstan' and R, including: the Continual Reassessment Method by O'Quigley et 
    al. (1990) <doi:10.2307/2531628>; EffTox by Thall & Cook (2004) 
    <doi:10.1111/j.0006-341X.2004.00218.x>; the two-parameter logistic method of
    Neuenschwander, Branson & Sponer (2008) <doi:10.1002/sim.3230>; and the 
    Augmented Binary method by Wason & Seaman (2013) <doi:10.1002/sim.5867>; and
    more. We provide functions to aid model-fitting and analysis. 
    The 'rstan' implementations may also serve as a cookbook to anyone looking 
    to extend or embellish these models. We hope that this package encourages 
    the use of Bayesian methods in clinical trials. There is a preponderance of 
    early phase trial designs because this is where Bayesian methods are used 
    most. If there is a method you would like implemented, please get in touch.
Functions and Examples in Sample Size Calculation in
        Clinical Research.
Provides the "r, q, p, and d" distribution functions for the triangle distribution.
Measuring angles between points in a landscape is much easier
    than measuring distances. When the location of three points is known the
    position of the observer can be determined based solely on the angles between
    these points as seen by the observer. This task (known as triangulation)
    however requires onerous calculations - these calculations are automated by this
    package.
A collection of high-performance functions for the triangular
    distribution that consists of the probability density function, cumulative
    distribution function, quantile function, random variate generator, moment
    generating function, characteristic function, and expected shortfall
    function. References: Samuel Kotz, Johan Ren Van Dorp (2004)
    <doi:10.1142/5720>, Melissa E. O'Neill (2014)
    <https://www.cs.hmc.edu/tr/hmc-cs-2014-0905.pdf>, David Blackman and
    Sebastiano Vigna (2018) <arXiv:1805.01407>, and Acerbi, Carlo and
    Tasche, Dirk. (2002) <doi:10.1111/1468-0300.00091>.
Functions to make manipulation of object attributes easier. 
    It also contains a few functions that extend the 'dplyr' package for data 
    manipulation, and it provides new pipe operators, including the pipe '%@>%' 
    similar to the 'magrittr' '%>%', but with the additional functionality to 
    enable attributes propagation.
A flexible color scale for ternary compositions with options for
  discretization, centering and scaling.
'Radix trees', or 'tries', are key-value data structures optimised for efficient lookups, similar in purpose
             to hash tables. 'triebeard' provides an implementation of 'radix trees' for use in R programming and in
             developing packages with 'Rcpp'.
A complete data set of historic GB trig points in British National Grid (OSGB36) coordinate reference system. Trig points (aka triangulation stations) are fixed survey points used to improve the accuracy of map making in Great Britain during the 20th Century. Trig points are typically located on hilltops so still serve as a useful navigational aid for walkers and hikers today.
Propensity score matching for non-binary treatments.
Trimmed k-means clustering. The method is described in Cuesta-Albertos et al. (1997) <doi:10.1214/aos/1031833664>.
Information on all of the TriMet stops in the Portland Metro Area. It includes information such as the longitude, latitude, cross street, and direction of the stop. TriMet has catalogued these stops, 6880 in total.
A lightweight toolkit to reduce the size of a list object. The
    object is minimized by recursively removing elements from the object 
    one-by-one. The process is constrained by a reference function call
    specified by the user, where the target object is given as an argument. 
    The procedure will not allow elements to be removed from the object, that 
    will cause results from the function call to diverge from the function 
    call with the original object.
Provides various commonly-used response time trimming
    methods, including the recursive / moving-criterion methods reported by
    Van Selst and Jolicoeur (1994). By passing trimming functions raw data files,
    the package will return trimmed data ready for inferential testing.
Creates point and probability forecasts from the trees in a random forest using a trimmed opinion pool.
Several statistical test functions as well as a function for exploratory data analysis to investigate classifiers allocating individuals to one of three disjoint and ordered classes. In a single classifier assessment the discriminatory power is compared to classification by chance. In a comparison of two classifiers the null hypothesis corresponds to equal discriminatory power of the two classifiers.
The package contains functions that 1) estimates
        gene-environment interaction between a SNP and a continuous
        non-genetic attribute by fitting a generalized additive model
        to case-parent trio data, 2) produces graphical displays of
        estimated interaction, 3) performs permutation test of
        gene-environment interaction; 4) simulates informative
        case-parent trios.
Fit a trio model via penalized maximum likelihood. The model is fit for a path of values of the penalty parameter. This package is based on Noah Simon, et al. (2011) <doi:10.1080/10618600.2012.681250>.
Functions for accessing and manipulating spatial data for animal
    tracking, with straightforward coercion from and to other formats. Filter
    for speed and create time spent maps from animal track data. There are
    coercion methods to convert between 'trip' and 'ltraj' from 'adehabitatLT', 
    and between 'trip' and 'psp' and 'ppp' from 'spatstat'. Trip objects
    can be created from raw or grouped data frames, and from types in the 'sp', 
    'sf', 'amt', 'trackeR', 'mousetrap', and other packages.
A constrained two-dimensional Delaunay triangulation package
  providing both triangulation and generation of voronoi mosaics of 
  irregular spaced data.
Data handling and estimation functions for animal movement
    estimation from archival or satellite tags. Helper functions are included
    for making image summaries binned by time interval from Markov Chain Monte Carlo
    simulations.
Social Relation Model (SRM) analyses for single or multiple
    round-robin groups are performed. These analyses are either based on one
    manifest variable, one latent construct measured by two manifest variables,
    two manifest variables and their bivariate relations, or two latent
    constructs each measured by two manifest variables. Within-group t-tests
    for variance components and covariances are provided for single groups.
    For multiple groups two types of significance tests are provided:
    between-groups t-tests (as in SOREMO) and enhanced standard errors based on
    Lashley and Bond (1997) <DOI:10.1037/1082-989X.2.3.278>. Handling for missing values is provided.
Tools for exploring effects of correlated features in predictive 
    models. The predict_triplot() function delivers instance-level explanations 
    that calculate the importance of the groups of explanatory variables. The 
    model_triplot() function delivers data-level explanations. The generic plot 
    function visualises in a concise way importance of hierarchical groups of 
    predictors. All of the the tools are model agnostic, therefore works for any
    predictive machine learning models. Find more details in Biecek (2018) 
    <arXiv:1806.08915>.
Uses read counts for biallelic single nucleotide polymorphisms (SNPs)
    to compare the likelihoods for the observed read counts given that a sample is 
    either diploid or triploid. It allows parameters to be specified to account for 
    sequencing error rates and allelic bias. For details of the algorithm, please see
    Delomas (2019) <doi:10.1111/1755-0998.13073>.
Computing diversity measures on tripartite graphs. This package first implements a parametrized family of such diversity measures which apply on probability distributions. Sometimes called "True Diversity", this family contains famous measures such as the richness, the Shannon entropy, the Herfindahl-Hirschman index, and the Berger-Parker index. Second, the package allows to apply these measures on probability distributions resulting from random walks between the levels of tripartite graphs. By defining an initial distribution at a given level of the graph and a path to follow between the three levels, the probability of the walker's position within the final level is then computed, thus providing a particular instance of diversity to measure.
Use alternating least squares to estimate a Temporally Regularized Matrix Factorization (Yu, Hsiang-Fu, Nikhil Rao, and Inderjit S. Dhillon, 2015) <arXiv:1509.08333v3> 
  (possibly) in the presence of missing values.
It includes functions like tropical addition, tropical multiplication for vectors and matrices. In tropical algebra, the tropical sum of two numbers is their minimum and the tropical product of two numbers is their ordinary sum. For more information see also I. Simon (1988) Recognizable sets with multiplicities in the tropical semi ring: Volume 324 Lecture Notes I Computer Science, pages 107-120 <doi: 10.1007/BFb0017135>.
A compilation of fish stock assessment methods for the
    analysis of length-frequency data in the context of data-poor
    fisheries. Includes methods and examples included in the FAO
    Manual by P. Sparre and S.C. Venema (1998), "Introduction to tropical fish
    stock assessment"
    (<http://www.fao.org/documents/card/en/c/9bb12a06-2f05-5dcb-a6ca-2d6dd3080f65/>),
    as well as other more recent methods.
Estimates the trophic position of a consumer relative 
    to a baseline species. It implements a Bayesian approach which combines an 
    interface to the 'JAGS' MCMC library of 'rjags' and stable isotopes. Users are
    encouraged to test the package and send bugs and/or errors to
    trophicposition-support@googlegroups.com.
Some of the basic tropical algebra functionality is provided for sparse matrices by applying sparse matrix storage techniques. Some of these are addition and multiplication of vectors and matrices, dot product of the vectors in tropical form and some general equations are also solved using tropical algebra.
Class definitions and constructors for pseudo-vectors containing
    all permutations, combinations and subsets of objects taken from a vector.
    Simplifies working with structures commonly encountered in combinatorics.
Recursive partytioning of transformation models with
  corresponding random forest for conditional transformation models 
  as described in 'Transformation Forests' (Hothorn and Zeileis, 2017, <arXiv:1701.02110>) 
  and 'Top-Down Transformation Choice' (Hothorn, 2018, <DOI:10.1177/1471082X17748081>).
Implements Bayesian methods, described in
    Hugh-Jones (2019) <doi:10.1007/s40881-019-00069-x>, for estimating the
    proportion of liars in coin flip-style experiments, where subjects
    report a random outcome and are paid for reporting a "good" outcome.
An implementation of the TrueSkill algorithm (Herbrich,
        R., Minka, T. and Grapel, T) in R; a Bayesian skill rating
        system with inference by approximate message passing on a
        factor graph. Used by Xbox to rank gamers and identify
        appropriate matches.
        http://research.microsoft.com/en-us/projects/trueskill/default.aspx
        Current version allows for one player per team. Will update as
        time permits.  Requires R version 3.0 as it is written with
        Reference Classes.  URL:
        https://github.com/bhoung/trueskill-in-r Acknowledgements to
        Doug Zongker and Heungsub Lee for their python implementations
        of the algorithm and for the liberal reuse of Doug's code
        comments (@dougz and @sublee on github).
A collection of functions to deal with the truncated univariate and multivariate normal and Student distributions, described in Botev (2017) <doi:10.1111/rssb.12162> and Botev and L'Ecuyer (2015) <doi:10.1109/WSC.2015.7408180>.
A collection of tools to evaluate probability density
        functions, cumulative distribution functions, quantile functions
        and random numbers for truncated random variables.  These functions are
        provided to also compute the expected value and variance. Nadarajah
        and Kotz (2006) developed most of the functions. QQ plots can be produced.
        All the probability functions in the stats, stats4 and evd
        packages are automatically available for truncation..
Goodness-of-fit tests and some adjusted exploratory tools
        allowing for left truncated data
Density, probability, quantile and random number
        generation functions for the truncated normal distribution.
Estimation of models for truncated Gaussian variables by maximum likelihood.
Semi-parametric estimation of truncated linear regression models
A wrapper around the 'Trundler' API, which gives
    access to historical retail product and pricing data, and can be found
    at <https://api.trundler.dev/>.
Does local optimization using two derivatives and trust regions.
    Guaranteed to converge to local minimum of objective function.
Trusted Timestamps (tts) are created by incorporating a hash of a file or dataset into a transaction on the decentralized blockchain (Stellar network). 
    The package makes use of a free service provided by <https://stellarapi.io>.
Trust region algorithm for nonlinear optimization. Efficient when
    the Hessian of the objective function is sparse (i.e., relatively few nonzero
    cross-partial derivatives). See Braun, M. (2014) <doi:10.18637/jss.v060.i04>.
Advanced tryCatch() and try() functions for better error handling
             (logging, stack trace with source code references and support for post-mortem analysis via dump files).
Stationary Gaussian ARMA processes and the stationary 'GARMA' distribution are fundamental in time series analysis. Here we give utilities to compute 
    the auto-covariance/auto-correlation for a stationary Gaussian ARMA process, as well as the probability functions (density, cumulative distribution, random 
    generation) for random vectors from this distribution.  We also give functions for the spectral intensity, and the permutation-spectrum test for testing 
    a time-series vector for the presence of a signal.
Contains R functions and datasets detailed in the book
        "Time Series Analysis with Applications in R (second edition)" by Jonathan Cryer and Kung-Sik Chan.
Tsallis distribution also known as the q-exponential family distribution. Provide distribution d, p, q, r functions, fitting and testing functions. Project initiated by Paul Higbie and based on Cosma Shalizi's code.
Accompanies the book Rainer Schlittgen and Cristina Sattarhoff (2020) <https://www.degruyter.com/view/title/575978>  "Angewandte Zeitreihenanalyse mit R, 4. Auflage" . The package contains the time series and functions used therein. It was developed over many years teaching courses about time series analysis.
Time series toolkit with identical behavior for all
  time series classes: 'ts','xts', 'data.frame', 'data.table', 'tibble', 'zoo',
  'timeSeries', 'tsibble', 'tis' or 'irts'. Also converts reliably between these classes.
Different estimators are provided to solve the blind source separation problem for multivariate time series with stochastic volatility (Matilainen, Nordhausen and Oja (2015) <doi:10.1016/j.spl.2015.04.033>; Matilainen, Miettinen, Nordhausen, Oja and Taskinen (2017) <doi:10.17713/ajs.v46i3-4.671>) and supervised dimension reduction problem for multivariate time series (Matilainen, Croux, Nordhausen and Oja (2017) <doi:10.1016/j.ecosta.2017.04.002>). Different functions based on AMUSE and SOBI are also provided for estimating the dimension of the white noise subspace.
Performs the two-sample comparisons using the following exact test procedures: the exact likelihood-ratio test (LRT) for equality of two normal populations proposed in Zhang et al. (2012); the combined test based on the LRT and Shapiro-Wilk test for normality via the Bonferroni correction technique; the newly proposed density-based empirical likelihood (DBEL) ratio test. To calculate p-values of the DBEL procedures, three procedures are used: (a) the traditional Monte Carlo (MC) method implemented in C++, (b) a new interpolation method based on regression techniques to operate with tabulated critical values of the test statistic; (c) a Bayesian type method that uses the tabulated critical values as the prior information and  MC generated DBEL-test-statistic's values as data.
A set of measures of dissimilarity between time series to perform time series clustering. Metrics based on raw data, on generating models and on the forecast behavior are implemented. Some additional utilities related to time series clustering are also provided, such as clustering algorithms and cluster evaluation metrics.
Utilities for comparing the equality of series on two databases.
	Comprehensive examples of all the 'TS*' packages is provided in the
	vignette Guide.pdf with the 'TSdata' package.
Likelihood-based methods for model fitting and assessment, prediction and intervention analysis of count time series following generalized linear models are provided. Models with the identity and with the logarithmic link function are allowed. The conditional distribution can be Poisson or Negative Binomial.
A set of functions to implement Time Series Cointegrated System (TSCS)
    spatial interpolation and relevant data visualization.
Illustrates the various 'TSdbi' packages with a vignette using time series 
	data from several sources. The vignette also illustrates some simple time series
	manipulation and plotting using packages 'tframe' and 'tfplot'.
A terribly-simple data base for numeric
  time series, written purely in R, so no external
  database-software is needed. Series are stored in
  plain-text files (the most-portable and enduring file
  type) in CSV format. Timestamps are encoded using R's
  native numeric representation for 'Date'/'POSIXct',
  which makes them fast to parse, but keeps them
  accessible with other software. The package provides
  tools for saving and updating series in this
  standardised format, for retrieving and joining data,
  for summarising files and directories, and for
  coercing series from and to other data types (such as
  'zoo' series).
Provides a common interface to time series databases. The
	objective is to define a standard interface so users can retrieve time 
	series data from various sources with a simple, common, set of 
	commands, and so programs can be written to be portable with respect 
	to the data source. The SQL implementations also provide a database 
	table design, so users needing to set up a time series database 
	have a reasonably complete way to do this easily. The interface 
	provides for a variety of options with respect to the representation 
	of time series in R. The interface, and the SQL implementations, also
	handle vintages of time series data (sometime called editions or 
	real-time data). There is also a (not yet well tested) mechanism to
	handle multilingual data documentation.
	Comprehensive examples of all the 'TS*' packages is provided in the
	vignette Guide.pdf with the 'TSdata' package.
ARIMA-model-based decomposition of quarterly and 
 monthly time series data.
 The methodology is developed and described, among others, in 
 Burman (1980) <DOI:10.2307/2982132> and 
 Hillmer and Tiao (1982) <DOI:10.2307/2287770>.
Calculate optimal Zhong's two-/three-stage Phase II designs (see Zhong (2012) <doi:10.1016/j.cct.2012.07.006>). Generate Target Toxicity decision table for Phase I dose-finding (two-/three-stage). This package also allows users to run dose-finding simulations based on customized decision table.
Determining training set for genomic selection using a genetic algorithm (Holland J.H. (1975) <DOI:10.1145/1216504.1216510>) or simple exchange algorithm (change an individual every iteration). Three different criteria are used in both algorithms, which are r-score (Ou J.H., Liao C.T. (2018) <DOI:10.6342/NTU201802290>), PEV-score (Akdemir D. et al. (2015) <DOI:10.1186/s12711-015-0116-6>) and CD-score (Laloe D. (1993) <DOI:10.1186/1297-9686-25-6-557>). Phenotypic data for candidate set is not necessary for all these methods. By using it, one may readily determine a training set that can be expected to provide a better training set comparing to random sampling.
Disaggregates low frequency time series data to higher frequency series. Implements the following methods for temporal disaggregation: Boot, Feibes and Lisman (1967) <DOI:10.2307/2985238>, Chow and Lin (1971) <DOI:10.2307/1928739>, Fernandez (1981) <DOI:10.2307/1924371> and Litterman (1983) <DOI:10.2307/1391858>.
A set of commonly used distance measures and some additional functions which, although initially not designed for this purpose, can be used to measure the dissimilarity between time series. These measures can be used to perform clustering, classification or other data mining tasks which require the definition of a distance measure between time series. U. Mori, A. Mendiburu and J.A. Lozano (2016), <doi:10.32614/RJ-2016-058>.
Implements a method for identifying subgroups with superior response relative to the overall sample.
Implements nonlinear autoregressive (AR) time series models. For univariate series, a non-parametric approach is available through additive nonlinear AR. Parametric modeling and testing for regime switching dynamics is available when the transition is either direct (TAR: threshold AR) or smooth (STAR: smooth transition AR, LSTAR). For multivariate series, one can estimate a range of TVAR or threshold cointegration TVECM models with two or three regimes. Tests can be conducted for TVAR as well as for TVECM (Hansen and Seo 2002 and Seo 2006).
Calculates total survey error (TSE) for one or more surveys, using common scale-dependent and/or scale-independent metrics.  On TSE, see: Weisberg, Herbert (2005, ISBN:0-226-89128-3); Biemer, Paul (2010) <doi:10.1093/poq/nfq058>.
Calculates total survey error (TSE) for one or more surveys, using both scale-dependent and scale-independent metrics.  Package works directly from the data set, with no hand calculations required: just upload a properly structured data set (see TESTIND and its documentation), properly input column names (see functions documentation), and run your functions.  For more on TSE, see: Weisberg, Herbert (2005, ISBN:0-226-89128-3); Biemer, Paul (2010) <doi:10.1093/poq/nfq058>; Biemer, Paul et.al. (2017, ISBN:9781119041672); etc.
A framework for dynamically combining forecasting models for time series forecasting predictive tasks. It leverages machine learning models from other packages to automatically combine expert advice using metalearning and other state-of-the-art forecasting combination approaches. The predictive methods receive a data matrix as input, representing an embedded time series, and return a predictive ensemble model. The ensemble use generic functions 'predict()' and 'forecast()' to forecast future values of the time series. Moreover, an ensemble can be updated using methods, such as 'update_weights()' or 'update_base_models()'. A complete description of the methods can be found in: Cerqueira, V., Torgo, L., Pinto, F., and Soares, C. "Arbitrated Ensemble for Time Series Forecasting." to appear at: Joint European Conference on Machine Learning and Knowledge Discovery in Databases. Springer International Publishing, 2017; and Cerqueira, V., Torgo, L., and Soares, C.: "Arbitrated Ensemble for Solar Radiation Forecasting." International Work-Conference on Artificial Neural Networks. Springer, 2017 <doi:10.1007/978-3-319-59153-7_62>.
Computes various entropies of given time series. This is the initial version that includes ApEn() and SampEn() functions for calculating approximate entropy and sample entropy. Approximate entropy was proposed by S.M. Pincus in "Approximate entropy as a measure of system complexity", Proceedings of the National Academy of Sciences of the United States of America, 88, 2297-2301 (March 1991). Sample entropy was proposed by J. S. Richman and J. R. Moorman in "Physiological time-series analysis using approximate entropy and sample entropy", American Journal of Physiology, Heart and Circulatory Physiology, 278, 2039-2049 (June 2000). This package also contains FastApEn() and FastSampEn() functions for calculating fast approximate entropy and fast sample entropy. These are newly designed very fast algorithms, resulting from the modification of the original algorithms. The calculated values of these entropies are not the same as the original ones, but the entropy trend of the analyzed time series determines equally reliably. Their main advantage is their speed, which is up to a thousand times higher. A scientific article describing their properties has been submitted to The Journal of Supercomputing and in present time it is waiting for the acceptance.
Time series analysis and computational finance.
Routines for the analysis of nonlinear time series. This
        work is largely inspired by the TISEAN project, by Rainer
        Hegger, Holger Kantz and Thomas Schreiber:
        <http://www.mpipks-dresden.mpg.de/~tisean/>.
Implements an Entropy measure of dependence based on the Bhattacharya-Hellinger-Matusita distance. Can be used as a (nonlinear) autocorrelation/crosscorrelation function for continuous and categorical time series. The package includes tests for serial dependence and nonlinearity based on it. Some routines have a parallel version that can be used in a multicore/cluster environment. The package makes use of S4 classes.
Multiscale multifractal analysis (MMA) (Gierałtowski et al.,
    2012)<DOI:10.1103/PhysRevE.85.021915> is a time series analysis method,
    designed to describe scaling properties of fluctuations within the signal
    analyzed. The main result of this procedure is the so called Hurst surface
    h(q,s) , which is a dependence of the local Hurst exponent h (fluctuation
    scaling exponent) on the multifractal parameter q and the scale of observation s
    (data window width).
Tools to perform some descriptive data analysis for assets. Manage the portfolio and capital of assets. It also downloads and organizes data from the Tehran Stock Exchange (TSE).
Calculates total survey error (TSE) for a survey under multiple, different weighting schemes, using both scale-dependent and scale-independent metrics.  Package works directly from the data set, with no hand calculations required: just upload a properly structured data set (see TESTWGT and its documentation), properly input column names (see functions documentation), and run your functions.  For more on TSE, see: Weisberg, Herbert (2005, ISBN:0-226-89128-3); Biemer, Paul (2010) <doi:10.1093/poq/nfq058>; Biemer, Paul et.al. (2017, ISBN:9781119041672); etc.
Forecasting of long memory time series in presence of structural break by using TSF algorithm by Papailias and Dias (2015) <doi:10.1016/j.ijforecast.2015.01.006>.
Extraction of Factors from Multivariate Time Series. See '?00tsfa-Intro' for more details.
A 'fame' interface for 'TSdbi'.
	Comprehensive examples of all the 'TS*' packages is provided in the
	vignette Guide.pdf with the 'TSdata' package.
Methods for extracting various features from time series data. The features provided are those from Hyndman, Wang and Laptev (2013) <doi:10.1109/ICDMW.2015.104>, Kang, Hyndman and Smith-Miles (2017) <doi:10.1016/j.ijforecast.2016.09.004> and from Fulcher, Little and Jones (2013) <doi:10.1098/rsif.2013.0048>. Features include spectral entropy, autocorrelations, measures of the strength of seasonality and trend, and so on. Users can also define their own feature functions.
A general regression neural network (GRNN) is a variant of a
    Radial Basis Function Network characterized by a fast single-pass learning.
    'tsfgrnn' allows you to forecast time series using a GRNN model Francisco 
    Martinez et al. (2019) <doi:10.1007/978-3-030-20521-8_17> and Weizhong Yan
    (2012) <doi:10.1109/TNNLS.2012.2198074>. When the forecasting horizon
    is higher than 1, two multi-step ahead forecasting strategies can be used.
    The model built is autoregressive, that is, it is only based on the 
    observations of the time series. You can consult and plot how the
    prediction was done. It is also possible to assess the forecasting accuracy
    of the model using rolling origin evaluation.
Allows to forecast time series using nearest neighbors regression
    Francisco Martinez, Maria P. Frias, Maria D. Perez-Godoy and Antonio J.
    Rivera (2017) <doi:10.1007/s10462-017-9593-z>. When the forecasting horizon
    is higher than 1, two multi-step ahead forecasting strategies can be used.
    The model built is autoregressive, that is, it is only based on the 
    observations of the time series. The nearest neighbors used in a prediction
    can be consulted and plotted.
To provide a high dimensional grouped variable selection approach for detection of whole-genome SNP effects and SNP-SNP interactions, as described in Fang et al. (2017, under review).
This gui shows realisations of times series, currently ARMA and GARCH processes. It might be helpful for teaching and studying.
Two-stage procedure compares hazard rate functions,
    which may or may not cross each other.
Provides a 'tbl_ts' class (the 'tsibble') for
    temporal data in an data- and model-oriented format. The 'tsibble'
    provides tools to easily manipulate and analyse temporal data, such as
    filling in time gaps and aggregating over calendar periods.
Provides diverse datasets in the 'tsibble' data structure. These datasets are useful for learning and demonstrating how tidy temporal data can tidied, visualised, and forecasted.
A shared tsibble data easily communicates between
    htmlwidgets on both client and server sides, powered by 'crosstalk'. A
    shiny module is provided to visually explore periodic/aperiodic
    temporal patterns.
Functions for analysing and forecasting intermittent demand/slow moving items time series.
An implementation of the time-series Susceptible-Infected-Recovered (TSIR) model using a number of different fitting options for infectious disease time series data. The manuscript based on this package can be found here <doi:10.1371/journal.pone.0185528>. The method implemented here is described by Finkenstadt and Grenfell (2000) <doi:10.1111/1467-9876.00187>.
A novel and fast two stage method for simultaneous multiple change point detection and variable selection for piecewise stationary autoregressive (PSAR) processes and linear regression model. It also simultaneously performs variable selection for each autoregressive model and hence the order selection.
Implementations of a number of functions used to mine numeric time-series data. It covers the implementation of SAX transformation, univariate motif discovery (based on the random projection method), multivariate motif discovery (based on graph clustering), and several functions used for the ease of visualizing the motifs discovered. The details of SAX transformation can be found in J. Lin. E. Keogh, L. Wei, S. Lonardi, Experiencing SAX: A novel symbolic representation of time series, Data Mining and Knowledge Discovery 15 (2) (2007) 107-144. Details on univariate motif discovery method implemented can be found in B. Chiu, E. Keogh, S. Lonardi, Probabilistic discovery of time series motifs, ACM SIGKDD, Washington, DC, USA, 2003, pp. 493-498. Details on the multivariate motif discovery method implemented can be found in A. Vahdatpour, N. Amini, M. Sarrafzadeh, Towards unsupervised activity discovery using multi-dimensional motif detection in time series, IJCAI 2009 21st International Joint Conference on Artificial Intelligence.
Methods to 
	retrieve data from several different sources. This include historical
	quote data from 'Yahoo' and 'Oanda', economic data from 'FRED', and
	'xls' and 'csv' data from different sources.
	Comprehensive examples of all the 'TS*' packages is provided in the
	vignette Guide.pdf with the 'TSdata' package.
Return the first four moments of the SMN distributions (Normal, Student-t, Pearson VII, Slash or Contaminated Normal).
Tools for specifying time series regression models
A toolkit implementing the Matrix Profile concept
    that was created by CS-UCR
    <http://www.cs.ucr.edu/~eamonn/MatrixProfile.html>.
Return the first four moments, estimation of parameters and sample of the TSMSN distributions (Skew Normal, Skew t, Skew Slash or Skew Contaminated Normal).
A 'MySQL' interface for 'TSdbi'.
	Comprehensive examples of all the 'TS*' packages is provided in the
	vignette Guide.pdf with the 'TSdata' package.
Temporal SNA tools for continuous- and discrete-time longitudinal networks having vertex, edge, and attribute dynamics stored in the 'networkDynamic' format. This work was supported by grant R01HD68395 from the National Institute of Health.
A "pure R" implementation of the t-SNE algorithm.
An ODBC interface for 'TSdbi'.
	Comprehensive examples of all the 'TS*' packages is provided in the
	vignette Guide.pdf with the 'TSdata' package.
Detection of outliers in time series following the 
    Chen and Liu (1993) <DOI:10.2307/2290724> procedure. 
    Innovational outliers, additive outliers, level shifts, 
    temporary changes and seasonal level shifts are considered.
Basic infrastructure and some algorithms for the traveling
    salesperson problem (also traveling salesman problem; TSP).
    The package provides some simple algorithms and
    an interface to the Concorde TSP solver and its implementation of the
    Chained-Lin-Kernighan heuristic. The code for Concorde
    itself is not included in the package and has to be obtained separately.
    Hahsler and Hornik (2007) <doi:10.18637/jss.v023.i02>.
Adjusts for correlations among the rows and columns via
        the Transposable Sphering Algorithm when conducting large-scale
        inference on the rows of a data matrix.
Prediction intervals for ARIMA and structural time series
    models using importance sampling approach with uninformative priors for model
    parameters, leading to more accurate coverage probabilities in frequentist
    sense. Instead of sampling the future observations and hidden states of the
    state space representation of the model, only model parameters are sampled,
    and the method is based solving the equations corresponding to the conditional
    coverage probability of the prediction intervals. This makes method relatively
    fast compared to for example MCMC methods, and standard errors of prediction
    limits can also be computed straightforwardly.
Instance feature calculation and evolutionary instance generation
    for the traveling salesman problem. Also contains code to "morph" two TSP
    instances into each other. And the possibility to conveniently run a couple
    of solvers on TSP instances.
A 'PostgreSQL' interface for 'TSdbi'.
	Comprehensive examples of all the 'TS*' packages is provided in the
	vignette Guide.pdf with the 'TSdata' package.
Functions for defining and conducting a time series prediction process including pre(post)processing, decomposition, modelling, prediction and accuracy assessment. The generated models and its yielded prediction errors can be used for benchmarking other time series prediction methods and for creating a demand for the refinement of such methods. For this purpose, benchmark data from prediction competitions may be used.
Time Series Qn is a package with applications of the Qn estimator of Rousseeuw and Croux (1993) <doi:10.1080/01621459.1993.10476408> to univariate and multivariate Time Series in time and frequency domains. More specifically, the robust estimation of autocorrelation or autocovariance matrix functions from Ma and Genton (2000, 2001) <doi:10.1111/1467-9892.00203>, <doi:10.1006/jmva.2000.1942> and Cotta (2017) <doi:10.13140/RG.2.2.14092.10883> are provided. The robust pseudo-periodogram of Molinares et. al. (2009) <doi:10.1016/j.jspi.2008.12.014> is also given. This packages also provides the M-estimator of the long-memory parameter d based on the robustification of the GPH estimator proposed by Reisen et al. (2017) <doi:10.1016/j.jspi.2017.02.008>.
Methods for representations (i.e. dimensionality reduction, preprocessing, feature extraction) of time series to help more accurate and effective time series data mining.
    Non-data adaptive, data adaptive, model-based and data dictated (clipped) representation methods are implemented. Also various normalisation methods (min-max, z-score, Box-Cox, Yeo-Johnson),
    and forecasting accuracy measures are implemented.
Additive hazards models with two stage residual inclusion method are fitted under either survival data or competing risks data. The estimator incorporates an instrumental variable and therefore can recover causal estimand in the presence of unmeasured confounding under some assumptions. A.Ying, R. Xu and J. Murphy. (2019) <doi:10.1002/sim.8071>.
Methods for handling the missing values outliers are introduced in
    this package. The recognized missing values and outliers are replaced 
    using a model-based approach. The model may consist of both autoregressive
    components and external regressors. The methods work robust and efficient,
    and they are fully tunable. The primary motivation for writing the package
    was preprocessing of the energy systems data, e.g. power plant production
    time series, but the package could be used with any time series data.
Time Series Segmented Residual Trends is a method for the automated detection of land degradation from remotely sensed vegetation and climate datasets. TSS-RESTREND incorporates aspects of two existing degradation detection methods: RESTREND which is used to control for climate variability, and BFAST which is used to look for structural changes in the ecosystem. The full details of the testing and justification of the TSS-RESTREND method (version 0.1.02) are published in Burrell et al., (2017). <doi:10.1016/j.rse.2017.05.018>. The changes to the method introduced in version 0.2.03 focus on the inclusion  of temperature as an additional climate variable. This allows for land  degradation assessment in temperature limited drylands. A paper that details this work is currently under review. There are also a number of bug fixes and speed improvements. Version 0.3.0 introduces additional attribution for eCO2,  climate change and climate variability the details of which are in press in Burrell et al., (2020).  The version under active development and additional example scripts showing  how the package can be applied can be found at <https://github.com/ArdenB/TSSRESTREND>.
Methods to 
	retrieve data in the Statistical Data and Metadata Exchange ('SDMX') format
	from several database. (For example,
	'EuroStat', the European Central Bank, the Organisation for Economic 
	Co-operation and Development, the 'Unesco' Institute for Statistics,
	and the International Labor Organization.)
	This is a wrapper for package 'RJSDMX'.
	Comprehensive examples of all the 'TS*' packages is provided in the
	vignette Guide.pdf with the 'TSdata' package.
Execution of various time series models and choosing the best one
    either by a specific error metric or by picking the best one by majority vote.
    The models are based on the "forecast" package, written by Prof. Rob Hyndman.
It performs the smoothing approach provided by penalized least squares for univariate and bivariate time series, as proposed by Guerrero (2007) and Gerrero et al. (2017). 
          This allows to estimate the time series trend by controlling the amount of resulting (joint) smoothness.
          ---
          Guerrero, V.M (2007)  <DOI:10.1016/j.spl.2007.03.006>.
          Guerrero, V.M; Islas-Camargo, A. and Ramirez-Ramirez, L.L. (2017) <DOI:10.1080/03610926.2015.1133826>.
Standard SQL query functions used by 
	SQL plugins packages for the 'TSdbi' interface to time series databases. 
	It will mainly be used by other packages rather than directly by end
	users. The one exception is the function 'TSquery' which can be used to
	construct a time series from a database containing observations over
	time (e.g. balance statements for multiple years), but where the database
	is not specifically designed to store time series (as with other 
	'TSdbi' SQL plugin packages).
	Comprehensive examples of all the 'TS*' packages is provided in the
	vignette Guide.pdf with the 'TSdata' package.
An 'SQLite' interface for 'TSdbi'.
	Comprehensive examples of all the 'TS*' packages is provided in the
	vignette Guide.pdf with the 'TSdata' package.
Functions for statistical analysis, modeling and simulation of time
 series with state space model, based on the methodology in Kitagawa
 (2020, ISBN: 978-0-367-18733-0).
Provides a set of tools for descriptive and predictive analysis of time series data. That includes functions for interactive visualization of time series objects and as well utility functions for automation time series forecasting.
Plot official statistics' time series conveniently: automatic legends, highlight windows, stacked bar chars with positive and negative contributions, sum-as-line option, two y-axes with automatic horizontal grids that fit both axes and other popular chart types. 'tstools' comes with a plethora of defaults to let you plot without setting an abundance of parameters first, but gives you the flexibility to tweak the defaults. In addition to charts, 'tstools' provides a super fast, 'data.table' backed time series I/O that allows the user to export / import long format, wide format and transposed wide format data to various file types.
A ternary search tree is a type of prefix tree with up to three children and the ability for incremental string search. The package uses this ability for word auto-completion and spell checking. Includes a dataset with the 10001 most frequent English words.
Interactive laboratory of Time Series based in Box-Jenkins methodology.
Includes: (i) tests and visualisations that can help the modeller explore time series components and perform decomposition; (ii) modelling shortcuts, such as functions to construct lagmatrices and seasonal dummy variables of various forms; (iii) an implementation of the Theta method; (iv) tools to facilitate the design of the forecasting process, such as ABC-XYZ analyses; and (v) "quality of life" functions, such as treating time series for trailing and leading values.
Fitting tree-structured varying coefficient models (Berger et al. (2018), <doi:10.1007/s11222-018-9804-8>). Simultaneous detection of covariates with varying coefficients and effect modifiers that induce varying coefficients if they are present.
An 'RStudio' add-in to visualize time series. Time series are searched in the global environment as data.frame objects with a column of type date and a column of type numeric. Interactive charts are produced using 'plotly' package.
Tools for timescale decomposition of the classic variance ratio of community ecology. Tools are as described in Zhao et al (in prep), extending commonly used methods introduced by Peterson et al (1975) <doi: 10.2307/1936306>.
Accompanies the text Applied Time Series Analysis with R, 2nd edition by Woodward, Gray, and Elliott. It is helpful for data analysis and for time series instruction.
Characterisation of the extremal dependence structure of time series, avoiding pre-processing and filtering as done typically with peaks-over-threshold methods. It uses the conditional approach of Heffernan and Tawn (2004) <DOI:10.1111/j.1467-9868.2004.02050.x> which is very flexible in terms of extremal and asymptotic dependence structures, and Bayesian methods improve efficiency and allow for deriving measures of uncertainty. For example, the extremal index, related to the size of clusters in time, can be estimated and samples from its posterior distribution obtained.
This interface was created to develop a standard procedure 
 to analyse temporal trend in the framework of the OSPAR convention.
 The analysis process run through 4 successive steps : 1) manipulate your data, 2)
 select the parameters you want to analyse, 3) build your regulated 
 time series, 4) perform diagnosis and analysis and 5) read the results. 
 Statistical analysis call other package function such as Kendall tests
 or cusum() function.
Computes a point pattern in R^2 or on a graph that is representative of a collection of many data patterns. The result is an approximate barycenter (also known as Fréchet mean or prototype) based on a transport-transform metric. Possible choices include Optimal SubPattern Assignment (OSPA) and Spike Time metrics. Details can be found in Müller, Schuhmacher and Mateu (2019) <arXiv:1909.07266>.
U.S. Department of the Treasury, Alcohol and Tobacco Tax and
    Trade Bureau (TTB) collects data and reports on monthly beer
    industry production and operations. This data package includes
    a collection of 10 years (2006 - 2015) worth of data on materials
    used at U.S. breweries in pounds reported by the Brewer's Report
    of Operations and the Quarterly Brewer's Report of Operations
    forms, ready for data analysis. This package also includes historical
    tax rates on distilled spirits, wine, beer, champagne, and tobacco
    products as individual data sets.
The analysis of microarray time series promises a deeper insight into the dynamics of the cellular response following stimulation. A common observation in this type of data is that some genes respond with quick, transient dynamics, while other genes change their expression slowly over time. The existing methods for detecting significant expression dynamics often fail when the expression dynamics show a large heterogeneity. Moreover, these methods often cannot cope with irregular and sparse measurements. The method proposed here is specifically designed for the analysis of perturbation responses. It combines different scores to capture fast and transient dynamics as well as slow expression changes, and performs well in the presence of low replicate numbers and irregular sampling times. The results are given in the form of tables including links to figures showing the expression dynamics of the respective transcript. These allow to quickly recognise the relevance of detection, to identify possible false positives and to discriminate early and late changes in gene expression. An extension of the method allows the analysis of the expression dynamics of functional groups of genes, providing a quick overview of the cellular response. The performance of this package was tested on microarray data derived from lung cancer cells stimulated with epidermal growth factor (EGF). Paper: Albrecht, Marco, et al. (2017)<DOI:10.1186/s12859-016-1440-8>.
The 'tinytest' package offers a light-weight zero-dependency unit-testing
 framework to which this package adds support of the 'diffobj' package for 'diff'-style
 comparison of R objects.
Interactive shiny application for working with ttest on data. Results for analysis are provided.
C source code and R wrappers for the tth/ttm TeX-to-HTML/MathML translators.
Computing the first two moments of the truncated multivariate t (TMVT) distribution under the double truncation. Appling the slice sampling algorithm to generate random variates from the TMVT distribution.
Several forms of likelihood ratio calculations are available.
A collection of over 50 technical indicators for creating technical trading rules. The package also provides fast implementations of common rolling-window functions, and several volatility calculations.
Time-Temperature Superposition analysis is often applied to frequency modulated data obtained by Dynamic
		Mechanic Analysis (DMA) and Rheometry in the analytical chemistry and physics
		areas. These techniques provide estimates of material mechanical properties
		(such as moduli) at different temperatures in a wider range of time. This
		package provides the Time-Temperature superposition Master Curve at a referred
		temperature by the three methods: the two wider used methods, Arrhenius based
		methods and WLF, and the newer methodology based on derivatives procedure.
		The Master Curve is smoothed by B-splines basis. The package output is composed
		of plots of experimental data, horizontal and vertical shifts, TTS data, and TTS
		data fitted using B-splines with bootstrap confidence intervals.
A screening process utilizing training and testing samples to filter out uninformative DNA methylation sites. Surrogate variables (SVs) of DNA methylation are included in the filtering process to explain unknown factor effects.
Tensor-train is a compact representation for higher-order tensors. Some algorithms for performing tensor-train decomposition are available such as TT-SVD, TT-WOPT, and TT-Cross. For the details of the algorithms, see I. V. Oseledets (2011) <doi:10.1137/090752286>, Yuan Longao, et al (2017) <arXiv:1709.02641>, I. V. Oseledets (2010) <doi:10.1016/j.laa.2009.07.024>.
Implementation of Time to Target plot based on the work 
             of Ribeiro and Rosseti (2015) <DOI:10.1007/s11590-014-0760-8>, 
             that describe a numerical method that gives the probability of 
             an algorithm A finds a solution at least as good as a given 
             target value in smaller computation time than algorithm B.
This package makes Travel To Work Area from a commuting flow data frame.
Get comments posted on YouTube videos, information on how many 
    times a video has been liked, search for videos with particular content, and 
    much more. You can also scrape captions from a few videos. To learn more about
    the YouTube API, see <https://developers.google.com/youtube/v3/>.
Get statistics and reports from YouTube. To learn more about
    the YouTube Analytics and Reporting API, see <https://developers.google.com/youtube/reporting/>.
Performs Three-Mode Principal Components Analysis,
    which carries out Tucker Models.
Provides R Markdown output formats to use Tufte styles for PDF and HTML output.
Custom template and output formats for use with rmarkdown. Produce
    Edward Tufte-style handouts in html formats with full support for rmarkdown
    features
Perform the conventional Tukey test from formula, lm, aov, aovlist and lmer objects.
Tukey regions are polytopes in the Euclidean space, viz. 
    upper-level sets of the Tukey depth function on given data. The bordering 
    hyperplanes of a Tukey region are computed as well as its vertices, facets, 
    centroid, and volume. In addition, the Tukey median set, which is the 
    non-empty Tukey region having highest depth level, and its barycenter 
    (= Tukey median) are calculated. Tukey regions are visualized in dimension 
    two and three. For details see Liu, Mosler, and Mozharovskyi 
    (2019, <doi:10.1080/10618600.2018.1546595>). See file LICENSE.note for 
    additional license information.
Provides wrapper functions to the multiple marginal model function mmm() of package 'multcomp' to implement the trend test of Tukey, Ciminera and Heyse (1985) <DOI:10.2307/2530666> for general parametric models.
Integrates several popular high-dimensional methods based on Linear Discriminant Analysis (LDA) and provides a comprehensive and user-friendly toolbox for linear, semi-parametric and tensor-variate classification as mentioned in Yuqing Pan, Qing Mai and Xin Zhang (2019) <arXiv:1904.03469>. Functions are included for covariate adjustment, model fitting, cross validation and prediction.
Provides an R-interface to the Tumblr web API (see Tumblr v2 API on <https://www.tumblr.com/docs/en/api/v2>). Tumblr is a microblogging platform and social networking website (<https://www.tumblr.com>).
A tool to obtain tumor growth rates from clinical trial patient data.  Output includes individual and summary data for tumor growth rate estimates as well as optional plots of the observed and predicted tumor quantity over time.
The ability to tune models is important. 'tune' contains functions and
    classes to be used in conjunction with other 'tidymodels' packages for 
    finding reasonable values of hyper-parameters in models, pre-processing
    methods, and post-processing steps.
Generic methods for parameter tuning of classification algorithms using multiple scoring functions.
Analyze music and speech, extract features like MFCCs, handle wave files and their representation in various ways, read mp3, read midi, perform steps of a transcription, ...
        Also contains functions ported from the 'rastamat' 'Matlab' package.
Tuning random forest with one line. The package is mainly based on the packages 'ranger' and 'mlrMBO'.
Functions to find all matches or non-matches, orphans, and
    duplicate or other replicated elements.
Algorithms for accelerating the convergence of slow,
        monotone sequences from smooth, contraction mapping such as the
        EM and MM algorithms. It can be used to accelerate any smooth,
        linearly convergent acceleration scheme.  A tutorial style
        introduction to this package is available in a vignette on the
        CRAN download page or, when the package is loaded in an R
        session, with vignette("turboEM").
Package for analyzing TURF (Total Unduplicated Reach and Frequency) data in R. 
    No looping in TURF algorithm results in fast processing times. Allows for individual-level 
	weights, depth specification, and user-truncated combination set(s). Allows user to substitute 
	Monte Carlo simulated combination set(s) after set(s) exceed a user-specified limit.
Package designed for working with vectors and lists of vectors,
    mainly for turning them into other indexed data structures.
An implementation of turtle graphics
    <http://en.wikipedia.org/wiki/Turtle_graphics>.
    Turtle graphics comes from Papert's language Logo and has
    been used to teach concepts of computer programming.
Helps the R users to get data from 'Tushare Pro'<https://tushare.pro>.
    'Tushare Pro' is a platform as well as a community with a lot of staffs working in financial area.
    We support financial data such as stock price, financial report statements and digital coins data.
DataCamp Light (<https://github.com/datacamp/datacamp-light>) is a light-weight implementation of the DataCamp UI,
  that allows you to embed interactive exercises inside HTML documents. The tutorial package makes it easy to create these
  HTML files from R Markdown files. An extension to knitr, tutorial detects appropriately formatted code chunks and replaces them
  with DataCamp Light readable chunks in the resulting HTML file.
Models of time-uncertain time series addressing frequency and non-frequency behavior of continuous and discrete (counting) data.
The model, developed at the Vienna University of Technology, is a lumped conceptual rainfall-runoff model, following the structure of the HBV model. 
             The model can also be run in a semi-distributed fashion and with dual representation of soil layer.
             The model runs on a daily or shorter time step and consists of a snow routine, a soil moisture routine and a flow routing routine. 
             See Parajka, J., R. Merz, G. Bloeschl (2007) <DOI:10.1002/hyp.6253> Uncertainty and multiple objective calibration in regional water balance modelling: case study in 320 Austrian catchments, Hydrological Processes, 21, 435-446.
Total Variation Denoising is a regularized denoising method which
    effectively removes noise from piecewise constant signals whilst preserving
    edges.  This package contains a C++ implementation of Condat's very fast 1D
    squared error loss TVD algorithm.  Additional methods and loss functions may
    be added in future versions.
Fits time-varying effect models (TVEM). These are a kind of application of varying-coefficient models in the context of longitudinal data, allowing the strength of linear, logistic, or Poisson regression relationships to change over time.  These models are described further in Tan, Shiyko, Li, Li & Dierker (2012) <doi:10.1037/a0025814>.  We thank Kaylee Litson, Patricia Berglund, and Yajnaseni Chakraborti for their valuable help with testing the package and documentation. The development of this package was part of a research project supported by National Institutes of Health grants P50 DA039838 from the National Institute of Drug Abuse and 1R01 CA229542-01 from the National Cancer Institute and the NIH Office of Behavioral and Social Science Research. Content is solely the responsibility of the authors and does not necessarily represent the official views of the funding institutions mentioned above. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
Probability mass (d), distribution (p), quantile (q), and random 
    number generating (r and rt) functions for the time-varying right-truncated 
    geometric (tvgeom) distribution. Also provided are functions to calculate the first 
    and second central moments of the distribution. The tvgeom distribution
    is similar to the geometric distribution, but the probability 
    of success is allowed to vary at each time step, and there are a limited 
    number of trials. This distribution is essentially a Markov chain, and it
    is useful for modeling Markov chain systems with a set 
    number of time steps.
Functions for managing cashflows and interest rate curves.
This is a statistical tool interactive that provides multivariate statistical tests that are more powerful than traditional Hotelling T2 test and LRT (likelihood ratio test) for the vector of normal mean populations with and without contamination and non-normal populations (Henrique J. P. Alves & Daniel F. Ferreira (2019) <DOI: 10.1080/03610918.2019.1693596>).
Provides tools for denoising noisy signal and images via
    Total Variation Regularization. Reducing the total variation of
    the given signal is known to remove spurious detail while preserving
    essential structural details. For the seminal work on the topic,
    see Rudin et al (1992) <doi:10.1016/0167-2789(92)90242-F>.
Fitting time-varying coefficient models for single and multi-equation regressions, using kernel smoothing techniques.
Contains various 'ggplot2' themes and color palettes based on TV shows 
    such as 'Game of Thrones', 'Brooklyn Nine-Nine', 'Avatar: The Last Airbender',
    'Spongebob Squarepants', and more.
Provides functions for propensity score
        estimating and weighting, nonresponse weighting, and diagnosis
        of the weights.
Maximum likelihood computations for Tweedie families, including the series expansion (Dunn and Smyth, 2005; <doi:10.1007/s11222-005-4070-y>) and the Fourier inversion  (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>), and related methods.
In order to create smooth animation between states of data,
    tweening is necessary. This package provides a range of functions for
    creating tweened data that can be used as basis for animation. Furthermore 
    it adds a number of vectorized interpolaters for common R data 
    types such as numeric, date and colour.
This is an improved implementation of the package 'StreamR' to
    capture tweets and store it into R, SQLite, 'postGIS' data base or GIS format. The package
    performs a description of harvested data and performs space time exploratory analysis.
Generates a game of 2048 that can be played in the
    console.  Supports grids of arbitrary sizes, undoing the last move,
    and resuming a game that was exited during the current session.
An R wrapper around the API of TheyWorkForYou, a parliamentary 
    monitoring site that scrapes and repackages Hansard (the UK's parliamentary 
    record) and augments it with information from the Register of Members' 
    Interests, election results, and voting records to provide a unified 
    source of information about UK legislators and their activities. See 
    <http://www.theyworkforyou.com> for details.
Twiddler is an interactive tool that automatically creates
        a Tcl/Tk GUI for manipulating variables in any R expression.
        See the documentation of the function twiddle to get started.
The Twilio web service provides an API for computer programs
    to interact with telephony. The included functions wrap the SMS and MMS 
    portions of Twilio's API, allowing users to send and receive text messages
    from R. See <https://www.twilio.com/docs/> for more information.
Provides an interface to the Twitter web API.
Provides an integration to the 'metatrader 5'. 
    The functionalities carry out automated trading using
    sentiment indexes computed from 'twitter' and/or 'stockwits'. 
    The sentiment indexes are based on the ph.d. dissertation 
    "Essays on Economic Forecasting Models" (Godeiro,2018) <https://repositorio.ufpb.br/jspui/handle/123456789/15198>
    The integration between the 'R' and the 'metatrader 5' allows sending buy/sell orders to the brokerage.
Include the Twitter status widgets in HTML pages created
  using R markdown. The package uses the Twitter javascript APIs to
  embed in your document Twitter cards associated to specific statuses.
  The main targets are regular HTML pages or dashboards.
Implementation of a Bayesian two-way latent structure model for integrative genomic clustering.  The model clusters samples in relation to distinct data sources, with each subject-dataset receiving a latent cluster label, though cluster labels have across-dataset meaning because of the model formulation.  A common scaling across data sources is unneeded, and inference is obtained by a Gibbs Sampler.  The model can fit multivariate Gaussian distributed clusters or a heavier-tailed modification of a Gaussian density.  Uniquely among integrative clustering models, the formulation makes no nestedness assumptions of samples across data sources -- the user can still fit the model if a study subject only has information from one data source. The package provides a variety of post-processing functions for model examination including ones for quantifying observed alignment of clusterings across genomic data sources.  Run time is optimized so that analyses of datasets on the order of thousands of features on fewer than 5 datasets and hundreds of subjects can converge in 1 or 2 days on a single CPU.  See "Swanson DM, Lien T, Bergholtz H, Sorlie T, Frigessi A, Investigating Coordinated Architectures Across Clusters in Integrative Studies: a Bayesian Two-Way Latent Structure Model, 2018, <doi:10.1101/387076>, Cold Spring Harbor Laboratory" at <https://www.biorxiv.org/content/early/2018/08/07/387076.full.pdf> for model details.
The TWN-list (Taxa Waterbeheer Nederland) is the Dutch standard for naming 
    taxons in Dutch Watermanagement. This package makes it easier to use the 
    TWN-list for ecological analyses. It  consists of two parts. First it makes the 
    TWN-list itself available in R. Second, it has a few functions that make it 
    easy to perform some basic and often recurring tasks for checking and consulting
    taxonomic data from the TWN-list.
A system to simulate clinical trials with time to event endpoints. Event simulation is based on Cox models allowing for covariates in addition to the treatment or group factor. Specific drop-out rates (separate from administrative censoring) can be controlled in the simulation. Other features include stratified randomization, non-proportional hazards, different accrual patterns, and event projection (timing to reach the target event) based on interim data.
This package implements the nonparametric test of equality
        between two copulas proposed by Remillard and Scaillet in their
        2009 JMVA paper.
Estimation of gene-treatment interactions in randomized clinical trials exploiting gene-treatment independence.
Application of two-regression algorithms for wearable
    research devices. It provides an easy way for users to read in
    device data files and apply an appropriate two-regression
    algorithm. More information is available from
    Hibbing PR, LaMunion SR, Kaplan AS, & Crouter SE (2017)
    <doi:10.1249/MSS.0000000000001532>.
Fast randomization based two sample tests. 
  Testing the hypothesis that two samples come from the same distribution using randomization to create p-values. Included tests are: Kolmogorov-Smirnov, Kuiper, Cramer-von Mises, Anderson-Darling, Wasserstein, and DTS. The default test (two_sample) is based on the DTS test statistic, as it is the most powerful, and thus most useful to most users. 
  The DTS test statistic builds on the Wasserstein distance by using a weighting scheme like that of Anderson-Darling. See the companion paper at <arXiv:2007.01360> or <https://codowd.com/public/DTS.pdf> for details of that test statistic, and non-standard uses of the package (parallel for big N, weighted observations, one sample tests, etc). We also include the permutation scheme to make test building simple for others.
For high-dimensional data whose main feature is a large number, p, of variables but a small sample size, the null hypothesis that the marginal distributions of p variables are the same for two groups is tested. We propose a test statistic motivated by the simple idea of comparing, for each of the p variables, the empirical characteristic functions computed from the two samples. If one rejects this global null hypothesis of no differences in distributions between the two groups, a set of permutation p-values is reported to identify which variables are not equally distributed in both groups.
Implements a variety of non-parametric methods for computing one-stage and two-stage confidence intervals, as well as point estimates of threshold values.
Conditional logistic regression with longitudinal follow up and
    individual-level random coefficients: A stable and efficient
    two-step estimation method.
Carries out analyses of two-way tables with one observation per cell, together with graphical displays
    for an additive fit and
    a diagnostic plot for removable 'non-additivity' via a power transformation of the response.
    It implements Tukey's Exploratory Data Analysis (1973) <ISBN: 978-0201076165> methods, including a
    1-degree-of-freedom test for row*column 'non-additivity', linear in the row and column effects.
Performs two-way tests in independent groups designs; Parametric Bootstrap based Generalized Test and Generalized Pivotal Quantity based Generalized Test (Weerahandi and Krishnamoorthy, 2019) <doi:10.1080/03610926.2017.1419264>. The package performs descriptive statistics and graphical approaches. Moreover, it assesses variance homogeneity and normality of data in each group via tests and plots. All 'twowaytests' functions are designed for two-way layout.
Efficient estimation of the population-level causal effects of
    stochastic interventions on a continuous-valued exposure. Both one-step and
    targeted minimum loss estimators are implemented for a causal parameter
    defined as the counterfactual mean of an outcome of interest under a
    stochastic intervention that may depend on the natural value of the
    exposure (i.e., a modified treatment policy). To accommodate settings in
    which two-phase sampling is employed, procedures for making use of inverse
    probability of censoring weights are provided to facilitate construction of
    inefficient and efficient one-step and targeted minimum loss estimators.
    The causal parameter and estimation methodology were first described by
    Díaz and van der Laan (2013) <doi:10.1111/j.1541-0420.2011.01685.x>).
    Estimation of nuisance parameters may be enhanced through the Super Learner
    ensemble model in 'sl3', available for download from GitHub using
    'remotes::install_github("tlverse/sl3")'.
Provides functions to produce rudimentary ascii graphics
        directly in the terminal window. Provides a basic plotting
        function (and equivalents of curve, density, acf and barplot)
        as well as boxplot and image functions.
This queue is a data structure that lets
  parallel processes send and receive messages,
  and it can help coordinate the work
  of complicated parallel tasks.
  Processes can push new messages to the queue,
  pop old messages, and obtain a
  log of all the messages ever pushed. File locking
  preserves the integrity of the data even when
  multiple processes access the queue simultaneously.
Provides a simple type annotation for R that is usable in scripts,
    in the R console and in packages. It is intended as a convention to allow other
    packages to use the type information to provide error checking,
    automatic documentation or optimizations.
Download and compile any version of the
  IANA Time Zone Database (also known as Olson database)
  and make it current in your R session.
  Beware: on Windows 'Cygwin' is required!
Despite there being a section in RFC 7231
    <https://tools.ietf.org/html/rfc7231#section-5.5.3> defining a suggested
    structure for 'User-Agent' headers this data is notoriously difficult
    to parse consistently. Tools are provided that will take in user agent
    strings and return structured R objects. This is a 'V8'-backed package
    based on the 'ua-parser' project <https://github.com/ua-parser>.
The Unmanned Aerial Vehicle Mission Planner provides an easy to use work flow for planning autonomous obstacle avoiding surveys of (almost) ready to fly unmanned aerial vehicles to retrieve aerial or spot related data. It creates either intermediate flight control files for the DJI phantom series or ready to upload control files for the pixhawk based flight controller as used in the 3DR Solo. Additionally it contains some useful tools for digitizing and data manipulation.
Two Phase I designs are implemented in the package: the classical 3+3 and the Continual Reassessment Method. Simulations tools are also available to estimate the operating characteristics of the methods with several user-dependent options.
Complete work flow for the analysis of pharmacokinetic pharmacodynamic (PKPD), physiologically-based pharmacokinetic (PBPK) and systems pharmacology models including: creation of ordinary differential equation-based models, pooled parameter estimation, individual/population based simulations, rule-based simulations for clinical trial design and modeling assays, deployment with a customizable 'Shiny' app, and non-compartmental analysis. System-specific analysis templates can be generated and each element includes integrated reporting with 'PowerPoint' and 'Word'.
Provides a set of functions that can be used to obtain better predictive performance on cost-sensitive and cost/benefits tasks (for both regression and classification). This includes re-sampling approaches that modify the original data set biasing it towards the user preferences.
Fit Bayesian hierarchical models of animal abundance and occurrence
    via the 'rstan' package, the R interface to the 'Stan' C++ library.
    Supported models include single-season occupancy, dynamic occupancy, and
    N-mixture abundance models. Covariates on model parameters are specified
    using a formula-based interface similar to package 'unmarked', while also
    allowing for estimation of random slope and intercept terms. References:
    Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>;
    Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
This suite of packages is developed to predicts resistome for unknown chemical compounds. It utilizes two algorithms viz. deterministic model and stochastic model (manuscript under preparation) for the prediction of drug class. Once the drug class is predicted, the resistome profile of Escherichia coli and Pseudomonas aeruginosa for the drug class is fetched from the database.
This package contains latex, knitr and R Markdown templates that
    adhere to the UC Berkeley Graduate Division's thesis guidelines. The
    templates are located in the inst/ directory.
R bindings of the 'uchardet', encoding detector library from Mozilla
  (<https://www.freedesktop.org/wiki/Software/uchardet/>). It takes a sequence
  of bytes in an unknown character encoding and without any additional
  information, and attempts to get the encoding of the text. All return names of
  the encodings are iconv-compatible.
Clustering and classification inference for high dimension low sample size (HDLSS)
    data with U-statistics. The package contains implementations of nonparametric statistical
    tests for sample homogeneity, group separation, clustering, and classification of 
    multivariate data. The methods have high statistical power and are tailored for data
    in which the dimension L is much larger than sample size n. See Gabriela B. Cybis,
    Marcio Valk and Sílvia RC Lopes (2018) <doi:10.1080/00949655.2017.1374387> and Marcio 
    Valk and Gabriela B. Cybis (2018) <arXiv:1805.12179>.
An algorithm for general-purpose unconstrained non-linear optimization.
             The algorithm is of quasi-Newton type with BFGS updating of the inverse
             Hessian and soft line search with a trust region type monitoring of the
             input to the line search algorithm. The interface of 'ucminf' is
             designed for easy interchange with 'optim'.
Comprehensive analysis and forecasting 
             of univariate time series using automatic 
             unobserved components models and algorithms.
             Harvey, AC (1989) <doi:10.1017/CBO9781107049994>.
             Pedregal, DJ and Young PC (2002) <doi:10.1002/9780470996430>.
             Durbin J and Koopman SJ (2012) <doi:10.1093/acprof:oso/9780199641178.001.0001>.
Changes the column names of the inputted dataset to the correct
    names from the Uniform Crime Report codebook for the "Offenses Known and
    Clearance by Arrest" datasets from 1998-2014.
Provides a web app for downloading, analyzing and
    visualizing datasets from UCSC Xena (<http://xena.ucsc.edu/>), which is a collection of
    UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE,
    and others.
Download and explore datasets from UCSC Xena data hubs, which are
    a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
    Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
A client for the Urban Dictionary <http://www.urbandictionary.com/> API.
The udder quarter infection data set contains infection times of individual cow udder quarters with Corynebacterium bovis (Laevens et al. 1997 <DOI:10.3168/jds.S0022-0302(97)76295-7>). Obviously, the four udder quarters are clustered within a cow, and udder quarters are sampled only approximately monthly, generating interval-censored data. The data set contains both covariates that change within a cow (e.g., front and rear udder quarters) and covariates that change between cows (e.g., parity [the number of previous calvings]). The correlation between udder infection times within a cow also is of interest, because this is a measure of the infectivity of the agent causing the disease. Various models have been applied to address the problem of interdependence for right-censored event times. These models, as applied to this data set, can be found back in the publications found in the reference list.
This natural language processing toolkit provides language-agnostic
    'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency
    parsing' of raw text. Next to text parsing, the package also allows you to train
    annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided
    at <https://universaldependencies.org/format.html>. The techniques are explained
    in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0
    with UDPipe', available at <doi:10.18653/v1/K17-3009>. 
    The toolkit also contains functionalities for commonly used data manipulations on texts 
    which are enriched with the output of the parser. Namely functionalities and algorithms 
    for collocations, token co-occurrence, document term matrix handling, 
    term frequency inverse document frequency calculations,
    information retrieval metrics (Okapi BM25), handling of multi-word expressions,
    keyword detection (Rapid Automatic Keyword Extraction, noun phrase extraction, syntactical patterns) 
    sentiment scoring and semantic similarity analysis.
Provides simple bindings to Unidata's udunits library.
A set of tools to read, process, and summarize Agilent Cary 620 uFTIR Microscope hyperspectral images
    primarily intended for microplastic analysis.
Maximum likelihood estimation of univariate Gaussian Mixture Autoregressive (GMAR),
    Student's t Mixture Autoregressive (StMAR), and Gaussian and Student's t Mixture Autoregressive (G-StMAR) models, 
    quantile residual tests, graphical diagnostics, forecast and simulate from GMAR, StMAR and G-StMAR processes. 
    Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2015) <doi:10.1111/jtsa.12108>, 
    Mika Meitz, Daniel Preve, Pentti Saikkonen (2018) <arXiv:1805.04010>,
    Savi Virolainen (2020) <arXiv:2003.05221>.
Construct a Hidden Markov Model with states learnt by unsupervised classification.
Implements functions to derive uncertainty intervals for (i) regression (linear and probit) parameters when outcome is missing not at random (non-ignorable missingness) introduced in Genbaeck, M., Stanghellini, E., de Luna, X. (2015) <doi:10.1007/s00362-014-0610-x> and Genbaeck, M., Ng, N., Stanghellini, E., de Luna, X. (2018) <doi:10.1007/s10433-017-0448-x>; and (ii) double robust and outcome regression estimators of average causal effects (on the treated) with possibly unobserved confounding introduced in Genbaeck, M., de Luna, X. (2018) <doi:10.1111/biom.13001>.
A set of custom 'R' 'Markdown' templates for documents and
   presentations with the University of Illinois at Urbana-Champaign (UIUC)
   color scheme and identity standards.
Full listing of UK baby names occurring more than three times per year between 1996 and 2015, and rankings of baby name popularity by decade from 1904 to 1994.
A set of tools to create a UK Biobank <http://www.ukbiobank.ac.uk/> dataset from a UKB fileset (.tab, .r, .html),
    visualize primary demographic data for a sample subset, query ICD diagnoses,
    retrieve genetic metadata, read and write standard file formats for genetic analyses.
Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the packages uses NRFA peak flow dataset version 9. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Proposal of the ‘extreme rank plot’ for extreme value analysis: with an emphasis on flood frequency studies", Hammond (2019, <doi:10.2166/nh.2019.157>). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Improving the FEH statistical procedures for flood frequency estimation", Environment Agency (2008, ISBN: 978 1 84432 920 5). "Low flow estimation in the United Kingdom", Institute of Hydrology (1992, ISBN 0 948540 45 1). Wallingford HydroSolutions, (2016, <http://software.hydrosolutions.co.uk/winfap4/Urban-Adjustment-Procedure-Technical-Note.pdf>). Data from the UK National River Flow Archive (<https://nrfa.ceh.ac.uk/>, terms and conditions: <https://nrfa.ceh.ac.uk/costs-terms-and-conditions>.
Allows users to access live UK energy market information via various APIs.
A time series of the national grid demand (high-voltage electric power transmission network) in the UK since 2011.
Access data from Land Registry Open Data
    <http://landregistry.data.gov.uk/> through 'SPARQL' queries. 'uklr'
    supports the house price index, transaction and price paid data.
Downloads data from the 'UK Police' public data API, 
    the full docs of which are available at <https://data.police.uk/docs/>. 
    Includes data on police forces and police force areas, crime reports, 
    and the use of stop-and-search powers.
Universally unique identifiers ('UUIDs') can be suboptimal
        for many uses-cases because they aren't the most character
        efficient way of encoding 128 bits of randomness; v1/v2 versions
        are impractical in many environments, as they require access to a
        unique, stable MAC address; v3/v5 versions require a unique seed
        and produce randomly distributed IDs, which can cause
        fragmentation in many data structures; v4 provides no other
        information than randomness which can cause fragmentation in many
        data structures. 'ULIDs' (<https://github.com/ulid/spec>) have
        128-bit compatibility with 'UUID', 1.21e+24 unique 'ULIDs' per
        millisecond, are lexicographically sortable, canonically encoded
        as a 26 character string, as opposed to the 36 character 'UUID',
        use Crockford's 'base32' for better efficiency and readability (5
        bits per character), are case insensitive, have no special
        characters (i.e. are 'URL' safe) and have a onotonic sort order
        (correctly detects and handles the same millisecond).
A generic reference Bayesian analysis of unidimensional mixture distributions obtained by a location-scale parameterisation of the model is implemented. The including functions simulate and summarize posterior samples for location-scale mixture models using a weakly informative prior. There is no need to define priors for scale-location parameters except two hyperparameters in which are associated with a Dirichlet prior for weights and a simplex.
Uniform manifold approximation and projection is a technique
    for dimension reduction. The algorithm was described by McInnes and
    Healy (2018) in <arXiv:1802.03426>. This package provides an interface
    for two implementations. One is written from scratch, including components
    for nearest-neighbor search and for embedding. The second implementation
    is a wrapper for 'python' package 'umap-learn' (requires separate
    installation, see vignette for more details).
By gaining the property of emergence through self-organization, the enhancement of SOMs(self organizing maps) is called Emergent SOM (ESOM). The result of the projection by ESOM is a grid of neurons which can be visualised as a three dimensional landscape in form of the Umatrix. Further details can be found in the referenced publications (see url). This package offers tools for calculating and visualising the ESOM as well as Umatrix, Pmatrix and UStarMatrix. All the functionality is also available through graphical user interfaces implemented in 'shiny'.
Calculates one-sample unbiased central moment estimates and 
    two-sample pooled estimates up to 6th order, including estimates of 
    powers and products of central moments. Provides the machinery for 
    obtaining unbiased central moment estimators beyond 6th order by generating
    expressions for expectations of raw sample moments and their powers and 
    products. 
    Gerlovina and Hubbard (2019) <doi:10.1080/25742558.2019.1701917>.
Does uniformly most powerful (UMP) and uniformly most
    powerful unbiased (UMPU) tests.  At present only distribution implemented
    is binomial distribution.  Also does fuzzy tests and confidence intervals
    (following Geyer and Meeden, 2005, <doi:10.1214/088342305000000340>)
    for the binomial
    distribution (one-tailed procedures based on UMP test and two-tailed
    procedures based on UMPU test).
The Ultimate Microrray Prediction, Reality and Inference
  Engine (UMPIRE) is a package to facilitate the simulation of realistic
  microarray data sets with links to associated outcomes. See Zhang and
  Coombes (2012) <doi:10.1186/1471-2105-13-S13-S1>. Version 2.0 adds the
  ability to simulate realistic mixed-typed clinical data.
Unmatched regression refers to the regression setting where
    covariates and predictors are collected separately/independently and so are not paired
    together, as in the usual regression setting.   Balabdaoui, Doss, and Durot (2020) <arXiv:2007.00830>
    study the unmatched regression setting where the univariate regression function is known to
    be monotone.     This package implements (two) gradient    descent method(s) to
    compute the estimator developed in  Balabdaoui, Doss, and Durot (2020).
Quickly create, run, and report structural equation and twin models.
    See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS.
    Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R.
    Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.
A dataset is said to be unbalanced when the class of interest (minority class) is much rarer than normal behaviour (majority class). The cost of missing a minority class is typically much higher that missing a majority class. Most learning systems are not prepared to cope with unbalanced data and several techniques have been proposed. This package implements some of most well-known techniques and propose a racing algorithm to select adaptively the most appropriate strategy for a given unbalanced task.
The package implements top-down and bottom-up algorithms
        for nonparametric function estimation in Gaussian noise using
        Unbalanced Haar wavelets.
If a procedure consists of several stages and there are several models that can be selected for each stage,
	uncertainty of the procedure can be decomposed by stages or models.
	This package includes the ANOVA-based method, the cumulative uncertainty-based method, and the balanced decomposition method.
	Yongdai Kim et al. (2019) <doi:10.1016/j.hydroa.2019.100024> is a related paper which is accessible via the URL below.
Functions for the determination of an uncertain interval, that is, a
    range of test scores that is inconclusive and does not allow a classification other
    than 'Uncertain' (Reference: J.A. Landsheer (2016) <doi:10.1371/journal.pone.0166007>).
Implements the Gaussian method of first and second order, the Kragten numerical method and the Monte Carlo simulation method for uncertainty estimation and analysis.
Consensus clustering by the unification of clustering results from multiple datasets using external specifications.
Dataset contains select attributes for each match result since 1949-1950 season for UNC men's basketball team.
Calculate several understandability metrics of BPMN models. BPMN stands for business process modelling notation and is a language for expressing business processes into business process diagrams. Examples of these understandability metrics are: average connector degree, maximum connector degree, sequentiality, cyclicity, diameter, depth, token split, control flow complexity, connector mismatch, connector heterogeneity, separability, structuredness and cross connectivity. See R documentation and paper on metric implementation included in this package for more information concerning the metrics.
Computes a universal numeric fingerprint (UNF) for an R data
    object. UNF is a cryptographic hash or signature that can be used to uniquely
    identify (a version of) a rectangular dataset, or a subset thereof. UNF can
    be used, in tandem with a DOI, to form a persistent citation to a versioned
    dataset.
Stereological unfolding of the joint size-shape-orientation distribution of spheroidal shaped particles.
Makes it easy to extract data from a survey. You can use an 
    explanatory variable and make multiple contingency tables for all variables
    in a data frame. You can also summarize response alternatives.
    URL: <https://en.wikipedia.org/wiki/Contingency_table>.
Use syntax inspired by the package 'glue' to extract matched substrings in a more intuitive and compact way than by using standard regular expressions.
Versatile method for ungrouping histograms (binned count data) 
 assuming that counts are Poisson distributed and that the underlying sequence 
 on a fine grid to be estimated is smooth. The method is based on the composite 
 link model and estimation is achieved by maximizing a penalized likelihood. 
 Smooth detailed sequences of counts and rates are so estimated from the binned 
 counts. Ungrouping binned data can be desirable for many reasons: Bins can be 
 too coarse to allow for accurate analysis; comparisons can be hindered when 
 different grouping approaches are used in different histograms; and the last 
 interval is often wide and open-ended and, thus, covers a lot of information 
 in the tail area. Age-at-death distributions grouped in age classes and 
 abridged life tables are examples of binned data. Because of modest assumptions, 
 the approach is suitable for many demographic and epidemiological applications. 
 For a detailed description of the method and applications see 
 Rizzi et al. (2015) <doi:10.1093/aje/kwv020>.
Verb-like functions to work with messy data, often derived from 
             spreadsheets or parsed PDF tables. Includes functions for unwrapping 
             values broken up across rows, relocating embedded grouping values, 
             and to annotate meaningful formatting in spreadsheet files.
Nonparametric estimation of a unimodal or U-shape covariate effect under additive hazards model.
Data from Unicode 13.0.0 and related utilities.
Efficient procedures for constructing uniform design of experiments under various space-filling criteria. It is based on a stochastic and adaptive threshold accepting algorithm with flexible initialization, adaptive threshold, and stochastic evolution. The package may also construct the augmented uniform designs in a sequential manner.
Uniform sampling of Directed Acyclic Graphs (DAG) using exact
 enumeration by relating each DAG to a sequence of outpoints (nodes with no
 incoming edges) and then to a composition of integers as suggested by
 Kuipers, J. and Moffa, G. (2015) <doi:10.1007/s11222-013-9428-y>.
Probability functions, family for glm() and Stan code for working with the unifed distribution (Quijano Xacur, 2019; <doi:10.1186/s40488-019-0102-6>).
In many phase I trials, the design goal is to find the dose associated with a certain target toxicity rate. In some trials, the goal can be to find the dose with a certain weighted sum of rates of various toxicity grades. For others, the goal is to find the dose with a certain mean value of a continuous response. This package provides the setup and calculations needed to run a dose-finding trial with non-binary endpoints and performs simulations to assess design’s operating characteristics under various scenarios. Three dose finding designs are included in this package: unified phase I design (Ivanova et al. (2009) <doi:10.1111/j.1541-0420.2008.01045.x>), Quasi-CRM/Robust-Quasi-CRM (Yuan et al. (2007) <doi:10.1111/j.1541-0420.2006.00666.x>, Pan et al. (2014) <doi:10.1371/journal.pone.0098147>) and generalized BOIN design (Mu et al. (2018) <doi:10.1111/rssc.12263>). The toxicity endpoints can be handled with these functions including equivalent toxicity score (ETS), total toxicity burden (TTB), general continuous toxicity endpoints, with incorporating ordinal grade toxicity information into dose-finding procedure. These functions allow customization of design characteristics to vary sample size, cohort sizes, target dose-limiting toxicity (DLT) rates, discrete or continuous toxicity score, and incorporate safety and/or stopping rules.
Uniform sampling on various geometric shapes, such as spheres, ellipsoids, simplices.
Goodness-of-fit tests for the uniform distribution.
Perform L1 or L2 isotonic and unimodal regression on 1D weighted or unweighted input vector and isotonic regression on 2D weighted or unweighted input vector. It also performs L infinity isotonic and unimodal regression on 1D unweighted input vector. Reference: Quentin F. Stout (2008) <doi:10.1016/j.csda.2008.08.005>. Spouge, J., Wan, H. & Wilbur, W.(2003) <doi:10.1023/A:1023901806339>. Q.F. Stout (2013) <doi:10.1007/s00453-012-9628-4>.
Define and use graphical elements of corporate design manuals in R. The 'unikn' package provides color functions (by defining dedicated colors and color palettes, and commands for changing, viewing, and using them) and styled text elements (e.g., for marking, underlining, or plotting colored titles). The pre-defined range of colors and text functions is based on the corporate design of the University of Konstanz <https://www.uni-konstanz.de/>, but can be adapted and extended for other institutions and purposes.
Implementation of "light" stemmers for French, German, Italian, Spanish, Portuguese, Finnish, Swedish. 
  They are based on the same work as the "light" stemmers found in 'SolR' <https://lucene.apache.org/solr/> or 'ElasticSearch' <https://www.elastic.co/fr/products/elasticsearch>. 
  A "light" stemmer consists in removing inflections only for noun and adjectives. 
  Indexing verbs for these languages is not of primary importance compared to nouns and adjectives. 
  The stemming procedure for French is described in (Savoy, 1999) <doi:10.1002/(SICI)1097-4571(1999)50:10%3C944::AID-ASI9%3E3.3.CO;2-H>.
Connect to Uniprot <https://www.uniprot.org/> to retrieve information about proteins using their accession number such information could be name or taxonomy information, For detailed information kindly read the publication <https://www.sciencedirect.com/science/article/pii/S1874391919303859>.
For each string in a set of strings, determine a unique tag that is a substring of fixed size k unique to that string, if it has one. If no such unique substring exists, the least frequent substring is used. If multiple unique substrings exist, the lexicographically smallest substring is used. This lexicographically smallest substring of size k is called the "UniqTag" of that string.
Univariate spline regression. It is possible to add the shape constraint of unimodality and predefined or
	self-defined penalties on the B-spline coefficients.
Provides the ability to read 'Unisens' data into R. 'Unisens' is a universal data format for multi sensor data.
The uc.check() function checks whether the roots of a given polynomial lie outside the Unit circle. You can also easily draw an unit circle.
United is a software tool which can be downloaded at the following
    website <http://www.schroepl.net/pbm/software/united/>. In general, it is
    a virtual manager game for football teams. This package contains helpful
    functions for determining an optimal formation for a virtual match in
    United. E.g. knowing that the opponent has a strong defensive it is
    advisable to beat him in the midfield. Furthermore, this package contains
    functions for computing the optimal usage of hardness in a game.
Simplifies regression tests by comparing objects produced by test
    code with earlier versions of those same objects.  If objects are unchanged
    the tests pass, otherwise execution stops with error details.  If in
    interactive mode, tests can be reviewed through the provided interactive
    environment.
Support for measurement units in R vectors, matrices
	and arrays: automatic propagation, conversion, derivation
	and simplification of units; raising errors in case of unit
	incompatibility. Compatible with the POSIXct, Date and difftime 
	classes. Uses the UNIDATA udunits library and unit database for 
	unit compatibility checking and conversion.
	Documentation about 'units' is provided in the paper by Pebesma, Mailund &
  Hiebert (2016, <doi:10.32614/RJ-2016-061>), included in this package as a
  vignette; see 'citation("units")' for details.
Concise TAP <http://testanything.org/> compliant unit testing package. Authored tests can be run using CMD check with minimal implementation overhead.
Assess essential unidimensionality using external validity
    information  using the procedure proposed by Ferrando & Lorenzo-Seva
    (2019) <doi:10.1177/0013164418824755>. Provides two indices for assessing
    differential  and incremental validity, both based on a second-order 
    modelling schema for the general factor.
User-friendly maximum likelihood estimation (Fisher (1921) 
    <doi:10.1098/rsta.1922.0009>) of univariate densities.
Provides S3 generic methods and some default implementations
    for Bayesian analyses that generate Markov Chain Monte Carlo (MCMC) samples.
    The purpose of 'universals' is to reduce package dependencies and conflicts.
    The 'nlist' package implements many of the methods for its 'nlist' class.
Well known outlier detection techniques in the univariate case. Methods to deal with skewed distribution are included too. The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of historical data is implemented as well. When available, survey weights can be used in outliers detection.
Pseudo-random number generation of 17 univariate distributions proposed by Demirtas. (2005) <DOI:10.22237/jmasm/1114907220>.
Bindings to system utilities found in most Unix systems such as
    POSIX functions which are not part of the Standard C Library.
Separate a data frame in two based on key columns. The function
 unjoin() provides an inside-out version of a nested data frame. This is used
 to identify duplication and normalize it (in the database sense) by linking
 two tables with the redundancy removed. This is a basic requirement for
 detecting topology within spatial structures that has motivated the need for
 this package as a building block for workflows within more applied projects.
Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates.
Fast flattening of hierarchical data structures (e.g. JSON and XML
             documents) into data.frames with a flexible spec language.
Assess the significance of identified clusters and estimates the true number of clusters by comparing the explained variation due to the clustering from the original data to that produced by clustering a unimodal reference distribution which preserves the covariance structure in the data. The reference distribution is generated using kernel density estimation and a Gaussian copula framework. A dimension reduction strategy and sparse covariance estimation optimize this method for the high-dimensional, low-sample size setting. This method is similar to them method described in Helgeson and Bair (2016) <arXiv:1610.01424> except a Gaussian copula approach is used to account for feature correlation.
Tools for converting data from complex or irregular layouts to a
    columnar structure.  For example, tables with multilevel column or row
    headers, or spreadsheets.  Header and data cells are selected by their
    contents and position, as well as formatting and comments where available,
    and are associated with one other by their proximity in given directions.
    Functions for data frames and HTML tables are provided.
Provides half-normal plots, reference plots, and Pareto plots
    of effects from an unreplicated experiment, along with various 
    pseudo-standard-error measures, simulated reference distributions, 
    and other tools. Many of these methods are described in 
    Daniel C. (1959) <doi:10.1080/00401706.1959.10489866> and/or
    Lenth R.V. (1989) <doi:10.1080/00401706.1989.10488595>, but some new
    approaches are added and integrated in one package.
Wraps the 'unrtf' utility to extract text from RTF files. Supports
    document conversion to HTML, LaTeX or plain text. Output in HTML is recommended
    because 'unrtf' has limited support for converting between character encodings.
Automatically converts language-specific verbal information, e.g., "1st half of the 19th century," to its standardized numerical counterparts, e.g., "1801-01-01/1850-12-31." It follows the recommendations of the 'MIDAS' ('Marburger Informations-, Dokumentations- und Administrations-System'), see <doi:10.11588/artdok.00003770>.
Performs a test for second-order stationarity of time series based
    on unsystematic sub-samples.
Hubbell's Unified Neutral Theory of Biodiversity.
Historical voting data of the United Nations General Assembly. This
    includes votes for each country in each roll call, as well as descriptions and
    topic classifications for each vote.
Implements empirical Bayes approaches to genotype
       polyploids from next generation sequencing data while
       accounting for allele bias, overdispersion, and sequencing
       error. The main functions are flexdog() and multidog(), 
       which allow the specification
       of many different genotype distributions. Also provided are functions to
       simulate genotypes, rgeno(), and read-counts, rflexdog(), as well as
       functions to calculate oracle genotyping error rates, oracle_mis(), and
       correlation with the true genotypes, oracle_cor(). These latter two
       functions are useful for read depth calculations. Run
       browseVignettes(package = "updog") in R for example usage. See
       Gerard et al. (2018) <doi:10.1534/genetics.118.301468> and
       Gerard and Ferrao (2020) <doi:10.1093/bioinformatics/btz852> for details 
       on the implemented methods.
Highly efficient Bayesian implementations of probit, logit, multinomial logit and binomial logit models. Functions for plotting and tabulating the estimation output are available as well. Estimation is based on Gibbs sampling where the Markov chain Monte Carlo algorithms are based on the latent variable representations and boosting algorithms outlined in Frühwirth-Schnatter S., Zens G., Wagner H. (2020) <arXiv:2011.06898>. The underlying implementation is written in C++.
An integrated package for building and testing uplift models
Provides a variety of plots and metrics to evaluate
    uplift models including the 'R uplift' package's Qini metric and Qini plot,
    a port of the 'python pylift' module's plotting function, and
    an alternative plot (in beta) useful for continuous outcomes.
    Background: Radcliffe (2007) <https://pdfs.semanticscholar.org/147b/32f3d56566c8654a9999c5477dded233328e.pdf>.
An implementation of the UPMASK method for performing membership
    assignment in stellar clusters in R. It is prepared to use photometry and
    spatial positions, but it can take into account other types of data. The
    method is able to take into account arbitrary error models, and it is
    unsupervised, data-driven, physical-model-free and relies on as few
    assumptions as possible. The approach followed for membership assessment is
    based on an iterative process, dimensionality reduction, a clustering
    algorithm and a kernel density estimation.
'UpSet.js' is a re-implementation of 'UpSetR' to create interactive set visualizations for more than three sets.
  This is a 'htmlwidget' wrapper around the 'JavaScript' library 'UpSet.js'.
Creates visualizations of intersecting sets using a novel matrix
    design, along with visualizations of several common set, element and attribute
    related tasks (Conway 2017) <doi:10.1093/bioinformatics/btx364>.
Variance approximations for the 
    Horvitz-Thompson total estimator in Unequal Probability Sampling
    using only first-order inclusion probabilities. 
    See Matei and Tillé (2005) and Haziza, Mecatti and Rao (2008) for details.
'Elasticsearch' is an open-source, distributed, document-based datastore
    (<https://www.elastic.co/products/elasticsearch>).
    It provides an 'HTTP' 'API' for querying the database and extracting datasets, but that
    'API' was not designed for common data science workflows like pulling large batches of
    records and normalizing those documents into a data frame that can be used as a training
    dataset for statistical models. 'uptasticsearch' provides an interface for 'Elasticsearch'
    that is explicitly designed to make these data science workflows easy and fun.
Provide a set of wrappers to call all the endpoints of UptimeRobot API
  which includes various kind of ping, keep-alive and speed tests.
  See <https://uptimerobot.com/> for more information.
Estimation and Inference for Unconditional Quantile Regression for cross-sectional and panel data (see Firpo et al. (2009) <DOI:10.3982/ECTA6822>).
Unit root and cointegration tests encountered in applied 
 econometric analysis are implemented.
Allows using two URL shortening services, which also provide
    expanding and analytic functions. Specifically developed for 'Bit.ly' (which requires OAuth2) and 'is.gd' (no API key).
A toolkit for all URL-handling needs, including encoding and decoding,
    parsing, parameter extraction and modification. All functions are
    designed to be both fast and entirely vectorised. It is intended to be
    useful for people dealing with web-related datasets, such as server-side
    logs, although may be useful for other situations involving large sets of
    URLs.
Seasonal unit roots and seasonal stability tests.
    P-values based on response surface regressions are available for both tests.
    P-values based on bootstrap are available for seasonal unit root tests.
S3 classes and methods for manipulation with georeferenced raster data: reading/writing, processing, multi-panel visualization.
A simple interface to the Geographic Header information
  from the "2010 US Census Summary File 2".  The entire Summary File 2
  is described at
  <https://catalog.data.gov/dataset/census-2000-summary-file-2-sf2>,
  but note that this package only provides access to parts of the
  geographic header ('geoheader') of the file.  In particular, only
  the first 101 columns of the geoheader are included and, more
  importantly, only rows with summary levels (SUMLEVs) 010 through 050
  (nation down through county level) are included.  In addition to
  access to (part of) the geoheader, the package also provides a
  decode function that takes a column name and value and, for certain
  columns, returns "the meaning" of that column (i.e., a "SUMLEV"
  value of 40 means "State"); without a value, the decode function
  attempts to describe the column itself.
Updated versions of the 1970's "US State Facts and
    Figures" objects from the 'datasets' package included with R. The new
    data is compiled from a number of sources, primarily from United
    States Census Bureau or the relevant federal agency.
The boundaries for geographical units in the United States of
    America contained in this package include state, county, congressional
    district, and zip code tabulation area. Contemporary boundaries are provided
    by the U.S. Census Bureau (public domain). Historical boundaries for the
    years from 1629 to 2000 are provided form the Newberry Library's 'Atlas of
    Historical County Boundaries' (licensed CC BY-NC-SA). Additional  data is
    provided in the 'USAboundariesData' package; this package provides an
    interface to access that data.
This package contains functions to read cancer data from SEER (http://seer.cancer.gov/) and IARC (http://www.iarc.fr) to create datasets at the county level based on US census information.
US Census 2000 Designated Places shapefiles and additional
        demographic data from the SF1 100 percent files. This data set
        contains polygon files in lat/lon coordinates and the
        corresponding demographic data for a number of different
        variables.
US 2000 Census Tract shapefiles and additional demographic
        data from the SF1 100 percent files. This data set contains
        polygon files in lat/lon coordinates and the corresponding
        demographic data for a number of different variables.
US Census 2010 shape files and additional demographic data
        from the SF1 100 percent files. This package contains a number
        of helper functions for the UScensus2010blk,
        UScensus2010blkgrp, UScensus2010tract, UScensus2010cdp
        packages.
Interface to easily access data via the United States Department of Agriculture (USDA)'s Livestock Mandatory Reporting ('LMR')
  Data API at <https://mpr.datamart.ams.usda.gov/>. The downloaded data can be saved for later off-line use. 
  Also provide relevant information and metadata for each of the input variables needed for sending the data inquiry.
An alternative for downloading various United States Department of
    Agriculture (USDA) data from <https://quickstats.nass.usda.gov/> through R. 
    You must sign up for an API token from the mentioned website in order for 
    this package to work.
Demographic data on the United States at the county and state levels spanning multiple years.
This is a framework that aims to provide methods and tools for assessing the impact of different sources of uncertainties (e.g.positional uncertainty) on performance of species distribution models (SDMs).)
Functions to re-arrange, extract, and work with distances.
A set of little functions that have been found useful to do little
    odds and ends such as plotting the results of K-means clustering, substituting
    special text characters, viewing parts of a data.frame, constructing formulas
    from text and building design and response matrices.
A set of general functions that I have used in various 
  projects and in other R packages. They support some miscellaneous operations 
  on data frames, matrices and vectors like adding a row on a ternary (3-value)
  data.frame based on positive and negative vector-indicators, rearranging a 
  list of data.frames by rownames, pruning rows or columns of a data.frame 
  that contain only one specific value given by the user,
  pruning and reordering a vector according to the common elements between its 
  names and elements of another given vector, finding the non-common elements 
  between two vectors (outer-section), 
  normalization of a vector, matrix or data.frame's numeric values in a specified range, 
  pretty printing of vector names and values in an R Markdown document.
  Also included is a function that returns the statistics needed for plotting a ROC curve.
Code snippets to fit models using the tidymodels framework can be easily created for a given data set.
Automate package and project setup tasks that are
    otherwise performed manually. This includes setting up unit testing,
    test coverage, continuous integration, Git, 'GitHub', licenses,
    'Rcpp', 'RStudio' projects, and more.
Compiled and cleaned the county-level estimates of fertilizer, 
    nitrogen and phosphorus, from 1945 to 2012 in United States of America (USA).  The commercial fertilizer data were originally 
    generated by USGS based on the sales data of commercial fertilizer. The manure data were estimated
    based on county-level population data of livestock, poultry, and other animals.
    See the user manual for detailed data sources and cleaning methods.  
    'usfertilizer' utilized the tidyverse to clean the original data and provide 
    user-friendly dataframe. Please note that USGS does not endorse this package. Also data from 1986 is not available for now.
Provides an overview of the demand for natural gas in the US by state and country level. Data source: US Energy Information Administration <https://www.eia.gov/>.
Provides a set of regular time-series datasets, describing the US electricity grid. That includes the total demand and supply, and as well as the demand by energy source (coal, solar, wind, etc.). Source: US Energy Information Administration (Dec 2019) <https://www.eia.gov/>.
Analyzes longitudinal data of HIV decline in patients on antiretroviral therapy using the canonical biphasic exponential decay model (pioneered, for example, by work in Perelson et al. (1997) <doi:10.1038/387188a0>; and Wu and Ding (1999) <doi:10.1111/j.0006-341X.1999.00410.x>). Model fitting and parameter estimation are performed, with additional options to calculate the time to viral suppression. Plotting and summary tools are also provided for fast assessment of model results.
A collection of data sets to accompany the
    textbook "Using R for Introductory Statistics," second
    edition.
Implements mixtures of unrestricted skew-t factor analyzer models via the EM algorithm.
The Universal Scalability Law (Gunther 2007)
    <doi:10.1007/978-3-540-31010-5> is a model to predict hardware and
    software scalability. It uses system capacity as a function of load to
    forecast the scalability for the system.
Obtain United States map data frames of varying region types (e.g. county, 
    state). The map data frames include Alaska and Hawaii conveniently placed to the
    bottom left, as they appear in most maps of the US. Convenience functions for plotting
    choropleths and working with FIPS codes are also provided.
Implements various independence tests for discrete, continuous, and infinite-dimensional data. The tests are based on a U-statistic permutation test, the USP of Berrett, Kontoyiannis and Samworth (2020) <arXiv:2001.05513>, and shown to be minimax rate optimal in a wide range of settings. As the permutation principle is used, all tests have exact, non-asymptotic Type I error control at the nominal level.
A set of functions leading to multivariate response L1 regression. 
    This includes functions on computing Euclidean inner products and norms, 
    weighted least squares estimates on multivariate responses, function to compute 
    fitted values and residuals. This package is a companion to the book "U-Statistics,
    M-estimation and Resampling", by Arup Bose and Snigdhansu Chatterjee, to appear 
    in 2017 as part of the "Texts and Readings in Mathematics" (TRIM) series of 
    Hindustan Book Agency and Springer-Verlag.
Forms a query to submit for US Treasury yield curve data, posting
    this query to the US Treasury web site's data feed service.  By default the
    download includes data yield data for 12 products from January 1, 1990,
    some of which are NA during this span.  The caller can pass parameters to
    limit the query to a certain year or year and month, but the full download
    is not especially large.  The download data from the service is in XML
    format.  The package's main function transforms that XML data into a numeric 
    data frame with treasury product items (constant maturity yields for 12 kinds 
    of bills, notes, and bonds) as columns and dates as row names. The function 
    returns a list which includes an item for this data frame as well as query-related
    values for reference and the update date from the service.
Three functions are provided: first function changes time from local to UTC, other changes from UTC to local and third returns difference between local and UTC. %h+% operator is also provided it adds hours to a time.
Process and print 'UTF-8' encoded international text (Unicode). Input, validate, normalize, encode, format, and display.
A collection of functions to make building customized ready-to-export tables for publication purposes easier and creating summaries of large datasets for review a breeze.
A set of tools for preparing and summarizing data for publication purposes. Includes functions for tabulating models, means to produce human-readable summary statistics from raw data, macros for calculating duration of time, and simplistic hypothesis testing tools.
A small set of functions for making visuals for publication in ggplot2. Includes minimalist themes with transparent backgrounds and a suite of tools for building Kaplan-Meier curves with risk tables.
Data utility functions for use in probability and statistics.  Includes functions for computing higher-moments for samples and their decompositions.
  Also includes utilities to examine functional mappings between factor variables and other variables in a data set.
Construct and plot objective hierarchies and associated value and utility functions. 
  Evaluate the values and utilities and visualize the results as colored objective hierarchies or tables. 
  Visualize uncertainty by plotting median and quantile intervals within the nodes of objective hierarchies.
  Get numerical results of the evaluations in standard R data types for further processing.
Contains functions for simulating phase 12 trial designs described by Chapple and Thall (2019) including simulation and the EFF-TOX trial and simulation and implementation of the U12 trial. Functions for implementing the EFF-TOX trial are found in the package 'Phase123'.
Predicts a smooth and continuous (individual) utility function from utility points, and computes measures of intensity for risk and higher order risk measures (or any other measure computed with user-written function) based on this utility function and its derivatives according to the method introduced in Schneider (2017) <http://hdl.handle.net/11858/00-1735-0000-002E-E306-0>.
The most used functions on IPEA (Instituto de Pesquisa Economica Aplicada). 
             Most of functions deal with brazilian names. 
             It can guess the women single's name, extract prepositions or extract the first name.
Multi-label learning strategies and others procedures to support multi-
  label classification in R. The package provides a set of multi-label procedures such as
  sampling methods, transformation strategies, threshold functions, pre-processing 
  techniques and evaluation metrics. A complete overview of the matter can be seen in
  Zhang, M. and Zhou, Z. (2014) <doi:10.1109/TKDE.2013.39> and Gibaja, E. and 
  Ventura, S. (2015) A Tutorial on Multi-label Learning.
Tools for generating and handling of UUIDs (Universally Unique Identifiers).
A method for estimating log-normalizing constants (or free
        energies) and expectations from multiple distributions (such as
        multiple generalized ensembles).
Supports the course Introduction to Methodology (POLSCI 4419/9715) at the University of Western Ontario.
An implementation of the Uniform Manifold Approximation and 
    Projection dimensionality reduction by McInnes et al. (2018) 
    <arXiv:1802.03426>. It also provides means to transform new data and to 
    carry out supervised dimensionality reduction. An implementation of the 
    related LargeVis method of Tang et al. (2016) <arXiv:1602.00370> is also 
    provided. This is a complete re-implementation in R (and C++, via the 'Rcpp'
    package): no Python installation is required. See the uwot website 
    (<https://github.com/jlmelville/uwot>) for more documentation and examples.
An R interface to V8: Google's open source JavaScript and WebAssembly 
    engine. This package can be compiled either with V8 version 6 and up, a NodeJS
    shared library, or the legacy 3.14/3.15 branch of V8.
An implementation of three procedures developed by 
    John Tukey: FUNOP (FUll NOrmal Plot), FUNOR-FUNOM 
    (FUll NOrmal Rejection-FUll NOrmal Modification), and vacuum cleaner. 
    Combined, they provide a way to identify, treat, and analyze outliers 
    in two-way (i.e., contingency) tables, as described in his 
    landmark paper "The Future of Data Analysis", Tukey, John W. (1962) 
    <https://www.jstor.org/stable/2237638>.
A lexicon and rule-based sentiment analysis tool that is specifically 
    attuned to sentiments expressed in social media, and works well on texts from other 
    domains. Hutto & Gilbert (2014) <https://www.aaai.org/ocs/index.php/ICWSM/ICWSM14/paper/view/8109/8122>.
Non-Domestic VAERS vaccine data for 01/01/2016 - 06/14/2016. If
    you want to explore the full VAERS data for 1990 - Present (data, symptoms,
    and vaccines), then check out the 'vaersND' package from the URL below. The
    URL and BugReports below correspond to the 'vaersND' package, of which
    'vaersNDvax' is a small subset (2016 only). 'vaersND' is not hosted on CRAN
    due to the large size of the data set. To install the Suggested 'vaers' and
    'vaersND' packages, use the following R code:
    'devtools::install_git("https://gitlab.com/iembry/vaers.git",
    build_vignettes = TRUE)' and
    'devtools::install_git("https://gitlab.com/iembry/vaersND.git",
    build_vignettes = TRUE)'. "VAERS is a national vaccine safety
    surveillance program co-sponsored by the US Centers for Disease Control and
    Prevention (CDC) and the US Food and Drug Administration (FDA). VAERS is a
    post-marketing safety surveillance program, collecting information about
    adverse events (possible side effects) that occur after the administration
    of vaccines licensed for use in the United States." For more information
    about the data, visit <https://vaers.hhs.gov/index>. For information about
    vaccination/immunization hazards, visit
    <http://www.questionuniverse.com/rethink.html/#vaccine>.
US VAERS vaccine data for 01/01/2018 - 06/14/2018. If you want to
    explore the full VAERS data for 1990 - Present (data, symptoms, and
    vaccines), then check out the 'vaers' package from the URL below. The URL
    and BugReports below correspond to the 'vaers' package, of which 'vaersvax'
    is a small subset (2018 only). 'vaers' is not hosted on CRAN due to the
    large size of the data set. To install the Suggested 'vaers' and 'vaersND'
    packages, use the following R code:
    'devtools::install_git("<https://gitlab.com/iembry/vaers.git>",
    build_vignettes = TRUE)' and
    'devtools::install_git("<https://gitlab.com/iembry/vaersND.git>",
    build_vignettes = TRUE)'. "The Vaccine Adverse Event Reporting System (VAERS)
    is a national early warning system to detect possible safety problems in
    U.S.-licensed vaccines. VAERS is co-managed by the Centers for Disease Control
    and Prevention (CDC) and the U.S. Food and Drug Administration (FDA)." For
    more information about the data, visit <https://vaers.hhs.gov/>. For
    information about
    vaccination/immunization hazards, visit
    <http://www.questionuniverse.com/rethink.html#vaccine>.
Provides access to the 'Vagalume' API <https://api.vagalume.com.br>. 
    The data extracted is basically lyrics of songs and information about
    artists/bands.
Fits generalized additive models (GAMs) using a variational approximations (VA) framework. In brief, the VA framework provides a fully or at least closed to fully tractable lower bound approximation to the marginal likelihood of a GAM when it is parameterized as a mixed model (using penalized splines, say). In doing so, the VA framework aims offers both the stability and natural inference tools available in the mixed model approach to GAMs, while achieving computation times comparable to that of using the penalized likelihood approach to GAMs. See Hui et al. (2018) <doi:10.1080/01621459.2018.1518235>.
A set of basic tools to transform functions into functions with
    input validation checks, in a manner suitable for both programmatic and
    interactive use.
A binding for the 'valection' program which offers various ways to 
  sample the outputs of competing algorithms or parameterizations, and fairly 
  assess their performance against each other. The 'valection' C library is 
  required to use this package and can be downloaded from:
  <http://labs.oicr.on.ca/boutros-lab/software/valection>. Cooper CI, et al; Valection: Design Optimization for Validation and Verification Studies; Biorxiv 2018; <doi:10.1101/254839>.
Alternative splicing produces a variety of different protein products from a given gene. 'VALERIE' enables visualisation of alternative splicing events from high-throughput single-cell RNA-sequencing experiments. 'VALERIE' computes percent spliced-in (PSI) values for user-specified genomic coordinates corresponding to alternative splicing events. PSI is the proportion of sequencing reads supporting the included exon/intron as defined by Shiozawa (2018) <doi:10.1038/s41467-018-06063-x>. PSI are inferred from sequencing reads data based on specialised infrastructures for representing and computing annotated genomic ranges by Lawrence (2013) <doi:10.1371/journal.pcbi.1003118>. Computed PSI for each single cell are subsequently presented in the form of a heatmap implemented using the 'pheatmap' package by Kolde (2010) <https://CRAN.R-project.org/package=pheatmap>. Board overview of the mean PSI difference and associated p-values across different user-defined groups of single cells are presented in the form of a line graph using the 'ggplot2' package by Wickham (2007) <https://CRAN.R-project.org/package=ggplot2>.
Methods and tools for analysing and validating the outputs
    and modelled functions of artificial neural networks (ANNs) in terms
    of predictive, replicative and structural validity. Also provides a
    method for fitting feed-forward ANNs with a single hidden layer.
Declare data validation rules and data quality indicators;
        confront data with them and analyze or visualize the results.
        The package supports rules that are per-field, in-record,
        cross-record or cross-dataset. Rules can be automatically
        analyzed for rule type and connectivity. See also Van der Loo
        and De Jonge (2018) <doi:10.1002/9781118897126>,
        chapter 6.
An implementation of statistical tests for the validation of rating systems as described in the ECB Working paper ''Advances in multivariate back-testing for credit risk underestimation'', by F. Coppens, M. Mayer, L. Millischer, F.  Resch, S. Sauer, K. Schulze (ECB WP series, forthcoming).
Rule sets with validation rules may contain redundancies or contradictions. 
  Functions for finding redundancies and problematic rules are provided, 
  given a set a rules formulated with 'validate'.
Functions for metrics and plots for model evaluation. Based on vectors of observed and predicted values. Method: Kristin Piikki, Johanna Wetterlind, Mats Soderstrom and Bo Stenberg (2021). <doi:10.1111/SUM.12694>.
The algorithm implemented in this package was
    designed to quickly estimates the distribution of the 
    log-rank especially for heavy unbalanced groups. VALORATE 
    estimates the null distribution and the p-value of the 
    log-rank test based on a recent formulation. For a given 
    number of alterations that define the size of survival 
    groups, the estimation involves a weighted sum of 
    distributions that are conditional on a co-occurrence term 
    where mutations and events are both present. The estimation 
    of conditional distributions is quite fast allowing the 
    analysis of large datasets in few minutes 
    <http://bioinformatica.mty.itesm.mx/valorate>.
Historical results for the state of Virginia lottery draw games. Data were downloaded from https://www.valottery.com/.
Read and manipulate genome intervals and signals. Provides
             functionality similar to command-line tool suites within R,
             enabling interactive analysis and visualization of genome-scale data. 
             Riemondy et al. (2017) <doi:10.12688/f1000research.11997.1>.
EQ-5D is a standard instrument (<https://euroqol.org/eq-5d-instruments/>) that measures the quality of life 
    often used in clinical and economic evaluations of health care technologies. Both adult versions of EQ-5D (EQ-5D-3L and EQ-5D-5L)
    contain a descriptive system and visual analog scale. The descriptive system measures the patient's health in 5 dimensions: 
    the 5L versions has 5 levels and 3L version has 3 levels. The descriptive system scores are usually converted to index values 
    using country specific values sets (that incorporates the country preferences). This package allows the calculation of both descriptive system
    scores to the index value scores. The value sets for EQ-5D-3L are from the references mentioned in the website <https://euroqol.org/eq-5d-instruments/eq-5d-3l-about/valuation/>
    The value sets for EQ-5D-3L for a total of 31 countries are used for the valuation (see the user guide for a complete list of references).
    The value sets for EQ-5D-5L are obtained from references mentioned in the <https://euroqol.org/eq-5d-instruments/eq-5d-5l-about/valuation-standard-value-sets/> and other sources.
    The value sets for EQ-5D-5L for a total of 17 countries are used for the valuation (see the user guide for a complete list of references).
    The package can also be used to map 5L scores to 3L index values for 10 countries: Denmark, France, Germany, Japan, Netherlands, Spain, Thailand, UK, USA, and Zimbabwe. 
    The value set and method for mapping are obtained from Van Hout et al (2012) <doi: 10.1016/j.jval.2012.02.008>.
Pricing of variable annuity life insurance
    contracts by means of Monte Carlo methods. Monte Carlo is used to price
    the contract in case the policyholder cannot surrender while
    Least Squares Monte Carlo is used if the insured can surrender.
    This package implements the pricing framework and algorithm described in
    Bacinello et al. (2011) <doi:10.1016/j.insmatheco.2011.05.003>.
    It also implements the state-dependent fee structure
    discussed in Bernard et al. (2014) <doi:10.1017/asb.2014.13> as well as 
    a function which prices the contract by resolving the partial differential equation 
    described in MacKay et al. (2017) <doi:10.1111/jori.12094>.
Contains logic for cell-specific gene set scoring of single cell RNA sequencing data.
Implementation of a Monte Carlo simulation engine for valuing synthetic portfolios of 
    variable annuities, which reflect realistic features of common annuity contracts in practice. 
    It aims to facilitate the development and dissemination of research related to the efficient 
    valuation of a portfolio of large variable annuities. The main valuation methodology was 
    proposed by Gan (2017) <doi:10.1515/demo-2017-0021>.
Vampirize the response biases from a dataset! Performs 
    factor analysis controlling the effects of social desirability
    and acquiescence using the method described in Ferrando, 
    Lorenzo-Seva & Chico (2009) <doi:10.1080/10705510902751374>.
Wrapper around the 'City of Vancouver' Open Data API <https://opendata.vancouver.ca/api/v2/console> to simplify and standardize access to 'City of Vancouver' open data. 
  Functionality to list the data catalogue and access data and geographic records.
Identify and analyze conserved waters within crystallographic 
  protein structures and molecular dynamics simulation trajectories. Statistical 
  parameters for each water cluster, informative graphs, and a PyMOL session 
  file to visually explore the conserved waters and protein are returned. 
  Hydrophilicity is the propensity of waters to congregate near specific protein 
  atoms and is related to conserved waters. An informatics derived set of 
  hydrophilicity values are provided based on a large, high-quality X-ray 
  protein structure dataset.
Provides low-level access to 'GDAL' functionality for R packages. The aim is to minimize
  the level of interpretation put on the 'GDAL' facilities, to enable direct use of it for a variety of purposes. 
  'GDAL' is the 'Geospatial Data Abstraction Library' a translator for raster and vector geospatial data formats 
  that presents a single raster abstract data model and single vector abstract data model to the calling application 
  for all supported formats <http://gdal.org/>. Other available packages 'rgdal' and 'sf' also provide access to 
  the 'GDAL' library, but neither can be used for these lower level tasks, and both do many other tasks.
Estimation, Hypothesis Testing, Prediction for Stationary Vector Autoregressive Models
Implementation of the variable banding procedure for modeling local dependence and estimating precision matrices that is introduced in Yu & Bien (2016) and is available at <https://arxiv.org/abs/1604.07451>.
Tool for easy and efficient discretization of continuous and categorical data. 
    The package calculates the most optimal binning of a given explanatory variable with respect to a 
    user-specified target variable. The purpose is to assign a unique Weight-of-Evidence value 
    to each of the calculated binpoints in order to recode the original variable. 
    The package allows users to impose certain restrictions on the functional form on the resulting 
    binning while maximizing the overall information value in the original data. 
    The package is well suited for logistic scoring models where input variables may be subject to 
    restrictions such as linearity by e.g. regulatory authorities. An excellent source describing in 
    detail the development of scorecards, and the role of Weight-of-Evidence coding in credit scoring 
    is (Siddiqi 2006, ISBN: 978–0-471–75451–0). The package utilizes the discrete nature of decision trees and 
    Isotonic Regression to accommodate the trade-off between flexible functional forms and maximum 
    information value.
Easily create list-like structures with constant, read-only 
    variables. Combines the flexibility of lists with read-only fields.
    Supports defensive programming by throwing errors on field assignment,
    helping mitigate the introduction of logical runtime bugs.
Fast algorithms for fitting Bayesian variable selection
    models and computing Bayes factors, in which the outcome (or
    response variable) is modeled using a linear regression or a
    logistic regression. The algorithms are based on the variational
    approximations described in "Scalable variational inference for
    Bayesian variable selection in regression, and its accuracy in
    genetic association studies" (P. Carbonetto & M. Stephens, 2012,
    <DOI:10.1214/12-BA703>). This software has been applied to large
    data sets with over a million variables and thousands of samples.
Performs clustering of quantitative variables,
    assuming that clusters lie in low-dimensional subspaces. Segmentation of
    variables, number of clusters and their dimensions are selected based on
    BIC. Candidate models are identified based on many runs of K-means
    algorithm with different random initializations of cluster centers.
Generation of domain variables, linearization of several non-linear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, Sample Survey Methods And Theory, vol. I: Methods and Applications; vol. II: Theory. 1953, New York: John Wiley and Sons), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y. G., 2015, <doi:10.1111/rssa.12116>). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Generating functions for both optimal and ordinary difference sequences, and the difference-based estimation functions.
Computes Value at risk and expected shortfall, two most popular measures of financial risk, for over one hundred parametric distributions,  including all commonly known distributions.  Also computed are the corresponding probability density function and cumulative distribution function.
Error variance estimation in ultrahigh dimensional datasets with four different methods, viz. Refitted cross validation, k-fold refitted cross validation, Bootstrap-refitted cross validation, Ensemble method.
Captures and compiles the genes and variants related to a disease, a phenotype or a clinical feature from the public databases including HPO (Human Phenotype Ontology, <http://human-phenotype-ontology.github.io/about.html>), Orphanet <http://www.orpha.net/consor/cgi-bin/index.php>, OMIM (Online Mendelian Inheritance in Man, <http://www.omim.org>), ClinVar <http://www.ncbi.nlm.nih.gov/clinvar>, and UniProt (Universal Protein Resource, <http://www.uniprot.org>) and PubMed abstracts. HPO provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. HPO currently contains approximately 11,000 terms and over 115,000 annotations to hereditary diseases. Orphanet is the reference portal for information on rare diseases and orphan drugs, whose aim is to help improve the diagnosis, care and treatment of patients with rare diseases. OMIM is a continuously updated catalog of human genes and genetic disorders and traits, with particular focus on the molecular relationship between genetic variation and phenotypic expression. ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. UniProt focuses on amino acid altering variants imported from Ensembl Variation databases. For Homo sapiens, the variants including human polymorphisms and disease mutations in the UniProt are manually curated  from UniProtKB/Swiss-Prot. Additionally, PubMed provides the primary and latest source of the information. Text mining was employed to capture the information from PubMed abstracts.
Variables are the fundamental parts of each programming language but handling them efficiently might be frustrating for programmers. This package contains some functions to help user (especially data explorers) to make more sense of their variables and take the most out of variables and hardware resources. These functions are written, collected and crafted over 7 years of experience in statistical data analysis on high-dimensional data, and for each of them there was a need. Functions in this package are suppose to be efficient and easy to use, hence they will be frequently updated to make them more convenient.
Performs analysis of various genetic parameters like genotypic and phenotypic coefficient of variance, heritability, genetic advance, genetic advance as a percentage of mean. The package also has functions for genotypic and phenotypic covariance, correlation and path analysis. Dataset has been added to facilitate example. For more information refer Singh, R.K. and Chaudhary, B.D. (1977, ISBN:81766330709788176633079).
Abstract descriptions of (yet) unobserved variables.
Implements variable screening techniques for ultra-high
    dimensional regression settings.  Techniques for independent (iid) data,
    varying-coefficient models, and longitudinal data are implemented. The package
     currently contains three screen functions: screenIID(), screenLD() and screenVCM(),
     and six methods for simulating dataset: simulateDCSIS(), simulateLD, simulateMVSIS(),
     simulateMVSISNY(), simulateSIRS() and simulateVCM(). The package is based on the work of
    Li-Ping ZHU, Lexin LI, Runze LI, and Li-Xing ZHU (2011) <DOI:10.1198/jasa.2011.tm10563>,
    Runze LI, Wei ZHONG, & Liping ZHU (2012) <DOI:10.1080/01621459.2012.695654>,
    Jingyuan LIU, Runze LI, & Rongling WU (2014) <DOI:10.1080/01621459.2013.850086>
    Hengjian CUI, Runze LI, & Wei ZHONG (2015) <DOI:10.1080/01621459.2014.920256>, and
    Wanghuan CHU, Runze LI and Matthew REIMHERR (2016) <DOI:10.1214/16-AOAS912>.
    Special thanks are due to Ling Zhang for providing detailed testing and proposing
    a method for speed improvement on the simulation of data with AR-1 structure.
Uses a Bayesian model to
    estimate the variability in a repeated
    measure outcome and use that as an outcome or a predictor
    in a second stage model.
Provides functions for the variance gamma
        distribution. Density, distribution and quantile functions.
        Functions for random number generation and fitting of the
        variance gamma to data. Also, functions for computing moments
        of the variance gamma distribution of any order about any
        location. In addition, there are functions for checking the
        validity of parameters and to interchange different sets of
        parameterizations for the variance gamma distribution.
This is a 'sparklyr' extension integrating 'VariantSpark' and R. 'VariantSpark' is 
  a framework based on 'scala' and 'spark' to analyze genome datasets, 
  see <https://bioinformatics.csiro.au/>. It was tested on datasets with 3000 samples 
  each one containing 80 million features in either unsupervised clustering approaches 
  and supervised applications, like classification and regression. The genome datasets
  are usually writing in VCF, a specific text file format used 
  in bioinformatics for storing gene sequence variations. So, 'VariantSpark' is a great 
  tool for genome research, because it is able to read VCF files, run analyses and return 
  the output in a 'spark' data frame.
Computes the random forest variable importance (VIMP) for the conditional inference random forest (cforest) of the 'party' package. Includes a function (varImp) that computes the VIMP for arbitrary measures from the 'measures' package. For calculating the VIMP regarding the measures accuracy and AUC two extra functions exist (varImpACC and varImpAUC).
Applying Monte Carlo permutation to generate pointwise variogram envelope and checking for spatial dependence at different scales using permutation test. Empirical Brown's method and Fisher's method are used to compute overall p-value for hypothesis test.
Multi-caller variant analysis pipeline for targeted analysis sequencing (TAS) data. Features a modular, automated workflow that can start with raw reads and produces a user-friendly PDF summary and a spreadsheet containing consensus variant information.
The goal of the package is to equip the 'jmcm' package (current version 0.2.1) 
    with estimations of the covariance of estimated parameters. Two methods are provided. 
    The first method is to use the inverse of estimated Fisher's information matrix, see 
    M. Pourahmadi (2000) <doi:10.1093/biomet/87.2.425>, M. Maadooliat, M. Pourahmadi and 
    J. Z. Huang (2013) <doi:10.1007/s11222-011-9284-6>, and W. Zhang, C. Leng, C. Tang (2015) 
    <doi:10.1111/rssb.12065>. The second method is bootstrap based, see Liu, R.Y. (1988) 
    <doi:10.1214/aos/1176351062> for reference.
A new mathematical formulation to merge observed data with gridded images of environmental variables using partial differential equations in a variational setting. The original method was created, developed and published by Ulloa, Samaniego, Campozano and Ballari (2018) <doi:10.1002/2017JD027982>.
A computational toolbox of heuristics approaches for performing variable ranking and feature selection based on mutual information well adapted for multivariate system epidemiology datasets. The core function is a general implementation of the minimum redundancy maximum relevance model. R. Battiti (1994) <doi:10.1109/72.298224>. Continuous variables are discretized using a large choice of rule. Variables ranking can be learned with a sequential forward/backward search algorithm. The two main problems that can be addressed by this package is the selection of the most representative variable within a group of variables of interest (i.e. dimension reduction) and variable ranking with respect to a set of features of interest.
In order to make it easy to use variance reduction algorithms for any simulation, this framework can help you.
    We propose user friendly and easy to extend framework. Antithetic Variates, Inner Control Variates,
    Outer Control Variates and Importance Sampling algorithms are available in the framework. User can
    write its own simulation function and use the Variance Reduction techniques in this package to
    obtain more efficient simulations. An implementation of Asian Option simulation is already 
    available within the package. See Kemal Dinçer Dingeç & Wolfgang Hörmann (2012) <doi:10.1016/j.ejor.2012.03.046>.
Methods for fitting semi-parametric mean and variance models, with normal or censored data. Also extended to allow a regression in the location, scale and shape parameters.
Estimation, lag selection, diagnostic testing, forecasting, causality analysis, forecast error variance decomposition and impulse response functions of VAR models and estimation of SVAR and SVEC models.
An algorithm which identifies the morphometric features that significantly discriminate two taxa and validates the morphological distinctness between them via a Monte-Carlo test, polar coordinates and overlap of the area under the density curve.
Feature selection using Sequential Forward Floating feature Selection and Jeffries-Matusita distance. It returns a suboptimal set of features to use for image classification. Reference: Dalponte, M., Oerka, H.O., Gobakken, T., Gianelle, D. & Naesset, E. (2013). Tree Species Classification in Boreal Forests With Hyperspectral Data. IEEE Transactions on Geoscience and Remote Sensing, 51, 2632-2645, <DOI:10.1109/TGRS.2012.2216272>.
Full model selection (detection of the relevant features and estimation of the number of clusters) for model-based clustering (see reference here <doi:10.1007/s11222-016-9670-1>). Data to analyze can be continuous, categorical, integer or mixed. Moreover, missing values can occur and do not necessitate any pre-processing. Shiny application permits an easy interpretation of the results.
Variable selection from random forests using both
        backwards variable elimination (for the selection of small sets
        of non-redundant variables) and selection based on the
        importance spectrum (somewhat similar to scree plots; for the
        selection of large, potentially highly-correlated variables).
        Main applications in high-dimensional data (e.g., microarray
        data, and other genomics and proteomics applications).
Creates a summary dataframe that can be used in 'RStudio' similar to the variable
    explorer in 'Stata', but which also includes the summary statistics. By default the result 
    is shown in the 'RStudio' Viewer Pane as a searchable data table. This is useful particularly 
    if you have a large dataset with a very large number of labelled variables with hard to 
    remember names. Can also be used to generate a table of summary statistics.
Vector autoregressive (VAR) model is a fundamental and effective approach
    for multivariate time series analysis. Shrinkage estimation methods can be
    applied to high-dimensional VAR models with dimensionality greater than
    the number of observations, contrary to the standard ordinary least squares
    method. This package is an integrative package delivering nonparametric,
    parametric, and semiparametric methods in a unified and consistent manner,
    such as the multivariate ridge regression in Golub, Heath, and Wahba (1979)
    <doi:10.2307/1268518>, a James-Stein type nonparametric shrinkage method in
    Opgen-Rhein and Strimmer (2007) <doi:10.1186/1471-2105-8-S2-S3>, and
    Bayesian estimation methods using noninformative and informative priors
    in Lee, Choi, and S.-H. Kim (2016) <doi:10.1016/j.csda.2016.03.007> and
    Ni and Sun (2005) <doi:10.1198/073500104000000622>.
Provides routines for identifying structural shocks in vector autoregressions (VARs) using sign restrictions.
Computes a portfolio of European options that replicates
        the cost of capturing the realised variance of an equity index.
An implementation of the Likelihood ratio Test (LRT) for testing that,
    in a (non)linear mixed effects model, the variances of a subset of the random
    effects are equal to zero. There is no restriction on the subset of variances
    that can be tested: for example, it is possible to test that all the variances
    are equal to zero. Note that the implemented test is asymptotic.
    This package should be used on model fits from packages 'nlme', 'lmer', and 'saemix'.
    Charlotte Baey, Paul-Henry Cournède and Estelle Kuhn (2019) <doi:10.1016/j.csda.2019.01.014>.
Implements the Wild bootstrap tests for autocorrelation in vector autoregressive models of Ahlgren, N. & Catani, P. 
	(2016, <doi:10.1007/s00362-016-0744-0>), the Combined LM test for ARCH in VAR models of Catani, P. & Ahlgren, N. 
	(2016, <doi:10.1016/j.ecosta.2016.10.006>), and Bootstrap determination of the co-integration rank (Cavaliere, G., Rahbek, A.,
	& Taylor, A. M. R., 2012, 2014).
Implements a maximum likelihood estimation (MLE)
    method for estimation and prediction of Gaussian process-based
    spatially varying coefficient (SVC) models 
    (Dambon et al. (2021a) <doi:10.1016/j.spasta.2020.100470>). 
    Covariance tapering (Furrer et al. (2006) <doi:10.1198/106186006X132178>) can 
    be applied such that the method scales to large data. Further, it implements
    a joint variable selection of the fixed and random effects (Dambon et al. 
    (2021b) <arXiv:2101.01932>).
Provide a collection of miscellaneous R functions
    related to the Vasicek distribution with the intent to make
    the lives of risk modelers easier.
Provides an interface to a 'HashiCorp' vault server over
  its http API (typically these are self-hosted; see
  <https://www.vaultproject.io>).  This allows for secure storage and
  retrieval of secrets over a network, such as tokens, passwords and
  certificates.  Authentication with vault is supported through
  several backends including user name/password and authentication via
  'GitHub'.
Efficient algorithm for solving discrete mixture
		regression model for rare variant association analysis.
		Uses variational Bayes algorithm to efficiently search over
		model space.  Outputs an approximate likelihood ratio test
		as well as variant level posterior probabilities of
		association.
Fit and simulate latent position and cluster
        models for network data, using a fast Variational Bayes approximation.
Efficient algorithm for solving ultra-sparse
		regularized regression models using a variational
		Bayes algorithm with a spike (l0) prior.  Algorithm
		is solved on a path, with coordinate updates, and is
		capable of generating very sparse models.  There are
		very general model diagnostics for controling type-1
		error included in this package.
Provides a new data structure, vector binary tree, to make
  your data visiting and management more efficient. if your data has
  very structurized column names with specific connecting pattern, it can 
  read, split, and factorize these names, then build the mapping from all
  string objects to an array or tensor, through vector binary tree, by
  which the batched data processing can be implemented easily. The methods
  of array and tensor are also applicable.
Provides new classes for (rotated) BB1, BB6, BB7, BB8, and 
  Tawn copulas, extends the existing Gumbel and Clayton families with 
  rotations, and allows to set up a vine copula model using the 'copula' API.
  Corresponding objects from the 'VineCopula' API can easily be converted.
ANOVA and REML estimation of linear mixed models is implemented, once following
 Searle et al. (1991, ANOVA for unbalanced data), once making use of the 'lme4' package.
 The primary objective of this package is to perform a variance component analysis (VCA)
 according to CLSI EP05-A3 guideline "Evaluation of Precision of Quantitative Measurement
 Procedures" (2014). There are plotting methods for visualization of an experimental design,
 plotting random effects and residuals. For ANOVA type estimation two methods for computing
 ANOVA mean squares are implemented (SWEEP and quadratic forms). The covariance matrix of 
 variance components can be derived, which is used in estimating confidence intervals. Linear
 hypotheses of fixed effects and LS means can be computed. LS means can be computed at specific
 values of covariables and with custom weighting schemes for factor variables. See ?VCA for a
 more comprehensive description of the features.
Visualization techniques, data sets, summary and inference
        procedures aimed particularly at categorical data. Special
        emphasis is given to highly extensible grid graphics. The
        package was package was originally inspired by the book 
	"Visualizing Categorical Data" by Michael Friendly and is 
	now the main support package for a new book, 
	"Discrete Data Analysis with R" by Michael Friendly and 
	David Meyer (2015).
Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data
    and the 'gnm' package for Generalized Nonlinear Models.
	In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and
	adds a 3D version in 'mosaic3d'.  Additionally, methods are provided for comparing and visualizing lists of
	'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by
  Michael Friendly and David Meyer.
Facilitates easy manipulation of variant call format (VCF) data.
    Functions are provided to rapidly read from and write to VCF files. Once
    VCF data is read into R a parser function extracts matrices of data. This
    information can then be used for quality control or other purposes. Additional
    functions provide visualization of genomic data. Once processing is complete
    data may be written to a VCF file (*.vcf.gz). It also may be converted into
    other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between
    VCF data and familiar R software.
Methods for faster extraction (about 5x faster in a few test cases) of variance-covariance matrices and standard errors from models. Methods in the 'stats' package tend to rely on the summary method, which may waste time computing other summary statistics which are summarily ignored.
Method to perform penalized variance component analysis.
Record test suite 'HTTP' requests and replays them during
    future runs. A port of the Ruby gem of the same name
    (<https://github.com/vcr/vcr/>). Works by hooking into the 'webmockr'
    R package for matching 'HTTP' requests by various rules ('HTTP' method,
    'URL', query parameters, headers, body, etc.), and then caching
    real 'HTTP' responses on disk in 'cassettes'. Subsequent 'HTTP' requests
    matching any previous requests in the same 'cassette' use a cached
    'HTTP' response.
Defines new notions of prototype and size that are
    used to provide tools for consistent and well-founded type-coercion
    and size-recycling, and are in turn connected to ideas of type- and
    size-stability useful for analysing function interfaces.
Comparison of variance - covariance patterns using relative principal component analysis (relative eigenanalysis), as described in Le Maitre and Mitteroecker (2019) <doi:10.1111/2041-210X.13253>. Also provides functions to compute group covariance matrices, distance matrices, and perform proportionality tests. A worked sample on the body shape of cichlid fishes is included, based on the dataset from Kerschbaumer et al. (2013) <doi:10.5061/dryad.fc02f>.
Analyze Peptide Array Data and characterize peptide
    sequence space. Allows for high level visualization of global signal, Quality control based
    on replicate correlation and/or relative Kd, calculation of peptide Length/Charge/Kd parameters,
    Hits selection based on RFU Signal, and amino acid composition/basic motif recognition with RFU
    signal weighting. Basic signal trends can be used to generate peptides that follow the observed
    compositional trends.
The qda() function from package 'MASS' is extended to calculate a weighted linear (LDA) and quadratic discriminant analysis (QDA) by changing the group variances and group means based on cell-wise uncertainties.
    The uncertainties can be derived e.g. through relative errors for each individual measurement (cell), not only row-wise or column-wise uncertainties.
    The method can be applied compositional data (e.g. portions of substances, concentrations) and non-compositional data.
Facilities for constructing variance dispersion graphs, fraction-
    of-design-space plots and similar graphics for exploring the properties of
    experimental designs. The design region is explored via random sampling, which
    allows for more flexibility than traditional variance dispersion graphs. A
    formula interface is leveraged to provide access to complex model formulae.
    Graphics can be constructed simultaneously for multiple experimental designs
    and/or multiple model formulae. Instead of using pointwise optimization to
    find the minimum and maximum scaled prediction variance curves, which can be
    inaccurate and time consuming, this package uses quantile regression as an
    alternative.
Uses a modification of the published FORTRAN code in "A Computer Program for Generating Variance Dispersion Graphs" by G. Vining, Journal of Quality Technology, Vol. 25 No. 1 January 1993, to produce variance dispersion graphs. Also produces fraction of design space plots, and contains data frames for several minimal run response surface designs.
Functions for creating variance dispersion graphs, fraction of design space plots, and contour plots of scaled prediction variances for second-order response surface designs in spherical and cuboidal regions. Also, some standard response surface designs can be generated.
An extension to the 'testthat' package that makes it easy
    to add graphical unit tests. It provides a Shiny application to
    manage the test cases.
Contains variable, diversity, and joining sequences and accompanying functions that enable both the extraction of and comparison between immune V-D-J genomic segments from a variety of species. Sources include IMGT from MP Lefranc (2009) <doi:10.1093/nar/gkn838> and Vgenerepertoire from publication DN Olivieri (2014) <doi:10.1007/s00251-014-0784-3>.
Provides statistical methods for the design and analysis of a calibration study, which aims for calibrating measurements using two different methods. The package includes sample size calculation, sample selection,  regression analysis with error-in measurements and change-point regression. The method is described in Tian, Durazo-Arvizu, Myers, et al. (2014) <DOI:10.1002/sim.6235>.
A package for applying affine and similarity transformations on vector spatial data (sp objects). Transformations can be defined from control points or directly from parameters. If redundant control points are provided Least Squares is applied allowing to obtain residuals and RMSE.
Automates set operations (i.e., comparisons of overlap) between multiple vectors.
    It also contains a function for automating reporting in 'RMarkdown', by generating markdown output for easy analysis, as well as an 'RMarkdown' template for use with 'RStudio'.
The base 'sets' tools follow the algebraic definition
 that each element of a set must be unique. 
 Since it's often helpful to compare all elements of two vectors,
 this toolset treats every element as unique for counting purposes.
 For ease of use, all functions in vecsets have an argument
 'multiple' which, when set to FALSE,
 reverts them to the base::set tools functionality.
A 2D statistical analysis is performed, both numerical and graphical, of a set of vectors. Since a vector has two components (module and azimuth) vector analysis is performed in three stages: modules are analyzed by means of linear statistics, azimuths are analyzed by circular statistics, and the joint analysis of modules and azimuths is done using density maps that allow detecting another distribution properties (i.e. anisotropy) and outliers. Tests and circular statistic parameters have associated a full range of graphing: histograms, maps of distributions, point maps, vector maps, density maps, distribution modules and azimuths.
This package performs a 3D statistical analysis, both numerical and graphical, of a set of vectors. Since a vector has three components (a module and two angles) vectorial analysis is performed in two stages: modules are analyzed by means of linear statistics and orientations are analyzed by spherical statistics. Tests and spherical statistic parameters are accompanied by a graphs as: density maps, distribution modules and angles. The tests, spherical statistic parameters and graphs allow us detecting another distribution properties (i.e. anisotropy) and outliers.
Block matrices and object arrays, as general purpose S4 data structures, with automatic formatting. Matrix arrays (that is, arrays of matrices), with binary operators for succinct/convenient matrix array multiplication. Set/sequence related functions, including index/interval finding functions. Also, SQL-like select functions, analytic geometry functions, head/tail generalizations and prototype pooling/convolution functions.
New wavelet methodology (vector wavelet coherence) (Oygur, T., Unal, G, 2020 <doi:10.1007/s40435-020-00706-y>) 
  to handle dynamic co-movements of multivariate time series via extending multiple and quadruple wavelet coherence methodologies. 
  This package can be used to perform multiple wavelet coherence, quadruple wavelet coherence, and n-dimensional vector wavelet coherence analyses.
The 'Vega-Lite' 'JavaScript' framework provides a higher-level grammar
    for visual analysis, akin to 'ggplot' or 'Tableau', that generates complete 'Vega'
    specifications. Functions exist which enable building a valid 'spec' from scratch
    or importing a previously created 'spec' file. Functions also exist to export 'spec'
    files and to generate code which will enable plots to be embedded in properly
    configured web pages. The default behavior is to generate an 'htmlwidget'.
Ordination methods, diversity analysis and other
  functions for community and vegetation ecologists.
Static and dynamic 3D plots to be used with ordination
    results and in diversity analysis, especially with the vegan package.
'Vega' and 'Vega-Lite' parse text in 'JSON' notation to render 
  chart-specifications into 'HTML'. This package is used to facilitate the 
  rendering. It also provides a means to interact with signals, events,
  and datasets in a 'Vega' chart using 'JavaScript' or 'Shiny'.
A set of functions to: (1) perform fuzzy clustering of vegetation data [De Caceres et al. (2010) <doi:10.1111/j.1654-1103.2010.01211.x>]; (2) to assess ecological community ressemblance on the basis of structure and composition [De Caceres et al. (2013): <doi:10.1111/2041-210X.12116>]; and (3) to perform community trajectory analysis [De Caceres et al. (2019): <doi:10.1002/ecm.1350>].
Handling of vegetation data from different sources (
	Turboveg <http://www.synbiosys.alterra.nl/turboveg/>; 
	the German national repository <http://www.vegetweb.de> and others. 
    Taxonomic harmonization (given appropriate taxonomic lists,
    e.g. the German taxonomic standard list "GermanSL", <http://germansl.infinitenature.org>).
This package computes diversity for community data sets
        using the methods outlined by Jost (2006, 2007). While there
        are differing opinions on the ideal way to calculate diversity
        (e.g. Magurran 2004), this method offers the advantage of
        providing diversity numbers equivalents, independent alpha and
        beta diversities, and the ability to incorporate 'order' (q) as
        a continuous measure of the importance of rare species in the
        metrics. The functions provided in this package largely
        correspond with the equations offered by Jost in the cited
        papers. The package computes alpha diversities, beta
        diversities, gamma diversities, and similarity indices.
        Confidence intervals for diversity measures are calculated
        using a bootstrap method described by Chao et al. (2008).  For
        datasets with many samples (sites, plots), sim.table creates
        tables of all pairwise comparisons possible, and for grouped
        samples sim.groups calculates pairwise combinations of within-
        and between-group comparisons.
Collection of common methods to determine growing season length in
  a simple manner. Start and end dates of the vegetation periods are calculated
  solely based on daily mean temperatures and the day of the year.
Import and handling data from vegetation-plot databases, especially
    data stored in 'Turboveg' (<https://www.synbiosys.alterra.nl/turboveg>).
    Also import/export routines for exchange of data with 'Juice'
    (<http://www.sci.muni.cz/botany/juice>) are implemented.
Elaboration of vehicular emissions inventories,
    consisting in four stages, pre-processing activity data, preparing 
    emissions factors, estimating the emissions and post-processing of emissions 
    in maps and databases. More details in Ibarra-Espinosa et al (2018) <doi:10.5194/gmd-11-2209-2018>.
    Before using VEIN you need to know the vehicular composition of your study area, in other words,
    the combination of of type of vehicles, size and fuel of the fleet. Then, it is recommended to
    start with the project to download a template to create a structure of directories and scripts.
Functions for downloading, reshaping, culling, cleaning, and analyzing fossil data from the Paleobiology Database <https://paleobiodb.org>.
A set of functions for generating HTML to
    embed hosted video in your R Markdown documents or Shiny applications.
Draws and displays Venn diagrams up to 7 sets, and any Boolean union of set intersections.
A set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.
Calculates and displays Venn and Euler Diagrams
Provides variable selection and estimation routines for models
    with main effects stratified on multiple binary factors. The 'vennLasso' package
    is an implementation of the method introduced in Huling, et al. (2017) <doi:10.1111/biom.12769>.
Calculate and plot Venn diagrams in 2D and 3D.
Utilities for verifying discrete, continuous and probabilistic forecasts, and forecasts expressed as parametric distributions are included.
Installs specified versions of R packages hosted on CRAN and
    provides functions to list available versions and the versions of currently
    installed packages. These tools can be used to help make R projects and
    packages more reproducible. 'versions' fits in the narrow gap between
    the 'devtools' install_version() function and the 'checkpoint' package.
    devtools::install_version() installs a stated package version from source files
    stored on the CRAN archives. However CRAN does not store binary versions of
    packages so Windows users need to have RTools installed and Windows and OSX
    users get longer installation times. 'checkpoint' uses the Revolution Analytics
    MRAN server to install packages (from source or binary) as they were available
    on a given date. It also provides a helpful interface to detect the packages
    in use in a directory and install all of those packages for a given date.
    'checkpoint' doesn't provide install.packages-like functionality however, and
    that's what 'versions' aims to do, by querying MRAN. As MRAN only goes back to
    2014-09-17, 'versions' can't install packages archived before this date.
When given a description of a polyhedral set by a system of linear inequalities Ax <= b, produce the list of the vertices of the set.
Creates Vertex Similarity matrix of an undirected graph based
  on the method stated by E. A. Leicht, Petter Holme, AND M. E. J. Newman in
  their paper <DOI:10.1103/PhysRevE.73.026120>.
Permits to apply the 'Vertex Sort' algorithm (Jothi et al. (2009) <10.1038/msb.2009.52>) to a graph in order to elucidate its hierarchical structure. It also allows graphic visualization of the sorted graph by exporting the results to a cytoscape friendly format. Moreover, it offers five different algorithms of graph randomization: 1) Randomize a graph with preserving node degrees, 2) with preserving similar node degrees, 3) without preserving node degrees, 4) with preserving node in-degrees and 5) with preserving node out-degrees.
Multi-precision library that allows to store and operate with arbitrarily big integers without
    loss of precision. It includes a large list of tools to work with them, like:
      - Arithmetic and logic operators
      - Modular-arithmetic operators
      - Computer Number Theory utilities
      - Probabilistic primality tests
      - Factorization algorithms
      - Random generators of diferent types of integers.
Simple functions for calculating the image gradient, image hessian, volume ratio filter, and Frangi vesselness filter of 3-dimensional volumes.
Integrated data management library that offers a variety of tools concerning the loading and manipulation of environmental data available from different Venezuelan governmental sources. Facilities are provided to plot temporal and spatial data as well as understand the health of a collection of meteorological data.
Declarative template-based framework for verifying that objects
  meet structural requirements, and auto-composing error messages when they do
  not.
R Codes and Datasets for Duchateau, L. and Janssen, P. and Rowlands, G. J. (1998). Linear Mixed Models. An Introduction with applications in Veterinary Research. International Livestock Research Institute.
Computation the value of one of two uniformly 
    distributed marginals if the copula probability value is known
    and the value of the second marginal is also known.
    Computation and plotting corresponding cumulative
    distribution function or survival function.
    The numerical definition of a common area limited by lines
    of the cumulative distribution function and survival function.
    Approximate quantification of the probability of this area.
    In addition to 'amh', the copula dimension may be larger than 2.
A set of visual input controls for Shiny apps to facilitate filtering across multiple outputs.
Variance function estimation for models proposed by W. Sadler in his variance function program 
  ('VFP', <http://www.aacb.asn.au/resources/useful-tools/variance-function-program-v14>). Here, the idea is
  to fit multiple variance functions to a data set and consequently assess which function reflects
  the relationship 'Var ~ Mean' best. For 'in-vitro diagnostic' ('IVD') assays modeling this relationship
  is of great importance when individual test-results are used for defining follow-up treatment of patients.
Realization of published methods to analyze visual field (VF) progression. Introduction to the plotting methods (designed by author TE) for VF output visualization. A sample dataset for two eyes, each with 10 follow-ups is included. The VF analysis methods could be found in -- Musch et al. (1999) <doi:10.1016/S0161-6420(99)90147-1>, Nouri-Mahdavi et at. (2012) <doi:10.1167/iovs.11-9021>, Schell et at. (2014) <doi:10.1016/j.ophtha.2014.02.021>, Aptel et al. (2015) <doi:10.1111/aos.12788>.
Empirical models for runoff, erosion, and phosphorus loss 
    across a vegetated filter strip, given slope, soils, climate, and 
    vegetation (Gall et al., 2018) <doi:10.1007/s00477-017-1505-x>. 
    It also includes functions for deriving climate parameters from 
    measured daily weather data, and for simulating rainfall. Models 
    implemented include MUSLE (Williams, 1975) and APLE (Vadas et al., 
    2009 <doi:10.2134/jeq2008.0337>).
An implementation of about 6 major classes of
    statistical regression models. The central algorithm is
    Fisher scoring and iterative reweighted least squares.
    At the heart of this package are the vector generalized linear
    and additive model (VGLM/VGAM) classes. VGLMs can be loosely
    thought of as multivariate GLMs. VGAMs are data-driven
    VGLMs that use smoothing. The book "Vector Generalized
    Linear and Additive Models: With an Implementation in R"
    (Yee, 2015) <DOI:10.1007/978-1-4939-2818-7> gives details of
    the statistical framework and the package. Currently only
    fixed-effects models are implemented. Many (150+) models and
    distributions are estimated by maximum likelihood estimation
    (MLE) or penalized MLE. The other classes are RR-VGLMs
    (reduced-rank VGLMs), quadratic RR-VGLMs, reduced-rank VGAMs,
    RCIMs (row-column interaction models)---these classes perform
    constrained and unconstrained quadratic ordination (CQO/UQO)
    models in ecology, as well as constrained additive ordination
    (CAO). Hauck-Donner effect detection is implemented.
    Note that these functions are subject to change;
    see the NEWS and ChangeLog files for latest changes.
Mainly data sets to accompany the VGAM package and
	the book "Vector Generalized Linear and
	Additive Models: With an Implementation in R" (Yee, 2015)
	<DOI:10.1007/978-1-4939-2818-7>.
	These are used to illustrate vector generalized
	linear and additive models (VGLMs/VGAMs), and associated models
	(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column
	Interaction Models, and constrained and unconstrained ordination
	models in ecology). This package now contains some
	old VGAM family functions which have been replaced by newer
	ones (often because they are now special cases).
Extending the functionalities of the 'VGAM' package with
         additional functions and datasets. At present, 'VGAMextra'
         comprises new family functions (ffs) to estimate several time
         series models by maximum likelihood using Fisher scoring, 
         unlike popular packages in CRAN relying on optim(), including
         ARMA-GARCH-like models, the Order-(p, d, q) ARIMAX model (non-
         seasonal), the Order-(p) VAR model, error correction models
         for cointegrated time series, and ARMA-structures with Student-t 
         errors. For independent data, new ffs to estimate the inverse-
         Weibull, the inverse-gamma, the generalized beta of the second
         kind and the general multivariate normal distributions are
         available. In addition, 'VGAMextra' incorporates new VGLM-links
         for the mean-function, and the quantile-function (as an alternative
         to ordinary quantile modelling) of several 1-parameter distributions,
         that are compatible with the class of VGLM/VGAM family functions.
         Currently, only fixed-effects models are implemented. All functions
         are subject to change; see the NEWS for further details on the
         latest changes.
Analyze the co-adaptation of codon usage between a virus and its host, calculate various codon usage bias measurements as: effective number of codons (ENc) Novembre (2002) <doi:10.1093/oxfordjournals.molbev.a004201>, codon adaptation index (CAI) Sharp  and  Li (1987) <doi:10.1093/nar/15.3.1281>, relative  codon deoptimization index (RCDI) Puigbò et al (2010) <doi:10.1186/1756-0500-3-87>, similarity index (SiD) Zhou et al (2013) <doi:10.1371/journal.pone.0077239>,  synonymous codon usage orderliness (SCUO) Wan et al (2004) <doi:10.1186/1471-2148-4-19> and, relative synonymous    codon usage (RSCU) Sharp et al (1986) <doi:10.1093/nar/14.13.5125>. Also, it provides a statistical dinucleotide over- and underrepresentation with three different models. Implement several methods for visualization of codon usage as ENc.GC3plot() and PR2.plot().
This package provides an implementation of Linear discriminant analysis and quadratic discriminant analysis that works fine in very high dimension (when there are many more variables than observations).
The "Vertical and Horizontal Inheritance Consistence Analysis" method is described in the following publication: "VHICA: a new method to discriminate between vertical and horizontal transposon transfer: application to the mariner family within Drosophila" by G. Wallau. et al. (2016) <DOI:10.1093/molbev/msv341>. The purpose of the method is to detect horizontal transfers of transposable elements, by contrasting the divergence of transposable element sequences with that of regular genes.
Provides direct access to linked names for the same entity across the world's major name authority files, including national and regional variations in language, character set, and spelling. For more information go to <https://viaf.org/>.
Compute group-specific intraclass correlation coefficients, 
    Bayesian testing of homogenous within-group variance, and spike-and-slab
    model selection to determine which groups share a common within-group 
    variance in a one-way random effects model <10.31234/osf.io/hpq7w>.
A shiny app for accurate estimation of vaccine induced immunogenicity 
    with bivariate linear modeling. Method is detailed in: Lhomme E, Hejblum BP, Lacabaratz C, 
    Wiedemann A, Lelièvre J-D, Levy Y, Thiebaut R & Richert L (2019). Submitted.
Converts Vietnam's provinces' names and ID
    across different formats. Handles diacritics and different spellings.
A set of tools to compute viewshed in 3D from Terrestrial Laser Scanner data and prepare the data prior to visibility estimation.
This package implements a fast regression algorithm for
        building linear model for large data as defined in the paper
        "VIF-Regression: A Fast Regression Algorithm for Large Data
        (2011), Journal of the American Statistical Association, Vol.
        106, No. 493: 232-247" by Dongyu Lin, Dean P. Foster, and Lyle
        H. Ungar.
Contains a function to support the following paper:
    Xiaoping Shi, Xiang-Sheng Wang, Dongwei Wei, Yuehua Wu (2016), <DOI:10.1007/s00180-015-0587-5>,
    A sequential multiple change-point detection procedure via VIF regression,
    Computational Statistics, 31(2): 671-691.
Conducts linear regression using variational Bayesian inference, particularly optimized for genome-wide association mapping and whole-genome prediction which use a number of DNA markers as the explanatory variables. Provides seven regression models which select the important variables (i.e., the variables related to response variables) among the given explanatory variables in different ways (i.e., model structures).
New tools for the visualization of missing and/or imputed values
    are introduced, which can be used for exploring the data and the structure of
    the missing and/or imputed values. Depending on this structure of the missing
    values, the corresponding methods may help to identify the mechanism generating
    the missing values and allows to explore the data including missing values.
    In addition, the quality of imputation can be visually explored using various
    univariate, bivariate, multiple and multivariate plot methods. A graphical user
    interface available in the separate package VIMGUI allows an easy handling of
    the implemented plot methods.
Calculate point estimates of and valid confidence intervals for
    nonparametric, algorithm-agnostic variable importance measures in high and low dimensions,
    using flexible estimators of the underlying regression functions. For more information
    about the methods, please see Williamson et al. (Biometrics, 2020),  Williamson et al. (arXiv, 2020+) <arXiv:2004.03683>, and Williamson and Feng (ICML, 2020).
An implementation of methods related to sparse clustering and variable importance 
    in clustering. The package currently allows to perform sparse k-means clustering with a group 
    penalty, so that it automatically selects groups of numerical features. It also allows to 
    perform sparse clustering and variable selection on mixed data (categorical and numerical 
    features), by preprocessing each categorical feature as a group of numerical features.
    Several methods for visualizing and exploring the results are also provided. 
    M. Chavent, J. Lacaille, A. Mourer and M. Olteanu (2020)<https://www.esann.org/sites/default/files/proceedings/2020/ES2020-103.pdf>.
Provides a programmatic interface in R for the US Department of 
    Transportation (DOT) National Highway Transportation Safety Administration 
    (NHTSA) vehicle identification number (VIN) API, located at 
    <https://vpic.nhtsa.dot.gov/api/>. 
    The API can decode up to 50 vehicle identification numbers in one call, and 
    provides manufacturer information about the vehicles, including make, model, 
    model year, and gross vehicle weight rating (GVWR).
Provides tools for the statistical analysis of vine copula models.
    The package includes tools for parameter estimation, model selection,
    simulation, goodness-of-fit tests, and visualization. Tools for estimation,
    selection and exploratory data analysis of bivariate copula models are also
    provided.
Implements D-vine quantile regression models with
  parametric or nonparametric pair-copulas. See 
  Kraus and Czado (2017) <doi:10.1016/j.csda.2016.12.009> and
  Schallhorn et al. (2017) <arXiv:1705.08310>.
Implementation of the vine graphical model for building
    high-dimensional probability distributions as a factorization of
    bivariate copulas and marginal density functions. This package
    provides S4 classes for vines (C-vines and D-vines) and methods
    for inference, goodness-of-fit tests, density/distribution
    function evaluation, and simulation.
A lattice violin-plot is overlayed with the arithmetic
        mean and standard deviation.
Produces violin plots with optional mean comparison with Tukey's honest significant difference and linear regression. This package aims to be a simple and quick visualization tool for comparing means and assessing trends of categorical factors.
A violin plot is a combination of a box plot and a kernel density plot. This package allows extensive customisation of violin plots.
viopoints draws one dimensional scatter plots with jitter
        using kernel density estimates in a similar way to violin
        plots.
A general framework for constructing variable importance plots from 
  various types of machine learning models in R. Aside from some standard model-
  specific variable importance measures, this package also provides model-
  agnostic approaches that can be applied to any supervised learning algorithm.
  These include 1) an efficient permutation-based variable importance measure, 
  2) variable importance based on Shapley values (Strumbelj and Kononenko, 
  2014) <doi:10.1007/s10115-013-0679-x>, and 3) the variance-based 
  approach described in Greenwell et al. (2018) <arXiv:1805.04755>. A 
  variance-based method for quantifying the relative strength of interaction 
  effects is also included (see the previous reference for details).
Generate a violin point plot, a combination of a violin/histogram
    plot and a scatter plot by offsetting points within a category based on their
    density using quasirandom noise.
Computation of volatility impulse response function for multivariate time series model using algorithm by Jin, Lin and Tamvakis (2012) <doi.org/10.1016/j.eneco.2012.03.003>.
Implementation of the 'viridis' - the default -, 'magma', 'plasma', 
    'inferno', and 'cividis' color maps for 'R'. 'viridis', 'magma', 'plasma', 
    and 'inferno' are ported from 'matplotlib' <http://matplotlib.org/>, a 
    popular plotting library for 'python'. 'cividis', was developed by Jamie R. 
    Nuñez and Sean M. Colby. These color maps are designed in such a way that 
    they will analytically be perfectly perceptually-uniform, both in regular 
    form and also when converted to black-and-white. They are also designed to 
    be perceived by readers with the most common form of color blindness (all 
    color maps in this package) and color vision deficiency ('cividis' only).
Implementation of the 'viridis' - the default -, 'magma', 'plasma', 
    'inferno', and 'cividis' color maps for 'R'. 'viridis', 'magma', 'plasma', 
    and 'inferno' are ported from 'matplotlib' <http://matplotlib.org/>, a 
    popular plotting library for 'python'. 'cividis', was developed by Jamie R. 
    Nuñez and Sean M. Colby. These color maps are designed in such a way that 
    they will analytically be perfectly perceptually-uniform, both in regular 
    form and also when converted to black-and-white. They are also designed to 
    be perceived by readers with the most common form of color blindness (all 
    color maps in this package) and color vision deficiency ('cividis' only). 
    This is the 'lite' version of the more complete 'viridis' package that can 
    be found at <https://cran.r-project.org/package=viridis>.
Experiments in which highly complex virome sequencing data is generated are difficult to visualize and unpack for a person without programming experience. 
    After processing of the raw sequencing data by a next generation sequencing (NGS) processing pipeline the usual output consists of contiguous sequences (contigs) in fasta format and an annotation file linking the 
    contigs to a reference sequence. The virome analysis browser app imports an annotation file and a corresponding fasta file containing the annotated contigs. 
    It facilitates browsing of annotations in multiple files and allows users to select and export specific annotated sequences from the associated fasta files. Various
    annotation quality thresholds can be set to filter contigs from the annotation files. Further inspection of selected contigs can be done in the form of automatic open
    reading frame (ORF) detection. Separate contigs and/or separate ORFs can be downloaded in nucleotide or amino acid format for further analysis.
The ability to generate virtual niches enables virtual ecology 
    experiments that have been advocated for evaluating species-environment 
    relationship models. Using multivariate normal distributions and matrix 
    algebra this package provides a unique computational framework to generate 
    integrated fundamental and realised niches, which is important given 
    differences in possible complexity of realised niche shapes that result 
    from biotic interactions Etherington and Omondiagbe (2019) <doi:10.21105/joss.01661>.
Tools to generate virtual environmental drivers with a given temporal autocorrelation, and to simulate pollen curves at annual resolution over millennial time-scales based on these drivers and virtual taxa with different life traits and niche features. It also provides the means to simulate quasi-realistic pollen-data conditions by applying simulated accumulation rates and given depth intervals between consecutive samples.
Provides a framework for generating virtual species distributions,
    a procedure increasingly used in ecology to improve species distribution
    models. This package integrates the existing methodological approaches with the
    objective of generating virtual species distributions with increased ecological
    realism.
Provides users with a simple and convenient
             mechanism to manage and query a 'Virtuoso' database using the 'DBI' (Data-Base Interface)
             compatible 'ODBC' (Open Database Connectivity) interface.
             'Virtuoso' is a high-performance "universal server," which can act
             as both a relational database, supporting standard Structured Query
             Language ('SQL') queries, while also supporting data following the
             Resource Description Framework ('RDF') model for Linked Data.
             'RDF' data can be queried using 'SPARQL' ('SPARQL' Protocol and 'RDF' Query Language)
             queries, a graph-based query that supports semantic reasoning.
             This allows users to leverage the performance of local or remote 'Virtuoso' servers using
             popular 'R' packages such as 'DBI' and 'dplyr', while also providing a 
             high-performance solution for working with large 'RDF' 'triplestores' from 'R.'
             The package also provides helper routines to install, launch, and manage
             a 'Virtuoso' server locally on 'Mac', 'Windows' and 'Linux' platforms using
             the standard interactive installers from the 'R' command-line.  By 
             automatically handling these setup steps, the package can make using 'Virtuoso'
             considerably faster and easier for a most users to deploy in a local
             environment. Managing the bulk import of triples
             from common serializations with a single intuitive command is another key
             feature of this package.  Bulk import performance can be tens to
             hundreds of times faster than the comparable imports using existing 'R' tools,
             including 'rdflib' and 'redland' packages.
Use VirusTotal, a Google service that analyzes files and URLs 
    for viruses, worms, trojans etc., provides category of the content hosted by a 
    domain from a variety of prominent services, provides passive DNS information,
    among other things. See <http://www.virustotal.com> for more information.
Implementation of Shiny app to visualize adverse events based on the Common Terminology Criteria for Adverse Events using stacked correspondence analysis as described in Diniz et. al (2021) <arXiv:2101.03454>.
Functionality for creating phase portraits of functions in the
    complex number plane. Works with R base graphics, whose full 
    functionality is available. Parallel processing is used for optimum 
    performance.
Create preliminary exploratory data visualisations of an entire 
    dataset to identify problems or unexpected features using 'ggplot2'.
A graphical R package designed to visualize behavioral observations over time. Based on raw time data extracted from video recorded sessions of experimental observations, ViSiElse grants a global overview of a process by combining the visualization of multiple actions timestamps for all participants in a single graph. Individuals and/or group behavior can easily be assessed. Supplementary features allow users to further inspect their data by adding summary statistics (mean, standard deviation, quantile or statistical test) and/or time constraints to assess the accuracy of the realized actions.
A Bayesian Phase I cancer vaccine
    trial design is implemented in this package. The design allows simultaneous evaluation
    of safety and immunogenicity outcomes in the context of vaccine studies.
    See Wang (2019) <DOI:10.1002/sim.8021> for the details of the Phase I cancer vaccine trial
    design.
Provides an R interface to the 'vis.js' JavaScript charting
    library. It allows an interactive visualization of networks.
Provides a convenient interface for constructing plots to visualize the fit of regression models arising from a wide variety of models in R ('lm', 'glm', 'coxph', 'rlm', 'gam', 'locfit', 'lmer', 'randomForest', etc.)
A library for creating time based charts, like Gantt or timelines. Possible outputs 
  include 'ggplot' diagrams, 'Plotly' graphs, 'Highchart' widgets and 'data.frames'. Results can be
  used in the 'RStudio' viewer pane, in 'RMarkdown' documents or in 'Shiny' apps. In the 
  interactive outputs created by 'Plotly.js' and 'Highcharts.js', you can interact with the 
  plot using mouse hover or zoom.
Provides a visualization for characterizing subgroups defined by a decision tree structure. The visualization simplifies the ability to interpret individual pathways to subgroups; each sub-plot describes the distribution of observations within individual terminal nodes and percentile ranges for the associated inner nodes.
Visualize and compute percentiles/probabilities of normal, t, f, chi square 
    and binomial distributions.
A collection of tools for analyzing the field of vision. It provides a framework for development and use of innovative methods for visualization, statistical analysis, and clinical interpretation of visual-field loss and its change over time. It is intended to be a tool for collaborative research.
Graphs the pdf or pmf and highlights what area or probability is
    present in user defined locations. Visualize is able to provide lower tail,
    bounded, upper tail, and two tail calculations. Supports strict and equal
    to inequalities.  Also provided on the graph is the mean and variance of
    the distribution.
Visualize the trends and historical downloads from packages in the 'CRAN' repository. Data is obtained by using the 'API' to query the database from the 'RStudio' 'CRAN' mirror.
Visual 2D point and contour plots for binary classification modeling under algorithms such as glm(), randomForest(), gbm(), nnet() and svm(), presented over two dimensions generated by FAMD and MCA methods. Package 'FactoMineR' for multivariate reduction functions and package 'MBA' for interpolation functions are used. The package can be used to visualize the discriminant power of input variables and algorithmic modeling, explore outliers, compare algorithm behaviour, etc. It has been created initially for teaching purposes, but it has also many practical uses.
Visualizes vowel variation in f0, F1, F2, F3 and duration.
Implements the novel testing approach by Janitza et al.(2015)
    <http://nbn-resolving.de/urn/resolver.pl?urn=nbn:de:bvb:19-epub-25587-4>
    for the permutation variable importance measure in a random forest and the
    PIMP-algorithm by Altmann et al.(2010) <doi:10.1093/bioinformatics/btq134>.
    Janitza et al.(2015) <http://nbn-resolving.de/urn/resolver.pl?urn=nbn:de:bvb:19-epub-25587-4>
    do not use the "standard" permutation variable
    importance but the cross-validated permutation variable
    importance for the novel test approach. The cross-validated
    permutation variable importance is not based on the out-of-bag
    observations but uses a similar strategy which is inspired by
    the cross-validation procedure. The novel test approach can be
    applied for classification trees as well as for regression
    trees. However, the use of the novel testing approach has not
    been tested for regression trees so far, so this routine is
    meant for the expert user only and its current state is rather
    experimental.
Provides templates and functions to simplify the production and maintenance of curriculum vitae.
Provides fitting routines for four versions of the
        Vitality family of mortality models.
Provides an easy to calculate local variable importance measure based on Ceteris Paribus profile 
  and global variable importance measure based on Partial Dependence Profiles.
Interactive visualization for Bayesian prior and posterior distributions. 
             When both distributions are provided the animation shows a transition from 
             prior to posterior. Finally, the animation splits the distribution using the provided 
             'breaks' into bars that show the probability for each region. 
             If no 'breaks' are providers it will use zero by default.
Provides an interface to the VK API <https://vk.com/dev/methods>.
      VK <https://vk.com/> is the largest European online social networking
      service, based in Russia.
Contains functions to set up risk-adjusted quality control charts in health care. For the variable life adjusted display (VLAD) proposed by Lovegrove et al. (1997) <doi:10.1016/S0140-6736(97)06507-0> signaling rules derived in Wittenberg et al. (2018) <doi:10.1002/sim.7647> are implemented. Additionally, for the risk-adjusted cumulative sum chart based on log-likelihood ratio statistic introduced by Steiner et al. (2000) <doi:10.1093/biostatistics/1.4.441> average run length and control limits can be computed with fast and accurate Markov chain approximations developed in Knoth et al. (2019) <doi:10.1002/sim.8104>.
Assists in producing a plot that more effectively expresses changes over time for two different types (long format and wide format) using a consistent calling scheme for longitudinal data. It provides the ability to projection supplementary information (supplementary objects and variables) that can often occur in longitudinal data to graphs, as well as provides a new interactive implementation to perform the additional interpretation, so it is also useful for longitudinal data visuals analysis (see <http://lib.pusan.ac.kr/resource/e-article/?app=eds&mod=detail&record_id=edsker.000004649097&db_id=edsker> for more information).
Using frequency matrices, very low frequency variants (VLFs) are assessed for amino acid and nucleotide sequences.  The VLFs are then compared to see if they occur in only one member of a species, singleton VLFs, or if they occur in multiple members of a species, shared VLFs.  The amino acid and nucleotide VLFs are then compared to see if they are concordant with one another.  Amino acid VLFs are also assessed to determine if they lead to a change in amino acid residue type, and potential changes to protein structures.
Functions, Classes & Methods for estimation, prediction, and
  simulation (bootstrap) of Variable Length Markov Chain ('VLMC') Models.
A framework to infer causality on a pair of time series of real numbers based on variable-lag Granger causality and transfer entropy. Typically, Granger causality and transfer entropy have an assumption of a fixed and constant time delay between the cause and effect. However, for a non-stationary time series, this assumption is not true. For example, considering two time series of velocity of person A and person B where B follows A. At some time, B stops tying his shoes, then running to catch up A. The fixed-lag assumption is not true in this case. We propose a framework that allows variable-lags between cause and effect in Granger causality and transfer entropy to allow them to deal with variable-lag non-stationary time series. Please see Chainarong Amornbunchornvej, Elena Zheleva, and Tanya Berger-Wolf (2019) <arXiv:1912.10829> when referring to this package in publications.
A port and extension to the original 'Matlab' code made public by Dragomiretskiy and Zosso, for conducting Variational Mode Decomposition (VMD) as described  within their 2013 publication (publication: <doi:10.1109/TSP.2013.2288675>, source: <https://goo.gl/fJH1d5>).
The tools you need to process, analyze, combine, integrate and
    plot your fishery data: the georeferenced dataset from the Vessel Monitoring
    System (VMS), from the Automatic Information System (AIS) or other tracking
    devices, as well as the catches or landings dataset from the Logbook or Vessel
    Register. Package 'vmsbase' is equipped by Viewer Tools to visually inspect data
    at different steps of the analyses and to produce effective outputs for reports
    and scientific publications. Viewers are conceived to show the VMS pings, to
    visualize single or multiple tracks for fishing vessels, or to represent the VMS
    data on Google Viewer, so that the user can produce easy to interpret and more
    realistic visualization of both fishing effort and effort behaviour. Package
    'vmsbase' represents the implementation of several R routines which have been
    developed by the "Tor Vergata" University of Rome Team involved in the Italian
    National Program for the Data Collection Framework for Fisheries Data between
    2009-2012.
Provide tools for finding multiple-objective optimal designs for
         estimating the shape of dose-response, the ED50 (the dose producing an effect
         midway between the expected responses at the extreme doses) and the MED (the
         minimum effective dose level) for the 2,3,4-parameter logistic models and for
         evaluating its efficiencies for the three objectives. The acronym VNM stands
         for V-algorithm using Newton Raphson method to search multiple-objective
         optimal design.
Create adjacency matrices of vocalisation graphs from
  dataframes containing sequences of speech and silence intervals,
  transforming these matrices into Markov diagrams, and generating
  datasets for classification of these diagrams by 'flattening' them
  and adding global properties (functionals) etc.  Vocalisation
  diagrams date back to early work in psychiatry (Jaffe and Feldstein,
  1970) and social psychology (Dabbs and Ruback, 1987) but have only
  recently been employed as a data representation method for machine
  learning tasks including meeting segmentation (Luz, 2012)
  <doi:10.1145/2328967.2328970> and classification (Luz,
  2013) <doi:10.1145/2522848.2533788>.
Differential expression (DE) analysis can be used to discover quantitative changes in expression levels between experimental groups. Such results are typically visualised using volcano plots, however in cases where more than two experimental groups are involved, visualising results can become convoluted and it quickly becomes difficult to see the wood for the trees. This package provides easy-to-use functions to extract and visualise outputs from DE between three groups (primarily aimed at 'limma' and 'DESeq2' outputs). We present novel methods to map DE results into polar coordinates to enable users to combine and simultaneously view three sets of results. These graphics also possess optional 'plotly' outputs for interactive and three-dimensional functionality, as seen in Lewis et. al. (2019) <doi:10.1016/j.celrep.2019.07.091>.
Provides an R interface for 'volesti' C++ package. 'volesti' computes estimations of volume 
             of polytopes given by (i) a set of points, (ii) linear inequalities or (iii) Minkowski sum of segments 
             (a.k.a. zonotopes). There are three algorithms for volume estimation as well as algorithms 
             for sampling, rounding and rotating polytopes. Moreover, 'volesti' provides algorithms for 
             estimating copulas useful in computational finance.
Volleyball match statistics of the German volleyball first division league (seasons 2013/2014 to 
    2018/2019). The data has been collected from the official volleyball first division homepage 
    (<www.volleyball-bundesliga.de>) and contains information on teams, staff, sets, matches, and player-in-match 
    statistics (extracted automatically from the official match reports).
The d3.js framework with the plugins d3-voronoi-map, d3-voronoi-treemap and d3-weighted-voronoi
        are used to generate Voronoi treemaps in R and in a shiny application.
        The computation of the Voronoi treemaps are based on Nocaj and Brandes (2012)
        <doi:10.1111/j.1467-8659.2012.03078.x>.
Facilitate Post Vortex Simulation Analysis by offering
    tools to collate multiple Vortex (v10) output files into one R object, and
    analyse the collated output statistically. Vortex is a software for
    the development of individual-based model for population dynamic simulation
    (see <https://scti.tools/vortex/>).
Contains selected data from two publications,
    Campbell 'et' 'al'. (2016) <DOI:10.1080/14486563.2015.1028486>
    and 'Pacioni' 'et' 'al'. (2017) <DOI:10.1071/PC17002>.
    The data is provided both as raw outputs from the population viability
    analysis software 'Vortex' and packaged as R objects.
    The R package 'vortexR' uses the raw data provided here to illustrate its
    functionality of parsing raw 'Vortex' output into R objects.
A 'Shiny' application for the interactive visualisation and
    analysis of networks that also provides a web interface for collecting
    social media data using 'vosonSML'.
A suite of tools for collecting and constructing networks from social media data.
    Provides easy-to-use functions for collecting data across popular platforms (Twitter, YouTube
    and Reddit) and generating different types of networks for analysis.
Voss package provides functionality for generating
        realizations of a fractal Brownian function on uniform 1D & 2D
        grid with classic and generic versions of the Voss algorithm
        (random sequential additions)
Counting election votes and determining election results by different methods, including
    the single transferable vote or ranked choice (Newland and F.S. Britton, 1997; 
    ISBN: 0903291185), approval, score, plurality, condorcet and two-round runoff methods.
'ProPublica' <https://projects.propublica.org/represent/> makes United States
    Congress member votes available and has developed their own unique cartogram to visually
    represent this data. Tools are provided to retrieve voting data, prepare voting data 
    for plotting with 'ggplot2', create vote cartograms and theme them.
Various methods to count ballots in voting systems are provided.
	Functions to check validity of ballots are also provided to ensure flexibility.
Calculates voter transitions comparing two elections, using the function solve.QP() in package 'quadprog'.
A wrapper around a CSS library called 'vov.css', intended for use 
  in 'shiny' applications. Simply wrap a UI element in one of the animation 
  functions to see it move.
Procedures for the manipulation, normalization, and plotting of phonetic and sociophonetic vowel formant data.  vowels is the backend for the NORM website.
Parametric and semiparametric inference for massively parallel
    models, i.e., a large number of models with common design matrix, as often
    occurs with brain imaging data.
Functions for the mass-univariate voxelwise analysis of medical imaging data that follows the NIfTI <http://nifti.nimh.nih.gov> format.
Tools for 3D point cloud voxelisation, projection, geometrical and morphological description of trees (DBH, height, volume, crown diameter), analyses of temporal changes between different measurement times, distance based clustering and visualisation of 3D voxel clouds and 2D projection. Most analyses and algorithms provided in the package are based on the concept of space exploration and are described in Lecigne et al. (2018, <doi:10.1093/aob/mcx095>).
Visual predictive checks are a commonly used diagnostic plot in pharmacometrics, showing how certain statistics (percentiles) for observed data compare to those same statistics for data simulated from a model. The package can generate VPCs for continuous, categorical, censored, and (repeated) time-to-event data.
An oceanographic data processing package for analyzing and visualizing Video 
    Plankton Recorder data. Works in concert with Visual Plankton (MATLAB) software 
    developed at 'WHOI'. This package was developed at 'Bedford Institute of Oceanography'.
    Functions are designed to process Visual Plankton output and create organized and 
    easily portable data products.
Estimation of varying regression segments and a change point in
    2-segment regression models with heteroscedastic variances, and with or
    without a smoothness constraint at the change point.
vrmlgen creates 3D scatter and bar plots, visualizations of 3D meshes, parametric functions and height maps in web-formats like the Virtual Reality Markup Language (VRML, filetype .wrl) and the LiveGraphics3D format.
The goal of 'vroom' is to read and write data (like
    'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial
    indexing step, then reads the values lazily , so only the data you
    actually use needs to be read.  The writer formats the data in
    parallel and writes to disk asynchronously from formatting.
A collection of statistical tests for martingale difference hypothesis
Performs variable selection/feature reduction under a clustering or classification framework. In particular, it can be used in an automated fashion using mixture model-based methods (tEIGEN and MCLUST are currently supported).
An implementation of Vasicek and Song goodness-of-fit tests. Several functions are provided to estimate differential Shannon entropy, i.e., estimate Shannon entropy of real random variables with density, and test the goodness-of-fit of some family of distributions, including uniform, Gaussian, log-normal, exponential, gamma, Weibull, Pareto, Fisher, Laplace and beta distributions; see Lequesne and Regnault (2020) <doi:10.18637/jss.v096.c01>.
Implementation of Visual Studio Team Services <https://www.visualstudio.com/team-services/> API calls. 
    It enables the extraction of information about repositories, build and release definitions and individual releases. 
    It also helps create repositories and work items within a project without logging into Visual Studio. 
    There is the ability to use any API service with a shell for any non-predefined call.
Three steps variable selection procedure based on random forests.
    Initially developed to handle high dimensional data (for which number of
    variables largely exceeds number of observations), the package is very
    versatile and can treat most dimensions of data, for regression and
    supervised classification problems. First step is dedicated to eliminate
    irrelevant variables from the dataset. Second step aims to select all
    variables related to the response for interpretation purpose. Third step
    refines the selection by eliminating redundancy in the set of variables
    selected by the second step, for prediction purpose.
    Genuer, R. Poggi, J.-M. and Tuleau-Malot, C. (2015)
    <https://journal.r-project.org/archive/2015-2/genuer-poggi-tuleaumalot.pdf>.
Automatically generates HTML variable documentation including variable names, labels, classes, value labels (if applicable), value ranges, and summary statistics. See the vignette "vtable" for a package overview.
Designed to facilitate the assimilation, analysis and synthesis of animal location and movement data collected by the VEMCO suite of acoustic transmitters and receivers. As well as database and geographic information capabilities the principal feature of VTrack is the qualification and identification of ecologically relevant events from the acoustic detection and sensor data. This procedure condenses the acoustic detection database by orders of magnitude, greatly enhancing the synthesis of acoustic detection data.
A 'data.frame' processor/conditioner that prepares real-world data for predictive modeling in a statistically sound manner.
    'vtreat' prepares variables so that data has fewer exceptional cases, making
    it easier to safely use models in production. Common problems 'vtreat' defends
    against: 'Inf', 'NA', too many categorical levels, rare categorical levels, and new
    categorical levels (levels seen during application, but not during training). Reference: 
    "'vtreat': a data.frame Processor for Predictive Modeling", Zumel, Mount, 2016, <DOI:10.5281/zenodo.1173313>.
A tool for calculating and drawing "variable trees". Variable trees display information about nested subsets of a data frame.
An interactive document on  the topic of variance analysis using 'rmarkdown' and 'shiny' packages. Runtime examples are provided in the package function as well as at  <https://predanalyticssessions1.shinyapps.io/chisquareVarianceTest/>.
Contains functions for visualization univariate data: ccdplot and qddplot.
Calculates the volume under the ROC surface and its (co)variance for ordered multi-class ROC analysis as well as certain bivariate ordinal measures of association.
Provides R functions to draw lines and curves with the width
             of the curve allowed to vary along the length of the curve.
Gaze data from the Visual World Paradigm requires significant
    preprocessing prior to plotting and analyzing the data. This package 
    provides functions for preparing visual world eye-tracking data for 
    statistical analysis and plotting. It can prepare data for linear 
    analyses (e.g., ANOVA, Gaussian-family LMER, Gaussian-family GAMM) as
    well as logistic analyses (e.g., binomial-family LMER and binomial-family GAMM).
    Additionally, it contains various plotting functions for creating grand average and
    conditional average plots. See the vignette for samples of the functionality.
    Currently, the functions in this package are designed for handling data
    collected with SR Research Eyelink eye trackers using Sample Reports created
    in SR Research Data Viewer.  While we would like to add functionality 
    for data collected with other systems in the future, the current package is 
    considered to be feature-complete; further updates will mainly entail maintenance
	and the addition of minor functionality.
Functions and data for use in visual word recognition research: 
	 Computation of neighbors (Hamming and Levenshtein
	 distances), average distances to neighbors (e.g., OLD20),
	 and Coltheart's N. Also includes the LD1NN algorithm to
	 detect bias in the composition of a lexical decision task. Most of
	 the functions support parallel execution. Supplies wordlists for 
	 several languages. Uses the string distance functions from the stringdist package by Mark van der Loo.
Set of functions that improves the graphical presentations of the functions: wave.correlation and spin.correlation (waveslim package, Whitcher 2012) and the wave.multiple.correlation and wave.multiple.cross.correlation (wavemulcor package, Fernandez-Macho 2012b). The plot outputs (heatmaps) can be displayed in the screen or can be saved as PNG or JPG images or as PDF or EPS formats. The W2CWM2C package also helps to handle the (input data) multivariate time series easily as a list of N elements (times series) and provides a multivariate data set (dataexample) to exemplify its use. A description of the package was published in a scientific paper: Polanco-Martinez and Fernandez-Macho (2014), <doi:10.1109/MCSE.2014.96>.
R interface to a W3C Markup Validation service.
  See <http://validator.w3.org/> for more information.
Downloads and tidies Aswath Damodaran's Cost of Capital Data.
A multivariate weather generator for daily climate variables based 
    on weather-states (Flecher et al. (2010) <doi:10.1029/2009WR008098>). 
    It uses a Markov chain for modeling the succession of weather states. 
    Conditionally to the weather states, the multivariate variables are modeled using the family 
    of Complete Skew-Normal distributions. Parameters are estimated on measured series. Must 
    include the variable 'Rain' and can accept as many other variables as desired.
A user-friendly factor-like interface for converting strings of
    text into numeric vectors and rectangular data structures.
Square pie charts (a.k.a. waffle charts) can be used
    to communicate parts of a whole for categorical quantities. To emulate the
    percentage view of a pie chart, a 10x10 grid should be used with each square
    representing 1% of the total. Modern uses of waffle charts do not
    necessarily adhere to this rule and can be created with a grid of any
    rectangular shape. Best practices suggest keeping the number of categories
    small, just as should be done when creating pie charts. Tools are provided
    to create waffle charts as well as stitch them together, and to use glyphs
    for making isotype pictograms.
Fit the fixed effect panel data model with heteroskedasticity and
    autocorrelation correction.
Full screen and partial loading screens for 'Shiny' with spinners, progress bars, and notifications.
Generates random data sets including: data.frames, lists,
        and vectors.
Read 'Quake' assets including bitmap images and textures in 'wal' file format. This package also provides support for extracting these assets from 'WAD' and 'PAK' file archives. It can also read models in 'MDL' and 'MD2' formats.
Compare complex R objects and reveal the key
    differences.  Designed particularly for use in testing packages where
    being able to quickly isolate key differences makes understanding test
    failures much easier.
Bayesian generalized linear models with time-varying coefficients 
    as in Helske (2020, <arXiv:2009.07063>). Gaussian, Poisson, and binomial 
    observations are supported. The Markov chain Monte Carlo (MCMC) computations are done using 
    Hamiltonian Monte Carlo provided by Stan, using a state space representation 
    of the model in order to marginalise over the coefficients for efficient sampling. 
    For non-Gaussian models, the package uses the importance sampling type estimators based on 
    approximate marginal MCMC as in Vihola, Helske, Franks (2020, <doi:10.1111/sjos.12492>).
A collection of functions to perform the Application
        Programming Interface (API) calls associated with the Walk
        Score website (www.walkscore.com) within the R environment.
        These functions can be used to query the Walk Score and Transit
        Score database for a wide variety of information using R
        scripts. This package includes the simple Walk Score and
        Transit Score API calls, which return the scores associated
        with an input location, as well as calls which return some data
        used to calculate the scores. These functions are especially
        useful for mass data collection and gathering Walk Score and
        Transit Score values for large lists of locations.
The 'shiny' application 'wallace' is a modular platform for reproducible modeling of species niches and distributions. 'wallace' guides users through a complete analysis, from the acquisition of species occurrence and environmental data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface.
A prediction model is calibrated if, roughly, for any percentage x we can expect that x subjects out of 100 experience the event among all subjects that have a predicted risk of x%. A calibration plot provides a simple, yet useful, way of assessing the calibration assumption. The Wally plot consists of a sequence of usual calibration plots. Among the plots contained within the sequence, one is the actual calibration plot which has been obtained from the data and the others are obtained from similar simulated data under the calibration assumption. It provides the investigator with a direct visual understanding of the shape and sampling variability that are common under the calibration assumption. The original calibration plot from the data is included randomly among the simulated calibration plots, similarly to a police lineup. If the original calibration plot is not easily identified then the calibration assumption is not contradicted by the data. The method handles the common situations in which the data contain censored observations and occurrences of competing events.
Provides API access to the Walmart Open API <https://developer.walmartlabs.com/>, 
    that contains data about stores, Value of the day and products which 
    includes names, sale prices, shipping rates and taxonomies.
A toolbox of common robust statistical tests, including robust
  descriptives, robust t-tests, and robust ANOVA. It is also available as a
  module for 'jamovi' (see <https://www.jamovi.org> for more information).
  Walrus is based on the WRS2 package by Patrick Mair, which is in turn based on
  the scripts and work of Rand Wilcox. These analyses are described in depth in
  the book 'Introduction to Robust Estimation & Hypothesis Testing'.
The outcome of various rehabilitation strategies for water distribution systems can be modeled with the Water Management Simulator (WaMaSim). Pipe breaks and the corresponding damage and rehabilitation costs are simulated. It is mainly intended to be used as educational tool for the Water Infrastructure Experimental and Computer Laboratory at ETH Zurich, Switzerland.
'MIME' types are shorthand descriptors for
      file contents and can be determined from "magic"
      bytes in file headers, file contents or intuited
      from file extensions. Tools are provided to
      perform curated "magic" tests as well as mapping
      'MIME' types from a database of over 1,500
      extension mappings.
This estimates precise weaning ages
	for a given skeletal population
	by analyzing the stable nitrogen isotope ratios of them.
	Bone collagen turnover rates estimated anew and
	the approximate Bayesian computation (ABC)
	were adopted in this package.
Tooling to group dates by a variety of periods
    including: yearly, monthly, by second, by week of the month, and more.
    The groups are defined in such a way that they also represent the
    distance between dates in terms of the period. This extracts valuable
    information that can be used in further calculations that rely on a
    specific temporal spacing between observations.
Mixed effects modeling with warping for functional data using B-
    spline. Warping coefficients are considered as random effects, and warping
    functions are general functions, parameters representing the projection onto B-
    spline basis of a part of the warping functions. Warped data are modelled by a
    linear mixed effect functional model, the noise is Gaussian and independent from
    the warping functions.
Urban water and sanitation survey dataset collected by Water and
    Sanitation for the Urban Poor (WSUP) with technical support from 
    Valid International. These citywide surveys have been collecting data 
    allowing water and sanitation service levels across the entire city to be 
    characterised, while also allowing more detailed data to be collected in 
    areas of the city of particular interest. These surveys are intended to 
    generate useful information for others working in the water and sanitation
    sector. Current release version includes datasets collected from a survey 
    conducted in Dhaka, Bangladesh in March 2017. This survey in Dhaka is one of 
    a series of surveys to be conducted by WSUP in various
    cities in which they operate including Accra, Ghana; Nakuru, Kenya; 
    Antananarivo, Madagascar; Maputo, Mozambique; and, Lusaka, Zambia. This 
    package will be updated once the surveys in other cities are completed and 
    datasets have been made available.
Time series outlier detection by mean of non parametric test. Outlier detection regarding two methodologies: single time series variability (a vector) and grouped similar time series (a data frame). Andrea Venturini(2011) Statistica-Universita' Bologna, Vol.71, pp.329-344.
Functions to compute Wasserstein barycenters
    of subset posteriors using the swapping algorithm developed by Puccetti, 
    Rüschendorf and Vanduffel (2020) <doi:10.1016/j.jmaa.2017.02.003>. The 
    Wasserstein barycenter is a geometric approach for combining subset 
    posteriors. It allows for parallel and distributed computation of the 
    posterior in case of complex models and/or big datasets, thereby increasing
    computational speed tremendously.
Tools and functions to calculate actual Evapotranspiration
    using surface energy balance models.
Imports U.S. Geological Survey (USGS) daily hydrologic data from USGS web services (see <https://waterservices.usgs.gov/> for more information), plots the data, addresses some common data problems, and calculates and plots anomalies.
Provides support for creating waterfall charts in R
    using both traditional base and lattice graphics.
A not uncommon task for quants is to create 'waterfall charts'. There seems to be no simple way to do this in 'ggplot2' currently. This package contains a single function (waterfall) that simply draws a waterfall chart in a 'ggplot2' object. Some flexibility is provided, though often the object created will need to be modified through a theme.
Lets you connect to any of the 'Consortium of Universities for the Advancement of Hydrological Science, Inc.' 
    ('CUAHSI') Water Data Center 'WaterOneFlow' web services
    and read any 'WaterML' time series data file. To see list of available
    web services, see <http://hiscentral.cuahsi.org>. All versions of 'WaterML'
    (1.0, 1.1 and 2.0) and both types of the web service protocol ('SOAP' and 'REST') are supported.
    The package has six data download functions: GetServices(): show all public web
    services from the HIS Central Catalog. HISCentral_GetSites() and HISCentral_GetSeriesCatalog():
    search for sites or time series from the HIS Central catalog based on geographic bounding box,
    server, or keyword. GetVariables(): Show a data.frame with all variables on the server.
    GetSites(): Show a data.frame with all sites on the server. GetSiteInfo(): Show what variables,
    methods and quality control levels are available at the specific site. GetValues(): Given a site
    code, variable code, start time and end time, fetch a data.frame of all the observation time
    series data values. The GetValues() function can also parse 'WaterML' data from a custom URL or
    from a local file. The package also has five data upload functions:
    AddSites(), AddVariables(), AddMethods(), AddSources(), and AddValues().
    These functions can be used for uploading data to a 'HydroServer Lite' Observations
    Data Model ('ODM') database via the 'JSON' data upload web service interface.
The main purpose of waterquality is to quickly and easily convert
    satellite-based reflectance imagery into one or many well-known water quality
    algorithms designed for the detection of harmful algal blooms or the following
    pigment proxies: chlorophyll-a, blue-green algae (phycocyanin), and turbidity.
    Johansen et al. (2019) <doi:10.21079/11681/35053>.
Methods for watersheds aggregation and spatial drainage network analysis.
Provides Water Year Hydrologic Classification Indices based on measured 
    unimpaired runoff (in million acre-feet). Data is provided by California Department of Water Resources
    and subject to revision.
Computes Bayesian wavelet shrinkage credible intervals for
	nonparametric regression.
	The method uses cumulants to derive Bayesian credible intervals for
	wavelet regression estimates.
	The first four cumulants of the posterior distribution of the
	estimates are expressed in terms of the observed data and integer
	powers of the mother wavelet functions.
	These powers are closely approximated by linear combinations of
	wavelet scaling functions at an appropriate finer scale.
	Hence, a suitable modification of the discrete wavelet transform allows
	the posterior cumulants to be found efficiently for any data set.
	Johnson transformations then yield the credible intervals themselves.
	Barber, S., Nason, G.P. and Silverman, B.W. (2002)
	<doi:10.1111/1467-9868.00332>.
Makes available code necessary to reproduce figures and
        tables in papers on the WaveD method for wavelet deconvolution
        of noisy signals as presented in The WaveD Transform in R,
        Journal of Statistical Software Volume 21, No. 3, 2007.
A wealth of Full Waveform (FW) Light Detection and Ranging (LiDAR) data are available to 
	the public from different sources, which is poised to boost the extensive 
	application of FW LiDAR data. However, we lack a handy and open source tool 
	that can be used by ecological and remote sensing communities for processing and analyzing FW LiDAR 
	data. To this end, we introduce 'waveformlidar', an R package dedicated to 
	FW LiDAR processing, analysis and visualization as a solution to the constraint.
	Specifically, this package provides several commonly used waveform processing methods
	such as Gaussian, adaptive Gaussian and Weibull decompositions, and 
	deconvolution approaches (Gold and Richard-Lucy (RL)) with customized settings. 
	In addition, we also develop some functions to derive commonly used waveform metrics
	for characterizing vegetation structure. Moreover, a new way to directly visualize 
	FW LiDAR data is developed through converting waveforms into points to form the Hyper
	Point cloud (HPC), which can be easily adopted and subsequently analyzed with existing 
	discrete-return LiDAR processing tools such as 'LAStools' and 'FUSION'. Basic explorations of 
	the HPC such as 3D voxelization of the HPC and conversion from original waveforms to 
	composite waveforms are also available in this package. All of these functions are 
	developed based on small-footprint FW LiDAR data, but they can be easily transplanted to
	the large footprint FW LiDAR data such as Geoscience Laser Altimeter System (GLAS) 
	and Global Ecosystem Dynamics Investigation (GEDI) data analysis. References: Zhou et al. (2017a) <doi:10.1016/j.isprsjprs.2017.04.021>;
	Zhou et al. (2017b) <doi:10.1016/j.rse.2017.08.012>; Zhou et al. (2018a) <doi:10.3390/rs10010039>;Zhou et al. (2018b) <doi:10.3390/rs10121949>.
Real probability distributions can be represented as the square of
    an orthogonal sum in the Hermite basis. This representation is formally
    similar to the representation of quantum mechanical states as wave
    functions, whose squared modulus is a probability density. This is
    described in more detail in "Wave function representation of probability
    distributions," by Madeleine B. Thompson <arXiv:1712.07764>. This package
    provides a reference implementation of the technique.
Fits hybrid Wavelet ANN model for time series forecasting using algorithm by Anjoy and Paul (2017) <DOI: 10.1007/s00521-017-3289-9>.
Fits hybrid Wavelet ARIMA model for time series forecasting using algorithm by Aminghafari and Poggi (2012) <doi:10.1142/S0219691307002002>.
Wavelet analysis and reconstruction of time series, cross-wavelets and phase-difference (with filtering options), significance with simulation algorithms.
Fits the combination of Wavelet-GARCH model for time series forecasting using algorithm by Paul (2015) <doi:10.3233/MAS-150328>.
Contains functions for computing and plotting
        discrete wavelet transforms (DWT) and maximal overlap discrete
        wavelet transforms (MODWT), as well as their inverses.
        Additionally, it contains functionality for computing and
        plotting wavelet transform filters that are used in the above
        decompositions as well as multiresolution analyses.
Wavelet routines that calculate single sets of wavelet multiple regressions and correlations, 
        and cross-regressions and cross-correlations from a multivariate time series.  
        Dynamic versions of the routines allow the wavelet local multiple (cross-)regressions and 
        (cross-)correlations to evolve over time.
Functions for calculating the
    fetch (length of open water distance along given directions)
    and estimating wave energy from wind and wave monitoring data.
For multivariate datasets, this function enables the estimation of missing data using the Weighted AVERage of all possible Regressions using the data available.
Originally designed application in the context of resource-limited plant research 
    and breeding programs, 'waves' provides an open-source solution to spectral data processing 
    and model development by bringing useful packages together into a streamlined pipeline. 
    This package is wrapper for functions related to the analysis of point visible and 
    near-infrared reflectance measurements. It includes visualization, filtering, aggregation, 
    preprocessing, cross-validation set formation, model training, and prediction functions to 
    enable open-source association of spectral and reference data. 
    Specialized cross-validation schemes are described in detail in Jarquín et al. (2017) 
    <doi:10.3835/plantgenome2016.12.0130>. Example data is from Ikeogu et al. (2017) 
    <doi:10.1371/journal.pone.0188918>.
Spatial data are generally auto-correlated, meaning that if two 
  units selected are close to each other, then it is likely that they share the
  same properties. For this reason, when sampling in the population it is often
  needed that the sample is well spread over space. A new method to draw a sample
  from a population with spatial coordinates is proposed. This method is called
  wave (Weakly Associated Vectors) sampling. It uses the less correlated vector
  to a spatial weights matrix to update the inclusion probabilities vector
  into a sample. For more details see Raphaël Jauslin and Yves Tillé (2019) <arXiv:1910.13152>.
Basic wavelet routines for time series (1D), image (2D) 
  and array (3D) analysis.  The code provided here is based on
  wavelet methodology developed in Percival and Walden (2000);
  Gencay, Selcuk and Whitcher (2001); the dual-tree complex wavelet
  transform (DTCWT) from Kingsbury (1999, 2001) as implemented by
  Selesnick; and Hilbert wavelet pairs (Selesnick 2001, 2002).  All
  figures in chapters 4-7 of GSW (2001) are reproducible using this 
  package and R code available at the book website(s) below.
Performs 1, 2 and 3D real and complex-valued wavelet transforms,
	nondecimated transforms, wavelet packet transforms, nondecimated
	wavelet packet transforms, multiple wavelet transforms,
	complex-valued wavelet transforms, wavelet shrinkage for
	various kinds of data, locally stationary wavelet time series,
	nonstationary multiscale transfer function modeling, density
	estimation.
Provides scalogram based wavelet tools for time series analysis: wavelet power spectrum, scalogram, windowed scalogram, windowed scalogram difference (see Bolos et al. (2017) <doi:10.1016/j.amc.2017.05.046>), scale index and windowed scale index (Benitez et al. (2010) <doi:10.1016/j.camwa.2010.05.010>).
Make sure packages are available at runtime without any setup. 
    Package installation, reproducibility and exchanging code can be 
    frustrating especially if code is used on older R versions. 
    Often it is hard to puzzle out which package versions are able to work 
    together after some years have passed and packages evolved further and 
    further. The 'wayback' package aims to make this process as painless 
    and robust as possible by using 'MRAN's 'CRAN' snapshots to build local
    package libraries from way back.
Supplies bootstrap alternatives to traditional hypothesis-test
  and confidence-interval procedures such as one-sample and two-sample
  inferences for means, medians, standard deviations, and proportions; simple
  linear regression; and more. Suitable for general audiences, including
  individual and group users, introductory statistics courses, and more advanced
  statistics courses that desire an introduction to bootstrap methods.
Provides efficient implementation of the Wild Binary Segmentation and Binary
    Segmentation algorithms for estimation of the number and locations of
    multiple change-points in the piecewise constant function plus Gaussian
    noise model.
Implements the diagnostic "theta" developed in Poetscher and Preinerstorfer (2020) "How Reliable are Bootstrap-based Heteroskedasticity Robust Tests?" <arXiv:2005.04089>. This diagnostic can be used to detect and weed out bootstrap-based procedures that provably have size equal to one for a given testing problem. The implementation covers a large variety of bootstrap-based procedures, cf. the above mentioned article for details. A function for computing bootstrap p-values is provided.
Search and download data from the World Bank Data API.
Implements detection for the number and locations of
    the change-points in a time series using the Wild Binary Segmentation and
    the Locally Stationary Wavelet model of Korkas and Fryzlewicz (2017) <doi:10.5705/ss.202015.0262>.
A flexible method for modeling cumulative effects of time-varying exposures, weighted according to their relative proximity in time, and represented by time-dependent covariates. The current implementation estimates the weight function in the Cox proportional hazards model. The function that assigns weights to doses taken in the past is estimated using cubic regression splines.
Analyze given data frame with multiple endpoints and return Kaplan-Meier survival probabilities together with the specified confidence interval.
Retrieval the leaf area index (LAI) and soil moisture (SM) from  microwave backscattering data using water cloud model (WCM) model . The WCM algorithm attributed to Pervot et al.(1993) <doi:10.1016/0034-4257(93)90053-Z>. The authors are grateful to SAC, ISRO, Ahmedabad for providing financial support to Dr. Prashant K Srivastava to conduct this research work.
Calculates Pearson, Spearman, polychoric, and polyserial correlation coefficients, in weighted or unweighted form. The package implements tetrachoric correlation as a special case of the polychoric and biserial correlation as a specific case of the polyserial.
The package contains the WCQ method for detection of QTL
        effects in a small mapping population. It also contains
        implementation of the Chen-Qin two-sample and one-sample test
        of means.
Search and download data from over 40 databases hosted by the World Bank, including the World Development Indicators ('WDI'), International Debt Statistics, Doing Business, Human Capital Index, and Sub-national Poverty indicators.
Provides efficient implementations of weighted dependence measures
  and related asymptotic tests for independence. Implemented measures are
  the Pearson correlation, Spearman's rho, Kendall's tau, Blomqvist's beta, and
  Hoeffding's D; see, e.g., Nelsen (2006) <doi:10.1007/0-387-28678-0> and
  Hollander et al. (2015, ISBN:9780470387375).
There are a number of binary files associated with the
    'Webdriver'/'Selenium' project (see <http://www.seleniumhq.org/download/>,
    <https://sites.google.com/a/chromium.org/chromedriver/>,
    <https://github.com/mozilla/geckodriver>,
    <http://phantomjs.org/download.html> and
    <https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver> for
    more information). This package provides functions to download these
    binaries and to manage processes involving them.
Fetch and clean data from the World Database on Protected
    Areas (WDPA). Data is obtained from Protected Planet
    <https://www.protectedplanet.net/en>.
Provides means for downloading historical weather data from 
    the Environment and Climate Change Canada website 
    (<https://climate.weather.gc.ca/historical_data/search_historic_data_e.html>). 
    Data can be downloaded from multiple stations and over large date ranges 
    and automatically processed into a single dataset. Tools are also provided 
    to identify stations either by name or proximity to a location.
Functions to convert between weather metrics, including conversions
    for metrics of temperature, air moisture, wind speed, and precipitation.
    This package also includes functions to calculate the heat index from
    air temperature and air moisture.
Handle instant weather forecasts and geographical information. It combines multiple sources of information to obtain instant weather forecasts.
Chemical information from around the web. This package interacts 
    with a suite of web services for chemical information. Sources include: Alan
    Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver,
    ChEBI, Chemical Translation Service, ChemIDplus, ChemSpider, ETOX,
    Flavornet, NIST Chemistry WebBook, OPSIN, PAN Pesticide Database, PubChem,
    SRS, Wikidata.
A client for the 'WebDriver' 'API'. It allows driving a
    (probably headless) web browser, and can be used to test web
    applications, including 'Shiny' apps. In theory it works with any
    'WebDriver' implementation, but it was only tested with 'PhantomJS'.
Functions for easily creating interactive web pages using
    'R Markdown' that students can use in self-guided learning.
Create a web app that makes it easier to test web clients
  without using the internet. It includes a web app framework with path
  matching, parameters and templates. Can parse various 'HTTP' request
  bodies. Can send 'JSON' data or files from the disk. Includes a web app
  that implements the <https://httpbin.org> web service.
The web version WebGestalt <http://www.webgestalt.org> supports 12 organisms, 354 gene identifiers and 321,251 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis and Network Topology Analysis. The user-friendly output report allows interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneously analyze multiple gene lists.
Displays geospatial data on an interactive 3D globe in the web browser.
Stubbing and setting expectations on 'HTTP' requests.
    Includes tools for stubbing 'HTTP' requests, including expected
    request conditions and response conditions. Match on
    'HTTP' method, query parameters, request body, headers and
    more. Can be used for unit tests or outside of a testing 
    context.
Lossless webp images are 26% smaller in size compared to PNG. Lossy
    webp images are 25-34% smaller in size compared to JPEG. This package reads
    and writes webp images into a 3 (rgb) or 4 (rgba) channel bitmap array using
    conventions from the 'jpeg' and 'png' packages.
This is a collection of tools for conducting both basic and advanced statistical power analysis including correlation, proportion, t-test, one-way ANOVA, two-way ANOVA, linear regression, logistic regression, Poisson regression, mediation analysis, longitudinal data analysis, structural equation modeling and multilevel modeling. It also serves as the engine for conducting power analysis online at <https://webpower.psychstat.org>.
Several analysis-related functions for the book entitled
    "Web-based Analysis without R in Your Computer"(written in Korean, ISBN 978-89-5566-185-9)
    by Keon-Woong Moon. The main function plot.htest() shows the distribution of statistic for
    the object of class 'htest'.
R is used by a vast array of people for a vast array of purposes
    - including web analytics. This package contains functions for consuming and
    munging various common forms of request log, including the Common and Combined
    Web Log formats and various Amazon access logs.
Functions that allow for accessing domains and a number of search engines.
Takes screenshots of web pages, including Shiny applications and R
    Markdown documents.
Provides a 'WebSocket' client interface for R.
    'WebSocket' is a protocol for low-overhead real-time communication:
    <https://en.wikipedia.org/wiki/WebSocket>.
Provides functions to query data from the 'WebTRIS' Traffic Flow API (from Highways England) into tidy data frames.
    The API documentation is available here: <http://webtris.highwaysengland.co.uk/api/swagger/ui/index>.
A Stata-style `webuse()` function for importing named datasets from Stata's online collection.
Parses http request data in application/json, multipart/form-data, 
    or application/x-www-form-urlencoded format. Includes example of hosting
    and parsing html form data in R using either 'httpuv' or 'Rhttpd'.
Provides functions to create factor variables with contrasts based on weighted effect coding, and their interactions. In weighted effect coding the estimates from a first order regression model show the deviations per group from the sample mean. This is especially useful when a researcher has no directional hypotheses and uses a sample from a population in which the number of observation per group is different.
Western Electric Company Rules (WECO) have been widely used for
    Shewhart control charts in order to increase the sensitivity of detecting
    assignable causes of process change. This package implements eight commonly
    used WECO rules and allow to apply the combination of these individual rules
    for detecting the deviation from a stable process. The package also provides
    a web-based graphical user interface to help users conduct the analysis.
Secondary analysis of case-control studies using a weighted estimating equation (WEE) approach: logistic regression for binary secondary outcomes, linear regression and quantile regression for continuous secondary outcomes.
Calculates the WEGE (Weighted Endemism including Global 
    Endangerment index) index for a particular area. Additionally it also 
    calculates rasters of KBA's (Key Biodiversity Area) criteria (A1a, A1b, A1e, 
    and B1), Weighted endemism (WE), the EDGE (Evolutionarily Distinct and
    Globally Endangered) score, Evolutionary Distinctiveness (ED) and Extinction
    risk (ER). Farooq, H., Azevedo, J., Belluardo F., Nanvonamuquitxo, C.,
    Bennett, D., Moat, J., Soares, A., Faurby, S. & Antonelli, A. (2020)
    <doi:10.1101/2020.01.17.910299>.
Performs a curve fit to 4-parameters Weibull distribution using Metropolis algorithm - Markov chain-Monte Carlo method. Special usage for fitting COVID-19 epidemic data on daily new cases and deaths. Also, builds the 4-parameters Weibull distribution curve using given parameters (shape, scale, location and area).
Provides a single function to fit data of an input data frame into one of the selected Weibull functions (w2, w3 and it's truncated versions), calculating the scale, location and shape parameters accordingly. The resulting plots and files are saved into the 'folder' parameter provided by the user. References: a) John C. Nash, Ravi Varadhan (2011). "Unifying Optimization Algorithms to Aid Software System Users: optimx for R" <doi:10.18637/jss.v043.i09>.
Performs a goodness-of-fit test of Weibull distribution (weibullness test) and provides the maximum likelihood estimates of the three-parameter Weibull distribution. Note that the threshold parameter is estimated based on the correlation from the Weibull plot. For more details, see Park (2018) <doi:10.1155/2018/6056975>. This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (No. NRF-2017R1A2B4004169).
Life data analysis in the graphical tradition of Waloddi Weibull. Methods derived from Robert B. Abernethy (2008, ISBN 0-965306-3-2), Wayne Nelson (1982, ISBN: 9780471094586) <DOI:10.1002/0471725234>, William Q. Meeker and  Lois A. Escobar (1998, ISBN: 1-471-14328-6), John I. McCool, (2012, ISBN: 9781118217986) <DOI:10.1002/9781118351994>.
Weighted descriptive statistics is the discipline of quantitatively describing the main features of real-valued fuzzy data which usually given from a fuzzy population. One can summarize this special kind of fuzzy data numerically or graphically using this package. To interpret some of the properties of one or several sets of real-valued fuzzy data, numerically summarize is possible by some weighted statistics which are designed in this package such as mean, variance, covariance and correlation coefficent. Also, graphically interpretation can be given by weighted histogram and weighted scatter plot using this package to describe properties of real-valued fuzzy data set.
Clusters state sequences and weighted data. It provides an optimized weighted PAM algorithm as well as functions for aggregating replicated cases, computing cluster quality measures for a range of clustering solutions and plotting clusters of state sequences.
This packages contains the Weighted Portmanteau Tests as
        described in "New Weighted Portmanteau Statistics for Time
        Series Goodness-of-Fit Testing' accepted for publication by the
        Journal of the American Statistical Association.
Fast computation of
 Receiver Operating Characteristic (ROC) curves
 and Area Under the Curve (AUC)
 for weighted binary classification problems
 (weights are example-specific cost values).
The weighted scores method and composite likelihood information criteria as an intermediate step for variable/correlation selection for longitudinal ordinal and count data in Nikoloulopoulos, Joe and Chaganty (2011)  <doi:10.1093/biostatistics/kxr005>, Nikoloulopoulos (2016) <doi:10.1002/sim.6871> and Nikoloulopoulos (2017) <arXiv:1510.07376>.
Calculates z-differences (O.Kuss (2013) <doi:10.1016/j.jclinepi.2013.06.001>) for each variable scale (continuous, binary, ordinal and nominal) with or without weights (e.g. generated by propensity score methods).
Generates weights to form equivalent groups in observational studies with point or longitudinal treatments by easing and extending the functionality of the R packages 'twang' for generalized boosted modeling (McCaffrey, Ridgeway & Morral, 2004) <doi:10.1037/1082-989X.9.4.403>, 'CBPS' for covariate balancing propensity score weighting (Imai & Ratkovic, 2014) <doi:10.1111/rssb.12027>, 'ebal' for entropy balancing (Hainmueller, 2012) <doi:10.1093/pan/mpr025>, 'optweight' for optimization-based weights (Zubizarreta, 2015) <doi:10.1080/01621459.2015.1023805>, 'ATE' for empirical balancing calibration weighting (Chan, Yam, & Zhang, 2016) <doi:10.1111/rssb.12129>, and 'SuperLearner' for stacked machine learning-based propensity scores (Pirracchio, Petersen, & van der Laan, 2015) <doi:10.1093/aje/kwu253>. Also allows for assessment of weights and checking of covariate balance by interfacing directly with 'cobalt'.
Estimation of observation-specific weights for incomplete longitudinal data and bootstrap procedure for weighted quantile regressions.
Estimates the Vevea and Hedges (1995)
    weight-function model. By specifying arguments, users can
    also estimate the modified model described in Vevea and Woods (2005), 
    which may be more practical with small datasets. Users 
    can also specify moderators to estimate a linear model. 
    The package functionality allows users to easily extract the 
    results of these analyses as R objects for other uses. In addition, 
    the package includes a function to launch both models as 
    a Shiny application. Although the Shiny application is also available online, 
    this function allows users to launch it locally if they choose.
Provides a variety of functions for producing simple weighted statistics, such as weighted Pearson's correlations, partial correlations, Chi-Squared statistics, histograms, and t-tests.  Also now includes some software for quickly recoding survey data and plotting point estimates from interaction terms in regressions (and multiply imputed regressions). NOTE: Weighted partial correlation calculations pulled to address a bug.
Functions for subject/instance weighted support vector machines (SVM). 
    It uses a modified version of 'libsvm' and is compatible with package 'e1071'.
Provides computational support for flow over weirs, such as sharp-crested, broad-crested, and embankments. Initially, the package supports broad- and sharp-crested weirs.
Implementation of Johansen's general formulation of Welch-James's statistic with Approximate Degrees of Freedom, which makes it suitable for testing 
    any linear hypothesis concerning cell means in univariate and multivariate mixed model designs when the data pose non-normality and non-homogeneous variance. Some 
    improvements, namely trimmed means and Winsorized variances, and bootstrapping for calculating an empirical critical value, have been added to the classical formulation. 
    The code departs from a previous SAS implementation by L.M. Lix and H.J. Keselman, available at <http://supp.apa.org/psycarticles/supplemental/met_13_2_110/SAS_Program.pdf> and
    published in Keselman, H.J., Wilcox, R.R., and Lix, L.M. (2003) <DOI:10.1111/1469-8986.00060>.
Convert 'WKT' to 'GeoJSON' and 'GeoJSON' to 'WKT'. Functions
    included for converting between 'GeoJSON' to 'WKT', creating both
    'GeoJSON' features, and non-features, creating 'WKT' from R objects
    (e.g., lists, data.frames, vectors), and linting 'WKT'.
Run mixed-effects models that include weights at every level. The WeMix package fits a weighted mixed model, also known as a multilevel, mixed, or hierarchical linear model (HLM). The weights could be inverse selection probabilities, such as those developed for an education survey where schools are sampled probabilistically, and then students inside of those schools are sampled probabilistically. Although mixed-effects models are already available in R, WeMix is unique in implementing methods for mixed models using weights at multiple levels. Both linear and logit models are supported. Models may have up to three levels.
Palettes generated mostly from 'Wes Anderson' movies.
The distributions of the weight of evidence (log Bayes factor) favouring case over noncase status in a test dataset (or test folds generated by cross-validation) can be used to quantify the performance of a diagnostic test (McKeigue (2019), <doi:10.1177/0962280218776989>). The package can be used with any test dataset on which you have observed case-control status and have computed prior and posterior probabilities of case status using a model learned on a training dataset. To quantify how the predictor will behave as a risk stratifier, the quantiles of the distributions of weight of evidence in cases and controls can be calculated and plotted.
Provides a computationally efficient way of fitting
	     weighted linear fixed effects estimators for causal
	     inference with various weighting schemes. Weighted linear
	     fixed effects estimators can be used to estimate the
	     average treatment effects under different identification
	     strategies. This includes stratified randomized
	     experiments, matching and stratification for
	     observational studies, first differencing, and
	     difference-in-differences. The package implements methods
	     described in Imai and Kim (2017) "When should We Use
	     Linear Fixed Effects Regression Models for Causal
	     Inference with Longitudinal Data?", available at
	     <https://imai.fas.harvard.edu/research/FEmatch.html>.
Implementation of Weighted Fast Greedy algorithm for community detection in networks with mixed types of attributes.
Provides a large English words list and tools to find words by patterns. In particular, anagram finder and scrabble word finder.
Provides a convenient data set, a set of helper functions, and a benchmark function for
    economically (profit) driven wind farm layout optimization. This enables researchers in the field
    of the NP-hard (non-deterministic polynomial-time hard) problem of wind farm layout optimization
    to focus on their optimization methodology contribution and also provides a realistic benchmark
    setting for comparability among contributions. See Croonenbroeck, Carsten & Hennecke, David (2020)
    <doi:10.1016/j.energy.2020.119244>.
A computationally efficient whole genome approach to detecting and estimating significant QTL in linkage maps using the flexible linear mixed modelling functionality of ASReml-R.
Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data as originally described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559>. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Weighted generalized estimating equations (WGEE) is an extension of generalized linear models to longitudinal clustered data by incorporating the correlation within-cluster when data is missing at random (MAR). The parameters in mean, scale correlation structures are estimated based on quasi-likelihood. Multiple model selection criterion are provided for selection of mean model and working correlation structure based on WGEE/GEE.
Functions for the analysis of whole-genome sequencing studies to simultaneously detect the existence, and estimate the locations of association signals at genome-wide scale. The functions allow genome-wide association scan, candidate region scan and single window test.
Functions for determining the effect of data weights on the variance of survey data: users will load a data set which has a weights column, and the package will calculate the design effect (DEFF), weighting loss, root design effect (DEFT), effective sample size (ESS), and/or weighted margin of error.
Inferences about counterfactuals are essential for prediction,
      answering what if questions, and estimating causal effects.
      However, when the counterfactuals posed are too far from the data at
      hand, conclusions drawn from well-specified statistical analyses
      become based largely on speculation hidden in convenient modeling
      assumptions that few would be willing to defend. Unfortunately,
      standard statistical approaches assume the veracity of the model
      rather than revealing the degree of model-dependence, which makes this
      problem hard to detect. WhatIf offers easy-to-apply methods to
      evaluate counterfactuals that do not require sensitivity testing over
      specified classes of models. If an analysis fails the tests offered
      here, then we know that substantive inferences will be sensitive to at
      least some modeling choices that are not based on empirical evidence,
      no matter what method of inference one chooses to use. WhatIf
      implements the methods for evaluating counterfactuals discussed in
      Gary King and Langche Zeng, 2006, "The Dangers of Extreme
      Counterfactuals," Political Analysis 14 (2) <DOI:10.1093/pan/mpj004>; 
      and Gary King and Langche Zeng, 2007, "When Can History Be Our Guide? The 
      Pitfalls of Counterfactual Inference," International Studies 
      Quarterly 51 (March) <DOI:10.1111/j.1468-2478.2007.00445.x>.
Scrape the fan-made J! Archive <https://www.j-archive.com/> 
    for Jeopardy episode contestants, categories, clues, answers, and scores.
Builds complex plots, heatmaps in particular, using natural semantics. Bigger plots can be assembled using directives such as 'LeftOf', 'RightOf', 'TopOf', and 'Beneath' and more. Other features include clustering, dendrograms and integration with 'ggplot2' generated grid objects. This package is particularly designed for bioinformaticians to assemble complex plots for publication.
Robust and reliable functions to return informative outputs to 
        console with the run or source location of a command. This can be from
        the  'RScript'/R terminal commands or 'RStudio' console, source editor, 
        'Rmarkdown' document and a Shiny application.
Retrieve geographical information for airports using their IATA or ICAO codes.
Provides a set of functions to make tracking the hidden movements 
  of the 'Jack' player easier. By tracking every possible path Jack might have 
  traveled from the point of the initial murder including special movement such 
  as through alleyways and via carriages, the police can more accurately narrow 
  the field of their search. Additionally, by tracking all possible hideouts from 
  round to round, rounds 3 and 4 should have a vastly reduced field of search.
Implements the whitening methods (ZCA, PCA, Cholesky,
 ZCA-cor, and PCA-cor) discussed in Kessy, Lewin, and Strimmer (2018)
 "Optimal whitening and decorrelation", <doi:10.1080/00031305.2016.1277159>,
 as well as the whitening approach to canonical correlation analysis allowing
 negative canonical correlations described in Jendoubi and Strimmer (2019)
 "A whitening approach to probabilistic canonical correlation analysis for omics
 data integration", <doi:10.1186/s12859-018-2572-9>.
Formal implementation of White test of heteroskedasticity and a bootstrapped version of it, developed under the methodology of Jeong, J., Lee, K. (1999) <https://yonsei.pure.elsevier.com/en/publications/bootstrapped-whites-test-for-heteroskedasticity-in-regression-mod>.
Shinohara (2014) <DOI:10.1016/j.nicl.2014.08.008>
    introduced 'WhiteStripe', an intensity-based normalization of T1 
    and T2 images, where normal 
    appearing white matter performs well, but requires segmentation.
    This method performs white matter mean and standard deviation
    estimates on data that has been rigidly-registered to the 'MNI'
    template and uses histogram-based methods.
Look up the username and full name of the current user,
    the current user's email address and 'GitHub' username,
    using various sources of system and configuration information.
Retrieve data from the 'Whoapi' (https://whoapi.com) store of
    domain information, including a domain's geographic location, registration
    status and search prominence.
Interactive tools for generating random samples. Users select an
    .xlsx, .csv, or delimited .txt file with population data and are walked through selecting the
    sample type (Simple Random Sample or Stratified), the number of backups
    desired, and a "stratify_on" value (if desired). The sample size is determined
    using a normal approximation to the hypergeometric distribution based on
    Nicholson (1956) <doi:10.1214/aoms/1177728270>. An .xlsx file is created
    with the sample and key metadata for reference. It is menu-driven and lets
    users pick an output directory. See vignettes for a detailed walk-through.
Utilities to generate bounding boxes from 'WKT' (Well-Known Text) objects and R data types, validate
             'WKT' objects and convert object types from the 'sp' package into 'WKT' representations.
Computationally easy modeling, interpolation, forecasting of massive temporal-spacial data.
Provides two functions 'frameableWidget()', and 'frameWidget()'.
  The 'frameableWidget()' is used to add extra code to a 'htmlwidget' which
  allows is to be rendered correctly inside a responsive 'iframe'.
  The 'frameWidget()' is a 'htmlwidget' which displays content of another 'htmlwidget'
  inside a responsive 'iframe'.
  These functions allow for easier embedding of 'htmlwidgets' in content management systems
  such as 'wordpress', 'blogger' etc.
  They also allow for separation of widget content from main HTML content where
  CSS of the main HTML could interfere with the widget.
Encapsulates the pattern of untidying data into a wide matrix,
  performing some processing, then turning it back into a tidy form. This
  is useful for several operations such as co-occurrence counts,
  correlations, or clustering that are mathematically convenient on wide matrices.
Retrieve and import data from different databases of the Federal Statistical Office of Germany (DESTATIS) using their SOAP XML web service <https://www-genesis.destatis.de/>.
The german Wikibook "GNU R" introduces R to new users.
        This package is a collection of functions and datas used in the
        german WikiBook "GNU R"
An API client for the 'Wikidata Query Service'
    <https://query.wikidata.org/>.
An API client for the Wikidata <http://wikidata.org/> store of
    semantic data.
Query Wikidata and get facts from current and historic Wikipedia main pages.
Scrape lake metadata tables from Wikipedia <http://www.wikipedia.org>.
Provides an interface to the Wikipedia web application programming
    interface (API), using internet connexion.Three functions provide details for
    a specific Wikipedia page : all links that are present, all pages that link
    to, all the contributions (revisions for main pages, and discussions for talk
    pages). Two functions provide details for a specific user : all contributions,
    and general information (as name, gender, rights or groups). It provides
    additional information compared to others packages, as WikipediR. It does not
    need login. The multiplex network that can be constructed from the results
    of the functions of WikipediaR can be modeled as Stochastic Block Model as in
    Barbillon P., Donnet, S., Lazega E., and Bar-Hen A. : Stochastic Block Models
    for Multiplex networks: an application to networks of researchers, ArXiv
    1501.06444, http://arxiv.org/abs/1501.06444.
A convenience wrapper for the Wikipedia page access statistics API 
  binding the 'pageviews' package and using an additional self composed data 
  source thus covering a time span from very late 2007 up to the present for 
  daily page views.
A wrapper for the MediaWiki API, aimed particularly at the
    Wikimedia 'production' wikis, such as Wikipedia. It can be used to retrieve
    page text, information about users or the history of pages, and elements of
    the category tree.
'Taxonomic' information from 'Wikipedia', 'Wikicommons',
    'Wikispecies', and 'Wikidata'. Functions included for getting
    taxonomic information from each of the sources just listed, as
    well performing taxonomic search.
This package provides functions to perform fast variable
        selection based on the Wilcoxon rank sum test in the
        cross-validation or Monte-Carlo cross-validation settings, for
        use in microarray-based binary classification.
An implementation of the 1-Sample Wilcoxon Sign rank test for medians. 
              It includes 2 functions, W_stat(), which computes the 
              exact probabilities of the Wilcoxon Sign Rank Test Statistic, W.
              The second function, Wilcox.m.test() allows the user to conduct the
              1-Sample Wilcoxon Sign Rank hypothesis test for medians, this also 
              allows the user to conduct the hypothesis test for the normal approximation, 
              based on the techniques of Bickel and Doksum (1973, ISBN:013850363X).
Dynamic interaction refers to spatial-temporal associations
    in the movements of two (or more) animals. This package provides tools for
    calculating a suite of indices used for quantifying dynamic interaction with
    wildlife telemetry data. For more information on each of the methods employed
    see the references within. The package (as of version 0.3) also has new tools for
    automating contact analysis in large tracking datasets. The package draws 
    heavily on the classes and methods developed in the 'adehabitat' packages.
Provides insight into how the best hand for a poker game changes based on the game dealt, players who stay in until the showdown and wildcards added to the base game.  At this time the package does not support player tactics, so draw poker variants are not included.
Tool-set of modules for creating web-based applications that use plot based strategies to visualize and analyze multi-omics data.
    This package utilizes the 'shiny' and 'plotly' frameworks to provide a user friendly dashboard for interactive plotting.
Obtain the native stack trace and fuse it with R's
    stack trace for easier debugging of R packages with native code.
Post-construction fatality monitoring studies at wind facilities are based on data from searches for bird and bat carcasses in plots beneath turbines. Bird and bat carcasses can fall outside of the search plot. Bird and bat carcasses from wind turbines often fall outside of the searched area. To compensate, area correction (AC) estimations are calculated to estimate the percentage of fatalities that fall within the searched area versus those that fall outside of it. This package provides two likelihood based methods and one physics based method (Hull and Muir (2010) <doi:10.1080/14486563.2010.9725253>, Huso and Dalthorp (2014) <doi:10.1002/jwmg.663>) to estimate the carcass fall distribution. There are also functions for calculating the proportion of area searched within one unit annuli, log logistic distribution functions, and truncated distribution functions.
Provides a tool to fit and compare the wind turbine power curves 
    with successful curve fitting techniques. Facilitates to examine and compare 
    the performance of a user-defined power curve fitting techniques. 
    Also, provide features to generate power curve discrete points from a graphical 
    power curves. Data on the power curves of the wind turbine from major 
    manufacturers are provided.
Analysing convergent evolution using the Wheatsheaf index, described in Arbuckle et al. (2014) <doi: 10.1111/2041-210X.12195>, and some other random but perhaps useful functions.
The genetic algorithm is designed to optimize wind farms of any shape. It requires a predefined amount of turbines, a unified rotor radius and an average wind speed value for each incoming wind direction. A terrain effect model can be included that downloads an 'SRTM' elevation model and loads a Corine Land Cover raster to approximate surface roughness.
Obtain information on peak flow data from the National River Flow Archive (NRFA) in the United Kingdom, either from the Peak Flow Dataset files <https://nrfa.ceh.ac.uk/peak-flow-dataset> once these have been downloaded to the user's computer or using the NRFA's API. These files are in a format suitable for direct use in the 'WINFAP' software, hence the name of the package.
Helps for interfacing with the operating system
    particularly for Windows.
Calculate the win ratio for prioritized outcomes and the 95% confidence interval based on Bebu and Lachin (2016) <doi:10.1093/biostatistics/kxv032>. Three type of outcomes can be analyzed: survival "failure-time" events, repeated survival "failure-time" events and continuous or ordinal "non-failure time" events that are captured at specific time-points in the study.
Fits a model to data separately for each treatment group and then calculates the win-Ratio as a function of follow-up time.
Provides simple, fast functions for maximum likelihood and Bayesian estimates of wildlife population parameters, suitable for use with simulated data or bootstraps. Early versions were indeed quick and dirty, but optional error-checking routines and meaningful error messages have been added. Includes single and multi-season occupancy, closed capture population estimation, survival, species richness and distance measures.
In the course of a genome-wide association study, the situation often arises that some phenotypes are known with greater precision than others.
    It could be that some individuals are known to harbor more micro-environmental variance than others.
    In the case of inbred strains of model organisms, it could be the case that more organisms were observed from some strains than others, so the strains with more organisms have better-estimated means.
    Package 'wISAM' handles this situation by allowing for weighting of each observation according to residual variance.
    Specifically, the 'weight' parameter to the function conduct_scan() takes the precision of each observation (one over the variance).
Perform the Wild Scale-Enhanced (WiSE) bootstrap.  Specifically, the user may supply a single or multiple equally-spaced time series and use the WiSE bootstrap to select a wavelet-smoothed model.  Conversely, a pre-selected smooth level may also be specified for the time series.  Quantities such as the bootstrap sample of wavelet coefficients, smoothed bootstrap samples, and specific hypothesis testing and confidence region results of the wavelet coefficients may be obtained.  Additional functions are available to the user which help format the time series before analysis.  This methodology is recommended to aid in model selection and signal extraction.
    Note:  This package specifically uses wavelet bases in the WiSE bootstrap methodology, but the theoretical construct is much more versatile.
A Shiny application for learning Bayesian Decision Networks from data. This package can be used for probabilistic reasoning (in the observational setting), causal inference (in the presence of interventions) and learning policy decisions (in Decision Network setting). Functionalities include end-to-end implementations for data-preprocessing, structure-learning, exact inference, approximate inference, extending the learned structure to Decision Networks and policy optimization using statistically rigorous methods such as bootstraps, resampling, ensemble-averaging and cross-validation. In addition to Bayesian Decision Networks, it also features correlation networks, community-detection, graph visualizations, graph exports and web-deployment of the learned models as Shiny dashboards.
A set of functions to run code 'with' safely and
    temporarily modified global state. Many of these functions were
    originally a part of the 'devtools' package, this provides a simple
    package with limited dependencies to provide access to these
    functions.
Provides a minimal R and C++ API for parsing
  well-known binary and well-known text representation of
  geometries to and from R-native formats. 
  Well-known binary is compact
  and fast to parse; well-known text is human-readable
  and is useful for writing tests. These formats are only
  useful in R if the information they contain can be 
  accessed in R, for which high-performance functions 
  are provided here.
Utility functions to convert between the 'Spatial' classes
  specified by the package 'sp', and the well-known binary '(WKB)'
  representation for geometry specified by the 'Open Geospatial Consortium'.
  Supports 'Spatial' objects of class 'SpatialPoints',
  'SpatialPointsDataFrame', 'SpatialLines', 'SpatialLinesDataFrame',
  'SpatialPolygons', and 'SpatialPolygonsDataFrame'. Supports 'WKB' geometry
  types 'Point', 'LineString', 'Polygon', 'MultiPoint', 'MultiLineString', and
  'MultiPolygon'. Includes extensions to enable creation of maps with
  'TIBCO Spotfire'.
Implementation of an adaptive weighted k-nearest neighbours (wk-NN) imputation algorithm for clinical register data developed to explicitly handle missing values of continuous/ordinal/categorical and static/dynamic features conjointly. For each subject with missing data to be imputed, the method creates a feature vector constituted by the information collected over his/her first 'window_size' time units of visits. This vector is used as sample in a k-nearest neighbours procedure, in order to select, among the other patients, the ones with the most similar temporal evolution of the disease over time. An ad hoc similarity metric was implemented for the sample comparison, capable of handling the different nature of the data, the presence of multiple missing values and include the cross-information among features.
Converts weekly data to monthly data.
     Users can use three types of week formats: ISO week, epidemiology week (epi week) and calendar date.
Provides extra utilities for well-known formats in the
  'wk' package that are outside the scope of that package. Utilities
  to parse coordinates from data frames, plot well-known geometry
  vectors, extract meta information from well-known geometry vectors,
  and calculate bounding boxes are provided.
It proposes a novel variable selection approach taking into account the correlations that may exist between the predictors of the design matrix in a high-dimensional linear model. Our approach consists in rewriting the initial high-dimensional linear model to remove the correlation between the predictors and in applying the generalized Lasso criterion. For further details we refer the reader to the paper <arXiv:2007.10768> (Zhu et al., 2020).
Estimate the parameters of weighted Lindley distribution, and provide some 
              useful results like goodness of fit or confidence interval etc.
              Ghitany, M., Alqallaf, F., Al-Mutairi, D., Husain, H. (2011) <doi:10.1016/j.matcom.2010.11.005>.
              Hyoung-Moon Kim. and Yu-Hyeong Jang. (2020) submitted.
              Wang, M., Wang, W. (2017) <doi:10.1080/03610918.2014.970696>.
Use various regression models for the analysis of win loss endpoints 
             adjusting for non-binary and multivariate covariates.
Distance discriminant analysis method is one of
        classification methods according to multiindex performance
        parameters.However,the traditional Mahalanobis distance
        discriminant method treats with the importance of all
        parameters equally,and exaggerates the role of parameters which
        changes a little.The weighted Mahalanobis distance is used in
        discriminant analysis method to distinguish the importance of
        each parameter.In the concrete application,firstly based on the
        principal component analysis scheme,a new group of parameters
        and their corresponding percent contributions of the parameters
        are calculated ,and the weighted matrix is regarded as the
        diagonal matrix of the contributions rates.Setting data to
        standardization,then the weighted Mahalanobis distance can be
        calculated.Besides the methods metioned above,bayes method is
        also given.
Analyzing the texture of an image from a multifractal wavelet leader analysis.
Calculate magnetic field at a given location and time according to 
  the World Magnetic Model (WMM). Both the main field and secular variation 
  components are returned. This functionality is useful for physicists and 
  geophysicists who need orthogonal components from WMM. Currently, this package 
  supports annualized time inputs between 2000 and 2020. If desired, users can
  specify which WMM version to use, e.g., the original WMM2015 release or the 
  recent out-of-cycle WMM2015 release. Methods used to implement WMM, including 
  the Gauss coefficients for each release, are described in the following 
  publications: Chulliat et al (2019) <doi:10.25921/xhr3-0t19>, 
  Chulliat et al (2015) <doi:10.7289/V5TB14V7>, 
  Maus et al (2010) <https://www.ngdc.noaa.gov/geomag/WMM/data/WMMReports/WMM2010_Report.pdf>, 
  McLean et al (2004) <https://www.ngdc.noaa.gov/geomag/WMM/data/WMMReports/TRWMM_2005.pdf>,
  and Macmillian et al (2000) <https://www.ngdc.noaa.gov/geomag/WMM/data/WMMReports/wmm2000.pdf>.
Power calculator for the two-sample Wilcoxon-Mann-Whitney rank-sum test for a continuous outcome (Mollan, Trumble, Reifeis et. al., Mar. 2020) <doi:10.1080/10543406.2020.1730866> <arXiv:1901.04597>, (Mann and Whitney 1947) <doi:10.1214/aoms/1177730491>, (Shieh, Jan, and Randles 2006) <doi:10.1080/10485250500473099>.
Calculates the minimal sample size for the Wilcoxon-Mann-Whitney test
    that is needed for a given power and two sided type I error rate. The method works for metric data with and without
    ties, count data, ordered categorical data, and even dichotomous data.
    But data is needed for the reference group to generate synthetic data for the treatment group based on a relevant effect.
    For details, see Brunner, E., Bathke A. C. and Konietschke, F: Rank- and Pseudo-Rank Procedures in Factorial Designs - Using R and SAS, Springer Verlag, to appear.
This is a set of minimization tools (maximum likelihood estimation and least square fitting) to solve examples in the Johan Gabrielsson and Dan Weiner's book "Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications" 5th ed. (ISBN:9198299107). Examples include linear and nonlinear compartmental model, turn-over model, single or multiple dosing bolus/infusion/oral models, allometry, toxicokinetics, reversible metabolism, in-vitro/in-vivo extrapolation, enterohepatic circulation, metabolite modeling, Emax model, inhibitory model, tolerance model, oscillating response model, enantiomer interaction model, effect compartment model, drug-drug interaction model, receptor occupancy model, and rebound phenomena model.
New tools for the imputation of missing values in high-dimensional
    data are introduced using the non-parametric nearest neighbor methods. It
    includes weighted nearest neighbor imputation methods that use specific
    distances for selected variables. It includes an automatic procedure of cross
    validation and does not require prespecified values of the tuning parameters.
    It can be used to impute missing values in high-dimensional data when the sample
    size is smaller than the number of predictors. For more information see Faisal
    and Tutz (2017) <doi:10.1515/sagmb-2015-0098>.
Estimates W-NOMINATE scores using parliamentary voting data
	(Poole et al 2007) <doi:10.18637/jss.v042.i14> supplied though a
	'rollcall' object from package 'pscl'.
Shows the relationship between an independent and dependent variable through Weight of Evidence and Information Value.
Implements an automated binning of numeric variables and factors with
 respect to a dichotomous target variable.
 Two approaches are provided: An implementation of fine and coarse classing that
 merges granular classes and levels step by step. And a tree-like approach that
 iteratively segments the initial bins via binary splits. Both procedures merge,
 respectively split, bins based on similar weight of evidence (WOE) values and
 stop via an information value (IV) based criteria.
 The package can be used with single variables or an entire data frame. It provides
 flexible tools for exploring different binning solutions and for deploying them to
 (new) data.
Implements a spatiotemporal boundary detection model with a dissimilarity
    metric for areal data with inference in a Bayesian setting using Markov chain
    Monte Carlo (MCMC). The response variable can be modeled as Gaussian (no nugget),
    probit or Tobit link and spatial correlation is introduced at each time point
    through a conditional autoregressive (CAR) prior. Temporal correlation is introduced
    through a hierarchical structure and can be specified as exponential or first-order
    autoregressive. Full details of the package can be found in the accompanying vignette.
    Furthermore, the details of the package can be found in "Diagnosing Glaucoma 
    Progression with Visual Field Data Using a Spatiotemporal Boundary Detection Method", 
    by Berchuck et al (2018), <arXiv:1805.11636>. The paper is in press at the Journal of 
    the American Statistical Association.
A hierarchy of classes and methods for manipulating matrices formed implicitly from the sums of the inverses of other matrices, a situation commonly encountered in spatial statistics and related fields. Enables easy use of the Woodbury matrix identity and the matrix determinant lemma to allow computation (e.g., solving linear systems) without having to form the actual matrix. More information on the underlying linear algebra can be found in Harville, D. A. (1997) <doi:10.1007/b98818>.
Tools for generating simulated sawn timber
    strength grading data with a main focus on statistical simulation based on
    covariance matrices. Simulation data
    for Norway spruce sawn timber from Austria and reference values of means and
    standard deviations of grade determining properties from literature
    for a number of European countries are provided, as well.
Students learning both econometrics and R may find the introduction 
    to both challenging. However, if the text is "Introductory Econometrics: 
    A Modern Approach" by Jeffrey M. Wooldridge, they are in luck! 
    The wooldridge data package aims to lighten the task by efficiently loading 
    any data set found in the text with a single command. Data sets have all been 
    compressed to a fraction of their original size and are well documented. 
    Documentation files contain the page numbers of the text where each set is used, 
    the original source, time of publication, and notes suggesting ideas for further 
    exploratory data analysis and research. If one need's to brush-up on model syntax, a 
    vignette contains R solutions to examples from each chapter of the text. 
    Data sets are from the 6th edition (Wooldridge 2016, ISBN-13: 978-1-305-27010-7), 
    and are backwards compatible with all versions of the text.
Create reproducible and transparent research projects in 'R'.
    This package is based on the Workflow for Open
    Reproducible Code in Science (WORCS), a step-by-step procedure based on best
    practices for
    Open Science. It includes an 'RStudio' project template, several
    convenience functions, and all dependencies required to make your project
    reproducible and transparent. WORCS is explained in the tutorial paper
    by Van Lissa, Brandmaier, Brinkman, Lamprecht, Struiksma, & Vreede (2020).
    <doi:10.17605/OSF.IO/ZCVBS>.
For a given Sentence-Aligned Parallel Corpus, it aligns words for each sentence pair. It considers one-to-many and symmetrization alignments. Moreover, it evaluates the quality of word alignment based on this package and some other software. It also builds an automatic dictionary of two languages based on given parallel corpus.
Learn vector representations of words by continuous bag of words and skip-gram implementations of the 'word2vec' algorithm. 
    The techniques are detailed in the paper "Distributed Representations of Words and Phrases and their Compositionality" by Mikolov et al. (2013), available at <arXiv:1310.4546>.
Tools for connecting to Wordbank, an open repository for
    developmental vocabulary data. For more information on the
    underlying data, see <http://wordbank.stanford.edu>.
Functionality to create pretty word clouds, visualize differences and similarity between documents, and avoid over-plotting in scatter plots with text.
A fast visualization tool for creating wordcloud
    by using 'wordcloud2.js'. 'wordcloud2.js' is a JavaScript library to create 
    wordle presentation on 2D canvas or HTML <https://timdream.org/wordcloud2.js/>.
Functions that help less experienced R users to make graph analysis for free associated words, or more generally for repeated nominal data for which a undirected graph analysis is meaningful. By corresponding to each word its centrality, it is possible to apply standard quantitative analysis methods in order to associate word selection with other   variables.
    The functions are implemented with the aid of the 'tibble', 'tidygraph', 'ggraph' and 'ggplot2' packages. Supported centrality functions are centrality_alpha(), centrality_authority(), centrality_betweenness(), centrality_closeness(), centrality_pagerank(), centrality_eigen(). A data set is included.
Matches words in one file with words in another file and shows index(row number) for the matches
An interface to WordNet using the Jawbone Java API to WordNet.
  WordNet (<https://wordnet.princeton.edu/>) is a large lexical database of
  English.  Nouns, verbs, adjectives and adverbs are grouped into sets of
  cognitive synonyms (synsets), each expressing a distinct concept.  Synsets
  are interlinked by means of conceptual-semantic and lexical relations.
  Please note that WordNet(R) is a registered tradename.  Princeton
  University makes WordNet available to research and commercial users
  free of charge provided the terms of their license
  (<https://wordnet.princeton.edu/license-and-commercial-use>) are followed,
  and proper reference is made to the project using an appropriate
  citation (<https://wordnet.princeton.edu/citing-wordnet>).
Methods for estimating profit, profit-maximizing price, demand and consumer surplus of Word-of-Mouth-campaigns on mean-field networks.
Collects several classical word pools used most often
    to provide lists of words in psychological studies of learning and memory. It
    provides a simple function, 'pickList' for selecting random samples of words
    within given ranges.
An API wrapper that helps R developers retrieve data from a WordPress site's API in tidy format, in addition to
    publishing content on the WordPress site (WordPress API documentation: <https://developer.wordpress.org/rest-api/>).
Serves for rendering MS Word documents with R inline code and inserting tables and plots.
Provides access to various word embedding methods (GloVe, 
    fasttext and word2vec) to extract word vectors using a unified framework to
    increase reproducibility and correctness.
An interactive laboratory for research on distributional semantic models ('DSM',
             see <https://en.wikipedia.org/wiki/Distributional_semantics> for more information).
Provides a workflow for your analysis projects by combining
  literate programming ('knitr' and 'rmarkdown') and version control
  ('Git', via 'git2r') to generate a website containing time-stamped,
  versioned, and documented results.
Managing both a 'parsnip' model and a preprocessor, such as a
    model formula or recipe from 'recipes', can often be challenging. The goal
    of 'workflows' is to streamline this process by bundling the model alongside
    the preprocessor, all within the same object.
World Flora Online is an online flora of all known plants, available from <http://www.worldfloraonline.org/>. Methods are provided of matching a list of plant names (scientific names, taxonomic names, botanical names) against a static copy of the World Flora Online Taxonomic Backbone data that can be downloaded from the World Flora Online website. The World Flora Online Taxonomic Backbone is an updated version of The Plant List (<http://www.theplantlist.org/>), a working list of plant names that has become static since 2013.
Functions to import data from more than 30,000 surface
    meteorological sites around the world managed by the National Oceanic and Atmospheric Administration (NOAA) Integrated Surface
    Database (ISD, see <https://www.ncdc.noaa.gov/isd>).
Retrieves taxonomic information from  <http://www.marinespecies.org> using WoRMS' RESTful Webservice. Utility functions aim at taxonomic consistency.
Client for World Register of Marine Species
    (<http://www.marinespecies.org/>). Includes functions for each
    of the API methods, including searching for names by name, date and
    common names, searching using external identifiers, fetching
    synonyms, as well as fetching taxonomic children and
    taxonomic classification.
R clients to the 'Web of Science' and 'InCites' 
  <https://clarivate.com/products/data-integration/> APIs, which 
  allow you to programmatically download publication and citation data
  indexed in the 'Web of Science' and 'InCites' databases.
Implementing weighted predictiveness curve to visualize the marker-by-treatment relationship and measure the performance of biomarkers for guiding treatment decision.
Supplies permutation-test alternatives to traditional hypothesis-test
  procedures such as two-sample tests for means, medians, and standard deviations;
  correlation tests; tests for homogeneity and independence; and more. Suitable for
  general audiences, including individual and group users, introductory statistics
  courses, and more advanced statistics courses that desire an introduction to
  permutation tests.
Weighted Piecewise Kernel Density Estimation for large data.
Data from the United Nation's World Population Prospects 2008
Data from the United Nation's World Population Prospects
        2010
Data from the United Nation's World Population Prospects 2012
Provides data from the United Nation's World Population Prospects 2015.
Provides data from the United Nation's World Population Prospects 2017.
Provides data from the United Nation's World Population Prospects 2019.
Explore data in the 'wpp2019' (or 2017, 2015, ...) package using a 'shiny' interface.
Functions to assist in the processing and
    exploration of data from environmental monitoring programs.
    The package name stands for "water quality" and reflects the
    original focus on time series data for physical and chemical
    properties of water, as well as the biota. Intended for
    programs that sample approximately monthly, quarterly or
    annually at discrete stations, a feature of many legacy data
    sets. Most of the functions should be useful for analysis of
    similar-frequency time series regardless of the subject
    matter.
Fits weighted quantile sum regression models, calculates weighted quantile sum index and estimated component weights.
Contains win-ratio analysis routines for prioritized composite time-to-event 
    outcomes, e.g., death and non-fatal events. These routines include functions to fit 
    the proportional win-fractions (PW) model and to compute and plot the standardized 
    score process to assess the proportionality assumption.
Supports systematic scrutiny, modification, and integration of
    data. The function status() counts rows that have missing values in 
    grouping columns (returned by na() ), have non-unique combinations of 
    grouping columns (returned by dup() ), and that are not locally sorted
    (returned by unsorted() ). Functions enumerate() and itemize() give 
    sorted unique combinations of columns, with or without occurrence counts,
    respectively. Function ignore() drops columns in x that are present in y,
    and informative() drops columns in x that are entirely NA; constant() returns
    values that are constant, given a key.  Data that have defined unique 
    combinations of grouping values behave more predictably during merge operations.
Tools for writing and debugging R code. Provides: 
    '%.>%' dot-pipe (an 'S3' configurable pipe), unpack/to (R style multiple assignment/return),
    'build_frame()'/'draw_frame()' ('data.frame' example tools),
    'qc()' (quoting concatenate), 
    ':=' (named map builder), 'let()' (converts non-standard evaluation interfaces to parametric standard
    evaluation interfaces, inspired by 'gtools::strmacro()' and 'base::bquote()'), and more.
A wrapper around Michel Scheffers's 'libassp' (<http://libassp.sourceforge.net/>). 
    The 'libassp' (Advanced Speech Signal Processor) library aims at providing
    functionality for handling speech signal files in most common audio formats
    and for performing analyses common in phonetic science/speech science. This
    includes the calculation of formants, fundamental frequency, root mean
    square, auto correlation, a variety of spectral analyses, zero crossing
    rate, filtering etc. This wrapper provides R with a large subset of
    'libassp's signal processing functions and provides them to the user in a
    (hopefully) user-friendly manner.
Additional options for making graphics in the context of analyzing high-throughput data are available here.
  This includes automatic segmenting of the current device (eg window) to accommodate multiple new plots, 
  automatic checking for optimal location of legends in plots, small histograms to insert as legends, 
  histograms re-transforming axis labels to linear when plotting log2-transformed data,
  a violin-plot <doi:10.1080/00031305.1998.10480559> function for a wide variety of input-formats, 
  principal components analysis (PCA) <doi:10.1080/14786440109462720> with bag-plots <doi:10.1080/00031305.1999.10474494> to highlight and compare the center areas for groups of samples, 
  generic MA-plots (differential- versus average-value plots) <doi:10.1093/nar/30.4.e15>, 
  staggered count plots and generation of mouse-over interactive html pages.
An implementation of the methodologies described in Alexander Petersen, Xi Liu and Afshin A. Divani (2019) <arXiv:1910.13418>, including global F tests, partial F tests, intrinsic 
        Wasserstein-infinity bands and Wasserstein density bands.
A powerful yet simple graphical tool available in the field of psychometrics is the Wright Map (also known as item maps or item-person maps), which presents the location of both respondents and items on the same scale. Wright Maps are commonly used to present the results of dichotomous or polytomous item response models. The 'WrightMap' package provides functions to create these plots from item parameters and person estimates stored as R objects. Although the package can be used in conjunction with any software used to estimate the IRT model (e.g. 'TAM', 'mirt', 'eRm' or 'IRToys' in 'R', or 'Stata', 'Mplus', etc.),  'WrightMap' features special integration with 'ConQuest' to facilitate reading and plotting its output directly.The 'wrightMap' function creates Wright Maps based on person estimates and item parameters produced by an item response analysis. The 'CQmodel' function reads output files created using 'ConQuest' software and creates a set of data frames for easy data manipulation, bundled in a 'CQmodel' object. The 'wrightMap' function can take a 'CQmodel' object as input or it can be used to create Wright Maps directly from data frames of person and item parameters.
Function for writing a SNNS pattern file from a data.frame
        or matrix.
Zero-dependency data frame to xlsx exporter based on 'libxlsxwriter'. 
    Fast and no Java or Excel required.
Cross-platform Perl based R function to create Excel 2003 (XLS) and Excel 2007 (XLSX)
             files from one or more data frames. Each data frame will be
             written to a separate named worksheet in the Excel spreadsheet.
             The worksheet name will be the name of the data frame it contains
             or can be specified by the user.
The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions. 
  Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc.  
  Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM) for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates). 
  Other functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc. 
  Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of large data-sets by combining very close values. 
  Many times large experimental datasets need some additional filtering, adequate functions are provided. 
  Batch reading (or writing) of sets of files and combining data to arrays is supported, too. 
  Convenient data normalization is supported in various different modes, parameter estimation via permutations or boot-strap as well as flexible testing of multiple pair-wise combinations using the framework of 'limma' is provided, too.
Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data. 
    Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted. 
    Quantitative proteomics (Schubert et al 2017 <doi:10.1038/nprot.2017.040>) measurements frequently contain multiple NA values, due to physical absence of given peptides in some samples, limitations in sensitivity or other reasons. 
    The functions provided here help to inspect graphically the data to investigate the nature of NA-values via their respective replicate measurements and to help/confirm the choice of NA-replacement by low random values. 
    Dedicated filtering and statistical testing using the framework of package 'limma' <doi:10.18129/B9.bioc.limma> can be run, enhanced by multiple rounds of NA-replacements to provide robustness towards rare stochastic events. 
    Multi-species samples, as frequently used in benchmark-tests (eg Navarro et al 2016 <doi:10.1038/nbt.3685>, Ramus et al 2016 <doi:10.1016/j.jprot.2015.11.011>), can be run with special options separating the data into sub-groups during normalization and testing. 
    Subsequently, ROC curves (Hand and Till 2001 <doi:10.1023/A:1010920819831>) can be constructed to compare multiple analysis approaches.
A collection of robust statistical methods based on Wilcox' WRS functions. It implements robust t-tests (independent and dependent samples), robust ANOVA (including between-within subject designs), quantile ANOVA, robust correlation, robust mediation, and nonparametric ANCOVA models based on robust location measures.
Water resources system simulator is a tool for simulation and analysis of large-scale water resources systems. 'WRSS' proposes functions and methods for construction, simulation and analysis of primary storage and hydropower water resources features (e.g. reservoirs, aquifers, and etc.) based on Standard Operating Policy (SOP).
A collection of implementations of classical and
    novel algorithms for weighted sampling without replacement.
Includes performance measurements and results of
    repeated experiment runs (for correctness checks) for code in the
    'wrswoR' package.
An adaptation for estuaries (tidal waters) of weighted regression
    on time, discharge, and season to evaluate trends in water quality time series.
Top-Down mass spectrometry aims to identify entire proteins as well as their (post-translational) modifications or ions bound (eg Chen et al (2018) <doi:10.1021/acs.analchem.7b04747>). 
    The pattern of internal fragments (Haverland et al (2017) <doi:10.1007/s13361-017-1635-x>) may reveal important information about the original structure of the proteins studied 
    (Skinner et al (2018) <doi:10.1038/nchembio.2515> and Li et al (2018) <doi:10.1038/nchem.2908>). 
    However, the number of possible internal fragments gets huge with longer proteins and subsequent identification of internal fragments remains challenging, 
    in particular since the the accuracy of measurements with current mass spectrometers represents a limiting factor.   
    This package attempts to deal with the complexity of internal fragments and allows identification of terminal and internal fragments from deconvoluted mass-spectrometry data.
Predicts individual race/ethnicity using surname, geolocation,
    and other attributes, such as gender and age. The method utilizes the Bayes'
    Rule to compute the posterior probability of each racial category for any given
    individual. The package implements methods described in Imai and Khanna (2015)
    "Improving Ecological Inference by Predicting Individual Ethnicity from Voter
    Registration Records" <DOI:10.1093/pan/mpw001>.
Non- and semiparametric regression for generalized additive, partial linear, and varying coefficient models as well as their combinations via smoothed backfitting. Based on Roca-Pardinas J and Sperlich S (2010) <doi:10.1007/s11222-009-9130-2>; Mammen E, Linton O and Nielsen J (1999) <doi:10.1214/aos/1017939138>; Lee YK, Mammen E, Park BU (2012) <doi:10.1214/12-AOS1026>.
Includes a variety of methods to compute objects related to the 'Wasserstein distance' (also known as 'Kantorovich distance' or 'Earth-Mover distance'). The main effort of this package is to allow for computations of 'Wasserstein barycenter' using regularised, unregularised and stochastic methods. It also provides convenient wrappers to call the 'transport' package with more general inputs. Handy visual tools are provided to showcase, barycenters, animations of optimal transport geodesics and animations of principal components in the 'Wasserstein space'.
Easily override the default visual choices in 'ggplot2' to make 
    your time series plots look more like the Wall Street Journal. Specific 
    theme design choices include omitting x-axis grid lines and displaying 
    sparse light grey y-axis grid lines. Additionally, this allows to label 
    the y-axis scales with your units only displayed on the top-most number, 
    while also removing the bottom most number (unless specifically 
    overridden). The goal is visual simplicity, because who has time to waste 
    looking at a cluttered graph?
Entropy weighted k-means (ewkm) by Liping Jing, Michael
        K. Ng and Joshua Zhexue Huang (2007)
        <doi:10.1109/TKDE.2007.1048> is a weighted subspace clustering
        algorithm that is well suited to very high dimensional data.
        Weights are calculated as the importance of a variable with
        regard to cluster membership.  The two-level variable
        weighting clustering algorithm tw-k-means (twkm) by Xiaojun
        Chen, Xiaofei Xu, Joshua Zhexue Huang and Yunming Ye (2013)
        <doi:10.1109/TKDE.2011.262> introduces two types of weights,
        the weights on individual variables and the weights on
        variable groups, and they are calculated during the clustering
        process.  The feature group weighted k-means (fgkm) by Xiaojun
        Chen, Yunminng Ye, Xiaofei Xu and Joshua Zhexue Huang (2012)
        <doi:10.1016/j.patcog.2011.06.004> extends this concept by
        grouping features and weighting the group in addition to
        weighting individual features.
A parallel implementation of Weighted Subspace Random Forest.  The
    Weighted Subspace Random Forest algorithm was proposed in the
    International Journal of Data Warehousing and Mining by Baoxun Xu,
    Joshua Zhexue Huang, Graham Williams, Qiang Wang, and Yunming Ye
    (2012) <DOI:10.4018/jdwm.2012040103>.  The algorithm can classify
    very high-dimensional data with random forests built using small
    subspaces.  A novel variable weighting method is used for variable
    subspace selection in place of the traditional random variable
    sampling.This new approach is particularly useful in building
    models from high-dimensional data.
We propose weighted SVM methods with penalization form. By
        adding weights to loss term, we can build up weighted SVM
        easily and examine classification algorithm properties under
        weighted SVM. Through comparing each of test error rates, we
        conclude that our Weighted SVM with boosting has predominant
        properties than the standard SVM have, as a whole.
Tools for a wavelet-based approach to analyzing spatial synchrony, principally in ecological data. Some tools will be useful for studying community synchrony. See, for instance, Sheppard et al (2016) <doi: 10.1038/NCLIMATE2991>, Sheppard et al (2017) <doi: 10.1051/epjnbp/2017000>, Sheppard et al (2019) <doi: 10.1371/journal.pcbi.1006744>.
Perform the calculation of W-test, diagnostic checking, calculate
    minor allele frequency (MAF) and odds ratio.
Computes the Weighted Topological Overlap with positive and negative signs (wTO) networks given a data frame containing the mRNA count/ expression/ abundance per sample, and a vector containing the interested nodes of interaction (a subset of the elements of the full data frame). It also computes the cut-off threshold or p-value based on the individuals bootstrap or the values reshuffle per individual. It also allows the construction of a consensus network, based on multiple wTO networks. The package includes a visualization tool for the networks.  More about the methodology can be found at <arXiv:1711.04702>.
Allows form managers to download entries from their respondents
    using Wufoo JSON API (<https://www.wufoo.com>). Additionally, the Wufoo reports - when public - can be
    also acquired programmatically. Note that building new forms within this package
    is not supported.
Methods to calculate and interpret climate change signals and time series from climate multi-model ensembles. Climate model output in binary 'NetCDF' format is read in and aggregated over a specified region to a data.frame for statistical analysis. Global Circulation Models, as the 'CMIP5' simulations, can be read in the same way as Regional Climate Models, as e.g. the 'CORDEX' or 'ENSEMBLES' simulations. The package has been developed at the 'Wegener Center for Climate and Global Change' at the University of Graz, Austria.
Provides a series of tools to compute and plot quantities related to classical and robust wavelet variance for time series and regular lattices. More details can be found, for example, in Serroukh, A., Walden, A.T., & Percival, D.B. (2000) <doi:10.2307/2669537> and Guerrier, S. & Molinari, R. (2016) <arXiv:1607.05858>.
Select data analysis plots, under a standardized calling interface implemented on top of 'ggplot2' and 'plotly'.  
   Plots of interest include: 'ROC', gain curve, scatter plot with marginal distributions, 
   conditioned scatter plot with marginal densities,
   box and stem with matching theoretical distribution, and density with matching theoretical distribution.
This tool, wood vision tool, is intended to facilitate preprocessing and analyzing 2-dimensional wood images toward automated recognition. The former includes some basics such as functions to RGB to grayscale, gray to binary, cropping, rotation(bilinear), median/mean/Gaussian filter, and Canny/Sobel edge detection. The latter includes gray level co-occurrence matrix (GLCM), Haralick parameters, local binary pattern (LBP), higher order local autocorrelation (HLAC), Fourier transform (radial and azimuthal integration), and Gabor filtering. The functions are intended to read data using  'readTIFF(x,info=T)' from 'tiff' package. The functions in this packages basically assumes the grayscale images as input data, thus the color images should be subjected to the function rgb2gray() before used for some other functions.
Book is "Linear Mixed Models: A Practical Guide Using
        Statistical Software" published in 2006 by Chapman Hall / CRC
        Press
Provides an array of white noise hypothesis tests for functional data and related visualizations. 
  These include tests based on the norms of autocovariance operators that are built under both strong and weak 
  white noise assumptions. Additionally, tests based on the spectral density operator and on principal component
  dimensional reduction are included, which are built under strong white noise assumptions. These methods are
  described in Kokoszka et al. (2017) <doi:10.1016/j.jmva.2017.08.004>, Characiejus and Rice (2019) 
  <doi:10.1016/j.ecosta.2019.01.003>, and Gabrys and Kokoszka (2007) <doi:10.1198/016214507000001111>, 
  respectively.
Calculate the (weighted) win loss statistics including the win ratio, win difference and win product 
 and their variances, with which the p-values are also calculated. The variance estimation is based on 
 Luo et al. (2015) <doi:10.1111/biom.12225> and Luo et al. (2017) <doi:10.1002/sim.7284>. This package also calculates general win loss statistics with 
 user-specified win loss function with variance estimation based on 
 Bebu and Lachin (2016) <doi:10.1093/biostatistics/kxv032>.
 This version corrected an error when outputting confidence interval for win difference.
Meta testing is the ability to test a function without having to 
    provide its parameter values.
    Those values will be generated, based on semantic naming of parameters, as 
    introduced by package 'wyz.code.offensiveProgramming'.
    Value generation logic can be completed with your own data types 
    and generation schemes. This to meet your most specific requirements and to 
    answer to a wide variety of usages, from general use case to very specific
    ones.
    While using meta testing, it becomes easier to generate stress test 
    campaigns, non-regression test campaigns and robustness test campaigns, as 
    generated tests can be saved and reused from session to session. 
    Main benefits of using 'wyz.code.metaTesting' is ability to discover valid 
    and invalid function parameter combinations, ability to infer valid 
    parameter values, and to provide smart summaries that allows you to focus
    on dysfunctional cases.
Allows to turn standard R code into offensive programming code. 
    Provides code instrumentation to ease this change and tools to assist and 
    accelerate code production and tuning while using offensive programming code 
    technics. 
    Should improve code robustness and quality. Function calls can be easily 
    verified on-demand or in batch mode to assess parameter types and length 
    conformities. 
    Should improve coders productivity as offensive programming reduces the code
    size due to reduced number of controls all along the call chain. 
    Should speed up processing as many checks will be reduced to one single check.
Allows to generate on-demand or by batch, any R documentation file,
    whatever is kind, data, function, class or package. It populates
    documentation sections, either automatically or by considering
    your input. Input code could be standard R code or offensive programming code. 
    Documentation content completeness depends on the type of code you use. With
    offensive programming code, expect generated documentation to be fully 
    completed, from a format and content point of view. With some standard R 
    code, you will have to activate post processing to fill-in any section that 
    requires complements. Produced manual page validity is automatically tested 
    against R documentation compliance rules. Documentation language 
    proficiency, wording style, and phrasal adjustments remains your job.
Allows to generate automatically 'testthat' code files from offensive 
    programming test cases. Generated test files are complete and ready to run.
    Using 'wyz.code.testthat' you will earn a lot of time, reduce the number of
    errors in test case production, be able to test immediately generated files 
    without any need to view or modify them, and enter a zero time latency between 
    code implementation and industrial testing. As with 'testthat', you may
    complete provided test cases according to your needs to push testing further, 
    but this need is nearly void when using 'wyz.code.offensiveProgramming'.
Provides a tool for extracting information (entities and relations between them) in text datasets. It also emphasizes the results exploration with graphical displays. It is a rule-based system and works with hand-made dictionaries and local grammars defined by users. 'x.ent' uses parsing with Perl functions and JavaScript to define user preferences through a browser and R to display and support analysis of the results extracted. Local grammars are defined and compiled with the tool Unitex, a tool developed by University Paris Est that supports multiple languages. See ?xconfig for an introduction.
The 'X13-ARIMA-SEATS' <https://www.census.gov/srd/www/x13as/> methodology and software is a widely used software and developed by the US Census Bureau. It can be accessed from 'R' with this package and 'X13-ARIMA-SEATS' binaries are provided by the 'R' package 'x13binary'.
A graphical user interface for the x12 package
The US Census Bureau provides a seasonal adjustment program now
 called 'X-13ARIMA-SEATS' building on both earlier programs called X-11 and
 X-12 as well as the SEATS program by the Bank of Spain. The US Census Bureau
 offers both source and binary versions -- which this package integrates for
 use by other R packages.
The x3p file format  is specified in ISO standard 5436:2000 to 
    describe 3d surface measurements. 'x3ptools' allows reading, writing and 
    basic modifications to the 3D surface measurements.
Create HTML5 slides with R Markdown and the JavaScript library
    'remark.js' (<https://remarkjs.com>).
Create beautifully color-coordinated and customized
    themes for your 'xaringan' slides, without writing any CSS. Complete
    your slide theme with 'ggplot2' themes that match the font and colors
    used in your slides.  Customized styles can be created directly in
    your slides' 'R Markdown' source file or in a separate external
    script.
Simulation of purebred and crossbred genomic data as well as pedigree and phenotypes are possible by this package. 'xbreed' can be used for the simulation of populations with flexible genome structures and trait genetic architectures. It can also be used to evaluate breeding schemes and generate genetic data to test statistical tools.
Functions to extract business financial information from
  an Extensible Business Reporting Language ('XBRL') instance file and the
  associated collection of files that defines its 'Discoverable' Taxonomy
  Set ('DTS').
Functions for Estimating a (c)DCC-GARCH Model in large dimensions
    based on a publication by Engle et,al (2017) <doi:10.1080/07350015.2017.1345683> and Nakagawa et,al (2018) <doi:10.3390/ijfs6020052>.
    This estimation method is consist of composite likelihood method by Pakel et al. (2014) <http://paneldataconference2015.ceu.hu/Program/Cavit-Pakel.pdf>
    and (Non-)linear shrinkage estimation of covariance matrices by Ledoit and Wolf (2004,2015,2016). (<doi:10.1016/S0047-259X(03)00096-4>,
    <doi:10.1214/12-AOS989>, <doi:10.1016/j.jmva.2015.04.006>).
Datasets and definitions of generic functions used in dependencies of the 'xergm' package.
Read and write XES Files to create event log objects used by the 'bupaR' framework. XES (Extensible Event Stream) is the `IEEE` standard for storing and sharing event data (see <http://standards.ieee.org/findstds/standard/1849-2016.html> for more info).
Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
This tool enables in-database scoring of 'XGBoost' models built in R, by translating trained model objects into SQL query. 
  'XGBoost' <https://xgboost.readthedocs.io/en/latest/index.html> provides parallel tree boosting (also known as gradient boosting machine, or GBM) algorithms
  in a highly efficient, flexible and portable way. GBM algorithm is introduced by Friedman (2001) <doi:10.1214/aos/1013203451>, 
  and more details on 'XGBoost' can be found in Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>.
Extreme Gradient Boosting, which is an efficient implementation
    of the gradient boosting framework from Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>.
    This package is its R interface. The package includes efficient linear
    model solver and tree learning algorithms. The package can automatically
    do parallel computation on a single machine which could be more than 10
    times faster than existing gradient boosting packages. It supports
    various objective functions, including regression, classification and ranking.
    The package is made to be extensible, so that users are also allowed to define
    their own objectives easily.
Interface to the XGobi and XGvis programs for graphical
        data analysis.
Supports a structured approach
    for exploring PKPD data <https://opensource.nibr.com/xgx>. It also
    contains helper functions for enabling the modeler to follow best R
    practices (by appending the program name, figure name location, and
    draft status to each plot). In addition, it enables the modeler to
    follow best graphical practices (by providing a theme that
    reduces chart ink, and by providing time-scale, log-scale, and
    reverse-log-transform-scale functions for more readable axes).
    Finally, it provides some data checking and summarizing functions for
    rapidly exploring pharmacokinetics and pharmacodynamics (PKPD) datasets.
Conduct the likelihood ratio tests for Hardy-Weinberg equilibrium at marker loci on the X chromosome.
Computes robust association measures that do not 
    presuppose linearity. The xi correlation (xicor) is based
    on cross correlation between ranked increments.
    The reference for the methods implemented here is 
    Chatterjee, Sourav (2020) <arXiv:1909.10140>
    This package includes the Galton peas example.
Provides a simple XML tree parser/generator. It includes
        functions to read XML files into R objects, get information out of
        and into nodes, and write R objects back to XML code. It's not as
        powerful as the 'XML' package and doesn't aim to be, but for simple
        XML handling it could be useful. It was originally developed for
        the R GUI and IDE 'RKWard' <https://rkward.kde.org>, to make plugin
        development easier.
Plotting ggplot2 graphs using the XKCD style.
The XKCD color survey asked participants to name colours. Randall Munroe published the top thousand(roughly) names and their sRGB hex values. This package lets you use them.
Download data from individual XKCD comics, written by Randall Munroe <https://xkcd.com/>.
Provides comprehensive functionality to read, write and format Excel data.
The expression of X-chromosome undergoes three possible biological processes: X-chromosome
             inactivation (XCI), escape of the X-chromosome inactivation (XCI-E),and skewed X-chromosome                    
             inactivation (XCI-S). To analyze the X-linked genetic association for phenotype such as                         
             continuous, binary, and time-to-event outcomes with the actual process unknown, we propose a unified            
             approach of maximizing the likelihood or partial likelihood over all of the potential biological             
             processes. The methods are described in Wei Xu, Meiling Hao (2017) <doi:10.1002/gepi.22097>. And 
             also see Dongxiao Han, Meiling Hao, Lianqiang Qu, Wei Xu (2019) <doi:10.1177/0962280219859037>.
Provides a tool for non linear mapping (non linear regression) using a mixture of regression model and an inverse regression strategy. The methods include the GLLiM model (see Deleforge et al (2015) <DOI:10.1007/s11222-014-9461-5>) based on Gaussian mixtures and a robust version of GLLiM, named SLLiM (see Perthame et al (2016) <https://hal.archives-ouvertes.fr/hal-01347455>) based on a mixture of Generalized Student distributions. The methods also include BLLiM (see Devijver et al (2017) <arXiv:1701.07899>) which is an extension of GLLiM with a sparse block diagonal structure for large covariance matrices (particularly interesting for transcriptomic data).
Provides a simple wrapper for some 'XLConnect' functions. 'XLConnect' is
    a package that allows for reading, writing, and manipulating 'Microsoft Excel'
    files. This package, 'xlsimple', adds some documentation and pre-defined formatting
    to the outputted 'Excel' file. Individual sheets can include a description on the
    first row to remind user what is in the data set. Auto filters and freeze
    rows are turned on. A brief readme file is created that provides a summary
    listing of the created sheets and, where provided, the description.
Provide R functions to read/write/format Excel 2007 and Excel 97/2000/XP/2003 file formats.
Reading and writing sheets of a single 'Excel' file into and from a list of data frames. Eases I/O of tabular data in bioinformatics while keeping them in a human readable format.
The xlsxjars package collects all the external jars
  required for the xlxs package. This release corresponds to POI
  3.10.1.
Extract Excel files from folder.
    Also display extracted data and compute a summary of it.
    Based on the 'readxl' package.
A toolbox for meta-analysis. This package includes a collection of functions for (1) implementing robust multivariate meta-analysis of continuous or binary outcomes; and (2) a bivariate Egger's test for detecting small study effects.
This is Xiaobei's miscellaneous classes and functions useful when
    developing R packages, particularly for OOP using R Reference Class.
Many approaches for both reading and
        creating XML (and HTML) documents (including DTDs), both local
        and accessible via HTTP or FTP.  Also offers access to an
        'XPath' "interpreter".
Work with XML files using a simple, consistent
    interface. Built on top of the 'libxml2' C library.
XML2R is a framework that reduces the effort required to transform
    XML content into number of tables while preserving parent to child
    relationships.
Import an XML document with nested object structures and convert
    it into a relational data model. The result is a set of R dataframes 
    with foreign key relationships. The data model and the data can be exported as
    SQL code of different SQL flavors.
Converts XML documents to R dataframes and dataframes to XML documents.
  A wide variety of options allows for different XML formats and flexible control
  of the conversion process. Results can be exported to CSV and Excel, if desired. 
  Also converts XML data to R lists.
Convert the output of 'utils::getParseData()' to an 'XML'
    tree, that one can search via 'XPath', and easier to manipulate in
    general.
'XML' package for creating and reading and manipulating 'XML', with an object model based on 'Reference Classes'.
The 'XML-RPC' is a remote procedure call protocol 
    based on 'XML'. The 'xmlrpc2' package is inspired by the 'XMLRPC'
	package but uses the 'curl' and 'xml2' packages instead 'RCurl' and 'XML'.
XMRs combine X-Bar control charts and Moving Range control charts. These functions also will recalculate the reference lines when significant change has occurred.
Fit a two-step kernel ridge regression model for
        predicting edges in networks, and carry out cross-validation
        using shortcuts for swift and accurate performance assessment
        (Stock et al, 2018 <doi:10.1093/bib/bby095> ).
Tests whether a set of counts fit a given expected ratio. For
    example, a genetic cross might be expected to produce four types in the
    relative frequencies of 9:3:3:1. To see whether a set of observed counts
    fits this expectation, one can examine all possible outcomes with xmulti() or a
    random sample of them with xmonte() and find the probability of an observation
    deviating from the expectation by at least as much as the observed. As a
    measure of deviation from the expected, one can use the log-likelihood
    ratio, the multinomial probability, or the classic chi-square statistic. A
    histogram of the test statistic can also be plotted and compared with the
    asymptotic curve.
Analysis of crossover interference in experimental crosses,
    particularly regarding the gamma model. See, for example,
    Broman and Weber (2000) <doi:10.1086/302923>.
Cross platform solution to open files, directories or 'URLs'
    with their associated programs.
Helps systematize and ease the process of 
    building unit tests with the 'testthat' package by providing 
    tools for generating expectations.
Allows to provide live interpretations and explanations of statistical 
    functions in R. These interpretations and explanations are shown when the explained function 
    is called by the user. They can interact with the values of the explained function's actual 
    results to offer relevant, meaningful insights. The 'xplain' interpretations and explanations 
    are based on an easy-to-use XML format that allows to include R code to interact with the 
    returns of the explained function.
Tools for interactive data exploration built using 'shiny'. Includes apps for descriptive 
    statistics, visualizing probability distributions, inferential statistics, linear regression, 
    logistic regression and RFM analysis.
Provides a set of functions devoted to multivariate exploratory statistics on textual data. Classical methods such as correspondence analysis and agglomerative hierarchical clustering are available. Chronologically constrained agglomerative hierarchical clustering enriched with labelled-by-words trees is offered. Given a division of the corpus into parts, their characteristic words and documents are identified. Further, accessing to 'FactoMineR' functions is very easy. Two of them are relevant in textual domain. MFA() addresses multiple lexical table allowing applications such as dealing with multilingual corpora as well as simultaneously analyzing both open-ended and closed questions in surveys. See <http://xplortext.unileon.es> for examples.
Diagnostics for non-linear mixed-effects (population) 
    models from 'NONMEM' <https://www.iconplc.com/innovation/nonmem/>. 
    'xpose' facilitates data import, creation of numerical run summary 
    and provide 'ggplot2'-based graphics for data exploration and model 
    diagnostics.
A model building aid for nonlinear mixed-effects 
    (population) model analysis using NONMEM, facilitating data set 
    checkout, exploration and visualization, model diagnostics, candidate 
    covariate identification and model comparison. The methods are described 
    in Keizer et al. (2013) <doi:10.1038/psp.2013.24>, and Jonsson et al. (1999) 
    <doi:10.1016/s0169-2607(98)00067-4>.
There is limited native support for external pointers in the R interface. 
    This package provides some basic tools to verify, create and modify 'externalptr' objects.
Support for interfaces from R to other languages,
    built around a class for evaluators and a combination of functions, classes and
    methods for communication. Will be used through a specific language interface
    package. Described in the book "Extending R".
Tools to analyze datasets previous to any statistical modeling.
    Has various functions designed to find inconsistencies and understanding the distribution of the data.
An implementation of the RuleFit algorithm as described in Friedman & Popescu 
  (2008) <doi:10.1214/07-AOAS148>. eXtreme Gradient Boosting ('XGBoost') is used 
  to build rules, and 'glmnet' is used to fit a sparse linear model on the raw and rule features. The result
  is a model that learns similarly to a tree ensemble, while often offering improved interpretability
  and achieving improved scoring runtime in live applications. Several algorithms for
  reducing rule complexity are provided, most notably hyperrectangle de-overlapping. All algorithms scale to 
  several million rows and support sparse representations to handle tens of thousands of dimensions.
Contains functions to identify tree-ring borders based on X-ray micro-density profiles and a Graphical User Interface to visualize density profiles and correct tree-ring borders.
A Julia interface structured according to the general
	     form described in package 'XR' and in the book "Extending R".
Fits hierarchical regularized regression models
    to incorporate potentially informative external data, Weaver and Lewinger (2019) <doi:10.21105/joss.01761>. 
    Utilizes coordinate descent to efficiently fit regularized regression models both with and without
    external information with the most common penalties used in practice (i.e. ridge, lasso, elastic net). 
    Support for standard R matrices, sparse matrices and big.matrix objects.
Digital repeat photography and near-surface remote sensing have been used by environmental scientists to study the environmental change for nearly a decade. However, a user-friendly, reliable, and robust platform to extract color-based statistics and time-series from a large stack of images is still lacking. Here, we present an interactive open-source toolkit, called 'xROI', that facilitate the process time-series extraction and improve the quality of the final data. 'xROI' provides a responsive environment for scientists to interactively a) delineate regions of interest (ROI), b) handle field of view (FOV) shifts, and c) extract and export time series data characterizing image color (i.e. red, green and blue channel digital numbers for the defined ROI). Using 'xROI', user can detect FOV shifts without minimal difficulty. The software gives user the opportunity to readjust the mask files or redraw new ones every time an FOV shift occurs. 'xROI' helps to significantly improve data accuracy and continuity.
A 'Python' interface structured according to the general
    form described in package 'XR' and in the book "Extending R".
This is a set of statistical quality control functions,  that allows plotting control charts and its iterations, process capability for variable and attribute control, highlighting the xrs_gr() function, like a first iteration for variable chart, meanwhile the we_rules() function detects non random patterns in sample.
An extension for the 'xml2' package to transform XML documents
    by applying an 'xslt' style-sheet.
The circadian period of a time series data is predicted and the statistical significance of the periodicity are calculated using the chi-square periodogram.
Builds generalized linear model with automatic data transformation. 
  The 'xspliner' helps to build simple, interpretable models that inherits informations provided by more complicated ones.
  The resulting model may be treated as explanation of provided black box, that was supplied prior to the algorithm.
Tools to download and merge data files on sub-national conflict, violence and protests from <http://www.x-sub.org>.
This is the tool set for crystallographer to design and analyze crystallization experiments, especially for ribosome from Mycobacterium tuberculosis.
The 'xtensor' C++ library for numerical analysis with
 multi-dimensional array expressions is provided as a header-only
 C++14 library. It offers an extensible expression system enabling
 lazy broadcasting; an API following the idioms of the C++ standard
 library; and tools to manipulate array expressions and build upon 'xtensor'.
Can be used for coloring output in terminals.
	It was developed for the standard Ubuntu terminal but should be compatible
	with any terminal using xterm or ANSI escape sequences. If run in windows,
	RStudio, or any other platform not supporting such escape sequences it
	gracefully passes on any output without modifying it.
Implemented is an algorithm to estimate the two-way fixed effect linear model. 
    The coefficients of interest are computed using the residuals from the 
    projection of all variables on the two sets of fixed effects. Our algorithm
    has three desirable features. First, it manages memory and computational 
    resources efficiently which speeds up the computation of the estimates. 
    Second, it allows the researcher to estimate multiple specifications 
    using the same set of fixed effects at a very low computational cost. 
    Third, the asymptotic variance of the parameters of interest can be 
    consistently estimated using standard routines on the residualized data. 
    Somaini P., Wolak F. A. (2016) <doi:10.1515/jem-2014-0008>
    Arellano, M. (1987) <https://ideas.repec.org/a/bla/obuest/v49y1987i4p431-34.html>.
Provide for uniform handling of R's different time-based data classes by extending zoo, maximizing native format information preservation and allowing for user level customization and extension, while simplifying cross-class interoperability.
Extends standard penalized regression (Lasso and Ridge) to allow differential shrinkage based on external information with the goal of achieving a better prediction accuracy. Examples of external information include the grouping of predictors, prior knowledge of biological importance, external p-values, function annotations, etc. The choice of multiple tuning parameters is done using an Empirical Bayes approach. A majorization-minimization algorithm is employed for implementation.
Calculates a number of valuation adjustments including CVA, DVA,
    FBA, FCA, MVA and KVA. A two-way margin agreement has been implemented. For
    the KVA calculation three regulatory frameworks are supported: CEM, (simplified) SA-CCR, OEM
	and IMM. The probability of default is implied through the credit spreads curve.
    Currently, only IRSwaps are supported. For more information, you can check
    one of the books regarding xVA: <http://www.cvacentral.com/books/credit-value-adjustment>.
Extrema-weighted feature extraction for varying length functional data. Functional data analysis method that performs dimensionality reduction based on predefined features and allows for quantile weighting. Method implemented as presented in van den Boom et al. (2018) <doi:10.1093/bioinformatics/bty120>.
A suite of psychometric analysis tools for research and operation, including:
    (1) computation of probability, information, and likelihood for the 3PL, GPCM, and GRM;
    (2) parameter estimation using joint or marginal likelihood estimation method;
    (3) simulation of computerized adaptive testing using built-in or customized algorithms;
    (4) assembly and simulation of multistage testing. 
    The full documentation and tutorials are at <https://github.com/xluo11/xxIRT>.
Methods for plotting multiple xylophone-style histograms 
    using base graphics.
High dimensional interaction search by brute force requires a
    quadratic computational cost in the number of variables. The xyz algorithm provably finds strong interactions in almost linear time.
    For details of the algorithm see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast interaction search in high-dimensional data <https://arxiv.org/pdf/1610.05108v1.pdf>.
Provides an alternative canonical correlation/redundancy
  analysis function, with associated print, plot, and summary methods.
  A method for generating helio plots is also included.
Another implementation of general regression neural network in R
    based on Specht (1991) <DOI:10.1109/72.97934>. It is applicable to the 
    functional approximation or the classification.
Performs nearest neighbor-based imputation using one or more alternative 
 approaches to processing multivariate data. These include methods based on canonical 
 correlation analysis, canonical correspondence analysis, and a multivariate adaptation 
 of the random forest classification and regression techniques of Leo Breiman and Adele 
 Cutler. Additional methods are also offered. The package includes functions for 
 comparing the results from running alternative techniques, detecting imputation targets 
 that are notably distant from reference observations, detecting and correcting 
 for bias, bootstrapping and building ensemble imputations, and mapping results.
This is a simple wrapper for the yakmo K-Means library (developed by Naoki Yoshinaga, see http://www.tkl.iis.u-tokyo.ac.jp/~ynaga/yakmo/). It performs fast and robust (orthogonal) K-Means.
This collection of data exploration tools was developed at
    Yale University for the graphical exploration of complex
    multivariate data; barcode and gpairs now have their own
    packages.  The new big.read.table() provided here may be
    useful for large files when only a subset is needed.
Implements the 'libyaml' 'YAML' 1.1 parser and emitter
  (<http://pyyaml.org/wiki/LibYAML>) for R.
A YAML-based
 mechanism for working with table metadata. It supports
 compact syntax for creating, modifying, exporting,
 importing, displaying, and plotting metadata coded as column 
 attributes. The 'yamlet' dialect is valid 'YAML' with
 defaults and conventions chosen to improve readability. 
 See ?yamlet, ?decorate.data.frame and ?modify.default.
 See ?read_yamlet ?write_yamlet, ?io_csv, and ?ggplot.decorated.
Setting layout through 'YAML' headers in 'R-Markdown' documents,
    enabling their automatic generation.
    Functions and methods may summarize 'R' objects in automatic reports, for
    instance check-lists and further reports applied to the packages 'taxlist'
    and 'vegtable'.
Functionality to compute the projection median via several
 algorithms. This package also provides functions to plot different
 multivariate medians and multivariate quantiles in two-dimensional and
 three-dimensional data respectively. See Chen, F. and Nason, G.P. (2020)
 "A new method for computing the projection median, its influence curve
 and techniques for the production of projected quantile plots." PLOS One
 (accepted for publication).
Another implementation of probabilistic neural network in R
    based on Specht (1990) <DOI:10.1016/0893-6080(90)90049-Q>. It is applicable to the 
    pattern recognition with a N-level response, where N > 2.
Tidy tools for quantifying how well model fits to a
    data set such as confusion matrices, class probability curve
    summaries, and regression metrics (e.g., RMSE).
A parser and a writer for 'WEKA' Attribute-Relation File Format
    <https://waikato.github.io/weka-wiki/arff_stable/> in pure R, with no dependencies. 
    As opposed to other R implementations, this package can read standard
    (dense) as well as sparse files, i.e. those where each row does only contain 
    nonzero components. Unlike 'RWeka', 'yarr' does not require any 'Java' installation
    nor is dependent on external software. This implementation is generalized from 
    those in packages 'mldr' and 'mldr.datasets'.
Contains a mixture of functions and data sets referred to in the introductory e-book "YaRrr!: The Pirate's Guide to R". The latest version of the e-book is available for free at <https://www.thepiratesguidetor.com>.
A collection of string functions designed for writing 
    compact and expressive R code. 'yasp' (Yet Another String Package) is simple,
    fast, dependency-free, and written in pure R. The package provides: a
    coherent set of abbreviations for paste() from package 'base' with a
    variety of defaults, such as p() for "paste" and pcc() for "paste and
    collapse with commas"; wrap(), bracket(), and others for wrapping a
    string in flanking characters; unwrap() for removing pairs of characters
    (at any position in a string); and sentence() for cleaning whitespace
    around punctuation and capitalization appropriate for prose sentences.
Provides functions to manage taxonomy when lineages
    are described with strings and ranks separated with special patterns
    like "|*__" or ";*__".
Yield curve or zero-coupon prices interpolation and extrapolation using the Nelson-Siegel, Svensson, Smith-Wilson models, and Hermite cubic splines.
Asks Yes-No questions with variable or custom responses.
The purpose of this package is to provide methods to interpret multiple
  linear regression and canonical correlation results including beta weights,structure coefficients, 
  validity coefficients, product measures, relative weights, all-possible-subsets regression,
  dominance analysis, commonality analysis, and adjusted effect sizes.
Deploy, maintain, and invoke models via the Yhat
    REST API.
Modelling the yield curve with some parametric models.
        The models implemented are: Nelson-Siegel, Diebold-Li and
        Svensson.  The package also includes the data of the term
        structure of interest rate of Federal Reserve Bank and European
        Central Bank.
The clustering by k-means of using the target variable.
             To determine the number of clusters with the variance of 
             the target variable in the cluster.
Compute the standard expected years of life lost (YLL),
    as developed by the Global Burden of Disease Study
    (Murray, C.J., Lopez, A.D. and World Health Organization, 1996).
    The YLL is based on comparing the age of death to an external standard life
    expectancy curve. It also computes the average YLL, which highlights premature
    causes of death and brings attention to preventable deaths
    (Aragon et al., 2008).
Write 'YAML' front matter for R Markdown and related
    documents. yml_*() functions write 'YAML' and use_*() functions let
    you write the resulting 'YAML' to your clipboard or to .yml files
    related to your project.
Build 'shiny' applications with the latest Bootstrap components
    and design utilities. Includes refreshed reactive inputs and outputs.
    Use responsive layouts to design and construct applications for devices
    of all sizes.
Analyzing performances of cricketers and cricket teams
             based on 'yaml' match data from Cricsheet <https://cricsheet.org/>.
On-disk embedded database with SQL versions of the original 
    datasets from Yotov, et al (2016, ISBN: 978-92-870-4367-2) and functions to 
    report regressions with clustered robust standard errors.
Although there exist some R packages tailored for YouTube API (e.g., 'tuber'), downloading YouTube video subtitle (i.e., caption) in a tidy form has never been a low-hanging fruit. Using 'youtube-transcript-api Python package' under the hood, this R package provides users with a convenient way of parsing and converting a desired YouTube caption into a handy 'tibble' data_frame object. Furthermore, users can easily save a desired YouTube caption data as a tidy Excel file without advanced programming background knowledge.
Semiparametric modeling of lifetime data with crossing survival curves via Yang and Prentice model with baseline hazard/odds modeled with Bernstein polynomials. Details about the model can be found in Demarqui et al. (2019) <arXiv:1910.04475>. Model fitting can be carried out via both maximum likelihood and Bayesian approaches. The package also provides point and interval estimation for the crossing survival times.
For any spending function specified by the user, this 
    package provides corresponding boundaries for interim testing using
    the adaptively weighted log-rank test developed by Yang and Prentice
    (2010 <doi:10.1111/j.1541-0420.2009.01243.x>). 
    The package uses a re-sampling method to obtain stopping boundaries 
    at the interim looks.The output consists of stopping boundaries 
    and observed values of the test statistics at the interim looks, 
    along with nominal p-values defined as the probability of the test 
    exceeding the specific observed test statistic value or critical 
    value, regardless of the test behavior at other looks. 
    The asymptotic validity of the stopping boundaries is established
    in Yang (2018 <doi:10.1002/sim.7958>).
Inference procedures accommodate a flexible range of hazard ratio patterns with a two-sample semi-parametric model. This model contains the proportional hazards model and the proportional odds model as sub-models, and accommodates non-proportional hazards situations to the extreme of having crossing hazards and crossing survivor functions. Overall, this package has four major functions: 1) the parameter estimation, namely short-term and long-term hazard ratio parameters; 2) 95 percent and 90 percent point-wise confidence intervals and simultaneous confidence bands for the hazard ratio function; 3) p-value of the adaptive weighted log-rank test; 4) p-values of two lack-of-fit tests for the model. See the included "read_me_first.pdf" for brief instructions. In this version (1.1), there is no need to sort the data before applying this package.
Semiparametric modeling of lifetime data with crossing survival curves via Yang and Prentice model with piecewise exponential baseline distribution. Details about the model can be found in Demarqui and Mayrink (2019) <arXiv:1910.02406>. Model fitting carried out via likelihood-based and Bayesian approaches. The package also provides point and interval estimation for the crossing survival times.
An implementation of equilibrium-based yield per recruit methods.
    Yield per recruit methods can used to estimate the optimal yield for a fish population
    as described by Walters and Martell (2004) <isbn:0-691-11544-3>.
    The yield can be based on the number of fish caught (or harvested) or 
    biomass caught for all fish or just large (trophy) individuals.
Miscellaneous functions for data analysis, portfolio management, graphics, data manipulation, statistical investigation, including descriptive statistics, creating leading and lagging variables, portfolio return analysis, time series difference and percentage change calculation, stacking data for higher efficient analysis.
Simple method for comparison of gene
        expression generated across different experiments, and on
        different platforms; that does not require global
        renormalization, and is not restricted to comparison of
        identical probes. YuGene works on a range of microarray dataset
        distributions, such as between manufacturers. The resulting
        output allows direct comparisons of gene expression between
        experiments and experimental platforms.
Simulation and Inference for SDEs and Other Stochastic Processes.
Provides a graphical user interface for the 'yuima' package.
Provides a number of functions to facilitate
  extracting information in 'YAML' fragments from one or 
  multiple files, optionally structuring the information
  in a 'data.tree'. 'YAML' (recursive acronym for "YAML ain't
  Markup Language") is a convention for specifying structured
  data in a format that is both machine- and human-readable.
  'YAML' therefore lends itself well for embedding (meta)data
  in plain text files, such as Markdown files. This principle
  is implemented in 'yum' with minimal dependencies (i.e. only
  the 'yaml' packages, and the 'data.tree' package can be
  used to enable additional functionality).
Yummly.com is one of the world's largest and most powerful recipe search sites and this package aims to provide R bindings for publicly available Yummly.com Recipe API (https://developer.yummly.com/).
Provides simple statistics from instruments and observations at sites in the NEON network, and acts as a simple interface for v0 of the National Ecological Observatory Network (NEON) API.
  Statistics are generated for meteorologic and soil-based observations, and are presented for daily, annual, and one-time observations at all available NEON sites.
  Users can also retrieve any dataset publicly hosted by NEON. Metadata for NEON sites and data products can be returned, as well as information on data product availability by site and date. 
  For more information on NEON, please visit <https://www.neonscience.org>. For detailed data product information, please see the NEON data product catalog at <https://data.neonscience.org/data-product-catalog>.
A suite of statistics for identifying areas of the genome under selective pressure. See Jacobs, Sluckin and Kivisild (2016) <doi:10.1534/genetics.115.185900>.
Interface to the 'ZooBank' API (<http://zoobank.org/Api>) client.
    'ZooBank' (<http://zoobank.org/>) is the official registry of zoological 
    nomenclature. Methods are provided for using each of the API endpoints, 
    including for querying by author, querying for publications, get 
    statistics on 'ZooBank' activity, and more.
Principled methods for the imputation of zeros, left-censored and missing data in
    compositional data sets (Palarea-Albaladejo and Martin-Fernandez (2015) <doi:10.1016/j.chemolab.2015.02.019>).
An implementation of z-curves - a method for estimating expected discovery 
    and replicability rates on the bases of test-statistics of published studies. The package 
    provides functions for fitting the new density and EM version 
    (Bartoš & Schimmack, 2020, <doi:10.31234/osf.io/urgtn>) as well as the original density 
    z-curve (Brunner & Schimmack, 2017, <doi:10.31219/osf.io/wr93f>). Furthermore, the package 
    provides summarizing and plotting functions for the fitted z-curve objects. See the 
    aforementioned articles for more information about the z-curves, expected discovery 
    and replicability rates, validation studies, and limitations.
Facilitates making a connection to the 
  'Zendesk' API and executing various queries. You can use it to
  get ticket data and ticket metrics. The 'Zendesk' documentation is 
  available at <https://developer.zendesk.com/rest_api
  /docs/support/introduction>. This package is not supported by 
  'Zendesk' (owner of the software).
Provides a %<-% operator to perform multiple,
    unpacking, and destructuring assignment in R. The 
    operator unpacks the right-hand side of an assignment
    into multiple values and assigns these values to 
    variables on the left-hand side of the assignment.
R package accompanying the book Working with dynamic models for agriculture and environment, by Daniel Wallach (INRA), David Makowski (INRA), James W. Jones (U.of Florida), Francois Brun (ACTA). 3rd edition 2018-09-27.
Implements the estimation of local (and global) association measures: Ducher's Z, pointwise mutual information, normalized pointwise mutual information and chi-squared residuals. The significance of local (and global) association is accessed using p-values estimated by permutations. Finally, using local association subgroup analysis, it identifies if the association between variables is dependent on the value of another variable.
Use behavioural variables to compute period, rhythmicity and other circadian parameters.
  Methods include computation of chi square periodograms (Sokolove and Bushell (1978) <DOI:10.1016/0022-5193(78)90022-X>),
  Lomb-Scargle periodograms (Lomb (1976) <DOI:10.1007/BF00648343>, Scargle (1982) <DOI:10.1086/160554>, Ruf (1999) <DOI:10.1076/brhm.30.2.178.1422>),
  and autocorrelation-based periodograms.
A framework that brings together an abundance of common
    statistical models found across packages into a unified interface, and
    provides a common architecture for estimation and interpretation, as well
    as bridging functions to absorb increasingly more models into the
    package. Zelig allows each individual package, for each
    statistical model, to be accessed by a common uniformly structured call and
    set of arguments. Moreover, Zelig automates all the surrounding building
    blocks of a statistical work-flow--procedures and algorithms that may be
    essential to one user's application but which the original package
    developer did not use in their own research and might not themselves
    support. These include bootstrapping, jackknifing, and re-weighting of data.
    In particular, Zelig automatically generates predicted and simulated
    quantities of interest (such as relative risk ratios, average treatment
    effects, first differences and predicted and expected values) to interpret
    and visualize complex models.
Provides an Interface to 'Zenodo' (<https://zenodo.org>) REST API, 
  including management of depositions, attribution of DOIs by 'Zenodo' and 
  upload of files.
This package provides an R wrapper for the Zendesk API
Graphical tools for visualizing high-dimensional data along a path
 of alternating one- and two-dimensional plots. Note that this
 includes interactive graphics plots based on 'loon' in turn based on 'tcltk'
 (included as part of the standard R distribution).  It also requires 'graph' from Bioconductor.
 For more detail on use and algorithms, see <doi:10.18637/jss.v095.i04>.
Uses bootstrap to test zero order correlation being equal to a 
    partial or semi-partial correlation (one or two tailed). Confidence 
    intervals for the parameter (zero order minus partial) can also be
    determined. Implements the bias-corrected and accelerated bootstrap
    method as described in "An Introduction to the Bootstrap" Efron (1983) 
    <0-412-04231-2>.
Functions to compute compositional turnover using zeta-diversity,
    the number of species shared by multiple assemblages. The package includes
    functions to compute zeta-diversity for a specific number of
    assemblages and to compute zeta-diversity for a range of numbers of
    assemblages. It also includes functions to explain how zeta-diversity
    varies with distance and with differences in environmental variables
    between assemblages, using generalised linear models, linear models
    with negative constraints, generalised additive models,shape
    constrained additive models, and I-splines.
Performs Zoom-Focus Algorithm (ZFA) to optimize testing regions for rare variant association tests in exome sequencing data.
The goal of 'zfit' is to improve the usage of basic model fitting
    functions within a piped work flow, in particular when passing
    and processing a data.frame using 'dplyr' or similar packages.
The method zGPS.AO (Zero Inflated Gamma Poisson Shrinker with AE 
    (Adverse Event) ontology) is based on the zero-inflated negative binomial 
    distribution. 
    It estimates the association between a specific vaccine and an adverse event 
    group, as well as associations between that vaccine and individual adverse 
    events within the adverse event group. This model handles the adverse event 
    count data with excess zeros and over-dispersion, and it allows borrowing 
    information from adverse event data in the same group. Details can be found 
    in  "Data Mining in Large Frequency Tables With Ontology, with an Application 
    to the Vaccine Adverse Event Reporting System." 
    Bangyao Zhao, Lili Zhao (2020) <arXiv:2010.12471>.
Microbiome count data (Operational Taxonomic Unit, OTUs) is usually overdispersed and has excessive zero counts. The 'ZIBBSeqDiscovery' assumes a zero-inflated beta-binomial model for the distribution of the count data, and employes link functions to adjust interested covariates. To fit the model, two approaches are proposed (i) a free approach which treats the overdispersion parameters for OTUs as independent, and (ii) a constrained approach which proposes a mean-overdispersion relationship to the count data. This package can be used to test the association between the composition of the microbiome counts and the interested covariates.
Detects abundance differences across clinical conditions. Besides, it takes the sparse nature of metagenomic data into account and handles compositional data efficiently.
Provides MCMC algorithms for the analysis of
        zero-inflated count models. The case of stochastic search
        variable selection (SVS) is also considered.  All MCMC samplers
        are coded in C++ for improved efficiency. A data set
        considering the demand for health care is provided.
Zillow, an online real estate company, provides real estate and
    mortgage data for the United States through a REST API. The ZillowR package
    provides an R function for each API service, making it easy to make API
    calls and process the response into convenient, R-friendly data structures.
    See <http://www.zillow.com/howto/api/APIOverview.htm> for the Zillow API
    Documentation.
Analyze count time series with excess zeros. 
    Two types of statistical models are supported: Markov regression by Yang et al.
    (2013) <doi:10.1016/j.stamet.2013.02.001> and state-space models by Yang et al. 
    (2015) <doi:10.1177/1471082X14535530>. They are also known as observation-driven and 
    parameter-driven models respectively in the time series literature. The functions used for 
    Markov regression or observation-driven models can also be used to fit ordinary regression models 
    with independent data under the zero-inflated Poisson (ZIP) or zero-inflated negative binomial (ZINB) 
    assumption. Besides, the package contains some miscellaneous functions to compute density, distribution, 
    quantile, and generate random numbers from ZIP and ZINB distributions.
Cross-Platform 'zip' Compression Library. A replacement
    for the 'zip' function, that does not require any additional
    external tools on any platform.
Some data treated by the Japanese R user require
    unique operations and processing. These are caused by address, Kanji,
    and traditional year representations. 'zipangu' transforms specific
    to Japan into something more general one.
Make working with ZIP codes in R painless with an integrated dataset of U.S. ZIP codes and functions for working with them. 
             Search ZIP codes by multiple geographies, including state, county, city & across time zones. Also included are functions for relating
             ZIP codes to Census data.
Estimation methods for zero-inflated Poisson factor analysis (ZIPFA) on sparse data. 
    It provides estimates of coefficients in a new type of zero-inflated regression. 
    It provides a cross-validation method to determine the potential rank of the data in the ZIPFA 
    and conducts zero-inflated Poisson factor analysis based on the determined rank.
Implementation of four extensions of the Zipf distribution: the Marshall-Olkin 
  Extended Zipf (MOEZipf) Pérez-Casany, M., & Casellas, A. (2013) <arXiv:1304.4540>, the Zipf-Poisson Extreme (Zipf-PE), the 
  Zipf-Poisson Stopped Sum (Zipf-PSS) and the Zipf-Polylog distributions. 
  In log-log scale, the two first extensions allow for top-concavity 
  and top-convexity while the third one only allows for top-concavity. 
  All the extensions maintain the linearity associated with the Zipf model in the tail.
Statistical models and utilities for the analysis of word frequency distributions.
	The utilities include functions for loading, manipulating and visualizing word frequency
	data and vocabulary growth curves.  The package also implements several statistical 
	models for the distribution of word frequencies in a population.  (The name of this package 
	derives from the most famous word frequency distribution, Zipf's law.)
Fit zero-inflated Poisson hidden (semi-)Markov models with or without covariates by directly minimizing the negative log likelihood function using the gradient descent algorithm. Multiple starting values should be used to avoid local minima.
Implements Python-style zip for R. Is a more flexible version of cbind.
Generates a data frame of US zip codes and their distance to the given zip code when given a starting 
  zip code and a radius in miles. Also includes functions for use with 'choroplethrZip' which are detailed in
  the vignette.
Calculate and plot scattering matrix coefficients for plane waves at interface.
Fits beta regression and zero-or-one inflated beta regression and obtains Bayesian Inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS.
'Zoltar' <https://www.zoltardata.com/> is a website that provides a repository of model forecast results
    in a standardized format and a central location. It supports storing, retrieving, comparing, and analyzing time
    series forecasts for prediction challenges of interest to the modeling community. This package provides functions
    for working with the 'Zoltar' API, including connecting and authenticating, getting information about projects,
    models, and forecasts, deleting and uploading forecast data, and downloading scores.
Create new analysis setups and deal with results of 
    Zonation conservation prioritization software <https://github.com/cbig/zonation-core>. 
    This package uses data available in the 'zdat' (7.7 MB) package 
    for building the vignettes.
An S3 class with methods for totally ordered indexed
             observations. It is particularly aimed at irregular time series
             of numeric vectors/matrices and factors. zoo's key design goals
             are independence of a particular index/date/time class and
             consistency with ts and base R by providing methods to extend
             standard generics.
The analysis and inference of faunal remains recovered from
    archaeological sites concerns the field of zooarchaeology. The zooaRch package
    provides analytical tools to make inferences on zooarchaeological data.
    Functions in this package allow users to read, manipulate, visualize, and
    analyze zooarchaeological data.
A free (open source) solution for analyzing digital
  images of plankton. In combination with ImageJ, a free image analysis
  system, it processes digital images, measures individuals, trains for
  automatic classification of taxa, and finally, measures plankton samples
  (abundances, total and partial size spectra or biomasses, etc.).
zm(), called with any active plot allow to enter an
    interactive session to zoom/navigate any plot. The development
    version, as well as binary releases can be found at
    https://github.com/cbarbu/R-package-zoom
Reproducible and remixable species distribution modelling.
    The package reads user submitted modules from an online repository, runs
    full species distribution modelling workflows and returns output that is
    fully reproducible. For examples and detailed discussion refer to: N.Golding
    et al. (2017) 'The zoon r package for reproducible and shareable species
    distribution modelling'. Methods in Ecology and Evolution.
    <doi:10.1111/2041-210X.12858>. The package 'SDMTools' is used for testing
    and, though this package is archived, you can access it here if 
    needed, <https://cran.r-project.org/src/contrib/Archive/SDMTools/>.
Combines a forecast of a time series, using the function forecast(), with the dynamic plots from dygraphs.
A tool for calculating z-scores and centiles for weight-for-age, 
    length/height-for-age, weight-for-length/height, BMI-for-age, 
    head circumference-for-age, age circumference-for-age, 
    subscapular skinfold-for-age, triceps skinfold-for-age based on the 
    WHO Child Growth Standards.
Generates well-known integer sequences. 'gmp' package is adopted for computing with arbitrarily large numbers. Every function has hyperlink to its corresponding item in OEIS (The On-Line Encyclopedia of Integer Sequences) in the function help page. For interested readers, see Sloane and Plouffe (1995, ISBN:978-0125586306).
Makes zebra-striped tables (tables with alternating row colors)
    in LaTeX and HTML formats easily from a data.frame, matrix, lm, aov, anova,
    glm, coxph, nls, fitdistr, mytable and cbind.mytable objects.
Functions for obtaining the density, random variates 
             and maximum likelihood estimates of the Zero-truncated Poisson lognormal
             distribution and their mixture distribution.
Read '.xls' and '.sbj' files which are written by the
   Microsoft Windows program 'z-Tree'. The latter is a software for
   developing and carrying out economic experiments
   (see <http://www.ztree.uzh.ch/> for more information).
How fast can you type R functions on your keyboard? Find out by running a 'zty.pe' game: export R functions as instructions to type to destroy opponents vessels.
Stein control variates can be used to improve Monte Carlo estimates of expectations when the derivatives of the log target are available. This package implements a variety of such methods, including zero-variance control variates (ZV-CV, Mira et al. (2013) <doi:10.1007/s11222-012-9344-6>), regularised ZV-CV (South et al., 2018 <arXiv:1811.05073>), control functionals (CF, Oates et al. (2017) <doi:10.1111/rssb.12185>) and semi-exact control functionals (SECF, South et al., 2020 <arXiv:2002.00033>). ZV-CV is a parametric approach that is exact for (low order) polynomial integrands with Gaussian targets. CF is a non-parametric alternative that offers better than the standard Monte Carlo convergence rates. SECF has both a parametric and a non-parametric component and it offers the advantages of both for an additional computational cost. Functions for applying ZV-CV and CF to two estimators for the normalising constant of the posterior distribution in Bayesian statistics are also supplied in this package. The basic requirements for using the package are a set of samples, derivatives and function evaluations.
Contains an efficient implementation of Sen's slope method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and Yue-Pilon's (Yue, 2002) prewhitening approaches to determining trends in climate data.
A minor collection of HTTP wrappers for the 'Zamzar File Conversion'
    API. The wrappers makes it easy to utilize the API and thus convert
    between more than 100 different file formats (ranging from audio files,
    images, movie formats, etc., etc.) through an R session.  
    For specifics regarding the API, please see <https://developers.zamzar.com/>.
Functions and datasets for bootstrapping from the
book "Bootstrap Methods and Their Application" by A. C. Davison and
D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
Various functions for classification, including k-nearest
neighbour, Learning Vector Quantization and Self-Organizing Maps.
Methods for Cluster analysis.  Much extended the original from
Peter Rousseeuw, Anja Struyf and Mia Hubert,
based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".
Reading and writing data stored by some versions of
'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka',
and for reading and writing some 'dBase' files.
Functions for kernel smoothing (and density estimation)
corresponding to the book:
Wand, M.P. and Jones, M.C. (1995) "Kernel Smoothing".
A powerful and elegant high-level data visualization
system inspired by Trellis graphics, with an emphasis on
multivariate data. Lattice is sufficient for typical graphics needs,
and is also flexible enough to handle most nonstandard requirements.
See ?Lattice for an introduction.
Functions and datasets to support Venables and Ripley,
"Modern Applied Statistics with S" (4th edition, 2002).
A rich hierarchy of matrix classes, including triangular,
symmetric, and diagonal matrices, both dense and sparse and with
pattern, logical and numeric entries.   Numerous methods for and
operations on these matrices, using 'LAPACK' and 'SuiteSparse' libraries.
Generalized additive (mixed) models, some of their extensions and
other generalized ridge regression with multiple smoothing
parameter estimation by (Restricted) Marginal Likelihood,
Generalized Cross Validation and similar, or using iterated
nested Laplace approximation for fully Bayesian inference. See
Wood (2017) <doi:10.1201/9781315370279> for an overview.
Includes a gam() function, a wide variety of smoothers, 'JAGS'
support and distributions beyond the exponential family.
Software for feed-forward neural networks with a single
hidden layer, and for multinomial log-linear models.
Recursive partitioning for classification,
regression and survival trees.  An implementation of most of the
functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.
Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
This device uses Cairo and GTK to draw to the screen,
file (png, svg, pdf, and ps) or memory (arbitrary GdkDrawable
or Cairo context). The screen device may be embedded into RGtk2
interfaces and supports all interactive features of other graphics
devices, including getGraphicsEvent().
A graphics device for R that produces 'Scalable Vector Graphics'.
'svglite' is a fork of the older 'RSvgDevice' package.
An extension to the 'testthat' package that makes it easy
to add graphical unit tests. It provides a Shiny application to
manage the test cases.
Many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP.  Also offers access to an
'XPath' "interpreter".
Please send bug reports to ismrp@jasp.ism.ac.jp.
Please send questions and comments to etiennead@gmail.com.
Please send questions and comments regarding pbdR to
RBigData@gmail.com
Please send bug reports to ismrp@jasp.ism.ac.jp
Please send questions and comments about Rcpp to
rcpp-devel@lists.r-forge.r-project.org
Please send questions and comments regarding RInside to
rcpp-devel@lists.r-forge.r-project.org
Raja Sekhara Reddy D.M <raja.duvvuru@gmail.com>
Dane R. Van Domelen <vandomed@gmail.com>
Renata T C Yokota <renatayokota@gmail.com>
Pedro Rafael Diniz Marinho <pedro.rafael.marinho@gmail.com>
Carlos J. Gil Bellosta <cgb@datanalytics.com>
Achmad Fauzi Bagus F <fauzi.pandya@gmail.com>
Cesar de Oliveira Ferreira Silva <cesaroliveira.f.silva@gmail.com>
Berent Ånund Strømnes Lunde <lundeberent@gmail.com>
Jose Roberto Ayala Solares <ichbinjras@gmail.com>
Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Pierre Lafaye De Micheaux <lafaye@unsw.edu.au>
Robin K. S. Hankin <hankin.robin@gmail.com>
Gabriel F. R. Vasconcelos <gabrielrvsc@yahoo.com.br>
Pedro Nascimento de Lima <pedrolima.n@gmail.com>
Pierre Lafaye de Micheaux <lafaye@unsw.edu.au>
Edwin Javier Castillo Carreño <edjcastilloca@unal.edu.co>
Stephanie van der Pas <svdpas@math.leidenuniv.nl>
Ricardo de Matos Simoes <ricardo_dematossimoes@dfci.harvard.edu>
Karel Van den Meersche <karel.van_den_meersche@cirad.fr>
Blondeau Da Silva Stephane <Stephane.Blondeau-Da-Silva@ac-limoges.fr>
Emilio Akira Morones Ishikawa <emiliomorones@gmail.com>
Luiz Antonio de Jesus Rocha <luiz.rocha@unifesp.br>
Anderson Rodrigo da Silva <anderson.agro@hotmail.com>
Ana Belen Nieto Librero <ananieto@usal.es>
Ricardo Puziol de Oliveira <rpuziol.oliveira@gmail.com>
Rafael de Andrade Moral <rafael.deandrademoral@mu.ie>
Andrey Duvan Rincon Torres <adrincont@unal.edu.co>
Guillaume Kon Kam King <guillaume.konkamking.work@gmail.com>
David Alejandro Martell Juarez <alex91599@gmail.com>
Jianzhao Gao and Xiaodan Fan <gaojz@nankai.edu.cn>
Rahim Alhamzawi  (University of Al-Qadisiyah) <rahim.alhamzawi@qu.edu.iq>
José Carlos Soage González <jsoage@uvigo.es>
Sy Han (Steven) Chiou <schiou@hsph.harvard.edu>
Francisco H. C. de Alencar <hildemardealencar@gmail.com>
Ivo Van Walle Developer <ivo.van.walle@gmail.com>
Ting Fung (Ralph) Ma <tingfung.ma@wisc.edu>
Luis Alfonso Perez Martos <lapm0001@gmail.com>
L. A. van der Ark <L.A.vanderArk@uva.nl>
Francesca Marta Lilja Di Lascio <marta.dilascio@unibz.it>
M. A. J. Zondervan-Zwijnenburg <m.a.j.zwijnenburg@uu.nl>
K. Gerald van den Boogaart <support@boogaart.de>
P. Lafaye de Micheaux <lafaye@unsw.edu.au>
Wim Van der Elst <Wim.vanderelst@gmail.com>
Sjoerd van der Spoel <R@sjoerdvanderspoel.nl>
Jonas M. B. Haslbeck <jonas.haslbeck@gmail.com>
Ernst van der Maaten <ernst.vandermaaten@gmail.com>
Carl A. B. Pearson <carl.pearson@lshtm.ac.uk>
Eduardo L. T. Conceicao <mail@eduardoconceicao.org>
Alec James van Rassel <alec.van-rassel.1@ulaval.ca>
Sean A. S. Anderson <seanas.anderson@mail.utoronto.ca>
Marcelino de la Cruz Rot <marcelino.delacruz@urjc.es>
A. Jonathan R. Godfrey <a.j.godfrey@massey.ac.nz>
Pedro H. C. Sant'Anna <pedro.h.santanna@vanderbilt.edu>
Don van den Bergh <donvdbergh@hotmail.com>
Kaique dos S. Alves <kaiquedsalves@gmail.com>
Alexandre Adalardo de Oliveira <ecovirtualpackage@gmail.com>
Ardo van den Hout <Ardo.vandenHout@ucl.ac.uk>
Matheus H. J. Saldanha <mhjsaldanha@gmail.com>
Manuel Oviedo de la Fuente <manuel.oviedo@usc.es>
Caíque de Oliveira de Souza <forestgrowthsoftware@gmail.com>
Clayton Vieira Fraga Filho <forestgrowthsoftware@gmail.com>
Eduardo San Miguel Martin
<eduardo.san.miguel.martin@gmail.com>
Nina M. D. Schiettekatte <nina.schiettekatte@gmail.com>
Agnese Maria Di Brisco <agnese.dibrisco@unimib.it>
Shaiful Anuar Abu Bakar <saab@um.edu.my>
Juan Pablo Marin Diaz <jpmarindiaz@gmail.com>
Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Vincent T van Hees <v.vanhees@accelting.com>
Xavier Fernández i Marín <xavier.fim@gmail.com>
Caspar J. van Lissa <c.j.vanlissa@uu.nl>
Kevin Allan Sales Rodrigues <kevin.asr@outlook.com>
Geraldine Van der Auwera <vdauwera@broadinstitute.org>
Anders Gonçalves da Silva <andersgs@gmail.com>
Martijn van de Pol <martijn@myscience.eu>
Rafael de Andrade Moral <rafael_moral@yahoo.com.br>
Austrian Institute of Technology <hyrim@ait.ac.at>
Sai Thein Than Tun <theinthantun.sai@gmail.com>
Marcelino de la Cruz <marcelino.delacruz@urjc.es>
Luiz Eduardo S. Gomes <gomes.leduardo@gmail.com>
Eufrasio de A. Lima Neto <eufrasio@de.ufpb.br>
Luiz Henrique Keng Queiroz Junior <keng@ufg.br>
Kleber Morais de Sousa <kleberfinancas@gmail.com>
Alejandro Quintela del Rio <aquintela@udc.es>
Thiago de Paula Oliveira <thiago.paula.oliveira@alumni.usp.br>
Danilo Roberti Alves de Almeida <daniloflorestas@gmail.com>
Jesús M. Rodríguez Rodríguez <jesusmro@ono.com>
Javier Royuela del Val <jroyval@lpi.tel.uva.es>
Rosineide Fernando da Paz <rfpaz2@gmail.com>
"Antoine Tremblay, Statistics Canada" <trea26@gmail.com>
Rune Haubo Bojesen Christensen <Rune.Haubo@gmail.com>
Vito M. R. Muggeo <vito.muggeo@unipa.it>
Jan van der Laan <djvanderlaan@unrealizedtime.nl>
"Robin K. S. Hankin" <hankin.robin@gmail.com>
Elizabeth Holmes - NOAA Federal <eli.holmes@noaa.gov>
Euloge C. Kenne Pagui <kenne@stat.unipd.it>
Fernando Ferraz do Nascimento <fernandofn@ufpi.edu.br>
Antonio Hermes M. da Silva-Junior <hermes@ccet.ufrn.br>
Manuel David Peris Diaz <manuel.perisdiaz@uwr.edu.pl>
Caspar J. van Lissa <c.j.vanlissa@gmail.com>
Alysha M De Livera <alyshad@unimelb.edu.au>
João Victor Gomes de Araujo Santana <jvg.santana@gmail.com>
Stephen L R Ellison <s.ellison@lgcgroup.com>
Héctor Manuel Sánchez Castellanos <sanchez.hmsc@berkeley.edu>
Bruno André Rodrigues coelho <bruno@brodrigues.co>
Krishna Harsha K H <khkrishnaharsha123@gmail.com>
Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>
L. Andries van der Ark <L.A.vanderArk@uva.nl>
Hannah De los Santos <hdelossantos653@gmail.com>
Sebastian J. Teran Hidalgo <sebastianteranhidalgo@gmail.com>
Eliot J B McIntire <eliot.mcintire@canada.ca>
T. R. dos Santos <thiagords@est.ufmg.br>
Julio Cesar Hernandez Sanchez <juliocesar_avila@usal.es>
Daiane Marcolino de Mattos <daiane.mattos@fgv.br>
José María Martínez Otzeta <josemaria.martinezo@ehu.eus>
Rune Haubo Bojesen Christensen <rune.haubo@gmail.com>
Joao Pedro Oliveira dos Santos <joaopsantos@pm.me>
Wouter van der Bijl <wouter@zoology.ubc.ca>
Euloge Clovis Kenne Pagui <kenne@stat.unipd.it>
Joaquin Bienvenido Ordieres Mere <j.ordieres@upm.es>
"Varhegyi, Nikole E. (nev4g)" <nev4g@virginia.edu>
Marieke van der Maaten-Theunissen <marieketheunissen@gmail.com>
Juan Pablo Ruiz Nicolini <juanpabloruiznicolini@gmail.com>
Gualberto Segundo Agamez Montalvo <gsagamez@gmail.com>
Juan Carlos Gonçalves Dosantos <juan.carlos.goncalves@udc.es>
Miguel Angelo Lellis Moreira <miguellellis@hotmail.com>
Blondeau Da Silva Stephane <blondeaudasilva@xlim.fr>
Robbie C.M. van Aert <R.C.M.vanAert@tilburguniversity.edu>
Peter J. van der Most <p.j.van.der.most@umcg.nl>
Wagner Santos de Lima <wagnersantos.ufs@hotmail.com>
"Shingo Yamamoto (gloops, Inc.)" <si.yamamoto@gloops.com>
Maria de los Angeles Resa <maria@stat.columbia.edu>
Achmad Fauzi Bagus F <uzi.fauz@gmail.com>
Manuel A. Mosquera Rodríguez <mamrguez@uvigo.es>
Pedro Mac Dowell Innecco <dmu@pedroinnecco.com>
Christian Alexander Mongeau Ospina <christian+rpkg-repec@mongeau.net>
Peter van den Berg <peter_v_d_berg@hotmail.com>
Sy Han (Steven) Chiou <schiou@utdallas.edu>
Manuel de Francisco Vera <manueldefrancisco@gmail.com>
Raymond K. W. Wong <raymondkww.dev@gmail.com>
Maria del Carmen Calatrava Moreno
<mc.calatrava.moreno@gmail.com>
Md Riaz Ahmed Khan <mdriazahmed.khan@jacks.sdstate.edu>
Pedro Rafael D. Marinho <pedro.rafael.marinho@gmail.com>
Manuel David Peris Diaz <madape@alumni.uv.es>
Mohammad Hadi Foroughmand Araabi <foroughmand@gmail.com>
Brazil Data Cube Team <brazildatacube@inpe.br>
Titus von der Malsburg <malsburg@posteo.de>
Rutger M. van den Bor <r.m.vandenbor@umcutrecht.nl>
Laercio Junio da Silva <laerciojdsilva@gmail.com>
Anderson Rodrigo da Silva <anderson.silva@ifgoiano.edu.br>
M. Yoga Satria Utama Developer <221709801@stis.ac.id>
Niels J. de Winter <niels.de.winter@vub.be>
Prof. Juan David Velasquez H. <jdvelasq@unal.edu.co>
Jose Manuel Vera Oteo <vera.josemanuel@gmail.com>
Lucas Roberto de Castro <lrcastro@estudante.ufla.br>
Willem Robert van Hage <willem.van.hage@synerscope.com>
Jonas Gregorio de Souza <jonas.gregorio@gmail.com>
Francisco Jesús Palomares Alabarce <fpalomares@correo.ugr.es>
Stephen A Sefick Jr. <ssefick@gmail.com>
Vinicius Quintas Souto Maior <vinicius@de.ufpe.br>
Daniel A. Dos Santos <pseudalopex_79@yahoo.com>
Jesus Maria Rodriguez Rodriguez <jesusmro@gmail.com>
Gabriel Henrique Oliveira Assuncao <gabrielhenryoliver@hotmail.com>
K. Gerald van den Boogaart <boogaart@math.tu-freiberg.de>
Silvestre Garcia de Jalon <s.garciadejalon@gmail.com>
Hafiz Zain Ul Haq <zainalibajwa4u@yahoo.com>
Antonio Fabio Di Narzo <antonio.fabio@gmail.com>
Dr. Ranjit Kumar Paul <ranjitstat@gmail.com>
Eraldo B. dos Anjos Filho <ebdaf1@de.ufpe.br>
Henrique Jose de Paula Alves <jpahenrique@gmail.com>
Luis D. Verde Arregoitia <luis@liomys.mx>
Oscar Alberto Quijano Xacur <oscar.quijano@use.startmail.com>
Angel Garcia de la Garza <agarciadlg@gmail.com>
"James P. Howard, II" <jh@jameshoward.us>
Giulio Valentino Dalla Riva <me@gvdallariva.net>
Joerg Schlarmann (aka Produnis) <schlarmann@produnis.de>
Olivier M. F. Martin <oliviermfmartin@tutanota.com>
Department of Mathematics and Statistics, University of
Agriculture Faisalabad, Faisalabad-Pakistan.
Package 'rjags' requires JAGS executabe file (compatiable
version) should be already installed.
Maintainers are not available to give advice on using a package
they did not author.
This version is a generalisation for (v=wnl) treatments. In the
version 1.0 we used rectangular right angular (m) association
schemes with (v=2nl) and m=4,5 and 7 associated classes. The
Association schemes used in this R-package are : Rectangular
association scheme; Generalized rectangular right angular
association scheme (4); Generalized rectangular right angular
association scheme (5); Generalized rectangular right angular
association scheme (7).
One minimum cost flow problem may have several or many solutions
that are equivalent in providing the same minimum total or mean
cost. Minor differences between computers or implementations
may have the minor consequence of altering which equivalent
solution is produced.
Supported by internal research project ING01-1516 from
'Universidad de Playa Ancha'
The author obtained financial resources as part of financing the
doctoral scholarship from the Polish National Science Centre
(DEC-2018/28/T/HS4/00095).
This publication was prepared for NCES under Contract No.
ED-IES-12-D-0002 with the American Institutes for Research.
Mention of trade names, commercial products, or organizations
does not imply endorsement by the U.S. Government.
Research funded by the Polish National Science Centre grant under
the contract number DEC-2015/19/N/HS4/00205.
The header file blaswrap.h, f2c.h and fgsg.h are from the
VisualStudio library created by Julie Langou.
Few parts are still preliminary and might be changed in the near
future. And more functions will be add as easier tools to
higher efficiency in analyzing.
While reporting issues on github start subject line with
[cran-package]
The authors are grateful to Mikhail Kanevski, Federico Amato and
Luciano Telesca for many fruitful discussions about the use and
the application of Fisher-Shannon method.
This software comes with NO warranty! It is NOT intended to be
used in clinical applications! For evaluation only!
The package is also based on the discussion
https://stats.stackexchange.com/questions/168964/building-a-regression-tree-with-r-from-scratch/168967#168967
research product of the RISCOPE project (ANR, project
No.16CE04-0011) <https://perso.math.univ-toulouse.fr/riscope/>.
Department of Genetics and Plant Breeding, University of
Agricultural Sciecnes, Dharwad.
Package 'R2jags' requires JAGS executable file installed
The authors are grateful to Mikhail Kanevski, Michael
Leuenberger, Carmen D. Vega Orozco and Fabian Guignard for many
fruitful discussions about the use of intrinsic dimension in
data mining.
Please, cite this package as: Marina Saez (2021). KarsTS: An
Interface For Microclimate Time Series Analysis. R package
version 2.4.1.
Department of Statistics, Bahauddin Zakariya University, Multan,
Pakistan.
Department of Statistics, Bahauddin Zakariya University, Multan,
Pakistan
The originale code was in matlab, see details below.
The developer version of 'keras' should be used, rather than the
CRAN version. The latter will cause tests to fail on an initial
run, but work on subsequent tries. To avoid this, use
devtools::install_github("rstudio/keras"). The user also must
have an installation of 'Python 3'.
the current version of the library has been developed as part of
the European Union's Horizon 2020 research and innovation
programme under grant agreement No. 727040 (Virt-EU).
For convenience, the package includes the necessary header files
for the Eigen distribution. (This is all that is needed to use
that functionality.) You can use an alternative installation of
Eigen on your system or the one we provide. The license for the
Eigen code is very permissive and allows us to distribute it
with this package. See <http://eigen.tuxfamily.org/index.php?
title=Main_Page> and also the License section on that page.
The current version (0.4.2) fixes a numerical issue with
symmetric implementation of the paco_links function.
In order to use this package you need your personal Project Vote
Smart API key. To get an API-key you need to sign up for access
to PVS' API (see http://votesmart.org/share/api for details).
Whenever you are using pvsR make sure that your personal PVS
API key is saved as a character string in the variable pvs.key
(pvs.key <- "yourkey"). If there is no valid PVS API key saved
in the variable pvs.key the functions in this package won't
work. This program is free software; you can redistribute it
and/or modify it under the terms of the GNU General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later
version. This program is distributed in the hope that it will
be useful, but WITHOUT ANY WARRANTY; without even the implied
warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the GNU General Public License for more details.
More information about the system requirements can be found in
the README file.
For details and derivation, see Braumoeller, Bear F. "Guarding
Against False Positives in Qualitative Comparative Analysis."
Forthcoming, Political Analysis.
Package is in active development; please report errors and
suggestions to rchlumsk@uwaterloo.ca.
NOTICE regarding the transfer of data from Retrosheet: The
information used here was obtained free of charge from and is
copyrighted by Retrosheet. Interested parties may contact
Retrosheet at "www.retrosheet.org".
See http://www.json.org/JSON_checker/test.zip for tests. We now
use code from the libjson project
(http://libjson.sourceforge.net).
The name "Scrabble" is a trademark of Hasbro, Inc. in the United
States and Canada; elsewhere, it is a trademark of Mattel.
The development of this package was supported by Carlos
Jaramillo, Center for Tropical Paleoecology and Archaeology at
Smithsonian Tropical Research Institute.
This publication was prepared for NCES under Contract No.
ED-IES-12-D-0009/0005 with Sanametrix and Westat. Mention of
trade names, commercial products, or organizations does not
imply endorsement by the U.S. Government.
The GPU computing version can be found soon, on following url
https://sites.google.com/site/mohamedlaibwebpage/Software.
revised for compliance with CRAN by K.Pal and C.M.Livi
The author acknowledges financial support from Sao Paulo Research
Foundation (FAPESP) grant 2016/18599-4
This is experimental software distributed free of charge and
comes with no warranty!  Exercise professional caution.
Package TSE works directly from the data set – no hand
calculations required.  Just upload a properly structured data
set (see TESTNUMB and its documentation), properly input column
names (see examples in the functions documentation), and run
your functions.
'TSEind' is a companion package to 'TSE'. Both calculate TSE for
your surveys, but use 'TSEind' if your surveys and the "gold
standard" survey have independent samples, and use 'TSE' if
your surveys and the "gold standard" survey have paired
samples.
'TSEwgt' is a companion package to 'TSE'. Each package calculates
TSE, but the former for multiple, different surveys, and the
latter for a single survey under multiple, different weighting
schemes.
This publication was prepared for NCES under Contract No.
ED-IES-12-D-0002 with American Institutes for Research. Mention
of trade names, commercial products, or organizations does not
imply endorsement by the U.S. government.
2018-03-13 21:10:22 UTC; Steven Harris Ranney
2020-09-22 06:18:07 UTC; Benjamin Schlegel
2012-06-11 14:36:21 UTC; Sophie Baillargeon
2021-01-04 09:56:11 UTC; Christian Blötner
2010-01-31 13:29:31 UTC; Jens Henrik Badsberg
2021-01-06 15:27:44 UTC; Sebastian Weirich
2020-02-13 05:58:54 UTC; Michael Kellermann
2018-05-10 17:12:26 UTC; Virasakdi's Surface
2020-07-14 07:43:10 UTC; Bernardo Sousa Pinto
2020-01-21 06:35:23 UTC; Md. Tofazzal Hossain
2018-10-24 16:05:44 UTC; Ashutosh Srivastava
2015-02-26 17:45:29 UTC; Sophie Baillargeon
2015-08-23 02:08:23 UTC; Fernando de Villar
2021-01-21 19:20:08 UTC; Christian Blötner
2020-08-24 13:32:49 UTC; Eleanor Pullenayegum
2020-04-22 19:29:14 UTC; Sebastian Schneider
2020-01-08 09:11:00 UTC; Nadezda Spiridovska
2021-01-04 14:56:17 UTC; Ilias Moutsopoulos
2018-04-29 13:45:20 UTC; Alberto Vico Moreno
2020-08-23 18:34:41 UTC; Gonzalo Vazquez-Bare
2020-12-30 19:05:48 UTC; Gonzalo Vazquez-Bare
2020-12-17 23:27:40 UTC; Gonzalo Vazquez-Bare
2017-01-03 15:34:03 UTC; Guybrush Threepwood
2019-05-02 03:37:50 UTC; hernandez michael
2018-12-13 11:53:36 UTC; Pedro Albuquerque
2020-05-07 11:07:40 UTC; Kanhaiiya Agrawal
2020-06-08 13:17:19 UTC; Kanhaiiya Agrawal
2018-06-05 15:09:00 UTC; Daniel Lewandowski
2019-08-02 17:03:10 UTC; Bernardo Sousa Pinto
2017-08-15 05:32:43 UTC; Aurnov Chattopadhyay
2016-03-19 23:54:53 UTC; Sophie Baillargeon
Image Magick (for reading non PPM format), dcraw
(for reading RAW images).
ADMIXTOOLS suite of command-line utilities for
population genetics. See
<https://reich.hms.harvard.edu/software> for the most recent
installation instructions and further information.
Alfresco Content Repository (Community or
Enterprise)
Python (>= 3.5.0), (Python) Altair (>= 4.0.0). To
use image functions, i.e. suggests: nodejs (> 8), and for
MacOS: X11
None, but greater than 12 GB of RAM highly
recommended.
ImageMagick (http://imagemagick.org) or
GraphicsMagick (http://www.graphicsmagick.org) or LyX
(http://www.lyx.org) for saveGIF(); (PDF)LaTeX for saveLatex();
SWF Tools (http://swftools.org) for saveSWF(); FFmpeg
(http://ffmpeg.org) or avconv (https://libav.org/avconv.html)
for saveVideo()
The exact (anti)clustering algorithms require that
the GNU linear programming kit (GLPK library) is installed
(<http://www.gnu.org/software/glpk/>). Rendering the vignette
requires pandoc.
C++11; for AWS S3 support on Linux, libcurl and
openssl (optional)
FFmpeg (>= 3.2); with at least libx264 and lame
(mp3) drivers. Debian/Ubuntu: libavfilter-dev, Fedora/CentOS:
ffmpeg-devel (via https://rpmfusion.org), MacOS Homebrew:
ffmpeg.
JAGS (>= 3.4.0) (see
http://mcmc-jags.sourceforge.net)
GNU make, Cargo (>= 1.42.0) [the Rust package
manager] for installation from sources: see file INSTALL
Rtools (>= 3.3) for Windows, Xcode (>= 9.0) for Mac
OS X
Preferred genomic operations engine: 'BEDTools',
'BEDOPS' and 'Tabix (>= 1.3)'.
JAGS >=4.3.0 <http://mcmc-jags.sourceforge.net/>,
Java JDK >=1.4 <https://www.java.com/en/download/manual.jsp>
Package 'bigsnpr' includes a few functions that
wrap existing software such as 'PLINK'
<www.cog-genomics.org/plink2>. Functions are provided to
download these software. Note that these external software
might not work for some operating systems (e.g. 'PLINK' might
not work on Solaris).
A system with a recent-enough C++11 compiler (such
as g++-4.8 or later).
Hugo (<https://gohugo.io>) and Pandoc
(<https://pandoc.org>)
OpenBUGS (>= 3.2.2), hence Windows or Linux
MAGeCK (=0.51, from
http://sourceforge.net/p/mageck/wiki/Home/), bowtie2
(http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
Python and TensorFlow are needed for Bayesian
inference computations; Python (>= 2.7.0) with header files and
shared library; TensorFlow (= v1.14;
https://www.tensorflow.org/); TensorFlow Probability (= v0.7.0;
https://www.tensorflow.org/probability/)
xclip (https://github.com/astrand/xclip) or xsel
(http://www.vergenet.net/~conrad/software/xsel/) for accessing
the X11 clipboard
libarmadillo: apt-get install -y libarmadillo-dev
(deb), libblas: apt-get install -y libblas-dev (deb),
liblapack: apt-get install -y liblapack-dev (deb),
libarpack++2: apt-get install -y libarpack++2-dev (deb),
gfortran: apt-get install -y gfortran (deb), libgmp3: apt-get
install -y libgmp3-dev (deb), libfftw3: apt-get install -y
libfftw3-dev (deb), libtiff5: apt-get install -y libtiff5-dev
(deb)
libcurl: libcurl-devel (rpm) or
libcurl4-openssl-dev (deb).
ImageMagick++: ImageMagick-c++-devel (rpm) or
libmagick++-dev (deb)
Julia (>= 0.6.0), Convex.jl, SCS.jl, ECOS.jl
pdfcrop (part of TexLive) is required to rebuild
the vignettes.
Java (>= 7.0); Stanford CoreNLP
<http://nlp.stanford.edu/ software/corenlp.shtml> (>= 3.5.2)
couchDB instance to connect to and work with.
pandoc (>= 2.0; https://pandoc.org), git, whoami
none, one or more of JAGS (>= 3.0.0), WinBUGS (>=
1.4), OpenBUGS (>= 3.2.2), Stan
NVIDIA CUDA GPU with compute capability 3.0 or
above and NVIDIA CUDA Toolkit 9.0 or above
GLPK library package (e.g., libglpk-dev on
Debian/Ubuntu)
FreeType, Xft, or zlib (only needed for platforms
other than OSX and Windows)
Julia (>= 1.5), DifferentialEquations.jl,
ModelingToolkit.jl
libpq >= 9.0: libpq-dev (deb) or postgresql-devel
(rpm)
LibreOffice (<https://www.libreoffice.org/>)
required to extract data from .doc files or perform .pptx
conversion.
Requires the OpenMP library for parallel computing.
If the OpenMP library is not available, the code is executed
sequentially and a warning is printed.
Python (>= 2.7 or >= 3.5) and elex package
EnergyPlus (>= 8.3, optional)
(<https://energyplus.net>); udunits2
fftw3 (libfftw3-dev (deb), or fftw-devel (rpm))
Display resolution >= 1280x800; RAM >= 4GB
libarmadillo: apt-get install -y libarmadillo-dev
(deb), libblas: apt-get install -y libblas-dev (deb),
liblapack: apt-get install -y liblapack-dev (deb),
libarpack++2: apt-get install -y libarpack++2-dev (deb),
gfortran: apt-get install -y gfortran (deb)
GNU Scientific Library (GSL). Note: users should
have GSL installed.
(license-free) MATLAB Runtime (MCR) V 9.6, Java
(>=8)
Python (>= 2.4), difflib, fuzzywuzzy ( >=0.15.0 ),
python-Levenshtein ( >=0.12.0 ). Detailed installation
instructions for each operating system can be found in the
README file.
Debian or Ubuntu system with access to Goto Blas,
Intel MKL, Atlas development build as well as a Nvidia GPU with
CUDA support
C++11, pandoc (>=1.12.3, needed for vignettes)
The SequenomMarkers() marker design function
requires 'vcftools' and 'Perl' on 'windows', and, in addition,
'awk' and 'bash' on '*nix'.
MongoDB (>= 3.4.0), Python (>= 2.7). Installation
instructions and links can be found in the README file.
libgit2 (>= 0.26): libgit2-devel (rpm) or
libgit2-dev (deb). A PPA is available for older Ubuntu LTS
versions.
By default, git2r uses a system installation of the
libgit2 headers and library. However, if a system installation
is not available, builds and uses a bundled version of the
libgit2 source. zlib headers and library. OpenSSL headers and
library (non-macOS). LibSSH2 (optional on non-Windows) to
enable the SSH transport.
GPGME: libgpgme-dev / libgpgme11-dev (deb),
gpgme-devel (rpm) gpgme (brew). On Linux 'haveged' is
recommended for generating entropy when using the GPG key
generator.
Python (>= 2.7.0) with header files and shared
library; TensorFlow (v1.14; https://www.tensorflow.org/);
TensorFlow Probability (v0.7.0;
https://www.tensorflow.org/probability/)
Python (>= 3.6) with header files and shared
library; H2O4GPU (https://github.com/h2oai/h2o4gpu)
Apache Hadoop >= 2.7.2
(https://hadoop.apache.org/releases.html#Download); Obsolete:
Hadoop core >= 0.19.1 and <= 1.0.3 or CDH3
(https://www.cloudera.com); standard unix tools (e.g., chmod)
LaTeX packages: adjustbox, array, calc, caption,
colortbl, fontspec, graphicx, hhline, hyperref, multirow,
siunitx, tabularx, threeparttable, ulem, wrapfig
Julia (>= 1.0) and Interpretable AI System Image
(>= 1.0.0)
ImageMagick (http://imagemagick.org) or
GraphicsMagick (http://www.graphicsmagick.org)
A C library with the fesetround/fegetround
functions.
gmp (optional), libxml2 (optional), glpk (optional)
C++11 and OpenCV 3 or newer: libopencv-dev (Debian,
Ubuntu) or opencv-devel (Fedora)
Impala driver to support a 'DBI'-compatible R
interface
pandoc (https://pandoc.org/) and phantomjs
(https://phantomjs.org/)
jupyter, jupyter_kernel_test (Python package for
testing)
libjq: jq-devel (rpm) or libjq-dev (deb)
Optional: libsecret on Linux (libsecret-1-dev on
Debian/Ubuntu, libsecret-devel on Fedora/CentOS)
MOSEK (http://www.mosek.com) and MOSEK license.
CUDA 8.0 tookit, OpenMP 4.0 capable compiler
Package vignettes based on R Markdown v2 or
reStructuredText require Pandoc (http://pandoc.org). The
function rst2pdf() require rst2pdf
(https://github.com/rst2pdf/rst2pdf).
procps (linux), ps (macos), wmic (windows)
ImageJ (>=1.48), ij.jar (see
http://imagej.nih.gov/ij/), Java (>=1.6.0)
libxml2: libxml2-dev (deb), libxml2-devel (rpm)
JAGS (>= 3.0.0) (see
http://mcmc-jags.sourceforge.net)
At least trial version of LocalSolver to be
downloaded from http://www.localsolver.com/download.html
A system with zoneinfo data (e.g.
/usr/share/zoneinfo) as well as a recent-enough C++11 compiler
(such as g++-4.8 or later). On Windows the zoneinfo included
with R is used.
Python 3.x with following modules: PyGMO, NumPy,
and cloudpickle
ADMB version 11 <http://admb-project.org/> for
use.admb=TRUE; see readme.txt
On a Unix-alike, one of the C functions
mach_absolute_time (macOS), clock_gettime or gethrtime. If none
of these is found, the obsolescent POSIX function gettimeofday
will be tried.
memory (>= 4GB) Ubuntu: build-essential,
libxml2-dev, libssl-dev, libcurl4-openssl-dev Windows: Rtools
(>= 3.5)
TensorFlow (https://www.tensorflow.org), Keras
(https://keras.io), TensorFlow Probability
(https://www.tensorflow.org/probability)
Apache Spark 2.0+, Apache Maven 3.5+, Java JDK 8,
MLeap Runtime 0.10.1+
A C++11 compiler. Versions 4.8.*, 4.9.* or later of
GCC will be fine.
gdal (optional), geos (optional), proj (optional),
udunits (optional), gsl (optional), gmp (optional), glu
(optional), jags (optional)
JAGS (>= 4.0.0) (see
http://mcmc-jags.sourceforge.net)
libcurl: libcurl-devel (rpm) or
libcurl4-openssl-dev (deb)
A valid account MUST be registered with Microsoft's
Cognitive Services website
<https://www.microsoft.com/cognitive-services/> in order to
obtain a (free) API key. Without an API key, this package will
not work properly.
pandoc, jupyter, jupyter nbconvert ("nbconvert"
python package), pywin32 (on windows)
neo4j - http://www.neo4j.com, cypher-shell -
https://github.com/neo4j/cypher-shell/releases
Python (>= 3.0.0), Neptune (https://neptune.ai/)
A compiler with C++11 support for the thread
library, Requires Rtools >= 33 (i.e. R >= 3.3.0) to build on
Windows.
A system installation of NLopt >= 2.4.0 (with
headers) will be used if available.
NetLogo (>= 5.3.1), Java (JDK 1.8), pandoc,
OpenSSL, udunits-2, PROJ.4, GEOS, GDAL, libxml2
Python (>= 2.7), nmslib ( >= 1.7.1), scipy ( >=
1.0.0), numpy ( >= 1.14.0). Detailed installation instructions
for each operating system can be found in the README file.
JAGS (http://mcmc-jags.sourceforge.net/) for
analysis of Bayesian hierarchical models
PhantomJS (http://phantomjs.org) for taking
screenshots
C++11, GNU make, An ODBC3 driver manager and
drivers.
GNU make, pandoc (>= 1.12.3), pandoc-citeproc
OpenCV 3 or newer: libopencv-dev (Debian, Ubuntu)
or opencv-devel (Fedora)
libarmadillo: apt-get install -y libarmadillo-dev
(deb), libblas: apt-get install -y libblas-dev (deb),
liblapack: apt-get install -y liblapack-dev (deb),
libarpack++2: apt-get install -y libarpack++2-dev (deb),
gfortran: apt-get install -y gfortran (deb), libjpeg-dev:
apt-get install -y libjpeg-dev (deb), libpng-dev: apt-get
install -y libpng-dev (deb), libfftw3-dev: apt-get install -y
libfftw3-dev (deb), libtiff5-dev: apt-get install -y
libtiff5-dev (deb)
To use the Localhost of OSRM, you need to build
OSRM
<https://github.com/Project-OSRM/osrm-backend/wiki/Building-OSRM>
locally
Python (>= 3.0.1); bencode-python3 (1.0.2)
pandoc (http://johnmacfarlane.net/pandoc) for
exporting markdown files to other formats.
For the MERLIN wrapper, MERLIN
(http://csg.sph.umich.edu/abecasis/Merlin/) must be installed
and pointed to in the PATH environment variable.
The 'Japanese.Rnw' vignette requires uplatex and
dvipdfmx.
OpenMPI (>= 1.5.4) on Solaris, Linux, Mac, and
FreeBSD. MS-MPI (Microsoft HPC Pack 2012) or MPICH2 (>=
1.4.1p1) on Windows.
OpenMPI (>= 1.5.4) on Solaris, Linux, Mac, and
FreeBSD. MS-MPI (Microsoft MPI v7.1 (SDK) and Microsoft HPC
Pack 2012 R2 MS-MPI Redistributable Package) on Windows.
OpenMPI (>= 1.5.4) on Solaris, Linux, Mac, and
FreeBSD. No MPI library required on Windows yet.
ssh (OpenSSH) or plink (PuTTY) on Solaris, Linux,
and Mac.
'OpenMPI' (>= 1.5.4) on Solaris, Linux, Mac, and
FreeBSD. 'MS-MPI' (Microsoft HPC Pack 2012 R2 MS-MPI
Redistributable Package) on Windows.
Linux, Mac OSX, and Windows, or 'ZeroMQ' library >=
4.0.4. Solaris 10 needs 'ZeroMQ' library 4.0.7 and 'OpenCSW'.
'Microsoft' 'PowerShell'
(<https://docs.microsoft.com/en-us/powershell/>), 'Microsoft'
'Power BI' (<https://powerbi.microsoft.com>)
Poppler C++ API: libpoppler-cpp-dev (deb) or
poppler-cpp-devel (rpm). The unit tests also require the
'poppler-data' package (rpm/deb)
Phoenix NLME with Phoenix Modeling Language (PML)
license
OpenSSL library and headers (openssl-dev or
similar)
For Windows users, Rtools (see
https://cran.r-project.org/bin/windows/Rtools/).
pandoc (>= 1.12.3) -
http://johnmacfarlane.net/pandoc
JAGS (>= 3.2.0) (see
http://mcmc-jags.sourceforge.net)
A POSIX system. Currently Linux and OS X are known
to work. GNU make.
proj 4.4.6 or higher (http://proj.maptools.org/)
pandoc (http://pandoc.org) for building Vignettes
and output reports as HTML
'python3' needs to built for the same architecture
R is built for (32 or 64 bit).
Python (>= 2.7.0) with header files and shared
library (UNIX) / static library (Windows)
OpenBugs for functions bugs() and openbugs() or
WinBUGS 1.4 for function bugs()
C++11, freetype2, libpng, libtiff, libjpeg
python >= 2.6, by default rasciidoc uses a system
installation of asciidoc. If a system installation of asciidoc
is not available, it downloads the sources from
(<http://gitlab.com/asciidoc>). GNU source-highlight is
recommended.
Java JRE 1.6 or higher ; Xuggle-xuggler-5.4.jar in
library paths and class paths.
A valid Bloomberg installation. The API headers and
dynamic library are downloaded from
<https://github.com/Rblp/blp> during the build step. See
<https://bloomberg.github.io/blpapi-docs/cpp/3.8> as well as
<https://www.bloomberg.com/professional/support/api-library/>
for API documentation. A compiler recent enough for (at least
partial) C++11 support is required; g++-4.6.* or later should
be sufficient and g++-4.9.* or later is preferred.
MOSEK (http://www.mosek.com) and MOSEK License for
use of Rmosek,
GMP (GNU MP bignum library from
<http://gmplib.org/>)
A 64-bit POSIX OS such as Linux or OS X with IANA
time zone data in /usr/share/zoneinfo as well as a
recent-enough C++11 compiler (such as g++-4.9 or later which is
preferred, g++-4.8 works too). On Windows the zoneinfo included
with R is used; and time parsing support is enabled via a
backport of std::get_time from the LLVM libc++ library.
GNU make, ncurses, pcre (>= 7 < 10), GLib (>=
2.0.0). On Windows, no prior installations are necessary, as
pre-built (i.e. cross-compiled) binaries of required libraries
are downloaded from a GitHub repository
(<https://github.com/PolMine/libcl>) during installation. On
macOS, static libraries of Glib are downloaded
(<https://github.com/PolMine/libglib>) if Glib is not present.
A POSIX system. Currently Linux and OS X are known
to work.
MeCab 0.996 (or mecab-ko 0.9.2) or higher, GNU make
GNU make, Windows: cmd.exe and cscript.exe,
Solaris: g++ is required
An available hiredis library (eg via package
libhiredis-dev on Debian/Ubuntu, hiredis-devel on
Fedora/RedHat, or directly from source from
<https://github.com/redis/hiredis>) is preferred but otherwise
built on demand.
A C++11 compiler; g++ (>= 4.9.*) or newer works.
Python (>= 3.0), retriever (>= 3.0.0) (version must
be listed to patch to allow parsing)
GNU GSL for the GSL random-number generators
mono 4.x or higher on OSX / Linux, .NET 4.x or
higher on Windows, 'msbuild' and 'nuget' available in the path
Subversion for install_svn, git for install_git
Presentations written in (R)Markdown require Pandoc
(http://pandoc.org).
'unrar' (Linux/macOS) or '7-Zip' (Windows) to work
with '.rar' files.
PROJ (>= 4.8.0, https://proj.org/download.html) and
GDAL (>= 1.11.4, https://gdal.org/download.html), with versions
either (A) PROJ < 6 and GDAL < 3 or (B) PROJ >= 6 and GDAL >=
3. For degraded PROJ >= 6 and GDAL < 3, use the configure
argument '--with-proj_api="proj_api.h"'.
GEOS (>= 3.2.0); for building from source: GEOS
from http://trac.osgeo.org/geos/; GEOS OSX frameworks built by
William Kyngesburye at http://www.kyngchaos.com/ may be used
for source installs on OSX.
Python (2.7 or >= 3.4), rgf_python, scikit-learn
(>= 0.18.0), scipy, numpy. Detailed installation instructions
for each operating system can be found in the README file.
OpenGL, GLU Library, XQuartz (on OSX), zlib
(optional), libpng (>=1.2.9, optional), FreeType (optional),
pandoc (>=1.14, needed for vignettes)
R built as a shared or static library, 'MPI'
library.
Java JDK 1.2 or higher (for JRI/REngine JDK 1.4 or
higher), GNU make
Oracle Java 7,Apache Kafka 2.8.0-0.8.1.1
C++11, cmake (>= 3.10), clang (optional), CUDA
(optional but recommended)
libmariadb-client-lgpl-dev or libmariadbclient-dev
or libmysqlclient-dev, with libssl-dev (deb),
mariadb-connector-c-devel or mariadb-devel (rpm),
mariadb-connector-c or mysql-connector-c (brew)
notepad.exe, mark.exe (>= 8.0) (or mark32.exe and
mark64.exe) and rel_32.exe (see README.txt)
pandoc (>=1.14, needed for the vignette)
libmariadb-client-dev | libmariadb-client-lgpl-dev
| libmysqlclient-dev (deb), mariadb-devel (rpm), mariadb |
mysql-connector-c (brew), mysql56_dev (csw)
The tools to run 'R CMD SHLIB' on 'Fortran' code.
The used 'Fortran' compiler must support pointer initialization
which is a feature of the 2008 standard. The compiler from
Oracle Developer Studio 12.6 on Solaris 10 currently does not
meet this requirement.
GNU Make, GCC Compiler Suite (C and Fortran)
Oracle Instant Client or Oracle Database Client
Poppler Glib interface headers and libraries
(<http://poppler.freedesktop.org/>) [Debian/Ubuntu:
libpoppler-glib-dev, Fedora: poppler-glib-devel]
C++11, GNU make, Windows: cmd.exe and cscript.exe
ProtoBuf libraries and compiler version 2.2.0 or
later; version 3.0.0 or later is supported as well. On
Debian/Ubuntu these can be installed as libprotoc-dev,
libprotobuf-dev and protobuf-compiler, while on Fedora/CentOS
protobuf-devel and protobuf-compiler are needed.
A user API key (which one can request from the
website at <http://www.pushbullet.com>), and one or more
devices to push messages to which may be any one of an (Android
or iOS) phone, a (Chrome or Firefox, or Opera or Safari)
browser or the (Windows or Mac) desktop application provided
the corresponding Pushbullet 'app' has been installed on any
one of these.
QuantLib library (>= 1.14) from
http://quantlib.org, Boost library from http://www.boost.org
The package depends on libraries from the RRD
project <http://oss.oetiker.ch/rrdtool/>. On Debian-based
systems, install 'librrd-dev', on CentOS based systems install
'rrdtool-devel', and on Fedora-based systems install
'rrdtool-devel'
<https://apps.fedoraproject.org/packages/rrdtool-devel>. For
more information, see the README.
need the RDRAND instruction on Intel CPU. and C
compiler must be able to compile a GNU-style in-line assembler.
Tcl/Tk (>= 8.5), Tktable (>= 2.9, optional)
"conda (python>=3.6 pytorch torchvision cpuonly
numpy ( >= 1.14.0) matplotlib pandas -c pytorch);
python-minimal, pandoc pandoc-citeproc, qpdf; Python (>=3.6),
pytorch (>=1.4), torchvision, cpuonly, numpy ( >= 1.14.0);
pandoc (>= 2.0), qpdf ( >= 7.0) on Solaris"
Python (>= 2.7); keras <https://keras.io/> (>= 2.1)
The Boost 'program_options' library
<https://boost.org> is required.
Python (>=2.6) in path and NumPy module installed,
ghostscript (>=9.0)
ZeroMQ >= 3.0.0: libzmq3-dev (deb) or zeromq-devel
(rpm)
Cargo (>= 1.40.0) for installation from sources:
see file INSTALL
GLPK library, including -dev or -devel part
Java (>= 8) and maxent.jar >= 3.4.1 to use Maxent
GDAL (>= 2.1.2), PROJ (>= 4.9.1), GEOS (>= 3.4.2),
Cairo, Curl, NetCDF, jq, Protocol Buffers, V8, OpenSSL,
Libxml2.
C++11, zlib headers and libraries, GNU make,
optionally also bzip2 and POSIX-compliant regex functions.
TensorFlow (https://www.tensorflow.org/),
TensorFlow Probability
(https://www.tensorflow.org/probability/)
(PDF)LaTeX (https://www.latex-project.org/) with
'pdfpages' package for studentGrowthPlot option in visualizeSGP
to bind together student growth plots into school catalogs
For playing sounds, a command line system tool for
playing wav-files is required.
Python (>=3.5.2) and the following python module:
nmrglue.
libssh >= 0.6.0 (the original, not libssh2)
Komodo Edit (http://www.openkomodo.com), SciViews-K
(http://www.sciviews.org/SciViews-K)
c("C++11", "\n fontconfig", "\n freetype2"), C++11
LilyPond (Only needed for rendering sheet music or
writing MIDI files)
Tesseract >= 3.03 (libtesseract-dev /
tesseract-devel) and Leptonica (libleptonica-dev /
leptonica-devel). On Debian you need to install the English
training data separately (tesseract-ocr-eng)
C++11, A modern compiler (>=gcc-4.9), And latexmk
is necessary to compile all output documents with the functions
provided by this package
pandoc (>= 1.12.3) suggested for using wordreg
function; LaTeX packages tikz, booktabs, dcolumn, rotating,
thumbpdf, longtable, paralist for the vignette
TensorFlow >= 1.13.0 (https://www.tensorflow.org/)
and TensorFlow IO >= 0.4.0 (https://github.com/tensorflow/io)
PhantomJS (https://phantomjs.org), pandoc (>=
1.12.3) - https://pandoc.org.
cmake (only when TileDB source build selected), git
(only when TileDB source build selected); on x86_64 platforms
pre-built TileDB Embedded libraries are available at GitHub and
are used if no TileDB installation is detected, and no other
option to build or download was specified by by the user.
Python (>= 2.7), python-gdal library (For Windows,
gdal installed via OSGeo4W <https://trac.osgeo.org/osgeo4w/>
recommended) clipboard
GNU Scientific Library version >= 1.8, C++11
under Linux, fftwtools needs libfftw3-dev
PARI/GP >= 2.3.0 [strongly recommended for
logkda()]
V8 engine version 6+ is needed for modern JS and
WASM support. On Debian / Ubuntu install either libv8-dev or
libnode-dev, on Fedora use v8-devel. The readme has
instructions for installing backports on Ubuntu Xenial and
Bionic. It is still possible to build this package against the
legacy libv8 version 3.14 branch, but these engines only
support traditional JavaScript (ES5).
To use image and spec-compilation functions, i.e.
suggests: nodejs (> 8), and for MacOS: X11
virtuoso-opensource (Linux). For Mac & Windows,
this package can automate Virtuoso installation.
PhantomJS (http://phantomjs.org) for taking
screenshots, ImageMagick (http://www.imagemagick.org) or
GraphicsMagick (http://www.graphicsmagick.org) and OptiPNG
(http://optipng.sourceforge.net) for manipulating images.
Java (>= 5.0); WordNet database files (direct
download:
<https://wordnetcode.princeton.edu/3.0/WNdb-3.0.tar.gz>; Debian
and Fedora package: wordnet)
Perl (>= 5.0), Unitex (>= 3.0
http://www-igm.univ-mlv.fr/~unitex/)
The standalone program xgobi must be installed
additionally, see file README, or INSTALL.windows under Windows
libxslt: libxslt1-dev (deb), libxslt-devel (rpm)
Accurate, Adaptable, and Accessible Error Metrics for Predictive
Models
Reliability and Scoring Routines for the Approach-Avoidance Task
Apps Based Activities for Communicating and Understanding
Statistics
Access to Abbyy Optical Character Recognition (OCR) API
Tools for Approximate Bayesian Computation (ABC)
Data Only: Tools for Approximate Bayesian Computation (ABC)
Array Based CpG Region Analysis Pipeline
Fit Accumulated Damage Models and Estimate Reliability using ABC
ABCDE_FBA: A-Biologist-Can-Do-Everything of Flux Balance
Analysis with this package
Implementation of Artificial Bee Colony (ABC) Optimization
Approximate Bayesian Computational Model for Estimating P2
Approximate Bayesian Computation via Random Forests
Asymptotically Bias-Corrected Regularized Linear Discriminant
Analysis
Useful Tools for Jurimetrical Analysis Used by the Brazilian
Jurimetrics Association
Measure a Subject's Abnormality with Respect to a Reference
Population
The Abnormal Blood Profile Score to Detect Blood Doping
Time Resolved Simulations of Antibody Repertoires
An R-Shiny Application for Creating Visual Abstracts
Inferring Directional Conservative Causal Core Gene Networks
Abrupt Change-Point or Aberration Detection in Point Series
Functions for Processing Accelerometer Data
Missing Value Imputation for Accelerometer Data
The Acute COPD Exacerbation Prediction Tool (ACCEPT)
Creation and Evaluation of Acceptance Sampling Plans
Tools for Autoregressive Conditional Duration Models
Optimal Bayesian Experimental Design using the ACE Algorithm
ACE and AVAS for Selecting Multiple Regression Transformations
Estimation of Dynamic Heritability and Comparison of Twin Models
Robust Estimation of the ACF from the M-Periodogram
Automated Retrieval of ACLED Conflict Event Data
Implements ACME Estimator of Bird and Bat Mortality by Wind
Turbines
Affymetrix SNP Probe-Summarization using Non-Negative Matrix
Factorization
Modelling Dependence with Multivariate Archimax (or any
User-Defined Continuous) Copulas
Convenience functions for analytical Customer Relationship
Management
A Cost-Minimal Regular Spanning Subgraph with TreeClust
Download, Manipulate, and Present American Community Survey and
Decennial Data from the US Census
Gene Enrichment Analysis from ACSN Maps or GMT Files
Algorithmic Complexity for Short Strings
Data Only: Algorithmic Complexity of Short Strings (Computed via
Coding Theorem Method)
A Companion Package for the Book "A Course in Statistics with R"
Asymptotic Classification Theory for Cognitive Diagnosis
Extract Circadian Rhythms Metrics from Actigraphy Data
Activity Fragmentation Metrics Extracted from Minute Level
Activity Data
Utilities for Parsing and Plotting Activities
Finding Cancer Driver Proteins with Enriched Mutations in
Post-Translational Modification Sites
A Driver Discovery Tool for Cancer Whole Genomes
Gaussian Process Based Design and Analysis for the Active
Subspace Method
Integrative Pathway Enrichment Analysis of Multivariate Omics
Data
Activity Index Calculation using Raw 'Accelerometry' Data
Advanced Processing and Chart Generation from activPAL Events
Files
Read in Activity Data and Plot Actograms
Actuarial Functions and Heavy Tailed Distributions
A Package for Displaying Visual Scenes as They May Appear to an
Animal with Lower Acuity
The R Package Ada for Stochastic Boosting
Applies Multiclass AdaBoost.M1, SAMME and Bagging
Discrete and Global Optimization Routines
Archetypoid Algorithms and Anomaly Detection
A Class of Adaptive Elastic Net Methods for Censored Data
Adaptive Approaches for Signal Detection in Pharmacovigilance
Adaptive Semiparametric Additive Regression with Simultaneous
Confidence Bands and Specification Tests
Implementation of a Generic Adaptive Monte Carlo Markov Chain
Sampler
Adaptive P-Value Thresholding for Multiple Hypothesis Testing
with Side Information
Automated Deconvolution Augmentation of Profiles for Tissue
Specific Cells
Adaptive Sampling for Positive Unlabeled and Label Noise
Learning
Binomial and Multinomial Additive Hazard Models
Fit Additive Hazards Models for Survival Analysis
Discover and Install Useful RStudio Addins
'RStudio' Addins for Show Outline of a R Markdown/'LaTeX'
Project
Additive Data Envelopment Analysis Models
Additivity Tests in the Two Way Anova with Single Sub-class
Numbers
Adds Labeled Center Line and Scale Lines/Regions to Trellis
Plots
Analysis of Accelerated Destructive Degradation Test Data
Analysis of Ecological Data: Exploratory and Euclidean Methods
in Environmental Sciences
Exploratory Analysis of Genetic and Genomic Data
An S4 Lattice-Based Package for the Representation of
Multivariate Data
Analysis of Habitat Selection by Animals
Exploratory Analyses for the Phylogenetic Comparative Method
A 'shiny' Application for the (Audio-)Visualization of Adverse
Event Profiles
Adequacy of Probabilistic Models and General Purpose
Optimization
Import from and Export to Amiga Disk Files
Assess Medication Adherence from Pharmaceutical Claims Data
Interactive Visualisation of Medication Adherence Patterns
Calculate Ad Hoc Distance Thresholds for DNA Barcoding
Identification
Adjusted Bayesian Quantile Regression Inference
Adjacency-Constrained Clustering of a Block-Diagonal Similarity
Matrix
Remove Automated and Repeated Downloads from 'RStudio' 'CRAN'
Download Logs
Adaptive Mixture of Student-t Distributions
An Interface for Running 'ADMIXTOOLS' Analyses
Admixture Graph Manipulation and Fitting
Algorithms using Alternating Direction Method of Multipliers
Alternating Direction Method of Multipliers to Solve Dense
Dubmatrix Problem
Regularized Model with Selecting the Number of Non-Zeros
Penalized Precision Matrix Estimation via ADMM
Ancient Demographic Modelling Using Radiocarbon
No-U-Turn MCMC Sampling for 'ADMB' and 'TMB' Models
Fast Clustering Using Adaptive Density Peak Detection
Use Least Squares Polynomial Regression and Statistical Testing
to Improve Savitzky-Golay
Design and Analysis of Locally or Globally Efficient Adaptive
Designs
Upper Clopper-Pearson Confidence Limits for Burn-in Studies
under Additional Available Information
Solving 1D Advection Bi-Flux Diffusion Equation
Interactive R Tutorials to Accompany Field (2016), "An Adventure
in Statistics"
Wavelet Analysis of Genomic Data from Admixed Populations
Change Point Analysis in ARIMA Forecasting
Download and Process AEMO Price and Demand Data
Statistical Modelling for Asymmetric Exponential Power
Distribution
A Computational Tool for Aerobiological Data
Model-Based Estimation of Confounder-Adjusted Attributable
Fractions
The Attributable Fraction (AF) Described as a Function of
Disease Heritability, Prevalence and Intervention Specific
Factors
Functions for Atomic Force Microscope Force-Distance Curves
Analysis
Tools for Modelling of Animal Flight Performance
Accelerated Failure Time Model with Generalized Estimating
Equations
Adaptive Set-Based Gene-Environment Interaction Test for Rare
Variants
Aggregate Numeric, Date and Categorical Variables
Relationship Matrices for Diploid and Autopolyploid Species
Adaptive Gauss Hermite Quadrature for Bayesian Inference
Aggregation Operators and Preordered Sets
Agreement Interval of Two Measurement Methods
Statistical Procedures for Agricultural Research
Tutorial Analysis of Some Agricultural Experiments
Evapotranspiration and Energy Fluxes Spatial Analysis
Calculate Concentration and Dispersion in Ordered Rating Scales
Stability Analysis for Agricultural Research
Estimation in Adaptive Group Sequential Trials
Miscellaneous plotting and utility functions
Adaptive and Automatic Gradient Boosting Computations
Regularization for semiparametric additive hazards regression
Additive Heredity Model: Method for the Mixture-of-Mixtures
Experiments
Functions and Data for the Book 'Applied Hierarchical Modeling
in Ecology' Vols 1 and 2
An Implementation of the Artificial Hydrocarbon Networks
Fast Searching for Multiple Keywords in Multiple Texts
Analytic Hierarchy Process for Survey Data
Hybrid Method for Multiple Criteria Decision-Making (MCDM)
Model Selection and Multimodel Inference Based on (Q)AIC(c)
Help Detect and Mitigate Bias in Machine Learning Models
Irish Weather Observing Stations Hourly Records for 2017
Download Mexico City Pollution, Wind, and Temperature Data
Suite of GR Hydrological Models for Precipitation-Runoff
Modelling
Teaching Hydrological Modelling with the GR Rainfall-Runoff
Models ('Shiny' Interface Included)
Convenience Tools for Working with Airport Data
Air Quality Measurements in Spain from 2011 to 2018
AIRR Data Representation Reference Library
Process and Display Data from Air Quality Sensors
Evaluation of Algorithm Collections Using Item Response Theory
Interpolation of Irregularly and Regularly Spaced Data
Adaptive Kmeans algorithm based on threshold
Anchored Kmedoids for Longitudinal Data Clustering
Atlas of Living Australia (ALA) Data and Resources in R
Immunoglobulin Clonal Lineage and Diversity Analysis
Adaptive Lasso for the Cox Regression with Interval Censored and
Possibly Left Truncated Data
PARAFAC Analysis of Fluorescence Excitation-Emission Matrices
Quantile Regression Using Asymmetric Laplace Distribution
Accumulated Local Effects (ALE) Plots and Partial Dependence
(PD) Plots
Estimating Absolute Protein Quantities from Label-Free LC-MS/MS
Proteomics Data
Connectivity to 'Alfresco' Content Management Repositories
Downloading Time Series from ALFRED Database for Various
Vintages
Determine Phytoplankton Functional Groups Based on Functional
Traits
Haplotype Two Snips Out of a Paired Group of Patients
Implement an Address Search Auto Completion Menu on 'Shiny' Text
Inputs Using the 'Algolia Places' 'Javascript' Library
Allows you to Easily Interact with the Algorithmia Platform
Converts Human gene symbols to entrez IDs
Visualizing Multiple Sequence Alignments with 'ggplot2'
Alignment of Phonetic Sequences Using the 'ALINE' Algorithm
Acknowledge all Contributors to a Project
Allele Imputation and Haplotype Reconstruction from Pedigree
Databases
Identifying Unique Multilocus Genotypes where Genotyping Error
and Missing Data may be Present
Allele Retention, Inbreeding, and Demography
A fast, unbiased and exact allelic exact test
Computes all of a word's possible spellings
Model Classifier for Binary Classification
Fit GLM's with High-Dimensional k-Way Fixed Effects
Algorithms for High-Throughput Sequencing of Antigen-Specific T
Cells
Generalization of the Convex Hull of a Sample of Points in the
Plane
Obtain Alpha-Outlier Regions for Well-Known Probability
Distributions
Partition/Decomposition of Breeding Values by Paths of
Information
Implementation of the 3D Alpha-Shape for the Reconstruction of
3D Sets from a Point Cloud
Lightweight R Interface to the Alpha Vantage API
Data to Accompany Applied Linear Regression 4th Edition
Multivariate Curve Resolution Alternating Least Squares
(MCR-ALS)
Accelerated line search algorithm for simultaneous orthogonal
transformation of several positive definite symmetric matrices
to nearly diagonal form
Companion to Applied Linear Statistical Models
Provides an Interface to the NREL Alternate Fuels Locator
Optimal Experimental Designs for Accelerated Life Testing
Alternative Estimators to Adjusted R-Squared
Compare Gene Expressions from 2-Treatment RNA-Seq Experiments
An Interface to the 'AutoNavi Maps' API Geocoding Services
Generate LaTeX Code for Auto-Multiple-Choice (AMC)
European Commission Annual Macro-Economic (AMECO) Database
Anomaly Detection with Normal Probability Functions
Additive and Multiplicative Effects Models for Networks and
Relational Data
This package includes pricing function for selected American
call options with underlying assets that generate payouts
American Politics-Inspired Color Palette Generator
Automated Fitting of Moderated Nonlinear Factor Analysis Through
the 'Mplus' Program
A Multidirectional Optimum Ecotope-Based Algorithm
Artificial Neural Network Training and Simulating
An Algorithm for Automatic Peak Detection in Noisy Periodic and
Quasi-Periodic Signals
Common Code for the 'AMPED' and 'PIMPLE' 'shiny' Apps for
Stakeholder Engagement and Harvest Strategies
Statistical Analysis of Amplicon Data of the Same Sample to
Identify Artefacts
Analysis of Codon Data under Stationarity using a Bayesian
Framework
Simple and Canonical Correspondence Analysis
Analogue and Weighted Averaging Methods for Palaeoecology
Additional Functions for Use with the Analogue Package
Compose Interoperable Analysis Pipelines & Put Them in
Production
Model Layer for Automatic Data Analysis via CSV File
Interpretation
Functions for Analysis of fMRI Datasets Stored in the ANALYZE or
NIFTI Format
Data Analysis and Automated R Notebook Generation
Assigning Ancestry Based on Population References
Statistical analysis of surveys with anchoring vignettes
An extended Bayesian Learning Technique developed by Dr. Geoff
Webb
Asynchronous Disk-Based Representation of Massive Data
Make Spectroscopic Data Processing Easier
Simulate a Bus Route Creel Survey of Anglers
Tools for 'ROMS' the Regional Ocean Modeling System
Inferring Dominance Hierarchies and Estimating Uncertainty
Extended Kalman Filters for Animal Movement
Networks Characterising the Physical Configurations of Animal
Habitats
Animal track reconstruction for high frequency 2-dimensional
(2D) or 3-dimensional (3D) movement data
A Gallery of Animations in Statistics and Utilities to Create
Animations
Animated Interactive Grammar of Graphics
Animation of Observed Trajectories Using Spline-Based
Interpolation
Animate Shiny and R Markdown Content when it Comes into View
Compute High Dimensional Orthant Probabilities
Artificial Neural Networks for Anomaly Detection
Extract Subsequences from GenBank Annotations
AnnotLists: A tool to annotate multiple lists from a specific
annotation file
A Non-Parametric Statistical Test to Compare Clustering
Structures
Interactive Document for Working with Analysis of Variance
Test ANOVA Replications by Means of the Prior Predictive p-Value
Create Datasets with Identical Summary Statistics
Import, Manipulate and Explore the Results of an 'Antares'
Simulation
Computation of the WHO Child Growth Standards
An R Package for Smith's Mean Measure of Divergence (MMD)
Statistical Methods for Anthropometric Data
Extract Text from Microsoft Word Documents
Query 'nycflights13'-Like Air Travel Data for Given Years and
Airports
Install and Load Any Package from CRAN, Bioconductor or Github
Anything to 'POSIXct' or 'Date' Converter
Analysis of Overdispersed Data using S3 Methods
Ontogenetic Shifts in Central-Place Foraging Insects
A-Optimal Block Designs for Comparing Test Treatments with
Controls
Inference in the Balanced One-Way ANOVA Model with Random Factor
Format Outputs of Statistical Tests According to APA Guidelines
Create American Psychological Association (APA) Style Tables
Create R Markdown Text for Results in the Style of the American
Psychological Association (APA)
Analysis of Unreplicated Orthogonal Experiments using All
Possible Comparisons
A New Age-Period-Cohort Model for Describing and Investigating
Inter-Cohort Differences and Life Course Dynamics
An Implementation of the Additive Polynomial Design Matrix
Phylogenetic Methods for Multiple Gene Data
Create Interactive Chart with the JavaScript 'ApexCharts'
Library
Multiple Testing Approach using Average Power Function (APF) and
Bayes FDR Robust Estimation
Analysis with Profile Hidden Markov Models
Auto-Adaptive Parentage Inference Software Tolerant to Missing
Parents
Datasets from Hosmer, Lemeshow and Sturdivant, "Applied Logistic
Regression" (3rd Ed., 2013)
Decorate a 'ggplot' with Associated Information
Another Plot Package: 'Bagplots', 'Iconplots', 'Summaryplots',
Slider Functions and Others
An Approach for Machine-Learning Modelling
Augmented and Penalized Minimization Method L0
Tools for Choice Model Estimation and Application
Adjusted Prediction Model Performance Estimation
Approximate Path for Penalized Likelihood Estimators
A Compilation of Applicability Domain Methods
Functions and Data Sets for 'Applied Predictive Modeling'
Amyloid Propensity Prediction Neural Network
Bayesian Prediction of Complex Computer Codes
Approximately Optimal Fine Balance Matching with Multiple Groups
Datasets from Draper and Smith "Applied Regression Analysis"
(3rd Ed., 1998)
Tools for the a Priori Comparison of Regression Modelling
Strategies
Amdahl's Profiler, Directed Optimization Made Easy
Inspect, Read, Edit and Run 'APSIM' "Next Generation" and
'APSIM' Classic
apsrtable model-output formatter for social science
Average Positive Predictive Values (AP) for Binary Outcomes and
Censored Event Times
Visualize Population Pyramids Aggregated by Age
Integrated Development Toolbox for Aquatic Chemical Model
Generation
Another Look at the Acceptance-Rejection Method
Simulate Auto Regressive Data from Precision Matricies
Rigorous Data Reduction and Error Propagation of Ar40 / Ar39
Data
Find Arbitrage Opportunities for Sports Matches
Fitting Univariate Censored Linear Regression Model with
Autoregressive Errors
Bayesian Modeling of Archaeological Chronologies
Post-Processing of the Markov Chain Simulated by 'ChronoModel',
'Oxcal' or 'BCal'
Example Datasets from Archaeological Research
Refitting and Stratigraphic Analysis in Archeology
Plant Root System Architecture Analysis Using DART and RSML
Files
Tools for Storing, Restoring and Searching for R Objects
Tools for Archiving, Managing and Sharing R Objects via GitHub
Autoregressive Cokriging Models for Multifidelity Codes
Load ARCOS Prescription Data Prepared by the Washington Post
Processing and Physical Activity Summaries of Minute Level
Activity Data
ARDL, ECM and Bounds-Test for Cointegration
Harmonise and Integrate Heterogeneous Areal Data
Plot Stacked Areas and Confidence Bands as Filled Polygons
Plots, Summary Statistics and Tools for Arena Simulation Users
Arena for the Exploration and Comparison of any ML Models
Fractional ARIMA (and Other Long Memory) Time Series Modeling
Accurate Estimation of Influenza Epidemics using Google Search
Data
Command Line Optional and Positional Argument Parser
Improved Communication to Users with Respect to Problems in
Function Arguments
Adaptable Regularized Hotelling's T^2 Test for High-Dimensional
Data
Efficient Computations of Standard Clustering Comparison
Measures
Archive and Unarchive Databases Using Flat Files
Data Analysis Using Regression and Multilevel/Hierarchical
Models
A Statistical Methodology to Select Covariates in
High-Dimensional Data under Dependence
Adaptive Rejection Metropolis Sampling (ARMS) via 'Rcpp'
Covariate-Adjusted Receiver Operating Characteristic Curve
Inference
Analysis of Large Affymetrix Microarray Data Sets
A Probe-Level Data File Format Used by 'aroma.affymetrix'
[deprecated]
Copy-Number Analysis of Large Microarray Data Sets
Core Methods and Classes Used by 'aroma.*' Packages Part of the
Aroma Framework
Geometric Morphometric Methods and Virtual Anthropology Tools
Fitting Autoregressive Censored Mixed-Effects Models
Tools for Simulating Direct Behavioral Observation Recording
Procedures Based on Alternating Renewal Processes
Fast Generators and Iterators for Permutations, Combinations,
Integer Partitions and Compositions
Apply a Function to a Margin of an Array
An Arsenal of 'R' Functions for Large-Scale Statistical
Summaries
Aligned Rank Transform for Nonparametric Factorial Analysis
Mining Association Rules and Frequent Itemsets
Classification Based on Association Rules
Mining NB-Frequent Itemsets and NB-Precise Rules
Visualizing Association Rules and Frequent Itemsets
Data Sets for "Applied Survival Analysis Using R""
A Collection of Statistical Tools for Biologists
Export R Objects to Several Markup Languages
Create 'Ascii' Screen Casts from R Scripts
Reads Fixed-Width ASCII Data Files (.txt or .dat) that Have
Accompanying Setup Files (.sps or .sas)
Simulations for Adaptive Seamless Designs
Interface to the Australian Statistical Geography Standard
Methods for Adaptive Shrinkage, using Empirical Bayes
Interface to the Algorithm Selection Benchmark Library
Linkage Map Construction using the MSTmap Algorithm
Animal Social Network Inference and Permutations for Ecologists
A collection of functions for estimating centrographic
statistics and computational geometries for spatial point
patterns
Bayesian Inference on Causal Genetic Variants using Affected
Sib-Pairs Data
An Adaptive Sum of Powered Correlation Test (aSPC) for Global
Association Between Two Random Vectors
A General Framework for Multivariate Analysis with Optimal
Scaling
Analysis of Symmetry of Parasitic Infections
Augments 'ASReml-R' in Fitting Mixed Models and Packages
Generally in Exploring Prediction Differences
Applied Singular Spectrum Analysis (ASSA)
Verbose Assertions for Tabular Data (Data.frames and
Data.tables)
Readable Check Functions to Ensure Code Integrity
A Lightweight Core of the 'assertive' Package
Assertions to Check Properties of Strings
Assertions to Check Properties of Dates and Times
Assertions to Check Properties of Matrices
Assertions to Check Properties of Models
Assertions to Check Properties of Numbers
Assertions to Check Properties of Variables
Assertive Programming for R Analysis Pipelines
Estimating Asset Correlations from Default Data
Optimal Pricing of Assets with Fixed Expiry Date
Population Assignment using Genetic, Non-Genetic or Integrated
Data in a Machine Learning Framework
Infer Geographic Origin from Isotopic Data
A Suite of R Functions Implementing Spline Smoothing Techniques
Adaptive Subgroup Selection in Group Sequential Trials
Implements New and Existing Association Indices for Constructing
Animal Social Networks
Interactive Document for Working with Association Rule Mining
Analysis
Calculate the Assortativity Coefficient of Weighted and Binary
Networks
Statistical Tests for Genetic Association Studies
A Computational Tool for Astrochronology
Astronomy: time and position functions, misc. utilities
Applied Statistical Time Series Analysis
Adaptive SURE Thresholding Using Side Information
Average Shifted Visual Predictive Checks
Kernel Density Estimation and Selection of Optimum Bandwidth
Asymmetric Linkage Disequilibrium (ALD) for Polymorphic Genetic
Data
Multidimensional Scaling of Asymmetric Data
Asymmetry Measures for Probability Density Functions
A Simple R Package for Classical Parametric Statistical Tests
and Confidence Intervals in Large Samples
Estimate Asymptomatic Cases via Capture/Recapture Methods
Regression Analysis of Sparse Asynchronous Longitudinal Data
Calculate Power Utilizing Asymptotic Likelihood Ratio Methods
Create Tables for Reporting Clinical Trials
Inference for Average Treatment Effects using Covariate
Balancing
Automatically Tuned Markov Chain Monte Carlo
Acoustic Traveltime Calculations for 1-D Atmospheric Models
Support Querying Axibase Time-Series Database
Correcting for Attenuation Due to Measurement Error
Threshold independent performance measures for probabilistic
classifiers
Variable Selection with Random Forest and the Area Under the
Curve
Standard Conform Pure Tone Audiometry (PTA) Plots
Model Audit - Verification, Validation, and Error Analysis
Analysis of Augmented Randomised Complete Block Designs
Analysis of Data with Mixed Measurement Error and
Misclassification in Covariates
eBird Data Extraction and Processing in R
Generates PFA Documents from R Code and Optionally Runs Them
Creates a Neighbourhood Using Locality Sensitive Hashing for
Gaussian Projections
Approximate Unconditional and Permutation Tests
Secure Authentication in Shiny with Auth0
Automatic Variable Reduction Using Principal Component Analysis
Learning to Rank Bagging Workflows with Metalearning
Automated Covariate Selection Using HDPS Algorithm
An Interface to the 'AutoDesk' 'API' Platform
Sparse Autoencoder for Automatic Learning of Representative
Features from Unlabeled Data
Semi-Automatic Grading of R and Rmd Scripts
Multiple Heat Maps for Projected Coordinates
Automagically Document and Install Packages Necessary to Run R
Code
Automated Transcriptome Classifier Pipeline: Comprehensive
Transcriptome Analysis
Automatic Generation of Interactive Visualizations for
Statistical Results
Development of Visualization Tools for Protein Sequence
Minimum Distance Estimation in Autoregressive Model
Retrieve Disease-Related Genes from Public Sources
Automatic Transformation of an 'R' Function into a 'shiny' App
Builds Stepwise GLMs via Train and Test Approach
An R Port of the 'ImageJ' Plugin 'Auto Threshold'
Automatic Model Selection and Prediction for Univariate Time
Series
Check if the Title of a Package is Available, Appropriate and
Interesting
Calculation of Average Population Attributable Fractions and
Confidence Intervals
Adaptation of Virtual Twins Method from Jared Foster
Convert Dates to Arbitrary Week Definitions
Amazon 'Kinesis' Consumer Application for Stream Processing
A Simple Client to the 'AWS' Key Management Service
Client for the Amazon Alexa Web Information Services API
'AWS Key Management Service' Client Package
Class and Methods Definitions for Packages 'aws', 'adimpro',
'fmri', 'dwi'
Novel Statistical Test for Aberration Enrichment
Authentication Services for Azure Active Directory
Interface to 'Container Instances', 'Docker Registry' and
'Kubernetes' in 'Azure'
Interface to the 'Azure Cosmos DB' 'NoSQL' Database Service
Interface to 'Kusto'/'Azure Data Explorer'
Interface to the 'Azure Machine Learning' 'SDK'
Interface to the Table Storage Service in 'Azure'
Interface to Azure Computer Vision Services
Interface to Azure Virtual Machine Instance Metadata
Adaptive differential evolution, b6e6rl variant
Bayesian Bacterial Growth Curve Analysis in R
Talking to 'Docker' and 'Singularity' Containers
Bayesian Bootstrap Predictive Mean Matching - Multiple and
Single Imputation for Discrete Data
Bubble Chart to Compare Biological Annotations by using DAVID
Modeling Framework for Cellular Communities in their
Environments
Bayesian Analysis of Computer Code Output (BACCO)
Bayesian Augmented Control for Clinical Trials
Bayesian Classification and Information Sharing (BaCIS) Tool for
the Design of Multi-Group Phase II Clinical Trials
Extracts the Backbone from Weighted Graphs
Reimplementations of Functions Introduced Since R-3.0.0
Learning Causal Cyclic Graphs from Unknown Shift Interventions
Exploring Portfolio-Based Conjectures About Financial
Instruments
Choice of the Hyperparameter Omega in the Bayesian Adjustment
for Confounding (BAC) Algorithm
Create Badges for 'Travis', 'Repostatus' 'Codecov.io' Etc in
Github Readme
Bayesian Average Error approach to Sample Size Determination
Bagged Cross-Validation for Kernel Density Bandwidth Selection
A Binary Regression Adaptive Goodness-of-Fit Test (BAGofT)
Filter Covariance and Correlation Matrices with
Bootstrapped-Averaged Hierarchical Ansatz
Bayes Factors for Informative Hypotheses
Library Driven Compound Profiling in Gas Chromatography - Mass
Spectrometry Data
Visualize Balances of Compositional Data
Balance Check for Multiple Covariates in Matched Observational
Studies
Balanced and Spatially Balanced Sampling
Statistical Inference and Sure Independence Screening via Ball
Statistics
Expression RNA-Seq Data Analysis Based on Linear Mixed Model
Functions and Datasets for "Bayesian Methods: A Social and
Behavioral Sciences Approach"
High Dimensional Bayesian Mediation Analysis
Protein Secondary Structure Prediction Using the Bamboo Method
Bayesian Meta-Analysis of Diagnostic Test Data
Bayesian Additive Models for Location, Scale, and Shape (and
Beyond)
Analysis and Visualization of Macroevolutionary Dynamics on
Phylogenetic Trees
Bayesian Model Optimized Reference Correction Method for
Assigned and Unassigned Protein NMR Spectra
Bayesian Age-Period-Cohort Modeling and Prediction
Functions for simple A/B split test and multi-armed bandit
analysis
Make Banner Comments with a Consistent Format
Batch Effect Removal and Addon Normalization (in Phenotype
Prediction using Gene Data)
Bayesian Prediction of Stochastic Processes
Label Creation for Tracking and Collecting Data from Biological
Samples
Species Identification using DNA Barcodes
A Bayesian Repulsive Biclustering Model for Periodontal Data
Access and Import Data from the French Open Data Portal
Contour Plots, 3D Plots, Vector Fields and Heatmaps
Bayesian Additive Regression Trees using Bayesian Model
Averaging
Causal Inference using Bayesian Additive Regression Trees
Regularized Wasserstein Distances and Barycenters
Bayesian Variable Selection and Model Averaging using Bayesian
Adaptive Sampling
Bayesian Variable Selection with Shrinking and Diffusing Priors
Convert Regression Between Base Function and 'rms' Package
Fast and URL-Safe Base64 Encoder and Decoder
Sabermetrics and Advanced Baseball Statistics
Infrastructure for Computing with Basis Functions
Plot Simple Features with 'base' Sensibilities
Trace Plots, Density Plots and Chain Comparisons for MCMC
Samples
Recovering a Basic Space from Issue Scales
Construct Rich Tables for Output to 'HTML'/'Excel'
Add Trendline and Confidence Interval of Basic Regression Models
to Plot
Classification of RNA Sequences using Complex Network Theory
Analysis and Visualization of Basketball Data
Age-Specific Survival Analysis from Incomplete
Capture-Recapture/Recovery Data
Big Data Statistical Analysis for High-Dimensional Models
Managing Packages Removal and Installation
Batching Routines in Parallel and Passing Command-Line Arguments
to R
Statistical Experiments on Batch Computing Clusters
Downloads and Organizes Financial Data for Multiple Tickers
Consistent Batch Means Estimation of Monte Carlo Standard Errors
Bayesian Tensor Factorization Linked to External Data
Convert Categorical Representations of Logicals to Actual
Logicals
An R Package for Data Reduction by Battery Reduction
Bayesian Estimation and Optimisation of Expected False Discovery
Rate
User Friendly Bayesian Data Analysis for Psychology
Bayesian Estimation of the Additive Main Effects and
Multiplicative Interaction Model
Bayesian Inference in the Analysis of Variance via Markov Chain
Monte Carlo in Gaussian Mixture Models
Bayesian Estimation of Bivariate Volatility Model
Bayesian Estimation of Mixtures of Multivariate Bernoulli
Distributions
Miscellaneous Functions for Bioinformatics and Bayesian
Statistics
An Implementation of Rubin's (1981) Bayesian Bootstrap
Bayesian Estimation using Bernstein Polynomial Fits Rate Matrix
Power Calculations and Bayesian Analysis of Count Distributions
and FECRT Data using MCMC
Bayesian Analysis of Censored Regression Models Under Scale
Mixture of Skew Normal Distributions
Simulation and Analysis of Adaptive Bayesian Clinical Trials
Two Arm Bayesian Clinical Trial Design with and Without
Historical Control Data
Functions and Datasets for the book "Bayesian Data Analysis"
Bayesian Dynamic Factor Analysis (DFA) with 'Stan'
Tools for the Bayesian Discount Prior Function
Computation of Bayes Factors for Common Designs
Fit Multivariate Response Generalized Additive Models using
Hamiltonian Monte Carlo
Bayesian Estimation of the GARCH(1,1) Model with Student-t
Innovations
Bayesian Analysis of Generalized Elliptical Semi-Parametric
Models and Flexible Measurement Error Models
Bayesian Modeling via Frequentist Goodness-of-Fit
Fast Bayesian Gaussian Process Regression Fitting
Bayesian Grouped Weighted Quantile Sum Regression
Bayesian Melding of GPS and DR Path for Animal Tracking
Bayesian Estimation of the ETAS Model for Earthquake Occurrences
Bayesian Gamma Regression: Joint Mean and Shape Modeling
Predict Brain Asymmetry Based on Handedness and Dichotic
Listening
Sample Size and Power for Comparing Inequality Constrained
Hypotheses
Plot Positive and Negative Predictive Values for Medical Tests
General-Purpose MCMC and SMC Samplers and Tools for Bayesian
Statistics
Bayesian Methods for Image Segmentation using a Potts Model
Linear Combinations of Bayesian Posterior Samples
Bayesian Analysis of Contingency Table Data
Adjust Longitudinal Regression Models Using Bayesian Methodology
Bayesian Preference Learning with the Mallows Rank Model
Bayesian Data Reconciliation of Separation Processes
Bayesian Mixture Survival Models using Additive
Mixture-of-Weibull Hazards, with Lasso Shrinkage and
Stratification
Non-Parametric Bayesian Analyses of Animal Movement
Bayesian Multi-Resolution Gaussian Process Approximations
BayesNI: Bayesian Testing Procedure for Noninferiority with
Binary Endpoints
Bayesian Analysis of Non-Stationary Gaussian Process Models
Variable Selection in a Hierarchical Bayesian Model for a Hazard
Function
Hierarchical Bayesian Model for a Hazard Function
Generate Postestimation Quantities for Bayesian MCMC Estimation
Hierarchical Bayesian analysis of ecological count data
Fast Projection Direction for Multivariate Changepoint Detection
Bayesian Regression Models with Global-Local Shrinkage Priors
Fits the Bayesian Piecewise Linear Log-Hazard Model
Bayes Factors for Hierarchical Linear Models with Continuous
Predictors
Bayesian Variable Selection Using Simplified Shotgun Stochastic
Search with Screening (S5)
Bayesian Analysis of Small Area Estimation
Bayes Linear Estimators for Finite Population
Different Models of Posterior Distributions of Adjusted Odds
Ratio
Bayesian Spatial Split Population Survival Model
Bayesian Survival Regression with Flexible Error and Random
Effects Distributions
Bayesian Survival Analysis for Right Censored Data
Effect Size Targeted Bayesian Two-Sample t-Tests via Markov
Chain Monte Carlo in Gaussian Mixture Models
Understand and Describe Bayesian Models and Posterior
Distributions
Bayesian Analysis of Item-Level Twin Data
Bayes Factors, Model Choice and Variable Selection in Linear
Models
Visually Learning the Graphical Structure of Bayesian Networks
and Performing MCMC with 'Stan'
R Utilities Accompanying the Software Package BayesX
R Package Distribution of the BayesX C++ Sources
Global Bayesian Foraminifera Core Top Calibration
R Functions for Bayesian Hazard Rate Estimation
Chronological Bayesian Models Integrating Optically Stimulated
Luminescence and Radiocarbon Age Dating
Computation of Bayes Factors for Common Biomedical Designs
Bayesian Analysis of Significantly Mutated Genes in Cancer
Bayesian Stability Analysis of Genotype by Environment
Interaction (GEI)
On Bayesian analysis of Threshold autoregressive model (BAYSTAR)
Solving and Optimizing Large-Scale Nonlinear Systems
Bayesian bandwidth estimation and semi-metric selection for the
functional kernel regression with unknown error density
Bayesian bandwidth estimation for multivariate kernel regression
with Gaussian error
Bayesian Estimation of Incoherent Neutron Scattering Backgrounds
Benthic Biotic Indices Calculation from Composition Data
Miscellaneous Helper Functions for B. Bischl
Tools for General Maximum Likelihood Estimation
Models for Continuous Traits Evolving in Macroevolutionary
Landscapes of any Shape
Bessel and Beta Regressions via Expectation-Maximization
Algorithm for Continuous Bounded Data
Bayesian Methods and Graphical Model Structures for Statistical
Modeling
Hierarchical Bayesian Analysis of North American BBS Data
Gene Regulatory Network Inference with Bc3net
Block Coordinate Ascent with One-Step Generalized Rosen
Algorithm
Bias Corrected Bootstrap Confidence Intervals
Bias-Corrected Bayesian Classification with Selected Features
Calculation of Option Prices Based on a Universal Solution
Search and Retrieve Data from the BC Data Catalogue
Business Cycle Dating and Plotting Tools
Bayesian composition estimator: estimating sample (taxonomic)
composition from biomarker data
The Bayesian Causal Effect Estimation Algorithm
B Cell Receptor Somatic Hyper Mutation Analysis
Causal Inference for a Binary Treatment and Continuous Outcome
using Bayesian Causal Forests
Semiparametric Bivariate Correlated Frailty Model
Bivariate Correlated Frailty Models with Varied Variances
Bayesian Constrained Generalised Linear Models
Bias-Corrected Estimates for Generalized Linear Models for
Dependent Data
Clinical Trial Calculation Based on BCHM Design
Radiocarbon Dating, Age-Depth Modelling, Relative Sea Level Rate
Estimation, and Non-Parametric Phase Modelling
Bayesian Palaeoclimate Reconstruction from Pollen Data
A Dirichlet Process Mixture Model for Clustering Longitudinal
Gene Expression Data
Map Layers and Spatial Utilities for British Columbia
Mixed Effect Model with the Box-Cox Transformation
Bayesian Analysis of Change Point Problems
Behavioral change point analysis of animal movement
Bayesian Multiple Changepoint Detection Using Metadata
Bayesian Continual Reassessment Method for Phase I
Dose-Escalation Trials
Bias-Corrected Methods for Estimating the ROC Surface of
Continuous Diagnostic Tests
A Bayesian Semiparametric Factor Analysis Model for Subtype
Identification (Clustering)
Bayesian Context Trees for Discrete Time Series
A User-Friendly Biodiversity Data Cleaning App for the
Inexperienced R User
Darwinizer: Darwin Core (DwC) Field Names Standardization
Efficient Determination of Sample Size in Balanced Design of
Experiments
Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
Transparent and Reproducible Artificial Data Generation
Bayesian Adaptive Designs for Phase II Trials with Binary
Endpoint
Optimisation of Bayesian Decision Problems
Inference and Design for Predictive Values in Diagnostic Tests
Bayesian Detection of Potential Risk Using Inference on Blinded
Safety Data
Remove Weekends and Holidays from ggplot2 Axes
Routines for Block Diagonal Symmetric Matrices
Bayesian Inference for Discrete Weibull Regression
Biometric Exploratory Analysis Creation House
Analysis of Multiplex Cytometric Bead Assays
Fast Bayesian Inference in Large Gaussian Graphical Models
Visualization via Beanplots (like Boxplot/Stripchart/Violin
Plot)
Bayesian Analysis of Heterogeneous Treatment Effect
Bayesian Estimation of Change-Points in the Slope of
Multivariate Time-Series
Quantifies effects of geo/eco distance on genetic
differentiation
Extract Genotypes from a PLINK .bed File
Genomic Region Processing using Tools Such as 'BEDTools',
'BEDOPS' and 'Tabix'
Easily Play Notification Sounds on any Platform
The Bee Swarm Plot, an Alternative to Stripchart
Canonical Data Structure for Behavioural Data
Download Historical Data from the Belgrade Stock Exchange
Boltzmann Entropy of a Landscape Gradient
Count Regression Models Based on the Bell Distribution
28 benchmark densities from Berlinet/Devroye (1994)
Benchmark and Frontier Analysis Using DEA and SFA
High Precise Measurement of R Expressions Execution Time
Benford Analysis for Data Validation and Forensic Analytics
Statistical Tests for Evaluating Conformity to Benford's Law
Bent-Cable Regression for Independent Data or Autoregressive
Time Series
Bayesian Exponential Random Graph Models
Function Collection Related to Plotting and Hydrology
Best Subset Selection /Ridge Regression in Linear, Logistic,
Poisson and CoxPH Models
Computations and Approximations for Bessel Functions
Bayesian Estimation Supersedes the t-Test
Best Subset GLM and Regression Utilities
Bayesian Estimation of Intervention Effects
Burden Estimate of Common Communicable Diseases in Settlements
of Displaced Populations
Mini Games from Adventures of Beta and Bit
Detecting rare variants for quantitative traits using nuclear
families
Functions for Working with Two- And Four-Parameter Beta
Probability Distributions
Partitioning Beta Diversity into Turnover and Nestedness
Components
Calculate Power and Sample Size with Beta Regression
Taxonomic Uncertainty on Multivariate Analyses of Ecological
Data
Simulation, Estimation and Forecasting of Beta-Skew-t-EGARCH
Models
Bayesian Evaluation of Variant Involvement in Mendelian Disease
Compare the Goodness of Fit of Benford's and Blondeau Da Silva's
Digit Distributions to a Given Dataset
Bayesian Spectral Inference for Stationary Time Series
Breaks For Additive Season and Trend (BFAST)
Flexible Bayes Factor Testing of Scientific Expectations
Search and Download Data from the Swiss Federal Statistical
Office (BFS)
Plot Maps from Switzerland by Swiss Federal Statistical Office
Bayesian Framework for Computational Modeling
A Suite of Packages for Analysis of Big Genomic Data
Binary Generalized Extreme Value Additive Models
BoardGameGeek's Board Game Data Analysis Tools
Bayesian Genomic Linear Models Applied to GE Genome Selection
Bayesian Estimation of Generalized Graded Unfolding Model
Parameters
Example BGM Files for the Atlantis Ecosystem Model
Gaussian Mixture Modeling Algorithms and the Belief-Based
Mixture Modeling
Markov Beta and Gamma Processes for Modeling Hazard Rates
Block Gibbs Sampler with Incomplete Multinomial Distribution
Bayesian Group Sparse Multi-Task Regression
Estimate the Burden of Healthcare-Associated Infections
Useful Functions for Box, Hunter and Hunter II
Bayesian Hierarchical Multi-Subject Multiscale Analysis of
Functional MRI Data
Bayesian Hierarchical Poisson Models for Multiple Grouped
Outcomes with Clustering
Structural Bayesian Vector Autoregression Models
Bayesian Multi-Plate High-Throughput Screening of Compounds
Bias correction of the parameter estimates of the beta
regression model
A GUI to Correct Measurement Bias in DNA Methylation Analyses
R Wrapper for Java Implementation of BiBit
Maximal Biclique Enumeration in Bipartite Graphs
Integrative Inference of De Novo Cis-Regulatory Modules
Bayesian Inference for Directed Acyclic Graphs
Calculates the Bidimensional Regression Between Two 2D
Configurations
Tools for Accessing the Botanical Information and Ecology
Network Database
Tools for Survey Statistics in Educational Assessment
Utilities for 'big.matrix' Objects from Package 'bigmemory'
Read, Write, Manipulate, Explore Chess PGN Files and R API to
UCI Chess Engines
Distances for Machine Learning and Statistics in the Context of
Big Data
Case-Control Analysis of Multi-Allelic Loci
Biochemically Intuitive Generalized Loewe Model
Extending Lasso Model Fitting to Big Data
Physical and Physiological Ecosystem Properties from Eddy
Covariance Data
Bounded Memory Linear and Generalized Linear Models
Making Optimal Matching Size-Scalable Using Optimal Calipers
Manage Massive Matrices with Shared Memory and Memory-Mapped
Files
A shared resource interface for Bigmemory Project packages
Interface with Google BigQuery with Shiny Compatibility
Big Quadratic Inverse Covariance Estimation
Generalized Linear Models (GLM) for Large Data Sets
An Interface to Google's 'BigQuery' 'API'
Statistical Tools for Filebacked Big Matrices
Big Survival Analysis Using Stochastic Gradient Descent
Table, Apply, and Split Functionality for Matrix and
'big.matrix' Objects
Nonparametric Analysis of Bivariate Gap Time with Competing
Risks
Sparse Estimation of Large Time Series Models
Top Scoring Pair based methods for classification
Dimension Reduction Methods for Multivariate Time Series
Co-Clustering Adjusted Rand Index and Bikm1 Procedure for
Contingency and Binary Data-Sets
Contains Data of Billboard Hot 100 Songs
Create Interactive Chart with the JavaScript 'Billboard' Library
Power for SNP analyses using silver standard cases
Estimates Mixture Models for Case-Control Data
Threshold Cut Point of Probability for a Binary Classifier Model
Creates, Merges, and Reads Binary Dosage Files
Variable Selection for Binary Data Using the EM Algorithm
Mean and Variance Modeling of Binary Data
Fit and Predict a Gaussian Process Model with (Time-Series)
Binary Response
Estimate the Correlation Between Two Irregular Time Series
Multi-Class Discriminant Analysis using Binary Predictors
Methods for Analyzing Binned Income Data
Evaluation and Experimental Design for Binomial Group Testing
Identification and Estimation using Group Testing
Calculation for Single Arm Group Sequential Test with Binary
Endpoint
Processes Binary Data Obtained from Fragment Analysis
Nonparametric Estimation for Interval-Grouped Data
Data Generation with Binary and Continuous Non-Normal Components
Simultaneous Generation of Multivariate Binary and Normal
Variates
Binomial Confidence Intervals For Several Parameterizations
Generates binomial random numbers via the coupling from the past
algorithm
Mixture Models for Binomial and Longitudinal Data
Binomial Random Forest Feature Selection
Efficient MCMC for Binomial Logit Models
Confidence Intervals and Sample Size Determination for a
Binomial Proportion under Simple Random Sampling and Pooled
Sampling
Concurrent Generation of Binary, Ordinal and Continuous Data
Depth-Dependent Binocular Visual Fields Simulation
Analyzing Replicated ChIP Sequencing Data Using Quasi-Likelihood
Cut Numeric Values into Evenly Distributed Groups
Piecewise Smooth Regression by Bootstrapped Binary Segmentation
Efficient Implementation of Binary Segmentation
Exact Binary Sequential Designs and Analysis
Data Preprocessing, Binning for Classification and Regression
Predict Environmental Conditions from Biological Observations
Analyse Audio Recordings and Automatically Extract Animal
Vocalizations
Summarising Multi Well Plate Cellular Assay
Interactive Circular Visualization of Genomic Data using
'htmlwidgets' and 'BioCircos.js'
Access the Bioconductor Project Package Repository
Feature Selection and Classification with the Embedded
Validation Procedures for Biomedical Data Analysis
Create and Manipulate BioCompute Objects
Package for Community Ecology and Suitability Analysis
Multilevel Modeling of Dendroclimatical Fluctuations
Biodiversity Assessment Using Functional Tools
Process Biogas Data and Predict Biogas Production
Point Data Quality Assessment and Coordinate Conversion
Mathematical Modelling of (Dynamic) Microbial Inactivation
Create Hyperlinks to Biological Databases and Resources
Modelling and Forecasting Biological Invasions
Utilities for the BIOM (Biological Observation Matrix) Format
Find Biomarkers in Two-Class Discrimination Problems
Estimating Aboveground Biomass and Its Uncertainty in Tropical
Forests
Generating Various Molecular Representations for Chemicals,
Proteins, DNAs, RNAs and Their Interactions
Ensemble Platform for Species Distribution Modeling
Sensitivity Analysis and Optimum Experiment Design for Microbial
Inactivation
Identification of Impulse-Like Gene Expression Changes in Short
Genomic Series Data
Biomarker Prognostic Enrichment Tool for Time-to-Event Trial
Simulation of deterministic and stochastic biochemical reaction
networks using Petri Nets
Biological Analysis and Visualization of Weather Radar Data
Search and Download Papers from the bioRxiv Preprint Server
From Biological Sequences and Simulations to Correlation
Analysis
From Biological Sequences to Multidimensional Scaling
A Toolbox for Manipulating Biological Sequences
Convert a Matrix of Raw Values into Nice and Tidy Data
Tools for Electromyogram Signals (EMG) Analysis
Biomarker Selection in Penalized Regression Models
Utility Functions, Datasets and Extended Examples for Survival
Analysis
Calculation of Freshwater Biotic Indices
Tools for Biometry and Applied Statistics in Agricultural
Science
Create Area-Proportional Venn Diagrams from Biological Lists
Visualising Bipartite Networks and Calculating Some (Ecological)
Indices
Bootstrap on Classical Biplots and Clustering Disjoint Biplot
Bivariate Probit with Partial Observability
Ranking Nodes in Bipartite and Weighted Networks
Methods to Analyse Ring Re-Encounter Data
Biodiversity Information Review and Decision Support
The R Package for "The Basics of Item Response Theory Using R"
Programmatic Access to Bank for International Settlements Data
Tools and Palettes for Bivariate Thematic Mapping
Estimating Cell Type Composition from Methylation Sequencing
Data
Tools to find bad commits with git bisect
Toolkit to Identify Candidate Synthetic Lethality
Approximate Bayesian Inference via Sparse Grid Quadrature
Evaluation (BISQuE) for Hierarchical Models
Decomposition of Bulk Expression with Single-Cell Sequencing
Classes and Methods for Fast Memory-Efficient Boolean Selections
A S3 Class for Vectors of 64bit Integers
Bayesian Integrative Models of Trait Evolution
Binarization and Trinarization of One-Dimensional Data
Quantize Floating-Point Numbers for Improved Compressibility
Estimating the Parameters of Some Bivariate Distributions
Sample size calculations for bivariate longitudinal data
Bivariate Alternating Recurrent Event Data Analysis
Tolerance Interval and EIV Regression - Method Comparison
Studies
Bivariate Residual Plots with Simulation Polygons
Generation of Bivariate Uniform Data and Its Relation to
Bivariate Binary Data
Conduct Univariate and Bivariate Wavelet Analyses
Functions to compute the biweight mean vector and covariance &
correlation matrices
Business Days Calculations and Utilities
An API Wrapper for the Bureau of Justice Statistics (BJS)
Parallel Chain Tools for Bayesian Kernel Machine Regression
Black Box Optimization and Exploration of Parameter Space
Processing Raw Black Carbon Concentration
Read and Write FWF Files in the Blaise Format
Blaker's Binomial and Poisson Confidence Limits
Plots (Slightly Extended) Bland-Altman Plots
Bayesian Inference with Laplace Approximations and P-Splines
Calculate and Analyze Blau Status for (Covert) Organizations
Black-Litterman and Copula Opinion Pooling Frameworks
A New Link Function that Blends Two Specified Link Functions
Analyze biotic homogenization of landscapes
Joint Analysis of Experiments with Mixtures and Random Effects
Bipartite Longitudinal Influence Network (BLIN) Estimation
Record Linkage for Empirically Motivated Priors
Binomial linear and linear-expit regression
Data Files and Functions Accompanying the Book "Bayesian Data
Analysis in Ecology using R, BUGS and Stan"
A Simple S3 Class for Representing Vectors of Binary Data
('BLOBS')
Co-Clustering Package for Binary, Categorical, Contingency and
Continuous Data-Sets
Estimation of Large Block Covariance Matrices
Spatial and Environmental Blocking for K-Fold Cross-Validation
Bayesian Calculation of Region-Specific Fixation Index to Detect
Local Adaptation
Block Forests: Random Forests for Blocks of Clinical and Omics
Covariate Data
blockmatrix: Tools to solve algebraic systems with partitioned
matrices
Creates strings that show a text message in 8 by 8 block letters
Generalized and Classical Blockmodeling of Valued Networks
Latent and Stochastic Block Model Estimation by a 'V-EM'
Algorithm
Randomization for Block Random Clinical Trials
Block Design for Response-Adaptive Randomization
Nested and Crossed Block Designs for Factorial and Unstructured
Treatment Sets
Block, Assign, and Diagnose Potential Interference in Randomized
Experiments
Create Blogs and Websites with R Markdown
Impute and Analyze Data with BLOQ Observations
Tools for Developing Binary Logistic Regression Models
Dose Escalation Design in Phase I Oncology Trial Using Bayesian
Logistic Regression Modeling
Stochastic Rainfall Generator Bartlett-Lewis Rectangular Pulse
Model
Interactive Document for Working with Binary Logistic Regression
Analysis
Request Data from the U.S. Bureau of Labor Statistics API
An API Wrapper for the Bureau of Labor Statistics (BLS)
Blyth-Still-Casella Exact Binomial Confidence Intervals
Bayesian Model Averaging for Basket Trials
Multivariate Extremes: Bayesian Estimation of the Spectral
Measure
Bayesian Multivariate Analysis of Summary Statistics
Benchmark dose analysis for dose-response data
Mediation Analysis with Missing Data Using Bootstrap
Miscellaneous Functions for Panel Data, Quantiles, and Printing
Results
Bayesian Sampling for Stick-Breaking Mixtures
Bayesian Estimation for Finite Mixture of Distributions
Bundle Methods for Regularized Risk Minimization Package
Bayesian Models for Rare Variant Association Analysis
Bayesian Multilevel Single Case Models using 'Stan'
Bayesian Approach for MTAR Models with Missing Data
Bayesian Multi-Trait Multi-Environment for Genomic Selection
Analysis
Learning Discrete Bayesian Network Classifiers from Data
Data Generator based on Bayesian Network Model
Bayesian Network Structure Learning, Parameter Learning and
Inference
Bayesian Network Meta-Analysis using 'JAGS'
Bayesian Neural Network for High-Dimensional Nonlinear Variable
Selection
Bagged k-Nearest Neighbors Survival Prediction
Bayesian Estimation for Normal Heteroscedastic Nonlinear
Regression Models
Ferguson-Klass Type Algorithm for Posterior Normalized Random
Measures
Bayesian Nonparametric Model for Clustering with Mixed Scale
Variables
Simulate Genotypes from the BN-PSD Admixture Model
A Bayesian Nonparametric Algorithm for Time Series Clustering
Pathway Enrichment Analysis Based on Bayesian Network
Bayesian Non- And Semi-Parametric Model Fitting
Spatial Implementation of Bayesian Networks and Mapping
Bayesian Network Structure Learning from Data with Missing
Values
Bayesian Networks Interactive Visualization and Explainable
Artificial Intelligence
Bayesian Output Analysis Program (BOA) for MCMC
Board Games and Tools for Building Board Games
Profilling of Peripheral Blood Mononuclear Cells using CyTOF
Bacterium and Virus Analysis of Orthologous Groups (BOG) is a
Package for Identifying Differentially Regulated Genes in the
Light of Gene Functions
Interface to the Boilerpipe Java Library
Bayesian Optimal INterval (BOIN) Design for Single-Agent and
Drug- Combination Phase I Clinical Trials
Functions for Elementary Bayesian Inference
Australian Government Bureau of Meteorology ('BOM') Data Client
Fixed Coupon Bond Valuation Allowing for Odd Coupon Periods and
Various Day Count Conventions
An Improved Multiple Testing Procedure for Controlling False
Discovery Rates
Authoring Books and Technical Documents with R Markdown
Generate Assorted Books and Documents with R 'bookdown' Package
Optimal Estimation of Partially Observed Boolean Dynamical
Systems
Construction, Simulation and Analysis of Boolean Networks
Boosting for Multivariate Longitudinal Response
Boosted Multivariate Trees for Longitudinal Data
A modular framework to bag or boost any estimation procedure
Bootstrap Functions (Originally by Angelo Canty for S)
A Bootstrap-Based Heterogeneity Test for Meta-Analysis
Bootstrapping Estimates of Clustering Stability
Combine Parameter Estimates via Parametric Bootstrap
Bootstrap Inference for Multiple Imputation
Bootstrapped Confidence Intervals for (Negative) Likelihood
Ratio Tests
Bootstrap-MRMR Technique for Informative Gene Selection
Bootstrap Methods for Various Network Estimation Routines
Bootstrap Prediction Intervals and Bias-Corrected Forecasting
A Bootstrap Test for the Probability of Ruin in the Classical
Risk Process
Bootstrap Subsamplings of Sparse Partial Least Squares -
Discriminant Analysis for Classification and Signature
Identification
Functions for the Book "An Introduction to the Bootstrap"
Bootstrap Algorithms for Finite Population Inference
Bootstrap cis-QTL Method that Corrects for the Winner's Curse
Fast, Exact Bootstrap Principal Component Analysis for High
Dimensional Data
Bootstrap Tolerance Levels for Credit Scoring Validation
Statistics
Transforming Behavioral Observation Records into Data Matrices
Bayesian Ordination and Regression AnaLysis
Estimate Causal Effects with Borrowing Between Data Sources
Wrapper Algorithm for All Relevant Feature Selection
A Bunch of Structure and Sequence Analysis
Best Orthogonalized Subset Selection (BOSS)
Analytic Solutions for (ground-water) Boussinesq Equation
Outlier Detection and Influence Diagnostics for Meta-Analysis
Functions to Create Publication-Quality Plots
Box-Cox-Type Transformations for Linear and Logistic Models with
Random Effects
Double Box Plot for Two-Axes Correlation
Nonparametric Bounds for the Average Causal Effect Due to Balke
and Pearl and Extensions
Biplot of Multivariate Data Based on Principal Components
Analysis
Beta Product Confidence Procedure for Right Censored Data
Bayesian Paired Comparison Analysis with Stan
bPeaks: an intuitive peak-calling strategy to detect
transcription factor binding sites from ChIP-seq data in small
eukaryotic genomes
Bayesian Phylogeographic and Ecological Clustering
Bayesian Model Selection Approach for Parsimonious Gaussian
Mixture Models
Bayesian Purity Model to Estimate Tumor Purity
Bayesian Projected Normal Regression Models for Circular Data
Computations Around Bayesian Predictive Power
Bayesian Quantile Regression for Ordinal Models
A Method to Estimate the Accuracy and Biogeographical Status of
Georeferenced Biological Data
Visualize Combined Action Response Surfaces and Report BRAID
Analyses
Fitting Dose Response with the BRAID Combined Action Model
Region-Level Connectivity Network Construction via Kernel
Canonical Correlation Analysis
Helper Functions to 'misc3d' and 'rgl' Packages for Brain
Imaging
Simulation and Estimation for Branching Processes
Bayesian Screening and Variable Selection
Model Agnostic Explainers for Individual Predictions
Methods for Fast Multiple Change-Point Detection and Estimation
An R Package for Multiple Break-Point Detection via the
Cross-Entropy Method
Core Functions to Read and Fit 13c Time Series from Breath Tests
Stan-Based Fit to Gastric Emptying Curves
Brain Cell Type Specific Gene Expression Analysis
Templating Framework for Report Generation
Bias Reduction in Binomial-Response Generalized Linear Models
Bias Reduction in Generalized Linear Models
An Implementation of the Bridge Distribution with Logit-Link as
in Wang and Louis (2003)
Genome-Wide RNA Degradation Analysis Using BRIC-Seq Data
Bridge Sampling for Marginal Likelihoods and Bayes Factors
Fast Inference for Large Spatial Datasets using BRISC
Bias Reduction with Missing Binary Response
Bayesian Regularization for Feed-Forward Neural Networks
Broken Stick Model for Irregular Longitudinal Data
Browse Over Longitudinal Data Graphically and Analytically in R
Convert Statistical Objects into Tidy Tibbles
Enhancements for 'broom' and 'easystats' Package Families
A Compression Format Optimized for the Web
Bayesian Analysis of Quantile Regression Models
Bayesian Inference on the Ratio of Two Poisson Rates
Interface to the 'OpenBUGS' MCMC Software
Normalisation Tools for Inter-Condition Variability of ChIP-Seq
Data
A 'Bootstrap 4' Version of 'shinydashboard'
Safety Assessment in Agricultural Field Trials
Bayesian State-Space Models for Animal Movement
Bayesian Spectral Analysis Models using Gaussian Process Priors
The Bayesian Spatial Bradley--Terry Model
Bayesian Survival Model with Lasso Shrinkage Using Generalized
Weibull Regression
Nonparametric Smoothing of the Hazard Function
Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'
Bayes Screening and Model Discrimination
Bayesian Proposal to Fit Spatial Econometric Models
Bayesian Nonparametric Spectral Density Estimation Using
B-Spline Priors
Adds Functionality to the R Markdown + Shiny Bootstrap Framework
Bayesian Semiparametric Models for Meta-Analysis
Asymptotic Covariance Matrices of Some BSS Mixing and Unmixing
Matrix Estimates
Bayesian Inference of Non-Linear and Non-Gaussian State Space
Models
Submitter and Monitor of the 'LSF Cluster'
Fitting a Log-Binomial Model using the Bekhit-Schöpe-Wagenpfeil
(BSW) Algorithm
Beyond the Border - Kernel Density Estimation for Urban
Geography
Bradley-Terry Model with Exponential Time Decayed Log-Likelihood
and Adaptive Lasso
Temporal Exponential Random Graph Models by Bootstrapped
Pseudolikelihood
Modelling Heterogeneity in Paired Comparison Data
Implementing BTYD Models with the Log Sum Exp Patch
Probabilistic Models for Assessing and Predicting your Customer
Base
Beautiful Bubbles for 'shiny' and 'rmarkdown' Backgrounds
Bucky's Archive for Data Analysis in the Social Sciences
Bias and Uncertainty Corrected Sample Size
A Deep Learning for Statistical Classification and Regression
Analysis with Random Effects
Stepwise Elimination and Term Reordering for Mixed-Effects
Regression
Organize & Run Build Scripts Comfortably
Buckley-James Regression for Survival Data with High-Dimensional
Covariates
Automatic Groove Identification via Bayesian Changepoint
Detection
Analyze Bunching in a Kink or Notch Setting
Markov model for bursty behavior in streams
Calculates Business Duration Between Two Dates
Bayesian Analysis of a Vector Autoregressive Model with
Stochastic Volatility and Time-Varying Parameters
Bayesian Inference of Vector Autoregressive Models
A Simple alternative to proportional Venn diagrams
The Stark-Parker algorithm for bounded-variable least squares
Solvers for Boundary Value Problems of Differential Equations
Bayesian Variable Selection in High Dimensional Settings using
Nonlocal Priors
Backward Procedure for Change-Point Detection
Describe Image Patterns in Natural Structures
Baumgartner Weiss Schindler Test of Equal Distributions
Tools for Case 1 Best-Worst Scaling (MaxDiff) Designs
Statistics About Bytes Contained in a File as a Circle Plot
Bivariate Zero-Inflated Negative Binomial Model Estimator
Extended Inference for Lasso and Elastic-Net Regularized Cox and
Generalized Linear Models
Methods for Detecting Safety Signals in Clinical Trials Using
Body-Systems (System Organ Classes)
Compare Two Classifications or Clustering Solutions of Varying
Structure
Infering large-scale gene networks with C3NET
C5.0 Decision Trees and Rule-Based Models
Simple, Multiple and Joint Correspondence Analysis
Project Specific Workspace Organization Templates
Bootstrap Confidence Regions for Simple and Multiple
Correspondence Analysis
Classification Accuracy and Consistency under Item Response
Theory
Conditional Density Estimation Network Construction and
Evaluation
A Package to Perform Covariate Augmented Dickey-Fuller Unit Root
Tests
Provides a GUI to Several Statistical Methods
Simulation of Plasma Caffeine Concentrations by Using Population
Pharmacokinetic Model
Conditional Akaike Information Criterion for 'lme4' and 'nlme'
Graphical Aid in Correspondence Analysis Interpretation and
Significance Testings
R Graphics Device using Cairo Graphics Library for Creating
High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG,
PostScript) and Display (X11 and Win32) Output
Comparison of Algorithms with Iterative Sample Size Estimation
Calculations for All Common Subsequences
High Dimensional Numerical and Symbolic Calculus
Simple Wrapper for Computationally Expensive Functions
Calculates the Wavelet-Based Organization Index
Create, Read, Write, and Work with 'iCalander' Files, Calendars
and Scheduling Data
Ready to Print Monthly and Yearly Calendars Made with 'ggplot2'
Automated Parameter Estimation for Complex (Ecological) Models
Calibration of Scatterplot and Biplot Axes
Calibration for Computer Experiments with Binary Responses
Weighting and Estimation for Panel Data with Non-Response
Bayesian Calibration of Complex Computer Codes
Mapping ML Scores to Calibrated Predictions
Improved Allele-Specific Copy Number of SNP Microarrays for
Downstream Segmentation
Finite Mixture Models and Meta-Analysis Tools - Based on C.A.MAN
'CamelUp' Board Game as a Teaching Aid for Introductory
Statistics
Mixed Computerized Adaptive Multistage Testing
Camera Trap Data Management and Preparation of Occupancy and
Spatial Capture-Recapture Analyses
Access, Retrieve, and Work with Canadian Census Data and
Geography
Estimation of Temporal Ordering of Cancer Abnormalities
Visualizing Generalized Canonical Discriminant and Canonical
Correlation Analysis
Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal
and Spatial Clonal Evolutionary History by Next-Generation
Sequencing
Compositional Analysis of Differentially Expressed Proteins in
Cancer
Accessing Statistics Canada Data Table and Vectors
Directly Extracts Complete CANSIM Data Tables
Visualization Package for CanvasXpress in R
Covariate Assisted Principal (CAP) Regression for Covariance
Matrix Outcomes
Comparative Analyses of Phylogenetics and Evolution in R
Capital Budgeting Analysis, Annuity Loan Calculations and
Amortization Schedules
A Virtual Patient Simulator in the Context of Calcium and
Phosphate Homeostasis
Numbers Figures and Creates Simple Captions
CAlibrating Penalities Using Slope HEuristics
Estimates population size from non-invasive sampling
Automatic Calibration by Evolutionary Multi Objective Algorithm
Covariate-Adaptive Randomization for Clinical Trials
Spatial Generalised Linear Mixed Models for Areal Unit Data
Data Used in the Vignettes Accompanying the CARBayes and
CARBayesST Packages
Spatio-Temporal Generalised Linear Mixed Models for Areal Unit
Data
Estimation of the Number of Fatalities from Carcass Searches
Cardiovascular and Autonomic Research Design
Companion to Applied Regression Data Sets
Identification of Cardinal Dates in Ecological Time Series
Cardiovascular Safety Exposure-Response Modeling in Early-Phase
Clinical Studies
High-Dimensional Regression and CAR Score Variable Selection
Statistical package for population size estimation in
capture-recapture models
Procedures for Computing Indices of Careless Responding
Continuous-Time Fractionally Integrated ARMA Process for
Irregularly Spaced Long-Memory Time Series Data
Estimation of caribou abundance based on large scale
aggregations monitored by radio telemetry
Functions for Statistics Classes at Carleton College
Ecological Quality Ratios Calculation and Plot
Carlson Elliptic Integrals and Incomplete Elliptic Integrals
A Collection of Database, Data Structure, Visualization, and
Utility Functions for R
Build Common Tables of Summary Statistics for Reports
CRISPR AnalyzeR for Pooled CRISPR Screens
Predicting Categorical and Continuous Outcomes Using One in Ten
Rule
Covariate Assisted Ranking and Screening for Large-Scale
Two-Sample Inference
Correlation-Adjusted Regression Survival (CARS) Scores
Tools for Understanding Highway Performance
Censored Autoregressive Model with Exogenous Covariates
Selection, Reverse-Engineering and Prediction in Cascade
Networks
Experimental Data of Cascade Experiments in Genomics
Casualty Actuarial Society Individual Claim Simulator
Fitting Flexible Smooth-in-Time Hazards and Risk Functions via
Logistic and Multinomial Regression
Identify Similar Cases for Qualitative Case Studies
Metodos De Estimacion Con Disenio Probabilistico y Estratificado
en Encuesta CASEN (Estimation Methods with Probabilistic
Stratified Sampling in CASEN Survey)
Detection of Statistically Significant Combinations of SNPs in
Association Mapping
Finds Missing Links and Metric Confidence Intervals in
Ecological Bipartite Networks
'caret' Applications for Spatial-Temporal Models
Analysis of categorical-variable datasets with missing values
Computerized Adaptive Testing and Decision Trees
Mapping of a Categorical Variable in a Panel Dataset
Covariate-Adjusted Tensor Classification in High-Dimensions
Taking the Pain Out of Catching and Handling Conditions
Test, Identify, Select and Mutate Categorical or Continuous
Values
Categorical Data Analysis Program Package
Datasetsfor Categorical Data Analysis by Agresti
Fishery Stock Assessment by Catch Dynamics Models
High Dimensional Factor Analysis and Confounder Adjusted Testing
and Estimation
Community Assembly by Traits: Individuals and Beyond
An R Package for Simulating IRT-Based Computerized Adaptive
Tests
Chronomics Analysis Toolkit (CAT): Periodicity Analysis
Formal Psychological Models of Categorization and Learning
Case-Control and TDT Meta-Analysis Package
Heatmap for Categorical Data using 'plotly'
Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc
Optimal Categorisation of Continuous Variables in Prediction
Models
Generation of IRT Response Patterns under Computerized Adaptive
Testing
Solution Paths for Linear and Logistic Regression Models with
SCOPE Penalty
Create Catseye Plots Illustrating the Normal Distribution of the
Means
Binary and Categorical Image Similarity Index
Special models for categorical variables
Computerized Adaptive Testing for Survey Research
Computation of the p-Value for the Exact Conditional
Cochran-Armitage Trend Test
Powerful Test for Survival Data under Non-Proportional Hazards
Accelerated Bayesian Analytics with DAGs
Nonparametric and Cox-Based Estimation of ATE in Competing Risks
Tools for Estimating Causal Dose Response Functions
Deriving Expressions of Joint Interventional Distributions and
Transport Formulas in Causal Models
Estimation of Causal Effects with Generalized Additive Models
Inferring Causal Effects using Bayesian Structural Time-Series
Models
Learning Stable Structures in Kinetic Systems
MBSTS Models for Causal Inference and Forecasting
An Interface to Specify Causal Graphs and Compute Bounds on
Causal Effects
Make, Update, and Query Binary Causal Models
Selection Bias Approach to Sensitivity Analysis for Causal
Effects
Estimation Methods for Causal Inference Based on Inverse
Probability Weighting
Control Charts with Guaranteed In-Control Performance and
Cautious Parameters Learning
CRISPR Pooled Screen Analysis using Beta-Binomial Test
Contextual Bayesian Anomaly Detection in R
Compare Baseline Characteristics Between Groups
Continuous Analog of a Binomial Distribution
Clustering of Multivariate Binary Data with Dimension Reduction
via L1-Regularized Likelihood Maximization
Simulation, Estimation and Segmentation of Composite Based
Structural Equation Models
Statistics Netherlands (CBS) Open Data API Client
Fits Cubic Bezier Spline Functions to Intertemporal and Risky
Choice Data
(Robust) Canonical Correlation Analysis via Projection Pursuit
Concordance Correlation Coefficient for Repeated (and
Non-Repeated) Measures
Combined Cluster and Discriminant Analysis
CCDr Algorithm for Learning Sparse Gaussian Bayesian Networks
Cox Model for Case-Cohort Data with Stratified
Subcohort-Selection
Transforming and Harmonizing CCHS Variables
Cross-Covariance Isolate Detect: a New Change-Point Method for
Estimating Dynamic Functional Connectivity
Convex Clustering Methods and Clustering Indexes
Estimation of Mean Costs in Censored Data
Significance Tests for Canonical Correlation Analysis (CCA)
One and two locus GWAS of binary phenotype with
case-control-population design
Removes the Cell-Cycle Effect from Single-Cell RNA-Sequencing
Data
Correct and Cluster Response Style Biased Data
Tools for the Continuous Convolution Trick in Nonparametric
Estimation
Consensus Analysis, Model-Based Clustering, and Cultural
Consensus Theory Applications
Cognitive Diagnostic Computerized Adaptive Testing
Retrieve Flu Season Data from the United States Centers for
Disease Control and Prevention ('CDC') 'FluView' Portal
Conditional Distance Correlation Based Feature Screening and
Conditional Independence Inference
Interface to the California Data Exchange Center
Quantile Regression for Random Variables on the Unit Interval
Coordinate Descent Algorithms for Lasso Penalized L1, L2, and
Logistic Regression
Cause-Deleted Life Expectancy Improvement Procedure
Tools to Download and Work with USDA Cropscape Data
Components of Canadian Monetary and Credit Aggregates
Phylogenetically Classifies Retention Mechanisms of Duplicate
Genes from Gene Expression Data
Constrained Dual Scaling for Detecting Response Styles
Sampling from Conditional C- and D-Vine Copulas
Benchmark functions for the Special Session and Competition on
Real-Parameter Single Objective Optimization at CEC-2013
R Interface for the C Implementation of CEC Benchmark Functions
Collection of Common Astronomical Conversion Routines and
Functions
Finds RNASeq Source Tissues Using In Situ Hybridisation Data
Translate Spreadsheet Cell Ranges to Rows and Columns
Functions to fit cell volume distributions and thereby estimate
cell growth rates and division times
Broken Adaptive Ridge AFT Model with Censored Data
Climate and Ecological Niche Factor Analysis
Estimation of the Time-Dependent ROC Curve and AUC for Censored
Survival Data
Linear Regression with a Randomly Censored Covariate
Finite Mixture of Multivariate Censored/Missing Data
Base de Datos de Facil Acceso del Censo 2017 de Chile (2017
Chilean Census Easy Access Database)
Fits Normal and Student-t Censored Regression Model
Changes United States Census Geographic Code into Name of
Location
Access the U.S. Census Bureau's Geocoding A.P.I. System
Show the Strength of Relationships Between Centre and Peripheral
Items
Non-Trivial Balance of Centrifuge Rotors
Cross-Entropy R Package for Optimization
Discriminant Analysis of Time Series in the Presence of
Within-Group Spectral Variability
Context Driven Exploratory Projection Pursuit
Outlier Detection Using the Iterated RMCD Method of Cerioli
(2010)
Identification and Analysis of ceRNA Regulation
Covariance Estimation Regularized by Nuclear Norm Penalties
Colony Formation Assay: Taking into Account Cellular Cooperation
Cause-Specific Framework for Competing-Risk Analysis
Counterfactual Decomposition: MC Integration of the G-Formula
Estimate quantiles using any order Cornish-Fisher expansion
Simple Similarity for User-Based Collaborative Filtering Systems
Canadian Forest Fire Danger Rating System
Collaborative Filtering by Reference Classes
Cystic Fibrosis Survival Prediction Model Based on Stanojevic
Model
Compare Groups, Analytically and Graphically
Calculate AUC-type measure when gold standard is continuous and
the corresponding optimal linear combination of variables with
respect to it
R-Based API for Accessing the MSKCC Cancer Genomics Data Server
(CGDS)
Array CGH Data Analysis and Visualization
Conditional Graphical LASSO for Gaussian Graphical Models with
Censored and Missing Values
Fits Conditional Generalized Linear Models
Clean and Analyze Continuous Glucose Monitor Data
Continuous Glucose Monitoring Data Analyzer
Powell Miscellaneous Functions for Teaching and Learning
Statistics
Statistical Methods and Models for Claims Reserving in General
Insurance
Nonparametric Change Detection in Multivariate Linear
Relationships
Geometrically Inspired Multivariate Changepoint Detection
Changepoint Analysis for Multivariate Time Series
Methods for Nonparametric Changepoint Detection
Change-Point Estimation for Expensive and High-Dimensional
Models
Change-Points Detections for Changes in Variance
Change Point Estimation for Clustered Signals
Markov Model for Online Multi-Channel Attribution
Shiny Web Application for the Multichannel Attribution Problem
Charge Transfer Rates and Charge Carrier Mobilities
Simplified Language for Plots and Charts
Check the Basic Validity of a (Function) Argument
Check-Fields and Check-Boxes for 'rmarkdown'
Checks if a Number is Valid Using the Luhn Algorithm
Install Packages from Snapshots on the Checkpoint Server for
Reproducibility
Check the Properties of Common R Objects
Analysis and Visualisation of Ecological Communities
Tools for Working with Data During Statistical Analysis
Calibration Functions for Analytical Chemistry
A Cheminformatics Modeling Laboratory for Fitting and Assessing
Machine Learning Models
Multivariate Statistical Analysis in Chemometrics
Exploratory Chemometrics for 2D Spectroscopy
Functions Supporting Packages ChemoSpec and ChemoSpec2D
Multiple Testing Methods for Exploratory Research
Read, Write, Create and Explore Chess Games
Change-in-Estimate Approach to Assess Confounding Effects
Closest History Flow Field Forecasting for Bivariate Time Series
Partitioning Chi-Squared and Tau Index for Three-Way Contingency
Tables
'Compressive' Hierarchical Kernel Clustering Toolbox
Data and Methods Around Reference Values in Pediatrics
Mapas de las Divisiones Politicas y Administrativas de Chile
(Maps of the Political and Administrative Divisions of Chile)
Processing Chill and Heat Models for Temperate Fruit Trees
Statistical Methods for Phenology Analysis in Temperate Fruit
Trees
Miscellaneous Tools for Chinese Text Mining and More
Nonparametric Methods for Identifying Differential Enrichment
Regions with ChIP-Seq Data
A Post Hoc Analysis for Pearson's Chi-Squared Test for Count
Data
Convert Antipsychotic Doses to Chlorpromazine Equivalents
Estimation and Hypothesis Testing for Threshold Regression
Thermodynamic Calculations and Diagrams for Geochemistry
Amend, Augment and Aid Analysis of John Snow's Cholera Map
Cholesky Decomposition of the Wishart Distribution
Simplify the Creation of Choropleth Maps in R
Contains an Administrative-Level-1 Map of the World
Contains Maps Used by the 'choroplethr' Package
Interface to Chromosome Counts Database API
Interactive Genomic Visualization of Biological Data
Chronological Objects which can Handle Dates and Times
Chunkwise Text-File Processing for 'dplyr'
Causal Inference in Case-Control Studies
Estimating and Testing Direct Effects in Directed Acyclic Graphs
using Estimating Equations
Weighted summary of cumulative incidence functions
Toolbox for Connectivity Informatics Technology Initiative
('CIFTI') Files
Tools for Reading and Visualizing CIFTI Brain Files
Causal Inference for Multiple Treatments with a Binary Outcome
A Computational Pipeline for Bulk 'ATAC-Seq' Profiles
Ready-to-Use Curated Gene Sets for 'cinaR'
Deciphering Central Informative Nodes in Network Analysis
Centered Isotonic Regression and Dose-Response Utilities
Curve Text Elements in 'Shiny' Using 'CircleType.js'
Maximum Likelihood Analysis of Circular Data
Statistical Analysis of Circular Data using Nonnegative
Trigonometric Sums (NNTS) Models
Detection of Outliers in Circular-Circular Regression
Spatial and Spatio-Temporal Bayesian Model for Circular Data
Circular Statistics, from "Topics in Circular Statistics" (2001)
Extreme Value Analysis for Circular Data
Analysis and Visualization of Circular Data
Common and Individual Structure Explained for Multiple Graphs
CIT Breast Cancer Molecular SubTypes Prediction
CIT Colon Cancer Molecular SubTypes Prediction
Confidence or Prediction Intervals, Quantiles, and Probabilities
for Statistical Models
Visualization of structure and contents of a database
Track Flows of Water Through an Urban System
Confidence Intervals Utilizing Uncertain Prior Information
Copula-Based Joint Analysis of Multiple Phenotypes
Client for the Comprehensive Knowledge Archive Network ('CKAN')
API
Composite Kernel Association Test for Pharmacogenetics Studies
Composite Kernel Machine Regression Based on Likelihood Ratio
Test
Optimal, Fast, and Reproducible Univariate Clustering
Measuring Morphological Diversity and Evolutionary Tempo
C++ Implementations of Phylogenetic Cladogenesis Calculations
Classical Age-Depth Modelling of Cores from Deposits
Time Series Modeling for Climate Change Proxies
Distribution-Free Tests of Non-Nested Models
Classes and Methods for "Class Comparison" Problems on
Microarrays
Classes and Methods for "Class Discovery" with Microarrays or
Proteomics
Construct Graphs of S4 Class Hierarchies
Generates a Visualization of Classifier Performance as a Grid of
Diagnostic Plots
Explore classification models in high dimensions
R Interface to the ClassyFire RESTful API
To Inspect and Manipulate Data; and to Keep Track of This
Process
Cleaning Geometries from Spatial Objects
A Tidy Data Model for Natural Language Processing
Simultaneous Variables Clustering and Regression
Composite Likelihood Estimation for Spatial Data
Clustering and Link Prediction Evaluation in R
Helpers for Developing Command Line Interfaces
Model-Based Clustering of Categorical Sequences
Mixtures of Continuous Time Markov Models
Fix Data and Create Report Tables from Different Objects
Analyzes Clickstreams Based on Markov Chains
Easily Download and Visualise Climate Data from CliFlo
Complex-Valued Wavelet Lifting Estimators of the Hurst Exponent
for Irregularly Sampled Time Series
Censoring Data and Likelihood-Based Correlation Estimation
Interface to Download Meteorological (and Hydrological) Datasets
Estimating Climate Stability from Climate Model Data
Climate Tools (Series Homogenization and Derived Products)
Climate Variability Indices for Ecological Modelling
Climate Classification According to Several Indices
Climate Downscaling Library for Daily Climate Model Output
Constrained L1-minimization for Inverse (covariance) Matrix
Estimation
Set of Tools to Compute Various Climate Indices
Simulation and Analysis Tools for Clinical Dose Response
Modeling
Clinical Trial Design and Data Analysis Functions
Summary Measures for Clinical Trials with Survival Outcomes
Recalibration Methods for Improved Clinical Utility of Risk
Scores
Hemodynamic Indexes Calculated from Clinical Monitoring
Calculating Likelihoods by Pedigree Paring
Read and Write from the System Clipboard
Constrained Inference for Linear Mixed Effects Models
Fitting Exact Conditional Logistic Regression with Lasso and
Elastic Net Penalties
Sparse Conditional Logistic Regression for Matched Studies
Seeking and Finding Clones in Copy Number and Sequencing Data
Composite Likelihood Inference and Diagnostics for Replicated
Spatial Ordinal Data
Interface to the Google Cloud Machine Learning Platform
Curve Linear Regression via Dimension Reduction
Central Limit Theorem Experiments (Theoretical and Simulation)
Cluster-Robust (Sandwich) Variance Estimators with Small-Sample
Corrections
Simultaneous Detection of Clusters and Cluster-Specific Genes in
High-Throughput Transcriptome Data
Statistical Methods for Analyzing Clustered Matched Pair Data
Clustering Dose-Response Curves and Fitting Appropriate Models
to Them
Clusters of Effects Curves in Quantile Regression Models
"Finding Groups in Data": Cluster Analysis Extended Rousseeuw et
al.
Performs Tests for Cluster Tendency of a Data Set
Analyze Clustered Data with Generalized Linear Models using the
Cluster Bootstrap
Causal Effects from Observational Studies with Clustered
Interference
Location and Visualization of Clustered Somatic Mutations
Random Cluster Generation (with Specified Degree of Separation)
Identifying clusters in genomics data by recursive partitioning
Execution of Multiple Clustering Algorithm
Optimal Distance-Based Clustering for Multidimensional Data with
Sequential Constraint
Unbiased Single-Cell Transcriptomic Data Cell Type
Identification
Evaluate Function Calls on HPC Schedulers (LSF, SGE, SLURM,
PBS/Torque)
Integrative Clustering for Heterogeneous Biomedical Datasets
A Parallel Clustering Non-Uniform Memory Access ('NUMA')
Optimized Package
Power Calculations for Cluster-Randomized and Cluster-Randomized
Crossover Trials
Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, K-Medoids
and Affinity Propagation Clustering
Reproducibility of Gene Expression Clusters
Calculate Cluster-Robust p-Values and Confidence Intervals
Searching for Optimal Clustering Procedure for a Data Set
Assessment of Stability of Individual Objects or Clusters in
Partitioning Solutions
Hierarchical Clustering with Spatial Constraints
K-means clustering with build-in missing data imputation
k-Prototypes Clustering for Mixed Variable-Type Data
Variable Selection in Clustering by Mixture Models for Discrete
Data
Methods for Joint Dimension Reduction and Clustering
Visualise Clusterings at Different Resolutions
Interactive Document for Working with Cluster Analysis
Clustering of Variables Around Latent Variables
Variable Selection for Gaussian Model-Based Clustering
Gaussian-Based Visualization of Gaussian and Non-Gaussian
Model-Based Clustering
Tools for Customer Lifetime Value Estimation
Covariance Matrix Adapting Evolutionary Strategy
Covariance Matrix Adaptation Evolution Strategy
Representation Tool For Output Of Connectivity Map (CMap)
Analysis
Matching Algorithms for Causal Inference with Clustered Data
Computer Model Calibration for Deterministic and Stochastic
Simulators
An Implementation of the 'Congruent Matching Cells' Method
Framework for Building Interfaces to Shell Commands
Reusable Assisting Functions for Child Mortality Estimation
Bi-Level Selection of Conditional Main Effects
Collective Matrix Factorization for Recommender Systems
Computational Methods for Numerical Analysis
Subdistribution Analysis of Competing Risks
Use IPW to Estimate Treatment Effect under Competing Risks
Analysis of Competing Risks Using Quantile Regressions
Misc Functions of the Center for Mathematical Research
Interactive Document for Working with Confusion Matrix
Statistical Methods for Composite Material Data
The Complex Multivariate Gaussian Distribution
Causal Modeling with Coincidence Analysis
Common Network Asset Indices Methodology (CNAIM)
Optimizing Consistency and Coverage in Configurational Causal
Modeling
Canonical Non-Symmetrical Correspondence Analysis in R
Complex-Valued Wavelet Lifting for Signal Denoising
Complex-Valued Wavelet Lifting for Univariate and Bivariate Time
Series Analysis
Pre-process DNA Copy Number (CN) Data for Detection of CN Events
Fast Algorithms for Frequency-Preserving Null Models in Ecology
Dirichlet-Multinomial Modelling of Relative Abundance Data
A Versatile Toolkit for Copy Number Variation Relationship Data
Analysis and Visualization
Bayesian "Now-Cast" Estimation of Event Probabilities in
Multi-Party Democracies
Biclustering via Latent Block Model Adapted to Overdispersed
Count Data
Constrained B-Splines (Sparse Matrix Based)
COmbat CO-Normalization Using conTrols (COCONUT)
Statistical Comparisons of Two or more Alpha Coefficients
Output Analysis and Diagnostics for MCMC
A Basic Set of Functions for Compositional Data Analysis
Markov chain Monte Carlo burn-in based on "bridge" statistics
Transformation-Free Linear Regression for Compositional Outcomes
and Predictors
Automated C Code Generation for 'deSolve', 'bvpSolve'
Automatic Codebooks from Metadata Encoded in Dataset Attributes
Analysis of R Code for Reproducible Research and Code
Comprehension
Generate 'CodeMeta' Metadata for R Packages
Deterministic Categorization of Items Based on External Code
Data
The CODEX (Comorbidity, Obstruction, Dyspnea, and Previous
Severe Exacerbations) Index: Short and Medium-Term Prognosis in
Patients Hospitalized for Chronic Obstructive Pulmonary Disease
(COPD) Exacerbations
Alternative Factor Coding Matrices for Linear Model Formulae
Robust Coefficient Alpha and Omega with Missing and Non-Normal
Data
Species coexistence modeling and analysis
Cognitive Mapping Tools Based on Coding of Textual Sources
Authentication for 'Shiny' Apps with 'Amazon Cognito'
Simulation of Cohort Platform Trials for Combination Treatments
Contextualization and Evaluation of COI-5P Barcode Data
Conditional Inference Procedures in a Permutation Test Framework
Get 'Cryptocurrencies' Market Cap Prices from Coin Market Cap
Simultaneous Confidence Interval for Multinomial Proportion
Consistent Monitoring of Stationarity and Cointegrating
Relationships
Parameter Estimation and Inference in a Cointegrating Regression
Constrained Optimization on Linear Function
Collapses Levels, Computes Information Value and WoE
Interactive Collapsible Tree Diagrams using 'D3.js'
Quickly and Neatly Collect Arguments from One Environment to
Pass to Another
Quantified Risk Assessment Data Collection
Check for Namespace Collisions Across Packages and Functions on
CRAN
Collocation Inference for Dynamic Systems
Collapsed Latent Position Cluster Model for Social Networks
Auxiliary Package for Package 'CollapsABEL'
Dengue Cases and Climate Variables in Colombo Sri Lanka
Colocalisation Tests of Two Genetic Traits
Conduct Co-Localization Analysis of Fluorescence Microscopy
Images
Distance Metrics for Image Color Similarity
Implementation of Colored Independent Component Analysis and
Spatial Colored Independent Component Analysis
Extract Colors from Windows BMP, JPEG, PNG, TIFF, and SVG Format
Images
Plot and add custom coloring to Venn diagrams for 2-dimensional,
3-dimensional and 4-dimensional data
Coloring Wildlife Distributions in Space-Time
Colorize Old Images Using the 'DeOldify' Image Colorization API
Color Palettes using Colormaps Node Module
Optimized Rendering of Fold Changes and Confidence Values
Color Palettes for EPL, MLB, NBA, NHL, and NFL Teams
A Toolbox for Manipulating and Assessing Colors and Palettes
Color Calculations with Emphasis on Spectral Data
Tools for colors in a Hue-Saturation-Value (HSV) color model
A Colour Picker Tool for Shiny and for Selecting Colours in
Plots
Creates Co-Occurrence Matrices of Spatial Data
Analysis of Concept Maps and Concept Landscapes
A Combined Association Test for Genes using Summary Statistics
Calculate Scores and Marks for Track and Field Combined Events
Estimation of Optimal Portfolio Weights by Combining Simple
Portfolio Strategies
Construction Methods of some Series of PBIB Designs
Exact Test from the Combinations of Mutually Exclusive
Alterations (CoMEt) Algorithm
Commonly Used Functions for R Shiny Applications
Computational Methods for Immune Cell-Type Subsets
Print Nicely Formatted Comments for Use in Script Files
Useful Libraries for Building a Java Based GUI under R
High Performance CommonMark and Github Markdown Rendering in R
JAR Files of the Apache Commons Mathematics Library
Comparative Phylogeographic Analysis using the Community Tree
Framework
Creates empty plots with compact axis notation
Comparison Functions for Clustering and Record Linkage
Compare Two Correlated C Indices with Right-censored Survival
Outcome
Interface to Diverse Estimation Methods of Causal Networks
Statistical Functions for the Design of Studies with Composite
Endpoints
Do a Git Style Diff of the Rows Between Two Dataframes with
Similar Structure
comparison of medical forms in CDISC ODM format
Correct for Verification Bias in Diagnostic Accuracy & Agreement
Multivariate Likelihood Ratio Calculation and Evaluation
Comparison of Cumulative Incidence Between Two Groups Under
Competing Risks
Comparison of Survival Curves Between Two Groups
Conformational Manipulations of Protein Atomic Structures
C++ Implementation of Component-Wise Boosting
Tools for Retrieval and Storage of Functional Genomics Data
A Graphical User Interface for Antitrust and Trade Practitioners
Calculate the Proportion of Permutations in Line with an
Informative Hypothesis
Create Complex UpSet Plots Using 'ggplot2' Components
Robust Linear Regression with Compositional Data as Covariates
Compositional, Multivariate and Univariate Time Series Outlier
Ensemble
Univariate Feature Selection and Compound Covariate for
Predicting Survival
Distribution Function of Quadratic Forms in Normal Variables
Composite-Likelihood Based Analysis of Random Fields
Flexible Framework for Simulating Community Assembly
Interface with the United Nations Comtrade API
Calculate the AQI from Pollutant Concentration
Human-Friendly Text from Unknown Strings
Optimisation with Continuous Convex Piecewise (Linear and
Quadratic) Functions
An Alternative to the Kruskal-Wallis Based on the Kendall Tau
Distance
Copy Number Profile Curve-Based Association Test
Computes & Plots Compatibility (Confidence), Surprisal, &
Likelihood Distributions
Approximate Conditional Inference for Logistic and Loglinear
Models
Parameter estimation in conditional GEE for recurrent event gap
times
Computation of P Values and Bayes Factors for Conditioning Data
Control How Many Times Conditions are Thrown
Conditional Density Estimation with Neural Network Conditional
Mixtures
Condition Number Regularized Covariance Estimation
Estimation of the Conditional Survival Function for Ordered
Multivariate Failure Time Data
Conditional Truncated Multivariate Normal Distribution
Query-Driven Pipeline Execution and Query Templates
Conditional Visualization for Statistical Models
Interactive Conditional Visualization for Supervised and
Unsupervised Models in Shiny
Primal or Dual Cone Projections with Routines for Constrained
Regression
Visualization and Analysis of Statistical Measures of Confidence
Confidence Estimation of Environmental State Classifications
Manage Environment Specific Configuration Values
Package to Parse an INI File, Including Variable Interpolation
An Implementation of Parsing and Writing Configuration File
(JSON/INI/YAML/TOML)
Descriptive Interpretations of Confidence Intervals
Confidence Interval for the Univariate Population Variance
without Normality Assumption
An Alternative Conflict Resolution Strategy
Transductive and Inductive Conformal Predictions for
Classification Problems
Sensitivity Analyses for Unmeasured Confounding in Meta-Analyses
Diagnostics for Confounding of Time-Varying and Other Joint
Exposures
Configural Frequencies Analysis Using Log-Linear Modeling
Estimates and Bounds for the False Discovery Proportion, by
Permutation
Distance Metrics for Trees Generated by Congreve and Lamsdell
Algorithms for Fitting Circles, Ellipses and Conics Based on the
Work by Prof. Nikolai Chernov
An Implementation of Conjoint Analysis Method
A package to check the cancellation axioms of conjoint
measurement
A Parametric Method for Generating Synthetic Data
Integrates with the 'RStudio' Connections Pane and 'pins'
Tools for Working with Connectivity Data
Conover-Iman Test of Multiple Comparisons Using Rank Sums
Computation of Parameters Used in Preliminary Assessment of
Conservation Status
Partial Linear Least-Squares Regression using Constrained
Splines
Compute the Median Ranking(s) According to the Kemeny's
Axiomatic Approach
Fits Regression & ARMA Models Subject to Constraints to the
Coefficient
Reference on Constants, Units and Uncertainty
Identify Event Sequences Using Time Series Joins
Constrained, Covariance-Matching Constrained and Universal Point
or Block Kriging
Models Spatially Continuous and Discrete Population Genetic
Structure
Social Contact Matrices for 152 Countries
Deque, Set, and Dict - R6 Based Container Classes with Iterators
Clustering and Classification with the Contaminated Normal
An Interface for Content-Based Identifiers
Simulation and Analysis of Contextual Multi-Armed Bandit
Policies
Contouring of Non-Regular Three-Dimensional Data
Create Contour Plots from Data or a Function
Plots x,y,z Co-Ordinates in a Contour Map
A Tiny Contribution Table Generator Based on 'ggplot2'
Quantile Comparison for Two-Sample Right-Censored Survival Data
Disciplined Convex Programming in R using 'Convex.jl'
Income Concentration Analysis with Complex Survey Samples
Probabilistic Species Co-Occurrence Analysis in R
Co-Operation: Fast Covariance, Correlation, and Cosine
Similarity Operations
Important Concepts of Cooperative Game Theory
Cooperative Aspects of Linear Production Programming Problems
Cooperative aspects of optimal trees in weighted graphs
Automated Cleaning of Occurrence Records from Biological
Collections
General Bivariate Copula Theory and Many Utility Functions
Fitting the copCAR Regression Model for Discrete Areal Data
Copula-Based Semiparametric Analysis for Time Series Data with
Detection Limits
Coverage Probability Excursion (CoPE) Sets
Sample Size Calculation for Two Primary Time-to-Event Endpoints
in Clinical Trials
Copula-Based Estimation and Statistical Process Control for
Serially Correlated Time Series
Copula Markov Model with Dependent Censoring
Association Analysis of Bivariate Survival Data Based on Copulas
Copula-Based Regression Models for Bivariate Censored Data
Copula Based Bivariate Beta-Binomial Model for Diagnostic Test
Accuracy Studies
Estimation of Distribution Algorithms Based on Copulas
Copula Mixed Models for Multivariate Meta-Analysis of Diagnostic
Test Accuracy Studies
Computing Response Similarity Indices for Multiple-Choice Tests
Apply 'colorffy' Color Gradients Within 'shiny' Elements
Collection of Rudimentary Bioinformatics Tools
Generate High-Dimensional Binary Data with Correlation
Structures
Community Estimation in G-Models via CORD
Set-Based Differential Covariance Testing for Genomics
Programmatic Analysis of Sediment Cores Using Computed
Tomography Imaging
Classification, Regression and Feature Evaluation
R Binding for the 'Certifiably Optimal RulE ListS (Corels)'
Learner
Core Functionality for Simulating Quantities of Interest from
Generalised Linear Models
TDT for compound heterozygous and recessive models
Hidden Markov Models of Character Evolution
Record Linkage, Incorporating Imputation for Missing Agreement
Patterns, and Modeling Correlation Patterns Between Fields
The Clustering of Regression Models Method
Collection of Scripts for Interface Between 'Cornerstone' and
'R'
Confounding Robust Independent Component Analysis for Noisy and
Grouped Data
The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Dataset
Efficient Estimation of Covariance and (Partial) Correlation
Statistics and Data Sets for Corpus Frequency Data
A 'Shiny' App for Exploration of Text Collections
Power Calculations for Assessing Correlates of Risk in Clinical
Efficacy Trials
Managing, Querying and Analyzing Tokenized Text
Implementation of 2D Correlation Analysis in R
Correlation Arrays and 2-Sample Correlation Matrices
Nonparametrics with Clustered Binary and Multinomial Data
Correcting the Coverage of Credible Sets from Bayesian Genetic
Fine Mapping
Finding Associations in Position-Wise Aligned DNA Sequence
Dataset
Correct Overloaded Peaks from GC-APCI-MS Data
Functions and Methods for Correspondence Regression
Speed Up Exploratory Data Analysis (EDA) with the Correlation
Funnel
Explore Correlations Between Variables in a Machine Learning
Model
Estimate Correlations Between Repeatedly Measured Endpoints
(E.g., Reliability) Based on Linear Mixed-Effects Models
Modeling Correlational Magnitude Transformations in
Discretization Contexts
Arbitrary Bounding of Series and Time Series Objects
Some Empiric and Nonparametric Copula Models
Tools for processing data after a Genome Wide Association Study
Bound Constrained Optimal Sample Allocation
Tools for estimating and predicting the cosinor model
Extended Tools for Cosinor Analysis of Rhythms
Functions for cosmological distances, times, luminosities, etc
Fit Regularized Nonparametric Regression Models Using COSSO
Penalty
Copula-Based Semiparametric Models for Spatio-Temporal Data
Connect to and Work with CouchDB Databases
Locates and Counts Pixels Within Color Range(s) in Images
Estimation and Inference Methods for Counterfactual Analysis
Comprehensive Automatized Evaluation of Distribution Models for
Count Data
Discrete Response Regression for High-Dimensional Data
Penalized Estimation of Flexible Hidden Markov Models for Time
Series of Counts
Flexible Univariate Count Models Based on Renewal Processes
Mean and Variance Modeling of Count Data
Convert Counts to Fragments per Kilobase of Transcript per
Million (FPKM)
Transform Counts in RNA-Seq Data Analysis
Quantify United States County-Level Flood Measurements
Convert from UTC to Local Time for United States Counties
Compiles Meterological Data for U.S. Counties
A Residue-Residue Contact Detecting Method
Local Polynomial Regression of State Dependent Covariates in
State-Space Models
Tests on Properties of Space-Time Covariance Functions
Brownian Motion Processes for 'nlme'-Models
Combine Partial Covariance / Relationship Matrices
Produce Forest Plots to Visualize Covariate Effects
Test for Equality of Covariance Matrices
Load and Analyze Live Data from the CoViD-19 Pandemic
Selected 'Drugbank' Drugs for COVID-19 Treatment Related Data in
R Format
The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Italy Dataset
Fetches Data on Covid-19 Mobility Trends from Different Sources
Pulls the Covid-19 Data from the New York Times Public Data
Source
COVID-19 Cases in Switzerland and Principality of Liechtenstein
Downloading, Reading and Analysing PNAD COVID19 Microdata
Mutation Analysis Toolkit for COVID-19 (Coronavirus Disease
2019)
Latent Class Models with Covariate Effects on Underlying and
Measured Variables
A simultaneous regression model for the mean and covariance
Robust Covariance Estimation via Nearest Neighbor Cleaning
Model-Free Covariate Selection in High Dimensions
Tests for Determining if the Covariance Structure of
2-Dimensional Data is Separable
VITA and IG Simulation for Given Covariance and Marginals
Statistical Tools for Covariance Analysis
Performs Segmented Linear Regression on Two Independent
Variables
Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Messages, Warnings, Strings with Ascii Animals
Duration-Based Quantities of Interest for the Cox Proportional
Hazards Model
Cox-Type Models for Interval-Censored Data
Cox Mixed-Effects Models for Genome-Wide Association Studies
Cox Regression with Firth's Penalized Likelihood
Sparse Estimation of Cox Proportional Hazards Models via
Approximated Information Criterion
Stochastic Gradient Descent log-Likelihood Estimation in Cox
Proportional Hazards Model
Cox Regression (Proportional Hazards Model) with Multiple Causes
and Mixed Effects
R-Squared Measure Based on Partial LR Statistic, for the Cox PH
Regression Model
Cox Proportional Hazards Regression for Right-Truncated Data
Confirmatory Path Analysis through the d-sep tests
Bayesian Meta Analysis for Studying Cross-Phenotype Genetic
Associations
Methods to perform Common Principal Component Analysis (CPCA)
Efficient and Customized Preconditioned Conjugate Gradient
Method for Solving System of Linear Equations
Concordance Probability Estimates in Survival Analysis
Association Between Methylation and a Phenotype of Interest
CpG Filtering Method Based on Intra-Class Correlation
Coefficients
Sequential and Batch Change Detection Using Parametric and
Nonparametric Methods
Correction of the P-Value after Multiple Coding in Generalized
Linear Models
Composition of Probabilistic Preferences (CPP)
Fast Implementation of Dijkstra Algorithm
The Conditional Probability Function of a Competing Event
Conditional Probit Model for Analysing Continuous Outcomes
Functions for Working with Danish CPR Numbers
Change-Point Detection by Sample-Splitting Methods
Nonparametric Change Point Estimation for Survival Data
Simulating Survival Data from Change-Point Hazard Distributions
A Toolbox for Using the CPS’s Voting and Registration Supplement
Quantile, Composite Quantile Regression and Regularized Versions
Conditional Maximum Likelihood for Quadratic Exponential Models
for Binary Panel Data
Power Calculation for Weighted Log-Rank Tests in Cure Rate
Models
Multivariate Nonparametric Cramer-Test for the
Two-Sample-Problem
Network Analysis of Dependencies of CRAN Packages
Download Logs from the 'RStudio' 'CRAN' Mirror
Package Directives and Collaboration Networks in CRAN
RStudio Addin for Searching Packages in CRAN Database Based on
Keywords
Conditional Random Sampling Sparse Matrices
Fit Continuous-Time Correlated Random Walk Models to Animal
Movement Data
Censored Regression with Conditional Heteroscedasticity
Clustering of Genomic Regions Analysis Method
Tools for Managing SSH and Git Credentials
Functions for calculating the CreditMetrics risk model
Toolkit for Credit Modeling, Analysis and Visualization
Evaluation of Credit Risk with Structural and Reduced Form
Models
Simple Conjoint Tidying, Analysis, and Visualization
Obtain and Visualize Regulome-Gene Expression Correlations in
Cancer
Conditional Random Fields for Labelling Sequential Data in
Natural Language Processing
Analyze Cricketers and Cricket Teams Based on ESPN Cricinfo
Statsguru
Group-Based Modelling of Longitudinal Data
Access Crime Data from the Open Crime Database
Statistical Methods for Crime Series Linkage
A Comprehensive Set of Functions to Clean, Analyze, and Present
Crime Data
Fits a Model that Partitions the Covariate Space into Blocks in
a Data- Adaptive Way
Continual Reassessment Method (CRM) for Phase I Clinical Trials
Fetch 'Scholary' Full Text from 'Crossref'
CCMN and Other Normalization Methods for Metabolomics Data
Object-Oriented Implementation of CRM Designs
Cellwise Robust M-Regression and SPADIMO
Downloads and Builds datasets for Climate Reference Network
Implementation Helper for '[' and '[<-' of Custom Matrix-Like
Types
A Dashboard to Visualize Scientific Workflows in 'Cromwell'
Schedule R Scripts and Processes with the 'cron' Job Scheduler
Open Data of Agricultural Production of Crops of Peru
Access Cropland Data Layer Data via the 'CropScape' Web Service
Climate Crop Zoning Based in Air Temperature for Brazil
Apply Functions to All Combinations of List Elements
Analysis and Search of Crossover Designs
Confidence intervals for crossover points of two simple
regression lines
Joint Distribution of Number of Crossings and Longest Run
Inter-Widget Interactivity for HTML Widgets
Verbal Autopsy Data Transformation for InSilicoVA and InterVA5
Algorithms
Classes and Methods for Cross Validation of "Class Prediction"
Algorithms
Rename and Encode Data Frames Using External Crosswalk Files
Constrained Regression Model for an Ordinal Response and Ordinal
Predictors
Bayesian Nonparametric Chinese Restaurant Process Clustering
with Entropy
Recurrence Quantification Analysis for Categorical and
Continuous Time-Series
Penalized Variable Selection in Competing Risks Regression
Competing risks regression for Stratified and Clustered data
Stepwise Covariate Selection for the Fine & Gray Competing Risks
Regression Model
A Robust and Powerful Test of Abnormal Stock Returns in
Long-Horizon Event Studies
Nonlinear Regression Parameters Estimation by 'CRS4HC' and
'CRS4HCe'
Tidying and Analyzing 'Coursera' Research Export Data
Doubly Robust Inverse Probability Weighted Augmented GEE
Estimator
Sample Size Estimation Functions for Cluster Randomized Trials
Interface to Climatic Research Unit Time-Series Version 3.21
Data
Changing the Reference Group without Re-Running the Model
Identifying Cryptic Relatedness in Genetic Association Studies
Calculate the Relative Crystallinity of Starch by XRD and FTIR
A Cross-Scale Analysis Tool for Model-Observation Visualization
and Integration
Bounds on Distributional Treatment Effect Parameters
Functions for Conditional Simulation in Regression-Scale Models
Frequent Contiguous Sequential Pattern Mining of Text
CRISPR-Based Salmonella Enterica Serotype Analyzer
Connectivity Scores with Factor Analysis
Cost-Sensitive Multi-Criteria Ensemble Selection for Uncertain
Cost Conditions
Correlates of State Policy Data Set in R
Complete Discrete Fourier Transform (DFT) and Periodogram
A Tool for the Correlates of State Policy Project Data
Data Only: The Correlates of State Policy Project Dataset
Methods to Test Hypotheses on the Distribution of Spatial Point
Processes
csSAM - cell-specific Significance Analysis of Microarrays
Selection of Number of Clusters via Normalized Clustering
Instability
Substantive significance testing for regression estimates and
marginal effects
Assessing Skill of Climate Forecasts on Seasonal-to-Decadal
Timescales
Combined Selection and Uncertainty Visualiser (CSUV)
Read and Write CSV Files with Selected Conventions
Import and Export CSV Data with a YAML Metadata Header
Interactive Application for Working with Contingency Tables
A Method for 'Connecting The Dots' in Weighted Graphs
Closed Testing with Globaltest for Pathway Analysis
A Text Mining Toolkit for Chinese Document
Estimating the Parameters of a Continuous-Time Markov Chain from
Discrete-Time Data
Modeling Animal Movement with Continuous-Time Discrete-Space
Markov Chains
Collaborative Targeted Maximum Likelihood Estimation
Censored and Truncated Quantile Regression
Retrieve and Analyze Clinical Trials in Public Registers
Assess the Stability of Candidate Housekeeping Genes
Continuous Time Structural Equation Modelling
Continuous Time SEM - 'OpenMx' Based Functions
Interactive Document for Working with Classification Tree
Analysis
A Class of Mixture Models for Ordinal Data
Adaptive Multivariate Integration over Hypercubes
Rule- And Instance-Based Regression Modeling
Charles's Utility Function using Formula
Tools, Measures and Statistical Tests for Cultural Evolution
Analyze Multivariate Phenotypes by Combining Univariate Results
Extends ddply to allow calculation of cumulative quantities
Change Point Detection in Genomic Sequences
Partial Function Application with %<%, %-<%, and %><%
Confidence Intervals for the Current Status Model
Multiple Curve Comparisons Using Parametric Bootstrap
Tukey Curve Depth and Distance in the Space of Curves
Cusp-Catastrophe Model Fitting Using Maximum Likelihood
Evaluation Metrics for Customer Scoring Models Depending on
Binary Classifiers
Customized Training for Lasso and Elastic-Net Regularized
Generalized Linear Models
Customizable Higher-Order Recipe Step Functions
Costs Allocation for the Installation of an Elevator
Cumulative Sum (CUSUM) Charts for Monitoring of Hospital
Performance
Compute Decision Interval and Average Run Length for CUSUM
Charts
CUTOFF: A Spatio-temporal Imputation Method
Determine and Evaluate Optimal Cutpoints in Binary
Classification Tasks
Optimal Equal-HR Method to Find Two Cutpoints for U-Shaped
Relationships in Cox Model
An R package to perform LPUE standardization and stock
assessment of the English Channel cuttlefish stock using a
two-stage biomass model
Compute Expected Shortfall and Value at Risk for Continuous
Distributions
Cross-Validated Area Under the ROC Curve Confidence Intervals
Estimation of the Calibration Equation with Error-in
Observations
Coefficient of Variation (CV) with Confidence Intervals (CI)
Efficient Design and Analysis of Cluster Randomized Trials
Tests for the Equality of Coefficients of Variation from
Multiple Groups
Lasso Penalized Precision Matrix Estimation
Cramer von Mises Tests for Discrete or Grouped Distributions
Calculate the predictive squared correlation coefficient
Compute Risk Scores for Cardiovascular Diseases
Fast Cross-Validation via Sequential Testing
Cross-validation tools for regression models
Regularized Estimators of Covariance Matrices with CV Tuning
Tools to Create, Modify and Manage 'CWB' Corpora
Miscellaneous Functions for Math, Plotting, Printing,
Statistics, Strings, and Tools
extend cxxfunction by saving the dynamic shared objects
Cycle Routing and Data for Cycling Advocacy
Survival Modeling with a Periodic Hazard Function
Cyclic Coordinate Descent for Logistic, Poisson and Survival
Analysis
Query 'Team Cymru' 'IP' Address, Autonomous System Number
('ASN'), Border Gateway Protocol ('BGP'), Bogon and 'Malware'
Hash Data Services
Cycle and Phase Identification for mastication data
Agent-Based Model for Taenia_solium Transmission and Control
Computes Signaling and Population Stats for Cytometry Data on
Cytobank using 'CytobankAPI'
Bridging and Extending the CytobankAPI Package in R to the
Cytobank Web Application
Plot Fan Plots for Cytometry Data using 'ggplot2'
Automated Cytometry Gating and Annotation
Use Open Data from the Czech Statistical Office in R
Tools for creating D3 JavaScript network, tree, dendrogram, and
Sankey graphs from R
Interactive Charts of Nested and Hierarchical Data with 'D3.js'
Create Interactive Collapsible Trees with the JavaScript 'D3'
Library
Data Analysis and Graphics Data and Functions
Data Sets and Functions, for Demonstrations with Expression
Arrays and Gene Sequences
Damped Anderson Acceleration with Epsilon Monotonicity for
Accelerating EM-Like Monotone Algorithms
Data Analysis using Bootstrap-Coupled Estimation
Data Analysis with Ceiling and/or Floor Data
Three-Way / Multigroup Data Analysis Through Densities
Functions Useful in the Design and ANOVA of Experiments
Design and Analysis of Experiments with R
Graphical Analysis of Structural Causal Models
Dynamical Assembly of Islands by Speciation, Immigration and
Extinction
moDel Agnostic Language for Exploration and eXplanation
The DALY Calculator - Graphical User Interface for Probabilistic
DALY Calculation in R
Dynamic Assembly Model of Colonization, Local Extinction and
Speciation
Interface to Drosophila Activity Monitor System Result Files
Dams in the United States from the National Inventory of Dams
(NID)
Dandelion Plot for R-Mode Exploratory Factor Analysis
Design and Analysis of Non-Inferiority Trials
Discriminant Adaptive Nearest Neighbor Classification
R Client for the Statistics Denmark Databank API
'purrr'-Like Apply Functions Over Input Elements
Data Quality Assessment for Process-Oriented Data
Estimating Dark Diversity and Site-Specific Species Pools
Importing and Analysing SNP and Silicodart Data Generated by
Genome-Wide Restriction Fragment Analysis
Statistical Tools to Analyze Your Darts Game
An Interface to the 'dash' Ecosystem for Authoring Reactive Web
Applications
Interactive Data Visualization with D3.js
Customise the Appearance of 'shinydashboard' Applications using
Themes
Core Interactive UI Components for 'Dash'
Interactive React-Based Pivot Tables for Dash
Core Interactive Table Component for 'dash'
Tools for Reading, Processing and Writing 'DSSAT' Files
General Purpose Hierarchical Data Structure
Functional Data Analysis with Linear Differential Equations
Wrapper for 'TCdata360' and 'Govdata360' API
Connecting to Various Database Platforms
JAR Dependencies for the 'DatabaseConnector' Package
Swarm Intelligence for Self-Organized Clustering
Interactive and Reproducible Data Cleaning
Tools for Easily Combining and Cleaning Data Sets
Compare Two Data Frames and Summarise the Difference
An Interactive Editor for Viewing, Entering, Filtering & Editing
Data
Make it Easier to Enter Questionnaire Data
Familiarity with Dataframes Before Data Manipulation
Estimating Finite State Machine Models from Data
Export Data from R so 'DataGraph' can Read it
A Suite of Checks for Identification of Potential Errors in a
Data Frame as Part of the Data Screening Process
A system for mapping foreign objects to R variables and
environments
Create and Append a Data Dictionary for an R Dataset
Create, Refine, and Cluster Data Nuggets
Easily Source Publicly Available Data on Derivatives
A Flexible Container to Transport and Manipulate Data and
Associated Resources
Efficient and Flexible Data Preprocessing Tools
Performs variable level data quality checks and generates
summary statistics
Reproducible Data Screening Checks and Report of Possible Errors
C3S Quality Control Tools for Historical Climate Data
Retrieval Functions for USGS and EPA Hydrologic and Water
Quality Data
Data Bank for Statistical Analysis and Visualization
Row by Row Data Processing Tool, Using 'DataSailr' Script
Datasets from the Book "An Introduction to Clustering with R"
Create Lightweight Schema.org Descriptions of Data
An Implementation of a SAS-Style Data Step
Provides a Link Between the 'Refinitiv Datastream' System and R
Data Visualisation Using an HTML Page and 'D3.js'
Traduce al Español Varios Conjuntos de Datos de Práctica
Functions for "Data Analysis in Vegetation Ecology"
Discriminant Analysis with Additional Information
Discrete Bayesian Additive Regression Trees Sampler
Goodness-of-fit and two sample comparison tests using sample
entropy
Detecting Breakpoints and Estimating Segments in Trend
A Double Bootstrap Method for Analyzing Linear Models with
Autoregressive Errors
Read and Write Files to SQLite Databases
methods of distance-based gene set functional enrichment
analysis
Compute the NPMLE of distribution from doubly censored data
Deterministic Blockmodeling of Signed, One-Mode and Two-Mode
Networks
Distance-Based Measures of Spatial Structures
Dynamic Bayesian Network Structure Learning, Parameter Learning
and Forecasting
Dynamic Bayesian Network Learning and Inference
Simplifies Plotting Data Inside Databases
Density Based Clustering of Applications with Noise (DBSCAN) and
Related Algorithms
Inferring Condition-Specific Networks via Differential Network
Inference
Dynamic Correlation Analysis for High Dimensional Data
Detrended Fluctuation and Detrended Cross-Correlation Analysis
Analyzing Dichotomous Choice Contingent Valuation Data
Metadata Validation for Data Coordinating Centers
Differential Community Detection in Paired Biological Networks
Clustering Big Data using Expectation Maximization Star (EM*)
Algorithm
Data Cloud Geometry (DCG): Using Random Walks to Find Community
Structure in Social Network Analysis
Differential Co-expression Analysis and Differential Regulation
Analysis of Gene Expression Microarray Data
Analysis of Ontologies and Protein Domain Annotations
Claims Reserving under the Double Chain Ladder Model
Data Cloning and MCMC Tools for Maximum Likelihood Methods
Functions for the Detection of Spatial Clusters of Diseases
Model-Based Detection of Disease Clusters
Information Matrix for Diagnostic Classification Models
Hierarchical Models Made Easy with Data Cloning
Modify Data Using Externally Defined Modification Rules
List Linear n-Peptide Constraints for Overlapping Protein
Regions
A Fast Implementation of Distance Covariance
Distance Covariance and Correlation for Time Series Analysis
Conventional Cross-validation statistics for climate-growth
model
Depth-Based Classification and Calculation of Data Depth
Variance Stabilization by Data-Driven Haar-Fisz (for
Microarrays)
The Data Defect Index for Samples that May not be IID
Distance & Density-Based Outlier Detection
Diagonally Dominant Principal Component Analysis
Analysis and Visualization of Droplet Digital PCR in R and on
the Web
Disease-Drived Differential Proteins Co-Expression Network
Analysis
Data-Driven Sparse Partial Least Squares Robust to Missing
Samples for Mono and Multi-Block Data Sets
Learning Bayesian Networks with Mixed Variables
Deconvolution density estimation with adaptive methods for a
variable prone to measurement error
Conventional and Fuzzy Data Envelopment Analysis
A Post-Clustering Denoiser for COI-5P Barcode Data
Bayesian Inference for Differential Equations
Debug Tool to Watch Objects/Expressions While Running an R
Script
Detecting Changes in Autocorrelated and Fluctuating Signals
DEComposition of Indirect and Direct Effects
Bindings for 'Mapbox' Ear Cutting Triangulation Library
Implementation of Multi Objective Decision Analysis
Quantitative Support of Decision Making under Uncertainty
Differential Co-Expression and Differential Expression Analysis
Decode Coded Variables to Plain Text and the Other Way Around
Time Series Prediction with PSF and Decomposition Methods (EMD
and EEMD)
Empirical Mode Decomposition for Cyclostratigraphy
Deconvolution Estimation in Measurement Error Models
Identifies Signatures Present in a Tumor Sample
Deductive Correction, Deductive Imputation, and Deterministic
Correction
Data Correction and Imputation Using Deductive Methods
Visualise and Explore the Deep Dependencies of R Packages
Sequential Design for Deep Gaussian Processes using MCMC
Clustering of Short Texts by Mixture of Unigrams and Its Deep
Extensions
Dirichlet-multinomial Evolutionary Event Profile Randomization
(DEEPR) test
Density Estimation by Extreme Value Distributions
Change the Default Arguments in R Functions
Create FDA-Style Data and Program Definitions
Integration of One-Dimensional Functions with Double Exponential
Formulas
Parameter Inference for Systems of Differential Equation
Models for Skewed Count Distributions Relevant to Networks
Detection of Isotope Pattern of a Mass Spectrometric Measurement
Multiple Imputation for Recurrent Events
Statistical Functions for the Delaporte Distribution
A Framework for Parallelizing Dependent Tasks
Sample Size and Power Calculations using the APPLE and SEPPLE
Methods
Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
Estimates Pseudotimes for Single Cell Expression Data
Estimation of Multivariate Densities Using Adaptive Partitions
Identification of Dichotomous Differential Item Functioning
(DIF) using Angoff's Delta Plot Method
Kernel Density Estimation using Lifetime Distributions
Functions to Calculate Relatedness on Diploid Genetic Data
Deming, Theil-Sen, Passing-Bablock and Total Least Squares
Regression
Analysis of Age-Structured Demographic Models
Extrapolate Gender, Age and Nationality of a Name
Providing Demographic Table with the P-Value, Standardized Mean
Difference Value
Forecasting Mortality, Fertility, Migration and Population Data
Kernel Density Estimation for Demonstration Purposes
Runs a 'Shiny' App as Demo or Lists All Demo 'Shiny' Apps
DEvelopment (of Multi-Linear QSPR/QSAR) MOdels VAlidated using
Test Set
Optimal Design Emulators via Point Processes
Extending 'dendrogram' Functionality in R
A Tool for Processing and Analyzing Dendrometer Data
Extra Functions to Cut, Label and Colour Dendrogram Clusters
A Set of Tools for Calculating Spatial Synchrony Between
Tree-Ring Chronologies
Linear and Nonlinear Methods for Analyzing Daily and Monthly
Dendroclimatological Data
Dendrogram seriation: ordering for visualisation
Modular Leaf Ordering Methods for Dendrogram Nodes
Parameter Estimates and Real-Time Prediction of a Single Dengue
Outbreak
Differential Expression Analysis Using a Bottom-Up Model
Statistical Analyses of De Novo Genetic Variants
Visualization of Multivariate Functions, Sets, and Data
Functional Linear Mixed Models for Densely Sampled Data
Density Estimation via Bayesian Inference Engines
Analysing Density Profiles from Resistance Drilling of Trees
Density.T.HoldOut: Non-combinatorial T-estimation Hold-Out for
density estimation
Clustering by Fast Search and Find of Density Peaks
Dens-Based Method for Partial Correlation Estimation in Large
Scale Brain Networks
Density Strips and Other Methods for Compactly Illustrating
Distributions
Simple Dengue Test and Vaccinate Cost Thresholds
Global Optimization by Differential Evolution
Differential Evolution Optimization in Pure R
Statistical Methods for the Analysis of Dependently Truncated
Data
A Utility Package to Help you Deal with "Pignas"
Deconvolute Mixed Genomes with Unknown Proportions
Dependent Mixture Models - Hidden Markov Models of GLMs and
Other Distributions in S4
Read, Plot and Analyse Output from the DEPONS Model
Nonparametric Depth Functions for Multivariate Analysis
Statistical Depth Functions for Multivariate Analysis
Functions and R Code to Accompany Derivatives Markets
Seasonal Adjustment by Frequency Analysis
An Interface to the 'DescribeDisplay' 'GGobi' Plugin
Describe Data in R Using Common Descriptive Statistics
Publication Quality Descriptive Statistics Tables
Produce Descriptive and Comparative Tables Easily
Interactive Functions to be Used as Shortcuts in 'RStudio'
Optimal deseasonalization for geophysical time series using AR
fitting
Design Clinical Trials with Potential Biomarker Effect
Computational tool for designing genetical genomics experiments
Matched Samples that are Balanced and Representative by Design
Desirability Functions for Ranking, Selecting, and Integrating
Data
Function Optimization and Ranking via Desirability Functions
Bagging with Distance-based Regression for Differential Gene
Expression Analyses
Solvers for Initial Value Problems of Differential Equations
('ODE', 'DAE', 'DDE')
Plotting Field Plans for Agricultural Experiments
Representation of DET Curve with Confidence Intervals
Create Details HTML Tag for Markdown and Package Documentation
Analyzing Wildlife Data with Detection Error
Detect Data Containing Personally Identifiable Information
Detect Runs of Homozygosity and Runs of Heterozygosity in
Diploid Genomes
Detect and Check for Separation and Infinite Maximum Likelihood
Estimates
Life Insurance Premium and Reserves Valuation
Implementation of the DetMCD Algorithm (Robust and Deterministic
Estimation of Location and Scatter)
Density Estimation and Random Number Generation with
Distribution Element Trees
Suite of Deterministic and Robust Algorithms for Linear
Regression
Start the detrendeR Graphical User Interface (GUI)
A Computer Program to Detect Markers Responding to Selection
Clear and Condense Argument Check for User-Defined Functions
Data sets from Devore's "Prob and Stat for Eng (7th ed)"
Quantify the Relationship Between Development Rate and
Temperature in Ectotherms
Tools to Make Developing R Packages Easier
Develop Treatment Rules with Observational Data
CML and Bayesian Calibration of Multistage Tests
Linear Discriminant Function and Canonical Correlation Analysis
Degrees of Freedom Adjustment for Robust Standard Errors
Phase I/II Adaptive Dose-Finding Design for Combination Studies
Compare Two Dataframes and Return Adds, Changes, and Deletes
Dose-Finding by the Continual Reassessment Method
Explore data.frames by plotting NA and classes of each variable
Differential Functioning of Items and Tests
Meta-Analysis of Phase I Dose-Finding Early Clinical Trials
Phase I/II Adaptive Dose-Finding Design for MTA
Detection and Analysis of Insect Defoliation Signals in Tree
Rings
Extrapolation and Bridging of Adult Information in Early Phase
Dose-Finding Paediatrics Studies
Phase I Control Charts (with Emphasis on Distribution-Free
Methods)
Bayesian Dose-Finding Designs using Pharmacokinetics (PK) for
Phase I Clinical Trials
Diewert and Fox's Method of Value Added Growth Decomposition
Capture-Recapture Estimation using Bayesian Model Averaging
Genetic Algorithm with Incomplete Dominance for Feature
Selection
Differential Gene Expression (DGE) Analysis Results Data Object
Differential Geometric Least Angle Regression
Double Generalized Linear Models Extending Poisson Regression
Simulating Data for PLS Mode B Structural Models
The Gumbel Distribution Functions and Gradients
Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression Models
Double Hierarchical Generalized Linear Models
Independence Testing via Hilbert Schmidt Independence Criterion
Diagnostic Plot and Multivariate Summary Statistics of Weighted
Samples from Importance Sampling
Meta-Analysis of Diagnostic Accuracy Studies with Several
Cutpoints
Block Diagonal Extraction or Replacement
Functions for Visualising Simple Graphs (Networks), Plotting
Flow Diagrams
Export DiagrammeR Graphviz Graphs as SVG
Parse, Format, and Validate International Phone Numbers
Required 'libphonenumber' jars for the 'dialr' Package
Tools for Creating Tuning Parameter Values
Calculate Ecological Information and Diatom Based Indices
Calculate probabilities of various dice-rolling events
Construction and Evaluation of Metamodels
Kriging Methods for Computer Experiments
Methods for Visualization of Computer Experiments Design and
Surrogate
Dictionaries for reading microdata surveys from IBGE
Finding Patterns of Monotonicity and Convexity in Data
R6 Based Key-Value Dictionary Implementation
Treatment Effects with Multiple Periods and Groups
A Simple Implementation and Demonstration of Gradient Boosting
Estimation in DID with Multiple Groups and Periods
Compute Recency Frequency Monetary Scores for your Customer Data
Defines some physical constants and dielectric functions
commonly used in optics, plasmonics
R Interface to the ZEIT ONLINE Content API
Detection of Differential Item Functioning (DIF) in Rasch Models
by Boosting Techniques
Fisher's z-Tests Concerning Difference of Correlations
Analyzing and Visualizing Differential Correlation Networks in
Biological Data
Calculates Confidence Intervals for two Dependent Proportions
Fast and Scalable Learning of Sparse Changes in High-Dimensional
Gaussian Graphical Model Structure
Given a List of Gene Symbols, Performs Differential Enrichment
Analysis
Solving Differential Equations (ODEs, SDEs, DDEs, DAEs)
Metrics of Difference for Comparing Pairs of Maps or Pairs of
Variables
Diffusion IRT Models for Response and Response Time Data
Multi-Fidelity Computer Experiments Using the Tuo-Wu-Yu Model
Detection of Statistically Significant Changes in Complex
Biological Networks
Display Differences Between Two Files using Codediff Library
Projects for Text Version Comparison and Analytics in R
Inference and Analysis for Generalized Quadratic Diffusions
Inference and Analysis for Diffusion Processes via Data
Imputation and Method of Lines
Inference and Analysis for Jump Generalized Quadratic Diffusions
Pattern Analysis Across Contingency Tables
A Penalty Approach to Differential Item Functioning in Rasch
Models
DIF and DDF Detection by Non-Linear Regression Models
Multilevel Mantel-Haenszel Statistics for Differential Item
Functioning Detection
Collection of Methods to Detect Dichotomous Differential Item
Functioning (DIF)
Differential Item Functioning via Shiny Application
Item Focussed Trees for the Identification of Items in
Differential Item Functioning
Create Compact Hash Digests of R Objects
Data-Informed Link Strength. Combine multiple-relationship
networks into a single weighted network. Impute (fill-in)
missing network links
DIME (Differential Identification using Mixture Ensemble)
Gathering Bibliographic Records from 'Digital Science
Dimensions' Using 'DSL' API
A Framework for Dimensionality Reduction
DiNAMIC A Method To Analyze Recurrent DNA Copy Number
Aberrations in Tumors
A Toolkit for Year-Quarter, Year-Month and Year-Isoweek Dates
Differential Pattern Analysis via Linear Modeling
Robust Tests for Differential Dispersion and Differential
Expression in RNA-Sequencing Data
Conduct Direction-Projection-Permutation Tests and Display Plots
Directional Penalties for Optimal Matching in Observational
Studies
A Dipping Sauce for Data Analysis and Visualizations
Hartigan's Dip Test Statistic for Unimodality - Corrected
Debiased Inverse Propensity Score Weighting
Bayesian Clustering of Multivariate Data Under the
Dirichlet-Process Prior
Estimating Controlled Direct Effects for Explaining Causal
Findings
A Collection of R Functions for Directional Data Analysis
Creates an Interactive Tree Structure of a Directory
Direction Analysis for Pathways and Kinases
Adjusted Means and Proportions by Direct Standardisation
Build Dirichlet Process Objects for Bayesian Modelling
Nonparametric Methods for Directional Data
Two-Steps Benchmarks for Time Series Disaggregation
Wrapper for the UN OCHA ReliefWeb Disaster Events API
A User-Friendly Pipeline for Biomarker Discovery in Single-Cell
Transcriptomics
Cox Models for Time-to-Event Data with Nonparametric Discrete
Group-Specific Frailties
Discrete Laplace Mixture Inference using the EM Algorithm
Test for Discretized Normality in Ordinal Data
Discordance and Concordance of Transcriptomic Responses
Functions for Discordant Kinship Modeling
Analyze Group Patterns using Graph Theory in Educational
Settings
Checks Title, Abstract and Keywords to Optimise Discoverability
Coordinate-Descent Algorithm for Learning Sparse Discrete
Bayesian Networks
Multiple Testing Procedures with Adaptation for Discrete Tests
Multiple testing procedures for discrete test statistics
Improved q-Values for Discrete Uniform and Homogeneous Tests
Create and Manipulate Discrete Random Variables
Discrete Weibull Distributions (Type 1 and 3)
Data preprocessing, discretization for classification
Model Wrappers for Discriminant Analysis
Tools of the Trade for Discriminant Analysis
Data for Comparing Species Distribution Modeling Methods
Modelling Spatial Variation in Disease Risk for Areal Data
Estimation Methods for Markets in Disequilibrium
Estimate the Gene Expression Levels and Component Proportions of
the Normal, Stroma (Immune) and Tumor Components of Bulk Tumor
Samples
Calculate Dissimilarity Matrix for Dataset with Mixed Attributes
Calculates Disproportionate Impact When Binary Success Data are
Disaggregated by Subgroups
Larger-than-RAM Disk-Based Data Manipulation Framework
A Pipeline to Analyze Resistance and Tolerance from Drug Disk
Diffusion Assays
Disparity Filter Algorithm for Weighted Networks
Create Disposable R Packages for Testing
Spatial Downscaling using the Dissever Algorithm
Fitting Sample Selection Models for Discrete Response Variables
Utilities for making pairwise comparisons of multivariate data
Distance Sampling Detection Function and Abundance Estimation
Calculates Study Size Required for Distance Sampling
Assessing Dissimilarity Between Multivariate Time Series
DiSTATIS Three Way Metric Multidimensional Scaling
Computations over Distributed Data without Aggregation
Distributional Method for the Dichotomisation of Continuous
Outcomes
Download Occurrence Data of Vascular Plants in Germany from the
FLORKART Database
'R Markdown' Format for Scientific and Technical Writing
Method Functions for Confidence Intervals and to Distill
Information from an Object
Unified Interface to Distance, Dissimilarity, Similarity
Matrices
Object Oriented Implementation of Distributions
The Complete R6 Probability Distributions Interface
Documentation for 'distr' Family of R Packages
Framework for the Visualization of Distributional Regression
Models
S4 Classes for Elliptically Contoured Distributions
Four Essential Functions for Statistical Distributions Analysis:
A New Functional Approach
Powerful Goodness-of-Fit Tests Based on the Likelihood Ratio
Object Oriented Implementation of Probability Models
Estimate and Manage Empirical Distributions
Distribution Classes for Distributions from Rmetrics
Simulation Classes Based on Package 'distr'
Extensions of Package 'distr' for Teaching
Stochastics/Statistics in Secondary School
Estimation and Testing Classes Based on Package 'distr'
A Collection of Full Defined Distribution Tails
A Test Environment for Database Requests
Provides tools for quality checks of georeferenced plant species
accessions
Diversity Dynamics using Fossil Sampling Data
Evolutionary Trait Divergence Between Sister Species and Other
Paired Lineages
Comparative 'Phylogenetic' Analyses of Diversification
A Comprehensive, General Purpose Population Genetics Analysis
Package
Building Diversity Models from Multiple Species Occupancy Models
Tools for Analysis of Diversity and Similarity in Biological
Systems
Nearest Neighbour Contingency Table Analysis
Dixon's Ratio Test for Outlier Detection
Multistage Record Linkage and Case Definition for
Epidemiological Analysis
Utilities for 'DIZ' R Package Development
Distance Measure Based Judgment and Learning
Time Series Regression Models with Distributed Lag Models
Implementation of Adaptive or Non-Adaptive Differentiable Lasso
and SCAD Penalties in Linear Models
Use Dirichlet Laplace Prior to Solve Linear Regression Problem
and Do Variable Selection
Bayesian and Likelihood Analysis of Dynamic Linear Models
Tools for Data Diagnosis, Exploration, Transformation
Distributed-Lag Linear Structural Equation Models
Measurement Nonequivalence Effect Size Calculator
Model Based Clustering of Binary Dissimilarity Measurements
Diffusion Model of Conflict (DMC) in Reaction Time Tasks
Daily Based Morgan-Morgan-Finney (DMMF) Soil Erosion Model
Dynamic Modeling and Parameter Estimation in ODE Models
DMR Detection by Non-Homogeneous Hidden Markov Model from
Methylation Array Data
Delete or Merge Regressors Algorithms for Linear and Logistic
Model Selection and High-Dimensional Data
Functions and data for "Data Mining with R"
Functions and Data for the Second Edition of "Data Mining with
R"
Tools for Analysing Forensic Genetic DNA Data
Integrative Analysis of Omics Data in Terms of Network,
Evolution and Ontology
Differential Network Local Consistency Analysis
Simulate Dynamic Networks using Exponential Random Graph Models
(ERGM) Family
Analysis of Discretely Observed Linear
Birth-and-Death(-and-Immigration) Markov Chains
Dimension Reduction for Outlier Detection
Data from the GLM Book by Dobson and Barnett
Groupwise Statistics, LSmeans, Linear Contrasts, Utilities
Measuring Concreteness in Natural Language
Distributed Representations of Sentences and Documents
Automatic Reporter for Descriptive Analysis
Automatic Reporter for Inference Analysis
Use Docker Images to Process Rmarkdown Blocks
Provides Docstring Capabilities to R Functions
Run 'roxygen2' on (Chunks of) Single Code Files
Extract Data Tables and Comments from 'Microsoft' 'Word'
Documents
Acceptance Sampling Ideas Originated by H.F. Dodge
Full Factorials, Orthogonal Arrays and Base Utilities for DoE
Packages
Creation of Arrays by Mixed Integer Programming
Wrapper Package for Design of Experiments Functionality
Analysis of Design of Experiments for Biological Research
Rare Variant Association Test Based on Position Density
Estimation
A Universal Foreach Parallel Adapter using the Future API of the
'future' Package
A Package to Calculate and Visualize Dominance Hierarchies
R Console Bindings for the 'Domino Command-Line Client'
Foreach Parallel Adaptor for the Rmpi Package
Nearest Neighbour Search with Variables on a Torus
Foreach Parallel Adaptor for the 'parallel' Package
Generic Reproducible Parallel Backend for 'foreach' Loops
Design of Observational Studies, Companion to the Second Edition
Causal Effect Identification from Multiple Incomplete Data
Sources
Interactive Designing of Dose Finding Studies
Planning and Analyzing Dose Finding Experiments
Foreach Parallel Adaptor for the 'snow' Package
Enhanced Foreign Function Interface Supporting Long Vectors
Enhanced Assignment Operator to Overwrite or Grow Objects
Gene-Set Analysis via Decorrelation by Orthogonal Transformation
Dot-and-Whisker Plots of Regression Results
Survivor Function Estimation for Doubly Interval-Censored
Failure Time Data
Test Against Parametric Regression Function
Differential Exon Usage Test for RNA-Seq Data via Empirical
Bayes Shrinkage of the Dispersion Parameter
Enable Operators Containing the '?' Symbol
Kernel Hazard Estimation with Best One-Sided and Double
One-Sided Cross-Validation
Functions Ported from 'MMR2' Toolbox Offered in Kevin Dowd's
Book Measuring Market Risk
Syntax Highlighting and Automatic Linking
Implement Download Buttons in 'rmarkdown'
Downscale of RS Images using Deep Learning
A Tool to Downsize Large Workflows for Testing
Automated Analysis of Multiplex Digital PCR Data
RStudio Addin for Teaching and Learning Data Manipulation Using
'dplyr'
Inference of Parameters of Normal Distributions from a Mixture
of Normals
Determinantal Point Process Mixture Models
Density, Probability, Quantile ('DPQ') Computations
DPQ (Density, Probability, Quantile) Distribution Computations
using MPFR
Piecewise Linear Segmentation by Dynamic Programming
Dirichlet Process Weibull Mixture Model for Survival Data
Methods for Dimension Reduction for Regression
Dose Response Data Analysis using the 4 Parameter Logistic (4pl)
Model
Deep Time Redox Analysis of the Geobiology Ontology Network
Statistical Tools to Identify Dragon Kings
Drag and Drop Elements in 'Shiny' using 'Dragula Javascript
Library'
A Pipeline Toolkit for Reproducible Computation at Scale
Wrapper Functions for Producing Graphics
Draw Samples with the Desired Properties from a Data Set
Computation of Rayleigh Densities of Arbitrary Dimension
Data Representation: Bayesian Approach That's Sparse
Regularized Estimation of Dynamic Linear Regression in the
Presence of Autocorrelated Residuals (DREGAR)
Doubly Robust Generalized Estimating Equations
Differential Risk Hotspots in a Linear Network
Calculates the Test-Statistic for the Drift Burst Hypothesis
Concept Drift and Concept Shift Detection for Predictive Models
Imputing Dropout Events in Single-Cell RNA-Sequencing Data
Drug Repurposing: Integration and Systematic Investigation of
Genomic High Throughput Data
Discontinuous Regression and Image Processing
Prioritizing Cancer Driver Genes Using Genomics Data
Dual Empirical Likelihood Inference under Density Ratio Models
in the Presence of Multiple Samples
Analyze Drop Out of an Experiment or Survey
Doubly-Robust Estimators for Ordinal Outcomes
Statistical Modeling and Assessment of Drought
Doubly-Robust Nonparametric Estimation and Inference
Implementation of a Machine Learning Framework for Predicting
Drugs Side Effects
Seasonal Adjustment of Daily Time Series
Dynamical Systems Approach to Infectious Disease Epidemiology
(Ecology/Evolution)
Dynamical Systems Approach to Immune Response Modeling
Discretization-Based Direct Random Sample Generation
Bayesian subgroup analysis in clinical trials
Dynamic Systems Estimation (Time Series Package)
What Skills and Qualifications are Required for Data Science
Related Jobs?
'DataSHIELD' Implementation on Local Datasets
Density Surface Modelling of Distance Sampling Data
Data Science Box of Pandora Miscellaneous
'DataSHIELD' Client for 'MOLGENIS Armadillo'
Spatial Modelling for Distance Sampling Data
Tests and Confidence Intervals on Directly Standardized Rates
for Several Methods
A Comprehensive R Interface for the DSSAT Cropping Systems Model
Analyze Two Choice Reaction Time Data with the D*M Method
Conditional Sensitivity Analysis for Matched Observational
Studies
Recursive Partitioning for Discrete-Time Survival Trees
Exploring Disease Similarity in Terms of Dysfunctional
Regulatory Mechanisms
A Wrapper of the JavaScript Library 'DataTables'
Cell Type Deconvolution from Gene Expressions
Diagnostic Test Assessment in the Absence of Gold Standard
Comparison of Binary Diagnostic Tests in a Paired Study Design
Doubly Truncated Data Analysis, Cumulative Incidence Functions
Doubly Truncated Data Analysis, Non Iterative
Analysis of Diffusion Weighted Imaging (DWI) Data
Dunnett-Tukey-Kramer Pairwise Multiple Comparison Test Adjusted
for Unequal Variances and Unequal Sample Sizes
Suite of functions related to discrete-time discrete-state
Markov Chains
Dose Transition Pathways for Continual Reassessment Method
Estimation and Comparison of Dynamic Treatment Regimes
Statistical Learning Methods for Optimizing Dynamic Treatment
Regimes
DTR Estimation and Inference via G-Estimation, Dynamic WOLS,
Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv)
Dynamic Treatment Regimes for Survival Analysis
A Class for Working with Time Series Based on 'data.table' and
'R6' with Largely Optional Reference Semantics
Manipulate Date, POSIXct and hms Vectors
Imputation of Time Series Based on Dynamic Time Warping
Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Time-Weighted Dynamic Time Warping for Satellite Image Time
Series Analysis
Imputation of Multivariate Time Series Based on Dynamic Time
Warping
Automatic Differentiation with Dual Numbers
Decimated and Undecimated 2D Complex Dual-Tree Wavelet Transform
Securely Wrangle Dataset According to Data Usage Agreement
Unpacking Assignment for Lists via Pattern Matching
DBI Package for the DuckDB Database Management System
Simple Client for the DuckDuckGo Instant Answer API
Create dummy/indicator variables flexibly and efficiently
Automatic Creation of Dummies with Support for Predictive
Modeling
Dunn's Test of Multiple Comparisons Using Rank Sums
Software implementation of step-down and step-up Dunnett test
procedures
Bayesian inference from count data using discrete uniform priors
Mixed Proportional Hazard Competing Risk Model
Analyze Dose-Volume Histograms and Check Constraints
Convenience Functions, Moving Window Statistics, and Graphics
Dynamic VAR - Based Control Charts for Batch Process Monitoring
Dynamic Water Balance a Hydrological Model
Fast Algorithms for Large Scale Generalized Distance Weighted
Discrimination
Read Binary Radar Files from 'DWD' (German Weather Service)
Parametric Regression for Discrete Response
Tools for DYRESM-CAEDYM Model Development: Calibration Assistant
and Post-Processing
Detection of Chaotic and Regular Intervals in the Data
Interface to 'Dygraphs' Interactive Time Series Charting Library
Quadratic Programming using Cyclic Projections
Dynamic Simulation and Testing for Single-Equation ARDL Models
Dynamically visualized probability distributions and their
moments
Modelling and Analysis of Dynamic Computer Experiments
Dynamic Hazard Models using State Space Models
Methods for Detection of Clusters in Hierarchical Clustering
Dendrograms
A Seamless Integration of 'R' and 'Dynare'
Implementation of the Dynamic TOPMODEL Hydrological Model
Full Interactive GUI for Dynamic Biplot in R
Denoising and clustering for dynamical image sequence (2D or
3D)+T
Dynamic Network Communities Detection and Generation
Complexity of Short and Coarse-Grained Time Series
Dimensionality Reduction Methods in a Common Format
Resisting Neighbor Label Attack in a Dynamic Network
A Multi-Modal Simulator for Spearheading Single-Cell Omics
Analyses
Visualising Statistical Models using Dynamic Nomograms
Companion Package to "Dynamic Prediction in Clinical Survival
Analysis"
Dynamic Simulations of Autoregressive Relationships
Methods for Estimating Optimal Dynamic Treatment Regimes
Common Functionality for the 'dynverse' Packages
Representing and Inferring Single-Cell Trajectories
Background and Pathway Data Used in 'DysPIA'
Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU Wien
Management and Processing Tools for Data Produced by the
Empatica E4
Fitting Dose-Response Models Using an Evolutionary Algorithm
Plots of the Empirical Attainment Function
Multiple Locus Association Mapping on a Genome-Wide Scale
Estimator Augmentation and Simulation-Based Inference
Dynamic Web-Based Analytics for the Energy Industry
Properties of Bayesian Early Gating Designs
Estimation of Transmissibility in the Early Stages of a Disease
Outbreak
Early Warning Signals Toolbox for Detecting Critical Transitions
in Timeseries
Parallel Implementation of 'ETERNA 3.40' for Prediction and
Analysis of Earth Tides
Derive a Color Palette from a Particular Location on Earth
Efficient Approximate Bayesian Computation Sampling Schemes
Generate Alluvial Plots with a Single Line of Code
Analysis of Variance and Other Important Complementary Analyses
Utility functions for working with mark-recapture data
Easy Model-Builder Functions for 'OpenMx'
Tools to Easily Read/Write NetCDF Files into/from
Multidimensional R Arrays
Sample Size Estimation for Experimental Designs
Reading, Formatting, and Organizing the Panel Study of Income
Dynamics (PSID)
Search and Retrieve Scientific Publication Records from PubMed
Helpful Functions from Oliver Wyman Actuarial Consulting
Easy Interface to the Statistical Disclosure Control Package
'sdcTable'
Ensemble Forecast Verification for Large Data Sets
Create Constraints for Small Test Assembly Problems
Spreadsheet Interface for Relational Databases
Data Management of Large Hierarchical Data
Educational Assessment Tools for Replication Methods
Miscellaneous Functions for the Analysis of Educational
Assessments
Entropy reweighting to create balanced samples
Sample Size Calculation Method for Cost-Effectiveness Studies
Based on Expected Value of Perfect Information
Empirical Bayes Thresholding and Related Methods
Empirical Bayes Estimation of Dynamic Bayesian Networks
Genotyping and SNP Detection using Next Generation Sequencing
Data
Empirical Bayesian Lasso and Elastic Net Methods for Generalized
Linear Models
Access and Analyze eBird Status and Trends Data
Estimate Ensemble Bayesian Model Averaging Forecasts using Gibbs
Sampling or EM-Algorithms
Ensemble-Based Methods for Class Imbalance Problem
Derive Polygenic Risk Score Based on Emprical Bayes Theory
Implementation of the Empirical Bayes Method
"Empirical Bayes Smoothing Splines with Correlated Errors"
Genotyping and SNP calling using single-sample next generation
sequencing data
An Automated Way to Estimate EC50 for Stratified Datasets
Excess Certainty Adjusted Probability Estimate
Programmatic Access to the European Central Bank's Statistical
Data Warehouse (SDW)
Translate English Words into Chinese, or Translate Chinese Words
into English
Simulation from Endpoint-Conditioned Continuous Time Markov
Chains
Elliptic Lambda Distribution and Option Pricing Model
Functions for Spatial Point Pattern Analysis
A Goodness-of-Fit Test for Elliptical Distributions with
Diagnostic Capabilities
Embedding Interactive Charts Generated with ECharts Library into
Shiny Applications
Create Interactive Graphs with 'Echarts JavaScript' Version 4
The Echelon Analysis and the Detection of Spatial Clusters using
Echelon Scan Method
Finding Rhythms Using Extended Circadian Harmonic Oscillators
(ECHO)
Efficient Calculation of Fine Structure Isotope Patterns via
Fourier Transforms of Simplex-Based Elemental Models
Ensemble Correlation-Based Low-Rank Matrix Completion
Environment Based Clustering for Interpretable Predictive Models
in High Dimensional Data
Interface to 'ECMWF' and 'CDS' Data Web Services
Integrating Ecological Remote Sensing Data to Derive EBV Metrics
Graphical Modelling and Ordination using Copulas
Estimating a Diet Matrix from Biotracer and Stomach Content Data
Dissimilarity-Based Functions for Ecological Analysis
A Community Modeling Foundation for Eco-Hydrology
Complexity Measures for Supervised Problems
"A practical guide to ecological modelling - using R as a
simulation platform"
Coalescent-Based Simulation of Ecological Communities
General Analysis of Various Economics Demand Systems
Estimation of Parameter-Dependent Network Centrality Measures
Simulate and Sample from Ecological Interaction Networks
Computational Methods for Economic Complexity
Ecological Regression using Aggregate and Individual Data
Conducts Analyses Informing Ecosystem Restoration Decisions
An R Interface to Brazilian Central Bank and Sidra APIs and the
IPEA Data
Simulating Community Assembly and Ecological Diversification
Using Ecospace Frameworks
Code and Data Accompanying the Eco-Stats Text
Characterising and Locating Ecotones and Communities
Procedures for Ecological Assessment of Surface Waters
Non-Parametric Multiple Change-Point Analysis of Multivariate
Data
Quantitative Estimates of Small Ectotherm Temperature Regulation
Effectiveness
Cointegration Based Timedelay Neural Network Model
Estimate ED50 and Its Confidence Interval
Experimental Design and Analysis for Tree Improvement
Download School District Geospatial Data, Perform Spatial
Analysis, and Create Formatted Exportable Maps
Automated School District Data Download and Processing
Get Evaporative Demand Drought Index Raster Data
Exploratory and Descriptive Event-Based Data Analysis
Read Data from European Data Format (EDF and EDF+) Files
Tool for the U.S. SEC EDGAR Retrieval and Parsing of Corporate
Filings
Datasets that Support the EDGE Server DIY Logic
More Powerful Unconditional Testing of Negative Binomial Means
for Digital Gene Expression Data
Bayesian Estimation of an Exploratory Deterministic Input, Noisy
and Gate Model
Network Reconstruction and Changepoint Detection
'RStudio' Addin for Editing a 'data.frame'
Simultaneous Edit-Imputation for Continuous Microdata
Parsing, Applying, and Manipulating Data Cleaning Rules
Dynamic Model Averaging with Grid Search
Implements the EDNE-Test for Equivalence
Empirical Distribution Ordering Inference Framework (EDOIF)
Provides Tools for Dimension Reduction Methods
Analysis of NCES Education Survey and Assessment Data
Compute and Decompose Inequality in Education
Exploring Election and Census Highly Informative Data Nationally
for Australia
Robust Analytical Methods for Evaluating Educational
Interventions using Randomised Controlled Trials Designs
Read and Preprocess Fluorescence Excitation-Emission Matrix
(EEM) Data
Ensemble Empirical Mode Decomposition and Its Variant Based ELM
Model
EEMD and Its Variant Based Time Delay Neural Network Model
Tools for Pre-Processing Emission-Excitation-Matrix (EEM)
Fluorescence Data
Convenience Functions for Education Data
Simulate and Evaluate Time Series for Environmental Epidemiology
Modelling Framework for the Estimation of Salmonid Abundance
Exploratory Factor Analysis Functions for Assessing
Dimensionality
Dimensionality Assessment Using Minimum Rank Factor Analysis
Fast and Flexible Implementations of Exploratory Factor Analysis
Tools
Utility Functions for Exploratory Factor Analysis
Wavelet-Based Enhanced FDR for Detecting Signals from Complete
or Incomplete Spatially Aggregated Data
Bayesian Effect Fusion for Categorical Predictors
Effect Displays for Linear, Generalized Linear, and Other Models
Indices of Effect Size and Standardized Parameters
Test changes of a grouped response relative to baseline
Visualization of Categorical Response Models
Efficient Initials for Computing the Maximal Eigenpair
The Causal Effects for a Causal Loglinear Model
Fetch Data from the Federal Reserve Economic Database
High-Level Functions to Read and Write Ensemble Forecast Time
Series in netCDF
Exploratory Graph Analysis - A Framework for Estimating the
Number of Dimensions in Multivariate Data Using Network
Psychometrics
Extensions for 'ggplot2': Custom Geom, Custom Themes, Plot
Alignment, Labelled Panels, Symmetric Scales, and Fixed Panel
Size
Hierarchical Modelling of Faecal Egg Counts
Import and Analyse Ego-Centered Network Data
Exploration and Graphics for RivEr Trends
Exploration and Graphics for RivEr Trends Confidence Intervals
Leveraging eQTLs to Identify Individual-Level Tissue of Interest
for a Complex Trait
Enhanced Help to Enable "Docstring"-Comments in Users Functions
Electronic Health Record (EHR) Data Processing and Analysis Tool
Delineating Temporal Dataset Shifts in Electronic Health Records
API Wrapper for 'US Energy Information Administration' Open Data
R Wrapper for the Energy Information Administration (EIA) API
Compares Ecological Inference, Goodman, Rows by Columns
Estimates
Generates (dense) matrices that have a given set of eigenvalues
Semiparametric Factor and Regression Models for Symmetric
Relational Data
Computes confidence intervals for principal components
Efficiently Impute Large Scale Incomplete Matrix
Effective Information and Causal Emergence
Ecological Inference and Higher-Dimension Data Management
Explanatory Item Response Modeling for Dichotomous and
Polytomous Items
An Algorithm for Reducing Errors-in-Variable Bias in Simple
Linear Regression
MCMC Procedures for Estimating Enzyme Kinetics Constants
Empirical Likelihood (EL) for Comparing Two Survival Functions
Enhanced Least Absolute Shrinkage and Selection Operator
Regression Model
General Purpose Interface to 'Elasticsearch'
Ising Network Estimation using Elastic Net and k-Fold
Cross-Validation
Elastic-Net for Sparse Estimation and Sparse PCA
A Lightweight Interface for Interacting with Elasticsearch from
R
Collection of Functions for Statistical Election Audits
Functions for election audits using stratified random samples
Estimation of Life Expectancies Using Multi-State Models
R Functions to Download and Clean Brazilian Electoral Data
Allocating Seats Methods and Party System Scores
An Framework for Reducing Elemental LAICPMS Data from Solid
Structures
Load Associated Press Election Results with Elex
Kumaraswamy Complementary Weibull Geometric (Kw-CWG) Probability
Distribution
Sampling from a Empirical Likelihood Bayesian Posterior of
Parameters Using Hamiltonian Monte Carlo
ELISA Data Analysis with Batch Correction
Equipment for Logarithmic and Linear Time Stepwise Multiple
Hypothesis Testing
Functions for Drawing Ellipses and Ellipse-Like Confidence
Regions
Weierstrass and Jacobi Elliptic Functions
Implementation of the Efficient Large-Scale Online Display
Advertising Algorithm
Preference Rating for Visual Stimuli Based on Elo Ratings
Optimized Elo Rating Method for Obtaining Dominance Ranks
Animal Dominance Hierarchies by Elo Rating
Entropy-Based Local Indicator of Spatial Association
Utilise Catastrophe Model Event Loss Table Outputs
Empirical Likelihood Analysis for the Cox Model and
Yang-Prentice (2005) Model
EM Algorithm for Maximum Likelihood Estimation by Non-Precise
Information
Data Management Tools for Real-Time Monitoring/Ecological
Momentary Assessment Data
Ensemble Boolean Model Biomarker Analysis
Extra Recipes for Encoding Categorical Predictors
Fast Embedding Guided by Self-Organizing Map
Tools to Analyze the Thermal Reaction Norm of Embryo Growth
Evolutionary Monte Carlo (EMC) algorithm
EM Algorithm for Model-Based Clustering of Finite Mixture
Gaussian Distribution
Empirical Mode Decomposition and Hilbert Spectral Analysis
Support Functions and Data for "Ecological Models and Data"
Estimating and Mapping Disaggregated Indicators
Exponentially Modified Gaussian (EMG) Distribution
EM Algorithms for Estimating Item Response Theory Models
Emissions and Statistics in R for Wastewater and Pollutants in
Combined Sewer Systems
Read and Write Ecological Metadata Language Files
Fitting log-Linear Models in Sparse Contingency Tables
Estimated Marginal Means, aka Least-Squares Means
A Mixture Model-Based Approach to the Clustering of Microarray
Expression Data
Mixture Models with Component-Wise Factor Analyzers
A Maximum Likelihood Approach to the Analysis of Modularity
Fitting Mixed Models with Known Covariance Structures
Tools for Environmental and Ecological Survey Design
Eye Movement Analysis Package for Fixation and Saccade Detection
Expected Maximum Profit Classification Performance Measure
Evaluates the Empirical Characteristic Function for Multivariate
Samples
Routines for Performing Empirical Calibration of Observational
Study Estimates
Simulation-Based False Discovery Rate in RNA-Seq
Empirical Likelihood Ratio for Censored/Truncated Data
Empirical Likelihood Ratio Test for Two Samples with Censored
Data
Epimed Solutions Collection for Data Editing, Analysis, and
Benchmark of Health Units
Some EM-Type Estimation Methods for the Heckman Selection Model
Tools for Fast Computing and Plotting Euclidean Minimum Spanning
Trees
Exact Multinomial Test: Goodness-of-Fit Test for Discrete
Multivariate data
Main Package of the EMU Speech Database Management System
The Expectation-Maximization Approach to Bayesian Variable
Selection
Portable Tools for 'UTF-8' Character Data
Encoding of Nucleotide Sequences into Numeric Feature Vectors
Ensemble Methods for Multiple Change-Point Detection
Represent Ordered Lists and Pairs as Strings
Easily Encrypt and Decrypt Data Frame/Tibble Columns or Files
using RSA Public/Private Keys
R Package for Fitting Multinomial Probit Models with Endogenous
Selection
Bayesian Measurement Models for Analyzing Endorsement
Experiments
Transmissions and Receptions in an End to End Network
E-Statistics: Multivariate Inference via the Energy of Data
Distribution Free Multivariate Control Chart Based on Energy
Test
Data Published by the United States Federal Energy Regulatory
Commission
Robust and Sparse Methods for High Dimensional Linear and
Logistic Regression
Data sets from "Introductory Statistics for Engineering
Experimentation"
English and European Soccer Results 1871-2016
Automated Runs and Evaluations of Ecological Niche Models
Analysis of Niche Evolution using Niche and Distribution Models
Utilities to Extract and Analyse Text Data from the Emergency
Nutrition Network Forum
Ensemble Partial Least Squares Regression
Methods to Enrich R Objects with Extra Components
Extensible Package for Parallel, Batch Training of Base Learners
for Ensemble Modeling
Probabilistic Forecasting using Ensembles and Bayesian Model
Averaging
Extensible Package for Cross-Validation-Based Integration of
Base Learners
Extensible Package for Principal-Component-Regression-Based
Heterogeneous Ensemble Meta-Learning
Extensible Classes and Methods for Penalized-Regression-Based
Integration of Base Learners
Ensemble Taxonomic Assignments of Amplicon Sequencing Data
Translate English Words into Chinese Words
Entropy Partitioning to Measure Diversity
Estimation of Entropy, Mutual Information and Related Quantities
Estimation of Entropy and Related Quantities
Tools for Exploring Differential Shannon Entropy, Differential
Coefficient of Variation and Differential Expression
MCMC Simulation and Convergence Evaluation using Entropy and
Kullback-Leibler Divergence Estimation
Miscellaneous Functions for Environmental Analyses
Detection of Structural Changes in Climate and Environment Time
Series
Various Utilities for Microbial Genomics and Metagenomics
Environmental Exposure on the Individual Level
Environmental Interpolation using Spatial Kernel Density
Estimation
GC/LC-MS Data Analysis for Environmental Science
Isotope Pattern, Profile and Centroid Calculation for Mass
Spectrometry
Peak Picking for High Resolution Mass Spectrometry Data
Environmental Probabilistic Risk Assessment Tools
Statistical Analysis of Environmental Space-Time Processes
Keep Track of User-Defined Environment Names
Methods for Identification of Outliers in Environmental Data
Package for Environmental Statistics, Including US EPA Guidance
Export or Graph and Tables to 'Microsoft' Office and Import
Figures and Tables
Data Management Package (Exposure and Occurrence Data in R)
Statistical Functions for the Censored and Uncensored
Epanechnikov Distribution
Ensemble Penalized Cox Regression for Survival Prediction
Implementation of the Everglades Phosphorus Gradient Model
Argentina's Permanent Household Survey Data and Manipulation
Utilities
Elementary Epidemiological Functions for Epidemiology and
Biostatistics
Handling, Visualisation and Analysis of Epidemiological Contacts
Epidemiological Tool for Contact Tracing
Tools to Retrieve Economic Policy Institute Data Library
Extracts
Estimate Time Varying Reproduction Numbers from Epidemic Curves
Analysis and Simulation of Plant Disease Progress Curves
Predicting Disease Spread from Flow Data
Interface Package for the 'EpiGraphDB' Platform
Spatial and Network Based Individual Level Models for Epidemics
Continuous Time Distance-Based and Network-Based Individual
Level Models for Epidemics
Miscellaneous Tools for the 'R4Epis' Project
Functions and Data for "Epidemics: Models and Data in R"
Mathematical Modeling of Infectious Disease Dynamics
Epistatic Network Modelling with Forward-Time Simulation
Estimate Real-Time Case Counts and Time-Varying Epidemiological
Parameters
Tools for the Analysis of Epidemiological Data
Basic Sensitivity Analysis of Epidemiological Results
Density Estimation with Soft Information by Exponential
Epi-splines
Detecting Epistatic Selection with Partially Observed Genotype
Data
Constructing an Epistemic Model for the Games with Two Players
Flexible Contingency Tables for Epidemiology
Small Helpers and Tricks for Epidemics Analysis
Early Detection of Public Health Threats from Twitter Data
A Toolkit for Using Whole Building Simulation Program
'EnergyPlus'
Endogenous Perturbation Analysis of Cancer
Exact Post Selection Inference with Applications to the Lasso
Ensemble Patch Transform, Visualization and Decomposition
Create Future 'EnergyPlus' Weather Files using 'CMIP6' Data
Methods for Calculating 'EQ-5D' Utility Index Scores
EQS Output Conversion to lavaan Functions
Tools for analyzing eQTL experiments: A complementary to Karl
Broman's 'qtl' package for genome-wide analysis
Testing the Equality of Two Covariance Matrices
Testing the Equality of a High Dimensional Set of Densities
Examine Measurement Invariance via Equivalence Testing and
Projection Method
Modeling, Confidence Intervals and Equivalence of Survival
Curves
Provides Tests and Graphics for Assessing Tests of Equivalence
Equivalence Test for the Means of Two Normal Distributions
Testing for Equivalence and Noninferiority
Uniformly Most Powerful Invariant Tests of Equivalence
Automated Spectral Deconvolution, Alignment, and Metabolite
Identification in GC/MS-Based Untargeted Metabolomics
Nonparametric Multiple Expectile Regression via ER-Boost
Fitting Tails by the Empirical Residual Coefficient of Variation
Fit, Simulate and Diagnose Exponential-Family Models for
Networks
Fit, Simulate and Diagnose Exponential-Family Models for
Networks with Count Edges
Fit, Simulate and Diagnose Exponential-Family Random Graph
Models to Egocentrically Sampled Network Data
Fit, Simulate and Diagnose Exponential-Family Models for
Rank-Order Relational Data
User-specified Terms for the statnet Suite of Packages
Local Health Department network data set
Exponential Random Graph Models for Small Networks
Significance Analysis of Event-Related Potentials Data
Event-Related Potential (ERP) Data Exploration Made Easy
Event-related potentials (ERP) analysis, graphics and utility
functions
Exploratory Reduced Reparameterized Unified Model Estimation
Empirically Informed Random Trajectory Generation in 3-D
Estimate Number of Latent Factors and Factor Matrix for Factor
Analysis
Extended Empirical Saddlepoint Density Approximations
Indicators of Electoral Systems and Party Systems
Effect Size Computation for Meta Analysis
Modular Approach to Dose Finding Clinical Trials
Adaptive Enrichment Designs with Sample Size Re-Estimation
Ensemble Tool for Predictions from Species Distribution Models
ESEA: Discovering the Dysregulated Pathways based on Edge Set
Enrichment Analysis
Data Preparation During and After the Use of the Experience
Sampling Methodology (ESM)
Explore and Visualize Your Data Interactively
Joint Quantile and Expected Shortfall Regression
Efficient Stepwise Selection in Decomposable Models
Download Data from the European Social Survey on the Fly
Calibrating Parameters for the Samejima's Continuous IRT Model
Efficient Sequential Testing with Evidence Ratios
Estimation of Heritability in High Dimensional Sparse Linear
Mixed Models using Variable Selection
Tools for Assessing Estimability of Linear Predictions
Perform the Joint Graphical Lasso and Selects Tuning Parameters
Maximum Likelihood Estimation for Probability Functions from
Data Sets
Fast Estimators for Design-Based Inference
Diagnostic Tools and Unit Tests for Statistical Estimators
Estimation of Four-Fold Table Cell Frequencies (Raw Data) from
Effect Size Measures
Estimating the Sample Mean and Standard Deviation from Commonly
Reported Quantiles in Meta-Analysis
An Implementation of Parametric and Nonparametric Event Study
Visualization and Estimation of Effect Sizes
Modeling Earthquake Data Using 'ETAS' Model
Mixed FLP and ML Estimation of ETAS Space-Time Point Processes
for Earthquake Description
Interaction with the 'Ethereum' Blockchain
Ethnicity Annotation from Whole Exome Sequencing Data
Extract-Transform-Load Framework for Medium Data
Utility Functions to Execute Standard Extract/Transform/Load
Operations (using Package 'ff') on Large Data
Computes Moments of Univariate Truncated t Distribution
Creates Safety Results Summary in XML to Upload to EudraCT
eulerian: A package to find eulerian paths from graphs
Area-Proportional Euler and Venn Diagrams with Ellipses
A Standard Dataset in the OMOP Common Data Model
R Interface to the Europe PubMed Central RESTful Web Service
Historical Populations of European Cities, 1500-1800
Bayesian Single Arm Sample Size Calculation Software
Extreme Value Analysis with Goodness-of-Fit Testing
Parsing and Evaluation Tools that Provide More Details than the
Default
Collection of Model Evaluation Measure Functions
Sensitivity Analyses for Unmeasured Confounding and Other Biases
in Observational Studies and Meta-Analyses
Modelling Actual, Potential and Reference Crop
Evapotranspiration
Functions for Extreme Value Distributions
Bayesian Analysis in Extreme Value Theory
Graphical User Interface for the 'EventDetectR' Package
Regression Models for Event History Outcomes
Streaming Events and their Early Classification
Generalised Additive Extreme Value Models
Evidential Analysis of Genetic Association Data
Analysis of Scientific Evidence Using Bayesian and Likelihood
Methods
Reporting Tools for Sensitivity Analysis of Evidence Factors in
Observational Studies
Evidence Factors in Observational Studies
Extreme Value Mixture Modelling, Threshold Estimation and
Boundary Corrected Kernel Density Estimation
Comparative and Population Genetic Analyses
Tools for Evolutionary Quantitative Genetics
Important Concepts of Evolutionary Game Theory
Evolutionary Parameter Estimation for 'Repast Simphony' Models
Mean of order p, peaks over random threshold Hill and high
quantile estimates
Extreme Value Theory for Open Set Classification - GPD and GEV
Classifiers
Evolutionary Learning of Globally Optimal Trees
Goodness-of-Fit Tests for the Exponential and Two-Parameter
Weibull Distributions
Escalation with Overdose Control using 2 Drug Combinations
Exact Tests and Confidence Intervals for 2x2 Tables
Exact P-Values and Matching Confidence Intervals for Simple
Discrete Parametric Cases
Inductive Confidence Intervals for the difference between two
proportions
Fast Extraction from Raster Datasets using Polygons
Monte Carlo Exact Tests for Log-linear models
Exact Distributions for Rank and Permutation Tests
Help for Writing Unit Tests Based on Function Examples
Question Generation in the 'MyLearn' XML Format
Confidence regions for exceedance sets and contour lines
Confidence Intervals for Exceedance Probability
Convenient Data Exchange with Microsoft Excel
A Wrapper of the 'JavaScript' Library 'jExcel'
Extracts Tabular Data from Excel Reports
Excerpt Structuring Comments from Your Code File and Set a Table
of Contents
Excursion Sets and Contour Credibility Regions for Random Fields
A Fast and Scalable Exhaustive Feature Selection Framework
Calls Copy Number Variants from Targeted Sequence Data
Convert Gene EXPression Data to FBA FLUXes
Expanding Ploidy and Allele-Frequency on Nested Subpopulations
Modular Differential Evolution for Experimenting with Operators
R Package for Designing and Analyzing Randomized Experiments
Modeling without data using expert opinion
Design of Discrete Choice and Conjoint Analysis
Exponential Integral and Incomplete Gamma Function
Explanation of Predictions for Classification and Regression
Models
Interactive Interfaces for Results Exploration
Multiple Effect Estimation of Chemicals in Environmental
Epidemiology
Exploratory Analysis with the Singular Value Decomposition
Spatial Analysis of Extra-Pair Paternity
Computing Expectations and Marginal Likelihoods for Permutations
An Exponential Stochastic Block Model for Interaction Lengths
Data Sets from "Forecasting with Exponential Smoothing"
Tables, Labels and Some Useful Functions from Spreadsheets and
'SPSS' Statistics
Fast, Reliable and Elegant Reproducible Research
Convenience Functions for Botanists to Create Specimens Indices
Extending the Range of Functions for Probability Distributions
Data Manipulation Extensions of 'Dplyr' and 'Tidyr'
Additional Families for Generalized Linear Models
Constructs the Exterior Match from Two Matched Control Groups
Maximum penalized likelihood estimation with extended lasso
penalty
An Extended Mallows Model and Its Hierarchical Version for
Ranked Data Aggregation
Extra-binomial approach for pooled sequencing data
Additional Univariate and Multivariate Distributions
Extra Binary Relational and Logical Operators
Astrobiology Equations Estimating Extraterrestrial Life
Extremely Randomized Trees (ExtraTrees) Method for
Classification and Regression
Summary Statistics for Geospatial Features
Extended RC Models for Contingency Tables
Estimation of Extreme Conditional Quantiles and Probabilities
Forecast Verification for Extreme Events
Extreme Value Statistics and Quantile Estimation
Estimation of Extreme Value Dependence for Time Series Data
Estimate Lower Extreme Quantile with the Censored Weibull MLE
and Censored Weibull Mixture
Econometric Analysis of Explosive Time Series
Open Source Ophthalmic Data Sets Curated for R
Import ASC Files from EyeLink Eye Trackers
Prepare/Analyse Eye Tracking Data for Reading
Organising and Analysing Eye-Tracking Data
Easy Analysis and Visualization of Factorial Experiments
Easy Interface to Effective Concentration Calculations
Task Oriented Interface for Exploratory Data Analysis
selects significant non-additive interaction between two
variables using fast GLM implementation
Avoid the Typical Working Directory Pain When Using 'knitr'
Easy Use of R via Shiny App for Basic Analyses of Experimental
Data
provide an easy to use framework to conduct simulation
Tunes AdaBoost, Elastic Net, Support Vector Machines, and
Gradient Boosting Machines
Core Tools for Packages in the 'fable' Framework
Overfitting Bayesian Mixtures of Factor Analyzers with
Parsimonious Covariance and Unknown Number of Components
Create Easily Canvas in 'shiny' and 'RMarkdown' Documents
Fast Covariance Estimation for Sparse Functional Data
A C++ Framework for Plant-Plant Interaction IBMs
Bayesian Sparse Factor Analysis model for the inference of
pathways responsive to drug treatment
Combination of Factorial Methods and Cluster Analysis
Extract and Visualize the Results of Multivariate Data Analyses
Automatic Description of Factorial Analysis
Multivariate Exploratory Data Analysis and Data Mining
Factorial Optimal Designs for Two-Colour cDNA Microarray
Experiments
Post-Processing MCMC Outputs of Bayesian Factor Analytic Models
Set of Assumptions for Factor and Principal Component Analysis
Factor Copula Models for Mixed Continuous and Discrete Data
Simultaneous Change-Point and Factor Analysis
Design and Analysis for Factorial Experiments
Design and Analysis of a 2x2 Factorial Trial
Graphical Presentation of Simple Contrasts
Bayesian quantile regression factor models
Identification of the Factors Affecting Species Richness
Bayesian Estimation of (Sparse) Latent Factor Stochastic
Volatility Models
Perform Factorial Analysis from 'FactoMineR' with a Shiny
Application
thin wrapper for the Factual.com server API
Variable Selection for Supervised Classification in High
Dimension
Distributions that are Sometimes Used in Hydrology
Data from the Book "Multivariate Statistical Modelling Based on
Generalized Linear Models", First Edition, by Ludwig Fahrmeir
and Gerhard Tutz
Fair Data Adaptation with Quantile Preservation
Flexible Tool for Bias Detection, Visualization, and Mitigation
Faisal Conjoint Model: A New Approach to Conjoint Analysis
Simulates Data from a Data Frame of Different Variable Types
Finding Allele-Specific Copy Number in Next-Generation
Sequencing Data
Finding Allele-Specific Copy Number in Whole-Exome Sequencing
Data
Family Age-at-Onset Data Simulation and Penetrance Estimation
Probabilities for Pedigrees Given DNA Data
A Convex Formulation for Modeling Interactions with Strong
Heredity
Maximum Likelihood and Bayesian Estimation of Univariate
Probability Distributions
A Flexible Algorithm for Model Selection
Family Sequence Kernel Association Test for Rare and Common
Variants
Factor Analysis for Multiple Testing (FAMT) : simultaneous tests
under dependence in high-dimensional data
Penalized Likelihood Factor Analysis via Nonconvex Penalty
Building Kriging Models from FANOVA Graphs
Visualisation of Sequential Probability Distributions Using Fan
Charts
ANSI Control Sequence Aware String Functions
Influential Case Detection Methods for Factor Analysis and
Structural Equation Models
Modelization for Functional AutoRegressive Processes
Functions and Datasets for Books by Julian Faraway
Fast and Robust Deconvolution of Tumor Infiltrating Lymphocyte
from Expression Profiles using Least Trimmed Squares
Interactive Interface to Data Envelopment Analysis Modeling
High Performance Colour Space Manipulation
Joint Segmentation of Correlated Time Series
Rmetrics - EBM and Asian Option Valuation
A Fast and Scalable Joint Estimator for Learning Multiple
Related Sparse Gaussian Graphical Models
Rmetrics - Analysing and Modelling Financial Assets
Analyze, Summarize, and Visualize Daily Streamflow Data
Fast Estimation of a Covariance Matrix by Banding the Cholesky
Factor
A Fast Solver for Parameterized LP Problems, Constrained L1
Minimization Approach to Sparse Precision Matrix Estimation and
Dantzig Selector
Fast Hierarchical Clustering Routines for R and 'Python'
Significant Interval Discovery with Categorical Covariates
Fine-Gray Regression via Forward-Backward Scan
Lasso and Elastic-Net Penalized Cox's Regression in High
Dimensions Models using the Cocktail Algorithm
Fast EM and Best-Subset Selection for CUB Models for Rating Data
Fast, Low Memory-Footprint Digests of R Objects
Fast Creation of Dummy (Binary) Columns and Rows from
Categorical Variables
Raster Image Processing and Vector Recognition
Fast and Exact Computation of Gaussian Stochastic Process
Fast 'Rcpp' Implementation of Gauss-Hermite Quadrature
Fast and Stable Fitting of Generalized Linear Models using
'RcppEigen'
Efficiently Using Gaussian Processes with Rcpp and RcppEigen
Fast Drawing and Shading of Graphs of Statistical Distributions
Robust Algorithm for Principal Component Analysis
Hierarchical Independent Component Analysis: a Multi-Scale
Sparse Non-Orthogonal Data-Driven Basis
FastICA Algorithms to Perform ICA and Projection Pursuit
A Fast Multiple-Kernel Method Based on a Low-Rank Approximation
Faster K-Medoids Clustering Algorithms: FastPAM, FastCLARA,
FastCLARANS
Fast Probabilistic Record Linkage with Missing Data
A Fast Way to Calculate the p-Value of One or Multiple
Log-Rank-Tests
Fast Nonconvex Deconvolution of Calcium Imaging Data
Fast Computation of Multivariate M-Estimators
Fast Marching Method for Modelling Evolving Boundaries
Fast Computation of some Matrices Useful in Statistics
Fast Mutual Information Based Independence Test
Extremely Fast Implementation of a Naive Bayes Classifier
FastPCS Robust Fit of Multivariate Location and Scatter
Finds the Critical Sequential Point of Stability for a Pearson
Correlation
Foundations and Applications of Statistics Using R (2nd Edition)
Fits the FastRCS Robust Multivariable Linear Regression Model
Fast Interactive Framework for Web Scripting Using R
Fast Utility Function for Time Parsing and Conversion
Two-Locus Family-Based Association Test with Polytomous Outcome
Quantification of Fate Bias in Multipotent Progenitors
Kiener Distributions and Fat Tails in Finance
Fault Trees for Risk and Reliability Analysis
Find the URL to the 'Favicon' for a Website
Functions and Datasets for "Forest Analytics with R"
An Extensible Approach to Flux Balance Analysis
Gene by Environment Interaction and Conditional Gene Tests for
Nuclear Families
Algorithm for Searching the Space of Gaussian Directed Acyclic
Graph Models Through Moment Fractional Bayes Factors
FISH Based Normalization and Copy Number inference of SNP
microarray data
Analyzing and Managing Facebook Ads from R
Association Football (Soccer) Ranking via Poisson Regression
Fast Algorithms to Bootstrap Receiver Operating Characteristics
Curves
The Full Bayesian Significance Test and the e-Value
Standard Evaluation-Based Multivariate Function Composition
Basics of Certificates and Structured Products Valuation
Full Length Circular RNA Sequence Extraction and Classification
Inference of Fuzzy Cognitive Maps (FCMs)
Rmetrics - Bivariate Dependence Structures with Copulae
Functional Concurrent Regression for Sparse Data
A Method to Search for Differentially Expressed Genes and to
Detect Recurrent Chromosomal Copy Number Aberrations
A Collection of Fluorescence Fluctuation Spectroscopy Analysis
Methods
Measuring functional diversity (FD) from multiple traits, and
other tools for functional ecology
Functional Data Analysis and Utilities for Statistical Computing
Autocorrelation Function for Functional Time Series
Functional Data Analysis for Density Functions by Transformation
to a Hilbert Space
Functional Data Analysis: K-Mean Alignment
Functional Data Analysis in a Mixed Model Framework
Analysis of Variance for Univariate and Multivariate Functional
Data
Outlier Detection Tools for Functional Data Analysis
Functional Data Analysis and Empirical Dynamics
Statistical Analysis of Functional and Spatial Data, Based on
Regression with PDE Regularization
Partially Observed Integrated Functional Depth
Interval Testing Procedure for Functional Data
Fast Implementation of the Diffusion Decision Model
Data Mining and R Programming for Beginners
Dynamic Model Averaging and Dynamic Model Selection for
Continuous Outcomes
Permutation-Based FDR Point and Confidence Interval Estimation
False Discovery Rate Procedures Under Discrete and Heterogeneous
Null Distributions
Estimate, Plot, and Summarize False Discovery Rates
Compute Sample Size that Meets Requirements for Average Power
and FDR
FDR-Control in Multiscale Change-Point Segmentation
Estimation of (Local) False Discovery Rates and Higher Criticism
Frequency Distribution Tables, Histograms and Polygons
False Discovery Exceedance Controlling Multiple Testing
Procedures
Classification and Feature Selection for microRNA/mRNA
Interactions
Feature Extraction and Statistics for Time Series
Local Inferential Feature Significance for Multivariate Kernel
Density Estimation
Measurement Level Independent Feature Correlation Matrix
Creates a Model Matrix via Feature Hashing with a Formula
Interface
Feature Importance for Partitional Clustering
Feature Extraction for Discretely-Sampled Functional Data
Interact with the 'Python' Module 'Featuretools'
Some Helper Functions that Help Create Features from Data
Data Package for the 2016 United States Federal Elections
Fechnerian Scaling of Discrete Object Sets
Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Client Package for the U.S. Federal Register API
Text Analysis of the US Code of Federal Regulations
Estimating Fixed Effects Individual Slope Models
Functional Help for Functions, Objects, and Packages
Fixed Effects Nonlinear Maximum Likelihood Models
Fixed Effects Logistic Model with High-Dimensional Parameters
Estimation and Fit Assessment of Frailty Exponential Random
Graph Models
Fertilizer Response Curve Analysis by Bootstrapping Residuals
Rmetrics - Pricing and Evaluating Exotic Option
Structured Products Valuation for
ExpressCertificates/Autocallables
Rmetrics - Modelling Extreme Events in Finance
Memory-Efficient Storage of Large Data on Disk and Fast Access
Functions
Basic Statistical Functions for Package 'ff'
Download Data from Kenneth French's Website
Force field simulation for a set of points
API Client for Fantasy Football League Platforms
Forgetting Factor Methods for Change Detection in Streaming Data
Fast FFT and DCT Based on the FFTW Library
Wrapper for 'FFTW3' Includes: One-Dimensional Univariate,
One-Dimensional Multivariate, and Two-Dimensional Transform
Rmetrics - Autoregressive Conditional Heteroskedastic Modelling
Utilities for Fundamental Geo-Spatial Data
Access Small ForestGEO Datasets For Examples
Partial Separability and Functional Gaussian Graphical Models
Feature Grouping and Selection Over an Undirected Graph
Fractional Hot Deck and Fully Efficient Fractional Imputation
Tests for Right and Interval-Censored Survival Data Based on the
Fleming-Harrington Class
Provide functions for forest inventory calculations
Focused Information Criteria for Model Comparison
Classical, Reloaded and Adaptive FastICA Algorithms
A Lightweight and Flexible Web Framework
File-Backed Matrix Class with Convenient Read and Write Access
Effective File Navigation from the R Console
Matrix Completion, Imputation, and Inpainting Methods
Rmetrics - Importing Economic and Financial Data
Quickly Create Elegant Regression Results Tables and Plots when
Modelling
Financial Analysis and Regression Diagnostic Analysis
Financial Instrument Model Infrastructure and Meta-Data
Classifies implicit trading activity from market quotes and
computes the probability of informed trading
Interface for the 'Finnish Biodiversity Information Facility'
API
Time Value of Money, Time Series Analysis and Computational
Finance
Covariance Matrix Estimation and Regularization for Finance
Find all root(s) of the equation and Find root(s) of the
equation by dichotomy
Functions to Find an Acceptable Python Binary
Find Code Snippets, R Scripts, R Markdown, PDF and Text Files
with Pattern Matching
A View Generator for Multidimensional Data
Fine-Scale Population Analysis (Rewrite for
Gene-Trait-Environment Interaction Analysis)
Functions to Operate on Binary Fingerprint Data
Computation of the Probability of Ruin Within a Finite Time
Horizon
Test for Finiteness of Moments in a Distribution
Financial Data from U.S. Securities and Exchange Commission
Companion to Tsay (2005) Analysis of Financial Time Series
Access to Average Purchase Price of Vehicles in Brazil
Integrates 'Google Firebase' Authentication Method with 'Shiny'
Prediction of Wildland Fire Behavior and Hazard
A Small Collection of Fish Population Datasets
The FisherEM Algorithm to Simultaneously Cluster and Visualize
High-Dimensional Data
Fisheye and Hyperbolic-space-alike Interactive Visualization
Tools in R
Iterative FISH-based Calibration of Hi-C Data
Dataset of Measurements of Fish Species at Kirkkojarvi Lake,
Finland
Fits Poisson-Sum-of-Gammas GLMs, Tweedie GLMs, and Delta
Log-Normal Models
Analytical Tool for Aquatic Respirometry
Fuzzy Inference System Design and Optimization
Transcriptomic Dynamics Models in Field Conditions
Fit ARMA or ARIMA Using Fast MLE Algorithm
Help to Fit of a Parametric Distribution to Non-Censored or
Censored Data
Mean and Covariance Matrix Estimation under Heavy Tails
Modeling Over Dispersed Binomial Outcome Data Using BMD and ABD
Genotype Calling for Bi-Allelic Marker Assays
FITS (Flexible Image Transport System) Utilities
Fit Hundreds of Theoretical Distributions to Empirical Data
fitTetra is an R package for assigning tetraploid genotype
scores
Fit Univariate Mixed and Usual Distributions
Data and Code Behind the Stories and Interactives at
'FiveThirtyEight'
Algorithms for Finding Fixed Point Vectors of Functions
The Distribution of Distances Between Discrete Events in Fixed
Time
An R Client for the "Fixer.io" Currency API
Fixed Sequence Multiple Testing Procedures
Fast Kalman Filtering Through Sequential Processing
Feature-Based Landscape Analysis of Continuous and Constrained
Optimization Problems
Highlight, Annotate, and Format your R Source Code
Fits Piecewise Constant Models with Data-Adaptive Knots
Interpretable Matching for Causal Inference
Functional Latent Data Models for Clustering Heterogeneous
Curves ('FLaMingos')
Implementation of optimal hierarchical clustering
Shed Light on Black Box Machine Learning Models
Transforms Contingency Tables to Data Frames, and Analyses Them
Obtaining a Flat Table from Pivot Tables
Tools for Working with XML Files as R Dataframes
R Markdown Format for Flexible Dashboards
Tools to Work with the Flexible Dirichlet Distribution
Generalized Additive Models with Flexible Response Functions
Flexible Latent Trait Metrics using the Filtered Monotonic
Polynomial Item Response Model
Finite Mixture Modeling of Generalized Nonlinear Models
Flexible Parametric Survival and Multi-State Models
Reconstruct Animal Paths from Solar Geolocation Loggers Data
Implement a Countdown in 'RMarkdown' Documents and 'shiny'
Applications
Robust Score Testing in GLMs, by Sign-Flip Contributions
Convert Files to and from Binary Objects (BLOBs)
Process Synchronization Using File Locks
Statistical Methods for the (Regional) Analysis of Flood
Frequency
Tools for Interacting with the Brazilian Flora 2020
Tools for characterizing flowering traits
Forecasts future values of a univariate time series
Streamlining Design and Deployment of Complex Workflows
The Environmental Costs of Flow Regulation
Daily Streamflow Trend and Change Point Screening
Path Algorithm for the General Fused Lasso Signal Approximator
Mining Rigs for Specialized Subset Sum, Multi-Subset Sum,
Multidimensional Subset Sum, Multidimensional Knapsack,
Generalized Assignment Problems
Influenza-Attributable Mortality with Distributed-Lag Models
Estimate Insect Survival from Fluorescence Data
Flux rate calculation from dynamic closed chamber measurements
Data Sets from "Forecasting: Methods and Applications" by
Makridakis, Wheelwright & Hyndman (1998)
Factorial Experiments with Minimum Level Changes
Efficient Estimation of Clustered Current Status Data
A Flexible Modelling Environment for Inverse Modelling,
Sensitivity, Identifiability and Monte Carlo Analysis
Fast Class Noise Detector with Multi-Factor-Based Learning
Rhythmic Patterns Modeling by FMM Models
Filtered Monotonic Polynomial IRT Models
R Access to the 'FMP Cloud' and 'Financial Modeling Prep' API
Functional MRI Quality Assurance Routines
Functions for Medical Statistics Book with some Demographic Data
Regression Models with Finite Mixtures of Skew Heavy-Tailed
Errors
Rmetrics - Analysing and Modeling Multivariate Financial Return
Distributions
Fast Nearest Neighbor Search Algorithms and Applications
Rmetrics - Nonlinear and Chaotic Time Series Modelling
Feature Ordering by Conditional Independence
Summarize CRAN Check Results in the Terminal
Fit Continuous-Time State-Space and Latent Variable Models for
Quality Control of Argos Satellite (and Other) Telemetry Data
and for Estimating Movement Behaviour
Creates and Manages Folder Functions for Portable Large-Scale R
Analysis
Fonts with 'Bitstream Vera Fonts' License
Additional 'ggplot2' Themes Using 'Hind' Fonts
Additional 'ggplot2' Themes Using 'M+' Fonts
Food Network Inference and Visualization
visualisation and analysis of food web networks
Rmetrics - Pricing and Evaluating Basic Options
Foraminifera and Community Ecology Analyses
Tools for Working with Categorical Variables (Factors)
Forecasting Functions for Time Series and Linear Models
Convenient Functions for Ensemble Time Series Forecasts
Time Series Forecasting with Machine Learning Methods
Forecasting for Stationary and Non-Stationary Time Series
Test Bench for the Comparison of Forecast Methods
Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata',
'Systat', 'Weka', 'dBase', ...
Statistical Methods in Forensic Genetics
Statistical tools for the interpretation of forensic DNA
mixtures
Systems Insights from Generation of Hydroclimatic Timeseries
Approximate False Positive Rate Control in Selection Frequency
for Random Forest
A Unified Framework for Random Forest Prediction Error
Estimation
Statistical Modelling for Plant Size Distributions
Forest Health Evaluation System at the Forest Stand Level in
China
Design-Based Global and Small-Area Estimations for Multiphase
Forest Inventories
Advanced Forest Plot Using 'grid' Graphics
Ecosystem and Canopy Structural Complexity Metrics from LiDAR
Implements the Forest-R.K. Algorithm for Classification Problems
Forest Spatial Structure Analysis Systems
Projecting Customer Retention Based on Fader and Hardie
Probability Models
Imputation of Missing Values Through a Forward Imputation
Algorithm
Functions from the 2nd Italian Forest Inventory (INFC)
Elementary arithemtic in formal series rings
Programmatic Utilities for Manipulating Formulas, Expressions,
Calls, Assignments and Other R Objects
Dynamic Generation and Quality Checks of Formula Objects
Forensic Pedigree Analysis and Relatedness Inference
Palaeoecological and Palaeogeographical Analysis Tools
Bayesian 4 Parameter Item Response Model
A Game for Human vs. Human or Human vs. AI
Restricted MLE for Functional Principal Components Analysis
Two Dimensional Functional Principal Component Analysis
Three Dimensional Functional Component Analysis
Reliable Comparison of Floating Point Numbers
Automatic Distribution Graphs Using Formulas
Segmentation using Optimal Partitioning and Function Pruning
Rmetrics - Portfolio Selection and Optimization
Computing the noncentrality parameter of the noncentral F
distribution
Data for "Forecasting: principles and practice"
Data for "Forecasting: Principles and Practice" (2nd Edition)
Data for "Forecasting: Principles and Practice" (3rd Edition)
Approximation of First-Passage-Time Densities for Diffusion
Processes
Testing Hypotheses via Fuzzy P-Value in Fuzzy Environment
Fractionally Differenced ARIMA aka ARFIMA(P,d,q) Models
Fraction Proliferation via a Quiescent Growth Model
Simulation and Parameter Estimation of Randomized Sierpinski
Carpets using the p-p-p-q-Model
Assessing and Visualizing Fragility of Clinical Results with
Binary Outcomes
Fitting Frailty Models with the EM Algorithm
Frailty Models via Hierarchical Likelihood
General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction; Evaluation of Failure-Time Surrogate Endpoints
General Semiparametric Shared Frailty Model
Simulation of the Growth of Framboidal and Sunflower Pyrite
Financial Risk Modelling and Portfolio Optimisation with R
Automatic Data Processing and Visualization for FRAP
Fuzzy Rule-Based Systems for Classification and Regression Tasks
Fast Regularized Canonical Correlation Analysis
Statistical Analysis for Random Objects and Non-Euclidean Data
Read and Write 'FreeSurfer' Neuroimaging File Formats
Tree Method for High Dimensional Longitudinal Data
Deterministic Computation of Text Box Metrics
Rmetrics - Regression Based Decision and Prediction
Generate Open or Closed Interpolating Curves
FREQ: Estimate population size from capture frequencies
Frequency Domain Based Analysis: Dynamic PCA
Functional Time Series: Dynamic Functional Principal Components
Frequency Profiles Computing and Plotting
Make Quick Descriptive Tables for Categorical Variables
Spectral Decomposition of Connectedness Measures
Implementation of Frequent-Directions Algorithm for Efficient
Matrix Sketching
Feature Selection Algorithms for Computer Aided Diagnosis
Create Custom 'Bootstrap' Themes to Use in 'Shiny'
Fractional Factorial Designs with 2-Level Factors
Catalogues of resolution IV 128 run 2-level fractional
factorials up to 33 factors that do have 5-letter words
The Entire Transcript from Friends in Tidy Format
Utilities for the Forest Research Institute of the State
Baden-Wuerttemberg
Regression Analysis of Fractional Responses
Regression Analysis of Fractional Responses Under Unobserved
Heterogeneity
Regression Analysis of Panel Fractional Responses
The Generalized Hyperbolic Distribution, Related Distributions
and Their Applications in Finance
Prediction of Minimum Temperature for Frost Forecasting in
Agriculture
Evaluation Tools for Assessing Climate Adaptation of Fruit Tree
Species
Cross-Platform File System Operations Based on 'libuv'
Simple Fisheries Stock Assessment Methods
Data to Support Fish Stock Assessment ('FSA') Package
Managing and Visualizing Brain Surface Data
Automated Feature Selection from 'caret'
Forward Stepwise Deep Autoencoder-Based Monotone NLDR
Robust Data Analysis Through Monitoring and Dynamic
Visualization
'Rcpp' Implementation of 'FSelector' Entropy-Based Feature
Selection Algorithms with a Sparse Matrix Support
Import and Analysis of OMR Data from FormScanner
An Interface Between the 'FSK-ML' Standard and 'R'
Wrapper Functions for 'FSL' ('FMRIB' Software Library) from
Functional MRI of the Brain ('FMRIB')
Feature Selection for Multivariate Time Series
Imputation of Time Series Based on Fuzzy Logic
Rosenthal's Fail Safe Number and Related Functions
Fused Sparse Structural Equation Models to Jointly Infer Gene
Regulatory Network
Generate Fully-Sequential Space-Filling Designs Inside a Unit
Hypercube
Lightning Fast Serialization of Data Frames
Unified Sequence-Based Association Tests Allowing for Multiple
Functional Annotation Scores
A Wrapper for the API of the Danish Parliament
Programs for Analyzing Fourier Transform-Ion Cyclotron Resonance
Mass Spectrometry Data
Features and Strings for Nonparametric Regression
Rmetrics - Trading and Rebalancing Financial Instruments
Feature Extraction from Biological Sequences
R Interface to 'tslib' (a Time Series Library in C++)
Spectral Density Estimation and Comparison for Functional Time
Series
Framework for Unified Estimation in Lognormal Models
FUzzy GEnetic, a machine learning algorithm to construct
prediction model based on fuzzy logic
Sensitivity Analysis Optimized for Matched Sets of Varied Sizes
Plot Full ROC Curves using Eyewitness Lineup Data
Full Text of 'Scholarly' Articles Across Many Data Sources
Clean and Visualize Over Expression Results from
'ConsensusPathDB'
Functional Cheng and Church Bi-Clustering
Convenience Functions by Michael Chirico
Model-Free Functional Chi-Squared and Exact Tests
Functional Profiling of Microarray Expression Data
Functional Clustering of Redundant Components of a System
Functional Ensemble Survival Tree for Dynamic Prediction
Clustering in the Discriminative Functional Subspace
Psychometric Functions from the Waller Lab
Gaussian Process Models for Scalar and Functional Inputs
Univariate and Multivariate Model-Based Clustering in
Group-Specific Functional Subspaces
Rmetrics - Modelling Trends and Unit Roots
Model-Based Co-Clustering of Functional Data
Exploratory Data Analysis and Data Preparation Tool-Box
Time-Based Joins to Analyze Sequences of Events
Funnel Plots for Comparing Institutional Performance
Simple Utility Providing Terminal Access to all R Functions
Functional Regression for Irregularly Timed Data
Apply Mapping Functions in Parallel using Futures
Block Splitting Algorithm for Estimation with Fused Penalty
Functions
Fused Lasso for High-Dimensional Regression over Groups
Embedding 'FusionCharts Javascript' Library in R
Clustering and Feature Screening using L1 Fusion Penalty
A framework for working in a functional programming paradigm in
R
Interim Analysis of Operational Futility in Randomized Trials
with Time-to-Event Endpoints and Fixed Follow-Up
Unified Parallel and Distributed Processing in R for Everyone
Apply Function to Elements in Parallel using Futures
A Future API for Parallel and Distributed Processing using
'batchtools'
A Future API for Parallel Processing using 'callr'
Find, Characterize, and Explore Extreme Events in Climate
Projections
Exact calculation of fuzzy decision rules for multiple testing
Join Tables Together on Inexact Matching
Multi-Criteria Decision Making Methods for Fuzzy Data
Apply Two Fuzzy Numbers on a Monotone Function
Fuzzy Quantification of Common and Rare Species
Fuzzy Rank Tests and Confidence Intervals
Fuzzy Similarity in Species Distributions
Fuzzy Stationary Probabilities from a Sequence of Observations
of an Unknown Markov Chain
Statistical Methods for Trapezoidal Fuzzy Numbers
Selecting Variables in Regression Models
Fire Weather Index System and Fire Behaviour Prediction System
Calculations
A package performing Dynamic Bayesian Network inference
Find and Fill Gaps in Metabolic Networks
Grain-Size Statistics and Description of Sediment
Interactively Visualize Genetic Mutation Data using a
Lollipop-Diagram
Abbreviating Items Measures using Genetic Algorithms
Framework for Generalized Subspace Pattern Mining
Genetic Similarity in User-Based Collaborative Filtering
GAD: Analysis of variance from general principles
A Genetic Algorithm for Learning Directed Acyclic Graphs
Gadget is the Globally-Applicable Area Disaggregated General
Ecosystem Toolbox
First Passage Time Simulation for Gaussian Diffusion Processes
Genetic and Isotopic Assignment Accounting for Habitat
Suitability
Machine Learning-Based Analysis of Potential Power Gain from
Passive Device Installation on Wind Turbine Generators
Graphical Extension with Accuracy in Parameter Estimation
(GAIPE)
Genomic Annotation in Livestock for Positional Candidate LOci
Genetic Algorithms and C-Steps Based LTS (Least Trimmed Squares)
Estimation
Genetic Approach to Maximize Clustering Criterion
Fit the Gambin Model to Species Abundance Distributions
Estimating multistate models using gamboost()
Functions and Data for a Course on Modern Regression and
Classification
Generalized Additive Models for Bivariate Conditional Dependence
Structures and Vine Copulas
Applies GAMbag, GAMrsm and GAMens Ensemble Classifiers for
Binary Classification
Palettes Inspired in the TV Show "Game of Thrones"
Statistical Estimation of Game-Theoretic Models
Genetic Algorithm for Sequential Symmetric Games
Tools for Calculating Allocations in Game Theory
Generalised Additive Models for Location Scale and Shape
Extra Additive Terms for Generalized Additive Models for
Location Scale and Shape
Fitting an Interval Response Variable Using `gamlss.family'
Distributions
Generating and Fitting K-Inflated 'discrete gamlss.family'
Distributions
Distributions for Generalized Additive Models for Location Scale
and Shape
Fitting Mixed (Inflated and Adjusted) Distributions
Fitting Mixture Distributions with GAMLSS
Fitting non linear parametric GAMLSS models
Spatial Terms in Generalized Additive Models for Location Scale
and Shape Models
Generating and Fitting Truncated `gamlss.family' Distributions
Bimodal Skew Symmetric Normal Distribution
Generalized Additive Mixed Models using 'mgcv' and 'lme4'
Comparing Nonlinear Curves and Surface Estimations by
Semiparametric Methods
Dose Rate Estimation from in-Situ Gamma-Ray Spectrometry
Measurements
Classic Gamma Regression: Joint Modeling of Mean and Shape
Parameters
Generalized Additive Mixed Model Analysis via Slice Sampling
Robust and Sparse Regression via Gamma-Divergence
Fit Regularization Path for Generalized Additive Models
Gene Association Network-based Pathway Analysis
Conservation Indicators using Spatial Information
Searching Parsimony Models with Genetic Algorithms
Gene and Region Counting of Mutations ("GARCOM")
Fitting and Forecasting Gegenbauer ARMA Time Series Models
Generalized Array Arithmetic for Ragged Arrays with Named
Margins
Genetic Algorithm (GA) for Variable Selection from
High-Dimensional Data
Greenhouse Gas Flux Calculation from Chamber Measurements
Analyzing Gastric Emptying from MRI or Scintigraphy
Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models
Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation
Lotka-Volterra Models for Gause's 'Struggle for Existence'
The Gaussian Covariate Method for Variable Selection
Difference measures for multivariate Gaussian probability
density functions
The Greatest Mathematician Since Antiquity
Inference, Goodness-of-Fit and Forecast for Univariate Gaussian
Hidden Markov Models
Collection of functions for Gaussian quadrature
Multi-Trait Dissimilarity with more Uniform Contributions
Generalize Lambda Distribution and Generalized Bootstrapping
Generalized Beta Distribution of the Second Kind: Properties,
Likelihood, Estimation
Estimation of the Generalised Beta Distribution of the Second
Kind from Grouped Data
Yield Curves of Brazil, China, and Russia
Generalized Beta and Beta Prime Distributions
Generalized Berk-Jones Test for Set-Based Inference in Genetic
Association Studies
Utilities for processing Rd objects and files
Inference of Ploidy from (Genotyping-by-Sequencing) GBS Data
Hyperparameter Search for Gradient Boosted Trees
Simulation of Real and Complex Numbers and Small Programming
Utilities
Guided Correction Approach for Inherited bias (GCAI.bias)
A Data Manipulation and Analysis Package for Calcium Indicator
Data
Simple Peak Alignment for Gas-Chromatography Data
Graph-based two-sample tests for categorical data
'GPU'/CPU Benchmarking in Debian-Based Systems
LASSO and Elastic Net (Adaptive) Penalized Least Squares,
Logistic Regression, HHSVM, Squared Hinge SVM and Expectile
Regression using a Fast GCD Algorithm
Analysis of Geostatistical Count Data using Gaussian Copulas
Concord method for Graphical Model Selection
Implements Generic Composite Similarity Measure
Geographical Detectors for Assessing Spatial Factors
Datasets for the Book Graphical Data Analysis with R
Earth Observation Data Cubes from Satellite Image Collections
Wrappers for 'GDAL' Utilities Executables
Wrappers for the Geospatial Data Abstraction Library (GDAL)
Utilities
Various R Programming Tools for Data Manipulation
A Toolbox for Geometric Data Analysis and More
Download, slice, and normalize GDELT data
Distances and Routes on Geographical Grids
Tools to Work with Google's 'DNS'-over-'HTTPS' ('DoH') API
IO for GAMS GDX Files using 'data.table'
Generalised Estimating Equations (GEE/WGEE) using 'Armadillo'
and S4
Adaptive Association Tests for Multiple Phenotypes using
Generalized Estimating Equations (GEE)
Bias-Corrected GEE for Cluster Randomized Trials
Marginal Proportional Hazards Mixture Cure Models with
Generalized Estimating Equations
Mediation Analysis for Generalized Linear Models Using the
Difference Method
Modified Variance Estimators for Generalized Estimating
Equations
Calculate Generalized Eigenvalues, the Generalized Schur
Decomposition and the Generalized Singular Value Decomposition
of a Matrix Pair with Lapack
Misspecified Models for Gene-Environment Interaction
File Conversion for 'Gem Infrasound Logger'
Network Meta-Analysis Using Bayesian Methods
Generalized Two-Stage Designs for Phase II Single-Arm Studies
General Engine for Eco-Evolutionary Simulations
Classes and Methods to Use Genetic Algorithms for Feature
Selection
Global ENvironmental ASsessment Information System (GENASIS)
computational tools
Analysis and Visualization Tools for Genetic Barcode Data
Clopper-Pearson Confidence Interval and Generalized Binomial
Distribution
Predict Gender from Names Using Historical Data
Predict Gender from Brazilian First Names
Segmentation and Classification of Accelerometer Data
Visualisation of Raw or Segmented Accelerometer Data
Gene Expression Clustering and Gene Network
Identification of Periodically Expressed Genes
Retrieves Gene Expression Dataset and Gene Symbols from GEO Code
A Pipeline to Define Gene Families in Legumes and Beyond
Profiling a gene list into GOslim or KEGG function pie
Belief Propagation in Genotype-Phenotype Networks
Genetic Epidemiology Design and Inference
Population Genetic Data Analysis Using Genepop
Generalized Correlations and Various Causal Paths
Goodness of Fit Tests for Logistic Regression Models
Test for Conditional Independence Based on the Generalized
Covariance Measure (GCM)
Credible Visualization for Two-Dimensional Projections of Data
Blinder-Oaxaca Decomposition for Generalized Linear Model
Generate Data Containing Fake Personally Identifiable
Information
Common S3 Generics not Provided by Base R Methods Related to
Model Fitting
Estimate Gender from Names in Spanish and Portuguese
Identify Favorable Subsets of Germplasm Collections
Spatial Graph-Theoretic Genetic Gravity Modelling
The Forward Imputation: A Sequential Distance-Based Approach for
Imputing Missing Data
Goodness-of-Fit for Univariate Hidden Markov Models
Fast, Robust, and Outlier Resistant Hierarchical Clustering
The Genie++ Hierarchical Clustering Algorithm with Noise Points
Detection
Easily Access Song Lyrics from Genius.com
Functions for generating and manipulating binned kernel density
estimates
Path Algorithm for Generalized Lasso Problems
Implements Generalized Meta-Analysis Using Iterated Reweighted
Least Squares Algorithm
Finding the DNA and Protein Sequences of Any Genomic or
Proteomic Loci
Methods for Analysing Forensic Ancestry Informative Markers
'Plot genome wide values for all chromosomes'
Models Dealing with Spatial Dependency in Genomic Data
Circular Genomic Permutation using Gwas p-Values of Association
Collection of Tools for Genomic Data Analysis
Plot Publication-Grade Gene and Genome Maps
Simulation of Discrete Random Variables with Given Correlation
Matrix and Marginal Distributions
A Genome-Wide Scan Statistic Framework for Whole-Genome Sequence
Data Analysis
Generalized Pathmox Approach Segmentation Tree Analysis
Power Calculations Under Genetic Model Misspecification
Generalized Ridge Trace Plots for Ridge Regression
Generates Data Sets for Class Demonstrations
A Generalized Multiclass Support Vector Machine
R Shiny App for Creating Simplified Trial Summary (TS) Domain
Spline Based Window Boundaries for Genomic Analyses
Analysis of Geostatistical Data using Bayes and Empirical Bayes
Methods
Loads Shapefiles of Official Spatial Data Sets of Brazil
A geometrical Approach to Differential expression and gene-set
enrichment
Stratified Heterogeneity Measure, Dominant Driving Force
Detection, Interaction Relationship Investigation
Fast, Dependency-Free Geodesic Distance Calculations
Methods for Calculating Gradient Surface Metrics
3D-Visualization of Geoelectric Resistivity Measurement Profiles
'ggplot2' Faceting Utilities for Geographical Data
Spatial Prediction for Function Value Data
Kriging Method for Spatial Functional Data
Select Sparse Geoadditive Models for Spatial Prediction
Geomultistar Generator from American Community Survey (ACS)
Geodatabases
Turn Geospatial Polygons into Regular or Hexagonal Grids
Convert Data from and to 'GeoJSON' or 'TopoJSON'
Web-Processing of Large Gridded Datasets
Data for topographic and Geologic Mapping
Tools for Reading and Writing ISO/OGC Geographic Metadata
Generate and Modify Interoperable Geometric Shapes
Convert Between R Objects and Geometric Structures
Mesh Generation and Surface Tessellation
Network Visualization in the 'ggplot2' Framework
Geometric Morphometric Analyses of 2D/3D Landmark Data
Multidimensional Queries Enriched with Geographic Data
Interface to the "Geonames" Spatial Query Web Service
Geophysics, Continuum Mechanics, Gravity Modeling
Calculating Geographic Range from Occurrence Data
Robust Geostatistical Analysis of Spatial Data
Open Source Geometry Engine ('GEOS') R API
Smallest Enclosing Disc for Latitude and Longitude Points
Classes and Methods for Working with Spectral Data with
Space-Time Attributes
Geostatistical Analysis and Design of Optimal Spatial Sampling
Networks
Spatio-Temporal; Inverse Distance Weighting and Radial Basis
Functions with Distance-Based Regression
An Introduction to Statistics for Geoscientists
Geostatistical Modelling with Likelihood and Bayes
Processing various types of data on GEO and TCGA
Tools to Improve the Use of Geostatistic
An R Plug-in for the Distributed Hydrological Model GEOtop
Methods for Handling and Analyzing Time Series of Satellite
Images
Google Encoded Polyline Algorithm Format
Download and Augment the Corpus of Plenary Protocols of the
German Bundestag
Indices and Graphics for Assess Seed Germination Process
Generalized Structured Component Analysis (GSCA)
Reproducible Data Retrieval from the GESIS Data Archive
Tools for Making and Combining Functions
Generalised Survival Trial Assessment Tool Environment
General Purpose G-Estimation for End of Study or Time-Varying
Outcomes
Fetching Tabular Data "Onload" in Compiled R Markdown HTML
Documents
Imports Datasets from BCB (Central Bank of Brazil) using Its
Official API
Reading Annual Financial Reports from Bovespa's DFP, FRE and FCA
System
Translating Coding Statements using get() and eval() for
Improved Run-Time Coding Efficiency
Access to Ethereum-Based Blockchains Through Geth Nodes
Get Landsat 8 Data from Amazon Public Data Sets
Import and Process Data from the 'Lattes' Curriculum Platform
Reading Bibliometric Data from Lattes Platform
Get Meteorological Data for Hydrologic Models
Quantifying Systematic Heterogeneity in Meta-Analysis
Parsing Command-Line Arguments and Simple Variable Interpolation
Fast and Cached Import of Data from 'Quandl' Using the 'json
API'
GetR: Calculate Guttman error trees in R
General-to-Specific (GETS) Modelling and Indicator Saturation
Methods
SPRE Statistics for Exploring Heterogeneity in Meta-Analysis
Get Data for Brazilian Bonds (Tesouro Direto)
Joint Test of Gene and GxE Interactions via Varying Coefficients
GEV Conditional Density Estimation Network
A visual, intuitive, easy to use software giving access to a new
type of information buried into your microarray data
Tools for Working with Hansen et al. Global Forest Change
Dataset
Gross Flows Estimation under Complex Surveys
Generalized Fiducial Inference for Extremes
Generalized Fiducial Inference for Low-Dimensional Robust Linear
Regression
Generalized Fiducial Inference for Normal Linear Mixed Models
Generalized Fisher's Combination Tests Under Dependence
Generalized Fiducial Inference for Ultrahigh-Dimensional
Regression
Implements Group Fused Multinomial Regression
Offline 'Google' Fonts for 'Markdown' and 'Shiny'
Graph-Constrained Functional Pruning Optimal Partitioning
Extra Coordinate Systems, 'Geoms', Statistical Transformations,
Scales and Fonts for 'ggplot2'
Categorical Scatter (Violin Point) Plots
Mini Bubble Plots for Comparison of Discrete Data with 'ggplot2'
Shorten the Distance from Data Visualization Idea to Actual Plot
Gabriel Graph Based Large-Margin Classifiers
Simpler Appearance Modification of 'ggplot2'
Visualization of a Correlation Matrix using 'ggplot2'
Analyze and Create Elegant Directed Acyclic Graphs
'ggplot2' Extension for Seasonal and Trading Day Adjustment with
'RJDemetra'
Create Dendrograms and Tree Diagrams Using 'ggplot2'
Visualizations of Distributions and Uncertainty
Interactive 'ggplot2' Layer and Theme Aesthetic Editor
Create Tidy Data Frames of Marginal Effects for 'ggplot' from
Model Outputs
Visualization Tools for Genealogical Data
Visualisation of High-Throughput Behavioural (i.e. Ethomics)
Data
Add Marginal Histograms to 'ggplot2', and More 'ggplot2'
Enhancements
Summarise a Distribution Through Coloured Intervals
Scales that Focus Specific Levels in your ggplot()
Formula Interface to the Grammar of Graphics
Data Visualization Tools for Statistical Analysis Results
Streamlined Creation of Segments on the Y-Axis of 'ggplot2'
Plots
Capture the Spirit of Your 'ggplot2' Calls
Create a Half Normal Plot Using 'ggplot2'
Compose Half-Half Plots Using Your Favourite Geoms
Graphics Layers for Plotting Image Data with 'ggplot2'
Visualise the Results of Inferential Statistics using 'ggplot2'
Explore the Innards of 'ggplot2' Objects
Data Visualization for IP Addresses and Networks
Make Interactive 'ggplot2'. Extension to 'ggplot2' and 'ggiraph'
Group Lasso Penalized Learning Using a Unified BMD Algorithm
Grammar of Graphics for Linear Model Diagnostic Plots
Plotting Lorenz Curve with the Blessing of 'ggplot2'
Graphical Markov Models with Mixed Graphs
Tools for Analyzing MCMC Simulations from Bayesian Inference
Variable Selection in Linear Mixed Models for SNP Data
Gaussian Graphical Models with Nonconvex Regularization
Gaussian Graphical Models Using Ridge Penalty Followed by
Thresholding and Reestimation
Plot Multiple Sequence Alignment using 'ggplot2'
Create Muller Plots of Evolutionary Dynamics
Geometries to Plot Networks with 'ggplot2'
Multiple Fill and Colour Scales in 'ggplot2'
A 'ggplot2' Extension to Make Normal Violin Plots
Plot Data on Oceanographic Maps using 'ggplot2'
A 'ggplot2' and 'gganimate' Version of Pac-Man
Variations of Parallel Coordinate Plots for Categorical Data
'ggplot' Visualizations for the 'partykit' Package
Easy Plotting of Periodic Data with 'ggplot2'
Multiple Summary Statistics for Binned Stats/Geometries
Create Elegant Data Visualisations Using the Grammar of Graphics
'RStudio' Addin for Teaching and Learning 'ggplot2'
Create Ggplots via a Graphical User Interface
Convert Plot to 'grob' or 'ggplot' Object
Extra Convenience Functions for 'Plotly'
'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME
Models
A Cross Between a 2D Density Plot and a Scatter Plot
Visualizing Social Science Data with 'ggplot2'
Polygons with Holes for the Grammar of Graphics
Annotate Statistical Tests for 'ggplot2'
Compare Big Datasets to the Uniform Distribution
Quickly Explore Your Data Using 'ggplot2' and 'table1' Summary
Tables
An Implementation of Grammar of Graphics for Graphs and Networks
Allows Interactive Visualization of Data Through a Web Browser
GUI
Gaussian-Based Genome Representative Selector with
Prioritization
Automatically Position Non-Overlapping Text Labels with
'ggplot2'
Panels and Interactive Versions of Diagnostic Plots using
'ggplot2'
Scientific Journal and Sci-Fi Themed Color Palettes for
'ggplot2'
'stats' for Seasonal Adjustment on the Fly with 'ggplot2'
A 'ggplot2' Extension for Drawing Publication-Ready Sequence
Logos
North Symbols and Scale Bars for Maps Created with 'ggplot2' or
'ggmap'
A 'ggplot2'-Plot of Composition of Solvency II SCR: SF and IM
New Data Visualisations for SOMs Networks
Extensions to 'ggplot2' for Radiation Spectra
'ggplot2' Based Plots with Statistical Details
Continuous Confidence Interval Plots using t-Distribution
Offers Various Swiss Maps as Data Frames and 'ggplot2' Objects
An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Improved Text Rendering Support for 'ggplot2'
Extra Themes, Scales and Geoms for 'ggplot2'
Time Series Visualisations Using the Grammar of Graphics
Combination Matrix Axis for 'ggplot2' to Create 'UpSet' Plots
Voronoi Diagrams and Heatmaps with 'ggplot2'
A Natural Language Interface to 'ggplot2'
Quantifying Evolution and Selection on Complex Traits
Functional Conditional Independence Testing with the GHCM
Missing Data Segments Imputation in Multivariate Streams
Graphical Horseshoe MCMC Sampler Using Data Augmented Block
Gibbs Sampler
Generalized Hyperbolic Distribution and Its Special Cases
Fit and Simulate Generalised Hypergeometric Ensembles of Graphs
Gene Set Uncertainty in Enrichment Analysis
Naive Gibbs Sampling with Metropolis Steps
Gibbs Sampler for One-Way Mixed-Effects ANOVA and ANCOVA Models
Multivariate Analysis with Optimal Scaling
Reads in 'Neuroimaging' 'GIFTI' Files with Geometry Information
GIFT Questions Format Generator from Dataframes
Take Shell Commands and Turn Them into R Functions
Random Variate Generator for the GIG Distribution
Gillespie's Stochastic Simulation Algorithm (SSA)
Gillespie's Stochastic Simulation Algorithm for Impatient People
Group Iterative Multiple Model Estimation
Supplemental Tools for the 'gimme' R Package
A New Gini Correlation Between Quantitative and Qualitative
Variables
Computing the Gini-Based Coefficients for Weighted and Negative
Attributes
Generalized Iterative Proportional Fitting for Relational Models
Download Map Data from GISCO API - Eurostat
Store and Retrieve Data.frames in a Git Repository
Rstudio Addin for Version Control and Assignment Management
using Git
A Helpful Way to Install R Packages Hosted on GitHub
Create Useful .gitignore Files for your Project
Add 'Git' Links to Your Web Based Assets
g-and-k and g-and-h Distribution Functions
Gaines and Kuklinski (2011) Estimators for Hybrid Experiments
Accessing the Official 'Google Knowledge Graph' API
Penalization in Large Scale Generalized Linear Array Models
Generate tables and plots to get summaries of data
Generalized Linear Autoregressive Moving Average Models
Graphical Lasso: Estimation of Gaussian Graphical Models
General Linear Ballistic Accumulator Models
An R Package for Estimating a Group-Effect in Latent Class
Analysis
Calculate Textures from Grey-Level Co-Occurrence Matrices
(GLCMs)
Estimation and Use of the Generalised (Tukey) Lambda
Distribution
Fitting Single and Mixture of Generalised Lambda Distributions
(RS and FMKL) using Various Methods
Fit GLD Regression Model and GLD Quantile Regression Model to
Empirical Data
Global and Individual Tests for Direct Effects
Learning Interactions via Hierarchical Group-Lasso
Regularization
Generalized Linear Latent Variable Models
'C' and 'Java' Source Code Generator for Fitted Glm Objects
Predicted Values and Discrete Changes for GLM
Adaptive LASSO and Network Regularized Generalized Linear Models
An Adaptive Test on High Dimensional Parameters in Generalized
Linear Models
All Hierarchical or Graphical Models for Generalized Linear
Model
Bayesian Fractional Polynomials for GLMs
Fitting Generalized Linear Models Subject to Constraints
Generalized Linear Models for Categorical Responses
Discretization and Grouping for Logistic Regression
GLRT P-Values in Generalized Linear Models
Graph-Constrained Regularization for Sparse Generalized Linear
Models
Fit GLM with LEP-Based Penalized Maximum Likelihood
Generalized Linear Mixed Models via Monte Carlo Likelihood
Approximation
Generalized Linear Mixed Models using Adaptive Gaussian
Quadrature
Bootstrap Resampling for Mixed Effects and Plain Models
Generalized Linear Mixed Model Analysis via Expectation
Propagation
Generalized Linear Mixed Models with Robust Random Fields for
Spatiotemporal Modeling
Variable Selection for Generalized Linear Mixed Models by
L1-Penalized Estimation
Generalized Linear Models with Clustering
Generalized Linear Mixed Model (GLMM) for Binary Randomized
Response Data
Generalized Linear Mixed Models using Template Model Builder
Lasso and Elastic-Net Regularized Generalized Linear Models
Fit a Penalized Constrained Continuation Ratio Model for
Predicting an Ordinal Response
Data and Code to Accompany Generalized Linear Models, 2nd
Edition
L1 Regularization Path for Generalized Linear Models and Cox
Proportional Hazards Model
Fit a Penalized Continuation Ratio Model for Predicting an
Ordinal Response
Dimension Reduction of Non-Normally Distributed Data
Creates Ideal Data for Generalized Linear Models
Truncated Lasso Regularized Generalized Linear Models
Model Selection and Multimodel Inference Made Easy
Variable Selection Deviation Measures and Instability Tests for
High-Dimensional Generalized Linear Models
Testing the additional predictive value of high-dimensional data
Bi-Level Optimization of Metabolic Network Models
Global Gene-Set Analysis for Association Studies
Inhomogeneous K- And Pair Correlation Functions Using Global
Estimators
Generate Functions to Get or Set Global Options
Objective functions for benchmarking the performance of global
optimization algorithms
Identify Global Objects in R Expressions
Plot 2D and 3D Views of the Earth, Including Major Coastline
Fitting and Testing Generalized Logistic Distributions
Generalized Logrank Tests for Interval-censored Failure Time
Data
Genome-Wide Association and Linkage Analysis under Heterogeneity
Generalized Least Squares with Measurement Error
Glucose Variability Measures from Continuous Glucose Monitoring
Data
Methods to Assess Generalized Latent Variable Model Fit
Genomic Mediation Analysis with Adaptive Confounding Adjustment
Distance and Travel Time Between Two Points from Google Maps
Simulation of Graphical Correlation Matrices
Fast Estimation of Gaussian Mixture Copula Models
Graph Based Multiple Comparison Procedures
Accessing a Geometallurgical Database with R
Short Term Forecasting via GMDH-Type Neural Network Algorithms
Binary Classification via GMDH-Type Neural Network Algorithms
Geometric Median, k-Median Clustering and Robust Median PCA
Inference and Clustering of Functional Data
Gaussian Mixture Graphical Model Learning and Inference
Descriptive Statistics, Transition Plots, and More
Unsupervised Gaussian Mixture and Minkowski and Spherical
K-Means with Constraints
Generalized Method of Moments and Generalized Empirical
Likelihood
Generalized Linear Mixed Model Association Tests
Likelihood-Based Boosting for Generalized Mixed Models
Multinomial Logit Models with Random Parameters
Various R Programming Tools for Model Fitting
Tools for 2D and 3D Plots of Single and Multi-Objective
Linear/Integer Programming Models
Generalised Management Strategy Evaluation Simulator
Generalized Mass Spectrum Missing Peaks Abundance Imputation
Interface Between GMT Map-Making Software and R
Estimate Gaussian Mixture Vector Autoregressive Model
Methods for Fitting Network Time Series Models
Computation of Generalized Nash Equilibria
Goodness of Fit Test for Continuous Distribution Functions
Estimate Natural Mortality for Different Life Stages
Access the 'Geographic Name Resolution Service'
Read Data from Files Readable by 'gnumeric'
Functions for Community Data and Ordinations
Fast DocumentTermMatrix and TermDocumentMatrix Creation
Goodness-of-Fit Tests for Functional Data
Goodness-of-Fit Tests for the Gamma Distribution
Testing Goodness-of-Fit with the Kernel Density Estimator
Khmaladze Martingale Transformation Goodness-of-Fit Test
Interactive Document for Working with Goodness of Fit Analysis
Tests of Fit for some Probability Distributions
Classical Goodness-of-Fit Tests for Univariate Distributions
Generalized Orthogonal GARCH (GO-GARCH) models
Gene Ontology Label Discernment and Identification
A Framework for Robust Shiny Applications
Animate Text using the 'Animate.css' Library
Association Analysis for Categorical Variables
R Scripts in the Google Cloud via Cloud Run, Cloud Build and
Cloud Scheduler
Access to the 'Google Cloud Vision' API for Image Recognition,
OCR and Labeling
Collect Data Programmatically by POST Methods to Google Forms
Retrieve Information from 'Google Knowledge Graph' API
Call Google's 'Natural Language' API, 'Cloud Translation' API,
'Cloud Speech' API and 'Cloud Text-to-Speech' API
An Interface to Google's Cloud Natural Language API
Encoding Coordinates into 'Google' Polylines
Working with Google's 'Public Data Explorer' DSPL Metadata Files
Access Google Sheets using the Sheets API V4
Access the 'Google Tag Manager' API using R
Accesses Google Maps APIs to Retrieve Data and Plot Maps
Visualization of Functional Analysis Data
Fit Generalized Odds Rate Mixture Cure Model with Interval
Censored Data
Evaluation of Inequality Constrained Hypotheses Using GORICA
Scroll Back to Top Icon in 'rmarkdown' and 'shiny'
functions to get public survey data in Japan
Structural Exploration of the Gene Ontology (GO) Knowledge Base
Gaussian Processes for Pareto Front Estimation and Optimization
Comprehensive Statistical Analysis of Plant Breeding Experiments
Differential Item Functioning in Generalized Partial Credit
Models
Bootstrap goodness-of-fit test for the generalized Pareto
distribution
Gaussian Process Regression for Functional Data Analysis
Solving Complex Game Problems using Gaussian Processes
Fast Gaussian Process Computation Using Vecchia's Approximation
Convert Chip ID of the GPL2015 into GeneBank Accession and
ENTREZID
Generalized Partial Linear Models (GPLM)
Various R Programming Tools for Plotting Data
Generalized Partially Linear Tree-Based Regression Model
Gaussian Process Modeling of Multi-Response and Possibly Noisy
Datasets
Analysing and plotting genotype-phenotype maps
Lyapunov Exponents and Kaplan-Yorke Dimension
Gaussian Process Ranking of Multiple Time Series
Gaussian Process Regression for Mortality Rates
Generalized Propensity Score Cumulative Distribution Function
Sequential Clustering Algorithm for Location Data
Maximum Likelihood Estimation of Multiple Membership Mixed
Models Used in Value-Added Modeling
Prediction of G Quadruplexes and Other Non-B DNA Motifs
Probability of Detection for Grab Sample Selection
Graph-Constrained Estimation and Hypothesis Tests
Helps Grade Assignment Submissions that are R Scripts
Interactive Color Gradient Picker Using 'htmlwidgets' and the
Modified JS Script 'jquery-gradient-picker'
Landscape Connectivity, Habitat, and Protected Area Networks
Creating Continuously Integrated Package Repositories from
Manifests
Inference on Granger-Causality in the Frequency Domain
Graphical Analysis of Variance Using ggplot2
Gene-Ranking Analysis of Pathway Expression
A Wrapper of the JavaScript Library 'vis-graph3d'
Build Graphs for Landscape Genetics Analysis
A Multi-Platform GUI for Drawing Customizable Graphs in R
An R Interface to the 'GraphHopper' Directions API
Statistical Methodology for Graphical Extreme Value Models
Graphical VAR for Experience Sampling Data
Additional Layout Algorithms for Network Visualizations
A Collection of Graphon Estimation Methods
Cluster Detection with Hypothesis Free Scan Statistic
Simulate Expression Data from 'igraph' Networks
Graceful 'ggplot'-Based Graphics and Other Functions for GAMs
Fitted Using 'mgcv'
Generating Time Series with Diverse and Controllable
Characteristics
Explore Probability Distributions for Bivariate Temporal
Granularities
Inference in Graphical Gaussian Models with Edge and Vertex
Symmetries
Parameter Inference and Optimal Designs for Grouped and/or
Right-Censored Count Data
Gradient-Based Recognition of Spatial Patterns in Environmental
Data
Routines for Writing Greek Letters and Mathematical Symbols on
the 'RStudio' and 'RGui'
Combine Categories Using Greenacre's Method
Mixed-Effects REML Incorporating Generalized Inverses
Adaptive Group-Regularized Logistic Elastic Net Regression
Simple and Scalable Statistical Modelling in R
Generalized Path Analysis for Social Networks
Gene ID Mapping for Genotype-Tissue Expression (GTEx) Data
Toolbox for Model Building and Forecasting
Fit a Grey-Zone Model with Survival Data
Miscellaneous Functions for "Grid" Graphics
Redraw Base Graphics Using 'grid' Graphics
Cluster-Preserving Multivariate Joint Grid Discretization
A Simulation Tool to Determine the Required Sample Size for
Repertory Grid Studies
Improved Text Rendering Support for 'Grid' Graphics
Uses Grieg-Smith method on 2 dimentional spatial data
Calculate Optical Parameters from Spindle Stage Measurements
Bayesian Inference for A|B and Bandit Marketing Tests
Creating Flexible, Reproducible 'PDF' Reports
Generalized Regression on Orthogonal Components
Gromov-Hausdorff Type Distances for Labeled Metric Spaces
Reproducible Scripts via Version-Specific Package Loading
Learn Group Bayesian Networks using Hierarchical Clustering
Regression Analysis of Grouped and Coarse Data
Grouped Statistical Analyses in a Tidy Way
Efficient Estimation of Grouped Survival Models
Independent Component Analysis for Grouped Data
Regularized Multivariate Regression for Identifying Master
Predictors Using the GroupRemMap Penalty
A GUI-Based Program to Compute Probabilities Regarding Group
Sequential Designs
Multiple Testing Procedure for Grouped Hypotheses
Grouped Weighted Quantile Sum Regression
Wavelet Functional ANOVA Through Markov Groves
Bayesian Non-Parametric Dependent Models for Time-Indexed
Functional Data
Multivariate Normal and Elliptically-Contoured Repeated
Measurements Models
Simple Metrics to Summarize Growth Curves
Plotting, Smoothing and Growth Trait Extraction for Longitudinal
Data
Bayesian reconstruction of growth velocity
Estimate Growth Rates from Experimental Data
Penalized Cox Model for High-Dimensional Data with Grouped
Predictors
Fitting User-Specified Models with Group Lasso Penalty
Standardization for Group Lasso Models with Categorical
Predictors
Regularization Paths for Regression Models with Grouped
Covariates
Patterns and Statistical Differences Between Two Groups of
Strings
Goodness-of-Fit Tests in High-Dimensional GLMs
Alternative Implementations of Base R Functions
GRS Test for Portfolio Efficiency, Its Statistical Power
Analysis, and Optimal Significance Level Calculation
Tools for the Analysis of Gutenberg-Richter Distributions of
Earthquake Magnitudes
Gene Set Analysis with Fisher Combined Method
Gene Set Analysis using the Gamma Method
Two Functions for Generalized SARIMA Time Series Simulation
Estimate Parameters in the Generalized SBM
Generalized Structure Component Analysis- Latent Class Analysis
& Latent Class Regression
Group Sequential Designs with Negative Binomial Outcomes
Robust Estimation in the Presence of Cellwise and Casewise
Contamination and Missing Data
Semi-Supervised Generalized Structural Equation Modeling
Group Sequential Design in Equivalence Studies
Download Google Sheets Using Just the URL
High Efficient Functions to Decode NFL Player IDs
Global Sea Level and Oxygen Isotope Data
Global Surface Summary of the Day ('GSOD') Weather Data Client
Group Sequential Refined Secondary Boundary
Spatial and Spatio-Temporal Geostatistical Modelling, Prediction
and Simulation
Graph-Based Sequential Change-Point Detection for Streaming Data
Utilities for Strings and Function Arguments
Estimation of the Generalized Symmetry Point, an Optimal
Cutpoint in Continuous Diagnostic Tests
Easily Create Presentation-Ready Display Tables
Generalizability Theory for Information Retrieval Evaluation
Calculate efficiencies of group testing algorithms with
correlated responses
Converting Transport Data from GTFS Format to GPS-Like Records
Routing with GTFS (General Transit Feed Specification) Data
Game-Theoretically OPtimal (GTOP) Reconciliation Method
Perform and Display Google Trends Queries
Presentation-Ready Data Summary and Analytic Result Tables
Genome and Transcriptome Wide Association Study
Nombres Inscritos en Chile (1920 - 2019)
Access 'The Guardian' Newspaper Open Data API
Maps, Data and Methods Related to Guerry (1833) "Moral
Statistics of France"
Adjust Estimates of Learning for Guessing
Implementation of Sampling Formulas for the Unified Neutral
Model of Biodiversity and Biogeography, with or without Guild
Structure
Statistical Analysis of Monthly Background Checks of Gun
Purchases
A User-Oriented Statistical Toolkit for Analytical Variance
Estimation
Download and Process Public Domain Works from Project Gutenberg
Fast Calculation of the Likelihood of a Stochastic Survival
Model
Perform Global Vector Autoregression Estimation and Inference
Regularized Categorical Effects/Categorical Effect
Modifiers/Continuous/Smooth Effects in GLMs
Global Validation of Linear Models Assumptions
Manhattan, Q-Q, and PCA Plots using 'ggplot2'
Identifying Significant SNPs in Genome Wide Association Studies
(GWAS) via Clustering
Exact Hardy-Weinburg testing for Genome Wide Association Studies
Nonlocal Prior Based Iterative SNP Selection Tool for
Genome-Wide Association Studies
Comprehensive and Easy to Use Quality Control of GWAS Results
A Shiny App to Aid Interpretation of Geometrically-Weighted
Degree Estimates in Exponential Random Graph Models
Controlling the genome-wide type I error rate in association
mapping experiments
Multi-Site Stochastic Models for Daily Precipitation and
Temperature
Calculation of probabilities for inadequate and excessive
gestational weight gain
Rewrite of gWidgets API for Simplified GUI Construction
Implementation of gWidgets2 for the RGtk2 Package
Toolkit Implementation of gWidgets2 for tcltk
Geographically Weighted Logistic Elastic Net Regression
Geographically Weighted Non-Negative Principal Components
Analysis
Geographically Weighted Partial Correlation Coefficient
Generalized Weighted Quantile Sum Regression
Generalized Waring Regression Model for Count Data
Fits geographically weighted regression models with diagnostic
tools
GroundWater Spatiotemporal Data Analysis Tool (GWSDAT)
Estimating Genome-Wide Significance for Whole Genome Sequencing
Studies, Either Single SNP Tests or Region-Based Tests
Run GWAS/GWEIS Scans Using Binary Dosage Files
Maximum Likelihood Estimation for Gene-by-Measured Environment
Interaction Models
R Interface for the 'H2O' Scalable Machine Learning Platform
Software to perform Haar Fisz transforms
Estimation, Simulation and Visualization of Hierarchical
Archimedean Copulae (HAC)
Wrapper for the 'Official Hacker News' API
Additional Tools for Splitting and Cleaning Data
Iterative Extrapolation of Species' Haplotype Accumulation
Curves for Genetic Diversity Assessment
Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass
Spectrometry Data
Utilities for using R scripts in Hadoop streaming
Analysis Framework for Monte Carlo Simulation Data in Physics
Analysis of Plant Pathogen Pathotype Complexities, Distributions
and Diversity
Highly Adaptive Lasso Conditional Density Estimation
Hierarchical Optimal Matching and Machine Learning Toolbox
Provides Easy Downloading Capabilities for the UK Parliament API
Inference of Trait Associations with SNP Haplotypes and Other
Attributes using the EM Algorithm
Inference of Chromosome-Length Haplotypes Using Genomic Data of
Single Gamete Cells
Analyzing Case-Parent Triad and/or Case-Control Data with SNP
Haplotypes
Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous
Reconstruction of Haplotype-Blocks from Time Series Data
Tool for Clustering Genotypes in Haplotypes
Manipulating DNA Sequences and Estimating Unambiguous Haplotype
Network with Statistical Parsimony
Calculate Upcoming Birthday Dates of Github Repos
Statistical Tests and Graphics for Hardy-Weinberg Equilibrium
Harmonic Mean p-Values and Model Averaging by Mean Maximum
Likelihood
Harmonic Regression to One or more Time Series
Wrangle Phylogenetic Distance Matrices and Other Utilities
Palettes Generated from All "Harry Potter" Movies
Full Feature Implementation of Hash/Associated
Arrays/Dictionaries
Generate Short Unique YouTube-Like IDs (Hashes) from Integers
Import and Export 'SPSS', 'Stata' and 'SAS' Files
Hawkes process simulation and calibration toolkit
Identifying Foggy and Cloudy Images by Quantifying Haziness
Damage functions from FEMA's HAZUS software for use in modeling
financial losses from natural disasters
Hierarchical Bayesian Modeling of Decision-Making Tasks
Hierarchical Bayesian Benefit-Risk Assessment Using Discrete
Choice Experiment
Hierarchical Bayesian Regression for GLMs
Hill/Bliss Independence Model for Combination Vaccines
Hierarchical Bayesian Analysis of Recognition Memory
Hierarchical Bayesian Small Area Estimation
Hierarchical Bayesian Space-Time models for Gaussian space-time
data
Interval estimation for the parameters of linear models with
heteroskedasticity (Wild Bootstrap)
Hierarchical Community Detection by Recursive Partitioning
Regression with a Large Number of Potential Explanatory
Variables
Change Point Estimation for Regression with Heteroscedastic Data
Causal Discovery from Discrete Data using Hidden Compact
Representation
Calculates Significance Criteria and Power for a Single Arm
Trial
Using Historical Controls for Designing Phase II Clinical Trials
Change-Point Analysis of High-Dimensional Time Series via Binary
Segmentation
High Dimensional Confidence Interval Based on Lasso and
Bootstrap
High Dimensional Supervised Classification and Clustering
Clustering High Dimensional Data with Hidden Markov Model on
Variable Blocks
Detect Change Points in Means of High Dimensional Data
Easy Manipulation of Out of Memory Data Sets
Sample Size Calculation for High Dimensional Classification
Study
Use Known Groups in High-Dimensional Data to Derive Scores for
Plots
Interface to the 'HDF5' Binary Data Format
Tests for High Dimensional Generalized Linear Models
Statistical Inference for Noisy Vector Autoregression
Distribution-Free Exact High Dimensional Low Sample Size
k-Sample Tests
Statistical Analysis Tools for High Dimension Molecular Data
(HDMD)
High-Dimensional Regression with Measurement Error
A Multiple Testing Procedure for High-Dimensional Mediation
Hypotheses
Benchmarking and Visualization Toolkit for Penalized Cox Models
Leland Wilkinson's Algorithm for Detecting Multidimensional
Outliers
Principal Component Analysis in High-Dimensional Data
Hierarchical Dirichlet Process Generalized Linear Models
Highest Density Regions and Conditional Density Estimation
High Dimensional Hypothesis Testing for Mean Vectors, Covariance
Matrices, and White Noise of Vector Time Series
The Lasso for the Tweedie's Compound Poisson Model Using an
IRLS-BMD Algorithm
Financial Projections and Planning for Health Care Practices
The Time Series Modeling Companion to 'healthyR'
Heat exchange calculations during physical activity
Fit Statistic for Binary Dependent Variable Models
Interactive Cluster Heat Maps Using 'plotly'
Robust Estimation Using Heavy-Tailed Distributions
Fit Normal or Student-t Heckman Selection Models
Markov Models for Health Economic Evaluations
Decode and Validate HEIMS Data from Department of Education,
Australia
Preprocess Data and Get Better Insights from Machine Learning
Models
Providing 'stringsAsFactors=FALSE' Variants of 'data.frame()'
and 'as.data.frame()'
Access London Natural History Museum Host-Helminth Record
Database
Tools for Environmental Analyses, Ecotoxicology and Various R
Functions
Hierarchical Ensemble Methods for Directed Acyclic Graphs
Visualizing Hypothesis Tests in Multivariate Linear Models
'sf'-Based Interface to the 'HERE' REST APIs
Marker-Based Estimation of Heritability Using Individual Plant
or Plot Data
Heritability of Gene Expression for Next-Generation Sequencing
Efficient Sequential and Batch Estimation of Univariate and
Bivariate Probability Density Functions and Cumulative
Distribution Functions along with Quantiles (Univariate) and
Spearman's Correlation (Bivariate)
Health-Economic Simulation Modeling and Decision Analysis
Test of No Main and/or Interaction Effects in Functional Data
Heteroskedastic Gaussian Process Modeling and Design under
Replication
MLE and Bayesian Estimation of Heteroskedastic Ordered Probit
(HETOP) Model
Heterogeneous Treatment Effects in Regression Analysis
Fisherian and Neymanian Methods for Detecting and Measuring
Treatment Effect Variation
Structural Handling of Finnish Personal Identity Numbers
Heuristics Including Take the Best and Unit-Weight Linear
Discovery of Process Models with the Heuristics Miner
Integrated Tool for Hairping Extraction of RNA Sequences
Holonomic Gradient Method and Gradient Descent
Identify and Correct Invalid HGNC Human Gene Symbols and MGI
Mouse Gene Symbols
Statistical Analysis and Data Display: Heiberger and Holland
Heller-Heller-Gorfine Tests of Independence and Equality of
Distributions
Age-Structured Spatio-Temporal Models for Infectious Disease
Counts
Calculate and Visualize the Herfindahl-Hirschman Index
The Hilbert-Huang Transform: Tools and Methods
Simulation from distributions supported by nested hyperplanes
Multiple Logistic Regression for 3D Chromatin Domain Border
Analysis
The All-Configurations, Maximum-Interaction F-Test for Hidden
Additivity
Functions to Perform Hierarchical Analysis of Distance Sampling
Data
Set Data Visualization Using Hierarchies
Hierarchical Multiplicative Partitioning of Complex Phenotypes
Partitioning Hierarchical Diversity and Differentiation Across
Metrics and Scales, from Genes to Ecosystems
Estimation and Tests of Hierarchical F-Statistics
A graphical user interface for calculating power and sample size
for hierarchical data
Convex Hierarchical Testing of Interactions
Two-Sample Tests for Equality of Means in High Dimension
Outlier Detection Algorithms for High-Dimensional Data
Testing Two-Sample Mean in High Dimension
Implementation of Voting Rules Electing the Candidate with
Highest Median Grade
Two-Sample Tests for High-Dimensional Mean Vectors
Determining and Evaluating High-Risk Zones
High-Throughput Screening for Plate Based Assays
Simultaneous Critical Values for t-Tests in Very High Dimensions
Statistical Inference for Online Learning and Stochastic
Approximation via HiGrad
Hilbert Similarity Index for High Dimensional Data
Integral Analysis of Diversity Based on Hill Numbers
Estimation of Heritability in Linear Mixed Models
Simulating the Development of h-Index Values
H-Index Calculator using Data from a Web of Science (WoS)
Citation Report
Tools for hypothesis testing based on Hypergeometric
Intersection distributions
Parentage Assignment using Bi-Allelic Genetic Markers
Non-Targeted Fluxomics on High-Resolution Mass-Spectrometry Data
Hierarchical Item Response Theory Models
Data Sets from the History of Statistics and Data Visualization
Construction of Regular and Irregular Histograms with Different
Options for Automatic Choice of Bins
Enhanced Command History Tracking for R Sessions and Dynamic
Documents
"Hit and Run" and "Shake and Bake" for Sampling Uniformly from
Convex Shapes
HIV calibrated model life tables for countries with generalized
HIV epidemics
Hierarchical Joint Analysis of Marginal Summary Statistics
Conversion Tools for HK80 Geographical Coordinate System
Ensemble Clustering using K Means and Hierarchical Clustering
Spatial Extreme Value Analysis with the Hierarchical Model of
Reich and Shaby (2012)
API to Retrieve Data from Hong Kong Stock Exchange
Diagnostic Tools for Hierarchical (Multilevel) Linear Models
Fit Statistical Models Using Hamiltonian Monte Carlo
Read Human Mortality Database and Human Fertility Database Data
from the Web
The H-Measure and Other Scalar Classification Performance
Metrics
High-Dimensional Mixed Graphical Models Estimation
Hidden Markov Models with Discrete Non-Parametric Observation
Distributions
Constructs Asymmetric Hidden Markov Models
Hidden Markov Model for Continuous Observations Processes
Markov Regime Switching Copula Models Estimation and Goodness of
Fit
A Fast Solver for Henderson Mixed Model Equation via Row
Operations
Determine the Number of States in Hidden Markov Models via
Marginal Likelihood
Analysing Accelerometer Data Using Hidden Markov Models
Hypothesis Testing and Power Calculations for Comparing
Metagenomic Samples from HMP
Statistical Object Oriented Data Analysis of RDP-Based Taxonomic
Trees from Human Microbiome Data
Flux Estimation with Static Chamber Data
Hierarchical Model of Species Communities
Group Association Test using a Hidden Markov Model
Half-Normal Plots with Simulation Envelopes
Collect and Retrieve Annotation Data for Various Genomic Data
Using Different Webservices
Holiday and Half-Day Data, for Use with the 'TimeWarp' Package
A Tidy Interface for Simulating Multivariate Data
Methods for Closed Testing with Simes Inequality, in Particular
Hommel's Method
Quick Access to Homologene and Gene Annotation Updates
Homogeneity tests for Regional Frequency Analysis
Transmissions and Receptions in a Hop by Hop Network
Hierarchical Ordered Probit Models with Application to Reporting
Heterogeneity
Supplemental Functions and Datasets for "Handbook of Regression
Methods"
Horn's (1965) Test to Determine the Number of Components/Factors
Flexible Non-Linear Regression with the HorseRule Algorithm
Nonlinear Regression using Horseshoe Prior
CSS Animations for 'shiny' Button Elements
A lower bound for the number of correct rejections
Heligman Pollard mortality model parameter estimation using
Bayesian Melding with Incremental Mixture Importance Sampling
High Performance Cluster Models Based on Kiefer-Wolfowitz
Recursion
High-Probability Lower Bounds for the Total Variance Distance
Miscellaneous convenience functions and dataset
Regularization Paths for Lasso or Elastic-Net Penalized Huber
Loss Regression and Quantile Regression
Toolkit for Data Analytics in Human Resources
Additional Themes, Theme Components and Utilities for 'ggplot2'
Nonparametric Assessment Between Competing Risks Hazard Ratios
Hazard Ratio Estimation using Cox Model Weighted by the
Estimated Propensity Score
High-Resolution Melting (HRM) Curve Analysis
Datasets, Functions and Scripts for Semiparametric Regression
Supporting Harezlak, Ruppert & Wand (2018)
Homogenous Segmentation for Spatial Lines Data
A Handbook of Statistical Analyses Using R (1st Edition)
A Handbook of Statistical Analyses Using R (2nd Edition)
A Handbook of Statistical Analyses Using R (3rd Edition)
Calculation of Covariance Between Markers for Half-Sib Families
Manage, Analyse and Simulate Hyperspectral Data
Homogeneity and Sparsity Detection Incorporating Prior
Constraint Information
Hierarchical Bayesian Species Distribution Models
Canonical Correlation Analysis based on Kernel Independence
Measures
A Path-Based BCD for Proximal Function of Latent Group Lasso
Phasing, Pedigree Reconstruction, Sire Imputation and
Recombination Events Identification of Half-sib Families Using
SNP Data
Hidden Smooth Polynomial Regression for Rupture Detection
Estimation of Recombination Rate and Maternal LD in Half-Sibs
Hierarchical Shrinkage Stan Models for Biomarker Selection
Reweighted Marginal Hypothesis Tests for Clustered Data
Bayesian Logistic Regression with Heavy-Tailed Priors
Convert 'HTML' to 'R' with a 'Shiny' App
Generates HTML Tag Strings for HTML5 Elements Included in
Mozilla's Documentation of HTML5
Simple Scraping and Tidy Webpage Summaries
Tidy Up and Test XPath Queries on HTML and XML Content
Facilitates Automated HTML Report Creation
Historical Tree Ensembles for Longitudinal Data
Clustering High-Throughput Transcriptome Sequencing (HTS) Data
High Throughput Sequencing of Stable Isotope Probing Data
Analysis
Distinct Colour Palettes Based on 'iwanthue'
compute HUM value and visualize ROC curves
Calculate Water Vapor Measures from Temperature and Dew Point
High-Performance Stemmer, Tokenizer, and Spell Checker
Zero-Inflated and Hurdle Modelling Using Bayesian Inference
Explore and Map County-Level Hurricane Exposure in the United
States
Easily Create and Style Tables for LaTeX, HTML and Other Formats
Testing Hardy-Weinberg Equilibrium for Multiallelic Genes
Models and Tests for Departure from Hardy-Weinberg Equilibrium
and Independence Between Loci
Bayesian investigation of Hardy-Weinberg Equilibrium via
estimation and testing
Objective Bayesian Testing for the Hardy-Weinberg Equilibrium
Problem
HTML Writer - Outputs R objects in HTML format
Build, Deploy and Evaluate Hybrid Ensembles
Implementation of the Hybrid Monte Carlo and Multipoint Hybrid
Monte Carlo sampling techniques
An R Package for the Stochastic Simulation of Disease Spreading
in Dynamic Networks
Hybrid Bayesian Networks Using R and JAGS
Tools and models for hydrological applications
Groundwater Data Presentation and Interpretation
Goodness-of-Fit Functions for Comparison of Simulated and
Observed Hydrological Time Series
Hydrologic Network Linking Data and Tools
Estimating Water Retention and Infiltration Model Parameters
using Experimental Data
Particle Swarm Optimisation, with Focus on Environmental Models
Interface to the Greek National Data Bank for
Hydrometeorological Information
Hydrologic Indices for Daily Time Series Data
Hydrological Tools for Handling Hydro-Meteorological Data from
Argentina and Chile
Time Series Management, Analysis and Interpolation for
Hydrological Modelling
Generic N-Dimensional Hyperplane Fitting with Heteroscedastic
Covariant Errors and Intrinsic Scatter
Machine Learning of Hyperrectangular Gating Strategies for
High-Dimensional Cytometry
Hypergeometric Function of a Matrix Argument
Overlap Detection in n-Dimensional Space
Attribute Sampling Plan with Exact Hypergeometric Probabilities
using Chebyshev Polynomials
Hyper-Ensemble Smote Undersampled Random Forests
Work with Hyperspectral Data, i.e. Spectra + Meta Information
(Spatial, Time, Concentration, ...)
High Dimensional Geometry and Set Operations Using Kernel
Density Estimation, Support Vector Machines, and Convex Hulls
Macroevolutionary phylogentic analysis of species trees and gene
trees
Confidence Intervals and Tests of Statistical Hypotheses
Wrapper for the 'Hypothes.is' Web Annotation Service
Multicriteria Risk Management using Zero-Sum Games with
Vector-Valued Payoffs that are Probability Distributions
Hybrid Methods for Addressing Uncertainty in RISK Assessments
Tools for Modeling Rate-Dependent Hysteretic Processes and
Ellipses
Get Pedestrian Frequency Data from the 'Hystreet' Project
Functions to Work with 'incidence2' Objects
Plotting N-T Plane for Decision on Performing an Interim
Analysis
Data and Functions for "An Intro. to Accept. Samp. & SPC/R"
Two-Stage Adaptive Dose-Finding Clinical Trial Design
Analysis of Intra Annual Density Fluctuations
Synthesizing Information Across Collaborating Research
Model Selection for Index of Asymmetry Distribution
Cleaning and Visualizing Implicit Association Test (IAT) Data
Compute Effect Sizes and Reliability for Implicit Association
Test (IAT) Data
Scoring Algorithm for the Implicit Association Test (IAT)
Implicit Association Test Scores Using Robust Statistics
Integrative Bayesian Analysis of Transcriptomic and CGH Data
R Wrapper for Istanbul Municipality Open Data Portal
Item Based Collaborative Filtering for Multi-Trait and
Multi-Environment Data
Functions for the Analysis of IBD Haplo Output
Convert Between Different IBD-State Labelling Schemes
Regression Methods for IBD Linkage with Covariates
Simulation of Chromosomal Regions Shared by Family Members
Irregular-lattice based ensemble empirical mode decomposition
Toolkits to Develop Individual-Based Models in Infectious
Disease
Individual Based Model Population Simulation
Generate Personality Insights Sunburst Diagrams
Iboot: iterated bootstrap tests and confidence sets
Model Agnostic Instance Level Variable Attributions
R API to Interactive Brokers Trader Workstation
Inequality Constrained Inference in Linear Normal Situations
A Copy Number and Expression-Based Classifier for Breast Tumours
Inequality and Concentration Indices and Curves
Standardized high-throughput evaluation of cell-based compound
screens
Infer Community Assembly Mechanisms by Phylogenetic-Bin-Based
Null Model Analysis
In-depth Characterization and Analysis of Mutational Signatures
('ICAMS')
Optimal Designs for Nonlinear Statistical Models by Imperialist
Competitive Algorithm (ICA)
Integrative Conditional Autoregressive Horseshoe Model
Calibrates and Reweights Units in Samples
Bayesian Semiparametric Models for Interval-Censored Data
Facilitating Estimation of the Intraclass Correlation
Coefficient
Calculation of Sample Size and Power for ICC
Cox Model with Interval-Censored Starting Time of a Covariate
Multilevel Model Intraclass Correlation for Slope Heterogeneity
Facilitates Clustered Binary Data Generation, and Estimation of
Intracluster Correlation Coefficient (ICC) for Binary Data
Computation of the Double-Entry Intraclass Correlation
An Ensemble Method for Interval-Censored Survival Data
International Classifcation of Diseases (ICD) Data
Metadata Processing for the German Modification of the ICD-10
Coding System
EM by the Method of Weights for Incomplete Categorical Data in
Generlized Linear Models
Identification of Cancer Dysfunctional Subpathway by Integrating
DNA Methylation, Copy Number Variation, and Gene Expression
Data
Individual Conditional Expectation Plot Toolbox
Apply Statistical Post-Processing to Improve Sea Ice Predictions
Incremental Cost-Effectiveness Inference using Two Unbiased
Samples
Analyzing High-Throughput Single Cell Sequencing Data
Parameter Estimation in Linear Transformation Model with
Interval-Censored Data and Covariate Measurement Error
Regression Models for Interval Censored Data
Accompanion to the Book on Interval Censoring by Bogaerts,
Komarek, and Lesaffre
Study Design and Data Analysis in the Presence of Error-Prone
Diagnostic Tests and Self-Reported Outcomes
DATRAS Trawl Survey Database Web Services
Functions to Support the ICES Transparent Assessment Framework
Estimation of number of clusters and identification of atypical
units
Fit Generalized Odds Rate Hazards Model with Interval Censored
Data
A Minimal Wrapper Around NIH's 'iCite' API
A Button-Based GUI for Financial and Economic Data Analysis
Integrative clustering of multiple genomic data types
Empirical Bayes Variable Selection via ICM/M Algorithm
Data Analysis for ODS and Case-Cohort Designs with
Interval-Censoring
Provides Easy Access to Complex Systems Datasets
Global Triangular and Penta-Hexagonal Grids Based on Tessellated
Icosahedra
Reproducible Data Retrieval from the ICPSR Archive
Simultaneous Confidence Intervals for Ranks
A Modified Random Survival Forest Algorithm
Tools for Exploring Multivariate Data via ICS/ICA
Outlier Detection Using Invariant Coordinate Selection
Data Smoothing by Interpolating Cubic Splines
A package for semiparametric regression analysis of
interval-censored data
Estimating and Testing the Number of Interesting Components in
Linear Dimension Reduction
Indirect Cross-Validation (ICV) for Kernel Density Estimation
R Interface to the US Census Bureau International Data Base API
Update Chinese ID Card Number to Eighteen Digits
Easy Manipulation of IDEAM's Climatological Data
Efficient Designs for Discrete Choice Experiments
Jacquard Condensed Coefficients of Identity
Bayesian Dynamic Spatio-Temporal Models, Including the
Integrodifference Equation Model
Various Methods for Estimating Intrinsic Dimension
Isolate-Detect Methodology for Multiple Change-Point Detection
Integrative Differential Network Analysis in Genomics
Idiograms with Marks and Karyotype Indices
Assessment of Individual Identity in Animal Signals
Infectious Disease Model Library and Utilities
Regression Model for Progressive Illness Death Data
Integrated Discovery of Oncogenic Signatures
'Utilities of Institute of Data Analyses and Process Design
(www.zhaw.ch/idp)'
Imprecise Dirichlet Process for Survival Analysis
Estimate Global Clustering in Infectious Disease
Convert Files to and from IDX Format to Vectors, Matrices and
Arrays
R Analysis package for iDynoMiCS Simulation Results
Irucka Embry's Miscellaneous USGS Functions
Functions to set and get the IEEE rounding mode
Irucka Embry's Miscellaneous Data Collection
Irucka Embry's Miscellaneous Text Collection
Robust Analysis for Absolute Abundance in Microbiome
An integrative factor analysis model for drug-pathway
association inference
Toolkit for Item Factor Analysis with 'OpenMx'
Italian Fiscal Code ('Codice Fiscale') Utilities
Machine Learning Time Series Forecasting
Instagram 2014 Vancouver Top Colour Dataset
Score Taxon-Level IgA Binding in IgA-Seq Experiments
Statistical Tests and Utilities for Genetic Association
Guided Analytics for Testing Manufacturing Parameters
Interpreting Glucose Data from Continuous Glucose Monitors
Read Binary Files Saved by 'Igor Pro' (Including 'Neuromatic'
Data)
A Collection of Network Data Sets for the 'igraph' Package
Convert iGraph graps to SoNIA .son files
Integrative Gene Set Enrichment Analysis Approaches
Download Data from the International House Price Database
Computing Individual Components of the Gini and the Theil
Indices
Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files
Lee-Carter Mortality Models using Iterative Fitting Algorithms
Integrated Methylation QTL Mapping and Allele-Specific Analysis
Binarize Images for Enhancing Optical Character Recognition
Implementation of the Canny Edge Detector for Images
Implementation of the Unsupervised Smooth Contour Line Detection
for Images
Find Corners in Digital Images with FAST-9
Implementation of the Harris Corner Detection for Images
Image Processing Functionality using the 'dlib' Package
Convolutional Neural Network for Face Detection
Aids in Processing and Plotting Data from a Lemna-Tec
Scananalyzer
Image Statistics Based on Processing Fluency
Image Processing Library Based on 'CImg'
Extra Image Processing Library Based on 'imager'
Independent Multiple-Sample Greedy Equivalence Search
Implementation
Simple 'htmlwidgets' Image Viewer with WebGL Brightness/Contrast
IMAGing engINEs, Tools for Application of Image Filters to Data
Matrices
Delimit and Characterize Color Phenotype of the Pearl Oyster
Preprocessing Algorithms for Imbalanced Datasets
Get Movie, Television Data from the 'imdb' Database
Likelihood Methods for Mediation Analysis
R Interface for International Monetary Fund(IMF) Data API
Download Data from the International Monetary Fund's Data API
Infinite Mixtures of Infinite Factor Analysers and Related
Models
Gaussian Mixture Model for Multi-Omics Data Integration
Candidate Prescriptions Discovery Based on Pathway Fingerprint
Item Response Models for Multiple Ratings
Iterative Max-Min Entropy Margin-Maximization with Interaction
Terms for Feature Selection
Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
Tunable Simulation of B- And T-Cell Receptor Repertoires
Calculation and Visualization of the Impact Effect Size Measure
Quantification of Population-Level Impact of Vaccination
Identifying Causal Effect for Multi-Component Intervention Using
Instrumental Variable Method
Imprecise Imputation for Statistical Matching
Compute Scores for Different Implicit Measures
Enables Importing/Loading of Packages or Functions While
Creating an Alias for Them
Download and Manage Open Data from INEGI
Classification Trees with Imprecise Probabilities
Imputation of Financial Time Series with Missing Values and/or
Outliers
A collection of methods for left-censored missing data
imputation
The Multifactor Dimensionality Reduction (MDR) Analysis for
Incomplete Data
Impute Missing Values in a Predictive Context
Imputation Methods for Multivariate Multinomial Data
Impute Missing Data in Time Series Data with PSF Based Method
A General Multivariate Imputation Framework
Robust Multiple Imputation with Generalized Additive Models for
Location Scale and Shape
Test Bench for the Comparison of Imputation Methods
Imputing the Last Largest Censored Observation(s) Under Weighted
Least Squares
Multi-Reader, Multi-Case Analysis Methods (ROC, Agreement, and
Other Metrics)
Immune Cell Gene Signatures for Profiling the Microenvironment
of Solid Tumours
Information Matrix Test for Generalized Partial Credit Models
Initialization Algorithms for Partitioning Cluster Analysis
Analysing Inbreeding Based on Genetic Markers
Recognize and Handle Data in Formats Used by Swedish Cancer
Centers
Pipe-Friendly Vector Replacement with Case Statements
Internal Control Analysis of Translatome Studies by Microarrays
Incremental Calculation of Dynamic Time Warping
Incremental Graphlet Counting for Network Optimisation
Compute, Handle, Plot and Model Incidence of Dated Events
Compute, Handle and Plot Incidence of Dated Events
Implements Empirical Bayes Incidence Curves
Comparison of Means for the Incomplete Paired Data
Insertion Deletion Analysis While Accounting for Possible
Missing Data
Non-Parametric Tests of Independence Between Random Vectors
Nonparametric Independence Tests Based on Entropy Estimation
Relationship Between Species and Groups of Sites
Elicitation of Independent Conditional Means Priors for
Generalised Linear Models
Obtaining and Estimating Unidimensional IRT Dual Models
Tests of Independence and Analysis of Dependence Between Point
Processes in Time
Integrate INEGI’s (Mexican Stats Office) API with R
Measuring Inequality, Concentration, and Poverty
Interpolation and Extrapolation for Species Diversity
Infine-dimensional model (IDM) to analyse phenotypic variation
in growth trajectories
Functions to extract inferential values of a fitted model object
Inference about the standardized mortality ratio when evaluating
the effect of a screening program on survival
Methods for Causal Inference with Interference
Estimate and Account for Tumor Purity in Cancer Methylation Data
Analysis
Melt Curve Fitting and Melt Shift Analysis
Tools for Detecting Influential Data in Mixed Effects Models
Case Influence in Structural Equation Models
Identify Influential Observations in Binary Classification
Software Tools to Quantify Structural Importance of Nodes in a
Network
Identification and Classification of the Most Influential Nodes
Information Decomposition of Two-Phase Experiments
Data Exploration with Information Theory (Weight-of-Evidence and
Information Value)
Performance Analysis and Companion Functions for Binary
Classification Models
Multiple Imputation for Informative Censoring
Sequence Statistics for Relational Event Models
Calculates the Probability of Informed Trading (PIN)
Effects and Importances of Model Ingredients
Translate ICD-9 into Injury Severity Score
Spatial Inference using Integrated Nested Laplace Approximation
Collection of Datasets for the USGS-INL Aquifer Monitoring
Networks
Functions to Inline C, C++, Fortran Function Calls from R
Convert Inline Comments to Documentation
Miscellaneous Functions for the USGS INL Project Office
Infix Operators for Detection, Subsetting and Replacement
Analyse Text Documents Using Ecological Tools
Quality Control of Climatological Daily Time Series
Tools to Easily Download Data from INSEE BDM Database
insideRODE includes buildin functions with deSolve solver and
C/FORTRAN interfaces to nlme, together with compiled codes
Easy Access to Model Information for Various Model Objects
Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm
High-Dimensional Changepoint Estimation via Sparse Projection
Inspection, Comparison and Visualisation of Data Frames
Validation of Arguments and Objects in User-Defined Functions
Inferring Shared Modules from Multiple Gene Expression Datasets
with Partially Overlapping Gene Sets
Check, Install and Load CRAN & USGS GRAN Packages
Using R to Install Stuff on Windows OS (Such As: R, 'Rtools',
'RStudio', 'Git', and More!)
A Collection of Insurance Datasets Useful in Risk Classification
in Non-life Insurance
Interactive Add-on Functionality for 'intamap'
Semiparametric Competing Risks Regression under Interval
Censoring
AUC Estimation of Interval Censored Survival Data
Integration of Multiple Data Sets with Clustering Techniques
Reconstruction of a Directed Acyclic Graph with Interventions
Integrating Multiple Modalities of High Throughput Assays Using
Item Response Theory
An Implementation of Interaction Graphs of Aleks Jakulin
Joint Modeling of the Gene-Expression and Bioassay Data, Taking
Care of the Effect Due to a Fingerprint Feature
Integrated Prediction using Uni-Variate and Multivariate Random
Forests
Intensity of Change for Comparing Categorical Maps from
Sequential Intervals
The Visualization of Interactive Circos Plot
Tests for marginal interactions in a 2 class response model
Comprehensive, User-Friendly Toolkit for Probing Interactions
Calculates Critical Test Statistics to Control False Discovery
Rates in Marginal Effects Plots
interactive network analysis and visualization
Compute Chi-Square Measures with Corrections
Interaction Analysis of Repeated Measure Data
GUI to Analyse qPCR Results after PMA Treatment or not
Exact Confidence Intervals in the Presence of Interference
Interference Color Charts for Polarized Light Microscopy
Coercion Routines for Network Data Objects
Scheduling Interim Analyses in Clinical Trials
App for Scheduling Interim Analyses in Clinical Trials
Converts Tabular Data to Interleaved Vectors
Importing Interlinearized Corpora and Dictionaries as Produced
by Descriptive Linguistics Software
Plot the Effects of Variables in Interaction Terms
Hourly interpolation of multiple temperature daily series
Fit Interpretable Machine Learning Models
Interpreting High Resolution Mass Spectra
Binary Classifier and Regression Model Interpretation Functions
Simulation of Inter-Related Genomic Datasets
Weighted Logrank Tests and NPMLE for Interval Censored Data
Time-Weighted Averaging for Interval Data
Tools for Working with Points and Intervals
Hypothesis Testing Using the Overlapping Interval Estimates
Interventional Inference for Dynamic Bayesian Networks
Tools and Statistical Procedures in Plant Science
A Numerical Implementation of Interval-Valued Kriging
Numerical Integration for Integrated Likelihood
Mediation Analysis using Interventional Effects
Integrative Clustering of Multiple Genomic Dataset
Quantify and Control Reproducibility in High-Throughput
Experiments
methods for analyzing introgression between divergent lineages
Analysis of Time-Ordered Event Data with Missed Observations
Interface to Popular R Functions for Data Science Pipelines
Interval and Enum-Type Representation of Vectors
Analyse Biological Invasion Costs with the 'InvaCost' Database
Inventory Analytics and Cost Calculations
Reverse Engineers Regular Expression Patterns for R Objects
Threshold regression that fits the (randomized drift) inverse
Gaussian distribution to survival data
Tools for Exploring Multiple Response Data
Graphical Tools for Exploring Data with 'iNZight'
Tools for Exploring Regression Models with 'iNZight'
A Unified Framework for Input-Output Operations in R
Calling Copy Number Alterations in Amplicon Sequencing Data
Calculate the Number of Required Flows for Semiconductor
Sequencing
Functions for Smoothing with Infinite Order Flat-Top Kernels
Iterative Pruning Population Admixture Inference Framework
Tools for Message Passing Between Processes
Iterative Pruning to Capture Population Structure
Kendall's Tau Partial Corr. for Survival Trait and Biomarkers
Inverse Probability of Censoring Weights to Deal with Treatment
Switch in Randomized Clinical Trials
Basic Functions to Check Readability, Consistency, and Content
of an Individual Participant Data File
Map Digitized Survival Curves Back to Individual Patient Data
Tools for subgroup analyses with multiple trial data using
aggregate statistics
Spatial Interpolation by Inverse Path Distance Weighting
Fast Implementation of the Iterative Proportional Fitting
Procedure in C
List Balancing for Reweighting and Population Synthesis
Miscellaneous Functions for Data Cleaning and Analysis
Intervention in Prediction Measure (IPM) for Random Forests
Interfaces to Phylogenetic Software in R
Manipulate, Validate and Resolve 'IP' Addresses
Inverse Probability Weighted Cox Model with Corrected Sandwich
Variance
Inverse Probability Weighted Estimation of Average Treatment
Effect with Misclassified Binary Outcome
Protein Quantification in Mass Spectrometry-Based Proteomics
Iterated Racing for Automatic Algorithm Configuration
Integrative Random Forest for Gene Regulatory Network Inference
A R Interface for the Instantaneous RATEs (IRATE) Model
Correlation Coefficients for Information Retrieval
Regression Methods for Interval-Valued Variables
Global Innovation Through Company Level Data
A Dynamic Bipartite Latent Space Model to Analyse Irish
Companies' Boards from 2003 to 2013
Classes and Methods for Seismic Data Analysis
Native R Kernel for the 'Jupyter Notebook'
Fast Truncated Singular Value Decomposition and Principal
Components Analysis for Large Dense and Sparse Matrices
Various Coefficients of Interrater Reliability and Agreement
Computing Chance-Corrected Agreement Coefficients (CAC)
Analysis of Longitudinal Data with Irregular Observation Times
Intraclass Correlations for Quantifying Inter-Rater Reliability
Coefficients of Interrater Reliability - Generalized for
Randomly Incomplete Datasets
Item Response Theory and Computerized Adaptive Testing Functions
Family of Bayesian EMM Algorithm for Item Response Models
A Collection of Functions Related to Item Response Theory (IRT)
Unidimensional Item Response Theory Modeling
Utilities and Probability Distributions Related to
Multidimensional Person Item Response Models
Estimation of Tree-Based Item Response Models
Extract Cell Density and Nearest Distance Based on 'PerkinElmer
InForm' Software Output
Iterative Selection of Blocks of Features - ISBF
Converts ISCO-08 to Job Prestige Scores, ISCO-88 and Job Name
Provides datasets for Introduction to Statistical Data Analysis
for the Life Sciences
Parse 'NOAA' Integrated Surface Data Files
Fitting Ising Models Using the ELasso Method
Sampling Methods and Distribution Functions for the Ising Model
Stochastic Island Biogeography Theory Made Easy
Data for an Introduction to Statistical Learning with
Applications in R
An Introduction to Statistical Modeling of Extreme Values
Index of Local Sensitivity to Nonignorability
Check if an 'externalptr' is a Null Pointer
Functions to Perform Isotonic Regression
Generate Isolines and Isobands from Regularly Spaced Elevation
Grids
Isotope Origin Clustering and Assignment Tools
Isomorphism Check for Multi-Stage Factorial Designs with
Randomization Restrictions
Confidence intervals for current status data based on
transformations and bootstrap
Correcting Drift and Carry-over in Continuous Isotopic
Measurements
Order-Restricted Inference for Microarray Experiments
Calculation of isotopic pattern for a given molecular formula
Statistical Toolbox for Radiometric Geochronology
Isoscape Computation and Inference of Spatial Origins using
Mixed Models
Isotonic Regression on Survival Analysis
Active Set and Generalized PAVA for Isotone Optimization
Penalized Isotonic Regression in one and two dimensions
Week of the year and weekday according to ISO 8601
Tools and Data for the International Soil Radiocarbon Database
Obtaining Open Data from Instituto Canario De Estadistica
(ISTAC) API
A Graphical Interface to Perform STOCSY Analyses on NMR Data
The Italian Survey on Household and Wealth, 2008 and 2010
Approximate Probability Densities by Iterated Laplace
Approximations
Efficient Iterator for Permutations and Combinations
itertools2: Functions creating iterators for efficient looping
Analysis of the International Trade Network
Statistical Learning for Individualized Treatment Regime
Variable Selection for Optimal Individualized Dynamic Treatment
Regime
Running Interrupted Time Series Analysis
Interpreting Time Series and Autocorrelated Data Using GAMMs
Time Series Analysis Using the Innovations Algorithm
Incorporating Uncertainties in Propensity Scores
Instrumental Variable Analysis in Case-Control Association
Studies
Profiling Compliers and Non-Compliers for Instrumental Variable
Analysis
Hypothesis Testing in Cluster-Randomized Encouragement Designs
Ensures Mutually Consistent Beliefs When Using IVs
Instrumental fixed effect panel data model
Estimate IV-Optimal Individualized Treatment Rules
Statistical Inference and Sensitivity Analysis for Instrumental
Variables Model
Instrumental Variables: Extrapolation by Marginal Treatment
Effects
Two-Stage Least-Squares Regression with Diagnostics
Create Independent Evidence in IV Analyses and Do Sensitivity
Analysis in Regression and IV Analysis
Structural Additive Cumulative Intensity Models with IV
Improved methods for causal inference and missing data problems
Simulation-Based Maximum Likelihood Parameter Estimation
Test Similarity Between Binary Data using Jaccard/Tanimoto
Coefficients
A Swift, Versatile Phylogenomic and High-Throughput Sequencing
Simulator
Jackknife Estimates of Kaplan-Meier Estimators or Integrals
Correcting Nonparametric Frontier Measurements for Outliers
Statistical Inference for Unsupervised Learning
Jaccard Index for Population Structure Identification
Blind Source Separation Methods Based on Joint Diagonalization
and Some BSS Performance Criteria
Supporting Files and Functions for the Book Bayesian Modelling
with 'JAGS'
A Wrapper Around 'rjags' to Streamline 'JAGS' Analyses
Analysis Tools for the 'JAMES' Framework
Simple Tools for Examining and Cleaning Dirty Data
Directory of Open Access Journals Client
Just a Rather Bayesian Evidence Synthesis
R modules for JASPAR databases: a collection of transcription
factor DNA-binding preferences, modeled as matrices
Jaya, a Gradient-Free Optimization Algorithm
Extended Classification of Weather Types
Colors Palettes for R and 'ggplot2', Additional Themes for
'ggplot2'
Monte Carlo Option Pricing Algorithms for Jump Diffusion Models
with Correlational Companies
'Java' Data Exchange for 'R' and 'rJava'
A Fast and Scalable Joint Estimator for Integrating Additional
Knowledge in Learning Multiple Related Sparse Gaussian
Graphical Models
One-to-One Gene-Probeset Mapping for Affymetrix Human
Microarrays
Tools and GUI for Analyzing Time Series Data of Just Finance and
Econometrics
Joint Generalized Estimating Equation Solver
Performs the Joint Graphical Lasso for Sparse Inverse Covariance
Estimation on Multiple Classes
Chinese Text Segmentation Data for jiebaR Package
Approximate Inclusion Probabilities for Survey Sampling
Joint Latent Class Trees for Joint Modeling of Time-to-Event and
Longitudinal Data
Joint Modeling of Longitudinal and Survival Data
Joint Modeling of Longitudinal and Time-to-Event Data under a
Bayesian Approach
Extended Joint Models for Longitudinal and Time-to-Event Data
Joint Mean-Covariance Models using 'Armadillo' and S4
Joint Models for Longitudinal and Competing Risks Data
Fitting Joint Mean and Dispersion Effects Models
Joint Modeling of Longitudinal and Survival Data - Power
Calculation
Joint Mean-Correlation Regression Approach for Discrete
Longitudinal Data
Time Series Analysis Toolkit Based on Symbolic Aggregate
Discretization, i.e. SAX
Permutation Tests for Nonparametric Statistics
Connect to the 'jamovi' Statistical Spreadsheet
Modelling and Simulating Judgments of Frequency
Joint Modelling of Repeated Measurements and Time-to-Event Data
Joint Modelling for Meta-Analytic (Multi-Study) Data
Joint Modelling of Multivariate Longitudinal Data and
Time-to-Event Outcomes
Joint Frailty-Copula Models for Tumour Progression and Death in
Meta-Analysis
Joint Analysis and Imputation of Incomplete Data
Joint Approximate Diagonalization of a Set of Square Matrices
Joint Mean and Covariance Estimation for Matrix-Variate Data
Semiparametric Joint Models for Longitudinal and Counting
Processes
End-to-End Sparse Gaussian Graphical Model Simulation,
Estimation, Visualization, Evaluation and Application
Joint N-Mixture Models for Site-Associated Species
Risk estimation using the joint probability method
Joint Segmentation of Multivariate (Copy Number) Signals
Perform Joins or Minus Queries on 'Excel' Files
Multilevel Joint Modelling Multiple Imputation
Unit-Level and Area-Level Small Area Estimation
Add Josa Based on Previous Letter in Korean
JavaScript Object Signing and Encryption
Journal Abbreviations for BibTeX Documents
Implements Under/Oversampling for Probability Estimation
Covariance and Inverse Covariance Matrix Estimation Using Joint
Penalty
Jump Q-Learning for Individualized Interval-Valued Dose Rule
Obtain 'jQuery' as an HTML Dependency Object
Exchange Commands Between R and 'JavaScript'
Joint Random Forest (JRF) for the Simultaneous Estimation of
Multiple Related Networks
Jack-Knife Support for Evolutionary Distinctiveness Indices I
and W
Item Response Theory Modeling and Scoring for Judgment Data
Basic Finance; NPV/IRR/Annuities/Bond-Pricing; Black Scholes
A 'RStudio' Addin to Send 'JavaScript' Code to the 'V8' Console
Semiparametric Joint Modeling of Survival and Longitudinal Data
Mediation Analysis Using Joint Significance
'RStudio' Addins and 'Shiny' Modules for Medical Research
A 'Base64' Encode/Decode Package with Support for JSON
Output/Input and UTF-8
Convert Between 'R' Objects and Javascript Object Notation
(JSON)
A Simple and Robust JSON Parser and Generator for R
A 'Java' Platform Integration for 'R' with Programming Languages
'Groovy', 'JavaScript', 'JRuby' ('Ruby'), 'Jython' ('Python'),
and 'Kotlin'
Create Tables from Different Types of Regression
Create Interactive Trees with the 'jQuery' 'jsTree' Plugin
A Wrapper of the JavaScript Library 'jsTree'
Analysis and Presentation of Social Scientific Data
Forecasting Long-Term Growth of the U.S. Stock Market and
Business Cycles
Seamless Integration Between R and 'Julia'
A Functionally Oriented Interface for Integrating 'Julia' with R
The Breakdown of Genomic Ancestry Blocks in Hybrid Lineages
Principal Component Analysis (PCA) and Whitening
Construct Complex Table with 'kable' and Pipe Syntax
Kernel Adaptive Density Estimation and Regression
Kernel Approaches for Nonlinear Genetic Association Regression
Package to identify and sort genes overexpressed
Kantorovich Distance Between Probability Measures
Encoding of Sequences Based on Frequency Matrix Chaos Game
Representation
Test the Homogeneity of Kappa Statistics
An R-Shiny Application for Calculating Cohen's and Fleiss' Kappa
Non-Additive Measure and Integral Manipulation Functions
Sample Size Estimation Functions for Studies of Interobserver
Agreement
Calculates "vectorial Kappa", an index of congruence between
patchy mosaics
K-Adaptive Partitioning for Survival data
An Interface for Microclimate Time Series Analysis
Kaya Identity Data for Nations and Regions
Khattree-Bahuguna's Univariate and Multivariate Skewness
Kernel Change Point Detection on the Running Statistics
Kernel Smoothing for Bivariate Copula Densities
Kernel Density Estimation with Parametric Starts and Asymmetric
Kernels
Nonparametric method for identifying discordant phylogenetic
trees
Multivariate Kernel Density Estimation with Vine Copulas
Tools for Working with Multidimensional Data
Kernel Estimator and Bandwidth Selection for Density and Its
Derivatives
Arrays with Better Control over Dimension Dropping
Collect, Assemble and Model Air Pollution, Weather and Health
Data
Calculate Solutions to the Kelvin Differential Equation using
Bessel Functions
Kendall rank correlation and Mann-Kendall trend test
Simulate and Visualize Kendall Random Walks and Related
Distributions
Kernel-Smoothed Nonparametric Methods for Environmental Exposure
Data Subject to Detection Limits
Knowledge Synthesis in Agriculture - From Experimental Network
to Meta-Analysis
R Interface to the Keras Deep Learning Library
Nonparametric kernel estimation of the distribution function.
Bandwidth selection and estimation of related functions
Expectile Regression in Reproducing Kernel Hilbert Space
Distance Weighted Discrimination (DWD) and Kernel Methods
Smoothed Bootstrap and Random Generation from Kernel Densities
Kernel Factory: An Ensemble of Kernel Machines
Kernel Density Estimation for Heaped and Rounded Data
Post-Selection Inference for Nonlinear Variable Selection
Statistical Learning with Kernel for Persistence Diagrams
Kernel Estimation of Hazard Function in Survival Analysis
A Kernel Regression-Based Multidimensional Wind Turbine Power
Curve
Kernel Machine Score Test for Semi-Competing Risks
Functions for Kernel Smoothing Supporting Wand & Jones (1995)
Bayesian Designs for Early Phase Clinical Trials
Keyboard and Mouse Input Simulation for Windows OS
Access the System Credential Store from R
Decrypt Passwords from Gnome Keyring, Windows Data Protection
API and macOS Keychain
Kalman Filter and Smoother for Exponential Family State Space
Models
Integrated Code Chunk Anchoring and Referencing for R Markdown
Documents
Kalman Filter, Smoother and Disturbance Smoother
Kernel Based Gradient Matching for Parameter Inference in
Ordinary Differential Equations
Colour Schemes for Scientific Data Visualization
A Simple Data Management and Sharing Tool
Kidney Functions: Clinical and Epidemiological
Functions for Behavioral Science Researchers
Framework for the Analysis of Kinetic Visual Field Data
Example Data from the Multi-Modal MRI 'Reproducibility' Resource
Example Functional Imaging Data from the Multi-Modal MRI
'Reproducibility' Resource
Example T1 Structural Data from the Multi-Modal MRI
'Reproducibility' Resource
a Keep It Simple Species Migration Model
Data Manipulation Functions Implemented in C
Spectral Response of Water Wells to Harmonic Strain and Pressure
Signals
A Wrapper for Querying KISTERS 'WISKI' Databases via the 'KiWIS'
API
Classifications and Codelists for Statistics Norway
Confidence intervals for the Kaplan-Meier estimator
Kaplan-Meier Estimator with Constraints for Right Censored Data
-- a Recursive Computational Algorithm
'Yingyang' K-Means and K-NN using NVIDIA CUDA
Fast K-Mer Counting and Clustering for Biological Sequence
Analysis
Kaplan-Meier Multiple Imputation for the Analysis of Cumulative
Incidence Functions in the Competing Risks Setting
Clustering longitudinal data using the likelihood as a metric of
distance
K-Means for Longitudinal Data using Shape-Respecting Distance
K-Means with Simultaneous Outlier Detection
Data sets from Klein and Moeschberger (1997), Survival Analysis
Generate Feasible Samples of a Knapsack Problem
A General-Purpose Package for Dynamic Report Generation in R
Data Language Engine for 'knitr' / 'rmarkdown'
An Accurate kNN Implementation with Multiple Distance Measures
Time Series Prediction using K-Nearest Neighbors Algorithm
(Parallel)
Interactive Document for Working with KNN Analysis
The Knockoff Filter for Controlled Variable Selection
Whole-Genome Sequencing Data Analysis via Knockoff Statistics
Non-Uniform Memory Access ('NUMA') Optimized, Parallel K-Means
Discriminating Well Surveyed Spatial Units from Exhaustive
Biodiversity Databases
Knowledge-Based Guided Regularized Random Forest
Get Data from the 'KOF Datenservice' API
A Genetic Algorithm for Fixed-Size Subset Selection
Functional Summary and Meta-Analysis of Gene Expression Data
Supervised and Unsupervised Self-Organising Maps
An Improved Evaluation of Kolmogorov's Distribution
Simply Beautiful PDF Letters from Markdown
KONP Tests: Powerful K-Sample Tests for Right-Censored Data
Text Analysis with Emphasis on POS Tagging, Readability and
Lexical Diversity
Language Support for 'koRpus' Package: English
Variable Selection by Revisited Knockoffs Procedures
Koul's Minimum Distance Estimation in Regression and Image
Segmentation Problems
Cubic Spline Fitting with Knot Selection
Kernel PC Algorithm for Causal Structure Detection
Determination of K Using Peak Counts of Features for Clustering
Method for Clustering Partially Observed Data
A Quantified Implementation of the Kraljic Matrix
Geospatial Kriging with Metropolis Sampling
Kriging-Based Inversion for Deterministic and Noisy Computer
Experiments
Measuring Agreement Using Krippendorff's Alpha Coefficient
Keen and Reliable Interface Subroutines for Bioinformatic
Analysis
K-Sample Rank Tests and their Combinations
Goodness-of-Fit Tests using Kernelized Stein Discrepancy
Computing P-Values of the K-S Test for (Dis)Continuous Null
Distribution
Identify Kinase Substrate Relationships Using Dynamic Data
Unbiased Estimators for Cumulant Products
Basic Functions in Knowledge Space Theory Using Matrix
Representation
Co-Tucker3 Analysis of Two Sequences of Matrices
Configurable Function for Solving Families of Nonlinear
Equations
Cubic Hermite Splines and Related Optimization Methods
Datasets and functions from the (now non-existing) Faculty of
Life Sciences, University of Copenhagen
Read/Write Files in Key-Value-Hierarchy Format
Calculation of Groundwater Mounding Beneath an Infiltration
Basin
Utility Functions for Statistical Analysis Report Generation and
Monte Carlo Studies
Multi-Scale Motions Separation with Kolmogorov-Zurbenko
Periodogram Signals
Kolmogorov-Zurbenko Fourier Transform and Applications
Kolmogorov-Zurbenko Spatial Smoothing and Applications
Sparse Generalized Linear Model with L0 Approximation for
Feature Selection
Fast Algorithms for Best Subset Selection
Friedman's Boosting Algorithm for Regularized Linear Regression
Ordination and Multivariate Analysis for Ecology
Relabelling MCMC Outputs of Mixture Models
Identification, Tuning, Visualisation and Analysis of Labour
Market Areas
Classify Multilingual Labour Market Free-Text to Standardized
Hierarchical Occupations
Simplex Optimization Algorithms for Laboratory and Manufacturing
Processes
Libreria Del Laboratorio Di Statistica Con R
Data Sets for the Book "Experimental Design for Laboratory
Biologists"
Gliding Box Lacunarity and Other Metrics for 2D Random Closed
Sets
Routines for Fit, Inference and Diagnostics in LAD Models
Estimation of Indicators on Social Exclusion and Poverty
Duncan test, Tukey test and Scott-Knott test
Interface to the Lake Multi-Scaled Geospatial and Temporal
Database
Local Approximate Gaussian Process Regression
Tools for the Analysis of Ecosystem Metabolism
Lake Temperatures Collected by Situ and Satellite Methods from
1985-2009
Modeling Data with Functional Programming
Collection of Internal Consistency Reliability Coefficients
Probabilistic Models to Analyze and Gaussianize Heavy-Tailed,
Skewed Data
Log-Analytic Methods for Multiplicative Effects
Liquid Association for Network Dynamics Detection
Landmark Estimation of Survival and Treatment Effect
Landmark Prediction of a Survival Outcome
Radiometric and Topographic Correction of Satellite Imagery
Landsat 8 Imagery Rescaled to Reflectance, Radiance and/or
Temperature
Landscape Metrics for Categorical Map Patterns
Langevin Analysis in One and Two Dimensions
Analyzing Linguistic Data: A Practical Introduction to
Statistics
Automated Setup and Auto Run for R Language Server
Laplace Deconvolution with Noisy Discrete Non-Equally Spaced
Observations on a Finite Time Interval
Complete Environment for Bayesian Inference
Local Average Response Functions for Instrumental Variable
Estimation of Treatment Effects
Serialization Interface for Large List Objects
Estimation of Lifetime Attributable Risk of Cancer from
Radiation Exposure
Least Angle Regression, Lasso and Forward Stagewise
Lasso-Zero for (High-Dimensional) Linear Regression
Modelling Interactions in High-Dimensional Data with
Backtracking
High-Dimensional Lasso Generalized Estimating Equations
Nonparametric P-Value Estimation for Predictors in Lasso
High-Dimensional Inference with the Penalized Score Test
L1 regularized regression (Lasso) solver using the Cyclic
Coordinate Descent algorithm aka Lasso Shooting
Sparsed Sliced Inverse Regression via Lasso
Draws Diagrams Useful for Checking Latent Scales
Latent Position and Cluster Models for Statistical Networks
Utilities for Scheduling Functions to Execute Later with Event
Loops
Functions to Calculate Common Laterality Statistics in
Primatology
Framework for Clustering Longitudinal Data
Density Estimation and Nonparametric Regression on Irregular
Regions
Extra Graphical Utilities Based on Lattice
Multi-Resolution Kriging Based on Markov Random Fields
Complex Survey Structural Equation Modeling (SEM)
Path Diagrams for Lavaan Models via DiagrammeR
Tools for Model Specification in the Latent Variable Framework
Lava Estimation for the Sum of Sparse and Dense Signals
Latent (Variable) Analysis with Bayesian Learning
Tools for Biostatistics, Public Policy, and Law
Loglikelihood Adjustment for Extreme Value Models
Persistent Large Data Array with Lazy-Loading on Demand
Progress Bar with Remaining Time Forecast Method
Applying the Lazy-Greedy Spanning Algorithm
Delayed Read for 'GDAL' Vector Data Sources
Learn Computer and Data Science using Algorithmic Trading
Latent Budget Analysis for Compositional Data
Limited Memory BFGS Minimizer with Bounds on Parameters with
optim() 'C' Interface
Length-biased correction to survival curve estimation
Log-Binomial Regression with Constrained Optimization
Latent Class Analysis (LCA) with Familial Dependence in Extended
Pedigrees
Variable Selection for Latent Class Analysis
Data sets for package ``LMERConvenienceFunctions''
A Bayesian Multi-Dimensional Couple-Based Latent Risk Model
Efficient Estimation of Discrete-Time Multivariate Frailty Model
Using Exact Likelihood Function for Grouped Survival Data
Extended Mixed Models Using Latent Classes and Latent Processes
Simple Tools to Compute Landscape Connectivity Metrics
A Tool for Selecting Genes Related to Survival Outcomes using
Longitudinal Gene Expression Data
Ordinal Outcomes: Generalized Linear Models with the Log Link
Bayesian Joint Latent Class and Regression Models
Univariate and Bivariate Latent Change Score Modeling
Local Correlation, Spatial Inequalities, Geographically Weighted
Regression and Other Tools
Collapsed Gibbs Sampling Methods for Topic Models
Selection of Statistically Similar Research Groups
Prototype of Multiple Latent Dirichlet Allocation Runs
Latent Dirichlet Allocation Coupled with Time Series Analyses
Tuning of the Latent Dirichlet Allocation Models Parameters
Interactive Visualization of Topic Models
Lan-DeMets Method for Group Sequential Boundaries
Linkage Disequilibrium Corrected by the Structure and the
Relatedness
Graphical Display of Pairwise Linkage Disequilibria Between SNPs
Hidden Markov Model for Financial Time-Series Based on Lambda
Distribution
An R Package for Calculating Linkage Disequilibrium
Finding Locally D-optimal optimal designs for some nonlinear and
generalized linear models
Methods for likelihood-based dimension reduction in regression
Linkage Disequilibrium Shrinkage Estimation for Polyploids
Exact tests for Linkage Disequilibrium and Hardy-Weinberg
Equilibrium
The Artificial Neural Networks Algorithm Leabra
Rapid Digital Image Analysis of Leaf Area
High-Performance 'WebGl' Rendering for Package 'leaflet'
Create Interactive Web Maps with the JavaScript 'Leaflet'
Library
'ESRI' Bindings for the 'leaflet' Package
Extra Functionality for 'leaflet' Package
An R Gallery for China and Other Geojson Choropleth Map in
Leaflet
Interactive Web-Maps Based on the Leaflet JavaScript Library
Leaflet Map Plugin for Drawing and Editing
Include Tables, Images and Graphs in Leaflet Pop-Ups
Calculates the Leaf Area Index (LAD) and Other Related Functions
Silhouette to Area Ratio of Tilted Surfaces
Finds "Local Subnetworks" Within an Interaction Network which
Show Enrichment for Differentially Expressed Genes
Constructing Gene Co-Expression Networks for Single-Cell
RNA-Sequencing Data Using Pseudotime Ordering
Likelihood Estimation of Admixture in Parents From Offspring
Genotypes
latent effect adjustment after primary projection
Border and Area Estimation of Data Measured with Additive Error
Functions for Learning Bayesian Inference
Data and Functions to Accompany the Book "Learning R"
Population Genetic Simulations & Numerical Analysis
Datasets for P. J. Aphalo's "Learn R" Book
An Interactive Environment for Learning Statistics
Modelling Pathways and Movement Potential Within a Landscape
(Version 1.7.4)
Utilities for Importing Data from Plain Text Accounting Files
Historical and Ahistorical Population Projection Matrix Analysis
Accessing Hong Kong Legislative Council API
Interface to the Comparative Legislators Database
Latent Environmental & Genetic InTeraction (LEGIT) Model
R Implementation of Leiden Clustering Algorithm
Implements the Leiden Algorithm via an R Interface
Length-Based Multispecies Analysis by Numerical Simulation
Access Landscape Evaporative Response Index Raster Data
Vectorised Nested if-else Statements Similar to CASE WHEN in
'SQL'
Data Handling and Analysis in Macroecology
Plot Lexis Diagrams for Demographic Purposes
Extractive Summarization of Text with the LexRank Algorithm
Estimation of the Local False Discovery Rates by Type II Maximum
Likelihood Estimation
Estimating Local False Discovery Rates Using the Method of
Moments
Estimating Local False Discovery Rates Using Empirical Bayes
Methods
Calculation of Low Flow Statistics for Daily Stream Flow Data
Locally Gaussian Distributions: Estimation and Methods
Simulation and Estimation of Log-GARCH Models
Tests for Genetic Association/Gene-Environment Interaction in
Longitudinal Studies
Example Datasets for a Learning Guide to R
Set-Based Tests for Genetic Association in Longitudinal Studies
A Set of Methods for Longitudinal Data Objects
Fit Sex-Specific Life History Models with Missing
Classifications
Linking Singe-Cell Transcriptomes Atween Contemporary
Subpopulation Genomes
Linear Test Statistics for Permutation Inference
Open Source Geometry Engine ('GEOS') C API
Linear Predictive Models Based on the 'LIBLINEAR' C/C++ Library
Linear Classification with Online Adaptation of Coordinate
Frequencies
Design of Optimum-Path Forest Classifiers
Libraries, Data Dictionaries, and a Data Step for R
Linearized Bregman Algorithms for Generalized Linear Models
Install, Update, Load Packages from CRAN, 'GitHub', and
'Bioconductor' in One Step
Library Snapshot for Packages and Dependencies in Use by Current
Session
Read, Create and Write 'PharmML' Standard Output (so) XML Files
Fast and Accurate Evaluation, Random Number Generation and
Parameter Estimation of Skew Stable Distributions
Light Cone Reconstruction of States - Predictive State
Estimation From Spatio-Temporal Data
Airborne LiDAR Data Manipulation and Visualization for Forestry
Applications
Financial and Actuarial Mathematics for Life Contingencies
Manage the Life Cycle of your Package Functions
Framework for Traditional Life Insurance Contracts
Two-Parameter HMD Model Life Table System
Compute the Top Decile Lift and Plot the Lift Curve
Wavelet Lifting Estimators of the Hurst Exponent for Regularly
and Irregularly Sampled Time Series
Containerize R Markdown Documents for Continuous Reproducibility
Tools for Communication with Lightning-Viz Server
Implementation of the 'Lights Out' Puzzle Game
Methods for Maximum Likelihood Estimation
Metabolomics Personalized Pathway Analysis Tool
For Implementation of Feed Reduction, Learning Examples, NLP and
Code Management
Linear Inverse Model examples and solution methods
Jitter/CI Plot with Ordered Points Below the Limit of Detection
Perform Polynomial Evaluation of Linearity
Binning and Plotting of Linearly Referenced Data
Static Univariate Frequentist and Bayesian Linear Calibration
Functions to Explore L-Systems (Lindenmayer Systems)
The Lindley Distribution and Its Modifications
Manipulate Formulas and Evaluate Marginal Effects
Linear Algorithm for Simulating Quantiles in Multiscale
Change-Point Segmentation Problem
Minimum Distance Estimation in Linear Regression Model
Gaussian Process Regression Models with Linear Inequality
Constraints
Easy Linguistics Document Writing with R Markdown
Linking Geographic Information Systems, Remote Sensing and Other
Command Line Tools
Plot Linkage Group Maps with Quantitative Trait Loci
Tools for Generating, Visualizing, and Analysing Link
Communities in Networks
Linked Emulator of a Coupled System of Simulators
Linkage information based genotype imputation method
Bivariate Correlations Calculation and Visualization
Generate Concentration-Time Profiles from Linear PK Systems
Interactive Interpretation of Linear Regression Models
Manipulation of Linear Systems of (in)Equalities
Lipid Annotation for LC-MS/MS DDA or DIA Data
Integrative Visualizations of the Lipidome
Implements Queue, PriorityQueue and Stack Classes
Statistical Methods for the Item Count Technique and List
Experiment
Incomplete Array with Arbitrary R Objects as Indices
A Toolbox for Working with R Arrays in a Functional Programming
Style
List-Based Rules for Dynamic Treatment Regimes
Tests of independence based on the Longest Increasing
Subsequence
'htmlwidget' for Interactive Views of R Lists
Lightweight Portable Message Queue Using 'SQLite'
Liu Regression with Liu Biasing Parameters and Statistics
Local Interpretable (Model-Agnostic) Visual Explanations
Leveraging Learning to Automatically Manage Algorithms
Local Log-linear Models for Capture-Recapture
Logit Leaf Model Classifier for Binary Classification
Data Analysis of Liquid-Liquid Systems using R
Add Standardized Regression Coefficients to lm-Objects
Linear Mixed-Effects Models using 'Eigen' and S4
Linear Mixed-Effects Models with Censored Responses
Information Matrices for 'lmeStruct' and 'glsStruct' Objects
Linear Mixed Effects Models for QTL Mapping for Multienvironment
and Multitrait Analysis
Compute the Personalized Activity Index Based on a Negative
Binomial Model
Compute the Personalized Activity Index Based on a Flexible
Bayesian Negative Binomial Model
Model Selection and Post-Hoc Analysis for (G)LMER Models
Bootstrap Methods for Nested Linear Mixed-Effects Models
Add smoothing spline modelling capability to nlme
Testing for a Subset of Variance Components in Linear Mixed
Models
Functions for estimation and inference of selection in
age-structured populations
Filter Methods for Parameter Estimation in Linear and Non Linear
Regression Models
Tools to Visualize and Screen 2D/3D Landmark Data
Advanced L-Moment Fitting of Distributions
L-Moments, Censored L-Moments, Trimmed L-Moments, L-Comoments,
and Many Distributions
(Precipitation) Frequency Analysis and Variability with
L-Moments from 'lmom'
Regional Frequency Analysis using L-Moments
An Algorithm for Gene Co-Expression Analysis
Data and Functions Used in Linear Models and Regression with R:
An Integrated Approach
Linear Ridge Regression with Ridge Penalty and Ridge Statistics
Exact Variable-Subset Selection in Linear Regression
Non-Parametric Causal Effects of Feasible Interventions Based on
Modified Treatment Policies
Linear Regression with Non-Constant Variances
A Package to Visualize Linear Models Features and Play with Them
Simultaneous CIs for Ratios of Means of Log-Normal Populations
with Zeros
Long Non-Coding RNA Differential Expression Analysis
LncRNA Identification and Analysis Using Heterologous Features
Predicting Modulator and Functional/Survival Analysis
Identifying the Pathways Regulated by LncRNA Sets of Interest
LogNormal Response Time Item Response Theory Models
Cleaner Workspaces with Shared Variable Environments
Nonparametric Methods for Generating High Quality Comparative
Effectiveness Evidence
Local Control Strategy for Robust Analysis of Cross-Sectional
Data
Localization Processes for Functional Data Analysis
Estimation of Marginal Treatment Effects using Local
Instrumental Variables
LIME-Based Explanations with Interpretable Inputs Based on
Ceteris Paribus Profiles
Identification of Location Game Equilibria in Networks
Functions for Performing Local FDR Estimation when Null and
Alternative are Poisson
Local Regression, Likelihood and Density Estimation
Test of Stationarity and Localized Autocovariance
Datasets for "Statistics: UnLocking the Power of Data"
Datasets for 'Statistics: Unlocking the Power of Data'
Fast Implementation of (Local) Population Stratification Methods
Dependency-Free Access to PNG Image Files
Genome-Wide Association Analysis of a Biomarker Accounting for
Limit of Detection
Limit of Detection Imputation for Single-Pollutant Models
Linear Model Fitting with LOD Covariates
A Fast and Lightweight Logging System for R, Based on 'log4j'
Log File Analysis in International Large-Scale Assessments
Relative Risk Regression Using the Log-Binomial Model
Log-Concave Density Estimation in Arbitrary Dimensions
Maximum Likelihood Estimation of a log-Concave Density Based on
Censored Data
Estimate a Log-Concave Probability Density from Iid Observations
Compute MLE of Log-Concave Density on R with Fixed Mode, and
Perform Inference for the Mode
Estimate a Log-Concave Probability Mass Function from Discrete
i.i.d. Observations
A Lightweight, Modern and Flexible Logging Utility
Salary Analysis by the Swiss Federal Office for Gender Equality
Binning Variables to Use in Logistic Regression
LOGICOIL: multi-state prediction of coiled-coil oligomeric
state
Logistic Regression with Misclassification in Dependent
Variables
Diagnostic Tests for Models with a Binomial Response
Adjusted Relative Risk from Logistic Regression
Infer network based on binary arrays using regularized logistic
regression
Functions for the Logitnormal Distribution
Logit Models w/Preference & WTP Space Utility Parameterizations
Computing Log-Transformed Kernel Density Estimates for Positive
Data
Double log normal distribution functions
Log-Multiplicative Models, Including Association Models
Functions for the Lognormal Distribution
Natural Logarithms of the Gamma Function for Large Values
Logrank Test for Aggregated Survival Data
Routines for Logspline Density Estimation
Kernel Regression Smoothing with Local or Global Plug-in
Bandwidth
Recursive Partitioning for Longitudinal Data and Right Censored
Data Using Baseline Covariates
Package for Plotting Categorical Longitudinal and Time-Series
Data
Model-Based Clustering and Classification for Longitudinal Data
Statistics for Long-Memory Processes (Book Jan Beran), and
Related Functionality
Sample Size Calculations for Longitudinal Data
Time-Dependent Prognostic Accuracy with Multiply Evaluated Bio
Markers or Scores
Recursive Partitioning of Longitudinal Data
Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
Models
Data Used to Illustrate 'Loon' Functionality
Making 'ggplot2' Plots Interactive with 'loon' and Vice Versa
loop decomposition of weighted directed graphs for life cycle
analysis, providing flexbile network plotting methods, and
analyzing food chain properties in ecology
A Collection of Tools to Conduct Levins' Loop Analysis
Comprehensive Feedback Loop Detection in ODE Models
Integration and Analysis of Chromatin Loop Data
Tools for Survival Analysis and Data Science
Logistic Ordinal Regression Differential Item Functioning using
IRT
LOw Rand and sparsE Covariance matrix estimation
The Lorentz Transform in Relativistic Physics
Tools for Deriving Income Inequality Estimates from Grouped
Income Data
Imputation of High-Dimensional Count Data using Side Information
Missing Morphometric Data Simulation and Estimation
Runs Lotka's Law which is One of the Special Applications of
Zipf's Law
A Simple Way to Specify Symmetric, Block Diagonal Matrices
Detecting New Signals under Background Mismodelling
Lassoed Principal Components for Testing Significance of
Features
Local Polynomial Density Estimation and Inference
Nonparametric Smoothing of Laplacian Graph Spectra
Local polynomial estimators of intensity function or its
derivatives
Local Projections Impulse Response Functions
LP Nonparametric High Dimensional K-Sample Comparison
'dplyr' Verbs for Lists and Other Verbs for Data Frames
Linear Parametric Models Applied to Hydrological Series
Nonparametric Estimation of Measurement Error Models
Merging Linkage Maps by Linear Programming
Modeler for linear programs (LP) and mixed integer linear
programs (MILP)
Calculates Power, Sample Size, or Detectable Effect for
Longitudinal Analyses
Linear Predictor Score, for Binary Inference from Multiple
Continuous Variables
Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs
R Interface to 'lp_solve' Version 5.5.2.0
Learned Pattern Similarity and Representation for Time Series
LP Nonparametric Approach to Non-Gaussian Non-Linear Time Series
Modelling
Lag Penalized Weighted Correlation for Time Series Clustering
Dose Response Signal Detection under Model Uncertainty
Sources an R "Module" with Caching & Encapsulation, Returning
Exported Vars
Different Types of Estimators to Deal with Multicollinearity
Fitting Linear Quantile Regression Mixed Models with
Relationship Matrix
A Likelihood Ratio Test Accounting for Genetic Heterogeneity
Locally Stationary Two-Dimensional Wavelet Process Estimation
Scheme
A Multiscale Test of Spatial Stationarity for LS2W Processes
Applied Latent Semantic Analysis (LSA) Functions
Daten, Beispiele und Funktionen zu 'Large-Scale Assessment mit
R'
Functions to Facilitate the Simulation of Large Scale Assessment
Data
Least-Squares Bilinear Clustering for Three-Way Data
Bandwidth Selection for Level Sets and HDR Estimation
Local Statistical Complexity - Automatic Pattern Discovery in
Spatio-Temporal Data
Solving Least Squares or Quadratic Programming Problems under
Equality/Inequality Constraints
Semi-Confirmatory Structural Equation Modeling via Penalized
Likelihood or Least Squares
Estimation of the log Likelihood of the Saturated Model
American options pricing with Least Squares Monte Carlo method
Value American and Real Options Through LSM Simulation
Nonparametric Estimation and Inference Procedures using
Partitioning-Based Least Squares Regression
Lysate and Secretome Peptide Feature Plotter
Linear Splines with Convenient Parametrisations
Classification using LS-PLS for Logistic Regression
Companion to "Learning Statistics with R"
The Accelerated Failure Time Model to Right Censored Data Based
on Least-Squares Principle
Model for Semisupervised Text Analysis Based on Word Embeddings
Simulation-Based Bayesian Inference for Latent Traits of Item
Response Models
Left-Truncated Mixtures of Gamma, Weibull, and Lognormal
Distributions
Longitudinal Targeted Maximum Likelihood Estimation
LTPD and AOQL Plans for Acceptance Sampling Inspection by
Variables
Ensemble Methods for Survival Data with Time-Varying Covariates
Survival Trees to Fit Left-Truncated and Right-Censored and
Interval-Censored Survival Data
Ridge and Liu Estimates based on LTS (Least Trimmed Squares)
Method
Sparse Principal Component Based on Least Trimmed Squares
Lightweight Sparklines for a LaTeX Document
Package to Download and Create the DB of LUCAS Data Harmonized
Printing Floating Point Numbers in a Human-Friendly Format
Latent Unknown Clustering with Integrated Data
Light Use Efficiency Model to Estimate Biomass and YIELD with
and Without Vapour Pressure Deficit
Comprehensive Luminescence Dating Data Analysis
Lunar Phase & Distance, Seasons and Other Environmental Factors
Latent Variable Gaussian Process Modeling with Qualitative and
Quantitative Input Variables
Stochastic EM Algorithms for Latent Variable Models with a
High-Dimensional Latent Space
An Automated Approach to Evaluating Dose-Effect Experiments
Following Litchfield and Wilcoxon (1949)
Bindings to Selected 'liblwgeom' Functions for Simple Features
Accurate Estimation of Clonal Coincidences and Abundances from
Biological Replicates
Exact Spike Train Inference via L0 Optimization
Movement to Behaviour Inference using Random Forest
Multi-Modal Similarity Matrix Factorization for Integrative
Multi-Omics Data Analysis
Multi-Modal Similarity Matrix Joint Factorization
Maximum Approximate Bernstein/Beta Likelihood Estimation
Binary and Multiclass Boosting Algorithms
Multi-Armed Bayesian Ordinal Utility-Based Sequential Trial
Mediation Analysis of Causality under Confounding
Machina Time Series Generation and Backtesting
Retrieve Data from MacLeish Field Station
Class prediction based on microarray data and clinical
parameters
Mediation Analysis for Count and Zero-Inflated Count Data
Fast Data Aggregation, Modification, and Filtering with Pipes
and 'data.table'
Automatic Differentiation of Multivariate Operations
MHC Allele-Based Differencing Between Populations
May All Data be Reproducible and Transparent (MADRaT) *
A Flexible Microarray Data Simulation Model
Data Class and Tools for Handling Spatial-Temporal Data
Pretty Scientific Plotting with Minor-Tick and Log Minor-Tick
Support
Magic Functions to Obtain Results from for Loops
Advanced Graphics and Image-Processing in R
GUI Tools for Interactive Image Processing with 'magick'
A Pipeline for Meta-Genome Wide Association
Implements the O'Connell-Dobson-Schouten Estimators of Agreement
for Multiple Observers
A Graphical User Interface for Microarray Data Analysis and
Annotation
Creates a Friendly User Interface for Emails Sending in 'shiny'
R Interface to Access the 'Majestic' API
k-Means Algorithm with a Majorization-Minimization Method
Create Dummy Variables from Categorical Data
Creates an empty package framework for the LCFD format
Exploring and Testing the Toolchain and System Libraries
Machine Learning Assisted Network Inference
An R Interface to Open-Access Malaria Data, Hosted by the
'Malaria Atlas Project'
Quantitative Analysis of Mass Spectrometry Data
MALDI Mass Spectrometry Data Robust Pre-Processing and Analysis
A wrapper around the Java machine learning tool MALLET
Calculation of Minimum Averaged Mean Squared Error (MAMSE)
Weights
Matrix Analysis and Normalization by Concordant Information
Enhancement
Multivariate Analysis for Neuroimaging Data
Multiple Allocation Model for Actor-Event Networks
Interactive Q-Q and Manhattan Plots Using 'plotly.js'
Access and Process Data and Documents of the Manifesto Project
An R Interface to the 'ROPTLIB' Library for Riemannian Manifold
Optimization
Add Even More Interactivity to Interactive Charts
Manly Mixture Modeling and Model-Based Clustering
Resampling-Based Analysis of Multivariate Data and Repeated
Measures Designs
Multiple Testing Procedures of Cox (2011) and Wong and Cox
(2007)
Tools for Matrix Algebra, Optimization and Inference
Mapping Markers to the Nearest Genomic Feature
Tools for Plotting Canadian Choropleth Maps and Choropleth
Alternatives
China Administrative Divisions Geospatial Shapefile Data
Interactive Maps Using 'Mapbox GL JS' and 'Deck.gl'
Interactive Editing of Spatial Data in R
Mapping Smoothed Effect Estimates from Individual-Level Data
Producing Administrative Boundary Map with Additional Features
Embedded
'sf'-Compatible Interface to 'Google Maps' APIs
Local Adaptation and Evaluation of Digital Soil Maps
Geographic Display of Survey Data Statistics
Mapping, pruning, and graphing tree models
Interactive Viewing of Spatial Data in R
Multiplicative AR(1) with Seasonal Processes
Migration and Range Change Estimation in R
Estimation of Meiotic Recombination Rates Using Marey Maps
Approximate Marginal Inference for Regression-Scale Models
Marine Ecosystem and Fishing Pressure Indicators
Render Markdown with the C Library 'Sundown'
Shiny Module for a Markdown Input with Result Preview
Mark-Recapture Analysis for Survival and Abundance Estimation
Market Matching and Causal Impact Inference
Tidy Calculation of Marketing Metrics Plus Quick Analysis
Markov Chain Models for Phylogenetic Trees
Easy Handling Discrete Time Markov Chains
Markov Chain-Based Cost-Optimal Control Charts
Statistical Significance of the Markowitz Portfolio
Multivariate Analysis Based on Relative Likelihoods
Import, Plot and Analyze Bathymetric and Topographic Data
A Parallelized General-Purpose Optimization Based on
Marquardt-Levenberg Algorithm
Simulation, Estimation, Model Selection and Forecasting for MARX
Models
Mandallaz' Model-Assisted Small Area Estimators
Masking, Unmasking and Restoring Confidential Data
Build Data Structures for Common Statistical Analysis
Support Functions and Datasets for Venables and Ripley's MASS
Body Mass Estimation Equations for Vertebrates
ML and MCMC Methods for Pedigree Reconstruction and Analysis
Model-Averaged Tail Area Wald (MATA-Wald) Confidence Interval
Multivariate and Propensity Score Matching with Balance
Optimization
Nonparametric Preprocessing for Parametric Causal Inference
Combining Matching and Linear Regression for Causal Inference
Optimal Multilevel Matching using a Network Algorithm
Matching and Weighting Multiply Imputed Datasets
A Code Converter from the Matlab/Octave Language to R
Support for the 'Mathpix' API (Image to 'LaTeX')
Measuring Association and Testing Independence Efficiently
An Interface for MATLAB using System Calls
Matrix Functions for Teaching and Learning Linear Algebra and
Multivariate Statistics
Matrix Clustering with Gaussian and Manly Mixture Models
Sparse and Dense Matrix Classes and Methods
Data.frame-Like Operations on Sparse and Dense Matrix Objects
Collection of functions for matrix calculations
Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix
Operations
Normalized Laplacian Matrix and Laplacian Map
Penalized Matrix-Normal Linear Discriminant Analysis
Modelling with Sparse And Dense Matrices
Simulations of Matrix Variate Distributions
Functions that Apply to Rows and Columns of Matrices (and to
Vectors)
Tests of Matrix Structure for Construct Validation
Fast Statistical Hypothesis Tests on Rows and Columns of
Matrices
Modern Calibration Functions for the Modern Analog Technique
(MAT)
Clustering with Matrix Gaussian and Matrix Transformation
Mixture Models
Decision Models with Multi Attribute Utility Theory
Three methods to identify differentially expressed gene sets,
ordinary least square test, Multivariate Analysis Of Variance
test with n contrasts and Random forest
Exact max-type Cochran-Armitage trend test(CATT)
The Group Sequential Max-Combo Test for Comparing Survival
Curves
Selecting the Best Set of Relevant Environmental Variables along
with the Optimal Regularization Multiplier for Maxent Niche
Modeling
Space-Filling Design under Maximin Distance
Maximum Likelihood Estimation and Related Tools
Model Species Distributions by Estimating the Probability of
Occurrence Using Presence-Only Data
Maximum Matching for General Weighted Graph
Fitting 'Maxent' Species Distribution Models with 'glmnet'
Approximate Maximisation of Nestedness in Bipartite Graphs
Orthogonal Data Projections with Maximal Skewness
Manage Spatial Metadata for Known Locations
Spatial Data Download and Utility Functions
Monotonic Association on Zero-Inflated Data
Maxwell Boltzmann Bose Einstein Fermi Dirac Distribution and
Destruction Rate Modelling
Multivariate Bias Correction of Climate Model Outputs
Companion Package for the Book "Model-Based Clustering and
Classification for Data Science" by Bouveyron et al. (2019,
ISBN:9781108644181).
Moment-Based Estimation for Hierarchical Models
Spatial Designs for Ecological and Environmental Surveys
Reading, Extracting, and Converting an Mbox File into a Tibble
Median Bias Reduction in Binomial-Response GLMs
Multivariate Bayesian Sparse Group Selection with Spike and Slab
Multivariate Bayesian Model with Shrinkage Priors
Multivariate Bayesian Structural Time Series
Bayesian Variable Selection Methods for Multivariate Data
A Monte Carlo Based Heterogeneity Test for Meta-Analysis
Tools for Two-Dimensional Monte-Carlo Simulations
Translates information from netcdf files with MC2 output into
inter-PVT transitions
Monte Carlo Simulation for Surface Backscattering
Monte Carlo Based Tests for the Behrens Fisher Problem as an
Alternative to Welch's t-Approximation
Matrix Computation Based Identification of Prime Implicants
Creates the MCC-F1 Curve and Calculates the MCC-F1 Metric and
the Best Threshold
Analysis of Matched Case Control Data with a Mismeasured
Exposure that is Accompanied by Instrumental Variables
Support for the Multicriteria Decision Aiding Process
Multi-Criteria Decision Making Methods for Crisp Data
Maximum Likelihood Estimation for Generalized Linear Mixed
Models
Machine Coded Genetic Algorithms for Real-Valued Optimization
Problems
Warnes and Raftery's MCGibbsit MCMC diagnostic
Multivariate Covariance Generalized Linear Models
Global optimization using Monte Carlo and Quasi Monte Carlo
simulation
Monte Carlo Hypothesis Tests with Sequential Stopping
Multiplicative Competitive Interaction (MCI) Model
Estimating Conditional Auto-Regressive (CAR) Models using Monte
Carlo Likelihood Methods
Multinomial Logit Models, with or without Random Effects or
Overdispersion
Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
Bayesian Analysis of Multivariate Counts Data in DNA
Metabarcoding and Ecology
Posterior Distribution of Extreme Value Models in R
Ensemble Sampler for Affine-Invariant MCMC
Hybrid Markov Chain Monte Carlo using Gaussian Processes
Functions to Store, Manipulate and Display Markov Chain Monte
Carlo (MCMC) Output
Precision of Discrete Parameters in Transdimensional MCMC
Markov Chain Monte Carlo Small Area Estimation
Prepare MCMCtree Analyses and Plot Bayesian Divergence Time
Analyses Estimates on Trees
Tools to Visualize, Manipulate, and Summarize MCMC Output
A Toolbox for the Multi-Criteria Minimum Spanning Tree Problem
Multiple Criteria Optimization Algorithms and Related Functions
Objects and Methods for Multi-Companion Matrices
Conjoint Analysis through Averaging of Multiple Analyses
Multiple Comparisons Using Normal Approximation
A Simplified Interface for Running Commands on Parallel
Processes
Design and Analysis of Dose-Finding Studies
A Supplement to the 'DoseFinding' Package for the General Case
Simulation-Based Design and Analysis of Dose-Finding Trials
Testing Generalized Linear Hypotheses for Generalized Linear
Model Parameters by Profile Deviance
Determine the Optimal Number of Clusters
Functions for Monte Carlo Methods with R
Visualize Results of Statistical Hypothesis Tests
Selecting Bandwidth for Kernel Density Estimator with Minimum
Distance Method
Produces Markdown Log File with a Built-in Function Call
Mixture and Flexible Discriminant Analysis
Inferring Causal Network from Mixed Observational Data Using a
Directed Acyclic Graph
Multivariate Data Analysis for Chemometrics
Measuring the Difference Between Two Empirical Distributions
Variable-Group Methods for Agglomerative Hierarchical Clustering
Multivariate Double Hierarchical Generalized Linear Models
Multi-Dimensional MA Normalization for Plate Effect
Graph-Constrained Regression with Enhanced Regularization
Parameters Selection
Improved Score Tests for Generalized Linear Models
Functions for Analysis of Data with General Recognition Theory
High Density Genetic Linkage Mapping using Multidimensional
Scaling
Searching for Optimal MDS Procedure for Metric and
Interval-Valued Data
Interactive Document for Working with Multidimensional Scaling
and Principal Component Analysis
Complement to 'Modern Data Science with R'
A Computationally Efficient Mean Shift Implementation
Make Quick Descriptive Tables for Continuous Variables
Performance Measures for Statistical Learning
Detection and Control of Tree-Ring Widths on Scanned Image
Sections
Maximum Entropy Bootstrap for Time Series
Fit the Mixture of Experts Latent Position Cluster Model to
Network Data
Measurement Error Correction in Linear Models with a Continuous
Outcome
Multi Calculator to Compute Scores of Adherence to Mediterranean
Diet
Bayesian Methods for Identifying the Most Harmful Medication
Errors
Extraction of Medication Information from Clinical Text
Flexible Mediation Analysis Using Natural Effect Models
Mediation Analysis Based on the Product Method
Simulation-Based Sensitivity Analysis for Causal Mediation
Studies
Medical Risk and Comorbidity Tools for ICD-9-CM Data
Tools for Obtaining and Cleaning Medicare Public Use Files
Prints a Random Quote from Marcus Aurelius' Book Meditations
Simple Mediation and Moderation Analysis
Access and Search MedRxiv and BioRxiv Preprint Data
Mixtures of Exponential-Distance Models with Covariates
Linear Mediation Analysis for Complex Surveys Using Balanced
Repeated Replication
Multivariate Data Handling in Ecology and Biogeography
Multivariate Data Handling with S4 Classes and Sparse Matrices
Accessing and Processing a 'Mega2' Genetic Database
Multiscale Clustering of Geometrical Network
Interactive model exploration using GGobi
Matching Event Data by Location, Time and Type
The Moving Epidemic Method Web Application
Spatial Pattern Detection in Genetic Distance Data Using Moran's
Eigenvector Maps
Management of Survey Data and Presentation of Analysis Results
In-Memory Caching for Repeated Computations
Testing for Structural Breaks under Long Memory and Testing for
Changes in Persistence
A 'rmarkdown' Template that Can be Highly Customized
Quantifying Ecological Memory in Palaeoecological Datasets and
Other Long Time-Series
Data Sets from Mixed-Effects Models in S
Creation of Empirical Density Functions Based on Multivariate
Data
Clustering and Visualizing Distance Matrices
Case-Wise and Cluster-Wise Derivatives for Mixed Effects Models
Mixed Effects Regression for Linear, Non-Linear and User-Defined
Models
Tools for Analyzing Mixed Effect Regression Models
Conveniently Issue Messages, Warnings, and Errors
Evaluating and Improving Matched Samples in Observational
Studies
Meta-Analysis for Diagnostic Test Studies
An Interactive Visualisation of Meta-Analysis as a Physical
Weighing Machine
Meta-analysis of genome-wide SNP association results
BLUE for Combining Location and Scale Information in a
Meta-Analysis
Bayesian Model Averaging for Random and Fixed Effects
Meta-Analysis
Probabilistic Latent Variable Models for Metabolomic Data
Datasets and Functions for Reproducing Meta-Analyses
Interface to the 'Metabolights' RESTful API
Annotation of Metabolites from Liquid Chromatography-Mass
Spectrometry Data
Basic Functions to Investigate Metabolomics Data Matrices
Normalize Metabolomic Data using QC Signal
Meta-CART: A Flexible Approach to Identify Moderators in
Meta-Analysis
Detection of Low-Quality Peaks in Untargeted Metabolomics Data
Tools for Parsing, Manipulating, and Graphing Taxonomic
Abundance Data
Analysis of the 'Elements of Metacommunity Structure'
Evaluate Periodicity in Large Scale Data
Annotate Mass over Charge Values with Databases and Formula
Prediction
Extract and Summarise Data from Published Figures
Tools to Read, Analyze and Visualize Metadynamics HILLS Files
from 'Plumed'
Tools to Read, Analyze and Visualize Metadynamics 3D HILLS Files
from 'Plumed'
Automated Intuitive Package for Meta-Ensemble Learning
Metapopulation simulations for conserving salmon through
portfolio optimization
Exploring Heterogeneity in Meta-Analysis using Random Forests
Fused Lasso Approach in Regression Coefficient Clustering
Meta-Analysis of Generalized Additive Models
Comprehensive Research Synthesis Tools for Systematic Reviews
and Meta-Analysis
An Implementation of Flower Pollination Algorithm in R
Easily Download Data and Metadata from 'DataONE'
Landscape and Range Expansion Simulation
Likelihood Inference in Meta-Analysis and Meta-Regression Models
Metagenomics Longitudinal Differential Abundance Method
Microbiome Data Analysis & Meta-Analysis with GAMLSS-BEZI &
Random Effects
Meta-Analysis of Diagnosis and Prognosis Research Studies
Bayesian Mixture Analysis for Metagenomic Community Profiling
Meta-Analysis of Studies with Non-Statistically Significant
Unreported Effects
Perform the Meta-Analysis for Pathway Enrichment Analysis (MAPE)
Creates CrossHairs Plots for Meta-Analyses
Regression Models for Meta Signal Detection Theory
Meta-Analysis using Structural Equation Modeling
Statistical Methods for Sensitivity Analysis in Meta-Analysis
Subtracting Summary Statistics of One or more Cohorts from
Meta-GWAS Results
Meta-Analysis of a Single Survival Curve
HTML Metadata Tags for 'R Markdown' and 'Shiny'
Meta-analysis for Classification Data and Correction to
Imperfect Reference
Utility Functions for Conducting and Interpreting Meta-Analyses
Variance-Covariance Matrix for Multivariate Meta-Analysis
Forest Plots, Funnel Plots, and Visual Funnel Plot Inference for
Meta-Analysis
Meta-Analytical Implementation to Identify Who Benefits Most
from Treatments
Spatio-Temporal Analysis and Mapping of Meteorological
Observations
Mixture-of-Experts Modeling for Complex Non-Normal Distributions
Fitting and Plotting Tools for the Maximum Entropy Theory of
Ecology (METE)
A Homogeneity Test under the Presence of Measurement Errors
Meth27QC: sample quality analysis, and sample control analysis
Analysis of Agreement in Method Comparison Studies
Identify and Rank CpG DNA Methylation Conservation Along the
Human Genome
Bias and Precision Plots to Compare Two Measurements with
Possibly Heteroscedastic Measurement Errors
Detection of Differentially Methylated Regions using
MethylCap-Seq Data
Statistical Methods for Normalizing Metabolomics Data
Separate Metabolites into Likely Measurement Artifacts and True
Metabolites
Tools for Easier Analysis of Meteorological Fields
Create Interactive Charts with the JavaScript 'MetricsGraphics'
Library
Weighted Metrics, Scoring Functions and Performance Measures for
Machine Learning
Find, Map, and Gather Environmental Data and Metadata
Interface with the Meteo France Synop Data API
A Fixed Memeory Moving Expanding Window Average
Identifying Master Gene Regulators from Gene Expression and
DNA-Binding Data
Leadership-Inference Framework for Multivariate Time Series
Multivariate Functional Principal Component Analysis for Data
Observed on Different Dimensional Domains
The Multiple Filter Test for Change Point Detection
Marginal Effects, Odds Ratios and Incidence Rate Ratios for GLMs
Simulating, Estimating and Diagnosing MGARCH (BEKK and mGJR)
Processes
Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation
Visualisations for Generalized Additive Models
Marginal Analysis of Misclassified Longitudinal Ordinal Data
Multivariate Response Generalized Linear Models
Model Averaging for Multivariate GLM with Null Models
Estimating Time-Varying k-Order Mixed Graphical Models
Missingness Aware Gaussian Mixture Models
mgpd: Functions for multivariate generalized Pareto distribution
(MGPD of Type II)
API Client for the MG-RAST Server of the US DOE KBase
A Matrix-Free Multigrid Preconditioner for Spline Smoothing
Safe, Multiple, Simultaneous String Substitution
Gene set analysis based on GSZ-scoring function and asymptotic
p-value
GWR and MGWR with Spatial Autocorrelation
General Markov Chain Monte Carlo for Bayesian Inference using
adaptive Metropolis-Hastings sampling
Multivariate Survival Function Estimation and Regression
Analysis of MHC Data in Non-Model Species
Multilevel Hidden Markov Models Using Bayesian Estimation
Inference for Hidden Markov and Semi-Markov Models
Multiple Hypothesis Test Based on Distribution of p Values
Tests Controlling the FDR / FWER under Certain Copula Models
Multiple Hypotheses Testing for Discrete Data
Multiple Hypotheses Testing for Multiple Families/Groups
Structure
Bayesian Model Selection in Logistic Regression for the
Detection of Adverse Drug Reactions
Missing Data Imputation and Model Checking
A Modular, Integrated Approach to Maximum Entropy Distribution
Modeling
Multivariate Imputation by Chained Equations
Some Additional Multiple Imputation Functions, Especially for
'mice'
Demand Analysis with the Almost Ideal Demand System (AIDS)
Analysis with the Constant Elasticity of Substitution (CES)
Function
Symmetric Normalized Quadratic Profit Function
Fast Imputations Using 'Rcpp' and 'Armadillo'
Multiple Imputation by Chained Equations with Multilevel Data
Missing not at Random Imputation Models for Multiple Imputation
by Chained Equation
Multiple Imputation by Chained Equations with Random Forests
The Works (in Luxembourguish) of Michel Rodange
Multivariate Independent Comparison of Observations
Promotion Time Cure Model with Mis-Measured Covariates
Do 16s Data Analysis and Generate Figures
Methods for Taxonomic Classification of Prokaryotes
Entity Resolution with Random Partition Priors for
Microclustering
Utilities for Official Spanish Microdata
Microbial Community Ecology Data Analysis
Linked Micromap Plots for General U. S. and Other Geographic
Areas
Microplots (Sparklines) in 'LaTeX', 'Word', 'HTML', 'Excel'
Finding Optimal Microsampling Designs for Non-Compartmental
Pharmacokinetic Analysis
Sequence Error Filtering Pipeline for FFPE Samples
Synthetic Control Methods with Micro- And Meso-Level Data
Estimation and Prediction Methods for High-Dimensional Mixed
Frequency Time Series Data
Multiple Imputation by Distance Aided Donor Selection
Microcluster-Based Detector of Anomalies in Edge Streams
Nearly Exact Sample Size Calculation for Exact Powerful
Nonrandomized Tests for Differences Between Binomial
Proportions
Multiples Comparisons Procedures Based on Studentized Midrange
and Range Distributions
Multiple Imputation for Exploratory Factor Analysis
Methods for the Indirect Estimation of Bilateral Migration
Create Credit State Migration (Transition) Matrices
Production Rules Based Classification of Migration
Graphical User Interface to the 'mi' Package
Learning Causal or Non-Causal Graphical Models Using Information
Theory
Multiple Imputation for Interval Censored Data
Model Implied Instrumental Variable (MIIV) Estimation of
Structural Equation Models
User-Friendly R Package for Supervised Machine Learning
Pipelines
MIcrosimulation Lung Cancer (MILC) model
Association Tests for Microbial Lineages on a Taxonomic Tree
Mixed Logistic Regression for Genome-Wide Analysis Studies
(GWAS)
Multiple-Instance Logistic Regression with LASSO Penalty
Main Effects and Interactions in Mixed and Incomplete Data
Mixture summary method for multiple imputation
Algorithm to Compute Monitor Independent Movement Summary Unit
(MIMS-Unit)
Calculate MIMS Dissolved Gas Concentrations Without Getting a
Headache
Determining the Minimal Background Area for Species Distribution
Models
Indicadores Economicos de Chile (Economic Outlook for Chile)
Data sets included in Utts and Heckard's Mind on Statistics
Convert Files Between Markdown or R Markdown Files and Mind Maps
Extract and Analyze Median Molecule Intensity from 'citrus'
Output
A Bayesian Design for Minimum Effective Dosing-Finding Trial
Maximal Information-Based Nonparametric Exploration for Variable
Analysis
Implementation of the Well-Known Game to Clear Bombs from a
Given Field (Matrix)
Create a Mini Version of CRAN Containing Only Selected Packages
Create Simple Yet Powerful HTML Documents with Light Weight CSS
Frameworks
Implementation of the minMSE Treatment Assignment Method for One
or Multiple Treatment Groups
R Interface to the Levenberg-Marquardt Nonlinear Least-Squares
Algorithm Found in MINPACK, Plus Support for Bounds
Derivative-free optimization algorithms by quadratic
approximation
MINimal VALidation for Stoichiometric Reactions
Multidimensional Iterative Proportional Fitting and Alternative
Models
Mutant Identification through Probabilistic High throughput
Enabled NOrmalization
Algebraic and Statistical Functions for Genetics
Left-Censored Recurrent Events Survival Models
Genome-Wide Discovery of Pre-miRNAs with few Labeled Examples
Computerized Adaptive Testing with Multidimensional Item
Response Theory
Joint Maximum Likelihood Estimation for High-Dimensional Item
Factor Analysis
SVD-Based Estimation for Exploratory Item Factor Analysis
Miscellaneous Useful Functions Including LaTeX Tables, Kalman
Filtering and Development Tools
Misclassified Interval Censored Time-to-Event Data
Computation of Generalized Linear Models with Misclassified
Covariates Using Side Information
Miscellaneous Functions for the Correlation Coefficient
Variable Selection for Multiply Imputed Data
Multiple Imputation with Sequential Penalized Regression
Microbiome Based Sum of Powered Score (MiSPU) Tests
Statistical Analysis of Misreporting on Sensitive Survey
Questions
Intuitive Missing Data Imputation Framework
Simulating and Analyzing Time to Event Data in the Presence of
Population Mortality
Nonparametric Missing Value Imputation using Random Forest
Missing Outcome Data in Health Economic Evaluation
Handling Missing Values with Multivariate Data Analysis
Handling Missing Data in Stochastic Block Models
Mixed effects Score Test for continuous outcomes
Data Sets, Functions and Examples from the Book: "Modern
Industrial Statistics" by Kenett, Zacks and Amberti
Methods in Structural Reliability Analysis
Mixture of Student t Distributions using Importance Sampling and
Expectation Maximization
Tools for Multiple Imputation in Multilevel Modeling
Tools for Multiple Imputation of Missing Data
Cybersecurity MITRE Standards Data and Digraphs
Multiple Imputation Using Weighted Quantile Sum Regression
Estimation/Multiple Imputation for Mixed Categorical and
Continuous Data
Multivariate Normal Mixture Models and Mixtures of Generalized
Linear Mixed Models Including Model Based Clustering
Clustering and Classification using Model-Based Mixture Models
Mixed Effects Cumulative Link and Logistic Regression Models
Mixture Model for the Deconvolution of Thermal Decay Curves
Estimation of the Order of Mixture Distributions
Cluster High Dimensional Categorical Datasets
Sparse Canonical Correlation Analysis for High-Dimensional Mixed
Data
Tools for Discrete Multivariate Mixed Membership Models
Statistical Tools for the Analysis of Psychophysical Data
Estimation Methods for Stochastic Differential Mixed Effects
Models
A Mixed-Effects Model for Analyzing Cluster-Level Non-Ignorable
Missing Data
Design and Analysis of Mixture Experiments
Evaluation of the FIM in NLMEMs using MCMC
Model Based Clustering, Classification and Discriminant Analysis
Using the Mixture of Generalized Hyperbolic Distributions
Genetics and Independence Testing of Mixed Genetic Panels
Omics Data Integration Using Kernel Methods
Simulated Maximum Likelihood Estimation of Mixed Logit Models
for Large Datasets
Mixed Model ANOVA and Statistics for Education
Classification with Matrix Variate Normal and t Distributions
An Extended Mixed-Effects Framework for Meta-Analysis
Finite Mixture Modeling for Raw and Binned Data
Plotting and Average Theta Functions for Multiple Class Mixed
Rasch Models
Functions to Fit Mixtures of Regressions
A Random-Forest-Based Approach for Imputing Clustered Incomplete
Data
Mixtures of Multivariate Shifted Asymmetric Laplace (SAL)
Distributions
Forensic Genetics DNA Mixture Separation
Simulating Data to Study Performance of Clustering Algorithms
Fitting Finite Mixture of Scale Mixture of Skew-Normal
Distributions
Mixtures of Power Exponential and Skew Power Exponential
Distributions for Use in Model-Based Clustering and
Classification
Sequential Quadratic Programming for Fast Maximum-Likelihood
Estimation of Mixture Proportions
DE Analysis of RNA-Seq Data by Mixtures of NB
Tools for Analyzing Finite Mixture Models
Curve Fitting and Mixture Toxicity Assessment
Mixture Models for Clustering and Classification
Mixture Regression Models for Left-Truncated and
Interval-Censored Data
MixTwice--a Package for Large-Scale Hypothesis Testing
Multi-Species sIZE Spectrum Modelling in R
2D and 3D movement-based kernel density estimates (MKDEs)
Kinetic Evaluation of Chemical Degradation Data
Power Analysis and Sample Size Calculation
Efficient multi-level k-circulant supersaturated designs
Maximum Likelihood Inference on Multi-State Trees
Variational Autoencoder Models for IRT Parameter Estimation
Abstract Classes for Building 'scikit-learn' Like API
Major League Baseball Player Statistics Calculator
Latent Class Item Response Theory (LC-IRT) Models under
Within-Item Multidimensionality
Interactive Document for Working with Discriminant Analysis
Exploratory Data Analysis and Manipulation of Multi-Label Data
Sets
R Ultimate Multilabel Dataset Repository
Expected/Observed Fisher Information and Bias-Corrected Maximum
Likelihood Estimate(s)
Machine learning algorithms with unified interface and confusion
matrices
Computation of the MLE for bivariate (interval) censored data
Maximum Likelihood Estimates of Gaussian Processes
Multilevel Exponential-Family Random Graph Models
Datasets for Use with Salvan, Sartori and Pace (2020)
Independent Component Analysis using Maximum Likelihood
Maximum Likelihood Estimation of DNA Methylation and
Hydroxymethylation Proportions
ML estimation under multivariate linear mixed models with
missing values
Model Selection in Multivariate Longitudinal Data Analysis
Estimating Frequencies, Prevalence and Multiplicity of Infection
Examples from Multilevel Modelling Software Review
Bayesian Model Averaging for Multinomial Logit Models
Multiplex Ligation-Dependent Probe Amplification Data Analysis
'Rcpp' Integration for the 'mlpack' Library
Multi-Label Prediction Using Gibbs Sampling (and Classifier
Chains)
Algorithms for Class Distribution Estimation
Analysis and Visualisation of Benchmark Experiments
Collection of Machine Learning Data Sets for 'mlr3'
Filter Based Feature Selection for 'mlr3'
Preprocessing Operators and Pipelines for 'mlr3'
Probabilistic Supervised Learning for 'mlr3'
Spatiotemporal Resampling Methods for 'mlr3'
Easily Install and Load the 'mlr3' Package Family
Composable Preprocessing Operators and Pipelines for Machine
Learning
Bayesian Optimization and Model-Based Optimization of Expensive
Black-Box Functions
Interactive Application for Working with Multiple Linear
Regression
Use the MLS Junk Generator Algorithm to Generate a Stream of
Pseudo-Random Numbers
Most Likely Transformations: Documentation and Regression Tests
Mean Length-Based Estimators of Mortality using TMB
Single-Sample Classifier of Medulloblastoma Subtypes for
Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
Gene Expression Datasets for the 'MM2S' Package
Inference of Linear Mixed Models Through MM Algorithm
Multiple Mediation Analysis for Big Data Sets
Data for Mathematical Modeling and Applied Calculus
Mathematical Morphology in Any Number of Dimensions
Arbitrary Dependency Mixed Multivariate Bayesian Models
Multivariate Multinomial Distribution Approximation and
Imputation for Incomplete Categorical Data
Robust Estimation of Copulas by Maximum Mean Discrepancy
Detecting Differentially Variable Genes Using the Mixture of
Marginal Distributions
Estimation of Multinormal Mixture Distribution
Fitting Markov-Modulated Linear Regression Models
Multivariate marginal models with shared regression parameters
Simultaneous Inference for Multiple Linear Contrasts in GEE
Models
Multi-Marker Molecular Signature for Treatment-specific Subgroup
Identification
Modern Measures of Population Differentiation
Implementation of Marker-Assisted Mini-Pooling with Algorithm
Integrative Analysis of Several Related Data Matrices
Monte-Carlo Methods for Prediction Functions
Various Similarity and Distance Metrics for Marked Point
Processes
Case Classification and Selection Based on Regression Results
Missing Multivariate Bayesian Variable Selection
Convert Dates to MMWR Day, Week, and Year
Easy Downloading Capabilities for the Members' Name Information
Service
Simulated Predicted Probabilities for Multinomial Logit Models
Interactive Shiny Presentation for Working with Multinomial
Logistic Regression
Multivariate Nonparametric Methods. An Approach Based on Spatial
Signs and Ranks
A Generator of Multivariate Non-Normal Random Numbers
Multivariate Normal Distributions with Power Integrand
The Multivariate Normal and t Distributions, and Their Truncated
Versions
MNREAD Parameters Estimation and Curve Plotting
Affine Invariant Tests of Multivariate Normality
Run Reports, Models, and Scripts from a Mobile Device
Calculates Transition Matrices and Mobility Indices
Spatial Simulation and Scale-Dependent Analysis of Biodiversity
Changes
General Nonlinear Multivariate Finite Mixtures
Multi-Objective Clustering Algorithm Guided by a-Priori
Biological Knowledge
Multi-Objective Optimization for Collecting Cluster Alternatives
Lightweight and Self-Contained Modules for Code Organization
Extraction of Bands from MODIS Surface Reflectance Product MOD09
NRT
A 'shiny' Module for Creating Charts of Various Types
Fit a Modified Connor-Mosimann Distribution to Elicited
Quantiles in Multinomial Problems
Multiscale Analysis for Density Functions
Stratified and Personalised Models Based on Model-Based Trees
and Forests
Estimation of Model-Based Predictions, Contrasts and Means
Data Sets Used Useful for Modeling Packages
Make Static HTML Website for Predictive Models
Classes and Methods for Training and Using Binary Prediction
Models
Model-free estimation of a psychometric function
A Framework for Creating, Managing and Training Multiple Caret
Models
Compare Models with Cross-Validated Log-Likelihood
Modeling and Map Production using Random Forest and Related
Stochastic Models
A Model Object Framework for Regression Analysis
Plots to Evaluate the Business Performance of Predictive Models
Modelling Functions that Work with the Pipe
Interactive Studio for Explanatory Model Analysis
Summary Tables and Plots for Statistical Models and Data:
Beautiful, Customizable, and Publication-Ready
Testing Infrastructure for Broom Model Generics
The Tidymodels Extension for Time Series Modeling
Ensemble Algorithms for Time Series Forecasting with Modeltime
Resampling Tools for Time Series Forecasting
Tools and Classes for Statistical Models
An Implementation of Two Modern Education-Based Value-Added
Models
Modeling and Analysis of Stochastic Systems
A 'shiny' Module for Reading Excel Sheets
Multivariate Outlier Detection and Imputation for Incomplete
Survey Data
Modified Versions of Mann Kendall and Spearman's Rho Trend Tests
Acquisition and Processing of MODIS Products
R tools for processing Level 2 Cloud Mask products from MODIS
Provides a Function to Download MODIS Snow Cover
Interface to the 'MODIS Land Products Subsets' Web Services
Find, Download and Process MODIS Land Products Data
Calculating Marginal Effects and Levels with Errors
Community Structure Detection via Modularity Maximization
'MatLab'-Style Modeling of Optimization Problems
Estimate ED50 Based on Modified Turning Point Method
Gaussian Parsimonious Clustering Models with Covariates and a
Noise Component
Multiobjective Genetic Algorithm for Variable Selection in
Regression
Dental Surface Complexity Measurement Tools
'OpenID Connect' Discovery and Authentication
Multiple Objective Latin Hypercube Design
Multivariate Outlier Detection in Contingency Tables
Bayesian Model Selection and Averaging for Non-Local and Local
Priors
Moment-Matching Methods for Weighted Sums of Chi-Squared Random
Variables
Moments, cumulants, skewness, kurtosis and related tests
Maximum Likelihood Analysis of Animal Movement Behavior Using
Multivariate Hidden Markov Models
Inference and Clustering for Mixture of Multinomial Principal
Component Analysis
Moments of Folded and Doubly Truncated Multivariate
Distributions
A Simple Graphical Representation of the Relative Occurrence and
Co-Occurrence of Events
Multi-Layer Perceptron Neural Network with Optional Monotonicity
Constraints
Perform Monothetic Clustering with Extensions to Circular Data
Estimation for MVN and Student-t Data with Monotone Missingness
Bayesian Monotonic Regression Using a Marked Point Process
Construction
Test for Monotonicity in Expected Asset Returns, Sorted by
Portfolios
Automatic Parallelized Monte Carlo Simulations
Functions and Datasets for the Book by Keon-Woong Moon
MOPSOCD: Multi-objective Particle Swarm Optimization with
Crowding Distance
Basic Quality Data Assurance for Epidemiological Research
Check Time Homogeneity and Markov Chain Order
A Toolbox for Conditional Inference Random Forests
Color schemes compatible with red-green color perception
difficulties
Estimate Parameters of Mixtures of Logistic Regressions
Calculations and Visualisations Related to Geometric
Morphometrics
Morphometric Maps, Bone Landmarking and Cross Sectional Geometry
Modelling Tools for Reproduction and Survival Data in
Ecotoxicology
Simple raw data generator based on user-specified summary
statistics
Analysis of Archaeological Mortality Data
The Double-Gap Life Expectancy Forecasting Model
Parametric Mortality Models, Life Tables and HMD
A Framework for Various Types of Mortality / Life Tables
Estimation and Projection of Age-Specific Mortality Rates
Project MOSAIC Statistics and Mathematics Teaching Utilities
Finding Rhythmic and Non-Rhythmic Trends in Multi-Omics Data
(MOSAIC)
Function-Based Numerical and Symbolic Differentiation and
Antidifferentiation
Common Utilities for Other MOSAIC-Family Packages
An Interface to Statistical Modeling Independent of Model
Architecture
Multi-Objective Simultaneous Model and Feature Selection
Multi-Omic Integration via Sparse Singular Value Decomposition
Moving Sum Based Procedures for Changes in the Mean
Learning Hybrid Bayesian Networks using Mixtures of Truncated
Basis Functions
Effect Size and Confidence Interval Calculator
Motif-Based Spectral Clustering of Weighted Directed Networks
Analyzing Paired Neuron Discharge Times for Time-Domain
Synchronization
Mountain Plots, Folded Empirical Cumulative Distribution Plots
Mouse-Tracking Measures from Trajectory Data
Visualizing and Analyzing Animal Track Data
Calculation of Accumulated Cost Surface and Least-Cost Paths
Related to Human Movement Across the Landscape
Animal Movement Modelling using Hidden Markov Models
Estimate Wind Speeds from Bird Trajectories
Mixtures of von Mises-Fisher Distributions
Weekly Notified Dengue Cases in Sri Lanka
Multinomial Probit Bayesian Additive Regression Trees
Treatment Allocation in Clinical Trials by the Maximal Procedure
Multivariate Process Capability Indices (MPCI)
Mean-Parametrized Conway-Maxwell Poisson (COM-Poisson)
Regression
Data Sets and Scripts for Modeling Psychophysical Data in R
A Two-Step Approach to Testing Overall Effect of
Gene-Environment Interaction for Multiple Phenotypes
The package can implement the network-based metabolite pathway
identification of pathways
Calculations of One Discrete Model in Several Time Steps
Modified Profile Likelihood Estimation for Weibull Shape and
Regression Parameters
Graphical Model Stability and Variable Selection Procedures
An R Package for Facilitating Large-Scale Latent Variable
Analyses in Mplus
Decision Trees with Structural Equation Models Fit in 'Mplus'
Most Probable Number and Other Microbial Enumeration Techniques
Symbolic Computation and More with Multivariate Polynomials
Statistics for analysing multiple simultaneous point processes
on the real line
Maximum Parsimony of Recombination to Infer Parental Genotypes
Estimating Through the Maximum Product Spacing Approach
Modeling Phylogenetic Signals using Eigenvector Maps
Mass-Preserving Spline Functions for Soil Data
Analyze Multinomial Processing Tree Models
Multiverse Analysis of Multinomial Processing Tree Models
Data Sets from Montgomery, Peck and Vining
Modelling and Quantitative Methods in Fisheries
Metabolomic Quantitative Trait Locus Mapping
Two Sample Mendelian Randomization using Robust Adjusted Profile
Score
Ratios of Coefficients in the General Linear Model
Bayesian Summary Data Models for Mendelian Randomization Studies
Magnetic Resonance Binning, Integration and Normalization
Scale Space Multiresolution Analysis of Random Signals
Methods for Analyzing Multiple Response Categorical Variables
(MRCVs)
Fits regression models when the outcome is partially missing
Marine Regions Data from 'Marineregions.org'
Markov Random Field Models for Image Analysis
Fitting and Predicting Large-Scale Nonlinear Regression Problems
using Multi-Resolution Functional ANOVA (MRFA) Approach
Markov Random Fields with Additional Covariates
Depth Measures in Multivariate, Regression and Functional
Settings
Multi-Resolution Estimation of the Hazard Rate
A Causal Mediation Method with Methylated Region (MR) as the
Mediator
Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for
Genome-Wide Association Study
Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for
Genome-Wide Association Study with Graphical User Interface
Multivariate Regression Models for Reserving
"Parallelized Minimum Redundancy, Maximum Relevance (mRMR)
Ensemble Feature Selection"
PC Algorithm with the Principle of Mendelian Randomization
Minimal Clinically Important Difference and Response Shift
Effect for Health-Related Quality of Life
MDL Multiresolution Linear Regression Framework
Regression Analysis for Very Large Data Sets via Merge and
Reduce
Multi-Resolution Scanning for Cross-Sample Differences
Multiple Responses Subgroup Identification using 'GUIDE'
Algorithm
A multiplicative-regression model for relative survival
A Sample Size Calculator for Micro-Randomized Trials
Package for Calculation of ARMSS, Local MSSS and Global MSSS
Multivariate Fay Herriot Models for Small Area Estimation
Difference Benchmarking for Multivariate Small Area Estimation
Multi-Step Adaptive Estimation Methods for Sparse Regressions
Statistical analysis for Methylation-sensitive Amplification
Polymorphism data
Multiscale Bernstein Polynomials for Densities
Hazard of Multi-Stage Clonal Expansion Models
Chart Generation for 'Microsoft Word' and 'Microsoft PowerPoint'
Documents
Multivariate Synthetic Control Method Using Time Series
Combine Data from Positive and Negative Ionization Mode Finding
Common Entities
Analyzing Gene Tree Quartets under the Multi-Species Coalescent
R Client for the Microsoft Cognitive Services Text Analytics
REST API
R Client for the Microsoft Cognitive Services 'Text-to-Speech'
REST API
R Client for the Microsoft Cognitive Services Web Language Model
REST API
Bayesian Inference for Multivariate Stochastic Differential
Equations
Parametric Estimation in Mixed-Effects Stochastic Differential
Equations
Data and Functions for the Book Modern Statistical Graphics
Multivariate Sparse Group Lasso for the Multivariate Multiple
Linear Regression with an Arbitrary Group Structure
A library to serialize or unserialize data in MessagePack format
Degrees of Freedom of Elastic Net, Adaptive Lasso and
Generalized Elastic Net
Extends Messages, Warnings and Errors by Adding Levels and Log
Files
MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
Micro Simulation Model for Cervical Cancer Prevention
Improved Techniques to Estimate Trend, Velocity and Acceleration
from Sea Level Records
Multi-State Markov and Hidden Markov Models in Continuous Time
Functions and Datasets for "Methods of Statistical Model
Estimation"
Building Augmented Data to Run Multi-State Models with 'msm'
Package
Multivariate Statistical Methods with R Applications
Data Sets and Functions Used in Multivariate Statistics: Old
School by John Marden
A Modified Sequential Probability Ratio Test (MSPRT)
Multi-State Reliability Demonstration Tests (MSRDT)
Helper Functions for Second Primary Cancer Analyses
Nonparametric Estimation for Multistate Models
Data Preparation, Estimation and Prediction in Multi-State
Models
A Collection of DIF Tests for Multistage Tests
Multiple Testing of Local Extrema for Detection of Change Points
Procedures to Generate Patterns under Multistage Testing
Multivariate Symmetric Uncertainty and Other Measurements
Multi-Trait Analysis of Rare-Variant Association Study
Read Data from Delimited 'MTConnect' Data Files and Perform some
Analysis
Mass Transportation Distance Rank Histogram
Sample Size and Power for Association Studies Involving
Mitochondrial DNA Haplogroups
Survival Prediction with Multi-Task Logistic Regression
Multi-Task Prediction using Stacking Algorithms
A Shiny Application for Automatic Measurements of Tree-Ring
Widths on Digital Images
All-Purpose Toolkit for Analyzing Multivariate Time Series (MTS)
and Estimating Multivariate Volatility Models
Multivariate Time Series Data Imputation
Methods in Mahalanobis-Taguchi (MT) System
Generate MUAC and BMI z-Scores and Percentiles for Children and
Adolescents
Data on Freedom of Information Act Requests
Interchange Tools for Multi-Parameter Spatiotemporal Data
Relative Risk Based on the Ratio of Median Unbiased Estimates
Hazard Function Estimation in Survival Analysis
Constructing Hierarchical Voronoi Tessellations and Overlay
Heatmap for Data Analysis
Exploring Data with Tree Data Structures
Generates Muller Plot from Population/Abundance/Frequency
Dynamics Data
Create, Modify and Visualize Multi-Layered Networks
Optimal Allocation in Stratified Sampling
Simultaneous Inference in General Parametric Models
Multivariate Version of the Diebold-Mariano Test
Multiple Equivalence Tests and Simultaneous Confidence Intervals
Optimal Exact Tests for Multiple Binary Endpoints
GEE Solver for Correlated Nominal or Ordinal Multinomial
Responses
Apply Functions to Multiple Multidimensional Arrays or Vectors
Finite Difference Method for Multi-Asset Option Valuation
Evaluating Multinomial Order Restrictions with Bridge Sampling
A Companion to the Multi-CAST Collection
A Generic Convex-Hull-Based Model Selection Method
Build MultiClass Pair-Based Classifiers using TSPs or RF
Flexible Modeling of Multivariate Count Data via the
Multivariate Conway-Maxwell-Poisson Distribution
Multiple Copy Number Variation Detection
Collinearity Detection in a Multiple Linear Regression Model
Add Multiple Colors to your Console & RMarkdown Output
Permutations of Multisets in Cool-Lex Order
A Graph-Based Test for Comparing Multivariate Distributions in
the Multi Sample Framework
Multivariate Analysis and Visualization for Biological Data
Multiscale Fisher's Independence Test for Multivariate
Dependence
Dealing with Several Images of a Same Object Constituted of
Different Zones
Read Fixed Width Format Files Containing Lines of Different Type
Enables Efficient Joining of Data File on Common Fields using
the Unix Utility Join
Estimation and Inference for Multi-Kink Quantile Regression
Transitive Index Numbers for Cross-Sections and Panel Data
Multidimensional Latent Class Item Response Theory Models
Multilevel and Mixed Effects Model Diagnostics and Effect Sizes
Capture-Mark-Recapture Analysis using Multiple Non-Invasive
Marks
Latent Variable Model to Infer Food Intake from Multiple
Biomarkers
Regression analysis of overdispersed correlated count data
Analysis and Mining of Multilayer Social Networks
Bayesian Network Meta-Analysis of Individual and Aggregate Data
Simultaneous Confidence Intervals for Multinomial Proportions
According to the Method by Sison and Glaz
Bayesian Inference for Multinomial Models with Inequality
Constraints
Robust Estimation of Overdispersed Multinomial Regression Models
Generation of Multivariate Ordinal Variates
Infrastructure to Assemble Multi-Panel Figures (from Grobs)
A Package to Test for Multi-Trait Association
Variable Importance Analysis with Population Intervention Models
Test and Detection of Explosive Behaviors for Time Series
Weighted Cox-Regression for Nested Case-Control Data
Algebraic Tools for the Analysis of Multiple Social Networks
Multiplier Data Envelopment Analysis and Cross Efficiency
Calculate Multivariate Richness via UTC and sUTC
Multiply Robust Methods for Missing Data Problems
Calculating and Visualizing ROC and PR Curves Across Multi-Class
Classifications
Bias, Precision, and Power for Multi-Level Random Regressions
Selecting Combinations of Predictors by Leveraging Multiple AUCs
for an Ordered Multilevel Outcome
Causal Mediation Analysis in Multisite Trials
Measures, Tests and Removes Multivariate Skewness
Clustering a Data Set using Multi-SOM Algorithm
MultiSV: an R package for identification of structural
variations in multiple populations based on whole genome
resequencing
Spectral Analysis Tools using the Multitaper Method
Penalized Estimation and Forecasting of Multiple Subject Vector
Autoregressive (multi-VAR) Models
Measuring Multivariate Dependence Using Distance Multivariance
Models Multivariate Cases Using Random Forests
Multiple Imputation for Multivariate Data
Variable Selection in a Multivariate Linear Model
Hypothesis Tests for Association Between Subgroups in Two Data
Views
Estimation of Multivariate Long-Memory Models Parameters
Common Multiple Testing Procedures and Gatekeeping Procedures
Metabolomics Univariate and Multivariate Analysis
Multiplicative Mixed Models using the Template Model Builder
Interpolate Munsell Renotation Data from Hue/Chroma to CIE/RGB
Murphy Diagrams for Forecast Comparisons
Murty's Algorithm for k-Best Assignments
Monetary Unit Sampling and Estimation Methods, Widely Used in
Auditing
Conversion of Nuclear Magnetic Resonance spectrum in audio file
A Graphical User Interface for the MuToss Project
Decipher Mutational Signatures from Somatic Mutational Catalogs
MultiClass Visualizable Classification using Combination of
Projections
An Introduction to Applied Multivariate Analysis with R
Statistical Methods for Analysing Multivariate Abundance Data
Modelling Multivariate Binary Data with Blocks of Specific
One-Factor Distribution
Workspace Organization, Code and Documentation Editing, Package
Prep and Editing, Etc
Multivariate Variance Components Tests for Multilevel Data
Multivariate Generalized Linear Mixed Models for Ranking Sports
Teams
Causal Inference using Multivariate Generalized Propensity Score
Influence Measures and Diagnostic Plots for Multivariate Linear
Models
Compute and Visualize Bivariate Associations
Multivariate Linear Model with Analytic p-Values
Multivariate, Locally Stationary Wavelet Process Estimation
Multivariate Meshes and Histograms in Arbitrary Dimensions
Multivariate and Univariate Meta-Analysis and Meta-Regression
A General Framework of Multivariate Mixed-Effects Selection
Models
Multi-State Adaptive Dynamic Principal Component Analysis for
Multivariate Process Monitoring
Multivariate Comparative Tools for Fitting Evolutionary Models
to Morphometric Data
Nelson-Aalen Estimator of the Cumulative Hazard in Multistate
Models
Bayesian Analysis Framework for MVN (Mixture) Distribution
Fast Multivariate Normal and Student's t Methods
Moving Grid Adjustment in Plant Breeding Field Trials
Powerful Tests for Multivariate Normality
Normality test for multivariate variables
Generate New Multivariate Normal Samples from Permutations
Goodness of Fit Tests for Multivariate Normality
Test for Multivariate Normal Distribution Based on a
Characterization
Multivariate Outlier Detection Based on Robust Methods
Multivariate Peaks-over-Threshold Modelling for Spatial Extreme
Events
Orthant Probability of the Multivariate Normal Distribution
Compute the Coefficient of Determination for Vector or Matrix
Outcomes
Mean and Variance of Truncated Normal Distribution
Generalized Shapiro-Wilk test for multivariate normality
Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for
Phylogenetic Comparative Hypotheses
Bayesian Inference for the Multivariate Skew-t Model
Estimation and Testing for the Multivariate t-Distribution
Causal Inference in Spatiotemporal Event Data
Multichannel Wavelet Deconvolution with Additive Long Memory
Noise
Penalized Moving-Window Lasso Method for Genome-Wide Association
Studies
Two Stage Moving-Window Ridge Method for Prediction and
Estimation
Efficient mixed-level k-circulant supersaturated designs
Feature Selection (Including Multiple Solutions) and Bayesian
Networks
Measurement Model of Derivatives in 'OpenMx'
Stepwise Variable Selection Procedures for Regression Analysis
Integrative immunoinformatics for Mycobacterial diseases in R
platform
Automatic Correlation and Regression Test in a 'data.frame'
Interface to Myrrix. Myrrix is a Complete, Real-Time, Scalable
Clustering and Recommender System, Evolved from Apache Mahout
Regression Models for Monozygotic Twin Data
Port of the 'Scilab' 'n1qn1' Module for Unconstrained BFGS
Optimization
Handling Methods for Naver News Text Crawling
Fast and Scalable Approximate k-Nearest Neighbor Search Methods
using 'N2' Library
Comprehensive Library for Working with Missing (NA) Values in
Vectors
Read Cancer Records in the NAACCR Format
Wraps 'libnabo', a Fast K Nearest Neighbour Library for Low
Dimensions
Nondetects and Data Analysis for Environmental Data
Operations to Ease Data Analyses Specific to Nigeria
High Performance Implementation of the Naive Bayes Algorithm
Nonparametric Additive Instrumental Variable Estimator and
Related IV Methods
Using Needleman-Wunsch to Match Sample Names
Provide namespace managment functions not (yet) present in base
R
Named Entity Recognition in Texts using 'NameTag'
Data Structures, Summaries, and Visualisations for Missing Data
High-Level Data Analysis and Manipulation in 'tidyverse' Style
Tools for Nanoparticle Simulation and Calculation of PDF and
Total Scattering Structure Function
Normalize NanoString miRNA and mRNA Data
Performs Quality Control, Data Normalization, and Batch Effect
Correction for 'NanoString nCounter' Data
Nanosecond-Resolution Time Support for R
A Flexible and Robust Sys.sleep() Replacement
Nonlinear Cointegrating Autoregressive Distributed Lag Model
Subset- And Name-Aware Array Utility Functions
Collection of datasets from the ASA 2006 data expo
NeuroAnatomy Toolbox for Analysis of 3D Image Data
NeuroAnatomy Toolbox ('nat') Extension for Assessing Neuron
Similarity and Clustering
NeuroAnatomy Toolbox ('nat') Extension for Handling Template
Brains
File System Utility Functions for 'NeuroAnatomy Toolbox'
Download House Price Data from Nationwide
Install the 'Natverse' Packages from Scratch
Estimating the Error Variance in a High-Dimensional Linear Model
Navigated Weighting for the Inverse Probability Weighting
Maximum Likelihood method in estimating effective population
size from genetic data
Determining the Best Number of Clusters in a Data Set
Vignette Engine Wrapping Jupyter Notebooks
NBD-Dirichlet Model of Consumer Buying Behavior for Marketing
Research
Design and Monitoring of Clinical Trials with Negative Binomial
Endpoint
Negative Binomial Linear Discriminant Analysis
Functions for Optimal Non-Bipartite Matching
Negative Binomial Models for RNA-Sequencing Data
Network-Based R-Statistics using Mixed Effects Models
Interactive Document for Working with Naive Bayes Classification
NCA Calculations and Population Model Diagnosis
Noncompartmental Analysis for Pharmacokinetic Report
Interface to Unidata netCDF (Version 4 or Earlier) Format Data
Files
Helper Functions for Use with the 'ncdf4' Package
Extract Metadata from 'NetCDF' Files as Data Frames
Miscellaneous Functions for Creating Adaptive Functions and
Scripts
Hierarchical Archimedean Copulas Constructed with Multivariate
Compound Distributions
Unified Algorithm for Non-convex Penalized Estimation for
Generalized Linear Models
Non-Central Squared Copula Models Estimation
Clustering of Omics Data of Multiple Types with a Multilayer
Network Representation
Regularization Paths for SCAD and MCP Penalized Regression
Models
Wicked-Fast Streaming 'JSON' ('ndjson') Reader
Interactive Presentation for Working with Normal Distribution
Efficient Network Enrichment Analysis Test
Calculating Effective Sizes Based on Known Demographic
Parameters of a Population
Negative Binomial and Beta Binomial Bayesian Regression Models
Estimating the Number of Essential Genes in a Genome
Classification, Regression, Clustering with K Nearest Neighbors
R Port of the 'Scilab' Neldermead Module
Querying and Managing 'Neo4J' Databases in 'R'
Access to the Neotoma Paleoecological Database Through R
Network Assisted Algorithm for Epigenetic Studies Using Mean and
Variance Combined Signals
Interface to 'Neptune' Experiment Tracking and Management Tool
Modeling, Imputing and Generating Synthetic Versions of Nested
Categorical Data in the Presence of Impossible Combinations
Inference of Species Associations from Co-Occurrence Data
Inferring Causal Effects on Collective Outcomes under
Interference
Analysis of Diffusion and Contagion Processes on Networks
Network Generator for Combinatorial Graph Problems
Network-Based Genome Wide Association Studies
Estimating network indices, including trophic structure of
foodwebs in R
Tools for Working with Samples of Networks
Build and Run Spatially Explicit Agent-Based Models
Network Meta-Analysis using Frequentist Methods
Dynamic Mixed-Membership Network Regression Model
Origin Estimation for Propagation Processes on Complex Networks
Permutation Testing Network Module Preservation Across Datasets
Actuarial Functions for Non-Life Insurance Modelling
Retrieve Network Statistics Including Available TCP Ports
Network Strengths and Weaknesses Analysis
Graphic Presentation of Complex Genomic and Network Data
Analysis
Network Reverse Engineering with Approximate Bayesian
Computation
Bayesian Package for Network Changepoint Analysis
Statistical Comparison of Two Networks Based on Three Invariance
Measures
Regression Model on Network-Linked Data with Statistical
Inference
Tools for using Network Reporting Estimators
Network Comparison Based on Structural Equivalence and Graphlets
Simulate Bipartite Graphs with Fixed Marginals Through
Sequential Importance Sampling
Methods and Measures for Brain, Cognitive, and Psychometric
Network Analysis
Tools for Identifying Important Nodes in Networks
Recursive Partitioning of Network Models
Visualization and Analysis Tools for Neural Networks
'Neuroconductor' Base Package with Helper Functions for 'nifti'
Objects
Data Structures and Handling for Neuroimaging Data
Functions to Generate fMRI Data Including Activated Data, Noise
Data and Resting State Data
Test for a Neutral Evolutionary Model in Cancer Sequencing Data
An Alternative to the Hodrick-Prescott Filter
Computes Pdf, Cdf, Quantile and Random Numbers, Measures of
Inference for 19 General Families of Distributions
True Discovery Guarantee by the New Focus Level Procedure
Extending the Newman Studentized Range Statistic to
Transcriptomics
Programmatically Collect Normalized News from (Almost) Any
Website
Semisupervised Model for Geographical Document Classification
Statistical Tests to Compare Curves with Recurrent Events
Parallel Analysis and Other Non Graphical Solutions to the
Cattell Scree Test
Numerical Formal Concept Analysis for Systematic Clustering
N-Factor Commodity Pricing Through Term Structure Estimation
Functions to Efficiently Access NFL Play by Play Data
The Standard Distribution Functions for the 3D NFW Profile
Bayesian Variable Selection for SNP Data using Normal-Gamma
A Simple General Purpose N-Gram Tokenizer
Fitting the Centered Autologistic and Sparse Spatial Generalized
Linear Mixed Models for Areal Data
Non-Gaussian State-Space with Exact Marginal Likelihood
Data from the US National Health and Nutrition Examination Study
Tools for working with the National Hydrography Dataset
National Hospital Discharge Survey 2010 Data
A Minimum-Dependency 'R' Interface to the 'NHL' API
Scores for Every Season Since the Founding of the NHL in 1917
Scrapes the 'NHL' API for Statistical Analysis
Non-Homogeneous Markov and Hidden Markov Multistate Models
Bayesian Non-Homogeneous Markov and Mixture Models for Multiple
Time Series
Non-Homogeneous Markov Switching Autoregressive Models
Modelling and Validation of Non Homogeneous Poisson Processes
Breast Cancer Survival and Therapy Benefits
NHS Data Dictionary Toolset for NHS Lookups
Tools for Working with NHS Number Checksums
NHS and Healthcare-Related Data for Education and Training
(Niche) (R)egion and Niche (Over)lap Metrics for
Multidimensional Ecological Niches
Tools for Ecological Niche Evolution Assessment Considering
Uncertainty
Common Analysis with Remote Sensing Data
Nonnegative Integer Solutions of Linear Diophantine Equations
with Applications
MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Distributions for Ecological Models in 'nimble'
Spatial Capture-Recapture (SCR) Methods Using 'nimble'
Sequential Monte Carlo Methods for 'nimble'
Principal Components Analysis using NIPALS or Weighted EMPCA,
with Gram-Schmidt Orthogonalization
National Information Platforms for Nutrition Anthropometric Data
Toolkit
Fast and Accurate Trisomy Prediction in Non-Invasive Prenatal
Testing
Novel Statistical Methods for Studying Near-Infrared
Spectroscopy (NIRS) Time Series Data
Nonlinear least squares examples from NIST
Fundamental Physical Constants and Unit Conversions from NIST
Finds the Best Subset of Points to Sample
Download Image Files from the 'NeuroImaging Tools and Resources
Collaboratory'
Data and Source Code From: Nitrogen Uptake and Allocation
Estimates for Spartina Alterniflora and Distichlis Spicata
Noninferiority Tests with Variable Margins
Snow Water Equivalent Modeling with the 'Delta.snow' Model and
Empirical Regression Models
Download and Analyze New Jersey Car Crash Data
Interface to the National Lakes Assessment
Solve Nonlinear Optimization with Nonlinear Constraints
Models for Non Linear Causality Detection in Time Series
Linear and Nonlinear Mixed Effects Models
Non-linear mixed-effects modelling in nlme using differential
equations
Datasets and utility functions enhancing functionality of nlme
package
Functions for Nonlinear Least Squares Solutions
Nonlinear Network, Clustering, and Variable Selection Based on
DCOL
Estimators of Non-Linear Cross-Validated Risks Optimized for
Small Samples
Nonlinear Regression for Agricultural Applications
Higher Order Inference for Nonlinear Heteroscedastic Models
Non-Linear Relative Risk Estimation and Plotting
Setup, Run and Analyze 'NetLogo' Model Simulations from 'R' via
'XML'
Robust Non-Linear Regression using AIC Scores
Fitting Structural Equation Mixture Models
Convenient Functions for Non-Linear Regression
Non-Linear Shrinkage Estimation of Population Eigenvalues and
Covariance Matrices
Nonlinear regression in predictive microbiology
Fitting Nonlinear Models with Scale Mixture of Skew-Normal
Distributions
An R Package for Fitting Separable Nonlinear Models
Non-Linear Model Fitting of Time Distribution of Biological
Phenomena
Utilities and Kinship Information for Research with the NLSY
A Nondecimated Lifting Transform for Signal Denoising
Wald Test of Nonlinear Restrictions and Nonlinear CI
Network Meta-Analysis of Multiple Diagnostic Tests
Network Meta-Analysis using Integrated Nested Laplace
Approximations
Detecting Outliers in Network Meta-Analysis
The Plate Plot for Network Meta-Analysis Results
Thresholds and Invariant Intervals for Network Meta-Analysis
Algorithms and Framework for Nonnegative Matrix Factorization
(NMF)
Normalized Mutual Information of Community Structure in Network
Miscellaneous Functions Used at 'Numeract LLC'
Goodness of Fit Checks for Binomial N-Mixture Models
Numerical Methods and Optimization in Finance
Understanding Nonlinear Mixed Effects Modeling for Population
Pharmacokinetics
Datasets and Functions to Benchmark Neural Network Packages
Feed-Forward Neural Networks and Multinomial Log-Linear Models
Prediction Intervals of Multi-Layer Neural Networks
Time Series Forecasting with Neural Networks
Non-Negative Garrote Estimation with Penalized Initial
Estimators
k-Nearest Neighbor Join for Spatial Data
Non-Negative Lasso and Elastic Net Penalized Generalized Linear
Models
The Lawson-Hanson algorithm for non-negative least squares
(NNLS)
Nearest Neighbor Based Multiple Imputation for Survival Data
with Missing Covariates
The Number Needed to Treat (NNT) for Survival Endpoint
Calculate Design Parameters for Biomarker Validation Studies
Supervised Data Transformation by Means of Neural Network Hidden
Layer
Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI'
Interface)
Algorithmic Framework for Representational Learning on Graphs
Node Harvest for Regression and Classification
Compares the Distribution of Sister Clades Through a Phylogeny
Implementation of the Natural and Orthogonal InterAction (NOIA)
model
Estimation of Intrinsic and Extrinsic Noise from Single-Cell
Data
Label Noise Filters for Data Preprocessing in Classification
Cross-Entropy Optimisation of Noisy Functions
Noise Quantification in High Throughput Sequencing Output
Noisy Stochastic Block Mode: Graph Inference by Multiple Testing
Hierarchical Cluster Analysis of Nominal Data
Biplot representations of categorical data
Calculate Total Points and Probabilities for Nomogram
Noncompartmental Analysis for Pharmacokinetic Data
Causal Inference in the Presence of Treatment Noncompliance
Under the Binary Instrumental Variable Model
Bayesian Analysis of Randomized Experiments with Non-Compliance
Weighted Average Ensemble without Training Labels
Invariant Causal Prediction for Nonlinear Models
Loading NONMEM Output Files with Functions for Visual Predictive
Checks (VPC) and Goodness of Fit (GOF) Plots
Create and Evaluate NONMEM Models in a Project Context
Multivariate Lomax (Pareto Type II) and Its Related
Distributions
A Collection of Nonparametric Hypothesis Tests
Nonparametric Methods for Measuring Efficiency and Productivity
Metagenome Coverage Estimation and Projections for 'Nonpareil'
Model Checking and Variable Selection in Nonparametric
Regression
Detecting Isotope, Adduct and Homologue Relations in LC-MS Data
Quantized simulation data of isotope pattern centroids
Normal aka Gaussian (1-d) Mixture Models (S3 Classes and
Methods)
Arctic Ice Studio's Nord and Group of Seven Inspired Colour
Palettes for 'ggplot2'
Dataset for Climate Analysis with Data from the Nordic Region
Analysis of multivariate normal datasets with missing values
Routines for Exponential Power Distribution
Normalisation of Multiple Variables in Large-Scale Datasets
Normalize Gene Expression Data using Evaluated Methods
Evaluates complex erf, erfc, Faddeeva, and density of sum of
Gaussian and Student's t
Neyman Smooth Tests of Normality for the Errors of ARMA Models
Assessing Normality of Stationary Process
Compute Node Overlap and Segregation in Ecological Networks
A Forward Agent-Based Transmission Chain Simulator
Send Alerts to your Cellphone and Phillips Hue Lights
Send push notifications to your smartphone via pushover.net
(ACCOUNT REQUIRED!)
Predicting Economic Variables using Dynamic Factor Models
Nonparametric Kernel Smoothing Methods for Mixed Data Types
Non-Parametric Measures of Actigraphy Data
Multiple Comparisons and Simultaneous Confidence Intervals
Nonparametric Analysis of Longitudinal Data in Factorial
Experiments
Nonparametric Analysis of Multivariate Data in Factorial Designs
Nonparametric Tests for Main Effects, Simple Effects and
Interaction Effect in a Factorial Design with Censored Data
Non-Parametric Bayesian Multiple Imputation for Categorical Data
Nonparametric Combination of Hypothesis Tests
Nonparametric Methods for Cognitive Diagnosis
Non Parametric Test for Detecting Changes in the Copula
Some Nonparametric CUSUM Tests for Change-Point Detection in
Possibly Multivariate Observations
Nonparametric Estimation in Mixture Cure Models
Exact Nonparametric Hypothesis Tests for the Mean, Variance and
Stochastic Inequality
Bayesian Nonparametrics for Automatic Gating of Flow-Cytometry
Data
Planning and Analysing Survival Studies under Non-Proportional
Hazards
Sample Size Calculation for the Proportional Hazards Mixture
Cure Model
Nonparametric Interaction Tests for Factorial Designs with
Repeated Measures
Plotting linkage and association results
Nonparametric Models for Longitudinal Data
Type-Specific Failure Rate and Hazard Rate on Competing Risks
Data
Two-Groups Mixture Model with Covariates
Non-Parametric Maximum Likelihood Estimate for Cohort Samplings
Nonparametric Maximum Likelihood Estimation for Random Effect
Models
Nonparametric Comparison of Multivariate Samples
Nonparametric Tests for Equality of Location Against Ordered
Alternatives
Normalized Power Prior Bayesian Analysis
Nonparametric Partially-Balanced Incomplete Block Design
Analysis
Vegetation Phenological Cycle and Anomaly Detection using Remote
Sensing Data
Nonparametric Regression via Smoothing Splines
Nonparametric Estimation of the Derivatives of a Regression
Function
Nonparametric Estimation of Regression Models with
Factor-by-Curve Interactions
Nonparametric Robust Estimation and Inference Methods using
Local Polynomial Regression and Kernel Density Estimation
Neyman-Pearson (NP) Classification Algorithms and NP Receiver
Operating Characteristic (NP-ROC) Curves
Kernel-Based Nonparametric ROC Regression Modelling
Nonparametric Rotations for Sphere-Sphere Regression
Convenience Functions and Tests for Working With the Net
Promoter Score (NPS)
Nonparametric and Stochastic Efficiency and Productivity
Analysis
Nonparametric Smoothing for contaminated data using
Simulation-Extrapolation
Validate Instrumental Variables using NPS
Generalization of Hewitt's Seasonality Test
Sample Size and Power Calculation for Common Non-Parametric
Tests in Survival Analysis
Nonparametric Bootstrap and Permutation Tests
Metrics for Multiple Testing with Correlated Outcomes
NRI for Risk Prediction Models with Time to Event and Binary
Response Data
Methods for Fitting and Simulating Non-Stationary ARFIMA Models
Simulation and Estimation of the Neyman-Scott Type Spatial
Cluster Models
Numerical Standard Errors Computation in R
Fetch Data from 'National Stock Exchange (India)'
A Clean API for Lazy and Non-Standard Evaluation
Elitist Non-dominated Sorting Genetic Algorithm based on R
An Implementation of Non-Dominated Sorting Genetic Algorithm III
for Feature Selection
Functions and Datasets to Accompany Hollander, Wolfe, and
Chicken - Nonparametric Statistical Methods, Third Edition
National Statistical Office of Mongolia's Open Data API Handler
Nonparametric and Semiparametric Mixture Estimation
Interface to National Sleep Research Resource
NUtrient Cycling and COMpetition Model Undisturbed Open Bog
Ecosystems in a Temperate to Sub-Boreal Climate
Validate, Compare and Format Identification Numbers from Brazil
Statistical Framework to Define Subgroups in Complex Datasets
Create a Kaplan-Meier Plot with Numbers at Risk
Numeric Routines for Optically Stimulated Luminescence Dating
Food Composition Information and Dietary Assessment
Structure Learning with Copula Graphical Model
Nonparametric Varying Coefficient Spike-and-Slab Lasso
The n-vector Approach to Geographical Position Calculations
using an Ellipsoidal Model of Earth
Create n-Dimensional, Quasi-Proportional Venn Diagrams
R functions for NetWorkSpaces and Sleigh
Accessing Data Stored in 'LaBB-CAT' Instances
Driving Offences in New Zealand Between 2009 and 2016
Reconstruction of Transmission Chains from Surveillance Data
General Purpose 'Oai-PMH' Services Client
Harvest Metadata Using OAI-PMH Version 2.0
Computation of the Orbit-Aware Quad Census
Outright Tool for the Analysis of Spatial Inequalities and
Segregation
Objective Bayesian Analysis for Spatial Regression Models
'RStudio' Addin for Removing Objects from the Global Environment
Based on Patterns and Object Type
Oblique Random Forests from Recursive Linear Model Splits
Oblique Random Forests for Right-Censored Time-to-Event Data
Estimate the Population Size for the Mb Capture-Recapture Model
An R package to assess agreement between observers
Collect and Process Physical Activity Direct Observation Data
Objective Bayesian Model Discrimination in Follow-Up Designs
Sensitivity analysis for Observational studies
Optimal Classification Roll Call Analysis Software
Querying and Managing Large Biodiversity Occurrence Datasets
High-Dimensional Multiscale Online Changepoint Detection
A Plotting Toolbox for 2D Oceanographic Data
Visualisation of Oceanographic Data and Model Output
Oceanographic Data Sets for 'oce' Package
Order Constrained Solutions in k-Means Clustering
Gaussian Model-Based Clustering with Outliers
Regression for Rank-Indexed Compositional Data
Interface to Open Collaboration Services (OCS) REST API
Manipulate and Map Origin-Destination Data
Open Document Databases (.odb) Management
Connect to ODBC Compatible Databases (using the DBI Interface)
Odds Ratios, Contingency Table, and Model Significance from a
Generalized Linear Model Object
Odds Ratio Calculation for GAM(M)s & GLM(M)s
Sensitivity Analysis of Ordinary Differential Equations
Convert 'ODK' or 'XLSForm' to 'SPSS' Data Frame
Optimal Design and Statistical Power of Multilevel Randomized
Trials
Statistical Methods for Outcome-Dependent Sampling Designs
Orthogonalizing EM: Penalized Regression for Big Tall Data
Enhanced 'R Markdown' Format for 'Word' and 'PowerPoint'
Manipulation of Microsoft Word and PowerPoint Documents
Detect Multiple Change Points from Time Series
A Meta-Analysis Approach with Filtering for Identifying
Gene-Level Gene-Environment Interactions with Genetic
Association Data
Estimation of Ordered Generalized Linear Models
Modeling of Ordinal Random Variables via Softmax Regression
OGA+HDIC+Trim and High-Dimensional Linear Regression Models
Ordered Homogeneity Pursuit Lasso for Group Variable Selection
Crosstab and Statistical Tests for OII MSc Stats Course
Multivariate Methods Based on the Oja Median and Related
Concepts
Crawler and Data Scraper for Open Journal System ('OJS')
OkCupid Profile Data for Introductory Statistics and Data
Science Courses
Retrieve Oklahoma Mesonet climatological data
A k-Nearest Neighbours Ensemble via Optimal Model Selection for
Regression
Odd Log-Logistic Generalized Gamma Probability Distribution
Tools for Building OLS Regression Models
filter the molecular descriptors for QSAR
Data Integration with Two-Way Orthogonal Partial Least Squares
Cell-Type-Specific Association Testing in Bulk Omics Experiments
Univariate Bootstrapping and Other Things
A Modified Fisher’s Method to Test Overall Gene-Level Effect
Model and Solve Mixed Integer Linear Programs
A Solver for 'ompr' that Uses the R Optimization Infrastructure
('ROI')
A Metabolomics Analysis Tool for Intuitive Figures and
Convenient Metadata Collection
Test of Between-Group Differences in the Onset of Senescence
Bayesian Logistic Regression for Oncology Dose-Escalation Trials
Maximum likelihood tree models for oncogenesis
Planning, Conducting, and Analysing Single-Arm Phase II Studies
Maximum Homogeneity Clustering for Univariate Data
Construction of Genetic Maps in Experimental Crosses: Full-Sib,
RILs, F2 and Backcrosses
One Rule Machine Learning Classification Algorithm with
Enhancements
Observers Needed to Evaluate Subjective Tests
Efficient Authenticated Interaction with the O*NET API
One-Way Tests in Independent Groups Designs
Online Bayesian Methods for Change Point Analysis
Online Change Point Detection in High-Dimensional Covariance
Structure
Forecast Modelling for Online Applications
Online Fitting of Time-Adaptive Lasso Vector Auto Regression
Functions for Visualising Sets of Ontological Terms
Functions for Calculating Ontological Similarities
Create Validation Tests for Automated Content Analysis
Class Unions, Matrix Operations, and Color Schemes for OOMPA
'Opal' Data Repository Client and 'DataSHIELD' Utils
Opasnet Modelling Environment Utility Functions
Tools for the Analysis of Air Pollution Data
Bindings to 'OpenCV' Computer Vision Library
Access the City of Toronto Open Data Portal
EBGM Disproportionality Scores for Adverse Event Data Mining
Data Sets and Supplemental Functions from 'OpenIntro' Textbooks
and Labs
Quantitative Analysis and Visualization of LUCC
A 'Prometheus' Client for R Using the 'OpenMetrics' Format
Open Machine Learning and Open Data Platform
Control Number of OpenMP Threads Dynamically
Apache OpenNLP Jars and Basic English Language Models
Interpretive Clustering for Repertory Grids
An R Client-Side Interface to the 'OpenSky' API
Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
An Open Source Implementation of the 'ArcGIS' Toolbox 'STARS'
An Open-Source Loader for Bruker's timsTOF Data Files
Tools for Creating and Analysing Air Trajectory Data
Utilities for Working with R's Operators
Routing Distribution, Broadcasts, Transmissions and Receptions
in an Opportunistic Network
Optimal Designs for the 5-Parameter Logistic Model
Optimal Combinations of Diagnostic Tests Based on AUC
'surv' Object Confidence Bands Optimized by Area
Optimal Block Designs for Two-Colour cDNA Microarray Experiments
Estimation of Optimal Number of Biomarkers for Two-Group
Microarray Based Classifications at a Given Error Tolerance
Level for Various Classification Rules
Circular, Periodic, or Framed Data Clustering: Fast, Optimal,
and Reproducible
Determine Optimal Clustering Algorithm and Number of Clusters
Optimal Designs for Estimating the Slope Divided by the
Intercept
Tools to Support Optimization Possibly with Bounds and Masks
Near-Optimal and Balanced Group-Sequential Designs for Clinical
Trials with Continuous Outcomes
Estimation of value and hedging strategy of call and put
options
Likelihood Based Optimal Partitioning and Indicator Species
Analysis
Computing Optimal Cutpoints in Diagnostic Tests
A Toolbox for Computing Efficient Designs of Experiments
Bayesian Methods for Optimal Threshold Estimation
Graphical and Numerical Checks for Mode-Finding Routines
Flexible Optimization of Complex Loss Functions with State and
Parameter Space Constraints
Optimos Prime Helps Calculate Autoecological Data for Biological
Species
Parallel Version of the L-BFGS-B Optimization Method
A Replacement and Extension of the 'optim' Function
R Port of the 'Scilab' Optimsimplex Module
Model Based Diagnostics for Multivariate Cluster Analysis
Expanded Replacement and Extension of the 'optim' Function
Optimal Two and Three Stage Designs for Single-Arm and Two-Arm
Randomized Controlled Trials with a Long-Term Binary Endpoint
Option Pricing with Efficient Simulation Algorithms
Utilizes the Black-Scholes Option Pricing Model to Perform
Strategic Option Analysis and Plot Option Strategies
Optimum Contribution Selection and Population Genetics
Linear, Quadratic, and Rational Optimization
Estimating the Optimal Number of Migration Edges from 'Treemix'
Optimal Partitioning of Similarity Relations
Optimization Toolbox for Solving Linear Systems
Optimal Row-Column Designs for Two-Colour cDNA Microarray
Experiments
Optimal Level of Significance for Regression and Other
Statistical Tests
Targeted Stable Balancing Weights Using Optimization
OPUS Miner Algorithm for Filtered Top-k Association Discovery
Statistical Methods for Modelling Operational Risk
Convenient Tools for Working with Oracle Databases
Computation of Graphlet Orbit Counts in Sparse Graphs
Several confidence intervals for the odds ratio
Subspace Clustering Based on Arbitrarily Oriented Projected
Cluster Generation
Order Restricted Clustering for Microarray Experiments
Estimate Procedure in Case of First Order Autocorrelation
Likelihood-Based Continual Reassessment Method (CRM) Dose
Finding Designs
Separating Location and Dispersion in Ordinal Regression Models
Identification of Differentially Expressed Genes
Estimate parent distributions with data of several order
statistics
Test, Check, Verify, Investigate the Monotonic Properties of
Vectors
Sampling from Order Statistics of New Families of Distributions
Efficiently Generates Random Order Statistic Variables
Least Squares, Logistic, and Cox-Regression with Ordered
Predictors
Ordinal Data Clustering, Co-Clustering and Classification
Ordinal Regression Analysis for Continuous Scales
Ordinal Forests: Prediction and Variable Ranking with Ordinal
Target Variables
Ordinal Regression for High-Dimensional Data
Co-Clustering of Ordinal Data via Latent Continuous Random
Variables
Biplot representations of ordinal variables
Analysis of Repeatability and Reproducibility Studies with
Ordinal Measurements
Compute least squares estimates of one bounded or two ordered
isotonic regression curves
Concurrent Generation of Ordinal and Normal Data with Given
Correlation Matrix and Marginal Distributions
Selection and/or Smoothing of Ordinal Predictors
An R Interface to the Onigmo Regular Expression Library
Connector to the Objective Revision Evaluation Service (ORES)
Analyse Text Files Created by Emacs' Org mode
Order-restricted Information Criterion-based Clustering
Algorithm
Fast Spatial Ancestry via Flexible Allele Frequency Surfaces
Operations Research LOCational Analysis Models
Spanish version of orloca package. Modelos de localizacion en
investigacion operativa
Advanced Plotting of Ordinal Regression Models
Rigorous - 'NIfTI' + 'ANALYZE' + 'AFNI' : Input / Output
Order Restricted Assessment Of Microarray Titration Experiments
Southern Ocean Frontal Distributions (Orsi)
Converting Odds Ratio to Relative Risk in Cohort Studies with
Partial Data Information
Semi-Parametric Dimension Reduction Models Using Orthogonality
Constrained Optimization
Dynamic Panel Models with Orthogonal Reparameterization of Fixed
Effects
Collection of functions for orthogonal and orthonormal
polynomials
Generation of Customizable, Discretized Time Series of
Oscillating Species
Orthogonal Signal Deconvolution for Spectra Deconvolution in
GC-MS and GCxGC-MS Data
Design, Planning and Analysis of Observational Studies
Finds an Optimal System of Distinct Representatives
Interface to the 'Open Science Framework' ('OSF')
Raw System Credential Store Access from R
Import 'OpenStreetMap' Data as Simple Features or Spatial
Objects
Object Oriented Simulator of Marine Ecosystems
Add a Scale Bar to 'OpenStreetMap' Plots
Orthogonal Sparse Non-Negative Matrix Tri-Factorization
Quadratic Programming Solver using the 'OSQP' Library
Interface Between R and the OpenStreetMap-Based Routing Service
OSRM
Mean Partition, Uncertainty Assessment, Cluster Validation and
Visualization Selection for Cluster Analysis
Optimal Trees Ensembles for Regression, Classification and Class
Membership Probability Estimation
One Time Password Generation and Verification
An R Wrapper for the 'OpenTripPlanner' REST API
Variable Selection for Optimal Treatment Decision
Summarizing OTU Table Regarding the Composition, Abundance and
Beta Diversity of Abundant and Rare Biospheres
North Temperate Lakes - Microbial Observatory 16S Time Series
Data and Functions
Ornstein-Uhlenbeck Models for Phylogenetic Comparative
Hypotheses
Bayesian Reconstruction of Disease Outbreaks by Combining
Epidemiologic and Genomic Data
Multivariate Outlier Detection and Replacement
Outlier Detection using quantile regression for Censored Data
Outlier Detection for Multi-replicated High-throughput Data
Explainable Outlier Detection Through Decision Tree Conditioning
Functions for Solving Multiple-criteria Decision-making Problems
Install and Run Programs, Outside of R, Inside of R
Analysis of Evolutionary Rates in an OU Framework
Overdispersion in Count Data Multiple Regression Analysis
Estimates of Coefficient of Overlapping for Animal Activity
Patterns
Estimation of Overlapping in Empirical Distributions
Test Overlapping of Polygons Against Random Rotation
Easily Extracting Information About Your Data
Optimal Weight Exchange Algorithm for Optimal Designs for Three
Models
Interface to 'OxCal' Radiocarbon Calibration
An Interface to the Oxford COVID-19 Government Response Tracker
API
An R API to the Oxford COVID-19 Database
Processing of Oxy-Bisulfite Microarray Data
Scans R Projects for Vulnerable Third Party Dependencies
Plot the Australian Coastline and States
Performance Attribution for Equity Portfolios
Pabon Lasso Graphs and Comparing Situations of a Unit in Two
Different Times
Partition-Assisted Clustering and Multiple Alignments of
Networks
PAC-Bayesian Estimation and Prediction in Sparse Additive
Models
Comfortable Search for R Packages on CRAN, Either Directly from
the R Console or with an R Studio Add-in
Computation and Visualization of Package Download Counts and
Percentiles
Track R Package Downloads from RStudio's CRAN Mirror
Decision Analysis Modelling Package with Parameters Estimation
Ability from Individual Patient Level Data
An Opinionated Framework for Using 'JavaScript'
A few Useful Functions for Statisticians
Multi-Block Partial Least Squares Discriminant Analysis
A Dependency Management System for Projects and their R Package
Dependencies
Penalized and Constrained Lasso Optimization
Procrustes Application to Cophylogenetic Analysis
Testing for Partial Copulas and the Simplifying Assumption in
Vine Copulas
Quickly Get Datetime Data Ready for Analysis
Attributable Fraction Function for Censored Survival Data
Book Companion for Processing and Analyzing Financial Data with
R
Generative Mechanism Estimation in Temporal Complex Networks
Read, Manipulate and Visualize 'Pairwise mApping Format' Data
Pairwise Association of Functional Annotations
Paginate the HTML Output of R Markdown with CSS for Print
An API Client for Wikimedia Traffic Data
The package can identify the dysregulated KEGG pathways based on
global influence from the internal effect of pathways and
crosstalk between pathways
Pathway Analysis Methods for Genomewide Association Data
Creation and Manipulation of Color Palettes
Confidence intervals for the ratio of locations and for the
ratio of scales of two paired samples
Rasch Model Parameters by Pairwise Algorithm
Confidence Intervals for Two Sample Comparisons
Another Approach to Package Installation
Multiple Indicator Cluster Survey (MICS) 2014 Child
Questionnaire Data for Punjab, Pakistan
Multiple Indicator Cluster Survey (MICS) 2014 Household
Questionnaire Data for Punjab, Pakistan
Multiple Indicator Cluster Survey (MICS) 2014 Household Listing
Questionnaire Data for Punjab, Pakistan
Multiple Indicator Cluster Survey (MICS) 2014 Women
Questionnaire Data for Punjab, Pakistan
Multiple Indicator Cluster Survey (MICS) 2017-18 Data for
Punjab, Pakistan
Multiple Indicator Cluster Survey (MICS) 2017-18 Birth History
of Children Questionnaire Data for Punjab, Pakistan
Multiple Indicator Cluster Survey (MICS) 2017-18 Children Age
5-17 Questionnaire Data for Punjab, Pakistan
Multiple Indicator Cluster Survey (MICS) 2017-18 Household
Questionnaire Data for Punjab, Pakistan
Multiple Indicator Cluster Survey (MICS) 2017-18 Maternal
Mortality Questionnaire Data for Punjab, Pakistan
Multiple Indicator Cluster Survey (MICS) 2017-18 Men
Questionnaire Data for Punjab, Pakistan
Significance Tests for Palaeoenvironmental Reconstructions
Download and Process Data from the Paleobiology Database
Analysis of Charcoal Records from the Global Charcoal Database
Geometric Morphometric Tools for Paleobiology
Paleontological and Phylogenetic Analyses of Evolution
Comprehensive Collection of Color Palettes
GPL Palettes Copied from 'Gimp' and 'Inkscape'
Fitting Point Process Models via the Palm Likelihood
Palmer Archipelago (Antarctica) Penguin Data
Partially Additive (Generalized) Linear Model Trees
Color Palettes, Colormaps, and Tools to Evaluate Them
Rank Aggregation with Partition Mallows Model
Principal Axes Methods for Contingency Tables with Partition
Structures on Rows and Columns
Prediction and Accuracy Measures for Nonlinear Models and for
Right-Censored Time-to-Event Data
Power Analysis for Random Effects in Mixed Models
Miscellaneous Functions for Passive Acoustic Analysis
Piece-Wise Exponential Additive Mixed Modeling Tools for
Survival Analysis
Implementation of the Panel Data Approach Method for Program
Evaluation
Pam: Prediction Analysis for Microarrays
Multiple Imputation for Multivariate Panel or Clustered Data
Benchmarking and Rescaling R2 using Noise Percentile Analysis
Preferential Attachment Based Common Neighbor Distribution
Derived Functional Associations
Long Term Prediction for Epidemic and Pandemic Data
Estimation of Linear AR(1) Panel Data Models with
Cross-Sectional Heteroskedasticity and/or Correlation
Random Effects and/or Sample Selection Models for Panel Count
Data
Matching Methods for Causal Inference with Time-Series
Cross-Sectional Data
Regression Models and Utilities for Repeated Measures and Panel
Data
A Semi-Parametric Test for Specifying Functional Form
View Medical Research Images using the Papaya JavaScript Library
A Toolbox for Writing Pretty Papers and Reports
Distance Recordings from a Paper Plane Folding/Flying Experiment
Define and Work with Parameter Spaces for Complex Algorithms
Parallel Distance Matrix Computation using Multiple Threads
Parallel Digital Soil Mapping using Machine Learning
Support for Parallel Computation, Logging, and Function
Automation
Unified Interface to Parallelization Back-Ends
A Parallel-Voting Algorithm for many Classifiers
Paralellised Versions of Constraint Based Causal Discovery
Algorithms
'Htmlwidget' for a Parallel Coordinates Plot
A Parallel-Voting Version of the Support-Vector-Machine
Algorithm
A Shiny GUI for some Parameter Estimation Examples
Helpers for Parameters in Black-Box Optimization, Tuning and
Machine Learning
Numeric and Visual Comparisons of Heterogeneity in Parametric
Models
Parametric Linkage and Other Pedigree Analysis in R
Run a Function Iteratively While Varying Parameters
Horn's Test of Principal Components/Factors
Interactive Parallel Categories Diagrams for 'easyalluvial'
'Htmlwidget' for 'd3.js' Parallel Coordinates Chart
Parallel implementation of the "segment" function of package
"DNAcopy"
The Pareto, Piecewise Pareto and Generalized Pareto Distribution
Computing, Fitting and Validating the PPS Distribution
Portfolio Allocation and Risk Management Applications
Parallel Mutual Information Estimation for Gene Network
Reconstruction
Recognize and Parse Dates in Various Formats, Including All ISO
8601 Formats
A Common API to Modeling and Analysis Functions
Estimation and Diagnostics for Partially Linear Censored
Regression Models Based on Heavy-Tailed Distributions
Partitioning Using Deletion, Substitution, and Addition Moves
A Graph Based Particle Simulator Based on D3-Force
Agglomerative Partitioning Framework for Dimension Reduction
Methods for Calculating the Loreau & Hector 2001 BEF Partition
Implements Measures for the Comparison of Two Partitions
Compute a distance metric between two partitions of a set
Periodic Autoregressive Time Series Models
Summarize Daily Physical Activity from 'SenseWear' Accelerometer
Data
Power and Sample Size for Linear Mixed Effect Models
Calculate Power and Sample Size for Two Sample Mean Tests
Assessing the Partial Association Between Ordinal Variables
Travel Smoothly Between Country Name and Code Formats
Package for Analysis of Space-Time Ecological Series
Phylogenetic Assembly with Soft Taxonomic Inferences
Probability and Statistics with R, Second Edition
Package to Patch '.dvi' or '.synctex' Files
Communication Between Editor and Viewer for Literate Programs
Basic Functions for Drawing Path Diagrams
Enrichment Analysis Utilizing Active Subnetworks
Compute Deviation and Correspondence Between Spatial Paths
Path Component Fit Indices for Latent Structural Equation Models
An Imputation Approach to Estimating Path-Specific Causal
Effects
Backwards Variable Selection for Paths using M Plus
Feature Extraction from Female Brown Anole Lizard Dorsal
Patterns
Class-Focused Pattern Metric Comparisons using Simulation
Quantification of Color Pattern Variation
Versatile Pie Charts, Ring Charts, Bar Charts and Box Plots
using Patterns, Colors and Images
Deciphering Biological Networks with Patterned Heterogeneous
Measurements
Bayesian Experimental Design for Systems Biology
Perceptual Analysis, Visualization and Organization of Spectral
Colour Data
Amazon Web Services Software Development Kit
Amazon Web Services Application Integration Services
Amazon Web Services Cost Management Services
Amazon Web Services Customer Engagement Services
Amazon Web Services Machine Learning Services
Amazon Web Services Management & Governance Services
Amazon Web Services Networking & Content Delivery Services
Amazon Web Services Security, Identity, & Compliance Services
Adding Progress Bar to '*apply' Functions
Pedigree/Family-Based Genetic Association Tests Analysis and
Power
Protracted Birth-Death Model of Diversification
Programming with Big Data -- Base Wrappers for Distributed
Matrices
Programming with Big Data -- Interface to MPI
Programming with Big Data -- MPI Profiling Tools
Programming with Big Data -- Remote Procedure Call
Programming with Big Data -- Scalable Linear Algebra Packages
Programming with Big Data -- Interface to 'ZeroMQ'
Partially Balanced Incomplete Block Designs
A Set of Datasets Used in My Classes or in the Book 'Modele
Liniowe i Mieszane w R, Wraz z Przykladami w Analizie Danych'
Estimating the Probability of Being in Response and Related
Outcomes
Access Data and Metadata from 'Microsoft' 'Power BI' Documents
Parametric Bootstrap, Kenward-Roger and Satterthwaite Based
Methods for Test in Mixed Models
Tracking the Progress of Mc*pply with Progress Bar
Permutation Based Non-Parametric Analysis of CRISPR Screen Data
The Probability of Being in Response Function and Its Variance
Estimates
Mapping Fisheries Data and Spatial Analysis Tools
GUI Tools Made Easy: Interact with Models and Explore Data
Probabilities for Bivariate Normal Distribution
Segmenting Multiple Time Series by Contemporaneous Linear
Transformation
Create 2D Principal Component Plots with Bootstrapping
Fast Principal Component Analysis for Outlier Detection
Tools for Principal Component Analysis-Based Data Structure
Comparisons
Calibration of P-Values for Point Null Hypothesis Testing
Methods for Graphical Models and Causal Inference
Match Cases to Controls Based on Genotype Principal Components
Finding the Number of Significant Principal Components
Dynamic Principal Components for Periodically Correlated
Functional Time Series
Proximity Catch Digraphs and Their Applications
Semiparametric regression analysis of panel count data using
monotone splines
Model Fitting to Progressively Censored Mixture Data
Principal Component of Explained Variance
Stan Models for the Paired Comparison Factor Model
Computation of Ancestry Scores with Mixed Families and Unrelated
Individuals
Preconditioned Conjugate Gradient Algorithm for solving Ax=b
Reconstruction of Causal Networks for Data with Random Genetic
Effects
Piecewise Constant Hazards Models for Censored and Truncated
Data
Bayesian Network Learning with the PCHC and Related Algorithms
Implementation of POSIXct Work-Alike for 365 and 360 Day
Calendars
IRT Models for Polytomous and Continuous Item Responses
Approximate Bayesian Computations for Phylogenetic Comparative
Methods
Simulation and Likelihood Calculation of Phylogenetic
Comparative Models
Fast Likelihood Calculation for Phylogenetic Comparative Models
Model Response Styles in Partial Credit Models
Estimation of an Ordinary Differential Equation Model by
Parameter Cascade Method
Principal Coordinates of Phylogenetic Structure
Analyzing Real-Time Quantitative PCR Data
Calculate the probability of correct selection (PCS)
Panel-Corrected Standard Error Estimation in R
Parallel Constraint Satisfaction Networks in R
Convenient Tool for Solving the Prize-Collecting Steiner Tree
Problem
Periodically Correlated and Periodically Integrated Time Series
Extract Sentences and Tables from PDFs with User Interface
Cluster Analysis via Nonparametric Density Estimation
Fetch Economic and Financial Time Series Data from Public
Sources
Read Portable Document Format (PDF) Files
Text Extraction, Rendering and Converting of PDF Documents
Phenotypic Index Measures for Oak Decline Severity
Proximal/Distal Modeling Framework for Pavlovian Conditioning
Phenomena
Pattern Discovery in PDB Structures of Metalloproteins
PDQ Functions via Gram Charlier, Edgeworth, and Cornish Fisher
Approximations
Threshold Model and Unit Root Tests in Cross-Section and Time
Series Data
Positive definite sparse covariance estimators
An Analysis Toolbox for Hermitian Positive Definite Matrices
Moment Condition Based Estimation of Linear Dynamic Panel Data
Models
Various Tools and Data for Quantitative Peace Science
Pareto Enrichment Analysis for Combining Heterogeneous Datasets
Two and Three Dimensional Kolmogorov-Smirnov Two-Sample Tests
Periodogram Peaks in Correlated Time Series
Compute the Annotation Error of Peak Calls
Peak Picking Methods Inspired by Biological Data
Monitor the Total and Peak RAM Used by an Expression or Function
Dynamic Programming Algorithm for Peak Detection in ChIP-Seq
Data
Joint Peak Detection in Several ChIP-Seq Samples
Optimal Segmentation Subject to Up-Down Constraints
Maximum Likelihood Inference for the Pearson VII Distribution
with Shape Parameter 3/2
Independent component analysis using score functions from the
Pearson system
Prediction Error Curves for Risk Prediction Models in Survival
Analysis
An implementation for association analysis with CNV data
Versatile Functions for Working with Pedigrees
Mutation Models for Pedigree Likelihood Computations
Public Economic Data and Quantitative Analysis
Pedigree, Genetic Merit and Phenotype Simulation
Creating and Working with Pedigrees and Marker Data
Luck-Corrected Peer Performance Analysis in R
Population and Evolutionary Genetics Analysis System
Population Proportion Estimation using Group Testing
Geophysical Inverse Theory and Optimization
Probabilistic Sex Estimate using Logistic Regression, Based on
VISual Traits of the Human Os Coxae
A Penalized EM algorithm incorporating missing-data mechanism
Portable Emissions (and Other Mobile) Measurement System
Utilities
L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation
in GLMs and in the Cox Model
Penalized Classification using Fisher's Linear Discriminant
Feature Selection SVM using Penalty Functions
Estimating Non-Simplified Vine Copulas Using Penalized Splines
Density Estimation with a Penalized Mixture Approach
Flexible Pair-Copula Estimation in D-Vines using Bivariate
Penalized Splines
Semiparametric Regression Analysis of Interval-Censored Data
using Penalized Splines
Estimating Regularized Multi-state Models Using L1 Penalties
Variable Selection in PH Cure Model with Time-Varying Covariates
Penalized Elastic Net S/MM-Estimator of Regression
Simulation of High-Dimensional Data and Parallelized Repeated
Penalized Regression
Data Sets for Keith McNulty's Handbook of Regression Modeling in
People Analytics
Parallelised Estimation of Prediction Error
Piecewise Exponential Distribution with Random Time Grids
Evaluation of Diversity in Nucleotide Libraries
Calculate Indices and Theoretical Physicochemical Properties of
Protein Sequences
Using Percolation and Conductance to Find Information Flow
Certainty in a Direct Network
Implementing Double Bootstrap Linear Regression Confidence
Intervals Using the 'perc-cal' Method
Estimate Percentiles from an Ordered Categorical Variable
Reconstruct Perfect Phylogenies from DNA Sequence Data
PerfMeas: Performance Measures for ranking and classification
tasks
Assessment of Regression Models Performance
Econometric Tools for Performance and Risk Analysis
An Infra-Structure for Performance Estimation of Predictive
Models
Functions for Generating Periodic Curves
Enterprise Streamlined 'Shiny' Application Framework
Permutational Algorithm to Simulate Survival Data
Permutational Group Sequential Test for Time-to-Event Data
Permutation Based Gene Expression Pathway Analysis
A Permutation Based Test for Biomarker Discovery in Microbiome
Data
Permutation Tests for Regression, (Repeated Measures)
ANOVA/ANCOVA and Comparison of Signals
The Symmetric Group: Permutations of a Finite Set
Functions for Generating Restricted Permutations of Data
Resampling-based prediction error estimation for regression
models
Automated Persomics Array Image Extraction
Estimation and Validation Methods for Subgroup Identification
and Personalized Medicine
Two-Part Estimation of Treatment Rules for Semi-Continuous Data
Pictographic Representation of Treatment Effects
Permutation of Species During Turnover Events
Sequence Iteration and Set Comprehension
Automatic Estimation of Number of Principal Components in PCA
Interface to Download Data on Pests and Hosts from 'EPPO'
Building, Visualizing, Exporting and Replaying Petri Nets
Reproducible Retrieval of Pew Research Center Datasets
Loading a JAGS Module for the Piecewise Exponential Distribution
Phylogenetics for the Environmental Sciences
Estimates False Discovery Proportion Under Arbitrary Covariance
Dependence
Penalized Independent Component Analysis for Univariate
Functional Data
Persistence Flamelets: Computation and Inferential Tools
Generate Random Samples from the Polya-Gamma Distribution
Penalized Generalized Estimating Equations in High-Dimension
Penalized Generalized Estimating Equations for Bivariate Mixed
Outcomes
Spatial Analysis and Data Mining for Field Ecologists
Generalized Least Square in comparative Phylogenetics
Nested Resolvable Designs and their Associated Uniform Designs
Estimating Multiple Gaussian Graphical Models (GGM) in Penalized
Gaussian Mixture Models (GMM)
Pseudo-Realizations for Gaussian Process Excursions
Build Dependency Graphs using Projection
Computes Powell's Generalized Synthetic Control Estimator
Functions for Generating PostgreSQL Statements/Scripts
Phase II Clinical Trial Design Using Bayesian Methods
Phase II Clinical Trial Design for Multinomial Endpoints
Enhanced RTF Wrapper for Use with Existing Table Packages
Pharmacometric Power calculations for mixed study designs
Simulating and Conducting Phase 123 Trials
Simulates SPSO and Efftox Phase 12 Trials with Correlated
Outcomes
Personalized Repeated Measurement Design for Phase I Clinical
Trials
Repeated Measurement Design for Phase I Clinical Trial
Phase Plane Analysis of One- And Two-Dimensional Autonomous ODE
Systems
PHATE - Potential of Heat-Diffusion for Affinity-Based
Transition Embedding
Permutation Testing in High-Dimensional Linear Models
High-Throughput Phenotyping with EHR using a Common Automated
Pipeline
Common Public Health Statistics and their Confidence Intervals
Estimate Phenological Metrics using Presence-Only Data
Auxiliary Functions for Phenological Data Analysis
Auxiliary functions for phenological data processing, modelling
and result handling
Insect Phenology Model Evaluation Based on Daily Temperatures
Auxiliary functions for phenological data analysis
Facilitates 'PhenoCam' Data Access and Time Series
Post-Processing
Continuous Development Models for Incremental Time-Series
Analysis
Extract Remote Sensing Vegetation Phenology
Tools to Manage a Parametric Function that Describes Phenology
and More
Projecting Satellite-Derived Phenology in Space
Process Digital Images of a Vegetation Cover
Unsupervised Gold-Standard Label Free Phenotyping Algorithm for
EHR Data
Flexible Phenotype Simulation from Different Genetic and Noise
Models
Evaluation of the Proportional Hazards Assumption with a
Standardized Score Process
Similarity and Distance Quantification Between Probability
Functions
Download Data from the Philadelphia District Attorney's Office
Tools for Inference in the Presence of a Monotone Likelihood
Convert Letters to Numbers and Back as on a Telephone Keypad
Tools for Phonetic and Acoustic Analyses
Spectral Transmittance and Spectral Reflectance Data
Read Spectral and Logged Data from Foreign Files
Plant Photobiology Related Functions and Data
Spectral Response Data for Light Sensors
Waveband Definitions for UV, VIS, and IR Radiation
Tools for Plant Ecophysiology & Modeling
R Interface to Geochemical Modeling Software
Run Phoenix NLME and Perform Post-Processing
An Extension (for Package 'SigTree') of Some of the Classes in
Package 'phylobase'
Base Package for Phylogenetic Structures and Comparative Data
Interactive Phylogenetic Trees Using the 'Phylocanvas'
JavaScript Library
Integrating Phylogenetics and Climatic Niche Modeling
Automatic Shift Detection using a Phylogenetic EM
Functions for Phylogenetically Based Statistical Analyses
Modelling Competitive Exclusion and Limited Dispersal in a
Statistical Phylogeographic Framework
Fast and Exact Algorithms for Computing Phylogenetic
Biodiversity Measures
Estimating Statistical Errors of Phylogenetic Metrics
Graph-Based Permutation Tests for Microbiome Data
Exploring the Phylogenetic Signal in Continuous Traits
Calculating Topological Properties of Phylogenies
The Phylogenetic Regression of Grafen (1989)
Marks Periods of 'Bedrest' in Actigraph Accelerometer Data
Process Accelerometer Data for Physical Activity Measurement
Calculate physiologic characteristics of awake and anesthetized
adults, children and infants
A Fast, Flexible Tool for Sorting Phylogenetic Trees
Phylogenetic Tools for Comparative Biology (and Other Things)
Pathwise Calibrated Sparse Shooting Algorithm
Bayesian Model to Find Changepoints Based on Rates and Count
Data
Managing Larger Data on a GitHub Repository
Prediction Intervals for Random-Effects Meta-Analysis
Fast and Stable Estimation of the Probability of Informed
Trading (PIN)
Sequence ('FASTA'), Annotation ('GFF') and Variants ('VCF') for
17 Samples of 'P. Infestans" and 1 'P. Mirabilis'
Identify, Ping, and Log Internet Provider Connection Data
Data About the Victims of the Pinochet Regime, 1973-1990
Clustering Algorithm for Data Integration and Disease Subtyping
Convert Chinese Characters into Pinyin, Sijiao, Wubi or Other
Codes
Dual-Agent Dose Escalation for Phase I Trials using the PIPE
Design
Permutation p-Value Estimation for Gene Set Tests
Calculate Pi Ratings for Teams Competing in Sport Matches
Small Example Response and Response Time Data from PISA 2018
Tools for Harnessing 'MLBAM' 'Gameday' Data and Visualizing
'pitchfx'
Pivotal Methods for Bayesian Relabelling and k-Means Clustering
A Fast, Easy-to-Use Tool for Manipulating Tables in Databases
and a Wrapper of MADlib
Tables so Beautifully Fine-Tuned You Will Believe It's Magic
The Parameter Converter of the Pharmacokinetic Models
Cache 'CRAN'-Like Metadata and R Packages
Make Static HTML Documentation for a Package
Download and Manage Optional Package Data
A Consistent and Intuitive Platform to Explore the Dependencies
of Packages on the Comprehensive R Archive Network Like
Repositories
Create Simple Packages Which Do not Upset R Package Checks
Simulate Package Installation and Attach
Check the Heaviness of Package Dependencies
Get Network Representation of an R Package
Public Key Infrastucture for R Based on the X.509 Standard
Least-Squares Estimator under k-Monotony Constraint for Discrete
Functions
A reporting pipeline for checking population pharmacokinetic
model assumption
Global Sensitivity Analysis in Physiologically Based Kinetic
Modeling
A Pairwise Likelihood Augmented Cox Estimator for Left-Truncated
Data
PLastic ACcumulation Estimate using R (PLACER)
Plot Raster Images Interactively on a Plain HTML Canvas
Functions for Calculating Dodge Romig, MIL STD 105E and MIL STD
414 Acceptance Sampling Plan
Simple and Accessible Data from all Known Planets
Modelling and Analysis of Leaf Gas Exchange Data
Partially Linear Additive Quantile Regression
Visualization of Plasmid Profile Results
Read, Tidy, and Display Data from Microtiter Plates
Dynamic Updating Methods for Player Ratings Estimation
Penalized Log-Density Estimation Using Legendre Polynomials
Pleiotropy Test for Multiple Traits on a Genetic Marker
Population Life Course Exposure to Health Effects Modeling
A GUI to View, Design and Export Various Graphs of Data
IRT Separate Calibration Linking Methods
Multiplicity control using Pooled LIS statistic
Bayesian Analysis of Finite Mixtures of Plackett-Luce Models for
Partial Rankings/Orderings
Estimate (Generalized) Linear Mixed Models with Factor
Structures
Polytomous Logit-Normit (Graded Logistic) Model Estimation
Multivariate Ordered Probit Model via Pairwise Likelihood
Plotting Multi-Dimensional Data - Using 'rgl'
Ternary Plots for Trinomial Regression Models
Easily Visualize Data from 'ERDDAP' Servers via the 'rerddap'
Package
Various Functions to Facilitate Visualization of Data and
Analysis
Tools for Visualizing Gaussian Mixture Models
New Plots Based on 'ggplot2' and Functions to Create Regular
Shapes
Visualization of Spatial and Spatio-Temporal Objects in Google
Earth
'ggplot2' Version of "I'm Feeling Lucky!"
Create Interactive Web Graphics via 'plotly.js'
Render 'Plotly' Maps without an Internet Connection
Plot Marginal Effects from Linear Models
Tidy Tools for Visualizing Mixture Models
Plot a Model's Residuals, Response, and Partial Dependence Plots
Plot Principal Component Histograms Around a Scatter Plot
Useful Networking Tools for Project Management
Creates an envelope that surrounds a set of points plotted in a
two dimensional space
Generate Useful ROC Curve Charts for Print and Interactive Use
Making Visual Exploratory Data Analysis with Nested Data Easier
Scale Graphics Devices Using Plot Dimensions
Graphing Nonlinear Relations Among Latent Variables from
Structural Equation Mixture Models
Spider Plots, ROC Curves, Pie Charts and More for Use in Other
Plots
Prediction Limits for Poisson Distribution
Log Linear by Linear Association models and Rasch family models
by pseudolikelihood estimation
Statistical inference in partial linear regression models
Partial Least Squares and Principal Component Regression
Partial Least Squares (PLS) Data Analysis Methods
Degrees of Freedom and Statistical Inference for Partial Least
Squares Regression
Linear and Smooth Predictor Modelling with Penalisation and
Variable Selection
Pleasure - Partial Least Squares Analysis with Permutation
Testing
Partial Least Squares Regression for Beta Regression Models
Partial Least Squares Regression for Cox Models and Related
Techniques
Partial Least Squares Regression for Generalized Linear Models
Variable Selection in Partial Least Squares
Simulate Probabilistic Long-Term Effects in Models with Temporal
Dependence
Pluralize and 'Singularize' Any (English) Word
Tools for Splitting, Applying and Combining Data
Interface to the 'PM4py' Process Mining Library
Calculate Pairwise Multiple Comparisons of Mean Rank Sums
Calculate Pairwise Multiple Comparisons of Mean Rank Sums
Extended
Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted
Analysis and Reactomics Analysis
'dplyr' Extension for Common Panel Data Maneuvers
Minimal Working Examples for Particle Metropolis-Hastings
Penalized Multi-Band Learning for Circadian Rhythm Analysis
Using Actigraphy
Interface to the Penn Machine Learning Benchmarks Data
Repository
Transforms Input Data from a PMML Perspective
Calculates the Minimum Sample Size Required for Developing a
Multivariable Prediction Model
Downloading, Reading and Analysing PNADC Microdata
Probit-Normal Marginalized Transition Random Effects Models
Downloading, Reading and Analysing PNS Microdata
Color Palettes Inspired by Nature in the US Pacific Northwest
An Elastic-Net Regularized Presence-Only Model
Finds the Price of Anarchy for Routing Games
Dose Finding in Drug Combination Phase I Trials Using PO-CRM
Probability of Detection for Qualitative PCR Methods
Common Functions for 'PHUSE' Open Data Repository
Principal Orthogonal ComplEment Thresholding (POET) Method
Downloading, Reading and Analysing POF Microdata
Bayesian Variable Selection for a Poisson-Logistic Model
PogromcyDanych / DataCrunchers is the Masive Online Open Course
that Brings R and Statistics to the People
Classification and Clustering of Sequencing Data Based on a
Poisson Model
Poisson lognormal and bivariate Poisson lognormal distribution
Validation of Local and Remote Data Tables
Interpretation of Point Forecasts as State-Dependent Quantiles
and Expectiles
Working Comfortably with Pointers and Shortcuts to R Objects
Analyzing Pointer Years and Components of Resilience
Input/Output Functionality for "PO" and "POT" Message
Translation Files
Data Generation with Poisson, Binary and Continuous Components
A Faster Implementation of the Poisson-Binomial Distribution
Data Generation with Poisson, Binary and Ordinal Components
Generation of Up to Four Different Types of Variables
Data Generation with Poisson, Binary, Ordinal and Normal
Components
Confidence Intervals with Poisson Double Sampling
Factorization of Sparse Counts Matrices Through Poisson
Likelihood
Simultaneous Generation of Count and Continuous Data
Simultaneous Generation of Multivariate Data with Poisson and
Normal Marginals
Simulating Homogenous & Non-Homogenous Poisson Processes
Fit high dimensional mixtures of Poisson GLMs
Efficient Computation of Ordinary and Generalized Poisson
Binomial Distributions
Robust M-Estimators Based on Transformations for Poisson Model
Significance analysis of sequencing data based on a Poisson log
linear model
Polytomous variable Latent Class Analysis
Policy Learning via Doubly Robust Empirical Welfare Maximization
over Trees
Datasets and Functions Featured in Pollock and Edwards, an R
Companion to Essentials of Political Analysis, Second Edition
Authentication and Administration for 'shiny' Apps
Tools for Acquiring and Analyzing Political Data
Estimate Pollinator Body Size and Co-Varying Ecological Traits
Calculate Crosstab and Topline Tables of Weighted Survey Data
Implementation of the Polya-Aeppli distribution
Bayesian Population Genomics in Autopolyploids
Find the Pole of Inaccessibility (Visual Center) of a Polygon
Linkage Analysis in Outcrossing Polyploids
Infrastructure for Manipulation Polynomial Matrices
A Collection of Functions to Implement a Class for Univariate
Polynomial Manipulations
Paternity Exclusion in Autopolyploid Species
The Pharmacokinetics (PK) of Multi-Component Drugs Using a
Metabolomics Approach
Helper Functions for Orthogonal Polynomials
QTL Analysis in Autopolyploid Bi-Parental F1 Populations
Genotype Calling with Uncertainty from Sequencing Data in
Polyploids and Diploids
Tools for Polyploid Microsatellite Analysis
Simulate and Test Marker Dosage for Dominant Markers in
Autopolyploids
Bayesian Mixture Models for Marker Dosage in Autopolyploids
Bootstrapped Basis Regression with Oracle Model Selection
Adaptive Association Tests for Multiple Phenotypes using
Proportional Odds Model (POM-aSPU)
Solver for Partially Observable Markov Decision Processes
(POMDP)
Pattern Oriented Modelling Information Criterion
Statistical Inference for Partially Observed Markov Processes
Person-Oriented Method and Perturbation on the Model
Pooled Mean Group Estimation of Dynamic Heterogenous Panels
Computing F-Statistics from Pool-Seq Data
Methods for Pooling P-Values from (Dependent) Tests
Gene-Based Association Tests using the Actual Impurity Reduction
(AIR) Variable Importance
A Poor Man's Dependency Free Recreation of 'dplyr'
A Flexible Syntax for Population Dynamic Modelling
Construction and Analysis of Matrix Population Models
Demographic Modelling Using Projection Matrices
Population (and Individual) Optimal Experimental Design
Functions for Epidemiological Analysis using Population Data
Useful functions for (batch) file conversion and data resampling
in microsatellite datasets
An Efficient Swiss Army Knife for Population Genomic Analyses
Accompaniment to the Book Population Genetics with R: An
Introduction for Life Scientists
A Simple Framework to Analyse Population and Landscape Genetic
Data
Estimate Kinship and FST under Arbitrary Population Structure
For interval estimation of mean of selected populations
Genetic Analysis of Populations with Mixed Reproduction
Reconstruct Human Populations of the Recent Past
Tools for Building, Visualizing, and Evaluating Self-Organizing
Maps
Estimate Smooth and Linear Trends from Population Count Survey
Data
Genomic Breeding Tools: Genetic Variance Prediction and
Cross-Validation
Ridge-Type Penalized Estimation of a Potpourri of Models
Acceder Con R a Los Datos Del Portal De Hacienda
Create Useful Summaries of the Portal Data
Portmanteau Tests for Univariate and Multivariate Time Series
Models
Portfolio Analysis, Including Numerical Methods for Optimization
of Portfolios
Automated Backtesting of Portfolios over Multiple Datasets
High Frequency Price Estimators by PortfolioEffect
High Frequency Portfolio Analytics by PortfolioEffect
Valid Post-Selection Inference for Linear LS Regression
Create Beautiful, Simple Personal Websites
Post Double Selection with Double Machine Learning
Generate PDF Conference Posters Using R Markdown
Non-Parametric Sampling with Parallel Monte Carlo
Tools for Interacting with 'PostgreSQL' / 'PostGIS' Databases
Estimating the Incubation Period Distribution of Post-Infectious
Syndrome
Parses Web Pages using Postlight Mercury
Utilities for Processing Posterior Samples Stored in
'mcmc.lists'
Generalized Pareto Distribution and Peaks Over Threshold
Markov Chain Monte Carlo for Potts Models
Phased or Unphased Linkage Disequilibrium
The Phylogenetic Ornstein-Uhlenbeck Mixed Model
Partition of Variation Variance Component Analysis Method
Full Pattern Summation of X-Ray Powder Diffraction Data
Computation of Power and Level Tables for Hypothesis Tests
Power and Sample-Size Distribution of 2-Stage Bioequivalence
Studies
Power Analysis Tool for Joint Testing Hazards with Competing
Risks Data
Power and Sample Size Calculation for eQTL Analysis
Power Calculations for GxE and GxG Interactions for GWAS
Power Analysis for Longitudinal Multilevel Models
Power/Sample Size Calculation for Mediation Analysis
Power analyses for the affected sib pair and the TDT design
Power and Sample Size Calculation for Survival Analysis of
Epidemiological Studies
Power and Sample Size for (Bio)Equivalence Studies
Power Analysis Tools for Multilevel Randomized Experiments
Probability Plot Correlation Coefficient Test
Projection Pursuit for Cluster Identification
Probabilistic and Possibilistic Cluster Analysis
Interfacing with ProPublica's 'Congress' API
Partial and Semi-Partial (Part) Correlation
Spatial Analysis of Pakistan Population Census
Generalised Additive Point Process Models
Projection Pursuit Based on Gaussian Mixtures and Evolutionary
Algorithms
Lookup Tables to Generate Poverty Likelihoods and Rates using
the Poverty Probability Index (PPI)
Privacy-Protecting Hazard Ratio Estimation in Distributed Data
Networks
Point Process Models with LASSO Penalties
Probabilistic Two Sample Mendelian Randomization
A Collection of Models that Employ a Prior Distribution on
Partitions
Process Performance Qualification (PPQ) Plans in Chemistry,
Manufacturing and Controls (CMC) Statistical Analysis
Projection Pursuit Classification Tree Visualization
web tool for estimating under-five deaths caused by poor-quality
antimalarials in sub-Saharan Africa
Efficient Mixed Model Analysis of Count Data in Large-Scale
Genomic Sequencing Studies
Functions for Clustering and Testing of Presence-Absence,
Abundance and Multilocus Genetic Data
Tools for Designing and Weighting Survey Samples
Provides a pragma / directive / keyword syntax for R
Prais-Winsten Estimator for AR(1) Serial Correlation
Kvantitatiivsete meetodite praktikumi asjad / Functions used in
the course "Quantitative methods in behavioural sciences"
(SHPH.00.004), University of Tartu
Tools for Information-Based Feature Selection
Testing Workbench for Precision-Recall Curves
Conduct a Prospective or Retrospective Design Analysis
Safety Diagnostics for Dose-Escalation Trial Designs
Precipitation Intensity, Concentration and Anomaly Analysis
Estimate Sample Size Based on Precision Rather than Power
Accurate Floating Point Sums and Products
Calculate Accurate Precision-Recall and ROC (Receiver Operator
Characteristics) Curves
Computational Prediction of Proteins Encoded by Circadian Genes
Genomic Prediction of Hybrid Performance
Draw Three Dimensional Predict Plot Using Package 'rgl'
Prediction Interval Functions for Assessing Replication Study
Results
Prediction for Future Data from any Continuous Distribution
Prediction Intervals for Three Basic Statistical Models
Calculate Predicted Means for Linear Models
Predict the Race of a Given Surname Using Census Data
Classification rule based on Bayesian mixture models with
feature selection bias corrected
Estimates Reliability of Individual Supervised Learning
Predictions
R Package for Pairwise Preference Elicitation
2-Stage Preference Trial Design and Analysis
Utilities to Fit Paired Comparison Models for Preferences
Pre-Knitting Processing and Post HTML-Rendering Processing
Dirichlet Process Bayesian Clustering, Profile Regression
Preparing Experimental Data for Statistical Analysis
Basic Functions for Pre-Processing Microarrays
Interactive Document for Preprocessing the Dataset
Utilities for Preparation of Data Analysis
R Markdown Templates to Preregister Scientific Studies
Registry of Victims of State Terrorism in Argentina
Probability-Scale Residuals and Residual Correlations
Indeterminacy of Networks via Press Perturbations
'RStudio' Addins to Prettify 'JavaScript', 'C++', 'Python', and
More
Creating Pretty Documents from R Markdown
Scale Bar, North Arrow, and Pretty Margins in R
Pretty, Human Readable Formatting of Quantities
Geostatistical Modelling of Spatially Referenced Prevalence Data
Estimating Regional Trends of a Prevalence from a DHS and
Similar Surveys
Prevalence to Incidence Calculations for Point-Prevalence
Studies in a Nosocomial Setting
Permutation Significance for Random Forests
Van Westendorp Price Sensitivity Meter Analysis
Parametric Simplex Method for Sparse Learning
Use Prime Factorization for Computations
Projected Refinement for Imputation of Missing Entries in PCA
Functions and Data for the Book, a Primer of Ecology with R
Visually Assessing the Specificity and Informativeness of Primer
Pairs
Eigenvalues and Singular Values and Vectors from Large Matrices
Fit a Principal Curve in Arbitrary Dimension
Finding and plotting simple basis vectors for multivariate data
Automatically Print R Objects to Appropriate Formats According
to the 'knitr' Output Format
Candidate Gene Prioritization for Non-Communicable Diseases
Based on Functional Information
Prioritizing Cancer Drugs for Interested Cancer
Generates Prior Distributions for Proportions
Systematic Conservation Prioritization in R
Analyzing Multiple Omics Data with an Offset Approach
Access Data from the Oregon State Prism Climate Project
Penalized Regression with Inferred Seasonality Module -
Forecasting Unemployment Initial Claims using 'Google Trends'
Data
Protocol Inspection and State Machine Analysis
Creates a Prisma Diagram using 'DiagrammeR'
Plot Flow Charts According to the "PRISMA" Statement
Downloads and Parses World Prison Brief Data
Differentially Private Regularized Logistic Regression
Estimation of Prevalence Ratios using Logistic Models
Point-Process Response Model for Optogenetics
Elementary Probability on Finite Sample Spaces
Tools for Post-Processing Class Probability Estimates
Statistical Tools for Probing Moderation Effects
Probabilistic weather forecast using the GOP method
Multivariate Generalized Kernel Smoothing and Related
Statistical Methods
Computing Logit & Probit Predicted Probabilities & Marginal
Effects
Unsupervised Multivariate Outlier Probabilities for Large
Datasets
Score Optimal Probabilistic Forecast Reconciliation
Interactive Document for Working with Basic Probability
Inference for the Stress-Strength Model R = P(Y<X)
Extraction of Bands from MODIS Calibrated Radiances MOD02 NRT
Several Methods for Procedural Name Generation
Rule-Based Conformance Checking of Business Process Event Data
Product Density Estimation for ICA using tilted Gaussian density
estimates
Product-Limit Estimation for Censored Event History Analysis
Indices of Productivity Using Data Envelopment Analysis (DEA)
An Alternative Display Profiling Data as Tree Structure
Compute and Visualize Profile Extrema Functions
Profile R Code and Visualize with 'Pprof'
Read, Manipulate, and Write Profiler Data
Profile Likelihood for a Parameter in Commonly Used Statistical
Models
Profiling Inference Functions for Various Model Classes
Profile Analysis of Multivariate Data in R
Fit Projected 2D Profiles to Galaxy Images
Downloading and Exploring Data from the PROFOUND Database
An Alternative Display for Profiling Information
Interactive Visualizations for Profiling R Code
Finding the Optimal Cluster Number Using Progeny Clustering
Prognostic ROC curves for evaluating the predictive capacity of
a binary test
An Inclusive, Unifying API for Progress Updates
Generic Coordinate System Transformations Using 'PROJ'
A simple interface to the PROJ.4 cartographic projections
library
Management of Deterministic and Stochastic Projects
A Project Infrastructure for Researchers
Automates the Creation of New Statistical Analysis Projects
Task Tracking and Project Management with GitHub
Calculates and Analyzes the Proliferative Index
Preference Ranking Organization METHod for Enrichment of
Evaluations
Abstractions for Promise-Based Asynchronous Programming
Analysis & Measurement of Promotion Effectiveness
Add Tooltips in 'Shiny' Apps with 'Hint.css'
Analyzing Combination of Proportions and Relative Risk
Various Confidence Interval Methods for Proportions
Parse 'Java' Properties Files for 'R Service Bus' Applications
Inference on Single Binomial Proportion and Bayesian
Computations
Feature (gene) selection based on the Proportional Overlapping
Scores
Calculating Proportionality Between Vectors of Compositional
Data
Propensity score methods for assigning treatment in randomized
trials
'ProPublica' U.S. Congress Bills API Wrapper
Patient Reported Outcomes Regression Analysis
Functions to Score Commonly-Used Patient-Reported Outcome (PRO)
Measures and Other Psychometric Instruments
Tools to Score Patient-Reported Outcome (PRO) and Other
Psychometric Measures
Penalized Regression with Second-Generation P-Values
Miscellaneous Functions for Processing and Sample Selection of
Spectroscopic Data
Search Tagged Peptides & Draw Highlighted Mass Spectra
Generates Various Protein Descriptors for Machine Learning
Algorithms
Optimization of a multi-stage proteomic study
Statistical Analysis of High Throughput Proteomics Data
Highly Optimized Protocol Buffer Serializers
Inference on Prototypes from Clusters of Features
Generating Various Numerical Representation Schemes for Protein
Sequences
Manipulate and Play 'ProTracker' Modules
Visualizing and Analyzing Mass Spectrometry Related Data in
Proteomics
Tools for Natural Language Processing in French
Statistical Toolbox for Sedimentary Provenance Analysis
Compare Provenance Collections to Explain Changed Script Outputs
Creates Adjacency Matrices for Lineage Searches
Summarizes Provenance Related to Inputs and Outputs of a Script
or Console Commands
Uses Provenance to Trace File Lineage for One or more R Scripts
Computes Proximity in Large Sparse Matrices
Minimal Protein Set Explaining Peptide Spectrum Matches
Precision-Recall and ROC Curves for Weighted and Unweighted Data
Stochastic Simulation of Streamflow Time Series using Phase
Randomization
Test of Periodicity using Response Surface Regression
Tabular Data Backed by Partitioned 'fst' Files
Datasets and Functions Used in the Book 'Przewodnik po Pakiecie
R'
List, Query, Manipulate System Processes
Penalized Parametric and Semiparametric Bayesian Survival Models
with Shrinkage and Grouping Priors
Analysis of Parent-Specific DNA Copy Numbers
Standardizing Physiological Composite Risk Endpoints
Adaptive, Sine-Multitaper Power Spectral Density and Cross
Spectrum Estimation
Download Regularly Maintained Political Science Data Sets
Parameter Space Exploration with Latin Hypercubes
Methods for Evaluating Principal Surrogates of Treatment
Response
Forecasting of Univariate Time Series Using the Pattern
Sequence-Based Forecasting (PSF) Algorithm
Prediction Model Selection and Performance Evaluation in
Multiple Imputed Datasets
Projected Spatial Gaussian Process Methods
Decision Tree Analysis for Probabilistic Subgroup Identification
with Multiple Treatments
Build Panel Data Sets from PSID Raw Data
Pakistan Social and Living Standards Measurement Survey 2014-15
Estimation of Characteristics of Seasonal and Sporadic
Infectious Disease Outbreaks Using Generalized Additive
Modeling with Penalized Basis Splines
Analysis of Physiologically Structured Population Models
PS-Integrated Methods for Incorporating RWE in Clinical Studies
Power and Sample Size for Health Researchers via Shiny
Test of Independence & Image Structural Similarity Measure PSSIM
Piecewise Exponential Model for Time to Progression and Time
from Progression to Death
Features Extracted from Position Specific Scoring Matrix (PSSM)
Flexible and Efficient Evaluation of Principal
Surrogates/Treatment Effect Modifiers
Flexible Identification of Phenotype-Specific Subpathways
Probabilistic Suffix Trees and Variable Length Markov Chains
Specification Tests for Parametric Propensity Score Models
Simulations of grouped responses relative to baseline
Propensity Score Weighting Methods for Dichotomous Treatments
Propensity Score Weighting for Causal Inference with
Observational Studies and Randomized Trials
Procedures for Psychological, Psychometric, and Personality
Research
Efficient and Publishing-Oriented Workflow for Psychological
Science
Structural Equation Modeling and Confirmatory Network Analysis
Recursive Partitioning Based on Psychometric Models
Psychrometric Properties of Moist and Dry Air
Tools to Accompany the 'psych' Package for Psychological
Research
Real Time Monitoring of Asset Markets: Bubbles and Crisis
Functions for Analyzing Psychophysical Data in R
Decentralized Unequivocality in Psychological Science
Persistence Terrace for Topological Data Analysis
Analyses of Protein Post-Translational Modifications
Poisson-Tweedie Generalized Linear Mixed Model
Construct Polygons Summarising the Location and Variability of
Point Sets
Tail Index Estimation for Power Law Distributions
Access the 'Public Transport Victoria' Timetable API
Percentile Estimation of Fetal Weight for Twins by Chorionicity
Quality Report Generation for MaxQuant and mzTab Results
Bayesian Variable Selection with Hierarchical Priors
Performs simulation study to look for publication bias, using a
technique described by Ioannidis and Trikalinos; Clin Trials.
2007;4(3):245-53
Fetch Sections of XML Scholarly Articles
A Toolbox for Public Health and Epidemiology
Sensitivity Analysis for Publication Bias in Meta-Analyses
Bayesian Meta-Analysis with Publications Bias and P-Hacking
Format Output of Various Routines in a Suitable Way for Reports
and Publication
Gathering Metadata About Publications, Grants, Clinical Trials
from 'PubMed' Database
Create and Query a Local 'PubTator' Database
High-Dimensional Variable Selection with Presence-Only Data
Parallel Utilities for Lambda Selection along a Regularization
Path
Identification of Transcriptional Dynamics using Pulse Models
via 4su-Seq Data and RNA-Seq Data
Meta-Analysis Methods Correcting for Publication Bias
A Collection of Physical and Chemical Adsorption Isotherm Models
A Unified Pipeline for Pupillometry Data
Bayesian Estimation of Tumor Purity and Clonality
Simple Method for Purging Mediation Effects among Independent
Variables
Tools at the Intersection of 'purrr' and 'dplyr'
Assembling Data Sets for Non-Linear Mixed Effects Modeling
Population Viability Analysis with Data Cloning
Creates and Plots P-Value Functions, S-Value Functions,
Confidence Distributions and Confidence Densities
Calculation and Application of p-Variation
Hierarchical Clustering with P-Values via Multiscale Bootstrap
Resampling
Simplifies the Analysis of Pressure Volume and Leaf Drying
Curves
Phylogenetic Eigenvectors Regression and Phylogentic
Signal-Representation Curve
An R package to interact with the Project Vote Smart API for
scientific research
Time Series Regression Using the Power Weighted Densities (PWD)
Approach
Design and Monitoring of Survival Trials Accounting for Complex
Situations
Utilities for Working with Air Quality Monitoring Data
Power and Sample Size Analysis for One-way and Two-way ANOVA
Models
Power Analyses for Common Designs (Power to the People)
Statistical Power Simulation for Testing the Rasch Model
Penn World Table (Versions 5.6, 6.x, 7.x)
Pena-Yohai Initial Estimator for Robust S-Regression
Interpolating Age-Specific Mortality Rates at All Ages
Types and Features for Object Oriented Programming
Automatic Item Generator for Quantitative Multiple-Choice Items
Heuristics for the Quadratic Assignment Problem (QAP)
Approximation to the Survival Functions of Quadratic Forms of
Gaussian Variables
Asymmetric Distributions and Quantile Estimation
Quantile Regression for Binary Longitudinal Data
Tests for Type I Error in Qualitative Comparative Analysis (QCA)
Estimate Power and Required Sample Size in QCA
Advanced Functionality for Performing and Evaluating Qualitative
Comparative Analysis
Quantitative Classification by Association Rules
Quality Control Charts under Repetitive Sampling
Fast and Easy Quality Control of EWAS Results Files
Quality Control of Genome Wide Association Study results
Sure Independence Screening via Quantile Correlation and
Composite Quantile Correlation
Bridging the Gap Between Qualitative Data and Quantitative
Analysis
Dictionaries and Word Lists for the 'qdap' Package
Regular Expression Removal, Extraction, and Replacement Tools
Modern Nonparametric Tools for Two-Sample Quantile and
Distribution Comparisons
Fitting a Quadrilateral Dissimilarity Model to Same-Different
Judgments
Density, Cumulative and Quantile Functions of Quadratic Forms
Quantitative Fatty Acid Signature Analysis
Quantitative Fatty Acid Signature Analysis in R
Pricing of Vanilla and Exotic Option Contracts
Smooth Additive Quantile Regression Models
Statistical Tools for Quantitative Genetic Analyses
Estimate Quantitative Genetics Parameters from Generalised
Linear Mixed Models
Graph Plotting Methods, Psychometric Data Visualization and
Graphical Model Estimation
A 'shiny' Application for Active Learning Instruction in
Introductory Quantitative Genetics
Generalized Quantitative Genetics Data Analyses
Q-Kernel-Based and Conditionally Negative Definite Kernel-Based
Machine Learning Tools
Utility Sparse Matrix Functions for Quantitative Language
Comparison
Reinforcement Learning using the Q Learning Algorithm
Statistical Transformations for Post-Processing Climate Model
Output
Analysis of Subjective Perspectives Using Q Methodology
Methods for Quantitative Magnetic Resonance Imaging ('qMRI')
Transport Data and Commands Across the 'FAME' / 'R' Border
Modelling and Analysis of Real-Time PCR Data
Interface to the 'qpmad' Quadratic Programming Solver
Permutation Based QQ Plot and Inflation Factor Estimation
Quantile-Quantile Plot Extensions for 'ggplot2'
Self Calibrating Quantile-Quantile Plots for Visual Testing
A 'Shiny' Gadget for Interactive 'QRA' Visualizations
Tools that Create D3 JavaScript Force Directed Graph from R
True Random Numbers using the ANU Quantum Random Numbers Server
A Novel Quantile Regression Approach for eQTL Discovery
Quantile Regression in Varying-Coefficient Models
Quick Response Code (QR Code) / Matrix Barcode Creator
10-Year Cardiovascular Disease Risk Calculator (QRISK3 2017)
Joint Estimation in Linear Quantile Regression
Quantile Regression for Linear Mixed-Effects Models
Provides R-Language Code to Examine Quantitative Risk Management
Concepts
Data Sets for Quantitative Risk Management Practice
Quantile Regression for Nonlinear Mixed-Effects Models
Quantitative Structure Activity Relationship (QSAR) Data Sets
Running Commands Remotely on 'Gridengine' Clusters
QTL Genome-Wide Composite Interval Mapping
QTL Genome-Wide Composite Interval Mapping with Graphical User
Interface
Quantitative Trait Locus Mapping in Experimental Crosses
Database Storage of Genotype Probabilities for QTL Mapping
Testing Pleiotropy in Multiparental Populations
Densitometric Analysis of Thin-Layer Chromatography Plates
Interactive Graphics for QTL Experiments
Tools for Mapping Multiple Complex Traits
Tools for Mapping of Quantitative Traits of Genetically Related
Individuals and Calculating Identity Coefficients from
Pedigrees
Quantile-Optimal Treatment Regimes with Censored Data
QuACN: Quantitative Analysis of Complex Networks
Exact permutation moments of quadratic form statistics
Functions to Solve Quadratic Programming Problems
Quadratic Programming with Absolute Value Constraints
Quadratic Root for any Quadratic Equation
Sparsity by Worst-Case Quadratic Penalties
Causal Inference with Qualitative and Ordinal Information on
Outcomes
Opinionated Approach for Digitizing Semi-Structured Qualitative
GIS Data
Automatic Generation of Qualitative Color Palettes
Implements Indices of Qualitative Variation Proposed by Wilcox
(1973)
Partitioning Uncertainty Components of an Incomplete Ensemble of
Climate Projections
Uncertainties of Climate Projections using Smoothing Splines
Streamline Descriptive Analysis of Quantitative Data Matrices
Dimension Reduction Techniques for Conditional Quantiles
Scaling Models and Classifiers for Textual Data
Plots for the Quantitative Analysis of Textual Data
Textual Statistics for the Quantitative Analysis of Textual Data
Quantification of Qualitative Survey Data
Nonparametric Confidence Intervals for Quantiles
Quantile Kriging for Stochastic Simulations with Replication
Mitigating the Adverse Impact of Batch Effects in Sample Pattern
Detection
Algorithms for Quantile- And Mean-Optimal Treatment Regimes
Quantile Regression Forests for 'ranger'
Quantile-Based Spectral Analysis of Time Series
Clustering Mutations using High Throughput Sequencing (HTS) Data
Performs Common Linear Algebra Operations Used in Quantum
Computing and Implements Quantum Algorithms
Interaction Prediction Between Groundwater and Quarry Extension
Using Discrete Choice Models and Artificial Neural Networks
Comparison of Phylogenetic Trees Using Quartet and Split
Measures
Analyzing RNA Sequencing Count Tables Using Quasi-Likelihood
Translate 'SQL' Queries into 'R' Expressions
Functions to Make Surveys Processing Easier
Analysis of Queueing Networks and Models
Calculation of Homology of Quandles, Racks, Biquandles and
Biracks
An 'R' Client for the 'USDA NASS Quick Stats API'
A System of Plotting Optimized for Speed and Modularity
Fits Psychometric Functions for Multiple Groups
Build Regression Models Quickly and Display the Results Using
'ggplot2'
QUick IDentification of DIagnostic CHaracters
Quantile Regression Outlier Diagnostics with K Left Out Analysis
A Way of Writing Functions that Quote their Arguments
Quasi Variances for Factor Effects in Statistical Models
Generalized Eigenvalues and QZ Decomposition
Bayesian Network Learning Improved Project
Fast and Light-Weight Caching (Memoization) of Objects and
Results to Speed Up Computations
Easy Handling of and Access to Files Organized in Structured
Directories
Methods for Accessing Huge Amounts of Data [deprecated]
Perform JIVE Decomposition for Multi-Source Data
Read and Write MAT Files and Call MATLAB from Within R
R Object-Oriented Programming with or without References
Dynamic Generation of Scientific Reports
Processing Pipeline for 'SamBada' from Pre- To Post-Processing
Estimation of R0 and Real-Time Reproduction Number from
Epidemics
Compressive Sampling: Sparse Signal Recovery Utilities
R2 Measure of Explained Variation under the Additive Hazards
Model
Estimate Structured Additive Regression Models with 'BayesX'
Multistage Sampling Allocation and PSU Selection
Bivariate (Two-Dimensional) Confidence Region and Frequency
Distribution
Multiple Peak Alignment for 2D Gas Chromatography Mass
Spectrometry Metabolomics Analysis
A Mini-Dictionary for 'R' and 'Markdown' Writing
Tools to Calculate Climate Targets for Financial Portfolios
Datasets to Align Financial Markets with Climate Goals
Tools to Match Financial Portfolios with Climate Data
Translation of Base R-Like Functions for 'data.table' Objects
Computes R Squared for Mixed (Multilevel) Models
R-Squared Measures for Multilevel Models
Simple R Interface to Microsoft PowerPoint using rcom or
RDCOMClient
Easily Create Presentation-Ready Rich Text Format (RTF) Table
and Figure
Wrapper for 'SUNDIALS' Solving ODE and Sensitivity Problem
Symbols for 'Markdown' and 'Shiny' Application
Goodness-of-Fit Tests for Capture-Recapture Models
Running 'WinBUGS' and 'OpenBUGS' from 'R' / 'S-PLUS'
Create Interactive 3D Visualizations of Molecular Data
Simulating Forest Growth using the 3-PG Model
Report Functions to Create HTML and PDF Files
Statistical Inference on Lineup Fairness
Work with the Bay Area Transportation Commission Application
Programming Interface
Encapsulated Classes with Reference Semantics
R6 Reference Class Based Data Structures
Generate Codes to Uniquely and Robustly Identify Individuals for
Animal Behavior Studies
Identification of Cell Types and Inference of Lineage Trees from
Single-Cell RNA-Seq Data
Pattern-Based Zoneless Method for Analysis and Visualization of
Racial Topography
Rapid A/Ci Response (RACiR) Data Analysis
Normalization and Study of Rank Abundance Distributions
Nuclear Decay Data for Dosimetric Calculations - ICRP 107
Interactive Gadgets for Radial Visualization Approaches
Basics Menu for Radiant: Business Analytics using R and Shiny
Data Menu for Radiant: Business Analytics using R and Shiny
Design Menu for Radiant: Business Analytics using R and Shiny
Model Menu for Radiant: Business Analytics using R and Shiny
Multivariate Menu for Radiant: Business Analytics using R and
Shiny
Tools for plotting skew-T diagrams and wind profiles
Inverse-Regression Estimation of Radioactive Doses
Query Random User Data from the Random User Generator API
Radon and Soil Gas Transport in 2D Porous Medium
Project Multidimensional Data in 2D Space
Random Approximate Elastic Net (RAEN) Variable Selection Method
Convenience Functions for Routine Data Exploration
A Wrapper of the 'JavaScript' Library 'agGrid'
Ridge Estimation of Precision Matrices from High-Dimensional
Data
Ridge Estimation of Vector Auto-Regressive (VAR) Processes
Pricing Equity Derivatives with Extensions of Black-Scholes
Bagplots, Boxplots and Rainbow Plots for Functional Data
Genome-Wide Association Study with SNP-Set Methods
Obtain and Analyze Daily Rainfall Data from the USA Climate
Prediction Center (CPC)
The Reinert Method for Textual Data Clustering
Stochastic Precipitation Downscaling with the RainFARM Method
Easy Spatial Microsimulation (Raking) in R
Retrieves Altmerics Data for Any Published Paper from
'Altmetric.com'
Interface to the JavaScript Library 'amCharts 4'
Estimation and Inference in Random Attention Models
Download and Read RAM Legacy Stock Assessment Database
Regularized Generalized Linear Models with Interaction Effects
Structural Equation Modeling Using the Reticular Action Model
(RAM) Notation
Bayesian Geostatistical Modeling with RAMPS
Reinforced Angle-Based Multicategory Support Vector Machines
Random number generator based on AES cipher
Covariate Balance Checks: Randomization Tests and Graphical
Diagnostics
Generate a Random p x p Correlation Matrix
Efficient Numerical Algorithm for Exact Inference in Meta
Analysis
Package Provides Access to Fake User Data
Random Network Model Selection and Parameter Tuning
A Parallel Analysis with Polychoric Correlation Matrices
Adaptive Estimation in the Linear Random Coefficients Models
Simulation and Analysis of Random Fields
Utilities for the Simulation and Analysis of Random Fields
Breiman and Cutler's Random Forests for Classification and
Regression
Explaining and Visualizing Random Forests in Terms of Variable
Importance
Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
Create a Random List for Crossover Studies
Easy-to-Use Tools for Common Forms of Random Assignment and
Sampling
Random Uniform Forests for Classification, Regression and
Unsupervised Learning
Get Random Quotes from Quotes on Design API
Toolbox for Pseudo and Quasi Random Number Generation and Random
Generator Tests
Occurrence Filtering, Geographic and Taxonomic Standardization
and Generation of Species Range Polygons
A Platform for the Study of Macro-Ecology of Life History Traits
Provides Templates for Metadata Files Associated with Species
Range Models
Aggregation of (Partial) Ordinal Rankings
Model-Based Clustering for Multivariate Partial Ranking Data
Rank-Based Tests for General Factorial Designs
The Ranking Project: Visualizations for Comparing Populations
Ranking Responses in a Single Response Question or a Multiple
Response Question
Ranking of Nodes with Kernelized Score Functions
Fast Nearest Neighbour Search (Wraps ANN Library) Using L2
Metric
Base Functions and Resources for Rapporteket
A Fast and Light Package to Compute Polygenic Risk Scores
Reliable Accurate Prenatal non-Invasive Diagnosis R package
Bindings to AppArmor and Security Related Linux Tools
Application Directories: Determine Where to Save Data, Caches,
and Logs
Miscellaneous (stats) helper functions with sane defaults for
reporting
Calculate Sketches using Random Projections to Reduce Large Data
Sets
Representative and Adequate Prioritization Toolkit in R
Estimate the Water Influx into Hydrocarbon Reservoirs
Linear Model with Tree-Based Lasso Regularization for Rare
Features
Testing Gene-Environment Interaction for Rare Genetic Variants
Ecological and biogeographical null model tests for comparing
rarefaction curves
Calculation of Rarity Indices for Species and Assemblages of
Species
Solvers for Large Scale Eigenvalue and SVD Problems
Random Subspace Ensemble Classification and Variable Screening
Diversity Indices for Numerical Matrices
Kernel Based Estimates on in-Memory Raster Images
A Raster Where Cells are Generic Objects
Easily and Rapidly Generate Raster Image Data with Support for
'Plotly.js'
Bayesian Estimation of the Evolutionary Rate Matrix
A Modification of Fleiss' Kappa in Case of Nominal and Ordinal
Variables
Confidence Intervals for Comparisons of Binomial or Poisson
Rates
Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Rationalizing Rational Expectations. Tests and Deviations
Calculating Ratios Between Two Data Sets and Correction for
Adhering Particles on Plants
Processing Acoustic Startle Experimental Data
Graphical User Interface for Data Science in R
Rare Variant Analysis and Genetic Simulations
Raven Hydrological Modelling Framework R Support and Analysis
Parameter Estimation for the Averaging Model of Information
Integration Theory
Interface to the Bird-Watching Dataset Proyecto AVIS
Easily Get True-Positive Rate and False-Positive Rate and KS
Statistic
Retrieve Raw R Code from Popular Tutorials and Websites
Create Maps and Visualize Data in 2D and 3D
'Bielefeld' Academic Search Engine ('BASE') Client
Age-Depth Modelling using Bayesian Statistics
Bayesian Trees for Conditional Mean and Variance
Bayesian Change-Point Detection and Time Series Decomposition
The Beta Random Number and Dirichlet Random Vector Generating
Functions
Tools for 'Box Geometry Model' (BGM) Files and Topology for the
Atlantis Ecosystem Model
Reading and Background Subtraction in Videos
Interface to the 'Biodiversity' 'Heritage' Library
Correct Bias in DNA Methylation Analyses
Read/Write, Transform, and Summarize 'BIOM' Data
An R Wrapper to the Overly Complicated 'Bitmoji' API
Handling Linear Gaussian Bayesian Networks
Download Data from the Reserve Bank of New Zealand Website
Extensible, Parallelizable Implementation of the Random Forest
Algorithm
Perform Rosenbaum bounds sensitivity tests for matched and
unmatched data
Regression-Based Approach for Testing the Type of Missing Data
Alternative Bootstrap-Based t-Test Aiming to Reduce Type-I Error
for Non-Negative, Zero-Inflated Data
Rbundler manages an application's dependencies systematically
and repeatedly
Residual Balancing Weights for Marginal Structural Models
Calculation of the Integrated Flow of Particles Between Polygons
Cancer Registry Data Analysis and Visualisation
Different Numeric Optimizations to Estimate Parameter
Coefficients
Access and Plot CanVec and CanVec+ Data for Rapid Basemap
Creation in Canada
Loglinear Models for Capture-Recapture Experiments
Dose Rate Modelling of Carbonate-Rich Samples
Calibration and Analysis of Radiocarbon Dates
Large, Sparse Optimal Matching with Refined Covariate Balance
Random Coefficient Binary Response Estimation
Optimal Subset Matching with Refined Covariate Balance
Parametric Bootstrapping to Control Rank Conditional Coverage
Miscellaneous R Functions for Swedish Regional Cancer Centers
R Cross Entropy Inspired Method for Optimization
Analytical Procedures in Support of Brazilian Public Sector
External Auditing
Download and Open Data Provided by the Copernicus Global Land
Service
Conjugate Gradient Minimization of Nonlinear Functions
Data on Base Packages for Current and Previous Versions of R
Chess Move, Generation/Validation, Piece Placement/ Movement,
and Check/Checkmate/Stalemate Detection
Discrete Choice (Binary, Poisson and Ordered) Models with Random
Parameters
Post-Processing of the Markov Chain Simulated by ChronoModel or
Oxcal
A 'DBI' Interface to the 'Yandex Clickhouse' Database Providing
Basic 'dplyr' Support
R tools for integrating with the www.clinicalcodes.org
repository
Graphical Toolbox for Clustering and Classification of Data
Frames
Run 'R CMD check' from 'R' and Capture Results
R Commander Plug-in for Repeated-Measures ANOVA
R Commander Plug-in for Case 1 (Object Case) Best-Worst Scaling
R Commander Plug-in for Dichotomous Choice Contingent Valuation
R Commander Plug-in for Discrete Choice Experiments
R Commander Plugin for (industrial) Design of Experiments
Plugin de R-Commander para el Manual 'EACSPIR'
Rcmdr Evidence Based Medicine Plug-in Package
R Commander Plug-in for the EZR (Easy R) Package
R Commander Plug-in for Fuzzy Clustering Methods (Fuzzy C-Means
and Gustafson Kessel)
R Commander Plug-in for Fitting Generalized Waring Regression
Models
R Commander Plug-in for Data Visualization with 'ggplot2'
Graphical User Interface for Conducting Meta-Analyses in R
R Commander Plug-in for University Level Applied Statistics
R Commander Plug-in for Robust Principal Component Analysis
Graphical POINT of view for questionnaire data Rcmdr Plug-In
R Commander Plug-in for Risk Demonstration
Rcmdr Receiver Operator Characteristic Plug-In PACKAGE
Tools for sampling in Official Statistical Surveys
Rcmdr Plugin for Designing and Analyzing Single-Case Experiments
R Commander Plug-in for the 'survival' Package
'Rcmdr' Plugin for Alpha-Sutte Indicator 'sutteForecastR'
R Commander Plugin for Teaching Statistical Methods
Graphical Integrated Text Mining Solution
R Commander Plug-in for the 'WorldFlora' Package
Interface to Colombos Compendia using the Exposed REST API
Functions to Support Extension Education Program Evaluation
A Collection of Small Text Corpora of Interesting Data
Cosmic Microwave Background Data Analysis
Regions of Common Profiles Modelling with Mixtures-of-Experts
High Performance Tools for Combinatorics and Computational
Mathematics
'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest
Neighbors
'Rcpp' Interface to the APT Package Manager
'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Rcpp bindings for the Boost Date_Time library
Factor Big Integers with the Parallel Quadratic Sieve
Examples using 'RcppClassic' to Interface R and C++
Read-Write Support for 'NumPy' Files via 'Rcpp'
'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
'date' C++ Header Library for Date and Time Functionality
Global Optimization by Differential Evolution in C++
'Rcpp' Integration of Additional Probability Distributions
'Rcpp' Integration for the 'Eigen' Templated Linear Algebra
Library
Compiles 'C++' Code using 'Rcpp', 'Eigen' and 'CppAD' to Produce
First and Second Order Partial Derivatives
Header-Only C++ Mathematical Optimization Library for
'Armadillo'
Examples using 'Rcpp' to Interface R and C++
'Rcpp' Bindings for the 'Faddeeva' Package
'Rcpp' Interface for Querying System Configuration Variables
'Rcpp' Integration for 'GNU GSL' Vectors and Matrices
'Rcpp' Bindings for 'hnswlib', a Library for Approximate Nearest
Neighbors
Solves Minimum Cost Bipartite Matching Problems
'Rcpp' Integration for the 'MLPACK' Library
'MsgPack' C++ Header Files and Interface Functions for R
'Rcpp' Package Illustrating Header-Only Access to 'NLopt'
'Rcpp' Integration for Numerical Computing Libraries
An Interruptible Progress Bar with OpenMP Support for C++ in R
Packages
R Bindings to the 'Quantuccia' Header-Only Essentials of
'QuantLib'
'Rcpp' Bindings for 'Redis' using the 'hiredis' Library
'Rcpp' Bindings for the 'simdjson' Header-Only Library for
'JSON' Parsing
Rcpp Bindings for Sequential Monte Carlo
'Rcpp' Integration of the 'Streamulus' 'DSEL' for Stream
Processing
Rcpp-Based Truncated Normal Distribution RNG and Family
'Rcpp' Bindings to Parser for Tom's Obvious Markup Language
'Rcpp' Integration of Different "Ziggurat" Normal RNG
Implementations
An Implementation of Crime Analysis Methods
An Integrated Regression Model for Normalizing 'NanoString
nCounter' Data
R Interface to the CSDP Semidefinite Programming Library
Airborne LiDAR Filtering Method Based on Cloth Simulation
Styling of Graphics using Cascading Style Sheets
Predict Fish Year-Class Strength from Survey Data
Simulations and Visualizations of Rubik's Cube (with Mods)
General Network (HTTP/FTP/...) Client Interface for R
Concentration-Response Data Analysis using Curvep
Hierarchical Partitioning for Canonical Analysis
DCA Tools for Decline Rate Analysis and EUR Forecast
Manipulation Testing Based on Density Discontinuity
Robust Data Envelopment Analysis (DEA) for R
Descent-Based Calibrated Optimal Direct Estimation
Interact with the UK AIR Pollution Database from DEFRA
Relevant Dimension Estimation (RDE) in Feature Spaces
Tools to Manipulate and Query Semantic Data
An Implementation of the 'DoubleClick for Publishers' API
Different Tensor Factorization (Decomposition) Techniques for
RDF Tensors (Three-Mode-Tensors)
API Client and Dataset Management for the Demographic and Health
Survey (DHS) Data
A Collection of Functions to Experiment Dice Rolls
R Interface to the 'DieHarder' RNG Test Suite
Dimension Reduction and Estimation Methods
Distance-Sampling Analyses for Density and Abundance Estimation
Measurement and Partitioning of Similarity-Sensitive
Biodiversity
Local Randomization Methods for RD Designs
Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format
Files
Analysis of RD Designs with Multiple Cutoffs or Scores
Generating Various Numerical Representation Schemes of DNA
Sequences
R Interface to the 'Deutsche Nationalbibliothek (German National
Library) API'
Get the Category of Content Hosted by a Domain
Low-Level Interface to the '.NET' Virtual Machine Along the
Lines of the R C/Call API
Create Doxygen Documentation for Source Code
Update and Manipulate Rd Documentation Objects
Robust Data-Driven Statistical Inference in
Regression-Discontinuity Designs
Programmatic Interface to the 'Dropbox' API
Univariate and Multivariate Damped Random Walk Processes
R Interface to DSDP Semidefinite Programming Library
An R wrapper for the Data Science Toolkit API
Data Transforming Augmentation for Linear Mixed Models
Select and Download Climate Data from 'DWD' (German Weather
Service)
Interactive Data Tables Based on 'React Table'
Reactive Transport Modelling in 1d, 2d and 3d
Read Data Stored in DBC (Compressed DBF) Files
Parse 'ActiGraph' 'GT3X'/'GT3X+' 'Accelerometer' Data
Download and Tidy Time Series Data from the Australian Bureau of
Statistics
Simple Unified Interface to Read Bitmap Images
(BMP,JPEG,PNG,TIFF)
Reads Mass Spectrometry Data in Bruker *flex Format
Read ESA SNAP Processed Raster Format in R
Suite of Functions to Flexibly Read Data from Files
Reading Machine Learning Benchmark Data Sets in Different
Formats
Reads Mass Spectrometry Data in mzXML Format
Fast Reader for 'Wavefront' OBJ 3D Scene Files
Download and Tidy Data from the Reserve Bank of Australia
Simply Read ASCII Single and Multicard Polling Datasets
Translate Models from System Dynamics Software into 'R'
Import and Handling for Plain and Formatted Text Files
Enhanced Reading and Writing for 'SQLite' Databases
Monotonize Point and Interval Functional Estimates by
Rearrangement
Clean Water Quality Data for NPDES Reasonable Potential Analyses
Empirical Bayes Estimation and Inference
R Client for the eBird Database of Bird Observations
Finite Mixture Modeling, Clustering & Classification
Build Regular Expressions in a Human Readable Way
Core Functionality for the 'rebus' Package
Date and Time Extensions for the 'rebus' Package
Numeric Extensions for the 'rebus' Package
Unicode Extensions for the 'rebus' Package
Relevant Component Analysis for Supervised Distance Metric
Learning
Recursive Mining for Frequent Pattern and Confident Association
Rules
3D Reconstruction of Archaeological Excavations
Redundancy Control in Pathways databases
Preprocessing Tools to Create Design Matrices
Ordination Methods for the Analysis of Beta-Diversity Indices
Compute the Rectangular Statistical Cartogram
Lab for Developing and Testing Recommender Algorithms
Book-Crossing Dataset (BX) for 'recommenderlab'
Reconstruct Individual-Level Data from Published KM Plots
Toolkit to Validate New Data for a Predictive Model
Record Linkage Functions for Linking and Deduplicating Data Sets
Inference Tools in Time Series Based on Record Statistics
Recommender System using Matrix Factorization
Computes Revisitation Metrics for Trajectory Data
Companion Package to the Book 'R: Einführung durch angewandte
Statistik'
Automated Construction of R Data Packages from REDCap Projects
Reconstruction of Daily Data - Precipitation
Post Processing of (Half-)Hourly Eddy-Covariance Measurements
Reading Data from NetCDF Files for 'REddyProc'
Simulation Methods for Legislative Redistricting
Tools for the IUCN Red List of Ecosystems and Species
Regression Trees with Random Effects for Longitudinal (Panel)
Data
Objective Bayes Intrinsic Conditional Autoregressive Model for
Areal Data
EWAS using Reference-Free DNA Methylation Mixture Deconvolution
Cluster and Merge Similar Values Within a Character Vector
Straightforward 'BibTeX' and 'BibLaTeX' Bibliography Management
Refining Data Table Using a Set of Formulas
Locate Trans and Intersex-Friendly Toilets
Tools for an Introductory Class in Regression and Modeling
Cluster analysis via regression coefficients
Risk Estimation for Genetic and Environmental Traits
Wrappers Around 'base::grep()' for Use with Pipes
Regular Expressions in 'shiny' Select Lists
A 'Shiny' App to Test Regular Expressions in an R Environment
Helper Functions for Regression Analysis
Curve Registration for Exponential Family Functional Data
Regression-Based Causal Mediation Analysis with an Interaction
Term
Network-Based Regularization for Generalized Linear Models
Gaussian Linear Models with Linear Covariance Structure
Expander Functions for Generating Full Gradient and Hessian from
Single-Slot and Multi-Slot Base Distributions
Toolkit for Compiling, (Post-Hoc) Testing, and Plotting
Regression Results
Random Subspace Method (RSM) for Linear Regression
Information Preserving Regression-Based Tools for Statistical
Disclosure Control
Non-Parametric Bayesian Spectrum Estimation for Multirate Data
Detect and Test Regular Sequences and Subsequences
Regularized Simultaneous Component Based Data Integration
Searching for Footprints of Selection using 'Extended Haplotype
Homozygosity' Based Tests
Data Only: Searching for Footprints of Selection using Haplotype
Homozygosity Based Tests
Downloads Tweets from a List of Tweet IDs
Functions from "Reinsurance: Actuarial and Statistical Aspects"
Item Analysis Package with Standard Errors
Relabel Loadings from MCMC Output for Confirmatory Factor
Analysis
Relative Importance of Regressors in Linear Models
Functions for Mapping Key-Value Pairs, Many-to-Many,
One-to-Many, and Many-to-One Relations
Maximum Likelihood Estimation of Relatedness using EM Algorithm
Data Structures and Algorithms for Relations
Explore the UK's National Power Grid Datasets
Functions for estimating parameters in software reliability
models
Reliability Diagrams Using Isotonic Regression
Package for some probability distributions
Relative Contribution of Effects in a Regression Model
Regional Spatial Modeling with Continuous Borders
Match Regular Expressions with a Nicer 'API'
Tidy Output from Regular Expression Matching
'RStudio' Addins to Simplify 'Markdown' Writing
Insert and Extract "Reminders" from Function Comments
Extensible Markov Model for Modelling Temporal Relationships
Between Clusters
Regularized Multivariate Regression for Identifying Master
Predictors
Empirical Orthogonal Teleconnections in R
Remote R: Control a Remote R Session from a Local One
R Package Installation from Remote Repositories, Including
'GitHub'
Refining Evaluation Methodology on Stage System
Fitting Linear Models with Endogenous Regressors using Latent
Instrumental Variables
Renewal Method for Extreme Values Extrapolation
Renewable Power Systems and the Environment
Interface to Allow Full Use of the Environment Modules System
for Unix
Reordering the dendrogram according to the class labels
Calculation of Mortgage Plan or Repayment Plan
Global tests for expression data of high-dimensional sets of
molecular features
Replicability Analysis for Multiple Studies of High Dimension
Statistical Metrics for Multisite Replication Studies
Average Bioequivalence with Expanding Limits (ABEL)
Two-Way ANOVA-Like Method to Analyze Replicated Point Patterns
Test Replications by Means of the Prior Predictive p-Value
Replication Timing Profiling using DNA Copy Number
Miscellaneous Tools for Reproducible Research
Generates a Project and Repo for Easy Initialization of a
Workshop
Repeated Measures Proportional Odds Logistic Regression
Lightweight Infrastructure for Handling Multiple R Markdown
Documents
A General Message and Error Reporting System
An Easy Way to Report Regression Analysis
Generate LaTeX Tables of Descriptive Statistics
R Interface to 'EPP-Lab', a Java Program for Exploratory
Projection Pursuit
Determine the representativity of two multidimensional data sets
Create Representative Records After Entity Resolution
Prepare Reproducible Example Code via the Clipboard
Reproduce Statistical Analyses and Meta-Analyses
A Set of Tools that Enhance Reproducibility Beyond Package
Management
Coordinate System Transformations for Generic Map Data
Examples of Recursive Lists and Nested or Split Data Frames
Powerful Classes for HTTP Requests and Responses
Installing and Loading R Packages for Reproducible Workflows
General Purpose Client for 'ERDDAP' Servers
Extracts Environmental Data from 'ERDDAP' Web Services
Reordering and/or Reflecting Factors for Simulation Studies with
Exploratory Factor Analysis
Data Sets for Mathematical Statistics with Resampling in R
Bootstrap Imputation for Single-Cell RNA-Seq Data
Retrieving Publications from PubMed Database Based on User Query
Memory-Based Learning in Spectral Chemometrics
Tools for Analysis, Design, and Operation of Water Supply
Storages
Flexibly Reshape Data: A Reboot of the Reshape Package
Electrical Properties of Resistor Networks
Resource Selection (Probability) Functions for Use-Availability
Data
Tools for Conducting and Analyzing Respirometry Experiments
Search and Retrieve Data from Eurostat Database
Functions for Working with the 'www.estimize.com' Web Services
Multivariate Normal Restricted by Affine Constraints
Restricted Statistical Estimation and Inference for Linear
Models
Tools for Type S (Sign) and Type M (Magnitude) Errors
Import Professional Baseball Data from 'Retrosheet'
Repeated Function Evaluation for Sensitivity Analysis
Ratio-of-Uniforms Sampling for Bayesian Extreme Value Analysis
Revealed Preferences and Microeconomic Rationality
R Markdown Format for 'reveal.js' Presentations
Linear Regression Stability to Significance Reversal
Reverse Geocoding with the Photon Geocoder for OpenStreetMap,
Google Maps, and Bing
Data Preparation and Diagnostics for Random Effects Within
Estimator
R Wrappers for EXPOKIT; Other Matrix Functions
R Interface to 'FACTS' on Unix-Like Systems
A Collection of Efficient and Extremely Fast R Functions
A Collection of Efficient and Extremely Fast R Functions II
Random Forest with Canonical Correlation Analysis
Get Seismic Data from the International Federation of Digital
Seismograph Networks
Multiple Imputation using Chained Random Forests
Rapid Feasible Generalized Least Squares
Space-Time Estimation of Forest Variables using the FIA Database
'Programmatic Interface to the 'openfisheries.org' API'
Exploratory Data Analysis for FishNet2 Data
Query Plane Tickets using the 'Kiwi' API
Recency, Frequency and Monetary Value Analysis
Merging of Satellite Datasets with Ground Observations using
Random Forests
MarkLogic NoSQL Database Server in-Database Analytics for R
Graphics for Spherical Distributions and Earthquake Focal
Mechanisms
Data Integration Feature for Force.com and Salesforce.com
Code Examples to Accompany the Book "R for Dummies"
BATWING for Calculating Forensic Trace-Suspect Match
Probabilities
Estimate Permutation p-Values for Random Forest Importance
Metrics
A 'FRACTRAN' Interpreter and Some Helper Functions
Feasible Solution Algorithm for Finding Best Subsets and
Interactions
Random Forests Model Selection and Performance Evaluation
Unbiased Variable Importance for Random Forests
Interactive Visualization Tool for Random Forests
Gabriel Multiple Comparison Test and Plot the Confidence
Interval on Barplot
Gamma convolutions for methylation array background correction
Interface to the Global 'Biodiversity' Information Facility API
LS-TreeBoost and LAD-TreeBoost for Gene Regulatory Network
Reconstruction
Hierarchical Modeling and Frequency Method Checking on
Overdispersed Gaussian, Poisson, and Binomial Data
Regularized and Sparse Generalized Canonical Correlation
Analysis for Multiblock Data
Preprocessing and Multivariate Analysis of Bidimensional Gas
Chromatography Data
Bindings for the 'Geospatial' Data Abstraction Library
Wrapper for 'Coinbase Pro (GDAX)' Cryptocurrency Exchange
NASA's Global Ecosystem Dynamics Investigation (GEDI) Data
Visualization and Processing
Random Sampling Distribution C++ Routines for Armadillo
Generates Multivariate Nonnormal Data and Determines How Many
Factors to Retain
Tools to Generate Daily-Precipitation Time Series
R Version of GENetic Optimization Using Derivatives
Geographic Profiling Methods for Serial Crime Analysis
Interface to Geometry Engine - Open Source ('GEOS')
Build, Import and Export GEXF Graph Files
Access WHO Global Health Observatory Data from R
R Interface to Global Biotic Interactions
Unsampled Data in R for Google Analytics Premium Accounts
Data and Functions from the Book R Graphics, Third Edition
Interface Between GRASS 7 Geographical Information System and R
Repetitive Group Sampling Plan Based on Cpk
Search and Retrieve Spatial Data from 'GUGiK'
Interface to the 'Handsontable.js' Library
Robust Hierarchical Co-Clustering to Identify Significant
Co-Cluster
Retrieve data sets from the HealthData.gov data API
Clustering Genetic Sequence Data Using the HierBAPS Algorithm
An R Implementation of the FIS MarketMap C-Toolkit
Random Heteroscedastic Nested Error Regression
Side Effect Risks in Hospital : Simulation and Estimation
Permits *apply() Style Dispatch for 'HPC'
Benchmarks for High-Performance Computing Environments
Heart Rate Variability Analysis of ECG Data
Ryan-Holm Step-Down Bonferroni or Sidak Procedure
Regularized Hotelling's T-square Test for Pathway (Gene Set)
Analysis
Wrapper for the 'Datamuse' API to Find Rhyming and Associated
Words
ri: R package for performing randomization-based inference for
experiments
Randomization Inference for Randomized Experiments
Randomization Inference for Treatment Effects on a Binary
Outcome
Radiomics Image Analysis Toolbox for Medial Images
Gene Annotation of Rice (Oryza Sativa L.spp.japonica)
Convert Biological ID from RAP or MSU to SYMBOL for Oryza Sativa
Computes and Compares Species Richnesses
Enrichment for Diseases in a Set of Genes
Drawing SVG Graphics to Visualize and Map Genome-Wide Data on
Idiograms
Ridge Regression with Automatic Selection of the Penalty
Parameter
R Package for Ridge Fusion in Statistical Learning
Ridit Analysis (An extension of the Kruskal-Wallis Test.)
Accesses Weather Data from the Iowa Environment Mesonet
Learning with Data on Riemannian Manifolds
Functions and C++ Header Files for Computation on Manifolds
An R Interface to the 'Tiingo' Stock Price API
Create Colour Palettes Based on Famous Artworks from the
Rijksmuseum
ILO Open Data via Ilostat Bulk Download Facility or SDMX Web
Service
Read 'ImageJ' Region of Interest (ROI) Files
An Installation Framework for Shiny Apps
C++ Classes to Embed R in C++ (and C) Applications
An Implementation of the 'Instagram' API Using Tidy Principles
View Images on Full Screen in 'RMarkdown' Documents and 'shiny'
Applications
Detects Fraud in Online Surveys by Tracing, Scoring, and
Visualizing IP Addresses
Calculate Persistent Homology with Ripser-Based Engines
Data Analysis and Parameter Estimation Using Item Response
Theory
Causal Inference and Prediction in Cohort-Based Analyses
Computes 26 Financial Risk Measures for Any Continuous
Distribution
Functions to Study Etiologic Heterogeneity
G-Computation to Estimate Interpretable Epidemiological Effects
Assessing Risk Predictions for Clustered Data
Risk Regression Models and Prediction Scores for Survival
Analysis with Competing Risks
Riskset ROC curve estimation from censored survival data
Risk Quantification for Stock Portfolios under the T-Copula
Model
Rendering Risk Literacy more Transparent
Isothermal Titration Calorimetry (ITC) Data Analysis
Integrated Taxonomic Information System Client
River Network Distance Computation and Applications
Load Estimation of River Compounds with Different Methods
In vitro in vivo correlation linear level A
Steady and Unsteady Open-Channel Flow Computation
A Clean, Whitespace-Sensitive Template Language for Writing HTML
Artificial Intelligence Systems and Observer Performance
Provides Access to Databases Through the JDBC Interface
Interface to 'JDemetra+' Seasonal Adjustment Software
'rmarkdown' Extension for Formatted 'RJDemetra' Outputs
Quality Assessment for Seasonal Adjustment
Miscellaneous Useful Functions for Statistics
R-Interface to Gene Drop Simulation from JPSGCS
Serialize R Objects to JSON, JavaScript Object Notation
Interface to the 'JWSACruncher' of 'JDemetra+'
Using Apache 'Kafka' Messaging Queue Through 'R'
External Jars Required for Package 'rkafka'
Datasets from 'KEEL' for it Use in 'RKEEL'
Kernel Operations on the GPU, with Autodiff, without Memory
Overflows
Ridge Group Sparse Optimization Problem for Estimation of a Meta
Model Based on Reproducing Kernel Hilbert Spaces
Random KNN Classification and Regression
Topological Analysis of Knotted Proteins, Biopolymers and 3D
Structures
Mann-Kendall Test, Seasonal and Regional Kendall Tests
Data Exchange Between R and 'LabKey' Server
Functions for Base Types and Core R and 'Tidyverse' Features
Read and Write 'las' and 'laz' Binary File Formats Used for
Remote Sensing Data
Create Interactive Linked Charts with Minimal Code
Analyze and Design Repeated Low-Dose Challenge Experiments
Bayesian LDA for Mixed-Membership Clustering Analysis
Common Functions for Run-Length Encoded Vectors
Estimates, Plots and Evaluates Leaf Angle Distribution
Functions, Calculates Extinction Coefficients
R Interface to RNG with Multiple Streams
Simulations and Statistical Inference for Linear Fractional
Stable Motions
Bayesian Exponential Smoothing Models with Trend Modifications
Ensemble Empirical Mode Decomposition (EEMD) and Its Complete
Variant (CEEMDAN)
Linked Inference of Genomic Experimental Relationships
Iterative Solvers for (Sparse) Linear System of Equations
A Toolbox for Non-Tabular Data Manipulation
Robust Regression with Data Driven Tuning Parameter
Rank-Based Estimation and Prediction in Random Effects Nested
Models
R Parallel Implementation of Local Outlier Factor(LOF)
Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive
Models
Monte-Carlo Methods for Simulating Luminescence Phenomena
Solving Ordinary Differential Equations to Understand
Luminescence
'Shiny' Applications for the R Package 'Luminescence'
Weighted Rasch Modeling and Extensions using Conditional Maximum
Likelihood
Exact Confidence Intervals for Random Effects Meta-Analyses
MAGIC - Markov Affinity-Based Graph Imputation of Cells
Makefile Generator for R Analytical Projects
Fit Multi-Modal Mallows' Models to Ranking Data
Continuous Optimization using Memetic Algorithms with Local
Search Chains (MA-LS-Chains) in R
Client for 'mapshaper' for 'Geospatial' Operations
Client for 'Mapzen' and Related Map APIs
Detect Marine Heat Waves and Marine Cold Spells
Estimate Original Hydrocarbon in Place and Reservoir Performance
The MCFS-ID Algorithm for Feature Selection and Interdependency
Discovery
Kuhn-Tucker and Multiple Discrete-Continuous Extreme Value
Models
HTML Output Formats and Templates for 'rmarkdown' Documents
Partial 'rmarkdown' Documents to Prettify your Reports
'R' 'Markdown' Format for 'shower' Presentations
Count Words, Chars and Non-Whitespace Chars in R Markdown Docs
Synchrony in Motion Energy Analysis (MEA) Time-Series
An Individual-Based Population Genetic Simulation Environment
Multiple Imputation with Denoising Autoencoders
Data Mining Classification and Regression Methods
A Robust Missing Imputation Method for Gene Expression Data
Combining Mixture Components for Clustering
Mixture Models with Heterogeneous and (Partially) Missing Data
Minimal Interface of the C++ 'MixtComp' Library for Mixture
Models with Heterogeneous and (Partially) Missing Data
Utility Functions for 'MixtComp' Outputs
Multiple Kernel Learning for Classification or Regression
Problems
Maximum Likelihood Principal Component Analysis
Connect R with MOA for Massive Online Analysis
R MPFR - Multiple Precision Floating-Point Reliable
Interface (Wrapper) to MPI (Message-Passing Interface)
Recursive Modified Pattern Search on Hyper-Rectangle
Causal Mediation Analysis Using Weighting Approach
Importing Data from Loligo Systems Software, Calculating
Metabolic Rates and Critical Tensions
RNA-Seq Analysis for Repeated-Measures Data
Root-mean-square goodness-of-fit test for simple null hypothesis
Amazing Random Facts About the World's Greatest Hacker
Quickly View Data Frames in 'Excel', Build Folder Paths and
Create Date Vectors
'Rcpp' Bindings to Native C++ Implementation of MS Numpress
Signal-Noise Separation in Random Matrices by using Eigenvalue
Spectrum Analysis
Distributions, Statistics and Tests derived from Random Matrix
Theory
Utilities for Nonlinear Regression and Repeated Measurements
Models
Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS
Tool
Tools to Conduct Meteorological Normalisation on Air Quality
Data
Database Interface and 'MySQL' Driver for R
Log-Linear Poisson Graphical Model with Hot-Deck Multiple
Imputation
RNA Secondary Structure Module Mining, Comparison and Plotting
RNA Secondary Structure Comparison and Module Mining
World Vector Map Data from Natural Earth Used in 'rnaturalearth'
Image Data Used in the Loon Package Demos
Visualization of High-Throughput Data on Large-Scale Biological
Networks
Wrapper for the National Bank of Poland API
EUtils libraries for use in the R environment
Obtain, Organize, and Visualize NCEP Weather Data
Testing Neighbor Effects in Marker-Based Regressions
Interval Mapping for Quantitative Trait Loci Underlying Neighbor
Effects
Entropy Based Method for the Detection of Significant Variation
in Gene Expression Data
Fast Network Modularity and Roles Computation by Simulated
Annealing (Rgraph C Library Wrapper for R)
Provides an Interface to the Agent-Based Modelling Platform
'NetLogo'
Tools for Comparing Text Messages Across Time and Media
Semantically Rich I/O for the 'NeXML' Format
Random Number Generation for Generalized Poisson Distribution
Seeding the Default RNG with a Numeric Vector
Utility Functions for Working with Random Number Generators
Toolbox for WELL Random Number Generators
Random number generator WELL19937a with 53 or 32 bit output
Image Registration Using the 'NiftyReg' Library
A Wrapper of the 'JavaScript' Library 'Nightly'
Perform the Complete Processing of a Set of Proton Nuclear
Magnetic Resonance Spectra
An R Interface to the NOAA Operational Model Archive and
Distribution System
Interface to the National 'Phenology' Network 'API'
UK National River Flow Archive Data from R
Interface to the Numerai Machine Learning Tournament API
Find Free Versions of Scholarly Publications via Unpaywall
Robust Analysis of High Dimensional Data
Interpolation Grids for Packages of the 'RobASt' - Family of
Packages
Conditionally Unbiased Bounded Influence Estimates
Robust Bayesian Variable Selection for Gene-Environment
Interactions
Forecasting Time Series with Robust Exponential Smoothing
Optimally Robust Estimation for Extreme Value Distributions
Robust Bootstrap Forecast Densities for GARCH Models
Interface for the RobinHood.com No Commission Investing Platform
Ocean Biodiversity Information System (OBIS) Client
Innovative and/or Additive Outlier Robust Kalman Filtering
Optimally Robust Influence Curves and Estimators for Location
and Scale
Infinitesimally Robust Estimators for Preprocessing -Omics Data
Robust Generalized Linear Models (GLM) using Mixtures
Generation of Dynamic Coappearance Matrices Within Texts
Robustness Checks for Omitted Variable Bias
A 'robots.txt' Parser and 'Webbot'/'Spider'/'Crawler'
Permissions Checker
Robust Periodogram and Periodicity Detection Methods
Three-Step Regression and Inference for Cellwise and Casewise
Contamination
Robust Regression with Compositional Covariates
Optimally Robust Influence Curves for Regression and Scale
Robust Regularized Singular Value Decomposition
Import an Observable Notebook as HTML Widget
Truncated Maximum Likelihood Fit and Robust Accelerated Failure
Time Regression for Gaussian and Log-Weibull Case
Robust Bayesian Linear Mixed-Effects Models using ABC
Robust Calibration of Imperfect Mathematical Models
Robust Methods using Exponential Tilt Model
An Object Oriented Solution for Robust Factor Analysis
Robust Estimation for Generalized Additive Models
Robust Gaussian Stochastic Process Emulation
Robust Methods for High-Dimensional Data
Perform the Robust Multivariable Mendelian Randomization
Analysis
An Extended Rao-Stirling Diversity Index to Handle Missing Data
Robust Clustering of Single Cell RNA-Seq Data
'eXtra' / 'eXperimental' Functionality for Robust Statistics
Visualize the Results of Risk-of-Bias (ROB) Assessments
Performance Assessment of Binary Classifier with Visualization
Non-Inferiority Test for Paired ROC Curves
ROC Curve Inference with and without Covariates
Robust Rank Correlation Coefficient and Test
Compute and Compare Diagnostic Test Statistics Across Groups
Visualizing the Performance of Scoring Classifiers
Receiver Operating Characteristic (ROC)-Guided Classification
and Survival Tree
Non-parametric estimation of ROC curves without Gold Standard
Test
Wrapper Functions for 'ODAM' (Open Data for Access and Mining)
Web Services
Provides Access to Databases Through the ODBC Interface
Ordinary Differential Equation (ODE) Solvers Written in R Using
S4 Classes
'ROI' Optimization Problems Based on 'globalOptTests'
'ROI' Access to 'MIPLIB' 2010 Benchmark Instances
'ROI' Optimization Problems Based on 'NETLIB-LP'
'alabama' Plug-in for the 'R' Optimization Infrastructure
'Clp (Coin-or linear programming)' Plugin for the 'R'
Optimization Interface
'DEoptim' and 'DEoptimR' Plugin for the 'R' Optimization
Interface
'ECOS' Plugin for the 'R' Optimization Infrastructure
'ipop' Plug-in for the 'R' Optimization Interface
'lp_solve' Plugin for the 'R' Optimization Infrastructure
'Multi-Solution' Binary Linear Problem Plug-in for the 'R'
Optimization Interface
'NEOS' Plug-in for the 'R' Optimization Interface
'nloptr' Plug-in for the 'R' Optimization Infrastructure
'optimx' Plug-in for the 'R' Optimization Infrastructure
'osqp' Plugin for the 'R' Optimization Infrastructure
'qpOASES' Plugin for the 'R' Optimization Infrastructure
'quadprog' Plug-in for the 'R' Optimization Infrastructure
'SCS' Plug-in for the 'R' Optimization Infrastructure
'SYMPHONY' Plug-in for the 'R' Optimization Interface
R Markdown Output Formats for Storytelling
Fast Rolling and Expanding Window Linear Regression
Convert Colour Specification to Colour Name
A Colour List and Colour Metric Based on the ISCC-NBS System of
Color Designation
Finding Optimal Three-Group Splits Based on a Survival Outcome
Subroutines to Estimate Rolling Window Multiple Correlation
Read and Search Interface to the 'HL7 FHIR' REST API
R Object Oriented Programming for Statistical Distribution
Finds Roots, Extrema and Inflection Points of a Curve
Nonlinear Root Finding, Equilibrium and Steady-State Analysis of
Ordinary Differential Equations
Distribution of Largest Root for Single and Double Wishart
Settings
Regression Optimized: Numerical Approach for Multivariate
Classification and Regression Trees
Model Selection with FDR Control of Selected Variables
Accesses Air Quality Data from the Open Data Platform OpenAQ
Download, Compile and Link 'OpenBLAS' Library with R
Query and Download 'Rapid7' 'Cybersecurity' Data Sets
Additional Operators to Help you Write Cleaner R Code
Reproducible Data Retrieval from the Roper Center Data Archive
Low-Level Support for Provenance Capture Between in-Memory R
Objects
Optimally Robust Estimation - Old Version
General Purpose Optimization in R using C++
Optimally Robust Estimation for Regression-Type Models
Matrix Reconstruction from a Few Entries
OCI Based Oracle Database Interface for R
Extended Rosenbrock-Type Densities for Markov Chain Monte Carlo
(MCMC) Sampler Benchmarking
Plot Raster Map Tiles from Open Street Map and Other Sources
Robust Sparse PCA using the ROSPCA Algorithm
Tests for Rotational Symmetry on the Hypersphere
Interface to the 'Open Tree of Life' API
Simplification of Decision Tables using Rough Sets
Data Analysis Using Rough Set and Fuzzy Rough Set Theories
A Simple Router for HTTP and WebSocket Requests
Royston's H Test: Multivariate Normality Test
Placido Analysis of Corneal Irregularity
Confirmatory Adaptive Clinical Trial Design and Analysis
Automatic Detection of Experimental Unit in Precision
Agriculture
Simple Interactive Controls for R using the 'tcltk' Package
Recursive Partitioning and Regression Trees
Least Absolute Deviation Regression Trees
Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
Tools for parsing and manipulating rpart objects, including
generating machine readable rules
Classification trees for ordinal responses
Recognising Visual Charting Patterns in Time Series Data
RobustPCA: Decompose a Matrix into Low-Rank and Sparse
Components
Tools for the Construction of Clinical Code Lists for Primary
Care Database Studies
RPCLR (Random-Penalized Conditional Logistic Regression)
Read, Write, Visualize and Manipulate PDB Files
Tools for Chromatographic Column Characterization and Modelling
Chromatographic Peak
Random Projection Ensemble Clustering Algorithm
Gamma and Exponential Generalized Linear Models with Elastic Net
Penalty
Computation and Plots of Influence Functions for Risk and
Performance Measures
Estimates of Standard Errors for Risk and Performance Measures
Reduced Piecewise Exponential Estimate/Test Software
Phylogenetic Comparative Tools for Missing Data and
Within-Species Variation
Get 'Silhouettes' of 'Organisms' from 'Phylopic'
Build Powerful Pivot Tables and Dynamically Slice & Dice your
Data
Interface to the Search API for 'PLoS' Journals
Bayesian Age-Depth Modelling of Cores Dated by Pb-210
Graphical User Interface (GUI) for Interactive R Analysis
Sessions
Recursive Partitioning for Modeling Survey Data
R Interface to the 'PostgreSQL' Database System
Sample Size Computations Controlling the Type-II Generalized
Family-Wise Error Rate
Resolvable partially pairwise balanced design and Space-filling
design via association scheme
Reads, Annotates, and Normalizes Reverse Phase Protein Array
Data
Reverse-Phase Protein Array Super Position and Concentration
Evaluation
Access the Global Plant Phenology Data Portal
Regularized PQL for Joint Selection in GLMMs
Database Preferences and Skyline Computation
Estimating Disease Prevalence from Registry Data
Functions for Working with 'Eprime' Text Files
WOE Transformation and Scorecard Builder
R Interface to the 'Protocol Buffers' 'API' (Version 2 or 3)
Rank Preserving Structural Failure Time Models
Goodness of Fit Tests for High-Dimensional Linear Regression
Models
Repeatability Estimation for Gaussian and Non-Gaussian Data
R Interface to the Pushbullet Messaging Service
Estimate the PVT Properties of Reservoir Fluids
Quantum Entanglement of Bipartite System
Quantitative Evaluation of the Native Fertility of Tropical
Soils
Relational Query Generator for Data Manipulation at Scale
Statistical Methods for the Randomized Response Technique
Real-Time Adaptive Penalization for Streaming Lasso Models
Robust Regression with Asymmetric Heavy-Tail Noise Distributions
Estimating Replication Rate for Genome-Wide Association Studies
Ridge Regression and Other Kernels for Genomic Selection
Scalable Robust Estimators with High Breakdown Point
Robust Methods for Multiway Data Analysis, Applicable also for
Compositional Data
Robust Multivariate Methods for High Dimensional Data
Scalable Robust Estimators with High Breakdown Point for
Incomplete Data
Import Data from a RRD (Round Robin Database) File
'DRNG' on Intel CPUs with the 'RdRand' Instruction for R
Environment for Evaluating Recommender Systems
Visualization for Norwegian Health Quality Registries
Generate Two- And Three-Phase Relative Permeability Estimates
Invoke 'Repast Simphony' Simulation Models
Realized Relatedness Estimation and Simulation
Residual Randomization Inference for Regression Models
Fitting Distributions to Given Data or Known Quantiles
Robust Regularized Linear Discriminant Analysis
Access Publisher Copyright & Self-Archiving Policies via the
'SHERPA/RoMEO' API
Phylogenetic Ridge Regression Methods for Comparative Studies
Linear Model Evaluation with Randomized Residuals in a
Permutation Procedure
Correlation and Regression Analyses for Randomized Response Data
Online Robust Reduced-Rank Regression Estimation
Robust Re-Scaling to Better Recover Latent Effects in Data
Reproducible Research with a Table of R Codes
Randomized Response Techniques for Complex Surveys
Bayesian Estimation of the Reduced Reparameterized Unified Model
with Gibbs Sampling
Data related to the book "R Statistical Application Development
by Example"
Linking R with the Open-Source 'SAGA-GIS' Software
Builds Empirical Remote Sensing Models of Water Quality
Variables and Analyzes Long-Term Trends
Ports the Workflow of "Resampling Stats" Add-in to R
Random Sampling Association Rules from a Transaction Dataset
Tools, Classes, and Methods for Interfacing with SaTScan
Stand-Alone Software
Handle R Requests from R Service Bus Applications with JSON
Payloads
Part Information from the Registry of Standard Biological Parts
An R Package for Stepwise Cluster Analysis
Rao-Scott Cochran-Armitage by Slices Trend Test
Bridge Between 'R' and 'Scala' with Callbacks
Shadow-Test Approach to Computerized Adaptive Testing
Scelestial: Steiner Tree Based Single-Cell Lineage Tree
Inference
SciMark 2.0 Benchmark for Scientific and Numerical Computing
Deploys Multiple 'Shiny' Apps using Configuration File
Deployment Interface for R Markdown Documents and Shiny
Applications
Generic implementation of the 'RStudio' connections contract
A Method to Download Department of Education College Scorecard
Data
Ray Shooting Depth (i.e. RS Depth) functions for bivariate
analysis
Tools for Reading SDMX Data and Metadata
Number of Newly Discovered Rare Species Estimation
Estimating the Proportion of Genetically Modified Seeds in
Seedlots via Multinomial Group Testing
Robust Structural Equation Modeling with Missing Data and
Auxiliary Variables
Strain Elevation Tension Spring Embedding
Report of Statistical Findings in 'bookdown'
Functions for Hierarchical Bayesian Estimation: A Flexible
Approach
Simulated Haploid Asexual Population Evolution
Siena - Simulation Investigation for Empirical Network Analysis
Analysis of Simulation Studies Including Monte Carlo Error
Download Data from Mexico's Air Quality Information System
Create Custom 'Rstudio' Keyboard Shortcuts
A Stemming Algorithm for the Portuguese Language
Submit R Calculations to a 'Slurm' Cluster
Loading Facebook and Instagram Advertising Data from
'Smartly.io'
Neural Networks using the Stuttgart Neural Network Simulator
(SNNS)
Get 'SNP' ('Single-Nucleotide' 'Polymorphism') Data on the Web
Efficient Score Statistics for Genome-Wide SNP Set Analysis
Import Various Northern and Southern Hemisphere Climate Indices
Adapt Numerical Records to Fit (in)Equality Restrictions
Sites, Population, and Records Cleaning Skills
Rational Approximations of Fractional Stochastic Partial
Differential Equations
Solvers for Large-Scale Eigenvalue and SVD Problems
Conversion Between Attitude Representations of DCM, Euler
Angles, Quaternions, and Euler Vectors
R's Shortest Path Problem with Forbidden Subpaths
Database Agnostic Package to Generate and Process 'SQL' Queries
in R
Statistical Downscaling Toolkit for Climate Change Scenario
using Non Parametric Quantile Mapping
Total Mediation Effect Size Measure (R-Squared Measure) under
Moderate or High-Dimensional Mediator Settings
A Collection of Methods for Singular Spectrum Analysis
Implementations of Semi-Supervised Learning Approaches for
Classification
Simulation of Supply Reservoir Systems using Standard Operation
Policy
Client Library for SpatioTemporal Asset Catalog
Persistent Fast Amortized Stack and Queue Data Structures
Bayesian Applied Regression Modeling via Stan
Tools for Developing R Packages Interfacing with 'Stan'
Spatial Temporal Aggregated Predictor Models via 'stan'
Pipe-Friendly Framework for Basic Statistical Tests
Random Orthonormal Matrix Generation and Optimization on the
Stiefel Manifold
Simulate and Develop Streaming Processing
Tools to Read and Manipulate Fisheries Data
Smooth Survival Models, Including Generalized Survival Models
A Convenience Interface for the Stripe Payment API
Supports Developing, Building and Deploying R Solution
Design of Rotatable Central Composite Experiments and Response
Surface Analysis
Robust Estimation of the Proportion of Treatment Effect
Explained by Surrogate Marker Information
Design and Analysis of Disease Surveillance Activities
Render SVG Images into PDF, PNG, PostScript, or Bitmap Arrays
An R SVG Graphics Device with Dynamic Tips and Hyperlinks
R Interface to SymPy Computer Algebra System
Extract Semantic Relations from Text by Querying and Reshaping
Syntax
Manage and manipulate large collections of R objects stored as
tape-like files
Detecting Trait Clustering in Environmental Gradients
Tools for analyzing sales report files of iTunes Connect
R Templates for Reproducible Data Analyses
Tools for Tensor Analysis and Decomposition
Automatic Text Classification via Supervised Learning
Functions for calculation of texture metrics for Grey Level
Co-occurrence Matrices
Supports the Analysis of RTI MicroPEM Output Files
Inequality, Welfare and Poverty Indices and Curves using the
EU-SILC Data
'STK++' Core Library Integration to 'R' using 'Rcpp'
Truncated Newton Function Minimization with Bounds Constraints
Create and Manage Todolist using 'Todoist.com' API
Interpolation of Data with Variable Spatial Support
Measuring Information Flow Between Time Series with Shannon and
Renyi Transfer Entropy
Datasets and Functions Relating to Star Trek
Analyze Download Logs from the CRAN RStudio Mirror
Triangle - A 2D Quality Mesh Generator and Delaunay Triangulator
Advanced and Parallel Random Number Generation via 'TRNG'
T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut
Implementation
Shiny Apps for Plotting and Exploratory Analysis
The R Implementation of the 't-walk' MCMC Algorithm
Bayesian Inference from the Conditional Genetic Stock
Identification Model
Implementation of Unobserved Components Model (UCM)
Learn Text 'Embeddings' with 'Starspace'
Univariate GARCH-MIDAS, Double-Asymmetric GARCH-MIDAS and
MEM-MIDAS
Data and Functions for USA State and County Unemployment Data
Runiversal - Package for converting R objects to Java variables
and XML
Interface Utilities, Model Templates, Parallel Computing Methods
and Additional Distributions for MCMC Models in JAGS
Fast Computation of Running Statistics for Time Series
R Interface to the 'UNU.RAN' Random Variate Generators
Beautiful Graphical Representation of Multiplication Tables on a
Modular Circle
Implementation of Unsupervised Neural Architectures
Detect and Remove Unwanted Variation using Negative Controls
Testing and Plotting Procedures for Biostatistics
R-Values for Ranking in High-Dimensional Settings
Manipulations of Triangular Meshes Based on the 'VCGLIB' API
Query 'R' Versions, Including 'r-release' and 'r-oldrel'
Search 'Vertnet', a 'Database' of Vertebrate Specimen Records
Rare Variants Association Analyses with Family Data
R Graphics Devices for Vector Graphics Output
Calling haplotype-based and variant-based pedigree
disequilibrium test for rare variants in pedigrees
High Performance Algorithms for Vine Copula Modeling
Radial Velocity Method for Detecting Exoplanets
Variable Metric Nonlinear Function Minimization
Calculates the Distance Between Voter and Multiple Polling
Locations
population control weighted rare-variants TDT
A package for accessing World Bank climate data
Detects spatial outliers using a Random Walk on Bipartite Graph
Read and Manipulate Data from 'RiverWare'
Import and Handling for 'WhatsApp' Chat Logs
Interface for the 'Wildbook' Wildlife Data Management Framework
Download, Edit and Include Wind and Sea Currents Data in
Ecological and Evolutionary Analysis
Lazy Search in R Packages, Task Views, CRAN, the Web. All-in-One
Download
Chinese Character Frequency in Real World
R We There Yet? Visualizing MCMC Convergence in Phylogenetics
'R x C Ecological Inference With Optional Incorporation of
Survey Information'
Functions to Parse and Create XMCDA Files
Queries and Extracts Images from Extensible Neuroimaging Archive
Toolkit Public/Private Datasets
Functions to Compute Chemical Reaction Similarity
Combined Total and Allele Specific Reads Sequencing Study
Maximum Likelihood Shrinkage using Generalized Ridge or Least
Angle Regression Methods
R Interface to the 'Yacas' Computer Algebra System
Legacy 'Ryacas' (Interface to 'Yacas' Computer Algebra System)
R package provide functions to translate English words into
Chinese
Companion to the Forthcoming Book - R you Ready?
Access to the YouTheria Mammal Trait Database
Grain size analysis, textural classifications and distribution
of unconsolidated sediments
R Module for Working with the 'Zabbix API'
Partitioning of Individual Autozygosity into Multiple
Homozygous-by-Descent Classes
Spherical Geometry Operators Using the S2 Geometry Library
Functions for University of Auckland Course STATS 201/208 Data
Analysis
A Set of Common Tools for Seasonal to Decadal Verification
Set of Common Tools for Forecast Verification
Spatial Two Stage Least Squares Estimation
Biclustering via Sparse Singular Value Decomposition
Incorporating Stability Selection
Somatic Copy Number Alteration Analysis Using Sequencing and SNP
Array Data
Background Removal and Spectrum Identification for SERS Data
Detection of Fixations in Eye-Tracking Data
Verify the Scale, Anisotropy and Direction of Weather Forecasts
Stability Analysis in Differentially Expressed Genes
Species Abundance Distributions with Independent-Species
Assumption
Maximum Likelihood Models for Species Abundance Distributions
Small Area Estimation with Measurement Error
Stochastic Approximation Expectation Maximization (SAEM)
Algorithm
Small Area Estimation for Rao and Yu Model
Simulation Tools for Small Area Estimation
Encrypt and Decrypt Strings, R Objects and Files
Create Interactive Graphics Related to Clinical Trial Safety
Clustering via Stochastic Approximation and Gaussian Mixture
Models
Akaike Information Criterion for Sparse Estimation
An Extension of the Taylor Diagram to Two-Dimensional Vector
Data
Provides Access to Salem Witchcraft Data
Elastic Net and (Adaptive) Lasso Penalized Sparse Asymmetric
Least Squares (SALES) and Coupled Sparse Asymmetric Least
Squares (COSALES) using Coordinate Descent and Proximal
Gradient Algorithms
An Implementation of 'Salesforce' APIs Using Tidy Principles
Search Algorithms and Loss Functions for Bayesian Clustering
Selection and Misclassification Bias Adjustment for Logistic
Regression Models
A Collection of Techniques Correcting for Sample Selection Bias
A Semi-Supervised Method for Prediction of Phenotype Event Times
Sample Design, Drawing & Data Analysis Using Data Frames
A Framework for Comparing the Performance of MCMC Samplers
Sample Size Calculation for Various t-Tests and Wilcoxon-Test
Sample Size Calculation for the Comparison of Means or
Proportions in Phase III Clinical Trials
Sample Size Calculations for Complex Surveys
Power and Sample Size Calculation for the
Cochran-Mantel-Haenszel Test
Sample Size Calculations for Case-Control Studies
Sample size calculations for normal means
Calculating sample size requirements when estimating the
difference between two binomial proportions
Sampling Data Within Different Study Designs for Cluster
Randomized Trials
Optimal Stratification of Sampling Frames for Multipurpose
Sampling Surveys
Sampling Surface Simulation for Areal Sampling Methods
SAM: Significance Analysis of Microarrays
Merge-Split Samplers for Conjugate Bayesian Nonparametric Models
Sensitivity Assessment to Unmeasured Confounding with Multiple
Treatments
Stochastic Augmentation of Matched Data Using Restriction
Methods
Sensitivity Analysis of a Meta-analysis with Unpublished but
Registered Analytical Investigations
Statistical Models for the Unsupervised Segmentation of
Time-Series ('SaMUraiS')
Statistical Analysis of Network Data with R, 2nd Edition
Downloads and Tidies the San Francisco Public Utilities
Commission Beach Water Quality Monitoring Program Data
C/C++ source code to trigger Address and Undefined Behaviour
Sanitizers
Keeps Track of all Performed Sanity Checks
Illustrate the Flow of Information or Material
Create Dependency Wheels and Sankey Diagrams
Stratified Analysis with Nonparametric Covariable Adjustment
Color Palettes Based on the Works of Sanzo Wada
Group Ordinal Method for Multiple Criteria Decision-Making
Import Air Quality Monitoring Data in a Fast and Easy Way
An R-GUI for Spatial Analysis of Surface Runoff using the
NRCS-CN Method
Simulation and Prediction with Seasonal ARIMA Models
Network-Based Interpretation of Changes in Compositional Data
XML Output Functions for Easy Creation of Moodle Questions
Snow Profile Analysis for Snowpack and Avalanche Research
Snow Profile Alignment, Aggregation, and Clustering
Fit and Compare Species-Area Relationship Models Using
Multimodel Inference
Import ASCII files directly into R using only a SAS input script
Data sets from "SAS System for Mixed Models"
Syntactically Awesome Style Sheets ('Sass')
Scientific Analysis of Trial Errors (SATE)
Handling and Manipulating Remote Sensing Data
Visualisation and Analysis of Ocean Data Derived from Satellites
Spanning Trees Used for Network Inference
Inference and Learning in Stochastic Automata
Bayesian Emulation, Calibration and Validation of Computer
Models
Single-Cell RNA-Seq Gene Expression Recovery
Small-Sample Adjustments for Wald Tests Using Sandwich
Estimators
Parameter-Free Domain-Agnostic Season Length Detection in Time
Series
Search Best ARIMA, GARCH, and MS-GARCH Model
Estimation of the Proportion of SB Explained by Confounders
Semiparametric Bayesian Gaussian Copula Estimation and
Imputation
Computing the Singular BIC for Multiple Models
sbioPN: Simulation of deterministic and stochastic spatial
biochemical reaction networks using Petri Nets
Sparse Bayesian Learning for QTL Mapping and Genome-Wide
Association Studies
Scalable Bayes with Median of Subset Posteriors
Semidefinite Programming for Fitting Block Models of Equal Block
Sizes
Inference for a Generalised SBM with a Split Merge Sampler
Text Prediction via Stupid Back-Off N-Gram Models
Machine Learning with AdaBoost on Decision Stumps
Detecting structural breaks using rectangle covering
(non-parametric method)
Satorra-Bentler Scaled Chi-Squared Difference Test
Stable Balancing Weights for Causal Inference and Estimation
with Incomplete Outcome Data
Scaffolding Interfaces to Packages in Other Programming
Languages
Compute scagnostics - scatterplot diagnostics
Scale Alignment for Between-Items Multidimensional Rasch Family
Models
Approximately Unbiased P-Values via Multiscale Bootstrap
Single-Case Data Analyses for Single and Multiple Baseline
Designs
Shape-Constrained Additive Regression: a Maximum Likelihood
Approach
Optimization Toolkit for Pharmacokinetic-Pharmacodynamic Models
Summary Based Conditional Association Test
Create Scatter Plots with Marginal Density or Box Plots
Identifies Mean, Variance, and Hierarchically Clustered
Biclusters
Single Cell Genomics for Enhancing Cell Composition Inference
from Bulk Genomics Data
Simultaneous Confidence Bands for the Mean of Functional Data
Stochastic Complexity-Based Conditional Independence Test for
Discrete Data
The Self-Consistent, Competing Risks (SC-CR) Algorithms
Estimating Hierarchical Linear Models for Single-Case Designs
Construct Reduced Trees with Predefined Nodal Structures
Stellar CharactEristics Pisa Estimation gRid
Stellar CharactEristics Pisa Estimation gRid for Binary Systems
Supervised Component Generalized Linear Regression
Analyse Citation Data from Google Scholar
Functions and datasets for math used in school
Tools for Analyzing Factorial Experiments
The Entire Transcript from the Office in Tidy Format
Standardized Climate Indices Such as SPI, SRI or SPEI
Colour Palettes Based on the Scientific Colour-Maps
Visualize 'Reproducibility' and 'Replicability' in a Comparison
of Scientific Studies
A Semi-Supervised Category Identification and Assignment Tool
Scientific Graphing Functions for Factorial Designs
Summarize Data for Scientific Publication
Measure Growth Patterns and Align Sampling Spots in Photographs
Inferring Functional Gene Co-Expression Networks from Single
Cell Data
Statistical Comparison of Multiple Algorithms in Multiple
Problems
Fitting Discrete Distribution Models to Count Data
Spectral Clustering-Based Method for Identifying B Cell Clones
A Package to Score Behavioral Questionnaires
Score Persons Using the Generalized Graded Unfolding Model
Peak Functions for Peak Detection in Univariate Time Series
Implementation of SCORE, SCORE+ and Mixed-SCORE
SCORER 2.0: an algorithm for distinguishing parallel dimeric and
trimeric coiled-coil sequences
Scoring Rules for Parametric and Simulated Distribution
Forecasts
Utilities for Scoring and Assessing Predictions
Semi-Supervised Calibration of Risk with Noisy Event Times
Inferring Developmental Chronologies from Single-Cell RNA
Sequencing Data
The Scott-Knott Effect Size Difference (ESD) Test
Implements the Scout Method for Covariance-Regularized
Regression
Calculation of the Conventional and Self-Calibrating Palmer
Drought Severity Index
Functions for Planning and Managing Inventories in a Supply
Chain
Shrinking Characteristics of Precision Matrix Estimators
Tools for Scraping Data from HTML and XML Documents
Screen and clean variable selection procedures
Analysis of High-Dimensional Categorical Data Such as SNP Data
Transcript-Based Unit Tests that are Easy to Create and Maintain
Determine a Script's Filename from Within the Script Itself
Simulating the Evolution of Biological Sequences
Single Cell RNA Sequencing Data Analysis Tools
Animate 'shiny' Elements when They Scroll into View using the
'scrollrevealjs' Library
Performs Bayesian Variable Selection on the Covariates in a
Semi-Competing Risks Model
Key Derivation Functions for R Based on Scrypt
In-Silico Knockout Experiments from Single-Cell Gene Regulatory
Networks
Construct and Compare scGRN from Single-Cell Transcriptomic Data
Extensions for Synthetic Controls Analysis
Variance Stabilizing Transformations for Single Cell UMI Data
Diving Calculations and Decompression Models
Utility Functions for Single-Cell RNA Sequencing Data
Shrinkage Discriminant Analysis and CAT Score Variable Selection
Spatially Discrete Approximation to Log-Gaussian Cox Processes
for Aggregated Disease Count Data
Create and (Interactively) Modify Nested Hierarchies
Tools for Statistical Disclosure Control in Research Data
Centers
Statistical Disclosure Control Methods for Anonymization of Data
and Risk Estimation
Statistical Disclosure Control for Spatial Data
Methods for Statistical Disclosure Control in Tabular Data
Statistical Disclosure Control Substitution Matrix Calculator
Shortcuts, Detours and Dead Ends (SDDE) Path Types in Genome
Similarity Networks
Simulation and Inference for Stochastic Differential Equations
Synthesizing List of Differentially Expressed Features
Subgroup Discovery with Evolutionary Fuzzy Systems
Statistical Tools for Toroidal Diffusions
Synthetic Data Generation for Linkage Methods Development
Filtering and Assessing the Sample Size of Tracking Data
A User-Friendly Application for Species Distribution Modeling
Species Distribution Modelling Predictor Datasets
Create Virtual Species for Species Distribution Modelling
Summarizing Distributions of Latent Structures
Scale-Dependent Hyperpriors in Structured Additive
Distributional Regression
Measures of Risk for the Compound Poisson Risk Process with
Diffusion
Semi-Definite Quadratic Linear Programming Solver
Spatially Balanced Samples of Spatial Objects
Species Distribution and Stability Future Models
Scenario Discovery Tools to Support Robust Decision Making
Lasso, Group Lasso, and Sparse-Group Lasso for Mixed Models
Seasonal Analysis and Graphics, Especially for Climatology
Score Equity Assessment- summary index computation
Toolbox for Clumped Isotope Seasonality Reconstructions
Graphical User Interface for Seasonal Adjustment
Statistical Estimation of Cluster Parameters (SECP)
Sampling Design for Spatially Explicit Capture-Recapture
Share Sensitive Information in R Packages
Encrypt Text Using a Shifting Substitution Cipher
Spatially Explicit Capture-Recapture for Linear Habitats
Several Examined and Concealed States-Dependent Speciation and
Extinction
Identify and Parse Web Security Policies Files
Handling of Data from the Clinical Data Management System
'secuTrial'
Visualisation Toolbox for 'easystats' and Extra Geoms, Themes
and Color Palettes for 'ggplot2'
Access Data from the SeeClickFix Web API
View Colors Used in R Objects in the Console
Seed Germination and Seedling Growth Indexes
Hydro and Thermal Time Seed Germination Models in R
Estimate Hidden Inputs using the Dynamic Elastic Net
Models for Drying and Soaking Kinetics of Seeds
reading and writing SEER*STAT data files
SEER and Atomic Bomb Survivor Data Analysis Tools
A Quick Way to Map U.S. Rates and Data of U.S. States, Counties,
Census Tracts, or Seer Registries using 2000 and 2010 U.S.
Census Boundaries
Supplemental U.S. 2010 Census Tract Boundaries for 20 Eastern
States (including DC and PR) without Registries for
'SeerMapper'
Supplemental U.S. 2010 Census Tract Boundaries for 19 States
with Seer Registries for 'SeerMapper'
Supplemental U.S. 2010 Census Tract Boundaries for 13 Western
States without Seer Registries for 'SeerMapper'
Supplemental U.S. 2000 Census Tract Boundaries for 20 States,
District and Territory without Seer Registries that are East of
the Mississippi River for Use with 'SeerMapper' Package
Supplemental U.S. 2000 Census Tract Boundaries for 19 States
with Seer Registries for 'SeerMapper'
Supplemental U.S. 2000 Census Tract Boundaries for 13 Western
States without Seer Registries for 'SeerMapper'
Bivariate Segmentation/Clustering Methods and Tools
Environmental Inequality Indices Based on Segregation Measures
Determine Event Boundaries in Event Segmentation Experiments
Regression Models with Break-Points / Change-Points Estimation
Similarity-Based Segmentation of Multidimensional Signals
Multiple Change-Point Detection for High-Dimensional GARCH
Processes
Modeling Non-Continuous Linear Responses of Ecological Data
Predict Information Cascade by Self-Exciting Point Process
Fast Rolling Functions for Seismology using 'Rcpp'
An Information About Deputies and Votings in Polish Diet from
Seventh to Eighth Term of Office
KoNLP static dictionaries and Sejong project resources
Selection Models for Amino Acid and/or Codon Evolution
Determines Species Probabilities Based on Functional Traits
Analysis of Field and Laboratory Foraging
A General Algorithm to Enhance the Performance of Variable
Selection Methods in Correlated Datasets
A Tool for Calculation and Optimization of the Expected Gain
from Multi-Stage Selection
Estimation of Weight Functions in Meta Analysis
Translate CSS Selectors to XPath Expressions
Select Point Pattern Models Based on Minimum Contrast, AIC and
Goodness of Fit
R Client Implementing the W3C WebDriver Specification
A Structural Equation Embedded Likelihood Framework for Causal
Discovery
Select Features Reliably with Cohen's Effect Sizes
Genotype Probabilities in Intermediate Generations of Inbreeding
Through Selfing
Regularization for Variable Selection in Model-Based Clustering
and Discriminant Analysis
Dashboard with Fomantic UI Support for Shiny
A Data-Driven Similarity Kernel on Probability Spaces
Automatic Calculation of Effects for Piecewise Structural
Equation Models
Hierarchical Models for Parametric and Semi-Parametric Analyses
of Semi-Competing Risks Data
Identifiability of Linear Structural Equation Models
Domain-Specific Language for Building and Estimating Structural
Equation Models
Constructing and Interacting with Databases of Presentations
Methods and Measures for Semantic Network Analysis
An Automated Cleaning Tool for Semantic and Linguistic Data
Dictionaries for the 'SemNetCleaner' Package
Path Diagrams and Visual Analysis of Various SEM Packages'
Output
Structural Equation Modeling Using Partial Least Squares
A Tool for Sensitivity Analysis in Structural Equation Modeling
Semiparametric Estimation of Stochastic Frontier Models
Useful Tools for Structural Equation Modeling
Recursive Partitioning for Structural Equation Models
Find, Download and Process Sentinel-2 Data
Sensitivity Analysis Tools for Regression Models
Access to 'Sensibo Sky' API V2 for Air Conditioners Remote
Control
Sensitivity Analysis for Comparative Methods
Global Sensitivity Analysis of Model Outputs
Sensitivity Analysis for 2x2xk Tables in Observational Studies
A Calibrated Sensitivity Analysis for Matched Observational
Studies
Sensitivity Analysis for Case-Control Studies
Sensitivity Analysis for Full Matching in Observational Studies
Sensitivity Analysis for Observational Studies with Multiple
Outcomes
Sensitivity Analysis in Observational Studies
Sensitivity analysis using weighted M-statistics
Principal Stratification Sensitivity Analysis Functions
Parametric Estimation and Sensitivity Analysis of Direct and
Indirect Effects
Computation of High-Order Sobol' Sensitivity Indices
Simultaneous Model-Based Clustering and Imputation via a
Progressive Expectation-Maximization Algorithm
Thurstonian Models for Sensory Discrimination
Sensitivity Analysis for Stratified Observational Studies
Text Tokenization using Byte Pair Encoding and Unigram Modelling
An Integrated Framework for Textual Sentiment Time Series
Aggregation and Prediction
Improved Standard Evaluation Interfaces for Common Data
Manipulation Tasks
Sequential Allocation for Prospective Experiments
Copy Number Profiling using Sequencing and CBS
Simulation and Group Sequential Monitoring of Randomized
Two-Stage Treatment Efficacy Trials with Time-to-Event
Endpoints
Sequential Method for Classification and Generalized Estimating
Equations Problem
A Tool to Associate FASTA Sequences and Features
Miscellaneous Tools for Sequence Analysis
Mixture Hidden Markov Models for Social Sequence Data and Other
Multivariate, Multichannel Categorical Time Series
Biological Sequences Retrieval and Analysis
Network Module-Based Model in the Differential Expression
Analysis for RNA-Seq
Efficiently Read Sequence Data (VCF Format, BCF Format, METAL
Format and BGEN Format) into R
Group Sequential Design Class for Clinical Trials
Generate RNA-Seq Data from Gene-Gene Association Networks
Simulation and visualization of restriction enzyme cutting
pattern from DNA sequences
Exact Bayesian Model Selection Methods for the Sparse Normal
Sequence Model
Exact Sequential Analysis for Poisson and Binomial Data
Observational Database Study Planning using Exact Sequential
Analysis for Poisson and Binomial Data
Copy Number Estimation from Tumor Genome Sequencing Data
Tools to Transform and Query Data with Apache Drill
Infrastructure for Ordering Objects Using Seriation
Lower Confidence Bounds for Binomial Series System
Estimating Infection Rates from Serological Data
Bayesian Modelling of Raman Spectroscopy
Analyze Data Generated from Syntech Servosphere Trials
A Simple HTTP Server to Serve Static Files or Dynamic Documents
Spatially Explicit Structural Equation Modeling
Functions for interacting with, saving and restoring R sessions
Functions for Set-Theoretic Multi-Method Research and Advanced
QCA
Set (Normal) Random Number Generator and Seed
Sets, Generalized Sets, Customizable Sets and Intervals
Group Testing Procedures for Signal Detection and
Goodness-of-Fit
Customise 'Shiny' Disconnected Screens and Error Messages
Advanced Methods for Stochastic Frontier Analysis
Constrained Triangulation for Simple Features
Sequential Full Factorial-Based Latin Hypercube Design
Converts Between R Objects and Simple Feature Objects
Straightforward Filtering Index for AP-MS Data Analysis (SFINX)
San Francisco International Airport Monthly Air Passengers
Utilities from 'Seminar fuer Statistik' ETH Zurich
Functions for Systems Factorial Technology Analysis of Data
Space Filling Based Tools for Data Mining
Modern Classes for Tracking and Movement Data
Spatial Graph Based Clustering Summaries for Spatial Point
Patterns
Stochastic Gradient Descent for Scalable Estimation
An Object-Oriented Framework for Geostatistical Modeling in S+
Fit a GLM (or Cox Model) with a Combination of Lasso and Group
Lasso Regularization
Fitting Semi-Parametric Generalized log-Gamma Regression Models
An R package for power and boundary calculations in
pre-licensure vaccine trials using a sequential generalized
likelihood ratio test
Stochastic Gradient Markov Chain Monte Carlo
Solves a Generic Stochastic Growth Model with a Representative
Agent
Sparse Gaussian Markov Random Field Mixtures for Anomaly
Detection
Student Growth Percentiles & Percentile Growth Trajectories
Exemplar Data Sets for Student Growth Percentiles (SGP) Analyses
Sparse Group Partial Least Square Methods
Calculate Second-Generation p-Values and Associated Measures
Seasonal Generalized Space Time Autoregressive (S-GSTAR) Model
Random Partition Distribution Indexed by Pairwise Information
Functions for Plotting Graphical Shapes, Colors
Change-Point Estimation using Shape-Restricted Splines
Collection and Analysis of Otolith Shape Data
Standardised Rigid Rotations of Articulated Three-Dimensional
Structures
Shape Selection for Landsat Time Series of Forest Dynamics
Prediction Explanation with Dependence-Aware Shapley Values
Statistical Significance of the Sharpe Ratio
Estimating Regulatory Scores and Identifying ATAC-STARR Data
Models and Data Sets for the Study of Species-Area Relationships
Estimate the Shattering Coefficient for a Particular Dataset
Tools to Support the Sheffield Elicitation Framework
Builds Chronologies from Oxygen Isotope Profiles in Shells
Bivalve Growth and Trace Element Accumulation Model
Exactly Computing the Tail of the Poisson-Binomial Distribution
Fast Enrichment Analysis via Circular Permutations
Inference in Regressions with Shift-Share Structure
Lorem-Ipsum Helper Function for 'shiny' Prototyping
Basic Routing for Shiny Web Applications
Delegate Jobs for Shiny Web Applications
'WebVR' Data Visualizations with 'RStudio Shiny' and 'Mozilla
A-Frame'
Easily Create Pretty Popup Messages (Modals) in 'Shiny'
Bootstrap 2 Web Components for Use with Shiny
Graphical User Interface ('shiny' App) for 'brms'
Combined Slider and Numeric Input for 'Shiny'
Add Loading Animations to a 'shiny' Output While It's
Recalculating
Create Interactive Network Visualizations in R and 'shiny'
Add More 'AdminLTE2' Components to 'shinydashboard'
Show a Nice Message When a 'Shiny' App Disconnects or Errors
Add a Download Button to a 'shiny' Plot or 'plotly'
Customize Your Web Apps with Fancy Effects
A Server-Side File System Viewer for Shiny
Use Interdependent Filters on Table Columns in Shiny Apps
Display 'HTML' Elements on Full Screen in 'Shiny' Apps
Easily Add Markdown Help Files to 'shiny' App Elements
Progress Bars for Downloads in 'shiny' Apps
Image Manipulation, with an Emphasis on Journaling
Item Response Theory Analysis with a 'shiny' Application
'jQuery UI' Interactions and Effects for Shiny
Easily Improve the User Experience of Your Shiny Apps in Seconds
An Interactive Application for ODE Parameter Inference Using
Gradient Matching
Record Everything that Happens in a 'Shiny' Application
Bootstrap Landing Home Pages for Shiny Applications
Authentication Management for 'Shiny' Applications
Implement Material Design in Shiny Applications
Compare and Merge Two Files with a 'Shiny' App
Compare Supervised Machine Learning Models Using Shiny App
Mobile Ready 'shiny' Apps with Standalone Capabilities
Molecular Biology Visualization Tools for 'Shiny' Apps
'RStudio' Addin for Quick Setup of ShinyDashboard Apps
Data Insights Through Inbuilt R Shiny App
Shiny User Interface for Multiple Source Capture Recapture
Models
Gadget to Use the Data Preprocessing 'recipes' Package
Interactively
Capture Screenshots of Entire Pages or Parts of Pages in 'Shiny'
Shiny Searchbar - An Input Widget for Highlighting Text and More
Creates an Executable Shortcut for Shiny Applications
Interactive Plotting for Mathematical Models of Infectious
Disease Spread
Interactive Visual and Numerical Diagnostics and Posterior
Analysis for Bayesian Models
Functions to Minimize Bonehead Moves While Working with 'shiny'
SHrinkage covariance Incorporating Prior knowledge
Miscellaneous Functions from Alexey Shipunov
Slope Heuristic for Block-Diagonal Covariance Selection in High
Dimensional Gaussian Graphical Models
Useful Shortcuts to Interact with 'RStudio' Scripts
Convert a SpatialLinesDataFrame Object to an 'igraph'-Class
Object
Global, Parameterwise and Joint Shrinkage Factor Estimation
Efficient Bayesian Inference for Time-Varying Parameter Models
with Shrinkage
The Shuffle Estimator for Explainable Variance
Confidence Intervals Compared via Shuffling
Systematic Identification of Bimodally Expressed Genes Using
RNAseq Data
Analysis of Single-Cell Viral Growth Curves
Subgroup Identification Based on Differential Effect Search
Substitution and Indel Distances to Infer Evolutionary
Relationships
Signal Extraction Approach for Sparse Multivariate Response
Regression
Sieve Analysis Methods for Proportional Hazards Models
Laboratory Sieve Test Reporting Functions
Statistical Inference for Enzyme Kinetics
Estimate the Parameters of a Discrete Crisis-Bargaining Game
Interface to 'Sigma.js' Graph Visualization Library
Extract, Analyze and Visualize Mutational Signatures for Genomic
Variations
Similarity Identification in Gene Expression
Consistent Significance Controlled Variable Selection in Linear
Regression
Perform Exact Sign Test and Asymptotic Sign Test in Large
Samples
Quality Control Metrics for Gene Signatures
Succinct and Correct Statistical Summaries for Reports
Identify and Visualize Significantly Responsive Branches in a
Phylogenetic Tree
Calculate ANSI S3.5-1997 Speech Intelligibility Index
Statistical Inference of Large-Scale Gaussian Graphical Model in
Gene Networks
Common Forms for Complex Hierarchical and Relational Data
Structures
Simultaneous Inference for Linear Models
Simulation of Piecewise Linear Fuzzy Numbers
Genotype Simulations for Rare or Common Variants Using
Haplotypes from 1000 Genomes
Simulate Outcomes Using Spatially Dependent Design Matrices
A Collection of functions for similarity analysis of vegetation
data
Simulation-Based Inference Methods for Infectious Disease Models
Simultaneous Inference for Diversity Indices
Simulate Cognitive Diagnostic Model ('CDM') Data
Simultaneous Comparisons for Multiple Endpoints
Simulation of Correlated Data with Multiple Variable Types
Including Continuous and Count Mixture Distributions
Safe Implementation of Monte Carlo Tests
Structure for Organizing Monte Carlo Simulation Designs
Modeling and Assessing Similarity of Drug Dissolutions Profiles
Assessment of Data Trial Distributions According to the
Carlisle-Stouffer Method
Simulation of Ecological (and Other) Dynamic Systems
Constrained Single Index Model Estimation
Simulation of Legal Exemption System for European Cartel Law
SIMEX- And MCSIMEX-Algorithm for Measurement Error Models
Generate Simulated Data for IRT-Enabled Exams
Import Financial Data from the 'SimFin' Project
Simulate Models Based on the Generalized Linear Model
Simulated Survival and Hazard Analysis for Time-Dependent
Exposure
A Framework for Data-Driven Stochastic Disease Spread
Simulations
Stochastic Simulation for Information Retrieval Evaluation:
Effectiveness Scores
Analysis via Simulation of Interrupted Time Series (ITS) Data
Helper Methods for 'simmer' Trajectories
Simulate Somatic Mutations in Cancer Genomes from Mutational
Processes
Subnetwork Integration for Multi-Modal Signatures
Simulation of Event Histories for Multi-State Models
Simulation of Correlated Data with Multiple Variable Types
Statistical Inference for Systems of Ordinary Differential
Equations using Separable Integral-Matching
A Method for Simulating Data from Perturbed Biological Pathways
Simulate and Plot Estimates from Cox Proportional Hazards Models
Tools to Simulate Phenotype(s) with Epistatic Interaction
Access Color Names Using a Standardized Nomenclature
Simple Graph Data Types and Basic Algorithms
Simulation of Pleiotropic, Linked and Epistatic Phenotypes
Set Up R Source Code Files for Use on Multiple Machines
Bayesian Inference and Sensitivity Analysis for Causal Effects
from 2 x 2 and 2 x 2 x K Tables in the Presence of Unmeasured
Confounding
Simple Visualisation with 'ggplot2' and 'leaflet' Wrappers
Regression Analysis of Proportional Data Using Simplex
Distribution
Provides Tools for Working with General Simplicial Complexes
Simulation of Complex Synthetic Data Information
Power Analysis for Generalised Linear Mixed Models by Simulation
Simulations to Predict the Number of RAD and GBS Loci
Simulation of Recurrent Event Data for Non-Constant Baseline
Hazard
Simulating Multistate Movements in River/Heterogeneous
Landscapes
Simulate Pedigrees Ascertained for a Rare Disease
Simulate Genetic Sequence Data for Pedigrees
Tools for Simulation Studies in Parallel
'Simulates Univariate and Semi-Competing Risks Data Given
Covariates and Piecewise Exponential Baseline Hazards'
Nonparametric Simulation of RNA-Seq Data
Test Surveys by Simulating Spatially-Correlated Populations
Data Transformation or Simulation with Empirical Covariance
Matrix
Datetimes as Integers for Discrete-Event Simulations
Simulate Longitudinal Dataset with Time-Varying Correlated
Covariates
Conduct Simulation Studies with a Minimal Amount of Source Code
Simulation with Kernel Density Estimation
A Constrained L1 Minimization Approach for Estimating Multiple
Sparse Gaussian or Nonparanormal Graphical Models
Simulation Tools for Planning Vitamin D Studies
A SINful Approach to Selection of Gaussian Graphical Markov
Models
An Enhanced Chart for Simple and Truthful Representation of
Single Observations over Multiple Classes
Conditional Least Squared (CLS) Method for the Model SINAR(1,1)
Sparse Identification of Nonlinear Dynamics
Create 'roxygen2' Skeleton with Information from Function Script
A Calculator for Single-Case Effect Sizes
Finding Needles (=differentially Expressed Genes) in Haystacks
(=single Cell Data)
Sum of Independent Non-Identical Binomial Random Variables
Functions for Calculating Daily Solar Radiation and
Evapotranspiration
Finding Feedback Effects in SEM and Testing for Their
Significance
Supplementary Item Response Theory Models
Sparse Interval Sliced Inverse Regression
Simulation of in Silico Multi-Omic Networks
Some Invalid Some Valid Instrumental Variables Estimator
Super Imposition by Translation and Rotation Growth Curve
Analysis
Site Adaptation of Solar Irradiance Modeled Series
Inferring an Animal's Sites of Interest from High Resolution
Data
Automatically Generate _site.yml File for 'R Markdown'
A Spatial Model of Intra-Tumor Heterogeneity
Parallel Pseudo Random Number Generator (PPRNG) 'sitmo' Header
Files
Format a number to a string with SI prefix
Six Sigma Tools for Quality Control and Improvement
Estimating the Sizes of Populations at Risk of HIV Infection
from Multiple Data Sources Using a Bayesian Hierarchical Model
Data and Variable Transformation Functions
Data Visualization for Statistics in Social Science
Collection of Convenient Functions for Common Statistical
Computations
Segment-Based Ordinary Kriging and Segment-Based Regression
Kriging for Spatial Prediction
SNP-Set (Sequence) Kernel Association Test
Sparse (Multicategory) Kernel Discriminant Analysis
Heteroskedasticity Diagnostics for Linear Regression Models
Densities and Sampling for the Skellam Distribution
Optimization of Skewed Distributions with Birth-Death Processes
The Skew Hyperbolic Student t-Distribution
Scale Mixture of Skew-Normal Linear Mixed Models
The Skillings-Mack Test Statistic for Block Designs with Missing
Observations
Measuring Agreement Using Sklar's Omega Coefficient
Design of Experiments Suite: Generate and Evaluate Optimal
Designs
Send Messages, Images, R Objects and Files to 'Slack'
Channels/Users
Estimation and Use of the Quantile-Based Skew Logistic
Distribution
Software for Analyzing Limiting Dilution Assays
Statistical Learning Based Estimation of Mutual Information
Data Sets from Ramsey and Schafer's "Statistical Sleuth (2nd
Ed)"
Data Sets from Ramsey and Schafer's "Statistical Sleuth (3rd
Ed)"
Fitting a Bayesian Sparse Latent Factor Model in Gene Expression
Analysis
Data Access Tools for the Soil and Landscape Grid of Australia
Maximin-Distance (Sliced) Latin Hypercube Designs
Selective Locally Linear Inference of Cellular Expression
Relationships
Create Interactive Carousels with the 'JavaScript' 'Slick'
Library
Single Cell Linkage by Distance Estimation is SLIDE
Compare Raster Images Side by Side with a Slider
Singular Linear Models for Longitudinal Data
Sparse Linear Method to Predict Ratings and Top-N
Recommendations
Change-in-Slope OP Algorithm with a Finite Number of States
Stochastic Linear Ornstein-Uhlenbeck Comparative Hypotheses
A Slow Version of the Rapid Automatic Keyword Extraction (RAKE)
Algorithm
Discrete Prolate Spheroidal (Slepian) Sequence Regression
Smoothers
Scalable and Robust Latent Trajectory Class Analysis
Smoothing Methods for Nonparametric Regression and Density
Estimation
Statistical Methods for the Analysis of Case-Control Point Data
Statistical Modeling of Animal Movements
Acquisition and Processing of NASA Soil Moisture Active-Passive
(SMAP) Data
Sequential Multiple Assignment Randomized Trial and Adaptive
Randomization
Bayesian Set of Best Dynamic Treatment Regimes and Sample Size
in SMARTs
Tools for Accessing Various Datasets Developed by the Foundation
SmarterPoland.pl
Sample Size for SMART Designs in Non-Surgical Periodontal Trials
Spatial Management and Assessment of Demersal Resources for
Trawl Fisheries
Online Unsupervised Outlier Detection Using Finite Mixtures with
Discounting Learning Algorithms
Fast and Robust Surrogate Variable Analysis
(Standardised) Major Axis Estimation and Testing Routines
Sparse Multiple Canonical Correlation Network Analysis Tool
Multiple Imputation of Covariates by Substantive Model
Compatible Fully Conditional Specification
A simple Monte Carlo optimizer using adaptive coordinate
sampling
Data Sets for Statistical Methods in Customer Relationship
Management by Kumar and Petersen (2012)
Data to Accompany Smithson & Merkle, 2013
Identification of Somatic Mutation-Driven Immune Cells
R functions and data from Chapter 5 of 'Statistical Methods for
Financial Engineering'
Filtering Algorithms for the State Space Models on the Stiefel
Manifold
Hidden Markov Random Field for Spatial Transcriptomic Data
Stochastic Modelling for Systems Biology
Statistical Methods for Interval-Censored Data
Provides two taxonomic coefficients from E. S. Smirnov
"Taxonomic analysis" (1969) book
Data Structure and Manipulations Tool for Host and Viral
Population
Visualize Data for Host and Viral Population from 'SMITIDstruct'
using 'HTMLwidgets'
Outlier Detection Using Statistical and Machine Learning Methods
Simulation and Estimation of Multi-State Discrete-Time
Semi-Markov and Markov Models
Soft Maximin Estimation for Large Scale Array-Tensor Models
The Swiss Municipal Data Merger Tool Maps Municipalities Over
Time
Fitting Univariate Censored Regression Model Under the Family of
Scale Mixture of Normal Distributions
Structural Modeling by using Overlapped Group Penalty
Small Molecule Octet/BLI Kinetics Experiment
Single and Multi-Objective Optimization Test Functions
Smoothing of Two-Dimensional Demographic Data, Optionally Taking
into Account Period and Cohort Effects
A Framework to Smooth L1 Penalized Regression Operators using
Nesterov Smoothing
Functions Relating to the Smoothing of Numerical Data
Estimation of Smooth Hazard Models for Interval-Censored Data
with Applications to Survival and Illness-Death Models
Smooth Hazard Ratio Curves Taking a Reference Value
Smoothed M-estimators for 1-dimensional location
Smooth Time-Dependent ROC Curve Estimation
Survival Regression with Smoothed Error Distribution
Smooth Estimation of GPD Shape Parameter
Nonparametric Estimation of the Trend and Its Derivatives in TS
A Collection of Oversampling Techniques for Class Imbalance
Problem Based on SMOTE
Some Movies to Illustrate Concepts in Statistics
Practicals for Use with Davison (2003) Statistical Models
Datasets for Agresti and Finlay's "Statistical Methods for the
Social Sciences"
Sparse Multi-Type Regularized Feature Modeling
The Skew-Normal and Related Distributions Such as the Skew-t
'RStudio' Addin for Network Analysis and Visualization
Play and Analyse the Game of Snakes and Ladders
Compress and Decompress 'Snappy' Encoded Data
Gadget N-body cosmological simulation code snapshot I/O
utilities
EM Algorithm for Multivariate Skew-Normal Distribution with
Overparametrization
Snipping Methods for Robust Estimation and Clustering
Calculate and Visualize 'SNOTEL' Snow Data and Seasonality
Snowball Stemmers Based on the C 'libstemmer' UTF-8 Library
Easier cluster computing (based on snow)
Fault Tolerant Simple Network of Workstations
SNPs-Based Whole Genome Association Studies
Knockoffs for Hidden Markov Models and Genetic Data
Maximally selected statistics for SNP data
Bivariate Gaussian Genotype Clustering and Calling for Illumina
Microarrays
Preparing Genotypic Datasets in Order to Run Genomic Analysis
Flexible writing of snpStats objects to flat files
Standard and Nonstandard Statistical Models and Methods for Test
Equating
Memory management in R by delayed assignments
Nonparametric Sobol Estimator with Bootstrap Bandwidth
Sobol Sequences with Better Two-Dimensional Projections
Specific Correspondence Analysis for the Social Sciences
Social Mixing Matrices for Infectious Disease Modelling
Generates social networks based on distance
Social Position Indicators Construction Toolbox
Operationalizing Social Determinants of Health Data for
Researchers
Utility Functions and Data Sets for Data Visualization
Functions and Examples for "Software for Data Analysis"
SODA: Main and Interaction Effects Selection for Logistic
Regression, Quadratic Discriminant and General Index Models
Interfaz interactiva con fines didacticos
Making Sophisticated and Aesthetical Figures in R
Matrix Completion via Iterative Soft-Thresholded SVD
Classification Random Forests for Soft Decision Trees
Assessment Models for Agriculture Soil Conditions and Crop
Suitability
Tools to Analyze Soil Carbon Database Created by Powell Center
Working Group
Models of Soil Organic Matter Decomposition
Functions for Soil Texture Plot, Classification and
Transformation
Implementation of Parametric Formulas for Soil Water Retention
or Conductivity Curve
Apply Sojourn Methods for Processing ActiGraph Accelerometer
Data
Supporting Objects for Sojourn Accelerometer Methods
Solar Position Algorithm for Solar Radiation Applications
Utilities Dealing with Solar Time Such as Sun Position and Time
of Sunrise
Calculating Solar Radiation and Related Variables Based on
Location, Time and Topographical Conditions
Topological k-NN Classifier Based on Self-Organising Maps
General-Purpose Optimisation With the Self-Organising Migrating
Algorithm
SOM Bound to Realize Euclidean and Relational Outputs
Controlling the Generalized Familywise Error Rate
SOM Algorithm for the Analysis of Multivariate Environmental
Data
An Individual-Based Model of Bird Song Evolution
Estimating Abundance of Clones from DNA Fragmentation Data
Bioacoustic Analysis and Publication Tools
Data Sonification - Turning Data into Sound
Single Objective Optimization Benchmark Functions
Non-Parametric Estimation of the Off-Pulse Interval of a Pulsar
Sequential Optimal Designs for Two-Colour cDNA Microarray
Experiments
Estimation using Sequential Offsetted Regression
A Bayesian Semiparametric Approach to Correlated ROC Surfaces
Static Adsorption Experiment Plotting and Analysis
Drag-and-Drop in 'shiny' Apps with 'SortableJS'
Turns a data frame into an HTML file containing a sortable
table
Estimation and Inference Methods for Sorted Causal Effects and
Classification Analysis
Search Contributed R Packages, Sort by Package
United States Presidential State of the Union Addresses
Semi-Automatic Analysis of Sound Correspondences
Stochastic Ordering Using Permutations (and Pairwise
Comparisons)
Fits a Non-Parametric Bayesian Source Attribution Model
A Graphical Model Approach to Identify Primary Genes in
Perturbed Biological Pathways
Tools for Reading, Tokenizing and Parsing R Code
Soybean Nested Association Mapping Dataset
Design and Simulation of seamless Phase II-III Clinical Trials
Latent Space Models for Multidimensional Networks
Standard and User-Defined RGB Color Spaces, with Conversion
Between RGB and CIE XYZ
CIE XYZ and some of Its Derived Color Spaces
Classes and Methods for Spatio-Temporal Data
Easily Obtain Spatial Data and Make Better Maps
Spherical Projections of Astronomical Data
Species-Richness Prediction and Diversity Estimation with R
Develop and Run Spatially Explicit Discrete Event Simulation
Models
Development Tools for 'SpaDES' and 'SpaDES' Modules
Core Utilities for Developing and Running Spatially Explicit
Discrete Event Models
Additional Tools for Developing Spatially Explicit Discrete
Event Simulation (SpaDES) Models
Artificial Spatial and Spatiotemporal Densities on Bounded
Windows
64-Bit Extension of the SPArse Matrix R Package 'spam'
Mixed-Effect Models, Particularly Spatial Models
Translate Quantities from Strings to Integer and Back. Misc
Functions on Spanish Data
Spatial Analysis of Field Trials Experiments using Geostatistics
and Spatial Autoregressive Model
Perform rare variants association analysis based on summation of
partition approaches
Perform Sparse Hierarchical Clustering and Sparse K-Means
Clustering
Read in 'SAS' Data ('.sas7bdat' Files) into 'Apache Spark'
Google 'BigQuery' Support for 'sparklyr'
Interface for 'TensorFlow' 'TFRecord' Files with 'Apache Spark'
Interface for 'XGBoost' on 'Apache Spark'
Spatial and Spatiotemporal Relative Risk
Power Analysis to Detect Spatial Relative Clusters
Sparse Biclustering of Transposable Data
'HJ-Biplot' using Different Ways of Penalization Plotting with
'ggplot2'
Learning Sparse Bayesian Networks from High-Dimensional Data
Utilities for Learning Sparse Bayesian Networks
Computation of Sparse Eigenvectors of a Matrix
Scaling Count and Binary Data with Sparse Factor Analysis
Functional Linear Mixed Models for Irregularly or Sparsely
Sampled Data
Design of Portfolio of Stocks to Track an Index
Computation of the Sparse Inverse Subset
The Sparse Latent Position Model for Nonnegative Interaction
Data
RcppEigen back end for sparse least trimmed squares regression
SPAtial Resolution-SEnsitive Models of Outbreak Dynamics
'Multiple Systems Estimation for Sparse Capture Data'
Multivariate Normal Functions for Sparse Covariance and
Precision Matrices
Fit Sparse Linear Regression Models via Nonconvex Optimization
Sparse Principal Component Analysis (SPCA)
Sparse Bayesian Models for Regression, Subgroup Analysis, and
Panel Data
Sparse-aware Maximum Likelihood for Structural Equation Models
Sparse Truncated Singular Value Decomposition (from 'SVDLIBC')
Solution Paths of Sparse High-Dimensional Support Vector Machine
with Lasso or Elastic-Net Regularization
Sparse Time Series Chain Graphical Models
Spike-and-Slab Variational Bayes for Linear and Logistic
Regression
Study Planning and Adaptation of Sample Size
Spatio-Temporal Modeling of Large Data Using a Spectral SPDE
Approach
Score Test and Meta-Analysis Based on Saddlepoint Approximation
Graph Edge Computations for Spatial Point Patterns
Functions for Kriging and Point Pattern Analysis
Blind Source Separation for Multivariate Spatial Data
Spatial Clustering using Fuzzy Geographically Weighted
Clustering
Computation of Spatial Covariance Matrices for Data on
Rectangles
Spatial Analysis and Modelling Utilities
Methods and Data for Spatial Epidemiology
A Shiny Web Application for the Analysis of Spatial and
Spatio-Temporal Disease Data
Multivariate Analysis of Spatial Data Using a Unifying Spatial
Fusion Framework
Kernel Density Estimation for Spatial Data
Performs spatial NBDA in a Bayesian context
Multivariate Nonparametric Methods Based on Spatial Signs and
Ranks
Tools for Assessment the Association Between Two Spatial
Processes
Robust Maximum Likelihood Estimation for Spatial Error Model
Segregation Measures for Multitype Spatial Point Patterns
Spatial Early Warning Signals of Ecosystem Degradation
Formats Spatial Data for Use in Htmlwidgets
Model-Based Clustering of Spatio-Temporal Data
Regularized Spatial Maximum Covariance Analysis
Regularized Principal Component Analysis for Spatial Data
Spatial Analysis of Field Trials with Splines
Group Animal Relocation Data by Spatial and Temporal
Relationship
Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Core Functionality of the 'spatstat' Package
Geometrical Functionality of the 'spatstat' Package
Interactive Graphics Functions for the 'spatstat' Package
Extension to 'spatstat' for Large Datasets on a Linear Network
Extension to 'spatstat' for Local Composite Likelihood
Sparse Three-Dimensional Arrays and Linear Algebra Utilities
Bayesian Spatial Survival Analysis with Parametric Proportional
Hazards Models
Univariate and Multivariate Spatial-Temporal Modeling
Bayesian Modeling and Analysis of Spatially Correlated Survival
Data
Statistical Process Control -- Calculation of ARL and Other
Control Chart Performance Measures
Statistical Process Control for Stochastic Textured Surfaces
Functions for Calibrating Control Charts
A New Reduced-Rank Linear Discriminant Analysis Method
Sparse Principal Component Analysis via Random Projections
(SPCAvRP)
Design and Analyze Studies using the Sequential Parallel
Comparison Design
Spatial Coverage Sampling and Random Sampling from Compact
Geographical Strata
Sparse Estimation of a Covariance Matrix
Analysis of Spatial Gradients in Radiocarbon Dates
Spatial Dependence: Weighting Schemes, Statistics
Spatial Downscaling Using Bias Correction Approach
Data Manipulation Verbs for the Spatial Classes
Spatio-Dynamic Wetland Plant Communities Model
A Wrapper for the Phonetic Software Praat
Tools for Nuclear Magnetic Resonance (NMR) Spectra Alignment,
Peak Based Processing, Quantitative Analysis and Visualizations
Jackknife Euclidean / Empirical Likelihood Inference for
Spearman's Rho
A Data Specification Format and Interface
Alternative spectral clustering, with automatic estimation of k
Change Points Detection with Spectral Clustering
Statistical package for species richness estimation
Reduction of Speckle Data from BTA 6-m Telescope
Metabolomics and Spectral Data Analysis and Mining
Conducting and Visualizing Specification Curve Analyses
Single-Equation Penalized Error-Correction Selector (SPECS)
Forecast Verification Routines for Ensemble Forecasts of Weather
and Climate
Storing, Manipulating and Analysis Spectroscopy and Associated
Data
Common Methods of Spectral Data Analysis
Pre-Process, Visualize and Analyse Process Analytical Data, by
Spectral Data Measurements Made During a Chemical Process
Approximate Gaussian Processes Using the Fourier Basis
Learning Graphs from Data via Spectral Constraints
Spectra Viewer, Organizer, Data Preparation and Property Blocks
Class and Methods for Hyperspectral Data
Fast Adaptive Spectral Clustering for Single and Multi-View Data
Estimation of the Relative Importance of Factors Affecting
Species Distribution Based on Stability Concept
Fitting Linear and Generalized Linear Models to Large Data Sets
Semiparametric efficient estimation for a two-sample treatment
effect
Calculation of the Standardised Precipitation-Evapotranspiration
Index
Correct the Spelling of a Given Word in the English Language
A Bi-Dimensional Implementation of the Empirical Mode
Decomposition for Spatial Data
Auxiliary Functions to Estimate Centers of Biodiversity
Perform Spatial Error Estimation and Variable Importance in
Parallel
Function-on-Scalar Regression with Group-Bridge Penalty
Semiparametric Spatial Filtering with Eigenvectors in
(Generalized) Linear Models
Feature Selection and Ranking by Simultaneous Perturbation
Stochastic Approximation
Pre-Processing and Analysis of Mid-Infrared Spectral Region
Interface Between GRASS 6+ Geographical Information System and R
Statistical Patterns in Genomic Sequences
Numerical Integration over Spheres and Balls in n-Dimensions;
Multivariate Polar Coordinates
Estimation of Spatial Autoregressive Models with and without
Heteroscedasticity
A Genetic-Based Assay for the Identification of Cell Lines
Parse and Test Robots Exclusion Protocol Files and Rules
Compute SPI Index using the Methods Genetic Algorithm and
Maximum Likelihood
Detecting Election Fraud from Irregularities in Vote-Share
Distributions
Prediction and variable selection using spike and slab
regression
Bayesian Variable Selection and Model Choice for Generalized
Additive Mixed Models
Semi-Parametric Gene-Environment Interaction via Bayesian
Variable Selection
Manual Tours, Manual Control of Dynamic Projections of Numeric
Multivariate Data
Sparse Generative Model and Its EM Algorithm
Wrapper for the Social Progress Index Data
Spatial and Space-Time Point Pattern Analysis
Tools to Work with the 'Splash' 'JavaScript' Rendering and
Scraping Service
Longitudinal Regression Trees and Forests
Split a Dataset for Training and Testing
Combined Evaluation and Split Access of Functions
Calculate Task Split Half Reliability Estimates
Best Split Selection Modeling for Low-Dimensional Data
Stack and Reshape Datasets After Splitting Concatenated Values
Econometric Models for Spatial Panel Data
Simultaneous Penalized Linear Mixed Effects Models
Sparse Partial Least Squares (SPLS) Regression and
Classification
Wrapper Functions for 'SPM' (Statistical Parametric Mapping)
Version 12 from the 'Wellcome' Trust Centre for 'Neuroimaging'
Semiparametric Maximum Likelihood Method for Interactions
Gene-Environment in Case-Mother Control-Mother Designs
Moran Eigenvector-Based Scalable Spatial Additive Mixed Models
Linear Network Preprocessing for Spatial Statistics
Scale Invariant Probabilistic Neural Networks
Spatial Regression Models for Large Datasets using Nearest
Neighbor Gaussian Processes
Interface to Species Occurrence Data Sources
SpongeBob-Case Converter : spOngEboB-CASe CoNVertER
Transform a Movie into a Synthetic Picture
Semiparametric proportional odds rate model
Sequential Pairwise Online Rating Techniques
Graphical User Interface for the Package 'SPOT'
SPatial and Optimally Temporal (SPOT) Sampling
Combining Different Spatial Datasets in Cancer Risk Estimation
Modeling Spatial Poisson and Related Point Processes
Sparse Arrays and Multivariate Polynomials
Simulating Spreading Activation in a Network
Statistical Package for Reliability Data Analysis
Selecting a Predictive Function for a Given Gene Expression Data
Bias Reduction in the Skew-Probit Model for a Binary Response
Calculate Species Richness and Extrapolation Metrics
Sparse Group Variable Selection for Gene-Environment
Interactions in the Longitudinal Study
Sparse and Non-Sparse Partial Robust M Regression and
Classification
Wald's Sequential Probability Ratio Test
Optimization of Sample Configurations using Spatial Simulated
Annealing
Selecting Spatial Scale of Covariates in Regression Models
Estimation and Prediction of Parameters of Various Soil
Hydraulic Property Models
Shape-Preserving Uni-Variate and Bi-Variate Spline Interpolation
Site Percolation on Square Lattices (SPSL)
Spatial Seemingly Unrelated Regression Models
Bernstein Polynomial Based Semiparametric Survival Analysis
Spatially Varying and Spatio-Temporal Dynamic Linear Models
Functions for Spatial Thinning of Species Occurrence Records for
Use in Ecological Models
Predicting Totals and Weighted Sums from Spatial Data
Functions and Datasets for "Introduction to Scientific
Programming and Simulation Using R"
SPatially aUTomatic deNoising for Ims toolKit
Wrapper for 'Python' Module 'sqlparse': Parse, Split, and Format
'SQL'
Rendering Parameterized SQL and Translation to Dialects
Utilities for Generating SQL Queries from Model Objects
Squared Extrapolation Methods for Accelerating EM-Like Monotone
Algorithms
Color-Based Plots for Multivariate Visualization
Politely Web Scrape Data from SquashInfo
Statistical Quantification of Individual Differences
Simplify Connections to Database Sources
Statistical Ranking Color Scheme for Multiple Pairwise
Comparisons
Structural Equation Modeling for the Social Relations Model
Nonparametric Smooth ROC Curves for Continuous Data
Smooth-Rough Partitioning of the Regression Coefficients
Adjust Srt File to Get Better Experience when Watching Movie
'dplyr'-Like Syntax for Summary Statistics of Survey Data
Fisheries Stock Assessment Simulation Testing with Stock
Synthesis
Sample Size Adjusted for Nonadherence or Variability of Input
Parameters
Robust Correlation Estimation and Testing Based on Spatial Signs
Sample Size Determination (SSD) for Unordered Categorical Data
Tools Developed for Structured Sufficient Dimension Reduction
(sSDR)
Sample Size Computation for Fixed N with Optimal Reward
Fitting of parametric models using summary statistics
Bayesian Graphical Estimation using Spike-and-Slab Priors
Local and remote system commands with output and error capture
Searching Shared HLA Amino Acid Residue Prevalence
Sample Size Calculations for Microarray Experiments
Sample Size Calculation for RNA-Seq Experimental Design
Semi-Supervised Classification, Regression and Clustering
Methods
Fit and Analyze Smooth Supersaturated Models
Skew Scale Mixtures of Normal Distributions
Bayesian State-Space Modeling of Mouse-Tracking Experiments via
Stan
Robust Estimation and Inference in Sample Selection Models
Scale-Shape Mixtures of Skew-Normal Distributions
Stream Suitable Online Support Vector Machines
Simulated Sampling Procedure for Community Ecology
Estimating Hidden Population Size using Respondent Driven
Sampling Data
Two-Dimensional Sociometric Status Determination with Rating
Scales
Sample Size Determination for Longitudinal Designs with Binary
Outcome
Sample Size Calculation using Restricted Mean Survival Time
Tools for Importing Files in the Triple-s (Standard Survey
Structure) Format
Same Species Sample Contamination Detection
Bootstrap Stacking of Random Forest Models for Heterogeneous
Data
Swiss Solvency Test (SST) Standard Models
Fitting Semi-Parametric log-Symmetric Regression Models
Shrinkage t Statistic and Correlation-Adjusted t-Score
Stability Analysis of Genotype by Environment Interaction (GEI)
Stabilizing Regression and Variable Selection
Probability Functions and Generalized Regression Models for
Stable Distributions
Estimate the Four Parameters of Stable Laws using Different
Methods
A Stable Gelman-Rubin Diagnostic for Markov Chain Monte Carlo
Stability Assessment of Statistical Learning Methods
Stable Specification Search in Structural Equation Models
Stability Measures for Feature Selection
Linear Regression with the Stable Distribution
'ODBC' Connection Class for Package stacomiR
Modelling the Population Dynamics of a Stage-Structured Species
in Continuous Time
Statistical Analysis of Mixed Ploidy Populations
Spatial Temporal Analysis of Moving Polygons
Tools for Standardizing Variables for Regression in R
Simultaneous Truth and Performance Level Estimation
Well-Formatted Regression and Summary Statistics Tables
Modelling Space Time AutoRegressive Moving Average (STARMA)
Processes
Spatiotemporal Arrays, Raster and Vector Data Cubes
Miscellaneous Functions for Working with 'stars' Rasters
Single to Double Arm Transition Design for Phase II Clinical
Trials
Automatically Retrieve Multidimensional Distributed Data Sets
Vector Logistic Smooth Transition Models / Realized Covariances
Construction
R-Based Visualization Techniques for Task-Based Applications
Relational Data from the 'Star Wars' API for Learning and
Teaching
Interactive Document for Working with Basic Statistical Analysis
Highest Density Regions and Other Functions of Distributions
Tools Inspired by 'Stata' to Manipulate Tabular Data
Client for Statistics Canada's Open Economic Data
Statistical Analysis of Chemistry, Histopathology, and
Reproduction Endpoints Including Repeated Measures and
Multi-Generation Studies
Extract Statistics from Articles and Recompute p Values
Statistical Complexity and Information Measures for Time Series
Analysis
Statistical Analysis for Environmental Data
Create United States Uniform Cartogram Heatmaps
Single Trial Analysis (STA) of Field Trials
Detailed Meteorological Data from Stations All Over the World
Working Examples for Reproducible Research Documents
Statistical Functions for Probability Distributions and
Regression
Easy Data Manipulation, Data Quality and Statistical Checks
Software Tools for the Statistical Analysis of Network Data
Common R Scripts and Utilities Used by the Statnet Project
Software
A Graphical User Interface for Network Modeling with 'Statnet'
Use Data from the Czech Public Finance Database
Statistical Tools for Social Network Analysis
Statistical Performance Measures to Evaluate Covariance Matrix
Estimates
Quotes on Statistics, Data Visualization and Science
Statistical Rank Aggregation: Inference, Evaluation, and
Visualization
Work with Open Road Traffic Casualty Data from Great Britain
Expressions and Dataframes with Statistical Details
Companion Software for the Coursera Statistics with R
Specialization
Calculate the Standardized Difference for Numeric, Binary and
Category Variables
ICA and Tests of Independence via Multivariate Distance
Covariance
Testing Steepness of Dominance Hierarchies
Steiner Tree Approach for Graph Analysis
Semi-Parametric Stein-Like Estimator with Instrumental Variables
Stemmatological Analysis of Textual Traditions
Spatio-Temporal Estimation and Prediction for Censored/Missing
Responses
Subpopulation Treatment Effect Pattern Plot (STEPP)
Stepwise Forward Variable Selection in Penalized Regression
L2 Penalized Logistic Regression with Stepwise Variable
Selection
Step-Wise Signal Extraction via Marginal Likelihood
Multiple Testing Method to Control Generalized Family-Wise Error
Rate and False Discovery Proportion
Stereo Camera Calibration and Reconstruction
Steve's Toy Data for Teaching About a Variety of Methodological,
Social, and Political Topics
Calculation of the Standardized Temperature Index
Persist Attributes Across Data Operations
Separable Gaussian Process Interpolation (Emulation)
Simultaneous Threshold Interaction Modeling Algorithm
Stineman, a Consistently Well Behaved Method of Interpolation
Tidy Manipulation of CSB Data for St. Louis
Spatio-Temporal Analysis of Point Patterns on Linear Networks
Enhanced Seasonal Decomposition of Time Series by Loess
Estimation of the Structural Topic Model
A Tool for Structural Topic Model Visualizations
Rapid and Accurate Genetic Prediction Modeling for Genome-Wide
Association or Whole-Genome Sequencing Study Data
Shiny Application for Creating STM Models
A 'Shiny' Application for Inspecting Structural Topic Models
Quantile-Quantile Plot with Several Gaussian Simulations
Discovery of Motifs in Spatial-Time Series
Fit a Spatial Occupancy Model via Gibbs Sampling
Stochastic Profiling using Maximum Likelihood Estimation
Stochastic Limited Memory Quasi-Newton Optimizers
Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Likelihood Estimation of Stochastic Volatility Models
R Functions for Solving Stoichiometric Equations
Selection Threshold Optimized Empirically via Splitting
Write Storm Bolts in R using the Storm Multi-Language Protocol
Functions for the Analysis of Star Trek Thematic Data
Stochastic Simulator for Reliability Modeling of Repairable
Systems
Selection of Training Populations by Genetic Algorithm
Stochastic Process Model for Analysis of Longitudinal and
Time-to-Event Outcomes
Space-Time Point Pattern Simulation, Visualisation and Analysis
A Framework for Investment Strategy Simulation
Stratigraphic Tree Analysis for Palaeontology
An Implementation of the Stratification Index
Optimum Sample Allocation in Stratified Random Sampling Scheme
Stratification and Matching for Large Observational Data Sets
Optimal Stratification in Stratified Sampling
Generic Framework to Analyze Trading Strategies
Univariate Stratification of Survey Populations
Builds Trees by Sampling Variables in Groups
Optimal Stratification of Univariate Populations
Enumeration and Uniform Sampling of Transmission Trees for a
Known Phylogeny
Anomaly Detection in High Dimensional and Temporal Data
Parametric Ordinary Differential Equations Model of Growth,
Death, and Respiration of Macroinvertebrate and Algae Taxa
Estimate Streamflow Depletion Due to Groundwater Pumping
Calculate Single Station Metabolism from Diurnal Oxygen Curves
Interface for MOA Stream Clustering Algorithms
Fetch and plot financial stress index and component data
Computation and Estimation of Reliability of Stress-Strength
Models
Creates an Adjacency Matrix from a List of Strings
Approximate String Matching, Fuzzy Text Search, and String
Distance Functions
Simple, Consistent Wrappers for Common String Operations
Structured Trellis Displays Without Strips for Lattice Graphics
Analysis of Short Tandem Repeat (STR) Massively Parallel
Sequencing (MPS) Data
R Codes and Datasets for Generalized Linear Mixed Models: Modern
Concepts, Methods and Applications by Walter W. Stroup
Testing, Monitoring, and Dating Structural Changes
False Discovery Control Procedure Integrating the Prior
Structure Information
Process Control and Internal Validation of Forensic STR Kits
Class and Methods for Structural Time Series Models
Subtests Using Algorithmic Rummaging Techniques
Tidy Handling and Navigation of the Student-Life Dataset
Study Strap and Multi-Study Learning Algorithms
Spatio-Temporal Uncertainty Propagation Across Multiple Scales
Student's t Vector Autoregression (StVAR)
Maximum-Likelihood Cultural Consensus Analysis with Sub-Cultures
Detect Subgroup with an Enhanced Treatment Effect
Methods for exploring treatment effect heterogeneity in subgroup
analysis of clinical trials
Graphical Displays for Subgroup Analysis in Clinical Trials
Combine Multiple GWAS by Using Gene-Environment Interactions
Automatic Lesion Incidence Estimation and Detection using
Multi-Modality Longitudinal Magnetic Resonance Images
Effect Modification in Observational Studies Using the Submax
Method
Within Outlying Mean Indexes: Refining the OMI Analysis
Identify Metabolic Subpathways Mediated by MicroRNAs
Identify Signal Subpathways Competitively Regulated by LncRNAs
Based on ceRNA Theory
Unconstrained Optimization using the Subplex Algorithm
Computes Copula using Ranks and Subsampling
Subsample Winner Algorithm for Variable Selection in Linear
Regression with a Large Number of Variables
Computing Subscores in Classical Test Theory and Item Response
Theory
Systematic Screening of Study Data for Subgroup Effects
Subgroup Treatment Effect Estimation in Clinical Trials
Subgroup Specific Optimal Dose Assignment
Cluster analysis to find molecular subtypes and their assessment
Prioritization of Candidate Cancer Subtype Specific Drugs
Visual Exploration of Protein Alignments Resulting from Multiple
Substitution Matrices
Identify Sudden Gains in Longitudinal Data
Tools for Making and Spoiling Sudoku Games
Suess and Laws Corrections for Marine Stable Carbon Isotope Data
Supporting Graphs for Analysing Time Series
Fast Region-Based Association Tests on Summary Statistics
Easy Calculation and Visualisation of Confidence Intervals
Building Polygenic Risk Score Using GWAS Summary Statistics
Tools to Quickly and Neatly Summarize Data
Spatio-Temporal Under-Five Mortality Methods for Estimation
Compute Sun Position, Sunlight Phases, Moon Position and Lunar
Phase
Quantification of the effect of geographic versus environmental
isolation on genetic differentiation
An Interface to 'SUNDIALS' Ordinary Differential Equation (ODE)
Solvers
Sub-National Geospatial Data Archive: Geoprocessing Toolkit
Constructing Suns-Voc from Outdoor Time-Series I-V Curves
The Self-Updating Process Clustering Algorithms
Supervised Clustering of Predictor Variables Such as Genes
Generating Robust Biclusters from a Bicluster Set (Ensemble
Biclustering)
A Comprehensive Test Suite for Testing Markov Chain
Nonconvergence
Exact Test and Visualization of Multi-Set Intersections
Superfast Likelihood Inference for Stationary Gaussian Time
Series
A Graphical Tool for Exploring Complex Datasets Using Heatmaps
Implements the supervised multidimensional scaling (superMDS)
proposal of Witten and Tibshirani (2011)
Build Machine Learning Models Like Using Python's Scikit-Learn
Library in R
Judd, McClelland, & Ryan Formatting for ANOVA Output
Simulation-Based Power Analysis for Factorial Designs
Supervised Classification Learning and Prediction using Patient
Rule Induction Method (PRIM)
Detecting Structural Change with Heteroskedasticity
Downloading Supplementary Data from Published Manuscripts
Basic Functions for Supporting an Implementation of Choice
Experiments
Calculates Likelihood Support Intervals for Common Data Types
Modeling Tool for 'Shiny' Applications Developed with Modules
Companion to "Statistics Using R: An Integrative Approach"
Bayesian Analysis of Seemingly Unrelated Regression Models
Surrogate Residuals for Ordinal and General Regression Models
A Novel Multi-Disease Automated Phenotyping Method for the EHR
Fitting Hansen Models to Investigate Convergent Evolution
Find Optimal Sampling Locations Based on Spatial Covariate(s)
Evaluation of Surrogate Endpoints in Clinical Trials
Estimation of the Proportion of Treatment Effect Explained by
Surrogate Outcome Information
Early Testing for a Treatment Effect using Surrogate Marker
Information
Evaluation of Failure Time Surrogate Endpoints in Individual
Patient Data Meta-Analyses
LaTeX descriptive statistic reporting for survey data
Inference for Model-Free Between-Group Parameters for Censored
Survival Data
Estimators of prediction accuracy for time-to-event data
Two-Sample Tests Based on Differences of Kaplan-Meier Curves
Concordance Based Bootstrap Methods for Outlier Detection in
Survival Analysis
C-statistics for risk prediction models with censored survival
data
Plots Survival Curves Element by Element
Discrete Time Survival and Longitudinal Data Analysis
Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Comparing Multiple Survival Functions with Crossing Hazards
Tools for the Bootstrap with Survey Data
Generate a Survey that can be Completed by Survey Respondents
Survey Standard Error Estimation for Cumulated Estimates and
their Differences in Complex Panel Designs
The Gini concentration test for survival data
Group Sequential Design for a Clinical Trial with Censored
Survival Data
Survival Analysis in Health Economic Evaluation
IDI and NRI for comparing competing risk prediction models with
censored survival data
Inference and Prediction in an Illness-Death Model
Penalised Maximum Likelihood for Survival Analysis Models
Penalised Likelihood for Survival Analysis with Dependent
Censoring
Time-dependent ROC curve estimation from censored survival data
Survival Prediction by Joint Analysis of Microarray Gene
Expression Data
Analysis of Proportional Hazards Model with Sparse Longitudinal
Covariates
Multiple Imputation Method in Survival Analysis
Miscellaneous Functions for Survival Data
Parametric Survival Simulation with Parameter Uncertainty
Multidimensional Penalized Splines for Survival and Net Survival
Models
Presmoothed Estimation in Survival Analysis
Estimating, Comparing and Visualising Time to Event Data
Weibull Regression for a Right-Censored Endpoint with
Interval-Censored Covariate
Flexible and Coherent Test/Estimation Procedure Based on
Restricted Mean Survival Times
Permutation Test for Comparing Restricted Mean Survival Time
Sensitivity Analysis with Time-to-Event Outcomes
Simulation of Simple and Complex Survival Data
Power Calculations for SNP Studies with Censored Outcomes
Compute Targeted Minimum Loss-Based Estimates in Right-Censored
Survival Settings
Visualization of the Local and Global Survival Model
Explanations
Forecasting Data using Alpha-Sutte Indicator
Measures of the Sturdiness of Regression Coefficients
Data-Driven Identification of SVAR Models
Interfaces to Various State-of-Art SVD and Eigensolvers
'SciViews' - Standard Dialog Boxes for Windows, MacOS and
Linuxes
SciViews GUI API - Dialog boxes using Tcl/Tk
R 'Htmlwidget' to Add Pan and Zoom to Almost any R Graphic
Manipulate SVG (Template) Files of Charts
3D Animated Interactive Visualizations Using SVG and WebGL
Functions to Ease Interactions Between R and IDE or Code Editors
SciViews GUI API - Functions to interface with Komodo Edit/IDE
Causal Effect Estimation and Diagnostics with Support Vector
Machines
Implementation of Support Vector Machines Plus (SVM+)
Wrappers for Tools in Other Packages for IDE Friendliness
'SciViews' - Unit, Integration and System Testing
Management of GUI Widgets, Windows, and Other GUI Resources
Linear Regression Model Diagnostics for Survey Data
Nomograms for Right-Censored Outcomes from Survey Designs
A package for complex surveys including plausible values
Design-Based Inference in Vector Generalised Linear Models
Subsampling Winner Algorithm for Classification
Dynamically Generates Documentation from a 'Swagger' Compliant
API
Visualization, Analysis and Adjustment of High-Dimensional Data
in Respect to Sample Annotations
A Null Model Adapted to Abundance Class Data in Ecology
Ensemble Learning Algorithms Based on Support Vector Machines
Read, Inspect, and Manipulate Color Swatch Files
Stepped Wedge Cluster Randomized Trial (SW CRT) Design
Sliding Window Discrete Fourier Transform (SWDFT)
Power Calculation for Stepped Wedge Cluster Randomized Trials
Southwest Fisheries Science Center Aerial DAS Data Processing
Southwest Fisheries Science Center Shipboard DAS Data Processing
Miscellaneous Functions for Southwest Fisheries Science Center
Simulation Extrapolation Inverse Probability Weighted
Generalized Estimating Equations
Scenario Weights for Importance Measurement
Data Import, Cleaning, and Conversions for Swimming Results
Tools for Creating Swimmers Plots using 'ggplot2'
Air Quality Data of Switzerland for One Year in 30 Min
Resolution
Get Swiss Federal and Cantonal Vote Results from Opendata.swiss
Multilevel Regression with Post-Stratification (MrP) for
Switzerland
Interface to the Webservices of the Swiss Parliament
A Simple and Flexible Switch-Case Construct for the 'R' Language
Switching nonparametric regression models for a single curve and
functional data
Installing, Managing, and Switching Between Distinct Sets of
Installed Packages
Retrieving, Organizing, and Analyzing Estuary Monitoring Data
Functions for Analyzing and Plotting Estuary Monitoring Data
Cost Constrained Flux Balance Analysis (ccFBA): MetabOlic
Modeling with ENzyme kineTics (MOMENT)
Cycle-Free Flux Balance Analysis (CycleFreeFlux)
Dynamic FBA : Dynamic Flux Balance Analysis
Syllable Counting and Readability Measurements
Syllabifier for CMU Dictionary Transcriptions
Hyphenation and Syllable Counting for Text Analysis
Language Support for 'sylly' Package: English
Autoregressive and Moving Average Symmetric Models
Symbolic Representation of Matrix Determinant
Testing for Symmetry of Data and Model Residuals
Symbolic Central and Noncentral Moments of the Multivariate
Normal Distribution
Symbolic Computation for Structural Equation Models
Methods for Computing Spatial, Temporal, and Spatiotemporal
Statistics
Subsample Temporal Data to Synchronal Events and Compute the MCI
A Synchronized Tausworthe RNG for R and Python
Analysis of Functional and Phylogenetic Patterns in
Metacommunities
Inference and Analysis of Sympatry Networks
Synthesize Dense or Sparse Functional Data/Snippets
Synthetic Likelihood Methods for Intractable Likelihoods
Synoptic Climate Classification and Spatial Regionalization of
Environmental Data
Synthetic RNA-Seq Network Generation and Mutual Information
Estimates
An 'SPSS' Syntax Generator for Multi-Variable Manipulation
Synthetic Control Group Method for Comparative Case Studies
Synthetic Microdata and Spatial MicroSimulation Modeling for ACS
Data
Generate Synthetic Data from Statistical Models
Import, Assemble, and Deduplicate Bibliographic Datasets
Synthetic Experience Tracking Insurance Claims
Generating Synthetic Versions of Sensitive Microdata for
Statistical Disclosure Control
Tools and Tests for Experiments with Partially Synthetic Data
Sets
Powerful and Reliable Tools for Running System Commands in R
Systematic Scenario Selection for Stress Testing
Send Log Messages to Remote 'syslog' Server
Estimating Systems of Simultaneous Equations
Extracts Sentiment and Sentiment-Derived Plot Arcs from Text
Functions for Applying the T^2-Test for Equivalence
Tools for Computational Optimal Transport
Create Summary Tables for Statistical Reports
Write Formatted Tables in Excel Workbooks
Build 'data.table' Expressions with Data Manipulation Verbs
Make and Apply Customized Rounding Specifications for Tables
Tables of Descriptive Statistics in HTML
Exports Reproducible Summary Tables to Multi-Tab Spreadsheet
Files (.xls or .xlsx)
Higher Criticism Test of Two Frequency Counts Tables
Combines 'data.table' and 'matrix' Classes
Create 'Table 1' to Describe Baseline Characteristics with or
without Propensity Score Weights
Represents tables as semi-graphic displays
Presentation-Quality Tables, Displayed Using 'ggplot2'
Tabulate Descriptive Statistics in Multiple Formats
Automatically Convert Hierarchical for-Human Tables to
Machine-Readable LongForm Dataframes
Fit 'TabNet' Models for Classification and Regression
Music Notation Syntax, Manipulation, Analysis and Transcription
in R
Efficient Tabulation with Stata-Like Output
Bindings for 'Tabula' PDF Table Extractor Library
Parsing Semi-Structured Log Files into Tabular Format
Tabu Search Algorithm for Binary Configurations
Positron Emission Tomography Time-Activity Curve Analysis
New and Extended Plots, Methods, and Panel Functions for
'lattice'
Helpers for Data Analysis and Presentation Focused on Undergrad
Psychology
Estimate the Probability in the Upper Tail of the Aggregate Loss
Distribution
Tool for Annotating Images in Preparation for Analysis
Analysis of Differential Calorimetry Scans
Design Shaded Contour Lines (or Tanaka) Maps
A Two-Stage Approach to Maximize Interpretability of Drug
Response Models Based on Multiple Molecular Data Types
Anonymization of Spatial Point Patterns and Raster Objects
Flexible Tree Taper Curves Based on Semiparametric Mixed Models
Wrapper for 'tapkee' Dimension Reduction Library
Bayesian Modeling of Autoregressive Threshold Time Series Models
Dynamic Function-Oriented 'Make'-Like Declarative Workflows
Replicate Tariff Method for Verbal Autopsy
Collection of Utility and Convenience Functions
Analysis and Prediction of Bicycle Rental Amount
Schedule R Scripts and Processes with the Windows Task Scheduler
Earthquake Traveltime Calculations for 1-D Earth Models
Efficient Computation and Testing of the Bergsma-Dassios Sign
Covariance
Get Data Out of 'Tautulli' (Formerly 'PlexPy')
A High-Performance Local Taxonomic Database Interface
Taxonomic Information from Around the Web
Tools for Working with 'Taxonomic' Databases
Functions to Work with NCBI Accessions and Taxonomy
Taxonomic Standardization of Plant Species Names
Estimation of Causal Effects with Outcomes Truncated by Death
Functions for tuberculosis diagnostics research
Tree Branches Evaluated Statistically for Tightness
TBF Methodology Extension for Multinomial Outcomes
Convert Tibbles or Data Frames to Xts Easily
Tree-Based Moving Average Forecasting Model
Rearrangement Distances Between Unrooted Phylogenetic Trees
Survival Analysis using a Transform-Both-Sides Model
MLE of a Truncated Normal Distribution with Censored Data
Retrieve Genomic and Clinical Data from TCGA
Time-Course Gene Set Analysis for RNA-Seq Data
Client for the Cancer Imaging Archive REST API
Spacekime Analytics, Time Complexity and Inferential Uncertainty
Testing in Conditional Likelihood Context
Data from the 2010 Tourism Forecasting Competition