Enhancing cross-language compatibility within the 'RStudio' environment and supporting seamless language understanding, 
    the 'deepRstudio' package leverages the power of the 'DeepL' API (see <https://www.deepl.com/docs-api>) to enable seamless, fast, 
    accurate, and affordable translation of code comments, documents, and text. This package offers the ability to translate selected text 
    into English (EN), as well as from English into various languages, namely Japanese (JA), Chinese (ZH), Spanish (ES), 
    French (FR), Russian (RU), Portuguese (PT), and Indonesian (ID). With much of the text being written in English, the emphasis 
    is on compatibility from English. It is also designed for developers working on multilingual projects and data analysts collaborating 
    with international teams, simplifying the translation process and making code more accessible and comprehensible to people with 
    diverse language backgrounds. This package uses the 'rstudioapi' package and 'DeepL' API, and is simply implemented, executed 
    from addins or via shortcuts on 'RStudio'. With just a few steps, content can be translated between supported languages, promoting better 
    collaboration and expanding the global reach of work. The functionality of this package works only on 'RStudio' using 'rstudioapi'.
Extends the functionality of other plotting packages like
    'ggplot2' and 'lattice' to help facilitate the plotting of data over long time
    intervals, including, but not limited to, geological, evolutionary, and ecological
    data. The primary goal of 'deeptime' is to enable users to add highly customizable
    timescales to their visualizations. Other functions are also included to assist
    with other areas of deep time visualization.
Allows for the specification of deep conditional transformation 
    models (DCTMs) and ordinal neural network transformation models, as 
    described in Baumann et al (2021) <doi:10.1007/978-3-030-86523-8_1> and 
    Kook et al (2022) <doi:10.1016/j.patcog.2021.108263>. Extensions such as
    autoregressive DCTMs (Ruegamer et al, 2022, <doi:10.48550/arXiv.2110.08248>)
    and transformation ensembles (Kook et al, 2022, <doi:10.48550/arXiv.2205.12729>)
    are implemented.
Abstract of Manuscript. Differential gene expression analysis using RNA sequencing (RNA-seq) data is a standard approach for making biological discoveries. Ongoing large-scale efforts to process and normalize publicly available gene expression data enable rapid and systematic reanalysis. While several powerful tools systematically process RNA-seq data, enabling their reanalysis, few resources systematically recompute differentially expressed genes (DEGs) generated from individual studies. We developed a robust differential expression analysis pipeline to recompute 3162 human DEG lists from The Cancer Genome Atlas, Genotype-Tissue Expression Consortium, and 142 studies within the Sequence Read Archive. After measuring the accuracy of the recomputed DEG lists, we built the Differential Expression Enrichment Tool (DEET), which enables users to interact with the recomputed DEG lists. DEET, available through CRAN and RShiny, systematically queries which of the recomputed DEG lists share similar genes, pathways, and TF targets to their own gene lists. DEET identifies relevant studies based on shared results with the user’s gene lists, aiding in hypothesis generation and data-driven literature review. Sokolowski, Dustin J., et al. "Differential Expression Enrichment Tool (DEET): an interactive atlas of human differential gene expression." Nucleic Acids Research Genomics and Bioinformatics (2023).
Provides mean squared error (MSE) and plot the kernel densities related to extreme value distributions with their estimated values.
    By using Gumbel and Weibull Kernel. See Salha et al. (2014) <doi:10.4236/ojs.2014.48061> and Khan and Akbar (2021) <doi:10.4236/ojs.2021.112018 >.
A simple syntax to change the default values for function
  arguments, whether they are in packages or defined locally.
Parses command line arguments and supplies values to scripts. Users can specify names to which parsed inputs are assigned, value types into which inputs are cast, long options or short options, input splitters and callbacks that define how options should be specified and how input values are supplied.
Creates 'define.xml' documents used for regulatory 
    submissions based on spreadsheet metadata.  Can also help
    create metadata and generate HTML data explorer.
Use numerical optimization to fit ordinary differential equations (ODEs) to time series data to examine the dynamic relationships between variables or the characteristics of a dynamical system. It can now be used to estimate the parameters of ODEs up to second order, and can also apply to multilevel systems. See <https://github.com/yueqinhu/defit> for details.
Simple functions to deflate nominal Brazilian Reais using several popular price indexes downloaded from the Brazilian Institute for Applied Economic Research.
Implements the 'deflist' class, a read-only list-like object that accesses its elements via a function.
    The 'deflist' class can be used to model deferred access to data or computations by routing indexed list access to a function.
    This approach is particularly useful when sequential list-like access to data is required but holding all the data in memory at once is not feasible.
    The package also provides utilities for memoisation and caching to optimize access to frequently requested elements.
Multi-binary response models are a class of models that allow for the estimation of multiple binary outcomes simultaneously. This package provides functions to estimate and simulate these models using the Discrete Exponential-Family Models [DEFM] framework. In it, we implement the models described in Vega Yon, Valente, and Pugh (2023) <doi:10.48550/arXiv.2211.00627>. DEFMs include Exponential-Family Random Graph Models [ERGMs], which characterize graphs using sufficient statistics, which is also the core of DEFMs. Using sufficient statistics, we can describe the data through meaningful motifs, for example, transitions between different states, joint distribution of the outcomes, etc.
Implements two out-of box classifiers presented in <doi:10.48550/arXiv.2112.01063> for 
    distinguishing forest and non-forest terrain images. Under these algorithms, there are 
    frequentist approaches: one parametric, using stable distributions, and another one- 
    non-parametric, using the squared Mahalanobis distance. The package also contains functions for 
    data handling and building of new classifiers as well as some test data set.
Methods for fitting nonstationary Gaussian process models by spatial deformation, as introduced by Sampson and Guttorp (1992) <doi:10.1080/01621459.1992.10475181>, and by dimension expansion, as introduced by Bornn et al. (2012) <doi:10.1080/01621459.2011.646919>. Low-rank thin-plate regression splines, as developed in Wood, S.N. (2003) <doi:10.1111/1467-9868.00374>, are used to either transform co-ordinates or create new latent dimensions.
Numerical quadrature of functions of one variable over a finite
  or infinite interval with double exponential formulas.
Compute degree days from daily min and max temperatures for
    modeling plant and insect development.
Genes that are differentially expressed between two or more experimental conditions can be detected in RNA-Seq. A high biological variability may impact the discovery of these genes once it may be divergent between the fixed effects. However, this variability can be covered by the random effects. 'DEGRE' was designed to identify the differentially expressed genes considering fixed and random effects on individuals. These effects are identified earlier in the experimental design matrix. 'DEGRE' has the implementation of preprocessing procedures to clean the near zero gene reads in the count matrix, normalize by 'RLE' published in the 'DESeq2' package, 'Love et al. (2014)' <doi:10.1186/s13059-014-0550-8> and it fits a regression for each gene using the Generalized Linear Mixed Model with the negative binomial distribution, followed by a Wald test to assess the regression coefficients.
Likelihood-based inference for skewed count distributions used in network modeling. "degreenet" is a part of the "statnet" suite of packages for network analysis.
Estimation of a density from grouped (tabulated) summary statistics evaluated in each of the big bins (or classes) partitioning the support of the variable. These statistics include class frequencies and central moments of order one up to four. The log-density is modelled using a linear combination of penalised B-splines. The multinomial log-likelihood involving the frequencies adds up to a roughness penalty based on the differences in the coefficients of neighbouring B-splines and the log of a root-n approximation of the sampling density of the observed vector of central moments in each class. The so-obtained penalized log-likelihood is maximized using the EM algorithm to get an estimate of the spline parameters and, consequently, of the variable density and related quantities such as quantiles, see Lambert, P. (2021) <arXiv:2107.03883> for details.
Performs reference based multiple imputation of recurrent event data
    based on a negative binomial regression model, as described
    by Keene et al (2014) <doi:10.1002/pst.1624>.
Provides probability mass, distribution, quantile, random-variate
    generation, and method-of-moments parameter-estimation functions for the
    Delaporte distribution with parameterization based on Vose (2008)
    <isbn:9780470512845>. The Delaporte is a discrete probability distribution
    which can be considered the convolution of a negative binomial distribution
    with a Poisson distribution. Alternatively, it can be considered a counting
    distribution with both Poisson and negative binomial components. It has been
    studied in actuarial science as a frequency distribution which has more
    variability than the Poisson, but less than the negative binomial.
Mechanisms to parallelize dependent tasks in a manner that
    optimizes the compute resources available. It provides access to "delayed"
    computations, which may be parallelized using futures. It is, to an extent,
    a facsimile of the 'Dask' library (<https://www.dask.org/>), for the 'Python'
    language.
Provides sample size and power calculations when the treatment time-lag effect is present and the lag duration is either homogeneous across the individual subject, or varies heterogeneously from individual to individual within a certain domain and following a specific pattern. The methods used are described in Xu, Z., Zhen, B., Park, Y., & Zhu, B. (2017) <doi:10.1002/sim.7157>.
Calculates the Delaunay triangulation and the Dirichlet
	or Voronoi tessellation (with respect to the entire plane) of
	a planar point set. Plots triangulations and tessellations in
	various ways.  Clips tessellations to sub-windows. Calculates
	perimeters of tessellations.  Summarises information about
	the tiles of the tessellation.	Calculates the centroidal
	Voronoi (Dirichlet) tessellation using Lloyd's algorithm.
Measure of agreement delta was originally by Martín & Femia (2004) <DOI:10.1348/000711004849268>. 
    Since then has been considered as agreement measure for different 
    fields, since their behavior is usually better than the usual kappa index
    by Cohen (1960) <DOI:10.1177/001316446002000104>. The main issue with delta 
    is that can not be computed by hand contrary to kappa. The current algorithm
    is based on the Version 5 of the delta windows program that can be found on
    <https://www.ugr.es/~bioest/software/delta/cmd.php?seccion=downloads>.
Infer progression of circadian rhythms in transcriptome data in
  which samples are not labeled with time of day and coverage of the circadian
  cycle may be incomplete. See Shilts et al. (2018) <doi:10.7717/peerj.4327>.
Analysis of agreement for nominal data between two raters using the Delta model. This model is proposed as an alternative to the widespread measure Cohen kappa coefficient, which performs poorly when the marginal distributions are very asymmetric (Martin-Andres and Femia-Marzo (2004), <doi:10.1348/000711004849268>; Martin-Andres and Femia-Marzo (2008) <doi:10.1080/03610920701669884>). The package also contains a function to perform a massive analysis of multiple raters against a gold standard. A shiny app is also provided to obtain the measures of nominal agreement between two raters.
The deltaPlotR package implements Angoff's Delta Plot method to detect dichotomous DIF. Several detection thresholds are included, either from multivariate normality assumption or by prior determination. Item purification is supported (Magis and Facon (2014) <doi:10.18637/jss.v059.c01>).
A collection of asymmetrical kernels belong to lifetime distributions for kernel density estimation is presented. 
    Mean Squared Errors (MSE) are calculated for estimated curves. For this purpose, R functions allow the distribution to be Gamma, Exponential or Weibull.
    For details see Chen (2000a,b), Jin and Kawczak (2003) and Salha et al. (2014) <doi:10.12988/pms.2014.4616>.
The distributed expectation maximization algorithms are used to solve parameters of multivariate Gaussian mixture models. The philosophy of the package is described in Guo, G. (2022) <doi:10.1080/02664763.2022.2053949>.
Developed to Solve the Multi-Criteria Decision Making Problems with Decision Making Trial and Evaluation Laboratory Technique in R.
Generalized Deming regression, Theil-Sen regression and Passing-Bablock regression functions.
Two general demographic decomposition methods are offered: Pseudo-continuous decomposition proposed by Horiuchi, Wilmoth, and Pletcher (2008) <doi:10.1353/dem.0.0033> and stepwise replacement decomposition proposed by Andreev, Shkolnikov and Begun (2002) <doi:10.4054/DemRes.2002.7.14>.
Designed to support the visualization, numerical computation,
     qualitative analysis, model-data fusion, and stochastic simulation for
     autonomous systems of differential equations. Euler and Runge-Kutta methods
     are implemented, along with tools to visualize the two-dimensional
     phaseplane. Likelihood surfaces and a simple Markov Chain Monte Carlo
     parameter estimator can be used for model-data fusion of differential
     equations and empirical models. The Euler-Maruyama method is provided for
     simulation of stochastic differential equations. The package was originally
     written for internal use to support teaching by Zobitz, and refined to
     support the text "Exploring modeling with data and differential equations
     using R" by John Zobitz (2021) <https://jmzobitz.github.io/ModelingWithR/index.html>.
Construction and analysis of matrix population models in R.
Connects to the <https://genderize.io/>, <https://agify.io/> and <https://nationalize.io/> APIs to estimate gender, age and nationality of a first name.
The Demographic Table in R combines contingency table for categorical variables, mean and standard deviation for continuous variables. t-test, chi-square test and Fisher's exact test calculated the p-value of two groups. The standardized mean difference were performed with 95 % confident interval, and writing table into document file.
Functions for creating demographic table with simple summary
        statistics, with optional comparison(s) over one or more groups.
        Numeric variables are summarized in means, standard deviations,
        medians, inter-quartile-ranges (IQR), skewness, Shapiro-Wilk
        normality test and ranges, and compared using two-sample t-test,
        Wilcoxon test, ANOVA and/or Kruskal-Wallis test.  Logical and
        factor variables are summarized in counts and percentages and
        compared using chi-squared test and/or Fisher's exact test.
Functions for demographic analysis including lifetable
        calculations; Lee-Carter modelling; functional data analysis of
        mortality rates, fertility rates, net migration numbers; and
        stochastic population forecasting.
Demonstration code showing how (univariate) kernel
	     density estimates are computed, at least conceptually,
	     and allowing users to experiment with different kernels,
	     should they so wish.  The method used follows directly
	     the definition, but gains efficiency by replacing the
	     observations by frequencies in a very fine grid covering
	     the sample range.  A canonical reference is
	     B. W. Silverman, (1998) <doi: 10.1201/9781315140919>.
	     NOTE: the density function in the
	     stats package uses a more sophisticated method based on the
	     fast Fourier transform and that function should be used if
	     computational efficiency is a prime consideration.
Estimate population kin counts and its distribution by type, age and sex.
    The package implements one-sex and two-sex framework for studying living-death availability,
    with time varying rates or not, and multi-stage model.
Mimics the demo functionality for 'Shiny' apps in a package. Apps stored to the package subdirectory inst/shiny can be called by demoShiny(topic).
Tool for the development of multi-linear QSPR/QSAR models (Quantitative structure-property/activity relationship). Theses models are used in chemistry, biology and pharmacy to find a relationship between the structure of a molecule and its property (such as activity, toxicology but also physical properties). The various functions of this package allows: selection of descriptors based of variances, intercorrelation and user expertise; selection of the best multi-linear regression in terms of correlation and robustness; methods of internal validation (Leave-One-Out, Leave-Many-Out, Y-scrambling) and external using test sets.
Implements the Determinantal point process (DPP) based optimal design
    emulator described in Pratola, Lin and Craigmile (2018) <arXiv:1804.02089> for
    Gaussian process regression models.  See <http://www.matthewpratola.com/software>
    for more information and examples.
Offers a set of functions for extending
    'dendrogram' objects in R, letting you visualize and compare trees of
    'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters
    - the color, size, type, etc of its branches, nodes and labels. (2)
    Visually and statistically compare different 'dendrograms' to one another.
There are various functions for managing and cleaning data before the application of different approaches. This includes identifying and erasing sudden jumps in dendrometer data not related to environmental change, identifying the time gaps of recordings, and changing the temporal resolution of data to different frequencies. Furthermore, the package calculates daily statistics of dendrometer data, including the daily amplitude of tree growth. Various approaches can be applied to separate radial growth from daily cyclic shrinkage and expansion due to uptake and loss of stem water. In addition, it identifies periods of consecutive days with user-defined climatic conditions in daily meteorological data, then check what trees are doing during that period.
Provides extra functions to manipulate dendrograms
    that build on the base functions provided by the 'stats' package. The main
    functionality it is designed to add is the ability to colour all the edges
    in an object of class 'dendrogram' according to cluster membership i.e. each
    subtree is coloured, not just the terminal leaves. In addition it provides
    some utility functions to cut 'dendrogram' and 'hclust' objects and to 
    set/get labels.
Computation of dendrometric and structural 
   parameters from forest inventory data. The objective is to provide an 
   user-friendly R package for researchers, ecologists, foresters, 
   statisticians, loggers and others persons who deal with forest inventory 
   data. Useful conversion of angle value from degree to radian, conversion from 
   angle to slope (in percentage) and their reciprocals as well as principal 
   angle determination are also included. Position and dispersion parameters 
   usually found in forest studies are implemented. The package contains 
   Fibonacci series, its extensions and the Golden Number computation.
   Useful references are Arcadius Y. J. Akossou, Soufianou Arzouma, 
   Eloi Y. Attakpa, Noël H. Fonton and Kouami Kokou (2013) <doi:10.3390/d5010099> 
   and W. Bonou, R. Glele Kakaï, A.E. Assogbadjo, H.N. Fonton, B. Sinsin (2009) 
   <doi:10.1016/j.foreco.2009.05.032> .
Provides functions for the calculation and plotting of synchrony in 
      tree growth from tree-ring width chronologies (TRW index). It combines
      variance-covariance (VCOV) mixed modelling with functions that quantify 
      the degree to which the TRW chronologies contain a common temporal 
      signal. It also implements temporal trends in spatial synchrony using a 
      moving window. These methods can also be used with other kind of ecological
      variables that have temporal autocorrelation corrected.
Provides novel dendroclimatological methods, primarily used by the
    Tree-ring research community. There are four core functions. The first one is 
    daily_response(), which finds the optimal sequence of days that are related 
    to one or more tree-ring proxy records. Similar function is daily_response_seascorr(), 
    which implements partial correlations in the analysis of daily response functions.
    For the enthusiast of monthly data, there is monthly_response() function.
    The last core function is compare_methods(), which effectively compares several 
    linear and nonlinear regression algorithms on the task of climate reconstruction.
Re-arranges a dendrogram to optimize visualisation-based cost functions.
An implementation of functions to optimize ordering of nodes in a dendrogram, without affecting the meaning of the dendrogram. A dendrogram can be sorted based on the average distance of subtrees, or based on the smallest distance value. These sorting methods improve readability and interpretability of tree structure, especially for tasks such as comparison of different distance measures or linkage types and identification of tight clusters and outliers. As a result, it also introduces more meaningful reordering for a coupled heatmap visualization. This method is described in "dendsort: modular leaf ordering methods for dendrogram representations in R", F1000Research 2014, 3: 177 <doi:10.12688/f1000research.4784.1>.
Provides a weekly, monthly, yearly summary of dengue cases by state/ province/ country.
Given count data from two conditions, it determines which transcripts are differentially expressed across the two conditions using Bayesian inference of the parameters of  a bottom-up model for PCR amplification. This model is  developed in Ndifon Wilfred, Hilah Gal, Eric Shifrut, Rina Aharoni, Nissan Yissachar, Nir Waysbort, Shlomit Reich Zeliger, Ruth Arnon, and Nir Friedman (2012), <http://www.pnas.org/content/109/39/15865.full>, and results in a distribution for the counts that is a superposition of the binomial and negative binomial distribution.
Estimate a low rank matrix from noisy data using singular values
    thresholding and shrinking functions. Impute missing values with matrix completion. The method is described in <arXiv:1602.01206>.
An integrated toolset for the analysis of de novo (sporadic)
    genetic sequence variants. denovolyzeR implements a mutational model that
    estimates the probability of a de novo genetic variant arising in each human
    gene, from which one can infer the expected number of de novo variants in a
    given population size. Observed variant frequencies can then be compared against
    expectation in a Poisson framework. denovolyzeR provides a suite of functions
    to implement these analyses for the interpretation of de novo variation in human
    disease.
Estimation of functional linear mixed models for densely sampled data based on functional principal component analysis.
Bayesian density estimates for univariate continuous random samples are provided using the Bayesian inference engine paradigm. The engine options are: Hamiltonian Monte Carlo, the no U-turn sampler, semiparametric mean field variational Bayes and slice sampling. The methodology is described in Wand and Yu (2020) <arXiv:2009.06182>.
Provides various tools for analysing density profiles
    obtained by resistance drilling. It can load individual or
    multiple files and trim the starting and ending part of each
    density profile. Tools are also provided to trim profiles
    manually, to remove the trend from measurements using several
    methods, to plot the profiles and to detect tree rings
    automatically. Written with a focus on forestry use of resistance
    drilling in standing trees.
With bivariate data, it is possible to calculate
    2-dimensional kernel density estimates that return polygons at given
    levels of probability. 'densityarea' returns these polygons for
    analysis, including for calculating their area.
An improved implementation (based on k-nearest neighbors) of the 
    density peak clustering algorithm, originally described by Alex Rodriguez 
    and Alessandro Laio (Science, 2014 vol. 344) <DOI: 10.1126/science.1242072>. 
    It can handle large datasets (> 100, 000 samples) very efficiently. It was 
    initially implemented by Thomas Lin Pedersen, with inputs from Sean Hughes 
    and later improved by Xiaojie Qiu to handle large datasets with kNNs.
Provide a Dens-based method for estimating functional connection in large scale brain networks using partial correlation.
Density ratio estimation.
    The estimated density ratio function can be used in many applications such as
    anomaly detection, change-point detection, covariate shift adaptation.
    The implemented methods are uLSIF (Hido et al. (2011) <doi:10.1007/s10115-010-0283-2>),
    RuLSIF (Yamada et al. (2011) <doi:10.1162/NECO_a_00442>),
    and KLIEP (Sugiyama et al. (2007) <doi:10.1007/s10463-008-0197-x>).
Graphical methods for compactly illustrating probability distributions, including density strips, density regions, sectioned density plots and varying width strips.
Provides the mathematical model described by "Serostatus Testing & Dengue Vaccine Cost-Benefit Thresholds"
    in <doi:10.1098/rsif.2019.0234>.  Using the functions in the package,
    that analysis can be repeated using sample life histories, either synthesized from local seroprevalence data
    using other functions in this package (as in the manuscript) or from some other source.
    The package provides a vignette which walks through the analysis in the publication, as well as a function
    to generate a project skeleton for such an analysis.
Implements the Differential Evolution algorithm for global
    optimization of a real-valued function of a real-valued parameter
    vector as described in Mullen et al. (2011) <doi:10.18637/jss.v040.i06>.
Differential Evolution (DE) stochastic heuristic algorithms for
    global optimization of problems with and without general constraints.
    The aim is to curate a collection of its variants that
    (1) do not sacrifice simplicity of design,
    (2) are essentially tuning-free, and
    (3) can be efficiently implemented directly in the R language.
    Currently, it provides implementations of the algorithms 'jDE' by
    Brest et al. (2006) <doi:10.1109/TEVC.2006.872133> for single-objective
    optimization and 'NCDE' by Qu et al. (2012) <doi:10.1109/TEVC.2011.2161873>
    for multimodal optimization (single-objective problems with
    multiple solutions).
Hash an expression with its dependencies and store its
	value, reloading it from a file as long as both the expression and
	its dependencies stay the same.
Dependent censoring regression models for survival multivariate data. These models are based on extensions of the frailty models, capable to accommodating the dependence between failure and censoring times, with Weibull and piecewise exponential marginal distributions. Theoretical details regarding the models implemented in the package can be found in Schneider et al. (2019) <doi:10.1002/bimj.201800391>.
Functions to compute coefficients measuring the dependence of two or more than two variables. The functions can be deployed to gain information about functional dependencies of the variables with emphasis on monotone functions. The statistics describe how well one response variable can be approximated by a monotone function of other variables. In regression analysis the variable selection is an important issue. In this framework the functions could be useful tools in modeling the regression function. Detailed explanations on the subject can be found in papers Liebscher (2014) <doi:10.2478/demo-2014-0004>; Liebscher (2017) <doi:10.1515/demo-2017-0012>; Liebscher (2019, submitted).
Estimation and testing methods for dependently truncated data.
 Semi-parametric methods are based on Emura et al. (2011)<Stat Sinica 21:349-67>, Emura & Wang (2012)<doi:10.1016/j.jmva.2012.03.012>,
 and Emura & Murotani (2015)<doi:10.1007/s11749-015-0432-8>.
 Parametric approaches are based on Emura & Konno (2012)<doi:10.1007/s00362-014-0626-2> and Emura & Pan (2017)<doi:10.1007/s00362-017-0947-z>.
 A regression approach is based on Emura & Wang (2016)<doi:10.1007/s10463-015-0526-9>. Quasi-independence tests are based on Emura & Wang (2010)<doi:10.1016/j.jmva.2009.07.006>.
 Right-truncated data for Japanese male centenarians are given by Emura & Murotani (2015)<doi:10.1007/s11749-015-0432-8>.
Pigna [_pìn'n'a_] is the Italian word for pine cone.  In
    jargon, it is used to identify a task which is boring, banal,
    annoying, painful, frustrating and maybe even with a not so beautiful
    or rewarding result, just like the obstinate act of trying to
    challenge yourself in extracting pine nuts from a pine cone, provided
    that, in the end, you will find at least one inside it. Here you can
    find a backpack of functions to be used to solve small everyday
    problems of coding or analyzing (clinical) data, which would be
    normally solved using quick-and-dirty patches. You will be able to
    convert 'Hmisc' and 'rms' summary()es into data.frames ready to be
    rendered by 'pander' and 'knitr'. You can access easy-to-use wrappers
    to activate essential but useful progress bars (from 'progress') into
    your loops or functionals. Easy setup and control Telegram's bots
    (from 'telegram.bot') to send messages or to divert error messages to
    a Telegram's chat. You also have some utilities helping you in the
    development of packages, like the activation of the same user
    interface of 'usethis' into your package, or call polite functions to
    ask a user to install other packages. Finally, you find a set of
    thematic sets of packages you may use to set up new environments
    quickly, installing them in a single call.
Plots dependency logos from a set of aligned input sequences.
Fits (multigroup) mixtures of latent or hidden Markov models on mixed categorical and continuous (timeseries) data. The 'Rdonlp2' package can optionally be used for optimization of the log-likelihood and is available from R-forge. See Visser et al. (2009, <DOI:10.1007/978-0-387-95922-1_13>) for examples and applications.
Fits latent (hidden) Markov models on mixed categorical and continuous (time series) data, otherwise known as dependent mixture models, see Visser & Speekenbrink (2010, <DOI:10.18637/jss.v036.i07>).
Methods for analyzing population dynamics and movement tracks simulated using the DEPONS model <https://www.depons.eu> (v.3.0), for manipulating input raster files, shipping routes and for analyzing sound propagated from ships.
Manage your source code dependencies
  by decorating your existing R code with special,
  'roxygen'-style comments.
Could be used to obtain spatial depths, spatial ranks and outliers of multivariate random variables. Could also be used to visualize DD-plots (a multivariate generalization of QQ-plots).
Data depth concept offers a variety of powerful and user friendly
    tools for robust exploration and inference for multivariate data. The offered
    techniques may be successfully used in cases of lack of our knowledge on
    parametric models generating data due to their nature. The
    package consist of among others implementations of several data depth techniques
    involving multivariate quantile-quantile plots, multivariate scatter estimators,
    multivariate Wilcoxon tests and robust regressions.
Implementation of different statistical tools for the 
        description and analysis of gene expression data based on the 
        concept of data depth, namely, the scale curves for 
        visualizing the dispersion of one or various groups of samples 
        (e.g. types of tumors), a rank test to decide whether two groups 
        of samples come from a single distribution and two methods of
        supervised classification techniques, the DS and TAD methods. 
        All these techniques are based on the Modified Band Depth, which
        is a recent notion of depth with a low computational cost, what 
        renders it very appropriate for high dimensional data such as 
        gene expression data.
Modeling the zero coupon yield curve using the dynamic De Rezende and
             Ferreira (2011) <doi:10.1002/for.1256> five factor model with variable
             or fixed decaying parameters. For explanatory purposes, the package also
             includes various short datasets of interest rates for the BRICS countries.
R-based solution for symbolic differentiation. It admits
    user-defined function as well as function substitution
    in arguments of functions to be differentiated. Some symbolic
    simplification is part of the work.
A set of pricing and expository functions that should
    be useful in teaching a course on financial derivatives.
Discrete event simulation (DES) involves modeling of systems
   having discrete, i.e. abrupt, state changes. For instance, when a job
   arrives to a queue, the queue length abruptly increases by 1.  This
   package is an R implementation of the event-oriented approach to DES;
   see the tutorial in Matloff (2008) 
   <http://heather.cs.ucdavis.edu/~matloff/156/PLN/DESimIntro.pdf>.
Tools to read, write, create, and manipulate DESCRIPTION
    files.  It is intended for packages that create or manipulate other
    packages.
Decompose a time series into seasonal, trend and irregular components using transformations to amplitude-frequency domain.
Weighted frequency and contingency tables of categorical
       variables and of the comparison of the mean value of a numerical
       variable by the levels of a factor, and methods to produce xtable
       objects of the tables and to plot them. There are also functions to
       facilitate the character encoding conversion of objects, to quickly
       convert fixed width files into csv ones, and to export a data.frame to
       a text file with the necessary R and SPSS codes to reread the data.
Helper functions for descriptive tasks such as making print-friendly bivariate 
  tables, sample size flow counts, and visualizing sample distributions. Also 
  contains 'R' approximations of some common 'SAS' and 'Stata' functions such 
  as 'PROC MEANS' from 'SAS' and 'ladder', 'gladder', and 'pwcorr' from 'Stata'.
Helps to describe a data frame in hand. Has been developed during PhD work of the maintainer. More information may be obtained from Garai and Paul (2023) <doi:10.1016/j.iswa.2023.200202>.
Produce publication quality graphics from output of 'GGobi'
    describe display plugin.
Allows users to quickly and easily describe data using
    common descriptive statistics.
Description of statistical associations between two variables : measures of local and global association between variables (phi, Cramér V, correlations, eta-squared, Goodman and Kruskal tau, permutation tests, etc.), multiple graphical representations of the associations between two variables (using 'ggplot2') and weighted statistics.
A system for analyzing descriptive representation, especially for comparing the composition of a political body to the population it represents. Users can compute the expected degree of representation for a body under a random sampling model, the expected degree of representation variability, as well as representation scores from observed political bodies. The package is based on Gerring, Jerzak, and Oncel (2023) <doi:10.1017/S0003055423000680>.
Estimate and return the needed parameters for visualizations designed for 'OpenBudgets.eu' <http://openbudgets.eu/> datasets. Calculate descriptive statistical measures in budget data of municipalities across Europe, according to the 'OpenBudgets.eu' data model. There are functions for measuring central tendency and dispersion of amount variables along with their distributions and correlations and the frequencies of categorical variables for a given dataset. Also, can be used generally to other datasets, to extract visualization parameters, convert them to 'JSON' format and use them as input in a different graphical interface.
Exploratory analysis of a data base. Using the functions of this package is possible to filter the data set detecting atypical values (outliers) and to perform exploratory analysis through visual inspection or dispersion measures. With this package you can explore the structure of your data using several parameters at the same time joining statistical parameters with different graphics. Finally, this package aid to confirm or reject the hypothesis that your data structure presents a normal distribution. Therefore this package is useful to get a previous insight of your data before to carry out statistical analysis.
Generate descriptive statistics such as measures of location,
    dispersion, frequency tables, cross tables, group summaries and multiple
    one/two way tables.
Provides functions to create descriptive statistics tables for continuous and categorical variables.
    By default, summary statistics such as mean, standard deviation, quantiles, minimum and maximum for continuous
    variables and relative and absolute frequencies for categorical variables are calculated. 'DescrTab2' features a sophisticated algorithm to
    choose appropriate test statistics for your data and provides p-values. On top of this, confidence intervals for group
    differences of appropriated summary measures are automatically produces for two-group comparison.
    Tables generated by 'DescrTab2' can be integrated in a variety of document formats, including .html, .tex and .docx documents.
    'DescrTab2' also allows printing tables to console and saving table objects for later use.
A toolbox for descriptive statistics, based on the computation of frequency and contingency tables. Several statistical functions and plot methods are provided to describe univariate or bivariate distributions of factors, integer series and numerical series either provided as individual values or as bins.
It generates summary statistics on the input dataset using different descriptive univariate 
    statistical measures on entire data or at a group level. Though there are other packages which does 
    similar job but each of these are deficient in one form or other, in the measures generated, in
    treating numeric, character and date variables alike, no functionality to view these measures on a
    group level or the way the output is represented. Given the foremost role of the descriptive statistics
    in any of the exploratory data analysis or solution development, there is a need for a more constructive, 
    structured and refined version over these packages. This is the idea behind the package and it brings 
    together all the required descriptive measures to give an initial understanding of the data quality, 
    distribution in a faster,easier and elaborative way.The function brings an additional capability to be 
    able to generate these statistical measures on the entire dataset or at a group level. It calculates measures 
    of central tendency (mean, median), distribution (count, proportion), dispersion (min, max, quantile, 
    standard deviation, variance) and shape (skewness, kurtosis). Addition to these measures, it provides information on 
    the data type, count on no. of rows, unique entries and percentage of missing entries. More importantly the measures 
    are generated based on the data types as required by them,rather than applying numerical measures on character and 
    data variables and vice versa. Output as a dataframe object gives a very neat representation, which often is useful 
    when working with a large number of columns. It can easily be exported as csv and analyzed further or presented as a 
    summary report for the data.
Easily create descriptive and comparative tables.
    It makes use and integrates directly with the tidyverse family of packages, and pipes.
    Tables are produced as (nested) dataframes for easy manipulation.
A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'BigCamelCase' style was consequently applied to functions borrowed from contributed R packages as well.
'RStudio' as of recently offers the option to define addins and assign shortcuts to them. This package contains addins for a few most frequently used functions in a data scientist's (at least mine) daily work (like str(), example(), plot(), head(), view(), Desc()). Most of these functions will use the current selection in the editor window and send the specific command to the console while instantly executing it. Assigning shortcuts to these addins will save you quite a few keystrokes.
Here, a function has been developed to generate parameters of the input designs, as well as incidence matrices. This is a general function that can be used to investigate the characterization properties of any block design.
Applying 'CUDA' 'GPUs' via 'Numba' for optimal clinical design. It allows the user to utilize a 'reticulate' 'Python' environment and run intensive Monte Carlo simulation to get the optimal cutoff for the clinical design with potential biomarker effect, which can guide the realistic clinical trials.
A 'shiny' application that enables the user to create a
    prototype UI, being able to drag and drop UI components before being
    able to save or download the equivalent R code.
A simple interface to build designs using the package 'DeclareDesign'. 
    In one line of code, users can specify the parameters of individual 
    designs and diagnose their properties. The designers can also be used 
    to compare performance of a given design across a range of combinations 
    of parameters, such as effect size, sample size, and assignment probabilities.
Includes functions for the construction of matched samples that are balanced and representative by design.  Among others, these functions can be used for matching in observational studies with treated and control units, with cases and controls, in related settings with instrumental variables, and in discontinuity designs.  Also, they can be used for the design of randomized experiments, for example, for matching before randomization.  By default, 'designmatch' uses the 'highs' optimization solver, but its performance is greatly enhanced by the 'Gurobi' optimization solver and its associated R interface.  For their installation, please follow the instructions at <https://www.gurobi.com/documentation/quickstart.html> and <https://www.gurobi.com/documentation/7.0/refman/r_api_overview.html>.  We have also included directions in the gurobi_installation file in the inst folder.
Generate balanced factorial designs with crossed and nested random and fixed effects <https://github.com/mmrabe/designr>.
Different sample size calculations with different study designs.
             These techniques are explained by Chow (2007)
             <doi:10.1201/9781584889830>.
Functions for (1) ranking, selecting, and prioritising  genes,
    proteins, and metabolites from high dimensional biology experiments, (2)
    multivariate hit calling in high content screens, and (3) combining data
    from diverse sources.
S3 classes for multivariate optimization using the desirability function by Derringer and Suich (1980).
In-line functions for multivariate optimization via desirability 
    functions (Derringer and Suich, 1980, <doi:10.1080/00224065.1980.11980968>)
    with easy use within 'dplyr' pipelines.
Written to help undergraduate as well as graduate students to get started
    with R for basic econometrics without the need to import specific functions
    and datasets from many different sources. Primarily, the package is meant to 
    accompany the German textbook Auer, L.v., Hoffmann, S., Kranz, T. (2023,
    ISBN: 978-3-662-68263-0) from which the exercises cover all the topics from the textbook
    Auer, L.v. (2023, ISBN: 978-3-658-42699-6).
Calculates the desparsified lasso as originally introduced in van de Geer et al. (2014) <doi:10.1214/14-AOS1221>, and provides inference suitable for high-dimensional time series, based on the long run covariance estimator in Adamek et al. (2020) <arXiv:2007.10952>. Also estimates high-dimensional local projections by the desparsified lasso, as described in Adamek et al. (2022) <arXiv:2209.03218>.
Functions that solve initial value problems of a system
        of first-order ordinary differential equations ('ODE'), of
        partial differential equations ('PDE'), of differential
        algebraic equations ('DAE'), and of delay differential
        equations.  The functions provide an interface to the FORTRAN
        functions 'lsoda', 'lsodar', 'lsode', 'lsodes' of the 'ODEPACK'
        collection, to the FORTRAN functions 'dvode', 'zvode' and 'daspk'
        and a C-implementation of solvers of the 'Runge-Kutta' family with
        fixed or variable time steps.  The package contains routines
        designed for solving 'ODEs' resulting from 1-D, 2-D and 3-D
        partial differential equations ('PDE') that have been converted
        to 'ODEs' by numerical differencing.
A function for plotting maps of agricultural field experiments that are laid out in grids.  See Ryder (1981) <doi:10.1017/S0014479700011601>.
Create a details HTML tag around R objects to place
    in a Markdown, 'Rmarkdown' and 'roxygen2' documentation.
Models for analyzing site occupancy and count data models
  with detection error, including single-visit based models,
  conditional distance sampling and time-removal models.
  Package development was supported by the
  Alberta Biodiversity Monitoring Institute
  and the Boreal Avian Modelling Project.
Non-normality could greatly distort the meta-analytic results, according to the simulation in Sun and Cheung (2020) <doi: 10.3758/s13428-019-01334-x>. This package aims to detect non-normality for two independent groups with only limited descriptive statistics, including mean, standard deviation, minimum, and maximum.
Allows users to quickly and easily detect data containing
    Personally Identifiable Information (PII) through convenience functions.
Researchers carried out a series of experiments passing a number 
  of essays to different GPT detection models. Juxtaposing detector predictions 
  for papers written by native and non-native English writers, the authors argue 
  that GPT detectors disproportionately classify real writing from non-native 
  English writers as AI-generated.
Detection of runs of homozygosity and of heterozygosity
    in diploid genomes using two methods: sliding windows (Purcell et al (2007)
    <doi:10.1086/519795>) and consecutive runs (Marras et al (2015)
    <doi:10.1111/age.12259>).
Provides pre-fit and post-fit methods for detecting separation and infinite maximum likelihood estimates in generalized linear models with categorical responses. The pre-fit methods apply on binomial-response generalized liner models such as logit, probit and cloglog regression, and can be directly supplied as fitting methods to the glm() function. They solve the linear programming problems for the detection of separation developed in Konis (2007, <https://ora.ox.ac.uk/objects/uuid:8f9ee0d0-d78e-4101-9ab4-f9cbceed2a2a>) using 'ROI' <https://cran.r-project.org/package=ROI> or 'lpSolveAPI' <https://cran.r-project.org/package=lpSolveAPI>. The post-fit methods apply to models with categorical responses, including binomial-response generalized linear models and multinomial-response models, such as baseline category logits and adjacent category logits models; for example, the models implemented in the 'brglm2' <https://cran.r-project.org/package=brglm2> package. The post-fit methods successively refit the model with increasing number of iteratively reweighted least squares iterations, and monitor the ratio of the estimated standard error for each parameter to what it has been in the first iteration. According to the results in Lesaffre & Albert (1989, <https://www.jstor.org/stable/2345845>), divergence of those ratios indicates data separation.
Methods for valuation of life insurance premiums and reserves (including variable-benefit and fractional coverage) based on  "Actuarial Mathematics" by Bowers, H.U. Gerber, J.C. Hickman, D.A. Jones and C.J. Nesbitt (1997, ISBN: 978-0938959465), "Actuarial Mathematics for Life Contingent Risks" by Dickson, David C. M., Hardy, Mary R. and Waters, Howard R  (2009) <doi:10.1017/CBO9780511800146>  and "Life Contingencies" by Jordan, C. W (1952) <doi:10.1017/S002026810005410X>. It also contains functions for  equivalent interest and discount rate calculation, present and future values of annuities, and loan amortization schedule.
Implementation of DetMCD, a new algorithm for robust and deterministic estimation of location and scatter. The benefits of robust and deterministic estimation are explained in Hubert, Rousseeuw and Verdonck (2012) <doi:10.1080/10618600.2012.672100>.
Provides 2D and 3D tour animations as HTML widgets. The user can interact with the widgets using orbit controls, tooltips, brushing, and timeline controls. Linked brushing is supported using 'crosstalk', and widgets can be embedded in Shiny apps or HTML documents.
Density estimation for possibly large data sets and conditional/unconditional random number generation or bootstrapping with distribution element trees. The function 'det.construct' translates a dataset into a distribution element tree. To evaluate the probability density based on a previously computed tree at arbitrary query points, the function 'det.query' is available. The functions 'det1' and 'det2' provide density estimation and plotting for one- and two-dimensional datasets. Conditional/unconditional smooth bootstrapping from an available distribution element tree can be performed by 'det.rnd'. For more details on distribution element trees, see: Meyer, D.W. (2016) <arXiv:1610.00345> or Meyer, D.W., Statistics and Computing (2017) <doi:10.1007/s11222-017-9751-9> and Meyer, D.W. (2017) <arXiv:1711.04632> or Meyer, D.W., Journal of Computational and Graphical Statistics (2018) <doi:10.1080/10618600.2018.1482768>.
DetLTS, DetMM (and DetS) Algorithms for Deterministic, Robust
    Linear Regression.
A Graphical User Interface (GUI) to import, save, detrend and 
    perform standard tree-ring analyses. The interactive detrending allows the user to check how
    well the detrending curve fits each time-series and change it when needed.
Detrend fluorescence microscopy image series for fluorescence
    fluctuation and correlation spectroscopy ('FCS' and 'FFS') analysis.
    This package contains functionality published in a 2016 paper
    <doi:10.1093/bioinformatics/btx434> but it has been extended since
    then with the Robin Hood algorithm and thus contains unpublished work.
Tissue-specific enrichment analysis to assess lists of candidate genes or RNA-Seq expression profiles. Pei G., Dai Y., Zhao Z. Jia P. (2019) deTS: Tissue-Specific Enrichment Analysis to decode tissue specificity. Bioinformatics, In submission.
Compare detrital zircon suites by uploading univariate,
      U-Pb age, or bivariate, U-Pb age and Lu-Hf data, in a 'shiny'-based
      user-interface. Outputs publication quality figures using 'ggplot2', and
      tables of statistics currently in use in the detrital zircon geochronology
      community.
A concise check of the format of one or multiple input arguments (data type, length or value) is provided. Since multiple input arguments can be tested simultaneously, a lengthly list of checks at the beginning of your function can be avoided, hereby enhancing the readability and maintainability of your code.
Provides a non-drawing graphic device for benchmarking purpose.
    In order to properly benchmark graphic drawing code it is necessary
    to factor out the device implementation itself so that results are not 
    related to the specific graphics device used during benchmarking. The 
    'devoid' package implements a graphic device that accepts all the required
    calls from R's graphic engine but performs no action. Apart from 
    benchmarking it is unlikely that this device has any practical use.
Data sets and sample analyses from Jay L. Devore (2008),
        "Probability and Statistics for Engineering and the Sciences
        (7th ed)", Thomson.
A set of functions to quantify the relationship between development
    rate and temperature and to build phenological models. The package comprises 
    a set of models and estimated parameters borrowed from a literature review 
    in ectotherms. The methods and literature review are described in Rebaudo 
    et al. (2018) <doi:10.1111/2041-210X.12935>, Rebaudo and Rabhi (2018) 
    <doi:10.1111/eea.12693>, and Regnier et al. (2021) <doi:10.1093/ee/nvab115>. 
    An example can be found in Rebaudo et al. (2017) 
    <doi:10.1007/s13355-017-0480-5>.
Collection of package development tools.
Develop and evaluate treatment rules based on: (1) the standard indirect approach of split-regression, which fits regressions separately in both treatment groups and assigns an individual to the treatment option under which predicted outcome is more desirable; (2) the direct approach of outcome-weighted-learning proposed by Yingqi Zhao, Donglin Zeng, A. John Rush, and Michael Kosorok (2012) <doi:10.1080/01621459.2012.695674>; (3) the direct approach, which we refer to as direct-interactions, proposed by Shuai Chen, Lu Tian, Tianxi Cai, and Menggang Yu (2017) <doi:10.1111/biom.12676>. Please see the vignette for a walk-through of how to start with an observational dataset whose design is understood scientifically and end up with a treatment rule that is trustworthy statistically, along with an estimation of rule benefit in an independent sample.
A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Classical Test and Item analysis, 
  Item Response analysis and data management for educational and psychological tests.
Conditional Maximum Likelihood Calibration and data management of multistage tests. 
  Supports polytomous items and incomplete designs with linear as well as multistage tests.
  Extended Nominal Response and Interaction models, DIF and profile analysis.
  See Robert J. Zwitser and Gunter Maris (2015)<doi:10.1007/s11336-013-9369-6>.
The 'df2yaml' aims to simplify the process of converting 'dataframe' to 'YAML' <https://yaml.org/>. 
    The 'dataframe' with multiple key columns and one value column will be converted to the multi-level hierarchy.
Contains the Detrended Fluctuation Analysis (DFA), Detrended Cross-Correlation Analysis (DCCA), Detrended Cross-Correlation Coefficient (rhoDCCA), Delta Amplitude Detrended Cross-Correlation Coefficient (DeltarhoDCCA), log amplitude Detrended Fluctuation Analysis (DeltalogDFA), two DFA automatic methods for identification of crossover points and a Deltalog automatic method for identification of reference channels.
Produces SPSS- and SAS-like output for linear discriminant 
  function analysis and canonical correlation analysis. The methods are described in
  Manly & Alberto (2017, ISBN:9781498728966),
  Rencher (2002, ISBN:0-471-41889-7), and
  Tabachnik & Fidell (2019, ISBN:9780134790541).
Computes small-sample degrees of freedom adjustment for
    heteroskedasticity robust standard errors, and for clustered standard errors
    in linear regression. See Imbens and Kolesár (2016)
    <doi:10.1162/REST_a_00552> for a discussion of these adjustments.
Phase I/II adaptive dose-finding design for combination
   studies where toxicity rates are supposed to increase with both agents.
Compares two dataframes with a common key
            and returns the delta records. The package will return
            three dataframes that contain the added, changed,
            and deleted records.
Provides functions to run the CRM and
        TITE-CRM in phase I trials and calibration tools for trial
        planning purposes.
Get Drug information from given differential expression profile. The package search for the bioactive compounds from reference databases such as LINCS containing the genome-wide gene expression signature (GES) from tens of thousands of drug and genetic perturbations (Subramanian et al. (2017) <DOI:10.1016/j.cell.2017.10.049>).
Implementation of automatically computing derivatives
    of functions (see Mailund Thomas (2017) <doi:10.1007/978-1-4842-2881-4>). Moreover, calculating gradients, Hessian and Jacobian matrices is possible.
Implements an algorithm to effortlessly split a column in an R data frame filled with multiple values separated by delimiters. This automates the process of creating separate columns for each unique value, transforming them into binary outcomes.
Provides extended data frames, with a special data frame column which contains two indexes, with potentially a nesting structure.
A set of functions to perform Raju, van der Linden and Fleer's
    (1995, <doi:10.1177/014662169501900405>) Differential Functioning of Items
    and Tests (DFIT) analyses. It includes functions to use the Monte Carlo Item
    Parameter Replication approach (Oshima, Raju, & Nanda, 2006, <doi:10.1111/j.1745-3984.2006.00001.x>)
    for obtaining the associated statistical significance
    tests cut-off points. They may also be used for a priori and post-hoc power
    calculations (Cervantes, 2017, <doi:10.18637/jss.v076.i05>).
Meta-analysis approaches for Phase I dose finding early phases clinical trials in order to better suit requirements in terms of maximum tolerated dose (MTD) and maximal dose regimen (MDR). This package has currently three different approaches: (a) an approach proposed by Zohar et al, 2011, <doi:10.1002/sim.4121> (denoted as ZKO), (b) the Variance Weighted pooling analysis (called VarWT) and (c) the Random Effects Model Based (REMB) algorithm, where user can input his/her own model based approach or use the existing random effect logistic regression model (named as glimem) through the 'dfmeta' package.
Efficient estimation of Dynamic Factor Models using the Expectation Maximization (EM) algorithm 
  or Two-Step (2S) estimation, supporting datasets with missing data. The estimation options follow advances in the 
  econometric literature: either running the Kalman Filter and Smoother once with initial values from PCA - 
  2S estimation as in Doz, Giannone and Reichlin (2011) <doi:10.1016/j.jeconom.2011.02.012> - or via iterated 
  Kalman Filtering and Smoothing until EM convergence - following Doz, Giannone and Reichlin (2012) 
  <doi:10.1162/REST_a_00225> - or using the adapted EM algorithm of Banbura and Modugno (2014) <doi:10.1002/jae.2306>, 
  allowing arbitrary patterns of missing data. The implementation makes heavy use of the 'Armadillo' 'C++' library and 
  the 'collapse' package, providing for particularly speedy estimation. A comprehensive set of methods supports 
  interpretation and visualization of the model as well as forecasting. Information criteria to choose the number 
  of factors are also provided - following Bai and Ng (2002) <doi:10.1111/1468-0262.00273>.
Phase I/II adaptive dose-finding design for single-agent
   Molecularly Targeted Agent (MTA), according to the paper "Phase
   I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau
   Determination using Adaptive Randomization", Riviere Marie-Karelle et
   al. (2016) <doi:10.1177/0962280216631763>.
Tools to identify, quantify, analyze, and visualize growth
    suppression events in tree rings that are often produced by insect
    defoliation. Described in Guiterman et al. (2020) <doi:10.1016/j.dendro.2020.125750>.
Derivative-Free optimization algorithms. These algorithms do not require gradient information. More importantly, they can be used to solve non-smooth optimization problems.
Provides R-implementation of Decision forest algorithm, which combines the predictions of
    multiple independent decision tree models for a consensus decision. In particular, Decision Forest is a novel 
    pattern-recognition method which can be used to analyze: (1) DNA microarray data; 
    (2) Surface-Enhanced Laser Desorption/Ionization Time-of-Flight Mass Spectrometry  (SELDI-TOF-MS) data; and 
    (3) Structure-Activity Relation (SAR) data.
    In this package, three fundamental functions are provided, as (1)DF_train, (2)DF_pred, and (3)DF_CV.  
    run Dforest() to see more instructions.
    Weida Tong (2003) <doi:10.1021/ci020058s>.
A tool for manipulating data using the generic formula. A single formula allows to easily add, replace and remove variables before running the analysis.
A unified method for designing and analysing dose-finding trials in paediatrics, while bridging information from adults, is proposed in the 'dfped' package. The dose range can be calculated under three extrapolation methods: linear, allometry and maturation adjustment, using pharmacokinetic (PK) data. To do this, it is assumed that target exposures are the same in both populations. The working model and prior distribution parameters of the dose-toxicity and dose-efficacy relationships can be obtained using early phase adult toxicity and efficacy data at several dose levels through 'dfped' package. Priors are used into the dose finding process through a Bayesian model selection or adaptive priors, to facilitate adjusting the amount of prior information to differences between adults and children. This calibrates the model to adjust for misspecification if the adult and paediatric data are very different. User can use his/her own Bayesian model written in Stan code through the 'dfped' package. A template of this model is proposed in the examples of the corresponding R functions in the package. Finally, in this package you can find a simulation function for one trial or for more than one trial. These methods are proposed by Petit et al, (2016) <doi:10.1177/0962280216671348>.
Statistical methods for retrospectively detecting changes
             in location and/or dispersion of univariate and multivariate 
             variables. Data values are assumed to be independent, can be 
             individual (one observation at each instant of time) or subgrouped 
             (more than one observation at each instant of time). 
             Control limits are computed, often using a permutation approach, 
             so that a prescribed false alarm probability is guaranteed  
             without making any parametric assumptions on the stable 
             (in-control) distribution. See G. Capizzi and G. Masarotto (2018) 
             <doi:10.1007/978-3-319-75295-2_1> for an introduction to the package.
Implementing Function-on-Scalar Regression model in which the response function is dichotomized and observed sparsely. This package provides smooth estimations of functional regression coefficients and principal components for the dichotomized functional response regression (dfrr) model.
Decomposing value added growth into explanatory factors.
    A cost constrained value added function is defined to specify the 
    production frontier. Industry estimates can also be aggregated using 
    a weighted average approach.
    Details about the methodology and data can be found in Diewert and Fox (2018)
    <doi:10.1093/oxfordhb/9780190226718.013.19>
    and Zeng, Parsons, Diewert and Fox (2018)
    <https://www.business.unsw.edu.au/research-site/centreforappliedeconomicresearch-site/Documents/emg2018-6_SZeng_EMG-Slides.pdf>.
Performs Bayesian model averaging for capture-recapture. This includes code to stratify records, check the strata for suitable overlap to be used for capture-recapture, and some functions to plot the estimated population size.
Feature selection from high dimensional data using a diploid
    genetic algorithm with Incomplete Dominance for genotype to phenotype mapping
    and Random Assortment of chromosomes approach to recombination.
Performs differential correlation analysis on input
    matrices, with multiple conditions specified by a design matrix. Contains
    functions to filter, process, save, visualize, and interpret differential
    correlations of identifier-pairs across the entire identifier space, or with
    respect to a particular set of identifiers (e.g., one). Also contains several
    functions to perform differential correlation analysis on clusters (i.e., modules)
    or genes. Finally, it contains functions to generate empirical p-values for the
    hypothesis tests and adjust them for multiple comparisons. Although the package
    was built with gene expression data in mind, it is applicable to other types of
    genomics data as well, in addition to being potentially applicable to data from
    other fields entirely. It is described more fully in the manuscript
    introducing it, freely available at <doi:10.1186/s12918-016-0349-1>.
Analyses gene expression data derived from experiments to detect differentially expressed genes by employing the concept of majority voting with five different statistical models. It includes functions for differential expression analysis, significance testing, etc. It simplifies the process of uncovering meaningful patterns and trends within gene expression data, aiding researchers in downstream analysis. Boyer, R.S., Moore, J.S. (1991) <doi:10.1007/978-94-011-3488-0_5>.
Provides a flexible container to manage and annotate Differential Gene 
    Expression (DGE) analysis results (Smythe et. al (2015) <doi:10.1093/nar/gkv007>).  
    The DGEobj has data slots for row (gene), col (samples), assays (matrix n-rows 
    by m-samples dimensions) and metadata (not keyed to row, col, or assays).  
    A set of accessory functions to deposit, query and retrieve subsets of a data 
    workflow has been provided.  Attributes are used to capture metadata such as 
    species and gene model, including reproducibility information such that a 3rd 
    party can access a DGEobj history to see how each data object was created or 
    modified.  Since the DGEobj is customizable and extensible it is not limited 
    to RNA-seq analysis types of workflows -- it can accommodate nearly any data 
    analysis workflow that starts from a matrix of assays (rows) by samples (columns).
Provides a function toolkit to facilitate reproducible RNA-Seq Differential Gene Expression (DGE)
    analysis (Law (2015) <doi:10.12688/f1000research.9005.3>).  The tools include both analysis 
    work-flow and utility functions: mapping/unit conversion, count normalization, accounting for 
    unknown covariates, and more.  This is a complement/cohort to the 'DGEobj' package that 
    provides a flexible container to manage and annotate Differential Gene Expression analysis results.
Spatial analyses involving binning require that every bin have the same area, but this is impossible using a rectangular grid laid over the Earth or over any projection of the Earth. Discrete global grids use hexagons, triangles, and diamonds to overcome this issue, overlaying the Earth with equally-sized bins. This package provides utilities for working with discrete global grids, along with utilities to aid in plotting such data.
Differential geometric least angle regression method for fitting sparse generalized linear models. In this version of the package, the user can fit models specifying Gaussian, Poisson, Binomial, Gamma and Inverse Gaussian family. Furthermore, several link functions can be used to model the relationship between the conditional expected value of the response variable and the linear predictor. The solution curve can be computed using an efficient predictor-corrector or a cyclic coordinate descent algorithm, as described in the paper linked to via the URL below.
Model fitting and evaluation tools for double generalized linear
    models (DGLMs). This class of models uses one generalized linear model (GLM)
    to fit the specified response and a second GLM to fit the deviance of the first
    model.
Model estimation, dispersion testing and diagnosis of hyper-Poisson
    Saez-Castillo, A.J. and Conde-Sanchez, A. (2013) 
    <doi:10.1016/j.csda.2012.12.009> and Conway-Maxwell-Poisson Huang, A. (2017)
    regression models.
Dynamic graphical models for multivariate time series data to estimate directed
    dynamic networks in functional magnetic resonance imaging (fMRI), see Schwab et
    al. (2017) <doi:10.1016/j.neuroimage.2018.03.074>.
A revision to the stats::ks.test() function and the associated
        ks.test.Rd help page. With one minor exception, it does not change the
        existing behavior of ks.test(), and it adds features necessary
        for doing one-sample tests with hypothesized discrete
        distributions. The package also contains cvm.test(), for doing
        one-sample Cramer-von Mises goodness-of-fit tests.
Interface to the 'python' package 'dgpsi' for Gaussian process, deep Gaussian process, 
             and linked deep Gaussian process emulations of computer models and networks using stochastic imputation (SI). 
             The implementations follow Ming & Guillas (2021) <doi:10.1137/20M1323771> and 
             Ming, Williamson, & Guillas (2023) <doi:10.1080/00401706.2022.2124311> and 
             Ming & Williamson (2023) <arXiv:2306.01212>. To get started with the package, 
             see <https://mingdeyu.github.io/dgpsi-R/>.
Gumbel distribution functions (De Haan L. (2007)
    <doi:10.1007/0-387-34471-3>) implemented with the techniques of automatic
    differentiation (Griewank A. (2008) <isbn:978-0-89871-659-7>).
    With this tool, a user should be able to quickly model extreme
    events for which the Gumbel distribution is the domain of attraction.
    The package makes available the density function, the distribution
    function the quantile function and a random generating function. In
    addition, it supports gradient functions. The package combines 'Adept'
    (C++ templated automatic differentiation) (Hogan R. (2017)
    <doi:10.5281/zenodo.1004730>) and 'Eigen' (templated matrix-vector
    library) for fast computations of both objective functions and exact
    gradients. It relies on 'RcppEigen' for easy access to 'Eigen' and
    bindings to R.
The 'DHARMa' package uses a simulation-based approach to create
    readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed
    models. Currently supported are linear and generalized linear (mixed) models from 'lme4'
    (classes 'lmerMod', 'glmerMod'), 'glmmTMB' 'GLMMadaptive' and 'spaMM', generalized additive models
    ('gam' from 'mgcv'), 'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and
    'lm' model classes. Moreover, externally created simulations, e.g. posterior predictive simulations
    from Bayesian software such as 'JAGS', 'STAN', or 'BUGS' can be processed as well.
    The resulting residuals are standardized to values between 0 and 1 and can be interpreted
    as intuitively as residuals from a linear regression. The package also provides a number of
    plot and test functions for typical model misspecification problems, such as
    over/underdispersion, zero-inflation, and residual spatial and temporal autocorrelation.
Draws stylized choropleth maps -- hexagonal maps and triangular multiclass hex maps -- for New Zealand District Health Boards and Regional Council areas. These allow faceted, coloured displays of quantitative information for comparison across District Health Boards or Regional Councils. The preprint Lumley (2019) <arXiv:1912.04435> is based on the methods in this package.
Identification of hub genes in a gene co-expression network from gene expression data. The differential network analysis for two contrasting conditions leads to the identification of various types of hubs like Housekeeping, Unique to stress (Disease) and Unique to control (Normal) hub genes.
Implements double hierarchical generalized linear models in which the mean, dispersion parameters for variance of random effects, and residual variance (overdispersion) can be further modeled as random-effect models.
The density, cumulative distribution, quantiles, 
    and i.i.d random variables of a heavy-headed distribution.
    For more information, please see the vignette.
Connect and pull data from a 'DHIS2 (District Health Information Software 2)' instance into R.
Tools for accessing data from National Library of Norway's dhlab (digital humanities laboratory).
    Provides wrappers for accessing our API services at <https://api.nb.no/dhlab/>.
    To learn more about dhlab, visit out site <https://www.nb.no/dh-lab/>.
Calculates key indicators such as fertility rates (Total Fertility Rate (TFR), General Fertility Rate (GFR), 
  and Age Specific Fertility Rate (ASFR)) using Demographic and Health Survey (DHS) women/individual data, 
  childhood mortality probabilities and rates such as Neonatal Mortality Rate (NNMR), Post-neonatal Mortality Rate (PNNMR), 
  Infant Mortality Rate (IMR), Child Mortality Rate (CMR), and Under-five Mortality Rate (U5MR), and adult mortality indicators 
  such as the Age Specific Mortality Rate (ASMR), Age Adjusted Mortality Rate (AAMR), Age Specific Maternal Mortality Rate (ASMMR),
  Age Adjusted Maternal Mortality Rate (AAMMR), Age Specific Pregnancy Related Mortality Rate (ASPRMR), 
  Age Adjusted Pregnancy Related Mortality Rate (AAPRMR), Maternal Mortality Ratio (MMR) and Pregnancy Related Mortality Ratio (PRMR).  
  In addition to the indicators, the 'DHS.rates' package estimates sampling errors indicators such as Standard Error (SE), 
  Design Effect (DEFT), Relative Standard Error (RSE) and Confidence Interval (CI). 
  The package is developed according to the DHS methodology of calculating the fertility indicators and 
  the childhood mortality rates outlined in the 
  "Guide to DHS Statistics" (Croft, Trevor N., Aileen M. J. Marshall, Courtney K. Allen, et al. 2018, <https://dhsprogram.com/Data/Guide-to-DHS-Statistics/index.cfm>) 
  and the DHS methodology of estimating the sampling errors indicators outlined in 
  the "DHS Sampling and Household Listing Manual" (ICF International 2012, <https://dhsprogram.com/pubs/pdf/DHSM4/DHS6_Sampling_Manual_Sept2012_DHSM4.pdf>).
We provide 70 data sets of females of reproductive age from 19 Asian countries, ranging in age from 15 to 49. The data sets are extracted from demographic and health surveys that were conducted over an extended period of time. Moreover, the functions also provide Whipple’s index as well as age reporting quality such as very rough, rough, approximate, accurate, and highly accurate.
Contains an implementation of the
	     d-variable Hilbert Schmidt independence criterion
	     and several hypothesis tests based on it, as described
	     in Pfister et al. (2017) <doi:10.1111/rssb.12235>.
A set of utilities for calculating the Deficit (frailty) Index (DI) in gerontological studies. 
             The deficit index was first proposed by Arnold Mitnitski and Kenneth Rockwood 
             and represents a proxy measure of aging and also can be served as
             a sensitive predictor of survival. For more information, see 
             (i)"Accumulation of Deficits as a Proxy Measure of Aging" 
             by Arnold B. Mitnitski et al. (2001), 
             The Scientific World Journal 1, <DOI:10.1100/tsw.2001.58>;
             (ii) "Frailty, fitness and late-life mortality in relation to chronological and biological age" 
             by Arnold B Mitnitski et al. (2001), 
             BMC Geriatrics2002 2(1), <DOI:10.1186/1471-2318-2-1>.
Fast functions for effective sample size, weighted multivariate 
    mean, variance, and quantile computation, and weight diagnostic plot for 
    generic importance sampling type or other probability weighted samples.
Diagnostics for linear L1 regression (also known as LAD - Least Absolute Deviations), including: estimation, confidence intervals, tests of hypotheses, measures of leverage, methods of diagnostics for L1 regression, special diagnostics graphs and measures of leverage. The algorithms are based in Dielman (2005)  <doi:10.1080/0094965042000223680>, Elian et al. (2000) <doi:10.1080/03610920008832518> and Dodge (1997) <doi:10.1006/jmva.1997.1666>. This package builds on the 'quantreg' package, which is a well-established package for tuning quantile regression models. There are also tests to verify if the errors have a Laplace distribution based on the work of Puig and Stephens (2000) <doi:10.2307/1270952>.
Provides methods by Steinhauser et al. (2016) <DOI:10.1186/s12874-016-0196-1> for meta-analysis of diagnostic accuracy studies with several cutpoints.
Several tools for handling block-matrix diagonals and similar
    constructs are implemented. Block-diagonal matrices can be extracted or removed
    using two small functions implemented here. In addition, non-square matrices
    are supported. Block diagonal matrices occur when two dimensions of a data set
    are combined along one edge of a matrix. For example, trade-flow data in the
    'decompr' and 'gvc' packages have each country-industry combination occur along
    both edges of the matrix.
Visualises simple graphs (networks) based on a transition matrix, utilities to plot flow diagrams, 
     visualising webs, electrical networks, etc.
     Support for the book "A practical guide to ecological modelling -
     using R as a simulation platform"
     by Karline Soetaert and Peter M.J. Herman (2009), Springer.
     and the book "Solving Differential Equations in R"
     by Karline Soetaert, Jeff Cash and Francesca Mazzia (2012), Springer.
     Includes demo(flowchart), demo(plotmat), demo(plotweb).
Build graph/network structures using functions for stepwise addition and
    deletion of nodes and edges. Work with data available in tables for bulk
    addition of nodes, edges, and associated metadata. Use graph selections
    and traversals to apply changes to specific nodes or edges. A wide
    selection of graph algorithms allow for the analysis of graphs. Visualize
    the graphs and take advantage of any aesthetic properties assigned to
    nodes and edges.
Allows for export of DiagrammeR Graphviz objects to SVG.
Performs Diallel Analysis with R using Griffing's and Hayman's approaches. Four different Methods (1: Method-I (Parents + F1's + reciprocals); 2: Method-II (Parents and one set of F1's); 3: Method-III (One set of F1's and reciprocals); 4: Method-IV (One set of F1's only)) and two Models (1: Fixed Effects Model; 2: Random Effects Model) can be applied using Griffing's approach.
Parse, format, and validate international phone
    numbers using Google's 'libphonenumber' java library,
    <https://github.com/google/libphonenumber>.
Collects 'libphonenumber' jars required for the
    'dialr' package.
Many models contain tuning parameters (i.e. parameters that
    cannot be directly estimated from the data). These tools can be used
    to define objects for creating, simulating, or validating values for
    such parameters.
Visualize one-factor data frame. 
  Beads plot consists of diamonds of each factor of each data series. 
  A diamond indicates average and range. 
  Look over a data frame with many numeric columns and a factor column.
Provides a 'dibble' that implements data cubes (derived from 
    'dimensional tibble'), and allows broadcasting by dimensional names.
This package provides utilities to calculate the probabilities of various dice-rolling events, such as the probability of rolling a four-sided die six times and getting a 4, a 3, and either a 1 or 2 among the six rolls (in any order); the probability of rolling two six-sided dice three times and getting a 10 on the first roll, followed by a 4 on the second roll, followed by anything but a 7 on the third roll; or the probabilities of each possible sum of rolling five six-sided dice, dropping the lowest two rolls, and summing the remaining dice.
Space-Filling Designs and space-filling criteria (distance-based and uniformity-based), with emphasis to computer experiments; <doi:10.18637/jss.v065.i11>.
Estimation, validation and prediction of models of different types : linear models, additive models, MARS,PolyMARS and Kriging.
Estimation, validation and prediction of kriging models. Important functions : km, print.km, plot.km, predict.km.
Efficient Global Optimization (EGO) algorithm as described in "Roustant et al. (2012)" <doi:10.18637/jss.v051.i01> and adaptations for problems with noise ("Picheny and Ginsbourger, 2012") <doi:10.1016/j.csda.2013.03.018>, parallel infill, and problems with constraints.
Performs cluster analysis using an ensemble
    clustering framework, Chiu & Talhouk (2018)
    <doi:10.1186/s12859-017-1996-y>.  Results from a diverse set of
    algorithms are pooled together using methods such as majority voting,
    K-Modes, LinkCluE, and CSPA. There are options to compare cluster
    assignments across algorithms using internal and external indices,
    visualizations such as heatmaps, and significance testing for the
    existence of clusters.
View 2D/3D sections, contour plots, mesh of excursion sets for computer experiments designs, surrogates or test functions.
Collapse red-green or green-blue distinctions to simulate
        the effects of different types of color-blindness.
This function provides an interface between 'Matlab' and 'R' in facilitating fast processing for reading and saving DICOM images.
Given  an initial set of points, this package minimizes the number of elements to discard from this set such that there exists at least one monotonic and convex mapping within pre-specified upper and lower bounds.
A key-value dictionary data structure based on R6 class which is designed to be similar usages with other languages dictionary (e.g. 'Python') with reference semantics and extendabilities by R6.
Efficient object-oriented R6 dictionary capable of holding objects of any class, including R6. Typed and untyped dictionaries are provided as well as the 'usual' dictionary methods that are available in other OOP languages, for example listing keys, items, values, and methods to get/set these.
An R interface to the 'Free Dictionary API' 
    <https://dictionaryapi.dev/>, 
    <https://github.com/meetDeveloper/freeDictionaryAPI>. Retrieve
    dictionary definitions for English words, as well 
    as additional information including phonetics, part of speech, origins, 
    audio pronunciation, example usage, synonyms and antonyms, returned in 
    'tidy' format for ease of use.
The standard Difference-in-Differences (DID) setup involves two periods and two groups -- a treated group and untreated group.  Many applications of DID methods involve more than two periods and have individuals that are treated at different points in time.  This package contains tools for computing average treatment effect parameters in Difference in Differences setups with more than two periods and with variation in treatment timing using the methods developed in Callaway and Sant'Anna (2021) <doi:10.1016/j.jeconom.2020.12.001>.  The main parameters are group-time average treatment effects which are the average treatment effect for a particular group at a a particular time.  These can be aggregated into a fewer number of treatment effect parameters, and the package deals with the cases where there is selective treatment timing, dynamic treatment effects, calendar time effects, or combinations of these.  There are also functions for testing the Difference in Differences assumption, and plotting group-time average treatment effects.
Estimates Two-way Fixed Effects difference-in-differences/event-study models using the approach proposed by Gardner (2021) <doi:10.48550/arXiv.2207.05943>. To avoid the problems caused by OLS estimation of the Two-way Fixed Effects model, this function first estimates the fixed effects and covariates using untreated observations and then in a second stage, estimates the treatment effects.
A basic, clear implementation of tree-based gradient boosting
    designed to illustrate the core operation of boosting models. Tuning
    parameters (such as stochastic subsampling, modified learning rate, or
    regularization) are not implemented. The only adjustable parameter is the
    number of training rounds. If you are looking for a high performance boosting
    implementation with tuning parameters, consider the 'xgboost' package.
Enables the user to build a citation network/graph from bibliographic data and, based on modularity and heterocitation metrics, assess the degree of awareness/cross-fertilization between two corpora/communities. This toolset is optimized for Scopus data.
Provides a big-data-friendly and memory-efficient difference-in-differences estimator for staggered (and non-staggered) treatment contexts.
Estimates Two-way Fixed Effects difference-in-differences/event-study models using the imputation-based approach proposed by Borusyak, Jaravel, and Spiess (2021).
This hosts the findRFM function which generates RFM scores on a 1-5 point scale for
             customer transaction data. The function consumes a data frame with Transaction Number,
             Customer ID, Date of Purchase (in date format) and Amount of Purchase as the attributes.
             The function returns a data frame with RFM data for the sales information.
Likelihood-based genome polarisation finds which alleles of genomic markers 
    belong to which side of the barrier. 
	Co-estimates which individuals belong to either side of the barrier and barrier strength.
	Uses expectation maximisation in likelihood framework. The method is described in 
	Baird et al. (2023) <doi:10.1111/2041-210X.14010>.
Estimates fractional trophic level from quantitative and qualitative diet data and calculates electivity indices in R. Borstein (2020) <doi:10.1007/s10750-020-04417-5>.
A wrapper for the ZEIT ONLINE Content API, available at <http://developer.zeit.de>. 'diezeit' gives access to articles and corresponding metadata from the ZEIT archive and from ZEIT ONLINE. A personal API key is required for usage.
Performs detection of Differential Item Functioning using the method DIFboost as proposed by Schauberger and Tutz (2016) <doi:10.1111/bmsp.12060>.
Estimation of DIFferential COexpressed NETworks using diverse and user metrics.
			 This package is basically used for three functions related to the estimation
			 of differential coexpression. 
			 First, to estimate differential coexpression where
			 the coexpression is estimated, by default, by Spearman correlation. For this,
			 a metric to compare two correlation distributions is needed. The package includes
			 6 metrics. Some of them needs a threshold. A new metric can also be specified as
			 a user function with specific parameters (see difconet.run). The significance is
			 be estimated by permutations.
			 Second, to generate datasets with controlled differential correlation data. This 
			 is done by either adding noise, or adding specific correlation structure.
			 Third, to show the results of differential correlation analyses. Please see
			 <http://bioinformatica.mty.itesm.mx/difconet> for further information.
Computations of Fisher's z-tests concerning different kinds of correlation differences. Additionally, approaches to estimating statistical power via Monte Carlo simulations are implemented.
A method for identifying pattern changes between 2 experimental
         conditions in correlation networks (e.g., gene co-expression networks),
         which builds on a commonly used association measure, such as Pearson's
         correlation coefficient. This package includes functions to calculate
         correlation matrices for high-dimensional dataset and to test
         differential correlation, which means the changes in the correlation
         relationship among variables (e.g., genes and metabolites) between 2
         experimental conditions.
Functions for comparing two data.frames against 
    each other. The core functionality is to provide a detailed breakdown of any differences 
    between two data.frames as well as providing utility functions to help narrow down the 
    source of problems and differences.
Shows you which rows have changed between two data frames with the same column structure. Useful for diffing slowly mutating data.
This is an R implementation of Fast and Scalable Learning of Sparse Changes in High-Dimensional Gaussian Graphical Model Structure (DIFFEE). The DIFFEE algorithm can be used to fast estimate the differential network between two related datasets. For instance, it can identify differential gene network from datasets of case and control. By performing data-driven network inference from two high-dimensional data sets, this tool can help users effectively translate two aggregated data blocks into knowledge of the changes among entities between two Gaussian Graphical Model. Please run demo(diffeeDemo) to learn the basic functions provided by this package. For further details, please read the original paper: Beilun Wang, Arshdeep Sekhon, Yanjun Qi (2018) <arXiv:1710.11223>.
Compare functional enrichment between two experimentally-derived groups of genes or proteins (Peterson, DR., et al.(2018)) <doi: 10.1371/journal.pone.0198139>. Given a list of gene symbols, 'diffEnrich'  will
  perform differential enrichment analysis using the Kyoto Encyclopedia of Genes
  and Genomes (KEGG) REST API. This package provides a number of functions that are 
  intended to be used in a pipeline. Briefly, the user provides a KEGG formatted species id for either human, mouse or rat, and the package will
  download and clean species specific ENTREZ gene IDs and map them to their respective
  KEGG pathways by accessing KEGG's REST API. KEGG's API is used to guarantee the most up-to-date pathway data from KEGG. Next, the user will identify significantly
  enriched pathways from two gene sets, and finally, the user will identify 
  pathways that are differentially enriched between the two gene sets. In addition to 
  the analysis pipeline, this package also provides a plotting function.
An interface to 'DifferentialEquations.jl' <https://diffeq.sciml.ai/dev/> from the R programming language.
  It has unique high performance methods for solving ordinary differential equations (ODE), stochastic differential equations (SDE),
  delay differential equations (DDE), differential-algebraic equations (DAE), and more. Much of the functionality,
  including features like adaptive time stepping in SDEs, are unique and allow for multiple orders of magnitude speedup over more common methods.
  Supports GPUs, with support for CUDA (NVIDIA), AMD GPUs, Intel oneAPI GPUs, and Apple's Metal (M-series chip GPUs).
  'diffeqr' attaches an R interface onto the package, allowing seamless use of this tooling by R users. For more information,
  see Rackauckas and Nie (2017) <doi:10.5334/jors.151>.
Metrics of difference for comparing pairs of variables or pairs of maps representing real or categorical variables at original and multiple resolutions.
Computes the ATM (Attractor Transition Matrix) structure and
    the tree-like structure describing the cell differentiation process
    (based on the Threshold Ergodic Set concept introduced by Serra and
    Villani), starting from the Boolean networks with synchronous updating
    scheme of the 'BoolNet' R package. TESs (Threshold Ergodic Sets) are
    the mathematical abstractions that represent the different cell types
    arising during ontogenesis. TESs and the powerful model of biological
    differentiation based on Boolean networks to which it belongs have
    been firstly described in "A Dynamical Model of Genetic Networks for
    Cell Differentiation" Villani M, Barbieri A, Serra R (2011) A
    Dynamical Model of Genetic Networks for Cell Differentiation. PLOS ONE
    6(3): e17703.
Package to fit diffusion-based IRT models to response and 
	response time data. Models are fit using marginal maximum 
	likelihood. Parameter restrictions (fixed value and equality 
	constraints) are possible. In addition, factor scores (person drift 
	rate and person boundary separation) can be estimated. Model fit 
	assessment tools are also available. The traditional diffusion model 
	can be estimated as well.
A wrapper for Google's 'diff-match-patch' library. It provides basic tools
    for computing diffs, finding fuzzy matches, and constructing / applying patches to strings.
Generate a colorized diff of two R objects for an intuitive
    visualization of their differences.
An implementation of major general-purpose mechanisms for privatizing
    statistics, models, and machine learners, within the framework of differential
    privacy of Dwork et al. (2006) <doi:10.1007/11681878_14>. Example mechanisms
    include the Laplace mechanism for releasing numeric aggregates, and the 
    exponential mechanism for releasing set elements. A sensitivity sampler 
    (Rubinstein & Alda, 2017) <arXiv:1706.02562> permits sampling target 
    non-private function sensitivity; combined with the generic mechanisms, it 
    permits turn-key privatization of arbitrary programs.
An R interface to the 'codediff' JavaScript library (a copy of which is included in the package,
  see <https://github.com/danvk/codediff.js> for information).
  Allows for visualization of the difference between 2 files, usually text files or R scripts, in a browser.
Enables the evaluation of diffusion distances for complex single-layer networks.
    Given a network one can define different types of Laplacian (or transition)
    matrices corresponding to different continuous-time random walks dynamics on the network. 
    This package enables the evaluation of Laplacians, stochastic matrices, and the 
    corresponding diffusion distance matrices. The metric structure induced by the network-driven
    process is richer and more robust than the one given by shortest-paths and allows to study 
    the geometry induced by different types of diffusion-like communication mechanisms taking 
    place on complex networks. 
    For more details see: De Domenico, M. (2017) <doi:10.1103/physrevlett.118.168301> and 
    Bertagnolli, G. and De Domenico, M. (2021) <doi:10.1103/PhysRevE.103.042301>.
Various diffusion models to forecast new product growth. Currently
    the package contains Bass, Gompertz and Gamma/Shifted Gompertz curves. See
    Meade and Islam (2006) <doi:10.1016/j.ijforecast.2006.01.005>.
Implements diffusion map method of data
    parametrization, including creation and visualization of
    diffusion map, clustering with diffusion K-means and
	  regression using adaptive regression model.
	  Richards (2009) <doi:10.1088/0004-637X/691/1/32>.
Implementation of network diffusion algorithms such as
  heat diffusion or Markov random walks. Network diffusion algorithms generally
  spread information in the form of node weights along the edges of a graph to other nodes.
  These weights can for example be interpreted as temperature, an initial amount
  of water, the activation of neurons in the brain, or the location of a random
  surfer in the internet. The information (node weights) is iteratively propagated
  to other nodes until a equilibrium state or stop criterion occurs.
Find, visualize and explore patterns of differential taxa in
    vegetation data (namely in a phytosociological table), using the
    Differential Value (DiffVal). Patterns are searched through
    mathematical optimization algorithms. Ultimately, Total Differential
    Value (TDV) optimization aims at obtaining classifications of
    vegetation data based on differential taxa, as in the traditional
    geobotanical approach.  The Gurobi optimizer, as well as the R package
    'gurobi', can be installed from
    <https://www.gurobi.com/products/gurobi-optimizer/>.  The useful
    vignette Gurobi Installation Guide, from package 'prioritizr', can be
    found here:
    <https://prioritizr.net/articles/gurobi_installation_guide.html>.
A HTML widget that shows differences between files
    (text, images, and data frames).
Statistical hypothesis testing of pattern heterogeneity
    via differences in underlying distributions across multiple
    contingency tables. Five tests are included: the comparative
    chi-squared test (Song et al. 2014) <doi:10.1093/nar/gku086>
    (Zhang et al. 2015) <doi:10.1093/nar/gkv358>, the Sharma-Song
    test (Sharma et al. 2021) <doi:10.1093/bioinformatics/btab240>, 
    the heterogeneity test, the marginal-change test (Sharma et al.
    2020) <doi:10.1145/3388440.3412485>, and the strength test
    (Sharma et al. 2020) <doi:10.1145/3388440.3412485>. Under the
    null hypothesis that row and column variables are statistically
    independent and joint distributions are equal, their test
    statistics all follow an asymptotically chi-squared distribution.
    A comprehensive type analysis categorizes the relation among the
    contingency tables into type null, 0, 1, and 2 (Sharma et al.
    2020) <doi:10.1145/3388440.3412485>. They can identify
    heterogeneous patterns that differ in either the first order
    (marginal) or the second order (differential departure from
    independence). Second-order differences reveal more
    fundamental changes than first-order differences across
    heterogeneous patterns.
Performs DIFlasso as proposed by Tutz and Schauberger (2015) <doi:10.1007/s11336-013-9377-6>, a method to detect DIF (Differential Item Functioning) in Rasch Models. It can handle settings with many variables and also metric variables.
Detection of differential item functioning (DIF) among dichotomously scored items and differential distractor functioning (DDF) among unscored items with non-linear regression  procedures based on generalized logistic regression models (Hladka & Martinkova, 2020, <doi:10.32614/RJ-2020-014>).
Clustered or multilevel data structures are common in the assessment of differential item functioning (DIF), particularly in the context of large-scale assessment programs. This package allows users to implement extensions of the Mantel-Haenszel DIF detection procedures in the presence of multilevel data based on the work of Begg (1999) <doi:10.1111/j.0006-341X.1999.00302.x>, Begg & Paykin (2001) <doi:10.1080/00949650108812115>, 
	and French & Finch (2013) <doi:10.1177/0013164412472341>.
Provides a collection of standard methods to detect differential item functioning among dichotomously scored items. Methods for uniform and non-uniform DIF, based on test-score or IRT methods, for comparing two or more than two groups of respondents, are available (Magis, Beland, Tuerlinckx and De Boeck,A General Framework and an R Package for the Detection of Dichotomous Differential Item Functioning, Behavior Research Methods, 42, 2010, 847-862 <doi:10.3758/BRM.42.3.847>).
Differential Item Functioning (DIF) Analysis with shiny application interfaces. You can run the functions in this package without any arguments and perform your DIF analysis using user-friendly interfaces.
Item focussed recursive partitioning for simultaneous selection of items and variables that induce Differential Item Functioning (DIF) in dichotomous or polytomous items.
Implementation of a function 'digest()' for the creation of hash
 digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32',
 'xxhash', 'murmurhash', 'spookyhash', 'blake3' and 'crc32c' algorithms) permitting
 easy comparison of R language objects, as well as functions such as'hmac()' to
 create hash-based message authentication code. Please note that this package
 is not meant to be deployed for cryptographic purposes for which more
 comprehensive (and widely tested) libraries such as 'OpenSSL' should be
 used.
Analyze and visualize the rhythmic behavior of animals using the 
  degree of functional coupling (See Scheibe (1999) <doi:10.1076/brhm.30.2.216.1420>),
  compute and visualize harmonic power, actograms, average activity and diurnality 
  index.
Deconvolution of bulk RNA-Seq data using context-specific deconvolution models based on Deep Neural Networks using scRNA-Seq data as input. These models are able to make accurate estimates of the cell composition of bulk RNA-Seq samples from the same context using the advances provided by Deep Learning and the meaningful information provided by scRNA-Seq data. See Torroja and Sanchez-Cabo (2019) <doi:10.3389/fgene.2019.00978> for more details.
The assay sensitivity is the minimum number of copies that the digital PCR assay can detect. Users provide serial dilution results in the format of counts of positive and total reaction wells. The output is the estimated assay sensitivity and the copy number per well in the initial dilute.
Import data from a digital image; it requires user input for
    calibration and to locate the data points. The end result is similar to
    'DataThief' and other other programs that 'digitize' published plots or
    graphs.
Provides statistical tests and support functions for detecting irregular digit patterns in numerical data. The package includes tools for extracting digits at various locations in a number, tests for repeated values, and (Bayesian) tests of digit distributions.
Simulation tool to estimate the rate of success that surveys possessing user-specific characteristics have in identifying archaeological sites (or any groups of clouds of objects), given specific parameters of survey area, survey methods, and site properties. The survey approach used is largely based on the work of Kintigh (1988) <doi:10.2307/281113>.
A robust identification of differential binding sites method for analyzing ChIP-seq (Chromatin Immunoprecipitation Sequencing) 
    comparing two samples that considers an ensemble of finite mixture models combined with a local false discovery rate (fdr) 
    allowing for flexible modeling of data. Methods for Differential Identification using Mixture Ensemble (DIME) is described in: 
    Taslim et al., (2011) <doi:10.1093/bioinformatics/btr165>.
Simple Principal Components Analysis (PCA) and Correspondence
    Analysis (CA) based on the Singular Value Decomposition (SVD). This
    package provides S4 classes and methods to compute, extract, summarize
    and visualize results of multivariate data analysis. It also includes
    methods for partial bootstrap validation described in Greenacre (1984)
    <isbn:978-0-12-299050-2> and Lebart et al. (2006)
    <isbn:978-2-10-049616-7>.
A set of tools to extract bibliographic content from 'Digital Science Dimensions' using 'DSL' API <https://www.dimensions.ai/dimensions-apis/>.
The 'DImodels' package is suitable for analysing data from biodiversity and ecosystem function studies using the Diversity-Interactions (DI) modelling approach introduced by Kirwan et al. (2009) <doi:10.1890/08-1684.1>. Suitable data will contain proportions for each species and a community-level response variable, and may also include additional factors, such as blocks or treatments. The package can perform data manipulation tasks, such as computing pairwise interactions (the DI_data() function), can perform an automated model selection process (the autoDI() function) and has the flexibility to fit a wide range of user-defined DI models (the DI() function).
The implemented methods are: Standard Bass model, Generalized Bass model (with rectangular shock, exponential shock, and mixed shock. You can choose to add from 1 to 3 shocks), Guseo-Guidolin model and Variable Potential Market model, and UCRCD model. The Bass model consists of a simple differential equation that describes the process of how new products get adopted in a population, the Generalized Bass model is a generalization of the Bass model in which there is a "carrier" function x(t) that allows to change the speed of time sliding. In some real processes the reachable potential of the resource available in a temporal instant may appear to be not constant over time, because of this we use Variable Potential Market model, in which the Guseo-Guidolin has a particular specification for the market function. The UCRCD model (Unbalanced Competition and Regime Change Diachronic) is a diffusion model used to capture the dynamics of the competitive or collaborative transition.
A collection of dimensionality reduction
    techniques from R packages and a common
    interface for calling the methods.
Estimate the Deterministic Input, Noisy "And" Gate (DINA)
    cognitive diagnostic model parameters using the Gibbs sampler described
    by Culpepper (2015) <doi:10.3102/1076998615595403>.
This function implements the DiNAMIC procedure for
        assessing the statistical significance of recurrent DNA copy
        number aberrations (Bioinformatics (2011) 27(5) 678 - 685).
In tumor tissue, underlying genomic instability can lead to DNA copy number alterations,
	e.g., copy number gains or losses. Sporadic copy number alterations occur randomly throughout the
	genome, whereas recurrent alterations are observed in the same genomic region across multiple
	independent samples, perhaps because they provide a selective growth advantage. Here we use
	cyclic shift permutations to identify recurrent copy number alterations in a single cohort or
	recurrent copy number differences in two cohorts based on a common set of genomic markers.
	Additional functionality is provided to perform downstream analyses, including the creation of
	summary files and graphics. DiNAMIC.Duo builds upon the original DiNAMIC package of Walter et al.
	(2011) <doi:10.1093/bioinformatics/btq717> and leverages the theory developed in Walter et al.
	(2015) <doi:10.1093/biomet/asv046>. An article describing DiNAMIC.Duo by Walter et al. (2022)
	can be found at <doi: 10.1093/bioinformatics/btac542>.
Decomposition of (income) inequality by population sub groups. 
    For a decomposition on a single variable the mean log deviation can be used
      (see Mookherjee Shorrocks (1982) <DOI:10.2307/2232673>).
    For a decomposition on multiple variables a regression based technique can be 
      used (see Fields (2003) <DOI:10.1016/s0147-9121(03)22001-x>).
    Recentered influence function regression for marginal effects of the (income 
      or wealth) distribution  (see Firpo et al. (2009) <DOI:10.3982/ECTA6822>).
    Some extensions to inequality functions to handle weights and/or missings.
An efficient and convenient set of functions to perform differential network estimation through the use of alternating direction method of multipliers optimization with a variety of loss functions.
S3 classes and methods to create and work
    with year-quarter, year-month and year-isoweek vectors. Basic
    arithmetic operations (such as adding and subtracting) are supported,
    as well as formatting and converting to and from standard R date
    types.
Individual gene expression patterns are encoded into a series of eigenvector patterns ('WGCNA' package). Using the framework of linear model-based differential expression comparisons ('limma' package), time-course expression patterns for genes in different conditions are compared and analyzed for significant pattern changes. For reference, see: Greenham K, Sartor RC, Zorich S, Lou P, Mockler TC and McClung CR. eLife. 2020 Sep 30;9(4). <doi:10.7554/eLife.58993>.
Implements the algorithm described in Jun Li and Alicia T. Lamere, 
    "DiPhiSeq: Robust comparison of expression levels on RNA-Seq data with large sample sizes"  (Unpublished). 
    Detects not only genes that show different 
    average expressions ("differential expression", DE), but also genes that show different 
    diversities of expressions in different groups ("differentially dispersed", DD). DD genes 
    can be important clinical markers. 'DiPhiSeq' uses a redescending penalty on the 
    quasi-likelihood function, and thus has superior robustness against outliers and other noise.
    Updates from version 0.1.0: (1) Added the option of using adaptive initial value for phi.
    (2) Added a function for estimating the proportion of outliers in the data.
    (3) Modified the input parameter names for clarity, and modified the output format for the main function.
An implementation by Chen, Li, and Zhang (2022) <doi: 10.1093/bioadv/vbac041> of the Depth Importance in Precision Medicine (DIPM) method 
             in Chen and Zhang (2022) <doi:10.1093/biostatistics/kxaa021> and Chen and 
             Zhang (2020) <doi:10.1007/978-3-030-46161-4_16>. The DIPM method is a classification 
             tree that searches for subgroups with especially poor or strong performance in a given treatment group.
Conducts a direction-projection-permutation test and displays diagnostic plots to facilitate the visual assessment of the test. See Wei et al. (2016) <doi:10.1080/10618600.2015.1027773> and Lam et al. (2018) <doi:10.1080/10618600.2017.1366915> for more details.
Improves the balance of optimal matching with near-fine balance by giving penalties on the unbalanced covariates with the unbalanced directions. Many directional penalties can also be viewed as Lagrange multipliers, pushing a matched sample in the direction of satisfying a linear constraint that would not be satisfied without penalization.
    Yu and Rosenbaum (2019) <doi:10.1111/biom.13098>.
Works as an "add-on" to packages like 'shiny', 'future', as well as 
    'rlang', and provides utility functions. Just like dipping sauce adding 
    flavors to potato chips or pita bread, 'dipsaus' for data analysis and 
    visualizations adds handy functions and enhancements to popular packages. 
    The goal is to provide simple solutions that are frequently asked for 
    online, such as how to synchronize 'shiny' inputs without freezing the app,
    or how to get memory size on 'Linux' or 'MacOS' system. The enhancements 
    roughly fall into these four categories: 1. 'shiny' input widgets; 2. 
    high-performance computing using the 'future' package; 3. 
    modify R calls and convert among numbers, strings, and other objects. 4. 
    utility functions to get system information such like CPU chip-set, memory 
    limit, etc.
Compute Hartigan's dip test statistic for unimodality /
 multimodality and provide a test with simulation based p-values,  where
 the original public code has been corrected.
Estimation of the average treatment effect when controlling for
    high-dimensional confounders using debiased inverse propensity score
    weighting (DIPW). DIPW relies on the propensity score following a sparse
    logistic regression model, but the regression curves are not required to be
    estimable. Despite this, our package also allows the users to estimate 
    the regression curves and take the estimated curves as input to our
    methods. Details of the methodology can be found in Yuhao Wang and
    Rajen D. Shah (2020) "Debiased Inverse Propensity Score Weighting for
    Estimation of Average Treatment Effects with High-Dimensional Confounders"
    <arXiv:2011.08661>. The package relies on the optimisation
    software 'MOSEK' <https://www.mosek.com/> which must be installed separately;
    see the documentation for 'Rmosek'.
Fit latent variable linear models, estimating score distributions for groups of people, following Cohen and Jiang (1999) <doi:10.2307/2669917>. In this model, a latent distribution is conditional on students item response, item characteristics, and conditioning variables the user includes. This latent trait is then integrated out. This software is intended to fit the same models as the existing software 'AM' <https://am.air.org/>. As of version 2, also allows the user to draw plausible values.
A Bayesian clustering method for replicated time series or replicated measurements from multiple experimental conditions, e.g., time-course gene expression data.  It estimates the number of clusters directly from the data using a Dirichlet-process prior.  See Fu, A. Q., Russell, S., Bray, S. and Tavare, S. (2013) Bayesian clustering of replicated time-course gene expression data with weak signals. The Annals of Applied Statistics. 7(3) 1334-1361. <doi:10.1214/13-AOAS650>.
Allows the computation of clustering coefficients for directed and weighted networks by using different approaches. 
    It allows to compute clustering coefficients that are not present in 'igraph' package. 
    A description of clustering coefficients can be found in "Directed clustering in weighted networks: a new perspective", Clemente, G.P., Grassi, R. (2017),  	
    <doi:10.1016/j.chaos.2017.12.007>.
A set of functions to estimate the controlled direct effect of treatment fixing a potential mediator to a specific value. Implements the sequential g-estimation estimator described in Vansteelandt (2009) <doi:10.1097/EDE.0b013e3181b6f4c9> and Acharya, Blackwell, and Sen (2016) <doi:10.1017/S0003055416000216>.
A collection of functions for directional data (including massive data, with millions of observations) analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000). Other references include a) Phillip J. Paine, Simon P. Preston Michail Tsagris and Andrew T. A. Wood (2018). "An elliptically symmetric angular Gaussian distribution". Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>. b) Tsagris M. and Alenazi A. (2019). "Comparison of discriminant analysis methods on the sphere". Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>. c) P. J. Paine, S. P. Preston, M. Tsagris and Andrew T. A. Wood (2020). "Spherical regression models with general covariates and anisotropic errors". Statistics and Computing 30(1): 153--165. <doi:10.1007/s11222-019-09872-2>. d) Tsagris M. and Alenazi A. (2022). "An investigation of hypothesis testing procedures for circular and spherical mean vectors". Communications in Statistics-Simulation and Computation (Accepted for publication). <doi:10.1080/03610918.2022.2045499>. e) Tsagris M. and Alzeley O. (2023). "Circular and spherical projected Cauchy distributions: A Novel Framework for Circular and Directional Data Modeling". <doi:10.48550/arXiv.2302.02468>.
An extensible framework
 for automatically placing direct labels onto multicolor 'lattice' or
 'ggplot2' plots.
 Label positions are described using Positioning Methods
 which can be re-used across several different plots.
 There are heuristics for examining "trellis" and "ggplot" objects
 and inferring an appropriate Positioning Method.
Represents the content of a directory as an interactive collapsible tree. Offers
    the possibility to assign a text (e.g., a 'Readme.txt') to each folder
    (represented as a clickable node), so that when the user hovers the pointer
    over a node, the corresponding text is displayed as a tooltip.
Direction analysis is a set of tools designed to identify
    combinatorial effects of multiple treatments/conditions on pathways
    and kinases profiled by microarray, RNA-seq, proteomics, or phosphoproteomics
    data. See Yang P et al (2014) <doi:10.1093/bioinformatics/btt616>; and Yang P et al. (2016) <doi:10.1002/pmic.201600068>.
Calculate adjusted means and proportions of a variable by groups defined by another variable by direct standardisation, standardised to the structure of the dataset.
Perform nonparametric Bayesian analysis using Dirichlet 
    processes without the need to program the inference algorithms. 
    Utilise included pre-built models or specify custom 
    models and allow the 'dirichletprocess' package to handle the 
    Markov chain Monte Carlo sampling. 
    Our Dirichlet process objects can act as building blocks for a variety 
    of statistical models including and not limited to: density estimation, 
    clustering and prior distributions in hierarchical models.
    See Teh, Y. W. (2011) 
    <https://www.stats.ox.ac.uk/~teh/research/npbayes/Teh2010a.pdf>, 
    among many other sources.
Implementation of Directional Metropolis Hastings Algorithm for
    MCMC.
Estimate parameters in Dirichlet-Multinomial and compute log-likelihoods.
Nonparametric kernel density estimation, bandwidth selection,
    and other utilities for analyzing directional data. Implements the estimator
    in Bai, Rao and Zhao (1987) <doi:10.1016/0047-259X(88)90113-3>, the
    cross-validation bandwidth selectors in Hall, Watson and Cabrera (1987)
    <doi:10.1093/biomet/74.4.751> and the plug-in bandwidth selectors in
    García-Portugués (2013) <doi:10.1214/13-ejs821>.
Semiparametric distributional regression methods (expectile, quantile and mode regression) for time-to-event variables with right-censoring; uses inverse probability of censoring weights or accelerated failure time models with auxiliary likelihoods. Expectile regression using inverse probability of censoring weights has been introduced in Seipp et al. (2021) "Weighted Expectile Regression for Right-Censored Data" <doi:10.1002/sim.9137>, mode regression for time-to-event variables has been introduced in Seipp et al. (2022) "Flexible Semiparametric Mode Regression for Time-to-Event Data" <doi:10.1177/09622802221122406>.
The twoStepsBenchmark() and threeRuleSmooth() functions allow you to 
    disaggregate a low-frequency time series with higher frequency time series, 
    using the French National Accounts methodology. The aggregated sum of the 
    resulting time series is strictly equal to the low-frequency time series within the 
    benchmarking window. Typically, the low-frequency time series is an annual one, 
    unknown for the last year, and the high frequency one is either quarterly or 
    monthly. See "Methodology of quarterly national accounts", Insee Méthodes 
    N°126, by Insee (2012, ISBN:978-2-11-068613-8, <https://www.insee.fr/en/information/2579410>).
First - Generates (potentially high-dimensional) high-frequency and low-frequency series for simulation studies in temporal disaggregation; Second - a toolkit utilizing temporal disaggregation and benchmarking techniques with a low-dimensional matrix of indicator series previously proposed in Dagum and Cholette (2006, ISBN:978-0-387-35439-2) ; and Third - novel techniques proposed by Mosley, Gibberd and Eckley (2021) <arXiv:2108.05783> for disaggregating low-frequency series in the presence of high-dimensional indicator matrices.
Estimation of incidence and case fatality for a chronic disease, given partial information, using a multi-state model. Given data on age-specific mortality and either incidence or prevalence, Bayesian inference is used to estimate the posterior distributions of incidence, case fatality, and functions of these such as prevalence.  The methods are described in Jackson et al. (2023) <doi:10.1093/jrsssa/qnac015>.
Area under the curve (AUC; Myerson et al., 2001) <doi:10.1901/jeab.2001.76-235> 
  is a popular measure used in discounting research. Although the calculation of
  AUC is standardized, there are differences in AUC based on some assumptions. 
  For example, Myerson et al. (2001) <doi:10.1901/jeab.2001.76-235> 
  assumed that (with delay discounting data) a researcher would impute an
  indifference point at zero delay equal to the value of the larger, later outcome.
  However, this practice is not clearly followed. This imputed zero-delay indifference
  point plays an important role in log and ordinal versions of AUC.
  Ordinal and log versions of AUC are described by Borges et al. (2016)<doi:10.1002/jeab.219>. 
  The package can calculate all three versions of AUC [and includes a new version: IHS(AUC)],
  impute indifference points when x = 0, calculate ordinal AUC in the case of Halton
  sampling of x-values, and account for probability discounting AUC.
An open, multi-algorithmic pipeline for easy, fast and efficient
  analysis of cellular sub-populations and the molecular signatures that
  characterize them. The pipeline consists of four successive steps: data
  pre-processing, cellular clustering with pseudo-temporal ordering, defining
  differential expressed genes and biomarker identification. More details on
  Ghannoum et. al. (2021) <doi:10.3390/ijms22031399>. This package implements
  extensions of the work published by Ghannoum et. al. (2019)
  <doi:10.1101/700989>.
Functions for fitting Cox proportional hazards models for grouped time-to-event data, where the shared group-specific frailties have a discrete nonparametric distribution. The methods proposed in the package is described by Gasperoni, F., Ieva, F., Paganoni, A. M., Jackson, C. H., Sharples, L. (2018) <doi:10.1093/biostatistics/kxy071>. There are also functions for simulating from these models, with a nonparametric or a parametric baseline hazard function.
Computes discrete fast Fourier transform of river discharge data and the derived metrics.
  The methods are described in J. L. Sabo, D. M. Post (2008) <doi:10.1890/06-1340.1> and J. L. Sabo, A. Ruhi, G. W. Holtgrieve, V. Elliott, M. E. Arias, P. B. Ngor, T. A. Räsänsen, S. Nam (2017) <doi:10.1126/science.aao1053>.
The discrete Laplace exponential family for use in fitting generalized linear models.
Make inference in a mixture of discrete Laplace distributions using the EM algorithm. This can e.g. be used for modelling the distribution of Y chromosomal haplotypes as described in [1, 2] (refer to the URL section).
Fit a mixture of Discrete Laplace distributions using plain numerical optimisation. This package has similar applications as the 'disclapmix' package that uses an EM algorithm.
Transform 'newswire' and earnings call transcripts as PDF obtained from 'Nexis Uni' to R data frames. Various 'newswires' and 'FairDisclosure' earnings call formats are supported. Further, users can apply several pre-defined dictionaries on the data based on Graffin et al. (2016)<doi:10.5465/amj.2013.0288> and Gamache et al. (2015)<doi:10.5465/amj.2013.0377>.
Tests whether multivariate ordinal data may stem from discretizing a multivariate normal distribution.
             The test is described by Foldnes and Grønneberg (2019) <doi:10.1080/10705511.2019.1673168>. 
             In addition, an adjusted polychoric correlation estimator is provided that takes marginal knowledge into account,
             as described by Grønneberg and Foldnes (2022) <doi:10.1037/met0000495>.
Functions for discordant kinship modeling (and other sibling-based quasi-experimental designs). Currently, the package contains data restructuring functions and functions for generating biometrically informed data for kin pairs.
Analyzes group patterns using discourse analysis data with
    graph theory mathematics. Takes the order of which individuals talk
    and converts it to a network edge and weight list. Returns the
    density, centrality, centralization, and subgroup information for each
    group. Based on the analytical framework laid out in Chai et al.
    (2019) <doi:10.1187/cbe.18-11-0222>.
Performs an exploratory data analysis through a 'shiny' interface. It includes basic methods such as the mean, median, mode, normality test, among others. It also includes clustering techniques such as Principal Components Analysis, Hierarchical Clustering and the K-Means Method.
Structure learning of Bayesian network using coordinate-descent
    algorithm. This algorithm is designed for discrete network assuming a multinomial data set,
    and we use a multi-logit model to do the regression.
    The algorithm is described in Gu, Fu and Zhou (2016) <arXiv:1403.2310>.
Multiple testing procedures described in the paper Döhler, Durand and Roquain (2018) "New FDR bounds for discrete and heterogeneous tests" <doi:10.1214/18-EJS1441>. The main procedures of the paper (HSU and HSD), their adaptive counterparts (AHSU and AHSD), and the HBR variant are available and are coded to take as input a set of observed p-values and their discrete support under the null. A function to compute such p-values and supports for Fisher's exact tests is also provided, along with a wrapper allowing to apply discrete procedures directly from contingency tables.
Implements fast Monte Carlo simulations for 
    goodness-of-fit (GOF) tests for discrete distributions. This 
    includes tests based on the Chi-squared statistic, the 
    log-likelihood-ratio (G^2) statistic, the Freeman-Tukey 
    (Hellinger-distance) statistic, the Kolmogorov-Smirnov 
    statistic, the Cramer-von Mises statistic as described in 
    Choulakian, Lockhart and Stephens (1994) <doi:10.2307/3315828>, 
    and the root-mean-square statistic, see Perkins, 
    Tygert, and Ward (2011) <doi:10.1016/j.amc.2011.03.124>.
Probability mass function, distribution function, quantile function, random generation and parameter estimation for the discrete inverse Weibull distribution.
Probability mass function, distribution function, quantile function, random generation and estimation for the skew discrete Laplace distributions.
We consider a multiple testing procedure used in many modern applications which is the q-value method proposed by Storey and Tibshirani (2003), <doi:10.1073/pnas.1530509100>. The q-value method is based on the false discovery rate (FDR), hence versions of the q-value method can be defined depending on which estimator of the proportion of true null hypotheses, p0, is plugged in the FDR estimator. We implement the q-value method based on two classical pi0 estimators, and furthermore, we propose and implement three versions of the q-value method for homogeneous discrete uniform P-values based on pi0 estimators which take into account the discrete distribution of the P-values.
Create, manipulate, transform, and simulate from discrete random
    variables. The syntax is modeled after that which is used in mathematical
    statistics and probability courses, but with powerful support for more
    advanced probability calculations. This includes the creation of joint
    random variables, and the derivation and manipulation of their conditional
    and marginal distributions.
Probability mass function, distribution function, quantile function, random generation and parameter estimation for the type I and III discrete Weibull distributions.
A collection of supervised discretization
        algorithms. It can also be grouped in terms of top-down or
        bottom-up, implementing the discretization algorithms.
Bindings for additional classification models for use with
    the 'parsnip' package. Models include flavors of discriminant
    analysis, such as linear (Fisher (1936)
    <doi:10.1111/j.1469-1809.1936.tb02137.x>), regularized (Friedman
    (1989) <doi:10.1080/01621459.1989.10478752>), and flexible (Hastie,
    Tibshirani, and Buja (1994) <doi:10.1080/01621459.1994.10476866>), as
    well as naive Bayes classifiers (Hand and Yu (2007)
    <doi:10.1111/j.1751-5823.2001.tb00465.x>).
Templates and data files to support "Discrete Choice Analysis with R",
    Páez, A. and Boisjoly, G. (2023) <doi:10.1007/978-3-031-20719-8>.
Provides data transformations, estimation utilities,
    predictive evaluation measures and simulation functions for discrete time
    survival analysis.
A simple approach to measure political sophistication based on open-ended survey responses. Discursive sophistication captures the complexity of individual attitude expression by quantifying its relative size, range, and constraint. For more information on the measurement approach see: Kraft, Patrick W. 2023. "Women Also Know Stuff: Challenging the Gender Gap in Political Sophistication." American Political Science Review (forthcoming).
Easy access to species distribution data for 6 regions in the world, for a total of 226 anonymised species. These data are described and made available by Elith et al (2020) <doi:10.17161/bi.v15i2.13384> to compare species distribution modelling methods.
Estimate, summarize, and perform predictions with the market in 
  disequilibrium model, as found in Gourieroux, C. (2000) <doi:10.1017/CBO9780511805608> and 
  Maddala, G. (1983) <doi:10.1017/CBO9780511810176>. The parameters are estimated with maximum likelihood.
Model cell type heterogeneity of bulk renal cell carcinoma. The observed gene expression in bulk tumor sample is modeled by a log-normal distribution with the location parameter structured as a linear combination of the component-specific gene expressions.
Implement the methods proposed by Ahmad & Dey (2007) <doi:10.1016/j.datak.2007.03.016> in calculating the dissimilarity matrix at the presence of mixed attributes. This Package includes functions to discretize quantitative variables, calculate conditional probability for each pair of attribute values, distance between every pair of attribute values, significance of attributes, calculate dissimilarity between each pair of objects.
Implements methods for calculating disproportionate impact: the percentage point gap, proportionality index, and the 80% index.
 California Community Colleges Chancellor's Office (2017).  Percentage Point Gap Method. <https://www.cccco.edu/-/media/CCCCO-Website/About-Us/Divisions/Digital-Innovation-and-Infrastructure/Research/Files/PercentagePointGapMethod2017.ashx>.
 California Community Colleges Chancellor's Office (2014).  Guidelines for Measuring Disproportionate Impact in Equity Plans. <https://www.cccco.edu/-/media/CCCCO-Website/Files/DII/guidelines-for-measuring-disproportionate-impact-in-equity-plans-tfa-ada.pdf>.
A disk-based data manipulation tool for working with 
  large-than-RAM datasets. Aims to lower the barrier-to-entry for 
  manipulating large datasets by adhering closely to popular and 
  familiar data manipulation paradigms like 'dplyr' verbs and 
  'data.table' syntax.
Methods for species distribution modeling, that is, predicting the environmental similarity of any site to that of the locations of known occurrences of a species.
Functionality for manipulating values of associative
  maps.  The package is designed to be used with the 'mvp' class of
  packages that use the STL map class: its purpose is to trap
  plausible idiom that is ill-defined (implementation-specific) and
  return an informative error, rather than returning a possibly
  incorrect result.  To cite the package in publications please use
  Hankin (2022) <doi:10.48550/ARXIV.2210.03856>.
The disparity filter algorithm is a network reduction technique to
    identify the 'backbone' structure of a weighted network without destroying
    its multi-scale nature. The algorithm is documented in M. Angeles Serrano,
    Marian Boguna and Alessandro Vespignani in "Extracting the multiscale
    backbone of complex weighted networks", Proceedings of the National Academy
    of Sciences 106 (16), 2009. This implementation of the algorithm supports
    both directed and undirected networks.
Simulates demic diffusion building on models previously developed
	for the expansion of Neolithic and other food-producing economies during
	the Holocene (Fort et al. (2012) <doi:10.7183/0002-7316.77.2.203>, Souza et al.
	(2021) <doi:10.1098/rsif.2021.0499>). Growth and emigration are modelled as
	density-dependent processes using logistic growth and an asymptotic threshold
	model. Environmental and terrain layers, which can change over time, affect
	carrying capacity, growth and mobility. Multiple centres of origin with
	their respective starting times can be specified.
Functions for estimating Gaussian dispersion regression models (Aitkin, 1987 <doi:10.2307/2347792>), overdispersed binomial logit models (Williams, 1987 <doi:10.2307/2347977>), and overdispersed Poisson log-linear models (Breslow, 1984 <doi:10.2307/2347661>), using a quasi-likelihood approach.
Create disposable R packages for testing.
    You can create, install and load multiple R packages with a single
    function call, and then unload, uninstall and destroy them with another
    function call. This is handy when testing how some R code or an R package
    behaves with respect to other packages.
Evaluate the presence of disposition effect and others irrational
    investor's behaviors based solely on investor's transactions and financial
    market data. Experimental data can also be used to perform the analysis.  
    Four different methodologies are implemented to account for the different
    nature of human behaviors on financial markets.  
    Novel analyses such as portfolio driven and time series disposition effect
    are also allowed.
A modular package for measuring disparity (multidimensional space occupancy). Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics. The package also provides functions for looking at disparity in a serial way (e.g. disparity through time) or per groups as well as visualising the results. Finally, this package provides several statistical tests for disparity analysis.
Similarity of dissolution profiles is assessed using the
    similarity factor f2 according to the EMA guideline (European
    Medicines Agency 2010) "On the investigation of bioequivalence".
    Dissolution profiles are regarded as similar if the f2 value is
    between 50 and 100. For the applicability of the similarity factor f2,
    the variability between profiles needs to be within certain limits.
    Often, this constraint is violated. One possibility in this situation
    is to resample the measured profiles in order to obtain a bootstrap
    estimate of f2 (Shah et al. (1998) <doi:10.1023/A:1011976615750>).
    Other alternatives are the model-independent non-parametric
    multivariate confidence region (MCR) procedure (Tsong et al. (1996)
    <doi:10.1177/009286159603000427>) or the T2-test for equivalence
    procedure (Hoffelder (2016)
    <https://www.ecv.de/suse_item.php?suseId=Z|pi|8430>). Functions for
    estimation of f1, f2, bootstrap f2, MCR / T2-test for equivalence
    procedure are implemented.
Set of tools for molecular probes selection and design of a microarray, e.g. the assessment of physical and chemical properties, blast performance, selection according to sensitivity and selectivity. Methods used in package are described in: Lorenz R., Stephan H.B., Höner zu Siederdissen C. et al. (2011) <doi:10.1186/1748-7188-6-26>; Camacho C., Coulouris G., Avagyan V. et al. (2009) <doi:10.1186/1471-2105-10-421>.
Calculate multiple or pairwise dissimilarity for orders q = 0-N 
    (CqN; Chao et al. 2008 <doi:10/fcvn63>) for a set of species assemblages or 
    interaction networks.
Spatial downscaling of coarse grid mapping to fine grid
    mapping using predictive covariates and a model fitted using the 'caret'
    package. The original dissever algorithm was published by Malone et al. 
    (2012) <doi:10.1016/j.cageo.2011.08.021>, and extended by Roudier et al.
    (2017) <doi:10.1016/j.compag.2017.08.021>.
Tools to fit sample selection models in case of discrete response 
  variables, through a parametric formulation which represents a natural 
  extension of the well-known Heckman selection model are provided in the 
  package. The response variable can be of Bernoulli, Poisson or Negative 
  Binomial type. The sample selection mechanism allows to choose among a 
  Normal, Logistic or Gumbel distribution.
A simple way of fitting detection functions to distance sampling
    data for both line and point transects. Adjustment term selection, left and
    right truncation as well as monotonicity constraints and binning are
    supported. Abundance and density estimates can also be calculated (via a
    Horvitz-Thompson-like estimator) if survey area information is provided. See
    Miller et al. (2019) <doi:10.18637/jss.v089.i01> for more information on
    methods and <https://examples.distancesampling.org/> for example analyses.
Provides tools for constructing, manipulating and using distance metrics.
Calculates distances from point locations to features.
    The usual approach for eg. resource selection function analyses is to
    generate a complete distance to features surface then sample it with your 
    observed and random points. Since these raster based approaches can be
    pretty costly with large areas, and often lead to memory issues in R, 
    the distanceto package opts to compute these distances using
    efficient, vector based approaches. As a helper, there's a decidedly 
    low-res raster based approach for visually inspecting your region's 
    distance surface. But the workhorse is distance_to.
Provides tools to assess the dissimilarity between multivariate time-series. It is based on the psi measure described  by Birks and Gordon (1985 <doi:10.1002/jqs.3390020110>), which computes dissimilarity between irregular time-series constrained by sample order. However, in this package the original idea has been extended to work with any kind of multivariate time-series, no matter whether they are regular, irregular, aligned or unaligned. Furthermore, the package allows to assess the significance of dissimilarity values by applying a restricted permutation test, allows to measure the contribution of individual variables to dissimilarity, and offers tools to transfer attributes (generally time or age, but other are possible) between sequences based on the similarity of their samples.
Implement DiSTATIS and CovSTATIS  (three-way multidimensional scaling).  DiSTATIS and CovSTATIS are used to analyze multiple distance/covariance matrices collected on the same set of observations. These methods are based on Abdi, H., Williams, L.J., Valentin, D., & Bennani-Dosse, M. (2012) <doi:10.1002/wics.198>.
Implementing algorithms and fitting models when sites (possibly remote) share
  computation summaries rather than actual data over HTTP with a master R process (using
  'opencpu', for example). A stratified Cox model and a singular value decomposition are
  provided. The former makes direct use of code from the R 'survival' package. (That is,
  the underlying Cox model code is derived from that in the R 'survival' package.)
  Sites may provide data via several means: CSV files, Redcap API, etc. An extensible
  design allows for new methods to be added in the future and includes facilities
  for local prototyping and testing. Web applications are provided (via 'shiny') for
  the implemented methods to help in designing and deploying the computations.
Creates discretised versions of continuous 
      distribution functions by mapping continuous values 
      to an underlying discrete grid, based on a (uniform) 
      frequency of discretisation, a valid discretisation 
      point, and an integration range. For a review of 
      discretisation methods, see 
      Chakraborty (2015) <doi:10.1186/s40488-015-0028-6>.
Contains a range of functions covering the present
  development of the distributional method for the dichotomisation of continuous outcomes. 
  The method provides estimates with standard error of a comparison of proportions 
  (difference, odds ratio and risk ratio) derived, with similar precision, from a comparison of means. 
  See the URL below or <arXiv:1809.03279> for more information.
Constructs confidence regions without the need to know the sampling distribution of bivariate data. The method was proposed by Zhiqiu Hu & Rong-cai Yang (2013) <doi:10.1371/journal.pone.0081179.g001>.
Scientific and technical article format for the web.
    'Distill' articles feature attractive, reader-friendly typography,
    flexible layout options for visualizations, and full support for
    footnotes and citations.
Some very simple method functions for confidence interval calculation, bootstrap resampling aimed at atmospheric science applications, and to distill pertinent information from a potentially complex object; primarily used in common with packages extRemes and SpatialVx.  To reference this package and for a tutorial on the bootstrap functions, please see Gilleland (2020) <doi: 10.1175/JTECH-D-20-0069.1> and Gilleland (2020) <doi: 10.1175/JTECH-D-20-0070.1>.
Provides several methods for model distillation and interpretability 
    for general black box machine learning models and treatment effect estimation
    methods. For details on the algorithms implemented, see <https://forestry-labs.github.io/distillML/index.html>
    Brian Cho, Theo F. Saarinen, Jasjeet S. Sekhon, Simon Walter.
Calculates Distinctiveness Centrality in social networks. 
	For formulas and descriptions, see Fronzetti Colladon and Naldi (2020) <doi:10.1371/journal.pone.0233276>.
Provides a high level API to interface over sources storing distance, dissimilarity, similarity matrices with matrix style extraction, replacement and other utilities. Currently, in-memory dist object backend is supported.
Geodesic distance between phylogenetic trees and
  associated functions. The theoretical background of 'distory'
  is published in Billera et al. (2001) "Geometry of the space of
  phylogenetic trees." <doi:10.1006/aama.2001.0759>.
Package including an interactive Shiny application for plotting 
    common univariate distributions.
S4-classes and methods for distributions.
Provides documentation in form of a common vignette to packages 'distr',
            'distrEx', 'distrMod', 'distrSim', 'distrTEst', 'distrTeach', and 'distrEllipse'.
Functions for visualizing distributional regression models fitted using the 'gamlss', 'bamlss' or 'betareg' R package. The core of the package consists of a 'shiny' application, where the model results can be interactively explored and visualized.
Distribution (S4-)classes for elliptically contoured distributions (based on
            package 'distr').
Extends package 'distr' by functionals, distances, and conditional distributions.
A different way for calculating pdf/pmf, cdf, quantile and random data such that the user is able to consider the name of related distribution as an argument and so easily can changed by a changing argument by user. It must be mentioned that the core and computation base of package 'DISTRIB' is package 'stats'. Although similar functions are introduced previously in package 'stats', but the package 'DISTRIB' has some special applications in some special computational programs.
Vectorised distribution objects with tools for manipulating, 
    visualising, and using probability distributions. Designed to allow model
    prediction outputs to return distributions rather than their parameters, 
    allowing users to directly interact with predictive distributions in a
    data-oriented workflow. In addition to providing generic replacements for
    p/d/q/r functions, other useful statistics can be computed including means,
    variances, intervals, and highest density regions.
Fits Gaussian Mixtures by applying evolution. As fitness function a mixture of the chi square test for distributions and a novel measure for approximating the common area under curves between multiple Gaussians is used. The package presents an alternative to the commonly used Likelihood Maximization as is used in Expectation Maximization. The algorithm and applications of this package are published under: Lerch, F., Ultsch, A., Lotsch, J. (2020) <doi:10.1038/s41598-020-57432-w>. The evolution is based on the 'GA' package: Scrucca, L. (2013) <doi:10.18637/jss.v053.i04> while the Gaussian Mixture Logic stems from 'AdaptGauss': Ultsch, A, et al. (2015) <doi:10.3390/ijms161025897>.
Tools to create and manipulate probability distributions
    using S3.  Generics pdf(), cdf(), quantile(), and random() provide
    replacements for base R's d/p/q/r style functions.  Functions and
    arguments have been named carefully to minimize confusion for students
    in intro stats courses. The documentation for each distribution
    contains detailed mathematical notes.
A library of density, distribution function, quantile function, (bounded) raw moments and random generation for a collection of distributions relevant for the firm size literature. Additionally, the package contains tools to fit these distributions using maximum likelihood and evaluate these distributions based on (i) log-likelihood ratio and (ii) deviations between the empirical and parametrically implied moments of the distributions. We add flexibility by allowing the considered distributions to be combined into piecewise composite or finite mixture distributions, as well as to be used when truncated. See Dewitte (2020) <https://hdl.handle.net/1854/LU-8644700> for a description and application of methods available in this package.
Provides new types of omnibus tests which are generally much more powerful than traditional tests (including the Kolmogorov-Smirnov, Cramer-von Mises and Anderson-Darling tests),see Zhang (2002) <doi:10.1111/1467-9868.00337>.
Utilities are provided which are of use in the
    packages I have developed for dealing with
    distributions. Currently these packages are GeneralizedHyperbolic,
    VarianceGamma, and SkewHyperbolic and NormalLaplace. Each of these
    packages requires DistributionUtils. Functionality includes sample
    skewness and kurtosis, log-histogram, tail plots, moments by
    integration, changing the point about which a moment is
    calculated, functions for testing distributions using inversion
    tests and the Massart inequality. Also includes an implementation
    of the incomplete Bessel K function.
Implements S4 classes for probability models based on packages 'distr' and
            'distrEx'.
In order to provide unified access to Linux distribution details
    in R, this package wraps the various files and commands that may exist
    on a system. It is similar in spirit to the 'lsb_release' command and the
    'Python' package of the same name.
Fast distributed/parallel estimation for multinomial logistic regression via Poisson factorization and the 'gamlr' package.  For details see: Taddy (2015, AoAS), Distributed Multinomial Regression, <arXiv:1311.6139>.
Tools to estimate and manage empirical distributions,
    which should work with survey data. One of the main features is the 
    possibility to create data cubes of estimated statistics, that include
    all the combinations of the variables of interest (see for example functions
    dcc5() and dcc6()).
S4-distribution classes based on package distr for distributions from packages
            'fBasics' and 'fGarch'.
S4-classes for setting up a coherent framework for simulation within the distr
            family of packages.
Provides flexible examples of LLN and CLT for teaching purposes in secondary
            school.
Evaluation (S4-)classes based on package distr for evaluating procedures
            (estimators/tests) at data/simulation in a unified way.
A full definition for Weibull tails and Full-Tails Gamma and tools for fitting these distributions to empirical tails. This package build upon the paper by del Castillo, Joan & Daoudi, Jalila & Serra, Isabel. (2012) <doi:10.1017/asb.2017.9>.
Provides convenient methods for accessing the data in 'dist' objects with minimal memory and computational overhead. 'disttools' can be used to extract the distance between any pair or combination of points encoded by a 'dist' object using only the indices of those points. This is an improvement over existing functionality, which requires either coercing a 'dist' object into a matrix or calculating the one dimensional index corresponding to a pair of observations. Coercion to a matrix is undesirable because doing so doubles the amount of memory required for storage. In contrast, there is no inherent downside to the latter solution. However, in part due to several edge cases, correctly and efficiently implementing such a solution can be challenging. 'disttools' abstracts away these challenges and provides a simple interface to access the data in a 'dist' object using the latter approach.
Testing and documenting code that communicates with remote
  databases can be painful. Although the interaction with R is usually relatively 
  simple (e.g. data(frames) passed to and from a database), because they rely on 
  a separate service and the data there, testing them can be difficult to set up,
  unsustainable in a continuous integration environment, or impossible without 
  replicating an entire production cluster. This package addresses that by 
  allowing you to make recordings from your database interactions and then play 
  them back while testing (or in other contexts) all without needing to spin up 
  or have access to the database your code would typically connect to.
Facilitate the analysis of teams in a corporate setting:
    assess the diversity per grade and job, present the results,
    search for bias (in hiring and/or promoting processes).
    It also provides methods to simulate the effect of bias, random team-data, etc.
    White paper: 'Philippe J.S. De Brouwer' (2021) <http://www.de-brouwer.com/assets/div/div-white-paper.pdf>.
    Book (chapter 36): 'Philippe J.S. De Brouwer' (2020, ISBN:978-1-119-63272-6) and 'Philippe J.S. De Brouwer' (2020) <doi:10.1002/9781119632757>.
Functions to describe sampling and diversity dynamics of fossil occurrence datasets (e.g. from the Paleobiology Database). The package includes methods to calculate range- and occurrence-based metrics of taxonomic richness, extinction and origination rates, along with traditional sampling measures. A powerful subsampling tool is also included that implements frequently used sampling standardization methods in a multiple bin-framework. The plotting of time series and the occurrence data can be simplified by the functions incorporated in the package, as well as other calculations, such as environmental affinities and extinction selectivity testing. Details can be found in: Kocsis, A.T.; Reddin, C.J.; Alroy, J. and Kiessling, W. (2019) <doi:10.1101/423780>.
Contains functions for the 'DivE' estimator <doi:10.1371/journal.pcbi.1003646>. The 'DivE' estimator is a heuristic approach to estimate the number of classes or the number of species (species richness) in a population.
Utilities to represent, visualize, filter, analyse, and summarize
	     time-depth recorder (TDR) data.  Miscellaneous functions for
	     handling location data are also provided.
A suite of 'loon' related packages providing data analytic tools for 
    Direct Interactive Visual Exploration in R ('diveR').
    These tools work with and complement those of the 'tidyverse' suite, 
    extending the grammar of 'ggplot2' to become a grammar of interactive
    graphics.
    The suite provides many visual tools designed for moderately (100s of variables)
    high dimensional data analysis, through 'zenplots' and novel tools in 'loon', and
    extends the 'ggplot2' grammar to provide parallel coordinates, Andrews plots, and arbitrary 
    glyphs through 'ggmulti'.
    The  'diveR' package gathers together and installs all these related packages
    in a single step.
Compares the fit of alternative models of continuous trait differentiation between sister species and other paired lineages. Differences in trait means between two lineages arise as they diverge from a common ancestor, and alternative processes of evolutionary divergence are expected to leave unique signatures in the distribution of trait differentiation in datasets comprised of many lineage pairs. Models include approximations of divergent selection, drift, and stabilizing selection. A variety of model extensions facilitate the testing of process-to-pattern hypotheses. Users supply trait data and divergence times for each lineage pair. The fit of alternative models is compared in a likelihood framework.
Computes the most common diversity measures used in social and other sciences, and includes new measures from interdisciplinary research.
Diversification is one of the most important concepts in portfolio management. This framework offers scholars, practitioners and policymakers a useful toolbox to measure diversification. Specifically, this framework provides recent diversification measures from the recent literature. These diversification measures are based on the works of Rudin and Morgan (2006) <doi:10.3905/jpm.2006.611807>, Choueifaty and Coignard (2008) <doi:10.3905/JPM.2008.35.1.40>, Vermorken et al. (2012) <doi:10.3905/jpm.2012.39.1.067>, Flores et al. (2017) <doi:10.3905/jpm.2017.43.4.112>, Calvet et al. (2007) <doi:10.1086/524204>, and Candelon, Fuerst and Hasse (2020).
Contains a number of comparative 'phylogenetic' methods,
  mostly focusing on analysing diversification and character
  evolution.  Contains implementations of 'BiSSE' (Binary State
  'Speciation' and Extinction) and its unresolved tree extensions,
  'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE',
  'GeoSSE', and 'BiSSE-ness' Other included methods include Markov
  models of discrete and continuous trait evolution and constant rate
  'speciation' and extinction.
Implements interaction forests [1], which are specific diversity forests and 
  the basic form of diversity forests that uses univariable, binary splitting [2].
  Interaction forests (IFs) are ensembles of decision trees that model quantitative and
  qualitative interaction effects using bivariable splitting. IFs come with the 
  Effect Importance Measure (EIM), which can be used to identify variable pairs that 
  feature quantitative and qualitative interaction effects with high predictive
  relevance. IFs and EIM focus on well interpretable forms of interactions.
  The package also offers plot functions for visualising the estimated forms of 
  interaction effects.
  Categorical, metric, and survival outcomes are supported.
  This is a fork of the R package 'ranger' (main author: Marvin N. Wright) that 
  implements random forests using an efficient C++  implementation.
  References:
  [1] Hornung, R. & Boulesteix, A.-L. (2022) Interaction Forests: Identifying and 
      exploiting interpretable quantitative and qualitative interaction effects.
	  Computational Statistics & Data Analysis 171:107460, <doi:10.1016/j.csda.2022.107460>.
  [2] Hornung, R. (2022) Diversity forests: Using split sampling to enable 
      innovative complex split procedures in random forests.
	  SN Computer Science 3(2):1, <doi:10.1007/s42979-021-00920-1>.
Predictions of alpha diversity are fitted from presence data, first abundance is modeled from occupancy models and then, several diversity indices are calculated and finally GLM models are used to predict diversity in different environments and select priority areas.
Provides tools to sort DICOM-format medical image files, and
    convert them to NIfTI-1 format.
A set of tools for empirical analysis of diversity (a number and frequency of different types in population) and similarity (a number and frequency of shared types in two populations) in biological or ecological systems.
Alpha and beta diversity for taxonomic (TD), functional (FD), and phylogenetic (PD) dimensions based on rasters. Spatial and temporal beta diversity can be partitioned into replacement and richness difference components. It also calculates standardized effect size for FD and PD alpha diversity and the average individual traits across multilayer rasters. The layers of the raster represent species, while the cells represent communities. Methods details can be found at Cardoso et al. 2022 <https://CRAN.R-project.org/package=BAT> and Heming et al. 2023 <https://CRAN.R-project.org/package=SESraster>.
Implements common measures of diversity and spatial segregation. This package has tools to compute the majority of measures are reviewed in Massey and Denton (1988) <doi:10.2307/2579183>. Multiple common measures of within-geography diversity are implemented as well. All functions operate on data frames with a 'tidyselect' based workflow.
Divide taxonomic occurrence data into geographic regions of fair
    comparison, with three customisable methods to standardise area and extent.
    Calculate common biodiversity and range-size metrics on subsampled data.
    Background theory and practical considerations for the methods are described
    in Antell and others (2023) <doi:10.31223/X5997Z>.
Function to test spatial segregation and association based in contingency table analysis of nearest neighbour counts following Dixon (2002) <doi:10.1080/11956860.2002.11682700>. Some 'Fortran' code has been included to the original dixon2002() function of the 'ecespa' package to improve speed.
For outlier detection in small and normally distributed 
    samples the ratio test of Dixon (Q-test) can be used. Density,
    distribution function, quantile function and random generation 
    for Dixon's ratio statistics are provided as wrapper functions.
    The core applies McBane's Fortran functions <doi:10.18637/jss.v016.i03> 
    that use Gaussian quadrature for a numerical solution.
An R package for record linkage and implementing epidemiological case definitions in R.
    Record linkage is implemented either through a multistage deterministic approach or a probabilistic approach. 
    Matching records are assigned to unique groups. There are mechanisms to address missing data and conflicting matches across linkage stages.
    Track and assign events (e.g. sample collection) and periods (e.g. hospital admission) to unique groups based on a case definition. 
    The tracking process permits several options such as episode lengths and recurrence.
    Duplicate events or records can then be identified for removal or further analyses.
Lightweight utility functions used for the R package
    development infrastructure inside the data integration centers ('DIZ')
    to standardize and facilitate repetitive tasks such as setting up a
    database connection or issuing notification messages and to avoid
    redundancy.
Utility functions used for the R package development
    infrastructure inside the data integration centers ('DIZ') to
    standardize and facilitate repetitive tasks such as setting up a
    database connection or issuing notification messages and to avoid
    redundancy.
Implements various decision support tools related to the Econometrics & Technometrics.
             Subroutines include correlation reliability test, Mahalanobis distance measure for outlier detection, combinatorial search (all possible subset regression), non-parametric efficiency analysis measures: DDF (directional distance function), DEA (data envelopment analysis), HDF (hyperbolic distance function), SBM (slack-based measure), and SF (shortage function), benchmarking, Malmquist productivity analysis, risk analysis, technology adoption model, new product target setting, network DEA, dynamic DEA, intertemporal budgeting, etc.
Provides functions to facilitate access to the 'DKAN' API (<https://dkan.readthedocs.io/en/latest/apis/index.html>), including the 'DKAN' REST API (metadata), and the 'DKAN' datastore API (data). Includes functions to list, create, retrieve, update, and delete datasets and resources nodes. It also includes functions to search and retrieve data from the 'DKAN' datastore.
Compute diffusion kernels on DNA polymorphisms, including SNP and bi-allelic genotypes.
Provides time series regression models with one predictor using finite distributed lag models, polynomial (Almon) distributed lag models, geometric distributed lag models with Koyck transformation, and autoregressive distributed lag models. It also consists of functions for computation of h-step ahead forecasts from these models. See Demirhan (2020)(<doi:10.1371/journal.pone.0228812>) and Baltagi (2011)(<doi:10.1007/978-3-642-20059-5>) for more information.
An implementation of the differentiable lasso (dlasso) and SCAD (dSCAD) using iterative ridge algorithm. This package allows selecting the tuning parameter by AIC, BIC, GIC and GIC.
The Dirichlet Laplace shrinkage prior in Bayesian linear regression and variable selection, featuring:
    utility functions in implementing Dirichlet-Laplace priors such as visualization; 
    scalability in Bayesian linear regression; 
    penalized credible regions for variable selection.
Interface for 'Rcpp' users to 'dlib' <http://dlib.net> which is a
    'C++' toolkit containing machine learning algorithms and computer vision tools.
    It is used in a wide range of domains including robotics, embedded devices,
    mobile phones, and large high performance computing environments. This package
    allows R users to use 'dlib' through 'Rcpp'.
Implementation of the Decorrelated Local Linear estimator proposed 
    in <arxiv:1907.12732>. It constructs the confidence interval for the derivative 
    of the function of interest under the high-dimensional sparse additive model.
Provides routines for Maximum likelihood,
    Kalman filtering and smoothing, and Bayesian
    analysis of Normal linear State Space models, also known as 
    Dynamic Linear Models.
A collection of data-limited management procedures that can be evaluated 
    with management strategy evaluation with the 'MSEtool' package, or applied to 
    fishery data to provide management recommendations.
Collection of functions for distributed lag linear and non-linear models.
A collection of tools that support data diagnosis, exploration, and transformation. 
    Data diagnostics provides information and visualization of missing values and outliers and 
    unique and negative values to help you understand the distribution and quality of your data. 
    Data exploration provides information and visualization of the descriptive statistics of 
    univariate variables, normality tests and outliers, correlation of two variables, and 
    relationship between target variable and predictor. Data transformation supports binning 
    for categorizing continuous variables, imputates missing values and outliers, resolving skewness. 
    And it creates automated reports that support these three tasks.
Algorithm to handle with optimal subset selection for distributed local principal component analysis. The philosophy of the package is described in Guo G. (2020) <doi:10.1080/02331888.2020.1823979>.
The goal of dlr is to provide a friendly wrapper around the common 
    pattern of downloading a file if that file does not already exist locally.
Inference functionalities for distributed-lag linear structural equation models (DLSEMs). DLSEMs are Markovian structural causal models where each factor of the joint probability distribution is a distributed-lag linear regression with constrained lag shapes (Magrini, 2018 <doi:10.2478/bile-2018-0012>; Magrini et al., 2019 <doi:10.1007/s11135-019-00855-z>). DLSEMs account for temporal delays in the dependence relationships among the variables through a single parameter per covariate, thus allowing to perform dynamic causal inference in a feasible fashion. Endpoint-constrained quadratic, quadratic decreasing, linearly decreasing and gamma lag shapes are available.
Implements the dynamic logistic state space model for binary outcome data proposed by Jiang et al. (2021) <doi:10.1111/biom.13593>.
 It provides a computationally efficient way to update the prediction whenever new data becomes available.
 It allows for both time-varying and time-invariant coefficients, and use cubic smoothing splines to model varying coefficients.
 The smoothing parameters are objectively chosen by maximum likelihood. The model is updated using batch data accumulated at pre-specified time intervals.
Monthly download stats of 'CRAN' and 'Bioconductor' packages.
	     Download stats of 'CRAN' packages is from the 'RStudio' 'CRAN mirror', see <https://cranlogs.r-pkg.org:443>.
	     'Bioconductor' package download stats is at <https://bioconductor.org/packages/stats/>.
Provides tools for working with multiple related
    tables, stored as data frames or in a relational database.  Multiple
    tables (data and metadata) are stored in a compound object, which can
    then be manipulated with a pipe-friendly syntax.
Dynamic model averaging for binary and continuous
        outcomes.
Functions to calculate Divisia monetary aggregates index as given in Barnett, W. A. (1980) (<DOI:10.1016/0304-4076(80)90070-6>).
Functions for fitting a Bayesian model for grouping binary
    dissimilarity matrices in homogeneous clusters. Currently, it includes
    methods only for binary data (<doi:10.18637/jss.v100.i16>).
DMC model simulation detailed in Ulrich, R., Schroeter, H., Leuthold, H., & Birngruber, T. (2015).
  Automatic and controlled stimulus processing in conflict tasks: Superimposed diffusion processes and delta functions.
  Cognitive Psychology, 78, 148-174. Ulrich et al. (2015) <doi:10.1016/j.cogpsych.2015.02.005>.
  Decision processes within choice reaction-time (CRT) tasks are often modelled using evidence accumulation models (EAMs),
  a variation of which is the Diffusion Decision Model (DDM, for a review, see Ratcliff & McKoon, 2008).
  Ulrich et al. (2015) introduced a Diffusion Model for Conflict tasks (DMC). The DMC model combines common
  features from within standard diffusion models with the addition of superimposed controlled and automatic activation.
  The DMC model is used to explain distributional reaction time (and error rate) patterns in common behavioural
  conflict-like tasks (e.g., Flanker task, Simon task). This R-package implements the DMC model and provides functionality
  to fit the model to observed data. Further details are provided in the following paper: 
  Mackenzie, I. G., & Dudschig, C. (2021). DMCfun: An R package for fitting Diffusion Model of Conflict (DMC) to reaction 
  time and error rate data. Methods in Psychology, 100074. <doi:10.1016/j.metip.2021.100074>.
Computational tools for meta-analysis of diagnostic accuracy test. Bootstrap-based computational methods of the confidence interval for AUC of summary ROC curve and some related AUC-based inference methods are available (Noma et al. (2021) <doi:10.1080/23737484.2021.1894408>).
The state-of-the-art algorithms for distance metric learning, including global and local methods such as Relevant Component Analysis, Discriminative Component Analysis, Local Fisher Discriminant Analysis, etc. These distance metric learning methods are widely applied in feature extraction, dimensionality reduction, clustering, classification, information retrieval, and computer vision problems.
Implementation of double machine learning (DML) algorithms in R, 
    based on Emmenegger and Buehlmann (2021) "Regularizing Double Machine Learning 
    in Partially Linear Endogenous Models" <arXiv:2101.12525> and Emmenegger and
    Buehlmann (2021) <arXiv:2108.13657> "Double Machine Learning for Partially 
    Linear Mixed-Effects Models with Repeated Measurements". 
    First part: our goal is to perform inference for the linear parameter in partially
    linear models with confounding variables.
    The standard DML estimator of the linear parameter has a two-stage least
    squares interpretation, which can lead to a large variance and overwide
    confidence intervals.
    We apply regularization to reduce the variance of the estimator,
    which produces narrower confidence intervals that are approximately valid.
    Nuisance terms can be flexibly estimated with machine learning algorithms.
    Second part: our goal is to estimate and perform inference for the linear 
    coefficient in a partially linear mixed-effects model
    with DML. Machine learning algorithms allows us to incorporate more
    complex interaction structures and high-dimensional variables.
Yang(2020,<doi:10.1016/j.jeconom.2020.01.018>) come up with Double Machine Learning model ,it is based on this model, using four machine learning methods-- bagging, Boosting, random forest and neural network, and then  based on the four models   for two different combinations of the integrated model -- linear model combination and random forest .
Dyadic mixed model analysis with multi-trait responses and
  pedigree-based partitioning of individual variation into a range of
  environmental and genetic variance components for individual and 
  maternal effects. Method documented in dmmOverview.pdf; dmm is an 
  implementation of dispersion mean model described by
  Searle et al. (1992) "Variance Components", Wiley, NY.
Implements the daily based Morgan-Morgan-Finney (DMMF) soil erosion model (Choi et al., 2017 <doi:10.3390/w9040278>) for estimating surface runoff and sediment budgets from a field or a catchment on a daily basis.
The framework provides functions to generate ODEs of reaction
    networks, parameter transformations, observation functions, residual functions,
    etc. The framework follows the paradigm that derivative information should be
    used for optimization whenever possible. Therefore, all major functions produce
    and can handle expressions for symbolic derivatives. The methods used in dMod
    were published in Kaschek et al, 2019, <doi:10.18637/jss.v088.i10>.
Perform estimation, prediction, and simulations using the Dynamic Multiple Quantile model of Catania and Luati (2023) <doi:10.1016/j.jeconom.2022.11.002>. Can be used to estimate a set of conditional time-varying quantiles of a time series that do not cross.
It provides functions to apply the deterministic tracking algorithm - DiST (Wong et al 2016) <doi:10.1214/15-AOAS880> and to plot tractography results.
Perform differential analysis for
        methylation array data. Detect differentially
        methylated regions (DMRs) from array M-values. 
        The core is a Non-homogeneous Hidden Markov Model
        for estimating spatial correlation and a novel Constrained 
        Gaussian Mixture Model for modeling the M-value pairs of each individual locus.
Model selection algorithms for regression and classification, where the predictors can be continuous or categorical and the number of regressors may exceed the number of observations. The selected model consists of a subset of numerical regressors and partitions of levels of factors. Szymon Nowakowski, Piotr Pokarowski, Wojciech Rejchel and Agnieszka Sołtys, 2023. Improving Group Lasso for High-Dimensional Categorical Data. In: Computational Science – ICCS 2023. Lecture Notes in Computer Science, vol 14074, p. 455-470. Springer, Cham. <doi:10.1007/978-3-031-36021-3_47>. Aleksandra Maj-Kańska, Piotr Pokarowski and Agnieszka Prochenka, 2015. Delete or merge regressors for linear model selection. Electronic Journal of Statistics 9(2): 1749-1778. <doi:10.1214/15-EJS1050>. Piotr Pokarowski and Jan Mielniczuk, 2015. Combined l1 and greedy l0 penalized least squares for linear model selection. Journal of Machine Learning Research 16(29): 961-992. <https://www.jmlr.org/papers/volume16/pokarowski15a/pokarowski15a.pdf>. Piotr Pokarowski, Wojciech Rejchel, Agnieszka Sołtys, Michał Frej and Jan Mielniczuk, 2022. Improving Lasso for model selection and prediction. Scandinavian Journal of Statistics, 49(2): 831–863. <doi:10.1111/sjos.12546>.
Several tests for differential methylation in methylation array data, including one-sided differential mean and variance test. Methods used in the package refer to Dai, J, Wang, X, Chen, H and others (2021) "Incorporating increased variability in discovering cancer methylation markers", Biostatistics, submitted.
Implementation of a transfer learning framework employing distribution mapping based domain transfer. Uses the renowned concept of histogram matching (see Gonzalez and Fittes (1977) <doi:10.1016/0094-114X(77)90062-3>, Gonzalez and Woods (2008) <isbn:9780131687288>) and extends it to include distribution measures like kernel density estimates (KDE; see Wand and Jones (1995) <isbn:978-0-412-55270-0>, Jones et al. (1996) <doi:10.2307/2291420). In the typical application scenario, one can use the underlying sample distributions (histogram or KDE) to generate a map between two distinct but related domains to transfer the target data to the source domain and utilize the available source data for better predictive modeling design. Suitable for the case where a one-to-one sample matching is not possible, thus one needs to transform the underlying data distribution to utilize the more available data for modeling.
For checking the dataset from EDC(Electronic Data Capture) in clinical trials.
             'dmtools' reshape your dataset in a tidy view and check events.
             You can reshape the dataset and choose your target to check, for example, the laboratory reference range.
Work within the 'dplyr' workflow to add random variates to your data frame. 
  Variates can be added at any level of an existing column.  Also, bounds can be specified 
  for simulated variates.
Functions and data accompanying the second edition of the book  "Data Mining with R, learning with case studies" by Luis Torgo, published by CRC Press.
Statistical methods for DNA mixture analysis. This package is a lite-version of the 'DNAmixtures' package to allow users without a 'HUGIN' software license to experiment with the statistical methodology. While the lite-version aims to provide the full functionality it is noticeably less efficient than the original 'DNAmixtures' package. For details on implementation and methodology see <https://dnamixtures.r-forge.r-project.org/>.
Integrates pathway information into the differential network analysis of two gene expression datasets as described in Grimes, Potter, and Datta (2019) <doi:10.1038/s41598-019-41918-3>. Provides summary functions to break down the results at the pathway, gene, or individual connection level. The differential networks for each pathway of interest can be plotted, and the visualization will highlight any differentially expressed genes and all of the gene-gene associations that are significantly differentially connected.
Generates DNA sequences based on Markov model techniques for matched sequences. This can be generalized to several sequences. The sequences (taxa) are then arranged in an evolutionary tree (phylogenetic tree) depicting how taxa diverge from their common ancestors. This gives the tests and estimation methods for the parameters of different models. Standard phylogenetic methods assume stationarity, homogeneity and reversibility for the Markov processes, and  often impose further restrictions on the parameters.
Computationally efficient tools for comparing all pairs of profiles
    in a DNA database. The expectation and covariance of the summary statistic
    is implemented for fast computing. Routines for estimating proportions of
    close related individuals are available. The use of wildcards (also called F-
    designation) is implemented. Dedicated functions ease plotting the results. 
    See Tvedebrink et al. (2012) <doi:10.1016/j.fsigen.2011.08.001>. 
    Compute the distribution of the numbers of alleles in DNA mixtures. 
    See Tvedebrink (2013) <doi:10.1016/j.fsigss.2013.10.142>.
The goal of 'dndR' is to provide a suite of Dungeons & Dragons related functions.
    This package is meant to be useful both to players and Dungeon Masters (DMs).
    All functions currently focus on Fifth Edition (a.k.a. "5e") but once the next edition is published functions will likely be expanded to include any rule changes.
The focus of the dnet by Fang and Gough (2014) <doi:10.1186/s13073-014-0064-8> is to make sense of omics data (such as gene expression and mutations) from different angles including: integration with molecular networks, enrichments using ontologies, and relevance to gene evolutionary ages. Integration is achieved to identify a gene subnetwork from the whole gene network whose nodes/genes are labelled with informative data (such as the significant levels of differential expression or survival risks). To help make sense of identified gene networks, enrichment analysis is also supported using a wide variety of pre-compiled ontologies and phylostratific gene age information in major organisms including: human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. Add-on functionalities are supports for calculating semantic similarity between ontology terms (and between genes) and for calculating network affinity based on random walk; both can be done via high-performance parallel computing.
Provides a modified hierarchical test (Liu (2017) <doi:10.1214/17-AOS1539>) for detecting the structural difference between two Semiparametric Gaussian graphical models. The multiple testing procedure asymptotically controls the false discovery rate (FDR) at a user-specified level. To construct the test statistic, a truncated estimator is used to approximate the transformation functions and two R functions including lassoGGM() and lassoNPN() are provided to compute the lasso estimates of the regression coefficients.
Provides density, distribution function, quantile function and random
             generation for the split normal and split-t distributions, and computes their
             mean, variance, skewness and kurtosis for the two distributions (Li, F,
             Villani, M. and Kohn, R. (2010) <doi:10.1016/j.jspi.2010.04.031>).
Provides some utils to get Korean text sample from news articles
            in Daum which is popular news portal service in Korea.
Using Local Moran's I for detection of differential network local consistency.
Discriminant Non-Negative Matrix Factorization aims to extend the Non-negative Matrix Factorization algorithm in order to extract features that enforce not only the spatial locality, but also the separability between classes in a discriminant manner. It refers to three article, Zafeiriou, Stefanos, et al. "Exploiting discriminant information in nonnegative matrix factorization with application to frontal face verification." Neural Networks, IEEE Transactions on 17.3 (2006): 683-695. Kim, Bo-Kyeong, and Soo-Young Lee. "Spectral Feature Extraction Using dNMF for Emotion Recognition in Vowel Sounds." Neural Information Processing. Springer Berlin Heidelberg, 2013. and Lee, Soo-Young, Hyun-Ah Song, and Shun-ichi Amari. "A new discriminant NMF algorithm and its application to the extraction of subtle emotional differences in speech." Cognitive neurodynamics 6.6 (2012): 525-535.
Functions are provided to fit temporal lag models to dynamic
    networks. The models are build on top of exponential random graph models (ERGM) framework. There are
    functions for simulating or forecasting networks for future time points.
    Abhirup Mallik & Zack W. Almquist (2019) Stable Multiple Time Step Simulation/Prediction From Lagged Dynamic Network Regression Models, Journal of Computational and Graphical Statistics, 28:4, 967-979, <DOI: 10.1080/10618600.2019.1594834>.
Flexibly convert data between long and wide format using just two
    functions: reshape_toLong() and reshape_toWide().
Provides Frequentist (EM) and Bayesian  (MCMC) Methods for Inference of  Birth-Death-Immigration Markov Chains.
A dimension reduction technique for outlier detection. DOBIN: a Distance 
    based Outlier BasIs using Neighbours, constructs a set of basis vectors for outlier 
    detection. This is not an outlier detection method; rather it is a pre-processing 
    method for outlier detection. It brings outliers to the fore-front using fewer basis 
    vectors (Kandanaarachchi, Hyndman 2020) <doi:10.1080/10618600.2020.1807353>.
Example datasets from the book "An Introduction to Generalised Linear Models" (Year: 2018, ISBN:9781138741515) by Dobson and Barnett.
Utility package containing:
    1) Facilities for working with grouped data: 'do' something to data
    stratified 'by' some variables.
    2) LSmeans (least-squares means), general linear estimates.
    3) Restrict functions to a smaller domain.
    4) Miscellaneous other utilities.
Models for detecting concreteness in natural language. This package is built in support of Yeomans (2021) <doi:10.1016/j.obhdp.2020.10.008>, which reviews linguistic models of concreteness in several domains. Here, we provide an implementation of the best-performing domain-general model (from Brysbaert et al., (2014) <doi:10.3758/s13428-013-0403-5>) as well as two pre-trained models for the feedback and plan-making domains.
Learn vector representations of sentences, paragraphs or documents by using the 'Paragraph Vector' algorithms,
    namely the distributed bag of words ('PV-DBOW') and the distributed memory ('PV-DM') model. 
    The techniques in the package are detailed in the paper "Distributed Representations of Sentences and Documents" by Mikolov et al. (2014), available at <arXiv:1405.4053>.
    The package also provides an implementation to cluster documents based on these embedding using a technique called top2vec. 
    Top2vec finds clusters in text documents by combining techniques to embed documents and words and density-based clustering.
    It does this by embedding documents in the semantic space as defined by the 'doc2vec' algorithm. Next it maps
    these document embeddings to a lower-dimensional space using the 'Uniform Manifold Approximation and Projection' (UMAP) clustering algorithm 
    and finds dense areas in that space using a 'Hierarchical Density-Based Clustering' technique (HDBSCAN). These dense
    areas are the topic clusters which can be represented by the corresponding topic vector which is an aggregate of the 
    document embeddings of the documents which are part of that topic cluster. In the same semantic space similar words can 
    be found which are representative of the topic.
    More details can be found in the paper 'Top2Vec: Distributed Representations of Topics' by D. Angelov available at <arXiv:2008.09470>.
Build a Dockerfile straight from your R session.
    'dockerfiler' allows you to create step by step a Dockerfile, and
    provide convenient tools to wrap R code inside this Dockerfile.
This is the core package that provides both the user API and developer API to deploy 
    the parallel cluster on the cloud using the container service. The user can call 
    clusterPreset() to define the cloud service provider and container and makeDockerCluster()
    to create the cluster. The developer should see "developer's cookbook" on how to define
    the cloud provider and container.
Gives you the ability to use arbitrary Docker images
    (including custom ones) to process Rmarkdown code chunks.
It provides the ability to generate images from documents
 of different types. Three main features are provided: functions for
 generating document thumbnails, functions for performing visual tests
 of documents and a function for updating fields and table of contents
 of a 'Microsoft Word' or 'RTF' document. In order to work, 'LibreOffice' must be
 installed on the machine and or 'Microsoft Word'. If the latter is
 available, it can be used to produce PDF documents or images
 identical to the originals; otherwise, 'LibreOffice' is used and
 the rendering can be sometimes different from the original
 documents.
Define a command-line interface by just giving it
    a description in the specific format.
A direct approach to optimal designs for copula models based on
    the Fisher information. Provides flexible functions for building joint PDFs,
    evaluating the Fisher information and finding optimal designs. It includes an
    extensible solution to summation and integration called 'nint', functions for
    transforming, plotting and comparing designs, as well as a set of tools for
    common low-level tasks.
Basic routines used in scientific coding, such as timing routines, vector/array handing functions and I/O support routines.
High quality documentation can make for a great experience for your users. You can use 'docreview' to check that your R package documentation passes a number of configurable checks relating to documentation content.
Provides the ability to display something analogous to
    Python's docstrings within R.  By allowing the user to document
    their functions as comments at the beginning of their function
    without requiring putting the function into a package we allow
    more users to easily provide documentation for their functions.
    The documentation can be viewed just like any other help files
    for functions provided by packages as well.
Creates 'testthat' tests from 'roxygen' examples using simple tags.
Have you ever been tempted to create 'roxygen2'-style documentation
    comments for one of your functions that was not part of one of your
    packages (yet)?
    This is exactly what this package is about: running 'roxygen2' on
    (chunks of) a single code file.
It is sometimes necessary to create documentation for all files in a directory. Doing so by hand can be very tedious. This task is made fast and reproducible using the functionality of 'documenter'. It aggregates all text files in a directory and its subdirectories into a single word document in a semi-automated fashion.
Connect to the 'DocuSign' Rest API <https://www.docusign.com/p/RESTAPIGuide/RESTAPIGuide.htm>, 
  which supports embedded signing, and sending of documents.
A set of helper functions for using R Markdown to create documents
    in docx format, especially documents for use in a classroom or workshop
    setting.
'Microsoft Word' 'docx' files provide an 'XML' structure that is fairly
    straightforward to navigate, especially when it applies to 'Word' tables and
    comments. Tools are provided to determine table count/structure, comment count
    and also to extract/clean tables and comments from 'Microsoft Word' 'docx' documents.
    There is also nascent support for '.doc' and '.pptx' files.
A variety of sampling plans are able to be compared using evaluations of their operating characteristics (OC), average outgoing quality (OQ), average total inspection (ATI) etc.
Distances on dual-weighted directed graphs using
    priority-queue shortest paths (Padgham (2019) <doi:10.32866/6945>).
    Weighted directed graphs have weights from A to B which may differ
    from those from B to A.  Dual-weighted directed graphs have two sets
    of such weights. A canonical example is a street network to be used
    for routing in which routes are calculated by weighting distances
    according to the type of way and mode of transport, yet lengths of
    routes must be calculated from direct distances.
Creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Provides diverse quality criteria. Provides utility functions for the class design, which is also used by other packages for designed experiments.
'CRAN' packages 'DoE.base' and 'Rmosek' and non-'CRAN' package 'gurobi' are enhanced with functionality for the creation of optimized arrays for experimentation, where optimization is in terms of generalized minimum aberration. It is also possible to optimally extend existing arrays to larger run size. The package writes 'MPS' (Mathematical Programming System) files for use with any mixed integer optimization software that can process such files. If at least one of the commercial products 'Gurobi' or 'Mosek' (free academic licenses available for both) is available, the package also creates arrays by optimization. For installing 'Gurobi' and its R package 'gurobi', follow instructions at <https://www.gurobi.com/products/gurobi-optimizer/> and <https://www.gurobi.com/documentation/7.5/refman/r_api_overview.html> (or higher version). For installing 'Mosek' and its R package 'Rmosek', follow instructions at <https://www.mosek.com/downloads/> and <https://docs.mosek.com/8.1/rmosek/install-interface.html>, or use the functionality in the stump CRAN R package 'Rmosek'.
Various kinds of designs for
 (industrial) experiments can be created. The package uses, and sometimes enhances,
        design generation routines from other packages. 
        So far, response surface designs from package 'rsm', Latin hypercube
        samples from packages 'lhs' and 'DiceDesign', and 
        D-optimal designs from package 'AlgDesign' have been implemented.
Performs analysis of popular experimental designs used in the field of biological research. The designs covered are completely randomized design, randomized complete block design, factorial completely randomized design, factorial randomized complete block design, split plot design, strip plot design and latin square design. The analysis include analysis of variance, coefficient of determination, normality test of residuals, standard error of mean, standard error of difference and multiple comparison test of means. The package has functions for transformation of data and yield data conversion. Some datasets are also added in order to facilitate examples.
The distributed online expectation maximization algorithms are used to solve parameters of Poisson mixture models. The philosophy of the package is described in Guo, G. (2022) <doi:10.1080/02664763.2022.2053949>.
Rare variant association test integrating variant position information. It aims to identify the presence of clusters of disease-risk variants in specific gene regions. For more details, please read the publication from Persyn et al. (2017)  <doi:10.1371/journal.pone.0179364>.
The 'future' package provides a unifying parallelization framework for R that supports many parallel and distributed backends. The 'foreach' package provides a powerful API for iterating over an R expression in parallel. The 'doFuture' package brings the best of the two together. There are two alternative ways to use this package. The first is the traditional 'foreach' approach by registering the 'foreach' adapter 'registerDoFuture()' and so that 'y <- foreach(...) %dopar% { ... }' runs in parallelizes with the 'future' framework. The other alternative is to use 'y <- foreach(...) %dofuture% { ... }', which does not require using 'registerDoFuture()' and has many advantages over '%dopar%'.
Work with data on Venetian doges and dogaresse and the noble families of the Republic of Venice, and use it for social network analysis, as used in Merelo (2022) <arXiv:2209.07334>.
Provides a parallel backend for the %dopar% function using
        the multicore functionality of the parallel package.
A wrapper on top of the 'Domino Command-Line Client'. It lets you
    run 'Domino' commands (e.g., "run", "upload", "download") directly from your
    R environment. Under the hood, it uses R's system function to run the 'Domino'
    executable, which must be installed as a prerequisite. 'Domino' is a service
    that makes it easy to run your code on scalable hardware, with integrated
    version control and collaboration features designed for analytical workflows
    (see <http://www.dominodatalab.com> for more information).
A wrapper on top of the 'Domino Data Python SDK' library. It lets 
    you query and access 'Domino Data Sources' directly from your R environment.
    Under the hood, 'Domino Data R SDK' leverages the API provided by the 
    'Domino Data Python SDK', which must be installed as a prerequisite.
    'Domino' is a platform that makes it easy to run your code on scalable 
    hardware, with integrated version control and collaboration features 
    designed for analytical workflows. See 
    <https://docs.dominodatalab.com/en/latest/api_guide/140b48/domino-data-api>
    for more information.
Methods to apply decomposition-based relative importance 
  analysis for R functions. This package supports the application of 
  decomposition methods by providing 'lapply'- or 'Map'-like meta-functions that 
  compute dominance analysis (Azen, R., & Budescu, D. V. (2003) 
  <doi:10.1037/1082-989X.8.2.129>; Grömping, U. (2007) 
  <doi:10.1198/000313007X188252>) or Shapley value regression 
  (Lipovetsky, S., & Conklin, M. (2001) <doi:10.1002/asmb.446>)
  based on the values returned from other functions.
Provides a parallel backend for the %dopar% function using
        the Rmpi package.
Finds the k nearest neighbours in a dataset of specified points, 
  adding the option to wrap certain variables on a torus.  The user chooses
  the algorithm to use to find the nearest neighbours. Two such algorithms,
  provided by the packages 'RANN' <https://cran.r-project.org/package=RANN>, 
  and 'nabor' <https://cran.r-project.org/package=nabor>, are suggested.
Tools for exploring the topography of 3d triangle meshes.
    The functions were developed with dental surfaces in mind, but could be 
    applied to any triangle mesh of class 'mesh3d'. More specifically, 'doolkit'
    allows to isolate the border of a mesh, or a subpart of the mesh using the 
    polygon networks method; crop a mesh; compute basic descriptors (elevation, 
    orientation, footprint area); compute slope, angularity and relief index
    (Ungar and Williamson (2000) <https://palaeo-electronica.org/2000_1/gorilla/issue1_00.htm>;
    Boyer (2008) <doi:10.1016/j.jhevol.2008.08.002>), inclination and occlusal
    relief index or gamma (Guy et al. (2013) <doi:10.1371/journal.pone.0066142>),
    OPC (Evans et al. (2007) <doi:10.1038/nature05433>), OPCR (Wilson et al. 
    (2012) <doi:10.1038/nature10880>), DNE (Bunn et al. (2011) <doi:10.1002/ajpa.21489>;
    Pampush et al. (2016) <doi:10.1007/s10914-016-9326-0>), form factor (Horton 
    (1932) <doi:10.1029/TR013i001p00350>), basin elongation (Schum (1956) 
    <doi:10.1130/0016-7606(1956)67[597:EODSAS]2.0.CO;2>), lemniscate ratio 
    (Chorley et al; (1957) <doi:10.2475/ajs.255.2.138>), enamel-dentine distance
    (Guy et al. (2015) <doi:10.1371/journal.pone.0138802>; Thiery et al. (2017) 
    <doi:10.3389/fphys.2017.00524>), absolute crown strength (Schwartz et al. 
    (2020) <doi:10.1098/rsbl.2019.0671>), relief rate (Thiery et al. (2019)
    <doi:10.1002/ajpa.23916>) and area-relative curvature; draw cumulative
    profiles of a topographic variable; and map a variable over a 3d triangle 
    mesh.
Provides a parallel backend for the %dopar% function using
        the parallel package.
Provides information on drug names (brand, 
    generic and street) for drugs tracked by the DEA. There are functions that 
    will search synonyms and return the drug names and types. The vignettes 
    have extensive information on the work done to create the data for the package.
Create and manage fault-tolerant task queues for the 'foreach' package using the 'Redis' key/value database.
Provides models to fit the dynamics of a regulated system experiencing exogenous inputs. 
    The underlying models use differential equations and linear mixed-effects regressions to estimate the 
    coefficients of the equation. With them, the functions can provide an estimated signal.
    The package provides simulation and analysis functions and also print, summary, plot and predict methods,
    adapted to the function outputs, for easy implementation and presentation of results.
Provides functions to perform
    reproducible parallel foreach loops, using independent
    random streams as generated by L'Ecuyer's combined
    multiple-recursive generator [L'Ecuyer (1999), <DOI:10.1287/opre.47.1.159>].
    It enables to easily convert standard '%dopar%' loops into
    fully reproducible loops, independently of the number
    of workers, the task scheduling strategy, or the chosen
    parallel environment and associated foreach backend.
Contains data sets, examples and software from the book Design of Observational Studies by Paul R. Rosenbaum, New York: Springer, <doi:10.1007/978-1-4419-1213-8>, ISBN 978-1-4419-1212-1.
Contains data sets, examples and software from the Second Edition of "Design of Observational Studies"; see Rosenbaum, P.R. (2010)  <doi:10.1007/978-1-4419-1213-8>.
Identification of causal effects from arbitrary observational and experimental probability distributions via do-calculus and standard probability manipulations using a search-based algorithm by Tikka et al. (2021) <doi:10.18637/jss.v099.i05>. Allows for the presence of mechanisms related to selection bias (Bareinboim, E. and Tian, J. (2015) <http://ftp.cs.ucla.edu/pub/stat_ser/r445.pdf>), transportability (Bareinboim, E. and Pearl, J. (2014) <http://ftp.cs.ucla.edu/pub/stat_ser/r443.pdf>), missing data (Mohan, K. and Pearl, J. and Tian., J. (2013) <http://ftp.cs.ucla.edu/pub/stat_ser/r410.pdf>) and arbitrary combinations of these. Also supports identification in the presence of context-specific independence (CSI) relations through labeled directed acyclic graphs (LDAG). For details on CSIs see Corander et al. (2019) <doi:10.1016/j.apal.2019.04.004>.
Provides the user with an interactive application which can be used to facilitate the planning of dose finding studies by applying the theory of optimal experimental design.
The DoseFinding package provides functions for the design and analysis
	     of dose-finding experiments (with focus on pharmaceutical Phase
	     II clinical trials). It provides functions for: multiple contrast
	     tests, fitting non-linear dose-response models (using Bayesian and
	     non-Bayesian estimation), calculating optimal designs and an
	     implementation of the MCPMod methodology (Pinheiro et al. (2014)
	     <doi:10.1002/sim.6052>).
Utilities for converting unstructured electronic prescribing instructions into structured medication data. Extracts drug dose, units, daily dosing frequency and intervals from English-language prescriptions. Based on Karystianis et al. (2015) <doi:10.1186/s12911-016-0255-x>.
Provides a parallel backend for the %dopar% function using
        the snow package of Tierney, Rossini, Li, and Sevcikova.
Constructs dynamic optimal shrinkage estimators for the weights of the global 
  minimum variance portfolio which are reconstructed at given reallocation 
  points as derived in Bodnar, Parolya, and Thorsén (2021) (<arXiv:2106.02131>).
  Two dynamic shrinkage estimators are available in this package. One using 
  overlapping samples while the other use nonoverlapping samples.
Estimates dose-response relations from summarized dose-response
    data and to combines them according to principles of (multivariate)
    random-effects models.
A small package containing helper utilities for creating functions
    for computing statistics.
Renders DOT diagram markup language in R and also provides the possibility to
    export the graphs in PostScript and SVG (Scalable Vector Graphics) formats.
    In addition, it supports literate programming packages such as 'knitr' and
    'rmarkdown'.
Provides .C64(), which is an enhanced version of .C()
    and .Fortran() from the foreign function interface. .C64() supports long
    vectors, arguments of type 64-bit integer, and provides a mechanism to
    avoid unnecessary copies of read-only and write-only arguments. This
    makes it a convenient and fast interface to C/C++ and Fortran code.
Load configuration from a '.env' file, that is
    in the current working directory, into environment variables.
Decorrelates a set of summary statistics (i.e., Z-scores or P-values per SNP) via Decorrelation by Orthogonal Transformation (DOT) approach and performs gene-set analyses by combining transformed statistic values; operations are performed with algorithms that rely only on the association summary results and the linkage disequilibrium (LD). For more details on DOT and its power, see Olga (2020) <doi:10.1371/journal.pcbi.1007819>.
A toolbox to create and manage metadata files and
    configuration profiles: files used to configure the parameters and
    initial settings for some computer programs.
Generate point data for representing people within spatial data. This
  collects a suite of tools for creating simple dot density maps. Several functions 
  from different spatial packages are standardized to take the same arguments so
  that they can be easily substituted for each other.
Quick and easy dot-and-whisker plots of regression results.
Contains the discrete nonparametric survivor function estimation algorithm of De Gruttola and Lagakos for doubly interval-censored failure time data and the discrete nonparametric survivor function estimation algorithm of Sun for doubly interval-censored left-truncated failure time data [Victor De Gruttola  & Stephen W. Lagakos (1989) <doi:10.2307/2532030>] [Jianguo Sun (1995) <doi:10.2307/2533008>].
Likelihood-based inference methods with doubly-truncated data are developed under various models.
 Nonparametric models are based on Efron and Petrosian (1999) <doi:10.1080/01621459.1999.10474187> and
 Emura, Konno, and Michimae (2015) <doi:10.1007/s10985-014-9297-5>.
 Parametric models from the special exponential family (SEF) are based on
 Hu and Emura (2015) <doi:10.1007/s00180-015-0564-z> and
 Emura, Hu and Konno (2017) <doi:10.1007/s00362-015-0730-y>.
 The parametric location-scale models are based on Dorre et al. (2020) <doi:10.1007/s00180-020-01027-6>.
Performs hypothesis tests concerning a regression function in a least-squares model, where the null is a parametric function, and the alternative is the union of large-dimensional convex polyhedral cones. See Bodhisattva Sen and Mary C Meyer (2016) <doi:10.1111/rssb.12178> for more details.
Differential exon usage test for RNA-Seq data via an empirical Bayes shrinkage method for the dispersion parameter the utilizes inclusion-exclusion data to analyze the propensity to skip an exon across groups. The input data consists of two matrices where each row represents an exon and the columns represent the biological samples. The first matrix is the count of the number of reads expressing the exon for each sample. The second matrix is the count of the number of reads that either express the exon or explicitly skip the exon across the samples, a.k.a. the total count matrix. Dividing the two matrices yields proportions representing the propensity to express the exon versus skipping the exon for each sample.
Implementation of the double/debiased machine learning framework of
    Chernozhukov et al. (2018) <doi:10.1111/ectj.12097> for partially linear
    regression models, partially linear instrumental variable regression models,
    interactive regression models and interactive instrumental variable
    regression models. 'DoubleML' allows estimation of the nuisance parts in
    these models by machine learning methods and computation of the Neyman
    orthogonal score functions. 'DoubleML' is built on top of 'mlr3' and the
    'mlr3' ecosystem. The object-oriented implementation of 'DoubleML' based on
    the 'R6' package is very flexible.
Overload utils::'?' to build unary and binary operators from existing functions, 
    piping operators of different precedence, and flexible syntaxes.
Creates the "table one" of bio-medical papers. Fill it with your data and the name of the variable which you'll make the group(s) out of and it will make univariate, bivariate analysis and parse it into HTML.
    It also allows you to visualize all your data with graphic representation.
Local linear hazard estimator and its multiplicatively bias correction, including three bandwidth selection methods: best one-sided cross-validation, double one-sided cross-validation, and standard cross-validation.
Implements maximum likelihood methods for 
    evaluating the durability of vaccine efficacy in a randomized, 
    placebo-controlled clinical trial with staggered enrollment of participants 
    and potential crossover of placebo recipients before the end of the trial. 
    Lin, D. Y., Zeng, D., and Gilbert, P. B. (2021) 
    <doi:10.1093/cid/ciab226>
    and 
    Lin, D. Y., Gu, Y., Zeng, D., Janes, H. E., and Gilbert, P. B. (2021) 
    <doi:10.1093/cid/ciab630>.
'Kevin Dowd's' book Measuring Market Risk is a widely read book 
          in the area of risk measurement by students and 
          practitioners alike. As he claims, 'MATLAB' indeed might have been the most 
          suitable language when he originally wrote the functions, but,
          with growing popularity of R it is not entirely 
	  valid. As 'Dowd's' code was not intended to be error free and were mainly 
	  for reference, some functions in this package have inherited those 
	  errors. An attempt will be made in future releases to identify and correct 
	  them. 'Dowd's' original code can be downloaded from www.kevindowd.org/measuring-market-risk/. 
          It should be noted that 'Dowd' offers both
          'MMR2' and 'MMR1' toolboxes. Only 'MMR2' was ported to R. 'MMR2' is more 
          recent version of 'MMR1' toolbox and they both have mostly similar 
          function. The toolbox mainly contains different parametric and non 
	  parametric methods for measurement of market risk as well as 
	  backtesting risk measurement methods.
Syntax highlighting of R code, specifically designed for the
    needs of 'RMarkdown' packages like 'pkgdown', 'hugodown', and
    'bookdown'. It includes linking of function calls to their
    documentation on the web, and automatic translation of ANSI escapes in
    output to the equivalent HTML.
Provides a wrapper for the download.file function,
    making it possible to download files over HTTPS on Windows, Mac OS X, and
    other Unix-like platforms. The 'RCurl' package provides this functionality
    (and much more) but can be difficult to install because it must be compiled
    with external dependencies. This package has no external dependencies, so
    it is much easier to install.
Implement download buttons in HTML output from 'rmarkdown' without the need for 'runtime:shiny'.
Uses species occupancy at coarse grain sizes to predict species occupancy at fine grain sizes. Ten models are provided to fit and extrapolate the occupancy-area relationship, as well as methods for preparing atlas data for modelling. See Marsh et. al. (2018) <doi:10.18637/jss.v086.c03>.
Toggles the test and production versions of a large
  data analysis project.
Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees.
    Provides methods to 1) reconstruct unmutated ancestral sequences,
    2) build B cell phylogenetic trees using multiple methods,
    3) visualize trees with metadata at the tips,
    4) reconstruct intermediate sequences,
    5) detect biased ancestor-descendant relationships among metadata types
    Workflow examples available at documentation site (see URL).
    Citations:
    Hoehn et al (2022) <doi:10.1371/journal.pcbi.1009885>,
    Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.
A Scannerless GLR parser/parser generator.  Note that GLR standing for "generalized LR", where L stands for "left-to-right" and
   R stands for "rightmost (derivation)".  For more information see <https://en.wikipedia.org/wiki/GLR_parser>. This parser is based on the Tomita
   (1987) algorithm. (Paper can be found at <https://aclanthology.org/P84-1073.pdf>).
   The original 'dparser' package documentation can be found at <https://dparser.sourceforge.net/>.  This allows you to add mini-languages to R (like
   RxODE's ODE mini-language Wang, Hallow, and James 2015 <DOI:10.1002/psp4.12052>) or to parse other languages like 'NONMEM' to automatically translate
   them to R code.   To use this in your code, add a LinkingTo dparser in your DESCRIPTION file and instead of using #include <dparse.h> use
   #include <dparser.h>.  This also provides a R-based port of the make_dparser <https://dparser.sourceforge.net/d/make_dparser.cat> command called
   mkdparser().  Additionally you can parse an arbitrary grammar within R using the dparse() function, which works on most OSes and is mainly for grammar
   testing.  The fastest parsing, of course, occurs at the C level, and is suggested.
Beta-binomial Mixture Model is used to infer the pattern from count data.
		It can be used for clustering of RNA methylation sequencing data.
Use dynamic programming method to solve l1 convex clustering with identical weights.
The automated clustering and quantification of the digital PCR
            data is based on the combination of 'DBSCAN' (Hahsler et al. (2019)
            <doi:10.18637/jss.v091.i01>) and 'c-means' (Bezdek et al. (1981) 
            <doi:10.1007/978-1-4757-0450-1>) algorithms.
            The analysis is independent of multiplexing geometry, dPCR system, 
            and input amount.
            The details about input data and parameters are available in the
            vignette.
Compares distributions with one another in terms of their fit to each sample in a dataset that contains multiple samples, as described in Joo, Aguinis, and Bradley (in press). Users can examine the fit of seven distributions per sample: pure power law, lognormal, exponential, power law with an exponential cutoff, normal, Poisson, and Weibull. Automation features allow the user to compare all distributions for all samples with a single command line, which creates a separate row containing results for each sample until the entire dataset has been analyzed.
Perform tree-ring analyses such as detrending, chronology
        building, and cross dating.  Read and write standard file formats
        used in dendrochronology.
A fast, consistent tool for working with data frame like
    objects, both in memory and out of memory.
An RStudio addin for teaching and learning data manipulation using the 'dplyr' package.
    You can learn each steps of data manipulation by clicking your mouse without coding.
    You can get resultant data (as a 'tibble') and the code for data manipulation.
Create, install, and summarise data packages that follow
    the Open Knowledge Foundation's Data Package Protocol.
This MCMC method takes a data numeric vector (Y) and assigns the elements of Y
  to a (potentially infinite) number of normal distributions. The individual normal distributions from a mixture of normals can be inferred.
  Following the method described in Escobar (1994) <doi:10.2307/2291223> we use a Dirichlet Process Prior (DPP) to describe stochastically our prior assumptions about the dimensionality of the data.
An implementation of common statistical analysis and models with
    differential privacy (Dwork et al., 2006a) <doi:10.1007/11681878_14>
    guarantees. The package contains, for example, functions providing
    differentially private computations of mean, variance, median, histograms,
    and contingency tables. It also implements some statistical models and
    machine learning algorithms such as linear regression (Kifer et al., 2012)
    <https://proceedings.mlr.press/v23/kifer12.html>
    and SVM (Chaudhuri et al., 2011)
    <https://jmlr.org/papers/v12/chaudhuri11a.html>. In addition, it implements
    some popular randomization mechanisms
    such as the Laplace mechanism (Dwork et al., 2006a)
    <doi:10.1007/11681878_14>, Gaussian mechanism (Dwork et al., 2006b)
    <doi:10.1007/11761679_29>, and exponential mechanism
    (McSherry & Talwar, 2007) <doi:10.1109/FOCS.2007.66>.
Multivariate Gaussian mixture model with a determinant point 
  process prior to promote the discovery of parsimonious components from 
  observed data. See Xu, Mueller, Telesca (2016) <doi:10.1111/biom.12482>.
Computations for approximations and alternatives for the 'DPQ'
  (Density (pdf), Probability (cdf) and Quantile) functions for probability
  distributions in R.
  Primary focus is on (central and non-central) beta, gamma and related
  distributions such as the chi-squared, F, and t.
  --
  For several distribution functions, provide functions implementing formulas from
  Johnson, Kotz, and Kemp (1992) <doi:10.1002/bimj.4710360207>  and
  Johnson, Kotz, and Balakrishnan (1995) for discrete or continuous
  distributions respectively.
  This is for the use of researchers in these numerical approximation
  implementations, notably for my own use in order to improve standard
  R pbeta(), qgamma(), ..., etc: {'"dpq"'-functions}.
An extension to the 'DPQ' package with computations for 'DPQ'
  (Density (pdf), Probability (cdf) and Quantile) functions, where
  the functions here partly use the 'Rmpfr' package and hence the
  underlying 'MPFR' and 'GMP' C libraries.
Provides a generalized method for printing tabular data within 
	the R environment in order to make the process of presenting high quality 
	tabular output seamless for the user.  Output is directed to the R graphics 
	device so that tables can be exported to any file format supported by the 
	graphics device. Utilizes a formula interface to specify the contents of 
	tables often found in manuscripts or business reports.  In addition, formula 
	interface provides inline formatting of the numeric cells of a table and 
	renaming column labels.
Generally, most of the packages specify the probability density function, cumulative distribution function, quantile function, and random numbers generation of the probability distributions. The present package allows to compute some important distributional properties, including the first four ordinary and central moments, Pearson's coefficient of skewness and kurtosis, the mean and variance, coefficient of variation, median, and quartile deviation at some parametric values of several well-known and extensively used probability distributions.
Piecewise linear segmentation of ordered data by a
        dynamic programming algorithm. The algorithm was developed for time
	series data, e.g. growth curves, and for genome-wide read-count data
        from next generation sequencing, but is broadly applicable.
        Generic implementations of dynamic programming routines allow
        to scan for optimal segmentation parameters and test custom
        segmentation criteria ("scoring functions").
Contains functions to perform copula estimation 
	by the non-parametric Bayesian method, 
	Dirichlet-based Polya Tree. See Ning (2018) <doi:10.1080/00949655.2017.1421194>.
A graphical user interface (GUI) to the functions implemented in the R package 'DQAstats'. Publication: Mang et al. (2021) <doi:10.1186/s12911-022-01961-z>.
Perform data quality assessment ('DQA') of electronic health
    records ('EHR'). Publication: Kapsner et al. (2021)
    <doi:10.1055/s-0041-1733847>.
Several fast random number generators are provided as C++
  header only libraries: The PCG family by O'Neill (2014
  <https://www.cs.hmc.edu/tr/hmc-cs-2014-0905.pdf>) as well as
  Xoroshiro128+ and Xoshiro256+ by Blackman and Vigna (2018
  <arXiv:1805.01407>). In addition fast functions for generating random
  numbers according to a uniform, normal and exponential distribution
  are included. The latter two use the Ziggurat algorithm originally
  proposed by Marsaglia and Tsang (2000, <doi:10.18637/jss.v005.i08>).
  The fast sampling methods support unweighted sampling both with and without
  replacement. These functions are exported to R and as a C++ interface and are
  enabled for use with the default 64 bit generator from the PCG family,
  Xoroshiro128+ and Xoshiro256+ as well as the 64 bit version of the 20 rounds
  Threefry engine (Salmon et al., 2011, <doi:10.1145/2063384.2063405>) as
  provided by the package 'sitmo'.
The new (dQTG.seq1 and dQTG.seq2) and existing (SmoothLOD, G', deltaSNP and ED) bulked segregant analysis methods are used to identify various types of quantitative trait loci for complex traits via extreme phenotype individuals in bi-parental segregation populations (F2, backcross, doubled haploid and recombinant inbred line). The numbers of marker alleles in extreme low and high pools are used in existing methods to identify trait-related genes, while the numbers of marker alleles and genotypes in extreme low and high pools are used in the new methods to construct a new statistic Gw for identifying trait-related genes. dQTG-seq2 is feasible to identify extremely over-dominant and small-effect genes in F2. Li P, Li G, Zhang YW, Zuo JF, Liu JY, Zhang YM (2022, <doi: 10.1016/j.xplc.2022.100319>).
Functions, methods, and datasets for fitting dimension
 reduction regression, using slicing (methods SAVE and SIR), Principal
 Hessian Directions (phd, using residuals and the response), and an
 iterative IRE.  Partial methods, that condition on categorical
 predictors are also available.  A variety of tests, and stepwise
 deletion of predictors, is also included.  Also included is
 code for computing permutation tests of dimension.  Adding additional
 methods of estimating dimension is straightforward.
 For documentation, see the vignette in the package.   With version 3.0.4,
 the arguments for dr.step have been modified.
Joint dimension reduction and spatial clustering is conducted for
    Single-cell RNA sequencing and spatial transcriptomics data, and more details can be referred to 
    Wei Liu, Xu Liao, Yi Yang, Huazhen Lin, Joe Yeong, Xiang Zhou, Xingjie Shi and Jin Liu. (2022) <doi:10.1093/nar/gkac219>. It is not only computationally efficient and scalable to the sample size increment, but also is capable of choosing the smoothness parameter and the number of clusters as well.
Models the relationship between dose levels and responses in a pharmacological experiment using the 4 Parameter Logistic model. Traditional packages on dose-response modelling such as 'drc' and 'nplr' often draw errors due to convergence failure especially when data have outliers or non-logistic shapes. This package provides robust estimation methods that are less affected by outliers and other initialization methods that work well for data lacking logistic shapes. We provide the bounds on the parameters of the 4PL model that prevent parameter estimates from diverging or converging to zero and base their justification in a statistical principle. These methods are used as remedies to convergence failure problems.  Gadagkar, S. R. and Call, G. B. (2015) <doi:10.1016/j.vascn.2014.08.006> Ritz, C. and Baty, F. and Streibig, J. C. and Gerhard, D. (2015) <doi:10.1371/journal.pone.0146021>.
Decodes meshes and point cloud data encoded by the Draco mesh
    compression library from Google. Note that this is only designed for basic
    decoding and not intended as a full scale wrapping of the Draco library.
Create, visualize, manipulate, and analyze bipartite mineral-chemistry
    networks for set of focal element(s) across deep-time on Earth. The method is 
    described in Spielman and Moore (2020) <doi:10.3389/feart.2020.585087>.
Statistical tests and test statistics to identify events in a
    dataset that are dragon kings (DKs). The statistical methods in this
    package were reviewed in Wheatley & Sornette (2015) <doi:10.2139/ssrn.2645709>.
These are data sets for the hit TV show, RuPaul's Drag Race. 
    Data right now include episode-level data, contestant-level data, and 
    episode-contestant-level data. This is a work in progress, and a love letter
    of a kind to RuPaul's Drag Race and the performers that have appeared on the show.
    This may not be the most productive use of my time, but I have tenure and what 
    are you going to do about it? I think there is at least some value in this package
    if it allows the show's fandom to learn more about the R programming language 
    around its contents.
Move elements between containers in 'Shiny' without explicitly using 'JavaScript'. It can be used to build custom inputs or to change the positions of user interface elements like plots or tables.
A general-purpose computational engine for data
  analysis, drake rebuilds intermediate data objects when their
  dependencies change, and it skips work when the results are already up
  to date.  Not every execution starts from scratch, there is native
  support for parallel and distributed computing, and completed projects
  have tangible evidence that they are reproducible.  Extensive
  documentation, from beginner-friendly tutorials to practical examples
  and more, is available at the reference website
  <https://docs.ropensci.org/drake/> and the online manual
  <https://books.ropensci.org/drake/>.
Analysis of preprocessed dramatic texts, with respect to literary research. 
  The package provides functions to analyze and visualize information about characters,
  stage directions, the dramatic structure and the text itself.
  The dramatic texts are expected to be in CSV format, which can be installed from within 
  the package, sample texts are provided. The package and the reasoning behind it are described in 
  Reiter et al. (2017) <doi:10.18420/in2017_119>.
Doubly robust average partial effect estimation. This implementation contains methods for adding additional smoothness to plug-in regression procedures and for estimating score functions using smoothing splines. Details of the method can be found in Harvey Klyne and Rajen D. Shah (2023) <arXiv:2308.09207>.
Creation and use of R Repositories via helper functions 
 to insert packages into a repository, and to add repository information 
 to the current R session. Two primary types of repositories are support:
 gh-pages at GitHub, as well as local repositories on either the same machine
 or a local network. Drat is a recursive acronym: Drat R Archive Template.
A set of user-friendly wrapper functions for creating consistent graphics and diagrams with lines, common shapes, text, and page settings.
  Compatible with and based on the R 'grid' package.
An interactive image editing tool that can be added as part of the HTML in Shiny,
    R markdown or any type of HTML document. Often times, plots, photos are embedded
    in the web application/file. 'drawer' can take screenshots of these image-like elements, or 
    any part of the HTML document and send to an image editing space called 'canvas' to allow users 
    immediately edit the screenshot(s) within the same document. Users can quickly 
    combine, compare different screenshots, upload their own images 
    and maybe make a scientific figure.
We present DRaWR, a network-based method for ranking genes or
    properties related to a given gene set. Such related genes or properties are
    identified from among the nodes of a large, heterogeneous network of biological
    information. Our method involves a random walk with restarts, performed on
    an initial network with multiple node and edge types, preserving more of the
    original, specific property information than current methods that operate
    on homogeneous networks. In this first stage of our algorithm, we find the
    properties that are the most relevant to the given gene set and extract a
    subnetwork of the original network, comprising only the relevant properties. We
    then rerank genes by their similarity to the given gene set, based on a second
    random walk with restarts, performed on the above subnetwork.
A tool to sample data with the desired properties.Samples can be 
    drawn by purposive sampling with determining distributional 
    conditions, such as deviation from normality (skewness and kurtosis), 
    and sample size in quantitative research studies.
    For purposive sampling, a researcher has something in mind and participants that 
    fit the purpose of the study are included (Etikan,Musa, & Alkassim, 2015) 
    <doi:10.11648/j.ajtas.20160501.11>.Purposive sampling can be useful for answering
    many research questions (Klar & Leeper, 2019) 
    <doi:10.1002/9781119083771.ch21>.
We offer an implementation of the series representation put 
  forth in "A series representation for multidimensional 
  Rayleigh distributions" by Wiegand and Nadarajah <DOI: 
  10.1002/dac.3510>. Furthermore we have implemented an 
  integration approach proposed by Beaulieu et al. for 3 and 
  4-dimensional Rayleigh densities (Beaulieu, Zhang,  "New 
  simplest exact forms for the 3D and 4D multivariate Rayleigh 
  PDFs with applications to antenna array geometrics", <DOI: 
  10.1109/TCOMM.2017.2709307>).
Feed longitudinal data into a Bayesian Latent Factor Model to obtain 
  a low-rank representation. Parameters are estimated using a Hamiltonian 
  Monte Carlo algorithm with STAN. See G. Weinrott, B. Fontez, N. Hilgert and 
  S. Holmes, "Bayesian Latent Factor Model for Functional Data Analysis", 
  Actes des JdS 2016.
Analysis of dose-response data is made available through a suite of flexible and versatile model fitting and after-fitting functions.
We provide a list of functions for replicating the results of the Monte Carlo simulations and empirical application of Jiang et al. (2022). 
    In particular, we provide corresponding functions for generating the three types of random data described in this paper, as well as all the estimation strategies. 
    Detailed information about the data generation process and estimation strategy can be found in Jiang et al. (2022)  <doi:10.48550/arXiv.2201.13004>.
Utility functions to be used to analyse datasets obtained from seed germination/emergence assays. Fits several types of seed germination/emergence models, including those reported in Onofri et al. (2018) "Hydrothermal-time-to-event models for seed germination", European Journal of Agronomy, 101, 129-139 <doi:10.1016/j.eja.2018.08.011>. Contains several datasets for practicing.
A specific and comprehensive framework for the analyses of time-to-event data in agriculture. Fit non-parametric and parametric time-to-event models. Compare time-to-event curves for different experimental groups. Plots and other displays. It is particularly tailored to the analyses of data from germination and emergence assays. The methods are described in Onofri et al. (2020) "A unified framework for the analysis of germination, emergence, and other time-to-event data in weed science"", Weed Science, 70, 259-271 <doi:10.1017/wsc.2022.8>.
Fit logistic functions to observed dose-response continuous
    data and evaluate goodness-of-fit measures. See Malyutina A., Tang J.,
    and Pessia A. (2023) <doi:10.18637/jss.v106.i04>.
Implements the locally efficient doubly robust difference-in-differences (DiD)
    estimators for the average treatment effect proposed by Sant'Anna and Zhao (2020)
    <doi:10.1016/j.jeconom.2020.06.003>. The estimator combines inverse probability weighting and outcome
    regression estimators (also implemented in the package) to form estimators with
    more attractive statistical properties. Two different estimation methods can be used
    to estimate the nuisance functions.
While it has been well established that drugs affect and help
  patients differently, personalized drug response predictions remain 
  challenging. Solutions based on single omics measurements have been proposed, 
  and networks provide means to incorporate molecular interactions into reasoning. 
  However, how to integrate the wealth of information contained in multiple omics 
  layers still poses a complex problem. 
  We present a novel network analysis pipeline, DrDimont, Drug response prediction 
  from Differential analysis of multi-omics networks. It allows for comparative 
  conclusions between two conditions and translates them into differential drug 
  response predictions. DrDimont focuses on molecular interactions. It establishes 
  condition-specific networks from correlation within an omics layer that are 
  then reduced and combined into heterogeneous, multi-omics molecular networks. 
  A novel semi-local, path-based integration step ensures integrative conclusions. 
  Differential predictions are derived from comparing the condition-specific 
  integrated networks. DrDimont's predictions are explainable, i.e., molecular 
  differences that are the source of high differential drug scores can be retrieved.
  Our proposed pipeline leverages multi-omics data for differential predictions,
  e.g. on drug response, and includes prior information on interactions.
  The case study presented in the vignette uses data published by
  Krug (2020) <doi:10.1016/j.cell.2020.10.036>. The package license applies only
  to the software and explicitly not to the included data.
Implement the statistical test proposed in Weng et al. (2021) to test whether
    the average treatment effect curve is constant and whether a discrete covariate is a significant effect modifier.
Fits (longitudinal) dose-response models utilizing a Bayesian model
  averaging approach as outlined in Gould (2019) <doi:10.1002/bimj.201700211>
  for both continuous and binary responses.  Functions
  for plotting and calculating various posterior quantities
  (e.g. posterior mean, quantiles, probability of minimum efficacious dose,
  etc.) are also implemented.  Copyright Eli Lilly and Company (2019).
Set of tools to facilitate package development and make R a more user-friendly place. Mostly for developers (or anyone who writes/shares functions). Provides a simple, powerful and flexible way to check the arguments passed to functions. 
    The developer can easily describe the type of argument needed. If the user provides a wrong argument, then an informative error message is prompted with the requested type and the problem clearly stated--saving the user a lot of time in debugging.
A penalized/non-penalized implementation for dynamic regression in the presence of autocorrelated residuals (DREGAR) using iterative penalized/ordinary least squares. It applies Mallows CP, AIC, BIC and GCV to select the tuning parameters.
An implementation of distributional random forests as introduced in Cevid & Michel & Meinshausen & Buhlmann (2020) <arXiv:2005.14458>.
Fit restricted mean models for the conditional association
  between an exposure and an outcome, given covariates. Three methods
  are implemented: O-estimation, where a nuisance model for the
  association between the covariates and the outcome is used;
  E-estimation where a nuisance model for the association
  between the covariates and the exposure is used, and doubly robust (DR)
  estimation where both nuisance models are used. In DR-estimation,
  the estimates will be consistent when at least one of the nuisance
  models is correctly specified, not necessarily both. For more information, see Zetterqvist and Sjölander (2015) <doi:10.1515/em-2014-0021>.
Performs the identification of differential risk hotspots (Briz-Redon et al. 2019) <doi:10.1016/j.aap.2019.105278> along a linear network. Given a marked point pattern lying on the linear network, the method implemented uses a network-constrained version of kernel density estimation (McSwiggan et al. 2017) <doi:10.1111/sjos.12255> to approximate the probability of occurrence across space for the type of event specified by the user through the marks of the pattern (Kelsall and Diggle 1995) <doi:10.2307/3318678>. The goal is to detect microzones of the linear network where the type of event indicated by the user is overrepresented.
Tutarials of R learning easily and happily.
Calculates the T-Statistic for the drift burst hypothesis from the working paper Christensen, Oomen and Reno (2018) <DOI:10.2139/ssrn.2842535>. The authors' MATLAB code is available upon request, see: <https://papers.ssrn.com/sol3/papers.cfm?abstract_id=2842535>.
Concept drift refers to the change in the data distribution or 
  in the relationships between variables over time.
  'drifter' calculates distances between variable distributions or 
  variable relations and identifies both types of drift. 
  Key functions are: 
  calculate_covariate_drift() checks distance between corresponding variables in two datasets,
  calculate_residuals_drift() checks distance between residual distributions for two models,
  calculate_model_drift() checks distance between partial dependency profiles for two models,
  check_drift() executes all checks against drift.
  'drifter' is a part of the 'DrWhy.AI' universe (Biecek 2018) <arXiv:1806.08915>.
Provides a R driver for Apache Drill<https://drill.apache.org>, which could connect to the Apache Drill cluster<https://drill.apache.org/docs/installing-drill-on-the-cluster> or drillbit<https://drill.apache.org/docs/embedded-mode-prerequisites> and get result(in data frame) from the SQL query and check the current configuration status. This link <https://drill.apache.org/docs> contains more information about Apache Drill.
Performs the drifting Markov models (DMM) which are 
    non-homogeneous Markov models designed for modeling the heterogeneities of
    sequences in a more flexible way than homogeneous Markov chains or even 
    hidden Markov models. In this context, we developed an R package dedicated to 
    the estimation, simulation and the exact computation of associated reliability 
    of drifting Markov models. The implemented methods are described in
    Vergne, N. (2008), <doi:10.2202/1544-6115.1326> and
    Barbu, V.S., Vergne, N. (2019) <doi:10.1007/s11009-018-9682-8> .
R codes for imputing dropout events. Many statistical methods in cell type identification, visualization and lineage reconstruction do not account for dropout events ('PCAreduce', 'SC3', 'PCA', 't-SNE', 'Monocle', 'TSCAN', etc). 'DrImpute' can improve the performance of such software by imputing dropout events.
This is a collection of functions for discontinuous regression
	     analysis and image processing (DRIP). This version removes the
	     dependence on the GNU Scientific Library.
Cancer genomes contain large numbers of somatic alterations but few
    genes drive tumor development. Identifying cancer driver genes is critical 
    for precision oncology. Most of current approaches either identify driver 
    genes based on mutational recurrence or using estimated scores predicting 
    the functional consequences of mutations. 'driveR' is a tool for 
    personalized or batch analysis of genomic data for driver gene prioritization 
    by combining genomic information and prior biological knowledge. As features, 
    'driveR' uses coding impact metaprediction scores, non-coding impact scores, 
    somatic copy number alteration scores, hotspot gene/double-hit gene 
    condition, 'phenolyzer' gene scores and memberships to cancer-related KEGG 
    pathways. It uses these features to estimate cancer-type-specific 
    probability for each gene of being a cancer driver using the related task of 
    a multi-task learning classification model. The method is described in detail 
    in Ulgen E, Sezerman OU. 2021. driveR: driveR: a novel method for 
    prioritizing cancer driver genes using somatic genomics data. BMC 
    Bioinformatics <doi:10.1186/s12859-021-04203-7>.
A toolkit for parsing dice notation, analyzing rolls,
    calculating success probabilities, and plotting outcome distributions.
Several functions are provided for dose-response (or concentration-response) characterization from omics data. 'DRomics' is especially dedicated to omics data obtained using a typical dose-response design, favoring a great number of tested doses (or concentrations) rather than a great number of replicates (no need of replicates). 'DRomics' provides functions 1) to check, normalize and or transform data, 2) to select monotonic or biphasic significantly responding items (e.g. probes, metabolites), 3) to choose the best-fit model among a predefined family of monotonic and biphasic models to describe each selected item, 4) to derive a benchmark dose or concentration and a typology of response from each fitted curve. In the available version data are supposed to be single-channel microarray data in log2, RNAseq data in raw counts, or already pretreated continuous omics data (such as metabolomic data) in log scale. In order to link responses across biological levels based on a common method, 'DRomics' also handles apical data as long as they are continuous and follow a normal distribution for each dose or concentration, with a common standard error. For further details see Larras et al (2018) <DOI:10.1021/acs.est.8b04752> at <https://hal.archives-ouvertes.fr/hal-02309919>.
Offers robust tools to identify and manage incomplete responses in survey datasets, thereby enhancing the quality and reliability of research findings.
Generates simulated data representing the LOX drop testing
    process (also known as impact testing). A simulated process allows for
    accelerated study of test behavior. Functions are provided to simulate
    trials, test series, and groups of test series. Functions for creating plots
    specific to this process are also included. Test attributes and criteria can
    be set arbitrarily. This work is not endorsed by or affiliated with NASA.
    See "ASTM G86-17, Standard Test Method for Determining Ignition Sensitivity
    of Materials to Mechanical Impact in Ambient Liquid Oxygen and Pressurized
    Liquid and Gaseous Oxygen Environments" <doi:10.1520/G0086-17>.
Efficient covariate-adjusted estimators of quantities that are useful for 
    establishing the effects of treatments on ordinal outcomes.
Provide tools for drought monitoring based on univariate and multivariate drought indicators.Statistical drought prediction based on Ensemble Streamflow Prediction (ESP), drought risk assessments, and drought propagation are also provided. Please see Hao Zengchao et al. (2017) <doi:10.1016/j.envsoft.2017.02.008>.
Estimation of the total population size from capture-recapture data efficiently and with low bias implementing the methods from Das M, Kennedy EH, and Jewell NP (2021) <arXiv:2104.14091>. The estimator is doubly robust against errors in the estimation of the intermediate nuisance parameters. Users can choose from the flexible estimation models provided in the package, or use any other preferred model.
Several quality measurements for investigating the performance of dimensionality reduction methods are provided here. In addition a new quality measurement called Gabriel classification error is made accessible, which was published in Thrun, M. C., Märte, J., & Stier, Q: "Analyzing Quality Measurements for Dimensionality Reduction" (2023), Machine Learning and Knowledge Extraction (MAKE), <DOI:10.3390/make5030056>.
An Implementation of Dimensionality Reduction
    via Regression using Kernel Ridge Regression.
Targeted minimum loss-based estimators of counterfactual means and
    causal effects that are doubly-robust with respect both to consistency and
    asymptotic normality (Benkeser et al (2017), <doi:10.1093/biomet/asx053>; MJ
    van der Laan (2014), <doi:10.1515/ijb-2012-0038>).
Performs drug demand forecasting by modeling drug dispensing data while taking into account predicted enrollment and treatment discontinuation dates. The number of skipped visits and the number of dispensed doses are modeled using zero-inflated Poisson or zero-inflated negative binomial distributions (Zeileis, Kleiber & Jackman (2008) <doi:10.18637/jss.v027.i08>) and a linear mixed-effects model (McCulloch & Searle (2001, ISBN:0-471-19364-X)), respectively.
Ingredient specific diagnostics for drug exposure records in the Observational Medical Outcomes Partnership (OMOP) common data model.
Prepare prescription data (such as from the Clinical Practice Research Datalink) into an analysis-ready format, with start and stop dates for each patient's prescriptions. Based on Pye et al (2018) <doi:10.1002/pds.4440>.
A systematic biology tool was developed to repurpose drugs via a drug-drug functional similarity network. 'DrugSim2DR' first predict drug-drug functional similarity  in the context of specific disease, and then using the similarity constructed a weighted drug similarity network. Finally, it used a network propagation algorithm on the network to identify drugs with significant target abnormalities as candidate drugs.
Summarise patient-level drug utilisation cohorts using data mapped 
    to the Observational Medical Outcomes Partnership (OMOP) common data model. 
    New users and prevalent users cohorts can be generated and their 
    characteristics, indication and drug use summarised.
Includes various functions for playing drum sounds. beat() plays a drum sound
  from one of the six included drum kits. tempo() sets spacing between calls to beat()
  in bpm. Together the two functions can be used to create many different drum patterns.
A systematic biology tool was developed to repurpose drugs via a subpathway crosstalk network. The operation modes include 1) calculating centrality scores of SPs in the context of gene expression data to reflect the influence of SP crosstalk, 2) evaluating drug-disease reverse association based on disease- and drug-induced SPs weighted by the SP crosstalk, 3) identifying cancer candidate drugs through perturbation analysis. There are also several functions used to visualize the results.
Performs various analyzes of descriptive statistics, including correlations, graphics and tables.
All datasets and functions required for the examples and exercises of the book "Data Science for Psychologists" (by Hansjoerg Neth, Konstanz University, 2022), available at <https://bookdown.org/hneth/ds4psy/>. The book and course introduce principles and methods of data science to students of psychology and other biological or social sciences. The 'ds4psy' package primarily provides datasets, but also functions for data generation and manipulation (e.g., of text and time data) and graphics that are used in the book and its exercises. All functions included in 'ds4psy' are designed to be explicit and instructive, rather than efficient or elegant.
Seasonal- and calendar adjustment of time series
    with daily frequency using the DSA approach developed by Ollech,
    Daniel (2018): Seasonal adjustment of daily time series. Bundesbank
    Discussion Paper 41/2018.
Exploration of simulation models (apps) of various infectious disease transmission dynamics scenarios.
    The purpose of the package is to help individuals learn 
    about infectious disease epidemiology (ecology/evolution) from a dynamical systems perspective.
    All apps include explanations of the underlying models and instructions on what to do with the models.
Simulation models (apps) of various within-host immune response scenarios.
    The purpose of the package is to help individuals learn 
    about within-host infection and immune response modeling from a dynamical systems perspective.
    All apps include explanations of the underlying models and instructions on what to do with the models.
Providing six different algorithms that can be used to split the 
    available data into training, test and validation subsets with similar distribution 
    for hydrological model developments. The dataSplit() function will help you divide 
    the data according to specific requirements, and you can refer to the par.default() 
    function to set the parameters for data splitting. The getAUC() function will help 
    you measure the similarity of distribution features between the data subsets.
    For more information about the data splitting algorithms, please refer to:
    Chen et al. (2022) <doi:10.1016/j.jhydrol.2022.128340>, 
    Zheng et al. (2022) <doi:10.1029/2021WR031818>.
Discretization-based random sampling algorithm that is useful for a complex model in high dimension is implemented. The normalizing constant of a target distribution is not needed. Posterior summaries are compared with those by 'OpenBUGS'. The method is described: Wang and Lee (2014) <doi:10.1016/j.csda.2013.06.011> and exercised in Lee (2009) <http://hdl.handle.net/1993/21352>.
This lightweight R package provides a method for normalizing and denoising protein expression data from droplet based single cell experiments. Raw protein Unique Molecular Index (UMI) counts from sequencing DNA-conjugated antibody derived tags (ADT) in droplets (e.g. 'CITE-seq') have substantial measurement noise. Our experiments and computational modeling revealed two major components of this noise: 1) protein-specific noise originating from ambient, unbound antibody encapsulated in droplets that can be accurately inferred via the expected protein counts detected in empty droplets, and 2) droplet/cell-specific noise revealed via the shared variance component associated with isotype antibody controls and background protein counts in each cell. This package normalizes and removes both of these sources of noise from raw protein data derived from methods such as 'CITE-seq', 'REAP-seq', 'ASAP-seq', 'TEA-seq', 'proteogenomic' data from the Mission Bio platform, etc. See the vignette for tutorials on how to integrate dsb with 'Seurat' and 'Bioconductor' and how to use dsb in 'Python'. Please see our paper Mulè M.P., Martins A.J., and Tsang J.S. Nature Communications 2022 <https://www.nature.com/articles/s41467-022-29356-8> for more details on the method.
Calculate posterior modes and credible intervals of parameters of the Dixon-Simon model for subgroup analysis (with binary covariates) in clinical trials. For details of the methodology, please refer to D.O. Dixon and R. Simon (1991), Biometrics, 47: 871-881.
The D-score is a quantitative measure of child development. 
    The D-score follows the Rasch model. See Jacobusse, van Buuren and 
    Verkerk (2006) <doi:10.1002/sim.2351>. The user can convert 
    milestone scores from many assessment instruments into the D-score 
    and the DAZ (D-score adjusted for age). Several tools assist in 
    mapping milestone names into the 9-position Global Scale of Early 
    Development (GSED) convention. Supports calculation of the D-score 
    using 'dutch' <doi:10.1177/0962280212473300>, 
    'gcdg' <doi:10.1136/bmjgh-2019-001724> and 'gsed' conversion keys.
    The user can calculate DAZ using 'phase1' (default), 'gcdg' and 'dutch' 
    age-conditional references.
The models of probability density functions are Gaussian or
    exponential distributions with polynomial correction terms.
    Using a maximum likelihood method, 'dsdp' computes parameters of Gaussian
    or exponential distributions together with degrees of polynomials by
    a grid search, and coefficient of polynomials by a variant of semidefinite
    programming. It adopts Akaike Information Criterion for model selection.
    See a vignette for a tutorial and more on our 'Github' repository 
    <https://github.com/tsuchiya-lab/dsdp/>.
Tools for multivariate, linear, time-invariant,
	time series models. This includes ARMA and state-space representations,
	and methods for converting between them. It also includes simulation
	methods and several estimation functions. The package has functions 
	for looking at model roots, stability, and forecasts at different 
	horizons. The ARMA model representation is general, so that VAR, VARX, 
	ARIMA, ARMAX, ARIMAX can all be considered to be special cases. Kalman
	filter and smoother estimates can be obtained from the state space
	model, and state-space model reduction techniques are implemented. 
	An introduction and User's Guide is available in a vignette.
Framework to fit distributional stochastic frontier models. Casts the stochastic frontier model into the flexible framework of distributional regression or otherwise known as General Additive Models of Location, Scale and Shape (GAMLSS). Allows for linear, non-linear, random and spatial effects on all the parameters of the distribution of the output, e.g. effects on the production or cost function, heterogeneity of the noise and inefficiency. Available distributions are the normal-halfnormal and normal-exponential distribution. Estimation via the fast and reliable routines of the 'mgcv' package. For more details see <doi:10.1016/j.csda.2023.107796>.
'DataSHIELD' is an infrastructure and series of R packages that 
    enables the remote and 'non-disclosive' analysis of sensitive research data. 
    This package defines the API that is to be implemented by 'DataSHIELD' compliant 
    data repositories.
Dataset containing information about job listings for data science job roles.
An abstract DList class helps storing large list-type objects in a distributed manner. Corresponding high-level functions and methods for handling distributed storage (DStorage) and lists allows for processing such DLists on distributed systems efficiently. In doing so it uses a well defined storage backend implemented based on the DStorage class.
Datasets and functions that can be used for data analysis practice, homework and projects in data science courses and workshops. 26 datasets are available for case studies in data visualization, statistical inference, modeling, linear regression, data wrangling and machine learning.
Dynamic slicing is a method designed for dependency detection between a categorical variable and a continuous variable. It could be applied for non-parametric hypothesis testing and gene set enrichment analysis.
'DataSHIELD' is an infrastructure and series of R packages that 
    enables the remote and 'non-disclosive' analysis of sensitive research data.
    This 'DataSHIELD Interface' implementation is for analyzing datasets living
    in the current R session. The purpose of this is primarily for lightweight
    'DataSHIELD' analysis package development.
Density surface modelling of line transect data. A Generalized
    Additive Model-based approach is used to calculate spatially-explicit estimates
    of animal abundance from distance sampling (also presence/absence and strip
    transect) data. Several utility functions are provided for model checking,
    plotting and variance estimation.
Tool collection for common and not so common data science use cases. This includes 
    custom made algorithms for data management as well as value calculations that are hard to find 
    elsewhere because of their specificity but would be a waste to get lost nonetheless. 
    Currently available functionality: find
    sub-graphs in an edge list data.frame, find mode or modes in a vector of values, extract 
    (a) specific regular expression group(s), generate ISO time stamps that play well with 
    file names, or generate URL parameter lists by expanding value combinations.
Performs parametric and non-parametric estimation and simulation of 
    drifting semi-Markov processes. The definition of parametric and non-parametric
    model specifications is also possible. Furthermore, three different types of
    drifting semi-Markov models are considered. These models differ in the number
    of transition matrices and sojourn time distributions used for the computation
    of a number of semi-Markov kernels, which in turn characterize the drifting 
    semi-Markov kernel. For the parametric model estimation and specification, 
    several discrete distributions are considered for the sojourn times: Uniform,
    Poisson, Geometric, Discrete Weibull and Negative Binomial. The non-parametric
    model specification makes no assumptions about the shape of the sojourn time
    distributions. Semi-Markov models are described in:
    Barbu, V.S., Limnios, N. (2008) <doi:10.1007/978-0-387-73173-5>.
    Drifting Markov models are described in:
    Vergne, N. (2008) <doi:10.2202/1544-6115.1326>.
    Reliability indicators of Drifting Markov models are described in:
    Barbu, V. S., Vergne, N. (2019) <doi:10.1007/s11009-018-9682-8>. 
    We acknowledge the DATALAB Project
    <https://lmrs-num.math.cnrs.fr/projet-datalab.html> (financed by the
    European Union with the European Regional Development fund (ERDF) and by
    the Normandy Region) and the HSMM-INCA Project (financed by the French
    Agence Nationale de la Recherche (ANR) under grant ANR-21-CE40-0005).
'DataSHIELD' is an infrastructure and series of R packages that 
    enables the remote and 'non-disclosive' analysis of sensitive research data.
    This package is the 'DataSHIELD' interface implementation to analyze data
    shared on a 'MOLGENIS Armadillo' server. 'MOLGENIS Armadillo' is a
    light-weight 'DataSHIELD' server using a file store and an 'RServe' server.
'DataSHIELD' is an infrastructure and series of R packages that 
    enables the remote and 'non-disclosive' analysis of sensitive research data.
    This package is the 'DataSHIELD' interface implementation for 'Opal', which is
    the data integration application for biobanks by 'OBiBa'. Participant data, once
    collected from any data source, must be integrated and stored in a central
    data repository under a uniform model. 'Opal' is such a central repository.
    It can import, process, validate, query, analyze, report, and export data.
    'Opal' is the reference implementation of the 'DataSHIELD' infrastructure.
Test for no adverse shift in two-sample comparison when we
    have a training set, the reference distribution, and a test set. The
    approach is flexible and relies on a robust and powerful test
    statistic, the weighted AUC. Technical details are in Kamulete, V. M.
    (2021) <arXiv:1908.04000>. Modern notions of outlyingness such as
    trust scores and prediction uncertainty can be used as the underlying
    scores for example.
You can retrieve 'Spotify' API Information such as artists, albums, tracks, features tracks, recommendations or related artists.
    This package allows you to search all the information by name and also includes a distance based algorithm to find similar songs.
	More information: <https://developer.spotify.com/documentation/web-api/> .
Perform a test of a simple null hypothesis about a 
    directly standardized rate and obtain the matching confidence 
    interval using a choice of methods.
The purpose of this package is to provide a comprehensive
    R interface to the Decision Support System for Agrotechnology
    Transfer Cropping Systems Model (DSSAT-CSM; see <https://dssat.net> for more information).
    The package provides cross-platform functions to read and
    write input files, run DSSAT-CSM, and read output files.
Draw samples from the direct sampling spatial prior model as
    described in G. White, D. Sun, P. Speckman (2019) <arXiv:1906.05575>. The basic model assumes a Gaussian
    likelihood and derives a spatial prior based on thin-plate splines.
Using the Theory of Belief Functions for evidence calculus. Basic probability assignments, or mass functions, can be defined on the subsets of a set of possible values and combined. A mass function can be extended to a larger frame. Marginalization, i.e. reduction to a smaller frame can also be done. These features can be combined to analyze small belief networks and take into account situations where information cannot be satisfactorily described by probability distributions.
Probability generating function,  formulae for the probabilities (discrete density) and random generation for discrete stable random variables.
A collection of functions to estimate parameters of a diffusion model via a D*M analysis. Build in models are: the Ratcliff diffusion model, the RWiener diffusion model, and Linear Ballistic Accumulator models. Custom models functions can be specified as long as they have a density function.
A d-statistic tests the null hypothesis of no treatment effect in a matched, nonrandomized study of the effects caused by treatments.  A d-statistic focuses on subsets of matched pairs that demonstrate insensitivity to unmeasured bias in such an observational study, correcting for double-use of the data by conditional inference. This conditional inference can, in favorable circumstances, substantially increase the power of a sensitivity analysis (Rosenbaum (2010) <doi:10.1007/978-1-4419-1213-8_14>).  There are two examples, one concerning unemployment from Lalive et al. (2006) <doi:10.1111/j.1467-937X.2006.00406.x>, the other concerning smoking and periodontal disease from Rosenbaum (2017) <doi:10.1214/17-STS621>.
For an observational study with binary treatment, binary outcome and K strata, implements a d-statistic that uses those strata most insensitive to unmeasured bias in treatment assignment.<doi:10.1093/biomet/asaa032>  The package has one function, dstat2x2xk.
Simultaneously detect the number and locations of change points in piecewise linear models under stationary Gaussian noise allowing autocorrelated random noise. The core idea is to transform the problem of detecting change points into the detection of local extrema (local maxima and local minima)through kernel smoothing and differentiation of the data sequence, see Cheng et al. (2020) <doi:10.1214/20-EJS1751>. A low-computational and fast algorithm call 'dSTEM' is introduced to detect change points based on the 'STEM' algorithm in D. Cheng and A. Schwartzman (2017) <doi:10.1214/16-AOS1458>.
Functions for direct surrogate variable analysis, which can identify hidden factors in high-dimensional biomedical data.
Data science methods used in wind energy applications. 
              Current functionalities include creating a multi-dimensional power curve model, 
              performing power curve function comparison, covariate matching, and energy decomposition. 
              Relevant works for the developed functions are: 
              funGP() - Prakash et al. (2022) <doi:10.1080/00401706.2021.1905073>, 
              AMK() - Lee et al. (2015) <doi:10.1080/01621459.2014.977385>, 
              tempGP() - Prakash et al. (2022) <doi:10.1080/00401706.2022.2069158>, 
              ComparePCurve() - Ding et al. (2021) <doi:10.1016/j.renene.2021.02.136>,
              deltaEnergy() - Latiffianti et al. (2022) <doi:10.1002/we.2722>,
              syncSize() - Latiffianti et al. (2022) <doi:10.1002/we.2722>,
              imptPower() - Latiffianti et al. (2022) <doi:10.1002/we.2722>,
              All other functions - Ding (2019, ISBN:9780429956508).
Data objects in R can be rendered as HTML tables using the
    JavaScript library 'DataTables' (typically via R Markdown or Shiny). The
    'DataTables' library has been included in this R package. The package name
    'DT' is an abbreviation of 'DataTables'.
Deconvolving cell types from high-throughput gene profiling data. For more information on dtangle see Hunt et al. (2019) <doi:10.1093/bioinformatics/bty926>.
Function to create forest plots. Functions to use posterior samples from Bayesian bivariate meta-analysis model, Bayesian hierarchical summary receiver operating characteristic (HSROC) meta-analysis model or Bayesian latent class (LC) meta-analysis model to create Summary Receiver Operating Characteristic (SROC) plots using methods described by Harbord et al (2007)<doi:10.1093/biostatistics/kxl004>.
Dose Titration Algorithm Tuning (DTAT) is a methodologic framework
             allowing dose individualization to be conceived as a continuous
             learning process that begins in early-phase clinical trials and
             continues throughout drug development, on into clinical practice.
             This package includes code that researchers may use to reproduce
             or extend key results of the DTAT research programme, plus tools
             for trialists to design and simulate a '3+3/PC' dose-finding study.
             Please see Norris (2017a) <doi:10.12688/f1000research.10624.3> and
             Norris (2017c) <doi:10.1101/240846>.
To calculate the sensitivity and specificity in the absence of gold standard using the Bayesian method.
    The Bayesian method can be referenced at Haiyan Gu and Qiguang Chen (1999) <doi:10.3969/j.issn.1002-3674.1999.04.004>.
Implement weighted higher-order initialization and angle-based iteration for multi-way spherical clustering under degree-corrected tensor block model. See reference Jiaxin Hu and Miaoyan Wang (2023) <doi:10.1109/TIT.2023.3239521>.
Comparison of the accuracy of two binary diagnostic tests in a "paired" study design, i.e. when each test is applied to each subject in the study.
Provides fast methods to work with Merton's distance to default 
  model introduced in Merton (1974) <doi:10.1111/j.1540-6261.1974.tb03058.x>. 
  The methods includes simulation and estimation of the parameters.
Implementation of different algorithms for analyzing
        randomly truncated data, one-sided and two-sided (i.e. doubly)
        truncated data. It serves to compute empirical cumulative 
        distributions and also kernel density and hazard functions 
        using different bandwidth selectors.
      Several real data sets are included.
Nonparametric estimator of the cumulative incidences of competing risks under double truncation. The estimator generalizes the Efron-Petrosian NPMLE (Non-Parametric Maximun Likelihood Estimator) to the competing risks setting. Efron, B. and Petrosian, V. (1999) <doi:10.2307/2669997>.
Non-iterative estimator for the cumulative distribution of a doubly truncated variable. de Uña-Álvarez J. (2018) <doi:10.1007/978-3-319-73848-2_37>.
The Discrete Transmuted Generalized Inverse Weibull (DTGIW) distribution is a new distribution for count data analysis. The DTGIW is discrete distribution based on Atchanut and Sirinapa (2021). <DOI: 10.14456/sjst-psu.2021.149>.
Diffusion Weighted Imaging (DWI) is a Magnetic Resonance Imaging
             modality, that measures diffusion of water in tissues like the human
             brain. The package contains R-functions to process diffusion-weighted
             data. The functionality includes diffusion tensor imaging (DTI),
             diffusion kurtosis imaging (DKI), modeling for high angular resolution
             diffusion weighted imaging (HARDI) using Q-ball-reconstruction and
             tensor mixture models, several methods for structural adaptive
             smoothing including POAS and msPOAS, and a streamline fiber tracking
             for tensor and tensor mixture models.
             The package provides functionality to manipulate and visualize results
             in 2D and 3D.
A series of functions which aid in both simulating and determining the properties of finite, discrete-time, discrete state markov chains.  Two functions (DTMC, MultDTMC) produce n iterations of a Markov Chain(s)  based on transition probabilities and an initial distribution.  The function FPTime determines the first passage time into each state.  The function statdistr determines the stationary distribution of a Markov Chain.
Compute the dynamic threshold panel model suggested by (Stephanie Kremer, Alexander Bick and Dieter Nautz (2013) <doi:10.1007/s00181-012-0553-9>) in which they extended the (Hansen (1999) <doi: 10.1016/S0304-4076(99)00025-1>) original static panel threshold estimation and the Caner and (Hansen (2004) <doi:10.1017/S0266466604205011>) cross-sectional instrumental variable threshold model, where generalized methods of moments type estimators are used.
Provides the dose transition pathways (DTP) to project in advance
    the doses recommended by a model-based design for subsequent patients (stay,
    escalate, deescalate or stop early) using all the accumulated toxicity
    information; See Yap et al (2017) <doi: 10.1158/1078-0432.CCR-17-0582>. DTP
    can be used as a design and an operational tool and can be displayed as a
    table or flow diagram. The 'dtpcrm' package also provides the modified
    continual reassessment method (CRM) and time-to-event CRM (TITE-CRM) with
    added practical considerations to allow stopping early when there is
    sufficient evidence that the lowest dose is too toxic and/or there is a
    sufficient number of patients dosed at the maximum tolerated dose.
Provides a data.table backend for 'dplyr'. The goal of
    'dtplyr' is to allow you to write 'dplyr' code that is automatically
    translated to the equivalent, but usually much faster, data.table
    code.
Track and
    document 'dplyr' data pipelines. As you filter, mutate, and join your
    way through a data set, 'dtrackr' seamlessly keeps track of your data
    flow and makes publication ready documentation of a data pipeline simple.
Methods to estimate the optimal treatment regime among all linear regimes via smoothed estimation methods, and construct element-wise confidence intervals for the optimal linear treatment regime vector, as well as the confidence interval for the optimal value via wild bootstrap procedures, if the population follows treatments recommended by the optimal linear regime. See more details in: Wu, Y. and Wang, L. (2021), "Resampling-based Confidence Intervals for Model-free Robust Inference on Optimal Treatment Regimes", Biometrics, 77: 465– 476, <doi:10.1111/biom.13337>.
We provide a comprehensive software to estimate general K-stage DTRs from SMARTs with Q-learning and a variety of outcome-weighted learning methods. Penalizations are allowed for variable selection and model regularization. With the outcome-weighted learning scheme, different loss functions - SVM hinge loss, SVM ramp loss, binomial deviance loss, and L2 loss - are adopted to solve the weighted classification problem at each stage; augmentation in the outcomes is allowed to improve efficiency. The estimated DTR can be easily applied to a new sample for individualized treatment recommendations or DTR evaluation.
Dynamic treatment regime estimation and inference via G-estimation, dynamic weighted ordinary least squares (dWOLS) and Q-learning. Inference via bootstrap and (for G-estimation) recursive sandwich estimation. Estimation and inference for survival outcomes via Dynamic Weighted Survival Modeling (DWSurv). Extension to continuous treatment variables (gdwols). Wallace et al. (2017) <DOI:10.18637/jss.v080.i02>; Simoneau et al. (2020) <DOI:10.1080/00949655.2020.1793341>.
Provides methods for estimating multi-stage optimal dynamic treatment regimes for survival outcomes with dependent censoring. Cho, H., Holloway, S. T., and Kosorok, M. R. (2020) <arXiv:2012.03294>.
It is a novel tool used to identify the candidate drugs against a particular disease based on the drug target set enrichment analysis. It assumes the most effective drugs are those with a closer affinity in the protein-protein interaction network to the specified disease. (See Gómez-Carballa et al. (2022) <doi: 10.1016/j.envres.2022.112890> and Feng et al. (2022) <doi: 10.7150/ijms.67815> for disease expression profiles; see Wishart et al. (2018) <doi: 10.1093/nar/gkx1037> and Gaulton et al. (2017) <doi: 10.1093/nar/gkw1074> for drug target information; see Kanehisa et al. (2021) <doi: 10.1093/nar/gkaa970> for the details of KEGG database.)
Basic time series functionalities such as listing of missing
    values, application of arbitrary aggregation as well as rolling (asymmetric)
    window functions and automatic detection of periodicity. As it is mainly
    based on 'data.table', it is fast and (in combination with the 'R6' package)
    offers reference semantics. In addition to its native R6 interface, it
    provides an S3 interface for those who prefer the latter. Finally yet
    importantly, its functional approach allows for incorporating
    functionalities from many other packages.
This package provides functions for 1D and 2D Discrete
        Cosine Transform (DCT), Discrete Sine Transform (DST) and
        Discrete Hartley Transform (DHT).
Manipulates date ('Date'), date time ('POSIXct') and time
    ('hms') vectors.  Date/times are considered discrete and are floored
    whenever encountered.  Times are wrapped and time zones are maintained
    unless explicitly altered by the user.
High-frequency time-series support via 'nanotime' and 'data.table'.
A comprehensive implementation of dynamic time warping
    (DTW) algorithms in R.  DTW computes the optimal (least cumulative
    distance) alignment between points of two time series.  Common DTW
    variants covered include local (slope) and global (window)
    constraints, subsequence matches, arbitrary distance definitions,
    normalizations, minimum variance matching, and so on.  Provides
    cumulative distances, alignments, specialized plot styles, etc.,
    as described in Giorgino (2009) <doi:10.18637/jss.v031.i07>.
Functions to impute large gaps within time series based on Dynamic Time Warping methods. It contains all required functions to create large missing consecutive values within time series and to fill them, according to the paper Phan et al. (2017), <DOI:10.1016/j.patrec.2017.08.019>. Performance criteria are added to compare similarity between two signals (query and reference).
Time series clustering along with optimized techniques related
    to the Dynamic Time Warping distance and its corresponding lower bounds.
    Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole
    clustering are available. Functionality can be easily extended with
    custom distance measures and centroid definitions. Implementations of
    DTW barycenter averaging, a distance based on global alignment kernels,
    and the soft-DTW distance and centroid routines are also provided. 
    All included distance functions have custom loops optimized for the 
    calculation of cross-distance matrices, including parallelization support.
    Several cluster validity indices are included.
Provides functionality for users who are learning R or the techniques of data analysis.  Written as a collection of wrapper functions, the 'DTwrapper' package facilitates many core operations of data processing.  This is achieved with relatively few requirements about the order of the processing steps or knowledge of specialized syntax.  'DTwrappers' creates coding results along with translations to data.table's code.  This enables users to benefit from the speed and efficiency of data.table's calculations.  Furthermore, the package also provides the translated code for educational purposes so that users can review working examples of coding syntax and calculations.
Provides a robust approach to land use mapping using multi-dimensional 
    (multi-band) satellite image time series. By leveraging the Time-Weighted Dynamic 
    Time Warping (TWDTW) distance metric in tandem with a 1 Nearest-Neighbor (1-NN) Classifier,
    this package offers functions to produce land use maps based on distinct seasonality patterns, 
    commonly observed in the phenological cycles of vegetation. The approach is described in 
    Maus et al. (2016) <doi:10.1109/JSTARS.2016.2517118> and Maus et al. (2019) <doi:10.18637/jss.v088.i05>.
    A primary advantage of TWDTW is its capability to handle irregularly sampled and noisy time series, 
    while also requiring minimal training sets. The package includes tools for training the 1-NN-TWDTW model, 
    visualizing temporal patterns, producing land use maps, and visualizing the results.
Functions to impute large gaps within multivariate time series based on Dynamic Time Warping methods. Gaps of size 1 or inferior to a defined threshold are filled using simple average and weighted moving average respectively. Larger gaps are filled using the methodology provided by Phan et al. (2017) <DOI:10.1109/MLSP.2017.8168165>: a query is built immediately before/after a gap and a moving window is used to find the most similar sequence to this query using Dynamic Time Warping. To lower the calculation time, similar sequences are pre-selected using global features. Contrary to the univariate method (package 'DTWBI'), these global features are not estimated over the sequence containing the gap(s), but a feature matrix is built to summarize general features of the whole multivariate signal. Once the most similar sequence to the query has been identified, the adjacent sequence to this window is used to fill the gap considered. This function can deal with multiple gaps over all the sequences componing the input multivariate signal. However, for better consistency, large gaps at the same location over all sequences should be avoided.
Automatic differentiation is achieved by using dual numbers without
  providing hand-coded gradient functions. The output value of a mathematical 
  function is returned with the values of its exact first derivative 
  (or gradient). For more details see Baydin, Pearlmutter, Radul, and Siskind
  (2018) <https://jmlr.org/papers/volume18/17-468/17-468.pdf>.
Provides a series of functions for fitting a dual sparse partial least squares (Dual-SPLS) regression. These functions differ by the choice of the underlying norm.
An implementation of the decimated two-dimensional complex dual-tree wavelet transform as described in Kingsbury (1999) <doi:10.1098/rsta.1999.0447> and Selesnick et al. (2005) <doi:10.1109/MSP.2005.1550194>. Also includes the undecimated version and spectral bias correction described in Nelson et al. (2018) <doi:10.1007/s11222-017-9784-0>. The code is partly based on the 'dtcwt' Python library.
Create shareable data sets from raw data files that
	     contain protected elements. Relying on master crosswalk
	     files that list restricted variables, package functions
	     warn users about possible violations of data usage
	     agreement and prevent writing protected elements.
Provides an operator for assigning nested components of a list to
  names via a concise pattern matching syntax. This is especially convenient for
  assigning individual names to the multiple values that a function may return
  in the form of a list, and for extracting deeply nested list components.
The DuckDB project is an embedded analytical data
    management system with support for the Structured Query Language (SQL). This package includes all of
    DuckDB and a R Database Interface (DBI) connector.
Provides friendly wrappers for creating 'duckdb'-backed connections
  to tabular datasets ('csv', parquet, etc) on local or remote file systems.
  This mimics the behaviour of "open_dataset" in the 'arrow' package, 
  but in addition to 'S3' file system also generalizes to any list of 'http' URLs.
Programmatic access to the DuckDuckGo Instant Answer API <https://api.duckduckgo.com/api>.
A drop-in replacement for 'dplyr', powered by 'DuckDB' for performance.
    Also defines a set of generics that provide a low-level
    implementer's interface for the high-level user interface of 'dplyr'.
Generates visualizations with Duke’s official suite of colors in a color blind friendly way.
Efficiently create dummies of all factors and character vectors in a data frame. Support is included for learning the categories on one data set (e.g., a training set) and deploying them on another (e.g., a test set).
Provides functions to randomly select, return, and print
  quotes or entire scenes from the American version of
  the show the Office. Receive laughs from one of of the 
  greatest sitcoms of all time on demand. Add these functions 
  to your  '.Rprofile' to get a good laugh everytime you start
  a new R session.
Computes Dunn's test (1964) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. 'dunn.test' makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. 'dunn.test' accounts for tied ranks.
Identifies code blocks that have a high level of similarity
  within a set of R files.
An easy-to-use yet powerful system for plotting grouped data effect sizes.
    Various types of effect size can be estimated, then plotted together with a
    representation of the original data. Select from many possible data representations
    (box plots, violin plots, raw data points etc.), and combine as desired.
    'Durga' plots are implemented in base R, so are compatible with base R methods
    for combining plots, such as 'layout()'. See Khan & McLean (2023) 
    <doi:10.1101/2023.02.06.526960>.
Functionality for analyzing dose-volume histograms (DVH)
        in radiation oncology: Read DVH text files, calculate DVH
        metrics as well as generalized equivalent uniform dose (gEUD),
        biologically effective dose (BED), equivalent dose in 2 Gy
        fractions (EQD2), normal tissue complication probability
        (NTCP), and tumor control probability (TCP). Show DVH
        diagrams, check and visualize quality assurance constraints
        for the DVH. Includes web-based graphical user interface.
Joint DNA-based disaster victim identification (DVI), as
    described in Vigeland and Egeland (2021)
    <doi:10.21203/rs.3.rs-296414/v1>. Identification is performed by
    optimising the joint likelihood of all victim samples and reference
    individuals. Individual identification probabilities, conditional on
    all available information, are derived from the joint solution in the
    form of posterior pairing probabilities. 'dvir' is part of the
    'pedsuite' collection of packages for pedigree analysis.
Contains functions that do something convenient (e.g. create BMI categories), functions for calculating moving-window statistics efficiently, and functions for generating various figures (e.g. histograms with fitted probability mass/density function).
A set of control charts for batch processes based on the VAR model. The package contains the implementation of T2.var and W.var control charts based on VAR model coefficients using the couple vectors theory. In each time-instant the VAR coefficients are estimated from a historical in-control dataset and a decision rule is made for online classifying of a new batch data. Those charts allow efficient online monitoring since the very first time-instant. The offline version is available too. In order to evaluate the chart's performance, this package contains functions to generate batch data for offline and online monitoring.See in Danilo Marcondes Filho and Marcio Valk (2020) <doi:10.1016/j.ejor.2019.12.038>.
Solving large scale distance weighted discrimination.
  The main algorithm is a symmetric Gauss-Seidel based alternating direction method of multipliers (ADMM) method. See Lam, X.Y., Marron, J.S., Sun, D.F., and Toh, K.C. (2018) <arXiv:1604.05473> for more details.
The 'DWD' provides gridded radar data for Germany in binary format. 
  'dwdradar' reads these files and enables a fast conversion into numerical format.
Infers networks with hubs using degree weighted Lasso method.
This linear model solution is useful when both predictor and response have associated uncertainty. The doubly weights linear model solution is invariant on which quantity is used as predictor or response. Based on the results by Reed(1989) <doi:10.1119/1.15963> and Ripley & Thompson(1987) <doi:10.1039/AN9871200377>.
The rapid development of single-cell transcriptomic technologies 
    has helped uncover the cellular heterogeneity within cell populations. 
    However, bulk RNA-seq continues to be the main workhorse for quantifying 
    gene expression levels due to technical simplicity and low cost. To most 
    effectively extract information from bulk data given the new knowledge 
    gained from single-cell methods, we have developed a novel algorithm to 
    estimate the cell-type composition of bulk data from a single-cell 
    RNA-seq-derived cell-type signature. Comparison with existing methods using 
    various real RNA-seq data sets indicates that our new approach is more 
    accurate and comprehensive than previous methods, especially for the 
    estimation of rare cell types. More importantly,our method can detect 
    cell-type composition changes in response to external perturbations, 
    thereby providing a valuable, cost-effective method for dissecting the 
    cell-type-specific effects of drug treatments or condition changes. 
    As such, our method is applicable to a wide range of biological and 
    clinical investigations. Dampened weighted least squares ('DWLS') is an 
    estimation method for gene expression deconvolution, in which the cell-type 
    composition of a bulk RNA-seq data set is computationally inferred. 
    This method corrects common biases towards cell types that are 
    characterized by highly expressed genes and/or are highly prevalent, to 
    provide accurate detection across diverse cell types. See: 
    <https://www.nature.com/articles/s41467-019-10802-z.pdf> for more 
    information about the development of 'DWLS' and the methods behind our 
    functions.
Fit a Poisson regression to carcass distance data and integrate over the searched area at a wind farm to estimate the fraction of carcasses falling in the searched area and format the output for use as the dwp parameter in the 'GenEst' or 'eoa' package for estimating bird and bat mortality, following Dalthorp, et al. (2022) <arXiv:2201.10064>.
Regression for a discrete response, where the conditional distribution is modelled via a discrete Weibull distribution.
Contains functions for the MCMC simulation of dyadic network models j2 (Zijlstra, 2017, <doi:10.1080/0022250X.2017.1387858>) and p2 (Van Duijn, Snijders & Zijlstra, 2004, <doi: 10.1046/j.0039-0402.2003.00258.x>), the multilevel p2 model (Zijlstra, Van Duijn & Snijders (2009) <doi: 10.1348/000711007X255336>), and the bidirectional (multilevel) counterpart of the the multilevel p2 model as described in Zijlstra, Van Duijn & Snijders (2009) <doi: 10.1348/000711007X255336>, the (multilevel) b2 model.
Tools for DYRESM-CAEDYM model development, including assisting with calibrating selected model parameters and visualising model output through time series plot, profile plot, contour plot, and scatter plot.
Finds regular and chaotic intervals in the data using 
    the 0-1 test for chaos proposed by Gottwald and Melbourne (2004) 
	<DOI:10.1137/080718851>.
An R interface to the 'dygraphs' JavaScript charting library
    (a copy of which is included in the package). Provides rich facilities
    for charting time-series data in R, including highly configurable
    series- and axis-display and interactive features like zoom/pan and
    series/point highlighting.
Solves quadratic programming problems using Richard L. Dykstra's cyclic projection algorithm. Routine allows for a combination of equality and inequality constraints. See Dykstra (1983) <doi:10.1080/01621459.1983.10477029> for details.
Add a "Did You Mean" feature to the R interactive. With this
    package, error messages for misspelled input of variable names or package names
    suggest what you really want to do in addition to notification of the mistake.
An application of Dynamic Mode Decomposition for prediction of time features. Automatic search for the best model across the space of all possible feature combinations and ranks of Singular Value Decomposition.
Time series regression.  The dyn class interfaces ts,
        irts(), zoo() and zooreg() time series classes to lm(), glm(),
        loess(), quantreg::rq(), MASS::rlm(), MCMCpack::MCMCregress(),
        quantreg::rq(), randomForest::randomForest() and other regression
        functions allowing those functions to be used with time series
        including specifications that may contain lags, diffs and
        missing values.
A comprehensive and dynamic configuration driven logging package for R. While there 
    are several excellent logging solutions already in the R ecosystem, I always feel constrained 
    in some way by each of them. Every project is designed differently to solve it's domain specific problem, 
    and ultimately the utility of a logging solution is its ability to adapt to this design. This is the 
    raison d'être for 'dyn.log': to provide a modular design, template mechanics and a configuration-based 
    integration model, so that the logger can integrate deeply into your design, even though it knows 
    nothing about it.
While autoregressive distributed lag (ARDL) models allow for extremely flexible dynamics, interpreting substantive significance of complex lag structures remains difficult. This package is designed to assist users in dynamically simulating and plotting the results of various ARDL models. It also contains post-estimation diagnostics, including a test for cointegration when estimating the error-correction variant of the autoregressive distributed lag model (Pesaran, Shin, and Smith 2001 <doi:10.1002/jae.616>).
Generalised model for population dynamics of invasive Aedes mosquitoes. Rationale and model structure are described here: Da Re et al. (2021) <doi:10.1016/j.ecoinf.2020.101180> and Da Re et al. (2022) <doi:10.1101/2021.12.21.473628>.
Returns dynamic fit index (DFI) cutoffs for latent variable models 
    that are tailored to the user's model statement, model type, and sample size.  
    This is the counterpart of the Shiny Application, <https://dynamicfit.app>.
Emulating and solving inverse problems for dynamic computer experiments.
	     It contains two major functionalities: (1) localized GP model for large-scale
	     dynamic computer experiments using the algorithm proposed by
	     Zhang et al. (2018) <arXiv:1611.09488>; (2) solving inverse problems
	     in dynamic computer experiments. The current version only supports 64-bit
	     version of R.
A collection of novel tools for generating species distribution and abundance models (SDM) that are dynamic through both space and time. These highly flexible functions incorporate spatial and temporal aspects across key SDM stages; including when cleaning and filtering species occurrence data, generating pseudo-absence records, assessing and correcting sampling biases and autocorrelation, extracting explanatory variables and projecting distribution patterns. Throughout, functions utilise Google Earth Engine and Google Drive to minimise the computing power and storage demands associated with species distribution modelling at high spatio-temporal resolution.
Contains methods for detection of clusters in hierarchical clustering dendrograms.
Easy-to-use and efficient interface for 
  Bayesian inference of complex panel (time series) data using dynamic 
  multivariate panel models by Helske and Tikka (2022) 
  <doi:10.31235/osf.io/mdwu5>. The package supports joint modeling of multiple 
  measurements per individual, time-varying and time-invariant effects, and a 
  wide range of discrete and continuous distributions. Estimation of these 
  dynamic multivariate panel models is carried out via 'Stan'. For an 
  in-depth tutorial of the package, see (Tikka and Helske, 2023) 
  <arxiv:2302.01607>.
Provides functions for inferring longitudinal dominance hierarchies, which describe dominance relationships and their dynamics in a single latent hierarchy over time. Strauss & Holekamp (in press).
It allows running 'Dynare' program from base R, R Markdown and Quarto. 'Dynare' is a software platform for handling a wide class of economic models, in particular dynamic stochastic general equilibrium ('DSGE') and overlapping generations ('OLG') models.  This package does not only integrate R and Dynare but also serves as a 'Dynare' Knit-Engine for 'knitr' package. The package requires 'Dynare' (<https://www.dynare.org/>) and 'Octave' (<https://www.octave.org/download.html>).  Write all your 'Dynare' commands in R or R Markdown chunk.
A set of tools to generate dynamic spectrogram visualizations in video format.
A multiple testing procedure aims to find the rare-variant association regions. When variants are rare, the single variant association test approach suffers from low power. To improve testing power, the procedure dynamically and hierarchically aggregates smaller genome regions to larger ones and performs multiple testing for disease associations with a controlled node-level false discovery rate. This method are members of the family of ancillary information assisted recursive testing introduced in Pura, Li, Chan and Xie (2021) <arXiv:1906.07757v2> and Li, Sung and Xie (2021) <arXiv:2103.11085v2>.
An R implementation and enhancement of the Dynamic TOPMODEL semi-distributed hydrological model originally proposed by Beven and Freer (2001) <doi:10.1002/hyp.252>. The 'dynatop' package implements code for simulating models which can be created using the 'dynatopGIS' package.
A set of algorithms based on Quinn et al. (1991) <doi:10.1002/hyp.3360050106> for processing river network and digital elevation data to build implementations of Dynamic TOPMODEL, a semi-distributed hydrological model proposed in Beven and Freer (2001) <doi:10.1002/hyp.252>. The 'dynatop' package implements simulation code for Dynamic TOPMODEL based on the output of 'dynatopGIS'.
Inference by sequential Monte Carlo for 
  dynamic tree regression and classification models
  with hooks provided for sequential design and optimization, 
  fully online learning with drift, variable selection, and 
  sensitivity analysis of inputs.  Illustrative 
  examples from the original dynamic trees paper 
  (Gramacy, Taddy & Polson (2011); <doi:10.1198/jasa.2011.ap09769>) are facilitated
  by demos in the package; see demo(package="dynaTree").
A GUI to solve dynamic biplots and classical biplot. Try matrices
    of 2-way and 3-way. The GUI can be run in multiple languages.
A two-stage procedure for the denoising and clustering of stack of noisy images acquired over time. Clustering only assumes that the data contain an unknown but small number of dynamic features. The method first denoises the signals using local spatial and full temporal information. The clustering step uses the previous output to aggregate voxels based on the knowledge of their spatial neighborhood. Both steps use a single keytool based on the statistical comparison of the difference of two signals with the null signal. No assumption is therefore required on the shape of the signals. The data are assumed to be normally distributed (or at least follow a symmetric distribution) with a known constant variance. Working pixelwise, the method can be time-consuming depending on the size of the data-array but harnesses the power of multicore cpus.
While there are many well-established measures for identifying critical fluctuations and phase transitions, these measures only work with many points of measurement and thus are unreliable when studying short and coarse-grained time series. This package provides a measure for complexity in a time series that does not rely on long time series (Kaiser (2017), <doi:10.17605/OSF.IO/GWTKX>).
Provides density functions for the joint distribution of
    choice, response time and confidence for discrete confidence judgments
    as well as functions for parameter fitting, prediction and simulation
    for various dynamical models of decision confidence.  All models are
    explained in detail by Hellmann et al.  (2023;
    Preprint available at <https://osf.io/9jfqr/>, published version: <doi:10.1037/rev0000411>).  Implemented models are the dynaViTE model, 
    dynWEV model, the 2DSD model (Pleskac & Busemeyer, 2010, <doi:10.1037/a0019737>),
    and various race models.  C++ code for dynWEV and 2DSD is based on the
    'rtdists' package by Henrik Singmann.
Computes dynamical correlation estimates and percentile
        bootstrap confidence intervals for pairs of longitudinal
        responses, including consideration of lags and derivatives.
Provides a common interface for applying dimensionality reduction methods,
  such as Principal Component Analysis ('PCA'), Independent Component Analysis ('ICA'), diffusion maps, 
  Locally-Linear Embedding ('LLE'), t-distributed Stochastic Neighbor Embedding ('t-SNE'), 
  and Uniform Manifold Approximation and Projection ('UMAP'). 
  Has built-in support for sparse matrices.
An anonymization algorithm to resist neighbor label attack in a dynamic network.
Based on random forest principle, 'DynForest' is able to include 
    multiple longitudinal predictors to provide individual predictions. 
    Longitudinal predictors are modeled through the random forest. The 
    methodology is fully described for a survival outcome in: 
    Devaux, Helmer, Genuer & Proust-Lima (2022) 
    <doi: 10.48550/arXiv.2208.05801>.
A novel, multi-modal simulation engine for
    studying dynamic cellular processes at single-cell resolution. 'dyngen'
    is more flexible than current single-cell simulation engines. It
    allows better method development and benchmarking, thereby stimulating
    development and testing of novel computational methods. Cannoodt et
    al. (2021) <doi:10.1038/s41467-021-24152-2>.
Dynamic linear models and time series regression.
Allows to perform the dynamic mixture estimation with state-space components and normal regression components, and clustering with normal mixture. Quasi-Bayesian estimation, as well as, that based on the Kerridge inaccuracy approximation are implemented. Main references: Nagy and Suzdaleva (2013) <doi:10.1016/j.apm.2013.05.038>; Nagy et al. (2011) <doi:10.1002/acs.1239>.
Demonstrate the results of a statistical model object as a dynamic nomogram in an RStudio panel or web browser. The package provides two generics functions: DynNom, which display statistical model objects as a dynamic nomogram; DNbuilder, which builds required scripts to publish a dynamic nomogram on a web server such as the <https://www.shinyapps.io/>. Current version of 'DynNom' supports stats::lm, stats::glm, survival::coxph, rms::ols, rms::Glm, rms::lrm, rms::cph, mgcv::gam and gam::gam model objects.
Computes the first stage GMM estimate of a dynamic linear model with p lags of the dependent variables.
Provides tools for describing parameters of algorithms in an abstract way.
  Description can include an id, a description, a domain (range or list of values),
  and a default value. 'dynparam' can also convert parameter sets to a 'ParamHelpers' format, 
  in order to be able to use 'dynparam' in conjunction with 'mlrMBO'.
The dynpred package contains functions for dynamic prediction in survival analysis.
A domain-specific language for specifying translating recursions
    into dynamic-programming algorithms. See 
    <https://en.wikipedia.org/wiki/Dynamic_programming> for a description
    of dynamic programming.
Intensive longitudinal data have become increasingly prevalent in
    various scientific disciplines. Many such data sets are noisy, multivariate,
    and multi-subject in nature. The change functions may also be continuous,
    or continuous but interspersed with periods of discontinuities (i.e.,
    showing regime switches). The package 'dynr' (Dynamic Modeling in R) is an
    R package that implements a set of computationally efficient algorithms for
    handling a broad class of linear and nonlinear discrete- and continuous-
    time models with regime-switching properties under the constraint of
    linear Gaussian measurement functions. The discrete-time models can
    generally take on the form of a state-space or difference equation model.
    The continuous-time models are generally expressed as a set of ordinary
    or stochastic differential equations. All estimation and computations
    are performed in C, but users are provided with the option to specify the
    model of interest via a set of simple and easy-to-learn model specification
    functions in R. Model fitting can be performed using single-subject time
    series data or multiple-subject longitudinal data. Ou, Hunter, & Chow
    (2019) <doi:10.32614%2FRJ-2019-012> provided a detailed introduction to the
    interface and more information on the algorithms.
Improves the concept of multivariate range boxes, which is highly susceptible for outliers and does not consider the distribution of the data. The package uses dynamic range boxes to overcome these problems.
Dynamic simulations and graphical depictions of autoregressive
    relationships.
Time-varying coefficient models for interval censored and
    right censored survival data including
    1) Bayesian Cox model with time-independent, time-varying or
    dynamic coefficients for right censored and interval censored data studied by
    Sinha et al. (1999) <doi:10.1111/j.0006-341X.1999.00585.x> and
    Wang et al. (2013) <doi:10.1007/s10985-013-9246-8>,
    2) Spline based time-varying coefficient Cox model for right censored data
    proposed by Perperoglou et al. (2006) <doi:10.1016/j.cmpb.2005.11.006>, and
    3) Transformation model with time-varying coefficients for right censored data
    using estimating equations proposed by
    Peng and Huang (2007) <doi:10.1093/biomet/asm058>.
Performs calculations with tree taper (or stem
    profile) equations, including model fitting. The package
    implements the methods from García, O. (2015) "Dynamic
    modelling of tree form"
    <http://mcfns.net/index.php/Journal/article/view/MCFNS7.1_2>.
    The models are parsimonious, describe well the tree bole shape
    over its full length, and are consistent with wood formation
    mechanisms through time.
Methods to estimate dynamic treatment regimes using Interactive
  Q-Learning, Q-Learning, weighted learning, and value-search methods based on 
  Augmented Inverse Probability Weighted Estimators and Inverse Probability
  Weighted Estimators. Dynamic Treatment Regimes: Statistical Methods for 
  Precision Medicine, Tsiatis, A. A., Davidian, M. D., Holloway, S. T., and Laber, E. B., 
  Chapman & Hall/CRC Press, 2020, ISBN:978-1-4987-6977-8.
Provides common functionality for the 'dynverse' packages. 
  'dynverse' is created to support the development, execution, and benchmarking of trajectory inference methods.
  For more information, check out <https://dynverse.org>.
Provides functionality to infer trajectories from single-cell data,
  represent them into a common format, and adapt them. Other biological information
  can also be added, such as cellular grouping, RNA velocity and annotation.
  Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.
It is used to identify dysregulated pathways based on a pre-ranked gene pair list. A fast algorithm is used to make the computation really fast. The data in package 'DysPIAData' is needed.
This dataset includes Background and Pathway data used in package 'DysPIA'.
In practice, we will encounter problems where the longitudinal performance of processes needs to be monitored over time. 
  Dynamic screening systems (DySS) are methods that aim to identify and give signals to processes with poor performance as early as possible. 
  This package is designed to implement dynamic screening systems and the related methods.
  References:
  Qiu, P. and Xiang, D. (2014) <doi:10.1080/00401706.2013.822423>;
  Qiu, P. and Xiang, D. (2015) <doi:10.1002/sim.6477>;
  Li, J. and Qiu, P. (2016) <doi:10.1080/0740817X.2016.1146423>;
  Li, J. and Qiu, P. (2017) <doi:10.1002/qre.2160>;
  You, L. and Qiu, P. (2019) <doi:10.1080/00949655.2018.1552273>;
  Qiu, P., Xia, Z., and You, L. (2020) <doi:10.1080/00401706.2019.1604434>;
  You, L., Qiu, A., Huang, B., and Qiu, P. (2020) <doi:10.1002/bimj.201900127>;
  You, L. and Qiu, P. (2021) <doi:10.1080/00224065.2020.1767006>.
Functions for latent class analysis, short time Fourier
	     transform, fuzzy clustering, support vector machines,
	     shortest path computation, bagged clustering, naive Bayes
	     classifier, generalized k-nearest neighbour ...
Process and manage the data from the Empatica E4. All functions operate on the EDA data stream, but other streams will be added soon. The Empatica E4 is a wearable physiological monitor made by Empatica (Empatica is not associated with any of this code). You can find more information about the E4 at Empatica's website <https://www.empatica.com/research/e4/>.
Fits dose-response models using an evolutionary
    algorithm to estimate the model parameters. The procedure currently
    can fit 3-parameter, 4-parameter, and 5-parameter log-logistic models
    as well as exponential models. Functions are also provided to plot,
    make predictions, and calculate confidence intervals for the resulting
    models. For details see "Nonlinear Dose-response Modeling of
    High-Throughput Screening Data Using an Evolutionary Algorithm",
    Ma, J., Bair, E., Motsinger-Reif, A.; Dose-Response
    18(2):1559325820926734 (2020) <doi:10.1177/1559325820926734>.
Computation and visualization of the empirical attainment function (EAF) for the analysis of random sets in multi-criterion optimization. M. López-Ibáñez, L. Paquete, and T. Stützle (2010) <doi:10.1007/978-3-642-02538-9_9>.
An implementation of multiple-locus association mapping on a genome-wide scale. 'Eagle' can handle inbred and  outbred study populations, populations of arbitrary unknown complexity, and data larger than the memory capacity of the computer. Since 'Eagle' is based on linear mixed models, it is best suited to the analysis of data on continuous traits. However, it can tolerate non-normal data. 'Eagle' reports, as its findings, the best set of snp in strongest association with a trait. For users unfamiliar with R, to perform an analysis, run 'OpenGUI()'. This  opens a web browser to the menu-driven user interface for the input of data, and for performing genome-wide analysis.
Estimator augmentation methods for statistical inference on high-dimensional data, 
    as described in Zhou, Q. (2014) <arXiv:1401.4425v2>
    and Zhou, Q. and Min, S. (2017) <doi:10.1214/17-EJS1309>.
    It provides several simulation-based inference methods: (a) Gaussian and 
    wild multiplier bootstrap for lasso, group lasso, scaled lasso, scaled group
    lasso and their de-biased estimators, (b) importance sampler for approximating
    p-values in these methods, (c) Markov chain Monte Carlo lasso sampler with 
    applications in post-selection inference.
A 'Shiny' web application for energy industry analytics.
      Take an overview of the industry, measure Key Performance Indicators,
      identify changes in the industry over time, and discover new relationships in the data.
Computes the most important properties of four 'Bayesian' early gating 
             designs (two single arm and two randomized controlled designs), such 
             as minimum required number of successes in the experimental group to 
             make a GO decision, operating characteristics and average operating 
             characteristics with respect to the sample size. 
             These might aid in deciding what design to use for the early phase trial.
Implements a simple, likelihood-based estimation of the reproduction number (R0) using a branching process with a Poisson likelihood. This model requires knowledge of the serial interval distribution, and dates of symptom onsets. Infectiousness is determined by weighting R0 by the probability mass function of the serial interval on the corresponding day. It is a simplified version of the model introduced by Cori et al. (2013) <doi:10.1093/aje/kwt133>.
The Early-Warning-Signals Toolbox provides methods for estimating
    statistical changes in time series that can be used for identifying nearby
    critical transitions.
Build regression models using the techniques in Friedman's
    papers "Fast MARS" and "Multivariate Adaptive Regression
    Splines" <doi:10.1214/aos/1176347963>.
    (The term "MARS" is trademarked and thus not used in
    the name of the package.)
Downloads a satellite image via Google Maps/Earth (these are
    originally from a variety of aerial photography sources), 
    translates the image into a perceptually uniform color space,
    runs one of a few different clustering algorithms on the colors in the image 
    searching for a user-supplied number of colors,
    and returns the resulting color palette.
Implementation in a simple and efficient way of fully customisable population genetics simulations,
    considering multiple loci that have epistatic interactions. Specifically suited to the modelling of
    multilocus nucleocytoplasmic systems (with both diploid and haploid loci), it is nevertheless possible
    to simulate purely diploid (or purely haploid) genetic models.
	Examples of models that can be simulated with Ease are numerous, for example models of genetic
	incompatibilities as presented by Marie-Orleach et al. (2022) <doi:10.1101/2022.07.25.501356>.
	Many others are conceivable, although few are actually explored, Ease having been developed
	in particular to provide a solution so that these kinds of models can be simulated simply.
Some utility functions for validation, data manipulation or color palettes. These functions can be helpful to reduce internal codes everywhere in package development.
Enables launching a series of simulations of a computer code from the R session, and to retrieve the simulation outputs in an appropriate format for post-processing treatments. Five sequential sampling schemes and three coupled-to-MCMC schemes are implemented.
Given the scores from decision makers, the analytic hierarchy process can be conducted easily.
Perform analysis of variance and other important complementary
  analyses.  The functions are easy to use.  Performs analysis in various
  designs, with balanced and unbalanced data.
Extracting desired data using the proper Census variable names can 
    be time-consuming. This package takes the pain out of that process by 
    providing functions to quickly locate variables and download labeled tables 
    from the Census APIs (<https://www.census.gov/data/developers/data-sets.html>).
Get high-resolution (1 km) daily climate data (precipitation,
    minimum and maximum temperatures) for points and polygons within
    Europe.
Univariate and multivariate methods for compositional data 
    analysis, based on logratios. The package implements the approach in the
    book Compositional Data Analysis in Practice by Michael Greenacre (2018),
    where accent is given to simple pairwise logratios. Selection can be made
    of logratios that account for a maximum percentage of logratio variance.
    Various multivariate analyses of logratios are included in the package.
Allows users to easily read multiple comma separated tables and create a data frame under the same name.
    Is able to read multiple comma separated tables from a local directory, a zip file or a zip file on a remote directory.
A unified interface for connecting to databases ('SQLite', 'MySQL', 'PostgreSQL').
    Just provide the database name and the package will ask you questions
    to help you configure the connection and setup your credentials.  Once
    database configuration and connection has been set up once, you won't
    have to do it ever again.
Descriptive analysis is essential for publishing medical articles.
  This package provides an easy way to conduct the descriptive analysis.
  1. Both numeric and factor variables can be handled. For numeric variables, normality test will be applied to choose the parametric and nonparametric test.
  2. Both two or more groups can be handled. For groups more than two, the post hoc test will be applied, 'Tukey' for the numeric variables and 'FDR' for the factor variables.
  3. T test, ANOVA or Fisher test can be forced to apply.
  4. Mean and standard deviation can be forced to display.
A function that reads in the GEO code of a list of probesets or gene symbols, a gene expression dataset GEO accession code, the name of the dataset feature discriminating the two conditions for the differential coexpression, and the values of the two different conditions for the differential coexpression, and returns the significant pairs of genes/probesets with highest differential coexpression (p-value < 0.005). If the input gene list is made of gene symbols, this package associates the probesets to these gene symbols, if found.  Platforms available: GPL80, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293,  GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>.
Interactive labelling of scatter plots, volcano plots and 
    Manhattan plots using a 'shiny' and 'plotly' interface. Users can hover 
    over points to see where specific points are located and click points 
    on/off to easily label them. Labels can be dragged around the plot to place 
    them optimally. Plots can be exported directly to PDF for publication.
Utilities for building certain kinds of common matrices and models in 
    the extended structural equation modeling package, 'OpenMx'.
Set of wrappers for the 'ncdf4' package to simplify and extend its
    reading/writing capabilities into/from multidimensional R arrays.
Easily load and install multiple packages from different sources, 
    including CRAN and GitHub. The libraries function allows you to load or attach 
    multiple packages in the same function call. The packages function will load one 
    or more packages, and install any packages that are not installed on your system 
    (after prompting you). Also included is a from_import function that allows you 
    to import specific functions from a package into the global environment.
Power analysis is used in the estimation of sample sizes for
    experimental designs. Most programs and R packages will only output the highest
    recommended sample size to the user. Often the user input can be complicated
    and computing multiple power analyses for different treatment comparisons can
    be time consuming. This package simplifies the user input and allows the user
    to view all of the sample size recommendations or just the ones they want to see.
    The calculations used to calculate the recommended sample sizes are from the
    'pwr' package.
Provides various functions for reading and preparing the Panel Study of Income Dynamics (PSID) for longitudinal analysis, including functions that read the PSID's fixed width format files directly into R, rename all of the PSID's longitudinal variables so that recurring variables have consistent names across years, simplify assembling longitudinal datasets from cross sections of the PSID Family Files, and export the resulting PSID files into file formats common among other statistical programming languages ('SAS', 'STATA', and 'SPSS').
Query NCBI Entrez and retrieve PubMed records in XML or text format. Process PubMed records by extracting and aggregating data from selected fields. A large number of records can be easily downloaded via this simple-to-use interface to the NCBI PubMed API.
Makes difficult operations easy. Includes these types of functions: 
    shorthand, type conversion, data wrangling, and work flow. 
    Also includes some helpful data objects: NA strings, U.S. state list, color blind charting colors. 
    Built and shared by Oliver Wyman Actuarial Consulting. Accepting proposed contributions through GitHub.
Performs analysis of regression in simple designs with quantitative treatments, 
             including mixed models and non linear models.
The main function, ProtectTable(), performs table suppression according to a 
 frequency rule with a data set as the only required input. Within this function, 
 protectTable(), protect_linked_tables() or runArgusBatchFile() in package 'sdcTable' is called. 
 Lists of level-hierarchy (parameter 'dimList') and other required input to these functions 
 are created automatically. 
 The suppression method Gauss (default) is implemented independently of 'sdcTable'.
 The function, PTgui(), starts a graphical user interface based on the 'shiny' package.
A meta-package that installs and loads a set of packages from 
    'easystats' ecosystem in a single step. This collection of packages provide 
    a unifying and consistent framework for statistical modeling, visualization, 
    and reporting. Additionally, it provides articles targeted at instructors for 
    teaching 'easystats', and a dashboard targeted at new R users for easily 
    conducting statistical analysis by accessing summary results, model fit indices, 
    and visualizations with minimal programming.
This SVG elements generator can easily generate 
    SVG elements such as rect, line, circle, ellipse, polygon, 
    polyline, text and group. Also, it can combine and 
    output SVG elements into a SVG file.
Set of tools to simplify application of atomic forecast
    verification metrics for (comparative) verification of ensemble forecasts
    to large data sets. The forecast metrics are imported from the
    'SpecsVerification' package, and additional forecast metrics are provided
    with this package. Alternatively, new user-defined forecast scores can be
    implemented using the example scores provided and applied using the
    functionality of this package.
Functions are provided to determine production frontiers and technical 
    efficiency measures through non-parametric techniques based upon regression trees. 
    The package includes code for estimating radial input, output, directional and 
    additive measures, plotting graphical representations of the scores and the production 
    frontiers by means of trees, and determining rankings of importance of input variables 
    in the analysis. Additionally, an adaptation of Random Forest by a set of individual 
    Efficiency Analysis Trees for estimating technical efficiency is also included. More 
    details in: <doi:10.1016/j.eswa.2020.113783>.
Provides simple functions to create constraints for small test assembly problems 
    (e.g. van der Linden (2005, ISBN: 978-0-387-29054-6)) using sparse matrices. Currently, 
    'GLPK', 'lpSolve', 'Symphony', and 'Gurobi' are supported as solvers. The 'gurobi' package is not available from 
    any mainstream repository; see <https://www.gurobi.com/downloads/>.
Use 'SQLite3' as a database system via a complete SQL free R interface, treating the data as if it was a single spreadsheet.
Import 'SPSS' data, handle and change 'SPSS' meta data, store and access large hierarchical data in 'SQLite' data bases.
The univariate statistical quality control tool aims to address measurement error effects when constructing exponentially weighted moving average p control charts. The method primarily focuses on binary random variables, but it can be applied to any continuous random variables by using sign statistic to transform them to discrete ones. With the correction of measurement error effects, we can obtain the corrected control limits of exponentially weighted moving average p control chart and reasonably adjusted exponentially weighted moving average p control charts. The methods in this package can be found in some relevant references, such as Chen and Yang (2022) <arXiv: 2203.03384>; Yang et al. (2011) <doi: 10.1016/j.eswa.2010.11.044>; Yang and Arnold (2014) <doi: 10.1155/2014/238719>; Yang (2016) <doi: 10.1080/03610918.2013.763980> and Yang and Arnold (2016) <doi: 10.1080/00949655.2015.1125901>.
Replication methods to compute some basic statistic operations (means, standard deviations,
  frequency tables, percentiles and generalized linear models) in complex survey designs comprising multiple
  imputed variables and/or a clustered sampling structure which both deserve special procedures at least in
  estimating standard errors. See the package documentation for a more detailed description along with references.
Miscellaneous functions for data cleaning and data analysis of educational assessments. Includes functions for descriptive 
   analyses, character vector manipulations and weighted statistics. Mainly a lightweight dependency for the packages 'eatRep', 
   'eatGADS', 'eatPrep' and 'eatModel' (which will be subsequently submitted to 'CRAN').
   The function for defining (weighted) contrasts in weighted effect coding refers to
   te Grotenhuis et al. (2017) <doi:10.1007/s00038-016-0901-1>.
   Functions for weighted statistics refer to
   Wolter (2007) <doi:10.1007/978-0-387-35099-8>.
Fitting and testing multi-attribute probabilistic choice
  models, especially the Bradley-Terry-Luce (BTL) model (Bradley &
  Terry, 1952 <doi:10.1093/biomet/39.3-4.324>; Luce, 1959),
  elimination-by-aspects (EBA) models (Tversky, 1972 <doi:10.1037/h0032955>),
  and preference tree (Pretree) models (Tversky & Sattath, 1979
  <doi:10.1037/0033-295X.86.6.542>).
Package implements entropy balancing, a data preprocessing procedure described in Hainmueller (2008, <doi:10.1093/pan/mpr025>) that allows users to reweight a dataset such that the covariate distributions in the reweighted data satisfy a set of user specified moment conditions. This can be useful to create balanced samples in observational studies with a binary treatment where the control group data can be reweighted to match the covariate moments in the treatment group. Entropy balancing can also be used to reweight a survey sample to known characteristics from a target population.
Empirical Bayes thresholding using the methods developed
    by I. M. Johnstone and B. W. Silverman. The basic problem is to
    estimate a mean vector given a vector of observations of the mean
    vector plus white noise, taking advantage of possible sparsity in
    the mean vector. Within a Bayesian formulation, the elements of
    the mean vector are modelled as having, independently, a
    distribution that is a mixture of an atom of probability at zero
    and a suitable heavy-tailed distribution. The mixing parameter can
    be estimated by a marginal maximum likelihood approach. This leads
    to an adaptive thresholding approach on the original data.
    Extensions of the basic method, in particular to wavelet
    thresholding, are also implemented within the package.
We provide the main R functions to compute the posterior interval for the noncentrality parameter of the chi-squared distribution. The skewness estimate of the posterior distribution is also available to improve the coverage rate of posterior intervals. Details can be found in Du and Hu (2020) <doi:10.1080/01621459.2020.1777137>.
Computes empirical Bayes confidence estimators and confidence
    intervals in a normal means model. The intervals are robust in the sense
    that they achieve correct coverage regardless of the distribution of the
    means. If the means are treated as fixed, the intervals have an average
    coverage guarantee. The implementation is based on Armstrong, Kolesár and
    Plagborg-Møller (2020) <arXiv:2004.03448>.
Infer the adjacency matrix of a
	network from time course data using an empirical Bayes
	estimation procedure based on Dynamic Bayesian Networks.
Provides the Empirical Bayesian Elastic Net for handling multicollinearity in generalized linear regression models.  As a special case of the 'EBglmnet'
  package (also available on CRAN), this package encourages a grouping effects to select relevant variables and estimate the corresponding non-zero effects.
Genotyping the population using next generation sequencing data is essentially important for the rare variant detection. In order to distinguish the genomic structural variation from sequencing error, we propose a statistical model which involves the genotype effect through a latent variable to depict the distribution of non-reference allele frequency data among different samples and different genome loci, while decomposing the sequencing error into sample effect and positional effect. An ECM algorithm is implemented to estimate the model parameters, and then the genotypes and SNPs are inferred based on the empirical Bayes method.
Provides empirical Bayesian lasso and elastic net algorithms for variable selection and effect estimation. Key features include sparse variable selection and effect estimation via generalized linear regression models, high dimensionality with p>>n, and significance test for nonzero effects. This package outperforms other popular methods such as lasso and elastic net methods in terms of power of detection, false discovery rate, and power of detecting grouping effects. Please reference its use as A Huang and D Liu (2016) <doi: 10.1093/bioinformatics/btw143>.
Tools to download, load, plot, and analyze eBird Status and
    Trends Data Products
    (<https://science.ebird.org/en/status-and-trends>). eBird
    (<https://ebird.org/home>) is a global database of bird observations
    collected by member of the public. eBird Status and Trends uses these
    data to model global bird abundances, range boundaries, and habitat
    associations at a high spatial and temporal resolution.
Create forecasts from multiple predictions using ensemble Bayesian model averaging (EBMA). EBMA models can be estimated using an expectation maximization (EM) algorithm or as fully Bayesian models via Gibbs sampling. The methods in this package are Montgomery, Hollenbach, and Ward (2015) <doi:10.1016/j.ijforecast.2014.08.001> and Montgomery, Hollenbach, and Ward (2012) <doi:10.1093/pan/mps002>.
Four ensemble-based methods (SMOTEBoost, RUSBoost, UnderBagging, and SMOTEBagging) for class imbalance problem are implemented for binary classification. Such methods adopt ensemble methods and data re-sampling techniques to improve model performance in presence of class imbalance problem. One special feature offers the possibility to choose multiple supervised learning algorithms to build weak learners within ensemble models. References: Nitesh V. Chawla, Aleksandar Lazarevic, Lawrence O. Hall, and Kevin W. Bowyer (2003) <doi:10.1007/978-3-540-39804-2_12>, Chris Seiffert, Taghi M. Khoshgoftaar, Jason Van Hulse, and Amri Napolitano (2010) <doi:10.1109/TSMCA.2009.2029559>, R. Barandela, J. S. Sanchez, R. M. Valdovinos (2003) <doi:10.1007/s10044-003-0192-z>, Shuo Wang and Xin Yao (2009) <doi:10.1109/CIDM.2009.4938667>, Yoav Freund and Robert E. Schapire (1997) <doi:10.1006/jcss.1997.1504>.
Provides simple, fast, and stable functions to fit the normal
    means model using empirical Bayes. For available models and details, see 
    function ebnm(). A detailed introduction to the package is provided
    by Willwerscheid and Stephens (2021) <arXiv:2110.00152>.
EB-PRS is a novel method that leverages information for effect sizes across all the markers to improve the prediction accuracy.  No parameter tuning is needed in the method, and no external information is needed. This R-package provides the calculation of polygenic risk scores from the given training summary statistics and testing data. We can use EB-PRS to extract main information, estimate Empirical Bayes parameters, derive polygenic risk scores for  each individual in testing data, and evaluate the PRS according to AUC and predictive r2. See Song et al. (2020) <doi:10.1371/journal.pcbi.1007565> for a detailed presentation of the method.
Empirical Bayes ranking applicable to parallel-estimation settings where the estimated parameters are asymptotically unbiased and normal, with known standard errors.  A mixture normal prior for each parameter is estimated using Empirical Bayes methods, subsequentially ranks for each parameter are simulated from the resulting joint posterior over all parameters (The marginal posterior densities for each parameter are assumed independent). Finally, experiments are ordered by expected posterior rank, although computations minimizing other plausible rank-loss functions are also given.
Implements a Bayesian-like approach to the high-dimensional sparse linear regression problem based on an empirical or data-dependent prior distribution, which can be used for estimation/inference on the model parameters, variable selection, and prediction of a future response. The method was first presented in Martin, Ryan and Mess, Raymond and Walker, Stephen G (2017) <doi:10.3150/15-BEJ797>. More details focused on the prediction problem are given in Martin, Ryan and Tang, Yiqi (2019) <arXiv:1903.00961>.
Presents a statistical method that uses a recursive algorithm for signal extraction. The method handles a non-parametric estimation for the correlation of the errors. See "Krivobokova", "Serra", "Rosales" and "Klockmann" (2021) <arXiv:1812.06948> for details.
Estimation tools for multidimensional Gaussian means using
    empirical Bayesian g-modeling. Methods are able to handle fully observed data as
    well as left-, right-, and interval-censored observations (Tobit
    likelihood); descriptions of these methods can be found in Barbehenn and
    Zhao (2023) <arXiv:2306.07239>. Additional, lower-level functionality based
    on Kiefer and Wolfowitz (1956) <doi:10.1214/aoms/1177728066> and Jiang and
    Zhang (2009) <doi:10.1214/08-AOS638> is provided that can be used to
    accelerate many empirical Bayes and nonparametric maximum likelihood
    problems.
The concept of Essential Biodiversity Variables (EBV, <https://geobon.org/ebvs/what-are-ebvs/>) 
    comes with a data structure based on the Network Common Data Form (netCDF). 
    The 'ebvcube' 'R' package provides functionality to easily create, access and 
    visualise this data. The EBV netCDFs can be downloaded from the EBV Data 
    Portal: Christian Langer/ iDiv (2020) <https://portal.geobon.org/>.
An implementation for estimating Effective control to 50% of growth
    inhibition (EC50) for multi isolates and stratified datasets. It implements 
    functions from the drc package in a way that is displayed a tidy data.frame 
    as output. Info about the drc package is available in Ritz C, Baty F, Streibig JC,
    Gerhard D (2015) <doi:10.1371/journal.pone.0146021>.
Support ecological analyses such as ordination and clustering. 
    Contains consistent and easy wrapper functions of 'stat', 'vegan', and 
    'labdsv' packages, and visualisation functions of ordination and clustering.
Fits Leroux model in spectral domain to estimate causal spatial effect as detailed in 
             Guan, Y; Page, G.L.; Reich, B.J.; Ventrucci, M.; Yang, S; (2020) <arXiv:2012.11767>.  
             Both the parametric and semi-parametric models are available.  The semi-parametric model 
             relies on 'INLA'.  The 'INLA' package can be obtained from <https://www.r-inla.org/>.
Provides an interface to the 'European Central Bank's Statistical
    Data Warehouse' API <https://sdw.ecb.europa.eu/>, allowing for programmatic 
    retrieval of a vast quantity of statistical data.
If translate English words into Chinese, there is a faster 
    way for R user. 'RYoudaoTranslate' package provides interface to 
    'Youdao' <http://youdao.com/> translation open API for R user. 'entcn' 
    package also provides similar features. But it does not support Chinese 
    words translation into English, I have made some improvements on the basis 
    of this software. You can pass in an English or Chinese word, ecce package 
    support both English and Chinese translation. It also support browse 
    translation results in website. In addition, also support obtain the pinyin 
    of the Chinese character, so that you can more easily understand the 
    pronunciation of the Chinese character.
Draw sample paths for endpoint-conditioned continuous time Markov chains via modified rejection sampling or uniformization.
Elliptic lambda distribution and lambda option pricing model
    have been evolved into a framework of
    stable-law inspired distributions,
    such as the extended stable lambda distribution for asset return,
    stable count distribution for volatility,
    and Lihn-Laplace process as a leptokurtic extension of Wiener process.
    This package contains functions for the computation of
    density, probability, quantile, random variable, fitting procedures,
    option prices, volatility smile. It also comes with sample financial data,
    and plotting routines.
Data sets for econometrics, including political science.
Computes and plots a transformed empirical CDF (ecdf) as a
    diagnostic for heavy tailed data, specifically data with power law decay on the
    tails.  Routines for annotating the plot, comparing data to a model, fitting a
    nonparametric model, and some multivariate extensions are given.
Some wrappers, functions and data sets for for spatial point pattern analysis (mainly based on 'spatstat'), used in the book "Introduccion al Analisis Espacial de Datos en Ecologia y Ciencias Ambientales: Metodos y Aplicaciones" and in the papers by De la Cruz et al. (2008) <doi:10.1111/j.0906-7590.2008.05299.x> and Olano et al. (2009) <doi:10.1051/forest:2008074>.
Functions and vignettes to update 
    data sets in 'Ecdat' and to create, manipulate, 
    plot, and analyze those and similar data sets.
A goodness-of-fit test for elliptical distributions with diagnostic
  capabilities. Gilles R. Ducharme, Pierre Lafaye de Micheaux (2019) <arXiv:1902.03622>.
A consistent tool for downloading ECH data, processing them and generating new indicators: poverty, education, employment, etc. All data are downloaded from the official site of the National Institute of Statistics at <https://www.gub.uy/instituto-nacional-estadistica/datos-y-estadisticas/encuestas/encuesta-continua-hogares>.
Embed interactive charts to their Shiny applications. These charts will be generated by ECharts library developed by Baidu (<http://echarts.baidu.com/>). Current version supports line chart, bar chart, pie chart, scatter plot, gauge, word cloud, radar chart, tree map, and heat map.
Easily create interactive charts by leveraging the 'Echarts Javascript' library which includes
    36 chart types, themes, 'Shiny' proxies and animations.
Deliver the full functionality of 'ECharts' with minimal overhead. 'echarty' users build R lists for 'ECharts' API. Lean set of powerful commands.
Functions for the echelon analysis developed proposed by Myers et al. (1997) <doi:10.1023/A:1018518327329>, and the detection of spatial clusters using echelon scan method proposed by Kurihara (2003) <doi:10.20551/jscswabun.15.2_171>.
Simulates cyclic voltammetry, linear-sweep voltammetry 
    (both with and without stirring of the solution), and single-pulse 
    and double-pulse chronoamperometry and chronocoulometry 
    experiments using the implicit finite difference method outlined in 
    Gosser (1993, ISBN: 9781560810261) and in Brown (2015) 
    <doi:10.1021/acs.jchemed.5b00225>. Additional functions provide 
    ways to display and to examine the results of these simulations.
    The primary purpose of this package is to provide tools for
    use in courses in analytical chemistry.
Capture code evaluations and script executions by expressions,
    outputs, and condition calls for logging.
Provides a function (echo_find()) designed to find rhythms 
    from data using extended harmonic oscillators. For more information,
    see H. De los Santos et al. (2020) <doi:10.1093/bioinformatics/btz617> .
Easily import multi-frequency acoustic data stored in 'HAC' files (see <http://biblio.uqar.ca/archives/30005500.pdf> for more information on the format), and produce echogram visualisations with predefined or customized color palettes. It is also possible to merge consecutive echograms; mask or delete unwanted echogram areas; model and subtract background noise; and more important, develop, test and interpret different combinations of frequencies in order to perform acoustic filtering of the echogram's data.
Implements choice models based on economic theory, including estimation using Markov chain Monte Carlo (MCMC), prediction, and more. Its usability is inspired by ideas from 'tidyverse'. Models include versions of the Hierarchical Multinomial Logit and Multiple Discrete-Continous (Volumetric) models with and without screening. The foundations of these models are described in Allenby, Hardt and Rossi (2019)  <doi:10.1016/bs.hem.2019.04.002>. Models with conjunctive screening are described in Kim, Hardt, Kim and Allenby (2022) <doi:10.1016/j.ijresmar.2022.04.001>. Models with set-size variation are described in Hardt and Kurz (2020) <doi:10.2139/ssrn.3418383>.
An R interface to United States Environmental 
    Protection Agency (EPA) Environmental Compliance 
    History Online ('ECHO') Application Program Interface
    (API). 'ECHO' provides information about EPA permitted 
    facilities, discharges, and other reporting info 
    associated with permitted entities. Data are obtained 
    from <https://echo.epa.gov/>.
Extends the Changes-in-Changes model a la Athey and Imbens
    (2006) <doi:10.1111/j.1468-0262.2006.00668.x> to multiple cohorts and
    time periods, which generalizes difference-in-differences estimation
    techniques to the entire distribution. Computes quantile treatment
    effects for every possible two-by-two combination in ecic(). Then,
    aggregating all bootstrap runs adds the standard errors in
    summary_ecic(). Results can be plotted with plot_ecic() aggregated
    over all cohort-group combinations or in an event-study style for
    either individual periods or individual quantiles.
Provides a function that quickly computes the fine structure
    isotope patterns of a set of chemical formulas to a given degree of
    accuracy (up to the limit set by errors in floating point arithmetic). A
    data-set comprising the masses and isotopic abundances of individual
    elements is also provided and calculation of isotopic gross structures
    is also supported.
Ensemble correlation-based low-rank matrix completion method (ECLRMC) is an extension to the LRMC based methods. Traditionally, the LRMC based methods give identical importance to the whole data which results in emphasizing on the commonality of the data and overlooking the subtle but crucial differences. This method aims to overcome the equality assumption problem that exists in the current LRMS based methods. Ensemble correlation-based low-rank matrix completion (ECLRMC) takes consideration of the specific characteristic of each sample and performs LRMC on the set of samples with a strong correlation. It uses an ensemble learning method to improve the imputation performance. Since each sample is analyzed independently this method can be parallelized by distributing imputation across many computation units or GPU platforms. This package provides three different methods (LRMC, CLRMC and ECLRMC) for data imputation. There is also an NRMS function for evaluating the result. Chen, Xiaobo, et al (2017) <doi:10.1016/j.knosys.2017.06.010>.
Companion package to the paper: An analytic approach for 
    interpretable predictive models in high dimensional data, in the presence of 
    interactions with exposures. Bhatnagar, Yang, Khundrakpam, Evans, Blanchette, Bouchard, Greenwood (2017) <DOI:10.1101/102475>. 
    This package includes an algorithm for clustering high dimensional data that can be affected by an environmental factor.
Functions for easy building of error correction models (ECM) for time series regression.
Programmatic interface to the European Centre for Medium-Range
    Weather Forecasts dataset web services (ECMWF; <https://www.ecmwf.int/>)
    and Copernicus's Climate Data Store (CDS; 
    <https://cds.climate.copernicus.eu>). Allows for easy downloads of weather 
    forecasts and climate reanalysis data in R.
A system for calculating the optimal sampling effort, based on the ideas of 
    "Ecological cost-benefit optimization" as developed by A. Underwood (1997, 
    ISBN 0 521 55696 1). Data is obtained from simulated ecological communities, 
    and the optimization follows the following procedure of four functions (1) 
    sim_beta() estimates statistical power and type 2 error by using Permutational 
    Multivariate Analysis of Variance, (2) plot_power() represents the results 
    of the previous function, (3) scompvar() calculates the variation components 
    necessary for (4) sim_cbo() to calculate the optimal combination of number 
    of sites and samples depending on either an economical budget or on a desired 
    statistical accuracy.
Essential Biodiversity Variables (EBV) are state variables with dimensions on time, space, and biological organization that document biodiversity change. Freely available ecosystem remote sensing products (ERSP) are downloaded and integrated with data for national or regional domains to derive indicators for EBV in the class ecosystem structure (Pereira et al., 2013) <doi:10.1126/science.1229931>, including horizontal ecosystem extents, fragmentation, and information-theory indices. To process ERSP, users must provide a polygon or geographic administrative data map. Downloadable ERSP include Global Surface Water (Peckel et al., 2016) <doi:10.1038/nature20584>, Forest Change (Hansen et al., 2013) <doi:10.1126/science.1244693>, and Continuous Tree Cover data (Sexton et al., 2013) <doi:10.1080/17538947.2013.786146>.
Work with the Ecological Community Data Design Pattern. 'ecocomDP' 
    is a flexible data model for harmonizing ecological community surveys, in a 
    research question agnostic format, from source data published across 
    repositories, and with methods that keep the derived data up-to-date as the 
    underlying sources change. Described in O'Brien et al. (2021), 
    <doi:10.1016/j.ecoinf.2021.101374>.
Creates 'graphs' of species associations (interactions) and ordination biplots from 
    co-occurrence data by fitting discrete gaussian copula graphical models. Methods described in
    Popovic, GC., Hui, FKC., Warton, DI., (2018) <doi:10.1016/j.jmva.2017.12.002>.
Biotracers and stomach content analyses are combined in a Bayesian hierarchical model
    to estimate a probabilistic topology matrix (all trophic link probabilities) and a diet matrix 
    (all diet proportions).
    The package relies on the JAGS software and the 'jagsUI' package to run a Markov chain Monte Carlo 
    approximation of the different variables.
Dissimilarity-based analysis functions including ordination and Mantel test functions, intended for use with spatial and community data. The original package description is in Goslee and Urban (2007) <doi:10.18637/jss.v022.i07>, with further statistical detail in Goslee (2010) <doi:10.1007/s11258-009-9641-0>.
Fit and sample from the ensemble model described in Spence et al (2018): "A general framework for combining ecosystem models"<doi:10.1111/faf.12310>.
Simulates the soil water balance (soil moisture, evapotranspiration, leakage and runoff), rainfall series by using the marked Poisson process and the vegetation growth through the normalized difference vegetation index (NDVI). Please see Souza et al. (2016) <doi:10.1002/hyp.10953>.
Calculates several indices, such as of diversity, fluctuation, etc., and they are used to estimate ecological indicators.
Provides measures to characterize the complexity of classification 
    and regression problems based on aspects that quantify the linearity of the 
    data, the presence of informative feature, the sparsity and dimensionality 
    of the datasets. This package provides bug fixes, generalizations and 
    implementations of many state of the art measures. The measures are 
    described in the papers: Lorena et al. (2019) <doi:10.1145/3347711> and 
    Lorena et al. (2018) <doi:10.1007/s10994-017-5681-1>.
Figures, data sets and examples from the book "A practical guide to ecological modelling - using R as a simulation platform" by Karline Soetaert and Peter MJ Herman (2009). Springer.
  All figures from chapter x can be generated by "demo(chapx)", where x = 1 to 11. 
  The R-scripts of the model examples discussed in the book are in subdirectory "examples", ordered per chapter.
  Solutions to model projects are in the same subdirectories.
Coalescent-Based Simulation of Ecological Communities as proposed
    by Munoz et al. (2017) <doi:10.13140/RG.2.2.31737.26728>. The package includes
    a tool for estimating parameters of community assembly by using Approximate 
    Bayesian Computation.
Estimates RxC (R by C) vote transfer matrices (ecological contingency tables) from aggregate data building on Thomsen (1987) and Park (2008) approaches.
   References:
   Park, W.-H. (2008). ''Ecological Inference and Aggregate Analysis of Election''. PhD Dissertation. University of Michigan. <https://deepblue.lib.umich.edu/bitstream/handle/2027.42/58525/wpark_1.pdf>
   Thomsen, S.R. (1987, ISBN:87-7335-037-2). ''Danish Elections 1920 79: a Logit Approach to Ecological Analysis and Inference''. Politica, Aarhus, Denmark.
Functions and data sets to perform and demonstrate community ecology statistical tests, including Hutcheson's t-test (Hutcheson (1970) <doi:10.1016/0022-5193(70)90124-4>, Zar (2010) ISBN:9780321656865).
Tools for general properties including price, quantity, elasticity, convexity, marginal revenue and manifold of various economics demand systems including Linear, Translog, CES, LES and CREMR.
Provides methods for estimating parameter-dependent network centrality measures with linear-in-means models. Both non linear least squares and maximum likelihood estimators are implemented. The methods allow for both link and node heterogeneity in network effects, endogenous network formation and the presence of unconnected nodes. The routines also compare the explanatory power of parameter-dependent network centrality measures with those of standard measures of network centrality. Benefits and features of the 'econet' package are illustrated using data from Battaglini and Patacchini (2018) and Battaglini, Patacchini, and Leone Sciabolazza (2020). For additional details, see the vignette <doi:10.18637/jss.v102.i08>.
Randomly generate a wide range of interaction networks with
             specified size, average degree, modularity, and topological
             structure. Sample nodes and links from within simulated networks
             randomly, by degree, by module, or by abundance. Simulations
             and sampling routines are implemented in 'FORTRAN', providing
             efficient generation times even for large networks. Basic
             visualization methods also included. Algorithms implemented
             here are described in de Aguiar et al. (2017) <arXiv:1708.01242>.
A collection of advanced tools, methods and models specifically  designed  for  analyzing different  types  of  ecological  networks - especially  antagonistic  (food  webs,  host-parasite),  mutualistic (plant-pollinator, plant-fungus, etc)  and competitive networks, as well as their variability in time and space. Statistical models are developed to describe and understand the mechanisms that determine species interactions, and to decipher the organization of these ecological networks (Ohlmann et al. (2019)  <doi:10.1111/ele.13221>, Gonzalez et al. (2020) <doi:10.1101/2020.04.02.021691>, Miele et al. (2021) <doi:10.48550/arXiv.2103.10433>, Botella et al (2021) <doi:10.1111/2041-210X.13738>).
Computes a series of indices commonly used in the fields of economic geography, economic complexity, and evolutionary economics to describe the location, distribution, spatial organization, structure, and complexity of economic activities. Functions include basic spatial indicators such as the location quotient, the Krugman specialization index, the Herfindahl or the Shannon entropy indices but also more advanced functions to compute different forms of normalized relatedness between economic activities or network-based measures of economic complexity. Most of the functions use matrix calculus and are based on bipartite (incidence) matrices consisting of region - industry pairs. These are described in Balland (2017) <http://econ.geo.uu.nl/peeg/peeg1709.pdf>.
A wrapper of different methods from Linear Algebra for the equations
  introduced in The Atlas of Economic Complexity and related literature. This
  package provides standard matrix and graph output that can be used seamlessly
  with other packages. See <doi:10.21105/joss.01866> for a summary
  of these methods and its evolution in literature.
Tools for using null models to analyse ecological
    networks (e.g. food webs, flower-visitation networks, seed-dispersal
    networks) and detect resource preferences or non-random interactions among
    network nodes. Tools are provided to run null models, test for and plot
    preferences, plot and analyse bipartite networks, and export null model
    results in a form compatible with other network analysis packages. The 
    underlying null model was developed by Agusti et al. (2003) Molecular 
    Ecology <doi:10.1046/j.1365-294X.2003.02014.x> and the full application to 
    ecological networks by Vaughan et al. (2018) econullnetr: an R package 
    using null models to analyse the structure of ecological networks and 
    identify resource selection. Methods in Ecology & Evolution, 
    <doi:10.1111/2041-210X.12907>.
Estimates power by simulation for multivariate
    abundance data to be used for sample size estimates. Multivariate
    equivalence testing by simulation from a Gaussian copula model.
    The package also provides functions for parameterising multivariate effect
    sizes and simulating multivariate abundance data jointly. The discrete
    Gaussian copula approach is described in
    Popovic et al. (2018) <doi:10.1016/j.jmva.2017.12.002>.
Estimating individual-level covariate-outcome associations 
 using aggregate data ("ecological inference") or a combination of 
 aggregate and individual-level data ("hierarchical related regression").
A toolbox for implementing the Ecological Dynamic Regime framework 
    (Sánchez-Pinillos et al., 2023 <doi:10.1002/ecm.1589>) to 
    characterize and compare groups of ecological trajectories in multidimensional 
    spaces defined by state variables. The package includes the RETRA-EDR algorithm 
    to identify representative trajectories, functions to generate, summarize, 
    and visualize representative trajectories, and several metrics to quantify 
    the distribution and heterogeneity of trajectories in an ecological dynamic 
    regime and quantify the dissimilarity between two or more ecological dynamic 
    regimes.
Three sets of data and functions for informing ecosystem restoration
    decisions, particularly in the context of the U.S. Army Corps of Engineers.
    First, model parameters are compiled as a data set and associated metadata 
    for over 500 habitat suitability models developed by the U.S. Fish and 
    Wildlife Service (USFWS 1980) <https://www.fws.gov/policy/ESMindex.html>. 
    Second, functions for conducting habitat suitability analyses both for the
    models described above as well as generic user-specified model 
    parameterizations. Third, a suite of decision support tools for conducting 
    cost-effectiveness and incremental cost analyses (Robinson et al. 1995)
    <https://www.iwr.usace.army.mil/Portals/70/docs/iwrreports/95-R-1.pdf>.
API wrapper to download statistical information from the Economic
             Statistics System (ECOS) of the Bank of Korea
             <https://ecos.bok.or.kr/api/#/>.
Classes and methods for implementing aquatic ecosystem models,
  for running these models, and for visualizing their results.
R interface to the Embedded COnic Solver (ECOS), an efficient
	     and robust C library for convex problems. Conic and equality
	     constraints can be specified in addition to integer and
	     boolean variable constraints for mixed-integer problems. This
	     R interface is inspired by the python interface and has
	     similar calling conventions.
Implements stochastic simulations of community assembly (ecological
    diversification) using customizable ecospace frameworks (functional trait
    spaces). Provides a wrapper to calculate common ecological disparity and
    functional ecology statistical dynamics as a function of species richness.
    Functions are written so they will work in a parallel-computing environment.
Collection of R functions and data sets for the support of spatial ecology analyses with a focus on pre, core and post modelling analyses of species distribution, niche quantification and community assembly. Written by current and former members and collaborators of the ecospat group of Antoine Guisan, Department of Ecology and Evolution (DEE) and Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland. Read Di Cola et al. (2016) <doi:10.1111/ecog.02671> for details.
Functions and data supporting the Eco-Stats text (Warton, 2022, Springer), and solutions to exercises. Functions include tools for using simulation envelopes in diagnostic plots, and a function for diagnostic plots of multivariate linear models. Datasets mentioned in the package are included here (where not available elsewhere) and there is a vignette for each chapter of the text with solutions to exercises.
Implementation of the scaling functions presented in "General statistical scaling laws for stability in ecological systems" by Clark et al in Ecology Letters <DOI:10.1111/ele.13760>. Includes functions for extrapolating variability, resistance, and resilience across spatial and ecological scales, as well as a basic simulation function for producing time series, and a regression routine for generating unbiased parameter estimates. See the main text of the paper for more details.
Analytical methods to locate and characterise ecotones, ecosystems and environmental patchiness along ecological gradients. Methods are implemented for isolated sampling or for space/time series. It includes Detrended Correspondence Analysis (Hill & Gauch (1980) <doi:10.1007/BF00048870>), fuzzy clustering (De Cáceres et al. (2010) <doi:10.1080/01621459.1963.10500845>), biodiversity indices (Jost (2006) <doi:10.1111/j.2006.0030-1299.14714.x>), and network analyses (Epskamp et al. (2012) <doi:10.18637/jss.v048.i04>) - as well as tools to explore the number of clusters in the data. Functions to produce synthetic ecological datasets are also provided.
A simple approach to using a probit or logit analysis to calculate
        lethal concentration (LC) or time (LT) and the appropriate fiducial 
        confidence limits desired for selected LC or LT for
        ecotoxicology studies (Finney 1971; Wheeler et al. 2006; 
        Robertson et al. 2007). The simplicity of 'ecotox' comes from the 
        syntax it implies within its functions which are similar to functions 
        like glm() and lm(). In addition to the simplicity of the syntax, 
        a comprehensive data frame is produced which gives the user a 
        predicted LC or LT value for the desired level and a suite of important 
        parameters such as fiducial confidence limits and slope.   
        Finney, D.J. (1971, ISBN: 052108041X);
        Wheeler, M.W., Park, R.M., and Bailer, A.J. (2006) <doi:10.1897/05-320R.1>;
        Robertson, J.L., Savin, N.E., Russell, R.M., and Preisler, H.K.
        (2007, ISBN: 0849323312).
Implementation of the EPA's Ecological Exposure Research Division (EERD) tools (discontinued in 1999) for Probit and Trimmed Spearman-Karber Analysis.
    Probit and Spearman-Karber methods from Finney's book "Probit analysis a statistical treatment of the sigmoid response curve" with options for most accurate results or identical results to the book.
    Probit and all the tables from Finney's book (code-generated, not copied) with the generating functions included.
    Control correction: Abbott, Schneider-Orelli, Henderson-Tilton, Sun-Shepard.
    Toxicity scales: Horsfall-Barratt, Archer, Gauhl-Stover, Fullerton-Olsen, etc.
The US EPA ECOTOX database is a freely available database
    with a treasure of aquatic and terrestrial ecotoxicological data.
    As the online search interface doesn't come with an API, this
    package provides the means to easily access and search the database
    in R. To this end, all raw tables are downloaded from the EPA website
    and stored in a local SQLite database.
Assists ecologists in the analysis of temporal changes of 
    ecosystems, defined as trajectories on a chosen multivariate space, by providing a set of 
    trajectory metrics and visual representations (see De Caceres et al. (2019) <doi:10.1002/ecm.1350> 
    and Sturbois et al. (2021) <doi:10.1016/j.ecolmodel.2020.109400>). Includes functions
    to estimate metrics for individual trajectories (length, directionality, angles, ...) as well as
    metrics to relate pairs of trajectories (dissimilarity and convergence).
An approach and software for modelling marine and freshwater ecosystems. It is articulated entirely around trophic levels. EcoTroph's key displays are bivariate plots, with trophic levels as the abscissa, and biomass flows or related quantities as ordinates. Thus, trophic ecosystem functioning can be modelled as a continuous flow of biomass surging up the food web, from lower to higher trophic levels, due to predation and ontogenic processes. Such an approach, wherein species as such disappear, may be viewed as the ultimate stage in the use of the trophic level metric for ecosystem modelling, providing a simplified but potentially useful caricature of ecosystem functioning and impacts of fishing. This version contains catch trophic spectrum analysis (CTSA) function and corrected versions of the mf.diagnosis and create.ETmain functions.
Functions for evaluating and visualizing
  ecological assessment procedures for surface waters
  containing physical, chemical and biological assessments
  in the form of value functions.
Computer simulations of classical ecological models as a
    learning resource.
Implements various procedures for finding 
	     multiple change-points from Matteson D. et al (2013)
	     <doi:10.1080/01621459.2013.849605>, Zhang W. et al (2017) 
	     <doi:10.1109/ICDMW.2017.44>, Arlot S. et al (2019).
	     Two methods make use of dynamic  
	     programming and pruning, with no distributional 
	     assumptions other than the existence of certain absolute 
	     moments in one method. Hierarchical and exact search methods 
	     are included. All methods return the set of estimated change-
	     points as well as other summary information.
Fit linear, logistic and Cox survival regression models penalised with adaptive multi-group ridge penalties.
  The multi-group penalties correspond to groups of covariates defined by (multiple) co-data sources.
  Group hyperparameters are estimated with an empirical Bayes method of moments, penalised with an extra level of hyper shrinkage.
  Various types of hyper shrinkage may be used for various co-data.
  Co-data may be continuous or categorical. 
  The method accommodates inclusion of unpenalised covariates, posterior selection of covariates and multiple data types.
  The model fit is used to predict for new samples.
  The name 'ecpc' stands for Empirical Bayes, Co-data learnt, Prediction and Covariate selection.
  See Van Nee et al. (2020) <arXiv:2005.04010>.
Framework for building evolutionary algorithms for both single- and multi-objective continuous or discrete optimization problems. A set of predefined evolutionary building blocks and operators is included. Moreover, the user can easily set up custom objective functions, operators, building blocks and representations sticking to few conventions. The package allows both a black-box approach for standard tasks (plug-and-play style) and a much more flexible white-box approach where the evolutionary cycle is written by hand.
Easy and rapid quantitative estimation of small terrestrial ectotherm temperature regulation effectiveness in R. ectotemp is built on classical formulas that evaluate temperature regulation by means of various indices, inaugurated by Hertz et al. (1993) <doi: 10.1086/285573>. Options for bootstrapping and permutation testing are included to test hypotheses about divergence between organisms, species or populations.
The cointegration based support vector regression model enables researchers to use data obtained from the cointegrating vector as input in the support vector regression model.
This cointegration based Time Delay Neural Network Model hybrid model allows the researcher to make use of the information extracted by the cointegrating vector as an input in the neural network model.
We implement (or re-implements in R) a variety of statistical tools. They are focused on non-parametric two-sample (or k-sample) distribution comparisons in the univariate or multivariate case. See the vignette for more info.
Functions of five estimation method for ED50 (50 percent effective dose) are provided, and they are respectively
    Dixon-Mood method (1948) <doi:10.2307/2280071>, Choi's original turning point method (1990) <doi:10.2307/2531453> and it's modified version given by
    us, as well as logistic regression and isotonic regression. Besides, the package also supports
    comparison between two estimation results.
Energy decomposition analysis for measuring contributions of components
             and factors on energy or carbon emission changes, as described in 
             B.W. Ang (2005) <doi:10.1016/j.enpol.2003.10.010>. Includes Log Mean 
             Devisia Index method and multi-year energy decomposition analysis using 
             five methods. Please refer P. Wu (2019) <doi:10.1016/j.jclepro.2019.02.200> 
             to use the package.
Provides data sets and R Codes for E.R. Williams, C.E. Harwood and A.C. Matheson (2023). Experimental Design and Analysis for Tree Improvement, CSIRO Publishing.
Import US Census Bureau, Education Demographic and Geographic Estimates Program,
  Composite School District Boundaries Files for 2013-2019 with the option to attach the 'EdBuild'
  master dataset of school district finance, student demographics, and community economic
  indicators for every school district in the United States. The master dataset is built
  from the US Census, Annual Survey of School System Finances (F33) and joins data from the
  National Center for Education Statistics, Common Core of Data; the US Census, Small Area
  Income and Poverty Estimates; and the US Census, Education Demographic and Geographic
  Estimates. Additional functions in the package create a dataset of all pairs of school
  district neighbors as either a dataframe or a shapefile and create formatted maps of
  selected districts at the state or neighbor level, symbolized by a selected variable
  in the 'EdBuild' master dataset. For full details about 'EdBuild' data processing please
  see 'EdBuild' (2020) <http://data.edbuild.org/>.
This is the course package for the exercise portion of the "Ecological Data Collection and Processing" course.
Compute a cyclist's Eddington number, including efficiently
    computing cumulative E over a vector. A cyclist's Eddington number
    <https://en.wikipedia.org/wiki/Arthur_Eddington#Eddington_number_for_cycling>
    is the maximum number satisfying the condition such that a cyclist has
    ridden E miles or greater in E days. The algorithm in this package is an
    improvement over the conventional approach because both summary statistics
    and cumulative statistics can be computed in linear time, since it does not
    require initial sorting of the data. These functions may also be used for
    computing h-indices for authors, a metric described by Hirsch (2005)
    <doi:10.1073/pnas.0507655102>. Both are specific applications of computing
    the side length of a Durfee square 
    <https://en.wikipedia.org/wiki/Durfee_square>.
Exploratory and descriptive analysis of event based data. Provides methods for describing and selecting process data, and for preparing event log data for process mining. Builds on the S3-class for event logs implemented in the package 'bupaR'.
Detects sustained change in digital bio-marker data using
    simultaneous confidence bands. Accounts for noise using an auto-regressive
    model. Based on Buehlmann (1998) "Sieve bootstrap for smoothing in
    nonstationary time series" <doi:10.1214/aos/1030563978>.
Import physiologic data stored in
    the European Data Format (EDF and EDF+) into R.
    Both EDF and EDF+ files are supported. Discontinuous
    EDF+ files are not yet supported.
Reads European Data Format files EDF and EDF+, see <http://www.edfplus.info>,
    BioSemi Data Format files BDF, see <http://www.biosemi.com/faq/file_format.htm>,
    and BDF+ files, see <http://www.teuniz.net/edfbrowser/bdfplus%20format%20description.html>.
    The files are read in two steps: first the header is read
    and then the signals (using the header object as a parameter).
This repository contains software for the calculation of goodness-of-fit test statistics and their P-values. The three statistics computed are the Empirical Distribution function statistics called Cramer-von Mises, Anderson-Darling, and Watson statistics. The statistics and their P-values can be used to assess an assumed distribution.The following distributions are available: Uniform, Normal, Gamma, Logistic, Laplace, Weibull, Extreme Value, and Exponential.
Easily creating empirical distribution functions from data: 'dfun', 'pfun',
    'qfun' and 'rfun'.
In the USA, companies file different forms with the U.S. 
    Securities and Exchange Commission (SEC) through EDGAR (Electronic 
    Data Gathering, Analysis, and Retrieval system). The EDGAR 
    database automated system collects all the different necessary 
    filings and makes it publicly available. This package facilitates
    retrieving, storing, searching, and parsing of all the available 
    filings on the EDGAR server. It downloads filings from SEC 
    server in bulk with a single query. Additionally, it provides 
    various useful functions: extracts 8-K triggering events, extract
    "Business (Item 1)" and "Management's Discussion and Analysis(Item 7)"
    sections of annual statements, searches filings for desired 
    keywords, provides sentiment measures, parses filing header 
    information, and provides HTML view of SEC filings.
A set of methods to access and parse live filing information from the
    U.S. Securities and Exchange Commission (SEC - <https://www.sec.gov/>) including
    company and fund filings along with all associated metadata.
Implements several algorithms for bundling edges in networks and flow and metro map layouts. This includes force directed edge bundling <doi:10.1111/j.1467-8659.2009.01450.x>, a flow algorithm based on Steiner trees<doi:10.1080/15230406.2018.1437359> and a multicriteria optimization method for metro map layouts <doi:10.1109/TVCG.2010.24>.
Generates interactive circle plots with the nodes around the
    circumference and linkages between the connected nodes using hierarchical
    edge bundling via the D3 JavaScript library. See <http://d3js.org/> for more
    information on D3.
Facilitates basic spatial edge correction to point pattern data.
Datasets from most recent CCIIO DIY entry
  in a tidy format. These support the Centers for Medicare and Medicaid
  Services' (CMS) risk adjustment Do-It-Yourself (DIY) process, which allows
  health insurance issuers to calculate member risk profiles under the Health
  and Human Services-Hierarchical Condition Categories (HHS-HCC) regression
  model. This regression model is used to calculate risk adjustment transfers.
  Risk adjustment is a selection mitigation program implemented under the
  Patient Protection and Affordable Care Act (ACA or Obamacare) in the USA.
  Under the ACA, health insurance issuers submit claims data to CMS	in order
  for CMS to calculate a risk score under the HHS-HCC regression model.
  However, CMS does not inform issuers of their average risk score until after
  the data submission deadline. These data sets can be used by issuers to
  calculate their average risk score mid-year. More information about risk
  adjustment and the HHS-HCC model can be found here:
  <https://www.cms.gov/mmrr/Articles/A2014/MMRR2014_004_03_a03.html>.
A system to facilitate designing comparative experiments using the 
  grammar of experimental designs <https://emitanaka.org/edibble-book/>. 
  An experimental design is treated as an intermediate, mutable object that is 
  built progressively by fundamental experimental components like units, treatments, and their relation.
The purpose of this package is to estimate the potential of urban agriculture to contribute to addressing several urban challenges at the city-scale. Within this aim, we selected 8 indicators directly related to one or several urban challenges. Also, a function is provided to compute new scenarios of urban agriculture. Methods are described by Pueyo-Ros, Comas & Corominas (2023) <doi:10.12688/openreseurope.16054.1>.
Perform a Bayesian estimation of the exploratory 
    deterministic input, noisy and gate (EDINA)
    cognitive diagnostic model described by Chen et al. (2018)
    <doi:10.1007/s11336-017-9579-4>.
Package EDISON (Estimation of Directed Interactions from
    Sequences Of Non-homogeneous gene expression) runs an MCMC
    simulation to reconstruct networks from time series data, using
    a non-homogeneous, time-varying dynamic Bayesian network.
    Networks segments and changepoints are inferred concurrently,
    and information sharing priors provide a reduction of the
    inference uncertainty.
The core of this package is a function eDT() which enhances DT::datatable() such that it can be used to interactively modify data in 'shiny'. By the use of generic 'dplyr' methods it supports many types of data storage, with relational databases ('dbplyr') being the main use case.
An 'RStudio' addin for editing a 'data.frame' or a 'tibble'. You can delete, add or update a 'data.frame'
    without coding. You can get resultant data as a 'data.frame'. In the package, modularized 'shiny' app codes are provided. 
    These modules are intended for reuse across applications.
Runs the eDITH (environmental DNA Integrating Transport 
  and Hydrology) model, which implements a mass balance of environmental DNA (eDNA) 
  transport at a river network scale coupled with a species distribution model 
  to obtain maps of species distribution. eDITH can work with both eDNA concentration 
  (e.g., obtained via quantitative polymerase chain reaction) or metabarcoding 
  (read count) data. Parameter estimation can be performed via Bayesian techniques 
  (via the 'BayesianTools' package) or optimization algorithms. An interface to the 
  'DHARMa' package for posterior predictive checks is provided. See Carraro et al. 
  (2018) <doi:10.1073/pnas.1813843115> and Carraro et al. (2020) 
  <doi:10.1038/s41467-020-17337-8> for methodological details.
Facilitates reading and manipulating (multivariate) data restrictions
    (edit rules) on numerical and categorical data. Rules can be defined with common R syntax
    and parsed to an internal (matrix-like format). Rules can be manipulated with
    variable elimination and value substitution methods, allowing for feasibility checks
    and more. Data can be tested against the rules and erroneous fields can be found based
    on Fellegi and Holt's generalized principle. Rules dependencies can be visualized with 
    using the 'igraph' package.
A client for the Environmental Data Initiative repository REST API. The 'EDI' data repository <https://portal.edirepository.org/nis/home.jsp> is for publication and reuse of ecological data with emphasis on metadata accuracy and completeness. It is built upon the 'PASTA+' software stack <https://pastaplus-core.readthedocs.io/en/latest/index.html#> and was developed in collaboration with the US 'LTER' Network <https://lternet.edu/>. 'EDIutils' includes functions to search and access existing data, evaluate and upload new data, and assist other data management tasks common to repository users.
Error-driven learning (based on the Widrow & Hoff (1960)<https://isl.stanford.edu/~widrow/papers/c1960adaptiveswitching.pdf> learning rule, and essentially the same as Rescorla-Wagner's learning equations (Rescorla & Wagner, 1972, ISBN: 0390718017), which are also at the core of Naive Discrimination Learning, (Baayen et al, 2011, <doi:10.1037/a0023851>) can be used to explain bottom-up human learning (Hoppe et al, <doi:10.31234/osf.io/py5kd>), but is also at the core of artificial neural networks applications in the form of the Delta rule. This package provides a set of functions for building small-scale simulations to investigate the dynamics of error-driven learning and it's interaction with the structure of the input. For modeling error-driven learning using the Rescorla-Wagner equations the package 'ndl' (Baayen et al, 2011, <doi:10.1037/a0023851>) is available on CRAN at <https://cran.r-project.org/package=ndl>. However, the package currently only allows tracing of a cue-outcome combination, rather than returning the learned networks. To fill this gap, we implemented a new package with a few functions that facilitate inspection of the networks for small error driven learning simulations. Note that our functions are not optimized for training large data sets (no parallel processing), as they are intended for small scale simulations and course examples. (Consider the python implementation 'pyndl' <https://pyndl.readthedocs.io/en/latest/> for that purpose.)
Bindings to edlib, a lightweight performant C/C++ library for exact pairwise sequence alignment using edit distance (Levenshtein distance). The algorithm computes the optimal alignment path, but also can be used to find only the start and/or end of the alignment path for convenience. Edlib was designed to be ultrafast and require little memory, with the capability to handle very large sequences. Three alignment methods are supported: global (Needleman-Wunsch), infix (Hybrid Wunsch), and prefix (Semi-Hybrid Wunsch). The original C/C++ library is described in "Edlib: a C/C++ library for fast, exact sequence alignment using edit distance", M. Šošić, M. Šikić, <doi:10.1093/bioinformatics/btw753>.
Perform dynamic model averaging with grid search as in Dangl and Halling (2012) <doi:10.1016/j.jfineco.2012.04.003> using parallel computing.
Implements various general algorithms to estimate missing elements
   of a Euclidean (squared) distance matrix.  
   Includes optimization methods based on semi-definite programming found in
   Alfakih, Khadani, and Wolkowicz (1999)<doi:10.1023/A:1008655427845>, 
   a non-convex position formulation by Fang and O'Leary (2012)<doi:10.1080/10556788.2011.643888>, and 
   a dissimilarity parameterization formulation by Trosset (2000)<doi:10.1023/A:1008722907820>.
   When the only non-missing
   distances are those on the minimal spanning tree, the guided random search
   algorithm will complete the matrix while preserving the minimal spanning tree following
   Rahman and Oldford (2018)<doi:10.1137/16M1092350>.
   Point configurations in specified dimensions can be determined from the completions. 
   Special problems such as the sensor localization problem, 
   as for example in Krislock and Wolkowicz (2010)<doi:10.1137/090759392>,
   as well as reconstructing
   the geometry of a molecular structure, as for example in 
   Hendrickson (1995)<doi:10.1137/0805040>, can also be solved.
   These and other methods are described in the thesis of Adam Rahman(2018)<https://hdl.handle.net/10012/13365>.
Collection of data sets from various assessments that can be used to 
    evaluate psychometric models. These data sets have been analyzed in the
    following papers that introduced new methodology as part of the application section:
    Yinghan Chen et al. (2021) <doi:10.1007/s11336-021-09750-9>,
    Yinyin Chen et al. (2020) <doi:10.1007/s11336-019-09693-2>,
    Culpepper, S. A. (2019a) <doi:10.1007/s11336-019-09683-4>,
    Culpepper, S. A. (2019b) <doi:10.1007/s11336-018-9643-8>,
    Culpepper, S. A., & Chen, Y. (2019) <doi:10.3102/1076998618791306>,
    Culpepper, S. A., & Balamuta, J. J. (2017) <doi:10.1007/s11336-015-9484-7>,
    and Culpepper, S. A. (2015) <doi:10.3102/1076998615595403>.
Implementations of (1) mutual dependence measures and mutual independence tests in 
    Jin, Z., and Matteson, D. S. (2017) <arXiv:1709.02532>;
    (2) independent component analysis methods based on mutual dependence measures in 
    Jin, Z., and Matteson, D. S. (2017) <arXiv:1709.02532> 
    and Pfister, N., et al. (2018) <doi:10.1111/rssb.12235>;
    (3) conditional mean dependence measures and conditional mean independence tests in 
    Shao, X., and Zhang, J. (2014) <doi:10.1080/01621459.2014.887012>,
    Park, T., et al. (2015) <doi:10.1214/15-EJS1047>,
    and Lee, C. E., and Shao, X. (2017) <doi:10.1080/01621459.2016.1240083>.
Package implements the EDNE-test for equivalence
    according to Hoffelder et al. (2015) <DOI:10.1080/10543406.2014.920344>.
    "EDNE" abbreviates "Euclidean Distance between the 
    Non-standardized Expected values".
    The EDNE-test for equivalence is a multivariate two-sample equivalence test. 
    Distance measure of the test is the Euclidean distance.
    The test is an asymptotically valid test for the family of distributions 
    fulfilling the assumptions of the multivariate central limit theorem 
    (see Hoffelder et al.,2015).
    The function EDNE.EQ() implements the EDNE-test for equivalence 
    according to Hoffelder et al. (2015).
    The function EDNE.EQ.dissolution.profiles() implements a variant 
    of the EDNE-test for equivalence analyses of dissolution profiles
    (see Suarez-Sharp et al.,2020 <DOI:10.1208/s12248-020-00458-9>).
    EDNE.EQ.dissolution.profiles() checks whether the quadratic mean of the 
    differences of the expected values of both dissolution profile populations 
    is statistically significantly smaller than 10 [\% of label claim]. 
    The current regulatory standard approach for equivalence analyses of 
    dissolution profiles is the similarity factor f2.
    The statistical hypotheses underlying EDNE.EQ.dissolution.profiles()
    coincide with the hypotheses for f2 (see Hoffelder et al.,2015, 
    Suarez-Sharp et al., 2020).
A non-parametric framework based on  estimation statistics principle. Its main purpose is to  infer orders of empirical distributions from different categories based on a probability of finding a value in one distribution that is greater than an expectation of another distribution. Given a set of ordered-pair of real-category values the framework is capable of 1) inferring orders of  domination  of  categories  and  representing  orders  in  the form of a graph; 2) estimating  magnitude  of  difference  between  a  pair  of categories in forms of mean-difference confidence intervals; and 3) visualizing  domination  orders  and  magnitudes  of  difference of categories. The publication of this package is at Chainarong Amornbunchornvej, Navaporn Surasvadi, Anon Plangprasopchok, and Suttipong Thajchayapong (2020) <doi:10.1016/j.heliyon.2020.e05435>.
A data transformation method which takes into account the special property of scale non-invariance with a breakpoint at 1 of the Euclidean distance.
Provides convenience functions and pre-programmed Stan models
    related to item response theory. Its purpose is to make fitting
    common item response theory models using Stan easy.
Read in and analyze functions for education survey and assessment data from the National Center for Education Statistics (NCES) <https://nces.ed.gov/>, including National Assessment of Educational Progress (NAEP) data <https://nces.ed.gov/nationsreportcard/> and data from the International Assessment Database: Organisation for Economic Co-operation and Development (OECD) <https://www.oecd.org/>, including Programme for International Student Assessment (PISA), Teaching and Learning International Survey (TALIS), Programme for the International Assessment of Adult Competencies (PIAAC), and International Association for the Evaluation of Educational Achievement (IEA) <https://www.iea.nl/>, including Trends in International Mathematics and Science Study (TIMSS), TIMSS Advanced, Progress in International Reading Literacy Study (PIRLS), International Civic and Citizenship Study (ICCS), International Computer and Information Literacy Study (ICILS), and Civic Education Study (CivEd).
Allows R users to retrieve and parse data from the Urban 
    Institute's Education Data API <https://educationdata.urban.org/> into a 
    'data.frame' for analysis.
Easily compute education inequality measures and the distribution 
  of educational attainments for any group of countries, using the data set 
  developed in Jorda, V. and Alonso, JM. (2017) <DOI:10.1016/j.worlddev.2016.10.005>. 
  The package offers the possibility to compute not only the Gini index, but 
  also generalized entropy measures for different values of the sensitivity 
  parameter. In particular, the package includes functions to compute the 
  mean log deviation, which is more sensitive to the bottom part of the 
  distribution; the Theil’s entropy measure, equally sensitive to all parts 
  of the distribution; and finally, the GE measure when the sensitivity 
  parameter is set equal to 2, which gives more weight to differences in 
  higher education. The decomposition of these measures in the components 
  between-country and within-country inequality is also provided. Two 
  graphical tools are also provided, to analyse the evolution of the
  distribution of educational attainments: The cumulative distribution 
  function and the Lorenz curve.
Implements the Edwards (1997) <doi:10.1002/j.1551-8833.1997.tb08229.x>
    Langmuir-based semi-empirical coagulation model, which predicts the concentration
    of organic carbon remaining in water after treatment with an Al- or Fe-based
    coagulant. Data and methods are provided to optimise empirical coefficients.
This software downloads and manages air quality data at the European level from the 
  European Environmental Agency (EEA) dataflows (<https://www.eea.europa.eu/data-and-maps/data/aqereporting-9>). 
	The package allows dynamically mapping the stations, summarising and time aggregating the measurements and building 
	spatial interpolation maps.
	See the webpage <https://www.eea.europa.eu/en> for further information on EEA's activities and history.
Analysing data from evaluations of educational interventions using a randomised controlled trial design. Various analytical tools to perform sensitivity analysis using different methods are supported (e.g. frequentist models with bootstrapping and permutations options, Bayesian models). The included commands can be used for simple randomised trials, cluster randomised trials and multisite trials. The methods can also be used more widely beyond education trials. This package can be used to evaluate other intervention designs using Frequentist and Bayesian multilevel models.
Analysis and visualization tools for electroencephalography (EEG) data. Includes functions for (i) plotting EEG data, (ii) filtering EEG data, (iii) smoothing EEG data; (iv) frequency domain (Fourier) analysis of EEG data, (v) Independent Component Analysis of EEG data, and (vi) simulating event-related potential EEG data.
Contains the example EEG data used in the package eegkit. Also contains code for easily creating larger EEG datasets from the EEG Database on the UCI Machine Learning Repository.
Read raw EEM data and prepares them for further analysis.
Forecasting time series with different decomposition based ARIMA models. For method details see Yu L, Wang S, Lai KK (2008). <doi:10.1016/j.eneco.2008.05.003>.
Forecasting univariate time series with different decomposition based Extreme Learning Machine models. For method details see Yu L, Wang S, Lai KK (2008). <doi:10.1016/j.eneco.2008.05.003>, Parida M, Behera MK, Nayak N (2018). <doi:10.1109/ICSESP.2018.8376723>.
Forecasting univariate time series with ensemble empirical mode decomposition (EEMD) with long short-term memory (LSTM). For method details see Jaiswal, R. et al. (2022). <doi:10.1007/s00521-021-06621-3>.
Application of Ensemble Empirical Mode Decomposition and its variant based Support Vector regression model for univariate time series forecasting. For method details see Das (2020).<http://krishi.icar.gov.in/jspui/handle/123456789/44138>.
Forecasting univariate time series with different decomposition based time delay neural network models. For method details see Yu L, Wang S, Lai KK (2008). <doi:10.1016/j.eneco.2008.05.003>.
Provides various tools for preprocessing Emission-Excitation-Matrix (EEM) for Parallel Factor Analysis (PARAFAC). Different
  methods are also provided to calculate common metrics such as humification index and fluorescence index.
Collection of convenience functions to make working with
    administrative records easier and more consistent. Includes functions to
    clean strings, and identify cut points. Also includes three example data 
    sets of administrative education records for learning how to process records 
    with errors.
Provides functions to create simulated time series of environmental
    exposures (e.g., temperature, air pollution) and health outcomes for use in
    power analysis and simulation studies in environmental epidemiology. This
    package also provides functions to evaluate the results of simulation studies
    based on these simulated time series. This work was supported by a grant
    from the National Institute of Environmental Health Sciences (R00ES022631) and
    a fellowship from the Colorado State University Programs for Research and
    Scholarly Excellence.
Contains logic for computing sparse principal components via the EESPCA method, 
    which is based on an approximation of the eigenvector/eigenvalue identity. 
    Includes logic to support execution of the TPower and rifle sparse PCA methods,
    as well as logic to estimate the sparsity parameters used by EESPCA, TPower and rifle
    via cross-validation to minimize the out-of-sample reconstruction error.
    H. Robert Frost (2021) <doi:10.1080/10618600.2021.1987254>.
A set of functions to estimate capture probabilities and
  densities from multipass pass removal data.
Functions for eleven procedures for determining the number of 
    factors, including functions for parallel analysis and the minimum average partial 
    test. There are also functions for conducting principal components analysis, principal 
    axis factor analysis, maximum likelihood factor analysis, image factor analysis, 
    and extension factor analysis, all of which can take raw data or correlation matrices 
    as input and with options for conducting the analyses using Pearson correlations, 
    Kendall correlations, Spearman correlations, gamma correlations, or polychoric 
    correlations. Varimax rotation, promax rotation, and Procrustes rotations can be
    performed. Additional functions focus on the factorability of a correlation matrix,
    the congruences between factors from different datasets, the assessment of local
    independence, the assessment of factor solution complexity, and internal consistency.
    Auerswald & Moshagen (2019, ISSN:1939-1463);
    Field, Miles, & Field (2012, ISBN:978-1-4462-0045-2);
    Mulaik (2010, ISBN:978-1-4200-9981-2);
    O'Connor (2000, <doi:10.3758/bf03200807>);
    O'Connor (2001, ISSN:0146-6216).
Performs parallel analysis (Timmerman & Lorenzo-Seva, 2011 
    <doi:10.1037/a0023353>) and hull method (Lorenzo-Seva, Timmerman, & Kiers, 
    2011 <doi:10.1080/00273171.2011.564527>) for assessing the dimensionality
    of a set of variables using minimum rank factor analysis (see ten Berge & 
    Kiers, 1991 <doi:10.1007/BF02294464> for more information). The package 
    also includes the option to compute minimum rank factor analysis by 
    itself, as well as the greater lower bound calculation.
Provides functions to perform exploratory factor analysis (EFA) procedures and compare their solutions. The goal is to provide state-of-the-art factor retention methods and a high degree of flexibility in the EFA procedures. This way, for example, implementations from R 'psych' and 'SPSS' can be compared. Moreover, functions for Schmid-Leiman transformation and the computation of omegas are provided. To speed up the analyses, some of the iterative procedures, like principal axis factoring (PAF), are implemented in C++.
A number of utility function for exploratory factor analysis are included in this package. In particular, it computes standard errors for parameter estimates and factor correlations under a variety of conditions.
An implementation of European Forestry Dynamics Model (EFDM) and
    an estimation algorithm for the transition probabilities.
    The EFDM is a large-scale forest model that simulates the development of
    the forest and estimates volume of wood harvested for any given forested
    area. This estimate can be broken down by, for example, species, site
    quality, management regime and ownership category.
    See Packalen et al. (2015) <doi:10.2788/153990>.
Enhanced False Discovery Rate (EFDR) is a tool to detect anomalies
    in an image. The image is first transformed into the wavelet domain in
    order to decorrelate any noise components, following which the coefficients
    at each resolution are standardised. Statistical tests (in a multiple
    hypothesis testing setting) are then carried out to find the anomalies. The
    power of EFDR exceeds that of standard FDR, which would carry out tests on
    every wavelet coefficient: EFDR choose which wavelets to test based on a
    criterion described in Shen et al. (2002). The package also provides
    elementary tools to interpolate spatially irregular data onto a grid of the
    required size. The work is based on Shen, X., Huang, H.-C., and Cressie, N.
    'Nonparametric hypothesis testing for a spatial signal.' Journal of the
    American Statistical Association 97.460 (2002): 1122-1140.
Estimate a total causal effect from observational data under 
    linearity and causal sufficiency. The observational data is supposed to 
    be generated from a linear structural equation model (SEM) with independent 
    and additive noise. The underlying causal DAG associated the SEM is required
    to be known up to a maximally oriented partially directed graph (MPDAG), 
    which is a general class of graphs consisting of both directed and 
    undirected edges, including CPDAGs (i.e., essential graphs) and DAGs. Such
    graphs are usually obtained with structure learning algorithms with added 
    background knowledge. The program is able to estimate every identified 
    effect, including single and multiple treatment variables. Moreover, the 
    resulting estimate has the minimal asymptotic covariance (and hence 
    shortest confidence intervals) among all estimators that are based on the 
    sample covariance.
Use structural equation modeling to estimate average and
    conditional effects of a treatment variable on an outcome variable, taking into
    account multiple continuous and categorical covariates.
Predicts cytoplasmic effector proteins using genomic data by searching for motifs of interest using regular expression searches and hidden Markov models (HMM) based in Haas et al. (2009) <doi:10.1038/nature08358>.
Graphical and tabular effect displays, e.g., of interactions, for 
  various statistical models with linear predictors.
Provide utilities to work with indices of effect size for a wide 
    variety of models and hypothesis tests (see list of supported models using 
    the function 'insight::supported_models()'), allowing computation of and 
    conversion between indices such as Cohen's d, r, odds, etc.
    References: Ben-Shachar et al. (2020) <doi:10.21105/joss.02815>.
Parametric and nonparametric statistics for single-case design. Regarding nonparametric statistics, the index suggested by Parker, Vannest, Davis and Sauber (2011) <doi:10.1016/j.beth.2010.08.006> was included. It combines both nonoverlap and trend to estimate the effect size of a treatment in a single case design.
Notice: The package EffectStars2 provides a more up-to-date implementation of effect stars! EffectStars provides functions to visualize regression models with categorical response as proposed by Tutz and Schauberger (2013) <doi:10.1080/10618600.2012.701379>. The effects of the variables are plotted with star plots in order to allow for an optical impression of the fitted model.
Provides functions for the method of effect stars as proposed by Tutz and Schauberger (2013) <doi:10.1080/10618600.2012.701379>. Effect stars can be used to visualize estimates of parameters corresponding to different groups, for example in multinomial logit models. Beside the main function 'effectstars' there exist methods for special objects, for example for 'vglm' objects from the 'VGAM' package.
In personalized medicine, one wants to know, for a given patient and his or her outcome for a predictor (pre-treatment variable), how likely it is that a treatment will be more beneficial than an alternative treatment. This package allows for the quantification of the predictive causal association (i.e., the association between the predictor variable and the individual causal effect of the treatment) and related metrics. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
An implementation for using efficient initials to compute the
    maximal eigenpair in R. It provides three algorithms to find the efficient
    initials under two cases: the tridiagonal matrix case and the general matrix
    case. Besides, it also provides two algorithms for the next to the maximal eigenpair under
    these two cases.
Fitting a causal loglinear model and calculating the causal effects for a causal loglinear model with the multiplicative interaction or without the multiplicative interaction, obtaining the natural direct, indirect and the total effect. It calculates also the cell effect, which is a new interaction effect.
A collection of functions to compute the standardized 
  effect sizes for experiments (Cohen d, Hedges g, Cliff delta, Vargha-Delaney A). 
  The computation algorithms have been optimized to allow efficient computation even 
  with very large data sets.
The European Eddy Fluxes Database Cluster distributes fluxes of different Green House Gases measured mainly using the eddy covariance technique acquired in sites involved in EU projects but also single sites in Europe, Africa and others continents that decided to share their measurements in the database <http://gaia.agraria.unitus.it>. The package provides two functions to load and row-wise bind CSV files distributed by the database. Currently only L2, L3, and L4 (L=Level), half-hourly and daily (aggregation) files are supported.
Interact with the FRED API, <https://fred.stlouisfed.org/docs/api/fred/>, 
      to fetch observations across economic series;
      find information about different economic sources, releases, series, etc.;
      conduct searches by series name, attributes, or tags; and determine the 
      latest updates. Includes functions for creating panels of related variables 
      with minimal effort and datasets containing data sources, releases, and 
      popular FRED tags.
Provides a function to check the
  importance of a feature based on a dependent classification
  variable. An ensemble of feature selection methods
  is used to determine the normalized importance value of
  all features. Combining these methods in one function
  (building the cumulative importance values) provides a 
  stable feature selection tool. This selection
  can also be viewed in a barplot using the barplot_fs() function
  and proved using the evaluation function efs_eval().
Functions for assigning Clarke or Parkes (Consensus) error grid
    zones to blood glucose values, and for plotting both types of error grids
    in both mg/mL and mmol/L units.
Implements the Exploratory Graph Analysis (EGA) framework for dimensionality
             and psychometric assessment. EGA estimates the number of dimensions in
	     psychological data using network estimation methods and community detection
             algorithms. A bootstrap method is provided to assess the stability of dimensions
	     and items. Fit is evaluated using the Entropy Fit family of indices. Unique 
             Variable Analysis evaluates the extent to which items are locally dependent (or
             redundant). Network loadings provide similar information to factor loadings and
	     can be used to compute network scores. A bootstrap and permutation approach are
             available to assess configural and metric invariance. Hierarchical structures
             can be detected using Hierarchical EGA. Time series and intensive longitudinal 
	     data can be analyzed using Dynamic EGA, supporting individual, group, and 
             population level assessments.
An easy-to-use implementation of the Engle-Granger
  two-step procedure for identifying pairs of cointegrated series.  It is
  geared towards the analysis of pairs of securities.  Summary and plot
  functions are provided, and the package is able to fetch closing prices of
  securities from Yahoo.  A variety of unit root tests are supported, and 
  an improved unit root test is included.
Miscellaneous functions to help customise 'ggplot2' objects. High-level functions are provided to post-process 'ggplot2' layouts and allow alignment between plot panels, as well as setting panel sizes to fixed values. Other functions include a custom 'geom', and helper functions to enforce symmetric scales or add tags to facetted plots.
An implementation of Bayesian hierarchical models
    for faecal egg count data to assess anthelmintic
    efficacy. Bayesian inference is done via MCMC sampling using 'Stan' <https://mc-stan.org/>.
Fits a variety of hidden Markov models, structured
	in an extended generalized linear model framework.  See
	T. Rolf Turner, Murray A. Cameron, and Peter J. Thomson
	(1998) <doi:10.2307/3315677>, and
	Rolf Turner (2008) <doi:10.1016/j.csda.2008.01.029>
	and the references cited therein.
User friendly interface based on the R package 'gstat' to fit
    exponential parametric models to empirical semi-variograms in order to
    model the spatial correlation structure of health data. Geo-located
    health outcomes of survey participants may be used to model spatial
    effects on health in an ego-centred approach.  The package contains a
    range of functions to help explore the spatial structure of the data
    as well as visualize the fit of exponential models for various
    metaparameter combinations with respect to the number of lag intervals
    and maximal distance.  Furthermore, the outcome of interest can be
    adjusted for covariates by fitting a linear regression in a
    preliminary step before the semi-variogram fitting process.
Tools for importing, analyzing and visualizing ego-centered
    network data. Supports several data formats, including the export formats of
    'EgoNet', 'EgoWeb 2.0' and 'openeddi'. An interactive (shiny) app for the
    intuitive visualization of ego-centered networks is provided. Also included
    are procedures for creating and visualizing Clustered Graphs 
    (Lerner 2008 <DOI:10.1109/PACIFICVIS.2008.4475458>).
Statistics and graphics for streamflow history,
    water quality trends, and the statistical modeling algorithm: Weighted
    Regressions on Time, Discharge, and Season (WRTDS).
Collection of functions to evaluate uncertainty of results from
    water quality analysis using the Weighted Regressions on Time Discharge and
    Season (WRTDS) method. This package is an add-on to the EGRET package that
    performs the WRTDS analysis. The WRTDS modeling
    method was initially introduced and discussed in Hirsch et al. (2010) <doi:10.1111/j.1752-1688.2010.00482.x>,
    and expanded in Hirsch and De Cicco (2015) <doi:10.3133/tm4A10>. The 
    paper describing the uncertainty and confidence interval calculations 
    is Hirsch et al. (2015) <doi:10.1016/j.envsoft.2015.07.017>.
Gene regulatory network constructed using combined score obtained from 
  individual network inference method. The combined score measures the significance 
  of edges in the ensemble network. Fisher's weighted method has been implemented to 
  combine the outcomes of different methods based on the probability values. 
  The combined score follows chi-square distribution with 2n degrees of freedom. <doi:10.22271/09746315.2020.v16.i3.1358>.
Genetic predisposition for complex traits is often manifested through multiple tissues of interest at different time points in the development. As an example, the genetic predisposition for obesity could be manifested through inherited variants that control metabolism through regulation of genes expressed in the brain and/or through the control of fat storage in the adipose tissue by dysregulation of genes expressed in adipose tissue. We present a method eGST (eQTL-based genetic subtyper) that integrates tissue-specific eQTLs with GWAS data for a complex trait to probabilistically assign a tissue of interest to the phenotype of each individual in the study. eGST estimates the posterior probability that an individual's phenotype can be assigned to a tissue based on individual-level genotype data of tissue-specific eQTLs and marginal phenotype data in a genome-wide association study (GWAS) cohort. Under a Bayesian framework of mixture model, eGST employs a maximum a posteriori (MAP) expectation-maximization (EM) algorithm to estimate the tissue-specific posterior probability across individuals. Methodology is available from: A Majumdar, C Giambartolomei, N Cai, MK Freund, T Haldar, T Schwarz, J Flint, B Pasaniuc (2019) <doi:10.1101/674226>.
Parametric proportional hazards fitting with left truncation and
        right censoring for common families of distributions, piecewise constant 
        hazards, and discrete models. Parametric accelerated failure time models
        for left truncated and right censored data. Proportional hazards
        models for tabular and register data. Sampling of risk sets in Cox 
        regression, selections in the Lexis diagram, bootstrapping. 
        Broström (2022) <doi:10.1201/9780429503764>.
Calculates 15 different goodness of fit criteria. These are; standard deviation ratio (SDR), coefficient of variation (CV), relative root mean square error (RRMSE), Pearson's correlation coefficients (PC), root mean square error (RMSE), performance index (PI), mean error (ME), global relative approximation error (RAE), mean relative approximation error (MRAE), mean absolute percentage error (MAPE), mean absolute deviation (MAD), coefficient of determination (R-squared), adjusted coefficient of determination (adjusted R-squared), Akaike's information criterion (AIC), corrected Akaike's information criterion (CAIC), Mean Square Error (MSE), Bayesian Information Criterion (BIC) and Normalized Mean Square Error (NMSE).
A tool for the preparation and enrichment of health datasets for analysis (Toner et al. (2023) <doi:10.1093/gigascience/giad030>). Provides functionality for assessing data quality and for improving the reliability and machine interpretability of a dataset. 
     'eHDPrep' also enables semantic enrichment of a dataset where metavariables are discovered from the relationships between input variables determined from user-provided ontologies.
By overloading the R help() function, this package allows users to use "docstring" style comments within their own defined functions. The package also provides additional functions to mimic the R basic example() function and the prototyping of packages.
Extended and enhanced hierarchical logistic regression models (called Huisman-Olff-Fresco in biology, see Huisman et al. 1993 Journal of Vegetation Science <doi:10.1111/jvs.12050>) models. Response curves along one-dimensional gradients including no response, monotone, plateau, unimodal and bimodal models.
Process and analyze electronic health record (EHR) data. The 'EHR'
    package provides modules to perform diverse medication-related studies using
    data from EHR databases. Especially, the package includes modules to perform
    pharmacokinetic/pharmacodynamic (PK/PD) analyses using EHRs, as outlined in
    Choi, Beck, McNeer, Weeks, Williams, James, Niu, Abou-Khalil, Birdwell, Roden, 
    Stein, Bejan, Denny, and Van Driest (2020) <doi:10.1002/cpt.1787>. Additional 
    modules will be added in future. In addition, this package provides various 
    functions useful to perform Phenome Wide Association Study (PheWAS) to explore 
    associations between drug exposure and phenotypes obtained from EHR data, as 
    outlined in Choi, Carroll, Beck, Mosley, Roden, Denny, and Van Driest (2018) 
    <doi:10.1093/bioinformatics/bty306>.
Software accompanying Gary King's book: A Solution to the Ecological Inference Problem. (1997). Princeton University Press. ISBN 978-0691012407.
Provides more than 550 data sets of actual election results. 
    Each of the data sets includes aggregate party and candidate outcomes at the voting
    unit (polling stations) level and two-way cross-tabulated results at the district level.
    These data sets can be used to assess ecological inference algorithms devised 
    for estimating RxC (global) ecological contingency tables using exclusively aggregate results 
    from voting units.
    Reference:
    Pavía (2022) <doi:10.1177/08944393211040808>.
Provides API access to data from the 'US Energy Information Administration' ('EIA') <https://www.eia.gov/>. 
    Use of the API requires a free API key obtainable at <https://www.eia.gov/opendata/register.php>.
    The package includes functions for searching 'EIA' data categories and importing time series and geoset time series datasets. 
    Datasets returned by these functions are provided in a tidy format or alternatively in more raw form. 
    It also offers helper functions for working with 'EIA' date strings and time formats and for inspecting different summaries of series metadata.
    The package also provides control over API key storage and caching of API request results.
Provides a function to query and extract data from the 'US Energy Information Administration' ('EIA') API V2  <https://www.eia.gov/opendata/>. The 'EIA' API provides a variety of information, in a time series format, about the energy sector in the US. The API is open, free, and requires an access key and registration at <https://www.eia.gov/opendata/>.
Model fitting and species biotic interaction network topology selection for explicit
  interaction community models. Explicit interaction community models are an extension of binomial
  linear models for joint modelling of species communities, that incorporate both the effects of
  species biotic interactions and the effects of missing covariates. Species interactions are modelled
  as direct effects of each species on each of the others, and are estimated alongside the effects of
  missing covariates, modelled as latent factors. The package includes a penalized maximum likelihood
  fitting function, and a genetic algorithm for selecting the most parsimonious species interaction
  network topology.
Provides a comprehensive suite of tools for estimating the candidate preferences of racial/ethnic voting blocs in elections. Includes functions for predicting voter race/ethnicity and conducting ecological inference. Race/ethnicity prediction builds on race prediction developed by Imai et al. (2016) <doi:10.1093/pan/mpw001>. Ecological inference methods are based on King (1997) <ISBN: 0691012407>, <https://gking.harvard.edu/eicamera/kinroot.html>; King et. al. (2004) <ISBN: 0521542804>, <https://gking.harvard.edu/files/abs/ecinf04-abs.shtml>.
Augments the 'eiCompare' package's Racially Polarized Voting (RPV) 
  functionality to streamline analyses and visualizations used to support 
  voting rights and redistricting litigation. The package implements methods 
  described in Barreto, M., Collingwood, L., Garcia-Rios, S., & Oskooii, K. A. (2022). 
  "Estimating Candidate Support in Voting Rights Act Cases: Comparing Iterative 
  EI and EI-R×C Methods" <doi:10.1177/0049124119852394>.
Estimation of the parameters in a model for
        symmetric relational data (e.g., the above-diagonal part of a
        square matrix), using a model-based eigenvalue decomposition
        and regression. Missing data is accommodated, and a posterior
        mean for missing data is calculated under the assumption that
        the data are missing at random. The marginal distribution of
        the relational data can be arbitrary, and is fit with an
        ordered probit specification. See Hoff (2007) <arXiv:0711.1146> 
        for details on the model.
Matrix algebra using the 'Eigen' C++ library: determinant, rank, inverse, pseudo-inverse, kernel and image, QR decomposition, Cholesky decomposition, linear least-squares problems. Also provides matrix functions such as exponential, logarithm, power, sine and cosine. Complex matrices are supported.
Efficiently impute large scale matrix with missing values via its unbiased low-rank matrix approximation. Our main approach is Hard-Impute algorithm proposed in <https://www.jmlr.org/papers/v11/mazumder10a.html>, which achieves highly computational advantage by truncated singular-value decomposition.
Methods and utilities for causal emergence.
    Used to explore and compute various information theory metrics for networks, such as effective information, effectiveness and causal emergence.
The summation notation suggested by Einstein (1916) <doi:10.1002/andp.19163540702> is a 
  concise mathematical notation that implicitly sums over repeated indices of n-dimensional arrays. Many ordinary
  matrix operations (e.g. transpose, matrix multiplication, scalar product, 'diag()', trace etc.)
  can be written using Einstein notation. The notation is particularly convenient for 
  expressing operations on arrays with more than two dimensions because the 
  respective operators ('tensor products') might not have a standardized name.
Provides EIOPA (European Insurance And Occupational Pensions Authority) risk-free rates. Please note that the author of this package is not affiliated with EIOPA. The data is accessed through a REST API available at <https://mehdiechchelh.com/api/>.
Provides methods for analyzing R by C ecological contingency
        tables using the extreme case analysis, ecological regression,
        and Multinomial-Dirichlet ecological inference models.  Also
        provides tools for manipulating higher-dimension data objects.
Analysis of dichotomous and polytomous response data using the explanatory item response modeling framework, as described in Bulut, Gorgun, & Yildirim-Erbasli (2021) <doi:10.3390/psych3030023>, Stanke & Bulut (2019) <doi:10.21449/ijate.515085>, and De Boeck & Wilson (2004) <doi:10.1007/978-1-4757-3990-9>. Generalized linear mixed modeling is used for estimating the effects of item-related and person-related variables on dichotomous and polytomous item responses.
Performs a compact genetic algorithm search to reduce errors-in-variables bias in linear regression. The algorithm estimates the regression parameters with lower biases and higher variances but mean-square errors (MSEs) are reduced.
This includes functions for analysis with error-prone covariates, including deconvolution, latent regression and errors-in-variables regression.  It implements methods by Rabe-Hesketh et al. (2003) <doi:10.1191/1471082x03st056oa>, Lockwood and McCaffrey (2014) <doi:10.3102/1076998613509405>, and Lockwood and McCaffrey (2017) <doi:10.1007/s11336-017-9556-y>, among others.
Structure mining from 'XGBoost' and 'LightGBM' models.
    Key functionalities of this package cover: visualisation of tree-based ensembles models,
    identification of interactions, measuring of variable importance,
    measuring of interaction importance, explanation of single prediction 
    with break down plots (based on 'xgboostExplainer' and 'iBreakDown' packages). 
    To download the 'LightGBM' use the following link: <https://github.com/Microsoft/LightGBM>.
    'EIX' is a part of the 'DrWhy.AI' universe.
Emissions are the mass of pollutants released into the atmosphere. Air quality models need emissions data, with spatial and temporal distribution, to represent air pollutant concentrations. This package, eixport, creates inputs for the air quality models 'WRF-Chem' Grell et al (2005) <doi:10.1016/j.atmosenv.2005.04.027>, 'MUNICH' Kim et al (2018) <doi:10.5194/gmd-11-611-2018> , 'BRAMS-SPM' Freitas et al (2005) <doi:10.1016/j.atmosenv.2005.07.017> and 'RLINE' Snyder et al (2013) <doi:10.1016/j.atmosenv.2013.05.074>. See the 'eixport' website (<https://atmoschem.github.io/eixport/>) for more information, documentations and examples. More details in Ibarra-Espinosa et al (2018) <doi:10.21105/joss.00607>.
Functions for estimating catalytic constant and Michaelis-Menten constant
            for enzyme kinetics model using Metropolis-Hasting algorithm within Gibbs 
            sampler based on the Bayesian framework.
Extensions of the kernel smoothing functions from the 'ks' package for compatibility with the tidyverse and geospatial ecosystems <doi:10.48550/arXiv.2203.01686>.
Empirical likelihood (EL) inference for two-sample problems. The following statistics are included: the difference of two-sample means, smooth Huber estimators, quantile (qdiff) and cumulative distribution functions (ddiff), probability-probability (P-P) and quantile-quantile (Q-Q) plots as well as receiver operating characteristic (ROC) curves. EL calculations are based on J. Valeinis, E. Cers (2011) <http://home.lu.lv/~valeinis/lv/petnieciba/EL_TwoSample_2011.pdf>.
Functions for computing critical values and implementing the one-sided/two-sided EL tests.
A novel concept for generating knowledge and gaining insights into laboratory data. You will be able to efficiently and easily explore your laboratory data from different perspectives.
Provides functions to align curves and to compute mean curves based on the 
    elastic distance defined in the square-root-velocity framework. For more details on 
    this framework see Srivastava and Klassen (2016, <doi:10.1007/978-1-4939-4020-2>). 
    For more theoretical details on our methods and algorithms see 
    Steyer et al. (2021, <arXiv:2104.11039>).
Performs some enhanced variable selection algorithms 
  based on the least absolute shrinkage and selection operator for regression model.
Provides functions for the computation of functional elastic shape 
  means over sets of open planar curves. The package is particularly suitable for 
  settings where these curves are only sparsely and irregularly observed. It uses 
  a novel approach for elastic shape mean estimation, where planar curves are
  treated as complex functions and a full Procrustes mean is estimated from the
  corresponding smoothed Hermitian covariance surface. This is combined with the 
  methods for elastic mean estimation proposed in Steyer, Stöcker, Greven	(2022)
  <doi:10.1111/biom.13706>. See Stöcker et. al. (2022) <arXiv:2203.10522> for details.
Connect to 'Elasticsearch', a 'NoSQL' database built on the 'Java'
    Virtual Machine. Interacts with the 'Elasticsearch' 'HTTP' API
    (<https://www.elastic.co/elasticsearch/>), including functions for
    setting connection details to 'Elasticsearch' instances, loading bulk data,
    searching for documents with both 'HTTP' query variables and 'JSON' based body
    requests. In addition, 'elastic' provides functions for interacting with API's
    for 'indices', documents, nodes, clusters, an interface to the cat API, and
    more.
Provides functions for fitting the entire
        solution path of the Elastic-Net and also provides functions
        for doing sparse PCA.
We developed a consistent and robust information criterion to conduct model selection for semiparametric models. It is free of distribution specification and powerful to locate the true model given large sample size. This package provides several usage of ELCIC with applications in generalized linear model (GLM), generalized estimating equation (GEE) for longitudinal data, and weighted GEE (WGEE) for missing longitudinal data under the mechanism of missing at random and drop-out. Chixaing Chen, Ming Wang, Rongling Wu, Runze Li (2020) <doi:10.5705/ss.202020.0254>.
This is a (somewhat bizarre) collection of functions written to do
        various sorts of statistical election audits.  There are also
        functions to generate simulated voting data, including methods to simulation different types 
        of voting errors which allow for simulations for checking the characteristics of
        these methods.
Digital simulation of electrochemical processes.
             Each function allows for implicit and explicit solution of the differential equation using methods like Euler, Backwards implicit, Runge Kutta 4, Crank Nicholson and Backward differentiation formula as well as different number of points for derivative approximation. Several electrochemical processes can be simulated such as: Chronoamperometry, Potential Step, Linear Sweep, Cyclic Voltammetry, Cyclic Voltammetry with electrochemical reaction followed by chemical reaction (EC mechanism) and CV with two following electrochemical reaction (EE mechanism). In update 1.1.0 has been added a general purpose CV function that allow to simulate up to 4 EE mechanism combined with chemical reaction for each species.Update 1.2.0 improved the accuracy of the measurements and allow personalized data resolution for simulation.
             Bibliography regarding this methods can be found in the following texts.
             Dieter Britz, Jorg Strutwolf (2016) <ISBN:978-3-319-30292-8>.
             Allen J. Bard, Larry R. Faulkner (2000) <ISBN:978-0-471-04372-0>.
Functions to compute state-specific and marginal life expectancies. The computation is based on a fitted continuous-time multi-state model that includes an absorbing death state; see Van den Hout (2017, ISBN:9781466568402). The fitted multi-state model model should be estimated using the 'msm' package using age as the time-scale.
This includes a dataset on the outcomes of the USA presidential elections since 1920, and various predictors, as used in <http://vanderwalresearch.com/blog/15-elections>.
Perform ballot-polling Bayesian audits for ranked voting elections
    using Dirichlet-tree prior distributions. Everest et al. (2022)
    <arXiv:2206.14605>, <arXiv:2209.03881>.
Offers a set of functions to easily download and clean 
    Brazilian electoral data from the Superior Electoral Court website. 
    Among others, the package retrieves data on local and
    federal elections for all positions (city councilor, mayor, state deputy,
    federal deputy, governor, and president) aggregated by
    state, city, and electoral zones.
Provides all electivity algorithms (including Vanderploeg and Scavia 
    electivity) that were examined in Lechowicz (1982) <doi:10.1007/BF00349007>, 
    plus the example data that were provided for moth resource utilisation.
Highest averages & largest remainders allocating seats methods and
    several party system scores.
    Implemented highest averages allocating seats methods are D'Hondt, Webster,
    Danish, Imperiali, Hill-Huntington, Dean, Modified Sainte-Lague,
    equal proportions and Adams.
    Implemented largest remainders allocating seats methods are Hare, Droop,
    Hangenbach-Bischoff, Imperial, modified Imperial and quotas & remainders.
    The main advantage of this package is that ties are always reported
    and not incorrectly allocated.
    Party system scores provided are competitiveness, concentration,
    effective number of parties, party nationalization score,
    party system nationalization score and volatility.
    References:
    Gallagher (1991) <doi:10.1016/0261-3794(91)90004-C>.
    Norris (2004, ISBN:0-521-82977-1).
    Consejo Nacional Electoral del Ecuador (2014)<http://cne.gob.ec/documents/Estadisticas/Atlas/ATLAS/CAPITULO%206%20web.pdf>.
    Laakso & Taagepera (1979) <https://journals.sagepub.com/doi/pdf/10.1177/001041407901200101>.
    Jones & Mainwaring (2003) <https://kellogg.nd.edu/sites/default/files/old_files/documents/304_0.pdf>.
    Pedersen (1979) <https://janda.org/c24/Readings/Pedersen/Pedersen.htm>.
    Golosov (2010) <https://ppq.sagepub.com/content/16/2/171.abstract>.
    Golosov (2014) <https://ppq.sagepub.com/content/early/2014/09/08/1354068814549342.abstract>.
Several web services are available that provide access to elevation
             data. This package provides access to many of those services and 
             returns elevation data either as an 'sf' simple features object 
             from point elevation services or as a 'raster' object from raster 
             elevation services. In future versions, 'elevatr' will drop 
             support for 'raster' and will instead return 'terra' objects. 
             Currently, the package supports access to the Amazon Web Services 
             Terrain Tiles <https://registry.opendata.aws/terrain-tiles/>, 
             the Open Topography Global Datasets 
             API <https://opentopography.org/developers/>, and the USGS 
             Elevation Point Query Service <https://apps.nationalmap.gov/epqs/>.
Provides R access to election results data. Wraps elex (https://github.com/newsdev/elex/), a Python package and command line tool for fetching and parsing Associated Press election results.
Density, distribution function, quantile function
    and random generation for the Kumaraswamy Complementary Weibull
    Geometric (Kw-CWG) lifetime probability distribution proposed
    in Afify, A.Z. et al (2017) <doi:10.1214/16-BJPS322>.
A toolset for generating Ecological Limit Function (ELF) models and evaluating potential species loss resulting from flow change, based on the 'elfgen' framework. ELFs describe the relation between aquatic species richness (fish or benthic macroinvertebrates) and stream size characteristics (streamflow or drainage area). Journal publications are available outlining framework methodology (Kleiner et al. (2020) <doi:10.1111/1752-1688.12876>) and application (Rapp et al. (2020) <doi:10.1111/1752-1688.12877>).
A tool to draw samples from a Empirical Likelihood Bayesian posterior
   of parameters using Hamiltonian Monte Carlo.
To run data analysis for enzyme-link immunosorbent assays (ELISAs). 
	Either the five- or four-parameter logistic model will be fitted for data of single ELISA. 
	Moreover, the batch effect correction/normalization will be carried out, when there are more than one batches of ELISAs. 
	Feng (2018) <doi:10.1101/483800>.
An alternative to Exploratory Factor Analysis (EFA) for
    metrical data in R. Drawing on characteristics of classical test
    theory, Exploratory Likert Scaling (ELiS) supports the user exploring
    multiple one-dimensional data structures. In common research practice,
    however, EFA remains the go-to method to uncover the (underlying)
    structure of a data set. Orthogonal dimensions and the potential of
    overextraction are often accepted as side effects. As described in
    Müller-Schneider (2001) <doi:10.1515/zfsoz-2001-0404>), ELiS confronts
    these problems. As a result, 'elisr' provides the platform to fully
    exploit the exploratory potential of the multiple scaling approach
    itself.
Create list comprehensions (and other types of comprehension) similar to those in
    'python', 'haskell', and other languages. List comprehension in 'R' converts a 
    regular for() loop into a vectorized lapply() function. Support for looping 
    with multiple variables, parallelization, and across non-standard objects included. Package 
    also contains a variety of functions to help with list comprehension.
Recently many new p-value based multiple test procedures have been proposed, and these new methods are more powerful than the widely used Hochberg procedure. These procedures strongly control the familywise error rate (FWER). This is a comprehensive collection of p-value based FWER-control stepwise multiple test procedures, including six procedure families and thirty multiple test procedures. In this collection, the conservative Hochberg procedure, linear time Hommel procedures, asymptotic Rom procedure, Gou-Tamhane-Xi-Rom procedures, and Quick procedures are all developed in recent five years since 2014. The package name "elitism" is an acronym of "e"quipment for "l"ogarithmic and l"i"near "ti"me "s"tepwise "m"ultiple hypothesis testing.
    See Gou, J. (2022), "Quick multiple test procedures and p-value adjustments", Statistics in Biopharmaceutical Research 14(4), 636-650.
Tool for Environment-Wide Association Studies (EnvWAS / EWAS) 
    which are repeated analysis. It includes three functions. One function for
    linear regression, a second for logistic regression and a last one for
    generalized linear models.
Correlation chart of two set (x and y) of data.  
  Using Quantiles.  Visualize the effect of factor.
Contains various routines for drawing
    ellipses and ellipse-like confidence regions, implementing the plots
    described in Murdoch and Chow (1996, <doi:10.2307/2684435>). There are
    also routines implementing the profile plots described in Bates and
    Watts (1988, <doi:10.1002/9780470316757>).
The ellipsis is a powerful tool for extending functions. Unfortunately 
    this power comes at a cost: misspelled arguments will be silently ignored. 
    The ellipsis package provides a collection of functions to catch problems
    and alert the user.
Provides functions for the simulation and
  the nonparametric estimation of elliptical distributions,
  meta-elliptical copulas and trans-elliptical distributions,
  following the article Derumigny and Fermanian (2022) <doi:10.1016/j.jmva.2022.104962>.
A suite of elliptic and related functions including Weierstrass and
 Jacobi forms.  Also includes various tools for manipulating and
 visualizing complex functions.
Given the omnipresence of the assumption of elliptical symmetry, it is essential to be able to test whether that assumption actually holds true or not for the data
            at hand. This package provides several statistical tests for elliptical symmetry that are described in Babic et al. (2021) <arXiv:2011.12560v2>.
Training and predict functions for Single Hidden-layer Feedforward Neural Networks (SLFN) using the Extreme Learning Machine (ELM) algorithm. The ELM algorithm differs from the traditional gradient-based algorithms for very short training times (it doesn't need any iterative tuning, this makes learning time very fast) and there is no need to set any other parameters like learning rate, momentum, epochs, etc. This is a reimplementation of the 'elmNN' package using 'RcppArmadillo' after the 'elmNN' package was archived. For more information, see "Extreme learning machine: Theory and applications" by Guang-Bin Huang, Qin-Yu Zhu, Chee-Kheong Siew (2006), Elsevier B.V, <doi:10.1016/j.neucom.2005.12.126>.
Training and prediction functions are provided for the Extreme Learning Machine algorithm (ELM). The ELM use a Single Hidden Layer Feedforward Neural Network (SLFN) with random generated weights and no gradient-based backpropagation. The training time is very short and the online version allows to update the model using small chunk of the training set at each iteration. The only parameter to tune is the hidden layer size and the learning function.
An implementation of the algorithm described in "Efficient Large-
    Scale Internet Media Selection Optimization for Online Display Advertising"
    by Paulson, Luo, and James (Journal of Marketing Research 2018; see URL below
    for journal text/citation and <http://faculty.marshall.usc.edu/gareth-james/Research/ELMSO.pdf>
    for a full-text version of the paper). The algorithm here is designed to 
    allocate budget across a set of online advertising opportunities using a 
    coordinate-descent approach, but it can be used in any resource-allocation 
    problem with a matrix of visitation (in the case of the paper, website page-
    views) and channels (in the paper, websites). The package contains allocation
    functions both in the presence of bidding, when allocation is dependent on 
    channel-specific cost curves, and when advertising costs are fixed at each channel.
A flexible framework for calculating Elo ratings and resulting
    rankings of any two-team-per-matchup system (chess, sports leagues, 'Go',
    etc.). This implementation is capable of evaluating a variety of matchups,
    Elo rating updates, and win probabilities, all based on the basic Elo
    rating system. It also includes methods to benchmark performance,
    including logistic regression and Markov chain models.
Allows calculating global scores for characteristics of visual stimuli as assessed by human raters. Stimuli are presented as sequence of pairwise comparisons ('contests'), during each of which a rater expresses preference for one stimulus over the other (forced choice). The algorithm for calculating global scores is based on Elo rating, which updates individual scores after each single pairwise contest. Elo rating is widely used to rank chess players according to their performance. Its core feature is that dyadic contests with expected outcomes lead to smaller changes of participants' scores than outcomes that were unexpected. As such, Elo rating is an efficient tool to rate individual stimuli when a large number of such stimuli are paired against each other in the context of experiments where the goal is to rank stimuli according to some characteristic of interest. Clark et al (2018) <doi:10.1371/journal.pone.0190393> provide details.
Provides functions to quantify animal dominance hierarchies. The major focus is on Elo rating and its ability to deal with temporal dynamics in dominance interaction sequences. For static data, David's score and de Vries' I&SI are also implemented. In addition, the package provides functions to assess transitivity, linearity and stability of dominance networks. See Neumann et al (2011) <doi:10.1016/j.anbehav.2011.07.016> for an introduction.
Obtain Bayesian posterior distributions of dominance hierarchy steepness (Neumann and Fischer (2023) <doi:10.1111/2041-210X.14021>). Steepness estimation is based on Bayesian implementations of either Elo-rating or David's scores.
Implements a Markov Chain Monte Carlo algorithm to approximate 
	exact conditional inference for logistic regression models. Exact 
	conditional inference is based on the distribution of the sufficient 
	statistics for the parameters of interest given the sufficient statistics 
	for the remaining nuisance parameters. Using model formula notation, users 
	specify a logistic model and model terms of interest for exact inference.
	See Zamar et al. (2007) <doi:10.18637/jss.v021.i03> for more details.
A framework that provides the methods for quantifying entropy-based local indicator of spatial association (ELSA) that can be used for both continuous and categorical data. In addition, this package offers other methods to measure local indicators of spatial associations (LISA). Furthermore, global spatial structure can be measured using a variogram-like diagram, called entrogram. For more information, please check that paper: Naimi, B., Hamm, N. A., Groen, T. A., Skidmore, A. K., Toxopeus, A. G., & Alibakhshi, S. (2019) <doi:10.1016/j.spasta.2018.10.001>.
Provides a tool to run Monte Carlo simulation of catastrophe model event loss tables, using a Poisson frequency and Beta severity distribution.
Empirical likelihood ratio tests for the Yang and Prentice (short/long term hazards ratio) models. 
             Empirical likelihood tests within a Cox model, for parameters defined via 
			 both baseline hazard function and regression parameters.
A generic function for running the Expectation-Maximization (EM) algorithm
  within a maximum likelihood framework, based on Dempster, Laird, and Rubin (1977) <doi:10.1111/j.2517-6161.1977.tb01600.x>
  is implemented. It can be applied after a model fitting using R's existing functions and packages.
The EM algorithm is a powerful tool for computing maximum likelihood estimates with incomplete data. This package will help to applying EM algorithm based on triangular and trapezoidal fuzzy numbers (as two kinds of incomplete data). A method is proposed for estimating the unknown parameter in a parametric statistical model when the observations are triangular or trapezoidal fuzzy numbers. This method is based on maximizing the observed-data likelihood defined as the conditional probability of the fuzzy data; for more details and formulas see Denoeux (2011) <doi:10.1016/j.fss.2011.05.022>.
Use 'emailjs' API easily in 'R'. This package is not official. <https://www.emailjs.com/docs/rest-api/send/>. You can send e-mail with 'emailjs' with function, based on 'httr'. You can also make a 'shiny' ui and server function. It can be used for making feedback form, inquiry, and so on.
An R client for the 'emailvalidation.io' e-mail verification API. The API requires registration of an API key. Basic features are free, some require a paid subscription. You can find the full API documentation at <https://emailvalidation.io/docs> .
DNA methylation is essential for human, and environment can change the DNA methylation
    and affect body status. Epigenome-Wide Mediation Analysis Study (EMAS) can find
    potential mediator CpG sites between exposure (x) and outcome (y) in epigenome-wide.
    For more information on the methods we used, please see the following references:
    Tingley, D. (2014) <doi:10.18637/jss.v059.i05>,
    Turner, S. D. (2018) <doi:10.21105/joss.00731>,
    Rosseel, D. (2012) <doi:10.18637/jss.v048.i02>.
Do data management functions common in real-time monitoring (also called: ecological momentary assessment, experience sampling, micro-longitudinal) data, including creating power curves for multilevel data, centering on participant means and merging event-level data into momentary data sets where you need the events to correspond to the nearest data point in the momentary data. This is VERY early release software, and more features will be added over time.
A light, simple tool for sending emails with minimal dependencies.
Variable selection methods have been extensively developed for analyzing high-dimensional omics data within both the frequentist and Bayesian frameworks. This package implemented the spike-and-slab quantile LASSO which has been developed along the line of Bayesian hierarchical model but deeply rooted in the frequentist regularization methods by utilizing the Expectation–Maximization (EM) algorithm. Therefore, the proposed method borrows strength from both the frequentist and Bayesian frameworks while overcoming their respective limitations. The spike-and-slab quantile LASSO can handle data irregularity in terms of skewness and outliers in the disease trait, compared to its nonrobust alternative, the spike-and-slab LASSO, which has also been implemented in the package. The core module of this package is developed in 'C++'.
Unsupervised, multivariate, binary clustering for meaningful annotation of data, taking into account the uncertainty in the data. A specific constructor for trajectory analysis in movement ecology yields behavioural annotation of trajectories based on estimated local measures of velocity and turning angle, eventually with solar position covariate as a daytime indicator, ("Expectation-Maximization Binary Clustering for Behavioural Annotation").
Predictors can be converted to one or more numeric
    representations using a variety of methods. Effect encodings using
    simple generalized linear models <arXiv:1611.09477> or nonlinear
    models <arXiv:1604.06737> can be used.  There are also functions for
    dimension reduction and other approaches.
Provides a smooth mapping of multidimensional points into
    low-dimensional space defined by a self-organizing map. Designed to work
    with 'FlowSOM' and flow-cytometry use-cases. See Kratochvil et al. (2019)
    <doi:10.12688/f1000research.21642.1>.
Tools to analyze the embryo growth and the sexualisation thermal reaction norms. See <doi:10.7717/peerj.8451> for tsd functions; see <doi:10.1016/j.jtherbio.2014.08.005> for thermal reaction norm of embryo growth.
EM algorithms and several efficient
        initialization methods for model-based clustering of finite
        mixture Gaussian distribution with unstructured dispersion
        in both of unsupervised and semi-supervised learning.
For multiscale analysis, this package carries out empirical mode decomposition and Hilbert spectral
        analysis. For usage of EMD, see Kim and Oh, 2009 (Kim, D and Oh, H.-S. (2009) EMD: A Package for Empirical 
        Mode Decomposition and Hilbert Spectrum, The R Journal, 1, 40-46).
Application of empirical mode decomposition based artificial neural network model for nonlinear and non stationary univariate time series forecasting. For method details see (i) Choudhury (2019) <https://www.indianjournals.com/ijor.aspx?target=ijor:ijee3&volume=55&issue=1&article=013>; (ii) Das (2020) <https://www.indianjournals.com/ijor.aspx?target=ijor:ijee3&volume=56&issue=2&article=002>.
Auxiliary functions and data sets for "Ecological Models and Data", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0).
Functions that support estimating, assessing and mapping regional
    disaggregated indicators. So far, estimation methods comprise direct estimation,
    the model-based unit-level approach Empirical Best Prediction (see "Small area
    estimation of poverty indicators" by Molina and Rao (2010) <doi:10.1002/cjs.10051>), 
    the area-level model (see "Estimates of income for small places: An 
    application of James-Stein procedures to Census Data" by Fay and Herriot (1979) 
    <doi:10.1080/01621459.1979.10482505>) and various extensions of it (adjusted variance 
    estimation methods, log and arcsin transformation, spatial, robust and measurement 
    error models), as well as their precision estimates. The assessment of the used model
    is supported by a summary and diagnostic plots. For a suitable presentation of
    estimates, map plots can be easily created. Furthermore, results can easily be
    exported to excel. For a detailed description of the package and the methods used
    see "The R Package emdi for Estimating and Mapping Regionally Disaggregated Indicators" 
    by Kreutzmann et al. (2019) <doi:10.18637/jss.v091.i07> and the second package vignette 
    "A Framework for Producing Small Area Estimates Based on Area-Level Models in R".
Package providing calculation of Earth Mover's Distance (EMD).
Description: Application of empirical mode decomposition based support vector regression model for nonlinear and non stationary univariate time series forecasting. For method details see (i) Choudhury (2019) <http://krishi.icar.gov.in/jspui/handle/123456789/44873>; (ii) Das (2020) <http://krishi.icar.gov.in/jspui/handle/123456789/43174>; (iii) Das (2023) <http://krishi.icar.gov.in/jspui/handle/123456789/77772>.
Provides basic distribution functions for a mixture model of a Gaussian and exponential distribution.
Simulate and fitting exponential multivariate Hawkes model. 
    This package simulates a multivariate Hawkes model, introduced by Hawkes (1971) <doi:10.2307/2334319>, with an exponential kernel and fits the parameters from the data. 
    Models with the constant parameters, as well as complex dependent structures, can also be simulated and estimated. 
    The estimation is based on the maximum likelihood method, introduced by introduced by Ozaki (1979) <doi:10.1007/BF02480272>, with 'maxLik' package.
A C++ implementation of the following evolutionary
    algorithms: Bat Algorithm (Yang, 2010 <doi:10.1007/978-3-642-12538-6_6>),
    Cuckoo Search (Yang, 2009 <doi:10.1109/nabic.2009.5393690>),
    Genetic Algorithms (Holland, 1992, ISBN:978-0262581110),
    Gravitational Search Algorithm (Rashedi et al., 2009 <doi:10.1016/j.ins.2009.03.004>),
    Grey Wolf Optimization (Mirjalili et al., 2014 <doi:10.1016/j.advengsoft.2013.12.007>),
    Harmony Search (Geem et al., 2001 <doi:10.1177/003754970107600201>),
    Improved Harmony Search (Mahdavi et al., 2007 <doi:10.1016/j.amc.2006.11.033>),
    Moth-flame Optimization (Mirjalili, 2015 <doi:10.1016/j.knosys.2015.07.006>),
    Particle Swarm Optimization (Kennedy et al., 2001 ISBN:1558605959),
    Simulated Annealing (Kirkpatrick et al., 1983 <doi:10.1126/science.220.4598.671>),
    Whale Optimization Algorithm (Mirjalili and Lewis, 2016 <doi:10.1016/j.advengsoft.2016.01.008>).
    'EmiR' can be used not only for unconstrained optimization problems, but also
    in presence of inequality constrains, and variables restricted to be integers.
Various Expectation-Maximization (EM) algorithms are implemented for item 
	response theory (IRT) models. The package includes IRT models for binary and ordinal
	responses, along with dynamic and hierarchical IRT models with binary responses. The
	latter two models are fitted using variational EM.  The package also includes 
	variational network and text scaling models.  The algorithms are described in Imai, Lo, 
	and Olmsted (2016) <DOI:10.1017/S000305541600037X>.
Processing tools to create emissions for use in numerical air 
  quality models. Emissions can be calculated both using emission factors 
  and activity data (Schuch et al 2018) <doi:10.21105/joss.00662> or using 
  pollutant inventories (Schuch et al., 2018) <doi:10.30564/jasr.v1i1.347>. 
  Functions to process individual point emissions, line emissions and 
  area emissions of pollutants are available as well as methods to 
  incorporate alternative data for Spatial distribution of emissions 
  such as satellite images (Gavidia Calderon et. al, 2018) 
  <doi:10.1016/j.atmosenv.2018.09.026> or openstreetmap data 
  (Andrade et al, 2015) <doi:10.3389/fenvs.2015.00009>.
Provides a fast and parallelised calculator to estimate combined wastewater emissions. 
    It supports the planning and design of urban drainage systems, without the requirement of 
    extensive simulation tools. The 'EmiStatR' package implements modular R methods. This enables 
    to add new functionalities through the R framework.
Work with Ecological Metadata Language ('EML') files. 
    'EML' is a widely used metadata standard in the ecological and
    environmental sciences, described in Jones et al. (2006),
    <doi:10.1146/annurev.ecolsys.37.091305.110031>.
This is a utility for transforming Ecological Metadata Language
        ('EML') files into 'JSON-LD' and back into 'EML.'  Doing so creates a
        list-based representation of 'EML' in R, so that 'EML' data can easily
        be manipulated using standard 'R' tools. This makes this package an
        effective backend for other 'R'-based tools  working with 'EML.' By
        abstracting away the complexity of 'XML' Schema, developers can
        build around native 'R' list objects and not have to worry about satisfying
        many of the additional constraints of set by the schema (such as element
        ordering, which is handled automatically). Additionally, the 'JSON-LD' 
        representation enables the use of developer-friendly 'JSON' parsing and
        serialization that may facilitate the use of 'EML' in contexts outside of 'R,'
        as well as the informatics-friendly serializations such as 'RDF' and
        'SPARQL' queries.
Provides implementations of computationally efficient maximum likelihood parameter estimation algorithms for models that represent linear dynamical systems. Currently, one such algorithm is implemented for the one-dimensional cumulative structural equation model with shock-error output measurement equation and assumptions of normality and independence. The corresponding scientific paper is yet to be published, therefore the relevant reference will be provided later.
End-member modelling analysis of grain-size data is an approach 
    to unmix a data set's underlying distributions and their contribution to 
    the data set. EMMAgeo provides deterministic and robust protocols for 
    that purpose.
Obtain estimated marginal means (EMMs) for many linear, generalized 
  linear, and mixed models. Compute contrasts or linear functions of EMMs,
  trends, and comparisons of slopes. Plots and other displays.
  Least-squares means are discussed, and the term "estimated marginal means"
  is suggested, in Searle, Speed, and Milliken (1980) Population marginal means 
  in the linear model: An alternative to least squares means, The American 
  Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Provides unsupervised selection and clustering of microarray data
    using mixture models. Following the methods described in McLachlan, Bean and
    Peel (2002) <doi:10.1093/bioinformatics/18.3.413> a subset of genes are selected
    based one the likelihood ratio statistic for the test of one versus two
    components when fitting mixtures of t-distributions to the expression data
    for each gene. The dimensionality of this gene subset is further reduced through
    the use of mixtures of factor analyzers, allowing the tissue samples to be
    clustered by fitting mixtures of normal distributions.
We provide functions to fit finite mixtures of multivariate normal or t-distributions to 
    data with various factor analytic structures adopted for the covariance/scale matrices. The 
    factor analytic structures available include mixtures of factor analyzers and mixtures of common 
    factor analyzers. The latter approach is so termed because the matrix of factor loadings is
    common to components before the component-specific rotation of the component factors to 
    make them white noise. Note that the component-factor loadings are not common after 
    this rotation. Maximum likelihood estimators of model parameters are obtained via the 
    Expectation-Maximization algorithm. See descriptions of the algorithms used in
    McLachlan GJ, Peel D (2000) <doi:10.1002/0471721182.ch8>
    McLachlan GJ, Peel D (2000) <ISBN:1-55860-707-2> 
    McLachlan GJ, Peel D, Bean RW (2003) <doi:10.1016/S0167-9473(02)00183-4> 
    McLachlan GJ, Bean RW, Ben-Tovim Jones L (2007) <doi:10.1016/j.csda.2006.09.015> 
    Baek J, McLachlan GJ, Flack LK (2010) <doi:10.1109/TPAMI.2009.149> 
    Baek J, McLachlan GJ (2011) <doi:10.1093/bioinformatics/btr112> 
    McLachlan GJ, Baek J, Rathnayake SI (2011) <doi:10.1002/9781119995678.ch9>.
The algorithm of semi-supervised learning based on finite Gaussian mixture models with a missing-data mechanism is designed for a fitting g-class Gaussian mixture model via maximum likelihood (ML). It is proposed to treat the labels of the unclassified features as missing-data and to introduce a framework for their missing as in the pioneering work of Rubin (1976) for missing in incomplete data analysis. This dependency in the missingness pattern can be leveraged to provide additional information about the optimal classifier as specified by Bayes’ rule.
Fit models of modularity to morphological landmarks. Perform model 
  selection on results. Fit models with a single within-module correlation or
  with separate within-module correlations fitted to each module.
The main functions are 'emmreml', and 'emmremlMultiKernel'. 'emmreml' solves a mixed model with known covariance structure using the 'EMMA' algorithm.  'emmremlMultiKernel' is a wrapper for 'emmreml' to handle multiple random components with known covariance structures. The function 'emmremlMultivariate' solves a multivariate gaussian mixed model with known covariance structure using the 'ECM' algorithm.
Collection of building blocks for the design and analysis
        of evolutionary multiobjective optimization algorithms.
Contains data about emojis with relevant metadata, and functions
    to work with emojis when they are in strings.
An implementation of using emoji and fontawesome for using in both
    base and 'ggplot2' graphics.
Statistical tools for environmental and ecological surveys.
    Simulation-based power and precision analysis; detection probabilities from
    different survey designs; visual fast count estimation.
Fixation and saccade detection in eye movement recordings. This package implements a dispersion-based algorithm (I-DT) proposed by Salvucci & Goldberg (2000) which detects fixation duration and position.
Functions for estimating EMP (Expected Maximum Profit Measure) in Credit Risk Scoring and Customer Churn Prediction, according to Verbraken et al (2013, 2014) <DOI:10.1109/TKDE.2012.50>, <DOI:10.1016/j.ejor.2014.04.001>.
The peak fitting of spectral data is performed by using the frame work of EM algorithm. We adapted the EM algorithm for the peak fitting of spectral data set by considering the weight of the intensity corresponding to the measurement energy steps    (Matsumura, T., Nagamura, N., Akaho, S., Nagata, K., & Ando, Y. (2019, 2021 and 2023) <doi:10.1080/14686996.2019.1620123>, <doi:10.1080/27660400.2021.1899449> <doi:10.1080/27660400.2022.2159753>. The package efficiently estimates the parameters of Gaussian mixture model during iterative calculation between E-step and M-step, and the parameters are converged to a local optimal solution. This package can support the investigation of peak shift with two advantages: (1) a large amount of data can be processed at high speed; and (2) stable and automatic calculation can be easily performed.
Evaluates the empirical characteristic function of univariate and multivariate samples.
    This package uses 'RcppArmadillo' for fast evaluation. It is also possible to export the code to be used in other packages at 'C++' level.
Routines for performing empirical calibration of observational
  study estimates. By using a set of negative control hypotheses we can
  estimate the empirical null distribution of a particular observational
  study setup. This empirical null distribution can be used to compute a
  calibrated p-value, which reflects the probability of observing an
  estimated effect size when the null hypothesis is true taking both random
  and systematic error into account. A similar approach can be used to
  calibrate confidence intervals, using both negative and positive controls. 
  For more details, see Schuemie et al. (2013) <doi:10.1002/sim.5925> and
  Schuemie et al. (2018) <doi:10.1073/pnas.1708282114>.
Empirical likelihood ratio tests for means/quantiles/hazards
 	from possibly censored and/or truncated data. Now does regression too.
	This version contains some C code.
Calculates the p-value for a mean-type hypothesis (or multiple mean-type hypotheses) based on 
        two samples with possible censored data.
Test hypotheses and construct confidence intervals for AUC (area under Receiver 
             Operating Characteristic curve) and pAUC (partial area under ROC curve), from the
			 given two samples of test data with disease/healthy subjects. The method used is
			 based on two sample empirical likelihood, as described in
			 <https://www.ms.uky.edu/~mai/research/eAUC1.pdf>.
Collection of functions related to benchmark with prediction models
	 for data analysis and editing of clinical and epidemiological data.
Provides the analysis of variance table including the expected mean squares (EMS) for various types of experimental design. When some variables are random effects or we use special experimental design such as nested design, repeated-measures design, or split-plot design, it is not easy to find the appropriate test, especially denominator for F-statistic which depends on EMS.
Background correction of spectral like data. Handles variations in
  scaling, polynomial baselines, interferents, constituents and replicate variation.
  Parameters for corrections are stored for further analysis, and spectra are corrected
  accordingly.
It provides a method based on EM algorithm to estimate the parameter of a mixture model, Sigmoid-Normal Model, where the samples come from several normal distributions (also call them subgroups) whose mean is determined by co-variable Z and coefficient alpha while the variance are homogeneous. Meanwhile, the subgroup each item belongs to is determined by co-variables X and coefficient eta through Sigmoid link function which is the extension of Logistic Link function. It uses bootstrap to estimate the standard error of parameters. When sample is indeed separable, removing estimation with abnormal sigma, the estimation of alpha is quite well. I used this method to explore the subgroup structure of HIV patients and it can be used in other domains where exists subgroup structure.
Some EM-type algorithms to estimate parameters for the well-known Heckman selection model are provided in the package. Such algorithms are as follow: ECM(Expectation/Conditional Maximization), ECM(NR)(the Newton-Raphson method is adapted to the ECM) and ECME(Expectation/Conditional Maximization Either). Since the algorithms are based on the EM algorithm, they also have EM’s main advantages, namely, stability and ease of implementation. Further details and explanations of the algorithms can be found in Zhao et al. (2020) <doi: 10.1016/j.csda.2020.106930>.
Fast and easily computes an Euclidean Minimum Spanning Tree (EMST) from data,
    relying on the R API for 'mlpack' - the C++ Machine Learning Library (Curtin et. al., 2013).
    'emstreeR' uses the Dual-Tree Boruvka (March, Ram, Gray, 2010, <doi:10.1145/1835804.1835882>), 
    which is theoretically and empirically the fastest algorithm for computing an EMST. This package also provides 
    functions and an S3 method for readily plotting Minimum Spanning Trees (MST) using either the 
    style of the 'base', 'scatterplot3d', or 'ggplot2' libraries.
Goodness-of-fit tests for discrete multivariate data. It is
        tested if a given observation is likely to have occurred under
        the assumption of an ab-initio model. Monte Carlo methods are provided to
        make the package capable of solving high-dimensional problems.
Allows one to estimate the output of a computer program,
 as a function of the input parameters, without actually running it.
 The computer program is assumed to be a Gaussian process, whose
 parameters are estimated using Bayesian techniques that give a PDF of
 expected program output.  This PDF is conditional on a training set
 of runs, each consisting of a point in parameter space and the model
 output at that point.  The emphasis is on complex codes that take
 weeks or months to run, and that have a large number of undetermined
 input parameters; many climate prediction models fall into this
 class.  The emulator essentially determines Bayesian posterior
 estimates of the PDF of the output of a model, conditioned on results
 from previous runs and a user-specified prior linear model.  The
 package includes functionality to evaluate quadratic forms 
 efficiently.
Provide the EMU Speech Database Management System (EMU-SDMS) with
    database management, data extraction, data preparation and data
    visualization facilities. See <https://ips-lmu.github.io/The-EMU-SDMS-Manual/>
    for more details.
Implements an S3 class for storing 'UTF-8' strings, based on regular character vectors.
    Also contains routines to portably read and write 'UTF-8' encoded text files,
    to convert all strings in an object to 'UTF-8',
    and to create character vectors with various encodings.
We describe fifteen different splice site sequence encoding schemes that have been used in earlier studies for mapping of splice site sequences into numeric feature vectors. These encoding schemes will also be helpful for transforming other nucleotide sequences into numeric forms, provided they are of equal length. These encoding schemes will help the computational biologist working in the field of classification (binary or multiclass) or prediction involving nucleic acid sequences of equal length.
Implements a segmentation algorithm for multiple change-point detection in univariate time series using the Ensemble Binary Segmentation of Korkas (2020) <arXiv:2003.03649>.
Interconverts between ordered lists and compact string notation.  
 Useful for capturing code lists, and pair-wise codes and decodes, for text storage.
 Analogous to factor levels and labels. Generics encode() and decode()
 perform interconversion, while codes() and decodes() extract components of an encoding.
 The function encoded() checks whether something is interpretable as an encoding.
 If a vector has an encoded 'guide' attribute, as_factor() uses it to coerce to factor.
Create encrypted html files that are fully self contained and do
  not require any additional software. Using the package you can encrypt
  arbitrary html files and also directly create encrypted 'rmarkdown' html reports.
It is important to ensure that sensitive data is protected. 
    This straightforward package is aimed at the end-user. 
    Strong RSA encryption using a public/private key pair is used to encrypt data frame or tibble columns.
    A public key can be shared to allow others to encrypt data to be sent to you. 
    This is particularly aimed a healthcare settings so patient data can be pseudonymised.
Various recursive two-stage models to address the endogeneity issue of treatment variables in observational study or mediators in experiments. The details of the models are discussed in Peng (2023) <doi:10.1287/isre.2022.1113>.
Likelihood-based approaches to estimate linear regression parameters and treatment effects in the presence of endogeneity. Specifically, this package includes James Heckman's classical simultaneous equation models-the sample selection model for outcome selection bias and hybrid model with structural shift for endogenous treatment. For more information, see the seminal paper of Heckman (1978) <DOI:10.3386/w0177> in which the details of these models are provided. This package accommodates repeated measures on subjects with a working independence approach. The hybrid model further accommodates treatment effect modification.
Fit the hierarchical and non-hierarchical Bayesian measurement models proposed by Bullock, Imai, and Shapiro (2011) <DOI:10.1093/pan/mpr031> to analyze endorsement experiments.  Endorsement experiments are a survey methodology for eliciting truthful responses to sensitive questions.  This methodology is helpful when measuring support for socially sensitive political actors such as militant groups.  The model is fitted with a Markov chain Monte Carlo algorithm and produces the output containing draws from the posterior distribution.
Maximum likelihood estimation of endogenous switching regression models from Heckman (1979) <doi:10.2307/1912352> and estimation of treatment effects.
Computes the expectation of the number of transmissions and receptions considering an End-to-End transport model with limited number of retransmissions per packet. It provides theoretical results and also estimated values based on Monte Carlo simulations. It is also possible to consider random data and ACK probabilities.
E-statistics (energy) tests and statistics for multivariate and univariate inference,
             including distance correlation, one-sample, two-sample, and multi-sample tests for
             comparing multivariate distributions, are implemented. Measuring and testing
             multivariate independence based on distance correlation, partial distance correlation,
             multivariate goodness-of-fit tests, k-groups and hierarchical clustering based on energy 
             distance, testing for multivariate normality, distance components (disco) for non-parametric 
             analysis of structured data, and other energy statistics/methods are implemented.
Provides a function for distribution free control chart based on the change point model, for multivariate statistical process control. The main constituent of the chart is the energy test that focuses on the discrepancy between empirical characteristic functions of two random vectors. This new control chart highlights in three aspects. Firstly, it is distribution free, requiring no knowledge of the random processes. Secondly, this control chart can monitor mean and variance simultaneously. Thirdly it is devised for multivariate time series which is more practical in real data application. Fourthly, it is designed for online detection (Phase II), which is central for real time surveillance of stream data. For more information please refer to O. Okhrin and Y.F. Xu (2017) <https://github.com/YafeiXu/working_paper/raw/master/CPM102.pdf>.
Data published by the United States Federal Energy Regulatory Commission including
    electric company financial data, natural gas company financial data, 
    hydropower plant data, liquified natural gas plant data, oil company financial data
    natural gas company financial data, and natural gas storage field data.
Compute energy landscapes using a digital elevation model raster and body mass of animals.
Fully robust versions of the elastic net estimator are introduced for linear and binary and multinomial regression, in particular high dimensional data. The algorithm searches for outlier free subsets on which the classical elastic net estimators can be applied. A reweighting step is added to improve the statistical efficiency of the proposed estimators. Selecting appropriate tuning parameters for elastic net penalties are done via cross-validation.
Allow numbers to be presented in an English language
        version, one, two, three, ...  Ordinals are also available,
        first, second, third, ... and indefinite article choice, "a" or "an".
Fits engression models for nonlinear distributional regression. Predictors and targets can be univariate or multivariate. Functionality includes estimation of conditional mean, estimation of conditional quantiles, or sampling from the fitted distribution. Training is done full-batch on CPU (the python version offers GPU-accelerated stochastic gradient descent). Based on "Engression: Extrapolation for nonlinear regression?" by Xinwei Shen and Nicolai Meinshausen (2023) <arxiv:2307.00835>.
Datasets from Nelson, Coffin and Copeland "Introductory
        Statistics for Engineering Experimentation" (Elsevier, 2003)
        with sample code.
Runs ecological niche models over all combinations of user-defined settings (i.e., tuning), performs cross validation to evaluate models, and returns data tables to aid in selection of optimal model settings that balance goodness-of-fit and model complexity. Also has functions to partition data spatially (or not) for cross validation, to plot multiple visualizations of results, to run null models to estimate significance and effect sizes of performance metrics, and to calculate niche overlap between model predictions, among others. The package was originally built for Maxent models (Phillips et al. 2006, Phillips et al. 2017), but the current version allows possible extensions for any modeling algorithm. The extensive vignette, which guides users through most package functionality but unfortunately has a file size too big for CRAN, can be found here on the package's Github Pages website: <https://jamiemkass.github.io/ENMeval/articles/ENMeval-2.0-vignette.html>.
Implements species distribution modeling and ecological niche
	modeling, including: bias correction, spatial cross-validation, model
	evaluation, raster interpolation, biotic "velocity" (speed and
	direction of movement of a "mass" represented by a raster), interpolating
	across a time series of rasters, and use of spatially imprecise records.
	The heart of the package is a set of "training" functions which
	automatically optimize model complexity based number of available
	occurrences. These algorithms include MaxEnt, MaxNet, boosted regression
	trees/gradient boosting machines, generalized additive models,
	generalized linear models, natural splines, and random forests. To enhance
	interoperability with other modeling packages, no new classes are created.
	The package works with 'PROJ6' geodetic objects and coordinate reference
	systems.
An algorithmic framework for measuring feature importance,
    outlier detection, model applicability domain evaluation,
    and ensemble predictive modeling with (sparse)
    partial least squares regressions.
A flexible tool for enrichment analysis based on user-defined sets. It allows users to perform over-representation analysis of the custom sets among any specified ranked feature list, hence making enrichment analysis applicable to various types of data from different scientific fields. 'EnrichIntersect' also enables an interactive means to visualize identified associations based on, for example, the mix-lasso model (Zhao et al., 2022 <doi:10.1016/j.isci.2022.104767>) or similar methods.
Provides an R interface to all 'Enrichr' databases. 'Enrichr' is a web-based tool for analysing gene sets and returns any enrichment of common annotated biological features. Quoting from their website 'Enrichment analysis is a computational method for inferring knowledge about an input gene set by comparing it to annotated gene sets representing prior biological knowledge.' See <https://maayanlab.cloud/Enrichr/> for further details.
Provides the "enrich" method to enrich list-like R objects with new, relevant components. The current version has methods for enriching objects of class 'family', 'link-glm', 'lm', 'glm' and 'betareg'. The resulting objects preserve their class, so all methods associated with them still apply. The package also provides the 'enriched_glm' function that has the same interface as 'glm' but results in objects of class 'enriched_glm'. In addition to the usual components in a `glm` object, 'enriched_glm' objects carry an object-specific simulate method and functions to compute the scores, the observed and expected information matrix, the first-order bias, as well as model densities, probabilities, and quantiles at arbitrary parameter values. The package can also be used to produce customizable source code templates for the structured implementation of methods to compute new components and enrich arbitrary objects.
An implementation of the clustering methods of categorical data
    discussed in Amiri, S., Clarke, B., and Clarke, J. (2015). Clustering categorical 
    data via ensembling dissimilarity matrices.  Preprint <arXiv:1506.07930>.
Extensible S4 classes and methods for batch training of regression and classification algorithms such as Random Forest, Gradient Boosting Machine, Neural Network, Support Vector Machines, K-Nearest Neighbors, Penalized Regression (L1/L2), and Bayesian Additive Regression Trees. These algorithms constitute a set of 'base learners', which can subsequently be combined together to form ensemble predictions. This package provides cross-validation wrappers to allow for downstream application of ensemble integration techniques, including best-error selection. All base learner estimation objects are retained, allowing for repeated prediction calls without the need for re-training. For large problems, an option is provided to save estimation objects to disk, along with prediction methods that utilize these objects. This allows users to train and predict with large ensembles of base learners without being constrained by system RAM.
Bayesian Model Averaging to create probabilistic forecasts
        from ensemble forecasts and weather observations
 <https://stat.uw.edu/sites/default/files/files/reports/2007/tr516.pdf>.
Extends the base classes and methods of EnsembleBase package for cross-validation-based integration of base learners. Default implementation calculates average of repeated CV errors, and selects the base learner / configuration with minimum average error. The package takes advantage of the file method provided in EnsembleBase package for writing estimation objects to disk in order to circumvent RAM bottleneck. Special save and load methods are provided to allow estimation objects to be saved to permanent files on disk, and to be loaded again into temporary files in a later R session. The package can be extended, e.g. by adding variants of the current implementation.
Ensemble Model Output Statistics to create probabilistic
        forecasts from ensemble forecasts and weather observations.
Extends the base classes and methods of 'EnsembleBase' package for Principal-Components-Regression-based (PCR) integration of base learners. Default implementation uses cross-validation error to choose the optimal number of PC components for the final predictor. The package takes advantage of the file method provided in 'EnsembleBase' package for writing estimation objects to disk in order to circumvent RAM bottleneck. Special save and load methods are provided to allow estimation objects to be saved to permanent files on disk, and to be loaded again into temporary files in a later R session. Users and developers can extend the package by extending the generic methods and classes provided in 'EnsembleBase' package as well as this package.
Extending the base classes and methods of EnsembleBase package for Penalized-Regression-based (Ridge and Lasso) integration of base learners. Default implementation uses cross-validation error to choose the optimal lambda (shrinkage parameter) for the final predictor. The package takes advantage of the file method provided in EnsembleBase package for writing estimation objects to disk in order to circumvent RAM bottleneck. Special save and load methods are provided to allow estimation objects to be saved to permanent files on disk, and to be loaded again into temporary files in a later R session. Users and developers can extend the package by extending the generic methods and classes provided in EnsembleBase package as well as this package.
Data sets for the chapter "Ensemble Postprocessing with R" of the book Stephane Vannitsem, Daniel S. Wilks, and Jakob W. Messner (2018) "Statistical Postprocessing of Ensemble Forecasts", Elsevier, 362pp. These data sets contain temperature and precipitation ensemble weather forecasts and corresponding observations at Innsbruck/Austria. Additionally, a demo with the full code of the book chapter is provided.
Functions to use ensembles of several machine learning models
    specified in caret package.
Creates ensemble taxonomic assignments of amplicon sequencing data 
  in R using outputs of multiple taxonomic assignment algorithms and/or
	reference databases. Includes flexible algorithms for mapping taxonomic 
	nomenclatures onto one another and for computing ensemble taxonomic 
	assignments.
Suite of tools to enable fast, efficient, high-throughput, R workflow integrable querying of 'Ensembl' REST API endpoints (<https://rest.ensembl.org/>).
Elastic net regression models are controlled by two parameters,
  lambda, a measure of shrinkage, and alpha, a metric defining the model's
  location on the spectrum between ridge and lasso regression.  
  glmnet provides tools for selecting lambda via cross
  validation but no automated methods for selection of alpha.  Elastic Net
  SearcheR automates the simultaneous selection of both lambda and alpha.
  Developed, in part, with support by NICHD R03 HD094912.
Add simple runtime contracts to R values. These ensure that values
    fulfil certain conditions and will raise appropriate errors if they do not.
Measurement and partitioning of diversity, based on Tsallis entropy, following Marcon and Herault (2015) <doi:10.18637/jss.v067.i08>.
  'entropart' provides functions to calculate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity.
  Estimation-bias corrections are available.
Contains methods for data analysis in entropic perspective. These entropic perspective methods are nonparametric, and perform better on non-ordinal data. Currently, the package has a function HeatMap() for visualizing distributional characteristics among multiple populations (groups).
Implements various estimators of entropy for discrete random 
  variables, including the shrinkage estimator by Hausser and Strimmer (2009),
  the maximum likelihood and the Millow-Madow estimator, various Bayesian
  estimators, and the Chao-Shen estimator.  It also offers an R interface to the
  NSB estimator.  Furthermore, the package provides functions for estimating the
  Kullback-Leibler divergence, the chi-squared divergence, mutual information,
  and the chi-squared divergence of independence.  It also computes the
  G statistic and the chi-squared statistic and corresponding p-values.
  Furthermore, there are functions for discretizing continuous random variables.
Contains methods for the estimation of Shannon's entropy, variants of Renyi's entropy, mutual information, Kullback-Leibler divergence, and generalized Simpson's indices. The estimators used have a bias that decays exponentially fast.
Tools for Markov Chain Monte Carlo (MCMC) simulation and performance analysis. Simulate MCMC algorithms including adaptive MCMC, evaluate their convergence rate, and compare candidate MCMC algorithms for a same target density, based on entropy and Kullback-Leibler divergence criteria. MCMC algorithms can be simulated using provided functions, or imported from external codes. This package is based upon work starting with Chauveau, D. and Vandekerkhove, P. (2013) <doi:10.1051/ps/2012004> and next articles.
Tools for measuring empirically the effects of entry in concentrated markets, based in Bresnahan and Reiss (1991) <https://www.jstor.org/stable/2937655>.
Small toolbox for data analyses in environmental chemistry and
    ecotoxicology. Provides, for example, calibration() to calculate calibration
    curves and corresponding limits of detection (LODs) and  limits of 
    quantification (LOQs) according to German DIN 32645 (2008). texture() makes
    it easy to estimate soil particle size distributions from hydrometer
    measurements (ASTM D422-63, 2007).
Tools for automatic model selection and diagnostics for Climate and Environmental data.  In particular the envcpt() function does automatic model selection between a variety of trend, changepoint and autocorrelation models.  The envcpt() function should be your first port of call.
Prints out information about the R working environment
    (system, R version,loaded and attached packages and versions) from a single
    function "env_doc()".  Optionally adds information on git repository,
    tags, commits and remotes (if available).
A collection of functions for microbial ecology and other
   applications of genomics and metagenomics. Companion package for the
   Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016
   <DOI:10.7287/peerj.preprints.1900v1>).
Estimates an ecological niche using occurrence data, covariates, and kernel
        density-based estimation methods. For a single species with presence and absence data,
        the 'envi' package uses the spatial relative risk function that is estimated using the
        'sparr' package. Details about the 'sparr' package methods can be found in the tutorial:
        Davies et al. (2018) <doi:10.1002/sim.7577>. Details about kernel density estimation can
        be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>. More information about
        relative risk functions using kernel density estimation can be found in J. F. Bithell
        (1991) <doi:10.1002/sim.4780101112>.
Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.
Fast and very memory-efficient calculation of isotope patterns,
    subsequent convolution to theoretical envelopes (profiles) plus valley
    detection and centroidization or intensoid calculation. Batch processing,
    resolution interpolation, wrapper, adduct calculations and molecular
    formula parsing.
	Loos, M., Gerber, C., Corona, F., Hollender, J., Singer, H. (2015) 
	<doi:10.1021/acs.analchem.5b00941>.
Provides a small set of functions for managing R environments, with defaults designed to encourage usage patterns that scale well to larger code bases. It provides: import_from(), a flexible way to assign bindings that defaults to the current environment; include(), a vectorized alternative to base::source() that also default to the current environment; and attach_eval() and attach_source(), a way to evaluate expressions in attached environments. Together, these (and other) functions pair to provide a robust alternative to base::library() and base::source().
Generation of bioclimatic rasters that are complementary to the typical 19 bioclim variables.
Methods to perform a Probabilistic Environmental Risk assessment from exposure to toxic substances - i.e. USEPA (1997) <https://www.epa.gov/risk/guiding-principles-monte-carlo-analysis> -.
Set of functions to keep track and find objects in user-defined environments
    by identifying environments by name --which cannot be retrieved with the built-in function environmentName().
    The package also provides functionality to obtain simplified information about function calling chains
    and to get an object's memory address.
A plot overlying the niche of multiple species is obtained: 1) to determine the niche conditions which favor a higher species richness, 2) to create a box plot with the range of environmental variables of the species, 3) to obtain a list of species in an area of the niche selected by the user and, 4) to estimate niche overlap among the species.
Contains utilities for the analysis of protein sequences in a phylogenetic context. 
    Allows   the generation of phylogenetic trees base on protein sequences in an alignment-independent way. 
    Two different methods have been implemented. One approach is based on the frequency analysis of n-grams, 
    previously described in Stuart et al. (2002) <doi:10.1093/bioinformatics/18.1.100>. The other approach is based on the species-specific neighborhood preference around amino acids. Features include the conversion of a protein set into a vector 
    reflecting these neighborhood preferences, pairwise distances (dissimilarity) between these vectors, 
    and the generation of trees based on these distance matrices.
Three semi-parametric methods for detection of outliers in environmental data based on kernel regression and subsequent analysis of smoothing residuals. The first method (Campulova, Michalek, Mikuska and Bokal (2018) <DOI: 10.1002/cem.2997>) analyzes the residuals using changepoint analysis, the second method is based on control charts (Campulova, Veselik and Michalek (2017) <DOI: 10.1016/j.apr.2017.01.004>) and the third method (Holesovsky, Campulova and Michalek (2018) <DOI: 10.1016/j.apr.2017.06.005>) analyzes the residuals using extreme value theory (Holesovsky, Campulova and Michalek (2018) <DOI: 10.1016/j.apr.2017.06.005>).
Runs a series of configurable tests against a user's compute 
  environment. This can be used for checking that things like a specific 
  directory or an environment variable is available before you start an analysis.
  Alternatively, you can use the package's situation report when filing error
  reports with your compute infrastructure.
Graphical and statistical analyses of environmental data, with 
  focus on analyzing chemical concentrations and physical parameters, usually in 
  the context of mandated environmental monitoring.  Major environmental 
  statistical methods found in the literature and regulatory guidance documents, 
  with extensive help that explains what these methods do, how to use them, 
  and where to find them in the literature.  Numerous built-in data sets from 
  regulatory guidance documents and environmental statistics literature.  Includes 
  scripts reproducing analyses presented in the book "EnvStats:  An R Package for 
  Environmental Statistics" (Millard, 2013, Springer, ISBN 978-1-4614-8455-4, 
  <https://link.springer.com/book/10.1007/978-1-4614-8456-1>).
A collection of functions that allows for easy and consistent use
  of environment variables. This includes setting, checking, retrieving,
  transforming, and validating values stored in environment variables.
Evidence of Absence software (EoA) is a user-friendly application for estimating bird and bat fatalities at wind farms and designing search protocols. The software is particularly useful in addressing whether the number of fatalities has exceeded a given threshold and what search parameters are needed to give assurance that thresholds were not exceeded. The models are applicable even when zero carcasses have been found in searches, following Huso et al. (2015) <doi:10.1890/14-0764.1>, Dalthorp et al. (2017) <doi:10.3133/ds1055>, and Dalthorp and Huso (2015) <doi:10.3133/ofr20151227>.
Provides wrap functions to export and import graphics and
             data frames in R to 'microsoft' office. And This package also 
             provide write out figures with lots of different formats.
             Since people may work on the platform without GUI support, the package 
             also provide function to easily write out figures
             to lots of different type of formats. Now this package provide function 
             to extract colors from all types of figures and pdf files.
This data management package provides some helper
    classes for publicly available data sources (HMD, DESTATIS) in
    Demography. Similar to ideas developed in the Bioconductor
    project <https://bioconductor.org> we strive to encapsulate data in easy
    to use S4 objects.
    If original data is provided in a text file, the resulting S4
    object contains all information from that text file. But the
    information is somehow structured (header, footer, etc).
    Further the classes provide methods to make a subset for selected
    calendar years or selected regions. The resulting subset
    objects still contain the original header and footer information.
A collection of nice plotting functions directly from a data.frame with limited customisation possibilities.
Analyzing censored variables usually requires the use of optimization algorithms. This package provides an alternative algebraic approach to the task of determining the expected value of a random censored variable with a known censoring point. Likewise this approach allows for the determination of the censoring point if the expected value is known. These results are derived under the assumption that the variable follows an Epanechnikov kernel distribution with known mean and range prior to censoring. Statistical functions related to the uncensored Epanechnikov distribution are also provided by this package.
Enables simulation of water piping networks using 'EPANET'.
    The package provides functions from the 'EPANET' programmer's toolkit as R
    functions so that basic or customized simulations can be carried out from R.
    The package uses 'EPANET' version 2.2 from Open Water Analytics
    <https://github.com/OpenWaterAnalytics/EPANET/releases/tag/v2.2>.
Reads water network simulation data in 'Epanet' text-based
    '.inp' and '.rpt' formats into R. Also reads results from 'Epanet-msx'.
    Provides basic summary information and plots.  The README file has a 
    quick introduction. See <http://www2.epa.gov/water-research/epanet> 
    for more information on the Epanet software for modeling
    hydraulic and water quality behavior of water piping systems.
Exploratory principal component analysis for large-scale dataset, including sparse principal component analysis and sparse matrix approximation.
The top-performing ensemble-based Penalized Cox Regression (ePCR) framework developed during the DREAM 9.5 mCRPC Prostate Cancer Challenge <https://www.synapse.org/ProstateCancerChallenge> presented in Guinney J, Wang T, Laajala TD, et al. (2017) <doi:10.1016/S1470-2045(16)30560-5> is provided here-in, together with the corresponding follow-up work. While initially aimed at modeling the most advanced stage of prostate cancer, metastatic Castration-Resistant Prostate Cancer (mCRPC), the modeling framework has subsequently been extended to cover also the non-metastatic form of advanced prostate cancer (CRPC). Readily fitted ensemble-based model S4-objects are provided, and a simulated example dataset based on a real-life cohort is provided from the Turku University Hospital, to illustrate the use of the package. Functionality of the ePCR methodology relies on constructing ensembles of strata in patient cohorts and averaging over them, with each ensemble member consisting of a highly optimized penalized/regularized Cox regression model. Various cross-validation and other modeling schema are provided for constructing novel model objects.
EPE's (Empresa de Pesquisa Energética) 4MD (Modelo de Mercado da Micro e Minigeração Distribuída - Micro and Mini Distributed Generation Market Model) model to forecast the adoption of Distributed Generation. Given the user's assumptions, it is possible to estimate how many consumer units will have distributed generation in Brazil over the next 10 years, for example. In addition, it is possible to estimate the installed capacity, the amount of investments that will be made in the country and the monthly energy contribution of this type of generation. <https://www.epe.gov.br/sites-pt/publicacoes-dados-abertos/publicacoes/PublicacoesArquivos/publicacao-689/topico-639/NT_Metodologia_4MD_PDE_2032_VF.pdf>.
Everglades Phosphorus Gradient Model predicts variations in water-column P concentration, peat accretion rate, and soil P concentration along a horizontal gradient imposed by an external phosphorus load and sheet-flow conditions. Potential biological responses are expressed in terms of marsh surface area exceeding threshold criteria for water-column and soil phosphorus concentrations. More information of the model can be found at <http://www.wwwalker.net/epgm/>.
Tools to download and manipulate the Permanent Household Survey from Argentina
    (EPH is the Spanish acronym for Permanent Household Survey).
    e.g: get_microdata() for downloading the datasets, get_poverty_lines() for downloading the official poverty baskets,
    calculate_poverty() for the calculation of stating if a household is in poverty or not, following the official methodology.
    organize_panels() is used to concatenate observations from different periods, and organize_labels()
    adds the official labels to the data. The implemented methods are based on INDEC (2016) <http://www.estadistica.ec.gba.gov.ar/dpe/images/SOCIEDAD/EPH_metodologia_22_pobreza.pdf>.
    As this package works with the argentinian Permanent Household Survey and its main audience is from this country,
    the documentation was written in Spanish.
Functions for demographic and epidemiological analysis in
  the Lexis diagram, i.e. register and cohort follow-up data. In
  particular representation, manipulation, rate estimation and
  simulation for multistate data - the Lexis suite of functions, which
  includes interfaces to 'mstate', 'etm' and 'cmprsk' packages.
  Contains functions for Age-Period-Cohort and Lee-Carter modeling and
  a function for interval censored data and some useful functions for
  tabulation and plotting, as well as a number of epidemiological data
  sets.
Contains elementary tools for analysis of
        common epidemiological problems, ranging from sample size
        estimation, through 2x2 contingency table analysis and basic
        measures of agreement (kappa, sensitivity/specificity).
        Appropriate print and summary statements are also written to
        facilitate interpretation wherever possible.  Source code is 	commented throughout to facilitate modification.  The target audience includes advanced undergraduate and graduate students
        in epidemiology or biostatistics courses, and clinical researchers.
Method and tool for generating time series forecasts using
        an ensemble wavelet-based auto-regressive neural network architecture. This method provides
        additional support of exogenous variables and also generates confidence interval. This 
        package provides EWNet model for time series forecasting based on the algorithm by
        Panja, et al. (2022) and Panja, et al. (2023) <arXiv:2206.10696> <doi:10.1016/j.chaos.2023.113124>.
Offers a tidy solution for epidemiological data. It houses a range of functions for epidemiologists and public health data wizards for data management and cleaning.
A collection of tools for representing epidemiological contact data, composed of case line lists and contacts between cases. Also contains procedures for data handling, interactive graphics, and statistics.
Routines for epidemiological contact tracing
    and visualisation of network of contacts.
Creates simple or stacked epidemic curves for hourly, daily, weekly or monthly outcome data.
The Economic Policy Institute (<https://www.epi.org/>) provides
    researchers, media, and the public with easily accessible, up-to-date, and
    comprehensive historical data on the American labor force. It is compiled
    from Economic Policy Institute analysis of government data sources. Use
    it to research wages, inequality, and other economic indicators over time
    and among demographic groups. Data is usually updated monthly.
The Delphi 'Epidata' API provides real-time access to epidemiological surveillance data for influenza, 'COVID-19', and other diseases for the USA at various geographical resolutions, both from official government sources such as the Center for Disease Control (CDC) and Google Trends and private partners such as Facebook and Change 'Healthcare'. It is built and maintained by the Carnegie Mellon University Delphi research group. To cite this API: David C. Farrow, Logan C. Brooks, Aaron 'Rumack', Ryan J. 'Tibshirani', 'Roni' 'Rosenfeld' (2015). Delphi 'Epidata' API. <https://github.com/cmu-delphi/delphi-epidata>.
Package for data exploration and result presentation. Full 'epicalc' package with data management functions is available at '<https://medipe.psu.ac.th/epicalc/>'.
Contains utilities and functions for the cleaning, processing and
    management of patient level public health data for surveillance
    and analysis held by the UK Health Security Agency, UKHSA.
Mathematical models of infectious diseases in humans and animals.
    Both, deterministic and stochastic models can be simulated and plotted.
Tools to quantify transmissibility throughout
    an epidemic from the analysis of time series of incidence as described in
    Cori et al. (2013) <doi:10.1093/aje/kwt133> and Wallinga and Teunis (2004) 
    <doi:10.1093/aje/kwh255>.
Analysis and visualization of plant disease progress curve data. Functions for
    fitting two-parameter population dynamics models (exponential, monomolecular, logistic
    and Gompertz) to proportion data for single or multiple epidemics using either linear
    or no-linear regression.  Statistical and visual outputs are provided to aid in model
    selection. Synthetic curves can be simulated for any of the models given the parameters.
    See Laurence V. Madden, Gareth Hughes, and Frank van den Bosch (2007) <doi:10.1094/9780890545058>
    for further information on the methods.
Provides functions and classes designed to handle and visualise
    epidemiological flows between locations. Also contains a statistical method
    for predicting disease spread from flow data initially described in
    Dorigatti et al. (2017) <doi:10.2807/1560-7917.ES.2017.22.28.30572>.
    This package is part of the RECON (<https://www.repidemicsconsortium.org/>)
    toolkit for outbreak analysis.
This is a collection of assorted functions and examples collected 
    from various projects. Currently we have functionalities for simplifying 
    overlapping time intervals, Charlson comorbidity score constructors for 
    Danish data, sibling design linear regression functionalities, and a method 
    for calculating the confidence intervals for functions of parameters from a 
    GLM.
The interface package to access data from the
    'EpiGraphDB' <https://epigraphdb.org> platform.
    It provides easy access to the 'EpiGraphDB' platform with functions that
    query the corresponding REST endpoints on the API <https://api.epigraphdb.org>
    and return the response data in the 'tibble' data frame format.
Provides tools for simulating from discrete-time individual level models for infectious disease data analysis. This epidemic model class contains spatial and contact-network based models with two disease types: Susceptible-Infectious (SI) and Susceptible-Infectious-Removed (SIR).
Provides tools for simulating from continuous-time individual level models of disease transmission, and carrying out infectious disease data analyses with the same models. The epidemic models considered are distance-based and/or contact network-based models within Susceptible-Infectious-Removed (SIR) or Susceptible-Infectious-Notified-Removed (SINR) compartmental frameworks. <doi:10.18637/jss.v098.i10>.
Using variational techniques we address some epidemiological
  problems as the incidence curve decomposition by inverting the renewal 
  equation as described in Alvarez et al. (2021) <doi:10.1073/pnas.2105112118> 
  and Alvarez et al. (2022) <doi:10.3390/biology11040540> or the estimation of 
  the functional relationship between epidemiological indicators. We also 
  propose a learning method for the short time forecast of the trend 
  incidence curve  as described in 
  Morel et al. (2022) <doi:10.1101/2022.11.05.22281904>.
Contains tools for formatting inline code, renaming redundant
  columns, aggregating age categories, adding survey weights, finding the earliest
  date of an event, plotting z-curves, generating population counts and 
  calculating proportions with confidence intervals. This is part of the 
  'R4Epis' project <https://r4epis.netlify.app/>.
The 'epilogi' variable selection algorithm is implemented for the case of continuous response and predictor variables. The relevant paper is: Lakiotaki K., Papadovasilakis Z., Lagani V., Fafalios S., Charonyktakis P., Tsagris M. and Tsamardinos I. (2023). "Automated machine learning for Genome Wide Association Studies". Bioinformatics. <doi:10.1002/sim.4780120902>.
Estimation of epidemiological parameters with 
 Laplacian-P-splines following the methodology of Gressani et al. (2022)
 <doi:10.1371/journal.pcbi.1010618>.
Functions, data sets and shiny apps for "Epidemics: Models and Data in R" by Ottar N. Bjornstad (ISBN 978-3-319-97487-3) <https://www.springer.com/gp/book/9783319974866>. The package contains functions to study the S(E)IR model, spatial and age-structured SIR models; time-series SIR and chain-binomial stochastic models; catalytic disease models; coupled map lattice models of spatial transmission and network models for social spread of infection. The package is also an advanced quantitative companion to the coursera Epidemics Massive Online Open Course <https://www.coursera.org/learn/epidemics>.
Functions, data sets and shiny apps for "Epidemics: Models and Data in R (2nd edition)" by Ottar N. Bjornstad (2022, ISBN: 978-3-031-12055-8) <https://link.springer.com/book/10.1007/978-3-319-97487-3>. The package contains functions to study the Susceptible-Exposed-Infected-Removed SEIR model, spatial and age-structured Susceptible-Infected-Removed SIR models; time-series SIR and chain-binomial stochastic models; catalytic disease models; coupled map lattice models of spatial transmission and network models for social spread of infection. The package is also an advanced quantitative companion to the 'Coursera' Epidemics Massive Online Open Course <https://www.coursera.org/learn/epidemics>.
Tools for simulating mathematical models of infectious disease dynamics.
    Epidemic model classes include deterministic compartmental models, stochastic
    individual-contact models, and stochastic network models. Network models use the
    robust statistical methods of exponential-family random graph models (ERGMs)
    from the Statnet suite of software packages in R. Standard templates for epidemic
    modeling include SI, SIR, and SIS disease types. EpiModel features an API for
    extending these templates to address novel scientific research aims. Full
    methods for EpiModel are detailed in Jenness et al. (2018, <doi:10.18637/jss.v084.i08>).
A collection of epidemic/network-related tools. Simulates transmission of diseases through contact networks. Performs Bayesian inference on network and epidemic parameters, given epidemic data.
Allows for forward-in-time simulation of epistatic networks with associated
    phenotypic output.
Estimates the time-varying reproduction number,
    rate of spread, and doubling time using a range of open-source tools
    (Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1>), and
    current best practices (Gostic et al. (2020)
    <doi:10.1101/2020.06.18.20134858>).  It aims to help users avoid some
    of the limitations of naive implementations in a framework that is
    informed by community feedback and is actively supported.
A collection of fast and flexible functions for analyzing
    omics data in observational studies. Multiple different approaches for
    integrating multiple environmental/genetic factors, omics data, and/or
    phenotype data are implemented. This includes functions for performing
    omics wide association studies with one or more variables of interest
    as the exposure or outcome; a function for performing a meet in the
    middle analysis for linking exposures, omics, and outcomes (as
    described by Chadeau-Hyam et al., (2010)
    <doi:10.3109/1354750X.2010.533285>); and a function for performing a
    mixtures analysis across all omics features using quantile-based
    g-Computation (as described by Keil et al., (2019)
    <doi:10.1289/EHP5838>).
Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Drafting an epidemiological report in 'Microsoft Word' format for a given disease,
  similar to the Annual Epidemiological Reports published by the European Centre 
  for Disease Prevention and Control. Through standalone functions, it is specifically 
  designed to generate each disease specific output presented in these reports and includes:
  - Table with the distribution of cases by Member State over the last five years;
  - Seasonality plot with the distribution of cases at the European Union / European Economic Area level, 
  by month, over the past five years;
  - Trend plot with the trend and number of cases at the European Union / European Economic Area level, 
  by month, over the past five years;
  - Age and gender bar graph with the distribution of cases at the European Union / European Economic Area level.
  Two types of datasets can be used:
  - The default dataset of dengue 2015-2019 data;
  - Any dataset specified as described in the vignette.
Searching genomic interactions with linear/logistic regression in a high-dimensional dataset is a time-consuming task. This package provides some efficient ways to scan epistasis in genome-wide interaction studies (GWIS). Both case-control status (binary outcome) and quantitative phenotype (continuous outcome) are supported (the main references: 1. Kam-Thong, T., D. Czamara, K. Tsuda, K. Borgwardt, C. M. Lewis, A. Erhardt-Lehmann, B. Hemmer, et al. (2011). <doi:10.1038/ejhg.2010.196>. 2. Kam-Thong, T., B. Pütz, N. Karbalai, B. Müller-Myhsok, and K. Borgwardt. (2011).  <doi:10.1093/bioinformatics/btr218>.)
DNA methylation (6mA) is a major epigenetic process by which alteration in gene expression took place without changing the DNA sequence. Predicting these sites in-vitro is laborious, time consuming as well as costly. This 'EpiSemble' package is an in-silico pipeline for predicting DNA sequences containing the 6mA sites. It uses an ensemble-based machine learning approach by combining Support Vector Machine (SVM), Random Forest (RF) and Gradient Boosting approach to predict the sequences with 6mA sites in it. This package has been developed by using the concept of Chen et al. (2019) <doi:10.1093/bioinformatics/btz015>.
Basic sensitivity analysis of the observed relative risks adjusting
    for unmeasured confounding and misclassification of the
    exposure/outcome, or both. It follows the bias analysis methods and
    examples from the book by Lash T.L, Fox M.P, and Fink A.K.
    "Applying Quantitative Bias Analysis to Epidemiologic Data",
    ('Springer', 2021).
Exploring time series for signal detection. It is specifically designed
    to detect possible outbreaks using infectious disease surveillance data
    at the European Union / European Economic Area or country level.
    Automatic detection tools used are presented in the paper
    "Monitoring count time series in R: aberration detection in public health surveillance",
    by Salmon (2016) <doi:10.18637/jss.v070.i10>.
    The package includes:
    - Signal Detection tool, an interactive 'shiny' application
      in which the user can import external data and perform basic signal detection analyses;
    - An automated report in HTML format, presenting the results of the time series analysis in tables and graphs.
      This report can also be stratified by population characteristics (see 'Population' variable).
    This project was funded by the European Centre for Disease Prevention and Control.
Provides set of functions aimed at epidemiologists. 
 The package includes commands for measures of association and impact for case control studies and cohort studies. 
 It may be particularly useful for outbreak investigations including univariable analysis and stratified analysis.
 The functions for cohort studies include the CS(), CSTable() and CSInter() commands. 
 The functions for case control studies include the CC(), CCTable() and CCInter() commands. 
 References - Cornfield, J. 1956. A statistical problem arising from retrospective studies. In Vol. 4 of Proceedings of the Third Berkeley Symposium, ed. J. Neyman, 135-148. Berkeley, CA - University of California Press.
 Woolf, B. 1955. On estimating the relation between blood group disease. 
 Annals of Human Genetics 19 251-253. Reprinted in Evolution of Epidemiologic Ideas Annotated Readings on Concepts and Methods, ed. S. Greenland, pp. 108-110. 
 Newton Lower Falls, MA Epidemiology Resources.
 Gilles Desve & Peter Makary, 2007. 'CSTABLE Stata module to calculate summary table for cohort study' Statistical Software Components S456879, Boston College Department of Economics.
 Gilles Desve & Peter Makary, 2007. 'CCTABLE Stata module to calculate summary table for case-control study' Statistical Software Components S456878, Boston College Department of Economics.
Constructing an epistemic model such that, for every player i and for every choice c(i) which is optimal, there is one type that expresses common belief in rationality.
Builds contingency tables that cross-tabulate multiple 
    categorical variables and also calculates various summary measures.
    Export to a variety of formats is supported, including: 'HTML', 
    'LaTeX', and 'Excel'.
Provides functions to test for gene x gene interactions in a
    bi-parental population of inbred lines. The data are fitted with the
    mixed linear model described in Rio et al. (2022) <doi:10.1101/2022.12.18.520958>, 
    that accounts for gene x gene interactions
    at both the fixed effect and variance levels. The package also
    provides graphical tools to display the gene x gene interaction trend at
    the mean level and the variance component analysis.
Tools for training and practicing epidemiologists including methods for two-way and multi-way contingency tables.
A collection of small functions useful for epidemics analysis and infectious disease modelling. This includes computation of basic reproduction numbers from growth rates, generation of hashed labels to anonymize data, and fitting discretized Gamma distributions.
A flexible framework for Agent-Based Models (ABM), the 'epiworldR' package provides methods for prototyping disease outbreaks and transmission models using a 'C++' backend, making it very fast. It supports multiple epidemiological models, including the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Removed (SIR), Susceptible-Exposed-Infected-Removed (SEIR), and others, involving arbitrary mitigation policies and multiple-disease models. Users can specify infectiousness/susceptibility rates as a function of agents' features, providing great complexity for the model dynamics. Furthermore, 'epiworldR' is ideal for simulation studies featuring large populations.
Collection of ancillary functions and utilities for Partial Linear Single Index Models for Environmental mixture analyses, which currently provides functions for scalar outcomes. The outputs of these functions include the single index function, single index coefficients, partial linear coefficients, mixture overall effect, exposure main and interaction effects, and differences of quartile effects. In the future, we will add functions for binary, ordinal, Poisson, survival, and longitudinal outcomes, as well as models for time-dependent exposures. See Wang et al (2020) <doi:10.1186/s12940-020-00644-4> for an overview.
A rich toolkit of using the whole building
    simulation program 'EnergyPlus'(<https://energyplus.net>), which
    enables programmatic navigation, modification of 'EnergyPlus' models
    and makes it less painful to do parametric simulations and analysis.
Evaluate a function over a data frame of expressions.
Facilitates the aggregation of species' geographic ranges from vector or raster spatial data, and that enables the calculation of various morphological and phylogenetic community metrics across geography. Citation: Title, PO, DL Swiderski and ML Zelditch (2022) <doi:10.1111/2041-210X.13914>.
Package provides a set of tools for robust estimation and inference for probit model with endogenous covariates. The current version contains a robust two-step estimator. For technical details, see Naghi, Varadi and Zhelonkin (2022), <doi:10.1016/j.ecosta.2022.05.001>.
Implements the Enhanced Portfolio Optimization (EPO) method as 
    described in Pedersen, Babu and Levine (2021)
    <doi:10.2139/ssrn.3530390>.
Estimates sparse matrices A or G using fast lasso regression from mRNA transcript levels Y and CNA profiles U. Two models are provided, EPoC A where
      AY + U + R = 0
  and EPoC G where
      Y = GU + E,
  the matrices R and E are so far treated as noise. For
  details see the manual page of 'lassoshooting' and the
  article Rebecka Jörnsten, Tobias Abenius, Teresia Kling, 
  Linnéa Schmidt, Erik Johansson, Torbjörn E M Nordling, 
  Bodil Nordlander, Chris Sander, Peter Gennemark, 
  Keiko Funa, Björn Nilsson, Linda Lindahl, Sven Nelander
  (2011) <doi:10.1038/msb.2011.17>.
Clinical coding and diagnosis of patients with kidney using
    clinical practice guidelines. The guidelines used are the evidence-based
    KDIGO guidelines, see <https://kdigo.org/guidelines/> for more information.
    This package covers acute kidney injury (AKI), anemia, and
    chronic kidney disease (CKD).
Provides a set of functions, which facilitates removing objects from an environment. 
             It allows to delete objects specified with regular expression or with other conditions (e.g. if object is numeric),
             using one function call.
Analysis and visualization of similarities between epilepsy ontologies based on text mining results by comparing ranked lists of co-occurring drug terms in the BioASQ corpus. The ranked result lists of neurological drug terms co-occurring with terms from the epilepsy ontologies EpSO, ESSO, EPILONT, EPISEM and FENICS undergo further analysis. The source data to create the ranked lists of drug names is produced using the text mining workflows described in Mueller, Bernd and Hagelstein, Alexandra (2016) <doi:10.4126/FRL01-006408558>, Mueller, Bernd et al. (2017) <doi:10.1007/978-3-319-58694-6_22> and Mueller, Bernd and Rebholz-Schuhmann, Dietrich (2020) <doi:10.1007/978-3-030-43887-6_52>.
Extra strength 'glue' for data-driven templates. String
    interpolation for 'Shiny' apps or 'R Markdown' and 'knitr'-powered
    'Quarto' documents, built on the 'glue' and 'whisker' packages.
Performs analysis of polynomial regression in simple designs with quantitative treatments.
Implements the conditional estimation procedure of
  Lee, Sun, Sun and Taylor (2016) <doi:10.1214/15-AOS1371>.
  This procedure allows hypothesis testing on the mean of
  a normal random vector subject to linear constraints.
For multiscale analysis, this package carries out ensemble patch transform, its visualization and multiscale decomposition. The detailed procedure is described in Kim et al. (2020), and Oh and Kim (2020). D. Kim, G. Choi, H.-S. Oh, Ensemble patch transformation: a flexible framework for decomposition and filtering of signal, EURASIP Journal on Advances in Signal Processing 30 (2020) 1-27 <doi:10.1186/s13634-020-00690-7>. H.-S. Oh, D. Kim, Image decomposition by bidimensional ensemble patch transform, Pattern Recognition Letters 135 (2020) 173-179 <doi:10.1016/j.patrec.2020.03.029>.
Provides functions supporting the reading and parsing of internal e-book content from EPUB files. 
    The 'epubr' package provides functions supporting the reading and parsing of internal e-book content from EPUB files. 
    E-book metadata and text content are parsed separately and joined together in a tidy, nested tibble data frame. 
    E-book formatting is not completely standardized across all literature. 
    It can be challenging to curate parsed e-book content across an arbitrary collection of e-books 
    perfectly and in completely general form, to yield a singular, consistently formatted output. 
    Many EPUB files do not even contain all the same pieces of information in their respective metadata. 
    EPUB file parsing functionality in this package is intended for relatively general application to arbitrary EPUB e-books. 
    However, poorly formatted e-books or e-books with highly uncommon formatting may not work with this package. 
    There may even be cases where an EPUB file has DRM or some other property that makes it impossible to read with 'epubr'. 
    Text is read 'as is' for the most part. The only nominal changes are minor substitutions, for example curly quotes changed to straight quotes. 
    Substantive changes are expected to be performed subsequently by the user as part of their text analysis. 
    Additional text cleaning can be performed at the user's discretion, such as with functions from packages like 'tm' or 'qdap'.
Query, download climate change projection data from the 'CMIP6' (Coupled
    Model Intercomparison Project Phase 6) project
    <https://pcmdi.llnl.gov/CMIP6/> in the 'ESGF' (Earth System Grid Federation)
    platform <https://esgf.llnl.gov>, and create future 'EnergyPlus'
    <https://energyplus.net> Weather ('EPW') files adjusted from climate changes
    using data from Global Climate Models ('GCM').
An ensemble method for the statistical detection of
    a rare class in two-class classification problems. The method uses an
    ensemble of classifiers where the constituent
    models of the ensemble use disjoint subsets (phalanxes) of explanatory
    variables. We provide an implementation of the phalanx-formation algorithm.
    Please see Tomal et al. (2015) <doi:10.1214/14-AOAS778>,
    Tomal et al. (2016) <doi:10.1021/acs.jcim.5b00663>, and
    Tomal et al. (2019) <arXiv:1706.06971> for more details.
Import data from 'Epidata' XML files '.epx' and convert it to R data structures.
EQ-5D is a popular health related quality of life instrument used 
    in the clinical and economic evaluation of health care. Developed by the 
    EuroQol group <https://euroqol.org/>, the instrument consists of two 
    components: health state description and evaluation. For the description 
    component a subject self-rates their health in terms of five dimensions; 
    mobility, self-care, usual activities, pain/discomfort, and 
    anxiety/depression using either a three-level (EQ-5D-3L,
    <https://euroqol.org/eq-5d-instruments/eq-5d-3l-about/>) or a five-level
    (EQ-5D-5L, <https://euroqol.org/eq-5d-instruments/eq-5d-5l-about/>) 
    scale. Frequently the scores on these five dimensions are converted to a 
    single utility index using country specific value sets, which can be used
    in the clinical and economic evaluation of health care as well as in 
    population health surveys. The eq5d package provides methods to calculate 
    index scores from a subject's dimension scores. 29 TTO and 11 VAS EQ-5D-3L
    value sets including those for countries in Szende et al (2007) 
    <doi:10.1007/1-4020-5511-0> and Szende et al (2014) 
    <doi:10.1007/978-94-007-7596-1>, 40 EQ-5D-5L EQ-VT value sets, the 
    EQ-5D-5L crosswalk value sets developed by van Hout et al. (2012) 
    <doi:10.1016/j.jval.2012.02.008>, the crosswalk value set for Russia and 
    reverse crosswalk value sets. Nine EQ-5D-Y value sets are also included 
    as are the NICE 'DSU' age-sex based EQ-5D-3L to EQ-5D-5L and EQ-5D-5L to 
    EQ-5D-3L mappings. Methods are also included for the analysis of EQ-5D 
    profiles along with a shiny web tool to enable the calculation, 
    visualisation and automated statistical analysis of EQ-5D data via a web 
    browser using EQ-5D dimension scores stored in CSV or Excel files.
Computation of the EQL for a given family of variance
        functions, Saddlepoint-approximations and related auxiliary
        functions (e.g. Hermite polynomials).
Tests the equality of two covariance matrices, used in paper "Two sample tests for high dimensional covariance matrices." Li and Chen (2012) <arXiv:1206.0917>.
The equality of a large number k of densities is tested by measuring the L2 distance between the corresponding kernel density estimators and the one based on the pooled sample. The test even works for sample sizes as small as 2.
Functions for examining measurement invariance via equivalence testing are included in this package. The traditionally used RMSEA (Root Mean Square Error of Approximation) cutoff values are adjusted based on simulation results. In addition, a projection-based method is implemented to test the equality of latent factor means across groups without assuming the equality of intercepts. For more information, see Yuan, K. H., & Chan, W. (2016) <doi:10.1037/met0000080>, Deng, L., & Yuan, K. H. (2016) <doi:10.1007/s11336-015-9491-8>, and Jiang, G., Mai, Y., & Yuan, K. H. (2017) <doi:10.3389/fpsyg.2017.01823>.
Provides function to transform latex math expressions 
 into format 'HTML' or 'Office Open XML Math'. The 'XML' 
 result can then be included in 'HTML', 'Microsoft Word' 
 documents or 'Microsoft PowerPoint' presentations by using 
 a 'Markdown' document or the R package 'officer'.
Contains methods for observed-score linking
  and equating under the single-group, equivalent-groups,
  and nonequivalent-groups with anchor test(s) designs.
  Equating types include identity, mean, linear, general
  linear, equipercentile, circle-arc, and composites of
  these. Equating methods include synthetic, nominal
  weights, Tucker, Levine observed score, Levine true
  score, Braun/Holland, frequency estimation, and chained
  equating. Plotting and summary methods, and methods for
  multivariate presmoothing and bootstrap error estimation
  are also provided.
Computation of direct, chain and average (bisector) equating coefficients with 
  standard errors using Item Response Theory (IRT) methods for dichotomous items 
  (Battauz (2013) <doi:10.1007/s11336-012-9316-y>, 
  Battauz (2015) <doi:10.18637/jss.v068.i07>). 
  Test scoring can be performed by true score equating and observed score equating methods. 
  DIF detection can be performed using a Wald-type test  
  (Battauz (2019) <doi:10.1007/s10260-018-00442-w>).
  The package includes tests to access the stability of the equating transformations
  (Battauz(2022) <doi:10.1111/stan.12277>).
Equating of multiple forms using Item Response Theory (IRT) methods (Battauz M. (2017) <doi:10.1007/s11336-016-9517-x> and Haberman S. J. (2009) <doi:10.1002/j.2333-8504.2009.tb02197.x>).
Saturation of ionic substances in urine is calculated based on
  sodium, potassium, calcium, magnesium, ammonia, chloride, phosphate, sulfate,
  oxalate, citrate, ph, and urate.  This program is intended for research use,
  only.  The code within is translated from EQUIL2 Visual Basic code based on
  Werness, et al (1985) "EQUIL2: a BASIC computer program for the calculation
  of urinary saturation" <doi:10.1016/s0022-5347(17)47703-2> to R. The Visual
  Basic code was kindly provided by Dr. John Lieske of the Mayo Clinic.
We provide a non-parametric and a parametric approach to investigate the equivalence (or non-inferiority) of two survival curves, obtained from two given datasets. The test is based on the creation of confidence intervals at pre-specified time points.
    For the non-parametric approach, the curves are given by Kaplan-Meier curves and the variance for calculating the confidence intervals is obtained by Greenwood's formula.
    The parametric approach is based on estimating the underlying distribution, where the user can choose between a Weibull, Exponential, Gaussian, Logistic, Log-normal or a Log-logistic distribution. Estimates for the variance for calculating the confidence bands are obtained by a (parametric) bootstrap approach. For this bootstrap censoring is assumed to be exponentially distributed and estimates are obtained from the datasets under consideration.
    All details can be found in K.Moellenhoff and A.Tresch: Survival analysis under non-proportional hazards: investigating non-inferiority or equivalence in time-to-event data <arXiv:2009.06699>.
Provides statistical tests and graphics for assessing tests
        of equivalence.  Such tests have similarity as the alternative
	hypothesis instead of the null.  Sample data sets are included.
Two methods for performing equivalence test for the means of two (test and reference) normal distributions are implemented. The null hypothesis of the equivalence test is that the absolute difference between the two means are greater than or equal to the equivalence margin and the alternative is that the absolute difference is less than the margin. Given that the margin is often difficult to obtain a priori, it is assumed to be a constant multiple of the standard deviation of the reference distribution. The first method assumes a fixed margin which is a constant multiple of the estimated standard deviation of the reference data and whose variability is ignored. The second method takes into account the margin variability. In addition, some tools to summarize and illustrate the data and test results are included to facilitate the evaluation of the data and interpretation of the results.
Making available in R the complete set of programs accompanying S. Wellek's (2010) monograph
             ''Testing Statistical Hypotheses of Equivalence and Noninferiority. Second Edition''
             (Chapman&Hall/CRC).
Implementation of uniformly most powerful invariant equivalence
    tests for one- and two-sample problems (paired and unpaired) as described 
    in Wellek (2010, ISBN:978-1-4398-0818-4). Also one-sided alternatives 
    (non-inferiority and non-superiority tests) are supported. Basically a variant 
    of a t-test with (relaxed) null and alternative hypotheses exchanged.
Multivariate modeling of data after deflation of interfering effects. EF Mosleth et al. (2021) <doi:10.1038/s41598-021-82388-w> and EF Mosleth et al. (2020) <doi:10.1016/B978-0-12-409547-2.14882-6>.
Provides a consistent representation of year-based time scales as a
    numeric vector with an associated 'era'. There are built-in era definitions
    for many year numbering systems used in contemporary and historic calendars 
    (e.g. Common Era, Islamic 'Hijri' years); year-based time scales used in 
    archaeology, astronomy, geology, and other palaeosciences (e.g. 
    Before Present, SI-prefixed 'annus'); and support for arbitrary user-defined
    eras. Years can converted from any one era to another using a generalised 
    transformation function. Methods are also provided for robust casting and 
    coercion between years and other numeric types, type-stable arithmetic with 
    years, and pretty-printing in tables.
Automated compound deconvolution, alignment across samples, and identification of metabolites by spectral library matching in Gas Chromatography - Mass spectrometry (GC-MS) untargeted metabolomics. Outputs a table with compound names, matching scores and the integrated area of the compound for each sample. Package implementation is described in Domingo-Almenara et al. (2016) <doi:10.1021/acs.analchem.6b02927>.
Provides a methodology simple and trustworthy for the analysis of extreme values and multiple threshold tests for a generalized Pareto distribution, together
    with an automatic threshold selection algorithm. See del Castillo, J, Daoudi, J and Lockhart, R (2014) <doi:10.1111/sjos.12037>.
Functions, datasets, and sample codes related to the book of 'Empirical Research in Economics: Growing up with R' by Dr. Changyou Sun are included. Marginal effects for binary or ordered choice models can be calculated. Static and dynamic Almost Ideal Demand System (AIDS) models can be estimated. A typical event analysis in finance can be conducted with several functions included.
Fits the Expectile Regression for Fixed Effect (ERFE)
    estimator. The ERFE model extends the within-transformation strategy
    to solve the incidental parameter problem within the expectile
    regression framework. The ERFE model estimates the regressor effects
    on the expectiles of the response distribution.  The ERFE estimate
    corresponds to the classical fixed-effect within-estimator when the
    asymmetric point is 0.5. The paper by Barry, Oualkacha, and
    Charpentier (2021, <arXiv:2108.04737>) gives more details about the
    ERFE model.
An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis. See Hunter, Handcock, Butts, Goodreau, and Morris (2008) <doi:10.18637/jss.v024.i03> and Krivitsky, Hunter, Morris, and Klumb (2023) <doi:10.18637/jss.v105.i06>.
A set of extensions for the 'ergm' package to fit weighted networks whose edge weights are counts. See Krivitsky (2012) <doi:10.1214/12-EJS696> and Krivitsky, Hunter, Morris, and Klumb (2021) <arXiv:2106.04997>.
Utilities for managing egocentrically sampled network data and a wrapper around the 'ergm' package to facilitate ERGM inference and simulation from such data. See Krivitsky and Morris (2017) <doi:10.1214/16-AOAS1010>.
A set of extensions for the 'ergm' package to fit multilayer/multiplex/multirelational networks and samples of multiple networks. 'ergm.multi' is a part of the Statnet suite of packages for network analysis. See Krivitsky, Koehly, and Marcum (2020) <doi:10.1007/s11336-020-09720-7> and Krivitsky, Coletti, and Hens (2022) <doi:10.48550/arXiv.2202.03685>.
A set of extensions for the 'ergm' package to fit weighted networks whose edge weights are ranks. See Krivitsky and Butts (2017) <doi:10.1177/0081175017692623> and Krivitsky, Hunter, Morris, and Klumb (2021) <arXiv:2106.04997>.
Calculates marginal effects and conducts process analysis in exponential family random graph models (ERGM).
    Includes functions to conduct mediation and moderation analyses and to diagnose
    multicollinearity.
    URL: <https://github.com/sduxbury/ergMargins>.
    BugReports: <https://github.com/sduxbury/ergMargins/issues>.
    Duxbury, Scott W (2021) <doi:10.1177/0049124120986178>.
    Long, J. Scott, and Sarah Mustillo (2018) <doi:10.1177/0049124118799374>.
    Mize, Trenton D. (2019) <doi:10.15195/v6.a4>.
    Karlson, Kristian Bernt, Anders Holm, and Richard Breen (2012) <doi:10.1177/0081175012444861>.
    Duxbury, Scott W (2018) <doi:10.1177/0049124118782543>.
    Duxbury, Scott W, Jenna Wertsching (2023) <doi:10.1016/j.socnet.2023.02.003>.
Provides tools for simulating draws from continuous time processes with well-defined exponential family random graph (ERGM) equilibria, i.e. ERGM generating processes (EGPs).  A number of EGPs are supported, including the families identified in Butts (2023) <doi:10.1080/0022250X.2023.2180001>, as are functions for hazard calculation and timing calibration.
Data for use with the Sage Introduction to Exponential
        Random Graph Modeling text by Jenine K. Harris.  Network data
        set consists of 1283 local health departments and the
        communication links among them along with several attributes.
Simulation and estimation of Exponential Random Graph Models (ERGMs)
  for small networks using exact statistics as shown in Vega Yon et al. (2020)
  <DOI:10.1016/j.socnet.2020.07.005>. As a difference from the 'ergm'
  package, 'ergmito' circumvents using Markov-Chain Maximum Likelihood Estimator
  (MC-MLE) and instead uses Maximum Likelihood Estimator (MLE) to fit ERGMs
  for small networks. As exhaustive enumeration is computationally feasible for
  small networks, this R package takes advantage of this and provides tools for
  calculating likelihood functions, and other relevant functions, directly,
  meaning that in many cases both estimation and simulation of ERGMs for
  small networks can be faster and more accurate than simulation-based
  algorithms.
Provides several validator functions for checking if arguments
    passed by users have valid types, lengths, etc. and for generating
    informative and well-formatted error messages in a consistent style. Also
    provides tools for users to create their own validator functions. The
    error message style used is adopted from
    <https://style.tidyverse.org/error-messages.html>.
Fits Rasch models (RM), linear logistic test models (LLTM), rating scale model (RSM), linear rating scale models (LRSM), partial credit models (PCM), and linear partial credit models (LPCM).  Missing values are allowed in the data matrix.  Additional features are the ML estimation of the person parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test, nonparametric Monte-Carlo Tests, itemfit and personfit statistics including infit and outfit measures, ICC and other plots, automated stepwise item elimination, simulation module for various binary data matrices.
Functions for signal detection and identification designed for Event-Related Potentials (ERP) data in a linear model framework. The functional F-test proposed in Causeur, Sheu, Perthame, Rufini (2018, submitted) for analysis of variance issues in ERP designs is implemented for signal detection (tests for mean difference among groups of curves in One-way ANOVA designs for example). Once an experimental effect is declared significant, identification of significant intervals is achieved by the multiple testing procedures reviewed and compared in Sheu, Perthame, Lee and Causeur (2016, <DOI:10.1214/15-AOAS888>). Some of the methods gathered in the package are the classical FDR- and FWER-controlling procedures, also available using function p.adjust. The package also implements the Guthrie-Buchwald procedure (Guthrie and Buchwald, 1991 <DOI:10.1111/j.1469-8986.1991.tb00417.x>), which accounts for the auto-correlation among t-tests to control erroneous detection of short intervals. The Adaptive Factor-Adjustment method is an extension of the method described in Causeur, Chu, Hsieh and Sheu (2012, <DOI:10.3758/s13428-012-0230-0>). It assumes a factor model for the correlation among tests and combines adaptively the estimation of the signal and the updating of the dependence modelling (see Sheu et al., 2016, <DOI:10.1214/15-AOAS888> for further details).
A set of user-friendly functions to aid in organizing, plotting
    and analyzing event-related potential (ERP) data.  Provides an easy-to-learn
    method to explore ERP data. Should be useful to those without a background
    in computer programming, and to those who are new to ERPs (or new to the
    more advanced ERP software available). Emphasis has been placed on highly
    automated processes using functions with as few arguments as possible.
    Expects processed (cleaned) data.
Computes the probability density and cumulative distribution functions of fourteen distributions used for the probabilistic hazard assessment. Estimates the model parameters of the distributions using the maximum likelihood and reports the goodness-of-fit statistics. The recurrence interval estimations of earthquakes are computed for each distribution.
Messages should provide users with readable information 
    about R objects without flooding their console. 
    'cc()' concatenates vector and data frame values 
    into a grammatically correct string using commas, an ellipsis and conjunction. 
    'cn()' allows the user to define a string which varies based on a count.
    'co()' combines the two to produce a customizable object aware string.
    The package further facilitates this process by providing five 'sprintf'-like 
    types such as '%n' for the length of an object and '%o' for its name as
    well as wrappers for pasting objects and issuing errors, warnings and messages.
Builds and analyzes error intervals for a particular model predictions assuming different distributions for noise in the data.
Provides environment hooks that obtain errors and warnings which
    occur during the execution of code to automatically search for solutions.
Errors in data can be located and removed using validation rules from package 
   'validate'. See also Van der Loo and De Jonge (2018) <doi:10.1002/9781118897126>,
   chapter 7.
Support for measurement errors in R vectors, matrices and arrays:
    automatic uncertainty propagation and reporting.
    Documentation about 'errors' is provided in the paper by Ucar, Pebesma &
    Azcorra (2018, <doi:10.32614/RJ-2018-075>), included in this package as a
    vignette; see 'citation("errors")' for details.
Perform a Bayesian estimation of the exploratory reduced
    reparameterized unified model (ErRUM) described by Culpepper and Chen (2018)
    <doi:10.3102/1076998618791306>.
Constructs a 'shiny' app function with interactive displays for summary and analysis of variance regression tables, and parallel coordinate plots of data and residuals.
Creates realistic random trajectories in a 3-D space between two given fix points, so-called conditional empirical random walks (CERWs). The trajectory generation is based on empirical distribution functions extracted from observed trajectories (training data) and thus reflects the geometrical movement characteristics of the mover. A digital elevation model (DEM), representing the Earth's surface, and a background layer of probabilities (e.g. food sources, uplift potential, waterbodies, etc.) can be used to influence the trajectories.
    Unterfinger M (2018). "3-D Trajectory Simulation in Movement Ecology: Conditional Empirical Random Walk". Master's thesis, University of Zurich. <https://www.geo.uzh.ch/dam/jcr:6194e41e-055c-4635-9807-53c5a54a3be7/MasterThesis_Unterfinger_2018.pdf>.
    Technitis G, Weibel R, Kranstauber B, Safi K (2016). "An algorithm for empirically informed random trajectory generation between two endpoints". GIScience 2016: Ninth International Conference on Geographic Information Science, 9, online. <doi:10.5167/uzh-130652>.
Computes various effect sizes of the difference, their variance, and confidence interval. This package treats Cohen's d, Hedges' d, biased/unbiased c (an effect size between a mean and a constant) and e (an effect size between means without assuming the variance equality).
These functions estimate the latent factors of a given matrix, no matter it is high-dimensional or not. It tries to first estimate the number of factors using bi-cross-validation and then estimate the latent factor matrix and the noise variances. For more information about the method, see Art B. Owen and Jingshu Wang 2015 archived article on factor model (<arXiv:1503.03515>).
Tools for fitting the Extended Empirical Saddlepoint (EES) density of Fasiolo et al. (2018) <doi:10.1214/18-EJS1433>.
It allows structuring electoral data of different size and structure 
        to calculate various indicators frequently used in the studies of electoral systems and party systems.
        Indicators of electoral volatility, electoral disproportionality, party nationalization and the 
        effective number of parties are included.
Implementations of the expected shortfall backtests of Bayer and Dimitriadis (2020) <doi:10.1093/jjfinec/nbaa013> 
    as well as other well known backtests from the literature. Can be used to assess the correctness of forecasts of the 
    expected shortfall risk measure which is e.g. used in the banking and finance industry for quantifying the market risk 
    of investments. A special feature of the backtests of  Bayer and Dimitriadis (2020) <doi:10.1093/jjfinec/nbaa013> 
    is that they only require forecasts of  the expected shortfall, which is in striking contrast to all other existing 
    backtests, making them particularly attractive for practitioners.
Implementation of the web-based 'Practical Meta-Analysis Effect Size
    Calculator' from David B. Wilson (<http://www.campbellcollaboration.org/escalc/html/EffectSizeCalculator-Home.php>)
    in R. Based on the input, the effect size can be returned as standardized mean 
    difference, Cohen's f, Hedges' g, Pearson's r or Fisher's
    transformation z, odds ratio or log odds, or eta squared effect size.
Methods for working with dose-finding clinical trials. We provide 
    implementations of many dose-finding clinical trial designs, including the 
    continual reassessment method (CRM) by O'Quigley et al. (1990) 
    <doi:10.2307/2531628>, the toxicity probability interval (TPI) design by Ji
    et al. (2007) <doi:10.1177/1740774507079442>, the modified TPI (mTPI) design
    by Ji et al. (2010) <doi:10.1177/1740774510382799>, the Bayesian optimal 
    interval design (BOIN) by Liu & Yuan (2015) <doi:10.1111/rssc.12089>, EffTox
    by Thall & Cook (2004) <doi:10.1111/j.0006-341X.2004.00218.x>; the design of
    Wages & Tait (2015) <doi:10.1080/10543406.2014.920873>, and the 3+3 
    described by Korn et al. (1994) <doi:10.1002/sim.4780131802>. All designs
    are implemented with a common interface. We also offer optional additional 
    classes to tailor the behaviour of all designs, including avoiding skipping 
    doses, stopping after n patients have been treated at the recommended dose,  
    stopping when a toxicity condition is met, or demanding that n patients are 
    treated before stopping is allowed. By daisy-chaining together these classes
    using the pipe operator from 'magrittr', it is simple to tailor the 
    behaviour of a dose-finding design so it behaves how the trialist wants.
    Having provided a flexible interface for specifying designs, we then provide
    functions to run simulations and calculate dose-paths for future cohorts of 
    patients.
The experiment selector cross-validated targeted maximum likelihood estimator (ES-CVTMLE) aims to select the experiment that optimizes the bias-variance tradeoff for estimating a causal average treatment effect (ATE) where different experiments may include a randomized controlled trial (RCT) alone or an RCT combined with real-world data. Using cross-validation, the ES-CVTMLE separates the selection of the optimal experiment from the estimation of the ATE for the chosen experiment. The estimated bias term in the selector is a function of the difference in conditional mean outcome under control for the RCT compared to the combined experiment. In order to help include truly unbiased external data in the analysis, the estimated average treatment effect on a negative control outcome may be added to the bias term in the selector. For more details about this method, please see Dang et al. (2022) <arXiv:2210.05802>.
Software of 'esDesign' is developed to implement the adaptive 
    enrichment designs with sample size re-estimation presented in 
    Lin et al. (2021) <doi: 10.1016/j.cct.2020.106216>. In details, 
    three-proposed trial designs are provided, including the AED1-SSR (or ES1-SSR),
    AED2-SSR (or ES2-SSR) and AED3-SSR (or ES3-SSR). In addition, this package 
    also contains several widely used adaptive designs, such as the Marker 
    Sequential Test (MaST) design proposed Freidlin et al. 
    (2014) <doi:10.1177/1740774513503739>, the adaptive enrichment designs 
    without early stopping (AED or ES), the sample size re-estimation 
    procedure (SSR) based on the conditional power proposed by 
    Proschan and Hunsberger (1995), and some useful functions. 
    In details, we can calculate the futility and/or efficacy stopping 
    boundaries, the sample size required, calibrate the value of the threshold 
    of the difference between subgroup-specific test statistics, conduct the 
    simulation studies in AED, SSR, AED1-SSR, AED2-SSR and AED3-SSR.
A tool which allows users to create and evaluate ensembles 
    of species distribution model (SDM) predictions. 
    Functionality is offered through R functions or a GUI (R Shiny app). 
    This tool can assist users in identifying spatial uncertainties and 
    making informed conservation and management decisions. The package is 
    further described in Woodman et al (2019) <doi:10.1111/2041-210X.13283>.
Environmental seismology is a scientific field that studies the  
    seismic signals, emitted by Earth surface processes. This package 
    provides all relevant functions to read/write seismic data files, prepare, 
    analyse and visualise seismic data, and generate reports of the processing 
    history.
Endpoint selection and sample size reassessment for multiple binary endpoints based on blinded and/or unblinded data. Trial design that allows an adaptive modification of the primary endpoint based on blinded information obtained at an interim analysis. The decision rule chooses the endpoint with the lower estimated required sample size. Additionally, the sample size is reassessed using the estimated event probabilities and correlation between endpoints. The implemented design is proposed in Bofill Roig, M., Gómez Melis, G., Posch, M., and Koenig, F. (2022). <doi:10.48550/arXiv.2206.09639>.
A collection of functions developed to support the tutorial on using Exploratory Structural Equiation Modeling (ESEM) (Asparouhov & Muthén, 2009) <https://www.statmodel.com/download/EFACFA810.pdf>) with Longitudinal Study of Australian Children (LSAC) dataset (Mohal et al., 2023) <doi:10.26193/QR4L6Q>. 
    The package uses 'tidyverse','psych', 'lavaan','semPlot' and provides additional functions to conduct ESEM. 
    The package provides general functions to complete ESEM, including esem_c(), creation of target matrix (if it is used) make_target(), generation of the Confirmatory Factor Analysis (CFA) model syntax esem_cfa_syntax(). 
    A sample data is provided - the package includes a sample data of the Strengths and Difficulties Questionnaire of the Longitudinal Study of Australian Children (SDQ LSAC) in sdq_lsac().  
    'ESEM' package vignette presents the tutorial demonstrating the use of ESEM on SDQ LSAC data.
The nonparametric trend and its derivatives in equidistant time 
    series (TS) with long-memory errors can be estimated. The 
    estimation is conducted via local polynomial regression using an 
    automatically selected bandwidth obtained by a built-in iterative plug-in 
    algorithm or a bandwidth fixed by the user.
    The smoothing methods of the package are described in Letmathe, S., Beran,
    J. and Feng, Y., (2021) <https://ideas.repec.org/p/pdn/ciepap/145.html>.
Presents a "Scenarios" class containing
        general parameters, risk parameters and projection results.
        Risk parameters are gathered together into a ParamsScenarios
        sub-object. The general process for using this package is to
        set all needed parameters in a Scenarios object, use the
        customPathsGeneration method to proceed to the projection, then
        use xxx_PriceDistribution() methods to get asset prices.
Computes shrinkage estimators for regression problems. Selects
    penalty parameter by minimizing bias and variance in the effect estimate, where bias and variance are estimated from the posterior predictive distribution. See Keller and Rice (2017) <doi:10.1093/aje/kwx225> for more details.
An implementation of extended state-space SIR models developed by
    Song Lab at UM school of Public Health. There are several functions available
    by 1) including a time-varying transmission modifier, 2) adding a time-dependent
    quarantine compartment, 3) adding a time-dependent antibody-immunization compartment.
    Wang L. (2020) <doi:10.6339/JDS.202007_18(3).0003>.
Misc functions programmed by Eduard Szöcs. 
    Provides read_regnie() to read gridded precipitation data from German Weather 
    Service  (DWD, see <http://www.dwd.de/> for more information).
Support in preparing a raw ESM dataset for statistical analysis. Preparation includes the handling of errors (mostly due to technological reasons) and the generating of new variables that are necessary and/or helpful in meeting the conditions when statistically analyzing ESM data. The functions in 'esmprep' are meant to hierarchically lead from bottom, i.e. the raw (separated) ESM dataset(s), to top, i.e. a single ESM dataset ready for statistical analysis. This hierarchy evolved out of my personal experience in working with ESM data.
Exploitation, processing and 2D-3D visualization of DICOM-RT files (structures, dosimetry, imagery) for medical physics and clinical research, in a patient-oriented perspective.
A 'shiny' gadget to create 'ggplot2' figures interactively with drag-and-drop to map your variables to different aesthetics.
    You can quickly visualize your data accordingly to their type, export in various formats,
    and retrieve the code to reproduce the plot.
Simultaneous modeling of the quantile and the expected shortfall of a response variable given 
    a set of covariates, see Dimitriadis and Bayer (2019) <doi:10.1214/19-EJS1560>.
An implementation of the ESS algorithm following Amol Deshpande, Minos Garofalakis,
	     Michael I Jordan (2013) <arXiv:1301.2267>. The ESS algorithm
	     is used for model selection in decomposable graphical models.
Functions for converting objects to scalars (vectors of length 1) 
    and a more inclusive definition of data that can be interpreted as numbers 
    (numeric and complex alike).
Provide an optimal histogram, in the sense of probability density estimation and features detection, by means of multiscale variational inference. In other words, the resulting histogram servers as an optimal density estimator, and meanwhile recovers the features, such as increases or modes, with both false positive and false negative controls. Moreover, it provides a parsimonious representation in terms of the number of blocks, which simplifies data interpretation. The only assumption for the method is that data points are independent and identically distributed, so it applies to fairly general situations, including continuous distributions, discrete distributions, and mixtures of both. For details see Li, Munk, Sieling and Walther (2016) <arXiv:1612.07216>.
Download data from the European Social Survey directly from their website <http://www.europeansocialsurvey.org/>. There are two families of functions that allow you to download and interactively check all countries and rounds available.
Este paquete pretende apoyar el proceso enseñanza-aprendizaje de estadística descriptiva e inferencial. Las funciones contenidas en el paquete 'estadistica' cubren los conceptos básicos estudiados en un curso introductorio. Muchos conceptos son ilustrados con gráficos dinámicos o web apps para facilitar su comprensión. This package aims to help the teaching-learning process of descriptive and inferential statistics. The functions contained in the package 'estadistica' cover the basic concepts studied in a statistics introductory course. Many concepts are illustrated with dynamic graphs or web apps to make the understanding easier. See: Esteban et al. (2005, ISBN: 9788497323741), Newbold et al.(2019, ISBN:9781292315034 ), Murgui et al. (2002, ISBN:9788484424673) .
Provides an interface to e-Stat API, the one-stop service for official statistics of the Japanese government.
Estimates item and person parameters for the Continuous Response Model (CRM; Samejima, 1973, <doi:10.1007/BF02291114>), computes item fit residual statistics, draws empirical 3D item category response curves, draws theoretical 3D item category response curves, and generates data under the CRM for simulation studies.
An implementation of sequential testing that uses evidence ratios
    computed from the weights of a set of models. These weights correspond either
    to Akaike weights computed from the Akaike Information Criterion (AIC) or the
    Bayesian Information Criterion (BIC) and following Burnham & Anderson
    (2004, <doi:10.1177/0049124104268644>) recommendations, or to pseudo-BMA
    weights computed from the WAIC or the LOO-IC of models fitted
    with 'brms' and following Yao et al. (2017, <arXiv:1704.02030v3>).
Provides tools for determining estimability of linear functions 
  of regression coefficients, and 'epredict' methods that handle 
  non-estimable cases correctly. Estimability theory is discussed in
  many linear-models textbooks including Chapter 3 of Monahan, JF (2008), 
  "A Primer on Linear Models", Chapman and Hall (ISBN 978-1-4200-6201-4).
Can be used to simultaneously estimate networks (Gaussian Graphical Models) in data from different groups or classes via Joint Graphical Lasso. Tuning parameters are selected via information criteria (AIC / BIC / extended BIC) or cross validation.
Bayesian estimation of spatial weight matrices in spatial econometric panel models. Allows for estimation of spatial autoregressive (SAR), spatial Durbin (SDM), and spatially lagged explanatory variable (SLX) type specifications featuring an unknown spatial weight matrix. Methodological details are given in Krisztin and Piribauer (2022) <doi:10.1080/17421772.2022.2095426>.
Total Time on Test plot and routines for parameter estimation of
    any lifetime distribution implemented in R via maximum likelihood (ML) given
    a data set. It is implemented thinking on parametric survival analysis, but
    it feasible to use in parameter estimation of probability density or mass
    functions in any field. The main routines 'maxlogL' and 'maxlogLreg' are
    wrapper functions specifically developed for ML estimation. There are
    included optimization procedures such as 'nlminb' and 'optim' from base
    package, and 'DEoptim' Mullen (2011) <doi: 10.18637/jss.v040.i06>. Standard
    errors are estimated with 'numDeriv' Gilbert (2011)
    <https://CRAN.R-project.org/package=numDeriv> or the option 'Hessian = TRUE'
    of 'optim' function.
Fast procedures for small set of commonly-used, design-appropriate estimators with robust standard errors and confidence intervals. Includes estimators for linear regression, instrumental variables regression, difference-in-means, Horvitz-Thompson estimation, and regression improving precision of experimental estimates by interacting treatment with centered pre-treatment covariates introduced by Lin (2013) <doi:10.1214/12-AOAS583>.
Extension of 'testthat' package to make unit tests on empirical distributions of estimators and functions for diagnostics of their finite-sample performance.
Estimation of four-fold table cell frequencies (raw data) from risk ratios (relative risks), risk differences and odds ratios. While raw data can be useful for doing meta-analysis, such data is often not provided by primary studies (with summary statistics being solely presented). Therefore, based on summary statistics (namely, risk ratios, risk differences and odds ratios), this package estimates the value of each cell in a 2x2 table according to the equations described in Di Pietrantonj C (2006) <doi:10.1002/sim.2287>.
Implements the methods of McGrath et al. (2020) 
    <doi:10.1177/0962280219889080> and Cai et al. (2021) 
    <doi:10.1177/09622802211047348> for estimating the sample mean and standard 
    deviation from commonly reported quantiles in meta-analysis. These methods 
    can be applied to studies that report the sample median, sample size, and 
    one or both of (i) the sample minimum and maximum values and (ii) the first 
    and third quartiles.
Includes R functions for the estimation of tumor clones percentages for both snp data and (whole) genome sequencing data. See Cheng, Y., Dai, J. Y., Paulson, T. G., Wang, X., Li, X., Reid, B. J., & Kooperberg, C. (2017). Quantification of multiple tumor clones using gene array and sequencing data. The Annals of Applied Statistics, 11(2), 967-991, <doi:10.1214/17-AOAS1026> for more details.
Estimation of production functions by the Olley-Pakes, Levinsohn-Petrin and Wooldridge methodologies. 
    The package aims to reproduce the results obtained with the Stata's user written opreg <http://www.stata-journal.com/article.html?article=st0145> and levpet <http://www.stata-journal.com/article.html?article=st0060> commands. 
    The first was originally proposed by Olley, G.S. and Pakes, A. (1996) <doi:10.2307/2171831>.
    The second by Levinsohn, J. and Petrin, A. (2003) <doi:10.1111/1467-937X.00246>.
	And the third by Wooldridge (2009) <doi:10.1016/j.econlet.2009.04.026>.
The new yield tables developed by the Northwest German Forest 
  Research Institute (NW-FVA) provide a forest management tool for the five 
  main commercial tree species oak, beech, spruce, Douglas-fir and pine for 
  northwestern Germany. The new method applied for deriving yield tables 
  combines measurements of growth and yield trials with growth simulations 
  using a state-of-the-art single-tree growth simulator. By doing so, the new 
  yield tables reflect the current increment level and the recommended 
  graduated thinning from above is the underlying management concept. The yield
  tables are provided along with methods for deriving the site index and for 
  interpolating between age and site indices and extrapolating beyond age and 
  site index ranges. The inter-/extrapolations are performed traditionally by 
  the rule of proportion or with a functional approach.
Creates simple to highly customized tables for a wide selection of descriptive statistics, with or without weighting the data.
Fits the space-time Epidemic Type Aftershock Sequence
    ('ETAS') model to earthquake catalogs using a stochastic 'declustering' 
    approach. The 'ETAS' model is a 'spatio-temporal' marked point process
    model and a special case of the 'Hawkes' process. The package is based 
    on a Fortran program by 'Jiancang Zhuang'
    (available at <http://bemlar.ism.ac.jp/zhuang/software.html>),
    which is modified and translated into C++ and C such that it 
    can be called from R. Parallel computing with 'OpenMP' is possible 
    on supported platforms.
The 2-D spatial and temporal Epidemic Type Aftershock Sequence ('ETAS') Model is widely used to 'decluster' earthquake data catalogs. Usually, the calculation of standard errors of the 'ETAS' model parameter estimates is based on the Hessian matrix derived from the log-likelihood function of the fitted model. However, when an 'ETAS' model is fitted to a local data set over a time period that is limited or short, the standard errors based on the Hessian matrix may be inaccurate. It follows that the asymptotic confidence intervals for parameters may not always be reliable. As an alternative, this package allows the building of bootstrap confidence intervals based on empirical quantiles for the parameters of the 2-D spatial and temporal 'ETAS' model.
Estimation of the components of an ETAS (Epidemic Type Aftershock Sequence) model for earthquake description. Non-parametric background seismicity can be estimated through FLP (Forward Likelihood Predictive). New version 2.0.0: covariates have been introduced to explain the effects of external factors on the induced seismicity; the parametrization has been changed; Chiodi, Adelfio (2017)<doi:10.18637/jss.v076.i03>.
Treatments of a one-way layout, being equivalent to a control, 
 can be selected with this package. Bonferroni adjusted "two one-sided 
 t-tests" (TOST) and related simultaneous confidence intervals are given for 
 both differences or ratios of means of normally distributed data. For the 
 case of equal variances and balanced sample sizes for the treatment groups, 
 the single-step procedure of Bofinger and Bofinger (1995) 
 <doi:10.1111/j.2517-6161.1995.tb02058.x> can be chosen. For non-normal data, 
 the Wilcoxon test is applied.
An implementation of the quantitative ethnobotany indices in R. The goal is to provide an easy-to-use platform for ethnobotanists to assess the cultural significance of plant species based on informant consensus. The package closely follows the paper by Tardio and Pardo-de-Santayana (2008). Tardio, J., and M. Pardo-de-Santayana, 2008. Cultural Importance Indices: A Comparative Analysis Based on the Useful Wild Plants of Southern Cantabria (Northern Spain) 1. Economic Botany, 62(1), 24-39. <doi:10.1007/s12231-007-9004-5>.
Reliable and rapid ethnicity annotation from whole exome and targeted sequencing data.
A predictable and pipeable framework for performing ETL 
    (extract-transform-load) operations on publicly-accessible medium-sized data 
    set. This package sets up the method structure and implements generic 
    functions. Packages that depend on this package download specific data sets 
    from the Internet, clean them up, and import them into a local or remote 
    relational database management system.
Provides functions to facilitate the use of the 'ff' package
    in interaction with big data in 'SQL' databases (e.g. in 'Oracle', 'MySQL',
    'PostgreSQL', 'Hive') by allowing easy importing directly into 'ffdf' objects
    using 'DBI', 'RODBC' and 'RJDBC'. Also contains some basic utility functions to
    do fast left outer join merging based on 'match', factorisation of data and a
    basic function for re-coding vectors.
The etm (empirical transition matrix) package permits to estimate the matrix of transition probabilities for any time-inhomogeneous multi-state model with finite state space using the Aalen-Johansen estimator. Functions for data preparation and for displaying are also included (Allignol et al., 2011 <doi:10.18637/jss.v038.i04>). Functionals of the Aalen-Johansen estimator, e.g., excess length-of-stay in an intermediate state, can also be computed (Allignol et al. 2011 <doi:10.1007/s00180-010-0200-x>).
Traditional meta-regression based method has been developed for using meta-analysis data, but it faced the challenge of inconsistent estimates. This package purpose a new statistical method to detect epistasis using incomplete information summary, and have proven it not only successfully let consistency of evidence, but also increase the power compared with traditional method (Detailed tutorial is shown in website).
Use R to interface with the 'ETRADE' API <https://developer.etrade.com/home>.
    Functions include authentication, trading, quote requests, account information, and option 
    chains. A user will need an ETRADE brokerage account and 'ETRADE' API approval. See README 
    for authentication process and examples.
Implementation of Energy Trees, a statistical model to perform 
    classification and regression with structured and mixed-type data. The
    model has a similar structure to Conditional Trees, but brings in Energy
    Statistics to test independence between variables that are possibly 
    structured and of different nature. Currently, the package covers functions
    and graphs as structured covariates. It builds upon 'partykit' to
    provide functionalities for fitting, printing, plotting, and predicting with
    Energy Trees. Energy Trees are described in Giubilei et al. (2022) 
    <arXiv:2207.04430>.
Provides a collection of functions to perform core tasks within
    Energy Trading and Risk Management (ETRM). Calculation of maximum smoothness 
    forward price curves for electricity and natural gas contracts with flow delivery, as presented in
    F. E. Benth, S. Koekebakker, and F. Ollmar (2007) <doi:10.3905/jod.2007.694791>
    and F. E. Benth,  J. S. Benth,  and S. Koekebakker (2008) <doi:10.1142/6811>.
    Portfolio insurance trading strategies for price risk management in the forward market, see
    F. Black (1976) <doi:10.1016/0304-405X(76)90024-6>, 
    T. Bjork (2009) <https://EconPapers.repec.org/RePEc:oxp:obooks:9780199574742>,  
    F. Black and R. W. Jones (1987) <doi:10.3905/jpm.1987.409131> and
    H. E. Leland (1980) <http://www.jstor.org/stable/2327419>.
Computes moments of univariate truncated t distribution.
    There is only one exported function, e_trunct(), which should be seen for details.
Convenience functions for implementing extended two-way 
  fixed effect regressions a la Wooldridge (2021, 2022)
  <doi:10.2139/ssrn.3906345>, <doi:10.2139/ssrn.4183726>.
Illustrates the concepts developed in Sarkar and Rashid (2019, ISSN:0025-5742) <http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwiH4deL3q3xAhWX73MBHR_wDaYQFnoECAUQAw&url=https%3A%2F%2Fwww.indianmathsociety.org.in%2Fmathstudent-part-2-2019.pdf&usg=AOvVaw3SY--3T6UAWUnH5-Nj6bSc>.
  This package helps a user guess four things (mean, MD, scaled MSD, and RMSD) before they get the SD. 
    1) The package displays the Empirical Cumulative Distribution Function (ECDF) of
  the given data. The user must choose the value of the mean by equating the areas of 
  two colored (blue and green) regions. The package gives feedback to improve the choice
  until it is correct. Alternatively, the reader may continue with a different guess for 
  the center (not necessarily the mean).
    2) The user chooses the values of the Mean Deviation (MD) based on the ECDF of the deviations
  by equating the areas of two newly colored (blue and green) regions, with feedback from the 
  package until the user guesses correctly.
    3) The user chooses the Scaled Mean Squared Deviation (MSD) based on the ECDF of the scaled 
  square deviations by equating the areas of two newly colored (blue and green) regions, with 
  feedback from the package until the user guesses correctly.
    4) The user chooses the Root Mean Squared Deviation (RMSD) by ensuring that its intersection 
  with the ECDF of the deviations is at the same height as the intersection between the scaled 
  MSD and the ECDF of the scaled squared deviations. Additionally, the intersection of two
  blue lines (the green dot) should fall on the vertical line at the maximum deviation. 
    5) Finally, if the mean is chosen correctly, only then the user can view the population 
  SD (the same as the RMSD) and the sample SD (sqrt(n/(n-1))*RMSD) by clicking the respective 
  buttons. If the mean is chosen incorrectly, the user is asked to correct it.
An interface for performing climate matching using the Euclidean "Climatch" algorithm. Functions provide a vector of climatch scores (0-10) for each location (i.e., grid cell) within the recipient region, the percent of climatch scores >= a threshold value, and mean climatch score. Tools for parallelization and visualizations are also provided. Note that the floor function that rounds the climatch score down to the nearest integer has been removed in this implementation and the “Climatch” algorithm, also referred to as the “Climate” algorithm, is described in: Crombie, J., Brown, L., Lizzio, J., & Hood, G. (2008). “Climatch user manual”. The method for the percent score is described in: Howeth, J.G., Gantz, C.A., Angermeier, P.L., Frimpong, E.A., Hoff, M.H., Keller, R.P., Mandrak, N.E., Marchetti, M.P., Olden, J.D., Romagosa, C.M., and Lodge, D.M. (2016). <doi:10.1111/ddi.12391>.
The remit of the European Clinical Trials Data Base (EudraCT <https://eudract.ema.europa.eu/> ), or ClinicalTrials.gov <https://clinicaltrials.gov/>, is to provide open access to summaries of all registered clinical trial results; thus aiming to prevent non-reporting of negative results and provide open-access to results to inform future research. The amount of information required and the format of the results, however, imposes a large extra workload at the end of studies on clinical trial units. In particular, the adverse-event-reporting component requires entering: each unique combination of treatment group and safety event; for every such event above, a further 4 pieces of information (body system, number of occurrences, number of subjects, number exposed) for non-serious events, plus an extra three pieces of data for serious adverse events (numbers of causally related events, deaths, causally related deaths). This package prepares the required statistics needed by EudraCT and formats them into the precise requirements to directly upload an XML file into the web portal, with no further data entry by hand.
Analyses 'EuFMDiS' output files in a Shiny App. The distributions of 
  relevant output parameters are described in form of tables (quantiles) and plots. 
  The App is called using eufmdis.adapt::run_adapt().
Contains match results from seven European men's football leagues, namely Premier League (England), Ligue 1 (France), 
	     Bundesliga (Germany), Serie A (Italy), Primera Division (Spain), Eredivisie (The Netherlands), Super Lig (Turkey).
	     Includes Seasons 2010/2011 until 2019/2020 and a set of interesting covariates. Can be used all purposes.
An eulerian path is a path in a graph which visits every edge exactly once. This package provides methods to handle eulerian paths or cycles.
Generate area-proportional Euler diagrams
    using numerical optimization. An Euler diagram is a generalization of a Venn
    diagram, relaxing the criterion that all interactions need to be
    represented. Diagrams may be fit with ellipses and circles via
    a wide range of inputs and can be visualized in numerous ways.
Computes maximum mean discrepancy two-sample test for univariate data using the Laplacian kernel, as described in Bodenham and Kawahara (2023) <doi:10.1007/s11222-023-10271-x>. The p-value is computed using permutations. Also includes implementation for computing the robust median difference statistic 'Q_n' from Croux and Rousseeuw (1992) <doi:10.1007/978-3-662-26811-7_58> based on Johnson and Mizoguchi (1978) <doi:10.1137/0207013>.
The EUNIS habitat classification is a comprehensive pan-European
    system for habitat identification
    <https://www.eea.europa.eu/data-and-maps/data/eunis-habitat-classification-1>.
    This is an R data package providing the EUNIS classification system.
    The classification is hierarchical and covers all types of habitats from
    natural to artificial, from terrestrial to freshwater and marine. The
    habitat types are identified by specific codes, names and descriptions and
    come with schema crosswalks to other habitat typologies.
Access to data on European Union laws and court decisions made easy with pre-defined 'SPARQL' queries and 'GET' requests. See Ovadek (2021) <doi:10.1080/2474736X.2020.1870150> .
Daily 'netCDF' data from e.g. regional climate models (RCMs) are not trivial
    to work with. This package, which relies on 'data.table', makes it easier
    to deal with large data from RCMs, such as from EURO-CORDEX 
    (<https://www.euro-cordex.net/>, <https://cordex.org/data-access/>). It has 
    functions to extract single grid cells from rotated pole grids as well as 
    the whole array in long format. Can handle non-standard calendars (360, 
    noleap) and interpolate them to a standard one. Potentially works with many 
    CF-conform 'netCDF' files.
Interface to Eurostat’s API (SDMX 2.1) with fast data.table-based import of
    data, labels, and metadata. On top of the core functionality, data search and data
    description/comparison functions are also provided.
    Use <https://github.com/alekrutkowski/eurodata_codegen> — a point-and-click app for rapid and
    easy generation of richly-commented R code — to import a Eurostat dataset or its subset
    (based on the eurodata::importData() function).
Interact with the Europeana Data Model via a variety of API
 endpoints that contains digital collections from thousands of institutions
 around Europe. This translates to millions of Cultural Heritage Objects in the
 form of image, text, video, sound and 3D, accompanied by rich metadata. The
 Data Model design principles are based on the core principles and best
 practices of the Semantic Web and Linked Data efforts to which Europeana
 contributes (see, e.g., Doerr, Martin, et al. The europeana data model (edm).
 World Library and Information Congress: 76th IFLA general conference
 and assembly. Vol. 10. 2010.). The package also provides methods for bulk
 downloads of specific subsets of items, including both their metadata
 and their associated media files.
An R Client for the Europe PubMed Central RESTful Web Service
    (see <https://europepmc.org/RestfulWebService> for more information). It
    gives access to both metadata on life science literature and open access
    full texts. Europe PMC indexes all PubMed content and other literature
    sources including Agricola, a bibliographic database of citations to the
    agricultural literature, or Biological Patents. In addition to bibliographic
    metadata, the client allows users to fetch citations and reference lists.
    Links between life-science literature and other EBI databases, including
    ENA, PDB or ChEMBL are also accessible. No registration or API key is
    required. See the vignettes for usage examples.
This dataset contains population estimates of all European cities 
    with at least 10,000 inhabitants during the period 1500-1800. These data are
    adapted from Jan De Vries, "European Urbanization, 1500-1800" (1984).
Bayesian sample size calculation software and examples for EuroSARC
    clinical trials which utilise Bayesian methodology. These trials rely on
    binomial based endpoints so the majority of programs found here relate to this
    sort of endpoint. Developed as part of the EuroSARC FP7 grant.
Tools to download data from the Eurostat database
    <https://ec.europa.eu/eurostat> together with search and manipulation
    utilities.
Goodness-of-fit tests for selection of r in the r-largest order
    statistics (GEVr) model. Goodness-of-fit tests for threshold selection in the
    Generalized Pareto distribution (GPD). Random number generation and density functions
    for the GEVr distribution. Profile likelihood for return level estimation
    using the GEVr and Generalized Pareto distributions. P-value adjustments for
    sequential, multiple testing error control. Non-stationary fitting of GEVr and
    GPD.
    Bader, B., Yan, J. & Zhang, X. (2016) <doi:10.1007/s11222-016-9697-3>.
    Bader, B., Yan, J. & Zhang, X. (2018) <doi:10.1214/17-AOAS1092>.
Evaluates the performance of binary classifiers.  Computes
    confusion measures (TP, TN, FP, FN), derived measures (TPR, FDR,
    accuracy, F1, DOR, ..), and area under the curve.  Outputs are well
    suited for nested dataframes.
Contains a set of clustering methods and evaluation metrics to select the best number of the clusters based on clustering stability. Two references describe the methodology: Fahimeh Nezhadmoghadam, and Jose Tamez-Pena (2021)<doi:10.1016/j.compbiomed.2021.104753>, and Fahimeh Nezhadmoghadam, et al.(2021)<doi:10.2174/1567205018666210831145825>.
Provides functions for evaluating (time series) model
	estimation methods. These facilitate Monte Carlo experiments of repeated
	simulations and estimations. Also provides methods for
	looking at the distribution of the results from these experiments,
	including model roots (which are an equivalence class invariant).
Provides various statistical methods for evaluating
    Individualized Treatment Rules under randomized data. The provided
    metrics include Population Average Value (PAV), Population Average
    Prescription Effect (PAPE), Area Under Prescription Effect Curve
    (AUPEC). It also provides the tools to analyze Individualized
    Treatment Rules under budget constraints. Detailed reference in Imai
    and Li (2019) <arXiv:1905.05389>.
The purpose of this package is to generate trees and validate unverified code. Trees are made by parsing a statement into a verification tree data structure. This will make it easy to port the statement into another language. Safe statement evaluations are done by executing the verification trees.
Parsing and evaluation tools that make it easy to recreate the
    command line behaviour of R.
Implements various quality evaluation statistics to assess the
    value of plant germplasm core collections using qualitative and 
    quantitative phenotypic trait data according to Odong et al. (2015) 
    <doi:10.1007/s00122-012-1971-y>.
Provides Some of the most important evaluation measures for evaluating a model. Just by giving the real and predicted class, measures such as accuracy, sensitivity, specificity, ppv, npv, fmeasure, mcc and ... will be returned.
Conducts sensitivity analyses for unmeasured confounding, selection bias, and measurement error (individually or in combination; VanderWeele & Ding (2017) <doi:10.7326/M16-2607>; Smith & VanderWeele (2019) <doi:10.1097/EDE.0000000000001032>; VanderWeele & Li (2019) <doi:10.1093/aje/kwz133>; Smith & VanderWeele (2021) <arXiv:2005.02908>). Also conducts sensitivity analyses for unmeasured confounding in meta-analyses (Mathur & VanderWeele (2020a) <doi:10.1080/01621459.2018.1529598>; Mathur & VanderWeele (2020b) <doi:10.1097/EDE.0000000000001180>) and for additive measures of effect modification (Mathur et al., under review).
Uses data and constants to calculate potential evapotranspiration (PET) and actual evapotranspiration (AET) from 21 different formulations including Penman, Penman-Monteith FAO 56, Priestley-Taylor and Morton formulations.
Different evidential classifiers, which provide
    outputs in the form of Dempster-Shafer mass functions. The methods are: 
    the evidential K-nearest neighbor rule, the evidential neural 
    network, radial basis function neural networks, logistic regression,
    feed-forward neural networks.
Various clustering algorithms that produce a credal partition,
    i.e., a set of Dempster-Shafer mass functions representing the membership of objects
    to clusters. The mass functions quantify the cluster-membership uncertainty of the     
    objects. The algorithms are: Evidential c-Means, Relational Evidential c-Means, 
    Constrained Evidential c-Means, Evidential Clustering, Constrained Evidential 
    Clustering, Evidential K-nearest-neighbor-based Clustering, Bootstrap Model-Based
    Evidential Clustering, Belief Peak Evidential Clustering, Neural-Network-based
    Evidential Clustering.
Combine pieces of evidence in the form of uncertainty representations.
Extends simulation, distribution, quantile and density
        functions to univariate and multivariate parametric extreme
        value distributions, and provides fitting functions which
        calculate maximum likelihood estimates for univariate and
        bivariate maxima models, and for univariate and bivariate
        threshold models.
Provides functions for the Bayesian analysis of extreme
        value models, using Markov chain Monte Carlo methods. Allows
		the construction of both uninformative and informed prior 
		distributions for common statistical models applied to extreme
        event data, including the generalized extreme value distribution.
Functions for setting up and analyzing event history data.
Event dataset repository including both real-life and artificial event logs. They can be used in combination with functionalities provided by the 'bupaR' packages. Janssenswillen et al. (2020) <http://ceur-ws.org/Vol-2703/paperTD7.pdf>.
A graphical user interface for open source event detection.
Detect events in time-series data. Combines multiple well-known R packages like 'forecast' and 'neuralnet' to deliver an easily configurable tool for multivariate event detection.
A user friendly, easy to understand way of doing event
    history regression for marginal estimands of interest,
    including the cumulative incidence and the restricted mean
    survival, using the pseudo observation framework for 
    estimation. For a review of the methodology, see Andersen and
    Pohar Perme (2010) <doi:10.1177/0962280209105020> or Sachs 
    and Gabriel (2022) <doi:10.18637/jss.v102.i09>. The
    interface uses the well known formulation of a generalized
    linear model and allows for features including plotting of 
    residuals, the use of sampling weights, and corrected
    variance estimation.
Functions for analysis of rate changes in sequential events.
Predicts enrollment and events at the design or analysis stage using specified enrollment and time-to-event models through simulations.
Implements event extraction and early classification of events in data streams in R. 
    It has the functionality to generate 2-dimensional data streams with events belonging to 
    2 classes. These events can be extracted and features computed. The event features extracted
    from incomplete-events can be classified using a partial-observations-classifier 
    (Kandanaarachchi et al. 2018) <doi:10.1371/journal.pone.0236331>.
Perform Event Studies from through our <https://EventStudyTools.com> Application Programming Interface, parse the results, visualize it, and / or use the results in further analysis.
Estimates linear panel event study models. Plots coefficients following the recommendations in Freyaldenhoven et al. (2021) <doi:10.3386/w29170>. Includes sup-t bands, testing for key hypotheses, least wiggly path through the Wald region. Allows instrumental variables estimation following Freyaldenhoven et al. (2019) <doi:10.1257/aer.20180609>.
Implements the hybrid framework for event prediction described in Fang & Zheng (2011, <doi:10.1016/j.cct.2011.05.013>). To estimate the survival function the event prediction is based on, a piecewise exponential hazard function is fit to the time-to-event data to infer the potential change points. Prior to the last identified change point, the survival function is estimated using Kaplan-Meier, and the tail after the change point is fit using piecewise exponential.
Provides several confidence interval and testing procedures using
    event-specific win ratios for semi-competing risks data with non-terminal
    and terminal events, as developed in Yang et al. (2021<doi:10.1002/sim.9266>). 
    Compared with conventional methods for survival data, these procedures are 
    designed to utilize more data for improved inference procedures with 
    semi-competing risks data. The event-specific win ratios were introduced in 
    Yang and Troendle (2021<doi:10.1177/1740774520972408>). In this package, 
    the event-specific win ratios and confidence intervals are obtained for each 
    event type, and several testing procedures are developed for the global null 
    of no treatment effect on either terminal or non-terminal events. Furthermore,
    a test of proportional hazard assumptions, under which the event-specific win 
    ratios converge to the hazard ratios, and a test of equal hazard ratios are 
    provided. For summarizing the treatment effect on all events, confidence 
    intervals for linear combinations of the event-specific win ratios are available
    using pre-determined or data-driven weights. Asymptotic properties of these 
    inference procedures are discussed in Yang et al (2021<doi:10.1002/sim.9266>). 
    Also, transformations are used to yield better control of the type one error 
    rates for moderately sized data sets.
Methods for fitting various extreme value distributions with parameters of 
      generalised additive model (GAM) form are provided. For details of distributions 
      see Coles, S.G. (2001) <doi:10.1007/978-1-4471-3675-0>, GAMs see Wood, S.N. (2017) 
      <doi:10.1201/9781315370279>, and the fitting approach see Wood, S.N., Pya, N. & 
      Safken, B. (2016) <doi:10.1080/01621459.2016.1180986>. Details of how evgam works
      and various examples are given in Youngman, B.D. (2022) <doi:10.18637/jss.v103.i03>.
Implementation of the epidemic volatility index (EVI), as 
    discussed by Kostoulas et. al. (2021). EVI is a new, conceptually simple, early warning tool for oncoming epidemic waves. 
    EVI is based on the volatility of newly reported cases per unit of time,
    ideally per day, and issues an early warning when the volatility change rate exceeds a threshold.
Evidential regression analysis for dichotomous and quantitative outcome data. The following references described the methods in this package:
        Strug, L. J., Hodge, S. E., Chiang, T., Pal, D. K., Corey, P. N., & Rohde, C. (2010) <doi:10.1038/ejhg.2010.47>.
        Strug, L. J., & Hodge, S. E. (2006) <doi:10.1159/000094709>.
        Royall, R. (1997) <ISBN:0-412-04411-0>.
Bayesian (and some likelihoodist) functions as alternatives to hypothesis-testing functions in R base using a user interface patterned after those of R's hypothesis testing functions. See McElreath (2016, ISBN: 978-1-4822-5344-3), Gelman and Hill (2007, ISBN: 0-521-68689-X) (new edition in preparation) and Albert (2009, ISBN: 978-0-387-71384-7) for good introductions to Bayesian analysis and Pawitan (2002, ISBN: 0-19-850765-8) for the Likelihood approach.  The functions in the package also make extensive use of graphical displays for data exploration and model comparison.
Provides tools for integrated sensitivity analysis of evidence factors in observational
	studies. When an observational study allows for multiple independent or nearly
	independent inferences which, if vulnerable, are vulnerable to different biases, we have 
	multiple evidence factors.  This package provides methods that respect type I error rate control. 
	Examples are provided of integrated evidence factors analysis in a longitudinal study with
	continuous outcome and in a case-control study. 
	Karmakar, B., French, B., and Small, D. S. (2019)<DOI:10.1093/biomet/asz003>.
Routines for combining causal effect estimates and study diagnostics across multiple data sites in a distributed study, without sharing patient-level data. 
  Allows for normal and non-normal approximations of the data-site likelihood of the effect parameter.
Contains a collection of examples of evidence factors in observational studies from the book Replication and Evidence Factors in Observational Studies by Paul R. Rosenbaum (2021) <doi:10.1201/9781003039648>.
It allows running 'EViews'(<https://eviews.com>) program from R, R Markdown and Quarto documents. 'EViews' (Econometric Views) is a statistical software for Econometric analysis.  This package integrates 'EViews' and R and also serves as an 'EViews' Knit-Engine for 'knitr' package. Write all your 'EViews' commands in R, R Markdown or Quarto documents.
Checks to see whether a supplied set of dice (their face values) are transitive, returning pair-win and group-roll win probabilities. Expected returns (mean magnitude of win/loss) are presented as well.
Allows users to model and draw inferences from extreme value inflated count data, and to evaluate these models and compare to non extreme-value inflated counterparts. The package is built to be compatible with standard presentation tools such as 'broom', 'tidy', and 'modelsummary'.
Functions for extreme value theory, which may be 
  divided into the following groups; exploratory data analysis, 
  block maxima, peaks over thresholds (univariate and bivariate), 
  point processes, gev/gpd distributions.
The usual distribution functions, maximum likelihood inference and
    model diagnostics for univariate stationary extreme value mixture models
    are provided. Kernel density estimation including various boundary
    corrected kernel density estimation methods and a wide choice of kernels,
    with cross-validation likelihood based bandwidth estimator.
    Reasonable consistency with the base functions in the 'evd' package is
    provided, so that users can safely interchange most code.
Comparative analysis of continuous traits influencing discrete states, and utility tools to facilitate comparative analyses.  Implementations of ABBA/BABA type statistics to test for introgression in genomic data. Wright-Fisher, phylogenetic tree, and statistical distribution Shiny interactive simulations for use in teaching.
Dynamic and Interactive Maps with R, powered by 'leaflet' <https://leafletjs.com>. 'evolMap' generates a web page with interactive and dynamic maps to which you can add geometric entities (points, lines or colored geographic areas), and/or markers with optional links between them. The dynamic ability of these maps allows their components to evolve over a continuous period of time or by periods.
Provides functions for covariance matrix comparisons, estimation of repeatabilities in measurements and matrices, and general evolutionary quantitative genetics tools. Melo D, Garcia G, Hubbe A, Assis A P, Marroig G. (2016) <doi:10.12688/f1000research.7082.3>.
Evolutionary game theory applies game theory to evolving populations 
    in biology, see e.g. one of the books by Weibull (1994, ISBN:978-0262731218) 
    or by Sandholm (2010, ISBN:978-0262195874) for more details. A comprehensive 
	set of tools to illustrate the core concepts of evolutionary game theory, 
	such as evolutionary stability or various evolutionary dynamics, for teaching 
	and academic research is provided.
Provides tools for calculating evolvability parameters from estimated G-matrices as defined 
    in Hansen and Houle (2008) <doi:10.1111/j.1420-9101.2008.01573.x> and fits phylogenetic 
    comparative models that link the rate of evolution of a trait to the state of another evolving 
    trait (see Hansen et al. 2021 Systematic Biology <doi:10.1093/sysbio/syab079>). The package was 
    released with Bolstad et al. (2014) <doi:10.1098/rstb.2013.0255>, which contains some examples of use.
Evolutionary process simulation using geometric morphometric data. Manipulation of landmark data files (TPS), shape plotting and distances plotting functions.
The EvoPER, Evolutionary Parameter Estimation for Individual-based Models is an extensible 
      package providing optimization driven parameter estimation methods using metaheuristics  and 
      evolutionary computation techniques (Particle Swarm Optimization, Simulated Annealing, Ant Colony Optimization 
      for continuous domains, Tabu Search, Evolutionary Strategies, ...)  which could be more efficient and require, 
      in some cases, fewer model evaluations than alternatives relying on experimental design.  Currently there 
      are built in support for models developed with 'Repast Simphony'  Agent-Based framework (<https://repast.github.io/>)  
      and with NetLogo (<https://ccl.northwestern.edu/netlogo/>) which are the most used frameworks for Agent-based modeling.
Performs automated morphological character partitioning for 
             phylogenetic analyses and analyze macroevolutionary parameter 
             outputs from clock (time-calibrated) Bayesian inference analyses, following 
             concepts introduced by Simões and Pierce (2021) <doi:10.1038/s41559-021-01532-x>.
Facilitates univariate and multivariate analysis of evolutionary sequences of phenotypic change. The package extends the modeling framework available in the 'paleoTS' package. Please see <https://klvoje.github.io/evoTS/index.html> for information about the package and the implemented models.
An implementation of the 'Evidential Neural Network for Regression' model recently introduced in Denoeux (2023) <doi:10.36227/techrxiv.21791831.v1>. In this model, prediction uncertainty is quantified by Gaussian random fuzzy numbers as introduced in Denoeux (2023) <doi:10.1016/j.fss.2022.06.004>. The package contains functions for training the network, tuning hyperparameters by cross-validation or the hold-out method, and making predictions. It also contains utilities for making calculations with Gaussian random fuzzy numbers (such as, e.g., computing the degrees of belief and plausibility of an interval, or combining Gaussian random fuzzy numbers).
The R package proposes extreme value index estimators for heavy tailed models 
             by mean of order p <DOI:10.1016/j.csda.2012.07.019>, peaks over random threshold
             <DOI:10.57805/revstat.v4i3.37> and a bias-reduced estimator 
             <DOI:10.1080/00949655.2010.547196>.
	     The package also computes moment, generalised Hill <DOI:10.2307/3318416> 
	     and mixed moment estimates for the extreme value index.
	     High quantiles and value at risk estimators based on these estimators are implemented.
Two classifiers for open set recognition and novelty detection based on extreme value theory. The first classifier is based on the generalized Pareto distribution (GPD) and the second classifier is based on the generalized extreme value (GEV) distribution. For details, see Vignotto, E., & Engelke, S. (2018) <arXiv:1808.09902>.
Commonly used classification and regression tree methods like the CART algorithm
             are recursive partitioning methods that build the model in a forward stepwise search.
	     Although this approach is known to be an efficient heuristic, the results of recursive
	     tree methods are only locally optimal, as splits are chosen to maximize homogeneity at
	     the next step only. An alternative way to search over the parameter space of trees is
	     to use global optimization methods like evolutionary algorithms. The 'evtree' package
	     implements an evolutionary algorithm for learning globally optimal classification and
	     regression trees in R. CPU and memory-intensive tasks are fully computed in C++ while
	     the 'partykit' package is leveraged to represent the resulting trees in R, providing
	     unified infrastructure for summaries, visualizations, and predictions.
Contains a large number of the goodness-of-fit tests for the Exponential and Weibull distributions classified into families: the tests based on the empirical distribution function, the tests based on the probability plot, the tests based on the normalized spacings, the tests based on the Laplace transform and the likelihood based tests.
An implementation of a variety of escalation with overdose control designs introduced by Babb, Rogatko and Zacks (1998) <doi:10.1002/(SICI)1097-0258(19980530)17:10%3C1103::AID-SIM793%3E3.0.CO;2-9>. It calculates the next dose as a clinical trial proceeds and performs simulations to obtain operating characteristics.
Function and data sets in the book entitled "R ile Temel Ekonometri", S.Guris, E.C.Akay, B. Guris(2020). The book published in Turkish. It is possible to makes Durbin two stage method for autocorrelation, generalized differencing method for correction autocorrelation, Hausman Test for identification and computes LM, LR and Wald test statistics for redundant variable by using the functions written in this package.
The purpose of Early Warning Systems (EWS) is to detect accurately the occurrence of a crisis, which is represented by a binary variable which takes the value of one when the event occurs, and the value of zero otherwise. EWS are a toolbox for policymakers to prevent or attenuate the impact of economic downturns. Modern EWS are based on the econometric framework of Kauppi and Saikkonen (2008) <doi:10.1162/rest.90.4.777>. Specifically, this framework includes four dichotomous models, relying on a logit approach to model the relationship between yield spreads and future recessions, controlling for recession risk factors. These models can be estimated in a univariate or a balanced panel framework as in Candelon, Dumitrescu and Hurlin (2014) <doi:10.1016/j.ijforecast.2014.03.015>. This package provides both methods for estimating these models and a dataset covering 13 OECD countries over a period of 45 years. In addition, this package also provides methods for the analysis of the propagation mechanisms of an exogenous shock, as well as robust confidence intervals for these response functions using a block-bootstrap method as in Lajaunie (2021). This package constitutes a useful toolbox (data and functions) for scholars as well as policymakers.
Performs unconditional exact tests and power calculations for 2x2 contingency tables.
  For comparing two independent proportions, performs Barnard's test (1945)
  <doi:10.1038/156177a0> using the original CSM test (Barnard, 1947 <doi:10.1093/biomet/34.1-2.123>),
  using Fisher's p-value referred to as Boschloo's test (1970) <doi:10.1111/j.1467-9574.1970.tb00104.x>,
  or using a Z-statistic (Suissa and Shuster, 1985, <doi:10.2307/2981892>).
  For comparing two binary proportions, performs unconditional exact test using McNemar's
  Z-statistic (Berger and Sidik, 2003, <doi:10.1191/0962280203sm312ra>),
  using McNemar's conditional p-value, using McNemar's Z-statistic with continuity correction,
  or using CSM test.  Calculates confidence intervals for the difference in proportion.
  This package interacts with pre-computed data available through the ExactData R package,
  which is available in a 'drat' repository.
  Install the ExactData R package from GitHub at <https://pcalhoun1.github.io/drat/>.
  The ExactData R package is approximately 85 MB.
Allows the user to determine minimum sample sizes that achieve target size and power at a specified alternative. For more information, see “Exact samples sizes for clinical trials subject to size and power constraints” by Lloyd, C.J. (2022) Preprint <doi:10.13140/RG.2.2.11828.94085>.
Calculates conditional exact tests (Fisher's exact test, Blaker's exact test, or  exact McNemar's test) and unconditional exact tests (including score-based tests on differences in proportions, ratios of proportions, and odds ratios, and Boshcloo's test) with appropriate matching confidence intervals, and provides power and sample size calculations. Gives melded confidence intervals for the binomial case (Fay, et al, 2015, <DOI:10.1111/biom.12231>). Gives boundary-optimized rejection region test (Gabriel, et al, 2018, <DOI:10.1002/sim.7579>), an unconditional exact test for the situation where the controls are all expected to fail. Gives confidence intervals compatible with exact McNemar's or sign tests (Fay and Lumbard, 2021, <DOI:10.1002/sim.8829>). For review of these kinds of exact tests see Fay and Hunsberger (2021, <DOI:10.1214/21-SS131>).
Researchers often use the bootstrap to understand a sample drawn
    from a population with unknown distribution. The exact bootstrap method is a
    practical tool for exploring the distribution of small sample size data. For
    a sample of size n, the exact bootstrap method generates the entire space of
    n to the power of n resamples and calculates all realizations of the selected
    statistic. The 'exactamente' package includes functions for implementing two
    bootstrap methods, the exact bootstrap and the regular bootstrap. The
    exact_bootstrap() function applies the exact bootstrap method following
    methodologies outlined in Kisielinska (2013) <doi:10.1007/s00180-012-0350-0>.
    The regular_bootstrap() function offers a more traditional bootstrap approach,
    where users can determine the number of resamples. The e_vs_r() function
    allows users to directly compare results from these bootstrap methods. To
    augment user experience, 'exactamente' includes the function exactamente_app()
    which launches an interactive 'shiny' web application. This application
    facilitates exploration and comparison of the bootstrap methods, providing
    options for modifying various parameters and visualizing results.
Calculates exact tests and confidence intervals for one-sample binomial and one- or two-sample Poisson cases (see Fay (2010) <doi:10.32614/rj-2010-008>).
This is a package for exact Confidence Intervals for the difference between two independent or dependent proportions.
Quickly and accurately summarizes raster values over polygonal areas ("zonal statistics").
Life Table Response Experiments (LTREs) are a method of comparative demographic analysis. The purpose is to quantify how the difference or variance in vital rates (stage-specific survival, growth, and fertility) among populations contributes to difference or variance in the population growth rate, "lambda." We provide functions for one-way fixed design and random design LTRE, using either the classical methods that have been in use for several decades, or an fANOVA-based exact method that directly calculates the impact on lambda of changes in matrix elements, for matrix elements and their interactions. The equations and descriptions for the classical methods of LTRE analysis can be found in "Matrix Population Models: Construction, Analysis, and Interpretation (2nd edition)" Caswell (2001, ISBN: 0878930965), and the fANOVA-based exact methods will be published in a forthcoming paper. We also provide some demographic functions, including generation time from Bienvenu and Legendre (2015) <doi:10.1086/681104>. For implementation of exactLTRE where all possible interactions are calculated, we use an operator matrix presented in Poelwijk, Krishna, and Ranganathan (2016) <doi:10.1371/journal.pcbi.1004771>.
A tool for conducting exact parametric regression-based causal mediation analysis of binary outcomes 
    as described in Samoilenko, Blais and Lefebvre (2018) <doi:10.1353/obs.2018.0013>;
    Samoilenko, Lefebvre (2021) <doi:10.1093/aje/kwab055>; and Samoilenko, Lefebvre (2023) <doi:10.1002/sim.9621>.
Computes exact p-values for multinomial goodness-of-fit tests based on multiple test statistics, namely, Pearson's chi-square, the log-likelihood ratio and the probability mass statistic. Implements the algorithm detailed in Resin (2020) <arXiv:2008.12682>. Estimates based on the classical asymptotic chi-square approximation or Monte-Carlo simulation can also be computed.
Computes exact conditional p-values and quantiles using an
 implementation of the Shift-Algorithm by Streitberg & Roehmel.
Contains all data sets for Exam PA: Predictive Analytics at 
    <https://exampa.net/>.
Take the examples written in your documentation of functions
    and use them to create shells (skeletons which must be manually
    completed by the user) of test files to be tested with the 'testthat'
    package. Sort of like python 'doctests' for R.
Automatic generation of exams based on exercises in Markdown or LaTeX format,
	possibly including R code for dynamic generation of exercise elements.
	Exercise types include single-choice and multiple-choice questions, arithmetic problems,
	string questions, and combinations thereof (cloze). Output formats include standalone
	files (PDF, HTML, Docx, ODT, ...), Moodle XML, QTI 1.2, QTI 2.1, Blackboard, Canvas, OpenOlat, ILIAS, TestVision,
	Particify, ARSnova, Kahoot!, Grasple, and TCExam. In addition to fully customizable PDF exams, a standardized PDF format
	(NOPS) is provided that can be printed, scanned, and automatically evaluated.
Randomized multiple-select and single-select
  question generation for the 'MyLearn' teaching and learning
  platform. Question templates
  in the form of the R/exams package (see <http://www.r-exams.org/>)
  are transformed into XML format required by 'MyLearn'.
Automatic generation of quizzes or individual questions for 'learnr' tutorials based on 'R/exams' exercises.
Automatic Generation of Exams in R for 'Sakai'.
  Question templates in the form of the 'exams' package (see <http://www.r-exams.org/>)
  are transformed into XML format required by 'Sakai'.
Provides methods for constructing confidence or credible regions
    for exceedance sets and contour lines.
Computes confidence intervals for the exceedance probability of normally distributed estimators. Currently only supports general linear models. Please see Segal (2019) <arXiv:1803.03356> for more information.
Allows access to data in running instance of Microsoft Excel
    (e. g. 'xl[a1] = xl[b2]*3' and so on). Graphics can be transferred with
    'xl[a1] = current.graphics()'. Additionally there are function for reading/writing 
    'Excel' files - 'xl.read.file'/'xl.save.file'. They are not fast but able to read/write 
    '*.xlsb'-files and password-protected files. There is an Excel workbook with 
    examples of calling R from Excel in the 'doc' folder. It tries to keep things as
    simple as possible - there are no needs in any additional
    installations besides R, only 'VBA' code in the Excel workbook.
    Microsoft Excel is required for this package.
A small group of functions to read in a data dictionary and the
    corresponding data table from 'Excel' and to automate the cleaning, re-coding
    and creation of simple calculated variables. This package was designed to
    be a companion to the macro-enabled 'Excel' template available
    on the GitHub site, but works with any similarly-formatted 'Excel' data.
Implements 'Excel' functions in 'R' for your calculation simplicity.You can use most of the aggregate functions, addressing functions,logical functions and text functions. Helps you a ton in learning how 'R' works as some 'Excel' users might be struggling with the program.
An R interface to 'jExcel' library to create web-based interactive tables and spreadsheets compatible with 'Excel' or any other spreadsheet software.
Implementation of a function which calculates the empirical excess mass 
	for given \eqn{\lambda} and given maximal number of modes (excessm()). Offering 
	powerful plot features to visualize empirical excess mass (exmplot()). This 
	includes the possibility of drawing several plots (with different maximal 
	number of modes / cut off values) in a single graph.
Implementation of method for estimating excess mortality and other health related outcomes from weekly or daily count data described in Acosta and Irizarry (2021) "A Flexible Statistical Framework for Estimating Excess Mortality".
Data that are collected through online sources such as Mechanical 
            Turk may require excluding rows because of IP address duplication, 
            geolocation, or completion duration. This package facilitates
            exclusion of these data for Qualtrics datasets.
Instead of counting observations before and after a subset() 
    call, the ExclusionTable() function reports the number before and after 
    each subset() call together with the number of observations that have been 
    excluded. This is especially useful in observational studies for keeping 
    track how many observations have been excluded for each in-/ or 
    exclusion criteria. You just need to provide ExclusionTable() with a 
    dataset and a list of logical filter statements.
Interactive tools to explore topographic-like data
    sets.  Such data sets take the form of a matrix in which the rows and
    columns provide location/frequency information, and the matrix elements
    contain altitude/response information.  Such data is found in cartography,
    2D spectroscopy and chemometrics.  The functions in this package create
    interactive web pages showing the contoured data, possibly with
    slices from the original matrix parallel to each dimension. The interactive
    behavior is created using the 'D3.js' 'JavaScript' library by Mike Bostock.
Functions that compute probabilistic excursion sets, contour credibility regions, contour avoiding regions, and simultaneous confidence bands for latent Gaussian random processes and fields. The package also contains functions that calculate these quantities for models estimated with the INLA package. The main references for excursions are Bolin and Lindgren (2015) <doi:10.1111/rssb.12055>, Bolin and Lindgren (2017) <doi:10.1080/10618600.2016.1228537>, and Bolin and Lindgren (2018) <doi:10.18637/jss.v086.i05>. These can be generated by the citation function in R.
Provides tools to set up modular ordinary and delay differential equation
  models for mosquito-borne pathogens, focusing on malaria. Modular design is achieved
  by S3 dispatch on parameter lists for each component which is used to compute
  the full set of differential equations which may be solved using
  any of the packages for numerical simulation of differential equations in R. The
  methods implemented by this package are described in Wu et al. (2022) <doi:10.1101/2022.11.07.22282044>.
Performs frequentist inference for the extremal index of a 
    stationary time series.  Two types of methodology are used.  One type is
    based on a model that relates the distribution of block maxima to the 
    marginal distribution of series and leads to the semiparametric maxima 
    estimators described in Northrop (2015) <doi:10.1007/s10687-015-0221-5> and 
    Berghaus and Bucher (2018) <doi:10.1214/17-AOS1621>.  Sliding block maxima
    are used to increase precision of estimation. A graphical block size 
    diagnostic is provided.  The other type of methodology uses a model for the 
    distribution of threshold inter-exceedance times (Ferro and Segers (2003) 
    <doi:10.1111/1467-9868.00401>). Three versions of this type of approach are 
    provided: the iterated weight least squares approach of Suveges (2007) 
    <doi:10.1007/s10687-007-0034-2>, the K-gaps model of 
    Suveges and Davison (2010) <doi:10.1214/09-AOAS292> and a similar approach
    of Holesovsky and Fusek (2020) <doi:10.1007/s10687-020-00374-3> 
    that we refer to as D-gaps. For the K-gaps and D-gaps models this package 
    allows missing values in the data, can accommodate independent subsets of 
    data, such as monthly or seasonal time series from different years, and can 
    incorporate information from right-censored inter-exceedance times.  
    Graphical diagnostics for the threshold level and the respective tuning
    parameters K and D are provided.
Routines for Bayesian estimation and analysis of dynamic quantile linear models utilizing the extended asymmetric Laplace error distribution, also known as extended dynamic quantile linear models (exDQLM) described in Barata et al (2020) <doi:10.1214/21-AOAS1497>.
Presents two methods to estimate the parameters 'mu', 'sigma', and 'tau' of an ex-Gaussian distribution. Those methods are Quantile Maximization Likelihood Estimation ('QMLE') and Bayesian. The 'QMLE' method allows a choice between three different estimation algorithms for these parameters : 'neldermead' ('NEMD'), 'fminsearch' ('FMIN'), and 'nlminb' ('NLMI'). For more details about the methods you can refer at the following list: Brown, S., & Heathcote, A. (2003) <doi:10.3758/BF03195527>; McCormack, P. D., & Wright, N. M. (1964) <doi:10.1037/h0083285>; Van Zandt, T. (2000) <doi:10.3758/BF03214357>; El Haj, A., Slaoui, Y., Solier, C., & Perret, C. (2021) <doi:10.19139/soic-2310-5070-1251>; Gilks, W. R., Best, N. G., & Tan, K. K. C. (1995) <doi:10.2307/2986138>.
The goal of this package is to provide an easy to use, fast and
    scalable exhaustive search framework. Exhaustive feature selections 
    typically require a very large number of models to be fitted and evaluated. 
    Execution speed and memory management are crucial factors here. This package 
    provides solutions for both. Execution speed is optimized by using a 
    multi-threaded C++ backend, and memory issues are solved by by only storing 
    the best results during execution and thus keeping memory usage constant.
Extracts Exchangeable Image File Format (EXIF) metadata, such as camera make and model, ISO speed and the date-time
             the picture was taken on, from JPEG images. Incorporates the 'easyexif' (https://github.com/mayanklahiri/easyexif)
             library.
Reads EXIF data using ExifTool <https://exiftool.org>
    and returns results as a data frame.
    ExifTool is a platform-independent Perl library plus a command-line
    application for reading, writing and editing meta information in a wide variety
    of files. ExifTool supports many different metadata formats including EXIF,
    GPS, IPTC, XMP, JFIF, GeoTIFF, ICC Profile, Photoshop IRB, FlashPix, AFCP and
    ID3, as well as the maker notes of many digital cameras by Canon, Casio, FLIR,
    FujiFilm, GE, HP, JVC/Victor, Kodak, Leaf, Minolta/Konica-Minolta, Motorola, Nikon,
    Nintendo, Olympus/Epson, Panasonic/Leica, Pentax/Asahi, Phase One, Reconyx, Ricoh,
    Samsung, Sanyo, Sigma/Foveon and Sony.
Reads, writes, and edits EXIF and other file metadata
    using ExifTool <https://exiftool.org/>, returning read results as
    a data frame. ExifTool supports many different metadata formats
    including EXIF, GPS, IPTC, XMP, JFIF, GeoTIFF, ICC Profile,
    Photoshop IRB, FlashPix, AFCP and ID3, Lyrics3, as well as the
    maker notes of many digital cameras by Canon, Casio, DJI, FLIR,
    FujiFilm, GE, GoPro, HP, JVC/Victor, Kodak, Leaf,
    Minolta/Konica-Minolta, Motorola, Nikon, Nintendo, Olympus/Epson,
    Panasonic/Leica, Pentax/Asahi, Phase One, Reconyx, Ricoh, Samsung,
    Sanyo, Sigma/Foveon and Sony.
The extended neighbourhood rule for the k nearest neighbour ensemble where the neighbours are determined in k steps. Starting from the first nearest observation of the test point, the algorithm identifies a single observation that is closest to the observation at the previous step. At each base learner in the ensemble, this search is extended to k steps on a random bootstrap sample with a random subset of features selected from the feature space. The final predicted class of the test point is determined by using a majority vote in the predicted classes given by all base models. Amjad Ali, Muhammad Hamraz, Naz Gul, Dost Muhammad Khan, Saeed Aldahmani, Zardad Khan (2022) <doi:10.48550/arXiv.2205.15111>.
Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. The method is presented in details in Plagnol et al (2012) <https://pubmed.ncbi.nlm.nih.gov/22942019/>.
Pacote para a analise de experimentos havendo duas variaveis
    explicativas quantitativas e uma variavel dependente quantitativa. Os
    experimentos podem ser sem repeticoes ou com delineamento estatistico.
    Sao ajustados 12 modelos de regressao multipla e plotados graficos de
    superficie resposta (Hair JF, 2016) <ISBN:13:978-0138132637>.(Package
    for the analysis of experiments having two explanatory quantitative
    variables and one quantitative dependent variable. The experiments can
    be without repetitions or with a statistical design. Twelve multiple
    regression models are fitted and response surface graphs are plotted
    (Hair JF, 2016) <ISBN:13:978-0138132637>).
Provides a shiny-based front end (the 'ExPanD' app) and
    a set of functions for exploratory data analysis. Run as a web-based 
    app, 'ExPanD' enables users to assess the robustness of empirical evidence 
    without providing them access to the underlying data. You can export a 
    notebook containing the analysis of 'ExPanD' and/or use the functions of the 
    package to support your exploratory data analysis workflow. Refer to the 
    vignettes of the package for more information on how to use 'ExPanD' and/or 
    the functions of this package.
Generates feature matrix outputs from R object inputs
    using a variety of expansion functions.  The generated
    feature matrices have applications as inputs
    for a variety of machine learning algorithms.
    The expansion functions are based on coercing the input
    to a matrix, treating the columns as features and
    converting individual columns or combinations into blocks of
    columns.
    Currently these include expansion of columns by
    efficient sparse embedding by vectors of lags,
    quadratic expansion into squares and unique products,
    powers by vectors of degree,
    vectors of orthogonal polynomials functions,
    and block random affine projection transformations (RAPTs).
    The transformations are
    magrittr- and cbind-friendly, and can be used in a
    building block fashion.  For instance, taking the cos() of
    the output of the RAPT transformation generates a
    stationary kernel expansion via Bochner's theorem, and this
    expansion can then be cbind-ed with other features.
    Additionally, there are utilities for replacing features,
    removing rows with NAs,
    creating matrix samples of a given distribution,
    a simple wrapper for LASSO with CV,
    a Freeman-Tukey transform,
    generalizations of the outer function,
    matrix size-preserving discrete difference by row,
    plotting, etc.
The amplitude-dependent autoregressive time series model (EXPAR) proposed by Haggan and Ozaki (1981) <doi:10.2307/2335819> was improved by incorporating the moving average (MA) framework for capturing the variability efficiently. Parameters of the EXPARMA model can be estimated using this package. The user is provided with the best fitted EXPARMA model for the data set under consideration.
A SQLite database is designed to store all information 
  of experiment-based data including metadata, experiment design, 
  managements, phenotypic values and climate records. The dataset can be
  imported from an excel file.
Modular implementation of the Differential Evolution algorithm for
    experimenting with different types of operators.
Package for analysis of simple experimental designs (CRD, RBD and LSD), experiments in double factorial schemes (in CRD and RBD), experiments in a split plot in time schemes (in CRD and RBD), experiments in double factorial schemes with an additional treatment (in CRD and RBD), experiments in triple factorial scheme (in CRD and RBD) and experiments in triple factorial schemes with an additional treatment (in CRD and RBD), performing the analysis of variance and means comparison by fitting regression models until the third power (quantitative treatments) or by a multiple comparison test, Tukey test, test  of Student-Newman-Keuls (SNK), Scott-Knott, Duncan test, t test (LSD) and Bonferroni t test (protected LSD) - for qualitative treatments; residual analysis (Ferreira, Cavalcanti and Nogueira, 2014) <doi:10.4236/am.2014.519280>.
Pacote para análise de delineamentos experimentais (DIC, DBC e DQL), experimentos em esquema fatorial duplo (em DIC e DBC), experimentos em parcelas subdivididas (em DIC e DBC), experimentos em esquema fatorial duplo com um tratamento adicional (em DIC e DBC), experimentos em fatorial triplo (em DIC e DBC) e experimentos em esquema fatorial triplo com um tratamento adicional (em DIC e DBC), fazendo analise de variancia e comparacao de multiplas medias (para tratamentos qualitativos), ou ajustando modelos de regressao ate a terceira potencia (para tratamentos quantitativos); analise de residuos (Ferreira, Cavalcanti and Nogueira, 2014) <doi:10.4236/am.2014.519280>.
Expectile and quantile regression of models with nonlinear effects
  e.g. spatial, random, ridge using least asymmetric weighed squares / absolutes
  as well as boosting; also supplies expectiles for common distributions.
Distributes samples in batches while making batches
    homogeneous according to their description. Allows for an arbitrary
    number of variables, both numeric and categorical. For quality control
    it provides functions to subset a representative sample.
Provides convenience functions for researching experiences 
    including user, customer, patient, employee, and other human experiences.
    It provides a suite of tools to simplify data exploration such as 
    benchmarking, comparing groups, and checking for differences. The outputs 
    translate statistical approaches in applied experience research to 
    human readable output.
Provides various statistical methods for
  designing and analyzing randomized experiments. One functionality
  of the package is the implementation of randomized-block and
  matched-pair designs based on possibly multivariate pre-treatment
  covariates. The package also provides the tools to analyze various
  randomized experiments including cluster randomized experiments,
  two-stage randomized experiments, randomized experiments with 
  noncompliance, and randomized experiments with missing data.
Contains all the datasets that were used in Social Science Experiments: A Hands-On Introduction and in its R Companion. Relevant materials can be found at <https://osf.io/b78je>.
Supports designing efficient discrete choice experiments (DCEs). Experimental designs can be formed on the basis of orthogonal arrays or search methods for optimal designs (Federov or mixed integer programs). Various methods for converting these experimental designs into a discrete choice experiment. Many efficiency measures! Draws from literature of Kuhfeld (2010) and Street et. al (2005) <doi:10.1016/j.ijresmar.2005.09.003>.
Enables users to incorporate expert opinion with parametric survival analysis using a Bayesian or frequentist approach. Expert Opinion can be provided on the survival probabilities at certain time-point(s) or for the difference in mean survival between two treatment arms.Please reference its use as Cooney, P., White, A. (2023) <doi:10.1177/0272989X221150212>.
Three functional modules, including genetic features, differential expression analysis and non-additive expression analysis were integrated into the package. And the package is suitable for RNA-seq and small RNA sequencing data. Besides, two methods of non-additive expression analysis were provided. One is the calculation of the additive (a) and dominant (d), the other is the evaluation of expression level dominance by comparing the total expression of the gene in hybrid offspring with the expression level in parents. For non-additive expression analysis of RNA-seq data, it is only applicable to hybrid offspring (including two sub-genomes) species for the time being.
Tools created for image analysis in researches. There are functions associated with image editing, segmentation, and obtaining biometric measurements (Este pacote foi idealizado para para a analise de imagens em pesquisas. Ha funcoes associadas a edicao de imagens, segmentacao, e obtencao de medidas biometricas).
The exponential integrals E_1(x), E_2(x), E_n(x) and
  Ei(x), and the incomplete gamma function G(a, x) defined for
  negative values of its first argument. The package also gives easy
  access to the underlying C routines through an API; see the package
  vignette for details. A test package included in sub-directory
  example_API provides an implementation. C routines derived from the
  GNU Scientific Library <https://www.gnu.org/software/gsl/>.
The Australian Regulatory Guidelines for Prescription
    Medicines (ARGPM), guidance on "Stability testing for prescription
    medicines", recommends to predict the shelf life of chemically derived
    medicines from stability data by taking the worst case situation at batch
    release into account. Consequently, if a change over time is observed,
    a release limit needs to be specified. Finding a release limit and the
    associated shelf life is supported, as well as the standard approach
    that is recommended by guidance Q1E "Evaluation of stability data"
    from the International Council for Harmonisation (ICH).
Generates explanations for classification and regression models and visualizes them.
 Explanations are generated for individual predictions as well as for models as a whole. Two explanation methods
 are included, EXPLAIN and IME. The EXPLAIN method is fast but might miss explanations expressed redundantly
 in the model. The IME method is slower as it samples from all feature subsets.
 For the EXPLAIN method see Robnik-Sikonja and Kononenko (2008) <doi:10.1109/TKDE.2007.190734>, 
 and the IME method is described in Strumbelj and Kononenko (2010, JMLR, vol. 11:1-18).
 All models in package 'CORElearn' are natively supported, for other prediction models a wrapper function is provided 
 and illustrated for models from packages 'randomForest', 'nnet', and 'e1071'.
Current layout algorithms such as Kamada Kawai do not take into consideration disjoint clusters in a network, often resulting in a high overlap among the clusters, resulting in a visual “hairball” that often is uninterpretable. The ExplodeLayout algorithm takes as input (1) an edge list of a unipartite or bipartite network, (2) node layout coordinates (x, y) generated by a layout algorithm such as Kamada Kawai, (3) node cluster membership generated from a clustering algorithm such as modularity maximization, and (4) a radius to enable the node clusters to be “exploded” to reduce their overlap. The algorithm uses these inputs to generate new layout coordinates of the nodes which “explodes” the clusters apart, such that the edge lengths within the clusters are preserved, while the edge lengths between clusters are recalculated. The modified network layout with nodes and edges are displayed in two dimensions. The user can experiment with different explode radii to generate a layout which has sufficient separation of clusters, while reducing the overall layout size of the network. This package is a basic version of an earlier version called [epl]<https://github.com/UTMB-DIVA-Lab/epl> that searched for an optimal explode radius, and offered multiple ways to separate clusters in a network (Bhavnani et al(2017) <PMID: 28815099>). The example dataset is for a bipartite network, but the algorithm can work also for unipartite networks.
Shiny interfaces and graphical functions for multivariate analysis results exploration.
Conduct numerous exploratory analyses in an instant with a 
    point-and-click interface. With one simple command, this tool 
    launches a Shiny App on the local machine. Drag and drop variables 
    in a data set to categorize them as possible independent, 
    dependent, moderating, or mediating variables. Then run dozens 
    (or hundreds) of analyses instantly to uncover any statistically 
    significant relationships among variables. Any relationship 
    thus uncovered should be tested in follow-up studies. 
    This tool is designed only to facilitate exploratory 
    analyses and should NEVER be used for p-hacking. Many of 
    the functions used in this package are previous versions of functions
    in the R Packages 'kim' and 'ezr'.
    Selected References:
    Chang et al. (2021) <https://CRAN.R-project.org/package=shiny>.
    Dowle et al. (2021) <https://CRAN.R-project.org/package=data.table>.
    Kim (2023) <https://jinkim.science/docs/kim.pdf>.
    Kim (2021) <doi:10.5281/zenodo.4619237>.
    Kim (2020) <https://CRAN.R-project.org/package=ezr>.
    Simmons et al. (2011) <doi:10.1177/0956797611417632>
    Tingley et al. (2019) <https://CRAN.R-project.org/package=mediation>.
    Wickham et al. (2020) <https://CRAN.R-project.org/package=ggplot2>.
Interactive data exploration with one line of code, automated
    reporting or use an easy to remember set of tidy functions for low code
    exploratory data analysis.
Simplifies some complicated and labor intensive processes involved in exploring and explaining data.  Allows you to quickly and efficiently visualize the interaction between variables and simplifies the process of discovering covariation in your data.  Also includes some convenience features designed to remove as much redundant typing as possible.
Computation of the matrix exponential, logarithm, sqrt,
  and related quantities, using traditional and modern methods.
Easily export 'R' graphs and statistical output to 'Microsoft
    Office' / 'LibreOffice', 'Latex' and 'HTML' Documents, using sensible defaults
    that result in publication-quality output with simple, straightforward commands.
    Output to 'Microsoft Office' is in editable 'DrawingML' vector format for
    graphs, and can use corporate template documents for styling. This enables
    the production of standardized reports and also allows for manual tidy-up
    of the layout of 'R' graphs in 'Powerpoint' before final publication. Export
    of graphs is flexible, and functions enable the currently showing R graph
    or the currently showing 'R' stats object to be exported, but also allow the
    graphical or tabular output to be passed as objects. The package relies on package
    'officer' for export to 'Office' documents,and output files are also fully compatible
    with 'LibreOffice'. Base 'R', 'ggplot2' and 'lattice' plots are supported, as
    well as a wide variety of 'R' stats objects, via wrappers to xtable(), broom::tidy() 
    and stargazer(), including aov(), lm(), glm(), lme(), glmnet() and coxph() as
    well as matrices and data frames and many more...
A variety of descriptive multivariate analyses with the singular value decomposition,
    such as principal components analysis, correspondence analysis, and multidimensional scaling.
    See An ExPosition of the Singular Value Decomposition in R (Beaton et al 2014) <doi:10.1016/j.csda.2013.11.006>.
The EXPOS model uses a digital elevation model (DEM) to estimate
    exposed and protected areas for a given hurricane wind direction and
    inflection angle. The resulting topographic exposure maps can be combined
    with output from the HURRECON model to estimate hurricane wind damage
    across a region. For details on the original version of the EXPOS model
    written in 'Borland Pascal', see: Boose, Foster, and Fluet (1994)
    <doi:10.2307/2937142>, Boose, Chamberlin, and Foster (2001)
    <doi:10.1890/0012-9615(2001)071[0027:LARIOH]2.0.CO;2>, and Boose,
    Serrano, and Foster (2004) <doi:10.1890/02-4057>.
Produces diversity estimates and species lists with associated global distribution for any angiosperm family and genus from 'Plants of the World Online' database <https://powo.science.kew.org/>, by interacting with the source code of each plant taxon page, and creates global maps of species richness.
A set of functions for computing expected permutation matrices given a matrix of likelihoods for each individual assignment. It has been written to accompany the forthcoming paper 'Computing expectations and marginal likelihoods for permutations'. Publication details will be updated as soon as they are finalized.
Allows to calculate the probabilities  of occurrences of an event in a 
 great number of repetitions of Bernoulli experiment, through the application of  
 the local and the integral theorem of De Moivre Laplace, and the theorem of Poisson. 
 Gives the possibility to show the results graphically and analytically, and to compare
 the results obtained by the application of the above  theorems with those calculated by
 the direct application of the Binomial formula. Is basically useful for educational
 purposes.
Given a continuous-time dynamic network, this package allows one to fit a stochastic blockmodel where nodes belonging to the same group create interactions and non-interactions of similar lengths. This package implements the methodology described by R. Rastelli and M. Fop (2019) <arXiv:1901.09828>.
Data sets from the book "Forecasting with exponential smoothing: the state space approach" by 
	Hyndman, Koehler, Ord and Snyder (Springer, 2008).
Package computes and displays tables with support for 'SPSS'-style 
        labels, multiple and nested banners, weights, multiple-response variables 
        and significance testing. There are facilities for nice output of tables 
        in 'knitr', 'Shiny', '*.xlsx' files, R and 'Jupyter' notebooks. Methods 
        for labelled variables add value labels support to base R functions and to 
        some functions from other packages. Additionally, the package brings 
        popular data transformation functions from 'SPSS' Statistics and 'Excel': 
        'RECODE', 'COUNT', 'COUNTIF', 'VLOOKUP' and etc. 
        These functions are very useful for data processing in marketing research 
        surveys. Package intended to help people to move data 
        processing from 'Excel' and 'SPSS' to R.
Provides a data class of 'tbl_es' to help aid in the formation and
    analyses of recurrent or novel experience studies. A 'tbl_es' has attributes
    which identify the key variables used for calculating metrics under an 
    actuarial perspective. Common metrics (such as actual-to-expected analysis) 
    can be quickly generated in aggregate or according to different qualitative 
    factors. If multiple factors are of interest, grouped metrics can be 
    automatically computed for each factor individually as well as for all 
    possible combinations. All resulting output can then be formatted for 
    presentations or left unformatted for subsequent analyses. Ultimately, this
    package aims to reduce time spent completing repetitive code therefore 
    increasing time for analysis and insight.
Analysis of experimental results and automatic report generation in both interactive HTML and LaTeX. This package ships with a rich interface for data modeling and built in functions for the rapid application of statistical tests and generation of common plots and tables with publish-ready quality.
Estimation for high conditional quantiles based on quantile regression.
A consistent, unified and extensible
    framework for estimation of parameters for probability distributions, including 
    parameter estimation procedures that allow for weighted samples; the current set of distributions included are: the standard beta, The four-parameter beta, Burr, gamma, Gumbel, Johnson SB and SU, Laplace, logistic, normal, symmetric truncated normal, truncated normal, symmetric-reflected truncated beta, standard symmetric-reflected truncated beta, triangular, uniform, and Weibull distributions; decision criteria and selections based on these decision criteria.
Creates family objects identical to stats
    family but for new links.
If one treated group is matched to one control reservoir in two different ways to produce two sets of treated-control matched pairs, then the two control groups may be entwined, in the sense that some control individuals are in both control groups.  The exterior match is used to compare the two control groups.
Estimates coefficients of extended LASSO penalized linear regression and generalized linear models. Currently lasso and elastic net penalized linear regression and generalized linear models are considered. This package currently utilizes an accurate approximation of L1 penalty and then a modified Jacobi algorithm to estimate the coefficients. There is provision for plotting of the solutions and predictions of coefficients at given values of lambda. This package also contains functions for cross validation to select a suitable lambda value given the data. Also provides a function for estimation in fused lasso penalized linear regression. For more details, see Mandal, B. N.(2014). Computational methods for L1 penalized GLM model fitting, unpublished report submitted to Macquarie University, NSW, Australia.
For multiple full/partial ranking lists, R package 'ExtMallows' can (1) detect whether the input ranking lists are over-correlated, and (2) use the Mallows model or extended Mallows model to integrate the ranking lists, and (3) use hierarchical extended Mallows model for rank integration if there are groups of over-correlated ranking lists.
By using a multispectral image and ESRI shapefile (Point/ Line/ Polygon), a data table will be generated for classification, regression or other processing. The data table will be contained by band wise raster values and shapefile ids (User Defined).
Density, distribution function, quantile function
    and random generation for a number of univariate
    and multivariate distributions. This package implements the
    following distributions: Bernoulli, beta-binomial, beta-negative
    binomial, beta prime, Bhattacharjee, Birnbaum-Saunders,
    bivariate normal, bivariate Poisson, categorical, Dirichlet,
    Dirichlet-multinomial, discrete gamma, discrete Laplace,
    discrete normal, discrete uniform, discrete Weibull, Frechet,
    gamma-Poisson, generalized extreme value, Gompertz,
    generalized Pareto, Gumbel, half-Cauchy, half-normal, half-t,
    Huber density, inverse chi-squared, inverse-gamma, Kumaraswamy,
    Laplace, location-scale t, logarithmic, Lomax, multivariate
    hypergeometric, multinomial, negative hypergeometric, 
    non-standard beta, normal mixture, Poisson mixture, Pareto,
    power, reparametrized beta, Rayleigh, shifted Gompertz, Skellam,
    slash, triangular, truncated binomial, truncated normal,
    truncated Poisson, Tukey lambda, Wald, zero-inflated binomial,
    zero-inflated negative binomial, zero-inflated Poisson.
Tools to using fonts other than the standard PostScript fonts.
    This package makes it easy to use system TrueType fonts and with PDF or
    PostScript output files, and with bitmap output files in Windows. extrafont
    can also be used with fonts packaged specifically to be used with, such as
    the fontcm package, which has Computer Modern PostScript fonts with math
    symbols.
Package for holding the database for the extrafont package
Provide estimation and data generation tools for some new multivariate frailty models.
             This version includes the gamma, inverse Gaussian, weighted Lindley, Birnbaum-Saunders
	     and truncated normal as the distribution for the frailty terms. 
             For the basal model, it is considered a parametric approach based on the exponential, 
             Weibull and the piecewise exponential distributions as well as a semiparametric approach. 
             For details, see Gallardo and Bourguignon (2022) <arXiv:2206.12973>.
Speed up common tasks, particularly logical or
  relational comparisons and routine follow up tasks such as finding the
  indices and subsetting. Inspired by mathematics, where something like:
  3 < x < 6 is a standard, elegant and clear way to assert that
  x is both greater than 3 and less than 6
  (see for example <https://en.wikipedia.org/wiki/Relational_operator>),
  a chaining operator is implemented. The chaining operator, %c%,
  allows multiple relational operations to be used in quotes on the right
  hand side for the same object, on the left hand side.
  The %e% operator allows something like set-builder notation 
  (see for example <https://en.wikipedia.org/wiki/Set-builder_notation>) 
  to be used on the right hand side.
  All operators have built in prefixes defined for all, subset, and which
  to reduce the amount of code needed for common tasks, such as return those
  values that are true.
Functions to 'numericise' 'R' objects (coerce to numeric
    objects), summarise 'MCMC' (Monte Carlo Markov Chain) samples and
    calculate deviance residuals as well as 'R' translations of some
    'BUGS' (Bayesian Using Gibbs Sampling), 'JAGS' (Just Another Gibbs
    Sampler), 'STAN' and 'TMB' (Template Model Builder) functions.
Finding life outside the planet Earth several is the ultimate goal of an astrobiologist. Using known astronomical measurements and assumptions the probability of extraterrestrial life existence could be estimated. Equations such as the Drake equation (1961) as stated in the paper of Molina (2019) <arXiv:1912.01783>, Seager (2013) <https://www.space.com/22648-drake-equation-alien-life-seager.html> and Foucher et al, (2017) <doi:10.3390/life7040040> are included in the 'extraterrestrial' package.
Provides summary statistics of local geospatial features within a given geographic area. 
	It does so by calculating the area covered by a target geospatial feature (i.e. buildings, parks, lakes, etc.). 
	The geospatial features can be of any type of geospatial data, including point, polygon or line data.
Maximum likelihood estimation of an extended class of row-column (RC) association models for two-dimensional contingency tables, which are formulated by a condition of reduced rank on a matrix of extended association parameters; see Forcina (2019) <arXiv:1910.13848>. These parameters are defined by choosing the logit type for the row and column variables among four different options and a transformation derived from suitable divergence measures.
A set of procedures for parametric and non-parametric modelling of the dependence structure of multivariate extreme-values is provided. The statistical inference is performed with non-parametric estimators, likelihood-based estimators and Bayesian techniques. It adapts the methodologies of Beranger and Padoan (2015) <arxiv:1508.05561>, Marcon et al. (2016) <doi:10.1214/16-EJS1162>, Marcon et al. (2017) <doi:10.1002/sta4.145>, Marcon et al. (2017) <doi:10.1016/j.jspi.2016.10.004> and Beranger et al. (2021) <doi:10.1007/s10687-019-00364-0>. This package also allows for the modelling of spatial extremes using flexible max-stable processes. It provides simulation algorithms and fitting procedures relying on the Stephenson-Tawn likelihood as per Beranger at al. (2021) <doi:10.1007/s10687-020-00376-1>.
An implementation of Extreme Bounds Analysis (EBA), a global sensitivity analysis that examines the robustness of determinants in regression models. The package supports both Leamer's and Sala-i-Martin's versions of EBA, and allows users to customize all aspects of the analysis.
Extreme value theory, nonparametric kernel estimation, tail
    conditional probabilities, extreme conditional quantile, adaptive estimation,
    quantile regression, survival probabilities.
An index measuring the amount of information brought by forecasts for extreme events, subject to calibration, is computed. This index is originally designed for weather or climate forecasts, but it may be used in other forecasting contexts. This is the implementation of the index in Taillardat et al. (2019) <arXiv:1905.04022>.
A set of procedures for estimating risks related to extreme events via risk measures such as Expectile, Value-at-Risk, etc. is provided. Estimation methods for univariate independent observations and temporal dependent observations are available. The methodology is extended to the case of independent multidimensional observations.  The statistical inference is performed through parametric and non-parametric estimators. Inferential procedures such as confidence intervals, confidence regions and hypothesis testing are obtained by exploiting the asymptotic theory. Adapts the methodologies derived in Padoan and Stupfler (2020) <arxiv:2004.04078>, Padoan and Stupfler (2020) <arxiv:2007.08944>, Daouia et al. (2018) <doi:10.1111/rssb.12254>, Drees (2000) <doi:10.1214/aoap/1019487617>, Drees (2003) <doi:10.3150/bj/1066223272>, de Haan and Ferreira (2006) <doi:10.1007/0-387-34471-3>, de Haan et al. (2016) <doi:10.1007/s00780-015-0287-6>.
General functions for performing extreme value analysis.  In particular, allows for inclusion of covariates into the parameters of the extreme-value distributions, as well as estimation through MLE, L-moments, generalized (penalized) MLE (GMLE), as well as Bayes.  Inference methods include parametric normal approximation, profile-likelihood, Bayes, and bootstrapping.  Some bivariate functionality and dependence checking (e.g., auto-tail dependence function plot, extremal index estimation) is also included.  For a tutorial, see Gilleland and Katz (2016) <doi: 10.18637/jss.v072.i08> and for bootstrapping, please see Gilleland (2020) <doi: 10.1175/JTECH-D-20-0070.1>.
Fit, plot and compare several (extreme value) distribution functions. 
    Compute (truncated) distribution quantile estimates and plot return periods on a linear scale.
   	On the fitting method, see Asquith (2011): Distributional Analysis with L-moment Statistics [...]  ISBN 1463508417.
Detect outliers in one-dimensional data.
Conducts inference in statistical models for extreme values (de Carvalho et al (2012), <doi:10.1080/03610926.2012.709905>; de Carvalho and Davison (2014), <doi:10.1080/01621459.2013.872651>; Einmahl et al (2016), <doi:10.1111/rssb.12099>).
Estimation of the sample univariate, cross and return time extremograms. The package can also adds empirical confidence bands to each of the extremogram plots via a permutation procedure under the assumption that the data are independent. Finally, the stationary bootstrap allows us to construct credible confidence bands for the extremograms.
Testing for and dating periods of explosive
    dynamics (exuberance) in time series using the univariate and panel
    recursive unit root tests proposed by Phillips et al. (2015)
    <doi:10.1111/iere.12132> and Pavlidis et al. (2016)
    <doi:10.1007/s11146-015-9531-2>.The recursive least-squares
    algorithm utilizes the matrix inversion lemma to avoid matrix
    inversion which results in significant speed improvements. Simulation
    of a variety of periodically-collapsing bubble processes. Details can be 
    found in Vasilopoulos et al. (2022) <doi:10.18637/jss.v103.i10>.
Analysis of trade in value added with international
    input-output tables. Includes commands for easy data extraction,
    matrix manipulation, decomposition of value added in gross exports and
    calculation of value added indicators, with full geographical and
    sector customization.  Decomposition methods include Borin and Mancini
    (2023) <doi:10.1080/09535314.2022.2153221>, Miroudot and Ye (2021)
    <doi:10.1080/09535314.2020.1730308>, Wang et al. (2013)
    <https://econpapers.repec.org/paper/nbrnberwo/19677.htm> and Koopman
    et al. (2014) <doi:10.1257/aer.104.2.459>.
There is no ophthalmic researcher who has not had headaches from 
    the handling of visual acuity entries. Different notations, untidy entries. 
    This shall now be a matter of the past. Eye makes it as easy as pie to work
    with VA data - easy cleaning, easy conversion between 
    Snellen, logMAR, ETDRS letters, and qualitative visual acuity 
    shall never pester you again. The eye 
    package automates the pesky task to count number of patients and eyes, 
    and can help to clean data with easy re-coding for right and left eyes. 
    It also contains functions to help reshaping eye side specific variables 
    between wide and long format. Visual acuity conversion is based on 
    Schulze-Bonsel et al. (2006) <doi:10.1167/iovs.05-0981>, 
    Gregori et al. (2010) <doi:10.1097/iae.0b013e3181d87e04>, 
    Beck et al. (2003) <doi:10.1016/s0002-9394(02)01825-1> and 
    Bach (2007) <http:michaelbach.de/sci/acuity.html>.
Open source data allows for reproducible research and helps advance
    our knowledge. The purpose of this package is to collate open source 
    ophthalmic data sets curated for direct use. This is real life data of 
    people with intravitreal injections with anti-vascular endothelial growth
    factor (anti-VEGF), due to age-related macular degeneration or diabetic 
    macular edema. Associated publications of the data sets: 
    Fu et al. (2020) <doi:10.1001/jamaophthalmol.2020.5044>, 
    Moraes et al (2020) <doi:10.1016/j.ophtha.2020.09.025>,
    Fasler et al. (2019) <doi:10.1136/bmjopen-2018-027441>, 
    Arpa et al. (2020) <doi:10.1136/bjophthalmol-2020-317161>,
    Kern et al. 2020, <doi:10.1038/s41433-020-1048-0>.
Imports plain-text ASC data files from EyeLink eye trackers 
    into (relatively) tidy data frames for analysis and visualization.
Import gaze data from  edf files generated by 
  the SR Research <https://www.sr-research.com/> EyeLink eye tracker. Gaze data,
  both recorded events and samples, is imported per trial. The package allows to extract
  events of interest, such as saccades, blinks, etc. as well as
  recorded variables and custom events (areas of interest, triggers) into separate tables.
  The package requires EDF API library that can be obtained at <https://www.sr-research.com/support/>.
Functions to prepare and analyse eye tracking data of reading
  exercises. The functions allow some basic data preparations and code fixations 
  as first and second pass. First passes can be further devided into forward and 
  reading. The package further allows for aggregating fixation times per AOI or 
  per AOI and per type of pass (first forward, first rereading, second). These 
  methods are based on Hyönä, Lorch, and Rinck (2003) <doi:10.1016/B978-044451020-4/50018-9> 
  and Hyönä, and Lorch (2004) <doi:10.1016/j.learninstruc.2004.01.001>. It is 
  also possible to convert between metric length and visual degrees.
Addresses tasks along the pipeline from raw
    data to analysis and visualization for eye-tracking data. Offers several
    popular types of analyses, including linear and growth curve time analyses,
    onset-contingent reaction time analyses, as well as several non-parametric
    bootstrapping approaches. For references to the approach see Mirman, 
    Dixon & Magnuson (2008) <doi:10.1016/j.jml.2007.11.006>, and
    Barr (2008) <doi:10.1016/j.jml.2007.09.002>.
A set of functions for organising and analysing datasets from
    experiments run using 'Eyelink' eye-trackers. Organising functions help
    to clean and prepare eye-tracking datasets for analysis, and mark up
    key events such as display changes and responses made by participants.
    Analysing functions help to create means for a wide range of standard
    measures (such as 'mean fixation durations'), which can then be fed into
    the appropriate statistical analyses and graphing packages as necessary.
Facilitates easy analysis of factorial experiments, including
    purely within-Ss designs (a.k.a. "repeated measures"), purely between-Ss
    designs, and mixed within-and-between-Ss designs. The functions in this package
    aim to provide simple, intuitive and consistent specification of data analysis
    and visualization. Visualization functions also include design visualization for
    pre-analysis data auditing, and correlation matrix visualization. Finally, this
    package includes functions for non-parametric analysis, including permutation
    tests and bootstrap resampling. The bootstrap function obtains predictions
    either by cell means or by more advanced/powerful mixed effects models, yielding
    predictions and confidence intervals that may be easily visualized at any level
    of the experiment's design.
A dataframe-friendly implementation of ComBat Harmonization which uses an empirical Bayesian framework to remove batch effects.
    Johnson WE & Li C (2007)  <doi:10.1093/biostatistics/kxj037> "Adjusting batch effects in microarray expression data using empirical Bayes methods."
    Fortin J-P, Cullen N, Sheline YI, Taylor WD, Aselcioglu I, Cook PA, Adams P, Cooper C, Fava M, McGrath PJ, McInnes M, Phillips ML, Trivedi MH, Weissman MM, & Shinohara RT (2017) <doi:10.1016/j.neuroimage.2017.11.024> "Harmonization of cortical thickness measurements across scanners and sites."
    Fortin J-P, Parker D, Tun<e7> B, Watanabe T, Elliott MA, Ruparel K, Roalf DR, Satterthwaite TD, Gur RC, Gur RE, Schultz RT, Verma R, & Shinohara RT (2017) <doi:10.1016/j.neuroimage.2017.08.047> "Harmonization of multi-site diffusion tensor imaging data."
A tool to operate a batch of univariate or multivariate Cox
    models and return tidy result.
Calculate cutoff values for model fit measures used in structural equation modeling (SEM) by simulating and testing data sets (cf. Hu & Bentler, 1999 <doi:10.1080/10705519909540118>) with the same parameters (population model, number of observations, etc.) as the model under consideration.
Because fungicide resistance is an important phenotypic trait for
    fungi and oomycetes, it is necessary to have a standardized method of
    statistically analyzing the Effective Concentration (EC) values. This
    package is designed for those who are not terribly familiar with R to be
    able to analyze and plot an entire set of isolates using the 'drc' package.
Enables users to create visualizations using functions 
    based on the data analysis task rather than on plotting mechanics. It hides
    the details of the individual 'ggplot2' function calls and 
    allows the user to focus on the end goal. Useful for quick preliminary explorations. 
    Provides functions for common exploration patterns. Some of the ideas in this
    package are motivated by Fox (2015, ISBN:1938377052).
Fit model for datasets with easy-to-interpret Gaussian process modeling, predict responses for new inputs.
    The input variables of the datasets can be quantitative, qualitative/categorical or mixed.
    The output variable of the datasets is a scalar (quantitative).
    The optimization of the likelihood function can be chosen by the users (see the documentation of EzGP_fit()).
    The modeling method is published in "EzGP: Easy-to-Interpret Gaussian Process Models for Computer Experiments with Both Quantitative and Qualitative Factors" 
    by Qian Xiao, Abhyuday Mandal, C. Devon Lin, and Xinwei Deng (2022) <doi:10.1137/19M1288462>.
An extension of 'knitr' that adds flexibility in several
    ways. One common source of frustration with 'knitr' is that it assumes
    the directory where the source file lives should be the working directory,
    which is often not true. 'ezknitr' addresses this problem by giving you
    complete control over where all the inputs and outputs are, and adds several
    other convenient features to make rendering markdown/HTML documents easier.
Serves as a platform for published fluorometric enzyme assay
 protocols. 'ezmmek' calibrates, calculates, and plots enzyme activities as they
 relate to the transformation of synthetic substrates. At present, 'ezmmek'
 implements two common protocols found in the literature, and is modular to accommodate
 additional protocols. Here, these protocols are referred to as the In-Sample
 Calibration (Hoppe, 1983; <doi:10.3354/meps011299>) and In-Buffer Calibration (German et al., 2011; <doi:10.1016/j.soilbio.2011.03.017>).
 protocols. By containing multiple protocols, 'ezmmek' aims to stimulate
 discussion about how to best optimize fluorometric enzyme assays. A standardized
 approach would make studies more comparable and reproducible.
Wrapper for the 'ggplot2' package that creates a variety of common
  charts (e.g. bar, line, area, ROC, waterfall, pie) while aiming to reduce
  typing.
Runs a Shiny App in the local machine for basic
    statistical and graphical analyses. The point-and-click interface 
    of Shiny App enables obtaining the same analysis outputs (e.g., plots and
    tables) more quickly, as compared with typing the required code in R,
    especially for users without much experience or expertise with coding.
    Examples of possible analyses include tabulating descriptive
    statistics for a variable, creating histograms by experimental groups,
    and creating a scatter plot and calculating the correlation between
    two variables.
Contains two functions that are intended to make
    tuning supervised learning methods easy. The eztune function uses a
    genetic algorithm or Hooke-Jeeves optimizer to find the best 
    set of tuning parameters. The user can choose the optimizer, the 
    learning method, and if optimization will be based on accuracy 
    obtained through validation error, cross validation, or resubstitution. 
    The function eztune.cv will compute a cross validated error rate. The purpose 
    of eztune_cv is to provide a cross validated accuracy or MSE when 
    resubstitution or validation data are used for optimization because 
    error measures from both approaches can be misleading.
Obtain Formula 1 data via the 'Ergast API' <https://ergast.com/mrd/> and the unofficial API <https://www.formula1.com/en/f1-live.html> via the 'fastf1' 'Python' library <https://docs.fastf1.dev/>.
Frequentist assisted by Bayes (FAB) confidence interval
    construction. See 'Adaptive multigroup confidence intervals with constant
    coverage' by Yu and Hoff <DOI:10.1093/biomet/asy009> and  
    'Exact adaptive confidence intervals for linear regression coefficients'
    by Hoff and Yu <DOI:10.1214/18-EJS1517>.
Frequentist assisted by Bayes (FAB) p-values and confidence 
 interval construction. See 
 Hoff (2019) <arXiv:1907.12589> 
 "Smaller p-values via indirect information",
 Hoff and Yu (2019) <doi:10.1214/18-EJS1517> 
 "Exact adaptive confidence intervals for linear regression coefficients", and
 Yu and Hoff (2018) <doi:10.1093/biomet/asy009> 
 "Adaptive multigroup confidence intervals with constant coverage".
Implementation of the Factorized Binary Search (FaBiSearch) methodology for the estimation of the number and the location of multiple change points in the network (or clustering) structure of multivariate high-dimensional time series. The method is motivated by the detection of change points in functional connectivity networks for functional magnetic resonance imaging (fMRI) data. FaBiSearch uses non-negative matrix factorization (NMF), an unsupervised dimension reduction technique, and a new binary search algorithm to identify multiple change points.  It requires minimal assumptions. Lastly, we provide interactive, 3-dimensional, brain-specific network visualization capability in a flexible, stand-alone function. This function can be conveniently used with any node coordinate atlas, and nodes can be color coded according to community membership, if applicable. The output is an elegantly displayed network laid over a cortical surface, which can be rotated in the 3-dimensional space. The main routines of the package are detect.cps(), for multiple change point detection, est.net(), for estimating a network between stationary multivariate time series, net.3dplot(), for plotting the estimated functional connectivity networks, and opt.rank(), for finding the optimal rank in NMF for a given data set. The functions have been extensively tested on simulated multivariate high-dimensional time series data and fMRI data. For details on the FaBiSearch methodology, please see Ondrus et al. (2021) <arXiv:2103.06347>. For a more detailed explanation and applied examples of the fabisearch package, please see Ondrus and Cribben (2022), preprint.
Provides a collection of commonly used univariate and multivariate
    time series forecasting models including automatically selected exponential 
    smoothing (ETS) and autoregressive integrated moving average (ARIMA) models.
    These models work within the 'fable' framework provided by the 'fabletools'
    package, which provides the tools to evaluate, visualise, and combine models 
    in a workflow consistent with the tidyverse.
Allows ATA (Automatic Time series analysis using the Ata method) models from the 'ATAforecasting' package to be used in a tidy workflow with the modeling interface of
    'fabletools'. This extends 'ATAforecasting' to provide enhanced model specification and management, performance evaluation methods, and
    model combination tools. The Ata method (Yapar et al. (2019) <doi:10.15672/hujms.461032>), an alternative to exponential smoothing (described in Yapar (2016)
    <doi:10.15672/HJMS.201614320580>, Yapar et al. (2017) <doi:10.15672/HJMS.2017.493>), is a new univariate time series forecasting method which provides
    innovative solutions to issues faced during the initialization and optimization stages of existing forecasting methods.
    Forecasting performance of the Ata method is superior to existing methods both in terms of easy implementation and accurate forecasting.
    It can be applied to non-seasonal or seasonal time series which can be decomposed into four components (remainder, level, trend and seasonal).
Allows prophet models from the 'prophet' package to be used in a tidy workflow with the modelling interface of 'fabletools'. This extends 'prophet' to provide enhanced model specification and management, performance evaluation methods, and model combination tools.
Provides tools, helpers and data structures for
    developing models and time series functions for 'fable' and extension
    packages. These tools support a consistent and tidy interface for time
    series modelling and analysis.
Model-based clustering of multivariate continuous data using Bayesian mixtures of factor analyzers (Papastamoulis (2019) <DOI:10.1007/s11222-019-09891-z> (2018) <DOI:10.1016/j.csda.2018.03.007>). The number of clusters is estimated using overfitting mixture models (Rousseau and Mengersen (2011) <DOI:10.1111/j.1467-9868.2011.00781.x>): suitable prior assumptions ensure that asymptotically the extra components will have zero posterior weight, therefore, the inference is based on the ``alive'' components. A Gibbs sampler is implemented in order to (approximately) sample from the posterior distribution of the overfitting mixture. A prior parallel tempering scheme is also available, which allows to run multiple parallel chains with different prior distributions on the mixture weights. These chains run in parallel and can swap states using a Metropolis-Hastings move. Eight different parameterizations give rise to parsimonious representations of the covariance per cluster (following Mc Nicholas and Murphy (2008) <DOI:10.1007/s11222-008-9056-0>). The model parameterization and number of factors is selected according to the Bayesian Information Criterion. Identifiability issues related to label switching are dealt by post-processing the simulated output with the Equivalence Classes Representatives algorithm (Papastamoulis and Iliopoulos (2010) <https://www.jstor.org/stable/25703571>, Papastamoulis (2016) <DOI:10.18637/jss.v069.c01>).
The goal of this package is to provide wrapper functions in the 
    data cleaning and cleansing processes. These function helps in messages and 
    interaction with the user, keep track of information in pipelines, help in 
    the wrangling, munging, assessment and visualization of data frame-like 
    material.
Helps you imagine your data before you collect it. Hierarchical data structures
   and correlated data can be easily simulated, either from random number generators or
   by resampling from existing data sources. This package is faster with 'data.table' and
   'mvnfast' installed.
Allows the user to implement easily canvas elements within a 'shiny' app or an 'RMarkdown' document. 
    The user can create shapes, images and text elements within the canvas which can also be used as a drawing tool for taking notes.
    The package relies on the 'fabricjs' 'JavaScript' library. See <http://fabricjs.com/>.
We implement the Fast Covariance Estimation for 
             Sparse Functional Data paper published in Statistics and Computing <doi: 10.1007/s11222-017-9744-8>.
Collect  marketing data from facebook Ads using the 'Windsor.ai' API <https://windsor.ai/api-fields/>.
    Use four spaces when indenting paragraphs within the Description.
Collect  your data on digital marketing campaigns from Facebook Leads Ads using the 'Windsor.ai' API <https://windsor.ai/api-fields/>.
Collect  your data on digital marketing campaigns from 'Facebook Organic' using the 'Windsor.ai' API <https://windsor.ai/api-fields/>.
Provides an interface to the 'Kairos' Face Recognition API <https://kairos.com/face-recognition-api>. The API detects faces in images and returns estimates for demographics like gender, ethnicity and age.
Linear cross-section factor model fitting with least-squares 
    and robust fitting the 'lmrobdetMM()' function from 'RobStatTM'; related
    volatility, Value at Risk and Expected Shortfall risk and performance 
    attribution (factor-contributed vs idiosyncratic returns);
    tabular displays of risk and performance reports;
    factor model Monte Carlo. The package authors would like to thank Chicago
    Research on Security Prices,LLC for the cross-section of about 300
    CRSP stocks data (in the data.table object 'stocksCRSP', and S&P GLOBAL MARKET
    INTELLIGENCE for contributing 14 factor scores (a.k.a "alpha factors".and
    "factor exposures") fundamental data on the 300 companies in the data.table
    object 'factorSPGMI'.  The 'stocksCRSP' and 'factorsSPGMI' data are not covered by
    the GPL-2 license, are not provided as open source of any kind, and they are
    not to be redistributed in any form.
We present 'FACT' (Feature Attributions for ClusTering), a
  framework for unsupervised interpretation methods that can be used with an 
  arbitrary clustering algorithm. The package is capable of re-assigning instances to
  clusters (algorithm agnostic), preserves the integrity of the data and does
  not introduce additional models. 'FACT' is inspired by the principles of
  model-agnostic interpretation in supervised learning. Therefore, some of the
  methods presented are based on 'iml', a R Package for Interpretable Machine
  Learning by Christoph Molnar, Giuseppe Casalicchio, and Bernd Bischl (2018)
  <doi:10.21105/joss.00786>.
Implements instrumental variable estimators for 2^K factorial experiments with noncompliance.
Perform Maximum Likelihood Factor analysis on a covariance matrix or data matrix.
Some functions of 'ade4' and 'stats' are combined in order to obtain a partition of the rows of a data table, with columns representing variables of scales: quantitative, qualitative or frequency. 
  First, a principal axes method is performed and then, a combination of Ward agglomerative hierarchical classification and K-means is performed, using some of the first coordinates obtained from the previous principal axes method. See, for example: 
      Lebart, L. and Piron, M. and Morineau, A.  (2006).
      Statistique Exploratoire Multidimensionnelle, Dunod, Paris.
  In order to permit to have different weights of the elements to be clustered, the function 'kmeansW', programmed in C++, is included. It is a modification of 'kmeans'.   
  Some graphical functions include the option: 'gg=FALSE'.  When 'gg=TRUE', they  use the 'ggplot2' and 'ggrepel' packages to avoid  the super-position of the labels.
Provides some easy-to-use functions to extract and visualize the
    output of multivariate data analyses, including 'PCA' (Principal Component
    Analysis), 'CA' (Correspondence Analysis), 'MCA' (Multiple Correspondence
    Analysis), 'FAMD' (Factor Analysis of Mixed Data), 'MFA' (Multiple Factor Analysis) and 'HMFA' (Hierarchical Multiple
    Factor Analysis) functions from different R packages. It contains also functions
    for simplifying some clustering analysis steps and provides 'ggplot2' - based
    elegant data visualization.
Brings a set of tools to help and automatically realise the description of principal component analyses (from 'FactoMineR' functions). Detection of existing outliers, identification of the informative components, graphical views and dimensions description are performed threw dedicated functions. The Investigate() function performs all these functions in one, and returns the result as a report document (Word, PDF or HTML).
Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis. F. Husson, S. Le and J. Pages (2017).
Computes factorial A-, D- and E-optimal designs for two-colour cDNA microarray experiments.
A well known identifiability issue in factor analytic models is the invariance with respect to orthogonal transformations. This problem burdens the inference under a Bayesian setup, where Markov chain Monte Carlo (MCMC) methods are used to generate samples from the posterior distribution. The package applies a series of rotation, sign and permutation transformations (Papastamoulis and Ntzoufras (2022) <DOI:10.1007/s11222-022-10084-4>) into raw MCMC samples of factor loadings, which are provided by the user. The post-processed output is identifiable and can be used for MCMC inference on any parametric function of factor loadings. Comparison of multiple MCMC chains is also possible.
Tests for Kaiser-Meyer-Olkin (KMO) and
    communalities in a dataset. It provides a final sample by removing
    variables in a iterable manner while keeping account of the variables
    that were removed in each step. It follows the best practices and assumptions according to
    Hair, Black, Babin & Anderson (2018, ISBN:9781473756540).
Estimation, model selection and goodness-of-fit of (1) factor copula models for mixed continuous and discrete data in Kadhem and Nikoloulopoulos (2021) <doi:10.1111/bmsp.12231>; (2) bi-factor and second-order copula models for item response data in Kadhem and Nikoloulopoulos (2023) <doi:10.1007/s11336-022-09894-2>; (3) factor tree copula models for item response data in Kadhem and Nikoloulopoulos (2022) <arXiv:2201.00339>.
Used for the design and analysis of a 2x2 factorial trial for
    a time-to-event endpoint.  It performs power calculations and significance
    testing as well as providing estimates of the relevant hazard ratios and the 
    corresponding 95% confidence intervals.  Important reference papers include
    Slud EV. (1994) <https://www.ncbi.nlm.nih.gov/pubmed/8086609>
    Lin DY, Gong J, Gallo P, Bunn PH, Couper D. (2016) <DOI:10.1111/biom.12507>
    Leifer ES, Troendle JF, Kolecki A, Follmann DA. (2020)
    <https://github.com/EricSLeifer/factorial2x2/blob/master/Leifer%20et%20al.%20paper.pdf>.
Functions to estimate a factor model using discrete and continuous proxy variables. The function 'dproxyme' estimates a factor model of discrete proxy variables using an EM algorithm (Dempster, Laird, Rubin (1977) <doi:10.1111/j.2517-6161.1977.tb01600.x>; Hu (2008) <doi:10.1016/j.jeconom.2007.12.001>; Hu(2017) <doi:10.1016/j.jeconom.2017.06.002> ). The function 'cproxyme' estimates a linear factor model (Cunha, Heckman, and Schennach (2010) <doi:10.3982/ECTA6551>).
Markov chain Monte Carlo (MCMC) sampler for fully Bayesian estimation of latent factor stochastic volatility models with interweaving <doi:10.1080/10618600.2017.1322091>. Sparsity can be achieved through the usage of Normal-Gamma priors on the factor loading matrix <doi:10.1016/j.jeconom.2018.11.007>.
Function factories are functions that make functions. They can be 
    confusing to construct. Straightforward techniques can produce functions 
    that are fragile or hard to understand. While more robust techniques exist 
    to construct function factories, those techniques can be confusing. This 
    package is designed to make it easier to construct function factories.
Perform factorial analysis with a menu and draw graphs interactively thanks to 'FactoMineR' and a Shiny application.
Multi-environment genomic prediction for training and test 
    environments using penalized factorial regression. Predictions are made 
    using genotype-specific environmental sensitivities as in Millet et al. 
    (2019) <doi:10.1038/s41588-019-0414-y>.
Allow clients to fetch 'analytics' through API for Portfolio 
    'Analytics'('PA'), Style Performance Risk('SPAR') and 'Vault' products of 
    'FactSet'. Visit 
    <https://github.com/factset/analyticsapi-engines-r-sdk/tree/master/Engines>
    for more information on the usage of package. Visit 
    <https://developer.factset.com/> for more information on products.
Generates 'RProtobuf' classes for 'FactSet' 'STACH V2' tabular 
    format which represents complex multi-dimensional array of data. These 
    classes help in the 'serialization' and 'deserialization' of 'STACH V2' 
    formatted data. See 'GitHub' repository documentation for more 
    information.
Allow clients to convert 'FactSet' 'STACH' formatted data to simpler 
    tabular formats in the form of data frames. This package also provides helper
    methods to extract the meta data from 'FactSet' 'STACH' formatted
    data. See documentation on the 'GitHub' repository for more information.
Compute maximum likelihood estimators of parameters in a Gaussian factor model using
  the the matrix-free methodology described in Dai et al. (2020) <doi:10.1080/10618600.2019.1704296>.
  In contrast to the factanal() function from 'stats' package, fad() can handle high-dimensional datasets where
  number of variables exceed the sample size and is also substantially faster than the EM algorithms.
The functions provided in the FADA (Factor Adjusted Discriminant Analysis) package aim at performing supervised classification of high-dimensional and correlated profiles. The procedure combines a decorrelation step based on a  
   factor modeling of the dependence among covariates and a classification method. The available methods are Lasso regularized logistic model
    (see Friedman et al. (2010)), sparse linear discriminant analysis (see
    Clemmensen et al. (2011)), shrinkage linear and diagonal discriminant
    analysis (see M. Ahdesmaki et al. (2010)). More methods of classification can be used on the decorrelated data provided by the package FADA.
Probability distributions that are sometimes useful in hydrology.
An implementation of a clustering algorithm for functional data based on adaptive density peak detection technique, in which the density is estimated by functional k-nearest neighbor density estimation based on a proposed semi-metric between functions. The proposed functional data clustering algorithm is computationally fast since it does not need iterative process. (Alex Rodriguez and Alessandro Laio (2014) <doi:10.1126/science.1242072>; Xiao-Feng Wang and Yifan Xu (2016) <doi:10.1177/0962280215609948>).
An easy framework to read FDA Adverse Event Reporting System XML/ASCII files <https://www.fda.gov/drugs/questions-and-answers-fdas-adverse-event-reporting-system-faers/fda-adverse-event-reporting-system-faers-latest-quarterly-data-files>.
Data and functions for the book "Multivariate Statistical 
              Modelling Based on Generalized Linear Models", first edition, by 
              Ludwig Fahrmeir and Gerhard Tutz.  Useful when using the book.
More comfortable interface to work with R data or source files
    in a key-value fashion.
An implementation of the fair data adaptation with quantile
    preservation described in Plecko & Meinshausen (2019) <arXiv:1911.06685>.
    The adaptation procedure uses the specified causal graph to pre-process the
    given training and testing data in such a way to remove the bias caused by
    the protected attribute. The procedure uses tree ensembles for quantile
    regression.
We provide here tools used by the Solar Durability and Lifetime Extension Center (SDLE)
    for FAIRifying data from materials science projects. Functions have been created for numerous tools common
    in the field in order to make the metadata more Findable, Accessible, Interoperable, and Reproducible.
Clustering for categorical and mixed-type of data, to preventing classification biases due to race, 
            gender or others sensitive attributes.
            This algorithm is an extension of the methodology proposed by "Santos & Heras (2020) <doi:10.28945/4643>".
Fair machine learning regression models which take sensitive attributes into account in
  model estimation. Currently implementing Komiyama et al. (2018) 
  <http://proceedings.mlr.press/v80/komiyama18a/komiyama18a.pdf>, Zafar et al.
  (2019) <https://www.jmlr.org/papers/volume20/18-262/18-262.pdf> and my own
  approach from Scutari, Panero and Proissl (2022)
  <https://link.springer.com/content/pdf/10.1007/s11222-022-10143-w.pdf>
  that uses ridge regression to enforce fairness.
Measure fairness metrics in one place for many models. Check how big is model's bias towards different races, sex, nationalities etc. Use measures such as Statistical Parity, Equal odds to detect the discrimination against unprivileged groups. Visualize the bias using heatmap, radar plot, biplot, bar chart (and more!). There are various pre-processing and post-processing bias mitigation algorithms implemented. Package also supports calculating fairness metrics for regression models. Find more details in (Wiśniewski, Biecek (2021)) <arXiv:2104.00507>.
Offers calculation, visualization and comparison of algorithmic fairness metrics. Fair machine learning is an emerging topic with the overarching aim to critically assess whether ML algorithms reinforce existing social biases. Unfair algorithms can propagate such biases and produce predictions with a disparate impact on various sensitive groups of individuals (defined by sex, gender, ethnicity, religion, income, socioeconomic status, physical or mental disabilities). Fair algorithms possess the underlying foundation that these groups should be treated similarly or have similar prediction outcomes. The fairness R package offers the calculation and comparisons of commonly and less commonly used fairness metrics in population subgroups. These methods are described by Calders and Verwer (2010) <doi:10.1007/s10618-010-0190-x>, Chouldechova (2017) <doi:10.1089/big.2016.0047>, Feldman et al. (2015) <doi:10.1145/2783258.2783311> , Friedler et al. (2018) <doi:10.1145/3287560.3287589> and Zafar et al. (2017) <doi:10.1145/3038912.3052660>. The package also offers convenient visualizations to help understand fairness metrics.
Allows user to obtain subsets of columns of data or vectors within a list.  These subsets will match the original data in terms of average and variation, but have a consistent length of data per column.  It is intended for use on automated data generation which may not always output the same N per replicate or sample.
This R package can be used to generate artificial data conditionally on pre-specified (simulated or user-defined) relationships between the variables and/or observations. Each observation is drawn from a multivariate Normal distribution where the mean vector and covariance matrix reflect the desired relationships. Outputs can be used to evaluate the performances of variable selection, graphical modelling, or clustering approaches by comparing the true and estimated structures (B Bodinier et al (2021) <arXiv:2106.02521>).
Use R as a minimal build system. This might come in
    handy if you are developing R packages and can not use a proper build
    system. Stay away if you can (use a proper build system).
Create fake datasets that can be used for prototyping and teaching.
    This package provides a set of functions to generate fake data
    for a variety of data types, such as dates, addresses,
    and names. It can be used for prototyping (notably in 'shiny') or as a tool
    to teach data manipulation and data visualization.
A set of function for clustering data observation with hybrid method Fuzzy ART and K-Means 
            by Sengupta, Ghosh & Dan (2011) <doi:10.1080/0951192X.2011.602362>.
This is a method for Allele-specific DNA Copy Number Profiling using Next-Generation Sequencing.  Given the allele-specific coverage at the variant loci, this program segments the genome into regions of homogeneous allele-specific copy number.  It requires, as input, the read counts for each variant allele in a pair of case and control samples. For detection of somatic mutations, the case and control samples can be the tumor and normal sample from the same individual.
This is a method for Allele-specific DNA Copy Number profiling for whole-Exome sequencing data.  Given the allele-specific coverage and site biases at the variant loci, this program segments the genome into regions of homogeneous allele-specific copy number.  It requires, as input, the read counts for each variant allele in a pair of case and control samples, as well as the site biases. For detection of somatic mutations, the case and control samples can be the tumor and normal sample from the same individual.  The implemented method is based on the paper: Chen, H., Jiang, Y., Maxwell, K., Nathanson, K. and Zhang, N. (under review). Allele-specific copy number estimation by whole Exome sequencing.
Given vectors of family sizes and number of affecteds per family, calculates the risk of disease recurrence in an unaffected person, conditional on a family having at least k affected members. Methods also model heterogeneity of disease risk across families by fitting a mixture model, allowing for high and low risk families.
Fatty acid metabolic analysis aimed to the estimation of FA import (I), de novo synthesis (S), fractional contribution of the 13C-tracers (D0, D1, D2), elongation (E) and desaturation (Des) based on mass isotopologue data.
Simulates age-at-onset traits associated with a segregating major gene in family data 
     obtained from population-based, clinic-based, or multi-stage designs. Appropriate ascertainment 
     correction is utilized to estimate age-dependent penetrance functions either parametrically from 
     the fitted model or nonparametrically from the data. The Expectation and Maximization algorithm 
     can infer missing genotypes and carrier probabilities estimated from family's genotype and
     phenotype information or from a fitted model. Plot functions include pedigrees of simulated 
     families and predicted penetrance curves based on specified parameter values.
     For more information see Choi, Y.-H., Briollais, L., He, W. and Kopciuk, K. (2021) FamEvent: An 
     R Package for Generating and Modeling Time-to-Event Data in Family Designs, 
     Journal of Statistical Software 97 (7), 1-30.
Provides functionality for testing familial hypotheses. Supports testing centers 
    belonging to the Huber family. Testing is carried out using the Bayesian bootstrap. One- and 
    two-sample tests are supported, as are directional tests. Methods for visualizing output are 
    provided.
Single unified interface for end-to-end modelling of regression, 
    categorical and time-to-event (survival) outcomes. Models created using
    familiar are self-containing, and their use does not require additional
    information such as baseline survival, feature clustering, or feature
    transformation and normalisation parameters. Model performance,
    calibration, risk group stratification, (permutation) variable importance,
    individual conditional expectation, partial dependence, and more, are
    assessed automatically as part of the evaluation process and exported in
    tabular format and plotted, and may also be computed manually using export
    and plot functions. Where possible, metrics and values obtained during the
    evaluation process come with confidence intervals.
Tools to study kinship networks, grandparenthood, and double burden (presence of children and oldest old parents) in virtual population produced by 'VirtualPop'.
Grows families of features by selecting features that maximize a weighted score calculated from empirical feature scores and graphical knowledge. The final weighted score for a feature is determined by summing a feature's family-weighted scores across all families in which the feature appears.
Estimate parameters of univariate probability distributions 
  with maximum likelihood and Bayesian methods.
Given a set of parameters describing model dynamics and a corresponding cost function,
    FAMoS performs a dynamic forward-backward model selection on a specified selection
    criterion. It also applies a non-local swap search method. Works on any cost function. 
    For detailed information see Gabel et al. (2019) <doi:10.1371/journal.pcbi.1007230>.
FamSKAT-RC is a family-based association kernel test for both 
    rare and common variants. This test is general and several special cases 
    are known as other methods: famSKAT, which only focuses on rare variants 
    in family-based data, SKAT, which focuses on rare variants in 
    population-based data (unrelated individuals), and SKAT-RC, which focuses 
    on both rare and common variants in population-based data. When one 
    applies famSKAT-RC and sets the value of phi to 1, famSKAT-RC becomes 
    famSKAT. When one applies famSKAT-RC and set the value of phi to 1 and the 
    kinship matrix to the identity matrix, famSKAT-RC becomes SKAT. When one 
    applies famSKAT-RC and set the kinship matrix (fullkins) to the identity 
    matrix (and phi is not equal to 1), famSKAT-RC becomes SKAT-RC. We also 
    include a small sample synthetic pedigree to demonstrate the method with.  
    For more details see Saad M and Wijsman EM (2014) <doi:10.1002/gepi.21844>.
The method proposed in this package takes into account the impact of dependence on the multiple testing procedures for high-throughput data as proposed by Friguet et al. (2009). The common information shared by all the variables is modeled by a factor analysis structure. The number of factors considered in the model is chosen to reduce the false discoveries variance in multiple tests. The model parameters are estimated thanks to an EM algorithm. Adjusted tests statistics are derived, as well as the associated p-values. The proportion of true null hypotheses (an important parameter when controlling the false discovery rate) is also estimated from the FAMT model. Graphics are proposed to interpret and describe the factors.
Computes the penalized maximum likelihood estimates of factor loadings and unique variances for various tuning parameters. The pathwise coordinate descent along with EM algorithm is used.  This package also includes a new graphical tool which outputs path diagram, goodness-of-fit indices and model selection criteria for each regularization parameter. The user can change the regularization parameter by manipulating scrollbars, which is helpful to find a suitable value of regularization parameter.
A collection of R functions to perform nonparametric 
    analysis of covariance for regression curves or surfaces. 
    Testing the equality or parallelism of nonparametric curves 
    or surfaces is equivalent to analysis of variance (ANOVA) or 
    analysis of covariance (ANCOVA) for one-sample functional data. 
    Three different testing methods are available in the package, 
    including one based on L-2 distance, one based on an ANOVA 
    statistic, and one based on variance estimators.
Provides the function fancycut() which is like cut() except
  you can mix left open and right open intervals with point values,
  intervals that are closed on both ends and intervals that are open on both ends.
A neighborhood-based, greedy search algorithm is performed to estimate a feature allocation by minimizing the expected loss based on posterior samples from the feature allocation distribution. The method is currently under peer review but an earlier draft is available in Dahl, Johnson, and Andros (2022+) <doi:10.48550/arXiv.2207.13824>.
Estimation and plotting of a function's FANOVA graph to identify the interaction structure and fitting, prediction and simulation of a Kriging model modified by the identified structure. The interactive function plotManipulate() can only be run on the 'RStudio IDE' with 'RStudio' package 'manipulate' loaded. 'RStudio' is freely available (<https://rstudio.com/>), and includes package 'manipulate'. The equivalent function plotTk() bases on CRAN Repository packages only. For further information on the method see Fruth, J., Roustant, O., Kuhnt, S. (2014) <doi:10.1016/j.jspi.2013.11.007>.
Visualise sequential distributions using a range of plotting
    styles. Sequential distribution data can be input as either simulations or
    values corresponding to percentiles over time. Plots are added to
    existing graphic devices using the fan function. Users can choose from four
    different styles, including fan chart type plots, where a set of coloured
    polygon, with shadings corresponding to the percentile values are layered
    to represent different uncertainty levels. Full details in R Journal article; Abel (2015) <doi:10.32614/RJ-2015-002>.
Counterparts to R string manipulation functions that account for
   the effects of ANSI text formatting control sequences.
Calculation of Evapotranspiration by FAO Penman-Monteith equation based on Allen, R. G., Pereira, L. S., Raes, D., Smith, M. (1998, ISBN:92-5-104219-5) "Crop evapotranspiration - Guidelines for computing crop water requirements - FAO Irrigation and drainage paper 56".
Download Data from the FAOSTAT Database of the Food and Agricultural Organization (FAO) of the United Nations.
    A list of functions to download statistics from FAOSTAT (database of the FAO <https://www.fao.org/faostat/>) 
    and WDI (database of the World Bank <https://data.worldbank.org/>), and to perform some harmonization operations.
Tools for detecting and summarize influential cases that
    can affect exploratory and confirmatory factor analysis models as well as
    structural equation models more generally (Chalmers, 2015, <doi:10.1177/0146621615597894>; 
    Flora, D. B., LaBrish, C. & Chalmers, R. P., 2012, <doi:10.3389/fpsyg.2012.00055>).
Create Frequently Asked Questions page for Shiny application.
Modelizations and previsions functions for
   Functional AutoRegressive processes using
   nonparametric methods: functional kernel,
   estimation of the covariance operator in
   a subspace, ...
Books are "Linear Models with R" published 1st Ed. August 2004, 2nd Ed. July 2014 by CRC press, ISBN 9781439887332, and "Extending the Linear Model with R" published by CRC press in 1st Ed. December 2005 and 2nd Ed. March 2016, ISBN 9781584884248 and "Practical Regression and ANOVA in R" contributed documentation on CRAN (now very dated).
Using the idea of least trimmed square, it could automatically detects and removes outliers from data before estimating the coefficients. It is a robust machine learning tool which can be applied to gene-expression deconvolution technique. Yuning Hao, Ming Yan, Blake R. Heath, Yu L. Lei and Yuying Xie (2019) <doi:10.1101/358366>.
Reads and writes 'ARFF' files. 'ARFF' (Attribute-Relation
    File Format) files are like 'CSV' files, with a little bit of added
    meta information in a header and standardized NA values. They are
    quite often used for machine learning data sets and were introduced
    for the 'WEKA' machine learning 'Java' toolbox. See
    <https://waikato.github.io/weka-wiki/formats_and_processing/arff_stable/>
    for further info on 'ARFF' and for
    <http://www.cs.waikato.ac.nz/ml/weka/> for more info on 'WEKA'.
    'farff' gets rid of the 'Java' dependency that 'RWeka' enforces, and
    it is at least a faster reader (for bigger files). It uses 'readr' as
    parser back-end for the data section of the 'ARFF' file. Consistency
    with 'RWeka' is tested on 'Github' and 'Travis CI' with hundreds of
    'ARFF' files from 'OpenML'.
Implements a consistent model selection strategy for high dimensional sparse regression when the covariate dependence can be reduced through factor models. By separating the latent factors from idiosyncratic components, the problem is transformed from model selection with highly correlated covariates to that with weakly correlated variables. It is appropriate for cases where we have many variables compared to the number of samples. Moreover, it implements a robust procedure to estimate distribution parameters wherever possible, hence being suitable for cases when the underlying distribution deviates from Gaussianity. See the paper on the 'FarmSelect' method, Fan et al.(2017) <arXiv:1612.08490>, for detailed description of methods and further references.
Performs robust multiple testing for means in the presence of known and unknown latent factors presented in Fan et al.(2019) "FarmTest: Factor-Adjusted Robust Multiple Testing With Approximate False Discovery Control" <doi:10.1080/01621459.2018.1527700>.
             Implements a series of adaptive Huber methods combined with fast data-drive tuning schemes proposed in Ke et al.(2019) "User-Friendly Covariance Estimation for Heavy-Tailed Distributions" <doi:10.1214/19-STS711> to estimate model parameters and construct test statistics that are robust against heavy-tailed and/or asymmetric error distributions. 
             Extensions to two-sample simultaneous mean comparison problems are also included. 
             As by-products, this package contains functions that compute adaptive Huber mean, covariance and regression estimators that are of independent interest.
Provides handy functions and data to support a course book for accounting research.
   Gow, Ian and Tongqing Ding (2022) "Accounting Research: An Introductory Course" <https://iangow.github.io/far_book/>.
Allows the user to execute interactively radial data envelopment analysis models. The user has the ability to upload a data frame, 
    select the input/output variables, choose the technology assumption to adopt and decide whether to run an input or an output oriented model. 
    When the model is executed a set of results are displayed which include efficiency scores, peers' determination, scale efficiencies' evaluation 
    and slacks' calculation. Fore more information about the theoretical background of the package, 
    please refer to Bogetoft & Otto (2011) <doi:10.1007/978-1-4419-7961-2>.
The encoding of colour can be handled in many different ways,
    using different colour spaces. As different colour spaces have
    different uses, efficient conversion between these representations are
    important. The 'farver' package provides a set of functions that gives
    access to very fast colour space conversion and comparisons
    implemented in C++, and offers speed improvements over the
    'convertColor' function in the 'grDevices' package.
An implementation of the two-sample multidimensional
    Kolmogorov-Smirnov test described by Fasano and Franceschini (1987)
    <doi:10.1093/mnras/225.1.155>. This test evaluates the null hypothesis
    that two i.i.d. random samples were drawn from the same underlying
    probability distribution. The data can be of any dimension, and can be
    of any type (continuous, discrete, or mixed).
It contains a function designed to the joint segmentation in the mean of several correlated series. The method is described in the paper X. Collilieux, E. Lebarbier and S. Robin. A factor model approach for the joint segmentation with between-series correlation (2015) <arXiv:1505.05660>.
This is an R implementation of "A Fast and Scalable Joint Estimator for Learning Multiple Related Sparse Gaussian Graphical Models" (FASJEM). The FASJEM algorithm can be used to estimate multiple related precision matrices. For instance, it can identify context-specific gene networks from multi-context gene expression datasets. By performing data-driven network inference from high-dimensional and heterogonous data sets, this tool  can help users effectively translate aggregated data into knowledge that take the form of graphs among entities. Please run demo(fasjem) to learn the basic functions provided by this package. For more details, please see <http://proceedings.mlr.press/v54/wang17e/wang17e.pdf>.
A collection of functions to manage, to investigate and to analyze data sets of financial 
  assets from different points of view.
The Flow Analysis Summary Statistics Tool for R, 'fasstr', provides various functions to tidy and screen daily stream discharge data, calculate and visualize various summary statistics and metrics, and compute annual trending and volume frequency analyses. 
     It features useful function arguments for filtering of and handling dates, customizing data and metrics, and the ability to pull daily data directly from the Water Survey of Canada hydrometric database (<https://collaboration.cmc.ec.gc.ca/cmc/hydrometrics/www/>).
A collection of acceleration schemes for proximal gradient methods for estimating penalized regression parameters described in
    Goldstein, Studer, and Baraniuk (2016) <arXiv:1411.3406>. Schemes such as Fast Iterative Shrinkage and Thresholding Algorithm (FISTA) by Beck and Teboulle (2009) <doi:10.1137/080716542> 
    and the adaptive stepsize rule introduced in Wright, Nowak, and Figueiredo (2009) <doi:10.1109/TSP.2009.2016892> are included. You provide the objective function and proximal mappings, and it takes care of the issues like stepsize selection, acceleration, and stopping conditions for you.
Implements the AdaptiveImpute matrix completion
    algorithm of 'Intelligent Initialization and Adaptive Thresholding for
    Iterative Matrix Completion',
    <https://amstat.tandfonline.com/doi/abs/10.1080/10618600.2018.1518238>.
    AdaptiveImpute is useful for embedding sparsely observed matrices,
    often out performs competing matrix completion algorithms, and
    self-tunes its hyperparameter, making usage easy.
Fast censored linear regression for the accelerated failure time (AFT) model of Huang (2013) <doi:10.1111/sjos.12031>.
The 'fastai' <https://docs.fast.ai/index.html> library 
             simplifies training fast and accurate neural networks 
             using modern best practices. It is based on research 
             in to deep learning best practices undertaken 
             at 'fast.ai', including 'out of the box' support
             for vision, text, tabular, audio, time series, and 
             collaborative filtering models.
Fast and numerically stable estimation of a covariance matrix by banding the Cholesky factor using a modified Gram-Schmidt algorithm implemented in RcppArmadilo. See <http://stat.umn.edu/~molst029> for details on the algorithm.
Methods for estimating time-varying infectious disease
	transmission rates from disease incidence time series, based on
	discretizations of an SIR model, as analyzed in Jagan et al. (2020)
	<doi:10.1371/journal.pcbi.1008124>.
This is a two-in-one package which provides interfaces to
        both R and 'Python'. It implements fast hierarchical, agglomerative
        clustering routines. Part of the functionality is designed as drop-in
        replacement for existing routines: linkage() in the 'SciPy' package
        'scipy.cluster.hierarchy', hclust() in R's 'stats' package, and the
        'flashClust' package. It provides the same functionality with the
        benefit of a much faster implementation. Moreover, there are
        memory-saving routines for clustering of vector data, which go beyond
        what the existing packages provide. For information on how to install
        the 'Python' files, see the file INSTALL in the source distribution.
        Based on the present package, Christoph Dalitz also wrote a pure 'C++'
        interface to 'fastcluster':
        <https://lionel.kr.hs-niederrhein.de/~dalitz/data/hclust/>.
A method which uses the Cochran-Mantel-Haenszel test with significant pattern mining to detect intervals in binary genotype data which are significantly associated with a particular phenotype, while accounting for categorical covariates.
We implement a cocktail algorithm, a good mixture of coordinate decent, the majorization-minimization principle and the strong rule, for computing the solution paths of the elastic net penalized Cox's proportional hazards model. The package is an implementation of Yang, Y. and Zou, H. (2013) DOI: <doi:10.4310/SII.2013.v6.n2.a1>.
Implements fast change point detection algorithm based on the
    paper "Sequential Gradient Descent and Quasi-Newton's Method for
    Change-Point Analysis" by Xianyang Zhang, Trisha Dawn
    <https://proceedings.mlr.press/v206/zhang23b.html>. The algorithm
    is based on dynamic programming with pruning and sequential gradient
    descent. It is able to detect change points a magnitude faster than
    the vanilla Pruned Exact Linear Time(PELT). The package includes examples
    of linear regression, logistic regression, Poisson regression, penalized
    linear regression data, and whole lot more examples with custom cost
    function in case the user wants to use their own cost function.
For ordinal rating data, consider the accelerated Expectation-Maximization algorithm to estimate and test models within the family of CUB models (where CUB stands for Combination of a discrete Uniform and a shifted Binomial distributions). The procedure is built upon Louis' identity for the observed information matrix.  Best-subset variable selection for CUB regression models is then implemented on such basis. The methods here implemented are illustrated and discussed in the preprint available from Researchgate by Simone R. (2020) <https://tinyurl.com/vvk563e>.
Provides an R interface to Bob Jenkin's streaming, 
 non-cryptographic 'SpookyHash' hash algorithm for use in digest-based 
 comparisons of R objects. 'fastdigest' plugs directly into R's internal 
 serialization machinery, allowing digests of all R objects the serialize() 
 function supports, including reference-style objects via custom hooks. Speed is
 high and scales linearly by object size; memory usage is constant and 
 negligible.
Creates dummy columns from columns that have categorical variables (character or factor types). You can also specify which columns to make dummies out of, or which columns to ignore. Also creates dummy rows from character, factor, and Date columns. This package provides a significant speed increase from creating dummy variables through model.matrix().
Fit Elastic Net, Lasso, and Ridge regression and do cross-validation in a fast way. We build the algorithm based on Least Angle Regression by Bradley Efron, Trevor Hastie, Iain Johnstone, etc. (2004)(<doi:10.1214/009053604000000067 >) and some algorithms like Givens rotation and Forward/Back Substitution. In this way, many matrices to be computed are retained as triangular matrices which can eventually speed up the computation. The fitting algorithm for Elastic Net is written in C++ using Armadillo linear algebra library.
Provides a drop-in replacement for rasterize() from the 'raster'
   package that takes 'sf'-type objects, and is much faster. There is support
   for the main options provided by the rasterize() function, including
   setting the field used and background value, and options for 
   aggregating multi-layer rasters. Uses the scan line algorithm attributed to
   Wylie et al. (1967) <doi:10.1145/1465611.1465619>.
Implements fast and exact computation of Gaussian stochastic process with the Matern kernel using forward filtering and backward smoothing algorithm. It allows for the cases with or without a noise.  See the reference: Mengyang Gu and Yanxun Xu (2017),  <arXiv:1711.11501>.
Fast, numerically-stable Gauss-Hermite quadrature rules and
    utility functions for adaptive GH quadrature. See Liu, Q. and Pierce, D. A.
    (1994) <doi:10.2307/2337136> for a reference on these methods.
Two 'Gray Level Co-occurrence Matrix' ('GLCM') implementations are included: The first is a fast 'GLCM' feature texture computation based on 'Python' 'Numpy' arrays ('Github' Repository, <https://github.com/tzm030329/GLCM>). The second is a fast 'GLCM' 'RcppArmadillo' implementation which is parallelized (using 'OpenMP') with the option to return all 'GLCM' features at once. For more information, see "Artifact-Free Thin Cloud Removal Using Gans" by Toizumi Takahiro, Zini Simone, Sagi Kazutoshi, Kaneko Eiji, Tsukada Masato, Schettini Raimondo (2019), IEEE International Conference on Image Processing (ICIP), pp. 3596-3600, <doi:10.1109/ICIP.2019.8803652>.
Fits generalized linear models efficiently using 'RcppEigen'. The iteratively reweighted least squares 
    implementation utilizes the step-halving approach of Marschner (2011) <doi:10.32614/RJ-2011-012> to help safeguard
    against convergence issues.
Contains Rcpp and RcppEigen implementations of matrix operations useful for Gaussian process models, such as the inversion of a symmetric Toeplitz matrix, sampling from multivariate normal distributions, evaluation of the log-density of a multivariate normal vector, and Bayesian inference for latent variable Gaussian process models with elliptical slice sampling (Murray, Adams, and MacKay 2010).
Provides functionality to produce graphs of probability density functions and cumulative distribution functions with few keystrokes, allows shading under the curve of the probability density function to illustrate concepts such as p-values and critical values, and fits a simple linear regression line on a scatter plot with the equation as the main title.
Implementation of FastICA algorithm to perform Independent
        Component Analysis (ICA) and Projection Pursuit.
TrainFastImputation() uses training data to describe a
    multivariate normal distribution that the data approximates or
    can be transformed into approximating and stores this information
    as an object of class 'FastImputationPatterns'. FastImputation()
    function uses this 'FastImputationPatterns' object to impute (make
    a good guess at) missing data in a single line or a whole data frame
    of data.  This approximates the process used by 'Amelia'
    <https://gking.harvard.edu/amelia> but is much faster when
    filling in values for a single line of data.
Maximum likelihood estimation for the semi-parametric joint modeling of competing risks and longitudinal data applying customized linear scan algorithms, proposed by Li and colleagues (2022) <doi:10.1155/2022/1362913>. 
             The time-to-event data is modelled using a (cause-specific) Cox proportional hazards regression model with time-fixed covariates. The longitudinal 
             outcome is modelled using a linear mixed effects model. The association is captured by shared random effects. The model 
             is estimated using an Expectation Maximization algorithm.
This 'Rcpp'-based package implements highly efficient functions for the calculation of the Jonckheere-Terpstra statistic. It can be used for a variety of applications, including feature selection in machine learning problems, or to conduct genome-wide association studies (GWAS) with multiple quantitative phenotypes. The code leverages 'OpenMP' directives for multi-core computing to reduce overall processing time.
A computationally efficient and statistically rigorous fast 
    Kernel Machine method for multi-kernel analysis. The approach is based on 
    a low-rank approximation to the nuisance effect kernel matrices. The 
    algorithm is applicable to continuous, binary, and survival traits and 
    is implemented using the existing single-kernel analysis software 'SKAT' 
    and 'coxKM'. 'coxKM' can be obtained from 
    <https://github.com/lin-lab/coxKM>.
R wrappers of C++ implementation of Faster K-Medoids clustering algorithms (FastPAM, FastCLARA and FastCLARANS) proposed in Erich Schubert, Peter J. Rousseeuw 2019 <doi:10.1007/978-3-030-32047-8_16>.
Compute labels for a test set according to the k-Nearest Neighbors classification. This is a fast way to do k-Nearest Neighbors classification because the distance matrix -between the features of the observations- is an input to the function rather than being calculated in the function itself every time.
Fitting a fast Laplace approximation for Spatial Generalized Linear Mixed Model as
  described in Park and Lee (2021) <https://github.com/sangwan93/fastLaplace/blob/main/FastLaplaceMain.pdf>.
Implements a Fellegi-Sunter probabilistic record linkage model that allows for missing data
    and the inclusion of auxiliary information. This includes functionalities to conduct a merge of two 
    datasets under the Fellegi-Sunter model using the Expectation-Maximization algorithm. In addition, 
    tools for preparing, adjusting, and summarizing data merges are included. The package implements methods 
    described in Enamorado, Fifield, and Imai (2019) ''Using a Probabilistic Model to Assist Merging of 
    Large-scale Administrative Records'', American Political Science Review and is available 
    at <http://imai.fas.harvard.edu/research/linkage.html>.
Provides very fast logistic regression with coefficient inferences plus other useful methods such as a forward stepwise model generator (see the benchmarks by visiting the github page at the URL below). The inputs are flexible enough to accomodate GPU computations. The coefficient estimation employs the fastLR() method in the 'RcppNumerical' package by Yixuan Qiu et al. This package allows their work to be more useful to a wider community that consumes inference.
Calculates marginal effects based on logistic model objects such as 'glm' or 'speedglm' at the average (default) or at given values using finite differences. It also returns confidence intervals for said marginal effects and the p-values, which can easily be used as input in stargazer. The function only returns the essentials and is therefore much faster but not as detailed as other functions available to calculate marginal effects. As a result, it is highly suitable for large datasets for which other packages may require too much time or calculating power.
A very fast Log-Rank-Test implementation that is several orders of magnitude faster than the implementation in the 'survival' package.
  Log-Rank-Tests can be computed individually or concurrently using threading.
Implements the new algorithm for fast computation of M-scatter matrices using a partial Newton-Raphson procedure for several estimators. The algorithm is described in Duembgen, Nordhausen and Schuhmacher (2016) <doi:10.1016/j.jmva.2015.11.009>.
Fast implementation of data structures, including a key-value
    store, stack, and queue. Environments are commonly used as key-value stores
    in R, but every time a new key is used, it is added to R's global symbol
    table, causing a small amount of memory leakage. This can be problematic in
    cases where many different keys are used. Fastmap avoids this memory leak
    issue by implementing the map using data structures in C++.
Package providing a fast match() replacement for cases
	that require repeated look-ups. It is slightly faster that R's
	built-in match() function on first match against a table, but
	extremely fast on any subsequent lookup as it keeps the hash
	table in memory.
Small set of functions to fast computation of some matrices and operations
  useful in statistics and econometrics. Currently, there are functions for efficient
  computation of duplication, commutation and symmetrizer matrices with minimal storage
  requirements. Some commonly used matrix decompositions (LU and LDL), basic matrix
  operations (for instance, Hadamard, Kronecker products and the Sherman-Morrison formula)
  and iterative solvers for linear systems are also available. In addition, the package
  includes a number of common statistical procedures such as the sweep operator, weighted
  mean and covariance matrix using an online algorithm, linear regression (using Cholesky,
  QR, SVD, sweep operator and conjugate gradients methods), ridge regression (with optimal
  selection of the ridge parameter considering several procedures), omnibus tests for 
  univariate normality, functions to compute the multivariate skewness, kurtosis, the 
  Mahalanobis distance (checking the positive defineteness), and the Wilson-Hilferty 
  transformation of chi squared variables. Furthermore, the package provides interfaces 
  to C code callable by another C code from other R packages.
A mutual information estimator based on k-nearest neighbor method proposed by A. Kraskov, et al. (2004) <doi:10.1103/PhysRevE.69.066138> to measure general dependence and the time complexity for our estimator is only squared to the sample size, which is faster than other statistics. Besides, an implementation of mutual information based independence test is provided for analyzing multivariate data in Euclidean space (T B. Berrett, et al. (2019) <doi:10.1093/biomet/asz024>); furthermore, we extend it to tackle datasets in metric spaces.
This is an extremely fast implementation of a Naive Bayes classifier. This 
    package is currently the only package that supports a Bernoulli distribution, a Multinomial 
    distribution, and a Gaussian distribution, making it suitable for both binary features, 
    frequency counts, and numerical features. Another feature is the support of a mix of 
    different event models. Only numerical variables are allowed, however, categorical variables 
    can be transformed into dummies and used with the Bernoulli distribution. 
    The implementation is largely based on the paper 
    "A comparison of event models for Naive Bayes anti-spam e-mail filtering" 
    written by K.M. Schneider (2003) <doi:10.3115/1067807.1067848>. Any issues can be 
    submitted to: <https://github.com/mskogholt/fastNaiveBayes/issues>.
We present an implementation of the algorithms required to simulate
  large-scale social networks and retrieve their most relevant metrics. Details 
  can be found in the accompanying scientific paper on the Journal 
  of Statistical Software, <doi:10.18637/jss.v096.i07>.
Implementation of a simple algorithm designed for online multivariate changepoint detection of a mean in sparse changepoint settings. The algorithm is based on a modified cusum statistic and guarantees control of the type I error on any false discoveries, while featuring O(1) time and O(1) memory updates per series as well as a proven detection delay.
The FastPCS algorithm of Vakili and Schmitt (2014) <doi:10.1016/j.csda.2013.07.021> for robust estimation of multivariate location and scatter and multivariate outliers detection.
Finds the critical sample size ("critical point of stability") for a 
    correlation to stabilize in Schoenbrodt and Perugini's definition of 
    sequential stability (see <doi:10.1016/j.jrp.2013.05.009>).
'FASTQC' is the most widely used tool for evaluating the quality of high throughput sequencing data.  
    It produces, for each sample, an html report and a compressed file containing the raw data. 
    If you have hundreds of samples, you are not going to open up each 'HTML' page. 
    You need some way of looking at these data in aggregate. 
    'fastqcr' Provides helper functions to easily parse, aggregate and analyze 
    'FastQC' reports for large numbers of samples. It provides a convenient solution for building 
    a 'Multi-QC' report, as well as, a 'one-sample' report with result interpretations.
New and faster implementations for quantile quantile plots. 
    The package also includes a function to prune data for quantile quantile 
    plots. This can drastically reduce the running time for large samples, 
    for 100 million samples, you can expect a factor 80X speedup.
Data sets and utilities to accompany the second edition of
    "Foundations and Applications of Statistics: an Introduction
    using R" (R Pruim, published by AMS, 2017), a text covering
    topics from probability and mathematical statistics at an advanced
    undergraduate level.  R is integrated throughout, and access to all
    the R code in the book is provided via the snippet() function.
The FastRCS algorithm of Vakili and Schmitt (2014) for robust fit of the multivariable linear regression model and outliers detection.
Provides  templates for reports in 'rmarkdown' and 
     functions to create tables and summaries of data.
Samples generalized random product graphs, a generalization of
    a broad class of network models. Given matrices X, S, and Y with with
    non-negative entries, samples a matrix with expectation X S Y^T and
    independent Poisson or Bernoulli entries using the fastRG algorithm of
    Rohe et al. (2017) <https://www.jmlr.org/papers/v19/17-128.html>. The
    algorithm first samples the number of edges and then puts them down
    one-by-one.  As a result it is O(m) where m is the number of edges, a
    dramatic improvement over element-wise algorithms that which require
    O(n^2) operations to sample a random graph, where n is the number of
    nodes.
A utility to scrape and load play-by-play data
    and statistics from the Premier Hockey Federation (PHF) <https://www.premierhockeyfederation.com/>, formerly
    known as the National Women's Hockey League (NWHL). Additionally, allows access to the National Hockey League's
    stats API <https://www.nhl.com/>.
A data package that hosts all models for the
    'nflfastR' package.
Infrastrcture for creating rich, dynamic web content using R scripts while maintaining very fast response time.
An implementation of the fast structural filtering with L0 penalty. It includes an adaptive polynomial estimator by minimizing the least squares error with constraints on the number of breaks in their (k + 1)-st discrete derivative, for a chosen integer k >= 0. It also includes generalized structure sparsity constraint, i.e., graph trend filtering. This package is implemented via the primal dual active set algorithm, which formulates estimates and residuals as primal and dual variables, and utilizes efficient active set selection strategies based on the properties of the primal and dual variables.
Computes fast (relative to other implementations) approximate 
    Shapley values for any supervised learning model. Shapley values help to 
    explain the predictions from any black box model using ideas from game 
    theory; see Strumbel and Kononenko (2014) <doi:10.1007/s10115-013-0679-x> 
    for details.
Functions for computing spillover measures, especially spillover
    tables and spillover indices, as well as their average, minimal, and maximal
    values.
It implements an improved and computationally faster version 
            of the original Stepwise Gaussian Graphical Algorithm for estimating 
            the Omega precision matrix from high-dimensional data. 
            Zamar, R., Ruiz, M., Lafit, G. and Nogales, J. (2021) 
            <doi:10.52933/jdssv.v1i2.11>.
An interface to the 'fastText' <https://github.com/facebookresearch/fastText> library for efficient learning of word representations and sentence classification. The 'fastText' algorithm is explained in detail in (i) "Enriching Word Vectors with subword Information", Piotr Bojanowski, Edouard Grave, Armand Joulin, Tomas Mikolov, 2017, <doi:10.1162/tacl_a_00051>; (ii) "Bag of Tricks for Efficient Text Classification", Armand Joulin, Edouard Grave, Piotr Bojanowski, Tomas Mikolov, 2017, <doi:10.18653/v1/e17-2068>; (iii) "FastText.zip: Compressing text classification models", Armand Joulin, Edouard Grave, Piotr Bojanowski, Matthijs Douze, Herve Jegou, Tomas Mikolov, 2016, <arXiv:1612.03651>.
An interface to the 'fastText' library
	<https://github.com/facebookresearch/fastText>. The package
	can be used for text classification and to learn word vectors.
	An example how to use 'fastTextR' can be found in the 'README' file.
Fast functions for timestamp
	manipulation that avoid system calls and take shortcuts
	to facilitate operations on very large data.
Implements fast, scalable optimization algorithms for
    fitting topic models ("grade of membership" models) and
    non-negative matrix factorizations to count data. The methods
    exploit the special relationship between the multinomial topic
    model (also, "probabilistic latent semantic indexing") and Poisson
    non-negative matrix factorization. The package provides tools to
    compare, annotate and visualize model fits, including functions to
    efficiently create "structure plots" and identify key features in
    topics. The 'fastTopics' package is a successor to the 'CountClust'
    package.
Easy installation, loading and management, of high-performance packages 
             for statistical computing and data manipulation in R. 
             The core 'fastverse' consists of 4 packages: 'data.table', 'collapse', 
             'kit' and 'magrittr', that jointly only depend on 'Rcpp'. 
             The 'fastverse' can be freely and permanently extended with 
             additional packages, both globally or for individual projects. 
             Separate package verses can also be created. Fast packages 
             for many common tasks such as time series, dates and times, strings, 
             spatial data, statistics, data serialization, larger-than-memory 
             processing, and compilation of R code are listed in the README file: 
             <https://github.com/fastverse/fastverse#suggested-extensions>.
A lightweight package to compute Maximal Overlap Discrete Wavelet 
    Transform (MODWT) and À Trous Discrete Wavelet Transform by leveraging the 
    power of 'Rcpp' to make these operations fast. This package was designed for use in forecasting, and
    allows users avoid the inclusion of future data when performing wavelet decomposition of time series.
    See Quilty and Adamowski (2018) <doi:10.1016/j.jhydrol.2018.05.003>.
Performs family-based association tests with a polytomous outcome under 2-locus and 1-locus models
             defined by some design matrix.
Application of 'FateID' allows computation and visualization of cell fate bias for multi-lineage single cell transcriptome data. Herman, J.S., Sagar, Grün D. (2018) <DOI:10.1038/nmeth.4662>.
Kiener distributions K1, K2, K3, K4 and K7 to characterize
    distributions with left and right, symmetric or asymmetric fat tails in market
    finance, neuroscience and other disciplines. Two algorithms to estimate with
    a high accuracy distribution parameters, quantiles, value-at-risk and expected
    shortfall. Include power hyperbolas and power hyperbolic functions.
Create datasets with factorial structure through simulation by specifying variable parameters. Extended documentation at <https://debruine.github.io/faux/>. Described in DeBruine (2020) <doi:10.5281/zenodo.2669586>.
Provides a replacement for dplyr::na_if().  Allows you to
    specify multiple values to be replaced with NA using a single
    function.
HTTP error helpers. Methods included for general purpose HTTP 
    error handling, as well as individual methods for every HTTP status
    code, both via status code numbers as well as their descriptive names.
    Supports ability to adjust behavior to stop, message or warning.
    Includes ability to use custom whisker template to have any configuration
    of status code, short description, and verbose message. Currently 
    supports integration with 'crul', 'curl', and 'httr'.
Estimate a FAVAR model by a Bayesian method, based on Bernanke et al. (2005) <DOI:10.1162/0033553053327452>.
Finds the URL to the 'favicon' for a website. This is useful if you
  want to display the 'favicon' in an HTML document or web application,
  especially if the website is behind a firewall.
A dataset of favourite numbers, selected from an online poll of over 30,000 people by Alex Bellos
             (http://pages.bloomsbury.com/favouritenumber).
Provides functions and datasets from the book "Forest Analytics with R".
A toolkit for Flux Balance Analysis and related
    metabolic modeling techniques. Functions are provided for: parsing
    models in tabular format, converting parsed metabolic models to input
    formats for common linear programming solvers, and
    evaluating and applying gene-protein-reaction mappings. In addition, there
    are wrappers to parse a model, select a solver, find the metabolic fluxes,
    and return the results applied to the original model. Compared to other
    packages in this field, this package puts a much heavier focus on
    providing reusable components that can be used in the design of new
    implementation of new techniques, in particular those that involve large
    parameter sweeps. For a background on the theory, see What is Flux Balance 
    Analysis <doi:10.1038/nbt.1614>.
Provides a collection of functions to 
    explore and to investigate basic properties of financial returns 
    and related quantities.
    The covered fields include techniques of explorative data analysis
    and the investigation of distributional properties, including
    parameter estimation and hypothesis testing. Even more there are
    several utility functions for data handling and management.
Does family-based gene by environment interaction tests, joint gene, gene-environment interaction test, and a test of a set of genes conditional on another set of genes.
Performs dose assignment and trial simulation for the FBCRM (Fully Bayesian Continual Reassessment Method) and MFBCRM (Mixture Fully Bayesian Continual Reassessment Method) phase I clinical trial designs. These trial designs extend the Continual Reassessment Method (CRM) and Bayesian Model Averaging Continual Reassessment Method (BMA-CRM) by allowing the prior toxicity skeleton itself to be random, with posterior distributions obtained from Markov Chain Monte Carlo. On average, the FBCRM and MFBCRM methods outperformed the CRM and BMA-CRM methods in terms of selecting an optimal dose level across thousands of randomly generated simulation scenarios. Details on the methods and results of this simulation study are available on request, and the manuscript is currently under review.
We propose an objective Bayesian algorithm for searching the space of Gaussian directed acyclic graph (DAG) models. The algorithm proposed makes use of moment fractional Bayes factors (MFBF) and thus it is suitable for learning sparse graph. The algorithm is implemented by using Armadillo: an open-source C++ linear algebra library.
Normalizes the data from a file containing the raw values of the SNP probes of microarray data by using the FISH probes and their corresponding copy number.
Open-source package for computing likelihood ratios in kinship testing and human identification cases (Chernomoretz et al. (2021) <doi:10.1016/j.fsir.2020.100132>). It has the core function of the software GENis, developed by Fundación Sadosky. It relies on a Bayesian Networks framework and is particularly well suited to efficiently perform large-size queries against databases of missing individuals (Darwiche (2009) <doi:10.1017/CBO9780511811357>).
It implements the Nelson-Siegel and the Nelson-Siegel-Svensson
	term structures.
Wrapper functions around the Facebook Marketing 'API' to create,
    read, update and delete custom audiences, images, campaigns, ad sets, ads and
    related content.
Implements a very fast C++ algorithm to quickly bootstrap receiver
    operating characteristics (ROC) curves and derived performance metrics,
    including the area under the curve (AUC) and the partial area under the curve as well as 
    the true and false positive rate. The analysis of paired receiver operating curves is supported as well,
    so that a comparison of two predictors is possible. You can also plot the
    results and calculate confidence intervals. On a typical desktop computer the time needed for 
    the calculation of 100000 bootstrap replicates given 500 observations requires time on the
    order of magnitude of one second.
Provides access to a range of functions for computing and visualizing the Full Bayesian Significance Test (FBST) and the e-value for testing a sharp hypothesis against its alternative, and the Full Bayesian Evidence Test (FBET) and the (generalized) Bayesian evidence value for testing a composite (or interval) hypothesis against its alternative. The methods are widely applicable as long as a posterior MCMC sample is available.
Provides a streamlined, standard evaluation-based approach to multivariate function composition. Allows for chaining commands via a forward-pipe operator, %>%.
Perform various floating catchment area methods to calculate a
    spatial accessibility index (SPAI) for demand point data. The distance
    matrix used for weighting is normalized in a preprocessing step using
    common functions (gaussian, gravity, exponential or logistic).
Provides tools to perform fuzzy formal concept
    analysis, presented in Wille (1982) <doi:10.1007/978-3-642-01815-2_23>
    and in Ganter and Obiedkov (2016) <doi:10.1007/978-3-662-49291-8>.  It
    provides functions to load and save a formal context, extract its
    concept lattice and implications.  In addition, one can use the
    implications to compute semantic closures of fuzzy sets and, thus,
    build recommendation systems.
Provides support for building Feldman-Cousins confidence intervals 
	[G. J. Feldman and R. D. Cousins (1998) <doi:10.1103/PhysRevD.57.3873>].
Provides functions to implement the Flexible cFDR (Hutchinson et al. (2021) <doi:10.1371/journal.pgen.1009853>) and Binary cFDR (Hutchinson et al. (2021) <doi:10.1101/2021.10.21.465274>) methodologies to leverage auxiliary data from arbitrary distributions, for example functional genomic data, with GWAS p-values to generate re-weighted p-values.
Bayesian estimation of forced choice models in Item Response Theory using 'rstan' (See Stan Development Team (2020) <https://mc-stan.org/>).
A financial calculator that provides very fast implementations
    of common financial indicators using 'Rust' code. It includes functions for
    bond-related indicators, such as yield to maturity ('YTM'), modified duration,
    and Macaulay duration, as well as functions for calculating time-weighted
    and money-weighted rates of return (using 'Modified Dietz' method) for multiple portfolios,
    given their market values and profit and loss ('PnL') data. 'fcl' is designed
    to be efficient and accurate for financial analysis and computation. The methods
    used in this package are based on the following references:
    <https://en.wikipedia.org/wiki/Modified_Dietz_method>,
    <https://en.wikipedia.org/wiki/Time-weighted_return>.
Algorithms for fuzzy clustering, cluster validity indices and plots for cluster validity and visualizing fuzzy clustering results.
Provides a selection of 3 different inference rules (including additionally the clamped types of the referred inference rules) and 4 threshold functions in order to obtain the inference of the FCM (Fuzzy Cognitive Map). Moreover, the 'fcm' package returns a data frame of the concepts' values of each state after the inference procedure. Fuzzy cognitive maps were introduced by Kosko (1986) <doi:10.1002/int.4550010405> providing ideal causal cognition tools for modeling and simulating dynamic systems.
Provides several functions to create and manipulate fuzzy
    cognitive maps. It is based on 'FCMapper' for Excel, distributed at <http://
    www.fcmappers.net/joomla/>, developed by Michael Bachhofer and Martin Wildenberg.
    Maps are inputted as adjacency matrices. Attributes of the maps and the
    equilibrium values of the concepts (including with user-defined constrained
    values) can be calculated. The maps can be graphed with a function that calls
    'igraph'. Multiple maps with shared concepts can be aggregated.
A toolbox to derive flexible cutoffs for fit indices in 'Covariance-based Structural Equation Modeling' based on the paper by 'Niemand & Mai (2018)' <doi:10.1007/s11747-018-0602-9>. Flexible cutoffs are an alternative to fixed cutoffs - rules-of-thumb - regarding an appropriate cutoff for fit indices such as 'CFI' or 'SRMR'. It has been demonstrated that these flexible cutoffs perform better than fixed cutoffs in grey areas where misspecification is not easy to detect. The package provides an alternative to the tool at <https://flexiblecutoffs.org> as it allows to tailor flexible cutoffs to a given dataset and model, which is so far not available in the tool. The package simulates fit indices based on a given dataset and model and then estimates the flexible cutoffs. Some useful functions, e.g., to determine the 'GoF-' or 'BoF-nature' of a fit index, are provided. So far, additional options for a relative use (is a model better than another?) are provided in an exploratory manner.
Provides a  collection of functions to 
	manage, to investigate and to analyze bivariate financial returns by  
	Copulae. Included are the families of Archemedean, Elliptical, 
	Extreme Value, and Empirical Copulae.
Over sixty clustering algorithms are provided in this package with consistent input and output, which enables the user to try out algorithms swiftly. Additionally, 26 statistical approaches for the estimation of the number of clusters as well as the mirrored density plot (MD-plot) of clusterability are implemented. The packages is published in Thrun, M.C., Stier Q.: "Fundamental Clustering Algorithms Suite" (2021), SoftwareX, <DOI:10.1016/j.softx.2020.100642>. Moreover, the fundamental clustering problems suite (FCPS) offers a variety of clustering challenges any algorithm should handle when facing real world data, see Thrun, M.C., Ultsch A.: "Clustering Benchmark Datasets Exploiting the Fundamental Clustering Problems" (2020), Data in Brief, <DOI:10.1016/j.dib.2020.105501>.
Dynamic prediction in functional concurrent regression with an application to child growth. Extends the pffr() function from the 'refund' package to handle the scenario where the functional response and concurrently measured functional predictor are irregularly measured.  Leroux et al. (2017), Statistics in Medicine, <doi:10.1002/sim.7582>.
A fold change rank based method is presented to search for genes with changing
             expression and to detect recurrent chromosomal copy number aberrations. This 
             method may be useful for high-throughput biological data (micro-array, sequencing, ...).
             Probabilities are associated with genes or probes in the data set and there is no
             problem of multiple tests when using this method. For array-based comparative genomic
             hybridization data, segmentation results are obtained by merging the significant
             probes detected.
This is a package for fluorescence fluctuation spectroscopy data analysis methods such as spFCS, FCCS, scanning-FCS, pCF, N&B and pCOMB, among others.
    In addition, several data detrending tools are provided. For an extensive user's guide for the use of FCSlib, please navigate to (<https://github.com/FCSlib/FCSlib/tree/master/Documentation>).
    Sample data can be found at (<https://github.com/FCSlib/FCSlib/tree/master/Sample%20Data>).
    The original paper where this package is presented can be found at (<doi:10.1093/bioinformatics/btaa876>).
Easy-to-use, very fast implementation of various functional bases. Easily used together with other packages.
    A functional basis is a collection of basis functions [\phi_1, ..., \phi_n] that can represent a smooth function, i.e. $f(t) = \sum c_k \phi_k(t)$.
    First- and second-order derivatives are also included. These are the mathematically correct ones, no approximations applied.
    As of version 1.1, this package includes B-splines, Fourier bases and polynomials.
Automatically suggests a correction when a typo occurs.
Estimation and inference using the Fractionally Cointegrated 
    Vector Autoregressive (VAR) model. It includes functions for model specification, 
    including lag selection and cointegration rank selection, as well as a comprehensive
    set of options for hypothesis testing, including tests of hypotheses on the 
    cointegrating relations, the adjustment coefficients and the fractional 
    differencing parameters. 
    An article describing the FCVAR model with examples is available on the Webpage 
    <https://sites.google.com/view/mortennielsen/software>.
Computes different multidimensional FD indices.  Implements a distance-based framework to measure FD that allows any number and type of functional traits, and can also consider species relative abundances.  Also contains other useful tools for functional ecology.
These functions were developed to support functional data
 analysis as described in Ramsay, J. O. and Silverman, B. W.
 (2005) Functional Data Analysis. New York: Springer and in 
 Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009). 
 Functional Data Analysis with R and Matlab (Springer). 
 The package includes data sets and script files working many examples 
 including all but one of the 76 figures in this latter book.  Matlab versions 
 are available by ftp from 
 <https://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/>.
Routines for exploratory and descriptive analysis of functional data such as depth measurements, atypical curves detection, regression models, supervised classification, unsupervised classification and functional analysis of variance.
Quantify the serial correlation across lags of a given functional 
    time series using the autocorrelation function and a partial autocorrelation
    function for functional time series proposed in 
    Mestre et al. (2021) <doi:10.1016/j.csda.2020.107108>.
    The autocorrelation functions are based on the L2 norm of the lagged covariance 
    operators of the series. Functions are available for estimating the 
    distribution of the autocorrelation functions under the assumption 
    of strong functional white noise.
Implementations of the k-means, hierarchical agglomerative and 
    DBSCAN clustering methods for functional data which allows for jointly 
    aligning and clustering curves. It supports functional data defined on 
    one-dimensional domains but possibly evaluating in multivariate codomains. 
    It supports functional data defined in arrays but also via the 'fd' and 
    'funData' classes for functional data defined in the 'fda' and 'funData' 
    packages respectively. It currently supports shift, dilation and affine 
    warping functions for functional data defined on the real line and uses the 
    SRSF framework to handle boundary-preserving warping for functional data 
    defined on a specific interval. Main reference for the k-means algorithm: 
    Sangalli L.M., Secchi P., Vantini S., Vitelli V. (2010) "k-mean alignment 
    for curve clustering" <doi:10.1016/j.csda.2009.12.008>. Main reference for 
    the SRSF framework: Tucker, J. D., Wu, W., & Srivastava, A. (2013) 
    "Generative models for functional data using phase and amplitude separation" 
    <doi:10.1016/j.csda.2012.12.001>.
Provides an implementation of concurrent or varying coefficient regression methods for 
    functional data. The implementations are done for both dense and sparsely observed functional
    data. Pointwise confidence bands can be constructed for each case. Further, the influence of
    past predictor values are modeled by a smooth history index function, 
    while the effects on the response are described by smooth varying coefficient functions, 
    which are very useful in analyzing real data such as COVID data.
    References: Yao, F., Müller, H.G., Wang, J.L. (2005) <doi: 10.1214/009053605000000660>.
                Sentürk, D., Müller, H.G. (2010) <doi: 10.1198/jasa.2010.tm09228>.
An implementation of the methodology described in
    Petersen and Mueller (2016) <doi:10.1214/15-AOS1363> for the functional
    data analysis of samples of density functions.  Densities are first
    transformed to their corresponding log quantile densities, followed by
    ordinary Functional Principal Components Analysis (FPCA).  Transformation
    modes of variation yield improved interpretation of the variability in the
    data as compared to FPCA on the densities themselves.  The standard
    fraction of variance explained (FVE) criterion commonly used for functional
    data is adapted to the transformation setting, also allowing for an
    alternative quantification of variability for density data through the
    Wasserstein metric of optimal transport.
Likelihood based analysis of 1-dimension functional data
        in a mixed-effects model framework. Matrix computation are
        approximated by semi-explicit operator equivalents with linear
        computational complexity. Markussen (2013) <doi:10.3150/11-BEJ389>.
Routines for model-based functional cluster analysis for functional data with optional covariates. The idea is to cluster functional subjects (often called functional objects) into homogenous groups by using spline smoothers (for functional data) together with scalar covariates. The spline coefficients and the covariates are modelled as a multivariate Gaussian mixture model, where the number of mixtures corresponds to the number of clusters. The parameters of the model are estimated by maximizing the observed mixture likelihood via an EM algorithm (Arnqvist and Sjöstedt de Luna, 2019) <arXiv:1904.10265>. The clustering method is used to analyze annual lake sediment from lake Kassjön (Northern Sweden) which cover more than 6400 years and can be seen as historical records of weather and climate.
Performs analysis of variance testing procedures for univariate and multivariate functional data (Cuesta-Albertos and Febrero-Bande (2010) <doi:10.1007/s11749-010-0185-3>, Gorecki and Smaga (2015) <doi:10.1007/s00180-015-0555-0>, Gorecki and Smaga (2017) <doi:10.1080/02664763.2016.1247791>, Zhang et al. (2018) <doi:10.1016/j.csda.2018.05.004>).
A collection of functions for outlier detection in functional data analysis. 
  Methods implemented include directional outlyingness by 
  Dai and Genton (2019) <doi:10.1016/j.csda.2018.03.017>,
  MS-plot by Dai and Genton (2018) <doi:10.1080/10618600.2018.1473781>,
  total variation depth and modified shape similarity index by 
  Huang and Sun (2019) <doi:10.1080/00401706.2019.1574241>, and sequential transformations by
  Dai et al. (2020) <doi:10.1016/j.csda.2020.106960 among others. Additional outlier detection
  tools and depths for functional data like functional boxplot, (modified) band depth etc.,
  are also available.
A versatile package that provides implementation of various
    methods of Functional Data Analysis (FDA) and Empirical Dynamics. The core of this
    package is Functional Principal Component Analysis (FPCA), a key technique for
    functional data analysis, for sparsely or densely sampled random trajectories
    and time courses, via the Principal Analysis by Conditional Estimation
    (PACE) algorithm. This core algorithm yields covariance and mean functions,
    eigenfunctions and principal component (scores), for both functional data and
    derivatives, for both dense (functional) and sparse (longitudinal) sampling designs.
    For sparse designs, it provides fitted continuous trajectories with confidence bands,
    even for subjects with very few longitudinal observations. PACE is a viable and
    flexible alternative to random effects modeling of longitudinal data. There is also a
    Matlab version (PACE) that contains some methods not available on fdapace and vice
    versa. Updates to fdapace were supported by grants from NIH Echo and NSF DMS-1712864 and DMS-2014626. Please cite our package if you use it (You may run the command citation("fdapace") to get the citation format and bibtex entry).
    References: Wang, J.L., Chiou, J., Müller, H.G. (2016) <doi:10.1146/annurev-statistics-041715-033624>;
    Chen, K., Zhang, X., Petersen, A., Müller, H.G. (2017) <doi:10.1007/s12561-015-9137-5>.
An implementation of regression models with partial differential regularizations, making use of the Finite Element Method. The models efficiently handle data distributed over irregularly shaped domains and can comply with various conditions at the boundaries of the domain. A priori information about the spatial structure of the phenomenon under study can be incorporated in the model via the differential regularization. See Sangalli, L. M. (2021) <doi:10.1111/insr.12444> "Spatial Regression With Partial Differential Equation Regularisation" for an overview. The release 1.1-9 requires R (>= 4.2.0) to be installed on windows machines.
Applications to visualization, outlier detection and classification. Software companion for Elías, Antonio, Jiménez, Raúl, Paganoni, Anna M. and Sangalli, Laura M., (2022), "Integrated Depth for Partially Observed Functional Data". Journal of Computational and Graphical Statistics. <doi:10.1080/10618600.2022.2070171>.
Provides algorithms to fit linear regression models under several popular penalization techniques and functional linear regression models based on Majorizing-Minimizing (MM) and Alternating Direction Method of Multipliers (ADMM) techniques.
    See Boyd et al (2010) <doi:10.1561/2200000016> for complete introduction to the method.
Performs alignment, PCA, and modeling of multidimensional and 
    unidimensional functions using the square-root velocity framework 
    (Srivastava et al., 2011 <arXiv:1103.3817> and Tucker et al., 2014 
    <DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic 
    analysis of functional data through phase and amplitude separation.
Implementation of the Interval Testing Procedure for functional data in different frameworks (i.e., one or two-population frameworks, functional linear models) by means of different basis expansions (i.e., B-spline, Fourier, and phase-amplitude Fourier). The current version of the package requires functional data evaluated on a uniform grid; it automatically projects each function on a chosen functional basis; it performs the entire family of multivariate tests; and, finally, it provides the matrix of the p-values of the previous tests and the vector of the corrected p-values. The functional basis, the coupled or uncoupled scenario, and the kind of test can be chosen by the user. The package provides also a plotting function creating a graphical output of the procedure: the p-value heat-map, the plot of the corrected p-values, and the plot of the functional data.
Regression models for functional data, i.e., scalar-on-function,
    function-on-scalar and function-on-function regression models, are fitted
    by a component-wise gradient boosting algorithm. 
	For a manual on how to use 'FDboost', see Brockhaus, Ruegamer, Greven (2017) <doi:10.18637/jss.v094.i10>.
Provides the probability density function (PDF), cumulative
  distribution function (CDF), and the partial derivatives of the PDF of the
  diffusion decision model (DDM; e.g.,
  Ratcliff & McKoon, 2008, <doi:10.1162/neco.2008.12-06-420>) with across-trial
  variability in the drift rate. Because the PDF, its partial derivatives, and
  the CDF of the DDM both contain an infinite sum, they need to be approximated.
  'fddm' implements all published approximations
  (Navarro & Fuss, 2009, <doi:10.1016/j.jmp.2009.02.003>;
  Gondan, Blurton, & Kesselmeier, 2014, <doi:10.1016/j.jmp.2014.05.002>;
  Blurton, Kesselmeier, & Gondan, 2017, <doi:10.1016/j.jmp.2016.11.003>;
  Hartmann & Klauer, 2021, <doi:10.1016/j.jmp.2021.102550>) plus
  new approximations. All approximations are implemented purely in 'C++'
  providing faster speed than existing packages.
A system provides a set of functions for
    working with data from the Federal Deposit Insurance Corporation
    (FDIC), including retrieving financial data for FDIC-insured
    institutions and accessing the data taxonomy.
Contains functions to simplify the use of data mining methods (classification, regression, clustering, etc.), for students and beginners in R programming. Various R packages are used and wrappers are built around the main functions, to standardize the use of data mining methods (input/output): it brings a certain loss of flexibility, but also a gain of simplicity. The package name came from the French "Fouille de Données en Master 2 Informatique Décisionnelle".
Allows to estimate dynamic model averaging, dynamic model selection and median probability model. The original methods are implemented, as well as, selected further modifications of these methods. In particular the user might choose between recursive moment estimation and exponentially moving average for variance updating. Inclusion probabilities might be modified in a way using 'Google Trends'. The code is written in a way which minimises the computational burden (which is quite an obstacle for dynamic model averaging if many variables are used). For example, this package allows for parallel computations and Occam's window approach. The package is designed in a way that is hoped to be especially useful in economics and finance. Main reference: Raftery, A.E., Karny, M., Ettler, P. (2010) <doi:10.1198/TECH.2009.08104>.
Forest data quality is a package containing nine methods of analysis for forest databases,
    from databases containing inventory data and growth models, the focus of the analyzes is related to the
    quality of the data present in the database with a focus on consistency , punctuality and completeness of data.
FDR functions for permutation-based estimators, including pi0 as well as FDR
             confidence intervals. The confidence intervals account for dependencies between
             tests by the incorporation of an overdispersion parameter, which is estimated
             from the permuted data. Also included are options for an analog parametric approach.
It is known that current false discovery rate (FDR) procedures can be very conservative when applied to multiple testing in the discrete paradigm where p-values (and test statistics) have discrete and heterogeneous null distributions. This package implements more powerful weighted or adaptive FDR procedures for FDR control and estimation in the discrete paradigm. The package takes in the original data set rather than just the p-values in order to carry out the adjustments for discreteness and heterogeneity of p-value distributions. The package implements methods for two types of test statistics and their p-values: (a) binomial test on if two independent Poisson distributions have the same means, (b) Fisher's exact test on if the conditional distribution is the same as the marginal distribution for two binomial distributions, or on if two independent binomial distributions have the same probabilities of success.
The user can directly compute and display false discovery rates from inputted p-values or z-scores under a variety of assumptions. p.fdr() computes FDRs, adjusted p-values and decision reject vectors from inputted p-values or z-values. get.pi0() estimates the proportion of data that are truly null. plot.p.fdr() plots the FDRs, adjusted p-values, and the raw p-values points against their rejection threshold lines.
Defines a collection of functions to compute average power and sample size for studies that use the false discovery rate as the final measure of statistical significance.
Estimates both tail area-based false 
   discovery rates (Fdr) as well as local false discovery rates (fdr) for a 
   variety of null models (p-values, z-scores, correlation coefficients,
   t-scores).  The proportion of null values and the parameters of the null 
   distribution are adaptively estimated from the data.  In addition, the package 
   contains functions for non-parametric density estimation (Grenander estimator), 
   for monotone regression (isotonic regression and antitonic regression with weights),
   for computing the greatest convex minorant (GCM) and the least concave majorant (LCM), 
   for the half-normal and correlation distributions, and for computing
   empirical higher criticism (HC) scores and the corresponding decision threshold.
Perform frequency distribution tables, associated histograms
             and polygons from vector, data.frame and matrix objects for
             numerical and categorical variables.
Multiple testing procedures for heterogeneous and discrete tests as described in Döhler and Roquain (2019) <arXiv:1912.04607v1>. The main algorithms of the paper are available as continuous, discrete and weighted versions.
Finite element modeling of beam structures and 2D geometries using constant strain triangles. Applies material properties and boundary conditions (load and constraint) to generate a finite element model. The model produces stress, strain, and nodal displacements; a heat map is available to demonstrate regions where output variables are high or low.  Also provides options for creating a triangular mesh of 2D geometries. Package developed with reference to: Bathe, K. J. (1996). Finite Element Procedures.[ISBN 978-0-9790049-5-7] -- Seshu, P. (2012). Textbook of Finite Element Analysis. [ISBN-978-81-203-2315-5] -- Mustapha, K. B. (2018). Finite Element Computations in Mechanics with R. [ISBN 9781315144474].
For each feature, a score is computed that can be useful
        for feature selection. Several random subsets are sampled from
        the input data and for each random subset, various linear
        models are fitted using lars method. A score is assigned to
        each feature based on the tendency of LASSO in including that
        feature in the models.Finally, the average score and the models
        are returned as the output. The features with relatively low
        scores are recommended to be ignored because they can lead to
        overfitting of the model to the training data. Moreover, for
        each random subset, the best set of features in terms of global
        error is returned. They are useful for applying Bolasso, the
        alternative feature selection method that recommends the
        intersection of features subsets.
Provides a collection of features, decomposition methods, 
    statistical summaries and graphics functions for the analysing tidy time
    series data. The package name 'feasts' is an acronym comprising of its key
    features: Feature Extraction And Statistics for Time Series.
Read and write feather files, a lightweight binary columnar
    data store designed for maximum speed.
Local inferential feature significance for multivariate kernel density estimation.
Uses three different correlation coefficients to
    calculate measurement-level adequate correlations in a feature matrix: 
    Pearson product-moment correlation coefficient,
    Intraclass correlation and Cramer's V.
Finds modelling features through a detailed analysis of model residuals using 'rpart' classification and regression trees. Scans the residuals of a model across subsets of the data to identify areas where the model prediction differs from the actual target variable. S. Chatterjee, A. S. Hadi (2006) <doi:10.1002/0470055464>.
Feature flags allow developers to turn features of their
    software on and off in form of configuration. This package provides
    functions for creating feature flags in code. It exposes an interface
    for defining own feature flags which are enabled based on custom criteria.
Feature hashing, also called as the hashing trick, is a method to transform 
  features of a instance to a vector. Thus, it is a method to transform a real dataset to a matrix. 
  Without looking up the indices in an associative array, 
  it applies a hash function to the features and uses their hash values as indices directly.
  The method of feature hashing in this package was proposed in Weinberger et al. (2009) <arXiv:0902.2206>. 
  The hashing algorithm is the murmurhash3 from the 'digest' package. 
  Please see the README in <https://github.com/wush978/FeatureHashing> for more information.
Implements a novel approach for measuring feature importance in k-means clustering. Importance of a feature is measured by the misclassification rate relative to the baseline cluster assignment due to a random permutation of feature values. An explanation of permutation feature importance in general can be found here: <https://christophm.github.io/interpretable-ml-book/feature-importance.html>.
Discretely-sampled function is first smoothed.  Features
        of the smoothed function are then extracted.  Some of the key
        features include mean value, first and second derivatives,
        critical points (i.e. local maxima and minima), curvature of
        cunction at critical points, wiggliness of the function, noise
        in data, and outliers in data.
The aim is to take in data.frame inputs and utilises methods, such as recursive feature engineering, to enable the features to be removed.
    What this does differently from the other packages, is that it gives you the choice to remove the variables manually, or it automated this process.
    Feature selection is a concept in machine learning, and statistical pipelines, whereby unimportant, or less predictive variables are eliminated from the analysis, see Boughaci (2018) <doi:10.1007/s40595-018-0107-y>.
A collection of functions that would help one to build features based on external data. Very useful for Data Scientists in data to day work. Many functions create features using parallel computation. Since the nitty gritty of parallel computation is hidden under the hood, the user need not worry about creating clusters and shutting them down.
Easily analyze relational data from the United States 2016 federal 
    election cycle as reported by the Federal Election Commission.
    This package contains data about candidates, committees, and a
    variety of different financial expenditures. Data is from <https://www.fec.gov/data/browse-data/?tab=bulk-data>.
Functions and example datasets for Fechnerian scaling of discrete
  object sets.  User can compute Fechnerian distances among objects representing
  subjective dissimilarities, and other related information.  See
  package?fechner for an overview.
Estimates causal effects with panel data using the counterfactual methods. It is suitable for panel or time-series cross-sectional analysis with binary treatments under (hypothetically) baseline randomization.It allows a treatment to switch on and off and limited carryover effects. It supports linear factor models, a generalization of gsynth and the matrix completion method. Implementation details can be found in Liu, Wang and Xu (2022) <arXiv:2107.00856>.
Functions to automate downloading geospatial data available
    from several federated data sources (mainly sources maintained by the
    US Federal government). Currently, the package enables extraction from
    seven datasets: The National Elevation Dataset digital elevation
    models (1 and 1/3 arc-second; USGS); The National Hydrography Dataset
    (USGS); The Soil Survey Geographic (SSURGO) database from the National
    Cooperative Soil Survey (NCSS), which is led by the Natural Resources
    Conservation Service (NRCS) under the USDA; the Global Historical
    Climatology Network (GHCN), coordinated by National Climatic Data
    Center at NOAA; the Daymet gridded estimates of daily weather
    parameters for North America, version 3, available from the Oak Ridge
    National Laboratory's Distributed Active Archive Center (DAAC); the
    International Tree Ring Data Bank; and the National Land Cover
    Database (NLCD).
Access data from the Federal Register API <https://www.federalregister.gov/developers/api/v1>.
Provides a flexible set of tools for matching two un-linked data sets. 
    'fedmatch' allows for three ways to match data: exact matches, fuzzy matches, and multi-variable matches. 
    It also allows an easy combination of these three matches via the tier matching function.
The Code of Federal Regulations (CFR) annual edition is the codification 
    of the general and permanent rules published in the Federal Register by the departments
    and agencies of the Federal Government of the United States of America. Simply, the 
    'fedregs' package facilitates word processing and sentiment analysis of the CFR using tidy 
    principles. Note: According to the Code of Federal Regulations XML Rendition User Guide Document: 
    "In general, there are no restrictions on re-use of information in Code of Federal Regulations
    material because U.S. Government works are not subject to copyright. OFR and GPO do not
    restrict downstream uses of Code of Federal Regulations data, except that independent providers
    should be aware that only the OFR and GPO are entitled to represent that they are the providers
    of the official versions of the Code of Federal Regulations and related Federal Register
    publications."
An API for automatic data queries to the fedstat <https://www.fedstat.ru>, using a small set of functions with a common interface.
Flow of funds are financial accounts that are provided by Federal Reserve quarterly. The package contains all
    datasets <https://www.federalreserve.gov/datadownload/Choose.aspx?rel=z1>, tables <https://www.federalreserve.gov/apps/fof/FOFTables.aspx> 
    and descriptions <https://www.federalreserve.gov/apps/fof/Guide/z1_tables_description.pdf> with functions to understand series <https://www.federalreserve.gov/apps/fof/SeriesStructure.aspx> and explore them.
Analysis of fragmented time directionality to investigate feedback in time series. Tools provided by the package allow the analysis of feedback for a single time series and the analysis of feedback for a set of time series collected across a spatial domain.
Provides the function feis() to estimate fixed effects individual 
    slope (FEIS) models. The FEIS model constitutes a more general version of 
    the often-used fixed effects (FE) panel model, as implemented in the 
    package 'plm' by Croissant and Millo (2008) <doi:10.18637/jss.v027.i02>. 
    In FEIS models, data are not only person demeaned like in conventional 
    FE models, but detrended by the predicted individual slope of each 
    person or group. Estimation is performed by applying least squares lm() 
    to the transformed data. For more details on FEIS models see Bruederl and 
    Ludwig (2015, ISBN:1446252442); Frees (2001) <doi:10.2307/3316008>; 
    Polachek and Kim (1994) <doi:10.1016/0304-4076(94)90075-2>; 
	Ruettenauer and Ludwig (2020) <doi:10.1177/0049124120926211>;
    Wooldridge (2010, ISBN:0262294354). To test consistency of conventional FE 
    and random effects estimators against heterogeneous slopes, the package 
    also provides the functions feistest() for an artificial regression test 
    and bsfeistest() for a bootstrapped version of the Hausman test.
Enhance R help system by fuzzy search and preview interface, pseudo-postfix operators, and more.
    The `?.` pseudo-postfix operator and the `?` prefix operator displays documents and contents (source or structure) of objects simultaneously to help understanding the objects.
    The `?p` pseudo-postfix operator displays package documents, and is shorter than help(package = foo).
Upload, download, and edit internet maps with the Felt API 
    (<https://feltmaps.notion.site/Felt-Public-API-reference-c01e0e6b0d954a678c608131b894e8e1>). 
    Allows users to create new maps, edit existing maps, and extract data.
    Provides tools for working with layers, which represent geographic data, and elements,
    which are interactive annotations. Spatial data accessed from the API is 
    transformed to work with 'sf'.
Efficient estimation of maximum likelihood models with multiple fixed-effects. Standard-errors can easily and flexibly be clustered and estimations exported.
A structured profile likelihood algorithm for the logistic fixed effects model and an approximate expectation maximization (EM) algorithm for the logistic mixed effects model. Based on He, K., Kalbfleisch, J.D., Li, Y. and Li, Y. (2013) <doi:10.1007/s10985-013-9264-6>.
R implementations of standard financial engineering codes;
  vanilla option pricing models such as Black-Scholes, Bachelier, CEV, and
  SABR.
Frailty Exponential Random Graph Models estimated through pseudo likelihood with frailty terms estimated using 'Stan' as per Box-Steffensmeier et. al (2017) <doi:10.7910/DVN/K3D1M2>.
    Goodness of fit for Frailty Exponential Random Graph Models is also available, with easy visualizations for comparison to fit Exponential Random Graph Models.
Data from various catalogs of astrophysical gamma-ray sources
    detected by NASA's Large Area Telescope (The Astrophysical Journal, 697, 1071,
    2009 June 1), on board the Fermi gamma-ray satellite. More information on
    Fermi and its data products is available from the Fermi Science Support Center
    (http://fermi.gsfc.nasa.gov/ssc/).
Diagnostic plots for optimisation, with a focus on projection pursuit. These show paths the optimiser 
    takes in the high-dimensional space in multiple ways: by reducing the dimension using principal component analysis, and
    also using the tour to show the path on the high-dimensional space. Several botanical colour palettes are included, reflecting the 
    name of the package. A paper describing the methodology can be found at <https://journal.r-project.org/archive/2021/RJ-2021-105/index.html>.
Quantify variability (such as confidence interval) of fertilizer response curves and optimum fertilizer rates using bootstrapping residuals with several popular non-linear and linear models.
Four fertility models are fitted using non-linear least squares. These are the Hadwiger, the Gamma, the Model1 and Model2, following the terminology of the following paper: Peristera P. and Kostaki A. (2007). "Modeling fertility in modern populations". Demographic Research, 16(6): 141--194. <doi:10.4054/DemRes.2007.16.6>. Model based averaging is also supported.
Processes data from The Social Networks and Fertility Survey,
    downloaded from <https://dataarchive.lissdata.nl>, including correcting 
    respondent errors and transforming network data into network objects to
    facilitate analyses and visualisation.
Original idea was presented in the reference paper. Varghese et al. (2020, 74(1):35-42) "Bayesian State-space Implementation of Schaefer Production Model for Assessment of Stock Status for Multi-gear Fishery". Marine fisheries governance and management practices are very essential to ensure the sustainability of the marine resources. A widely accepted resource management strategy towards this is to derive sustainable fish harvest levels based on the status of marine fish stock. Various fish stock assessment models that describe the biomass dynamics using time series data on fish catch and fishing effort are generally used for this purpose. In the scenario of complex multi-species marine fishery in which different species are caught by a number of fishing gears and each gear harvests a number of species make it difficult to obtain the fishing effort corresponding to each fish species. Since the capacity of the gears varies, the effort made to catch a resource cannot be considered as the sum of efforts expended by different fishing gears. This necessitates standardisation of fishing effort in unit base.
Contains functions to fetch data from various data sources.
    The user first creates a catalog of objects from a data source,
    then fetches data from the catalog.  The package provides an easy
    way to access data from many different types of sources.
Collect  your data on digital marketing campaigns from Google Analytics using the 'Windsor.ai' API <https://windsor.ai/api-fields/>.
Collect  your data on digital marketing campaigns from Salesforce using the 'Windsor.ai' API <https://windsor.ai/api-fields/>.
Provides functions for analysing
  and modelling extreme events in financial time Series. The
  topics include: (i) data pre-processing, (ii) explorative 
  data analysis, (iii) peak over threshold modelling, (iv) block
  maxima modelling, (v) estimation of VaR and CVaR, and (vi) the
  computation of the extreme index.
Functions, S4 classes/methods and a graphical user interface (GUI) to design surveys to substantiate freedom from disease using a modified hypergeometric function (see Cameron and Baldock, 1997, <doi:10.1016/s0167-5877(97)00081-0>). Herd sensitivities are computed according to sampling strategies "individual sampling" or "limited sampling" (see M. Ziller, T. Selhorst, J. Teuffert, M. Kramer and H. Schlueter, 2002, <doi:10.1016/S0167-5877(01)00245-8>). Methods to compute the a-posteriori alpha-error are implemented. Risk-based targeted sampling is supported.
Downloads all the datasets (you can exclude the daily ones or specify a list of those you are targeting specifically) from Kenneth French's Website at <https://mba.tuck.dartmouth.edu/pages/faculty/ken.french/data_library.html>, process them and convert them to list of 'xts' (time series).
Format the raw data from the ESPN fantasy football API
    <https://fantasy.espn.com/apis/v3/games/ffl/> as data frames.
    Retrieve data on public leagues, rosters, athletes, and matches.
General linear modeling with multiple responses (MANCOVA). An overall p-value for each model term is calculated by the 50-50 MANOVA method by Langsrud (2002) <doi:10.1111/1467-9884.00320>, which handles collinear responses. Rotation testing, described by Langsrud (2005) <doi:10.1007/s11222-005-4789-5>, is used to compute adjusted single response p-values according to familywise error rates and false discovery rates (FDR). The approach to FDR is described in the appendix of Moen et al. (2005) <doi:10.1128/AEM.71.4.2086-2094.2005>. Unbalanced designs are handled by Type II sums of squares as argued in Langsrud (2003) <doi:10.1023/A:1023260610025>. Furthermore, the Type II philosophy is extended to continuous design variables as described in Langsrud et al. (2007) <doi:10.1080/02664760701594246>. This means that the method is invariant to scale changes and that common pitfalls are avoided.
Implements numerical entropy-pooling for portfolio construction and 
    scenario analysis as described in Meucci, Attilio (2008) and Meucci, Attilio (2010) 
    <doi:10.2139/ssrn.1696802>.
Helps access various Fantasy Football APIs by handling
    authentication and rate-limiting, forming appropriate calls, and
    returning tidy dataframes which can be easily connected to other data
    sources.
Uses bootstrap resampling to run fantasy football season
    simulations supported by historical rankings and 'nflfastR' data,
    calculating optimal lineups, and returning aggregated results.
An implementation of the adaptive forgetting factor scheme described in Bodenham and Adams (2016) <doi:10.1007/s11222-016-9684-8> which adaptively estimates the mean and variance of a stream in order to detect multiple changepoints in streaming data. The implementation is in 'C++' and uses 'Rcpp'. Additionally, implementations of the fixed forgetting factor scheme from the same paper, as well as the classic cumulative sum ('CUSUM') and exponentially weighted moving average ('EWMA') methods, are included.
Create, visualize, and test fast-and-frugal decision trees (FFTs) using the algorithms and methods described by Phillips, Neth, Woike & Gaissmaier (2017), <doi:10.1017/S1930297500006239>. 
    FFTs are simple and transparent decision trees for solving binary classification problems. 
    FFTs can be preferable to more complex algorithms because they require very little information, are easy to understand and communicate, and are robust against overfitting.
Provides a simple and efficient wrapper around the fastest
        Fourier transform in the west (FFTW) library <http://www.fftw.org/>.
Provides a wrapper for several 'FFTW' functions. This package provides access to the two-dimensional 'FFT', the multivariate 'FFT', and the one-dimensional real to complex 'FFT' using the 'FFTW3' library. The package includes the functions fftw() and mvfftw() which are designed to mimic the functionality of the R functions fft() and mvfft(). The 'FFT' functions have a parameter that allows them to not return the redundant complex conjugate when the input is real data.
This is a package for implementation of Flury-Gautschi
        algorithms.
Analyze and model heteroskedastic behavior in financial time series.
Read and Parse for Fundamental Geo-Spatial Data (FGD) which downloads XML file 
    from providing site (<https://fgd.gsi.go.jp/download/menu.php>). The JPGIS format file 
    provided by FGD so that it can be handled as an R spatial object such as 'sf' and 
    'raster', 'terra' or 'stars'.
    Supports the FGD version 4.1, and accepts fundamental items and digital elevation models.
To help you access, transform, analyze, and
    visualize ForestGEO data, we developed a collection of R packages
    (<https://forestgeo.github.io/fgeo/>). This package, in particular,
    helps you to install and load the entire package-collection with a
    single R command, and provides convenient ways to find relevant
    documentation. Most commonly, you should not worry about the
    individual packages that make up the package-collection as you can
    access all features via this package. To learn more about ForestGEO
    visit <http://www.forestgeo.si.edu/>.
To help you access, transform, analyze, and
    visualize ForestGEO data, we developed a collection of R packages
    (<https://forestgeo.github.io/fgeo/>). This package, in particular,
    helps you to implement analyses of plot species distributions,
    topography, demography, and biomass. It also includes a torus
    translation test to determine habitat associations of tree species as
    described by Zuleta et al. (2018) <doi:10.1007/s11104-018-3878-0>. To
    learn more about ForestGEO visit <https://forestgeo.si.edu/>.
To help you access, transform, analyze, and visualize
    ForestGEO data, we developed a collection of R packages
    (<https://forestgeo.github.io/fgeo/>). This package, in particular,
    helps you to plot ForestGEO data. To learn more about ForestGEO visit
    <https://forestgeo.si.edu/>.
To help you access, transform, analyze, and visualize
    'ForestGEO' data, we developed a collection of R packages
    (<https://forestgeo.github.io/fgeo/>). This package, in particular,
    helps you to easily import, filter, and modify 'ForestGEO' data. To
    learn more about 'ForestGEO' visit <https://forestgeo.si.edu/>.
Access small example datasets from Luquillo, a
    ForestGEO site in Puerto Rico
    (<https://forestgeo.si.edu/sites/north-america/luquillo>).
'FastGit' <https://doc.fastgit.org/> works like a mirror of 'GitHub' to make significant acceleration. 'fgitR' is a package to do git operation with 'FastGit' automatically.
An implementation of the methodologies described in Xi Liu, Afshin A. Divani, and Alexander Petersen (2022) <doi:10.1016/j.csda.2022.107421>, including 
                truncated functional linear and truncated functional logistic regression models.
The function estimates a multivariate regression model for outcomes with network dependence.
Estimates a functional graphical model and a partially separable Karhunen-Loève decomposition for a multivariate Gaussian process. See Zapata J., Oh S. and Petersen A. (2019) <arXiv:1910.03134>.
Growth models and forest production require existing data
    manipulation and the creation of new data, structured from basic forest
    inventory data. The purpose of this package is provide functions to support
    these activities.
Rapidly create a GUI interface for a function you created by automatically creating widgets for arguments of the function. Automatically parses help routines for context-sensitive help to these arguments. The interface essentially a wrapper to some Tcl/Tk routines to both simplify and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be incorporated into the interface for greater customization for the more experienced.
Impute general multivariate missing data with the fractional hot deck imputation based on Jaekwang Kim (2011) <doi:10.1093/biomet/asq073>.
Useful tools for conveniently downloading FHIR resources in xml format 
    and converting them to R data.frames. The package uses FHIR-search to download bundles 
    from a FHIR server, provides functions to save and read xml-files containing such bundles 
    and allows flattening the bundles to data.frames using XPath expressions. FHIR® is the registered trademark 
    of HL7 and is used with the permission of HL7. Use of the FHIR trademark does not constitute endorsement of this product by HL7.
Fitting (hierarchical) hidden Markov models to financial data
    via maximum likelihood estimation. See Oelschläger, L. and Adam, T.
    "Detecting bearish and bullish markets in financial time series using 
    hierarchical hidden Markov models" (2021, Statistical Modelling) 
    <doi:10.1177/1471082X211034048> for a reference.
Functions to compare two or more survival curves with:
             a) The Fleming-Harrington test for right-censored data based on permutations and on counting processes.
             b) An extension of the Fleming-Harrington test for interval-censored data based on a permutation distribution and on a score vector distribution.
Provide functions for forest inventory calculations.
        Common volumetric equations (Smalian, Newton and Huber) as well
        stacking factor and form
Routines for estimating tree fiber (tracheid) length distributions in the standing tree
           based on increment core samples. Two types of data can be used with the package, increment 
           core data measured by means of an optical fiber analyzer (OFA), e.g. such as the Kajaani 
          Fiber Lab, or measured by microscopy. Increment core data analyzed by OFAs consist of the cell
          lengths of both cut and uncut fibres (tracheids) and fines (such as ray parenchyma cells)
           without being able to identify which cells are cut or if they are fines or fibres. The
          microscopy measured data consist of the observed lengths of the uncut fibres in the increment
         core. A censored version of a mixture of the fine and fiber length distributions is proposed to
         fit the OFA data, under distributional assumptions (Svensson et al., 2006) <doi:10.1111/j.1467-9469.2006.00501.x>. The package offers two choices for the
        assumptions of the underlying density functions of the true fiber (fine) lenghts of those fibers
        (fines) that at least partially appear in the increment core, being the generalized gamma and 
        the log normal densities.
Compares how well different models estimate a quantity of interest (the "focus") so that different models may be preferred for different purposes.  Comparisons within any class of models fitted by maximum likelihood are supported, with shortcuts for commonly-used classes such as generalised linear models and parametric survival models.  The methods originate from Claeskens and Hjort (2003) <doi:10.1198/016214503000000819> and Claeskens and Hjort (2008, ISBN:9780521852258).
Algorithms for classical symmetric and deflation-based FastICA, reloaded deflation-based FastICA algorithm and an algorithm for adaptive deflation-based FastICA using multiple nonlinearities. For details, see Miettinen et al. (2014) <doi:10.1109/TSP.2014.2356442> and Miettinen et al. (2017) <doi:10.1016/j.sigpro.2016.08.028>. The package is described in Miettinen, Nordhausen and Taskinen (2018) <doi:10.32614/RJ-2018-046>.
Create secure, encrypted, and password-protected static HTML 
  documents that include the machinery for secure in-browser authentication 
  and decryption.
Provides methods for fitting and inspection of Bayesian Multinomial Logistic Normal Models using MAP estimation 
 and Laplace Approximation as developed in Silverman et. Al. (2022) <https://www.jmlr.org/papers/v23/19-882.html>. Key functionality is implemented in C++ for 
 scalability. 'fido' replaces the previous package 'stray'.
A shiny design of experiments (DOE) app that aids in the creation of traditional, 
 un-replicated, augmented and partially-replicated designs applied to agriculture, 
 plant breeding, forestry, animal and biological sciences.
For curve, surface and function fitting with an emphasis
 on splines, spatial data, geostatistics,  and spatial statistics. The major methods
 include cubic, and thin plate splines, Kriging, and compactly supported
 covariance functions for large data sets. The splines and Kriging methods are
 supported by functions that can determine the smoothing parameter
 (nugget and sill variance) and other covariance function parameters by cross
 validation and also by restricted maximum likelihood. For Kriging
 there is an easy to use function that also estimates the correlation
 scale (range parameter).  A major feature is that any covariance function
 implemented in R and following a simple format can be used for
 spatial prediction. There are also many useful functions for plotting
 and working with spatial data as images. This package also contains
 an implementation of sparse matrix methods for large spatial data
 sets and currently requires the sparse matrix (spam) package. Use
 help(fields) to get started and for an overview.  The fields source
 code is deliberately commented and provides useful explanations of
 numerical details as a companion to the manual pages. The commented
 source code can be viewed by expanding the source code version
 and looking in the R subdirectory. The reference for fields can be generated
 by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development
 of this package was supported in part by the National Science Foundation  Grant
 1417857,  the National Center for Atmospheric Research, and Colorado School of Mines.
 See the Fields URL
 for a vignette on using this package and some background on spatial statistics.
Simulates plot data in field trials for multiple 
	traits across multiple environments. Its core function generates plot errors comprising 1) 
	a spatially correlated error term, 2) a random error term, and 3) an extraneous error 
	term. Spatially correlated errors are simulated using either bivariate interpolation 
	or a two-dimensional autoregressive process of order one (AR1:AR1). The three error 
	terms are combined at a user-defined ratio. Plot phenotypes can be generated 
	by combining the simulated errors with genetic values (e.g. true, simulated 
	or predicted). 'FieldSimR' provides wrapper functions to simulate genetic values for 
	multiple traits across multiple environments using the 'R' package 'AlphaSimR'.
A very flexible framework for building server side logic in
    R. The framework is unopinionated when it comes to how HTTP requests
    and WebSocket messages are handled and supports all levels of app
    complexity; from serving static content to full-blown dynamic
    web-apps. Fiery does not hold your hand as much as e.g. the shiny
    package does, but instead sets you free to create your web app the way
    you want.
A research estimation tool for analysts that work with sample-based
    inventory data from the U.S. Department of Agriculture, Forest Service,
    Forest Inventory and Analysis (FIA) Program.
A set of tools for data wrangling, spatial data analysis,
    statistical modeling (including direct, model-assisted, photo-based, and
    small area tools), and USDA Forest Service data base tools. These tools are
    aimed to help Foresters, Analysts, and Scientists extract and perform
    analyses on USDA Forest Service data.
Work with configs with a source precedence. Either create own R6
  instance or work with convenient functions at a package level.
With the functions in this package you can check the
  validity of the following financial instrument identifiers:
  FIGI (Financial Instrument Global Identifier
  <https://www.openfigi.com/about/figi>),
  CUSIP (Committee on Uniform Security Identification Procedures
  <https://www.cusip.com/identifiers.html#/CUSIP>),
  ISIN (International Securities Identification Number
  <https://www.cusip.com/identifiers.html#/ISIN>),
  SEDOL (Stock Exchange Daily Official List
  <https://www2.lseg.com/SEDOL-masterfile-service-tech-guide-v8.6>).
  You can also calculate the FIGI checksum of 11-character strings,
  which can be useful if you want to create your own FIGI identifiers.
An easy-to-use web client/wrapper for the 'Figma API' <https://www.figma.com/developers/api>. 
  It allows you to bring all data from a 'Figma' file to your 'R' session. This includes the data of all objects
  that you have drawn in this file, and their respective canvas/page metadata.
For including external figures into an assembled 
    {patchwork}. This enables the creation of more complex figures that include 
    images alongside plots.
We view a figure as a collection of graphs/tables assembled on a page and optionally annotated with metadata
    (titles, headers and footers). Functions and supporting documentation are offered to streamline a variety of figure production task.
Transform output files of some tools to the 'microtable' object of 'microtable' class in 'microeco' package. The 'microtable' class is the basic class in 'microeco' package and is necessary for the downstream microbial community data analysis.
Stores large arrays in files to avoid occupying large
    memories. Implemented with super fast gigabyte-level multi-threaded 
    reading/writing via 'OpenMP'. Supports multiple non-character data 
    types (double, float, complex, integer, logical, and raw).
A wrapper for the Filebin API. Filebin implements convenient file
    sharing on the web.
Implements a simple key-value style database where character string keys
  are associated with data values that are stored on the disk. A simple interface is provided for inserting,
  retrieving, and deleting data from the database. Utilities are provided that allow 'filehash' databases to be
  treated much like environments and lists are already used in R. These utilities are provided to encourage
  interactive and exploratory analysis on large datasets. Three different file formats for representing the
  database are currently available and new formats can easily be incorporated by third parties for use in the
  'filehash' framework.
Simple key-value database using SQLite as the back end.
Place an exclusive or shared lock on a file. It uses 'LockFile'
    on Windows and 'fcntl' locks on Unix-like systems.
Interface for working with large matrices stored in files,
        not in computer memory. Supports multiple non-character
        data types (double, integer, logical and raw) of
        various sizes (e.g. 8 and 4 byte real values).
        Access to parts of the matrix is done by indexing, 
        exactly as with usual R matrices.
        Supports very large matrices.
        Tested on multi-terabyte matrices.
        Allows for more than 2^32 rows or columns.
        Allows for quick addition of extra columns to a filematrix.
        Cross-platform as the package has R code only.
Create descriptive file names with ease. New file names are
    automatically (but optionally) time stamped and placed in date stamped
    directories. Streamline your analysis pipeline with input and output file
    names that have informative tags and proper file extensions.
Functions for printing the contents of a folder as columns in a ragged-bottom data.frame and for
  viewing the details (size, time created, time modified, etc.) of a folder's top level contents.
This started out as a package for file and string
    manipulation.  Since then, the 'fs' and 'strex' packages emerged,
    offering functionality previously given by this package (but it's done
    better in these new ones).  Those packages have hence almost pushed
    'filesstrings' into extinction.  However, it still has a small number
    of unique, handy file manipulation functions which can be seen in the
    vignette.  One example is a function to remove spaces from all file
    names in a directory.
A population genetic simulator, which is able to generate synthetic datasets for single-nucleotide polymorphisms (SNP) for multiple populations. The genetic distances among populations can be set according to the Fixation Index (Fst) as explained in Balding and Nichols (1995) <doi:10.1007/BF01441146>. This tool is able to simulate outlying individuals and missing SNPs can be specified. For Genome-wide association study (GWAS), disease status can be set in desired level according risk ratio.
Filling in the missing entries of a partially observed data is one of fundamental problems in various disciplines of mathematical science. For many cases, data at our interests have canonical form of matrix in that the problem is posed upon a matrix with missing values to fill in the entries under preset assumptions and models. We provide a collection of methods from multiple disciplines under Matrix Completion, Imputation, and Inpainting. See Davenport and Romberg (2016) <doi:10.1109/JSTSP.2016.2539100> for an overview of the topic.
Edit vectors to fill missing values, based on the vector itself.
Filtering of raw acoustic telemetry transmissions
    from three acoustic telemetry companies (ATS, Lotek, Teknologic). The 
    filtering steps check for false positives caused by reflected transmissions 
    from surfaces and false pings from other noise generating equipment. The 
    filter is unique for each technology type. The package was written in 
    concert with the Interagency Telemetry Advisory Group (iTAG) and makes use 
    of the JSATS California Fish Tracking Database:
    <https://oceanview.pfeg.noaa.gov/CalFishTrack/>.
Generate search filters to query scientific bibliographic sources, 
    such as PubMed and Web of Science, for non-human primate related 
    publications.
Provides a collection of utility functions 
    to download and manage data sets from the Internet or from other 
    sources.
Generate regression results tables and plots in final 
    format for publication. Explore models and export directly to PDF 
    and 'Word' using 'RMarkdown'.
Calculate the final size of a susceptible-infectious-recovered epidemic in a population with demographic variation in contact patterns and susceptibility to disease, as discussed in Miller (2012) <doi:10.1007/s11538-012-9749-6>.
Functions for financial analysis and financial modeling, 
             including batch graphs generation, beta calculation, 
             descriptive statistics, annuity calculation, bond pricing 
             and financial data download.
Infrastructure for defining meta-data and
    relationships for financial instruments.
Contains financial math functions and introductory derivative functions included in the Society of Actuaries and Casualty Actuarial Society 'Financial Mathematics' exam, and some topics in the 'Models for Financial Economics' exam.
This package accomplishes two tasks: a) it classifies
        implicit trading activity from quotes in OTC markets using the
        algorithm of Lee and Ready (1991); b) based on information for
        trade initiation, the package computes the probability of
        informed trading of Easley and O'Hara (1987).
A programmatic interface to the 'Finnish Biodiversity Information
    Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
    Finnish biodiversity data from multiple sources in a single open access
    portal for researchers, citizen scientists, industry and government.
    'FinBIF' allows users of biodiversity information to find, access, combine
    and visualise data on Finnish plants, animals and microorganisms. The
    'finbif' package makes the publicly available data in 'FinBIF' easily
    accessible to programmers. Biodiversity information is available on taxonomy
    and taxon occurrence. Occurrence data can be filtered by taxon, time,
    location and other variables. The data accessed are conveniently
    preformatted for subsequent analyses.
Learning bipartite and k-component bipartite graphs from financial
     datasets. This package contains implementations of the algorithms described
     in the paper: Cardoso JVM, Ying J, and Palomar DP (2022).
     <https://openreview.net/pdf?id=WNSyF9qZaMd>
     "Learning bipartite graphs: heavy tails and multiple components,
     Advances in Neural Informations Processing Systems" (NeurIPS).
Package for time value of money calculation, time series analysis and computational finance.
Parse and create Darwin Core (<http://rs.tdwg.org/dwc/>) Simple
    and Archives. Functionality includes reading and parsing all the
    files in a Darwin Core Archive, including the datasets and metadata;
    read and parse simple Darwin Core files; and validation of Darwin
    Core Archives.
Estimation and regularization for covariance matrix of asset
    returns. For covariance matrix estimation, three major types of factor
    models are included: macroeconomic factor model, fundamental factor model and
    statistical factor model. For covariance matrix regularization, four regularized
    estimators are included: banding, tapering, hard-thresholding and soft-
    thresholding. The tuning parameters of these regularized estimators are selected
    via cross-validation.
Creates a HTML widget which displays the results of searching for a pattern in files in a given folder. The results can be viewed in the 'RStudio' viewer pane, included in a 'R Markdown' document or in a 'Shiny' app. Also provides a 'Shiny' application allowing to run the widget and to navigate in the results.
Creates a HTML widget which displays the results of searching for a pattern in files in a given 'git' repository, including all its branches. The results can also be returned in a dataframe.
The heterogeneous treatment effect estimation procedure 
        proposed by Imai and Ratkovic (2013)<DOI: 10.1214/12-AOAS593>.  
        The proposed method is applicable, for
        example, when selecting a small number of most (or least)
        efficacious treatments from a large number of alternative
        treatments as well as when identifying subsets of the
        population who benefit (or are harmed by) a treatment of
        interest. The method adapts the Support Vector Machine
        classifier by placing separate LASSO constraints over the
        pre-treatment parameters and causal heterogeneity parameters of
        interest. This allows for the qualitative distinction between
        causal and other parameters, thereby making the variable
        selection suitable for the exploration of causal heterogeneity. 	
        The package also contains a class of functions, CausalANOVA, 
        which estimates the average marginal interaction effects (AMIEs)
        by a regularized ANOVA as proposed by Egami and Imai (2019)<DOI:10.1080/01621459.2018.1476246>. 
        It contains a variety of regularization techniques to facilitate 
	analysis of large factorial experiments.
Finds 'CRAN' packages by the topic requested. The topic can be given as a character string or as a regular expression and will help users to locate 'CRAN' packages matching their specified requirement. findPackage(<string>) returns a data frame of packages with description containing the input string.
Package designed to find an acceptable python binary.
Scans all directories and subdirectories of a path for code snippets, R scripts,
    R Markdown, PDF or text files containing a specific pattern.  Files found can be copied to a new folder.
Developed by CDC/ATSDR (Centers for Disease Control and Prevention/
    Agency for Toxic Substances and Disease Registry), 
    Social Vulnerability Index (SVI) serves as a tool to assess the resilience 
    of communities by taking into account socioeconomic and demographic factors. 
    Provided with year(s), region(s) and a geographic level of interest, 
    'findSVI' retrieves required variables from US census data and calculates SVI 
    for communities in the specified area based on CDC/ATSDR SVI documentation. 
    Reference for the calculation methods: Flanagan BE, Gregory EW, Hallisey EJ, 
    Heitgerd JL, Lewis B (2011) <doi:10.2202/1547-7355.1792>.
A tool to explore wide data sets, by detecting, ranking
    and plotting groups of statistically dependent columns.
Statistical tool set for population genetics. The package provides following functions: 1) empirical Bayes estimator of Fst and other measures of genetic differentiation, 2) regression analysis of environmental effects on genetic differentiation using bootstrap method, 3) interfaces to read and manipulate 'GENEPOP' format data files and allele/haplotype frequency format files.
Statistical tool set for population genetics. The package provides following functions: 1) estimators of genetic differentiation (FST), 2) regression analysis of environmental effects on genetic differentiation using generalized least squares (GLS) method, 3) interfaces to read and manipulate 'GENEPOP' format data files). For more information, see Kitada, Nakamichi and Kishino (2020) <doi:10.1101/2020.01.30.927186>.
The ability to tune models is important. 'finetune' enhances
    the 'tune' package by providing more specialized methods for finding
    reasonable values of model tuning parameters.  Two racing methods
    described by Kuhn (2014) <arXiv:1405.6974> are included. An iterative
    search method using generalized simulated annealing (Bohachevsky,
    Johnson and Stein, 1986) <doi:10.1080/00401706.1986.10488128> is also
    included.
Functions to manipulate binary fingerprints
 of arbitrary length. A fingerprint is represented by an object of S4 class 'fingerprint'
 which is internally represented a vector of integers, such
 that each element represents the position in the fingerprint that is set to 1.
 The bitwise logical functions in R are overridden so that they can be used directly
 with 'fingerprint' objects. A number of distance metrics are also
 available (many contributed by Michael Fadock). Fingerprints 
 can be converted to Euclidean vectors (i.e., points on the unit hypersphere) and
 can also be folded using OR.  Arbitrary fingerprint formats can be handled via line
 handlers. Currently handlers are provided for CDK, MOE and BCI fingerprint data.
Quantifies the provenance of the sediments in a catchment or study area. Based on a comprehensive characterization of the sediment sources and the end sediment mixtures a mixing model algorithm is applied to the sediment mixtures in order to estimate the relative contribution of each potential source. The package includes several statistical methods such as Kruskal-Wallis test, discriminant function analysis ('DFA'), principal component plot ('PCA') to select the optimal subset of tracer properties. The variability within each sediment source is also considered to estimate the statistical distribution of the sources contribution.
Learning graphs for financial markets with optimization algorithms.
    This package contains implementations of the algorithms described in the paper:
    Cardoso JVM, Ying J, and Palomar DP (2021) <https://papers.nips.cc/paper/2021/hash/a64a034c3cb8eac64eb46ea474902797-Abstract.html>
    "Learning graphs in heavy-tailed markets", Advances in Neural Informations Processing Systems (NeurIPS).
In the Cramér–Lundberg risk process perturbed by a Wiener
    process, this packages provides approximations to the probability of
    ruin within a finite time horizon.  Currently, there are three methods
    implemented: The first one uses saddlepoint approximation (two
    variants are provided), the second one uses importance sampling and
    the third one is based on the simulation of a dual process.  This last
    method is not very accurate and only given here for completeness.
The purpose of this package is to tests whether a given 
             moment of the distribution of a given sample is finite or not. For 
             heavy-tailed distributions with tail exponent b, only moments of 
             order smaller than b are finite. Tail exponent and heavy-
             tailedness are notoriously difficult to ascertain. But the 
             finiteness of moments (including fractional moments) can be tested 
             directly. This package does that following the test suggested by 
             Trapani (2016) <doi:10.1016/j.jeconom.2015.08.006>.
Providing classes, methods, and functions to deal with financial networks. 
    Users can easily store information about both physical and legal persons by using pre-made classes that are studied for integration with scraping packages such as 'rvest' and 'RSelenium'.
    Moreover, the package assists in creating various types of financial networks depending on the type of relation between its units depending on the relation under scrutiny (ownership, board interlocks, etc.), the desired tie type (valued or binary), and renders them in the most common formats (adjacency matrix, incidence matrix, edge list, 'igraph', 'network').
R API client package for 'Fingrid Open Data' on the 
    electricity market and the power system. get_data() function
    holds the main application logic to retrieve time-series data.
    API calls require free user account registration.
Automated time series forecasting developed by Microsoft Finance. The Microsoft Finance Time 
    Series Forecasting Framework, aka Finn, can be used to forecast any component of the income 
    statement, balance sheet, or any other area of interest by finance. Any numerical quantity over time, 
    Finn can be used to forecast it. While it can be applied outside of the finance domain, Finn was built 
    to meet the needs of financial analysts to better forecast their businesses within a company, and has 
    a lot of built in features that are specific to the needs of financial forecasters. Happy forecasting!
Download and display company financial data from the U.S. Securities
    and Exchange Commission's EDGAR database. It contains a suite of functions with
    web scraping and XBRL parsing capabilities that allows users to extract data from EDGAR 
    in an automated and scalable manner. See <https://www.sec.gov/edgar/searchedgar/companysearch.html>
    for more information.
R companion to Tsay (2005)
 Analysis of Financial Time Series, second edition (Wiley).
 Includes data sets, functions and script files
 required to work some of the examples.  Version 0.3-x
 includes R objects for all data files used in the text
 and script files to recreate most of the analyses in
 chapters 1-3 and 9 plus parts of chapters 4 and 11.
Provides a lightweight suite
             of functions for retrieving information
             about 5-digit or 2-digit US FIPS codes.
Computes implicitly induced quantities from prior/hyperparameter    
    specifications of three Mixtures of Finite Mixtures models: Dirichlet 
    Process Mixtures (DPMs; Escobar and West (1995) 
    <doi:10.1080/01621459.1995.10476550>), Static Mixtures of Finite Mixtures 
    (Static MFMs; Miller and Harrison (2018) 
    <doi:10.1080/01621459.2016.1255636>), and Dynamic Mixtures of Finite 
    Mixtures (Dynamic MFMs; Frühwirth-Schnatter, Malsiner-Walli and Grün (2020)
    <arXiv:2005.09918>). For methodological details, please refer to 
    Greve, Grün, Malsiner-Walli and Frühwirth-Schnatter (2020)
    <arXiv:2012.12337>) as well as the package vignette.
The algorithm assigns rareness/ outlierness score to every sample in voluminous datasets.
    The algorithm makes multiple estimations of the proximity between a pair of samples, in low-dimensional spaces. To compute proximity, FiRE uses Sketching, a variant of locality sensitive hashing. For more details: Jindal, A., Gupta, P., Jayadeva and Sengupta, D., 2018. Discovery of rare cells from voluminous single cell expression data. Nature Communications, 9(1), p.4719. <doi:10.1038/s41467-018-07234-6>.
Authenticate users in 'Shiny' applications using 'Google Firebase'
    with any of the many methods provided; email and password, email link, or
    using a third-party provider such as 'Github', 'Twitter', or 'Google'.
    Use 'Firebase Storage' to store files securely, and leverage 'Firebase Analytics'
    to easily log events and better understand your audience.
Fire behavior prediction models, including the Scott & Reinhardt's (2001) Rothermel Wildland Fire Modelling System <DOI:10.2737/RMRS-RP-29> and Alexander et al.'s (2006) Crown Fire Initiation & Spread model <DOI:10.1016/j.foreco.2006.08.174>. Also contains sample datasets, estimation of fire behavior prediction model inputs (e.g., fuel moisture, canopy characteristics, wind adjustment factor), results visualization, and methods to estimate fire weather hazard.
Proposes non-parametric estimates of the Fisher information measure and the 
              Shannon entropy power. More theoretical and implementation details can be found
              in Guignard et al. <doi:10.3389/feart.2020.00255>. A 'python' version of this
              work is available on 'github' and 'PyPi' ('FiShPy').
Provides raw and curated data on the codes,
    classification and conservation status of freshwater fishes in British
    Columbia. Marine fishes will be added in a future release.
A collection of four datasets 
    based around the population dynamics of migratory fish. Datasets 
    contain both basic size information on a per fish basis, as well as
    otolith data that contains a per day record of fish growth history.
    All data in this package was collected by the author, from 
    2015-2016, in the Wellington region of New Zealand.
The FisherEM algorithm, proposed by Bouveyron & Brunet (2012) <doi:10.1007/s11222-011-9249-9>,
        is an efficient method for the clustering of high-dimensional data. FisherEM models and 
        clusters the data in a discriminative and low-dimensional latent subspace. It also provides
        a low-dimensional representation of the clustered data. A sparse version of Fisher-EM
        algorithm is also provided.
Base maps are transformed to focus on a specific location using an
    azimuthal logarithmic distance transformation.
Dataset of 302 measurements of 11 fish species to accompany the
    manuscript "Length-weight relationships of six freshwater fish species
    from lake Kirkkojarvi, Finland".
Functions for applying a wide range of fisheries stock assessment methods.
Fits models to catch and effort data. Single-species models are 1) delta log-normal, 2) Tweedie, or 3) Poisson-gamma (G)LMs.
Provides an alternative to facilitate the construction of a phylogeny for fish species from a list of species
   or a community matrix using as a backbone the phylogenetic tree proposed by Rabosky et al. (2018) <doi:10.1038/s41586-018-0273-1>.
Calculates metabolic rate of fish and other aquatic organisms measured using
             an intermittent-flow respirometry approach. The tool is used to run a set of graphical
             QC tests of raw respirometry data, correct it for background respiration and chamber
             effect, filter and extract target values of absolute and mass-specific metabolic rate.
             Experimental design should include background respiration tests and measuring of one
             or more metabolic rate traits. The R package is ideally integrated with the pump
             controller 'PumpResp' and the DO meter 'SensResp' (open-source hardware by FishResp).
             Raw respirometry data can be also imported from 'AquaResp' (free software), 'AutoResp'
             ('LoligoSystems'), 'OxyView' ('PreSens'), 'Pyro Oxygen Logger' ('PyroScience') and
             'Q-box Aqua' ('QubitSystems'). More information about the R package 'FishResp'is
             available in the publication by Morozov et al. (2019) <doi:10.1093/conphys/coz003>.
An interface to the Fish Tree of Life API to download taxonomies,
    phylogenies, fossil calibrations, and diversification rate information for
    ray-finned fishes.
Implementation of color palettes based on fish species.
Fuzzy inference systems are based on fuzzy rules, which have a good capability for managing progressive phenomenons. 
  This package is a basic implementation of the main functions to use a Fuzzy Inference System (FIS) provided by the open source software 'FisPro' <https://www.fispro.org>. 
  'FisPro' allows to create fuzzy inference systems and to use them for reasoning purposes, especially for simulating a physical or biological system.
Provides functionality for constructing
    statistical models of transcriptomic dynamics in field conditions.
    It further offers the function to predict expression of a gene given 
    the attributes of samples and meteorological data. Nagano, A. J., Sato, 
    Y., Mihara, M., Antonio, B. A., Motoyama, R., Itoh, H., Naganuma, Y., and 
    Izawa, T. (2012). <doi:10.1016/j.cell.2012.10.048>. Iwayama, K., Aisaka, Y., 
    Kutsuna, N., and Nagano, A. J. (2017). <doi:10.1093/bioinformatics/btx049>.
The fit.models function and its associated methods (coefficients, print,
  summary, plot, etc.) were originally provided in the robust package to compare robustly
  and classically fitted model objects. See chapters 2, 3, and 5 in Insightful (2002)
  'Robust Library User's Guide' <http://robust.r-forge.r-project.org/Robust.pdf>). The aim
  of the fit.models package is to separate this fitted model object comparison functionality
  from the robust package and to extend it to support fitting methods (e.g., classical,
  robust, Bayesian, regularized, etc.) more generally.
Many 'Fitbit' users, and R-friendly 'Fitbit' users
    especially, have found themselves curious about their 'Fitbit' data.
    'Fitbit' aggregates a large amount of personal data, much of which is
    interesting for personal research and to satisfy curiosity, and is
    even potentially useful in medical settings. The goal of 'fitbitr' is
    to make interfacing with the 'Fitbit' API as streamlined as possible,
    to make it simple for R users of all backgrounds and comfort levels to
    analyze their 'Fitbit' data and do whatever they want with it!
    Currently, 'fitbitr' includes methods for pulling data on activity,
    sleep, and heart rate, but this list is likely to grow in the future
    as the package gains more traction and more requests for new methods
    to be implemented come in.  You can find details on the 'Fitbit' API
    at <https://dev.fitbit.com/build/reference/web-api/>.
Scrapes data from Fitbit <http://www.fitbit.com>. This does not use the official
    API, but instead uses the API that the web dashboard uses to generate the graphs
    displayed on the dashboard after login at <http://www.fitbit.com>.
Connection to the 'Fitbit' Web API <https://dev.fitbit.com/build/reference/web-api/> by including 'ggplot2' Visualizations, 'Leaflet' and 3-dimensional 'Rayshader' Maps. The 3-dimensional 'Rayshader' Map requires the installation of the 'CopernicusDEM' R package which includes the 30- and 90-meter elevation data.
Fit data to an ellipse, hyperbola, or parabola. Bootstrapping is available when needed. The conic curve can be rotated through an  arbitrary angle and the fit will still succeed. Helper functions are  provided to convert generator coefficients from one style to another, generate test data sets, rotate conic section parameters, and so on. References include Nikolai Chernov (2014) "Fitting ellipses, circles, and lines by  least squares" <https://people.cas.uab.edu/~mosya/cl/>; A. W. Fitzgibbon, M. Pilu, R. B. Fisher (1999) "Direct Least Squares Fitting of Ellipses" IEEE Trans. PAMI,  Vol. 21, pages 476-48; N. Chernov, Q. Huang, and H. Ma (2014) "Fitting quadratic curves to data points", British Journal of Mathematics & Computer Science, 4, 33-60; N. Chernov and H. Ma  (2011) "Least squares fitting of quadratic curves and surfaces", Computer Vision, Editor S. R. Yoshida, Nova Science Publishers, pp. 285-302.
Extends the fitdistr() function (of the MASS package) with several functions 
  to help the fit of a parametric distribution to non-censored or censored data. 
  Censored data may contain left censored, right censored and interval censored values, 
  with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), 
  the package provides moment matching (MME), quantile matching (QME), maximum goodness-of-fit 
  estimation (MGE) and maximum spacing estimation (MSE) methods (available only for 
  non-censored data). Weighted versions of MLE, MME, QME and MSE are available. See e.g. 
  Casella & Berger (2002), Statistical inference, Pacific Grove, for a general introduction 
  to parametric estimation.
Estimation of a dynamic lognormal - Generalized Pareto mixture via the Approximate Maximum Likelihood and the Cross-Entropy methods. See Bee, M. (2023) <doi:10.1016/j.csda.2023.107764>.
Robust estimation methods for the mean vector, scatter matrix,
    and covariance matrix (if it exists) from data (possibly containing NAs) 
    under multivariate heavy-tailed distributions such as angular Gaussian 
    (via Tyler's method), Cauchy, and Student's t distributions. Additionally, 
    a factor model structure can be specified for the covariance matrix. The
    latest revision also includes the multivariate skewed t distribution.
    The package is based on the papers: Sun, Babu, and Palomar (2014);
    Sun, Babu, and Palomar (2015); Liu and Rubin (1995);
    Zhou, Liu, Kumar, and Palomar (2019); Pascal, Ollila, and Palomar (2021).
A toolbox for estimating vector fields from intensive
    longitudinal data, and construct potential landscapes thereafter. The
    vector fields can be estimated with two nonparametric methods: the
    Multivariate Vector Field Kernel Estimator (MVKE) by Bandi & Moloche
    (2018) <doi:10.1017/S0266466617000305> and the Sparse Vector Field
    Consensus (SparseVFC) algorithm by Ma et al.  (2013)
    <doi:10.1016/j.patcog.2013.05.017>. The potential landscapes can be
    constructed with a simulation-based approach with the 'simlandr'
    package (Cui et al., 2021) <doi:10.31234/osf.io/pzva3>, or the
    Bhattacharya et al. (2011) method for path integration
    <doi:10.1186/1752-0509-5-85>.
Fits the lifespan datasets of biological systems such as yeast, fruit flies, and other similar biological units with well-known finite mixture models introduced by Farewell V. (1982) <doi:10.2307/2529885> and Al-Hussaini et al. (2000) <doi:10.1080/00949650008812033>. Estimates parameter space fitting of a lifespan dataset with finite mixtures of parametric distributions. Computes the following tasks; 1) Estimates parameter space of the finite mixture model 
             by implementing the expectation maximization (EM) algorithm. 2) Finds a sequence of four goodness-of-fit measures consist of Akaike Information Criterion (AIC), Bayesian Information Criterion (BIC), Kolmogorov-Smirnov (KS), and log-likelihood (log-likelihood) statistics. 3)The initial values is determined by k-means clustering.
Contains Probability Mass Functions, Cumulative Mass
    Functions, Negative Log Likelihood value, parameter estimation and
    modeling data using Binomial Mixture Distributions (BMD) (Manoj et al
    (2013) <doi:10.5539/ijsp.v2n2p24>) and Alternate Binomial
    Distributions (ABD) (Paul (1985) <doi:10.1080/03610928508828990>),
    also Journal article to use the package(<doi:10.21105/joss.01505>).
Methods and functions for fitting ordinary differential equations (ODE) model in 'R'. Sensitivity equations are used to compute the gradients of ODE trajectories with respect to underlying parameters, which in turn allows for more stable fitting. Other fitting methods, such as MCMC (Markov chain Monte Carlo), are also available.
Fits Weibull or sigmoidal models to percent loss conductivity (plc) curves as a function of plant water potential, computes confidence intervals of parameter estimates and predictions with bootstrap or parametric methods, and provides convenient plotting methods.
Genotyping assays for bi-allelic markers (e.g. SNPs) produce
	signal intensities for the two alleles. 'fitPoly' assigns genotypes 
	(allele dosages) to a collection of polyploid samples based on these
	signal intensities. 'fitPoly' replaces the older package 'fitTetra' that was
	limited (a.o.) to only tetraploid populations whereas 'fitPoly' accepts any
	ploidy level. Reference: Voorrips RE, Gort G, Vosman B (2011)
	<doi:10.1186/1471-2105-12-172>.
Fits Zeta distributions (discrete power laws) to data that arises
    from forensic surveys of clothing on the presence of glass and paint in
    various populations. The general method is described to some extent in
    Coulson, S.A., Buckleton, J.S., Gummer, A.B., and Triggs, C.M. (2001) 
    <doi:10.1016/S1355-0306(01)71847-3>, although the implementation differs.
Convenient classes to model fitness landscapes and fitness
    seascapes. A low-level package with which most users will not interact but
    upon which other packages modeling fitness landscapes and fitness seascapes
    will depend.
Utilities to read and write files in the FITS (Flexible
  Image Transport System) format, a standard format in astronomy (see
  e.g. <https://en.wikipedia.org/wiki/FITS> for more information).
  Present low-level routines allow: reading, parsing, and modifying
  FITS headers; reading FITS images (multi-dimensional arrays);
  reading FITS binary and ASCII tables; and writing FITS images
  (multi-dimensional arrays).  Higher-level functions allow: reading
  files composed of one or more headers and a single (perhaps
  multidimensional) image or single table; reading tables into
  data frames; generating vectors for image array axes; scaling and
  writing images as 16-bit integers.  Known incompletenesses are
  reading random group extensions, as well as
  complex and array descriptor data types in binary tables.
Systematic fit of hundreds of theoretical univariate distributions to empirical data via maximum likelihood estimation. Fits are reported and summarized by a data.frame, a csv file or a 'shiny' app (here with additional features like visual representation of fits). All output formats provide assessment of goodness-of-fit by the following methods: Kolmogorov-Smirnov test, Shapiro-Wilks test, Anderson-Darling test.
Extends the fitdist() (from 'fitdistrplus') adding the Anderson-Darling ad.test() (from 'ADGofTest') and Kolmogorov Smirnov Test ks.test() inside, trying the distributions from 'stats' package by default and offering a second function which uses mixed distributions to fit, this distributions are split with unsupervised learning, with Mclust() function (from 'mclust').
Wrapper for computing parameters for univariate distributions using MLE. It creates an object that stores d, p, q, r functions as well as parameters and statistics for diagnostics. Currently supports automated fitting from base and actuar packages. A manually fitting distribution fitting function is included to support directly specifying parameters for any distribution from ancillary packages.
An easy package for scraping and processing Australia Rules Football (AFL)
    data. 'fitzRoy' provides a range of functions for accessing publicly available data 
    from 'AFL Tables' <https://afltables.com/afl/afl_index.html>, 'Footy Wire' <https://www.footywire.com> and
    'The Squiggle' <https://squiggle.com.au>. Further functions allow for easy processing, 
    cleaning and transformation of this data into formats that can be used for analysis.
Datasets and code published by the data journalism website 
    'FiveThirtyEight' available at <https://github.com/fivethirtyeight/data>. 
    Note that while we received guidance from editors at 'FiveThirtyEight', this 
    package is not officially published by 'FiveThirtyEight'.
Fixed income mathematics made easy. A rich set of functions 
    that helps with calculations of interest rates and fixed income.
    It has objects that abstract interest rates, compounding factors, day count rules,
    forward rates and term structure of interest rates.
    Many interpolation methods and parametric curve models commonly used by practitioners
    are implemented.
For functions that take and return vectors (or scalars), this package provides 8 algorithms for finding fixed point vectors (vectors for which the inputs and outputs to the function are the same vector). These algorithms include Anderson (1965) acceleration <doi:10.1145/321296.321305>, epsilon extrapolation methods (Wynn 1962 <doi:10.2307/2004051>) and minimal polynomial methods (Cabay and Jackson 1976 <doi:10.1137/0713060>).
Determine and test the fixed-point property in binary mixture data.
  This package was originally developed in the context of detecting mixture of 
  cognitive processing strategies, based on observed response time distributions. 
  The method is explain in more detail by Van Maanen, De Jong, Van Rijn (2014) 
  <doi:10.1371/journal.pone.0106113> and Van Maanen, Couto, Lebreton, (2016) 
  <doi:10.1371/journal.pone.0167377>.
Distribution functions and test for over-representation of short
    distances in the Liland distribution. Simulation functions are included for
    comparison.
An R client for the "fixer.io" currency conversion and exchange 
  rate API. The API requires registration and some features are only available 
  on paid accounts. The full API documentation is available at 
  <https://fixer.io/documentation>.
Fast and user-friendly estimation of econometric models with multiple fixed-effects. Includes ordinary least squares (OLS), generalized linear models (GLM) and the negative binomial.
    The core of the package is based on optimized parallel C++ code, scaling especially well for large data sets. The method to obtain the fixed-effects coefficients is based on Berge (2018) <https://wwwen.uni.lu/content/download/110162/1299525/file/2018_13>.
    Further provides tools to export and view the results of several estimations with intuitive design to cluster the standard-errors.
A set of functions that facilitate basic data manipulation and cleaning for statistical analysis including functions for finding and fixing duplicate rows and columns, missing values, outliers, and special characters in column and row names and functions for checking data consistency, distribution, quality, reliability, and structure.
Several generalized / directional Fixed Sequence Multiple Testing
    Procedures (FSMTPs) are developed for testing a sequence of pre-ordered
    hypotheses while controlling the FWER, FDR and Directional Error (mdFWER).
    All three FWER controlling generalized FSMTPs are designed under arbitrary
    dependence, which allow any number of acceptances. Two FDR controlling
    generalized FSMTPs are respectively designed under arbitrary dependence and
    independence, which allow more but a given number of acceptances. Two mdFWER
    controlling directional FSMTPs are respectively designed under arbitrary
    dependence and independence, which can also make directional decisions based
    on the signs of the test statistics. The main functions for each proposed
    generalized / directional FSMTPs are designed to calculate adjusted p-values
    and critical values, respectively. For users' convenience, the functions also
    provide the output option for printing decision rules.
Generate mock data in R using YAML configuration.
An implementation of the Fizz Buzz algorithm, as defined e.g. in <https://en.wikipedia.org/wiki/Fizz_buzz>. 
    It provides the standard algorithm with 3 replaced by Fizz and 5 replaced by Buzz, with the option of specifying start 
    and end numbers, step size and the numbers being replaced by fizz and buzz, respectively. This package gives 
    interviewers the optional answer of "I use fizzbuzzR::fizzbuzz()" when interviewing rather than having to write an algorithm
    themselves.
This is a fast and flexible implementation of the Kalman
        filter and smoother, which can deal with NAs. It is entirely written in C and relies fully on linear algebra subroutines contained in
        BLAS and LAPACK. Due to the speed of the filter, the fitting of
        high-dimensional linear state space models to large datasets
        becomes possible. This package also contains a plot function
        for the visualization of the state vector and graphical
        diagnostics of the residuals.
Fast and flexible Kalman filtering and smoothing implementation utilizing sequential processing, designed for efficient parameter estimation through maximum likelihood estimation. Sequential processing is a univariate treatment of a multivariate series of observations and can benefit from computational efficiency over traditional Kalman filtering when independence is assumed in the variance of the disturbances of the measurement equation. Sequential processing is described in the textbook of Durbin and Koopman (2001, ISBN:978-0-19-964117-8). 'FKF.SP' was built upon the existing 'FKF' package and is, in general, a faster Kalman filter/smoother.
Implements the method of Hofmeyr, D.P. (2021) <DOI:10.1109/TPAMI.2019.2930501> for fast evaluation of univariate kernel smoothers based on recursive computations.
  Applications to the basic problems of density and regression function estimation are provided, as well as some projection pursuit methods
  for which the objective is based on non-parametric functionals of the projected density, or conditional density of a response given projected
  covariates.
  The package is accompanied by an instructive paper in the Journal of Statistical Software <doi:10.18637/jss.v101.i03>.
Tools and features for "Exploratory Landscape Analysis (ELA)" of
	single-objective continuous optimization problems.
    Those features are able to quantify rather complex properties, such as the
    global structure, separability, etc., of the optimization problems.
Three methods are implemented in R to facilitate the aggregations of flags in official statistics.  
            From the underlying flags the highest in the hierarchy, the most frequent, or with the highest total weight
            is propagated to the flag(s) for EU or other aggregates. Below there are some reference documents for the topic: 
            <https://sdmx.org/wp-content/uploads/CL_OBS_STATUS_v2_1.docx>,
            <https://sdmx.org/wp-content/uploads/CL_CONF_STATUS_1_2_2018.docx>,
            <http://ec.europa.eu/eurostat/data/database/information>,
            <http://www.oecd.org/sdd/33869551.pdf>,
            <https://sdmx.org/wp-content/uploads/CL_OBS_STATUS_implementation_20-10-2014.pdf>.
Implements the fused lasso additive model as proposed in Petersen, A., Witten, D., and Simon, N. (2016). Fused Lasso Additive Model. Journal of Computational and Graphical Statistics, 25(4): 1005-1025.
Efficient implementations of the algorithms in the 
    Almost-Matching-Exactly framework for interpretable matching in causal
    inference. These algorithms match units via a learned, weighted Hamming
    distance that determines which covariates are more important to match on.
    For more information and examples, see the Almost-Matching-Exactly website.
A generative art system for producing tree-like
    images using an L-system to create the structures. The package 
    includes tools for generating the data structures and visualise
    them in a variety of styles.
Provides a variety of original and flexible user-friendly 
    statistical latent variable models for the simultaneous clustering and 
    segmentation of heterogeneous functional data (i.e time series, or more 
    generally longitudinal data, fitted by unsupervised algorithms, including 
    EM algorithms. Functional Latent Data Models for Clustering heterogeneous 
    curves ('FLaMingos') are originally introduced and written in 'Matlab' by
    Faicel Chamroukhi 
    <https://github.com/fchamroukhi?utf8=?&tab=repositories&q=mix&type=public&language=matlab>. 
    The references are mainly the following ones.
    Chamroukhi F. (2010) <https://chamroukhi.com/FChamroukhi-PhD.pdf>.
    Chamroukhi F., Same A., Govaert, G. and Aknin P. (2010) <doi:10.1016/j.neucom.2009.12.023>.
    Chamroukhi F., Same A., Aknin P. and Govaert G. (2011). <doi:10.1109/IJCNN.2011.6033590>.
    Same A., Chamroukhi F., Govaert G. and Aknin, P. (2011) <doi:10.1007/s11634-011-0096-5>.
    Chamroukhi F., and Glotin H. (2012) <doi:10.1109/IJCNN.2012.6252818>.
    Chamroukhi F., Glotin H. and Same A. (2013) <doi:10.1016/j.neucom.2012.10.030>.
    Chamroukhi F. (2015) <https://chamroukhi.com/FChamroukhi-HDR.pdf>.
    Chamroukhi F. and Nguyen H-D. (2019) <doi:10.1002/widm.1298>.
Tools for fluctuations analysis of mutant cells counts. Main reference is A. Mazoyer, R. Drouilhet, S. Despreaux and B. Ycart (2017)  <doi:10.32614/RJ-2017-029>.
Provide the implementation of a family of Lasso variants including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating high dimensional sparse linear model. We adopt the alternating direction method of multipliers and convert the original optimization problem into a sequential L1 penalized least square minimization problem, which can be efficiently solved by linearization algorithm. A multi-stage screening approach is adopted for further acceleration. Besides the sparse linear model estimation, we also provide the extension of these Lasso variants to sparse Gaussian graphical model estimation including TIGER and CLIME using either L1 or adaptive penalty. Missing values can be tolerated for Dantzig selector and CLIME. The computation is memory-optimized using the sparse matrix output. For more information, please refer to <https://www.jmlr.org/papers/volume16/li15a/li15a.pdf>.
Create a flip over style Flash Card with desired data frame for Shiny application.
Fast implementation of hierarchical clustering
Methods for matrix factorization based on Wang and Stephens (2021) 
    <https://jmlr.org/papers/v22/20-589.html>.
Shed light on black box machine learning models by the help
    of model performance, variable importance, global surrogate models,
    ICE profiles, partial dependence (Friedman J. H. (2001)
    <doi:10.1214/aos/1013203451>), accumulated local effects (Apley D. W.
    (2016) <arXiv:1612.08468>), further effects plots, interaction
    strength, and variable contribution breakdown (Gosiewska and Biecek
    (2019) <arxiv:1903.11420>).  All tools are implemented to work with
    case weights and allow for stratified analysis.  Furthermore, multiple
    flashlights can be combined and analyzed together.
Provides functions for creating flashcard decks of terms and 
    definitions. This package creates HTML slides using 'revealjs' that can be 
    viewed in the 'RStudio' viewer or a web browser.  Users can create 
    flashcards from either existing built-in decks or create their own from CSV
    files or vectors of function names.
Contingency Tables are a pain to work with when you want to run regressions.
  This package takes them, flattens them into a long data frame, so you can more easily analyse them!
  As well, you can calculate other related statistics. All of this is done so in a 'tidy' manner,
  so it should tie in nicely with 'tidyverse' series of packages.
Transformations that allow obtaining a flat table from
    reports in text or Excel format that contain data in the form of pivot
    tables. They can be defined for a single report and applied to a set
    of reports.
On import, the XML information is converted to a dataframe that reflects the hierarchical XML structure. Intuitive functions allow to navigate within this transparent XML data structure (without any knowledge of 'XPath'). 'flatXML' also provides tools to extract data from the XML into a flat dataframe that can be used to perform statistical operations. It also supports converting dataframes to XML.
Streamlines the process of updating changelogs (NEWS.md)
    and versioning R packages developed in git repositories.
The main function kcca implements a general framework for
  k-centroids cluster analysis supporting arbitrary distance measures
  and centroid computation. Further cluster methods include hard
  competitive learning, neural gas, and QT clustering. There are
  numerous visualization methods for cluster results (neighborhood
  graphs, convex cluster hulls, barcharts of centroids, ...), and
  bootstrap methods for the analysis of cluster stability.
Allows maximum likelihood fitting of cluster-weighted models, a class of mixtures of regression models with random covariates. 
            Methods are described in Angelo Mazza, Antonio Punzo, Salvatore Ingrassia (2018) <doi:10.18637/jss.v086.i02>.
Format for converting an R Markdown document to a grid
    oriented dashboard. The dashboard flexibly adapts the size of it's
    components to the containing web page.
Provides tools to work with the Flexible Dirichlet
    distribution. The main features are an E-M algorithm for computing the maximum
    likelihood estimate of the parameter vector and a function based on conditional
    bootstrap to estimate its asymptotic variance-covariance matrix. It contains
    also functions to plot graphs, to generate random observations and to handle
    compositional data.
Flexible Dotplot and Pacman plot for multimodal data.
Standard generalized additive models assume a response function, 
    which induces an assumption on the shape of the distribution of the 
    response. However, miss-specifying the response function results in biased 
    estimates. Therefore in Spiegel et al. (2017) 
    <doi:10.1007/s11222-017-9799-6> we propose to estimate the response function
    jointly with the covariate effects. This package provides the underlying 
    functions to estimate these generalized additive models with flexible 
    response functions. The estimation is based on an iterative algorithm. In 
    the outer loop the response function is estimated, while in the inner loop 
    the covariate effects are determined. For the response function a strictly
    monotone P-spline is used while the covariate effects are estimated based on
    a modified Fisher-Scoring algorithm. Overall the estimation relies on the 
    'mgcv'-package.
Provides functions to switch the 'BLAS'/'LAPACK' optimized backend
    and change the number of threads without leaving the R session, which needs
    to be linked against the 'FlexiBLAS' wrapper library
    <https://www.mpi-magdeburg.mpg.de/projects/flexiblas>.
Application of the filtered monotonic polynomial (FMP) item response
    model to flexibly fit item response models. The package includes tools that
    allow the item response model to be build on any monotonic transformation of
    the latent trait metric, as described by Feuerstahler (2019) <doi:10.1007/s11336-018-9642-9>.
A general framework for finite mixtures of regression
  models using the EM algorithm is implemented. The E-step and all
  data handling are provided, while the M-step can be supplied by the
  user to easily define new models. Existing drivers implement
  mixtures of standard linear models, generalized linear models and
  model-based clustering.
The fitting of mixtures of generalized nonlinear models is implemented as an extension of the existing package 'flexmix'.
A general estimation framework for multi-state Markov processes with flexible specification of the transition intensities.
    The log-transition intensities can be specified through Generalised Additive Models which allow for virtually any type of covariate
    effect. Elementary specifications such as time-homogeneous processes and simple parametric forms are also supported. There are 
    no limitations on the type of process one can assume, with both forward and backward transitions allowed and virtually any number
    of states.
Model selection tools and 'selfStart' functions to fit parametric curves in 'nls', 'nlsList' and 'nlme' frameworks.
Binding to the C++ implementation of the flexible polyline
    encoding by HERE <https://github.com/heremaps/flexible-polyline>. The
    flexible polyline encoding is a lossy compressed representation of a list of
    coordinate pairs or coordinate triples. The encoding is achieved by:
    (1) Reducing the decimal digits of each value;
    (2) encoding only the offset from the previous point;
    (3) using variable length for each coordinate delta; and
    (4) using 64 URL-safe characters to display the result.
Functions to fit regression models for bounded continuous and discrete responses. In case of bounded continuous  responses (e.g., proportions and rates), available models are the flexible beta (Migliorati, S., Di Brisco, A. M., Ongaro, A. (2018) <doi:10.1214/17-BA1079>), the variance-inflated beta (Di Brisco, A. M., Migliorati, S., Ongaro, A. (2020) <doi:10.1177/1471082X18821213>), the beta (Ferrari, S.L.P., Cribari-Neto, F. (2004) <doi:10.1080/0266476042000214501>), and their augmented versions to handle the presence of zero/one values (Di Brisco, A. M., Migliorati, S. (2020) <doi:10.1002/sim.8406>) are implemented. In case of bounded discrete responses (e.g., bounded counts, such as the number of successes in n trials),  available models are the flexible beta-binomial (Ascari, R., Migliorati, S. (2021) <doi:10.1002/sim.9005>), the beta-binomial, and the binomial are implemented. Inference is dealt with a Bayesian approach based on the Hamiltonian Monte Carlo (HMC) algorithm (Gelman, A., Carlin, J. B., Stern, H. S., Rubin, D. B. (2014) <doi:10.1201/b16018>). Besides, functions to compute residuals, posterior predictives, goodness of fit measures, convergence diagnostics, and graphical representations are provided.
Package for parametric relative survival analyses. It allows to model non-linear and 
        non-proportional effects and both non proportional and non linear effects, using splines (B-spline and truncated power basis), Weighted Cumulative Index of Exposure effect, with correction model for 
        the life table. Both non proportional and non linear effects are described in 
			Remontet, L. et al. (2007) <doi:10.1002/sim.2656> and 
			Mahboubi, A. et al. (2011) <doi:10.1002/sim.4208>.
An easy way to conduct flexible scan.
    Monte-Carlo method is used to test the spatial clusters given the cases, population, and shapefile.
    A table with formal style and a map with clusters are included in the result report.
    The method can be referenced at: Toshiro Tango and Kunihiko Takahashi (2005) <doi:10.1186/1476-072X-4-11>.
A drop-in replacement for 'flexdashboard' 'Rmd' documents, which
  implements an after-knit-hook to split the generated single page application
  in one document per main section to reduce rendering load in the web browser
  displaying the document. Put all 'JavaScript' stuff needed in all sections 
  before the first headline featuring navigation menu attributes. This package 
  is experimental and maybe replaced by a solution inside 'flexdashboard'.
Flexible parametric models for time-to-event data,
    including the Royston-Parmar spline model, generalized gamma and
    generalized F distributions.  Any user-defined parametric
    distribution can be fitted, given at least an R function defining
    the probability density or hazard. There are also tools for
    fitting and predicting from fully parametric multi-state models,
    based on either cause-specific hazards or mixture models.
Flexible parametric mixture and non-mixture cure models for time-to-event data.
Use a grammar for creating and customizing pretty tables. 
 The following formats are supported: 'HTML', 'PDF', 'RTF', 
 'Microsoft Word', 'Microsoft PowerPoint' and R 'Grid Graphics'. 
 'R Markdown', 'Quarto' and the package 'officer' can be used to produce 
 the result files. The syntax is the same for the user regardless of 
 the type of output to be produced. A set of functions allows the 
 creation, definition of cell arrangement, addition of headers or 
 footers, formatting and definition of cell content with text and 
 or images. The package also offers a set of high-level functions 
 that allow tabular reporting of statistical models and the 
 creation of complex cross tabulations.
Provides an interface to the Flickr API <https://www.flickr.com/services/api/>
      and allows R users to download data on Flickr.
Functions to create and manipulate 
    FIFO (First In First Out), LIFO (Last In First Out), and NINO (Not In or Never Out) 
    stacks in R.
Provides functionality to plot airplane flight paths on maps. The plotted flight paths follow the great circle of the Earth.
Download flight and airport data from Brazil’s Civil Aviation Agency
             (ANAC) <https://www.gov.br/anac>. The data includes detailed 
             information on all aircrafts, aerodromes, airports, and airport 
             movements registered in ANAC, on airfares and on every international
             flight to and from Brazil, as well as domestic flights within the country.
Likelihood-free inference method for stochastic models.
    Uses a deterministic optimizer on simple simulations of the model
    that are performed with a prior drawn randomness by applying the inverse transform method.
    Is designed to work on its own and also by using the Julia package 'Jflimo'
    available on the git page of the project: <https://metabarcoding.org/flimo>.
Given a multivariate dataset and some knowledge about the dependencies 
              between its features, it is customary to fit a statistical model to the features 
              to infer parameters of interest. Such a procedure implicitly assumes that the 
              sample is exchangeable. This package provides a flexible non-parametric test 
              of this exchangeability assumption, allowing the user to specify the feature 
              dependencies by hand as long as features can be grouped into disjoint independent sets. 
              This package also allows users to test a dual hypothesis, which is, given that the 
              sample is exchangeable, does a proposed grouping of the features into disjoint sets
              also produce statistically independent sets of features? See Aw, Spence and Song (2023) 
              for the accompanying paper.
It implements many univariate and multivariate permutation (and
    rotation) tests. Allowed tests: the t one and two samples, ANOVA, linear
    models, Chi Squared test, rank tests (i.e. Wilcoxon, Mann-Whitney,
    Kruskal-Wallis), Sign test and Mc Nemar. Test on Linear Models are
    performed also in presence of covariates (i.e. nuisance parameters).
    The permutation and the rotation methods to get the null distribution of
    the test statistics are available. It also implements methods for
    multiplicity control such as Westfall & Young minP procedure and Closed
    Testing (Marcus, 1976) and k-FWER. Moreover, it allows to test for fixed
    effects in mixed effects models.
Flipbooks present code step-by-step and side-by-side with its output.  'flipbookr' helps creators build flipbooks efficiently because code pipelines are automatically parsed and prepped for presentation as flipbooks.
Allows the user to create a countdown in 'RMarkdown' documents and 'shiny' applications. 
    The package is a wrapper of the 'JavaScript' library 'flipdown.js'. See <https://pbutcher.uk/flipdown/> for more info.
Include a countdown <https://github.com/PButcher/flipdown> in all R contexts with the convenience of 'htmlwidgets'.
A flexible permutation framework for making 
    inference such as point estimation, confidence 
    intervals or hypothesis testing, on any kind of data, 
    be it univariate, multivariate, or more complex such 
    as network-valued data, topological data, functional 
    data or density-valued data.
Provides robust tests for testing in GLMs, by sign-flipping score contributions. The tests are robust against overdispersion, heteroscedasticity and, in some cases, ignored nuisance variables. See Hemerik, Goeman and Finos (2020) <doi:10.1111/rssb.12369>.
Fits the Fused Lasso Latent Feature model, which is used for modeling multi-sample aCGH data to identify regions of copy number variation (CNV).  Produces a set of features that describe the patterns of CNV and a set of weights that describe the composition of each sample.  Also provides functions for choosing the optimal tuning parameters and the appropriate number of features, and for estimating the false discovery rate.
R comes with a suite of utilities for linear algebra with "numeric"
    (double precision) vectors/matrices. However, sometimes single precision (or
    less!) is more than enough for a particular task.  This package extends R's
    linear algebra facilities to include 32-bit float (single precision) data.
    Float vectors/matrices have half the precision of their "numeric"-type
    counterparts but are generally faster to numerically operate on, for a
    performance vs accuracy trade-off.  The internal representation is an S4
    class, which allows us to keep the syntax identical to that of base R's.
    Interaction between floats and base types for binary operators is generally
    possible; in these cases, type promotion always defaults to the higher
    precision.  The package ships with copies of the single precision 'BLAS' and
    'LAPACK', which are automatically built in the event they are not available
    on the system.
Converts files to and from flobs.  A flob is a file that was
    read into binary in integer-mode as little endian, saved as the single
    element of a named list (where the name is the name of the original
    file) and then serialized before being coerced into a blob.  Flobs are
    useful for writing and reading files to and from databases.
Implements synchronization between R processes (spawned by using the "parallel" package for instance) using file locks. Supports both exclusive and shared locking.
Includes several statistical methods for the estimation of parameters and high quantiles of river flow distributions. The focus is on regional estimation based on homogeneity assumptions and computed from multivariate observations (multiple measurement stations).
	For details see Kinsvater et al. (2017) <arXiv:1701.06455>.
Plotting flood quantiles and their corresponding probabilities (return periods) on the probability papers.
    The details of relevant methods are available in Chow et al (1988, ISBN: 007070242X, 9780070702424), and
    Bobee and Ashkar (1991, ISBN: 0918334683, 9780918334688).
Provides an efficient 'C++' code for computing an
 optimal segmentation model
 with Poisson loss,
 up-down constraints,
 and label constraints,
 as described by Kaufman et al. (2022) <arXiv:2210.02580>.
Tools to quickly compile taxonomic and distribution data from
    the Brazilian Flora 2020.
Log-ratio Lasso regression for continuous, binary, and survival outcomes with compositional features. See Fei and others (2023) <doi:10.1101/2023.05.02.538599>.
Visualize as flow diagrams the logic of functions, expressions or 
  scripts in a static way or when running a call, visualize the dependencies between
  functions or between modules in a shiny app, and more.
Provides functionality to perform machine-learning-based modeling in a computation pipeline.
    Its functions contain the basic steps of machine-learning-based knowledge discovery workflows,
    including model training and optimization, model evaluation, and model testing.
    To perform these tasks, the package builds heavily on existing machine-learning packages,
    such as 'caret' <https://github.com/topepo/caret/> and associated packages.
    The package can train multiple models, optimize model hyperparameters by performing a grid search
    or a random search, and evaluates model performance by different metrics.
    Models can be validated either on a test data set, or in case of a small sample size
    by k-fold cross validation or repeated bootstrapping.
    It also allows for 0-Hypotheses generation by performing permutation experiments.
    Additionally, it offers methods of model interpretation and item categorization
    to identify the most informative features from a high dimensional data space.
    The functions of this package can easily be integrated into computation pipelines
    (e.g. 'nextflow' <https://www.nextflow.io/>) and hereby improve scalability,
    standardization, and re-producibility in the context of machine-learning.
This framework allows you to design and implement complex
    pipelines, and deploy them on your institution's computing cluster. This has
    been built keeping in mind the needs of bioinformatics workflows. However, it is
    easily extendable to any field where a series of steps (shell commands) are to
    be executed in a (work)flow.
An application to calculate the daily environmental costs of river flow regulation by dams based on García de Jalon et al. 2017 <doi:10.1007/s11269-017-1663-0>.
Screens daily streamflow time series for temporal trends and
    change-points. This package has been primarily developed for assessing the
    quality of daily streamflow time series. It also contains tools for plotting
    and calculating many different streamflow metrics. The package can be used to
    produce summary screening plots showing change-points and significant temporal
    trends for high flow, low flow, and/or baseflow statistics, or it can be used
    to perform more detailed hydrological time series analyses. The package was
    designed for screening daily streamflow time series from Water Survey Canada
    and the United States Geological Survey but will also work with streamflow time
    series from many other agencies.
Useful functions to standardize software outputs from ProteomeDiscoverer, Spectronaut, DIA-NN and MaxQuant on precursor, modified peptide and proteingroup level and to trace software differences for identifications such as varying proteingroup denotations for common precursor.
Simulation and analysis of Fully-Latent Principal Stratification (FLPS) with measurement models. Sales & Pane (2019). <doi:10.1214/18-AOAS1196>.
Implements a path algorithm for the Fused Lasso Signal Approximator.
    For more details see the help files or the article by Hoefling (2009) <arXiv:0910.0526>.
Specialized solvers for combinatorial optimization problems in the Subset Sum family. The solvers differ from the mainstream in the options of (i) restricting subset size, (ii) bounding subset elements, (iii) mining real-value multisets with predefined subset sum errors, (iv) finding one or more subsets in limited time. A novel algorithm for mining the one-dimensional Subset Sum induced algorithms for the multi-Subset Sum and the multidimensional Subset Sum. The multi-threaded framework for the latter offers exact algorithms to the multidimensional Knapsack and the Generalized Assignment problems. Historical updates include (a) renewed implementation of the multi-Subset Sum, multidimensional Knapsack and Generalized Assignment solvers; (b) availability of bounding solution space in the multidimensional Subset Sum; (c) fundamental data structure and architectural changes for enhanced cache locality and better chance of SIMD vectorization; (d) option of mapping floating-point instance to compressed 64-bit integer instance with user-controlled precision loss, which could yield substantial speedup due to the dimension reduction and efficient compressed integer arithmetic via bit-manipulations; (e) distributed computing infrastructure for multidimensional subset sum; (f) arbitrary-precision zero-margin-of-error multidimensional Subset Sum accelerated by a simplified Bloom filter. The package contains a copy of xxHash from <https://github.com/Cyan4973/xxHash>. Package vignette (<arXiv:1612.04484v3>) detailed a few historical updates. Functions prefixed with 'aux' (auxiliary) are independent implementations of published algorithms for solving optimization problems less relevant to Subset Sum.
Functions to estimate the mortality attributable to 
    influenza and temperature, using distributed-lag nonlinear models
    (DLNMs), as first implemented in 
    Lytras et al. (2019) <doi:10.2807/1560-7917.ES.2019.24.14.1800118>.
    Full descriptions of underlying DLNM methodology in Gasparrini et al. 
    <doi:10.1002/sim.3940> (DLNMs), 
    <doi:10.1186/1471-2288-14-55> (attributable risk from DLNMs) and 
    <doi:10.1002/sim.5471> (multivariate meta-analysis).
Use spectrophotometry measurements performed on insects as a way to infer pathogens 
      virulence. Insect movements cause fluctuations in fluorescence signal, and functions are 
      provided to estimate when the insect has died as the moment when variance in autofluorescence 
      signal drops to zero. The package provides functions to obtain this estimate together with 
      functions to import spectrophotometry data from a Biotek microplate reader. Details of the method 
      are given in Parthuisot et al. (2018) <doi:10.1101/297929>.
A model for leaf fluorescence, reflectance and transmittance spectra. It implements
    the model introduced by Vilfan et al. (2016) <DOI:10.1016/j.rse.2016.09.017>. Fluspect-B
    calculates the emission of ChlF on both the illuminated and shaded side of the leaf.
    Other input parameters are chlorophyll and carotenoid concentrations, leaf water, dry matter 
    and senescent material (brown pigments) content, leaf mesophyll structure parameter and ChlF 
    quantum efficiency for the two photosystems, PS-I and PS-II.
Functions for the calculation of greenhouse gas flux rates 
	from closed chamber concentration measurements. The package follows 
	a modular concept: Fluxes can be calculated in just two simple steps 
	or in several steps if more control in details is wanted. Additionally 
	plot and preparation functions as well as functions for modelling
	gpp and reco are provided.
Compute energy fluxes in trophic networks, from resources to their consumers, and can be applied to systems ranging from simple two-species interactions to highly complex food webs. It implements the approach described in Gauzens et al. (2017) <doi:10.1101/229450> to calculate energy fluxes, which are also used to calculate equilibrium stability.
Functions for range estimation in birds based on Pennycuick (2008)
    and Pennycuick (1975), 'Flight' program which compliments Pennycuick (2008)
    requires manual entry of birds which can be tedious when there are thousands
    of birds to estimate. Implemented are two ODE methods discussed in Pennycuick (1975)
    and time-marching computation method "constant muscle mass" as in Pennycuick (1998).
    See Pennycuick (1975, ISBN:978-0-12-249405-5), Pennycuick (1998) <doi:10.1006/jtbi.1997.0572>,
    and Pennycuick (2008, ISBN:9780080557816).
Functions for range estimation in birds based on Pennycuick (2008)
    and Pennycuick (1975), 'Flight' program which compliments Pennycuick (2008)
    requires manual entry of birds which can be tedious when there are hundreds
    of birds to estimate. Implemented are two ODE methods discussed in Pennycuick (1975)
    and time-marching computation methods as in Pennycuick (1998) and Pennycuick (2008).
    See Pennycuick (1975, ISBN:978-0-12-249405-5), Pennycuick (1998) <doi:10.1006/jtbi.1997.0572>,
    and Pennycuick (2008, ISBN:9780080557816).
All data sets from "Forecasting: methods and applications" by Makridakis, Wheelwright & Hyndman (Wiley, 3rd ed., 1998) <https://robjhyndman.com/forecasting/>.
Creation of an input model (fitted distribution) via the frequentist model averaging (FMA) approach and generate random-variates from the distribution specified by "myfit" which is the fitted input model via the FMA approach. See W. X. Jiang and B. L. Nelson (2018), "Better Input Modeling via Model Averaging," Proceedings of the 2018 Winter Simulation Conference, IEEE Press, 1575-1586.
The Fill-Mask Association Test ('FMAT') is an integrative, versatile,
    and probability-based method that uses Masked Language Models
    to measure conceptual associations or relations
    (e.g., attitudes, biases, stereotypes, social norms, cultural values)
    as propositional representations in natural language.
    The supported language models include
    'BERT' (Devlin et al., 2018) <arXiv:1810.04805>
    and its model variants available at 'Hugging Face'
    <https://huggingface.co/models?pipeline_tag=fill-mask>.
    'Python' ('conda') environment and the 'transformers' module can be
    installed automatically using the FMAT_load() function.
    Methodological references and technical details are provided at
    <https://psychbruce.github.io/FMAT/>.
Implements basic financial market objects like currencies, currency
  pairs, interest rates and interest rate indices. You will be able to use
  Benchmark instances of these objects which have been defined using their most
  common conventions or those defined by International Swap Dealer Association
  (ISDA, <https://www.isda.org>) legal documentation.
Generate cost effective minimally changed run sequences 
              for symmetrical as well as asymmetrical factorial 
              designs.
Current status data abounds
            in the field of epidemiology and public health, where the only observable data for a subject is
            the random inspection time and the event status at inspection. Motivated by such a current status
            data from a periodontal study where data are inherently clustered,
            we propose a unified methodology to analyze such complex data.
Provides a friendly (flexible) Markov Chain Monte Carlo (MCMC)
         framework for implementing Metropolis-Hastings algorithm in a modular way
         allowing users to specify automatic convergence checker, personalized
         transition kernels, and out-of-the-box multiple MCMC chains using
         parallel computing. Most of the methods implemented in this package can
         be found in Brooks et al. (2011, ISBN 9781420079425). Among the methods
         included, we have: Haario (2001) <doi:10.1007/s11222-011-9269-5>
         Adaptive Metropolis, Vihola (2012) <doi:10.1007/s11222-011-9269-5>
         Robust Adaptive Metropolis, and Thawornwattana et
         al. (2018) <doi:10.1214/17-BA1084> Mirror transition kernels.
Implements common date calculations relevant for specifying
  the economic nature of financial market contracts that are typically defined
  by International Swap Dealer Association (ISDA, <http://www2.isda.org>) legal
  documentation. This includes methods to check whether dates are business
  days in certain locales, functions to adjust and shift dates and time length
  (or day counter) calculations.
Provides functions to help in fitting models to data, to
  perform Monte Carlo, sensitivity and identifiability analysis. It is
  intended to work with models be written as a set of differential
  equations that are solved either by an integration routine from
  package 'deSolve', or a steady-state solver from package
  'rootSolve'. However, the methods can also be used with other types of
  functions.
Create local, regional, and global explanations for any machine learning model with forward marginal effects. You provide a model and data, and 'fmeffects' computes feature effects. The package is based on the theory in: C. A. Scholbeck, G. Casalicchio, C. Molnar, B. Bischl, and C. Heumann (2022) <arXiv:2201.08837>.
Heterogeneity pursuit methodologies for regularized finite mixture regression by effects-model formulation proposed by Li et al. (2021) <arXiv:2003.04787>.
Generate planar and spherical triangle meshes,
    compute finite element calculations for 1- and 2-dimensional flat and curved
    manifolds with associated basis function spaces, methods for lines and
    polygons, and transparent handling of coordinate reference systems and
    coordinate transformation, including 'sf' and 'sp' geometries. The core
    'fmesher' library code was originally part of the 'INLA' package, and
    implements parts of "Triangulations and Applications" by
    Hjelle and Daehlen (2006) <doi:10.1007/3-540-33261-8>.
A fast class noise detector which provides noise score for each observations. The package takes advantage of 'RcppArmadillo' to speed up the calculation of distances between observations.
Provides a collection of functions to fit and explore single, multi-component and restricted Frequency Modulated Moebius (FMM) models. 'FMM' is a nonlinear parametric regression model capable of fitting non-sinusoidal shapes in rhythmic patterns. Details about the mathematical formulation of 'FMM' models can be found in Rueda et al. (2019) <doi:10.1038/s41598-019-54569-1>.
Estimates Filtered Monotonic Polynomial IRT Models as described by Liang and Browne (2015) <DOI:10.3102/1076998614556816>.
Use R to access to the 'FMP Cloud' API <https://fmpcloud.io/> and 
    'Financial Modeling Prep' API <https://financialmodelingprep.com/developer/docs/>.
    Data available includes stock prices, market indexes, company fundamentals,
    13F holdings data, and much more. A valid API token must be set to enable
    functions.
Functions that support stable prediction and classification with radiomics data through factor-analytic modeling. For details, see Peeters et al. (2019) <arXiv:1903.11696>.
Contains R-functions to perform an fMRI analysis as described in
             Polzehl and Tabelow (2019) <DOI:10.1007/978-3-030-29184-6>,
             Tabelow et al. (2006) <DOI:10.1016/j.neuroimage.2006.06.029>,
             Polzehl et al. (2010) <DOI:10.1016/j.neuroimage.2010.04.241>,
             Tabelow and Polzehl (2011) <DOI:10.18637/jss.v044.i11>.
Methods for performing fMRI quality assurance (QA) measurements of
  test objects. Heavily  based on the fBIRN procedures detailed by Friedman and 
  Glover (2006) <doi:10.1002/jmri.20583>.
Data-driven fMRI denoising with projection scrubbing (Pham et al 
    (2022) <doi:10.1016/j.neuroimage.2023.119972>). Also includes routines for 
    DVARS (Derivatives VARianceS) (Afyouni and Nichols (2018) 
    <doi:10.1016/j.neuroimage.2017.12.098>), motion scrubbing (Power et al 
    (2012) <doi:10.1016/j.neuroimage.2011.10.018>), aCompCor (anatomical 
    Components Correction) (Muschelli et al (2014)
    <doi:10.1016/j.neuroimage.2014.03.028>), detrending, and nuisance
    regression. Projection scrubbing is also applicable to other
    outlier detection tasks involving high-dimensional data.
Supports fMRI (functional magnetic resonance imaging) 
    analysis tasks including reading in 'CIFTI', 'GIFTI' and 
    'NIFTI' data, temporal filtering, nuisance regression, and 
    aCompCor (anatomical Components Correction) (Muschelli et al.
    (2014) <doi:10.1016/j.neuroimage.2014.03.028>).
Several utility functions for the book entitled 
	"Practices of Medical and Health Data Analysis using R"
	(Pearson Education Japan, 2007) with Japanese demographic
	data and some demographic analysis related functions.
Fit linear regression models where the random errors follow a finite mixture of of Skew Heavy-Tailed Errors.
Some basic procedures for dealing
        with log maximally skew stable distributions, which are also
        called finite moment log stable distributions.
The FMT method computes posterior residual variances to be used in
  the denominator of a moderated t-statistic from a linear model analysis of
  gene expression data. It is an extension of the moderated t-statistic
  originally proposed by Smyth (2004) <doi:10.2202/1544-6115.1027>.
  LOESS local regression and empirical Bayesian method are used to estimate
  gene specific prior degrees of freedom and prior variance based on average
  gene intensity levels. The posterior residual variance in the denominator is
  a weighted average of prior and residual variance and the weights are prior
  degrees of freedom and residual variance degrees of freedom. The degrees of
  freedom of the moderated t-statistic is simply the sum of prior and residual
  variance degrees of freedom.
Contains a set of functions that can be used to apply
  formats to data frames or vectors.  The package aims to provide to 
  functionality similar to that of SAS® formats. Formats are assigned to
  the format attribute on data frame columns.  Then when the fdata() 
  function is called, a new data frame is created with the column data
  formatted as specified.  The package also contains a value() function
  to create a user-defined format, similar to a SAS® user-defined format.
A collection of functions inspired by Venables and Ripley (2002) <doi:10.1007/978-0-387-21706-2>
             and Azzalini and Capitanio (1999) <arXiv:0911.2093> to manage, investigate and analyze
             bivariate and multivariate data sets of financial returns.
Implements methods for network estimation and forecasting of high-dimensional time series 
    exhibiting strong serial and cross-sectional correlations under a factor-adjusted vector autoregressive model.
    See Barigozzi, Cho and Owens (2022) <arXiv:2201.06110> for further descriptions of FNETS methodology and 
    Owens, Cho and Barigozzi (2023) <arXiv:2301.11675> accompanying the R package.
Cover-tree and kd-tree fast k-nearest neighbor search algorithms and related applications
        including KNN classification, regression and information measures are implemented.
Provides a collection of functions for testing various aspects of
	univariate time series including independence and neglected
	nonlinearities. Further provides functions to investigate the chaotic
	behavior of time series processes and to simulate different types of chaotic
	time series maps.
Feature Ordering by Conditional Independence (FOCI) is a variable selection algorithm based on the measure of conditional dependence.
    For more information, see the paper: Azadkia and Chatterjee (2019),"A simple measure of conditional dependence" <arXiv:1910.12327>.
Takes a distance matrix and plots it as an 
    interactive graph. One point is focused at the center of the graph,
    around which all other points are plotted in their exact distances as
    given in the distance matrix. All other non-focus points are plotted 
    as best as possible in relation to one another. Double click on any 
    point to choose a new focus point, and hover over points to see their
    ID labels. If color label categories are given, hover over colors in 
    the legend to highlight only those points and click on colors to 
    highlight multiple groups. For more information on the rationale 
    and mathematical background, as well as an interactive introduction,
    see <https://lea-urpa.github.io/focusedMDS.html>.
The CRAN check results and where your package stands in the
    CRAN submission queue in your R terminal.
Supports the use of standardized folder names.
Datasets for teaching quantitative approaches and
    modeling in archaeology and paleontology. This package provides
    several types of data related to broad topics (cultural evolution,
    radiocarbon dating, paleoenvironments, etc.), which can be used to
    illustrate statistical methods in the classroom (multivariate data
    analysis, compositional data analysis, diversity measurement, etc.).
Extend 'shiny.semantic' with extra 'Fomantic UI' components.
    Create pages in a format similar to 'shiny', form validation and more.
Easily and flexibly insert 'Font Awesome' icons into 'R Markdown'
    documents and 'Shiny' apps. These icons can be inserted into HTML content
    through inline 'SVG' tags or 'i' tags. There is also a utility function for
    exporting 'Font Awesome' icons as 'PNG' images for those situations where
    raster graphics are needed.
Provides fonts licensed under the 'Bitstream Vera Fonts'
    license for the 'fontquiver' package.
Computer Modern font for use with extrafont package
A placeholder for the Liberation fontset intended for the
    `fontquiver` package. This fontset covers the 12 combinations of
    families (sans, serif, mono) and faces (plain, bold, italic, bold
    italic) supported in R graphics devices.
Provides a set of fonts with permissive licences. This is
    useful when you want to avoid system fonts to make sure your
    outputs are reproducible.
Displays a weighted undirected food graph from an adjacency matrix.
    Can perform confidence-interval bootstrap inference with mutual information
    or maximal information coefficient.
    Based on my Master 1 internship at the Bordeaux Population Health center.
    References : Reshef et al. (2011) <doi:10.1126/science.1205438>,
    Meyer et al. (2008) <doi:10.1186/1471-2105-9-461>,
    Liu et al. (2016) <doi:10.1371/journal.pone.0158247>.
Aids in analysing data from a food frequency questionnaire known as 
    the Harvard Service Food Frequency Questionnaire (HSFFQ).
    Functions from this package use answers from the HSFFQ to generate 
    estimates of daily consumed micronutrients, calories, macronutrients on 
    an individual level.
    The package also calculates food quotients on individual and group levels. 
    Foodquotient calculation is an often tedious step in the calculation of 
    total human energy expenditure (TEE) using the doubly labeled water method, 
    which is the gold standard for measuring TEE.
Enhances the functionality of the mvbutils::foodweb() program. The matrix-format output of the original program contains identical row names and column names, each name representing a retrieved function. This format is enhanced by using the find_funs() program [see Sebastian (2017) <https://sebastiansauer.github.io/finds_funs/>] to concatenate the package name to the function name. Each package is assigned a unique color, that is used to color code the text naming the packages and the functions. This color coding is extended to the entries of value "1" within the matrix, indicating the pattern of ancestor and descendent functions.
Provides functionality for manipulating functions and translating them
    in metaprogramming.
Basic analysis of all penalties taken in the German men's Bundesliga
  between the start of its inaugural season and May 2017. The main functions are
  suitable printing and plotting functions. Flexible selection of a player is
  supported via grep. Missed penalties can easily be included or excluded, depending
  on the user's wishes.
This is the first package allowing for the estimation,
             visualization and prediction of the most well-known 
             football models: double Poisson, bivariate Poisson,
             Skellam, student_t, diagonal-inflated bivariate Poisson, and
             zero-inflated Skellam. The package allows Hamiltonian
             Monte Carlo (HMC) estimation through the underlying Stan
             environment and Maximum Likelihood estimation (MLE, for 
             'static' models only). The model construction relies on
             the most well-known football references, such as 
             Dixon and Coles (1997) <doi:10.1111/1467-9876.00065>,
             Karlis and Ntzoufras (2003) <doi:10.1111/1467-9884.00366> and
             Egidi, Pauli and Torelli (2018) <doi:10.1177/1471082X18798414>.
A handy tool to calculate carbon footprints from
    air travel based on three-letter International Air Transport Association (IATA) airport codes or latitude and longitude.
    footprint first calculates the great-circle distance between departure and arrival 
    destinations. It then uses the Department of Environment, Food & Rural Affairs (DEFRA) 
    greenhouse gas conversion factors for business air travel to estimate the carbon footprint.
    These conversion factors consider trip length, flight class (e.g. economy, business), and emissions 
    metric (e.g. carbon dioxide equivalent, methane).
Tools for quickly processing and analyzing 
	field observation data and air quality data. This 
	tools contain functions that facilitate analysis 
	in atmospheric chemistry (especially in ozone 
	pollution). Some functions of time series are also 
	applicable to other fields. For detail please view 
	homepage<https://github.com/tianshu129/foqat>.
	Scientific Reference:
	1. The Hydroxyl Radical (OH) Reactivity: Roger Atkinson and Janet Arey (2003) <doi:10.1021/cr0206420>.
	2. Ozone Formation Potential (OFP): <http://ww2.arb.ca.gov/sites/default/files/barcu/regact/2009/mir2009/mir10.pdf>, Zhang et al.(2021) <doi:10.5194/acp-21-11053-2021>.
	3. Aerosol Formation Potential (AFP): Wenjing Wu et al. (2016) <doi:10.1016/j.jes.2016.03.025>.
	4. TUV model: <https://www2.acom.ucar.edu/modeling/tropospheric-ultraviolet-and-visible-tuv-radiation-model>.
Several functions to compute indicators for organization and efficiency in visual foraging, multi-target visual search, and cancellation tasks. The current version of this package includes the following indicators: best-r, mean Inter-target Distance, Percentage Above Optimal (PAO) scan path, and intersections in the scan path. For more detailed descriptions, see Mark et al. (2004) <doi:10.1212/01.WNL.0000131947.08670.D4>.
SHE, FORAM Index and ABC Method analyses and custom plot
        functions for community data.
Helpers for reordering factor levels (including moving
    specified levels to front, ordering by first appearance, reversing,
    and randomly shuffling), and tools for modifying factor levels
    (including collapsing rare levels into other, 'anonymising', and
    manually 'recoding').
For cleaning and analysis of graphs, such as animal closing force 
    measurements. 
    'forceR' was initially written and optimized to deal with insect bite force 
    measurements, but can be used for any time series. Includes a full workflow 
    to load, plot and crop data, correct amplifier and baseline drifts, 
    identify individual peak shapes (bites), rescale (normalize) peak curves, 
    and find best polynomial fits to describe and analyze force curve shapes.
Support for the foreach looping construct.  Foreach is an
        idiom that allows for iterating over elements in a collection,
        without the use of an explicit loop counter.  This package in
        particular is intended to be used for its return value, rather
        than for its side effects.  In that sense, it is similar to the
        standard lapply function, but doesn't require the evaluation
        of a function.  Using foreach without side effects also
        facilitates executing the loop in parallel.
Implementation of Forecastable Component Analysis ('ForeCA'),
    including main algorithms and auxiliary function (summary, plotting, etc.) to
    apply 'ForeCA' to multivariate time series data. 'ForeCA' is a novel dimension
    reduction (DR) technique for temporally dependent signals. Contrary to other
    popular DR methods, such as 'PCA' or 'ICA', 'ForeCA' takes time dependency
    explicitly into account and searches for the most ''forecastable'' signal.
    The measure of forecastability is based on the Shannon entropy of the spectral
    density of the transformed signal.
Methods and tools for displaying and analysing
             univariate time series forecasts including exponential smoothing
             via state space models and automatic ARIMA modelling.
Provides geometric- and regression-based forecast
    combination methods under a unified user interface for the packages 'ForecastCombinations'
    and 'GeomComb'. Additionally, updated tools and convenience functions for data pre-processing are available in order to deal with 
    common problems in forecast combination (missingness, collinearity). For method details see Hsiao C, Wan SK (2014). <doi:10.1016/j.jeconom.2013.11.003>, Hansen BE (2007). <doi:10.1111/j.1468-0262.2007.00785.x>,
    Elliott G, Gargano A, Timmermann A (2013). <doi:10.1016/j.jeconom.2013.04.017>, 
    and Clemen RT (1989). <doi:10.1016/0169-2070(89)90012-5>.
Aim: Supports the most frequently used methods to combine forecasts. Among others: Simple average, Ordinary Least Squares, Least Absolute Deviation, Constrained Least Squares, Variance-based, Best Individual model, Complete subset regressions and Information-theoretic (information criteria based).
A web application for displaying, analysing and forecasting univariate time series. Includes basic methods such as mean, naïve, seasonal naïve and drift, as well as more complex methods such as Holt-Winters Box,G and Jenkins, G (1976) <doi:10.1111/jtsa.12194> and ARIMA Brockwell, P.J. and R.A.Davis (1991) <doi:10.1007/978-1-4419-0320-4>.
Convenient functions for ensemble forecasts in R combining
    approaches from the 'forecast' package. Forecasts generated from auto.arima(), ets(),
    thetaf(), nnetar(), stlm(), tbats(), and snaive() can be combined with equal weights, weights
    based on in-sample errors (introduced by Bates & Granger (1969) <doi:10.1057/jors.1969.103>),
    or cross-validated weights. Cross validation for time series data with user-supplied models
    and forecasting functions is also supported to evaluate model accuracy.
Implementation to perform forecasting of locally stationary wavelet processes by examining the local second order structure of the time series.
The purpose of 'forecastML' is to simplify the process of multi-step-ahead forecasting with standard machine learning algorithms. 'forecastML' supports lagged, dynamic, static, and grouping features for modeling single and grouped numeric or factor/sequence time series. In addition, simple wrapper functions are used to support model-building with most R packages. This approach to forecasting is inspired by Bergmeir, Hyndman, and Koo's (2018) paper "A note on the validity of cross-validation for evaluating autoregressive time series prediction" <doi:10.1016/j.csda.2017.11.003>.
Methods to compute linear h-step ahead prediction coefficients based
    on localised and iterated Yule-Walker estimates and empirical mean squared
    and absolute prediction errors for the resulting predictors. Also, functions
    to compute autocovariances for AR(p) processes, to simulate tvARMA(p,q) time
    series, and to verify an assumption from Kley et al. (2019), Electronic of Statistics,
    forthcoming. Preprint <arXiv:1611.04460>.
Provides a test bench for the comparison of forecasting
    methods in uni-variate time series. Forecasting methods are compared using 
    different error metrics. Proposed forecasting methods and alternative error 
    metrics can be used. Detailed discussion is provided in the vignette.
Classical (bottom-up and top-down), optimal and heuristic combination forecast 
    point (Di Fonzo and Girolimetto, 2023) <doi:10.1016/j.ijforecast.2021.08.004> and 
    probabilistic (Girolimetto et al. 2023) <arXiv:2303.17277> reconciliation procedures 
    for cross-sectional, temporal, and cross-temporal linearly constrained time series.
Offers a set of tools for visualizing and analyzing size and power properties of the test for equal predictive accuracy, the Diebold-Mariano test that is based on heteroskedasticity and autocorrelation-robust (HAR) inference. A typical HAR inference is involved with non-parametric estimation of the long-run variance, and one of its tuning parameters, the truncation parameter, trades off a size and power. Lazarus, Lewis, and Stock (2021)<doi:10.3982/ECTA15404> theoretically characterize the size-power frontier for the Gaussian multivariate location model. 'ForeComp' computes and visualizes the finite-sample size-power frontier of the Diebold-Mariano test based on fixed-b asymptotics together with the Bartlett kernel. To compute the finite-sample size and power, it works with the best approximating ARMA process to the given dataset. It informs the user how their choice of the truncation parameter performs and how robust the testing outcomes are.
Routines for forecasting univariate time series using Theta Models.
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.
The 'forensIT' package is a comprehensive statistical toolkit tailored for handling missing person cases. By leveraging information theory metrics, it enables accurate assessment of kinship, particularly when limited genetic evidence is available. With a focus on optimizing statistical power, 'forensIT' empowers investigators to effectively prioritize family members, enhancing the reliability and efficiency of missing person investigations.
Include assessing site classes based on the stand height growth and establishing a nonlinear mixed-effect biomass model under different site classes based on the whole stand model to achieve more accurate estimation of carbon sequestration. In particular, a carbon sequestration potential productivity calculation method based on the potential mean annual increment is proposed. This package is applicable to both natural forests and plantations. It can quantitatively assess stand’s potential productivity, realized productivity, and possible improvement under certain site, and can be used in many aspects such as site quality assessment, tree species suitability evaluation, and forest degradation evaluation. Reference: Lei X, Fu L, Li H, et al (2018) <doi:10.11707/j.1001-7488.20181213>. Fu L, Sharma R P, Zhu G, et al (2017) <doi:10.3390/f8040119>.
Approximate false positive rate control in selection frequency for
    random forest using the methods described by Ender Konukoglu and Melanie Ganz (2014) <arXiv:1410.2838>.
    Methods for calculating the selection frequency threshold at false positive rates
    and selection frequency false positive rate feature selection.
Supervised, multivariate, and non-parametric discretization algorithm based on tree ensembles learning and moment matching optimization. This version of the algorithm relies on random forest algorithm to learn a large set of split points that conserves the relationship between attributes and the target class, and on moment matching optimization to transform this set into a reduced number of cut points matching as well as possible statistical properties of the initial set of split points. For each attribute to be discretized, the set S of its related split points extracted through random forest is mapped to a reduced set C of cut points of size k. This mapping relies on minimizing, for each continuous attribute to be discretized, the distance between the four first moments of S and the four first moments of C subject to some constraints. This non-linear optimization problem is performed using k values ranging from 2 to 'max_splits', and the best solution returned correspond to the value k which optimum solution is the lowest one over the different realizations. ForestDisc is a generalization of RFDisc discretization method initially proposed by Berrado and Runger (2009) <doi:10.1109/AICCSA.2009.5069327>, and improved by Berrado et al. in 2012 by adopting the idea of moment matching optimization related by Hoyland and Wallace (2001) <doi: 10.1287/mnsc.47.2.295.9834>.
Code for fitting and assessing models for the growth of trees. In 
    particular for the Bayesian neighborhood competition linear regression model 
    of Allen (2020): methods for model fitting and generating fitted/predicted 
    values, evaluating the effect of competitor species identity using 
    permutation tests, and evaluating model performance using spatial 
    cross-validation.
Estimates the conditional error distributions of random forest
    predictions and common parameters of those distributions, including
    conditional misclassification rates, conditional mean squared prediction
    errors, conditional biases, and conditional quantiles, by out-of-bag
    weighting of out-of-bag prediction errors as proposed by Lu and Hardin
    (2021). This package is compatible with several existing packages that
    implement random forests in R.
Developed for the following tasks. 1 ) Computing the probability density function,
             cumulative distribution function, random generation, and estimating the parameters
 			 of the eleven mixture models. 2 ) Point estimation of the parameters of two - 
			 parameter Weibull distribution using twelve methods and three - parameter Weibull 
			 distribution using nine methods. 3 ) The Bayesian inference for the three - 
			 parameter Weibull distribution. 4 ) Estimating parameters of the three - parameter
			 Birnbaum - Saunders, generalized exponential, and Weibull distributions fitted to
			 grouped data using three methods including approximated maximum likelihood, 
			 expectation maximization, and maximum likelihood. 5 ) Estimating the parameters
			 of the gamma, log-normal, and Weibull mixture models fitted to the grouped data
			 through the EM algorithm, 6 ) Estimating parameters of the nonlinear height curve
			 fitted to the height - diameter observation, 7 ) Estimating parameters, computing
			 probability density function, cumulative distribution function, and generating
			 realizations from gamma shape mixture model introduced by Venturini et al. (2008)
			 <doi:10.1214/07-AOAS156> , 8 ) The Bayesian inference, computing probability
			 density function, cumulative distribution function, and generating realizations
			 from four-parameter Johnson SB distribution, 9 ) Robust multiple linear regression
			 analysis when error term follows skewed t distribution, 10 ) Estimating 
			 parameters of a given distribution fitted to grouped data using method of maximum
			 likelihood, and 11 ) Estimating parameters of the Johnson SB distribution through 
			 the Bayesian, method of moment, conditional maximum likelihood, and two - percentile 
			 method.
Set of tools for detecting and analyzing Airborne Laser Scanning-derived Tropical Forest Canopy Gaps. Details were published in Silva and others (2019) <doi:10.1111/2041-210X.13211>.
Assessing forest ecosystem health is an effective way for forest
    resource management.The national forest health evaluation system at the forest 
    stand level using analytic hierarchy process, has a high application value 
    and practical significance. The package can effectively and easily realize the 
    total assessment process, and help foresters to further assess and management 
    forest resources.
Extensive global and small-area estimation procedures for multiphase
    forest inventories under the design-based Monte-Carlo approach are provided.
    The implementation has been published in the Journal of Statistical Software (<doi:10.18637/jss.v097.i04>) 
    and includes estimators for simple and cluster sampling
    published by Daniel Mandallaz in 2007 (<doi:10.1201/9781584889779>),
    2013 (<doi:10.1139/cjfr-2012-0381>, <doi:10.1139/cjfr-2013-0181>,
    <doi:10.1139/cjfr-2013-0449>, <doi:10.3929/ethz-a-009990020>)
    and 2016 (<doi:10.3929/ethz-a-010579388>). It provides point estimates,
    their external- and design-based variances and confidence intervals, as well as a
    set of functions to analyze and visualize the produced estimates.
    The procedures have also been optimized for the use of remote sensing data
    as auxiliary information, as demonstrated in 2018 by Hill et al. (<doi:10.3390/rs10071052>).
Interactive forest plot for clinical trial safety analysis
    using 'metalite', 'reactable', 'plotly', and Analysis Data Model (ADaM)
    datasets. Includes functionality for adverse event filtering,
    incidence-based group filtering, hover-over reveals, and search and sort
    operations. The workflow allows for metadata construction, data preparation,
    output formatting, and interactive plot generation.
Processing forest inventory data with methods such as simple random sampling, stratified random sampling and systematic sampling. There are also functions for yield and growth predictions and model fitting, linear and nonlinear grouped data fitting, and statistical tests. References: Kershaw Jr., Ducey, Beers and Husch (2016). <doi:10.1002/9781118902028>.
Produces forest plots using 'ggplot2' from models produced by functions
    such as stats::lm(), stats::glm() and survival::coxph().
A forest plot that allows for
    multiple confidence intervals per row,
    custom fonts for each text element,
    custom confidence intervals,
    text mixed with expressions, and more.
    The aim is to extend the use of forest plots beyond meta-analyses.
    This is a more general version of the original 'rmeta' package's forestplot()
    function and relies heavily on the 'grid' package.
Create forest plot based on the layout of the data. Confidence interval in multiple columns by groups can be done easily. Editing plot, inserting/adding text, applying theme to the plot and much more.
Provides a toolkit for calculating forest and canopy structural complexity metrics from
    terrestrial LiDAR (light detection and ranging). References:  Atkins et al. 2018 <doi:10.1111/2041-210X.13061>; Hardiman et al. 2013 <doi:10.3390/f4030537>;
    Parker et al. 2004 <doi:10.1111/j.0021-8901.2004.00925.x>.
Provides functions that calculates common types of splitting
    criteria used in random forests for classification problems, as well as 
    functions that make predictions based on a single tree or a Forest-R.K. model; 
    the package also provides functions to generate importance plot for a 
    Forest-R.K. model, as well as the 2D multidimensional-scaling plot of 
    data points that are colour coded by their predicted class types by the 
    Forest-R.K. model. This package is based on: 
    Bernard, S., Heutte, L., Adam, S., (2008, ISBN:978-3-540-85983-3) 
    "Forest-R.K.: A New Random Forest Induction Method", 
    Fourth International Conference on Intelligent Computing,
    September 2008, Shanghai, China, pp.430-437.
A series of utility functions to help with 
    reshaping hierarchy of data tree, and reform the structure of data tree.
Tools for analyzing remote sensing forest data, including functions for detecting treetops from canopy models, outlining tree crowns, and calculating textural metrics.
Project Customer Retention based on Beta Geometric, Beta Discrete Weibull and Latent Class 
    Discrete Weibull Models.This package is based on Fader and Hardie (2007) 
    <doi:10.1002/dir.20074> and Fader and Hardie et al. (2018) <doi:10.1016/j.intmar.2018.01.002>.
Helper functions with a consistent interface to coerce and verify
    the types and shapes of values for input checking.
The goal of this collection of functions is to provide an easy to use tool for the measurement of foraminifera and other unicellulars organisms size. With functions developed to guide foraminiferal test biovolume calculations and cell biomass estimations. The volume function includes several microalgae models geometric adaptations based on Hillebrand et al. (1999) <doi:10.1046/j.1529-8817.1999.3520403.x>, Sun and Liu (2003) <doi:10.1093/plankt/fbg096> and Vadrucci, Cabrini and Basset (2007) <doi:10.1285/i1825229Xv1n2p83>.
Tabacchi et al. (2011) published a very detailed study producing a uniform system of functions to estimate tree volume and
    phytomass components (stem, branches, stool). The estimates of the 2005 Italian forest inventory (<https://www.inventarioforestale.org/it/>) 
    are based on these functions. The study documents the domain of applicability of each function and the equations to quantify estimates
    accuracies for individual estimates as well as for aggregated estimates. This package makes the functions available in the R environment. 
    Version 2 exposes two distinct functions for individual and summary estimates. To facilitate access to the functions, tree species 
    identification is now based on EPPO species codes (<https://data.eppo.int/>).
Format BibTeX entries and files in an opinionated way.
Provides a small set of tools for formatting tasks when creating 
    documents in R Markdown or Quarto Markdown. Convert the elements of a 
    numerical vector to character strings in one of several forms: powers-of-ten 
    notation in engineering or scientific form delimited for rendering as inline 
    equations; integer or decimal notation delimited for equation rendering; 
    numbers with measurement units (non-delimited) where units are selected to 
    eliminate the need for powers-of-ten or scientific notation. Useful for 
    rendering a numerical scalar in an inline R code chunk as well as formatting 
    columns of data frames displayed in a table.
Provides a function tidy_source() to format R source code. Spaces
    and indent will be added to the code automatically, and comments will be
    preserved under certain conditions, so that R code will be more
    human-readable and tidy. There is also a Shiny app as a user interface in
    this package (see tidy_app()).
Provides functions to create formattable vectors and data frames.
    'Formattable' vectors are printed with text formatting, and formattable
    data frames are printed with multiple types of formatting in HTML
    to improve the readability of data presented in tabular form rendered in
    web pages.
We provide a framework for rendering complex tables to ASCII,
    and a set of formatters for transforming values or sets of values into
    ASCII-ready display strings.
'Shiny' apps can often make use of the same key elements, this package provides modules for common tasks (data upload, wrangling data, figure generation and saving the app state). These modules can react and interact as well as generate code to create reproducible analyses.
Provides analytics directly from 'R'. It requires:
    'FormShare App': <https://github.com/qlands/FormShare >= 2.22.0> .
    Analytics plugin: <https://github.com/qlands/formshare_analytics_plugin> .
    Remote SQL plugin: <https://github.com/qlands/formshare_sql_plugin> .
Infrastructure for extended formulas with multiple parts on the
             right-hand side and/or multiple responses on the left-hand side
	     (see <doi:10.18637/jss.v034.i01>).
These utilities facilitate the programmatic manipulations of
    formulas, expressions, calls, assignments and other R language objects. 
    These objects all share the same structure: a left-hand side, operator and 
    right-hand side. This packages provides methods for accessing and 
    modifying this structures as well as extracting and replacing names and 
    symbols from these objects.
Many statistical models and analyses in R are implemented through formula objects. The formulaic package creates a unified approach for programmatically and dynamically generating formula objects. Users may specify the outcome and inputs of a model directly, search for variables to include based upon naming patterns, incorporate interactions, and identify variables to exclude. A wide range of quality checks are implemented to identify issues such as misspecified variables, duplication, a lack of contrast in the inputs, and a large number of levels in categorical data.  Variables that do not meet these quality checks can be automatically excluded from the model.  These issues are documented and reported in a manner that provides greater accountability and useful information to guide an investigation of the data.
Perform mathematical operations on R formula (add, subtract, multiply, etc.) and substitute parts of formula.
Simplifies the creation and customization of forest plots (alternatively called dot-and-whisker plots). Input classes accepted by 'forplo' are data.frame, matrix, lm, glm, and coxph. 'forplo' was written in base R and does not depend on other packages.
Forensic applications of pedigree analysis, including
    likelihood ratios for relationship testing, general relatedness
    inference, marker simulation, and power analysis. General computation
    of exclusion powers is based on Egeland et al. (2014)
    <doi:10.1016/j.fsigen.2013.05.001>. Several functions deal
    specifically with family reunion cases, implementing and developing
    ideas from Kling et al. (2017) <doi:10.1016/j.fsigen.2017.08.006>. A
    novelty of 'forrel' is the ability to model background inbreeding in
    forensic pedigree computations.  This can have significant impact in
    applications, as exemplified in Vigeland and Egeland (2019)
    <doi:10.1016/j.fsigss.2019.10.175>. 'forrel' is part of the ped suite,
    a collection of packages for pedigree analysis. In particular,
    'forrel' imports 'pedtools' for creating and manipulating pedigrees
    and markers, 'pedprobr' for likelihood computations, and 'pedmut' for
    mutation modelling.  Pedigree data may be created from scratch, or
    loaded from text files. Data import from the 'Familias' software
    (Egeland et al. (2000) <doi:10.1016/S0379-0738(00)00147-X>) is
    supported.
Identifies potential data outliers and their impact on estimates and analyses. Uses the forward search approach of Atkinson and Riani, "Robust Diagnostic Regression Analysis",          2000,<ISBN: o-387-95017-6> to prepare descriptive statistics of a dataset that is to be analyzed by stats::lm(), stats::glm(), nlme::lme() or survival::coxph().  Includes graphics functions to display the descriptive statistics.
The goal of 'forstringr' is to enable complex string
    manipulation in R especially to those more familiar with LEFT(),
    RIGHT(), and MID() functions in Microsoft Excel. The package combines
    the power of 'stringr' with other manipulation packages such as
    'dplyr' and 'tidyr'.
Process automation of point cloud data derived from terrestrial-based technologies such as Terrestrial Laser Scanner (TLS) or Simultaneous Localization and Mapping (SLAM). 'FORTLS' enables (i) detection of trees and estimation of tree-level attributes (e.g. diameters and heights), (ii) estimation of stand-level variables (e.g. density, basal area, mean and dominant height), (iii) computation of metrics related to important forest attributes estimated in Forest Inventories at stand-level, and (iv) optimization of plot design for combining TLS data and field measured data. Documentation about 'FORTLS' is described in Molina-Valero et al. (2022, <doi:10.1016/j.envsoft.2022.105337>).
A collection of fortunes from the R community.
Robust analysis using forward search in linear and
        generalized linear regression models, as described in Atkinson, A.C. and Riani, M. (2000), Robust Diagnostic Regression Analysis, First Edition. New York: Springer.
Anonymized data from surveys conducted by Forwards <https://forwards.github.io/>, the R Foundation task force on women and other under-represented groups. Currently, a single data set of responses to a survey of attendees at useR! 2016 <https://www.r-project.org/useR-2016/>, the R user conference held at Stanford University, Stanford, California, USA, June 27 - June 30 2016.
A set of analytical tools useful in analysing ecological and geographical data sets, both ancient and modern. The package includes functions for estimating species richness (Chao 1 and 2, ACE, ICE, Jacknife), shared species/beta diversity, species area curves and geographic distances and areas.
Functions to automate the detection and resolution of taxonomic and stratigraphic errors in fossil occurrence datasets. Functions were developed using data from the Paleobiology Database.
Simulating taxonomy and fossil data on phylogenetic trees under mechanistic
    models of speciation, preservation and sampling.
A shiny application based on 'FossilSim'. Used for simulating
    tree, taxonomic and fossil data under mechanistic models of speciation,
    preservation and sampling.
A tool to use a principal component analysis on radially averaged
  two dimensional Fourier spectra to characterize image texture. The method
  within the context of ecology was first described by Couteron et al. (2005)
  <doi:10.1111/j.1365-2664.2005.01097.x> and expanded upon by
  Solorzano et al. (2018) <doi:10.1117/1.JRS.12.036006>
  using a moving window approach.
Interface to 'Palantir Foundry', including
    reading and writing structured or unstructured datasets, and more
    <https://www.palantir.com/platforms/foundry/>.
The four-gamete test is based on the infinite-sites model which assumes that the probability of the same mutation occurring twice (recurrent or parallel mutations) and the probability of a mutation back to the original state (reverse mutations) are close to zero. Without these types of mutations, the only explanation for observing the four dilocus genotypes (example below) is recombination (Hudson and Kaplan 1985, Genetics 111:147-164). Thus, the presence of all four gametes is also called phylogenetic incompatibility.
Computes Fourier integrals of functions of one and two variables using the Fast Fourier transform. The Fourier transforms must be evaluated on a regular grid for fast evaluation.
Estimate Barton & Lord's (1981) <doi:10.1002/j.2333-8504.1981.tb01255.x> 
    four parameter IRT model with lower and upper asymptotes using Bayesian
    formulation described by Culpepper (2016) <doi:10.1007/s11336-015-9477-6>.
A game for two players: Who gets first four in a row (horizontal, vertical or diagonal) wins. As board game published by Milton Bradley, designed by Howard Wexler and Ned Strongin.
Implements parsimonious hidden Markov models for four-way data via expectation-
    conditional maximization algorithm, as described in Tomarchio et al. (2020) <arXiv:2107.04330>.
    The matrix-variate normal distribution is used as emission distribution. For each hidden
    state, parsimony is reached via the eigen-decomposition of the covariance matrices of the
    emission distribution. This produces a family of 98 parsimonious hidden Markov models.
Spatio-temporal Fixation Pattern Analysis (FPA) is a new method of analyzing eye 
  movement data, developed by Mr. Jinlu Cao under the supervision of Prof. Chen Hsuan-Chih at 
  The Chinese University of Hong Kong, and Prof. Wang Suiping at the South China Normal 
  Univeristy. The package "fpa" is a R implementation which makes FPA analysis much easier. 
  There are four major functions in the package: ft2fp(), get_pattern(), plot_pattern(), and 
  lineplot(). The function ft2fp() is the core function, which can complete all the preprocessing 
  within moments. The other three functions are supportive functions which visualize the eye 
  fixation patterns.
Computes the power and sample size (PASS) required to test for the
    difference in the mean function between two groups under a repeatedly measured longitudinal 
    or sparse functional design. See the manuscript by Koner and Luo (2023) <https://salilkoner.github.io/assets/PASS_manuscript.pdf> 
    for details of the PASS formula and computational details. The details of the testing
    procedure for univariate and multivariate response are presented in
    Wang (2021) <doi:10.1214/21-EJS1802> and Koner and Luo (2023) 
    <arXiv:2302.05612> respectively.
Various methods for clustering and cluster validation.
  Fixed point clustering. Linear regression clustering. Clustering by 
  merging Gaussian mixture components. Symmetric 
  and asymmetric discriminant projections for visualisation of the 
  separation of groupings. Cluster validation statistics
  for distance based clustering including corrected Rand index. 
  Standardisation of cluster validation statistics by random clusterings and 
  comparison between many clustering methods and numbers of clusters based on
  this.  
  Cluster-wise cluster stability assessment. Methods for estimation of 
  the number of clusters: Calinski-Harabasz, Tibshirani and Walther's 
  prediction strength, Fang and Wang's bootstrap stability. 
  Gaussian/multinomial mixture fitting for mixed 
  continuous/categorical variables. Variable-wise statistics for cluster
  interpretation. DBSCAN clustering. Interface functions for many 
  clustering methods implemented in R, including estimating the number of
  clusters with kmeans, pam and clara. Modality diagnosis for Gaussian
  mixtures. For an overview see package?fpc.
Run three dimensional functional principal component analysis and return the three dimensional functional principal component scores. The details of the method are explained in Lin et al.(2015) <doi:10.1371/journal.pone.0132945>.
Functions to represent functional objects under a Reproducing Kernel Hilbert Space (RKHS) framework as described 
  in Muñoz & González (2010). Autoregressive Hilbertian Model for functional time series using RKHS and predictive confidence bands construction 
  as proposed in Hernández et al (2021).
Comparisons of floating point numbers are problematic due to errors
    associated with the binary representation of decimal numbers.
    Despite being aware of these problems, people still use numerical methods
    that fail to account for these and other rounding errors (this pitfall is
    the first to be highlighted in Circle 1 of Burns (2012)
    'The R Inferno' <https://www.burns-stat.com/pages/Tutor/R_inferno.pdf>).
    This package provides new relational operators useful for performing
    floating point number comparisons with a set tolerance.
Probabilistic distance clustering (PD-clustering) is an iterative, distribution free, probabilistic clustering method. PD-clustering assigns units to a cluster according to their probability of membership, under the constraint that the product of the probability and the distance of each point to any cluster centre is a constant. PD-clustering is a flexible method that can be used with non-spherical clusters, outliers, or noisy data. PDQ is an extension of the algorithm for clusters of different size. GPDC and TPDC uses a dissimilarity measure based on densities. Factor PD-clustering (FPDC) is a factor clustering method that involves a linear transformation of variables and a cluster optimizing the PD-clustering criterion. It works on high dimensional data sets.
Tools to help text files importation. It can return 
 the number of lines; print the first and last lines; convert 
 encoding. Operations are made without reading the entire file 
 before starting, resulting in good performances with large files. 
 This package provides an alternative to a simple use of the 
 'head', 'tail', 'wc' and 'iconv' programs that are not always 
 available on machine where R is installed.
Given the values of sampled units and selection probabilities 
             the desraj function  in the package computes the estimated value of the total
             as well as estimated variance.
This data contains a large variety of information on players and their
  current attributes on Fantasy Premier League
  <https://fantasy.premierleague.com/>. In particular, it contains a
  `next_gw_points` (next gameweek points) value for each player
  given their attributes in the current week. Rows represent player-gameweeks,
  i.e. for each player there is a row for each gameweek. This
  makes the data suitable for modelling a player's next gameweek points, given
  attributes such as form, total points, and cost at the current gameweek.
  This data can therefore be used to create Fantasy Premier League bots that
  may use a machine learning algorithm and a linear programming solver
  (for example) to return the best possible transfers and team to pick for
  each gameweek, thereby fully automating the decision making process in
  Fantasy Premier League. This function simply supplies the required data
  for such a task.
Easy way to plot regular/weighted/conditional distributions by using formulas. The core of the package concerns distribution plots which are automatic: the many options are tailored to the data at hand to offer the nicest and most meaningful graphs possible -- with no/minimum user input. Further provide functions to plot conditional trends and box plots. See <https://lrberge.github.io/fplot/> for more information.
Read and process a large delimited file block by
    block. A block consists of all the contiguous rows that have the same value
    in the first field. The result can be returned as a list or a data.table,
    or even directly printed to an output file.
A dynamic programming algorithm for the fast segmentation of univariate signals into piecewise constant profiles.
  The 'fpop'  package is a wrapper to a C++ implementation of the fpop (Functional Pruning Optimal Partioning) algorithm described in Maidstone et al. 2017
  <doi:10.1007/s11222-016-9636-3>. The problem of detecting changepoints in an univariate sequence is formulated 
  in terms of minimising the mean squared error over segmentations. The fpop algorithm exactly minimizes the mean squared error 
  for a penalty linear in the number of changepoints.
Weighted-L2 FPOP Maidstone et al. (2017) <doi:10.1007/s11222-016-9636-3> and pDPA/FPSN Rigaill (2010) <arXiv:1004.0887> algorithm for detecting multiple changepoints in the mean of a vector. Also includes a few model selection functions using Lebarbier (2005) <doi:10.1016/j.sigpro.2004.11.012> and the 'capsushe' package.
A collection of functions to optimize portfolios and to analyze them from different points of view.
Returns the noncentrality parameter of the noncentral F
        distribution if probability of type I and type II error,
        degrees of freedom of the numerator and the denominator are
        given.  It may be useful for computing minimal detectable
        differences for general ANOVA models.  This program is
        documented in the paper of A. Baharev, S. Kemeny, On the
        computation of the noncentral F and noncentral beta
        distribution; Statistics and Computing, 2008, 18 (3), 333-340.
All data sets required for the examples and exercises in
        the book "Forecasting: principles and practice" by Rob J
        Hyndman and George Athanasopoulos. All packages required to run
        the examples are also loaded.
All data sets required for the examples and exercises
  in the book "Forecasting: principles and practice" (2nd ed, 2018)
  by Rob J Hyndman and George Athanasopoulos <https://otexts.com/fpp2/>.
  All packages required to run the examples are also loaded.
All data sets required for the examples and exercises in the book
    "Forecasting: principles and practice" by Rob J Hyndman and George Athanasopoulos
    <https://OTexts.com/fpp3/>.  All packages required to run the examples are also
    loaded.
Efficient approximation of first-passage-time densities for diffusion processes based on the First-Passage-Time Location (FPTL) function.
The main goal of this package is drawing the membership function of the fuzzy p-value which is defined as a fuzzy set on the unit interval for three following problems: (1) testing crisp hypotheses based on fuzzy data, see Filzmoser and Viertl (2004) <doi:10.1007/s001840300269>, (2) testing fuzzy hypotheses based on crisp data, see Parchami et al. (2010) <doi:10.1007/s00362-008-0133-4>, and (3) testing fuzzy hypotheses based on fuzzy data, see Parchami et al. (2012) <doi:10.1007/s00362-010-0353-2>. In all cases, the fuzziness of data or / and the fuzziness of the boundary of null fuzzy hypothesis transported via the p-value function and causes to produce the fuzzy p-value. If the p-value is fuzzy, it is more appropriate to consider a fuzzy significance level for the problem. Therefore, the comparison of the fuzzy p-value and the fuzzy significance level is evaluated by a fuzzy ranking method in this package.
A collection of functions for calculating Floristic Quality
    Assessment (FQA) metrics using regional FQA databases that have been
    approved or approved with reservations as ecological planning models
    by the U.S. Army Corps of Engineers (USACE). For information on FQA
    see Spyreas (2019) <doi:10.1002/ecs2.2825>. These databases are stored
    in a sister R package, 'fqadata'. Both packages were developed for the
    USACE by the U.S. Army Engineer Research and Development Center’s
    Environmental Laboratory.
Contains regional Floristic Quality Assessment databases that
    have been approved or approved with reservations by the U.S. Army
    Corps of Engineers (USACE). Paired with the 'fqacalc' R package, these
    data sets allow for Floristic Quality Assessment metrics to be
    calculated. For information on FQA see Spyreas (2019)
    <doi:10.1002/ecs2.2825>. Both packages were developed for the USACE by
    the U.S.  Army Engineer Research and Development Center's
    Environmental Laboratory.
Methods to "add" two tables; also an alternative
     interpretation of named vectors as generalized tables, so that
     c(a=1,b=2,c=3) + c(b=3,a=-1) will return c(b=5,c=3).  Uses
     'disordR' discipline (Hankin, 2022, <arxiv:2210.03856>).
     Extraction and replacement methods are provided.  The underlying
     mathematical structure is the Free Abelian group, hence the name.
     To cite in publications please use Hankin (2023)
     <arxiv:2307:13184>.
Maximum likelihood estimation of the parameters of a fractionally
   differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989);
   including inference and basic methods.  Some alternative algorithms to estimate "H".
Calculate numerical asymptotic distribution functions of likelihood ratio 
    statistics for fractional unit root tests and tests of cointegration rank. 
    For these distributions, the included functions calculate critical values 
    and P-values used in unit root tests, cointegration tests, and rank tests 
    in the Fractionally Cointegrated Vector Autoregression (FCVAR) model.
    The functions implement procedures for tests described in the following articles:
    Johansen, S. and M. Ø. Nielsen (2012) <doi:10.3982/ECTA9299>,
    MacKinnon, J. G. and M. Ø. Nielsen (2014) <doi:10.1002/jae.2295>.
Aim is to provide fractional Brownian vector field generation algorithm, Hurst parameter estimation method and fractional kriging model for multivariate data modeling.
Functions for fitting data to a quiescent growth model,
        i.e. a growth process that involves members of the population
        who stop dividing or propagating.
Implements various methods for estimating fractal dimension of time series and 2-dimensional data <doi:10.1214/11-STS370>.
The parameters p and q are estimated with the aid of a randomized Sierpinski Carpet which is built on a [p-p-p-q]-model. Thereby, for three times a simulation with a p-value and once with a q-value is assumed. Hence, these parameters are estimated and displayed. Moreover, functions for simulating random Sierpinski-Carpets with constant and variable probabilities are included. For more details on the method please see Hermann et al. (2015) <doi:10.1002/sim.6497>.
Various functions for performing fractal and multifractal analysis including performing fractal regression. Please refer to Peng and colleagues (1994) <doi:10.1103/physreve.49.1685>, Kantelhardt and colleagues (2002)<doi:10.1016/S0378-4371(02)01383-3>, and Likens and colleagues (2019) <doi:10.1016/j.physa.2019.121580>.
Estimate the of fractal dimension of a black area in 2D and 3D (slices) images using the box-counting method. See Klinkenberg B. (1994) <doi:10.1007/BF02065874>.
Turn numeric,data.frame,matrix into fraction form.
The main function of this package allows numerical vector objects to
  be displayed with their values in vulgar fractional form.  This is convenient if
  patterns can then be more easily detected.  In some cases replacing the components
  of a numeric vector by a rational approximation can also be expected to remove
  some component of round-off error.  The main functions form a re-implementation
  of the functions 'fractions' and 'rational' of the MASS package, but using a
  radically improved programming strategy.
Provides functions for converting decimals to a
    matrix of numerators and denominators or a character vector of
    fractions.  Supports mixed or improper fractions, finding common
    denominators for vectors of fractions, limiting denominators to powers
    of ten, and limiting denominators to a maximum value.  Also includes
    helper functions for finding the least common multiple and greatest
    common divisor for a vector of integers.  Implemented using C++ for
    maximum speed.
A collection of user-friendly functions for assessing and visualizing fragility of individual studies (Walsh et al., 2014 <doi:10.1016/j.jclinepi.2013.10.019>; Lin, 2021 <doi:10.1111/jep.13428>), conventional pairwise meta-analyses (Atal et al., 2019 <doi:10.1016/j.jclinepi.2019.03.012>), and network meta-analyses of multiple treatments with binary outcomes (Xing et al., 2020 <doi:10.1016/j.jclinepi.2020.07.003>). The included functions are designed to: 1) calculate the fragility index (i.e., the minimal event status modifications that can alter the significance or non-significance of the original result) and fragility quotient (i.e., fragility index divided by sample size) at a specific significance level; 2) give the cases of event status modifications for altering the result's significance or non-significance and visualize these cases; 3) visualize the trend of statistical significance as event status is modified; 4) efficiently derive fragility indexes and fragility quotients at multiple significance levels, and visualize the relationship between these fragility measures against the significance levels; and 5) calculate fragility indexes and fragility quotients of multiple datasets (e.g., a collection of clinical trials or meta-analyses) and produce plots of their overall distributions. The outputs from these functions may inform the robustness of clinical results in terms of statistical significance and aid the interpretation of fragility measures. The usage of this package is detailed in Lin and Chu (2022 <doi:10.1371/journal.pone.0268754>).
Performs fragment analysis using genetic data coming from capillary electrophoresis machines. These are files with FSA extension which stands for FASTA-type file, and .txt files from Beckman CEQ 8000 system, both contain DNA fragment intensities read by machinery. In addition to visualization, it performs automatic scoring of SSRs (Sample Sequence Repeats; a type of genetic marker very common across the genome) and other type of PCR markers (standing for Polymerase Chain Reaction) in biparental populations such as F1, F2, BC (backcross), and diversity panels (collection of genetic diversity).
Contains functions for fitting shared frailty models with a semi-parametric
    baseline hazard with the Expectation-Maximization algorithm. Supported data formats 
    include clustered failures with left truncation and recurrent events in gap-time
    or Andersen-Gill format. Several frailty distributions, such as the the gamma, positive stable
    and the Power Variance Family are supported.
Implements the h-likelihood estimation procedures for general frailty models including competing-risk models and joint models.
The penalized and non-penalized Minorize-Maximization (MM) method for frailty models to fit the clustered data, multi-event data and recurrent data. Least absolute shrinkage and selection operator (LASSO), minimax concave penalty (MCP) and smoothly clipped absolute deviation (SCAD) penalized functions are implemented. All the methods are computationally efficient. These general methods are proposed based on the following papers,
    Huang, Xu and Zhou (2022) <doi:10.3390/math10040538>,
    Huang, Xu and Zhou (2023) <doi:10.1177/09622802221133554>.
Simulates and fits semiparametric shared frailty models under a
    wide range of frailty distributions using a consistent and
    asymptotically-normal estimator. Currently supports: gamma, power variance
    function, log-normal, and inverse Gaussian frailty models.
Tools to support sensible statistics for functional response analysis.
Provides a friendly interface for modifying data frames with a sequence of piped commands built upon the 'tidyverse' Wickham et al., (2019) <doi:10.21105/joss.01686> . The majority of commands wrap 'dplyr' mutate statements in a convenient way to concisely solve common issues that arise when tidying small to medium data sets. Includes smart defaults and allows flexible selection of columns via 'tidyselect'.
Point and interval estimation in dual frame surveys. In contrast
    to classic sampling theory, where only one sampling frame is considered,
    dual frame methodology assumes that there are two frames available for
    sampling and that, overall, they cover the entire target population. Then,
    two probability samples (one from each frame) are drawn and information
    collected is suitably combined to get estimators of the parameter of
    interest.
With no external dependencies and
    support for 335 languages; all languages spoken by
    more than one million speakers. 'Franc' is a port
    of the 'JavaScript' project of the same name,
    see <https://github.com/wooorm/franc>.
Accompanying package of the book 'Financial Risk Modelling
        and Portfolio Optimisation with R', second edition. The data sets used in the book are contained in this package.
Automatically process Fluorescence Recovery After Photobleaching (FRAP) data and generate consistent, publishable figures. Note: this package does not replace 'ImageJ' (or its equivalence) in raw image quantification. Some references about the methods: Sprague, Brian L. (2004) <doi:10.1529/biophysj.103.026765>; Day, Charles A. (2012) <doi:10.1002/0471142956.cy0219s62>.
Generating fractional binomial random variables and computing density, cumulative distribution, and quantiles of fractional binomial distributions. (Lee, J. (2023) <arXiv:2209.01516>.)
An implementation of various learning algorithms based on fuzzy rule-based systems (FRBSs) for dealing with classification and regression tasks. Moreover, it allows to construct an FRBS model defined by human experts. 
    FRBSs are based on the concept of fuzzy sets, proposed by Zadeh in 1965, which aims at
    representing the reasoning of human experts in a set of IF-THEN rules, to
    handle real-life problems in, e.g., control, prediction and inference, data
    mining, bioinformatics data processing, and robotics. FRBSs are also known
    as fuzzy inference systems and fuzzy models. During the modeling of an
    FRBS, there are two important steps that need to be conducted: structure
    identification and parameter estimation. Nowadays, there exists a wide
    variety of algorithms to generate fuzzy IF-THEN rules automatically from
    numerical data, covering both steps. Approaches that have been used in the
    past are, e.g., heuristic procedures, neuro-fuzzy techniques, clustering
    methods, genetic algorithms, squares methods, etc. Furthermore, in this
    version we provide a universal framework named 'frbsPMML', which is adopted
    from the Predictive Model Markup Language (PMML), for representing FRBS
    models. PMML is an XML-based language to provide a standard for describing
    models produced by data mining and machine learning algorithms. Therefore,
    we are allowed to export and import an FRBS model to/from 'frbsPMML'.
    Finally, this package aims to implement the most widely used standard
    procedures, thus offering a standard package for FRBS modeling to the R
    community.
Contains the core functions associated with Fast
        Regularized Canonical Correlation Analysis. Please see the following for
        details: Raul Cruz-Cano, Mei-Ling Ting Lee, 
        Fast regularized canonical correlation analysis, 
        Computational Statistics & Data Analysis, 
        Volume 70, 2014, Pages 88-100, 
        ISSN 0167-9473 <doi:10.1016/j.csda.2013.09.020>.
Provides implementation of statistical methods for random objects 
    lying in various metric spaces, which are not necessarily linear spaces. 
    The core of this package is Fréchet regression for random objects with 
    Euclidean predictors, which allows one to perform regression analysis 
    for non-Euclidean responses under some mild conditions. 
    Examples include distributions in L^2-Wasserstein space, 
    covariance matrices endowed with power metric (with Frobenius metric 
    as a special case), Cholesky and log-Cholesky metrics.  
    References: Petersen, A., & Müller, H.-G. (2019) <doi:10.1214/17-AOS1624>.
An R client for the 'Federal Reserve Economic Data'
    ('FRED') API <https://research.stlouisfed.org/docs/api/>.  Functions
    to retrieve economic time series and other data from 'FRED'.
Unified regularized estimating equation solver. Currently the package includes one solver with the l1 penalty only. More solvers and penalties are under development. Reference: Yi Yang, Yuwen Gu, Yue Zhao, Jun Fan (2021) <arXiv:2110.11074>.
The free algebra in R with non-commuting indeterminates.
     Uses 'disordR' discipline
     (Hankin, 2022, <doi:10.48550/ARXIV.2210.03856>).  To cite the
     package in publications please use Hankin (2022)
     <doi:10.48550/ARXIV.2211.04002>.
Estimates and provides inference for quantities that assess high dimensional mediation and potential surrogate markers including the direct effect of treatment, indirect effect of treatment, and the proportion of treatment effect explained by a surrogate/mediator; details are described in Zhou et al (2022) <doi:10.1002/sim.9352> and Zhou et al (2020) 
    <doi:10.1093/biomet/asaa016>. This package relies on the optimization software 'MOSEK', 
    <https://www.mosek.com>.
An R client for the 'freecurrencyapi.com' currency conversion API. The API requires registration of an API key. You can find the full API documentation at <https://freecurrencyapi.com/docs> .
Implements the formulae required to calculate freedom
    from disease according to Cameron and Baldock (1998)
    <doi:10.1016/S0167-5877(97)00081-0>. These are the
    methods used at the Swedish national veterinary institute (SVA) to
    evaluate the performance of our nation animal disease
    surveillance programmes.
The free group in R; juxtaposition is represented by a
  plus.  Includes inversion, multiplication by a scalar,
  group-theoretic power operation, and Tietze forms.  To cite the
  package in publications please use Hankin (2022)
  <doi:10.48550/ARXIV.2212.05883>.
Provides tools for describing and analysing free sorting data. Main methods are computation of consensus partition and factorial analysis of the dissimilarity matrix between stimuli (using multidimensional scaling approach).
Provides functions to read and write neuroimaging data in various file formats, with a focus on 'FreeSurfer' <http://freesurfer.net/> formats. This includes, but is not limited to, the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file format. Contains a brain surface mesh, given by a list of vertices and a list of faces.
This tree-based method deals with high dimensional longitudinal 
	data with correlated features through the use of a piecewise random effect 
	model. FREE tree also exploits the network structure of the features, by 
	first clustering them using Weighted Gene Co-expression Network Analysis 
	('WGCNA'). It then conducts a screening step within each cluster of features 
	and a selecting step among the surviving features, which provides a relatively
	unbiased way to do feature selection. By using dominant principle components 
	as regression variables at each leaf and the original features as splitting 
	variables at splitting nodes, FREE tree delivers easily interpretable results
	while improving computational efficiency.
A collection of functions for linear and non-linear regression 
  modelling. It implements a wrapper for several regression models available 
  in the base and contributed packages of R.
Functions for finding smooth interpolating curves connecting
    a series of points in the plane.  Curves may be open or closed,
    that is, with the first and last point of the curve at the initial point.
Download data sets from Kenneth's French finance data library site <http://mba.tuck.dartmouth.edu/pages/faculty/ken.french/data_library.html>, reads all the data subsets from the file. Allows R users to collect the data as
    'tidyverse'-ready data frames.
Real capture frequencies will be fitted to various distributions which provide the basis of estimating population sizes, their standard error, and symmetric as well as asymmetric confidence intervalls.
Generates a frequency distribution. The frequency
    distribution includes raw frequencies, percentages in each category, and
    cumulative frequencies. The frequency distribution can be stored as a data
    frame.
Input has to be in the form of vectors of lower class limits and upper class limits and frequencies; the output will give a cumulative frequency distribution table with cumulative frequency plot.
Implementation of dynamic principal component
    analysis (DPCA), simulation of VAR and VMA processes and frequency domain tools. 
    These frequency domain methods for dimensionality reduction of multivariate time series
    were introduced by David Brillinger in his book Time Series (1974). We follow implementation
    guidelines as described in Hormann, Kidzinski and Hallin (2016),
    Dynamic Functional Principal Component <doi:10.1111/rssb.12076>.
Implementations of functional dynamic principle components analysis. Related graphic tools and frequency domain methods.
  These methods directly use multivariate dynamic principal components implementation,
  following the guidelines from Hormann, Kidzinski and Hallin (2016), Dynamic Functional Principal Component <doi:10.1111/rssb.12076>.
New approaches to parallel coordinates plots for
   multivariate data visualization, including applications to clustering,
   outlier hunting and regression diagnostics.  Includes general functions
   for multivariate nonparametric density and regression estimation, 
   using parallel computation.
Interval estimation of the population allele frequency from qPCR analysis based on the restriction enzyme digestion (RED)-DeltaDeltaCq method (Osakabe et al. 2017, <doi:10.1016/j.pestbp.2017.04.003>), as well as general DeltaDeltaCq analysis. Compatible with the Cq measurement of DNA extracted from multiple individuals at once, so called "group-testing", this model assumes that the quantity of DNA extracted from an individual organism follows a gamma distribution. Therefore, the point estimate is robust regarding the uncertainty of the DNA yield.
Tools for generating an informative type of line graph, the frequency profile, 
    which allows single behaviors, multiple behaviors, or the specific behavioral patterns 
    of individual subjects to be graphed from occurrence/nonoccurrence behavioral data.
Quickly make tables of descriptive statistics (i.e., counts, 
    percentages, confidence intervals) for categorical variables. This 
    package is designed to work in a Tidyverse pipeline, and consideration
    has been given to get results from R to Microsoft Word ® with minimal pain.
Generate 'SPSS'/'SAS' styled frequency tables. Frequency tables are 
    generated with variable and value label attributes where applicable with optional
    html output to quickly examine datasets.
Accompanies a paper (Barunik, Krehlik (2018) <doi:10.1093/jjfinec/nby001>) dedicated to spectral decomposition of connectedness measures and their interpretation. We implement all the developed estimators as well as the historical counterparts. For more information, see the help or GitHub page (<https://github.com/tomaskrehlik/frequencyConnectedness>) for relevant information.
Implement frequent-directions algorithm for efficient matrix sketching. 
  (Edo Liberty (2013) <doi:10.1145/2487575.2487623>).
A study based on the screened selection design (SSD) is an exploratory phase II randomized trial with two or more arms but without concurrent control. The primary aim of the SSD trial is to pick a desirable treatment arm (e.g., in terms of the median survival time) to recommend to the subsequent randomized phase IIb (with the concurrent control) or phase III. Though The survival endpoint is often encountered in phase II trials, the existing SSD methods cannot deal with the survival endpoint. Furthermore, the existing SSD won’t control the type I error rate.  The proposed designs can “partially” control or provide the empirical type I error/false positive rate by an optimal algorithm (implemented by the optimal() function) for each arm. All the design needed components (sample size, operating characteristics) are supported.
Contains a set of utilities for building and testing statistical models (linear, logistic,ordinal or COX) for Computer Aided Diagnosis/Prognosis applications. Utilities include data adjustment, univariate analysis, model building, model-validation, longitudinal analysis, reporting and visualization.
Customize 'Bootstrap' and 'Bootswatch' themes, like colors, fonts, grid layout, 
  to use in 'Shiny' applications, 'rmarkdown' documents and 'flexdashboard'.
Procedure for solving the maximin problem for identical design across heterogeneous data groups. Particularly efficient when the design matrix is either orthogonal or has tensor structure. Orthogonal wavelets can be specified for 1d, 2d or 3d data simply by name. For tensor structured design the tensor components (two or three) may be supplied. The package also provides an efficient implementation of the generic magging estimator.
A simple way to unload none-base packages and remove all global
    variables.
Regular and non-regular Fractional Factorial 2-level designs 
        can be created. Furthermore, analysis tools for Fractional
        Factorial designs with 2-level factors are offered (main
        effects and interaction plots for all factors simultaneously,
        cube plot for looking at the simultaneous effects of three
        factors, full or half normal plot, alias structure in a more
        readable format than with the built-in function alias).
Catalogues of resolution IV regular
        fractional factorial designs in 128 runs are provided 
        for up to 33 2-level factors. The catalogues are complete, 
        excluding resolution IV designs without 5-letter words, 
        because these do not add value for a search for unblocked 
        clear designs. The previous package version
        1.0 with complete catalogues up to 24 runs (24 runs and a
        namespace added later) can be downloaded from the authors
        website.
Computes relative importance of main and interaction effects. Also, sum of the modified generalized weights is computed. Ibrahim et al. (2022) <doi:10.1134/S1064229322080051>.
Read and write Frictionless Data Packages. A 'Data Package'
    (<https://specs.frictionlessdata.io/data-package/>) is a simple container
    format and standard to describe and package a collection of (tabular) data. 
    It is typically used to publish FAIR 
    (<https://www.go-fair.org/fair-principles/>) and open datasets.
The complete scripts from the American sitcom Friends in tibble 
    format. Use this package to practice data wrangling, text analysis and 
    network analysis.
Miscellaneous utilities, tools and helper
    functions for finding and searching files on disk, searching for and
    removing R objects from the workspace.
    Does not import or depend on any third party package, but on core R 
    only (i.e. it may depend on packages with priority 'base').
A tool for spatial/spatio-temporal modelling and prediction with large datasets. The approach models the field, and hence the covariance function, using a set of basis functions. This fixed-rank basis-function representation facilitates the modelling of big data, and the method naturally allows for non-stationary, anisotropic covariance functions. Discretisation of the spatial domain into so-called basic areal units (BAUs) facilitates the use of observations with varying support (i.e., both point-referenced and areal supports, potentially simultaneously), and prediction over arbitrary user-specified regions. `FRK` also supports inference over various manifolds, including the 2D plane and 3D sphere, and it provides helper functions to model, fit, predict, and plot with relative ease. Version 2.0.0 and above also supports the modelling of non-Gaussian data (e.g., Poisson, binomial, negative-binomial, gamma, and inverse-Gaussian) by employing a generalised linear mixed model (GLMM) framework.  Zammit-Mangion and Cressie <doi:10.18637/jss.v098.i04> describe `FRK` in a Gaussian setting, and detail its use of basis functions and BAUs, while Sainsbury-Dale et al. <arXiv:2110.02507> describe `FRK` in a non-Gaussian setting; two vignettes are available that summarise these papers and provide additional examples.
When fitting a set of linear regressions which have some same variables, we can separate the matrix and reduce the computation cost. This package aims to fit a set of repeated linear regressions faster. More details can be found in this blog Lijun Wang (2017) <https://stats.hohoweiya.xyz/regression/2017/09/26/An-R-Package-Fit-Repeated-Linear-Regressions/>.
Fast, numerically robust computation of weighted moments via 'Rcpp'. 
   Supports computation on vectors and matrices, and Monoidal append of moments. 
   Moments and cumulants over running fixed length windows can be computed, 
   as well as over time-based windows.
   Moment computations are via a generalization of Welford's method, as described
   by Bennett et. (2009) <doi:10.1109/CLUSTR.2009.5289161>.
Maximum Likelihood Estimation of
   Stochastic Frontier Production and Cost Functions.
   Two specifications are available:
   the error components specification with time-varying efficiencies
   (Battese and Coelli, 1992, <doi:10.1007/BF00158774>)
   and a model specification in which the firm effects are directly 
   influenced by a number of variables (Battese and Coelli, 1995,
   <doi:10.1007/BF01205442>).
It calculates the alpha-quantile proposed by Daouia and Simar (2007) <doi:10.1016/j.jeconom.2006.07.002> and order-m efficiency score in multi-dimension proposed by Daouia and Gijbels (2011) <doi:10.1016/j.jeconom.2010.12.002> and computes several summaries and representation of the associated frontiers in 2d and 3d.
An R API to MET Norway's 'Frost' API <https://frost.met.no/index.html> 
    to retrieve data as data frames. The 'Frost' API, and the underlying data, is 
    made available by the Norwegian Meteorological Institute (MET Norway). The data
    and products are distributed under the 
    Norwegian License for Open Data 2.0 (NLOD) <https://data.norge.no/nlod/en/2.0>
    and Creative Commons 4.0 <https://creativecommons.org/licenses/by/4.0/>.
Functions for automatically performing 
             a reanalysis series
             on a data set using CNA, and for calculating the fit-robustness
             of the resulting models, as described in 
             Parkkinen and Baumgartner (2021) <doi:10.1177/0049124120986200>.
Climate is a critical component limiting growing range of plant species, which
    also determines cultivar adaptation to a region. The evaluation of climate influence on
    fruit production is critical for decision-making in the design stage of orchards and 
    vineyards and in the evaluation of the potential consequences of future climate. Bio-
    climatic indices and plant phenology are commonly used to describe the suitability of 
    climate for growing quality fruit and to provide temporal and spatial information about 
    regarding ongoing and future changes. 'fruclimadapt' streamlines the assessment of 
    climate adaptation and the identification of potential risks for grapevines and fruit 
    trees. Procedures in the package allow to i) downscale daily meteorological variables
    to hourly values (Forster et al (2016) <doi:10.5194/gmd-9-2315-2016>),
    ii) estimate chilling and forcing heat accumulation (Miranda et al (2019)
    <https://ec.europa.eu/eip/agriculture/sites/default/files/fg30_mp5_phenology_critical_temperatures.pdf>),
    iii) estimate plant phenology (Schwartz (2012) <doi:10.1007/978-94-007-6925-0>), iv) 
    calculate bioclimatic indices to evaluate fruit tree and grapevine adaptation (e.g. Badr 
    et al (2017) <doi:10.3354/cr01532>), v) estimate the incidence of weather-related disorders 
    in fruits (e.g. Snyder and de Melo-Abreu (2005, ISBN:92-5-105328-6) and vi)
    estimate plant water requirements (Allen et al (1998, ISBN:92-5-104219-5)).
A cross-platform interface to file system operations, built
    on top of the 'libuv' C library.
A variety of simple fish stock assessment methods.
The datasets to support the Fish Stock Assessment ('FSA') package.
A flexible and interfaced framework for importing, processing and ploting Applied Biosystems data files. Application to Reverse-Transcriptase Multiplex Ligation-dependent Probe Amplification (RT-MLPA) gene-expression profiling and classification is illustrated in Mareschal, Ruminy et al (2015) <doi:10.1016/j.jmoldx.2015.01.007>. Gene-fusion detection and Sanger sequencing are illustrated in Mareschal, Palau et al (2021) <doi:10.1182/bloodadvances.2020002517>. Examples are provided for genotyping applications as well.
Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <http://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.
Automated feature selection using variety of models
        provided by 'caret' package.
        This work was funded by Poland-Singapore bilateral cooperation
        project no 2/3/POL-SIN/2012.
FS-DAM performs feature extraction through latent variables identification. Implementation is based on autoencoders with monotonicity and orthogonality constraints.
Provides interface to the 'MATLAB' toolbox 'Flexible Statistical Data Analysis
    (FSDA)' which is comprehensive and computationally efficient
    software package for robust statistics in regression, multivariate
    and categorical data analysis. The current R version implements tools
    for regression: (forward search, S- and MM-estimation, least trimmed
    squares (LTS) and least median of squares (LMS)), for multivariate analysis
    (forward search, S- and MM-estimation), for cluster analysis and cluster-wise regression.
    The distinctive feature of our package is the possibility of
    monitoring the statistics of interest as a function of breakdown point,
    efficiency or subset size, depending on the estimator. This is
    accompanied by a rich set of graphical features, such as dynamic
    brushing, linking, particularly useful for exploratory data analysis.
Functions for selecting attributes from a given
    dataset. Attribute subset selection is the process of identifying and
    removing as much of the irrelevant and redundant information as
    possible.
'Rcpp' (free of 'Java'/'Weka') implementation of 'FSelector' entropy-based feature selection 
 algorithms based on an MDL discretization (Fayyad U. M., Irani K. B.: Multi-Interval Discretization of Continuous-Valued Attributes for Classification Learning.
 In 13'th International Joint Conference on Uncertainly in Artificial Intelligence (IJCAI93), pages 1022-1029, Chambery, France, 1993.) <https://www.ijcai.org/Proceedings/93-2/Papers/022.pdf>
 with a sparse matrix support.
Routines for estimation or simultaneous estimation and variable selection of
  several functional semiparametric models with scalar response, such as the functional single-index model, 
  the semi-functional partial linear model or the semi-functional partial linear single-index model. 
  In addition, it includes algorithms for dealing with scalar covariates with linear effect coming from the discretization
  of a curve in the cases of the linear model, the multi-functional partial linear model
  and the multi-functional partial linear single-index model.
Import data of tests and questionnaires from FormScanner. FormScanner is an open source software that converts scanned images to data using optical mark recognition (OMR) and it can be downloaded from <http://sourceforge.net/projects/formscanner/>. The spreadsheet file created by FormScanner is imported in a convenient format to perform the analyses provided by the package. These analyses include the conversion of multiple responses to binary (correct/incorrect) data, the computation of the number of corrected responses for each subject or item, scoring using weights,the computation and the graphical representation of the frequencies of the responses to each item and the report of the responses of a few subjects.
Feature subset selection algorithms modularized in search algorithms and measure utilities. Full list and more information available at <https://dicits.ugr.es/software/FSinR/>.
Performs fast detection of interactions in large-scale data using the
    method of random intersection trees introduced in
    Shah, R. D. and Meinshausen, N. (2014) <http://www.jmlr.org/papers/v15/shah14a.html>. 
    The algorithm finds potentially high-order interactions in high-dimensional binary
    two-class classification data, without requiring lower order interactions
    to be informative.  The search is particularly fast when the matrices of
    predictors are sparse.  It can also be used to perform market basket analysis
    when supplied with a single binary data matrix.  Here it will find collections
    of columns which for many rows contain all 1's.
Functions for importing, creating, editing and
    exporting 'FSK' files <https://foodrisklabs.bfr.bund.de/fskx-food-safety-knowledge-exchange-format/>
    using the 'R' programming environment. Furthermore, it enables users
    to run simulations contained in the 'FSK' files and visualize the results.
Wrapper functions that interface with 'FSL' 
    <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>, a powerful and commonly-used 'neuroimaging'
    software, using system commands. The goal is to be able to interface with 'FSL'
    completely in R, where you pass R objects of class 'nifti', implemented by
    package 'oro.nifti', and the function executes an 'FSL' command and returns an R
    object of class 'nifti' if desired.
Randomized and balanced allocation of units to treatment groups using the Finite Selection Model (FSM). The FSM was originally proposed and developed at the RAND corporation by Carl Morris to enhance the experimental design for the now famous Health Insurance Experiment. See Morris (1979) <doi:10.1016/0304-4076(79)90053-8> for details on the original version of the FSM.
Implements feature selection routines for multivariate time series (MTS). 
    The list of implemented algorithms includes: 
    own lags (independent MTS components), 
    distance-based (using external structure, e.g. Pfeifer and Deutsch (1980) <doi:10.2307/1268381>),
    cross-correlation (see  Schelter et al. (2006, ISBN:9783527406234)),
    graphical LASSO (see Haworth and Cheng (2014) <https://www.gla.ac.uk/media/Media_401739_smxx.pdf>),
    random forest (see Pavlyuk (2020) "Random Forest Variable Selection for Sparse Vector Autoregressive Models" in Contributions to Statistics, in production),
    least angle regression (see Gelper and Croux (2008) <https://lirias.kuleuven.be/retrieve/16024>), 
    mutual information (see  Schelter et al. (2006, ISBN:9783527406234), Liu et al. (2016) <doi:10.1109/ChiCC.2016.7554480>),
    and partial spectral coherence (see Davis et al.(2016) <doi:10.1080/10618600.2015.1092978>). 
    In addition, the package implements functions for ensemble feature selection (using feature ranking and majority voting).
    The package is implemented within Dmitry Pavlyuk's research project No. 1.1.1.2/VIAA/1/16/112 "Spatiotemporal urban traffic modelling using big data".
Filling large gaps in low or uncorrelated multivariate time series uses a new fuzzy weighted similarity measure. It contains all required functions to create large missing consecutive values within time series and then fill these gaps, according to the paper Phan et al. (2018), <DOI:10.1155/2018/9095683>. Performance indicators are also provided to compare similarity between two univariate signals (incomplete signal and imputed signal).
Estimation of Rosenthal's fail safe number including confidence intervals. The relevant papers are the following. Konstantinos C. Fragkos, Michail Tsagris and Christos C. Frangos (2014). "Publication Bias in Meta-Analysis: Confidence Intervals for Rosenthal's Fail-Safe Number". International Scholarly Research Notices, Volume 2014. <doi:10.1155/2014/825383>. Konstantinos C. Fragkos, Michail Tsagris and Christos C. Frangos (2017). "Exploring the distribution for the estimator of Rosenthal's fail-safe number of unpublished studies in meta-analysis". Communications in Statistics-Theory and Methods, 46(11):5672--5684. <doi:10.1080/03610926.2015.1109664>.
Fuzzy set ordination is a multivariate analysis used in ecology to
    relate the composition of samples to possible explanatory variables.  While
    differing in theory and method, in practice, the use is similar to 'constrained
    ordination.'  The package contains plotting and summary functions as well as
    the analyses.
Estimating the number of factors in Exploratory Factor Analysis (EFA) with out-of-sample prediction errors using a cross-validation scheme. Haslbeck & van Bork (Preprint) <https://psyarxiv.com/qktsd>.
Support for fuzzy spatial objects, their operations, and fuzzy spatial inference models based on Spatial Plateau Algebra. 
    It employs fuzzy set theory and fuzzy logic as foundation to deal with spatial fuzziness. 
    It mainly implements underlying concepts defined in the following research papers: 
    (i) "Spatial Plateau Algebra: An Executable Type System for Fuzzy Spatial Data Types" <doi:10.1109/FUZZ-IEEE.2018.8491565>; 
    (ii) "A Systematic Approach to Creating Fuzzy Region Objects from Real Spatial Data Sets" <doi:10.1109/FUZZ-IEEE.2019.8858878>; 
    (iii) "Spatial Data Types for Heterogeneously Structured Fuzzy Spatial Collections and Compositions" <doi:10.1109/FUZZ48607.2020.9177620>;
    (iv) "Fuzzy Inference on Fuzzy Spatial Objects (FIFUS) for Spatial Decision Support Systems" <doi:10.1109/FUZZ-IEEE.2017.8015707>;
    (v) "Evaluating Region Inference Methods by Using Fuzzy Spatial Inference Models" <doi:10.1109/FUZZ-IEEE55066.2022.9882658>.
Social Relations Analysis with roles ("Family SRM") are computed,
    using a structural equation modeling approach. Groups ranging from three members
    up to an unlimited number of members are supported and the mean structure can
    be computed. Means and variances can be compared between different groups of
    families and between roles.
An optimizer of Fused-Sparse Structural Equation Models, which is 
 the state of the art jointly fused sparse maximum likelihood function 
 for structural equation models proposed by Xin Zhou and Xiaodong Cai (2018 
 <doi:10.1101/466623>).
Provides three methods proposed by Shang and Apley (2019) <doi:10.1080/00224065.2019.1705207> to generate fully-sequential space-filling designs inside a unit hypercube. A 'fully-sequential space-filling design' means a sequence of nested designs (as the design size varies from one point up to some maximum number of points) with the design points added one at a time and such that the design at each size has good space-filling properties. Two methods target the minimum pairwise distance criterion and generate maximin designs, among which one method is more efficient when design size is large. One method targets the maximum hole size criterion and uses a heuristic to generate what is closer to a minimax design.
Multithreaded serialization of compressed data frames using the 'fst' format. The
    'fst' format allows for full random access of stored data and a wide range of compression
    settings using the LZ4 and ZSTD compressors.
Provides efficient methods to compute local and genome wide
    genetic distances (corresponding to the so called Hudson Fst
    parameters) through moment method, perform chromosome segmentation
    into homogeneous Fst genomic regions, and selection sweep detection
    for multi-population comparison. When multiple profile segmentation is
    required, the procedure can be parallelized using the future package.
Has two functions to help with calculating feature selection stability. 'Lump' is a function that groups subset vectors into a dataframe, and adds NA to shorter vectors so they all have the same length.
    'ASM' is a function that takes a dataframe of subset vectors and the original vector of features as inputs, and calculates the Stability of the feature selection.
    The calculation for 'asm' uses the Adjusted Stability Measure proposed in: 'Lustgarten', 'Gopalakrishnan', & 'Visweswaran' (2009)<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2815476/>.
The 'fstlib' library provides multithreaded serialization of compressed data frames using the
    'fst' format. The 'fst' format allows for random access of stored data and compression with the 'LZ4' and 'ZSTD'
    compressors.
A program to generate smoothed quantiles for the Fst-heterozygosity distribution. Designed for use with large numbers of loci (e.g., genome-wide SNPs). The best case for analyzing the Fst-heterozygosity distribution is when many populations (>10) have been sampled. See Flanagan & Jones (2017) <doi:10.1093/jhered/esx048>.
Functions for sequencing studies allowing for multiple functional annotation scores. Score type tests and an efficient perturbation method are used for individual gene/large gene-set/genome wide analysis. Only summary statistics are needed.
Calculation and plotting of instantaneous unavailabilities of basic events along with the top event of fault trees are issues important in reliability analysis of complex systems. Here, a fault tree is provided in terms of its minimal cut sets, along with reliability and maintainability distribution functions of the basic events. All the methods are derived from Horton (2002, ISBN: 3-936150-21-4), Niloofar and Lazarova-Molnar (2022).
A wrapper for the API of the Danish Parliament. It makes it 
    possible to get data from the API easily into a data frame. Learn more at 
    <http://www.ft.dk/dokumenter/aabne_data>.
Build display tables easily by extending the functionality of the
    'flextable' package. Features include spanning header, grouping rows,
    parsing markdown and so on.
A collection of functions for trading and rebalancing financial
	instruments. It implements various technical indicators to analyse time series such
	as moving averages or stochastic oscillators.
Extracts features from biological sequences. It contains most features which are presented in related work and also includes features which have never been introduced before. It extracts numerous features from nucleotide and peptide sequences. Each feature converts the input sequences to discrete numbers in order to use them as predictors in machine learning models. There are many features and information which are hidden inside a sequence. Utilizing the package, users can convert biological sequences to discrete models based on chosen properties. References: 'iLearn' 'Z. Chen et al.' (2019) <DOI:10.1093/bib/bbz041>. 'iFeature' 'Z. Chen et al.' (2018) <DOI:10.1093/bioinformatics/bty140>. <https://CRAN.R-project.org/package=rDNAse>. 'PseKRAAC' 'Y. Zuo et al.' 'PseKRAAC: a flexible web server for generating pseudo K-tuple reduced amino acids composition' (2017) <DOI:10.1093/bioinformatics/btw564>. 'iDNA6mA-PseKNC' 'P. Feng et al.' 'iDNA6mA-PseKNC: Identifying DNA N6-methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC' (2019) <DOI:10.1016/j.ygeno.2018.01.005>. 'I. Dubchak et al.' 'Prediction of protein folding class using global description of amino acid sequence' (1995) <DOI:10.1073/pnas.92.19.8700>. 'W. Chen et al.' 'Identification and analysis of the N6-methyladenosine in the Saccharomyces cerevisiae transcriptome' (2015) <DOI:10.1038/srep13859>.
Functions for visualizing, modeling, forecasting and hypothesis testing of functional time series.
Functions for estimating spectral density operator of functional
    time series (FTS) and comparing the spectral density operator of two
    functional time series, in a way that allows detection of differences of
    the spectral density operator in frequencies and along the curve length.
Provides utilities to facilitate handling of Fude Polygon data 
    downloadable from the Ministry of Agriculture, Forestry and Fisheries 
    website <https://open.fude.maff.go.jp>.
Lognormal models have broad applications in various research areas such as economics, actuarial science, biology, environmental science and psychology. The estimation problem in lognormal models has been extensively studied. This R package 'fuel' implements thirty-nine existing and newly proposed estimators. See Zhang, F., and Gou, J. (2020), A unified framework for estimation in lognormal models, Technical report.
Fuel economy data from the EPA, 1985-2015,
    conveniently packaged for consumption by R users.
As in music, a fugue statistic repeats a theme in small variations.  Here, the psi-function that defines an m-statistic is slightly altered to maintain the same design sensitivity in matched sets of different sizes.  The main functions in the package are sen() and senCI().  For sensitivity analyses for m-statistics, see Rosenbaum (2007) Biometrics 63 456-464 <doi:10.1111/j.1541-0420.2006.00717.x>.
Provides core functions and utilities for packages and other code
    developed by Jordan Mark Barbone.
We facilitate the analysis of full factorial mating designs with mixed-effects models. There are now six vignettes containing detailed examples.
Enable researchers to adjust identification rates using the 1/(lineup size) method, generate the full receiver operating characteristic (ROC) curves, and statistically compare the area under the curves (AUC). 
  References: Yueran Yang & Andrew Smith. (2020). "fullROC: An R package for generating and analyzing eyewitness-lineup ROC curves". <doi:10.13140/RG.2.2.20415.94885/1>  ,
              Andrew Smith, Yueran Yang, & Gary Wells. (2020). "Distinguishing between investigator discriminability and eyewitness discriminability: A method for creating full receiver operating characteristic curves of lineup identification performance". Perspectives on Psychological Science, 15(3), 589-607. <doi:10.1177/1745691620902426>.
This is a collection of R games and other funny stuff, such as the
    classic Mine sweeper and sliding puzzles.
Provides functions to have visualization and clean-up of enriched gene ontologies (GO) terms, 
    protein complexes and pathways (obtained from multiple databases) using 'ConsensusPathDB' 
    from gene set over-expression analysis. Performs clustering of pathway based on similarity 
    of over-expressed gene sets and visualizations similar to Ingenuity Pathway Analysis (IPA) 
    when up and down regulated genes are known. The methods are described in a paper currently
    submitted by Orecchioni et al, 2020 in Nanoscale.
The FunCC algorithm allows to apply the FunCC algorithm to simultaneously cluster the rows and the columns of a data matrix whose inputs are functions.
Compute alpha and beta contributional diversity metrics,
    which is intended for linking taxonomic and functional microbiome
    data. See 'GitHub' repository for the tutorial:
    <https://github.com/gavinmdouglas/FuncDiv/wiki>. Citation: Gavin M.
    Douglas, Sunu Kim, Morgan G. I. Langille, B. Jesse Shapiro (2023)
    <doi:10.1093/bioinformatics/btac809>.
Provides functional control charts 
    for statistical process monitoring of functional data, 
    using the methods of Capezza et al. (2020) <doi:10.1002/asmb.2507> and 
    Centofanti et al. (2021) <doi:10.1080/00401706.2020.1753581>.
    The package is thoroughly illustrated in the paper of 
    Capezza et al (2023) <doi:10.1080/00224065.2023.2219012>.
YACFP (Yet Another Convenience Function Package). get_age() is a fast & accurate tool for measuring fractional years between two dates. abbr_to_colClass() is a much more concise way of feeding many types to a colClass argument in a data reader. stale_package_check() tries to identify any library() calls to unused packages.
Statistical hypothesis testing methods for
 inferring model-free functional dependency using asymptotic
 chi-squared or exact distributions. Functional test
 statistics are asymmetric and functionally optimal, unique
 from other related statistics. Tests in this package reveal
 evidence for causality based on the causality-by-
 functionality principle. They include asymptotic functional
 chi-squared tests (Zhang & Song 2013) <arXiv:1311.2707>,
 an adapted functional chi-squared test (Kumar & Song 2022) 
 <doi:10.1093/bioinformatics/btac206>, 
 and an exact functional test (Zhong & Song 2019)
 <doi:10.1109/TCBB.2018.2809743> (Nguyen et al. 2020)
 <doi:10.24963/ijcai.2020/372>. The normalized functional
 chi-squared test was used by Best Performer 'NMSUSongLab'
 in HPN-DREAM (DREAM8) Breast Cancer Network Inference
 Challenges (Hill et al. 2016) <doi:10.1038/nmeth.3773>. A
 function index (Zhong & Song 2019)
 <doi:10.1186/s12920-019-0565-9> (Kumar et al. 2018)
 <doi:10.1109/BIBM.2018.8621502> derived from the
 functional test statistic offers a new effect size measure
 for the strength of functional dependency, a better
 alternative to conditional entropy in many aspects. For
 continuous data, these tests offer an advantage over
 regression analysis when a parametric functional form
 cannot be assumed; for categorical data, they provide a
 novel means to assess directional dependency not possible
 with symmetrical Pearson's chi-squared or Fisher's exact
 tests.
Analyzes the function calls in an R package and creates a hive plot of the calls, dividing them among functions that only make outgoing calls (sources), functions that have only incoming calls (sinks), and those that have both incoming calls and make outgoing calls (managers).  Function calls can be mapped by their absolute numbers, their normalized absolute numbers, or their rank.  FuncMap should be useful for comparing packages at a high level for their overall design.  Plus, it's just plain fun.  The hive plot concept was developed by Martin Krzywinski (www.hiveplot.com) and inspired this package.  Note: this package is maintained for historical reasons. HiveR is a full package for creating hive plots.
A collection of functions which fit functional neural network models. In
            other words, this package will allow users to build deep learning models 
            that have either functional or scalar responses paired with functional and 
            scalar covariates. We implement the theoretical discussion found 
            in Thind, Multani and Cao (2020) <arXiv:2006.09590> through the help of a main fitting and 
            prediction function as well as a number of helper functions to assist with 
            cross-validation, tuning, and the display of estimated functional weights.
An implementation of revised functional regression models for multiple genetic variation data, such as single nucleotide polymorphism (SNP) data, which provides revised functional linear regression models, partially functional interaction regression analysis with penalty-based techniques and corresponding drawing functions, etc.(Ruzong Fan, Yifan Wang, James L. Mills, Alexander F. Wilson, Joan E. Bailey-Wilson, and Momiao Xiong (2013) <doi:10.1002/gepi.21757>).
Curry, Compose, and other higher-order functions
Find functions in an unstructured directory and explore their dependencies. 
    Sourcing of R source files is performed without side-effects: from R scripts that have 
    executable code and function definitions only functions are sourced.
S4 classes for univariate and multivariate functional data with
    utility functions. See <doi:10.18637/jss.v093.i05> for a detailed description 
    of the package functionalities and its interplay with the MFPCA package for 
    multivariate functional principal component analysis 
    <https://CRAN.R-project.org/package=MFPCA>.
Computes six functional diversity indices. These are namely,
  Functional Divergence (FDiv), Function Evenness (FEve), Functional Richness
  (FRic), Functional Richness intersections (FRic_intersect), Functional
  Dispersion (FDis), and Rao's entropy (Q) (reviewed in Villéger et al. 2008
  <doi:10.1890/07-1206.1>). Provides efficient, modular, and parallel functions
  to compute functional diversity indices
  (preprint: <doi:10.32942/osf.io/dg7hw>).
The funFEM algorithm (Bouveyron et al., 2014) allows to cluster functional data by modeling the curves within a common and discriminative functional subspace.
Computes fungible coefficients and Monte Carlo data. Underlying theory for these functions is described in the following publications:
    Waller, N. (2008). Fungible Weights in Multiple Regression. Psychometrika, 73(4), 691-703, <DOI:10.1007/s11336-008-9066-z>.
    Waller, N. & Jones, J. (2009). Locating the Extrema of Fungible Regression Weights.
    Psychometrika, 74(4), 589-602, <DOI:10.1007/s11336-008-9087-7>.
    Waller, N. G. (2016). Fungible Correlation Matrices:
    A Method for Generating Nonsingular, Singular, and Improper Correlation Matrices for
    Monte Carlo Research. Multivariate Behavioral Research, 51(4), 554-568, <DOI:10.1080/00273171.2016.1178566>.
    Jones, J. A. & Waller, N. G. (2015). The normal-theory and asymptotic distribution-free (ADF)
    covariance matrix of standardized regression coefficients: theoretical extensions
    and finite sample behavior. Psychometrika, 80, 365-378, <DOI:10.1007/s11336-013-9380-y>.
    Waller, N. G.  (2018).  Direct Schmid-Leiman transformations and rank-deficient loadings matrices.  Psychometrika, 83, 858-870. <DOI:10.1007/s11336-017-9599-0>.
Construction and smart selection of Gaussian process models
	for analysis of computer experiments
	with emphasis on treatment of functional inputs that are regularly sampled. This package
	offers: (i) flexible modeling of functional-input regression
	problems through the fairly general Gaussian process model; (ii)
	built-in dimension reduction for functional inputs; (iii)
	heuristic optimization of the structural parameters of the model
	(e.g., active inputs, kernel function, type of distance).
	Metamodeling background is provided in
	Betancourt et al. (2020) <doi:10.1016/j.ress.2020.106870>.
	The algorithm for structural parameter optimization is described
	in <https://hal.archives-ouvertes.fr/hal-02532713>.
Similar to base's unique function, only optimized for working with 
    data frames, especially those that contain date-time columns.
Provides four addons for analyzing trends and
    unit roots in financial time series: (i) functions for the density
    and probability of the augmented Dickey-Fuller Test, (ii) functions 
    for the density and probability of MacKinnon's unit root test 
    statistics, (iii) reimplementations for the ADF and MacKinnon
    Test, and (iv) an 'urca' Unit Root Test Interface for Pfaff's
    unit root test suite.
Compare variables of interest between (potentially large
    numbers of) spatial interactions and meta-variables. Spatial variables
    are summarized using K, or other, functions, and projected for use in
    a modified random forest model. The model allows comparison of
    functional and non-functional variables to each other and to noise,
    giving statistical significance to the results. Included are
    preparation, modeling, and interpreting tools along with example
    datasets, as described in VanderDoes et al., (2023)
    <doi:10.1101/2023.07.18.549619>.
Allows generating heatmap-like visualisations for benchmark data 
  frames. Funky heatmaps can be fine-tuned by providing annotations of the 
  columns and rows, which allows assigning multiple palettes or geometries
  or grouping rows and columns together in categories.
  Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.
The funLBM algorithm allows to simultaneously cluster the rows and the columns of a data matrix where each entry of the matrix is a function or a time series.
Fits a functional mediation model with a scalar distal outcome. The method is described in detail by Coffman, Dziak, Litson, Chakraborti, Piper & Li (2021) <arXiv:2112.03960>. The model is similar to that of Lindquist (2012) <doi:10.1080/01621459.2012.695640> although allowing a binary outcome as an alternative to a numerical outcome.  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.
Time-based joins to analyze sequence of events, 
    both in memory and out of memory. after_join() joins two 
    tables of events, while funnel_start() and funnel_step() 
    join events in the same table. With the type argument, you
    can switch between different funnel types, like first-first
    and last-firstafter.
An implementation of methods presented by Spiegelhalter (2005) <doi:10.1002/sim.1970> Funnel plots for comparing institutional performance, for standardised ratios, ratios of counts and proportions with additive overdispersion adjustment.
A set of simplified functions for creating funnel plots for proportion data. This package supports user defined benchmarks, confidence limits and estimation methods (i.e. exact or approximate) based on Spiegelhalter (2005) <doi:10.1002/sim.1970>. Additional routines for returning scored unit level data according to a set of specifications is also implemented for convenience. Specifically, both a categorical and a continuous score variable is returned to the sample data frame, which identifies which observations are deemed extreme or in control. Typically, such variables are useful as stratifications or covariates in further exploratory analyses. Lastly, the plotting routine returns a base funnel plot ('ggplot2'), which can also be tailored.
Functional principal component analysis under the Linear Mixed Models representation of smoothing splines. The method utilizes the Demmler-Reinsch basis and assumes error independence. For more details see: F. Rosales (2016) <https://ediss.uni-goettingen.de/handle/11858/00-1735-0000-0028-87F9-6>.
High-order functions for data manipulation : sort or group data, given one
    or more auxiliary functions. Functions are inspired by other pure
    functional programming languages ('Haskell' mainly). The package also 
    provides built-in function operators for creating compact anonymous
    functions, as well as the possibility to use the 'purrr' package syntax.
A small utility which wraps Rscript and provides access to all R
    functions from the shell.
Computes functional rarity indices as proposed by Violle et al.
    (2017) <doi:10.1016/j.tree.2017.02.002>. Various indices can be computed
    using both regional and local information. Functional Rarity combines both
    the functional aspect of rarity as well as the extent aspect of rarity.
    'funrar' is presented in Grenié et al. (2017) <doi:10.1111/ddi.12629>.
Performs functional regression, and some related
    approaches, for intensive longitudinal data (see the book by Walls & Schafer, 
    2006, Models for Intensive Longitudinal Data, Oxford) when such data is not
    necessarily observed on an equally spaced grid of times.  The
    approach generally follows the ideas of Goldsmith, Bobb, Crainiceanu,
    Caffo, and Reich (2011)<DOI:10.1198/jcgs.2010.10007> and the approach taken in their sample code, but
    with some modifications to make it more feasible to use with long rather
    than wide, non-rectangular longitudinal datasets with unequal and
    potentially random measurement times.  It also allows easy plotting of the
    correlation between the smoothed covariate and the outcome as a function of
    time, which can add additional insights on how to interpret a functional
    regression.  Additionally, it also provides several permutation tests for
    the significance of the functional predictor.  The heuristic interpretation
    of ``time'' is used to describe the index of the functional predictor, but
    the same methods can equally be used for another unidimensional continuous
    index, such as space along a north-south axis.  Note that most of the functionality
	of this package has been superseded by added features after 2016 in the 'pfr' function by
    Jonathan Gellar, Mathew W. McLean, Jeff Goldsmith, and Fabian Scheipl, in the 
	'refund' package built by Jeff Goldsmith and co-authors and maintained by Julia Wrobel.
	The development of the funreg package in 2015 and 2016 was part of a research 
	project supported by Award R03 CA171809-01 from the National Cancer Institute and Award P50 
	DA010075 from the National Institute on Drug Abuse. The content is solely the responsibility of the
    authors and does not necessarily represent the official views of the
    National Institute on Drug Abuse, the National Cancer Institute, or the
    National Institutes of Health.
Estimation of functional spaces based on traits of organisms.
    The package includes functions to impute missing trait values (with or
    without considering phylogenetic information), and to create,
    represent and analyse two dimensional functional spaces based on
    principal components analysis, other ordination methods, or raw
    traits. It also allows for mapping a third variable onto the
    functional space.  See 'Carmona et al. (2021)' 
    <doi:10.1038/s41586-021-03871-y>, 'Puglielli et al.  (2021)'
    <doi:10.1111/nph.16952>, 'Carmona et al. (2021)'
    <doi:10.1126/sciadv.abf2675>, 'Carmona et al. (2019)'
    <doi:10.1002/ecy.2876> for more information.
Helpers for parsing out the R functions
  and packages used in R scripts and notebooks.
Implementation of two sample comparison procedures based on median-based statistical tests 
    for functional data, introduced in Smida et al (2022) <doi:10.1080/10485252.2022.2064997>. 
    Other competitive state-of-the-art approaches proposed by Chakraborty and Chaudhuri (2015) <doi:10.1093/biomet/asu072>,
    Horvath et al (2013) <doi:10.1111/j.1467-9868.2012.01032.x> or Cuevas et al (2004) <doi:10.1016/j.csda.2003.10.021>
    are also included in the package, as well as procedures to run test result comparisons and power analysis 
    using simulations.
Computes the functional tangential angle pseudo-depth and its robustified version from the paper by Kuhnt and Rehage (2016). See Kuhnt, S.; Rehage, A. (2016): An angle-based multivariate functional pseudo-depth for shape outlier detection, JMVA 146, 325-340, <doi:10.1016/j.jmva.2015.10.016> for details.
Nonparametric estimators and tests for time series analysis. The functions use bootstrap techniques and robust nonparametric difference-based estimators to test for the presence of possibly non-monotonic trends and for synchronicity of trends in multiple time series.
A collection of toys to do things like generate Collatz sequences, convert a fraction to "continued fraction" form, calculate a fraction which is a close approximation to some value (e.g., 22/7 or 355/113 for pi), and so on.
Contains four main functions (i.e., four pieces of furniture):
    table1() which produces a well-formatted table of descriptive statistics common as Table 1
    in research articles, tableC() which produces a well-formatted table of correlations,
    tableF() which provides frequency counts, and washer() which 
    is helpful in cleaning up the data. These furniture-themed functions are designed 
    to simplify common tasks in quantitative analysis. Other data summary and cleaning tools 
    are also available.
Implementations of the family of map() functions from 'purrr'
    that can be resolved using any 'future'-supported backend, e.g.
    parallel on the local machine or distributed on a compute cluster.
Implementation of fused Markov graphical model (FMGM; Park and Won, 2022). The functions include building mixed graphical model (MGM) objects from data, inference of networks using FMGM, stable edge-specific penalty selection (StEPS) for the determination of penalization parameters, and the visualization. For details, please refer to Park and Won (2022) <arXiv:2208.14959>.
Use Rmarkdown First method to build your package. Start your
    package with documentation, functions, examples and tests in the same
    unique file. Everything can be set from the Rmarkdown template file
    provided in your project, then inflated as a package. Inflating the
    template copies the relevant chunks and sections in the appropriate
    files required for package development.
Enables high-dimensional penalized regression across heterogeneous 
    subgroups. Fusion penalties are used to share information about the linear 
    parameters across subgroups. The underlying model is described 
    in detail in Dondelinger and Mukherjee (2017) <arXiv:1611.00953>.
FusionCharts provides awesome and minimalist functions to make beautiful interactive charts <https://www.fusioncharts.com/>.
Provides the Big Merge Tracker and COSCI algorithms for convex clustering and 
    feature screening using L1 fusion penalty. See Radchenko, P. and Mukherjee, G. (2017) <doi:10.1111/rssb.12226> and 
    T.Banerjee et al. (2017) <doi:10.1016/j.jmva.2017.08.001> for more details.
The fusion learning method uses a model selection algorithm to learn from multiple data sets across different experimental platforms through group penalization. The responses of interest may include a mix of discrete and continuous variables. The responses may share the same set of predictors, however, the models and parameters differ across different platforms. Integrating information from different data sets can enhance the power of model selection. Package is based on Xin Gao, Raymond J. Carroll (2017) <arXiv:1610.00667v1>.
Provides a simple yet powerful logging utility. Based loosely on
    log4j, futile.logger takes advantage of R idioms to make logging a
    convenient and easy to use replacement for cat and print statements.
A scoped options management framework. Used in other packages.
Randomized clinical trials commonly follow participants for a time-to-event efficacy endpoint for a fixed period of time. Consequently, at the time when the last enrolled participant completes their follow-up, the number of observed endpoints is a random variable. Assuming data collected through an interim timepoint, simulation-based estimation and inferential procedures in the standard right-censored failure time analysis framework are conducted for the distribution of the number of endpoints--in total as well as by treatment arm--at the end of the follow-up period. The future (i.e., yet unobserved) enrollment, endpoint, and dropout times are generated according to mechanisms specified in the simTrial() function in the 'seqDesign' package. A Bayesian model for the endpoint rate, offering the option to specify a robust mixture prior distribution, is used for generating future data (see the vignette for details). Inference can be restricted to participants who received treatment according to the protocol and are observed to be at risk for the endpoint at a specified timepoint. Plotting functions are provided for graphical display of results.
The purpose of this package is to provide a lightweight and
    unified Future API for sequential and parallel processing of R
    expression via futures.  The simplest way to evaluate an expression
    in parallel is to use `x %<-% { expression }` with `plan(multisession)`.
    This package implements sequential, multicore, multisession, and
    cluster futures.  With these, R expressions can be evaluated on the
    local machine, in parallel a set of local machines, or distributed
    on a mix of local and remote machines.
    Extensions to this package implement additional backends for
    processing futures via compute cluster schedulers, etc.
    Because of its unified API, there is no need to modify any code in order
    switch from sequential on the local machine to, say, distributed
    processing on a remote compute cluster.
    Another strength of this package is that global variables and functions
    are automatically identified and exported as needed, making it
    straightforward to tweak existing code to make use of futures.
Implementations of apply(), by(), eapply(), lapply(), Map(), .mapply(), mapply(), replicate(), sapply(), tapply(), and vapply() that can be resolved using any future-supported backend, e.g. parallel on the local machine or distributed on a compute cluster.  These future_*apply() functions come with the same pros and cons as the corresponding base-R *apply() functions but with the additional feature of being able to be processed via the future framework.
Implementation of the Future API on top of the 'batchtools' package.
    This allows you to process futures, as defined by the 'future' package,
    in parallel out of the box, not only on your local machine or ad-hoc
    cluster of machines, but also via high-performance compute ('HPC') job
    schedulers such as 'LSF', 'OpenLava', 'Slurm', 'SGE', and 'TORQUE' / 'PBS',
    e.g. 'y <- future.apply::future_lapply(files, FUN = process)'.
Implementation of the Future API on top of the 'callr' package.  This allows you to process futures, as defined by the 'future' package, in parallel out of the box, on your local (Linux, macOS, Windows, ...) machine.  Contrary to backends relying on the 'parallel' package (e.g. 'future::multisession') and socket connections, the 'callr' backend provided here can run more than 125 parallel R processes.
Backends implementing the 'Future' API, as defined by the 'future' package, should use the tests provided by this package to validate that they meet the minimal requirements of the 'Future' API.  The tests can be performed easily from within R or from outside of R from the command line making it straightforward to include them in package tests and in Continuous Integration (CI) pipelines.
Inputs a directory of climate projection files and, for each,
    identifies and characterizes heat waves for specified study locations. The
    definition used to identify heat waves can be customized. Heat wave
    characterizations include several metrics of heat wave length, intensity,
    and timing in the year. The heat waves that are identified can be
    explored using a function to apply user-created functions across all
    generated heat wave files.This work was supported in part by grants from
    the National Institute of Environmental Health Sciences (R00ES022631), the
    National Science Foundation (1331399), and the Colorado State University
    Vice President for Research.
Test function arguments with a wide array of inputs, and produce
  reports summarizing messages, warnings, errors, and returned values.
The main goal of this package is drawing the membership function of the fuzzy p-value which is defined as a fuzzy set on the unit interval for three following problems: (1) testing crisp hypotheses based on fuzzy data, (2) testing fuzzy hypotheses based on crisp data, and (3) testing fuzzy hypotheses based on fuzzy data. In all cases, the fuzziness of data or/and the fuzziness of the boundary of null fuzzy hypothesis transported via the p-value function and causes to produce the fuzzy p-value. If the p-value is fuzzy, it is more appropriate to consider a fuzzy significance level for the problem. Therefore, the comparison of the fuzzy p-value and the fuzzy significance level is evaluated by a fuzzy ranking method in this package.
Calculation of AHP (Analytic Hierarchy Process -
    <http://en.wikipedia.org/wiki/Analytic_hierarchy_process>)
    with classic and fuzzy weights based on Saaty's pairwise
    comparison method for determination of weights.
It provides classifiers which can be used for discrete variables and for continuous variables based on the Naive Bayes and Fuzzy Naive Bayes hypothesis. Those methods were developed by researchers belong to the 'Laboratory of Technologies for Virtual Teaching and Statistics (LabTEVE)' and 'Laboratory of Applied Statistics to Image Processing and Geoprocessing (LEAPIG)' at 'Federal University of Paraiba, Brazil'. They considered some statistical distributions and their papers were published in the scientific literature, as for instance, the Gaussian classifier using fuzzy parameters, proposed by 'Moraes, Ferreira and Machado' (2021) <doi:10.1007/s40815-020-00936-4>.
An interface for training Fuzzy DBScan with both Fuzzy Core and Fuzzy Border.
    Therefore, the package provides a method to initialize and run the algorithm and a
    function to predict new data w.t.h. of 'R6'.
    The package is build upon the paper "Fuzzy Extensions of the DBScan algorithm"
    from Ienco and Bordogna (2018) <doi:10.1007/s00500-016-2435-0>.
    A predict function assigns new data according to the same criteria as the algorithm itself.
    However, the prediction function freezes the algorithm to preserve the trained
    cluster structure and treats each new prediction object individually.
Fuzzy forests, a new algorithm based on random forests,
    is designed to reduce the bias seen in random forest feature selection
    caused by the presence of correlated features.  Fuzzy forests uses
    recursive feature elimination random forests to select
    features from separate blocks of correlated features where the
    correlation within each block of features is high
    and the correlation between blocks of features is low.
    One final random forest is fit using the surviving features.
    This package fits random forests using the 'randomForest' package and
    allows for easy use of 'WGCNA' to split features into distinct blocks.
    See D. Conn, Ngun, T., C. Ramirez, and G. Li (2019) <doi:10.18637/jss.v091.i09>
    for further details.
Join tables together based not on whether columns
  match exactly, but whether they are similar by some comparison.
  Implementations include string distance and regular expression
  matching.
Provides methods to solve Fuzzy Linear Programming Problems with
             fuzzy constraints (following different approaches proposed by 
             Verdegay, Zimmermann, Werners and Tanaka), fuzzy costs, and fuzzy
             technological matrix.
Contains functions for operations with fuzzy cognitive maps using t-norm and s-norm operators. T-norms and S-norms are described by Dov M. Gabbay and George Metcalfe (2007) <doi:10.1007/s00153-007-0047-1>. System indicators are described by Cox, Earl D. (1995) <isbn:1886801010>. Executable examples are provided in the "inst/examples" folder.
S4 classes and methods
    to deal with fuzzy numbers. They allow for computing any arithmetic
    operations (e.g., by using the Zadeh extension principle),
    performing approximation of arbitrary fuzzy numbers by trapezoidal
    and piecewise linear ones, preparing plots for publications, computing
    possibility and necessity values for comparisons, etc.
One can easily draw the membership function of f(x,y) by package 'FuzzyNumbers.Ext.2' in which f(.,.) is supposed monotone and x and y are two fuzzy numbers. This work is possible using function f2apply() which is an extension of function fapply() from Package 'FuzzyNumbers' for two-variable monotone functions. Moreover, this package has the ability of computing the core, support and alpha-cuts of the fuzzy-valued final result.
Estimates fuzzy measures of poverty and deprivation. It also estimates the sampling variance of these measures using bootstrap or jackknife repeated replications.
Fuzzy clustering of species in an ecological community as common or
    rare based on their abundance and occupancy. It also includes functions to
    compute confidence intervals of classification metrics and plot results. See
    Balbuena et al. (2020, <doi:10.1101/2020.08.12.247502>).
Design and simulate fuzzy logic systems using Type-1 and Interval Type-2 Fuzzy Logic.
    This toolkit includes with graphical user interface (GUI) and an adaptive neuro-
    fuzzy inference system (ANFIS). This toolkit is a continuation from the previous
    package ('FuzzyToolkitUoN'). Produced by the Intelligent Modelling & Analysis Group (IMA)
    and Lab for UnCertainty In Data and decision making (LUCID), University of Nottingham. 
    A big thank you to the many people who have contributed to the development/evaluation of the toolbox.
    Please cite the toolbox and the corresponding paper <doi:10.1109/FUZZ48607.2020.9177780> when using it.
    More related papers can be found in the NEWS.
Does fuzzy tests and confidence intervals (following Geyer
    and Meeden, Statistical Science, 2005, <doi:10.1214/088342305000000340>)
    for sign test and Wilcoxon signed rank and rank sum tests.
Estimators for fuzzy linear regression. The functions estimate parameters of 
    fuzzy linear regression models with crisp or fuzzy independent variables (triangular
    fuzzy numbers are supported). Implements multiple methods for parameter estimation and 
    algebraic operations with triangular fuzzy numbers. Includes functions for 
    summarising, printing and plotting the model fit. Calculates predictions from the 
    model and total error of fit. Individual methods are described in
    Diamond (1988) <doi:10.1016/0020-0255(88)90047-3>,
	Hung & Yang (2006) <doi:10.1016/j.fss.2006.08.004>,
	Lee & Tanaka (1999) <doi:10.15807/jorsj.42.98>,
	Nasrabadi, Nasrabadi & Nasrabady (2005) <doi:10.1016/j.amc.2004.02.008>,
	Skrabanek, Marek & Pozdilkova (2021) <doi:10.3390/math9060685>,
	Tanaka, Hayashi & Watada (1989) <doi:10.1016/0377-2217(89)90431-1>,
	Zeng, Feng & Li (2017) <doi:10.1016/j.asoc.2016.09.029>.
The classical (i.e. Efron's, see Efron and Tibshirani (1994, ISBN:978-0412042317)  "An Introduction to the Bootstrap") bootstrap is widely used for both the real (i.e. "crisp") and fuzzy data.
 The main aim of the algorithms implemented in this package  is to overcome a problem with repetition of a few distinct values and to create fuzzy numbers, which are "similar" (but not the same) to values from the initial sample.
 To do this, different characteristics of triangular/trapezoidal numbers are kept (like the value, the ambiguity, etc., see Grzegorzewski et al. <doi:10.2991/eusflat-19.2019.68>, Grzegorzewski et al. (2020) <doi:10.2991/ijcis.d.201012.003>, Grzegorzewski et al. (2020) <doi:10.34768/amcs-2020-0022>, Grzegorzewski and Romaniuk (2022) <doi:10.1007/978-3-030-95929-6_3>,  Romaniuk and Hryniewicz (2019) <doi:10.1007/s00500-018-3251-5>).
 Some additional procedures related to these resampling methods are also provided,
 like calculation of the Bertoluzza et al.'s distance (aka the mid/spread distance, see Bertoluzza et al. (1995) "On a new class of distances between fuzzy numbers")
 and estimation of the p-value of the one- and two- sample bootstrapped test for the mean (see Lubiano et al. (2016, <doi:10.1016/j.ejor.2015.11.016>)).
 Additionally, there are procedures which randomly generate trapezoidal fuzzy numbers using some well-known statistical distributions.
Functions to compute fuzzy versions of species occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis, and prevalence-independent favourability obtained from probability of presence), as well as pair-wise fuzzy similarity (based on fuzzy logic versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model consensus and comparison (overlap and fuzzy similarity, loss or gain), and for data preparation, such as obtaining unique abbreviations of species names, cleaning and gridding (thinning) point occurrence data onto raster maps, selecting absences under specified criteria, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, selecting relevant variables for models, assessing the false discovery rate, or analysing and dealing with multicollinearity. Initially described in Barbosa (2015) <doi:10.1111/2041-210X.12372>.
Random simulations of fuzzy numbers are still a challenging problem. The aim of this package is to provide the respective 
 procedures to simulate fuzzy random variables, especially in the case of the piecewise linear fuzzy numbers (PLFNs, 
 see Coroianua et al. (2013) <doi:10.1016/j.fss.2013.02.005> for the further details).
 Additionally, the special resampling algorithms known as the epistemic bootstrap are provided (see Grzegorzewski and Romaniuk
 (2022) <doi:10.34768/amcs-2022-0021>, Grzegorzewski and Romaniuk (2022) <doi:10.1007/978-3-031-08974-9_39>)
 together with the functions to apply statistical tests and estimate various characteristics based on the epistemic bootstrap.
 The package also includes a real-life data set of epistemic fuzzy triangular numbers.
 The fuzzy numbers used in this package are consistent with the 'FuzzyNumbers' package.
An implementation of a method for computing fuzzy numbers representing stationary probabilities of an unknown Markov chain,
        from which a sequence of observations along time has been obtained. The algorithm is based on the proposal presented by James Buckley 
        in his book on Fuzzy probabilities (Springer, 2005), chapter 6. Package 'FuzzyNumbers' is used to represent the output probabilities.
The aim of the package is to provide some basic functions
 for doing statistics with trapezoidal fuzzy numbers. In particular,
  the package contains several functions for simulating trapezoidal 
  fuzzy numbers, as well as for calculating some central tendency 
  measures (mean and two types of median), some scale measures 
  (variance, ADD, MDD, Sn, Qn, Tn and some M-estimators) and 
  one diversity index and one inequality index. Moreover, 
  functions for calculating the 1-norm distance, the mid/spr 
  distance and the (phi,theta)-wabl/ldev/rdev distance between 
  fuzzy numbers are included, and a function to calculate the 
  value phi-wabl given a sample of trapezoidal fuzzy numbers.
The aim of the package is to contain the package 'FuzzyStatTra' in 
    Encapsulated Object Oriented Programming using R6. 'FuzzyStatTra' contains Statistical 
    Methods for Trapezoidal Fuzzy Numbers, whose aim is to provide some basic functions 
    for doing statistical analysis with trapezoidal fuzzy numbers. For more details, you 
    can visit the website of the SMIRE+CoDiRE (Statistical Methods with Imprecise Random 
    Elements and Comparison of Distributions of Random Elements) Research Group 
    (<https://bellman.ciencias.uniovi.es/smire+codire/>). The most related paper can be 
    found in References. Now, those functions are organized in specific classes and methods. 
    This object-based approach is an important step in making statistical computing more 
    accessible to users.
The main goal of this package is to present various fuzzy statistical tools. It intends to provide an implementation of the theoretical and empirical approaches presented in the thesis entitled "The signed distance measure in fuzzy statistical analysis. Some theoretical, empirical and programming advances" (Thesis to be published soon. For the theoretical approaches, see Berkachy R. and Donze L. (2019) <doi:10.1007/978-3-030-03368-2_1>. For the empirical approaches, see Berkachy R. and Donze L. (2016) <ISBN: 978-989-758-201-1>). Important (non-exhaustive) implementation highlights of this package are as follows: (1) a numerical procedure to estimate the fuzzy difference and the fuzzy square. (2) two numerical methods of fuzzification. (3) a function performing different possibilities of distances, including the signed distance and the generalized signed distance for instance. (4) numerical estimations of fuzzy statistical measures such as the variance, the moment, etc. (5) two methods of estimation of the bootstrap distribution of the likelihood ratio in the fuzzy context. (6) an estimation of a fuzzy confidence interval by the likelihood ratio method. (7) testing fuzzy hypotheses and/or fuzzy data by fuzzy confidence intervals in the Kwakernaak - Kruse and Meyer sense. (8) a general method to estimate the fuzzy p-value with fuzzy hypotheses and/or fuzzy data. (9) a method of estimation of global and individual evaluations of linguistic questionnaires. (10) numerical estimations of multi-ways analysis of variance models in the fuzzy context. The unbalance in the considered designs are also foreseen.
Fuzzy string matching implementation of the 'fuzzywuzzy' <https://github.com/seatgeek/fuzzywuzzy> 'python' package. It uses the Levenshtein Distance <https://en.wikipedia.org/wiki/Levenshtein_distance> to calculate the differences between sequences.
An implementation of the fractional weighted bootstrap to be used as a drop-in for functions in
   the 'boot' package. The fractional weighted bootstrap (also known as the Bayesian bootstrap) involves drawing
   weights randomly that are applied to the data rather than resampling units from the data. See Xu et al. (2020)
   <doi:10.1080/00031305.2020.1731599> for details.
A simple method
    to select the best model or best subset of variables using
    different types of data (binary, Gaussian or Poisson) and
    applying it in different contexts (parametric or non-parametric).
Provides three functions to calculate the outputs of the two main components of the Canadian Forest Fire Danger Rating System (CFFDRS): the Fire Weather Index (FWI) System and the Fire Behaviour Prediction (FBP) System.
Implementation of fast algorithms for wild cluster bootstrap 
             inference developed in 'Roodman et al' (2019, 'STATA' Journal,
             <doi:10.1177/1536867X19830877>) and 'MacKinnon et al' (2022), 
             which makes it feasible to quickly calculate bootstrap test 
             statistics based on a large number of bootstrap draws even for 
             large samples. Multiple bootstrap types as described in 'MacKinnon, 
             Nielsen & Webb' (2022) are supported. 
             Further, 'multiway' clustering, regression weights, 
             bootstrap weights, fixed effects and 'subcluster' bootstrapping
             are supported. Further, both restricted ('WCR') and unrestricted
             ('WCU') bootstrap are supported. Methods are provided for a variety 
             of fitted models, including 'lm()', 'feols()' 
             (from package 'fixest') and 'felm()' (from package 'lfe'). 
             Additionally implements a 'heteroskedasticity-robust' ('HC1') wild 
             bootstrap.
             Last, the package provides an R binding to 'WildBootTests.jl',
             which provides additional speed gains and functionality, 
             including the 'WRE' bootstrap for instrumental variable models 
             (based on models of type 'ivreg()' from package 'ivreg')
             and hypotheses with q > 1.
Creates a scatter plot after residualizing using a set of covariates. The residuals are calculated using the 'fixest' package which allows very fast estimation that scales. Details of the (Yule-)Frisch-Waugh-Lovell theorem is given in Basu (2023) <arXiv:2307.00369>.
Fresh biomass determination is the key to evaluating crop genotypes' response to diverse input and stress conditions and forms the basis for calculating net primary production. However, as conventional phenotyping approaches for measuring fresh biomass is time-consuming, laborious and destructive, image-based phenotyping methods are being widely used now. In the image-based approach, the fresh weight of the above-ground part of the plant depends on the projected area. For determining the projected area, the visual image of the plant is converted into the grayscale image by simply averaging the Red(R), Green (G) and Blue (B) pixel values. Grayscale image is then converted into a binary image using Otsu’s thresholding method Otsu, N. (1979) <doi:10.1109/TSMC.1979.4310076> to separate plant area from the background (image segmentation). The segmentation process was accomplished by selecting the pixels with values over the threshold value belonging to the plant region and other pixels to the background region. The resulting binary image consists of white and black pixels representing the plant and background regions. Finally, the number of pixels inside the plant region was counted and converted to square centimetres (cm2) using the reference object (any object whose actual area is known previously) to get the projected area. After that, the projected area is used as input to the machine learning model (Linear Model, Artificial Neural Network, and Support Vector Regression) to determine the plant's fresh weight.
Simulates a population under the Fisher-Wright model (fixed or stochastic population size) with a one-step neutral mutation process (stepwise mutation model, logistic mutation model and exponential mutation model supported). The stochastic population sizes are random Poisson distributed and different kinds of population growth are supported. For the stepwise mutation model, it is possible to specify locus and direction specific mutation rate (in terms of upwards and downwards mutation rate). Intermediate generations can be saved in order to study e.g. drift.
The 'fxl' Charting package is used to prepare and design single case design figures that are typically prepared in spreadsheet software. With 'fxl', there is no need to leave the R environment to prepare these works.
Exchange rate regression and structural change tools
             for estimating, testing, dating, and monitoring
	     (de facto) exchange rate regimes.
The goal of this package is to provide an improved version of 
    WA-PLS (Weighted Averaging Partial Least Squares) by including the 
    tolerances of taxa and the frequency of the sampled climate variable. 
    This package also provides a way of leave-out cross-validation that 
    removes both the test site and sites that are both geographically 
    close and climatically close for each cycle, to avoid the risk of 
    pseudo-replication.
In Australia, a financial year (or fiscal year) is the period from 1 July to 30 June
     of the following calendar year. As such, many databases need to represent and 
     validate financial years efficiently. While the use of integer years with a convention that  
     they represent the year ending is common, it may lead to ambiguity with calendar years.
     On the other hand, string representations may be too inefficient and do not easily admit
     arithmetic operations. This package tries to make validation of financial years quicker while
     retaining clarity.
Create and maintain delayed-data packages (ddp's).  Data stored in
  a ddp are available on demand, but do not take up memory until requested.
  You attach a ddp with g.data.attach(), then read from it and assign to it in
  a manner similar to S-PLUS, except that you must run g.data.save() to
  actually commit to disk.
Full descriptive statistics, physical description of sediment,
            metric or phi sieves.
Interface for 'g3-lollipop' JavaScript library.
    Visualize genetic mutation data using an interactive lollipop diagram in Studio or your browser.
Flexible general-purpose toolbox implementing genetic algorithms (GAs) for stochastic optimisation. Binary, real-valued, and permutation representations are available to optimize a fitness function, i.e. a function provided by users depending on their objective function. Several genetic operators are available and can be combined to explore the best settings for the current task. Furthermore, users can define new genetic operators and easily evaluate their performances. Local search using general-purpose optimisation algorithms can be applied stochastically to exploit interesting regions. GAs can be run sequentially or in parallel, using an explicit master-slave parallelisation or a coarse-grain islands approach.
Scale abbreviation using Genetic Algorithms that maximally capture the variance in the original data.
Help to the occasional R user for synthesis and enhanced graphical visualization of redundancy analysis (RDA) and principal component analysis (PCA) methods and objects.
  Inputs are : data frame, RDA (package 'vegan') and PCA (package 'FactoMineR') objects.
  Outputs are : synthesized results of RDA, displayed in console and saved in tables ; displayed and saved objects of PCA graphic visualization of individuals and variables projections with multiple graphic parameters.
  Method note : for the RDA output synthesis, several functions of the package 'RVAideMemoire', developed by Maxime Hervé, are exploited.
The genetic algorithm can be used directly to find the similarity of users and more effectively to increase the efficiency of the collaborative filtering method.
  By identifying the nearest neighbors to the active user, before the genetic algorithm, and by identifying suitable starting points, an effective method for user-based collaborative filtering method has been developed.
  This package uses an optimization algorithm (continuous genetic algorithm) to directly find the optimal similarities between active users (users for whom current recommendations are made) and others.
  First, by determining the nearest neighbor and their number, the number of genes in a chromosome is determined. Each gene represents the neighbor's similarity to the active user.
  By estimating the starting points of the genetic algorithm, it quickly converges to the optimal solutions.
  The positive point is the independence of the genetic algorithm on the number of data that for big data is an effective help in solving the problem.
This package analyses complex ANOVA models with any
        combination of orthogonal/nested and fixed/random factors, as
        described by Underwood (1997). There are two restrictions: (i)
        data must be balanced; (ii) fixed nested factors are not
        allowed. Homogeneity of variances is checked using Cochran's C
        test and 'a posteriori' comparisons of means are done using
        Student-Newman-Keuls (SNK) procedure.
Sparse large Directed Acyclic Graphs learning with a combination of a convex program and a tailored genetic algorithm (see Champion et al. (2017) <https://hal.archives-ouvertes.fr/hal-01172745v2/document>).
A statistical ecosystem modelling package, taking many features of
             the ecosystem into account. Gadget works by running an internal
             model based on many parameters, and then comparing the data from
             the output of this model to real data to get a goodness-of-fit
             likelihood score. These parameters can then be adjusted, and the
             model re-run, until an optimum is found, which corresponds to the
             model with the lowest likelihood score. Gadget allows the user to
             include a number of features into an ecosystem model: One or more
             species, each of which may be split into multiple stocks; multiple
             areas with migration between areas; predation between and within
             species; maturation; reproduction and recruitment; multiple
             commercial and survey fleets taking catches from the populations.
             For more details see <https://gadget-framework.github.io/gadget2/>.
             This is the C++ Gadget2 runtime, making it available for R.
A framework to assist creation of marine ecosystem models,
             generating either 'R' or 'C++' code which can then be optimised using
             the 'TMB' package and standard 'R' tools. Principally designed to
             reproduce gadget2 models in 'TMB', but can be extended beyond
             gadget2's capabilities.
             Kasper Kristensen, Anders Nielsen, Casper W. Berg, Hans Skaug, Bradley M. Bell (2016) <doi:10.18637/jss.v070.i05> "TMB: Automatic Differentiation and Laplace Approximation.".
             Begley, J., & Howell, D. (2004) <https://core.ac.uk/download/pdf/225936648.pdf> "An overview of Gadget, the globally applicable area-disaggregated general ecosystem toolbox. ICES.".
A group of sample points are evaluated against a
        user-defined expression, the sample points are lists of
        parameters with values that may be substituted into that
        expression. The genetic algorithm attempts to make the result
        of the expression as low as possible (usually this would be the
        sum of residuals squared).
Fits linear regression, logistic and multinomial regression models, Poisson regression, Cox model via Global Adaptive Generative Adjustment Algorithm.  
 For more detailed information, see Bin Wang, Xiaofei Wang and Jianhua Guo (2022) <arXiv:1911.00658>. 
 This paper provides the theoretical properties of Gaga linear model when the load matrix is orthogonal. 
 Further study is going on for the nonorthogonal cases and generalized linear models. 
 These works are in part supported by the National Natural Foundation of China (No.12171076).
Performs genetic algorithm (Scrucca, L (2013) <doi:10.18637/jss.v053.i04>) 
             assisted genomic best liner unbiased prediction for genomic selection.
             It also provides a binning method in natural population for genomic selection
             under the principle of linkage disequilibrium for dimensional reduction.
Tools for using genetic markers, stable isotope data, and habitat
    suitability data to calculate posterior probabilities of breeding origin of
    migrating birds.
Provides an effective machine learning-based tool that quantifies the gain of passive device installation on wind turbine generators.
  H. Hwangbo, Y. Ding, and D. Cabezon (2019) <arXiv:1906.05776>.
Constructs gains tables and lift charts for prediction algorithms. Gains tables and lift charts are commonly used in direct marketing applications.  The method is described in Drozdenko and Drake (2002), "Optimal Database Marketing", Chapter 11.
Implements graphical extension with accuracy in parameter estimation (AIPE) on RMSEA for sample size planning in structural equation modeling based on Lin, T.-Z. & Weng, L.-J. (2014) <doi: 10.1080/10705511.2014.915380>. And, it can also implement AIPE on RMSEA and power analysis on RMSEA.
The Global Biodiversity Information Facility 
    (GBIF, <https://www.gbif.org>) sources data from an international network of 
    data providers, known as 'nodes'. Several of these nodes - the 'living 
    atlases' (<https://living-atlases.gbif.org>) - maintain their own
    web services using a codebase originally developed by the Atlas of Living 
    Australia (ALA, <https://www.ala.org.au>). 'galah' enables the R community 
    to directly access data and resources hosted by GBIF and its partner nodes.
Estimates generalized additive latent and
    mixed models using maximum marginal likelihood, 
    as defined in Sorensen et al. (2023) 
    <doi:10.1007/s11336-023-09910-z>, which is an extension of Rabe-Hesketh and
    Skrondal (2004)'s unifying framework for multilevel latent variable 
    modeling <doi:10.1007/BF02295939>. Efficient computation is done using sparse 
    matrix methods, Laplace approximation, and automatic differentiation. The 
    framework includes generalized multilevel models with heteroscedastic 
    residuals, mixed response types, factor loadings, smoothing splines, 
    crossed random effects, and combinations thereof. Syntax for model 
    formulation is close to 'lme4' (Bates et al. (2015) 
    <doi:10.18637/jss.v067.i01>) and 'PLmixed' (Rockwood and Jeon (2019) 
    <doi:10.1080/00273171.2018.1516541>).
Collection of packages for work with API 'Google Ads' <https://developers.google.com/google-ads/api/docs/start>, 
    'Yandex Direct' <https://yandex.ru/dev/direct/>, 'Yandex Metrica' <https://yandex.ru/dev/metrika/>, 
    'MyTarget' <https://target.my.com/help/advertisers/api_arrangement/ru>, 'Vkontakte' <https://vk.com/dev/methods>, 
    'Facebook' <https://developers.facebook.com/docs/marketing-apis/> and 'AppsFlyer' <https://support.appsflyer.com/hc/en-us/articles/207034346-Using-Pull-API-aggregate-data>. 
    This packages allows you loading data from ads account and manage your ads materials.
The accurate annotation of genes and Quantitative Trait Loci (QTLs) located within candidate markers and/or regions (haplotypes, windows, CNVs, etc) is a crucial step the most common genomic analyses performed in livestock, such as Genome-Wide Association Studies or transcriptomics. The Genomic Annotation in Livestock for positional candidate LOci (GALLO) is an R package designed to provide an intuitive and straightforward environment to annotate positional candidate genes and QTLs from high-throughput genetic studies in livestock. Moreover, GALLO allows the graphical visualization of gene and QTL annotation results, data comparison among different grouping factors (e.g., methods, breeds, tissues, statistical models, studies, etc.), and QTL enrichment in different livestock species including cattle, pigs, sheep, and chicken, among others.
Includes the ga.lts() function that estimates
        LTS (Least Trimmed Squares) parameters using genetic algorithms
        and C-steps. ga.lts() constructs a genetic algorithm to form a
        basic subset and iterates C-steps as defined in Rousseeuw and
        van-Driessen (2006) to calculate the cost value of the LTS
        criterion. OLS (Ordinary Least Squares) regression is known to
        be sensitive to outliers. A single outlying observation can
        change the values of estimated parameters. LTS is a resistant
        estimator even the number of outliers is up to half of the
        data. This package is for estimating the LTS parameters with
        lower bias and variance in a reasonable time. Version >=1.3 
        includes the function medmad for fast outlier detection in
        linear regression.
An R interface to the Galvanize 'Highbond' API <https://docs-apis.highbond.com>.
Functions for fitting and working with generalized
		additive models, as described in chapter 7 of "Statistical Models in S" (Chambers and Hastie (eds), 1991), and "Generalized Additive Models" (Hastie and Tibshirani, 1990).
Data sets and scripts used in the book 'Generalized Additive 
             Models: An Introduction with R', Wood (2006,2017) CRC.
Fits unimodal and multimodal gambin distributions to species-abundance distributions
    from ecological data, as in in Matthews et al. (2014) <DOI:10.1111/ecog.00861>. 
    'gambin' is short for 'gamma-binomial'. The main function is fit_abundances(), which estimates 
    the 'alpha' parameter(s) of the gambin distribution using maximum likelihood. Functions are 
    also provided to generate the gambin distribution and for calculating likelihood statistics.
Simulates a gambling game under the gambler's ruin setup, after asking for the money you have and the money you want to win, along with your win probability in each round of the game.
Boosting models for fitting generalized additive models for
  location, shape and scale ('GAMLSS') to potentially high dimensional
  data.
Contains infrastructure for using mboost::gamboost() in order to estimate multistate models.
Functions and data are provided that support a course
        that emphasizes statistical issues of inference and generalizability.  
        The functions are designed to make it straightforward to illustrate
        the use of cross-validation, the training/test approach, simulation, 
        and model-based estimates of accuracy.  Methods considered are
        Generalized Additive Modeling, Linear and Quadratic Discriminant
        Analysis, Tree-based methods, and Random Forests.
Implementation of various inference and simulation tools to
    apply generalized additive models to bivariate dependence structures and
    non-simplified vine copulas.
Implements the GAMbag, GAMrsm and GAMens ensemble
    classifiers for binary classification (De Bock et al., 2010) <doi:10.1016/j.csda.2009.12.013>. The ensembles
    implement Bagging (Breiman, 1996) <doi:10.1023/A:1010933404324>, the Random Subspace Method (Ho, 1998) <doi:10.1109/34.709601>
    , or both, and use Hastie and Tibshirani's (1990, ISBN:978-0412343902) generalized additive models (GAMs)
    as base classifiers. Once an ensemble classifier has been trained, it can
    be used for predictions on new data. A function for cross validation is also
    included.
Finds adaptive strategies for sequential symmetric 
    games using a genetic algorithm. Currently, any symmetric two by two matrix
    is allowed, and strategies can remember the history of an opponent's play
    from the previous three rounds of moves in iterated interactions between
    players. The genetic algorithm returns a list of adaptive strategies given
    payoffs, and the mean fitness of strategies in each generation.
Implementation of a common set of punctual solutions  for Cooperative Game Theory.
Many situations can be modeled as game theoretic situations. Some procedures are included in this package to calculate the most important allocations rules in Game Theory: Shapley value, Owen value or nucleolus, among other. First, we must define as an argument the value of the unions of the envolved agents with the characteristic function.
The gamma lasso algorithm provides regularization paths corresponding to a range of non-convex cost functions between L0 and L1 norms.  As much as possible, usage for this package is analogous to that for the glmnet package (which does the same thing for penalization between L1 and L2 norms).  For details see: Taddy (2017 JCGS), 'One-Step Estimator Paths for Concave Regularization', <arXiv:1308.5623>.
Functions for fitting the Generalized Additive Models for Location Scale and Shape introduced by Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The models use a distributional regression approach where all the parameters of the conditional distribution of the response variable are modelled using explanatory variables.
Interface for extra smooth functions including tensor products, neural networks and decision trees.
This is an add-on package to GAMLSS. The purpose of this
        package is to allow users to fit interval response variables in
        GAMLSS models. The main function gen.cens() generates a
        censored version of an existing GAMLSS family distribution.
This is an add on package to 'GAMLSS'. The main purpose of this package is generating and fitting inflated distributions at any desired point (0, 1, 2, ...). The function gen.Kinf() generates K-inflated version of an existing discrete 'GAMLSS' family distribution.
Data used as examples in the current two books on Generalised Additive Models for Location Scale and Shape introduced by Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>.
Demos for smoothing and gamlss.family distributions.
A set of distributions which can be used for modelling the response variables in Generalized Additive Models for Location Scale and Shape, Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The distributions can be continuous, discrete or mixed distributions. Extra distributions can be created, by transforming, any continuous distribution defined on the real line, to a distribution defined on ranges 0 to infinity or 0 to 1, by using a 'log' or a 'logit' transformation respectively.
Computational intensive calculations for Generalized Additive Models for Location Scale and Shape, <doi:10.1111/j.1467-9876.2005.00510.x>.
This is an add-on package to 'gamlss'. The purpose of this package is to allow users to fit GAMLSS (Generalised Additive Models for Location Scale and Shape) models when the response variable is defined either in the intervals [0,1), (0,1] and [0,1] (inflated at zero and/or one distributions), or in the positive real line including zero (zero-adjusted distributions). The mass points at zero and/or one are treated as extra parameters with the possibility to include a linear predictor for both. The package also allows transformed or truncated distributions from the GAMLSS family to be used for the continuous part of the distribution. Standard methods and GAMLSS diagnostics can be used with the resulting fitted object.
Interface for extra high-dimensional smooth functions for Generalized Additive Models for Location Scale and Shape (GAMLSS) including (adaptive) lasso, ridge, elastic net and least angle regression.
The main purpose of this package is to allow fitting of
        mixture distributions with generalised additive models for location 
        scale and shape models see Chapter 7 of Stasinopoulos et al. (2017) <doi:10.1201/b21973-4>.
It allows us to fit Gaussian Markov Random Field within the
    Generalized Additive Models for Location Scale and Shape algorithms.
This is an add on package to GAMLSS. The purpose of this
        package is to allow users to defined truncated distributions in
        GAMLSS models. The main function gen.trun() generates truncated
        version of an existing GAMLSS family distribution.
Density, distribution function, quantile function and random generation for the bimodal skew symmetric normal distribution of Hassan and El-Bassiouni (2016) <doi:10.1080/03610926.2014.882950>.
Estimate generalized additive mixed models via a version of
         function gamm() from 'mgcv', using 'lme4' for estimation.
Process in-situ Gamma-Ray Spectrometry for Luminescence
    Dating. This package allows to import, inspect and correct the energy
    shifts of Gamma-ray spectra. It provides methods for estimating the
    gamma dose rate by the use of a calibration curve as described in
    Mercier and Falguères (2007).  The package only supports Canberra CNF
    and TKA files.
Performs Gamma regression, where both mean and shape parameters follows lineal regression structures.
Uses a slice sampling-based Markov chain Monte Carlo to
        conduct Bayesian fitting and inference for generalized additive
        mixed models.  Generalized linear mixed models and generalized 
        additive models are also handled as special cases of generalized
        additive mixed models. The methodology and software is described 
        in Pham, T.H. and Wand, M.P. (2018). Australian and New Zealand
        Journal of Statistics, 60, 279-330 <DOI:10.1111/ANZS.12241>.
Robust regression via gamma-divergence with L1, elastic net and ridge.
To calculate the relative risk (RR) for the generalized additive model.
Using overlap grouped-lasso penalties, 'gamsel' selects whether a term in a 'gam' is nonzero, linear, or a non-linear spline (up to a specified max df per variable). It fits the entire regularization path on a grid of values for the overall penalty lambda, both for gaussian and binomial families.
Generalized additive model selection via approximate Bayesian inference is provided. Bayesian mixed model-based penalized splines with spike-and-slab-type coefficient prior distributions are used to facilitate fitting and selection. The approximate Bayesian inference engine options are: (1) Markov chain Monte Carlo and (2) mean field variational Bayes. Markov chain Monte Carlo has better Bayesian inferential accuracy, but requires a longer run-time. Mean field variational Bayes is faster, but less accurate. The methodology is described in He and Wand (2023) <arXiv:2201.00412>.
Neural networks are applied to create a density value function which approximates density values for a data source. The trained neural network is analyzed for different levels. For each level metric subspaces with density values above a level are determined. The obtained set of metric subspaces and the trained neural network are assembled into a data model. A prerequisite is the definition of a data source, the generation of generative data and the calculation of density values. These tasks are executed using package 'ganGenerativeData' <https://cran.r-project.org/package=ganGenerativeData>.
Generative Adversarial Networks are applied to generate generative data for a data source. In iterative training steps the distribution of generated data converges to that of the data source. Direct applications of generative data are the created functions for data classifying and missing data completion. Reference: Goodfellow et al. (2014) <arXiv:1406.2661v1>.
A network-based gene weighting algorithm for pathway enrichment analysis, using either RNA-seq or microarray data. Zhaoyuan Fang, Weidong Tian and Hongbin Ji (2012) <doi:10.1038/cr.2011.149>.
This is a dataset package for GANPA, which implements a
        network-based gene weighting approach to pathway analysis. This
        package includes data useful for GANPA, such as a functional
        association network, pathways, an expression dataset and
        multi-subunit proteins.
As first reported [Zhao, J. H. 2007. "gap: Genetic Analysis Package". J Stat Soft 23(8):1-18.
        <doi:10.18637/jss.v023.i08>], it is designed as an integrated package for genetic data
        analysis of both population and family data. Currently, it contains functions for
        sample size calculations of both population-based and family-based designs, probability
        of familial disease aggregation, kinship calculation, statistics in linkage analysis,
        and association analysis involving genetic markers including haplotype analysis with or
        without environmental covariates. Over years, the package has been developed in-between
        many projects hence also in line with the name (gap).
Datasets associated with the 'gap' package. Currently,
             it includes an example data for regional association
             plot (CDKN), an example data for a genomewide association
             meta-analysis (OPG), data in studies of Parkinson's diease (PD),
             ALHD2 markers and alcoholism (aldh2), APOE/APOC1 markers
             and Schizophrenia (apoeapoc), cystic fibrosis (cf), a
             Olink/INF panel (inf1), Manhattan plots with (hr1420, mhtdata)
             and without (w4) gene annotations.
Methodology that combines feature selection, model tuning, and parsimonious model selection with Genetic Algorithms (GA) proposed in {Martinez-de-Pison} (2015) <DOI:10.1016/j.asoc.2015.06.012>. To this objective, a novel GA selection procedure is introduced based on separate cost and complexity evaluations.
Provides functions to estimate the disparities across categories (e.g. Black and white) that persists if a treatment variable (e.g. college) is equalized. Makes estimates by treatment modeling, outcome modeling, and doubly-robust augmented inverse probability weighting estimation, with standard errors calculated by a nonparametric bootstrap. Cross-fitting is supported. Survey weights are supported for point estimation but not for standard error estimation; those applying this package with complex survey samples should consult the data distributor to select an appropriate approach for standard error construction, which may involve calling the functions repeatedly for many sets of replicate weights provided by the data distributor. The methods in this package are described in Lundberg (2021) <doi:10.31235/osf.io/gx4y3>.
Tools to fill missing values in satellite data and to develop new
    gap-fill algorithms. The methods are tailored to data (images) observed
    at equally-spaced points in time. The package is illustrated with MODIS
    NDVI data.
The gap encodes the distance between clusters and improves
    interpretation of cluster heatmaps. The gaps can be of the same
    distance based on a height threshold to cut the dendrogram. Another
    option is to vary the size of gaps based on the distance between
    clusters.
An excerpt of the data available at Gapminder.org. For each
    of 142 countries, the package provides values for life expectancy, GDP
    per capita, and population, every five years, from 1952 to 2007.
Provides functions to estimate model parameters and forecast future volatilities using the Unified GARCH-Ito [Kim and Wang (2016) <doi:10.1016/j.jeconom.2016.05.003>] and Realized GARCH-Ito [Song et. al. (2020) <doi:10.1016/j.jeconom.2020.07.007>] models. Optimization is done using augmented Lagrange multiplier method.
Functions for estimating a GARCHSK model and GJRSK model based on a publication by Leon et,al (2005)<doi:10.1016/j.qref.2004.12.020> and Nakagawa and Uchiyama (2020)<doi:10.3390/math8111990>. These are a GARCH-type model allowing for time-varying volatility, skewness and kurtosis.
Flexible and robust estimation and inference of generalised autoregressive conditional heteroscedasticity (GARCH) models with covariates ('X') based on the results by Francq and Thieu (2018) <doi:10.1017/S0266466617000512>. Coefficients can straightforwardly be set to zero by omission, and quasi maximum likelihood methods ensure estimates are generally consistent and inference valid, even when the standardised innovations are non-normal and/or dependent over time, see <https://journal.r-project.org/archive/2021/RJ-2021-057/RJ-2021-057.pdf> for an overview of the package.
Gene and Region Counting of Mutations (GARCOM) package computes mutation (or alleles) counts per gene per individuals based on gene annotation or genomic base pair boundaries. It comes with features to accept data formats in plink(.raw) and VCF. It provides users flexibility to extract and filter individuals, mutations and genes of interest.
Provides utilities for working with Google APIs
    <https://developers.google.com/apis-explorer>.  This includes
    functions and classes for handling common credential types and for
    preparing, executing, and processing HTTP requests.
An event-Based framework for building 'Shiny' apps.
    Instead of relying on standard 'Shiny' reactive objects, this 
    package allow to relying on a lighter set of triggers, so that 
    reactive contexts can be invalidated with more control.
Methods for estimating univariate long memory-seasonal/cyclical
             Gegenbauer time series processes. See for example (2022) <doi:10.1007/s00362-022-01290-3>.
             Refer to the vignette for details of fitting these processes.
Organize a so-called ragged array as generalized arrays, which
	is simply an array with sub-dimensions denoting the subdivision of
	dimensions (grouping of members within dimensions).
	By the margins (names of dimensions and sub-dimensions) in generalized
	arrays, operators and utility functions provided in this package
	automatically match the margins,
	doing map-reduce style parallel computation
	along margins.  Generalized arrays are also cooperative to R's native
	functions that work on simple arrays.
Simulate, estimate and forecast using univariate and multivariate GAS models 
  as described in Ardia et al. (2019) <doi:10.18637/jss.v088.i06>.
Provides a genetic algorithm for finding variable
    subsets in high dimensional data with high prediction performance. The
    genetic algorithm can use ordinary least squares (OLS) regression models or
    partial least squares (PLS) regression models to evaluate the prediction
    power of variable subsets. By supporting different cross-validation
    schemes, the user can fine-tune the tradeoff between speed and quality of
    the solution.
Functions for greenhouse gas flux calculation from chamber
    measurements.
Estimation, forecasting, and simulation of generalized
    autoregressive score (GAS) models of Creal, Koopman, and Lucas (2013)
    <doi:10.1002/jae.1279> and Harvey (2013) <doi:10.1017/cbo9781139540933>.
    Model specification allows for various data types and distributions,
    different parametrizations, exogenous variables, joint and separate modeling
    of exogenous variables and dynamics, higher score and autoregressive orders,
    custom and unconditional initial values of time-varying parameters, fixed
    and bounded values of coefficients, and missing values. Model estimation is
    performed by the maximum likelihood method and the Hessian matrix.
Train a Gaussian stochastic process model of an unknown function, possibly observed with error, via maximum likelihood or maximum a posteriori (MAP) estimation, run model diagnostics, and make predictions, following Sacks, J., Welch, W.J., Mitchell, T.J., and Wynn, H.P. (1989) "Design and Analysis of Computer Experiments", Statistical Science, <doi:10.1214/ss/1177012413>.  Perform sensitivity analysis and visualize low-order effects, following Schonlau, M. and Welch, W.J. (2006), "Screening the Input Variables to a Computer Model Via Analysis of Variance and Visualization", <doi:10.1007/0-387-28014-6_14>.
Provides the standard operations for signal processing on graphs: 
    graph Fourier transform, spectral graph wavelet transform, 
    visualization tools. It also implements a data driven method
    for graph signal denoising/regression, for details see 
    De Loynes, Navarro, Olivier (2019) <arxiv:1906.01882>. 
    The package also provides an interface to the SuiteSparse Matrix Collection, 
    <https://sparse.tamu.edu/>, a large and widely used set of sparse matrix 
    benchmarks collected from a wide range of applications.
Fits gastric emptying time series from MRI or 'scintigraphic' measurements
   using nonlinear mixed-model population fits with 'nlme' and Bayesian methods with 
   Stan; computes derived parameters such as t50 and AUC.
Manipulation of genetic data (SNPs). Computation of GRM and dominance matrix, LD, heritability with efficient algorithms for linear mixed model (AIREML). Dandine et al <doi:10.1159/000488519>.
Allows user to choose/gate a region on the plot and returns points
    within it.
Estimates statistically significant marker combination values within
        which one immunologically distinctive group (i.e., disease case) is more associated than
        another group (i.e., healthy control), successively, using various combinations (i.e.,
        "gates") of markers to examine features of cells that may be different between
        groups. For a two-group comparison, the 'gateR' package uses the spatial relative risk
        function estimated using the 'sparr' package. Details about the 'sparr' package
        methods can be found in the tutorial: Davies et al. (2018) <doi:10.1002/sim.7577>. Details
        about kernel density estimation can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>.
        More information about relative risk functions using kernel density estimation can be
        found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.
Fits a Gaussian process model to data. Gaussian processes
 are commonly used in computer experiments to fit an interpolating model.
 The model is stored as an 'R6' object and can be easily updated with new 
 data. There are options to run in parallel, and 'Rcpp'
 has been used to speed up calculations.
 For more info about Gaussian process software, see Erickson et al. (2018)
 <doi:10.1016/j.ejor.2017.10.002>.
A collection of tools and data for analyzing the Gause microcosm experiments, and for fitting Lotka-Volterra models to time series data. Includes methods for fitting single-species logistic growth, and multi-species interaction models, e.g. of competition, predator/prey relationships, or mutualism. See documentation for individual functions for examples. In general, see the lv_optim() function for examples of how to fit parameter values in multi-species systems. Note that the general methods applied here, as well as the form of the differential equations that we use, are described in detail in the Quantitative Ecology textbook by Lehman et al., available at <http://hdl.handle.net/11299/204551>, and in Lina K. Mühlbauer, Maximilienne Schulze, W. Stanley Harpole, and Adam T. Clark. 'gauseR': Simple methods for fitting Lotka-Volterra models describing Gause's 'Struggle for Existence' in the journal Ecology and Evolution.
Given the standard linear model the traditional way of deciding whether to include the jth covariate is to apply the F-test to decide whether the corresponding beta coefficient is  zero. The Gaussian covariate method is completely different. The question as to whether the beta coefficient is or is not zero is replaced by the question as to whether the covariate is better or worse than i.i.d. Gaussian noise. The P-value for the covariate is the probability that Gaussian noise is better. Surprisingly this can be given exactly and it is the same a the P-value for the classical model based on the F-distribution. The Gaussian covariate P-value is model free, it is the same for any data set. Using the idea it is possible to do covariate selection for a small number of covariates 25 by considering all subsets.  Post selection inference causes no problems as the P-values hold whatever the data. The idea extends to stepwise regression again with exact probabilities. In the simplest version the only parameter is a specified cut-off P-value which can be interpreted as the probability of a false positive being included in the final selection. For more information see the web site below and the accompanying papers: L. Davies and L. Duembgen, "Covariate Selection Based on a Model-free Approach to Linear Regression with Exact Probabilities", 2022, <arxiv:2202.01553>. L. Davies, "Linear Regression, Covariate Selection and the Failure of Modelling", 2022, <arXiv:2112.08738>.
A collection difference measures for multivariate Gaussian
        probability density functions, such as the Euclidea mean, the
        Mahalanobis distance, the Kullback-Leibler divergence, the
        J-Coefficient, the Minkowski L2-distance, the Chi-square
        divergence and the Hellinger Coefficient.
Display a random fact about Carl Friedrich Gauss
 based the on collection curated by Mike Cavers via the
 <http://gaussfacts.com> site.
Inference, goodness-of-fit test, and prediction densities and intervals for univariate Gaussian Hidden Markov Models (HMM). The goodness-of-fit is based on a Cramer-von Mises statistic and uses parametric bootstrap to estimate the p-value. The description of the methodology is taken from Chapter 10.2 of Remillard (2013) <doi:10.1201/b14285>.
Functions to fit two-dimensional Gaussian functions, predict values from
    fits, and produce plots of predicted data via either 'ggplot2' or base R 
    plotting.
A collection of functions to perform Gaussian quadrature
        with different weight functions corresponding to the orthogonal
        polynomials in package orthopolynom.  Examples verify the
        orthogonality and inner products of the polynomials.
A statistical disclosure control tool to protect tables by suppression 
    using the Gaussian elimination secondary suppression algorithm. A suggestion is 
    to start by working with functions SuppressSmallCounts() and 
    SuppressDominantCells(). These functions use primary suppression functions for 
    the minimum frequency rule and the dominance rule, respectively. Novel 
    functionality for suppression of disclosive cells is also included. General 
    primary suppression functions can be supplied as input to the general working 
    horse function, GaussSuppressionFromData(). Suppressed frequencies can be 
    replaced by synthetic decimal numbers as described in 
    Langsrud (2019) <doi:10.1007/s11222-018-9848-9>.
R function gawdis() produces multi-trait dissimilarity with more uniform contributions of different traits. de Bello et al. (2021) <doi:10.1111/2041-210X.13537> presented the approach based on minimizing the differences in the correlation between the dissimilarity of each trait, or groups of traits, and the multi-trait dissimilarity. This is done using either an analytic or a numerical solution, both available in the function.
A collection of algorithms and functions 
  for fitting data to a generalized lambda distribution 
  via moment matching methods, and generalized 
  bootstrapping.
Package GB2 explores the Generalized Beta distribution of the second kind. Density, cumulative distribution function, quantiles and moments of the distributions are given. Functions for the full log-likelihood, the profile log-likelihood and the scores are provided. Formulas for various indicators of inequality and poverty under the GB2 are implemented. The GB2 is fitted by the methods of maximum pseudo-likelihood estimation using the full and profile log-likelihood, and non-linear least squares estimation of the model parameters. Various plots for the visualization and analysis of the results are provided. Variance estimation of the parameters is provided for the method of maximum pseudo-likelihood estimation. A mixture distribution based on the compounding property of the GB2 is presented (denoted as "compound" in the documentation). This mixture distribution is based on the discretization of the distribution of the underlying random scale parameter. The discretization can be left or right tail. Density, cumulative distribution function, moments and quantiles for the mixture distribution are provided. The compound mixture distribution is fitted using the method of maximum pseudo-likelihood estimation. The fit can also incorporate the use of auxiliary information. In this new version of the package, the mixture case is complemented with new functions for variance estimation by linearization and comparative density plots.
Estimation of the generalized beta distribution of the second 
    kind (GB2) and related models using grouped data in form of income shares. 
    The GB2 family is a general class of distributions that provides an accurate 
    fit to income data. 'GB2group' includes functions to estimate the GB2, the 
    Singh-Maddala, the Dagum, the Beta 2, the Lognormal and the Fisk distributions. 
    'GB2group' deploys two different econometric strategies to estimate these 
    parametric distributions, the equally weighted minimum distance (EWMD) estimator and the  
    optimally weighted minimum distance (OMD) estimator. Asymptotic standard errors are reported for the 
    OMD estimates. Standard errors of the EWMD estimates are obtained by Monte 
    Carlo simulation. See Jorda et al. (2018) <arXiv:1808.09831> for a detailed 
    description of the estimation procedure.
DNA methylation of 5-methylcytosine (5mC) is the result of a multi-step, enzyme-dependent process. Predicting these sites in-vitro is laborious, time consuming as well as costly. This ' Gb5mC-Pred ' package is an in-silico pipeline for predicting DNA sequences containing the 5mC sites. It uses a machine learning approach which uses Stochastic Gradient Boosting approach for prediction of the sequences with 5mC sites. This package has been developed by using the concept of Navarez and Roxas (2022) <doi:10.1109/TCBB.2021.3082184>.
Density, distribution function, quantile function, and random generation for the generalized Beta and Beta prime distributions. The family of generalized Beta distributions is conjugate for the Bayesian binomial model, and the generalized Beta prime distribution is the posterior distribution of the relative risk in the Bayesian 'two Poisson samples' model when a Gamma prior is assigned to the Poisson rate of the reference group and a Beta prime prior is assigned to the relative risk. References: Laurent (2012) <doi:10.1214/11-BJPS139>, Hamza & Vallois (2016) <doi:10.1016/j.spl.2016.03.014>, Chen & Novick (1984) <doi:10.3102/10769986009002163>.
Supplies a set of functions to interface with bikeshare data
    following the General Bikeshare Feed Specification, allowing users to query
    and accumulate tidy datasets for specified cities/bikeshare programs.
A high performance interface to the Global Biodiversity
  Information Facility, 'GBIF'.  In contrast to 'rgbif', which can
  access small subsets of 'GBIF' data through web-based queries to
  a central server, 'gbifdb' provides enhanced performance for R users
  performing large-scale analyses on servers and cloud computing
  providers, providing full support for arbitrary 'SQL' or 'dplyr'
  operations on the complete 'GBIF' data tables (now over 1 billion
  records, and over a terabyte in size). 'gbifdb' accesses a copy
  of the 'GBIF' data in 'parquet' format, which is already readily
  available in commercial computing clouds such as the Amazon Open
  Data portal and the Microsoft Planetary Computer, or can be 
  accessed directly without downloading, or downloaded
  to any server with suitable bandwidth and storage space.
  The high-performance techniques for local and remote access 
  are described in <https://duckdb.org/why_duckdb>
  and <https://arrow.apache.org/docs/r/articles/fs.html> respectively.
Offers the Generalized Berk-Jones (GBJ) test for set-based inference in genetic
	association studies. The GBJ is designed as an alternative to tests such as Berk-Jones (BJ),
    Higher Criticism (HC), Generalized Higher Criticism (GHC), Minimum p-value (minP), and Sequence
    Kernel Association Test (SKAT). All of these other methods (except for SKAT) are also implemented 
    in this package, and we additionally provide an omnibus test (OMNI) which integrates information from each of the tests.
    The GBJ has been shown to outperform other tests in genetic association studies when signals
    are correlated and moderately sparse. Please see the vignette for a quickstart guide or the paper at
    <doi:10.1080/01621459.2019.1660170> for full details.
An implementation of extensions to Freund and Schapire's AdaBoost 
  algorithm and Friedman's gradient boosting machine. Includes regression 
  methods for least squares, absolute loss, t-distribution loss, quantile 
  regression, logistic, multinomial logistic, Poisson, Cox proportional hazards 
  partial likelihood, AdaBoost exponential loss, Huberized hinge loss, and 
  Learning to Rank measures (LambdaMart). Originally developed by Greg Ridgeway.
Automates delta log-normal boosted regression tree abundance
    prediction. Loops through parameters provided (LR (learning rate), TC
    (tree complexity), BF (bag fraction)), chooses best, simplifies, &
    generates line, dot & bar plots, & outputs these & predictions & a
    report, makes predicted abundance maps, and Unrepresentativeness
    surfaces.  Package core built around 'gbm' (gradient boosting machine)
    functions in 'dismo' (Hijmans, Phillips, Leathwick & Jane Elith, 2020
    & ongoing), itself built around 'gbm' (Greenwell, Boehmke, Cunningham
    & Metcalfe, 2020 & ongoing, originally by Ridgeway). Indebted to
    Elith/Leathwick/Hastie 2008 'Working Guide'
    <doi:10.1111/j.1365-2656.2008.01390.x>; workflow follows Appendix S3.
    See <http://www.simondedman.com/> for published guides and papers
    using this package.
Writes SAS code to get predicted values from every tree of a gbm.object.
Estimation and analysis of group-based multivariate trajectory models (Nagin, 2018 <doi:10.1177/0962280216673085>; Magrini, 2022 <doi:10.1007/s10182-022-00437-9>). The package implements an Expectation-Maximization (EM) algorithm allowing unbalanced panel and missing values, and provides several functionalities for prediction and graphical representation.
Basic infrastructure and several algorithms for 1d-4d bin packing
    problem. This package provides a set of c-level classes and solvers for
    1d-4d bin packing problem, and an r-level solver for 4d bin packing problem,
    which is a wrapper over the c-level 4d bin packing problem solver.
    The 4d bin packing problem solver aims to solve bin packing problem, a.k.a
    container loading problem, with an additional constraint on weight.
    Given a set of rectangular-shaped items, and a set of rectangular-shaped bins
    with weight limit, the solver looks for an orthogonal packing solution
    such that minimizes the number of bins and maximize volume utilization.
    Each rectangular-shaped item i = 1, .. , n is characterized by length l_i,
    depth d_i, height h_i, and weight w_i, and each rectangular-shaped bin
    j = 1, .. , m is specified similarly by length l_j, depth d_j, height h_j,
    and weight limit w_j.
    The item can be rotated into any orthogonal direction, and no further
    restrictions implied.
Provides utilities for processing Rd objects and files.
        Extract argument descriptions and other parts of the help pages
        of functions.
Functions for inference of ploidy from (Genotyping-by-sequencing) GBS data, including a function to infer allelic ratios and allelic proportions in a Bayesian framework.
An implementation of hyperparameter optimization for Gradient
    Boosted Trees on binary classification and regression problems. The current
    version provides two optimization methods: Bayesian optimization and random
    search. Instead of giving the single best model, the final output is an 
    ensemble of Gradient Boosted Trees constructed via the method of ensemble 
    selection.
Plot density and distribution functions with automatic selection of
       suitable regions. Numerically invert (compute quantiles) distribution
       functions. Simulate real and complex numbers from distributions of their
       magnitude and arguments. Optionally, the magnitudes and/or arguments may
       be fixed in almost arbitrary ways. Create polynomials from roots given in
       Cartesian or polar form. Small programming utilities: check if an object
       is identical to NA, count positional arguments in a call, set
       intersection of more than two sets, check if an argument is unnamed,
       compute the graph of S4 classes in packages.
Provides shortcuts in extracting useful data points and summarizing waveform data. It is optimized for speed to work efficiently with large data sets so you can get to the analysis phase more quickly. It also utilizes a user-friendly format for use by both beginners and seasoned R users.
Aligns peak based on peak retention times and matches homologous peaks
    across samples. The underlying alignment procedure comprises three sequential steps.
    (1) Full alignment of samples by linear transformation of retention times to 
    maximise similarity among homologous peaks (2) Partial alignment of peaks within 
    a user-defined retention time window to cluster homologous peaks (3) Merging rows
    that are likely representing homologous substances (i.e. no sample shows peaks in 
    both rows and the rows have similar retention time means). The algorithm is described in detail
    in Ottensmann et al., 2018 <doi:10.1371/journal.pone.0198311>.
These are two-sample tests for categorical data utilizing similarity information among the categories.  They are useful when there is underlying structure on the categories.
'GPU'/CPU Benchmarking on Debian-package based systems
 This package benchmarks performance of a few standard linear algebra
 operations (such as a matrix product and QR, SVD and LU decompositions)
 across a number of different 'BLAS' libraries as well as a 'GPU' implementation.
 To do so, it takes advantage of the ability to 'plug and play' different
 'BLAS' implementations easily on a Debian and/or Ubuntu system.  The current
 version supports
  - 'Reference BLAS' ('refblas') which are un-accelerated as a baseline
  - Atlas which are tuned but typically configure single-threaded
  - Atlas39 which are tuned and configured for multi-threaded mode
  - 'Goto Blas' which are accelerated and multi-threaded
  - 'Intel MKL' which is a commercial accelerated and multithreaded version.
 As for 'GPU' computing, we use the CRAN package
  - 'gputools'
 For 'Goto Blas', the 'gotoblas2-helper' script from the ISM in Tokyo can be
 used. For 'Intel MKL' we use the Revolution R packages from Ubuntu 9.10.
Provides methods for model selection, estimation, bootstrap inference, and simulation for the 
    multilevel factor model, based on the principal component estimation and generalised 
    canonical correlation approach. Details can be found in "Generalised Canonical Correlation 
    Estimation of the Multilevel Factor Model." Lin and Shin (2023) <doi:10.2139/ssrn.4295429>.
Contains the Global Charcoal database data. Data include charcoal
    series (age, depth, charcoal quantity, associated units and methods) and
    information on sedimentary sites (localisation, depositional environment, biome,
    etc.) as well as publications informations. Since 4.0.0 the GCD mirrors the online SQL database at <http://paleofire.org>.
Implements a generalized coordinate descent (GCD) algorithm
    for computing the solution paths of the hybrid Huberized support vector
    machine (HHSVM) and its generalizations. Supported models include the
    (adaptive) LASSO and elastic net penalized least squares, logistic
    regression, HHSVM, squared hinge loss SVM and expectile regression.
Generalized competing event model based on Cox PH model and Fine-Gray model.
    This function is designed to develop optimized risk-stratification methods for competing
    risks data, such as described in:
    1. Carmona R, Gulaya S, Murphy JD, Rose BS, Wu J, Noticewala S,McHale MT, Yashar CM, Vaida F,
    and Mell LK (2014) <DOI:10.1016/j.ijrobp.2014.03.047>.
    2. Carmona R, Zakeri K, Green G, Hwang L, Gulaya S, Xu B, Verma R, Williamson CW, Triplett DP, Rose
    BS, Shen H, Vaida F, Murphy JD, and Mell LK (2016) <DOI:10.1200/JCO.2015.65.0739>.
    3. Lunn, Mary, and Don McNeil (1995) <DOI:10.2307/2532940>.
Scrapes Google Citation pages and creates data frames of 
    citations over time.
Provides a variety of functions to analyze and model
    geostatistical count data with Gaussian copulas, including
 1) data simulation and visualization; 
 2) correlation structure assessment (here also known as the Normal To Anything); 
 3) calculate multivariate normal rectangle probabilities; 
 4) likelihood inference and parallel prediction at predictive locations.
 Description of the method is available from: Han and DeOliveira (2018) <doi:10.18637/jss.v087.i13>.
Estimation of covariance matrices as solutions of 
             continuous time Lyapunov equations. 
             Sparse coefficient matrix and diagonal noise are estimated 
             with a proximal gradient 
             method for an l1-penalized loss minimization problem.
             Varando G, Hansen NR (2020) <arXiv:2005.10483>.
Orders panels in scatterplot matrices and parallel coordinate
 displays by some merit index. Package contains various indices of merit,
 ordering functions, and enhanced versions of pairs and parcoord which
 color panels according to their merit level.
Likelihood inference in Gaussian copula marginal
        regression models.
An implementation of the International Bureau of Weights and Measures (BIPM) generalized consensus estimators used to assign the reference value in a key comparison exercise. This can also be applied to any interlaboratory study. Given a set of different sources, primary laboratories or measurement methods this package provides an evaluation of the variance components according to the selected statistical method for consensus building. It also implements the comparison among different consensus builders and evaluates the participating method or sources against the consensus reference value. Based on a diverse set of references, DerSimonian-Laird (1986) <doi:10.1016/0197-2456(86)90046-2>, for a complete list of references look at the reference section in the package documentation.
Data sets used in the book "R Graphics Cookbook" by Winston
    Chang, published by O'Reilly Media.
Run a Gibbs sampler for a multivariate Bayesian sparse group selection model with Dirac, continuous and hierarchical spike prior for detecting pleiotropy on the traits. This package is designed for summary statistics containing estimated regression coefficients and its estimated covariance matrix. The methodology is available from: Baghfalaki, T., Sugier, P. E., Truong, T., Pettitt, A. N., Mengersen, K., & Liquet, B. (2021) <doi:10.1002/sim.8855>.
Easy import, manipulation, and model-free analysis of
    microbial growth curve data, as commonly output by plate readers.
    Tools for reshaping common plate reader outputs into 'tidy' formats and
    merging them with design information, making data easy to work with using 
    'gcplyr' and other packages. Also streamlines common growth curve
    processing steps, like smoothing and calculating derivatives, and
    facilitates model-free characterization and analysis of growth data.
    See methods at <https://mikeblazanin.github.io/gcplyr/>.