Automatic open data acquisition from resources of IGN
    ('Institut National de Information Geographique et forestiere')
    (<https://www.ign.fr/>). Available datasets include various types of
    raster and vector data, such as digital elevation models, state
    borders, spatial databases, cadastral parcels, and more. There also
    access to point clouds data ('LIDAR') and specifics API
    (<https://apicarto.ign.fr/api/doc/>).
There are two interesting games in this package, one is 2048 games(for windows), using up and down to control the direction until there is a 2048 figure. And the other is 'what to eat today',preparing for people who choose difficulties, including most of the delicious Cantonese cuisine.
By analyzing time series, it is possible to observe significant changes in the behavior of observations that frequently characterize events. Events present themselves as anomalies, change points, or motifs. In the literature, there are several methods for detecting events. However, searching for a suitable time series method is a complex task, especially considering that the nature of events is often unknown. This work presents Harbinger, a framework for integrating and analyzing event detection methods. Harbinger contains several state-of-the-art methods described in Salles et al. (2020) <doi:10.5753/sbbd.2020.13626>.
Building modeling packages is hard. A large amount of effort
    generally goes into providing an implementation for a new method that
    is efficient, fast, and correct, but often less emphasis is put on the
    user interface. A good interface requires specialized knowledge about
    S3 methods and formulas, which the average package developer might not
    have. The goal of 'hardhat' is to reduce the burden around building
    new modeling packages by providing functionality for preprocessing,
    predicting, and validating input.
Contains tools for exploring Hardy-Weinberg equilibrium (Hardy, 1908;  Weinberg, 1908) for bi and multi-allelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) with bi-allelic variants are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included (Graffelman & Weir, 2016) <doi:10.1038/hdy.2016.20>, including Bayesian procedures. Some exact and permutation procedures also work with multi-allelic variants. Special test procedures that jointly address Hardy-Weinberg equilibrium and equality of allele frequencies in both sexes are supplied, for the bi and multi-allelic case. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of bi-allelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots. The functionality of the package is explained in detail in a related JSS paper <doi:10.18637/jss.v064.i03>.
The harmonic mean p-value (HMP) test combines p-values and corrects for multiple testing while controlling the strong-sense family-wise error rate. It is more powerful than common alternatives including Bonferroni and Simes procedures when combining large proportions of all the p-values, at the cost of slightly lower power when combining small proportions of all the p-values. It is more stringent than controlling the false discovery rate, and possesses theoretical robustness to positive correlations between tests and unequal weights. It is a multi-level test in the sense that a superset of one or more significant tests is certain to be significant and conversely when the superset is non-significant, the constituent tests are certain to be non-significant. It is based on MAMML (model averaging by mean maximum likelihood), a frequentist analogue to Bayesian model averaging, and is theoretically grounded in generalized central limit theorem. For detailed examples type vignette("harmonicmeanp") after installation. Version 3.0 addresses errors in versions 1.0 and 2.0 that led function p.hmp to control the familywise error rate only in the weak sense, rather than the strong sense as intended.
Several functions are provided to harmonize CN8 (Combined Nomenclature 
	8 digits) and PC8 (Production Communautaire 8 digits) product codes over 
	time and the classification systems HS6 and BEC. Harmonization of CN8 
	codes are possible by default from 1995 to 2022 and of PC8 from 2001 to 
	2021, respectively.
Implementation of the Harmony algorithm for single cell integration, described in Korsunsky et al <doi:10.1038/s41592-019-0619-0>. Package includes a standalone Harmony function and interfaces to external frameworks.
'Harmony' is a tool using AI which allows you to compare items from questionnaires and identify similar content. You can try 'Harmony' at <https://harmonydata.ac.uk/app/> and you can read our blog at <https://harmonydata.ac.uk/blog/> or at <https://fastdatascience.com/how-does-harmony-work/>. Documentation at <https://harmonydata.ac.uk/harmony-r-released/>.
Provides tools for processing and analyzing .har and .sl4 files, making it easier 
    for 'GEMPACK' users and 'GTAP' researchers to handle large economic datasets. 
    It simplifies the management of multiple experiment results, enabling faster 
    and more efficient comparisons without complexity. Users can extract, restructure, 
    and merge data seamlessly, ensuring compatibility across different tools. 
    The processed data can be exported and used in 'R', 'Stata', 'Python', 'Julia', or 
    any software that supports Text, CSV, or 'Excel' formats.
Harriet was Charles Darwin's pet tortoise (possibly). 'harrietr'
    implements some function to manipulate distance matrices and phylogenetic trees
    to make it easier to plot with 'ggplot2' and to manipulate using 'tidyverse'
    tools.
Implementation of characteristic palettes inspired in the Wizarding World and the Harry Potter movie franchise.
Aimed at applying the Harvest classification tree algorithm, modified algorithm of classic classification tree.The harvested tree has advantage of deleting redundant rules in trees, leading to a simplify and more efficient tree model.It was firstly used in drug discovery field, but it also performs well in other kinds of data, especially when the region of a class is disconnected. This package also improves the basic harvest classification tree algorithm by extending the field of data of algorithm to both continuous and categorical variables. To learn more about the harvest classification tree algorithm, you can go to http://www.stat.ubc.ca/Research/TechReports/techreports/220.pdf for more information.
Implements a data structure similar to hashes in Perl and dictionaries in Python but with a purposefully R flavor. For objects of appreciable size, access using hashes outperforms native named lists and vectors.
An R port of the hashids library.  hashids generates YouTube-like hashes from integers or vector of integers.  Hashes generated from integers are relatively short, unique and non-seqential.  hashids can be used to generate unique ids for URLs and hide database row numbers from the user.  By default hashids will avoid generating common English cursewords by preventing certain letters being next to each other.  hashids are not one-way: it is easy to encode an integer to a hashid and decode a hashid back into an integer.
Apply an adaptation of the SuperFastHash algorithm to any R
    object. Hash whole R objects or, for vectors or lists, hash R objects to obtain
    a set of hash values that is stored in a structure equivalent to the input. See
    <http://www.azillionmonkeys.com/qed/hash.html> for a description of the hash
    algorithm.
The Ljung-Box test is one of the most important tests for time series diagnostics and model selection. 
    The  Hassani SACF (Sum of the Sample Autocorrelation Function) Theorem , however, indicates that the sum of sample autocorrelation function is always fix for 
    any stationary time series with arbitrary length. This package confirms for sensitivity of the Ljung-Box test to 
    the number of lags involved in the test and therefore it should be used with extra caution.
    The Hassani SACF Theorem has been described in : Hassani, Yeganegi and M. R. (2019) <doi:10.1016/j.physa.2018.12.028>.
A non-parametric test founded upon the principles of the Kolmogorov-Smirnov (KS) 
  test, referred to as the KS Predictive Accuracy (KSPA) test. The KSPA test is able to serve
  two distinct purposes. Initially, the test seeks to determine whether there exists a 
  statistically significant difference between the distribution of forecast errors, and 
  secondly it exploits the principles of stochastic dominance to determine whether the 
  forecasts with the lower error also reports a stochastically smaller error than forecasts 
  from a competing model, and thereby enables distinguishing between the predictive accuracy 
  of forecasts. KSPA test has been described in : Hassani and Silva (2015) <doi:10.3390/econometrics3030590>.
Returns a Hasse diagram of the layout structure (Bate and Chatfield (2016)) <doi:10.1080/00224065.2016.11918173> or the restricted layout structure (Bate and Chatfield (2016)) <doi:10.1080/00224065.2016.11918174> of an experimental design.
Predict hatch and emergence timing for a wide range of wild fishes using the effective value framework (Sparks et al., (2019) <DOI:10.1139/cjfas-2017-0468>). 'hatchR' offers users access to established phenological models and the flexibility to incorporate custom parameterizations using external datasets.
Import foreign statistical formats into R via the embedded
    'ReadStat' C library, <https://github.com/WizardMac/ReadStat>.
The package allows to simulate Hawkes process both in univariate and multivariate settings. It gives functions to compute different moments of the number of jumps of the process on a given interval, such as mean, variance or autocorrelation of process jumps on time intervals separated by a lag.
Implements an estimation method for Hawkes processes when count data are only observed in discrete time, using a spectral approach derived from the Bartlett spectrum, see Cheysson and Lang (2020) <arXiv:2003.04314>. Some general use functions for Hawkes processes are also included: simulation of (in)homogeneous Hawkes process, maximum likelihood estimation, residual analysis, etc.
The conditional treatment effect for competing risks data in observational studies is estimated. While it is described as a constant difference between the hazard functions given the covariates, we do not assume specific functional forms for the covariates. Rava, D. and Xu, R. (2021) <arXiv:2112.09535>.
Provides a set of functions to estimate haziness of an image based on RGB bands. It returns a haze factor, varying from 0 to 1, a metric for fogginess and cloudiness. The package also presents additional functions to estimate brightness, darkness and contrast rasters of the RGB image. This package can be used for several applications such as inference of weather quality data and performing environmental studies from interpreting digital images.
Implements hierarchically regularized entropy balancing proposed by Xu and Yang (2022) <doi:10.1017/pan.2022.12>. The method adjusts the covariate distributions of the control group to match those of the treatment group. 'hbal' automatically expands the covariate space to include higher order terms and uses cross-validation to select variable penalties for the balancing conditions.
Perform hierarchical Bayesian Aldrich-McKelvey scaling using Hamiltonian Monte
    Carlo via 'Stan'. Aldrich-McKelvey ('AM') scaling is a method for estimating the ideological 
    positions of survey respondents and political actors on a common scale using positional survey 
    data. The hierarchical versions of the Bayesian 'AM' model included in this package outperform 
    other versions both in terms of yielding meaningful posterior distributions for respondent 
    positions and in terms of recovering true respondent positions in simulations. The package 
    contains functions for preparing data, fitting models, extracting estimates, plotting key 
    results, and comparing models using cross-validation. The original version of the default 
    model is described in Bølstad (2024) <doi:10.1017/pan.2023.18>.
Fit an array of decision-making tasks with computational models in
    a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of
    various computational models with a single line of coding
    (Ahn et al., 2017) <doi:10.1162/CPSY_a_00002>.
Implements assessment of benefit-risk balance using Bayesian Discrete Choice Experiment. For more details see the article by Mukhopadhyay et al. (2019) <DOI:10.1080/19466315.2018.1527248>.
Calculate expected relative risk and proportion protected assuming normally distributed log10 transformed antibody dose for a several component vaccine. Uses Hill models for each component which are combined under Bliss independence. See Saul and Fay, 2007 <DOI:10.1371/journal.pone.0000850>.
Contains functions for fitting hierarchical versions of
        EVSD, UVSD, DPSD, DPSD with d' restricted to be positive, and
        our gamma signal detection model to recognition memory
        confidence-ratings data.
Functions to compute small area estimates based on a basic area or
    unit-level model. The model is fit using restricted maximum likelihood, or
    in a hierarchical Bayesian way. In the latter case numerical integration is
    used to average over the posterior density for the between-area variance.
    The output includes the model fit, small area estimates and corresponding
    mean squared errors, as well as some model selection measures. Additional functions
    provide means to compute aggregate estimates and mean squared errors, to minimally
    adjust the small area estimates to benchmarks at a higher aggregation
    level, and to graphically compare different sets of small area estimates.
Implementing Hierarchical Bayesian Small Area Estimation 
    models using the 'brms' package as the computational backend. The 
    modeling framework follows the methodological foundations described in area-level 
    models. This package is designed to facilitate a principled Bayesian workflow, 
    enabling users to conduct prior predictive checks, model fitting, posterior 
    predictive checks, model comparison, and sensitivity analysis in a coherent and 
    reproducible manner. It supports flexible model specifications via 'brms' and 
    promotes transparency in model development, aligned with the recommendations of 
    modern Bayesian data analysis practices, implementing methods described in 
    Rao and Molina (2015) <doi:10.1002/9781118735855>.
Fits Hierarchical Bayesian space-Time models for Gaussian data. Furthermore, its functions have been implemented for analysing the fitting qualities of those models.
The HBV hydrological model (Bergström, S. and Lindström, G., (2015) <doi:10.1002/hyp.10510>) has been split in modules to allow the user to build his/her own model. This version was developed by the author in IANIGLA-CONICET (Instituto Argentino de Nivologia, Glaciologia y Ciencias Ambientales - Consejo Nacional de Investigaciones Cientificas y Tecnicas) for hydroclimatic studies in the Andes. HBV.IANIGLA incorporates routines for clean and debris covered glacier melt simulations.
Texts for H.C. Andersens fairy tales, ready for
    text analysis. Fairy tales in German, Danish, English, Spanish and
    French.
Calculates the interval estimates for the parameters of linear models with heteroscedastic regression using bootstrap - (Wild Bootstrap) and double bootstrap-t (Wild Bootstrap). It is also possible to calculate confidence intervals using the percentile bootstrap and percentile bootstrap double. The package can calculate consistent estimates of the covariance matrix of the parameters of linear regression models with heteroscedasticity of unknown form. The package also provides a function to consistently calculate the covariance matrix of the parameters of linear models with heteroscedasticity of unknown form. The bootstrap methods exported by the package are based on the master's thesis of the first author, available at <https://raw.githubusercontent.com/prdm0/hcci/master/references/dissertacao_mestrado.pdf>. The hcci package in previous versions was cited in the book VINOD, Hrishikesh D. Hands-on Intermediate Econometrics Using R: Templates for Learning Quantitative Methods and R Software. 2022, p. 441, ISBN 978-981-125-617-2 (hardcover). The simple bootstrap schemes are based on the works of Cribari-Neto F and Lima M. G. (2009) <doi:10.1080/00949650801935327>, while the double bootstrap schemes for the parameters that index the linear models with heteroscedasticity of unknown form are based on the works of Beran (1987) <doi:10.2307/2336685>. The use of bootstrap for the calculation of interval estimates in regression models with heteroscedasticity of unknown form from a weighting of the residuals was proposed by Wu (1986) <doi:10.1214/aos/1176350142>. This bootstrap scheme is known as weighted or wild bootstrap.
Hierarchical community detection on networks by a recursive spectral partitioning strategy, which is shown to be effective and efficient in Li, Lei, Bhattacharyya, Sarkar, Bickel, and Levina (2018) <arXiv:1810.01509>. The package also includes a data generating function for a binary tree stochastic block model, a special case of stochastic block model that admits hierarchy between communities.
Simulate and analyze hierarchical composite endpoints. Includes implementation for the kidney hierarchical composite endpoint as defined in Heerspink HL et al (2023) “Development and validation of a new hierarchical composite end point for clinical trials of kidney disease progression” (Journal of the American Society of Nephrology 34 (2): 2025–2038, <doi:10.1681/ASN.0000000000000243>). Win odds, also called Wilcoxon-Mann-Whitney or success odds, is the main analysis method. Other win statistics (win probability, win ratio, net benefit) are also implemented in the univariate case, provided there is no censoring. The win probability analysis is based on the Brunner-Munzel test and uses the DeLong-DeLong-Clarke-Pearson variance estimator, as described by Brunner and Konietschke (2025) in “An unbiased rank-based estimator of the Mann–Whitney variance including the case of ties” (Statistical Papers 66 (1): 20, <doi:10.1007/s00362-024-01635-0>). Stratification and covariate adjustment are performed based on the methodology presented by Koch GG et al. in “Issues for covariance analysis of dichotomous and ordered categorical data from randomized clinical trials and non-parametric strategies for addressing them” (Statistics in Medicine 17 (15-16): 1863–92). For a review, see Gasparyan SB et al (2021) “Adjusted win ratio with stratification: Calculation methods and interpretation” (Statistical Methods in Medical Research 30 (2): 580–611, <doi:10.1177/0962280220942558>).
By binding R functions and the 'Highmaps' <https://www.highcharts.com.cn/products/highmaps> chart library, 'hchinamap' package provides a simple way to map China and its provinces. The map of China drawn by this package contains complete Chinese territory, especially the Nine-dotted line, South Tibet, Hong Kong, Macao and Taiwan.
A collection of datasets of human-computer interaction (HCI) experiments. 
    Each dataset is from an HCI paper, with all fields described and the original publication 
    linked. All paper authors of included data have consented to the inclusion of their data 
    in this package. The datasets include data from a range of HCI studies, such as pointing 
    tasks, user experience ratings, and steering tasks. 
    Dataset sources: 
    Bergström et al. (2022) <doi:10.1145/3490493>;
    Dalsgaard et al. (2021) <doi:10.1145/3489849.3489853>;
    Larsen et al. (2019) <doi:10.1145/3338286.3340115>;
    Lilija et al. (2019) <doi:10.1145/3290605.3300676>;
    Pohl and Murray-Smith (2013) <doi:10.1145/2470654.2481307>;
    Pohl and Mottelson (2022) <doi:10.3389/frvir.2022.719506>.
Univariate agglomerative hierarchical clustering with a comprehensive list of choices of a linkage function in O(n*log n) time. The better algorithmic time complexity is paired with an efficient 'C++' implementation.
Facilitates hierarchical clustering analysis with functions
    to read data in 'txt', 'xlsx', and 'xls' formats, apply normalization
    techniques to the dataset, perform hierarchical clustering and
    construct scatter plot from principal component analysis to evaluate
    the groups obtained.
Software for performing the reduction, exploratory and model selection phases of the procedure proposed by Cox, D.R. and Battey, H.S. (2017) <doi:10.1073/pnas.1703764114> for sparse regression when the number of potential explanatory variables far exceeds the sample size. The software supports linear regression, likelihood-based fitting of generalized linear regression models and the proportional hazards model fitted by partial likelihood.
This code provides a method to fit the hidden compact representation model as well as to identify the causal direction on discrete data. 
    We implement an effective solution to recover the above hidden compact representation under the likelihood framework. 
    Please see the Causal Discovery from Discrete Data using Hidden Compact Representation from NIPS 2018 by Ruichu Cai, Jie Qiao, Kun Zhang, Zhenjie Zhang and Zhifeng Hao (2018) <https://nips.cc/Conferences/2018/Schedule?showEvent=11274> for a description of some of our methods.
Given a database of previous treatment/placebo estimates, their standard errors and sample sizes,
      the program calculates a significance criteria and power estimate that takes into account the among
      trial variation.
It provides functions to design historical controlled trials with survival outcome by group sequential method. The options for interim look boundaries are efficacy only, efficacy & futility or futility only. It also provides the function to monitor the trial for any unplanned look. The package is based on Jianrong Wu, Xiaoping Xiong (2016) <doi:10.1002/pst.1756> and Jianrong Wu, Yimei Li (2020) <doi:10.1080/10543406.2019.1684305>.
A novel searching scheme for tuning parameter in high-dimensional 
             penalized regression. We propose a new estimate of the regularization
             parameter based on an estimated lower bound of the proportion of false 
             null hypotheses (Meinshausen and Rice (2006) <doi:10.1214/009053605000000741>).
             The bound is estimated by applying the empirical null distribution of the higher 
             criticism statistic, a second-level significance testing, which is constructed
             by dependent p-values from a multi-split regression and aggregation method
             (Jeng, Zhang and Tzeng (2019) <doi:10.1080/01621459.2018.1518236>). An estimate 
             of tuning parameter in penalized regression is decided corresponding to the lower 
             bound of the proportion of false null hypotheses. Different penalized 
             regression methods are provided in the multi-split algorithm.
Provides functions for designing phase II clinical trials adjusting for the heterogeneity of the population using known subgroups or historical controls.
Functions to perform dimensionality reduction for classification if the covariance matrices of the classes are unequal.
Functions and datasets to support Smilde, Marini, Westerhuis and Liland (2025, ISBN: 978-1-394-21121-0) 
   "Analysis of Variance for High-Dimensional Data - Applications in Life, Food and Chemical Sciences". 
   This implements and imports a  collection of methods for HD-ANOVA data analysis with common interfaces, result- and plotting 
   functions, multiple real data sets and four vignettes covering a range different applications.
Provides seamless access to the WEkEO Harmonised Data Access (HDA) API, enabling 
  users to query, download, and process data efficiently from the HDA platform. 
  With 'hdar', researchers and data scientists can integrate the extensive HDA 
  datasets into their R workflows, enhancing their data analysis capabilities. 
  Comprehensive information on the API functionality and usage is available 
  at <https://gateway.prod.wekeo2.eu/hda-broker/docs>.
User-friendly functions for leveraging (multiple) historical data set(s) for generalized
    linear models. The package contains functions for sampling from the posterior distribution of a
    generalized linear model using the prior induced by the Bayesian hierarchical model, power prior 
    by Ibrahim and Chen (2000) <doi:10.1214/ss/1009212673>, normalized power prior by Duan et al. (2006) 
    <doi:10.1002/env.752>, normalized asymptotic power prior by Ibrahim et al. (2015) <doi:10.1002/sim.6728>, 
    commensurate prior by Hobbs et al. (2011) <doi:10.1111/j.1541-0420.2011.01564.x>, robust meta-analytic-predictive 
    prior by Schmidli et al. (2014) <doi:10.1111/biom.12242>, the latent exchangeability prior by Alt et al. (2023) 
    <doi:10.48550/arXiv.2303.05223>, and a normal (or half-normal) prior. Functions for computing the marginal 
    log-likelihood under each of the implemented priors are also included. The package compiles all 
    the 'CmdStan' models once during installation using the 'instantiate' package.
Functions implementing change point detection methods using the maximum pairwise Bayes factor approach.
    Additionally, the package includes tools for generating simulated datasets for comparing and evaluating change point detection techniques.
Binary segmentation methods for detecting and estimating multiple change-points in the mean or second-order structure of high-dimensional time series as described in Cho and Fryzlewicz (2014) <doi:10.1111/rssb.12079> and Cho (2016) <doi:10.1214/16-EJS1155>.
Perform mediation analysis in the presence of high-dimensional
    mediators based on the potential outcome framework. High dimensional
    Bayesian mediation (HDBM), developed by Song et al (2018)
    <doi:10.1101/467399>, relies on two Bayesian sparse linear mixed models to
    simultaneously analyze a relatively large number of mediators for a
    continuous exposure and outcome assuming a small number of mediators are
    truly active. This sparsity assumption also allows the extension of
    univariate mediator analysis by casting the identification of active
    mediators as a variable selection problem and applying Bayesian methods
    with continuous shrinkage priors on the effects.
Mediation analysis is used to identify and quantify intermediate effects from factors that intervene the observed relationship between an exposure/predicting variable and an outcome. We use a Bayesian adaptive lasso method to take care of the hierarchical structures and high dimensional exposures or mediators.
Ridge regression provide biased estimators of the regression parameters with lower variance. The HDBRR ("High Dimensional Bayesian Ridge Regression") function fits Bayesian Ridge regression without MCMC, this one uses the SVD or QR decomposition for the posterior computation.
A two-step double-robust method to estimate the conditional average treatment effects (CATE) with potentially high-dimensional covariate(s). In the first stage, the nuisance functions necessary for identifying CATE are estimated by machine learning methods, allowing the number of covariates to be comparable to or larger than the sample size. The second stage consists of a low-dimensional local linear regression, reducing CATE to a function of the covariate(s) of interest. The CATE estimator implemented in this package not only allows for high-dimensional data, but also has the “double robustness” property: either the model for the propensity score or the models for the conditional means of the potential outcomes are allowed to be misspecified (but not both). This package is based on the paper by Fan et al., "Estimation of Conditional Average Treatment Effects With High-Dimensional Data" (2022), Journal of Business & Economic Statistics <doi:10.1080/07350015.2020.1811102>.
Efficient implementations of the following multiple changepoint detection algorithms: Efficient Sparsity Adaptive Change-point estimator by Moen, Glad and Tveten (2023) <doi:10.48550/arXiv.2306.04702> , Informative Sparse Projection for Estimating Changepoints by Wang and Samworth (2017) <doi:10.1111/rssb.12243>, and the method of Pilliat et al (2023) <doi:10.1214/23-EJS2126>.
Fits regression models on high dimensional data to estimate coefficients and use bootstrap method to obtain confidence intervals. Choices for regression models are Lasso, Lasso+OLS, Lasso partial ridge, Lasso+OLS partial ridge.
Discriminant analysis and data clustering methods for high
    dimensional data, based on the assumption that high-dimensional data live in
    different subspaces with low dimensionality proposing a new parametrization of
    the Gaussian mixture model which combines the ideas of dimension reduction and
    constraints on the model.
Clustering of high dimensional data with Hidden Markov Model on Variable Blocks (HMM-VB) fitted via Baum-Welch algorithm. Clustering is performed by the Modal Baum-Welch algorithm (MBW), which finds modes of the density function. Lin Lin and Jia Li (2017) <https://jmlr.org/papers/v18/16-342.html>.
Objective: Implement new methods for detecting change points in high-dimensional time series data. These new methods can be applied to non-Gaussian data, account for spatial and temporal dependence, and detect a wide variety of change-point configurations, including changes near the boundary and changes in close proximity. Additionally, this package helps address the “small n, large p” problem, which occurs in many research contexts. This problem arises when a dataset contains changes that are visually evident but do not rise to the level of statistical significance due to the small number of observations and large number of parameters. The problem is overcome by treating the dimensions as a whole and scaling the test statistics only by its standard deviation, rather than scaling each dimension individually. Due to the computational complexity of the functions, the package runs best on datasets with a relatively large number of attributes but no more than a few hundred observations.
Provides functions for fitting various penalized parametric and semi-parametric mixture cure models with different penalty functions, testing for a significant cure fraction, and testing for sufficient follow-up as described in Fu et al (2022)<doi:10.1002/sim.9513> and Archer et al (2024)<doi:10.1186/s13045-024-01553-6>. False discovery rate controlled variable selection is provided using model-X knock-offs.
A procedure that fits derivative curves based on a sequence of quotient differences.  In a hierarchical setting the package produces estimates of subject-specific and group-specific derivative curves.  In a non-hierarchical setting the package produces a single derivative curve.
Hard drive data: Class of data allowing the easy importation/manipulation of out of memory data sets. The data sets are located on disk but look like in-memory, the syntax for manipulation is similar to 'data.table'. Operations are performed "chunk-wise" behind the scene.
'HDF5' is a data model, library and file format for storing
    and managing large amounts of data. This package provides a nearly
    feature complete, object oriented  wrapper for the 'HDF5' API
    <https://support.hdfgroup.org/documentation/hdf5/latest/_r_m.html> using R6 classes.
    Additionally, functionality is added so that 'HDF5' objects behave very
    similar to their corresponding R counterparts.
Some methods to manipulate 'HDF5' files, extending the 'hdf5r' package. Reading and writing R objects to 'HDF5' formats follow the specification of 'AnnData' <https://anndata.readthedocs.io/en/latest/fileformat-prose.html>.
Provides a forecasting method that efficiently maps vast
    numbers of (scalar-valued) signals into an aggregate density forecast
    in a time-varying and computationally fast manner. The method proceeds
    in two steps: First, it transforms a predictive signal into a density
    forecast and, second, it combines the resulting candidate density
    forecasts into an ultimate aggregate density forecast. For a detailed
    explanation of the method, please refer to Adaemmer et al. (2023)
    <doi:10.2139/ssrn.4342487>.
Provides an interface to 'HDFql' <https://www.hdfql.com/> 
    and helper functions for reading data from and writing data to 'HDF5' files. 'HDFql' 
    provides a high-level language for managing 'HDF5' data that is platform independent.
    For more information, see the reference manual 
    <https://www.hdfql.com/resources/HDFqlReferenceManual.pdf>.
Offers methods for visualizing, modelling, and forecasting high-dimensional functional time series, also known as functional panel data. Documentation about 'hdftsa' is provided via the paper by Cristian F. Jimenez-Varon, Ying Sun and Han Lin Shang (2024, <doi:10.1080/10618600.2024.2319166>).
Test the significance of coefficients in high dimensional generalized linear models.
Implementation of multiple approaches to perform inference in high-dimensional models.
A correlation-based batch process for fast, accurate imputation for 
    high dimensional missing data problems via chained random forests.
    See Waggoner (2023) <doi:10.1007/s00180-023-01325-9> for more on 'hdImpute',
    Stekhoven and Bühlmann (2012) <doi:10.1093/bioinformatics/btr597> for more on 'missForest', 
    and Mayer (2022) <https://github.com/mayer79/missRanger> for more on 'missRanger'.
A generic function and a set of methods to calculate highest density intervals for a variety of classes of objects which can specify a probability density distribution, including MCMC output, fitted density objects, and functions.
We provide an R tool for computation and nonparametric plug-in estimation of Highest Density Regions (HDRs) and general level sets in the directional setting. Concretely, circular and spherical HDRs can be reconstructed from a data sample following Saavedra-Nieves and Crujeiras (2021) <doi:10.1007/s11634-021-00457-4>. This library also contains two real datasets in the circular and spherical settings. The first one concerns a problem from animal orientation studies and the second one is related to earthquakes occurrences.
The model is high-dimensional vector autoregression with measurement error, also known as linear gaussian state-space model. Provable sparse expectation-maximization algorithm is provided for the estimation of transition matrix and noise variances. Global and simultaneous testings are implemented for transition matrix with false discovery rate control. For more information, see the accompanying paper: Lyu, X., Kang, J., & Li, L. (2023). "Statistical inference for high-dimensional vector autoregression with measurement error", Statistica Sinica.
Joint models have been widely used to study the associations between longitudinal biomarkers and a survival outcome. However, existing joint models only consider one or a few longitudinal 
    biomarkers and cannot deal with high-dimensional longitudinal biomarkers. This package can be used to fit our recently developed penalized joint model that can handle high-dimensional longitudinal biomarkers. 
    Specifically, an adaptive lasso penalty is imposed on the parameters for the effects of the longitudinal biomarkers on the survival outcome, which allows for variable selection. 
    Also, our algorithm is computationally efficient, which is based on the Gaussian variational approximation method.
Testing homogeneity of k multivariate distributions is a classical and challenging problem in
             statistics, and this becomes even more challenging when the dimension of the data exceeds the sample size.
             We construct some tests for this purpose which are exact level (size) alpha tests based on clustering. 
             These tests are easy to implement and distribution-free in finite sample situations. Under appropriate 
             regularity conditions, these tests have the consistency property in HDLSS asymptotic regime, where the 
             dimension of data grows to infinity while the sample size remains fixed. We also consider a multiscale 
             approach, where the results for different number of partitions are aggregated judiciously. Details are in 
             Biplab Paul, Shyamal K De and Anil K Ghosh (2021) <doi:10.1016/j.jmva.2021.104897>; Soham Sarkar and Anil K Ghosh (2019) 
             <doi:10.1109/TPAMI.2019.2912599>; William M Rand (1971) <doi:10.1080/01621459.1971.10482356>;  
             Cyrus R Mehta and Nitin R Patel (1983) <doi:10.2307/2288652>; Joseph C Dunn (1973) 
             <doi:10.1080/01969727308546046>; Sture Holm (1979) <doi:10.2307/4615733>; 
             Yoav Benjamini and Yosef Hochberg (1995) <doi: 10.2307/2346101>.
Implementation of selected high-dimensional statistical and
    econometric methods for estimation and inference. Efficient estimators and
    uniformly valid confidence intervals for various low-dimensional causal/
    structural parameters are provided which appear in high-dimensional
    approximately sparse models. Including functions for fitting heteroscedastic
    robust Lasso regressions with non-Gaussian errors and for instrumental variable
    (IV) and treatment effect estimation in a high-dimensional setting. Moreover,
    the methods enable valid post-selection inference and rely on a theoretically
    grounded, data-driven choice of the penalty.
    Chernozhukov, Hansen, Spindler (2016) <arXiv:1603.01700>.
We use the Alternating Direction Method of Multipliers (ADMM) for parameter estimation in high-dimensional, single-modality mediation models. To improve the sensitivity and specificity of estimated mediation effects, we offer the sure independence screening (SIS) function for dimension reduction. The available penalty options include Lasso, Elastic Net, Pathway Lasso, and Network-constrained Penalty. The methods employed in the package are based on Boyd, S., Parikh, N., Chu, E., Peleato, B., & Eckstein, J. (2011). <doi:10.1561/2200000016>, Fan, J., & Lv, J. (2008) <doi:10.1111/j.1467-9868.2008.00674.x>, Li, C., & Li, H. (2008) <doi:10.1093/bioinformatics/btn081>, Tibshirani, R. (1996) <doi:10.1111/j.2517-6161.1996.tb02080.x>, Zhao, Y., & Luo, X. (2022) <doi:10.4310/21-sii673>, and Zou, H., & Hastie, T. (2005) <doi:10.1111/j.1467-9868.2005.00503.x>.
Penalized regression for generalized linear models for
  measurement error problems (aka. errors-in-variables). The package
  contains a version of the lasso (L1-penalization) which corrects
  for measurement error (Sorensen et al. (2015) <doi:10.5705/ss.2013.180>). 
  It also contains an implementation of the Generalized Matrix Uncertainty 
  Selector, which is a version the (Generalized) Dantzig Selector for the 
  case of measurement error (Sorensen et al. (2018) <doi:10.1080/10618600.2018.1425626>).
A suite of functions for performing mediation
    analysis with high-dimensional mediators. In addition to centralizing code 
    from several existing packages for high-dimensional mediation analysis, we 
    provide organized, well-documented functions for a handle of methods 
    which, though programmed their original authors, have not previously been 
    formalized into R packages or been made presentable for public use. The 
    methods we include cover a broad array of approaches and objectives, and are
    described in detail by both our companion manuscript---"Methods for 
    Mediation Analysis with High-Dimensional DNA Methylation Data: Possible 
    Choices and Comparison"---and the original publications that proposed them. 
    The specific methods offered by our package include the Bayesian sparse 
    linear mixed model (BSLMM) by Song et al. (2019); high-dimensional mediation
    analysis (HDMA) by Gao et al. (2019); high-dimensional multivariate 
    mediation (HDMM) by Chén et al. (2018); high-dimensional linear mediation 
    analysis (HILMA) by Zhou et al. (2020); high-dimensional mediation analysis
    (HIMA) by Zhang et al. (2016); latent variable mediation analysis (LVMA) by 
    Derkach et al. (2019); mediation by fixed-effect model (MedFix) by 
    Zhang (2021); pathway LASSO by Zhao & Luo (2022); principal component 
    mediation analysis (PCMA) by Huang & Pan (2016); and sparse principal 
    component mediation analysis (SPCMA) by Zhao et al. (2020). Citations for 
    the corresponding papers can be found in their respective functions.
High-dimensional matrix factor models have drawn much attention in view of the fact that observations are usually well structured to be an array such as in macroeconomics and finance. In addition, data often exhibit heavy-tails and thus it is also important to develop robust procedures. We aim to address this issue by replacing the least square loss with Huber loss function. We propose two algorithms to do robust factor analysis by considering the Huber loss. One is based on minimizing the Huber loss of the idiosyncratic error's Frobenius norm, which leads to a weighted iterative projection approach to compute and learn the parameters and thereby named as Robust-Matrix-Factor-Analysis (RMFA), see the details in He et al. (2023)<doi:10.1080/07350015.2023.2191676>. The other one is based on minimizing the element-wise Huber loss, which can be solved by an iterative Huber regression algorithm (IHR), see the details in He et al. (2023) <arXiv:2306.03317>. In this package, we also provide the algorithm for alpha-PCA by Chen & Fan (2021) <doi:10.1080/01621459.2021.1970569>, the Projected estimation (PE) method by Yu et al. (2022)<doi:10.1016/j.jeconom.2021.04.001>. In addition, the methods for determining the pair of factor numbers are also given.
A multiple-testing procedure for high-dimensional mediation hypotheses. Mediation analysis is of rising interest in epidemiology and clinical trials. Among existing methods for mediation analyses, the popular joint significance (JS) test yields an overly conservative type I error rate and therefore low power. In the R package 'HDMT' we implement a multiple-testing procedure that accurately controls the family-wise error rate (FWER) and the false discovery rate (FDR) when using JS for testing high-dimensional mediation hypotheses. The core of our procedure is based on estimating the proportions of three component null hypotheses and deriving the corresponding mixture distribution of null p-values. Results of the data examples include better-behaved quantile-quantile plots and improved detection of novel mediation relationships on the role of DNA methylation in genetic regulation of gene expression. With increasing interest in mediation by molecular intermediaries such as gene expression, the proposed method addresses an unmet methodological challenge. Methods used in the package refer to James Y. Dai, Janet L. Stanford & Michael LeBlanc (2020) <doi:10.1080/01621459.2020.1765785>.
Estimates parameters in Mixture Transition Distribution (MTD) models, a class of high-order Markov chains. The set of relevant pasts (lags) is selected using either the Bayesian Information Criterion or the Forward Stepwise and Cut algorithms. Other model parameters (e.g. transition probabilities and oscillations) can be estimated via maximum likelihood estimation or the Expectation-Maximization algorithm. Additionally, 'hdMTD' includes a perfect sampling algorithm that generates samples of an MTD model from its invariant distribution. For theory, see Ost & Takahashi (2023) <http://jmlr.org/papers/v24/22-0266.html>.
Creates nomogram visualizations for penalized Cox regression
    models, with the support of reproducible survival model building,
    validation, calibration, and comparison for high-dimensional data.
Contains functions to construct high-dimensional orthogonal maximin distance designs in two, four, eight, and sixteen levels from rotating the Kronecker product of sub-Hadamard matrices.
An implementation of an algorithm for outlier detection that can handle a) data with a mixed categorical and continuous variables, b) many columns of data, c) many rows of data, d) outliers that mask other outliers, and e) both unidimensional and multidimensional datasets. Unlike ad hoc methods found in many machine learning papers, HDoutliers is based on a distributional model that uses probabilities to determine outliers.
In high-dimensional settings:
	Estimate the number of distant spikes based on the Generalized Spiked Population (GSP) model.
	Estimate the population eigenvalues, angles between the sample and population eigenvectors, correlations between the sample and population PC scores, and the asymptotic shrinkage factors.
	Adjust the shrinkage bias in the predicted PC scores.
	Dey, R. and Lee, S. (2019) <doi:10.1016/j.jmva.2019.02.007>.
Implementation of MCMC algorithms to estimate the Hierarchical Dirichlet Process Generalized Linear Model (hdpGLM) presented in the paper Ferrari (2020) Modeling Context-Dependent Latent Heterogeneity, Political Analysis <DOI:10.1017/pan.2019.13> and <doi:10.18637/jss.v107.i10>.
Implements an efficient algorithm to fit and tune penalized quantile regression models using the generalized coordinate descent algorithm. Designed to handle high-dimensional datasets effectively, with emphasis on precision and computational efficiency. This package implements the algorithms proposed in Tang, Q., Zhang, Y., & Wang, B. (2022) <https://openreview.net/pdf?id=RvwMTDYTOb>.
Computation of highest density regions in one and two dimensions, kernel estimation of univariate density functions conditional on one covariate,and multimodal regression.
Factor models have been widely applied in areas such as economics and finance, and the well-known heavy-tailedness of macroeconomic/financial data should be taken into account when conducting factor analysis. We propose two algorithms to do robust factor analysis by considering the Huber loss. One is based on minimizing the Huber loss of the idiosyncratic error's L2 norm, which turns out to do Principal Component Analysis (PCA) on the weighted sample covariance matrix and thereby named as Huber PCA. The other one is based on minimizing the element-wise Huber loss, which can be solved by an iterative Huber regression algorithm. In this package we also provide the code for traditional PCA, the Robust Two Step (RTS) method by He et al. (2022) and the Quantile Factor Analysis (QFA) method by Chen et al. (2021) and He et al. (2023).
Functions for calculating the hazard discrimination summary and its
    standard errors, as described in Liang and Heagerty (2016) <doi:10.1111/biom.12628>.
Constructs shrinkage estimators of high-dimensional mean-variance portfolios and performs 
    high-dimensional tests on optimality of a given portfolio. The techniques developed in 
    Bodnar et al. (2018 <doi:10.1016/j.ejor.2017.09.028>, 2019 <doi:10.1109/TSP.2019.2929964>, 
    2020 <doi:10.1109/TSP.2020.3037369>, 2021 <doi:10.1080/07350015.2021.2004897>) 
    are central to the package. They provide simple and feasible estimators and tests for optimal 
    portfolio weights, which are applicable for 'large p and large n' situations where p is the 
    portfolio dimension (number of stocks) and n is the sample size. The package also includes tools
    for constructing portfolios based on shrinkage estimators of the mean vector and covariance matrix
    as well as a new Bayesian estimator for the Markowitz efficient frontier recently developed by 
    Bauder et al. (2021) <doi:10.1080/14697688.2020.1748214>.
Contains ten datasets used in the chapters and exercises of Paul, Alice (2023) "Health Data Science in R" <https://alicepaul.github.io/health-data-science-using-r/>.
A method for identifying responses to experimental stimulation in mass or flow cytometry that uses high dimensional analysis of measured parameters and can be performed with an end-to-end unsupervised approach. In the context of in vitro stimulation assays where high-parameter cytometry was used to monitor intracellular response markers, using cell populations annotated either through automated clustering or manual gating for a combined set of stimulated and unstimulated samples, 'HDStIM' labels cells as responding or non-responding. The package also provides auxiliary functions to rank intracellular markers based on their contribution to identifying responses and generating diagnostic plots.
Implements an efficient algorithm to fit and tune penalized Support Vector Machine models using the generalized coordinate descent algorithm. Designed to handle high-dimensional datasets effectively, with emphasis on precision and computational efficiency. This package implements the algorithms proposed in Tang, Q., Zhang, Y., & Wang, B. (2022) <https://openreview.net/pdf?id=RvwMTDYTOb>.
Efficient sampling from high-dimensional truncated Gaussian
 distributions, or multivariate truncated normal (MTN). Techniques include 
 zigzag Hamiltonian Monte Carlo as in Akihiko Nishimura, Zhenyu Zhang and 
 Marc A. Suchard (2024) <doi:10.1080/01621459.2024.2395587>, and  harmonic Monte in Ari Pakman 
 and Liam Paninski (2014) <doi:10.1080/10618600.2013.788448>.
Provides uniform testing procedures for existence and heterogeneity of threshold 
    effects in high-dimensional nonparametric panel regression models. The package accompanies
    the paper Chen, Keilbar, Su and Wang (2023) "Inference on many jumps in nonparametric panel
    regression models". arXiv preprint <doi:10.48550/arXiv.2312.01162>.
An implementation for high-dimensional time series analysis methods, including factor model for vector time series 
      proposed by Lam and Yao (2012) <doi:10.1214/12-AOS970> and Chang, Guo and Yao (2015)
      <doi:10.1016/j.jeconom.2015.03.024>, martingale difference test proposed by 
      Chang, Jiang and Shao (2023) <doi:10.1016/j.jeconom.2022.09.001>, principal 
      component analysis for vector time series proposed by Chang, Guo and Yao (2018) <doi:10.1214/17-AOS1613>,
      cointegration analysis proposed by Zhang, Robinson and Yao (2019)
      <doi:10.1080/01621459.2018.1458620>, unit root test proposed by Chang, Cheng and Yao (2022)
      <doi:10.1093/biomet/asab034>, white noise test proposed by Chang, Yao and Zhou (2017)
      <doi:10.1093/biomet/asw066>, CP-decomposition for matrix time 
      series proposed by Chang et al. (2023) <doi:10.1093/jrsssb/qkac011> and
      Chang et al. (2024) <doi:10.48550/arXiv.2410.05634>, and statistical inference for
      spectral density matrix proposed by Chang et al. (2022) 
      <doi:10.48550/arXiv.2212.13686>.
The Tweedie lasso model implements an iteratively reweighed least square (IRLS) strategy that incorporates a blockwise majorization decent (BMD) method, for efficiently computing solution paths of the (grouped) lasso and the (grouped) elastic net methods.
A protocol that facilitates the processing and analysis of Hydrogen-Deuterium Exchange Mass Spectrometry data using p-value statistics and Critical Interval analysis. 
    It provides a pipeline for analyzing data from 'HDXExaminer' (Sierra Analytics, Trajan Scientific), 
    automating matching and comparison of protein states through Welch's T-test and the Critical Interval statistical framework. 
    Additionally, it simplifies data export, generates 'PyMol' scripts, and ensures calculations meet publication standards. 
    'HDXBoxeR' assists in various aspects of hydrogen-deuterium exchange data analysis, including reprocessing data, calculating parameters, identifying significant peptides, 
    generating plots, and facilitating comparison between protein states. 
    For details check papers by Hageman and Weis (2019) <doi:10.1021/acs.analchem.9b01325> 
    and Masson et al. (2019) <doi:10.1038/s41592-019-0459-y>.
    'HDXBoxeR' citation: Janowska et al. (2024) <doi:10.1093/bioinformatics/btae479>.
Create dynamic, data-driven text. Given two values, a list of 
    talking points is generated and can be combined using string
    interpolation. Based on the 'glue' package.
Allows for painless use of the 'Metopio' health atlas APIs
    <https://metopio.com/health-atlas> to explore and import data.
    'Metopio' health atlases store open public health data. See what topics
    (or indicators) are available among specific populations, periods, and
    geographic layers. Download relevant data along with geographic 
    boundaries or point datasets. Spatial datasets are returned as 'sf' 
    objects.
Health Calculator helps to find different parameters like basal metabolic rate, body mass index etc. related to fitness and health of a person.
Antitrust analysis of
    healthcare markets. Contains functions to implement the 
    semiparametric estimation technique described in Raval, Rosenbaum,
    and Tenn (2017) "A Semiparametric Discrete Choice Model: An Application
    to Hospital Mergers" <doi:10.1111/ecin.12454>.
A system for identifying diseases or events from healthcare databases and
    preparing data for epidemiological studies. It includes capabilities not
    supported by 'SQL', such as matching strings by 'stringr' style regular
    expressions, and can compute comorbidity scores (Quan et al. (2005)
    <doi:10.1097/01.mlr.0000182534.19832.83>) directly on a database server. The
    implementation is based on 'dbplyr' with full 'tidyverse' compatibility.
Compute 21 summary measures of health inequality and its
    corresponding confidence intervals for ordered and non-ordered
    dimensions using disaggregated data. Measures for ordered dimensions
    (e.g., Slope Index of Inequality, Absolute Concentration Index) also
    accept individual and survey data.
Provides a shiny interface for a free, open-source managerial
    accounting-like system for health care practices. This package allows
    health care administrators to project revenue with monthly adjustments
    and procedure-specific boosts up to a 3-year period. Granular data
    (patient-level) to aggregated data (department- or hospital-level) can
    all be used as valid inputs provided historical volume and revenue
    data is available. For more details on managerial accounting
    techniques, see Brewer et al. (2015, ISBN:9780078025792).
Efficient tools for parsing and standardizing Australian 
    addresses from textual data. It utilizes optimized algorithms to accurately identify and 
    extract components of addresses, such as street names, types, and postcodes, especially  
    for large batched data in contexts where sending addresses to internet services may be 
    slow or inappropriate. The core functionality is built on fast string processing techniques 
    to handle variations in address formats and abbreviations commonly found in Australian 
    address data. Designed for data scientists, urban planners, and logistics analysts, the 
    package facilitates the cleaning and normalization of address information, supporting 
    better data integration and analysis in urban studies, geography, and related fields.
Hospital data analysis workflow tools, modeling, and automations. This library
    provides many useful tools to review common administrative hospital data. Some 
    of these include average length of stay, readmission rates, average net pay
    amounts by service lines just to name a few. The aim is to provide a simple
    and consistent verb framework that takes the guesswork out of everything.
Hospital machine learning and ai data analysis workflow tools, modeling, and automations. 
    This library provides many useful tools to review common administrative 
    hospital data. Some of these include predicting length of stay, and readmits.
    The aim is to provide a simple and consistent verb framework that takes the 
    guesswork out of everything.
Provides data for functions typically used in the 'healthyR' package.
Hospital time series data analysis workflow tools, modeling, and automations. 
    This library provides many useful tools to review common administrative time 
    series hospital data. Some of these include average length of stay, and 
    readmission rates. The aim is to provide a simple and consistent verb 
    framework that takes the guesswork out of everything.
The 'healthyverse' is a set of packages that work in
    harmony because they share common data representations and 'API'
    design. This package is designed to make it easy to install and load
    multiple 'healthyverse' packages in a single step.
Makes it easy to download a large number of files such as PDF files 
    and CSV files, while automatically slowing down requests, letting you know 
    where it is up to, and adjusting for files that have already been downloaded.
The heatex package calculates heat storage in the body and
        the components of heat exchange (conductive, convective,
        radiative, and evaporative) between the body and the
        environment during physical activity based on the principles of
        partitional calorimetry. The program enables heat exchange
        calculations for a range of environmental conditions when
        wearing various clothing ensembles.
Implements the simpler and faster heat index, which matches the values of the original 1979 heat index and its 2022 extension for air temperatures above 300 K (27 C, 80 F) and with only minor differences at lower temperatures. Also implements an algorithm for calculating the thermodynamic (and psychrometric) wet-bulb (and ice-bulb) temperature.
An improved heatmap package. Completely
    compatible with the original R function 'heatmap',
    and provides more powerful and convenient features.
Generates a fit plot for diagnosing misspecification in models of
    binary dependent variables, and calculates the related heatmap fit
    statistic described in Esarey and Pierce (2012) <DOI:10.1093/pan/mps026>.
A set of tools supporting more flexible heatmaps. The graphics is grid-like using
  the old graphics system. The main function is heatmap.n2(), which is a wrapper around the various functions
  constructing individual parts of the heatmap, like sidebars, picket plots, legends etc. The function supports zooming
  and splitting, i.e., having (unlimited) small heatmaps underneath each other in one plot deriving from the same data set,
  e.g., clustered and ordered by a supervised clustering method.
Create interactive cluster 'heatmaps' that can be saved as a stand-
    alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and
    available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to
    show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical
    method for visualizing high-dimensional data, in which a table of numbers
    are encoded as a grid of colored cells. The rows and columns of the matrix
    are ordered to highlight patterns and are often accompanied by 'dendrograms'.
    'Heatmaps' are used in many fields for visualizing observations, correlations,
    missing values patterns, and more. Interactive 'heatmaps' allow the inspection
    of specific value by hovering the mouse over a cell, as well as zooming into
    a region of the 'heatmap' by dragging a rectangle around the relevant area.
    This work is based on the 'ggplot2' and 'plotly.js' engine. It produces
    similar 'heatmaps' to 'heatmap.2' with the advantage of speed
    ('plotly.js' is able to handle larger size matrix), the ability to zoom from
    the 'dendrogram' panes, and the placing of factor variables in the sides of the
    'heatmap'.
The different methods for defining, detecting, and categorising the extreme events 
    known as heatwaves or cold-spells, as first proposed in Hobday et al. (2016) <doi: 10.1016/j.pocean.2015.12.014> 
    and Hobday et al. (2018) <https://www.jstor.org/stable/26542662>. The functions in this package work on both air 
    and water temperature data. These detection algorithms may be used on non-temperature data as well.
Provides a case conversion between common cases like CamelCase and 
    snake_case. Using the 'rust crate heck' <https://github.com/withoutboats/heck>
    as the backend for a highly performant case conversion for 'R'.
It performs maximum likelihood estimation for the Heckman selection model (Normal, Student-t or Contaminated normal) using an EM-algorithm <doi:10.1016/j.jmva.2021.104737>. It also performs influence diagnostic through global and local influence for four possible perturbation schema.
Tools for the estimation of Heckman selection models with robust 
  variance-covariance matrices. It includes functions for computing the bread 
  and meat matrices, as well as clustered standard errors for generalized Heckman 
  models, see Fernando de Souza Bastos and Wagner Barreto-Souza and Marc G. Genton 
  (2022, ISSN: <https://www.jstor.org/stable/27164235>). The package also offers 
  cluster-robust inference with sandwich estimators, and tools for handling issues 
  related to eigenvalues in covariance matrices.
Implements Heckman selection models using a Bayesian approach via 'Stan' and compares the performance of normal, Student’s t, and contaminated normal distributions in addressing complexities and selection bias (Heeju Lim, Victor E. Lachos, and Victor H. Lachos, Bayesian analysis of flexible Heckman selection models using Hamiltonian Monte Carlo, 2025, under submission).
This tool identifies hydropeaking events from raw time-series flow record, a rapid flow variation induced by the hourly-adjusted electricity market. The novelty of 'HEDA' is to use vector angle instead of the first-order derivative to detect change points which not only largely improves the computing efficiency but also accounts for the rate of change of the flow variation. More details <doi:10.1016/j.jhydrol.2021.126392>.
Helper functions designed to make
    dynamically generating R Markdown documents easier by providing a
    simple and tidy way to create report pieces, shape them to your data,
    and combine them for exporting into a single R Markdown document.
This algorithm is described in detail in the paper "Hedging Forecast Combinations With an Application to the Random Forest" by Beck et al. (2024) <https://papers.ssrn.com/sol3/papers.cfm?abstract_id=5032102>. The package provides a function hedgedrf() that can be used to train a Hedged Random Forest model on a dataset, and a function predict.hedgedrf() that can be used to make predictions with the model.
Hedgehog will eat all your bugs.
  'Hedgehog' is a property-based testing package in the spirit
  of 'QuickCheck'. With 'Hedgehog', one can test properties
  of their programs against randomly generated input, providing
  far superior test coverage compared to unit testing. One of the
  key benefits of 'Hedgehog' is integrated shrinking of
  counterexamples, which allows one to quickly find the cause of
  bugs, given salient examples when incorrect behaviour occurs.
An implementation of the modelling and reporting features described 
    in reference textbook and guidelines (Briggs, Andrew, et al. Decision 
    Modelling for Health Economic Evaluation. Oxford Univ. Press, 2011;
    Siebert, U. et al. State-Transition Modeling. Medical Decision Making 
    32, 690-700 (2012).): deterministic and probabilistic sensitivity analysis, 
    heterogeneity analysis, time dependency on state-time and model-time 
    (semi-Markov and non-homogeneous Markov models), etc.
In streaming data analysis, it is crucial to detect significant shifts in the data distribution or the accuracy of predictive models over time, a phenomenon known as concept drift. The package aims to identify when concept drift occurs and provide methodologies for adapting models in non-stationary environments. 
  It offers a range of state-of-the-art techniques for detecting concept drift and maintaining model performance. Additionally, the package provides tools for adapting models in response to these changes, ensuring continuous and accurate predictions in dynamic contexts.
  Methods for concept drift detection are described in Tavares (2022) <doi:10.1007/s12530-021-09415-z>.
Decode elements of the Australian Higher Education Information Management System (HEIMS) data for clarity and performance. HEIMS is the record system of the Department of Education, Australia to record enrolments and completions in Australia's higher education system, as well as a range of relevant information. For more information, including the source of the data dictionary, see <http://heimshelp.education.gov.au/sites/heimshelp/dictionary/pages/data-element-dictionary>.
Calculate and visualize Healthy Eating Index (HEI) scores
    from National Health and Nutrition Examination Survey 24-hour dietary
    recall data utilizing three methods recommended by the National Cancer
    Institute (2024)
    <https://epi.grants.cancer.gov/hei/hei-methods-and-calculations.html#:~:text=To%20use%20the%20simple%20HEI,the%20total%20scores%20across%20individuals.>.
    Effortlessly analyze HEI scores across different demographic groups
    and years.
Contains the National Health and Nutrition Examination Survey
    24-hour dietary recall data and Healthy Eating Index scoring standards
    used by the 'heiscore' package.
Create publication-quality, 2-dimensional visualizations of alpha-helical peptide
  sequences. Specifically, allows the user to programmatically generate
  helical wheels and wenxiang diagrams to provide a bird's eye, top-down view of
  alpha-helical oligopeptides. See Wadhwa RR, et al. (2018)
  <doi:10.21105/joss.01008> for more information.
Empirical value of the Hellinger correlation, a measure of dependence between
	     two continuous random variables. More details can be found in Geenens and Lafaye De Micheaux (2019) <arXiv:1810.10276v4>.
Batch processing framework for 'ellmer' chat models.
    Provides both sequential and parallel processing of chat interactions
    with features including tool calling and structured data extraction.
    Enables workflow management through progress tracking and recovery and 
    automatic retry with backoff. Additional quality-of-life features 
    include verbosity (or echo) control and sound notifications.
    Parallel processing is implemented via the 'future' framework.
    Includes methods for retrieving progress status, chat texts, and chat objects.
Base R's default setting for 'stringsAsFactors' within
    'data.frame()' and 'as.data.frame()' is supposedly the most often complained
    about piece of code in the R infrastructure. The 'hellno' package provides
    an explicit solution without changing R itself or having to mess around with
    options. It tries to solve this problem by providing alternative
    'data.frame()' and 'as.data.frame()' functions that are in fact simple
    wrappers around base R's 'data.frame()' and 'as.data.frame()' with
    'stringsAsFactors' option set to 'HELLNO' ( which in turn equals FALSE )
    by default.
A dummy package to demonstrate how to interface to a jar
        file that resides inside an R package.
Template R package with minimal setup to use Rust code in R without
    hacks or frameworks. Includes basic examples of importing cargo dependencies,
    spawning threads and passing numbers or strings from Rust to R. Cargo crates
    are automatically 'vendored' in the R source package to support offline
    installation. The GitHub repository for this package has more details and also 
    explains how to set up CI. This project was first presented at 'Erum2018' to 
    showcase R-Rust integration <https://jeroen.github.io/erum2018/>; for a real
    world use-case, see the 'gifski' package on 'CRAN'.
Contains miscellaneous functions useful for managing 'NetCDF' files (see <https://en.wikipedia.org/wiki/NetCDF>), get moon phase and time for sun rise and fall, tide level, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Tools for accessing various open data APIs in the Helsinki
    region in Finland. Current data sources include the Service Map API,
    Linked Events API, and Helsinki Region Infoshare statistics API.
An implementation of several Hierarchical Ensemble Methods (HEMs) for Directed Acyclic Graphs (DAGs). 'HEMDAG' package: 1) reconciles flat predictions with the topology of the ontology; 2) can enhance the predictions of virtually any flat learning methods by taking into account the hierarchical relationships between ontology classes; 3) provides biologically meaningful predictions that always obey the true-path-rule, the biological and logical rule that governs the internal coherence of biomedical ontologies; 4) is specifically designed for exploiting the hierarchical relationships of DAG-structured taxonomies, such as the Human Phenotype Ontology (HPO) or the Gene Ontology (GO), but can be safely applied to tree-structured taxonomies as well (as FunCat), since trees are DAGs; 5) scales nicely both in terms of the complexity of the taxonomy and in the cardinality of the examples; 6) provides several utility functions to process and analyze graphs; 7) provides several performance metrics to evaluate HEMs algorithms. (Marco Notaro, Max Schubach, Peter N. Robinson and Giorgio Valentini (2017) <doi:10.1186/s12859-017-1854-y>).
Import and classify canopy fish-eye images, estimate angular gap fraction and derive canopy attributes like leaf area index and openness.  Additional information is provided in the study by Chianucci F., Macek M. (2023) <doi:10.1016/j.agrformet.2023.109470>.
Provides HE plot and other functions for visualizing hypothesis
    tests in multivariate linear models. HE plots represent sums-of-squares-and-products 
    matrices for linear hypotheses and for error using ellipses (in two
    dimensions) and ellipsoids (in three dimensions). It also provides other tools for analysis and graphical display of the models
    such as robust methods and homogeneity of variance covariance matrices.
    The related 'candisc' package provides visualizations in a reduced-rank canonical discriminant space when
    there are more than a few response variables.
Set of R functions to be coupled with the 'xeus-r' 'jupyter' kernel
    in order to drive execution of code in notebook input cells, how R objects
    are to be displayed in output cells, and handle two way communication
    with the front end through comms.
Constructs paths to your project's files.
    Declare the relative path of a file within your project with 'i_am()'.
    Use the 'here()' function as a drop-in replacement for 'file.path()',
    it will always locate the files relative to your project root.
Interface to the 'HERE' REST APIs <https://developer.here.com/develop/rest-apis>:
  (1) geocode and autosuggest addresses or reverse geocode POIs using the 'Geocoder' API;
  (2) route directions, travel distance or time matrices and isolines using the 'Routing', 'Matrix Routing' and 'Isoline Routing' APIs;
  (3) request real-time traffic flow and incident information from the 'Traffic' API;
  (4) find request public transport connections and nearby stations from the 'Public Transit' API;
  (5) request intermodal routes using the 'Intermodal Routing' API;
  (6) get weather forecasts, reports on current weather conditions, astronomical
  information and alerts at a specific location from the 'Destination Weather' API.
  Locations, routes and isolines are returned as 'sf' objects.
Implements marker-based estimation of heritability when observations on genetically identical replicates are available. These can be either observations on individual plants or plot-level data in a field trial. Heritability can then be estimated using a mixed model for the individual plant or plot data. For comparison, also mixed-model based estimation using genotypic means and estimation of repeatability with ANOVA are implemented. For illustration the package contains several datasets for the model species Arabidopsis thaliana.
Probability functions and other utilities for the generalized Hermite distribution.
Facilitates estimation of full univariate and bivariate 
  probability density functions and cumulative distribution functions along with
  full quantile functions (univariate) and nonparametric correlation 
  (bivariate) using Hermite series based estimators. These estimators are 
  particularly useful in the sequential setting (both stationary and 
  non-stationary) and one-pass batch estimation setting for large data sets. 
  Based on: Stephanou, Michael, Varughese, Melvin and Macdonald, Iain. "Sequential quantiles via Hermite series density estimation." Electronic Journal of Statistics 11.1 (2017): 570-607 <doi:10.1214/17-EJS1245>, 
  Stephanou, Michael and Varughese, Melvin. "On the properties of Hermite series based distribution function estimators." Metrika (2020) <doi:10.1007/s00184-020-00785-z> and Stephanou, Michael and Varughese, Melvin. "Sequential estimation of Spearman rank correlation using Hermite series estimators." Journal of Multivariate Analysis (2021) <doi:10.1016/j.jmva.2021.104783>.
An implementation of the sandwich smoother proposed in Fast Bivariate Penalized Splines by Xiao et al. (2012) <doi:10.1111/rssb.12007>.    A hero is a specific type of sandwich.  Dictionary.com (2018) <https://www.dictionary.com> describes a hero as: a large sandwich, usually consisting of a small loaf of bread or long roll cut in half lengthwise and containing a variety of ingredients, as meat, cheese, lettuce, and tomatoes. Also implements the spatio-temporal sandwich smoother of French and Kokoszka (2021) <doi:10.1016/j.spasta.2020.100413>.
A modular and computationally efficient R package for  
  parameterizing, simulating, and analyzing health economic simulation 
  models. The package supports cohort discrete time state transition models 
  (Briggs et al. 1998) <doi:10.2165/00019053-199813040-00003>,
  N-state partitioned survival models (Glasziou et al. 1990)
  <doi:10.1002/sim.4780091106>, and individual-level continuous 
  time state transition models (Siebert et al. 2012) <doi:10.1016/j.jval.2012.06.014>,
  encompassing both Markov (time-homogeneous and time-inhomogeneous) and 
  semi-Markov processes. Decision uncertainty from a cost-effectiveness analysis is 
  quantified with standard graphical and tabular summaries of a probabilistic 
  sensitivity analysis (Claxton et al. 2005, Barton et al. 2008) <doi:10.1002/hec.985>, 
  <doi:10.1111/j.1524-4733.2008.00358.x>. Use of C++ and data.table
  make individual-patient simulation, probabilistic sensitivity analysis, 
  and incorporation of patient heterogeneity fast.
Provides tools for estimating sample sizes primarily based on heritability, while also considering additional parameters such as statistical power and fold change. The package normalizes heritability values according to trait-specific heritability and classification to enhance accuracy in sample size estimation.
Distribution free heteroscedastic tests for functional data. 
    The following tests are included in this package: test of no main treatment or contrast
    effect and no simple treatment effect given in 
    Wang, Higgins, and Blasi (2010) <doi:10.1016/j.spl.2009.11.016>,
    no main time effect, and no interaction effect based on 
    original observations given in Wang and Akritas (2010a) 
    <doi:10.1080/10485250903171621>
    and tests based on ranks given in Wang and Akritas (2010b)
    <doi:10.1016/j.jmva.2010.03.012>.
A method for estimating the correlation matrix of the Gaussian copula from the observed data. This package also contains a penalized estimation of the corresponding precision matrix, and enables to generate random vectors that are distributed according to a Gaussian copula.
A comprehensive suite of spatial 
  functions created to analyze and assess data heterogeneity and climate variability 
  in spatial datasets. This package is specifically designed to address the challenges associated
  with characterizing and understanding complex spatial patterns in environmental and climate-related data.
The goal of this package is to user-friendly realizing Gaussian 
             graphical model-based heterogeneity analysis.
             Recently, several Gaussian graphical model-based heterogeneity 
             analysis techniques have been developed. A common methodological limitation 
             is that the number of subgroups is assumed to be known a priori, which 
             is not realistic. In a very recent study (Ren et al., 2022), a novel approach 
             based on the penalized fusion technique is developed to fully 
             data-dependently determine the number and structure of subgroups in 
             Gaussian graphical model-based heterogeneity analysis. It opens the door for utilizing 
             the Gaussian graphical model technique in more practical settings. Beyond 
             Ren et al. (2022), more estimations and functions are added, so 
             that the package is self-contained and more comprehensive and can 
             provide ``more direct'' insights to practitioners (with the 
             visualization function). Reference: 
             Ren, M., Zhang S., Zhang Q. and Ma S. (2022). Gaussian Graphical 
             Model-based Heterogeneity Analysis via Penalized Fusion. 
             Biometrics, 78 (2), 524-535.
Published meta-analyses routinely present one of the
   measures of heterogeneity introduced in Higgins and Thompson
   (2002) <doi:10.1002/sim.1186>. For critiquing articles
   it is often better to convert to another of
   those measures. Some
   conversions are provided here and confidence intervals are also
   available.
A multi-core R package that allows for the statistical modeling of multi-group multivariate mixed data using Gaussian graphical models. Combining the Gaussian copula framework with the fused graphical lasso penalty, the 'heteromixgm' package can handle a wide variety of datasets found in various sciences. The package also includes an option to perform model selection using the AIC, BIC and EBIC information criteria, a function that plots partial correlation graphs based on the selected precision matrices, as well as simulate mixed heterogeneous data for exploratory or simulation purposes and one multi-group multivariate mixed agricultural dataset pertaining to maize yields. The package implements the methodological developments found in Hermes et al. (2024) <doi:10.1080/10618600.2023.2289545>.
Performs Gaussian process regression with heteroskedastic noise following the model by Binois, M., Gramacy, R., Ludkovski, M. (2016) <doi:10.48550/arXiv.1611.05902>, with implementation details in Binois, M. & Gramacy, R. B. (2021) <doi:10.18637/jss.v098.i13>. The input dependent noise is modeled as another Gaussian process. Replicated observations are encouraged as they yield computational savings. Sequential design procedures based on the integrated mean square prediction error and lookahead heuristics are provided, and notably fast update functions when adding new observations.
Homomorphic encryption (Brakerski and Vaikuntanathan (2014) <doi:10.1137/120868669>) using Ring Learning with Errors (Lyubashevsky et al. (2012) <https://eprint.iacr.org/2012/230>) is a form of Learning with Errors (Regev (2005) <doi:10.1145/1060590.1060603>) using polynomial rings over finite fields. Functions to generate the required polynomials (using 'polynom'), with various distributions of coefficients are provided. Additionally, functions to generate and take coefficient modulo are provided.
Cellular responses to perturbations are highly heterogeneous
    and depend largely on the initial state of cells. Connecting
    post-perturbation cells via cellular trajectories to untreated cells
    (e.g. by leveraging metabolic labeling information) enables
    exploitation of intercellular heterogeneity as a combined knock-down
    and overexpression screen to identify pathway modulators, termed
    Heterogeneity-seq (see 'Berg et al' <doi:10.1101/2024.10.28.620481>).
    This package contains functions to generate cellular trajectories based
    on scSLAM-seq (single-cell, thiol-(SH)-linked alkylation of RNA for
    metabolic labelling sequencing) time courses, functions to identify
    pathway modulators and to visualize the results.
Provides a function to assess and test for heterogeneity in the utility of a surrogate marker with respect to a baseline covariate. The main function can be used for either a continuous or discrete baseline covariate. More details will be available in the future in: Parast, L., Cai, T., Tian L (2021). "Testing for Heterogeneity in the Utility of a Surrogate Marker." Biometrics, In press.
Provides functions to assess and test for heterogeneity in the utility of a surrogate marker with respect to a baseline covariate using censored (survival data), and to test for heterogeneity across multiple time points.  More details are available in Parast et al (2024) <doi:10.1002/sim.10122>.
Functions for the fitting and summarizing of heteroscedastic t-regression.
Tests for a treatment effect using surrogate marker information accounting for heterogeneity in the utility of the surrogate. Details are described in Parast et al (2022) <arXiv:2209.08315>.
Computes diagnostics for linear regression when treatment effects are heterogeneous.
    The output of 'hettreatreg' represents ordinary least squares (OLS) 
    estimates of the effect of a binary treatment as a weighted average of the average treatment effect 
    on the treated (ATT) and the average treatment effect on the untreated (ATU). 
    The program estimates the OLS weights on these parameters, computes the associated model diagnostics, 
    and reports the implicit OLS estimate of the average treatment effect (ATE). 
    See Sloczynski (2019), <http://people.brandeis.edu/~tslocz/Sloczynski_paper_regression.pdf>.
Implements methods developed by Ding, Feller, and Miratrix (2016) <doi:10.1111/rssb.12124> <arXiv:1412.5000>,
    and Ding, Feller, and Miratrix (2018) <doi:10.1080/01621459.2017.1407322> <arXiv:1605.06566>
    for testing whether there is unexplained variation in treatment effects across observations, and for characterizing
    the extent of the explained and unexplained variation in treatment effects. The package includes wrapper functions
    implementing the proposed methods, as well as helper functions for analyzing and visualizing the results of the test.
Structural handling of Finnish identity codes (natural persons and 
    organizations); extract information, check ID validity and diagnostics.
Implements the Clarke-Wright algorithm to find a quasi-optimal solution to the Capacitated Vehicle Routing Problem. See Clarke, G. and Wright, J.R. (1964) <doi:10.1287/opre.12.4.568> for details. The implementation is accompanied by helper functions to inspect its solution.
Implements various heuristics like Take The Best and
    unit-weight linear, which do two-alternative choice: which of
    two objects will have a higher criterion?  Also offers functions
    to assess performance, e.g. percent correct across all row pairs
    in a data set and finding row pairs where models disagree.
    New models can be added by implementing a fit and predict function--
    see vignette.  Take The Best was first described in: Gigerenzer, G.
    & Goldstein, D. G. (1996) <doi:10.1037/0033-295X.103.4.650>.  All
    of these heuristics were run on many data sets and analyzed in:
    Gigerenzer, G., Todd, P. M., & the ABC Group (1999).
    <ISBN:978-0195143812>.
Provides the heuristics miner algorithm for process discovery 
   as proposed by Weijters et al. (2011) <doi:10.1109/CIDM.2011.5949453>. The
   algorithm builds a causal net from an event log created with the 'bupaR' 
   package. Event logs are a set of ordered sequences of events for which 
   'bupaR' provides the S3 class eventlog(). The discovered causal nets 
   can be visualised as 'htmlwidgets' and it is possible to annotate them with
   the occurrence frequency or processing and waiting time of process 
   activities.
Binning and plotting functions for hexagonal bins.
Kernel density estimation with hexagonal grid for bivariate data.
      Hexagonal grid has many beneficial properties like equidistant neighbours
      and less edge bias, making it better for spatial analyses than the more
      commonly used rectangular grid.
      Carr, D. B. et al. (1987) <doi:10.2307/2289444>.
      Diggle, P. J. (2010) <doi:10.1201/9781420072884>.
      Hill, B. (2017) <https://blog.bruce-hill.com/meandering-triangles>.
      Jones, M. C. (1993) <doi:10.1007/BF00147776>.
Contains most of the hex font files from the 'GNU Unifont Project' <https://unifoundry.com/unifont/> compressed by 'xz'.  'GNU Unifont' is a duospaced bitmap font that attempts to cover all the official Unicode glyphs plus several of the artificial scripts in the '(Under-)ConScript Unicode Registry' <https://www.kreativekorp.com/ucsur/>.  Provides a convenience function for loading in several of them at the same time as a 'bittermelon' bitmap font object for easy rendering of the glyphs in an 'R' terminal or graphics device.
Helper functions for creating reproducible hexagon sticker purely in R.
Simple and integrated tool that automatically extracts and folds all hairpin sequences from raw genome-wide data. It predicts the secondary structure of several overlapped segments, with longer length than the mean length of sequences of interest for the species under processing, ensuring that no one is lost nor inappropriately cut.
Display hexagonally binned scatterplots for multi-class data, using coloured triangles to show class proportions.
Functions to view files in raw binary form like in a hex editor.  Additional functions to specify and read arbitrary binary formats.
Provides functionality to download and cache files from 'Hugging Face Hub' <https://huggingface.co/models>. 
    Uses the same caching structure so files can be shared between different client libraries.
A data only package containing commercial domestic flights that
    departed Houston (IAH and HOU) in 2011.
Provides functions for the estimation, plotting, predicting and cross-validation of hierarchical feature regression models as described in Pfitzinger (2024). Cluster Regularization via a Hierarchical Feature Regression. Econometrics and Statistics (in press). <doi:10.1016/j.ecosta.2024.01.003>.
Implementation of the Hysteretic and Gatekeeping Depressions Model (HGDM) which calculates variable connected/contributing areas and resulting discharge volumes in prairie basins dominated by depressions ("slough" or "potholes"). The small depressions are combined into a single "meta" depression which explicitly models the hysteresis between the storage of water and the connected/contributing areas of the depressions. The largest (greater than 5% of the total depressional area) depression (if it exists) is represented separately to model its gatekeeping, i.e. the blocking of upstream flows until it is filled. The methodolgy is described in detail in Shook and Pomeroy (2025, <doi:10.1016/j.jhydrol.2025.132821>).
Implements the hub graphical lasso and hub covariance graph proposal by Tan, KM., London, P., Mohan, K., Lee, S-I., Fazel, M., and Witten, D. (2014). Learning graphical models with hubs. Journal of Machine Learning Research 15(Oct):3297-3331.
Implemented here are procedures for fitting hierarchical generalized linear models (HGLM). It can be used for linear mixed models and generalized linear mixed models with random effects for a variety of links and a variety of distributions for both the outcomes and the random effects. Fixed effects can also be fitted in the dispersion part of the mean model. As statistical models, HGLMs were initially developed by Lee and Nelder (1996) <https://www.jstor.org/stable/2346105?seq=1>. We provide an implementation (Ronnegard, Alam and Shen 2010) <https://journal.r-project.org/archive/2010-2/RJournal_2010-2_Roennegaard~et~al.pdf> following Lee, Nelder and Pawitan (2006) <ISBN: 9781420011340> with algorithms extended for spatial modeling (Alam, Ronnegard and Shen 2015) <https://journal.r-project.org/archive/2015/RJ-2015-017/RJ-2015-017.pdf>.
This data-only package was created for distributing data used in the examples of the 'hglm' package.
The holonomic gradient method (HGM, hgm) gives a way to evaluate normalization
  constants of unnormalized probability distributions by utilizing holonomic 
  systems of differential or difference equations. The holonomic gradient descent (HGD, hgd) gives a method
  to find maximal likelihood estimates by utilizing the HGM.
Graphical model is an informative and powerful tool to explore the conditional dependence relationships among variables. The traditional Gaussian graphical model and its extensions either have a Gaussian assumption on the data distribution or assume the data are homogeneous. However, there are data with complex distributions violating these two assumptions. For example, the air pollutant concentration records are non-negative and, hence, non-Gaussian. Moreover, due to climate changes, distributions of these concentration records in different months of a year can be far different, which means it is uncertain whether datasets from different months are homogeneous. Methods with a Gaussian or homogeneous assumption may incorrectly model the conditional dependence relationships among variables. Therefore, we propose a heterogeneous graphical model for non-negative data (HGMND) to simultaneously cluster multiple datasets and estimate the conditional dependence matrix of variables from a non-Gaussian and non-negative exponential family in each cluster.
A set of routines to quickly download and import the
    HUGO Gene Nomenclature Committee (HGNC) data set on mapping of
    gene symbols to gene entries in other genomic databases or resources.
Contains functions for
 identifying and correcting HGNC human gene symbols and MGI mouse gene symbols 
 which have been converted to date format by Excel, withdrawn, or aliased.
 Also contains functions for reversibly converting between HGNC
 symbols and valid R names.
It is used to travel graphs, by using DFS and BFS to get the path from node to each leaf node.
  Depth first traversal(DFS) is a recursive algorithm for searching all the vertices of a graph or tree data structure.
  Traversal means visiting all the nodes of a graph.
  Breadth first traversal(BFS) algorithm is used to search a tree or graph data structure for a node that meets a set of criteria.
  It starts at the tree’s root or graph and searches/visits all nodes at the current depth level before moving on to the nodes at the next depth level.
  Also, it provides the matrix which is reachable between each node.
  Implement reference about Baruch Awerbuch (1985) <doi:10.1016/0020-0190(85)90083-3>.
Estimation of high-dimensional multi-response regression with heterogeneous noises under Heterogeneous group square-root Lasso penalty. For details see: Ren, Z., Kang, Y., Fan, Y. and Lv, J. (2018)<arXiv:1606.03803>.
A handy collection of utility functions designed to aid in
    package development, plotting and scientific research.  Package
    development functionalities includes among others tools such as
    cross-referencing package imports with the description file, analysis
    of redundant package imports, editing of the description file and the
    creation of package badges for GitHub.  Some of the other
    functionalities include automatic package installation and loading,
    plotting points without overlap, creating nice breaks for plots,
    overview tables and many more handy utility functions.
This model divides coefficients into three types,
        i.e., local fixed effects, global fixed effects, and random effects (Hu et al., 2022)<doi:10.1177/23998083211063885>.
        If data have spatial hierarchical structures (especially are overlapping on some locations),
        it is worth trying this model to reach better fitness.
Support software for Statistical Analysis and Data Display (Second Edition, Springer, ISBN 978-1-4939-2121-8, 2015) and (First Edition, Springer, ISBN 0-387-40270-5, 2004) by Richard M. Heiberger and Burt Holland.  This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis.  The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print.  All chapters have exercises.  All functions introduced in the book are in the package.  R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Meyer and Held (2017) <doi:10.1093/biostatistics/kxw051> present an
    age-structured spatio-temporal model for infectious disease counts. The
    approach is illustrated in a case study on norovirus gastroenteritis in
    Berlin, 2011-2015, by age group, city district and week, using additional
    contact data from the POLYMOD survey. This package contains the data and
    code to reproduce the results from the paper, see 'demo("hhh4contacts")'.
Based on the aggregated shares retained by individual firms or actors within a market or space, the Herfindahl-Hirschman Index (HHI) measures the level of concentration in a space. This package allows for intuitive and straightforward computation of HHI scores, requiring placement of objects of interest directly into the function. The package also includes a plot function for quick visual display of an HHI time series using any measure of time (year, quarter, month, etc.). For usage, please cite the Journal of Open Source Software paper associated with the package: Waggoner, Philip D. (2018) <doi:10.21105/joss.00828>.
Allows users to create high-quality heatmaps from labelled, hierarchical data. Specifically, for data with a two-level hierarchical structure, it will produce a heatmap where each row and column represents a category at the lower level. These rows and columns are then grouped by the higher-level group each category belongs to, with the names for each category and groups shown in the margins. While other packages (e.g. 'dendextend') allow heatmap rows and columns to be arranged by groups only, 'hhmR' also allows the labelling of the data at both the category and group level.
In medical research, supervised heterogeneity analysis has important implications. Assume that there are two types of features. Using both types of features, our goal is to conduct the first supervised heterogeneity analysis that satisfies a hierarchical structure. That is, the first type of features defines a rough structure, and the second type defines a nested and more refined structure. A penalization approach is developed, which has been motivated by but differs significantly from penalized fusion and sparse group penalization. 
             Reference: 
             Ren, M., Zhang, Q., Zhang, S., Zhong, T., Huang, J. & Ma, S. (2022). "Hierarchical cancer heterogeneity analysis based on histopathological imaging features". Biometrics, <doi:10.1111/biom.13426>.
Develops algorithms for fitting, prediction, simulation 
  and initialization of the following models
  (1)- hidden hybrid Markov/semi-Markov model, 
  introduced by Guedon (2005) <doi:10.1016/j.csda.2004.05.033>, 
  (2)- nonparametric mixture of B-splines emissions (Langrock et al., 2015
  <doi:10.1111/biom.12282>), 
  (3)- regime switching regression model 
  (Kim et al., 2008 <doi:10.1016/j.jeconom.2007.10.002>) and auto-regressive 
  hidden hybrid Markov/semi-Markov model, 
  (4)- spline-based nonparametric 
  estimation of additive state-switching models  
  (Langrock et al., 2018 <doi:10.1111/stan.12133>)
  (5)- robust emission model proposed by 
  Qin et al, 2024 <doi:10.1007/s10479-024-05989-4>
  (6)- several emission distributions, including mixture of multivariate normal  
  (which can also handle missing data using EM algorithm) and multi-nomial emission 
  (for modeling polymer or DNA sequences)
  (7)- tools for prediction of future state sequence, computing the score of a new sequence,
  splitting the samples and sequences to train and test sets, computing the information measures of 
  the models, computing the residual useful lifetime (reliability) and many other useful tools ...
  (read for more description: Amini et al., 2022 <doi:10.1007/s00180-022-01248-x> and its 
  arxiv version: <doi:10.48550/arXiv.2109.12489>).
Builds on the EMD package to provide additional tools for empirical mode decomposition (EMD) and Hilbert spectral analysis. It also implements the ensemble empirical decomposition (EEMD) and the complete ensemble empirical mode decomposition (CEEMD) methods to avoid mode mixing and intermittency problems found in EMD analysis.  The package comes with several plotting methods that can be used to view intrinsic mode functions, the HHT spectrum, and the Fourier spectrum.
A user-friendly tool to fit Bayesian regression models. It can fit 3 types of Bayesian models using individual-level, summary-level, and individual plus pedigree-level (single-step) data for both Genomic prediction/selection (GS) and Genome-Wide Association Study (GWAS), it was designed to estimate joint effects and genetic parameters for a complex trait, including:
    (1) fixed effects and coefficients of covariates,
    (2) environmental random effects, and its corresponding variance, 
    (3) genetic variance, 
    (4) residual variance, 
    (5) heritability, 
    (6) genomic estimated breeding values (GEBV) for both genotyped and non-genotyped individuals,
    (7) SNP effect size, 
    (8) phenotype/genetic variance explained (PVE) for single or multiple SNPs, 
    (9) posterior probability of association of the genomic window (WPPA), 
    (10) posterior inclusive probability (PIP). 
    The functions are not limited, we will keep on going in enriching it with more features. 
    References: Meuwissen et al. (2001) <doi:10.1093/genetics/157.4.1819>; Gustavo et al. (2013) <doi:10.1534/genetics.112.143313>; Habier et al. (2011) <doi:10.1186/1471-2105-12-186>; Yi et al. (2008) <doi:10.1534/genetics.107.085589>; Zhou et al. (2013) <doi:10.1371/journal.pgen.1003264>; Moser et al. (2015) <doi:10.1371/journal.pgen.1004969>; Lloyd-Jones et al. (2019) <doi:10.1038/s41467-019-12653-0>; Henderson (1976) <doi:10.2307/2529339>; Fernando et al. (2014) <doi:10.1186/1297-9686-46-50>.
A tool for Hierarchical Climate Regionalization applicable to any correlation-based clustering.
             It adds several features and a new clustering method (called, 'regional' linkage) to hierarchical
             clustering in R ('hclust' function in 'stats' library): data regridding, coarsening spatial resolution,
             geographic masking, contiguity-constrained clustering, data filtering by mean and/or variance
             thresholds, data preprocessing (detrending, standardization, and PCA), faster correlation function
             with preliminary big data support, different clustering methods, hybrid hierarchical clustering,
             multivariate clustering (MVC), cluster validation, visualization of regionalization results, and
             exporting region map and mean timeseries into NetCDF-4 file.
             The technical details are described in Badr et al. (2015) <doi:10.1007/s12145-015-0221-7>.
Identifies chromatin interaction modules by constructing a Hi-C contact network based on statistically significant interactions, followed by network clustering. The method enables comparison of module connectivity across two Hi-C datasets and is capable of detecting cell-type-specific regulatory modules. By integrating network analysis with chromatin conformation data, this approach provides insights into the spatial organization of the genome and its functional implications in gene regulation. Author: Sora Yoon (2025) <https://github.com/ysora/HiCociety>.
Provides an example HiC dataset and two examples of 'HiCociety' 
  outputs from a function named hic2community(). 
  The data are intended for demonstration purposes only and kept small 
  enough to be distributed via CRAN.
The Harmonised Index of Consumer Prices (HICP) is the key economic figure to measure inflation in the euro area.
              The methodology underlying the HICP is documented in the HICP Methodological Manual (<https://ec.europa.eu/eurostat/web/products-manuals-and-guidelines/w/ks-gq-24-003>).
              Based on the manual, this package provides functions to access and work with HICP data from Eurostat's public database (<https://ec.europa.eu/eurostat/data/database>).
Computes the ACMIF test and Bonferroni-adjusted p-value of interaction in two-factor studies.  Produces corresponding interaction plot and analysis of variance tables and p-values from several other tests of non-additivity.
Contains functions for the analysis of Discrete Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated Poisson Process. It includes functions for simulation, parameter estimation, and the Viterbi algorithm. See the topic "HiddenMarkov" for an introduction to the package, and "Change Log" for a list of recent changes. The algorithms are based of those of Walter Zucchini.
Generates HIDECAN plots that summarise and combine 
  the results of genome-wide association studies (GWAS) and transcriptomics 
  differential expression analyses (DE), along with manually curated candidate genes of interest. The HIDECAN plot 
  is presented in Angelin-Bonnet et al. (2023) (currently in review).
Performs linear discriminant analysis in high dimensional
        problems based on reliable covariance estimators for problems
        with (many) more variables than observations. Includes routines
        for classifier training, prediction, cross-validation and
        variable selection.
Calculate clinical scores for hidradenitis suppurativa (HS), a
  dermatologic disease.  The scores are typically used for evaluation of
  efficacy in clinical trials.  The scores are not commonly used in clinical
  practice.  The specific scores implemented are Hidradenitis Suppurativa 
  Clinical Response (HiSCR) (Kimball, et al. (2015) <doi:10.1111/jdv.13216>),
  Hidradenitis Suppurativa Area and Severity Index Revised (HASI-R) (Goldfarb,
  et al. (2020) <doi:10.1111/bjd.19565>), hidradenitis suppurativa Physician
  Global Assessment (HS PGA) (Marzano, et al. (2020) <doi:10.1111/jdv.16328>),
  and the International Hidradenitis Suppurativa Severity Score System (IHS4)
  (Zouboulis, et al. (2017) <doi:10.1111/bjd.15748>).
Pure set data visualization approaches are often limited in
    scalability due to the combinatorial explosion of distinct set families as
    the number of sets under investigation increases. hierarchicalSets applies
    a set centric hierarchical clustering of the sets under investigation and
    uses this hierarchy as a basis for a range of scalable visual
    representations. hierarchicalSets is especially well suited for collections
    of sets that describe comparable comparable entities as it relies on the
    sets to have a meaningful relational structure.
Bipartite graph-based hierarchical clustering, developed for pharmacogenomic 
    datasets and datasets sharing the same data structure. The goal is to 
    construct a hierarchical clustering of groups of samples based on 
    association patterns between two sets of variables. In the context of
    pharmacogenomic datasets, the samples are cell lines, and the two sets of 
    variables are typically expression levels and drug sensitivity values. 
    For this method, sparse canonical correlation analysis from 
    Lee, W., Lee, D., Lee, Y. and Pawitan, Y. (2011) <doi:10.2202/1544-6115.1638> 
    is first applied to extract association patterns for each group of samples. 
    Then, a nuclear norm-based dissimilarity measure is used to construct a 
    dissimilarity matrix between groups based on the extracted associations. 
    Finally, hierarchical clustering is applied.
Estimates hierarchical F-statistics from haploid or
    diploid genetic data with any numbers of levels in the hierarchy, following the
    algorithm of Yang (Evolution(1998), 52:950).
    Tests via randomisations the significance
    of each F and variance components, using the likelihood-ratio statistics G
    (Goudet et al. (1996) <https://academic.oup.com/genetics/article/144/4/1933/6017091>).
    Estimates genetic diversity statistics
    for haploid and diploid genetic datasets in various formats, including inbreeding and
    coancestry coefficients, and population specific F-statistics following
    Weir and Goudet (2017) <https://academic.oup.com/genetics/article/206/4/2085/6072590>.
Fits sparse interaction models for continuous and binary responses subject to the strong (or weak) hierarchy restriction that an interaction between two variables only be included if both (or at least one of) the variables is included as a main effect.  For more details, see Bien, J., Taylor, J., Tibshirani, R., (2013) "A Lasso for Hierarchical Interactions." Annals of Statistics. 41(3). 1111-1141.
Machine learning hierarchical risk clustering portfolio allocation strategies. 
 The implemented methods are:
  Hierarchical risk parity (De Prado, 2016) <DOI: 10.3905/jpm.2016.42.4.059>.
  Hierarchical clustering-based asset allocation (Raffinot, 2017)  
  <DOI: 10.3905/jpm.2018.44.2.089>.
  Hierarchical equal risk contribution portfolio (Raffinot, 2018)
  <DOI: 10.2139/ssrn.3237540>.
  A Constrained Hierarchical Risk Parity Algorithm with Cluster-based Capital Allocation (Pfitzingera and Katzke, 2019)
  <https://www.ekon.sun.ac.za/wpapers/2019/wp142019/wp142019.pdf>.
Provides semiparametric sufficient dimension reduction for central mean subspaces for heterogeneous data defined by combinations of binary factors (such as chronic conditions). Subspaces are estimated to be hierarchically nested to respect the structure of subpopulations with overlapping characteristics. This package is an implementation of the proposed methodology of Huling and Yu (2021) <doi:10.1111/biom.13546>.
An implementation of the nonnegative garrote method that incorporates hierarchical relationships among variables. The core function, HiGarrote(), offers an automated approach for analyzing experiments while respecting hierarchical structures among effects. For methodological details, refer to Yu and Joseph (2024) <doi:10.48550/arXiv.2411.01383>. This work is supported by U.S. National Science Foundation grant DMS-2310637.
A wrapper for the 'Highcharts' library including
    shortcut functions to plot R objects. 'Highcharts'
    <https://www.highcharts.com/> is a charting library offering
    numerous chart types with a simple configuration syntax.
Tests for two high-dimensional population mean vectors. The user has the option to compute the asymptotic, the permutation or the bootstrap based p-value of the test. Some references are: Chen S.X. and Qin Y.L. (2010). <doi:10.1214/09-AOS716>, Cai T.T., Liu W., and Xia Y. (2014) <doi:10.1111/rssb.12034> and Yu X., Li D., Xue L. and Li, R. (2023) <doi:10.1080/01621459.2022.2061354>.
Implements the high-dimensional two-sample test 
    proposed by Zhang (2019) <http://hdl.handle.net/2097/40235>. 
    It also implements the test proposed by Srivastava, Katayama, 
    and Kano (2013) <doi:10.1016/j.jmva.2012.08.014>. These tests 
    are particularly suitable to high dimensional data from two populations 
    for which the classical multivariate Hotelling's T-square test fails due 
    to sample sizes smaller than dimensionality. In this case, the ZWL and ZWLm 
    tests proposed by Zhang (2019) <http://hdl.handle.net/2097/40235>, 
    referred to as zwl_test() in this package, provide a reliable and powerful test.
Computes the scores and ranks candidates according to voting rules electing the highest median grade.
    Based on "Tie-breaking the highest median: alternatives to the majority judgment", A. Fabre, Social Choice & Welfare (forthcoming as of 2020). The paper is available here: <https://github.com/bixiou/highest_median/raw/master/Tie-breaking%20Highest%20Median%20-%20Fabre%202019.pdf>.
    Functions to plot the voting profiles can be found on github: <https://github.com/bixiou/highest_median/blob/master/packages_functions_data.R>.
A modern idiomatic header-only 'C++'' interface for 'libhdf5'. Original software can be found at <https://github.com/highfive-devs/highfive/>.
Provide functionality to manage, clean and match highfrequency
    trades and quotes data, calculate various liquidity measures, estimate and
    forecast volatility, detect price jumps and investigate microstructure noise and intraday
    periodicity. A detailed vignette can be found in the open-access paper 
    "Analyzing Intraday Financial Data in R: The highfrequency Package" 
    by Boudt, Kleen, and Sjoerup (2022, <doi:10.18637/jss.v104.i08>).
Syntax highlighter for R code based on the results of the R
    parser. Rendering in HTML and latex markup. Custom Sweave driver
    performing syntax highlighting of R code chunks.
Code Syntax Highlighting made easy for code snippets or complete
    files. Whether you're documenting your data analysis or creating interactive
    'shiny' apps.
A tool to format R markdown with CSS ids for HTML output. 
    The tool may be most helpful for those using markdown to create reproducible
    documents. The biggest limitations in formatting is the knowledge of CSS
    by the document authors.
Input multiple versions of a source document, 
    and receive HTML code for a highlighted version of the source document
    indicating the frequency of occurrence of phrases in the different versions.
    This method is described in Chapter 3 of 
    Rogers (2024) <https://digitalcommons.unl.edu/dissertations/AAI31240449/>.
Provides various tests for comparing high-dimensional mean vectors in two sample populations.
Perform high dimensional Feature Selection in the presence of survival outcome.
            Based on Feature Selection method and different survival analysis, it will obtain the best 
            markers with optimal threshold levels according to their effect on disease progression
            and produce the most consistent level according to those threshold values. 
            The functions' methodology is based on by Sonabend et al (2021) <doi:10.1093/bioinformatics/btab039>  and Bhattacharjee  et al (2021) <arXiv:2012.02102>.
The classical Markowitz's mean-variance portfolio formulation ignores 
    heavy tails and skewness. High-order portfolios use higher order moments to
    better characterize the return distribution. Different formulations and fast 
    algorithms are proposed for high-order portfolios based on the mean, variance, 
    skewness, and kurtosis.
    The package is based on the papers:
    R. Zhou and D. P. Palomar (2021). "Solving High-Order Portfolios via 
    Successive Convex Approximation Algorithms." <arXiv:2008.00863>.
    X. Wang, R. Zhou, J. Ying, and D. P. Palomar (2022). "Efficient and Scalable 
    High-Order Portfolios Design via Parametric Skew-t Distribution." <arXiv:2206.02412>.
Provides syntax highlighting for R source code. Currently it
    supports LaTeX and HTML output. Source code of other languages is supported
    via Andre Simon's highlight package (<https://gitlab.com/saalen/highlight>).
Functions for determining and evaluating high-risk zones and
    simulating and thinning point process data, as described in 'Determining
    high risk zones using point process methodology - Realization by building
    an R package' Seibold (2012) <http://highriskzone.r-forge.r-project.org/Bachelorarbeit.pdf> 
    and 'Determining high-risk zones for unexploded World War II bombs by using point 
    process methodology', Mahling et al. (2013) <doi:10.1111/j.1467-9876.2012.01055.x>.
R interface to 'HiGHS', an optimization solver for solving mixed integer 
        optimization problems with quadratic or linear objective and linear constraints.
HIGHT(HIGh security and light weigHT) algorithm is a block cipher encryption algorithm developed to provide confidentiality in computing environments that demand low power consumption and lightweight, such as RFID(Radio-Frequency Identification) and USN(Ubiquitous Sensor Network), or in mobile environments that require low power consumption and lightweight, such as smartphones and smart cards. Additionally, it is designed with a simple structure that enables it to be used with basic arithmetic operations, XOR, and circular shifts in 8-bit units. This algorithm was designed to consider both safety and efficiency in a very simple structure suitable for limited environments, compared to the former 128-bit encryption algorithm SEED. In December 2010, it became an ISO(International Organization for Standardization) standard. The detailed procedure is described in Hong et al. (2006) <doi:10.1007/11894063_4>.
Implements the method developed by Cao and Kosorok (2011) for the 
    significance analysis of thousands of features in high-dimensional 
    biological studies. It is an asymptotically valid data-driven procedure 
    to find critical values for rejection regions controlling the 
    k-familywise error rate, false discovery rate, and the tail probability 
    of false discovery proportion.
Environmental health studies are increasingly measuring multiple pollutants
    to characterize the joint health effects attributable to exposure mixtures.
    However, the underlying dose-response relationship between toxicants and
    health outcomes of interest may be highly nonlinear, with possible nonlinear
    interaction effects. Hierarchical integrative group least absolute shrinkage
    and selection operator (HiGLASSO), developed by Boss et al (2020)
    <arXiv:2003.12844>, is a general framework to identify noteworthy nonlinear 
    main and interaction effects in the presence of group structures among a set
    of exposures.
Implements the Hierarchical Incremental GRAdient Descent (HiGrad) algorithm,
    a first-order algorithm for finding the minimizer of a function in online learning just like stochastic gradient descent (SGD).
    In addition, this method attaches a confidence interval to assess the uncertainty of its predictions.
    See Su and Zhu (2018) <arXiv:1802.04876> for details.
Provides utilities for encoding and decoding coordinates to/from Hilbert curves
  based on the iterative encoding implementation described in Chen et al. (2006) <doi:10.1002/spe.793>.
Quantifying similarity between high-dimensional single cell samples is challenging, and usually requires
    some simplifying hypothesis to be made. By transforming the high dimensional space into a high dimensional grid,
    the number of cells in each sub-space of the grid is characteristic of a given sample. Using a Hilbert curve
    each sample can be visualized as a simple density plot, and the distance between samples can be calculated from
    the distribution of cells using the Jensen-Shannon distance. Bins that correspond to significant differences
    between samples can identified using a simple bootstrap procedure.
Makes it easy to extract and combine variables from the HILDA (Household, Income and Labour Dynamics in Australia) survey maintained by the Melbourne Institute <https://melbourneinstitute.unimelb.edu.au/hilda>.
Calculate taxonomic, functional and phylogenetic diversity measures 
    through Hill Numbers proposed by Chao, Chiu and Jost (2014) 
    <doi:10.1146/annurev-ecolsys-120213-091540>.
A set of tools to create georeferenced hillshade relief 
    raster maps using ray-tracing and other advanced hill-shading 
    techniques. It includes a wrapper function to create a georeferenced,
    ray-traced hillshade map from a digital elevation model, and other
    functions that can be used in a rayshader pipeline.
Allows to estimate and test high-dimensional mediation effects based on advanced mediator screening and penalized regression techniques. Methods used in the package refer to Zhang H, Zheng Y, Zhang Z, Gao T, Joyce B, Yoon G, Zhang W, Schwartz J, Just A, Colicino E, Vokonas P, Zhao L, Lv J, Baccarelli A, Hou L, Liu L. Estimating and Testing High-dimensional Mediation Effects in Epigenetic Studies. Bioinformatics. (2016) <doi:10.1093/bioinformatics/btw351>. PMID: 27357171.
For supersonic aircraft, flying subsonic over land,
    find the best route between airports. Allow for coastal buffer and
    potentially closed regions. Use a minimal model of aircraft
    performance: the focus is on time saved versus subsonic flight, rather
    than on vertical flight profile. For modelling and forecasting, not for planning your
    flight!
H-index and h-alpha are a bibliometric indicators. This package 
  provides functions to simulate how these indicators may develop over time for
  a given set of researchers and to visualize the simulation data. 
  The implementation is based on the 'STATA' ado h-index and is described in 
  more detail in Bornmann et al. (2019) <arXiv:1905.11052>.
H(x) is the h-index for the past x years. Here, the h(x) of a scientist/department/etc. can be calculated using the exported excel file from a Web of Science citation report of a search. Also calculated is the year of first publication, total number of publications, and sum of times cited for the specified period. Therefore, for h-10: the date of first publication, total number of publications, and sum of times cited in the past 10 years are calculated. Note: the excel file has to first be saved in a .csv format.
Hypergeometric Intersection distributions are a
    broad group of distributions that describe the probability of picking
    intersections when drawing independently from two (or more) urns
    containing variable numbers of balls belonging to the same n
    categories. <arXiv:1305.0717>.
Can be used for paternity and maternity assignment and outperforms 
  conventional methods where closely related individuals occur in the pool of 
  possible parents. The method compares the genotypes of offspring with any 
  combination of potentials parents and scores the number of mismatches of these 
  individuals at bi-allelic genetic markers (e.g. Single Nucleotide Polymorphisms). 
  It elaborates on a prior exclusion method based on the Homozygous Opposite Test 
  (HOT; Huisman 2017 <doi:10.1111/1755-0998.12665>) by introducing the 
  additional exclusion criterion HIPHOP (Homozygous Identical Parents, 
  Heterozygous Offspring are Precluded; Cockburn et al., in revision). Potential 
  parents are excluded if they have more mismatches than can 
  be expected due to genotyping error and mutation, and thereby one can identify the 
  true genetic parents and detect situations where one (or both) of the true 
  parents is not sampled. Package 'hiphop' can deal with (a) the case where there 
  is contextual information about parentage of the mother (i.e. a female has been 
  seen to be involved in reproductive tasks such as nest building), but paternity 
  is unknown (e.g. due to promiscuity), (b) where both parents need to be assigned, 
  because there is no contextual information on which female laid eggs and which 
  male fertilized them (e.g. polygynandrous mating system where multiple females 
  and males deposit young in a common nest, or organisms with external fertilisation 
  that breed in aggregations).
    For details: Cockburn, A., Penalba, J.V.,Jaccoud, D.,Kilian, A., Brouwer, L.,
       Double, M.C., Margraf, N., Osmond, H.L., van de Pol, M. and Kruuk, L.E.B. 
       (in revision). HIPHOP: improved paternity assignment among close relatives 
       using a simple exclusion method for bi-allelic markers. 
       Molecular Ecology Resources, DOI to be added upon acceptance.
An 'RStudio' Addin for Hippie Expand (AKA Hippie Code
  Completion or Cyclic Expand Word). This type of completion searches for 
  matching tokens within the user's current source editor file, regardless of
  file type. By searching only within the current source file, 'hippie' offers a
  fast way to identify and insert completions that appear around the user's
  cursor.
Read hierarchical fixed width files like those commonly used by 
    many census data providers. Also allows for reading of data in chunks,
    and reading 'gzipped' files without storing the full file in memory.
Identifying labeled compounds in a 13C-tracer experiment in
    non-targeted fashion is a cumbersome process. This package facilitates
    such type of analyses by providing high level quality control plots,
    deconvoluting and evaluating spectra and performing a multitude of
    tests in an automatic fashion.  The main idea is to use changing
    intensity ratios of ion pairs from peak list generated with 'xcms' as
    candidates and evaluate those against base peak chromatograms and
    spectra information within the raw measurement data automatically.
    The functionality is described in Hoffmann et al. (2018)
    <doi:10.1021/acs.analchem.8b00356>.
Implementation of a class of hierarchical item response
  theory (IRT) models where both the mean and the variance of latent preferences
  (ability parameters) may depend on observed covariates. The current
  implementation includes both the two-parameter latent trait model for binary data and the
  graded response model for ordinal data. Both are fitted via the Expectation-Maximization (EM)
  algorithm. Asymptotic standard errors are derived from the observed information
  matrix.
Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification. Beaulieu and O'Meara (2016) <doi:10.1093/sysbio/syw022>.
In some cases you will have data in a histogram format, where
  you have a vector of all possible observations, and a vector of how many
  times each observation appeared. You could expand this into a single 1D
  vector, but this may not be advisable if the counts are extremely large.
  'HistDat' allows for the calculation of summary statistics without the need
  for expanding your data.
The 'HistData' package provides a collection of small data sets
    that are interesting and important in the history of statistics and data
    visualization. The goal of the package is to make these available, both for
    instructional use and for historical research. Some of these present interesting
    challenges for graphics or analysis in R.
In the framework of Symbolic Data Analysis, a relatively new
    approach to the statistical analysis of multi-valued data, we consider
    histogram-valued data, i.e., data described by univariate histograms. The
    methods and the basic statistics for histogram-valued data are mainly based
    on the L2 Wasserstein metric between distributions, i.e., the Euclidean metric
    between quantile functions. The package contains unsupervised classification
    techniques, least square regression and tools for histogram-valued data and for
    histogram time series. An introducing paper is Irpino A. Verde R. (2015) <doi: 10.1007/s11634-014-0176-4>.
Using the MDL principle, it is possible to estimate
	parameters for a histogram-like model. The package contains
	the implementation of such an estimation method.
Automatic construction of regular and irregular histograms as described in Rozenholc/Mildenberger/Gather (2010).
Historical borrowing in clinical trials can improve
  precision and operating characteristics. This package supports
  a hierarchical model and a mixture model to borrow historical
  control data from other studies to better characterize the
  control response of the current study. It also quantifies
  the amount of borrowing through benchmark models (independent
  and pooled). Some of the methods are discussed by
  Viele et al. (2013) <doi:10.1002/pst.1589>.
Historical borrowing in clinical trials can improve
  precision and operating characteristics. This package supports
  a longitudinal hierarchical model to borrow historical
  control data from other studies to better characterize the
  control response of the current study. It also quantifies
  the amount of borrowing through longitudinal benchmark models (independent
  and pooled). The hierarchical model approach to historical borrowing
  is discussed by Viele et al. (2013) <doi:10.1002/pst.1589>.
These sample data sets are intended for historians
    learning R. They include population, institutional, religious,
    military, and prosopographical data suitable for mapping,
    quantitative analysis, and network analysis.
A histogram slider input binding for use in 'Shiny'. Currently supports creating histograms from numeric, date, and 'date-time' vectors.
The "Hit and Run" Markov Chain Monte Carlo method for sampling uniformly from convex shapes defined by linear constraints, and the "Shake and Bake" method for sampling from the boundary of such shapes. Includes specialized functions for sampling normalized weights with arbitrary linear constraints. Tervonen, T., van Valkenhoef, G., Basturk, N., and Postmus, D. (2012) <doi:10.1016/j.ejor.2012.08.026>. van Valkenhoef, G., Tervonen, T., and Postmus, D. (2014) <doi:10.1016/j.ejor.2014.06.036>.
We provide the monthly number of HIV and antiretroviral therapy (ART) cases of male, female, children and transgender as well as for the whole of Pakistan reported at various treatment centers in Pakistan from January 2016 to December 2021. Related works include: 
  a) Imran, M., Nasir, J. A., & Riaz, S. (2018). Regional pattern of HIV cases in Pakistan. Journal of Postgraduate Medical Institute, 32(1), 9-13. 
  <https://jpmi.org.pk/index.php/jpmi/article/view/2108>.
Hadoop InteractiVE facilitates distributed 
             computing via the MapReduce paradigm through R and Hadoop. An easy to use 
             interface to Hadoop, the Hadoop Distributed File System (HDFS), 
	     and Hadoop Streaming is provided.
Creates and plots 2D and 3D hive plots. Hive plots are a unique method of displaying networks of many types in which node properties are mapped to axes using meaningful properties rather than being arbitrarily positioned.  The hive plot concept was invented by Martin Krzywinski at the Genome Science Center (www.hiveplot.net/).  Keywords: networks, food webs, linnet, systems biology, bioinformatics.
Provides functions to implement a hierarchical approach which is designed to perform joint analysis of summary statistics using the framework of Mendelian Randomization or transcriptome analysis. Reference: Lai Jiang, Shujing Xu, Nicholas Mancuso, Paul J. Newcombe, David V. Conti (2020). "A Hierarchical Approach Using Marginal Summary Statistics for Multiple Intermediates in a Mendelian Randomization or Transcriptome Analysis." <bioRxiv><doi:10.1101/2020.02.03.924241>.
This is a collection of functions for converting coordinates between WGS84UTM, WGS84GEO, HK80UTM, HK80GEO and HK1980GRID Coordinate Systems used in Hong Kong SAR, based on the algorithms described in Explanatory Notes on Geodetic Datums in Hong Kong by Survey and Mapping Office Lands Department, Hong Kong Government (1995).
Datasets related to Hong Kong, including information on the 2019 elected District Councillors (<https://www.districtcouncils.gov.hk> and <https://dce2019.hk01.com/>) and traffic collision data from the Hong Kong Department of Transport (<https://www.td.gov.hk/>). All
    of the data in this package is available in the public domain.
Several procedures for the hierarchical kernel extreme value process of Reich and Shaby (2012) <DOI:10.1214/12-AOAS591>, including simulation, estimation and spatial extrapolation. The spatial latent variable model <DOI:10.1214/11-STS376> is also included.
Functions, Shiny apps and data for the book "Introduction to Statistics" by
   Wolfgang Karl Härdle, Sigbert Klinke, and Bernd Rönz (2015) <doi:10.1007/978-3-319-17704-5>.
A streamlined tool for eplet analysis of donor and recipient HLA (human leukocyte antigen) mismatch. Messy, low-resolution HLA typing data is cleaned, and imputed to high-resolution using the NMDP (National Marrow Donor Program) haplotype reference database <https://haplostats.org/haplostats>. High resolution data is analyzed for overall or single antigen eplet mismatch using a reference table (currently supporting 'HLAMatchMaker' <http://www.epitopes.net> versions 2 and 3). Data can enter or exit the workflow at different points depending on the user's aims and initial data quality.
A toolkit for the analysis and management of data for genes in the so-called "Human Leukocyte Antigen" (HLA) region. Functions extract reference data from the Anthony Nolan HLA Informatics Group/ImmunoGeneTics HLA 'GitHub' repository (ANHIG/IMGTHLA) <https://github.com/ANHIG/IMGTHLA>, validate Genotype List (GL) Strings, convert between UNIFORMAT and GL String Code (GLSC) formats, translate HLA alleles and GLSCs across ImmunoPolymorphism Database (IPD) IMGT/HLA Database release versions, identify differences between pairs of alleles at a locus, generate customized, multi-position sequence alignments, trim and convert allele-names across nomenclature epochs, and extend existing data-analysis methods.
Provides access to datasets published by 'Hlídač státu' <https://www.hlidacstatu.cz/>, 
    a Czech watchdog, via their API.
A suite of diagnostic tools for hierarchical
    (multilevel) linear models. The tools include
    not only leverage and traditional deletion diagnostics (Cook's
    distance, covratio, covtrace, and MDFFITS) but also 
    convenience functions and graphics for residual analysis. Models
    can be fit using either lmer in the 'lme4' package or lme in the 'nlme' package.
Fits latent space models for single networks and hierarchical latent space models for ensembles of networks as described in Sweet, Thomas & Junker (2013).
Higher-order latent trait theory (item response theory). We
    implement the generalized partial credit model with a second-order latent
    trait structure. Latent regression can be done on the second-order latent
    trait. For a pre-print of the methods,
    see, "Latent Regression in Higher-Order Item Response Theory with the R
    Package hlt" <https://mkleinsa.github.io/doc/hlt_proof_draft_brmic.pdf>.
For estimation of a variable of interest using two sources of auxiliary information available in a nested structure. For reference see Saarela et al. (2016)<doi:10.1007/s13595-016-0590-1> and Saarela et al. (2018) <doi:10.3390/rs10111832>.
Provides interpretable high-dimensional mean comparison methods (HMC). 
    For example, users can apply these methods to assess the difference in 
    gene expression between two treatment groups. It is not a gene-by-gene 
    comparison. Instead, the methods focus on the interplay between features 
    and identify those that are predictive of the group label. The tests are 
    valid frequentist procedures and yield sparse estimates indicating which 
    features contribute to the group differences.
Fitting hidden Markov models of learning under the cognitive diagnosis framework.
  The estimation of the hidden Markov diagnostic classification model,
  the first order hidden Markov model, the reduced-reparameterized unified learning model,
  and the joint learning model for responses and response times.
Provide users with a framework to learn the intricacies of the Hamiltonian Monte Carlo algorithm with hands-on experience by tuning and fitting their own models.  All of the code is written in R.  Theoretical references are listed below:.
    Neal, Radford (2011) "Handbook of Markov Chain Monte Carlo" ISBN: 978-1420079418, 
    Betancourt, Michael (2017) "A Conceptual Introduction to Hamiltonian Monte Carlo" <arXiv:1701.02434>, 
    Thomas, S., Tu, W. (2020) "Learning Hamiltonian Monte Carlo in R" <arXiv:2006.16194>,
    Gelman, A., Carlin, J. B., Stern, H. S., Dunson, D. B., Vehtari, A., & Rubin, D. B. (2013) "Bayesian Data Analysis" ISBN: 978-1439840955, 
    Agresti, Alan (2015) "Foundations of Linear and Generalized Linear Models ISBN: 978-1118730034, 
    Pinheiro, J., Bates, D. (2006) "Mixed-effects Models in S and S-Plus" ISBN: 978-1441903174.
Holistic Multimodel Domain Analysis (HMDA) is a robust and transparent framework designed for exploratory machine learning research, aiming to enhance the process of feature assessment and selection. HMDA addresses key limitations of traditional machine learning methods by evaluating the consistency across multiple high-performing models within a fine-tuned modeling grid, thereby improving the interpretability and reliability of feature importance assessments. Specifically, it computes Weighted Mean SHapley Additive exPlanations (WMSHAP), which aggregate feature contributions from multiple models based on weighted performance metrics. HMDA also provides confidence intervals to demonstrate the stability of these feature importance estimates. This framework is particularly beneficial for analyzing complex, multidimensional datasets common in health research, supporting reliable exploration of mental health outcomes such as suicidal ideation, suicide attempts, and other psychological conditions. Additionally, HMDA includes automated procedures for feature selection based on WMSHAP ratios and performs dimension reduction analyses to identify underlying structures among features. For more details see Haghish (2025) <doi:10.13140/RG.2.2.32473.63846>.
Wrapper for Stan that offers a number of in-built models to implement a hierarchical Bayesian longitudinal model for repeat observation data. Model choice selects the differential equation that is fit to the observations. Single and multi-individual models are available. O'Brien et al. (2024) <doi:10.1111/2041-210X.14463>.
Utilities for reading data from the Human Mortality Database (<https://www.mortality.org>), Human Fertility Database (<https://www.humanfertility.org>), and similar databases from the web or locally into an R session as data.frame objects. These are the two most widely used sources of demographic data to study basic demographic change, trends, and develop new demographic methods. Other supported databases at this time include the Human Fertility Collection (<https://www.fertilitydata.org>), The Japanese Mortality Database (<https://www.ipss.go.jp/p-toukei/JMD/index-en.html>), and the Canadian Human Mortality Database (<http://www.bdlc.umontreal.ca/chmd/>). Arguments and data are standardized.
Classification performance metrics that are derived from the ROC
    curve of a classifier. The package includes the H-measure performance metric
    as described in <http://link.springer.com/article/10.1007/s10994-009-5119-5>,
    which computes the minimum total misclassification cost, integrating over any
    uncertainty about the relative misclassification costs, as per a user-defined
    prior. It also offers a one-stop-shop for other scalar metrics of performance,
    including sensitivity, specificity and many others, and also offers plotting
    tools for ROC curves and related statistics.
A set of objects and functions for Bayes Linear emulation and history matching.
  Core functionality includes automated training of emulators to data, diagnostic functions
  to ensure suitability, and a variety of proposal methods for generating 'waves' of points.
  For details on the mathematical background, there are many papers available on the topic
  (see references attached to function help files or the below references); for details of 
  the functions in this package, consult the manual or help files.
  Iskauskas, A, et al. (2024) <doi:10.18637/jss.v109.i10>.
  Bower, R.G., Goldstein, M., and Vernon, I. (2010) <doi:10.1214/10-BA524>.
  Craig, P.S., Goldstein, M., Seheult, A.H., and Smith, J.A. (1997) <doi:10.1007/978-1-4612-2290-3_2>.
Contains many functions useful for data
	analysis, high-level graphics, utility operations, functions for
	computing sample size and power, simulation, importing and annotating datasets,
	imputing missing values, advanced table making, variable clustering,
	character string manipulation, conversion of R objects to LaTeX and html code,
	recoding variables, caching, simplified parallel computing, encrypting and decrypting data using a safe workflow, general moving window statistical estimation, and assistance in interpreting principal component analysis.
An algorithm for time series analysis that leverages hidden Markov models, cluster analysis, and mixture distributions to segment data, detect patterns and predict future sequences.
Easy to use library to setup, apply and make inference with discrete time and discrete space Hidden Markov Models.
Fits hidden Markov models with discrete non-parametric 
	observation distributions to data sets.  The observations may
	be univariate or bivariate. Simulates data from such models.
	Finds most probable underlying hidden states, the most
	probable sequences of such states, and the log likelihood
	of a collection of observations given the parameters of
	the model.  Auxiliary predictors are accommodated in the
        univariate setting.
Estimation procedures and goodness-of-fit test for several Markov regime switching models and mixtures of  bivariate copula models. The goodness-of-fit test is based on a Cramer-von Mises statistic and uses Rosenblatt's transform and parametric bootstrap to estimate the p-value. The proposed methodologies are described in Nasri, Remillard and Thioub (2020) <doi:10.1002/cjs.11534>.
Consider the linear mixed model with normal random effects. A typical method to solve Henderson's Mixed Model Equations (HMME) is recursive estimation of the fixed effects and random effects. We provide a fast, stable, and scalable solver to the HMME without computing matrix inverse. See Kim (2017) <arXiv:1710.09663> for more details.
Contains functions for hidden Markov models with observations having extra zeros as defined in the following two publications, Wang, T., Zhuang, J., Obara, K. and Tsuruoka, H. (2016) <doi:10.1111/rssc.12194>; Wang, T., Zhuang, J., Buckby, J., Obara, K. and Tsuruoka, H. (2018) <doi:10.1029/2017JB015360>. The observed response variable is either univariate or bivariate Gaussian conditioning on presence of events, and extra zeros mean that the response variable takes on the value zero if nothing is happening. Hence the response is modelled as a mixture distribution of a Bernoulli variable and a continuous variable. That is, if the Bernoulli variable takes on the value 1, then the response variable is Gaussian, and if the Bernoulli variable takes on the value 0, then the response is zero too. This package includes functions for simulation, parameter estimation, goodness-of-fit, the Viterbi algorithm, and plotting the classified 2-D data. Some of the functions in the package are based on those of the R package 'HiddenMarkov' by David Harte. This updated version has included an example dataset and R code examples to show how to transform the data into the objects needed in the main functions. We have also made changes to increase the speed of some of the functions.
Functions for specifying and fitting marginal models for contingency tables proposed by Bergsma and Rudas (2002) <doi:10.1214/aos/1015362188> here called hierarchical multinomial marginal models (hmmm) and their extensions presented by Bartolucci, Colombi and Forcina (2007) <https://www.jstor.org/stable/24307737>; multinomial Poisson homogeneous (mph) models and homogeneous linear predictor (hlp) models for contingency tables proposed by Lang (2004) <doi:10.1214/aos/1079120140> and Lang (2005) <doi:10.1198/016214504000001042>. Inequality constraints on the parameters are allowed and can be tested.
Provide functions to make estimate the number of states for a hidden Markov 
    model (HMM) using marginal likelihood method proposed by the authors.
    See the Manual.pdf file a detail description of all functions, and a detail tutorial.
Analysing time-series accelerometer data to quantify length and 
             intensity of physical activity using hidden Markov models. 
             It also contains the traditional cut-off point method.
             Witowski V, Foraita R, Pitsiladis Y, Pigeot I, Wirsik N (2014).
             <doi:10.1371/journal.pone.0114089>.
Datasets and code examples that accompany our book Visser & Speekenbrink (2021), "Mixture and Hidden Markov Models with R", <https://depmix.github.io/hmmr/>.
Reliability Analysis and Maintenance Optimization using Hidden Markov Models (HMM). The use of HMMs to model the state of a system which is not directly observable and instead certain indicators (signals) of the true situation are provided via a control system. A hidden model can provide key information about the system dependability, such as the reliability of the system and related measures. An estimation procedure is implemented based on the Baum-Welch algorithm. Classical structures such as K-out-of-N systems and Shock models are illustrated. Finally, the maintenance of the system is considered in the HMM context and two functions for new preventive maintenance strategies are considered. Maintenance efficiency is measured in terms of expected cost. Methods are described in Gamiz, Limnios, and Segovia-Garcia (2023) <doi:10.1016/j.ejor.2022.05.006>.
Fitting hidden Markov models using automatic differentiation 
  and Laplace approximation, allowing for fast inference and flexible covariate
  effects (including random effects and smoothing splines) on model parameters.
  The package is described by Michelot (2022) <doi:10.48550/arXiv.2211.14139>.
Using Dirichlet-Multinomial distribution to provide several functions for formal hypothesis testing, power and sample size calculations for human microbiome experiments.
Tools to model, compare, and visualize populations of taxonomic tree objects.
Statistical analysis of static chamber concentration data for trace gas flux estimation.
Implements an S3 class for storing and formatting time-of-day
    values, based on the 'difftime' class.
Hierarchical Modelling of Species Communities (HMSC) is
   a model-based approach for analyzing community ecological data. 
   This package implements it in the Bayesian framework with Gibbs
   Markov chain Monte Carlo (MCMC) sampling (Tikhonov et al. (2020)
   <doi:10.1111/2041-210X.13345>).
A collection of datasets and supporting functions accompanying Health Metrics and the Spread of Infectious Diseases by Federica Gazzelloni (2024). This package provides data for health metrics calculations, including Disability-Adjusted Life Years (DALYs), Years of Life Lost (YLLs), and Years Lived with Disability (YLDs), as well as additional tools for analyzing and visualizing health data. Federica Gazzelloni (2024) <doi:10.5281/zenodo.10818338>.
The HMS (Hierarchic Memetic Strategy) is a composite global optimization
  strategy consisting of a multi-population evolutionary strategy and some
  auxiliary methods. The HMS makes use of a dynamically-evolving data structure
  that provides an organization among the component populations. It is a tree
  with a fixed maximal height and variable internal node degree. Each component
  population is governed by a particular evolutionary engine. This package
  provides a simple R implementation with examples of using different genetic
  algorithms as the population engines. References: J. Sawicki, M. Łoś,
  M. Smołka, J. Alvarez-Aramberri (2022) <doi:10.1007/s11047-020-09836-w>.
Tracks elapsed clock time using a `hms::hms()` scalar. 
 It was was originally developed to time Bayesian model runs. 
 It should not be used to estimate how long extremely fast code takes to execute 
 as the package code adds a small time cost.
The heterogeneous multi-task feature learning is a data integration method to conduct joint feature selection across multiple related data sets with different distributions. The algorithm can combine different types of learning tasks, including linear regression, Huber regression, adaptive Huber, and logistic regression. The modified version of Bayesian Information Criterion (BIC) is produced to measure the model performance. Package is based on Yuan Zhong, Wei Xu, and Xin Gao (2022) <https://www.fields.utoronto.ca/talk-media/1/53/65/slides.pdf>.
Hierarchical and single-level non-negative matrix factorization. Several NMF algorithms are available.
Generates (half-)normal plots with simulation envelopes using different diagnostics from a range of different fitted models. A few example datasets are included.
Cross-species identification of novel gene candidates using the NCBI web service is provided. Further, sets of miRNA target genes can be identified by using the targetscan.org API.
Suite of tools for managing cached files, targeting
    use in other R packages. Uses 'rappdirs' for cross-platform paths.
    Provides utilities to manage cache directories, including targeting
    files by path or by key; cached directories can be compressed and
    uncompressed easily to save disk space.
Allows to evaluate Higher Order Assortativity of complex networks defined through objects of class 'igraph' from the package of the same name. The package returns a result also for directed and weighted graphs. References, Arcagni, A., Grassi, R., Stefani, S., & Torriero, A. (2017) <doi:10.1016/j.ejor.2017.04.028> Arcagni, A., Grassi, R., Stefani, S., & Torriero, A. (2021) <doi:10.1016/j.jbusres.2019.10.008> Arcagni, A., Cerqueti, R., & Grassi, R. (2023) <doi:10.48550/arXiv.2304.01737>.
Provides easy access to essential climate change datasets to non-climate experts. Users can download the latest raw data from authoritative sources and view it via pre-defined 'ggplot2' charts. Datasets include atmospheric CO2, methane, emissions, instrumental and proxy temperature records, sea levels, Arctic/Antarctic sea-ice, Hurricanes, and Paleoclimate data. Sources include: NOAA Mauna Loa Laboratory <https://gml.noaa.gov/ccgg/trends/data.html>, Global Carbon Project <https://www.globalcarbonproject.org/carbonbudget/>, NASA GISTEMP <https://data.giss.nasa.gov/gistemp/>, National Snow and Sea Ice Data Center <https://nsidc.org/home>, CSIRO <https://research.csiro.au/slrwavescoast/sea-level/measurements-and-data/sea-level-data/>, NOAA Laboratory for Satellite Altimetry <https://www.star.nesdis.noaa.gov/socd/lsa/SeaLevelRise/> and HURDAT Atlantic Hurricane Database <https://www.aoml.noaa.gov/hrd/hurdat/Data_Storm.html>, Vostok Paleo carbon dioxide and temperature data: <doi:10.3334/CDIAC/ATG.009>.
Built by Hodges lab members for current and future Hodges lab members. Other individuals are welcome to use as well. Provides useful functions that the lab uses everyday to analyze various genomic datasets. Critically, only general use functions are provided; functions specific to a given technique are reserved for a separate package. As the lab grows, we expect to continue adding functions to the package to build on previous lab members code.
Estimates treatment effects  using covariate adjustment methods in Randomized Clinical Trials (RCT) motivated by higher-order influence functions (HOIF). Provides point estimates, oracle bias, variance, and approximate variance for HOIF-adjusted estimators. For methodology details, see Zhao et al. (2024) <doi:10.48550/arXiv.2411.08491>.
Higher order likelihood inference is a promising approach for
    analyzing small sample size data. The 'holi' package provides web applications
    for higher order likelihood inference. It currently supports linear, logistic,
    and Poisson generalized linear models through the rstar_glm() function, based
    on Pierce and Bellio (2017) <doi:10.1111/insr.12232> and 'likelihoodAsy'.
    The package offers two main features: LA_rstar(), which launches an interactive
    'shiny' application allowing users to fit models with rstar_glm() through their
    web browser, and sim_rstar_glm_pgsql(), which streamlines the process of
    launching a web-based 'shiny' simulation application that saves results to a
    user-created 'PostgreSQL' database.
Holistic generalized linear models (HGLMs) extend generalized linear models (GLMs) by enabling the possibility to add further constraints to the model. The 'holiglm' package simplifies estimating HGLMs using convex optimization. Additional information about the package can be found in the reference manual, the 'README' and the accompanying paper <doi:10.18637/jss.v108.i07>.
Offers a convenient way to compute parameters 
    in the framework of the theory of vocational choice introduced by
    J.L. Holland, (1997). A comprehensive summary to this theory 
    of vocational choice is given in Holland, J.L. (1997). Making vocational
    choices. A theory of vocational personalities and work environments. 
    Lutz, FL: Psychological Assessment.
Enables chat completion and text annotation with local and 'OpenAI' <https://openai.com/> language models, supporting batch processing, multiple annotators, and consistent output formats.
We provide functions for identifying the core community phylogeny in any microbiome, drawing phylogenetic Venn diagrams, calculating the core Faith’s PD for a set of communities, and calculating the core UniFrac distance between two sets of communities. All functions rely on construction of a core community phylogeny, which is a phylogeny where branches are defined based on their presence in multiple samples from a single type of habitat. Our package provides two options for constructing the core community phylogeny, a tip-based approach, where the core community phylogeny is identified based on incidence of leaf nodes and a branch-based approach, where the core community phylogeny is identified based on incidence of individual branches. We suggest use of the microViz package.
Provides pipe-friendly (%>%) wrapper functions for MASS::mvrnorm() to create simulated multivariate data sets
    with groups of variables with different degrees of variance, covariance, and effect size.
A 'shiny' application, which allows you to perform single- and
    multi-omics analyses using your own omics datasets. After the upload 
    of the omics datasets and a metadata file, single-omics is performed
    for feature selection and dataset reduction. These datasets are used 
    for pairwise- and multi-omics analyses, where automatic tuning is 
    done to identify correlations between the datasets - the end goal 
    of the recommended 'Holomics' workflow.
    Methods used in the package were implemented in the package 'mixomics'
    by Florian Rohart,Benoît Gautier,Amrit Singh,Kim-Anh Lê Cao (2017) <doi:10.1371/journal.pcbi.1005752>
    and are described there in further detail.
Performs a homogeneity analysis (multiple correspondence analysis) and various extensions. Rank restrictions on the category quantifications can be imposed (nonlinear PCA). The categories are transformed by means of optimal scaling with options for nominal, ordinal, and numerical scale levels (for rank-1 restrictions). Variables can be grouped into sets, in order to emulate regression analysis and canonical correlation analysis.
A simple implementation of doughnut plots - pie charts with a blank center. The package is named after Homer Simpson - arguably the best-known lover of doughnuts.
Provides methods for closed testing using Simes local tests. In particular, calculates adjusted p-values for Hommel's multiple testing method, and provides lower confidence bounds for true discovery proportions. A robust but more conservative variant of the closed testing procedure that does not require the assumption of Simes inequality is also implemented. The methods have been described in detail in Goeman et al (Biometrika 106, 841-856, 2019).
Most common exact, asymptotic and resample based tests are provided for testing the 
            homogeneity of variances of k normal distributions under normality. 
            These tests are Barlett, Bhandary & Dai, Brown & Forsythe, Chang et al., Gokpinar & Gokpinar, Levene, Liu and Xu, Gokpinar. 
            Also, a data generation function from multiple normal distribution is provided using any multiple normal parameters.  
            Bartlett, M. S. (1937) <doi:10.1098/rspa.1937.0109> 
            Bhandary, M., & Dai, H. (2008) <doi:10.1080/03610910802431011>
            Brown, M. B., & Forsythe, A. B. (1974).<doi:10.1080/01621459.1974.10482955>
            Chang, C. H., Pal, N., & Lin, J. J. (2017) <doi:10.1080/03610918.2016.1202277>
            Gokpinar E. & Gokpinar F. (2017) <doi:10.1080/03610918.2014.955110>
            Liu, X., & Xu, X. (2010) <doi:10.1016/j.spl.2010.05.017>
            Levene, H. (1960) <https://cir.nii.ac.jp/crid/1573950400526848896>
            Gökpınar, E. (2020) <doi:10.1080/03610918.2020.1800037>.
A wrapper for the homologene database by the National Center for
    Biotechnology Information ('NCBI'). It allows searching for gene homologs across 
    species. Data in this package can be found at <ftp://ftp.ncbi.nih.gov/pub/HomoloGene/build68/>.
    The package also includes an updated version of the homologene database where 
    gene identifiers and symbols are replaced with their latest (at the time of
    submission) version and functions to fetch latest annotation data to keep updated.
Homomorphic computations in R for privacy-preserving applications. Currently only
             the Paillier Scheme is implemented.
Implements the Brakerski-Fan-Vercauteren (BFV, 2012) <https://eprint.iacr.org/2012/144>, Brakerski-Gentry-Vaikuntanathan (BGV, 2014) <doi:10.1145/2633600>, and Cheon-Kim-Kim-Song (CKKS, 2016) <https://eprint.iacr.org/2016/421.pdf> schema for Fully Homomorphic Encryption. The included vignettes demonstrate the encryption procedures.
Provides functions to conduct robust inference in difference-in-differences and event study designs by implementing the methods developed in Rambachan & Roth (2023) <doi:10.1093/restud/rdad018>, "A More Credible Approach to Parallel Trends" [Previously titled "An Honest Approach..."]. Inference is conducted under a weaker version of the parallel trends assumption. Uniformly valid confidence sets are constructed based upon conditional confidence sets, fixed-length confidence sets and hybridized confidence sets.
A utility to quickly obtain clean and tidy men's
    basketball play by play data. Provides functions to access
    live play by play and box score data from ESPN<https://www.espn.com> with shot locations
    when available. It is also a full NBA Stats API<https://www.nba.com/stats/> wrapper.
    It is also a scraping and aggregating interface for Ken Pomeroy's 
    men's college basketball statistics website<https://kenpom.com>. It provides users with an
    active subscription the capability to scrape the website tables and
    analyze the data for themselves.
Computes the expectation of the number of transmissions and receptions considering a Hop-by-Hop transport model with limited number of retransmissions per packet. It provides the theoretical results shown in Palma et. al.(2016) <DOI:10.1109/TLA.2016.7555237> and also estimated values based on Monte Carlo simulations. It is also possible to consider random data and ACK probabilities.
Calculate Hopkins statistic to assess the clusterability of data. See Wright (2023) <doi:10.32614/RJ-2022-055>.
Supplement for the book "Handbook of Regression Methods" by D. S. Young.  Some datasets used in the book are included and documented.  Wrapper functions are included that simplify the examples in the textbook, such as code for constructing a regressogram and expanding ANOVA tables to reflect the total sum of squares.
A stand-alone function that generates a user specified number of random datasets and computes eigenvalues using the random datasets (i.e., implements Horn's [1965, Psychometrika] parallel analysis <doi:10.1007/BF02289447>). Users then compare the resulting eigenvalues (the mean or the specified percentile) from the random datasets (i.e., eigenvalues resulting from noise) to the eigenvalues generated with the user's data. Can be used for both principal components analysis (PCA) and common/exploratory factor analysis (EFA). The output table shows how large eigenvalues can be as a result of merely using randomly generated datasets. If the user's own dataset has  actual eigenvalues greater than the corresponding eigenvalues, that lends support to retain that factor/component. In other words, if the i(th) eigenvalue from the actual data was larger than the percentile of the (i)th eigenvalue generated using randomly generated data, empirical support is provided to retain that factor/component. Horn, J. (1965). A rationale and test for the number of factors in factor analysis. Psychometrika, 32, 179-185.
We provide extensions to the classical dataset "Example 4:
             Death by the kick of a horse in the Prussian Army" first
	           used by Ladislaus von Bortkeiwicz in his treatise on
	           the Poisson distribution "Das Gesetz der kleinen Zahlen",
	           <DOI:10.1017/S0370164600019453>.  As well as an
	           extended time series for the horse-kick death data, we also
             provide, in parallel, deaths by falling from a horse and by
	     drowning.
Contains functions for applying the horseshoe prior to high-
    dimensional linear regression, yielding the posterior mean and credible
    intervals, amongst other things. The key parameter tau can be equipped with
    a prior or estimated via maximum marginal likelihood estimation (MMLE).
    The main function, horseshoe, is for linear regression. In addition, there
    are functions specifically for the sparse normal means problem, allowing
    for faster computation of for example the posterior mean and posterior
    variance. Finally, there is a function available to perform variable
    selection, using either a form of thresholding, or credible intervals.
Provides the posterior estimates of the regression coefficients when horseshoe prior is specified. 
             The regression models considered here are logistic model for binary response and 
             log normal accelerated failure time model for right censored survival response. 
             The linear model analysis is also available for completeness. 
             All models provide deviance information criterion and widely applicable information criterion. 
             See <doi:10.1111/rssc.12377> Maity et. al. (2019) <doi:10.1111/biom.13132> Maity et. al. (2020).
Automatically displays the order and spatial weighting matrix of the distance between locations. This concept was derived from the research of Mubarak, Aslanargun, and Siklar (2021) <doi:10.52403/ijrr.20211150> and Mubarak, Aslanargun, and Siklar (2022) <doi:10.17654/0972361722052>. Distance data between locations can be imported from 'Ms. Excel', 'maps' package or created in 'R' programming directly. This package also provides 5 simulations of distances between locations derived from fictitious data, the 'maps' package, and from research by Mubarak, Aslanargun, and Siklar (2022) <doi:10.29244/ijsa.v6i1p90-100>.
Set of tools to help interested researchers to build hospital networks 
  from data on hospitalized patients transferred between hospitals. Methods provided 
  have been used in Donker T, Wallinga J, Grundmann H. (2010) <doi:10.1371/journal.pcbi.1000715>, 
  and Nekkab N, Crépey P, Astagneau P, Opatowski L, Temime L. (2020) <doi:10.1038/s41598-020-71212-6>.
A data set of the Portuguese 'NHS' hospitals.
Performs multiple hot-deck imputation of categorical and continuous variables in a data frame.
A set of R functions which implements Hotelling's T^2 test and some variants of it. Functions are also included for Aitchison's additive log ratio and centred log ratio transformations.
Functions to calculate the Hotelling’s T-squared statistic and corresponding confidence ellipses. Provides the semi-axes of the Hotelling’s T-squared ellipses at 95% and 99% confidence levels. Enables users to obtain the coordinates in two or three dimensions at user-defined confidence levels, allowing for the construction of 2D or 3D ellipses with customized confidence levels. Bro and Smilde (2014) <DOI:10.1039/c3ay41907j>. Brereton (2016) <DOI:10.1002/cem.2763>.
Contains data for software hotspot analysis, along with a function performing the analysis itself.
The hotspots package is designed to look within a set of measured values of a variable and identify values that are disproportionately high based on both the deviance of any given value from a statistical distribution and its similarity to other values. Because this relative magnitude of each value is taken into account, a value that is a statistical outlier may not always be a hot spot if other values are similarly large.
Lecțiile prof/cls trebuie completate cu un câmp "ora", astfel ca
    oricare două lecții prof/cls/ora să nu se suprapună într-o aceeași oră.
    The prof/cls lessons must be completed with a "hour" field ('ora), so that
    any two prof/cls/ora lessons do not overlap in the same hour.
    <https://vlad.bazon.net/>.
Monthly median home listing, sale price per square foot, and number of units sold for 2984 counties in the contiguous United States From 2008 to January 2016.  Additional data sets containing geographical information and links to Wikipedia are also included.
A wrapper around a CSS library called 'Hover.css', intended for use 
  in 'shiny' applications.
Audio interactivity within 'shiny' applications using 'howler.js'. Enables the
    status of the audio player to be sent from the UI to the server, and events such as
    playing and pausing the audio can be triggered from the server.
When performing multiple imputations, while 5-10 imputations are
             sufficient for obtaining point estimates, a larger number of
             imputations are needed for proper standard error estimates.
             This package allows you to calculate how many imputations are
             needed, following the work of von Hippel (2020)
             <doi:10.1177/0049124117747303>.
Helping to calculate cricket specific problems in a tidy & simple manner.
Multivariate conditional and marginal densities, moments, cumulative distribution functions as well as binary choice and sample selection models based on Hermite polynomial approximation which was proposed and described by A. Gallant and D. W. Nychka (1987) <doi:10.2307/1913241>.
By binding R functions and the 'Highcharts' <http://www.highcharts.com/> charting library, 'hpackedbubble' package provides a simple way to draw split packed bubble charts.
Probabilistic models describing the behavior 
	of workload and queue on a High Performance Cluster and computing GRID 
	under FIFO service discipline basing on modified Kiefer-Wolfowitz 
	recursion. Also sample data for inter-arrival times, service times, 
	number of cores per task and waiting times of HPC of Karelian 
	Research Centre are included, measurements took place from 06/03/2009 to 02/30/2011.
	Functions provided to import/export workload traces in Standard Workload Format (swf).
	Stability condition of the model may be verified either exactly, or approximately.
	Stability analysis: see Rumyantsev and Morozov (2017) <doi:10.1007/s10479-015-1917-2>,
	workload recursion: see Rumyantsev (2014) <doi:10.1109/PDCAT.2014.36>.
Provides two functions that implement the one-sided and
    two-sided versions of the Hodrick-Prescott filter. The one-sided
    version is a Kalman filter-based implementation, whereas the two-
    sided version uses sparse matrices for improved efficiency.
    References:
    Hodrick, R. J., and Prescott, E. C. (1997) <doi:10.2307/2953682>
    Mcelroy, T. (2008) <doi:10.1111/j.1368-423X.2008.00230.x>
    Meyer-Gohde, A. (2010) <https://ideas.repec.org/c/dge/qmrbcd/181.html>
    For more references, see the vignette.
Compute house price indexes and series using a variety of different methods and
    models common through the real estate literature.  Evaluate index 'goodness' based
    on accuracy, volatility and revision statistics. Background on basic model construction
    for repeat sales models can be found at: Case and Quigley (1991) 
    <https://ideas.repec.org/a/tpr/restat/v73y1991i1p50-58.html> and for hedonic pricing models at: 
    Bourassa et al (2006) <doi:10.1016/j.jhe.2006.03.001>. The package author's working paper on the 
    random forest approach to house price indexes can be found at: <http://www.github.com/andykrause/hpi_research>.
An implementation of high-probability lower bounds for the total variance distance 
             as introduced in Michel & Naef & Meinshausen (2020) <arXiv:2005.06006>. An estimated 
             lower-bound (with high-probability) on the total variation distance between two probability distributions from which
             samples are observed can be obtained with the function HPLB.
Provides a nonparametric smoothed kernel estimator for the future conditional hazard rate function when time-dependent covariates are present, a bandwidth selector for the estimator's implementation and pointwise and uniform confidence bands. Methods used in the package refer to Bagkavos, Isakson, Mammen, Nielsen and Proust-Lima (2025)  <doi:10.1093/biomet/asaf008>.
Miscellaneous convenience functions and wrapper functions 
	to convert frequencies between Hz, semitones, mel and Bark, 
	to create a matrix of dummy columns from a factor, 
	to determine whether x lies in range [a,b], 
	and to add a bracketed line to an existing plot.
	This package also contains an example data set of a stratified sample
	of 80 talkers of Dutch.
Offers efficient algorithms for fitting regularization paths for lasso or elastic-net penalized regression models with Huber loss, quantile loss or squared loss. Reference: Congrui Yi and Jian Huang (2017) <doi:10.1080/10618600.2016.1256816>.
Methods for data engineering in the human resources (HR) corporate domain. Designed for HR analytics practitioners and workforce-oriented data sets.
A compilation of extra 'ggplot2' themes, scales and utilities, including a 
    spell check function for plot label fields and an overall emphasis on typography. 
    A copy of the 'Google' font 'Roboto Condensed' is also included.
Nonparametric cumulative-incidence based estimation of the ratios of sub-hazard ratios to cause-specific hazard ratios using the approach from Ng et al. (2020).
Computes the hemodynamic response function (HRF) for task 
    functional magnetic resonance imaging (fMRI) data. Also includes functions
    for constructing a design matrix from task fMRI event timings, and for
    comparing multiple design matrices in a general linear model (GLM). A
    wrapper function is provided for GLM analysis of CIFTI-format data. Lastly,
    there are supporting functions which provide visual summaries of the
    HRFs and design matrices.
A program that conducts group variable selection for quantile and robust mean 
              regression (Sherwood and Li, 2022). The group lasso penalty (Yuan and Lin, 2006) is used for
              group-wise variable selection. Both of the quantile and mean regression models are based on the Huber loss.
              Specifically, with the tuning parameter in the Huber loss approaching to 0, the quantile check 
              function can be approximated by the Huber loss for the median and the tilted version of 
              Huber loss at other quantiles. Such approximation provides computational efficiency and stability, and
              has also been shown to be statistical consistent.
Functions for testing affine hypotheses on the regression coefficient vector in regression models with heteroskedastic errors: (i) a function for computing various test statistics (in particular using HC0-HC4 covariance estimators based on unrestricted or restricted residuals); (ii) a function for numerically approximating the size of a test based on such test statistics and a user-supplied critical value; and, most importantly, (iii) a function for determining size-controlling critical values for such test statistics and a user-supplied significance level (also incorporating a check of conditions under which such a size-controlling critical value exists). The three functions are based on results in Poetscher and Preinerstorfer (2021) "Valid Heteroskedasticity Robust Testing" <doi:10.48550/arXiv.2104.12597>, which will appear as <doi:10.1017/S0266466623000269>.
It is used to construct run sequences with minimum changes for half replicate of two level factorial run order. Experimenter can save time and resources by minimizing the number of changes in levels of individual factor and therefore the total number of changes. It consists of the function minimal_hrtlf(). This technique can be employed to any half replicate of two level factorial run order where the number of factors are greater than two. In Design of Experiments (DOE) theory, two level of a factor can be represented as integers e.g. - 1 for low and 1 for high. User is expected to enter total number of factors to be considered in the experiment. minimal_hrtlf() provides the required run sequences for the input number of factors.  The output also gives the number of changes of each factor along with total number of changes in the run sequence. Due to restricted randomization the minimally changed run sequences of half replicate of two level factorial run order will be affected by trend effect. The output also provides the Trend Factor value of the run order. Trend factor value will lies between 0 to 1. Higher the values, lesser the influence of trend effects on the run order.
The presence of outliers in a dataset can substantially bias the
    results of statistical analyses. To correct for outliers, micro edits are 
    manually performed on all records. A set of constraints and decision rules
    is typically used to aid the editing process. However, straightforward
    decision rules might overlook anomalies arising from disruption of linear
    relationships. Computationally efficient methods are provided to 
    identify historical, tail, and relational anomalies at the data-entry 
    level (Sartore et al., 2024; <doi:10.6339/24-JDS1136>). A score statistic
    is developed for each anomaly type, using a distribution-free approach
    motivated by the Bienaymé-Chebyshev's inequality, and fuzzy logic is used
    to detect cellwise outliers resulting from different types of anomalies.
    Each data entry is individually scored and individual scores are combined
    into a final score to determine anomalous entries. In contrast to fuzzy
    logic, Bayesian bootstrap and a Bayesian test based on empirical 
    likelihoods are also provided as studied by Sartore et 
    al. (2024; <doi:10.3390/stats7040073>). These algorithms allow for a more 
    nuanced approach to outlier detection, as it can identify outliers at 
    data-entry level which are not obviously distinct from the rest of the 
    data.
    ---
    This research was supported in part by the U.S. Department of Agriculture,
    National Agriculture Statistics Service. The findings and conclusions in
    this publication are those of the authors and should not be construed to
    represent any official USDA, or US Government determination or policy.
The book "Semiparametric Regression with R" by J. Harezlak, D. Ruppert & M.P. Wand (2018, Springer; ISBN: 978-1-4939-8851-8) makes use of datasets and scripts to explain semiparametric regression concepts. Each of the book's scripts are contained in this package as well as datasets that are not within other R packages. Functions that aid semiparametric regression analysis are also included.
A Hierarchical Spatial Autoregressive Model (HSAR), based on a Bayesian Markov Chain Monte Carlo (MCMC) algorithm (Dong and Harris (2014) <doi:10.1111/gean.12049>). The creation of this package was supported by the Economic and Social Research Council (ESRC) through the Applied Quantitative Methods Network: Phase II, grant number ES/K006460/1.
Functions, data sets, analyses and examples from the book 
  ''A Handbook of Statistical Analyses Using R'' (Brian S. Everitt and Torsten
  Hothorn, Chapman & Hall/CRC, 2006). The first chapter
  of the book, which is entitled ''An Introduction to R'', 
  is completely included in this package, for all other chapters,
  a vignette containing all data analyses is available.
Functions, data sets, analyses and examples from the 
  second edition of the book 
  ''A Handbook of Statistical Analyses Using R'' (Brian S. Everitt and Torsten
  Hothorn, Chapman & Hall/CRC, 2008). The first chapter
  of the book, which is entitled ''An Introduction to R'', 
  is completely included in this package, for all other chapters,
  a vignette containing all data analyses is available. In addition,
  the package contains Sweave code for producing slides for selected
  chapters (see HSAUR2/inst/slides).
Functions, data sets, analyses and examples from the 
  third edition of the book 
  ''A Handbook of Statistical Analyses Using R'' (Torsten Hothorn and Brian S.
  Everitt, Chapman & Hall/CRC, 2014). The first chapter
  of the book, which is entitled ''An Introduction to R'', 
  is completely included in this package, for all other chapters,
  a vignette containing all data analyses is available. In addition,
  Sweave source code for slides of selected chapters is included in 
  this package (see HSAUR3/inst/slides). The publishers web page is 
  '<https://www.routledge.com/A-Handbook-of-Statistical-Analyses-using-R/Hothorn-Everitt/p/book/9781482204582>'.
The theoretical covariance between pairs of markers is calculated
    from either paternal haplotypes and maternal linkage disequilibrium (LD) or 
    vise versa. A genetic map is required. Grouping of markers is based on the 
    correlation matrix and a representative marker is suggested for each group.
    Employing the correlation matrix, optimal sample size can be derived for 
    association studies based on a SNP-BLUP approach.
    The implementation relies on paternal half-sib families and biallelic 
    markers. If maternal half-sib families are used, the roles of sire/dam are 
    swapped. Multiple families can be considered.
    Wittenburg, Bonk, Doschoris, Reyer (2020) "Design of Experiments for 
    Fine-Mapping Quantitative Trait Loci in Livestock Populations" 
    <doi:10.1186/s12863-020-00871-1>.
    Carlson, Eberle, Rieder, Yi, Kruglyak, Nickerson (2004) "Selecting a 
    maximally informative set of single-nucleotide polymorphisms for association
    analyses using linkage disequilibrium" <doi:10.1086/381000>.
User-friendly and fast set of functions for estimating parameters of hierarchical Bayesian species distribution models (Latimer and others 2006 <doi:10.1890/04-0609>). Such models allow interpreting the observations (occurrence and abundance of a species) as a result of several hierarchical processes including ecological processes (habitat suitability, spatial dependence and anthropogenic disturbance) and observation processes (species detectability). Hierarchical species distribution models are essential for accurately characterizing the environmental response of species, predicting their probability of occurrence, and assessing uncertainty in the model results.
We present this package for fitting structural equation models using the hierarchical likelihood method. This package allows extended structural equation model, including dynamic structural equation model. We illustrate the use of our packages with well-known data sets. Therefore, this package are able to handle two serious problems inadmissible solution and factor indeterminacy <doi:10.3390/sym13040657>.
Implementation of S4 class of sets and multisets of numbers.
    The implementation is based on the hash table from the package 'hash'.
    Quick operations are allowed when the set is a dynamic object.
    The implementation is discussed in detail in Ceoldo and Wit (2023) <arXiv:2304.09809>.
To test the homogeneity of stratum effects in stratified paired binary data.
Identification of recombination events, haplotype reconstruction, sire imputation and pedigree reconstruction using half-sib family SNP data.
Spatial heterogeneity can be specified in various ways. 'hspm' is an ambitious project that aims at implementing various methodologies to control for heterogeneity in spatial models. The current version of 'hspm' deals with spatial and (non-spatial) regimes models. In particular, the package allows to estimate a general spatial regimes model with additional endogenous variables, specified in terms of a spatial lag of the dependent variable, the spatially lagged regressors, and, potentially, a spatially autocorrelated error term. Spatial regime models are estimated by instrumental variables and generalized methods of moments (see Arraiz et al., (2010) <doi:10.1111/j.1467-9787.2009.00618.x>, Bivand and Piras, (2015) <doi:10.18637/jss.v063.i18>, Drukker et al., (2013) <doi:10.1080/07474938.2013.741020>, Kelejian and Prucha, (2010) <doi:10.1016/j.jeconom.2009.10.025>).
Several functions that allow by different methods to infer a piecewise polynomial regression model under regularity constraints, namely continuity or differentiability of the link function. The implemented functions are either specific to data with two regimes, or generic for any number of regimes, which can be given by the user or learned by the algorithm. A paper describing all these methods will be submitted soon. The reference will be added to this file as soon as available.
Paternal recombination rate and maternal linkage disequilibrium 
    (LD) are estimated for pairs of biallelic markers such as single nucleotide 
    polymorphisms (SNPs) from progeny genotypes and sire haplotypes. The 
    implementation relies on paternal half-sib families. If maternal half-sib 
    families are used, the roles of sire/dam are swapped. Multiple families can 
    be considered. For parameter estimation, at least one sire has to be double 
    heterozygous at the investigated pairs of SNPs.
    Based on recombination rates, genetic distances between markers can be 
    estimated. Markers with unusually large recombination rate to markers in 
    close proximity (i.e. putatively misplaced markers) shall be discarded in 
    this derivation.
    A workflow description is attached as vignette.
    *A pipeline is available at GitHub*
    <https://github.com/wittenburg/hsrecombi>
    Hampel, Teuscher, Gomez-Raya, Doschoris, Wittenburg (2018) "Estimation of 
    recombination rate and maternal linkage disequilibrium in half-sibs" 
    <doi:10.3389/fgene.2018.00186>.
    Gomez-Raya (2012) "Maximum likelihood estimation of linkage disequilibrium 
    in half-sib families" <doi:10.1534/genetics.111.137521>.
Linear and logistic regression models penalized with hierarchical
  shrinkage priors for selection of biomarkers (or more general variable
  selection), which can be fitted using Stan (Carpenter et al. (2017)
  <doi:10.18637/jss.v076.i01>). It implements the horseshoe and regularized
  horseshoe priors (Piironen and Vehtari (2017) <doi:10.1214/17-EJS1337SI>),
  as well as the projection predictive selection approach to recover a sparse
  set of predictive biomarkers (Piironen, Paasiniemi and Vehtari (2020)
  <doi:10.1214/20-EJS1711>).
Fast, model-agnostic implementation of different H-statistics
    introduced by Jerome H. Friedman and Bogdan E. Popescu (2008)
    <doi:10.1214/07-AOAS148>.  These statistics quantify interaction
    strength per feature, feature pair, and feature triple.  The package
    supports multi-output predictions and can account for case weights.
    In addition, several variants of the original statistics are provided.
    The shape of the interactions can be explored through partial
    dependence plots or individual conditional expectation plots. 'DALEX'
    explainers, meta learners ('mlr3', 'tidymodels', 'caret') and most
    other models work out-of-the-box.
A collection of reweighted marginal hypothesis tests for clustered data, based
    on reweighting methods of Williamson, J., Datta, S., and Satten, G. (2003) <doi:10.1111/1541-0420.00005>.
    The tests in this collection are clustered analogs to well-known hypothesis tests
    in the classical setting, and are appropriate for data with cluster- and/or group-size 
    informativeness. The syntax and output of functions are modeled after common, 
    recognizable functions native to R. Methods used in the package refer to 
    Gregg, M., Datta, S., and Lorenz, D. (2020) <doi:10.1177/0962280220928572>, 
    Nevalainen, J., Oja, H., and Datta, S. (2017) <doi:10.1002/sim.7288>
    Dutta, S. and Datta, S. (2015) <doi:10.1111/biom.12447>, 
    Lorenz, D., Datta, S., and Harkema, S. (2011) <doi:10.1002/sim.4368>, 
    Datta, S. and Satten, G. (2008) <doi:10.1111/j.1541-0420.2007.00923.x>, 
    Datta, S. and Satten, G. (2005) <doi:10.1198/016214504000001583>.
Estimating heterogeneous treatment effects with tree-based machine
    learning algorithms and visualizing estimated results in flexible and 
    presentation-ready ways. For more information, see Brand, Xu, Koch, 
    and Geraldo (2021) <doi:10.1177/0081175021993503>. Our current package 
    first started as a fork of the 'causalTree' package on 'GitHub' and we 
    greatly appreciate the authors for their extremely useful and free package.
Two papers published in the early 2000's (Zeeberg, B.R., Feng, W., Wang, G. et al. 
  (2003) <doi:10.1186/gb-2003-4-4-r28>) and (Zeeberg, B.R., Qin, H., Narashimhan, S., et al. (2005)
  <doi:10.1186/1471-2105-6-168>) implement 'GoMiner' and 'High Throughput GoMiner'
  ('HTGM') to map lists of genes to the Gene Ontology (GO) <https://geneontology.org>. Until recently,
  these were hosted on a server at The National Cancer Institute (NCI). In order to continue
  providing these services to the bio-medical community, I have developed stand-alone versions.
  The current package 'HTGM' builds upon my recent package 'GoMiner'.
  The output of 'GoMiner' is a heatmap showing the relationship of a single list
  of genes and the significant categories into which they map. 'High Throughput GoMiner'
  ('HTGM') integrates the results of the individual 'GoMiner' analyses. The output of 'HTGM'
  is a heatmap showing the relationship of the significant categories derived from each gene list.
  The heatmap has only 2 axes, so the identity of the genes are unfortunately
  "integrated out of the equation." Because the graphic for the heatmap is implemented
  in Scalable Vector Graphics (SVG) technology, it is relatively easy to hyperlink each
  picture element to the relevant list of genes. By clicking on the desired picture
  element, the user can recover the "lost" genes.
The Gene Ontology (GO) Consortium <https://geneontology.org/> organizes genes
  into hierarchical categories based on biological process (BP), molecular function (MF) and
  cellular component (CC, i.e., subcellular localization). Tools such as 'GoMiner' (see Zeeberg, B.R.,
  Feng, W., Wang, G. et al. (2003) <doi:10.1186/gb-2003-4-4-r28>) can leverage GO to perform
  ontological analysis of microarray and proteomics studies, typically generating a list of
  significant functional categories. Microarray studies are usually analyzed with BP, whereas
  proteomics researchers often prefer CC. To capture the benefit of both of those ontologies,
  I developed a two-dimensional version of 'High-Throughput GoMiner' ('HTGM2D'). I generate a
  2D heat map whose axes are any two of BP, MF, or CC, and the value within
  a picture element of the heat map reflects the Jaccard metric p-value for the number of genes
  in common for the corresponding pair.
The Gene Ontology (GO) Consortium <https://geneontology.org/> organizes genes
  into hierarchical categories based on biological process (BP), molecular function (MF) and
  cellular component (CC, i.e., subcellular localization). Tools such as 'GoMiner' (see Zeeberg, B.R.,
  Feng, W., Wang, G. et al. (2003) <doi:10.1186/gb-2003-4-4-r28>) can leverage GO to perform
  ontological analysis of microarray and proteomics studies, typically generating a list of
  significant functional categories. To capture the benefit of all three ontologies,
  I developed 'HTGM3D', a three-dimensional version of 'GoMiner'.
Efficient Bayesian multinomial logistic regression based on heavy-tailed
  (hyper-LASSO, non-convex) priors. The posterior of coefficients and hyper-parameters
  is sampled with restricted Gibbs sampling for leveraging the high-dimensionality and
  Hamiltonian Monte Carlo for handling the high-correlation among coefficients. A detailed
  description of the method: Li and Yao (2018), 
  Journal of Statistical Computation and Simulation, 88:14, 2827-2851, <arXiv:1405.3319>.
Convert a html document to plain texts by stripping off all html tags.
Provides a 'Shiny' app allowing to convert 'HTML' code to 'R' code (e.g. '<span>Hello</span>' to 'tags$span("Hello")'), for usage in a 'Shiny' UI.
Generates valid HTML tag strings for HTML5 elements documented by Mozilla. 
    Attributes are passed as named lists, with names being the attribute name and values being the attribute value. 
    Attribute values are automatically double-quoted. To declare a DOCTYPE, wrap html() with function doctype().
    Mozilla's documentation for HTML5 is available here: <https://developer.mozilla.org/en-US/docs/Web/HTML/Element>.
    Elements marked as obsolete are not included.
Create compressed, interactive 'HTML' (Hypertext Markup Language) reports with embedded 'Python' code, custom 'JS' ('JavaScript') and 'CSS' (Cascading Style Sheets), and wrappers for
	'CanvasXpress' plots, networks and more. Based on <https://pypi.org/project/py-report-html/>, its sister project.
Tables with state-of-the-art layout elements such as row spanners,
    column spanners, table spanners, zebra striping, and more. While allowing
    advanced layout, the underlying css-structure is simple in order to maximize
    compatibility with common word processors. The package also contains a few
    text formatting functions that help outputting text compatible with HTML/LaTeX.
Facilitates automated HTML report creation, in particular
        framed HTML pages and dynamically sortable tables.
A framework for creating HTML widgets that render in various
    contexts including the R console, 'R Markdown' documents, and 'Shiny'
    web applications.
Analysis of Surface Plasmon Resonance (SPR) and Biolayer Interferometry data, with automations for high-throughput SPR. This version of the package fits the 1: 1 binding model, with and without bulkshift. It offers optional local or global Rmax fitting. The user must provide a sample sheet and a Carterra output file in Carterra's current format. There is a utility function to convert from Carterra's old output format. The user may run a custom pipeline or use the provided 'Runscript', which will produce a pdf file containing fitted Rmax, ka, kd and standard errors, a plot of the sensorgram and fits, and a plot of residuals. The script will also produce a .csv file with all of the relevant parameters for each spot on the SPR chip.
Detection of haplotype patterns that include single nucleotide polymorphisms (SNPs) and non-contiguous haplotypes that are associated with a phenotype. Methods for implementing HTRX are described in Yang Y, Lawson DJ (2023) <doi:10.1093/bioadv/vbad038> and Barrie W, Yang Y, Irving-Pease E.K, et al (2024) <doi:10.1038/s41586-023-06618-z>.
Provides methods for analysing and forecasting hierarchical and 
    grouped time series. The available forecast methods include bottom-up,
    top-down, optimal combination reconciliation (Hyndman et al. 2011) 
    <doi:10.1016/j.csda.2011.03.006>, and trace minimization reconciliation
    (Wickramasuriya et al. 2018) <doi:10.1080/01621459.2018.1448825>.
A Poisson mixture model is implemented to cluster genes from high-
    throughput transcriptome sequencing (RNA-seq) data. Parameter estimation is
    performed using either the EM or CEM algorithm, and the slope heuristics are
    used for model selection (i.e., to choose the number of clusters).
Takes the MinT implementation of the 'hts'<https://cran.r-project.org/package=hts> package and adapts it to allow degenerate hierarchical structures. Instead of the "nodes" argument, this function takes an S matrix which is more versatile in the structures it allows. For a demo, see Steinmeister and Pauly (2024)<doi:10.15488/17729>. The MinT algorithm is based on Wickramasuriya et al. (2019)<doi:10.1080/01621459.2018.1448825>.
The seed germination process starts with water uptake by the seed and ends with the protrusion of radicle and plumule under varying temperatures and soil water potential. Hydrotime is a way to describe the relationship between water potential and seed germination rates at germination percentages. One important quantity before applying hydrotime modeling of germination percentages is to consider the proportion of viable seeds that could germinate under saturated conditions. This package can be used to apply correction factors at various water potentials before estimating parameters like stress tolerance, and uniformity of the hydrotime model. Three different distributions namely, Gaussian, Logistic, and Extreme value distributions have been considered to fit the model to the seed germination time course. Details can be found in Bradford (2002) <https://www.jstor.org/stable/4046371>, and Bradford and Still(2004) <https://www.jstor.org/stable/23433495>.
Seed germinates through the physical process of water uptake by dry seed driven by the difference in water potential between the seed and the water. There exists seed-to-seed variability in the base seed water potential. Hence, there is a need for a distribution such that a viable seed with its base seed water potential germinates if and only if the soil water potential is more than the base seed water potential. This package estimates the stress tolerance and uniformity parameters of the seed lot for germination under various temperatures by using the hydro-time model of counts of germinated seeds under various water potentials. The distribution of base seed water potential has been considered to follow Normal, Logistic and Extreme value distribution. The estimated proportion of germinated seeds along with the estimates of stress and uniformity parameters are obtained using a generalised linear model. The significance test of the above parameters for within and between temperatures is also performed in the analysis. Details can be found in Kebreab and Murdoch (1999) <doi:10.1093/jxb/50.334.655> and Bradford (2002) <https://www.jstor.org/stable/4046371>.
Functions for the management and treatment of hydrology and 
  meteorology time-series stored in a 'Sqlite' data base.
A novel decision tree algorithm in the hypothesis testing framework. The algorithm examines the distribution difference between two child nodes over all possible binary partitions. The test statistic of the hypothesis testing is equivalent to the generalized energy distance, which enables the algorithm to be more powerful in detecting the complex structure, not only the mean difference. It is applicable for numeric, nominal, ordinal explanatory variables and the response in general metric space of strong negative type. The algorithm has superior performance compared to other tree models in type I error, power, prediction accuracy, and complexity.
In order to improve performance for HTTP API clients, 'httpcache'
    provides simple tools for caching and invalidating cache. It includes the
    HTTP verb functions GET, PUT, PATCH, POST, and DELETE, which are drop-in
    replacements for those in the 'httr' package. These functions are cache-aware
    and provide default settings for cache invalidation suitable for RESTful
    APIs; the package also enables custom cache-management strategies.
    Finally, 'httpcache' includes a basic logging framework to facilitate the
    measurement of HTTP request time and cache performance.
Find and explain the meaning of 'HTTP' status codes.
    Functions included for searching for codes by full or partial number,
    by message, and get appropriate dog and cat images for many
    status codes.
A suite of functions to ping 'URLs' and to time
    'HTTP' 'requests'. Designed to work with 'httr'.
Tools for emitting the 'Problem Details' structure defined in
  'RFC' 7807 <https://tools.ietf.org/html/rfc7807> for reporting errors from
  'HTTP' servers in a standard way.
HTTP Request protocols. Implements the GET, POST and multipart POST request.
Testing and documenting code that communicates with remote servers
    can be painful. Dealing with authentication, server state,
    and other complications can make testing seem too costly to
    bother with. But it doesn't need to be that hard. This package enables one
    to test all of the logic on the R sides of the API in your package without
    requiring access to the remote service. Importantly, it provides three
    contexts that mock the network connection in different ways, as well as
    testing functions to assert that HTTP requests were---or were
    not---made. It also allows one to safely record real API responses to use as
    test fixtures. The ability to save responses and load them offline also
    enables one to write vignettes and other dynamic documents that can be
    distributed without access to a live server.
Testing and documenting code that communicates with remote servers
    can be painful. This package helps with writing tests for packages that
    use 'httr2'. It enables testing all of the logic
    on the R sides of the API without requiring access to the
    remote service, and it also allows recording real API responses to use as
    test fixtures. The ability to save responses and load them offline also
    enables writing vignettes and other dynamic documents that can be
    distributed without access to a live server.
Provides low-level socket and protocol support for handling
    HTTP and WebSocket requests directly from within R. It is primarily
    intended as a building block for other packages, rather than making it
    particularly easy to create complete web applications using httpuv
    alone.  httpuv is built on top of the libuv and http-parser C
    libraries, both of which were developed by Joyent, Inc. (See LICENSE
    file for libuv and http-parser license information.)
Useful tools for working with HTTP organised by HTTP verbs
    (GET(), POST(), etc). Configuration functions make it easy to control
    additional request components (authenticate(), add_headers() and so
    on).
Tools for creating and modifying HTTP requests, then
    performing them and processing the results. 'httr2' is a modern
    re-imagining of 'httr' that uses a pipe-based interface and solves
    more of the problems that API wrapping packages face.
Collection of functions to help retrieving data from
    'Hub'Eau' the free and public French National APIs on water
    <https://hubeau.eaufrance.fr/>.
Functions for combining model outputs (e.g. predictions or
    estimates) from multiple models into an aggregated ensemble model
    output.
Core set of low-level utilities common across the 
  'hubverse'. Used to interact with 'hubverse' schema, Hub configuration files 
  and model outputs and designed to be primarily used internally by other 
  'hubverse' packages. See Reich et al. (2022) <doi:10.2105/AJPH.2022.306831> 
  for an overview of Collaborative Hubs.
Provides functions to access data from the US Department of Housing and Urban Development <https://www.huduser.gov/portal/dataset/fmr-api.html>.
Creating effective colour palettes for figures is 
    challenging. This package generates and plot palettes of optimally 
    distinct colours in perceptually uniform colour space, based on 
    'iwanthue' <http://tools.medialab.sciences-po.fr/iwanthue/>. 
    This is done through k-means clustering of CIE Lab colour space, 
    according to user-selected constraints on hue, chroma, and 
    lightness.
Provides a general framework for
        high-dimensional undirected graph estimation. It integrates
        data preprocessing, neighborhood screening, graph estimation,
        and model selection techniques into a pipeline. In
        preprocessing stage, the nonparanormal(npn) transformation is
        applied to help relax the normality assumption. In the graph
        estimation stage, the graph structure is estimated by
        Meinshausen-Buhlmann graph estimation or the graphical lasso,
        and both methods can be further accelerated by the lossy
        screening rule preselecting the neighborhood of each variable
        by correlation thresholding. We target on high-dimensional data
        analysis usually d >> n, and the computation is
        memory-optimized using the sparse matrix output. We also
        provide a computationally efficient approach, correlation
        thresholding graph estimation. Three
        regularization/thresholding parameter selection methods are
        included in this package: (1)stability approach for
        regularization selection (2) rotation information criterion (3)
        extended Bayesian information criterion which is only available
        for the graphical lasso.
An open-source R package to deploys reproducible and flexible labels using layers. 
  The 'huito' package is part of the 'inkaverse' project for developing different procedures and
  tools used in plant science and experimental designs. 
  Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Tools for computing HUM (Hypervolume Under the Manifold) value to estimate features ability
             to discriminate the class labels, visualizing the ROC curve for two or three class labels
             (Natalia Novoselova, Cristina Della Beffa, Junxi Wang, Jialiang Li, Frank Pessler, Frank Klawonn
             (2014) <doi:10.1093/bioinformatics/btu086>).
Format quantities of time or bytes into human-friendly strings.
Human names are complicated and nonstandard things. Humaniformat,
    which is based on Anthony Ettinger's 'humanparser' project (https://github.com/
    chovy/humanparser) provides functions for parsing human names, making a best-
    guess attempt to distinguish sub-components such as prefixes, suffixes, middle
    names and salutations.
An almost direct port of the 'python' 'humanize' package <https://github.com/jmoiron/humanize>.
  This package contains utilities to convert values into human readable forms.
Generates high-entropy integer synthetic populations from marginal and (optionally) seed data using quasirandom sampling,
  in arbitrary dimensionality (Smith, Lovelace and Birkin (2017) <doi:10.18564/jasss.3550>).
  The package also provides an implementation of the Iterative Proportional Fitting (IPF) algorithm (Zaloznik (2011) <doi:10.13140/2.1.2480.9923>).
Vapor pressure, relative humidity, absolute humidity, specific humidity, and mixing ratio are commonly used water vapor measures in meteorology. This R package provides functions for calculating saturation vapor pressure (hPa), partial water vapor pressure (Pa), relative humidity (%), absolute humidity (kg/m^3), specific humidity (kg/kg), and mixing ratio (kg/kg) from temperature (K) and dew point (K). Conversion functions between humidity measures are also provided.
Low level spell checker and morphological analyzer based on the 
    famous 'hunspell' library <https://hunspell.github.io>. The package can analyze
    or check individual words as well as parse text, latex, html or xml documents.
    For a more user-friendly interface use the 'spelling' package which builds on
    this package to automate checking of files, documentation and vignettes in all
    common formats.
Contains various functions for data analysis, notably helpers and diagnostics for Bayesian modelling using Stan.
When considering count data, it is often the case that many more zero counts than would be expected of some given distribution are observed. It is well established that data such as this can be reliably modelled using zero-inflated or hurdle distributions, both of which may be applied using the functions in this package. Bayesian analysis methods are used to best model problematic count data that cannot be fit to any typical distribution. The package functions are flexible and versatile, and can be applied to varying count distributions, parameter estimation with or without explanatory variable information, and are able to allow for multiple hurdles as it is also not uncommon that count data have an abundance of large-number observations which would be considered outliers of the typical distribution. In lieu of throwing out data or misspecifying the typical distribution, these extreme observations can be applied to a second, extreme distribution. With the given functions of this package, such a two-hurdle model may be easily specified in order to best manage data that is both zero-inflated and over-dispersed.
The HURRECON model estimates wind speed, wind direction, enhanced 
    Fujita scale wind damage, and duration of EF0 to EF5 winds as a function 
    of hurricane location and maximum sustained wind speed. Results may be 
    generated for a single site or an entire region. Hurricane track and 
    intensity data may be imported directly from the US National Hurricane 
    Center's HURDAT2 database. For details on the original version of the 
    model written in Borland Pascal, see: 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>.
Allows users to create time series of tropical storm
    exposure histories for chosen counties for a number of hazard metrics
    (wind, rain, distance from the storm, etc.). This package interacts
    with data available through the 'hurricaneexposuredata' package, which
    is available in a 'drat' repository. To access this data package, see the 
    instructions at <https://github.com/geanders/hurricaneexposure>. 
    The size of the 'hurricaneexposuredata' package is
    approximately 20 MB. This work was supported in part by grants from the National
    Institute of Environmental Health Sciences (R00ES022631), the National Science
    Foundation (1331399), and a NASA Applied Sciences Program/Public Health Program
    Grant (NNX09AV81G).
Provides utility functions for, and drawing on, the 'data.table' package. The package also collates useful miscellaneous functions extending base R not available elsewhere. The name is a portmanteau of 'utils' and the author.
Provides utility functions that are simply, frequently used, 
    but may require higher performance that what can be obtained from base R.
    Incidentally provides support for 'reverse geocoding', such as matching a point
    with its nearest neighbour in another array. Used as a complement to package
    'hutils' by sacrificing compilation or installation time for higher running 
    speeds. The name is a portmanteau of the author and 'Rcpp'.
Creates styled tables for data presentation. Export to HTML, LaTeX,
  RTF, 'Word', 'Excel', and 'PowerPoint'. Simple, modern interface to manipulate 
  borders, size, position, captions, colours, text styles and number formatting.
  Table cells can span multiple rows and/or columns.
  Includes  a 'huxreg' function for creation of regression tables, and 'quick_*' 
  one-liners to print data to a new document.
Facilitates building topology preserving maps for data analysis.
Fits models for genotypic disequilibria, as described in
  Huttley and Wilson (2000) <doi:10.1093/genetics/156.4.2127>, Weir (1996) and Weir and Wilson (1986).
  Contrast terms are available that account for first order interactions
  between loci.  Also implements, for a single locus in a single
  population, a conditional exact test for Hardy-Weinberg equilibrium.
General (multi-allelic) Hardy-Weinberg equilibrium problem from an objective Bayesian testing standpoint. This aim is achieved through the identification of a class of priors specifically designed for this testing problem. A class of intrinsic priors under the full model is considered. This class is indexed by a tuning quantity, the training sample size, as discussed in Consonni, Moreno and Venturini (2010). These priors are objective, satisfy Savage's continuity condition and have proved to behave extremely well for many statistical testing problems.
Inference concerning equilibrium and random mating in 
    autopolyploids. Methods are available to test for equilibrium 
    and random mating at any even ploidy level (>2) in the presence
    of double reduction at biallelic loci. For autopolyploid populations
    in equilibrium, methods are available to estimate the degree of 
    double reduction. We also provide functions to calculate genotype 
    frequencies at equilibrium, or after one or several rounds of 
    random mating, given rates of double reduction. The main function is
    hwefit(). This material is based upon work supported by the
    National Science Foundation under Grant No. 2132247. The opinions,
    findings, and conclusions or recommendations expressed are those of
    the author and do not necessarily reflect the views of the National
    Science Foundation. For details of these methods, see 
    Gerard (2022a) <doi:10.1111/biom.13722> and
    Gerard (2022b) <doi:10.1101/2022.08.11.503635>.
The half-weight index gregariousness (HWIG) is an association 
             index used in social network analyses. It extends the half-weight 
             association index (HWI), correcting for level of gregariousness 
             in individuals. It is calculated using group by individual 
             data according to methods described in Godde et al. (2013) 
             <doi:10.1016/j.anbehav.2012.12.010>.
Provides a way to display word clouds in R. The word cloud is a html widget, so you can use it in interactive documents and 'shiny' applications.
Easy-to-use and versatile functions to output R objects in
        HTML format.
Programmatic interface to the Harmonized World Soil Database 
    'HWSD' web services (<https://daac.ornl.gov/cgi-bin/dsviewer.pl?ds_id=1247>).
    Allows for easy downloads of 'HWSD' soil data directly to your R workspace 
    or your computer. Routines for both single pixel data downloads and
    gridded data are provided.
Provides methods to test whether time series is consistent
	with white noise. Two new tests based on Haar wavelets and general
	wavelets described by Nason and Savchev (2014)
	<doi:10.1002/sta4.69> are provided and, for comparison purposes
	this package also implements the
	B test of Bartlett (1967) <doi:10.2307/2333850>. Functionality
	is provided to compute an approximation to the theoretical
	power of the general wavelet test in the case of general
	ARMA alternatives.
The Hybrid design is a combination of model-assisted design (e.g., the modified 
             Toxicity Probability Interval design) with dose-toxicity model-based design for 
             phase I dose-finding studies. The hybrid design controls the overdosing 
             toxicity well and leads to a recommended dose closer to the true maximum tolerated 
             dose (MTD) due to its ability to calibrate for an intermediate dose. More details 
             can be found in Liao et al. 2022 <doi:10.1002/ijc.34203>.
A set of tools to analyze and visualize the relationships between host-associated microbiomes of hybrid organisms and those of their progenitor species. Though not necessary, installing the microViz package is recommended as a check for phyloseq objects. To install microViz from R Universe use the following command: install.packages("microViz", repos = c(davidbarnett = "https://david-barnett.r-universe.dev", getOption("repos"))). To install microViz from GitHub use the following commands: install.packages("devtools") followed by devtools::install_github("david-barnett/microViz").
Simulates stochastic hybrid models for transmission of infectious
    diseases in dynamic networks. It is a metapopulation model in which each
    node in the network is a sub-population and disease spreads within nodes
    and among them, combining two approaches: stochastic simulation algorithm
    (<doi:10.1146/annurev.physchem.58.032806.104637>) and individual-based
    approach, respectively. Equations that models spread within nodes are
    customizable and there are two link types among nodes: migration and
    influence (commuting). More information in Fernando S. Marques,
    Jose H. H. Grisi-Filho, Marcos Amaku et al. (2020) <doi:10.18637/jss.v094.i06>.
Using hybrid data, this package created a vividly colored hybrid heat map.
    The input is two files which are auto-selected.
    The first file has three columns, the first two for pairs of species,
    with the third column for the hybrid experiment code (an integer).
    The second file is a list of code and their descriptions in two 
    columns. The output is a figure showing the hybrid heat map with a color legend.
Method and tool for generating hybrid time series forecasts using
        an error remodeling approach. These forecasting approaches utilize a recursive 
        technique for modeling the linearity of the series using a linear method 
        (e.g., ARIMA, Theta, etc.) and then models (forecasts) the residuals of the linear forecaster
        using non-linear neural networks (e.g., ANN, ARNN, etc.). The hybrid architectures comprise three steps: 
        firstly, the linear patterns of the series are forecasted which are followed by an error re-modeling step, 
        and finally, the forecasts from both the steps are combined to produce the final output. This method additionally 
        provides the confidence intervals as needed. Ten different models can be implemented using this package.
        This package generates different types of hybrid error correction models for time series forecasting 
        based on the algorithms by Zhang. (2003), Chakraborty et al. (2019), Chakraborty et al. (2020), 
        Bhattacharyya et al. (2021), Chakraborty et al. (2022), and Bhattacharyya et al. (2022)
        <doi:10.1016/S0925-2312(01)00702-0> <doi:10.1016/j.physa.2019.121266> 
        <doi:10.1016/j.chaos.2020.109850> <doi:10.1109/IJCNN52387.2021.9533747> 
        <doi:10.1007/978-3-030-72834-2_29> <doi:10.1007/s11071-021-07099-3>.
An S4 class and several functions which utilize internally stored
    datasets and gauging data enable 1d water level interpolation. The S4 class
    (WaterLevelDataFrame) structures the computation and visualisation
    of 1d water level information along the German federal waterways Elbe and
    Rhine. 'hyd1d' delivers 1d water level data - extracted from the 'FLYS'
    database - and validated gauging data - extracted from the hydrological
    database 'WISKI7' - package-internally. For computations near real time
    gauging data are queried externally from the 'PEGELONLINE REST API' 
    <https://pegelonline.wsv.de/webservice/dokuRestapi>.
Raster based flood modelling internally using 'hyd1d', an R package
    to interpolate 1d water level and gauging data. The package computes flood
    extent and duration through strategies originally developed for 'INFORM',
    an 'ArcGIS'-based hydro-ecological modelling framework. It does not provide
    a full, physical hydraulic modelling algorithm, but a simplified, near real
    time 'GIS' approach for flood extent and duration modelling. Computationally
    demanding annual flood durations have been computed already and data
    products were published by Weber (2022) <doi:10.1594/PANGAEA.948042>.
Calculate an optimal embedding of a set of data points into low-dimensional hyperbolic space. This uses the strain-minimizing hyperbolic embedding of Keller-Ressel and Nargang (2019), see <arXiv:1903.08977>.
Functions for basic hydraulic calculations related to 
    water flow in circular pipes both flowing full (under pressure), and 
    partially full (gravity flow), and trapezoidal open channels. For 
    pressure flow this includes friction loss calculations by solving 
    the Darcy-Weisbach equation for head loss, flow or diameter, 
    plotting a Moody diagram, matching a pump characteristic curve to a system 
    curve, and solving for flows in a pipe network using the Hardy-Cross method. 
    The Darcy-Weisbach friction factor is calculated using the Colebrook 
    (or Colebrook-White equation), the basis of the Moody diagram, the original 
    citation being Colebrook (1939) <doi:10.1680/ijoti.1939.13150>. For gravity 
    flow, the Manning equation is used, again solving for missing parameters. 
    The derivation of and solutions using the Darcy-Weisbach equation and the
    Manning equation are outlined in many fluid mechanics texts such as 
    Finnemore and Maurer (2024, ISBN:978-1-264-78729-6). Some gradually- and 
    rapidly-varied flow functions are included. For the Manning equation
    solutions, this package uses modifications of original code from the 'iemisc' 
    package by Irucka Embry.
The 'hydReng' package provides a set of functions for hydraulic engineering tasks and natural hazard assessments. It includes basic hydraulics (wetted area, wetted perimeter, flow, flow velocity, flow depth, and maximum flow) for open channels with arbitrary geometry under uniform flow conditions. For structures such as circular pipes, weirs, and gates, the package includes calculations for pressure flow, backwater depth, and overflow over a weir crest. Additionally, it provides formulas for calculating bedload transport. The formulas used can be found in standard literature on hydraulics, such as Bollrich (2019, ISBN:978-3-410-29169-5) or Hager (2011, ISBN:978-3-642-77430-0).
Estimates frictional constants for hydraulic analysis 
    of rivers. This HYDRaulic ROughness CALculator (HYDROCAL) was previously 
    developed as a spreadsheet tool and accompanying documentation by McKay and
    Fischenich (2011, <https://erdc-library.erdc.dren.mil/jspui/bitstream/11681/2034/1/CHETN-VII-11.pdf>).
Pfafstetter Hydrological Codes 
    as cited in Verdin and Verdin (1999) <doi: 10.1016/S0022-1694(99)00011-6> 
    are decoded for upstream or downstream queries.
Compute duration curves of daily flow series, both real and modeled, to be compared through indexes of flow duration curves. The package functions include comparative plots and goodness of fit tests. Flow duration curve indexes are based on: Yilmaz et al., (2008) <DOI:10.1029/2007WR006716>.
Events from individual hydrologic time series are extracted, and events from multiple time series can be matched to each other.
	Tang, W. & Carey, S. K. (2017) <doi:10.1002/hyp.11185>.
	Kaur, S., Horne, A., Stewardson, M.J., Nathan, R., Costa, A.M., Szemis, J.M., & Webb, J.A. (2017) <doi:10.1080/24705357.2016.1276418>.
	Ladson, A., Brown, R., Neal, B., & Nathan, R. J. (2013) <doi:10.7158/W12-028.2013.17.1>.
Contains one function for drawing Piper diagrams (also
    called Piper-Hill diagrams) of water analyses for major ions.
S3 functions implementing both statistical and graphical goodness-of-fit measures between observed and simulated values, mainly oriented to be used during the calibration, validation, and application of hydrological models. Missing values in observed and/or simulated values can be removed before computations. Comments / questions / collaboration of any kind are very welcomed.
A collection of utilities that support creation of network attributes for hydrologic networks. Methods and algorithms implemented are documented in Moore et al. (2019) <doi:10.3133/ofr20191096>), Cormen and Leiserson (2022) <ISBN:9780262046305> and Verdin and Verdin (1999) <doi:10.1016/S0022-1694(99)00011-6>.
State-of-the-art Multi-Objective Particle Swarm Optimiser (MOPSO), based on the algorithm developed by Lin et al. (2018) <doi:10.1109/TEVC.2016.2631279> with improvements described by Marinao-Rivas & Zambrano-Bigiarini (2020) <doi:10.1109/LA-CCI48322.2021.9769844>. This package is inspired by and closely follows the philosophy of the single objective 'hydroPSO' R package ((Zambrano-Bigiarini & Rojas, 2013) <doi:10.1016/j.envsoft.2013.01.004>), and can be used for global optimisation of non-smooth and non-linear R functions and R-base models (e.g., 'TUWmodel', 'GR4J', 'GR6J'). However, the main focus of 'hydroMOPSO' is optimising environmental and other real-world models that need to be run from the system console (e.g., 'SWAT+'). 'hydroMOPSO' communicates with the model to be optimised through its input and output files, without requiring modifying its source code. Thanks to its flexible design and the availability of several fine-tuning options, 'hydroMOPSO' can tackle a wide range of multi-objective optimisation problems (e.g., multi-objective functions, multiple model variables, multiple periods). Finally, 'hydroMOPSO' is designed to run on multi-core machines or network clusters, to alleviate the computational burden of complex models with long execution time.
An important environmental impact on running water ecosystems 
    is caused by hydropeaking - the discontinuous release of turbine water 
    because of peaks of energy demand. An event-based algorithm is implemented 
    to detect flow fluctuations referring to increase events (IC) and decrease 
    events (DC). For each event, a set of parameters related to the fluctuation 
    intensity is calculated. The framework is introduced in Greimel et al. (2016) 
    "A method to detect and characterize sub-daily flow fluctuations" 
    <doi:10.1002/hyp.10773> and can be used to identify different fluctuation 
    types according to the potential source: e.g., sub-daily flow fluctuations 
    caused by hydropeaking, rainfall, or snow and glacier melt.
    This is a companion to the package 'hydroroute', which is used to detect and 
    follow hydropower plant-specific hydropeaking waves at the sub-catchment 
    scale and to describe how hydropeaking flow parameters change along the
    longitudinal flow path as proposed and validated in Greimel et al. (2022).
Statistical functions used in the French 'HydroPortail' <https://hydro.eaufrance.fr/>.
    This includes functions to estimate distributions, quantile curves and uncertainties, along with various other utilities.
    Technical details are available (in French) in Renard (2016) <https://hal.inrae.fr/hal-02605318>.
Implements an empirical approach referred to as PeakTrace which uses multiple hydrographs to detect and follow hydropower plant-specific hydropeaking waves at the sub-catchment scale and to describe how hydropeaking flow parameters change along the longitudinal flow path. The method is based on the identification of associated events and uses (linear) regression models to describe translation and retention processes between neighboring hydrographs. Several regression model results are combined to arrive at a power plant-specific model. The approach is proposed and validated in Greimel et al. (2022) <doi:10.1002/rra.3978>. The identification of associated events is based on the event detection implemented in 'hydropeak'.
Calculates a suite of hydrologic indices for daily time series data that are widely used in hydrology and stream ecology.
Read, plot, manipulate and process hydro-meteorological data records (with special features for Argentina and Chile data-sets).
Read, plot, manipulate and process hydro-meteorological data from Argentina and Chile.
S3 functions for management, analysis, interpolation and plotting of time series used in hydrology and related environmental sciences. In particular, this package is highly oriented to hydrological modelling tasks. The focus of this package has been put in providing a collection of tools useful for the daily work of hydrologists (although an effort was made to optimise each function as much as possible, functionality has had priority over speed). Bugs / comments / questions / collaboration of any kind are very welcomed, and in particular, datasets that can be included in this package for academic purposes.
Focuses on data processing and visualization in hydrology and
    climate forecasting. Main function includes data extraction, data downscaling,
    data resampling, gap filler of precipitation, bias correction of forecasting
    data, flexible time series plot, and spatial map generation. It is a good pre-
    processing and post-processing tool for hydrological and hydraulic modellers.
Facilitates the analysis and evaluation of hydrologic model output and 
    time-series data with functions focused on comparison of modeled (simulated) and observed data, 
    period-of-record statistics, and trends.
High level functions for hyperplane fitting (hyper.fit()) and visualising (hyper.plot2d() / hyper.plot3d()). In simple terms this allows the user to produce robust 1D linear fits for 2D x vs y type data, and robust 2D plane fits to 3D x vs y vs z type data. This hyperplane fitting works generically for any N-1 hyperplane model being fit to a N dimension dataset. All fits include intrinsic scatter in the generative model orthogonal to the hyperplane.
Generalized additive models with a numeric hyper column
       tabulated on a common grid. Sign-adjustment based on the
       correlation of model prediction and a selected slice of the
       hyper column. Visualization of the integrand surface over the
       hyper column.
A suite of routines for the hyperdirichlet distribution
   and reified Bradley-Terry; supersedes the 'hyperdirichlet' package;
   uses 'disordR' discipline <doi:10.48550/ARXIV.2210.03856>.  To cite
   in publications please use Hankin 2017 <doi:10.32614/rj-2017-061>,
   and for Generalized Plackett-Luce likelihoods use Hankin 2024
   <doi:10.18637/jss.v109.i08>.
Implements Data Envelopment Analysis (DEA) with a hyperbolic orientation using a non-linear programming solver. It enables flexible estimations with weight restrictions, non-discretionary variables, and a generalized distance function. Additionally, it allows for the calculation of slacks and super-efficiency scores. The methods are detailed in Öttl et al. (2023), <doi:10.1016/j.dajour.2023.100343>. Furthermore, the package provides a non-linear profitability estimation built upon the DEA framework.
Maintenance has been discontinued for this package. It has been
	     superseded by 'GeneralizedHyperbolic'. 'GeneralizedHyperbolic' 
	     includes all the functionality of 'HyperbolicDist' and more 
	     and is based on a more rational design. 'HyperbolicDist' 
	     provides functions for the hyperbolic and related 
	     distributions. Density, distribution and quantile functions 
	     and random number generation are provided for the hyperbolic 
	     distribution, the generalized hyperbolic distribution, 
	     the generalized inverse Gaussian distribution and the 
	     skew-Laplace distribution. Additional functionality is 
	     provided for the hyperbolic distribution, including 
	     fitting of the hyperbolic to data.
Provides functions and methods for organizing data in hypercubes
  (i.e., a multi-dimensional cube). Cubes are generated from molten data frames.
  Each cube can be manipulated with five operations: rotation (change.dimensionOrder()),
  dicing and slicing (add.selection(), remove.selection()), drilling down (add.aggregation()),
  and rolling up (remove.aggregation()).
Implements various tools for storing and analyzing hypergraphs.
  Handles basic undirected, unweighted hypergraphs, and various ways of 
  creating hypergraphs from a number of representations, and
  converting between graphs and hypergraphs.
Given a high-dimensional dataset that typically represents a cytometry dataset, and a subset of the datapoints, this algorithm outputs an hyperrectangle so that datapoints within the hyperrectangle best correspond to the specified subset. In essence, this allows the conversion of clustering algorithms' outputs to gating strategies outputs.
The Gaussian hypergeometric function for complex numbers.
Computation of generalized hypergeometric function with tunable high precision in a vectorized manner, with the floating-point datatypes from 'mpfr' or 'gmp' library. The computation is limited to real numbers.
Evaluates the hypergeometric functions of a matrix argument,
    which appear in random matrix theory. This is an implementation of
    Koev & Edelman's algorithm (2006) <doi:10.1090/S0025-5718-06-01824-2>.
Uses support vector machines to identify a perfectly separating hyperplane (linear or curvilinear) between two entities in high-dimensional space. If this plane exists, the entities do not overlap. Applications include overlap detection in morphological, resource or environmental dimensions. More details can be found in: Brown et al. (2020) <doi:10.1111/2041-210X.13363> .
Comfortable ways to work with hyperspectral data sets.
    I.e. spatially or time-resolved spectra, or spectra with any other kind
    of information associated with each of the spectra. The spectra can be data
    as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS,
    etc. More generally, any data that is recorded over a discretized variable,
    e.g. absorbance = f(wavelength), stored as a vector of absorbance values
    for discrete wavelengths is suitable.
Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and hole detection. Uses stochastic geometry approach to high-dimensional kernel density estimation, support vector machine delineation, and convex hull generation. Applications include modeling trait and niche hypervolumes and species distribution modeling.
Work with model files (setup, input, output) from
    the hydrological catchment model HYPE: Streamlined file import and export, standard 
    evaluation plot routines, diverse post-processing and aggregation routines 
    for hydrological model analysis. The HYPEtools package is also archived at <doi:10.5281/zenodo.7627955>
    and can be cited in publications with Brendel et al. (2024) <doi:10.1016/j.envsoft.2024.106094>.
An implementation of Random Forest-based two-sample tests as introduced in Hediger & Michel & Naef (2022).
Add, share and manage annotations for 'Shiny' applications and R Markdown documents via 'hypothes.is'.
Interact with the application programming interface for the web
    annotation service 'Hypothes.is' (See <http://hypothes.is> for more
    information.) Allows users to download data about public annotations, and
    create, retrieve, update, and delete their own annotations.
Translation between experimental null hypotheses, hypothesis matrices, and contrast matrices as used in linear regression models. The package is based on the method described in Schad et al. (2019) <doi:10.1016/j.jml.2019.104038> and Rabe et al. (2020) <doi:10.21105/joss.02134>.
Functions for generating tables required for drawing and calculating hypsometric curves and hypsometric integrals.
    These functions accept as input the DEM of the region of interest (your watershed) and a spatial data frame file specifying delineation of sub-catchments within the watershed.
    They then generate output in the form of PNG images and HTML files contained in a folder named "HYPSO_OUTPUT" created in the current directory.
    S. K. Sharma, S. Gajbhiye, et al. (2018) <doi:10.1007/978-981-10-5801-1_19>.
    Omvir Singh, A. Sarangi, and Milap C. Sharma (2006) <doi:10.1007/s11269-008-9242-z>.
    James A. Vanderwaal and Herbert Ssegane (2013) <doi:10.1111/jawr.12089>.
Construction and analysis of multivalued zero-sum matrix games over the abstract space of probability distributions, which describe the losses in each scenario of defense vs. attack action. The distributions can be compiled directly from expert opinions or other empirical data (insofar available). The package implements the methods put forth in the EU project HyRiM (Hybrid Risk Management for Utility Networks), FP7 EU Project Number 608090. The method has been published in Rass, S., König, S., Schauer, S., 2016. Decisions with Uncertain Consequences-A Total Ordering on Loss-Distributions. PLoS ONE 11, e0168583. <doi:10.1371/journal.pone.0168583>, and applied for advanced persistent thread modeling in Rass, S., König, S., Schauer, S., 2017. Defending Against Advanced Persistent Threats Using Game-Theory. PLoS ONE 12, e0168675. <doi:10.1371/journal.pone.0168675>. A volume covering the wider range of aspects of risk management, partially based on the theory implemented in the package is the book edited by S. Rass and S. Schauer, 2018. Game Theory for Security and Risk Management: From Theory to Practice. Springer, <doi:10.1007/978-3-319-75268-6>, ISBN 978-3-319-75267-9.
We provide a stage-wise selection method using genetic algorithms, designed to efficiently identify main and two-way interactions within high-dimensional linear regression models. Additionally, it implements simulated annealing algorithm during the mutation process. The relevant paper can be found at: Ye, C.,and Yang,Y. (2019) <doi:10.1109/TIT.2019.2913417>.
Enhance package 'testthat' by allowing tests to be attached to the function/object they test. 
    This allows to keep functional and unit test code together.
Estimate parameters of the hysteretic threshold autoregressive
    (HysTAR) model, using conditional least squares.
    In addition, you can generate time series data from the HysTAR model.
    For details, see Li, Guan, Li and Yu (2015) <doi:10.1093/biomet/asv017>.
Fit, summarize and plot sinusoidal hysteretic processes using:
    two-step simple harmonic least squares, ellipse-specific non-linear least
    squares, the direct method, geometric least squares or linear least squares. See 
    Yang, F and A. Parkhurst, "Efficient Estimation of Elliptical Hysteresis with 
    Application to the Characterization of Heat Stress" <DOI:10.1007/s13253-015-0213-6>.
An R API wrapper for the 'Hystreet' project <https://hystreet.com>. 'Hystreet' provides pedestrian counts in different cities in Germany.
Error type I and Optimal critical values to test statistical hypothesis based on Neyman-Pearson Lemma and Likelihood ratio test 
    based on random samples from several distributions. The families of distributions are Bernoulli, Exponential, Geometric, Inverse Normal, 
    Normal, Gamma, Gumbel, Lognormal, Poisson, and Weibull.
    This package is an ideal resource to help with the teaching of Statistics.
    The main references for this package are Casella G. and Berger R. (2003,ISBN:0-534-24312-6 , "Statistical Inference. Second Edition", Duxbury Press) and 
    Hogg, R., McKean, J., and Craig, A. (2019,ISBN:013468699, "Introduction to Mathematical Statistic. Eighth edition", Pearson).
Search and download Swiss data and metadata from the I14Y 
  interoperability platform of Switzerland using its public APIs 
  <https://www.i14y.admin.ch/api/index.html>.
Up-to-date data from the 'Unicode CLDR Project' (where 'CLDR'
    stands for 'Common Locale Data Repository') are available here as a series
    of easy-to-parse datasets. Several functions are provided for extracting
    key elements from the tabular datasets.
Suite of functions that help simulate elections under different electoral systems, which are then used to compute incentives generated by these systems in terms of the inter- and intra-party dimensions of electoral competition.
Contains data frames and functions used in the book "An Introduction to Acceptance Sampling and SPC with R". This book is available electronically at <https://bookdown.org/>. A physical copy will be published by CRC Press.
Simulate and implement early phase two-stage adaptive dose-finding design for binary and quasi-continuous toxicity endpoints. See Chiuzan et al. (2018) for further reading <DOI:10.1080/19466315.2018.1462727>.
Calculate false ring proportions from data frames of intra annual 
  density fluctuations.
Provides functions to conduct a model-agnostic asymptotic hypothesis test for the identification of interaction effects in black-box machine learning models. The null hypothesis assumes that a given set of covariates does not contribute to interaction effects in the prediction model. The test statistic is based on the difference of variances of partial dependence functions (Friedman (2008) <doi:10.1214/07-AOAS148> and Welchowski (2022) <doi:10.1007/s13253-021-00479-7>) with respect to the original black-box predictions and the predictions under the null hypothesis. The hypothesis test can be applied to any black-box prediction model, and the null hypothesis of the test can be flexibly specified according to the research question of interest. Furthermore, the test is computationally fast to apply as the null distribution does not require resampling or refitting black-box prediction models.
An interface to the algorithms of 'Interpretable AI'
    <https://www.interpretable.ai> from the R programming language.
    'Interpretable AI' provides various modules, including 'Optimal Trees' for
    classification, regression, prescription and survival analysis, 'Optimal
    Imputation' for missing data imputation and outlier detection, and 'Optimal
    Feature Selection' for exact sparse regression. The 'iai' package is an
    open-source project. The 'Interpretable AI' software modules are proprietary
    products, but free academic and evaluation licenses are available.
Provides a monthly summary of Iowa liquor (class E) sales from January 2015
    to October 2020. See the package website for more information, 
    documentation and examples. Data source: 
    Iowa Data portal <https://data.iowa.gov/resource/m3tr-qhgy.csv>.
The matrix factor model has drawn growing attention for its advantage in achieving two-directional dimension reduction simultaneously for matrix-structured observations. In contrast to the Principal Component Analysis (PCA)-based methods, we propose a simple Iterative Alternating Least Squares (IALS) algorithm for matrix factor model, see the details in He et al. (2023) <arXiv:2301.00360>.
Implementation of some of the formulations for the thermodynamic
	and transport properties released by the International Association for
	the Properties of Water and Steam (IAPWS). More specifically, the
	releases R1-76(2014), R5-85(1994), R6-95(2018), R7-97(2012), R8-97,
	R9-97, R10-06(2009), R11-24, R12-08, R15-11, R16-17(2018),
	R17-20 and R18-21 at <https://iapws.org>.
An implementation of the International Association for the
    Properties of Water (IAPWS) Formulation 1995 for the Thermodynamic Properties of Ordinary
    Water Substance for General and Scientific Use and on the releases for viscosity,
    conductivity, surface tension and melting pressure.
Data sets, functions and scripts with examples to implement autoregressive models for irregularly observed time series. The models available in this package are the irregular autoregressive model (Eyheramendy et al.(2018) <doi:10.1093/mnras/sty2487>), the complex irregular autoregressive model (Elorrieta et al.(2019) <doi:10.1051/0004-6361/201935560>) and the bivariate irregular autoregressive model (Elorrieta et al.(2021) <doi:10.1093/mnras/stab1216>).
Tools to assess model fit and identify misfitting items for Rasch models (RM) and partial credit models (PCM). Included are item fit statistics, item characteristic curves, item-restscore association, conditional likelihood ratio tests, assessment of measurement error, estimates of the reliability and test targeting as described in Christensen et al. (Eds.) (2013, ISBN:978-1-84821-222-0).
Calculate AIC's and AICc's of unimodal model (one normal distribution) and bimodal model(a mixture of two normal distributions) which fit the distribution of indices of asymmetry (IAS), and plot their density, to help determine IAS distribution is unimodal or bimodal.
Implements the standard D-Scoring algorithm
    (Greenwald, Banaji, & Nosek, 2003) for Implicit Association Test (IAT)
    data and includes plotting capabilities for exploring raw IAT data.
Quickly score raw data outputted from an Implicit Association Test (IAT; Greenwald, McGhee, & Schwartz, 1998) <doi:10.1037/0022-3514.74.6.1464>. IAT scores are calculated as specified by Greenwald, Nosek, and Banaji (2003) <doi:10.1037/0022-3514.85.2.197>.    The output of this function is a data frame that consists of four rows containing the following information: (1) the overall IAT effect size for the participant's dataset, (2) the effect size calculated for odd trials only, (3) the effect size calculated for even trials only, and (4) the proportion of trials with reaction times under 300ms (which is important for exclusion purposes). Items (2) and (3) allow for a measure of the internal consistency of the IAT. Specifically, you can use the subsetted IAT effect sizes for odd and even trials to calculate Cronbach's alpha across participants in the sample.    The input function consists of three arguments. First, indicate the name of the dataset to be analyzed. This is the only required input. Second, indicate the number of trials in your entire IAT (the default is set to 220, which is typical for most IATs). Last, indicate whether congruent trials (e.g., flowers and pleasant) or incongruent trials (e.g., guns and pleasant) were presented first for this participant (the default is set to congruent).    Data files should consist of six columns organized in order as follows: Block (0-6), trial (0-19 for training blocks, 0-39 for test blocks), category (dependent on your IAT), the type of item within that category (dependent on your IAT), a dummy variable indicating whether the participant was correct or incorrect on that trial (0=correct, 1=incorrect), and the participant’s reaction time (in milliseconds).    A sample dataset (titled 'sampledata') is included in this package to practice with.
This minimalist package is designed to quickly score raw data outputted from an Implicit Association Test (IAT; Greenwald, McGhee, & Schwartz, 1998) <doi:10.1037/0022-3514.74.6.1464>. IAT scores are calculated as specified by Greenwald, Nosek, and Banaji (2003) <doi:10.1037/0022-3514.85.2.197>. Outputted values can be interpreted as effect sizes. The input function consists of three arguments. First, indicate the name of the dataset to be analyzed. This is the only required input. Second, indicate the number of trials in your entire IAT (the default is set to 219, which is typical for most IATs). Last, indicate whether congruent trials (e.g., flowers and pleasant) or incongruent trials (e.g., guns and pleasant) were presented first for this participant (the default is set to congruent). The script will tell you how long it took to run the code, the effect size for the participant, and whether that participant should be excluded based on the criteria outlined by Greenwald et al. (2003). Data files should consist of six columns organized in order as follows: Block (0-6), trial (0-19 for training blocks, 0-39 for test blocks), category (dependent on your IAT), the type of item within that category (dependent on your IAT), a dummy variable indicating whether the participant was correct or incorrect on that trial (0=correct, 1=incorrect), and the participant’s reaction time (in milliseconds). Three sample datasets are included in this package (labeled 'IAT', 'TooFastIAT', and 'BriefIAT') to practice with.
Compute several variations of the Implicit Association Test (IAT) scores, including the D scores (Greenwald, Nosek, Banaji, 2003, <doi:10.1037/0022-3514.85.2.197>) and the new scores that were developed using robust statistics (Richetin, Costantini, Perugini, and Schonbrodt, 2015, <doi:10.1371/journal.pone.0129601>).
An implementation of the iterative bootstrap procedure of 
    Kuk (1995) <doi:10.1111/j.2517-6161.1995.tb02035.x> to correct the estimation bias of a fitted model object. This
    procedure has better bias correction properties than the 
    bootstrap bias correction technique.
A statistical method based on Bayesian Additive Regression Trees with Global 
    Standard Error Permutation Test (BART-G.SE) for descriptor selection 
    and symbolic regression. It finds the symbolic formula of the regression function 
    y=f(x) as described in Ye, Senftle, and Li (2023) <arXiv:2110.10195>.
A collection of useful functions and datasets for the Data Science
  Course at IBAW.
Call wrappers for Istanbul Metropolitan
    Municipality's Open Data Portal (Turkish: İstanbul Büyükşehir
    Belediyesi Açık Veri Portalı) at <https://data.ibb.gov.tr/en/>.
Implements the item based collaborative filtering (IBCF) method for continues phenotypes in the context of plant breeding where data are collected for various traits that were studied in various environments proposed by Montesinos-López et al. (2017) <doi:10.1534/g3.117.300309>.
Implements multiple variants of the Information Bottleneck ('IB') method 
    for clustering datasets containing mixed-type variables (nominal, ordinal, and 
    continuous). The package provides deterministic, agglomerative, generalized, 
    and standard 'IB' clustering algorithms that preserve relevant information while 
    forming interpretable clusters. The Deterministic Information Bottleneck is described in 
    Costa et al. (2024) <doi:10.48550/arXiv.2407.03389>. The standard 'IB' method 
    originates from Tishby et al. (2000) <doi:10.48550/arXiv.physics/0004057>, 
    the agglomerative variant from Slonim and Tishby (1999) <https://papers.nips.cc/paper/1651-agglomerative-information-bottleneck>, 
    and the generalized 'IB' for Gaussian variables from Chechik et al. (2005) <https://www.jmlr.org/papers/volume6/chechik05a/chechik05a.pdf>.
A collection of several utility functions related to binary incomplete block designs. Contains function to generate A- and D-efficient binary incomplete block designs with given numbers of treatments, number of blocks and block size. Contains function to generate an incomplete block design with specified concurrence matrix. There are functions to generate balanced treatment incomplete block designs and incomplete block designs for test versus control treatments comparisons with specified concurrence matrix. Allows performing analysis of variance of data and computing estimated marginal means of factors from experiments using a connected incomplete block design. Tests of hypothesis of treatment contrasts in incomplete block design set up is supported.
This R package implements methods for estimation and inference under Incomplete Block Designs and Balanced Incomplete Block Designs within a design-based finite-population framework. Based on 'Koo and Pashley' (2024) <arXiv:2405.19312>, it includes block-level estimators and extends to unit-level effects using 'Horvitz-Thompson' and 'Hájek' estimators. The package also provides asymptotic confidence intervals to support valid statistical inference.
Identity by Descent (IBD) distributions in pedigrees. A Hidden Markov
    Model is used to compute identity coefficients, simulate IBD segments and
    to derive the distribution of total IBD sharing and segment count across
    chromosomes. The methods are applied in Kruijver (2025) 
    <doi:10.3390/genes16050492>. The probability that the total IBD sharing
    is zero can be computed using the method of Donnelly (1983)
    <doi:10.1016/0040-5809(83)90004-7>.
Simulation of segments shared identical-by-descent (IBD) by
    pedigree members. Using sex specific recombination rates along the
    human genome (Halldorsson et al. (2019)
    <doi:10.1126/science.aau1043>), phased chromosomes are simulated for
    all pedigree members. Applications include calculation of realised
    relatedness coefficients and IBD segment distributions. 'ibdsim2' is
    part of the 'pedsuite' collection of packages for pedigree analysis.
    A detailed presentation of the 'pedsuite', including a separate
    chapter on 'ibdsim2', is available in the book 'Pedigree analysis in
    R' (Vigeland, 2021, ISBN:9780128244302). A 'Shiny' app for visualising
    and comparing IBD distributions is available at
    <https://magnusdv.shinyapps.io/ibdsim2-shiny/>.
Some basic functions to implement belief functions including:
    transformation between belief functions using the method introduced by
    Philippe Smets <arXiv:1304.1122>, evidence combination, evidence
    discounting, decision-making, and constructing masses. Currently, thirteen
    combination rules and six decision rules are supported. It can also be
    used to generate different types of random masses when working on belief
    combination and conflict management.
The initial basic feasible solution (IBFS) is a significant step to achieve the minimal total cost (optimal solution) of the transportation problem. However, the existing methods of IBFS do not always provide a good feasible solution which can reduce the number of iterations to find the optimal solution. This initial basic feasible solution can be obtained by using any of the following methods. 
             a) North West Corner Method. 
             b) Least Cost Method. 
             c) Row Minimum Method. 
             d) Column Minimum Method. 
             e) Vogel's Approximation Method.
             etc.
             For more technical details about the algorithms please refer below URLs.
             <https://theintactone.com/2018/05/24/ds-u2-topic-8-transportation-problems-initial-basic-feasible-solution/>.
             <https://www.brainkart.com/article/Methods-of-finding-initial-Basic-Feasible-Solutions_39037/>.
             <https://myhomeworkhelp.com/row-minima-method/>.
             <https://myhomeworkhelp.com/column-minima-method/>.
Implementation of some Individual Based Models (IBMs, sensu Grimm and Railsback 2005) 
  and methods to create new ones, particularly for population dynamics models (reproduction, 
  mortality and movement). The basic operations for the simulations are implemented in Rcpp for speed.
Authentication can be the most difficult part about
  working with a new API. 'ibmAcousticR' facilitates making a
  connection to the 'IBM Acoustic' email campaign management API
  and executing various queries. The 'IBM Acoustic' API 
  documentation is available at
  <https://developer.ibm.com/customer-engagement/docs/>. This
  package is not supported by 'IBM'.
It provides a generic set of tools for initializing a synthetic
         population with each individual in specific disease states, and
         making transitions between those disease states according to the rates
         calculated on each timestep. The new version 1.0.0 has C++ code 
         integration to make the functions run faster. It has also a higher level
         function to actually run the transitions for the number of timesteps
         that users specify. Additional functions will follow for changing
         attributes on demographic, health belief and movement.
Functionality required to efficiently use R with IBM(R) Db2(R)
        Warehouse offerings (formerly IBM dashDB(R)) and IBM Db2 for z/OS(R) in
        conjunction with IBM Db2 Analytics Accelerator for z/OS.
        Many basic and complex R operations are pushed down into the database, 
        which removes the main memory boundary of R and allows to make full 
        use of parallel processing in the underlying database.
        For executing R-functions in a multi-node environment in parallel the idaTApply() function
        requires the 'SparkR' package (<https://spark.apache.org/docs/latest/sparkr.html>).
        The optional 'ggplot2' package is needed for the plot.idaLm() function only.
Simulation of the random evolution of heterogeneous populations using stochastic Individual-Based Models (IBMs) <doi:10.48550/arXiv.2303.06183>. 
    The package enables users to simulate population evolution, in which individuals are characterized by their age and some characteristics, and the population is modified by different types of events, including births/arrivals, death/exit events, or changes of characteristics. The frequency at which an event can occur to an individual can depend on their age and characteristics, but also on the characteristics of other individuals (interactions). 
    Such models have a wide range of applications. For instance, IBMs can be used for simulating the evolution of a heterogeneous insurance portfolio with selection or for validating  mortality forecasts. 
    This package overcomes the limitations of time-consuming IBMs simulations by implementing new efficient algorithms  based on thinning methods, which are compiled using the 'Rcpp' package while providing a user-friendly interface.
Generates Personality Insights sunburst diagrams based on
    'IBM Watson' Personality Insights service output.
Multivariate smoothing using iterative bias reduction with kernel, thin plate splines, Duchon splines or low rank splines.
Model agnostic tool for decomposition of predictions from black boxes.
    Supports additive attributions and attributions with interactions.
    The Break Down Table shows contributions of every variable to a final prediction. 
    The Break Down Plot presents variable contributions in a concise graphical way. 
    This package works for classification and regression models. 
    It is an extension of the 'breakDown' package (Staniak and Biecek 2018) <doi:10.32614/RJ-2018-072>,
    with new and faster strategies for orderings. 
    It supports interactions in explanations and has interactive visuals (implemented with 'D3.js' library). 
    The methodology behind is described in the 'iBreakDown' article (Gosiewska and Biecek 2019) <arXiv:1903.11420>
    This package is a part of the 'DrWhy.AI' universe (Biecek 2018) <arXiv:1806.08915>.
Provides native R access to Interactive Brokers Trader Workstation API.
Several functions to calculate two important indexes (IBR (Integrated Biomarker Response) and IBRv2 (Integrated Biological Response version 2)), it also calculates the standardized values for enzyme activity for each index, and it has a graphing function to perform radarplots that make great data visualization for this type of data. Beliaeff, B., & Burgeot, T. (2002). <https://pubmed.ncbi.nlm.nih.gov/12069320/>. Sanchez, W., Burgeot, T., & Porcher, J.-M. (2013).<doi:10.1007/s11356-012-1359-1>. Devin, S., Burgeot, T., Giambérini, L., Minguez, L., & Pain-Devin, S. (2014). <doi:10.1007/s11356-013-2169-9>. Minato N. (2022). <https://minato.sip21c.org/msb/>.
Calculate B-spline basis functions with a given set of knots and order, or a B-spline function with a given set of knots and order and set of de Boor points (coefficients), or the integral of a B-spline function.
Fit a full or subsampling bagging survival tree on a mixture of population (susceptible and nonsusceptible)
             using either a pseudo R2 criterion or an adjusted Logrank criterion. The predictor is 
             evaluated using the Out Of Bag Integrated Brier Score (IBS) and several scores of importance
             are computed for variable selection. The thresholds values for variable selection are 
             computed using a nonparametric permutation test. 
             See 'Cyprien Mbogning' and 'Philippe Broet' (2016)<doi:10.1186/s12859-016-1090-x> for 
             an overview about the methods implemented in this package.
Implements inequality constrained inference. This includes parameter estimation in normal (linear) models under linear equality and inequality constraints, as well as normal likelihood ratio tests involving inequality-constrained hypotheses. For inequality-constrained linear models, averaging over R-squared for different orderings of regressors is also included.
Implementation of the classifier described in the paper Ali HR et al (2014) <doi:10.1186/s13059-014-0431-1>. It uses copy number and/or expression form breast cancer data, trains a Tibshirani's 'pamr' classifier with the features available and predicts the iC10 group.
Training datasets for iC10; which implements the classifier described in the paper 'Genome-driven integrated classification of breast cancer validated in over 7,500 samples' (Ali HR et al., Genome Biology 2014). It uses copy number and/or expression form breast cancer data, trains a pamr classifier (Tibshirani et al.) with the features available and predicts the iC10 group. Genomic annotation for the training dataset has been obtained from Mark Dunning's lluminaHumanv3.db package.
Independent Component Analysis (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and Joint Approximate Diagonalization of Eigenmatrices (JADE).
A simple wrapper around the 'ical.js' library executing 
    'Javascript' code via 'V8' (the 'Javascript' engine driving the 'Chrome' 
    browser and 'Node.js' and accessible via the 'V8' R package). 
    This package enables users to parse 'iCalendar' files ('.ics', '.ifb', 
    '.iCal', '.iFBf') into lists and 'data.frames' to ultimately do statistics
    on events, meetings, schedules, birthdays, and the like.
To implement a general framework to quantitatively infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysis, abbreviated as 'iCAMP' (Ning et al 2020) <doi:10.1038/s41467-020-18560-z>. It can quantitatively assess the relative importance of different community assembly processes, such as selection, dispersal, and drift, for both communities and each phylogenetic group ('bin'). Each bin usually consists of different taxa from a family or an order. The package also provides functions to implement some other published methods, including neutral taxa percentage (Burns et al 2016) <doi:10.1038/ismej.2015.142> based on neutral theory model and quantifying assembly processes based on entire-community null models ('QPEN', Stegen et al 2013) <doi:10.1038/ismej.2013.93>. It also includes some handy functions, particularly for big datasets, such as phylogenetic and taxonomic null model analysis at both community and bin levels, between-taxa niche difference and phylogenetic distance calculation, phylogenetic signal test within phylogenetic groups, midpoint root of big trees, etc. Version 1.3.x mainly improved the function for 'QPEN' and added function 'icamp.cate()' to summarize 'iCAMP' results for different categories of taxa (e.g. core versus rare taxa).
Analysis and visualization of experimentally elucidated mutational
    signatures -- the kind of analysis and visualization in Boot et al.,
    "In-depth characterization of the cisplatin mutational signature in 
    human cell lines and in esophageal and liver tumors", Genome Research 2018, 
    <doi:10.1101/gr.230219.117> and
    "Characterization of colibactin-associated mutational signature in an 
    Asian oral squamous cell carcinoma and in other mucosal tumor types",
    Genome Research 2020 <doi:10.1101/gr.255620.119>.
    'ICAMS' stands for In-depth Characterization 
    and Analysis of Mutational Signatures. 'ICAMS' has functions to read in 
    variant call files (VCFs) and to collate the corresponding catalogs of 
    mutational spectra and to analyze and plot catalogs of mutational spectra
    and signatures. Handles both "counts-based" and "density-based" (i.e.
    representation as mutations per megabase) mutational spectra or signatures.
Running Focused Identification of the Germplasm Strategy (FIGS) to make best subsets from Genebank Collection.
Implements the integrative conditional autoregressive horseshoe model 
    discussed in Jendoubi, T., Ebbels, T.M. Integrative analysis of time course metabolic data and biomarker discovery. 
    BMC Bioinformatics 21, 11 (2020) <doi:10.1186/s12859-019-3333-0>.
    The model consists in three levels: Metabolic pathways level modeling interdependencies between
    variables via a conditional auto-regressive (CAR) component, integrative analysis level to identify
    potential associations between heterogeneous omic variables via a Horseshoe prior and experimental
    design level to capture experimental design conditions through a mixed-effects model.
    The package also provides functions to simulate data from the model, construct pathway matrices,
    post process and plot model parameters.
Provides user-friendly tools for calibration in survey sampling.
    The package is production-oriented, and its interface is inspired by the famous
    popular macro 'Calmar' for SAS, so that 'Calmar' users can quickly get used to
    'icarus'. In addition to calibration (with linear, raking and logit methods),
    'icarus' features functions for calibration on tight bounds and penalized
    calibration.
Implementation of the methodology proposed in 'Data-driven design of targeted gene panels for estimating immunotherapy biomarkers', Bradley and Cannings (2021) <arXiv:2102.04296>. This package allows the user to fit generative models of mutation from an annotated mutation dataset, and then further to produce tunable linear estimators of exome-wide biomarkers. It also contains functions to simulate mutation annotated format (MAF) data, as well as to analyse the output and performance of models.
Assist in the estimation of the Intraclass Correlation Coefficient
    (ICC) from variance components of a one-way analysis of variance and also
    estimate the number of individuals or groups necessary to obtain an ICC
    estimate with a desired confidence interval width.
Provides functions to calculate the requisite sample size for studies where ICC is 
    the primary outcome. Can also be used for calculation of power. In both cases it
    allows the user to test the impact of changing input variables by calculating the outcome
    for several different values of input variables. Based off the work of Zou.
    Zou, G. Y. (2012). Sample size formulas for estimating intraclass correlation coefficients with
    precision and assurance. Statistics in medicine, 31(29), 3972-3981.
Calibration and risk-set calibration methods for fitting Cox proportional hazard model when a binary covariate is measured intermittently. Methods include functions to fit calibration models from interval-censored data and modified partial likelihood for the proportional hazard model, Nevo et al. (2018+) <arXiv:1801.01529>.
A function and vignettes for computing an intraclass correlation
    described in Aguinis & Culpepper (2015) <doi:10.1177/1094428114563618>.
    This package quantifies the share of variance in a dependent variable that
    is attributed to group heterogeneity in slopes.
Assists in generating binary clustered data, estimates of Intracluster Correlation coefficient (ICC) for binary response in 16 different methods, and 5 different types of confidence intervals.
Estimates the intraclass correlation coefficient (ICC) for count data to assess repeatability (intra-methods concordance) and concordance (between-method concordance). In the concordance setting, the ICC is equivalent to the concordance correlation coefficient estimated by variance components. The ICC is estimated using the estimates from generalized linear mixed models. The within-subjects distributions considered are: Poisson; Negative Binomial with additive and proportional extradispersion; Zero-Inflated Poisson; and Zero-Inflated Negative Binomial with additive and proportional extradispersion. The statistical methodology used to estimate the ICC with count data can be found in Carrasco (2010) <doi:10.1111/j.1541-0420.2009.01335.x>.
The functions compute the double-entry intraclass correlation, which is an index of profile similarity (Furr, 2010; McCrae, 2008). The double-entry intraclass correlation is a more precise index of the agreement of two empirically observed profiles than the often-used intraclass correlation (McCrae, 2008). Profiles comprising correlations are automatically transformed according to the Fisher z-transformation before the double-entry intraclass correlation is calculated. If the profiles comprise scores such as sum scores from various personality scales, it is recommended to standardize each individual score prior to computation of the double-entry intraclass correlation (McCrae, 2008). See Furr (2010) <doi:10.1080/00223890903379134> or McCrae (2008) <doi:10.1080/00223890701845104> for details.
Implements the conditional inference forest approach 
  to modeling interval-censored survival data. It also provides 
  functions to tune the parameters and evaluate the model fit. See 
  Yao et al. (2019) <arXiv:1901.04599>.
Assists in generating categorical clustered outcome data, estimating the Intracluster Correlation Coefficient (ICC) for nominal or ordinal data with 2+ categories under the resampling and method of moments (MoM) methods, with confidence intervals.
Estimates the intraclass correlation coefficient for trajectory data using a matrix of distances between trajectories. The distances implemented are the extended Hausdorff distances (Min et al. 2007) <doi:10.1080/13658810601073315> and the discrete Fréchet distance (Magdy et al. 2015) <doi:10.1109/IntelCIS.2015.7397286>.
Data from the United States Center for Medicare and Medicaid
    Services (CMS) is included in this package. There are ICD-9 and ICD-10
    diagnostic and procedure codes, and lists of the chapter and sub-chapter 
    headings and the ranges of ICD codes they encompass. There are also two 
    sample datasets. These data are used by the 'icd' package for finding
    comorbidities.
Provides convenient access to the German modification of the International Classification of Diagnoses, 10th revision (ICD-10-GM). It provides functionality to aid in the identification, specification and historisation of ICD-10 codes. Its intended use is the analysis of routinely collected data in the context of epidemiology, medical research and health services research. The underlying metadata are released by the German Institute for Medical Documentation and Information <https://www.dimdi.de>, and are redistributed in accordance with their license.
Provides tools for mapping International Classification of Diseases codes to comorbidity, 
    enabling the identification and analysis of various medical conditions within healthcare data.
Provides an estimator for generalized linear models with incomplete
    data for discrete covariates. The estimation is based on the EM algorithm by the
    method of weights by Ibrahim (1990) <DOI:10.2307/2290013>.
Categorization and scoring of injury severity typically involves
    trained personnel with access to injured persons or their medical records. 'icdpicr' contains a function
    that provides automated calculation of Abbreviated Injury Scale ('AIS') and Injury Severity Score ('ISS')
    from International Classification of Diseases ('ICD') codes and may be a useful substitute to manual injury 
    severity scoring. 'ICDPIC' was originally developed in 'Stata', and 'icdpicr' is an open-access update 
    that accepts both 'ICD-9' and 'ICD-10' codes.
Identify Cancer Dysfunctional Sub-pathway by integrating gene expression, DNA methylation and copy number variation, and pathway topological information. 1)We firstly calculate the gene risk scores by integrating three kinds of data: DNA methylation, copy number variation, and gene expression.  2)Secondly, we perform a greedy search algorithm to identify the key dysfunctional sub-pathways within the pathways for which the discriminative scores were locally maximal. 3)Finally, the permutation test was used to calculate statistical significance level for these key dysfunctional sub-pathways.
Implements Individual Conditional Expectation (ICE) plots, a tool for visualizing the model estimated by any supervised learning algorithm. ICE plots refine Friedman's partial dependence plot by graphing the functional relationship between the predicted response and a covariate of interest for individual observations. Specifically, ICE plots highlight the variation in the fitted values across the range of a covariate of interest, suggesting where and to what extent they may exist.
Provides user-friendly and configurable print debugging via a
    single function, ic(). Wrap an expression in ic() to print the
    expression, its value and (where available) its source location.
    Debugging output can be toggled globally without modifying code.
Estimate test-retest reliability for complex sampling strategies 
    and extract variances using IntraClass Effect Decomposition. Developed by
    Brandmaier et al. (2018) "Assessing reliability in neuroimaging research through intra-class effect decomposition (ICED)" <doi:10.7554/eLife.35718> 
    Also includes functions to simulate data based on sampling strategy. 
    Unofficial version release name: "Good work squirrels".
Given two unbiased samples of patient level data on cost and effectiveness
  for a pair of treatments, make head-to-head treatment comparisons by (i) generating the
  bivariate bootstrap resampling distribution of ICE uncertainty for a specified value of
  the shadow price of health, lambda, (ii) form the wedge-shaped ICE confidence region with
  specified confidence fraction within [0.50, 0.99] that is equivariant with respect to
  changes in lambda, (iii) color the bootstrap outcomes within the above confidence wedge
  with economic preferences from an ICE map with specified values of lambda, beta and gamma
  parameters, (iv) display VAGR and ALICE acceptability curves, and (v) illustrate variation
  in ICE preferences by displaying potentially non-linear indifference(iso-preference) curves
  from an ICE map with specified values of lambda, beta and either gamma or eta parameters.
A toolkit that allows scientists to work with data from single cell sequencing technologies such as scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST). Single (i) Cell R package ('iCellR') provides unprecedented flexibility at every step of the analysis pipeline, including normalization, clustering, dimensionality reduction, imputation, visualization, and so on. Users can design both unsupervised and supervised models to best suit their research. In addition, the toolkit provides 2D and 3D interactive visualizations, differential expression analysis, filters based on cells, genes and clusters, data merging, normalizing for dropouts, data imputation methods, correcting for batch differences, pathway analysis, tools to find marker genes for clusters and conditions, predict cell types and pseudotime analysis. See Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.05.05.078550>  and Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.03.31.019109> for more details.
Regression models for interval censored data. Currently supports
    Cox-PH, proportional odds, and accelerated failure time models. Allows for
    semi and fully parametric models (parametric only for accelerated failure
    time models) and Bayesian parametric models. Includes functions for easy visual
    diagnostics of model fits and imputation of censored data.
Contains datasets and several smaller functions suitable for analysis of interval-censored data. The package complements the book Bogaerts, Komárek and Lesaffre (2017, ISBN: 978-1-4200-7747-6) "Survival Analysis with Interval-Censored Data: A Practical Approach" <https://www.routledge.com/Survival-Analysis-with-Interval-Censored-Data-A-Practical-Approach-with/Bogaerts-Komarek-Lesaffre/p/book/9781420077476>. Full R code related to the examples presented in the book can be found at <https://ibiostat.be/online-resources/icbook/supplemental>. Packages mentioned in the "Suggests" section are used in those examples.
We consider studies in which information from error-prone
    diagnostic tests or self-reports are gathered sequentially to determine the
    occurrence of a silent event. Using a likelihood-based approach
    incorporating the proportional hazards assumption, we provide functions to
    estimate the survival distribution and covariate effects. We also provide 
    functions for power and sample size calculations for this setting.
    Please refer to Xiangdong Gu, Yunsheng Ma, and Raji Balasubramanian (2015) 
    <doi: 10.1214/15-AOAS810>, Xiangdong Gu and Raji Balasubramanian (2016) 
    <doi: 10.1002/sim.6962>, Xiangdong Gu, Mahlet G Tadesse, Andrea S Foulkes,
    Yunsheng Ma, and Raji Balasubramanian (2020) <doi: 10.1186/s12911-020-01223-w>.
The app will calculate the ICER (incremental cost-effectiveness 
             ratio) Rawlins (2012) <doi:10.1016/B978-0-7020-4084-9.00044-6> from the mean 
             costs and quality-adjusted life years (QALY) Torrance and Feeny (2009) <doi:10.1017/S0266462300008461>
             for a set of treatment options, and draw the efficiency frontier 
             in the costs-effectiveness plane. The app automatically identifies 
             and excludes dominated and extended-dominated options from the ICER 
             calculation.
A collection of functions that facilitate computational steps
  related to advice for fisheries management, according to ICES guidelines.
  These include methods for calculating reference points and model diagnostics.
Programmatic connection to the 'OpenAltimetry API' <https://openaltimetry.earthdatacloud.nasa.gov/data/openapi/swagger-ui/index.html/> to download and process 'ATL03' (Global Geolocated Photon Data), 'ATL06' (Land Ice Height), 'ATL07' (Sea Ice Height), 'ATL08' (Land and Vegetation Height), 'ATL10' (Sea Ice Freeboard), 'ATL12' (Ocean Surface Height) and 'ATL13' (Inland Water Surface Height) 'ICESat-2' Altimeter Data. The user has the option to download the data by selecting a bounding box from a 1- or 5-degree grid globally utilizing a shiny application. The 'ICESat-2' mission collects altimetry data of the Earth's surface. The sole instrument on 'ICESat-2' is the Advanced Topographic Laser Altimeter System (ATLAS) instrument that measures ice sheet elevation change and sea ice thickness, while also generating an estimate of global vegetation biomass. 'ICESat-2' continues the important observations of ice-sheet elevation change, sea-ice freeboard, and vegetation canopy height begun by 'ICESat' in 2003.
Provides user tokens for ICES web services that require
  authentication and authorization.  Web services covered by this
  package are ICES VMS database, the ICES DATSU web services, and the
  ICES SharePoint site <https://www.ices.dk/data/tools/Pages/WebServices.aspx>.
R interface to access the web services of the ICES (International
             Council for the Exploration of the Sea) DATRAS trawl survey
             database <https://datras.ices.dk/WebServices/Webservices.aspx>.
Functions to Interact with the ICES Data Submission Utility (DATSU)
  <https://datsu.ices.dk/web/index.aspx>.
Run quality checks on data sets using the same checks that are conducted
  on the ICES Data Submission Utility (DATSU) <https://datsu.ices.dk>.
R interface to access the web services of the ICES Stock Assessment
             Graphs database <https://sg.ices.dk>.
R interface to access the web services of the ICES Stock Database <https://sd.ices.dk>.
Functions to support the ICES Transparent Assessment Framework
  <https://taf.ices.dk> to organize data, methods, and results used in ICES
  assessments. ICES is an organization facilitating international collaboration
  in marine science.
R interface to access the Vocabularies REST API of the ICES
  (International Council for the Exploration of the Sea) Vocabularies database
  <https://vocab.ices.dk/services/>.
It is a package that helps to estimate the number of real clusters in data as well as to identify atypical units. The underlying methods are based on distances rather than on unit x variables.
Calculate various information criteria in literature for "lm" and "glm" objects.
Generalized Odds Rate Hazards (GORH) model is a flexible model of fitting survival data, including the Proportional Hazards (PH) model and the Proportional Odds (PO) Model as special cases. This package fit the GORH model with interval censored data.
An implementation of 'Ichimoku Kinko Hyo', also commonly known as
    'cloud charts'. Static and interactive visualizations with tools for
    creating, backtesting and development of quantitative 'ichimoku' strategies.
    As described in Sasaki (1996, ISBN:4925152009), the technique is a refinement
    on candlestick charting, originating from Japan and now in widespread use in
    technical analysis worldwide. Translating as 'one-glance equilibrium chart',
    it allows the price action and market structure of financial securities to
    be determined 'at-a-glance'. Incorporates an interface with the OANDA
    fxTrade API <https://developer.oanda.com/> for retrieving historical and
    live streaming price data for major currencies, metals, commodities,
    government bonds and stock indices.
A GUI designed to support the analysis of financial-economic time
    series data.
We consider the non-parametric maximum likelihood estimation of the underlying distribution function, assuming log-concavity, based on mixed-case interval-censored data. The algorithm implemented is base on Chi Wing Chu, Hok Kan Ling and Chaoyu Yuan (2024, <doi:10.48550/arXiv.2411.19878>).
A variational Bayesian approach for fast integrative
    clustering and feature selection, facilitating the analysis of
    multi-view, mixed type, high-dimensional datasets with applications in
    fields like cancer research, genomics, and more.
Empirical Bayes variable selection via ICM/M algorithm for normal, binary logistic, and Cox's regression. The basic problem is to fit high-dimensional regression which sparse coefficients. This package allows incorporating the Ising prior to capture structure of predictors in the modeling process. More information can be found in the papers listed in the URL below.
Allows for the non-parametric estimation of transition intensities in interval-censored
    multi-state models using the approach of Gomon and Putter (2024) <doi:10.48550/arXiv.2409.07176> or 
    Gu et al. (2023) <doi:10.1093/biomet/asad073>.
Sieve semiparametric likelihood methods for analyzing 
 interval-censored failure time data from an outcome-dependent sampling (ODS) 
 design and from a case-cohort design. 
 Zhou, Q., Cai, J., and Zhou, H. (2018) <doi:10.1111/biom.12744>; 
 Zhou, Q., Zhou, H., and Cai, J. (2017)  <doi:10.1093/biomet/asw067>.
Single Layer Feed-forward Neural networks (SLFNs) have many applications in various fields of statistical modelling, especially for time-series forecasting. However, there are some major disadvantages of training such networks via the widely accepted 'gradient-based backpropagation' algorithm, such as convergence to local minima, dependencies on learning rate and large training time. These concerns were addressed by Huang et al. (2006) <doi:10.1016/j.neucom.2005.12.126>, wherein they introduced the Extreme Learning Machine (ELM), an extremely fast learning algorithm for SLFNs which randomly chooses the weights connecting input and hidden nodes and analytically determines the output weights of SLFNs. It shows good generalized performance, but is still subject to a high degree of randomness. To mitigate this issue, this package uses a dimensionality reduction technique given in Hyvarinen (1999) <doi:10.1109/72.761722>, namely, the Independent Component Analysis (ICA) to determine the input-hidden connections and thus, remove any sort of randomness from the algorithm. This leads to a robust, fast and stable ELM model. Using functions within this package, the proposed model can also be compared with an existing alternative based on the Principal Component Analysis (PCA) algorithm given by Pearson (1901) <doi:10.1080/14786440109462720>, i.e., the PCA based ELM model given by Castano et al. (2013) <doi:10.1007/s11063-012-9253-x>, from which the implemented ICA based algorithm is greatly inspired.
Implementation of icosahedral grids in three dimensions. The spherical-triangular tessellation can be set to create grids with custom resolutions. Both the primary triangular and their inverted penta-hexagonal grids can be calculated. Additional functions are provided that allow plotting of the grids and associated data, the interaction of the grids with other raster and vector objects, and treating the grids as a graphs.
Survival analysis of interval-censored data with proportional hazards, and an explicit smooth estimate of the baseline log-hazard with P-splines.
Reproducible, programmatic retrieval of datasets from the
    Inter-university Consortium for Political and Social Research archive.
Provides functions to compute and plot Krippendorff's inter-coder 
    reliability coefficient alpha and bootstrapped uncertainty estimates 
    (Krippendorff 2004, ISBN:0761915443). The bootstrap routines are set up to
    make use of parallel threads where supported.
Algorithms to construct simultaneous confidence intervals for the ranks of means mu_1,...,mu_n based on an independent Gaussian sample using multiple testing techniques.
Implements a modification to the Random Survival Forests algorithm for obtaining variable importance in high dimensional datasets. The proposed algorithm is appropriate for settings in which a silent event is observed through sequentially administered, error-prone self-reports or laboratory based diagnostic tests.  The modified algorithm incorporates a formal likelihood framework that accommodates sequentially administered, error-prone self-reports or laboratory based diagnostic tests. The original Random Survival Forests algorithm is modified by the introduction of a new splitting criterion based on a likelihood ratio test statistic.
Implementation of Tyler, Critchley, Duembgen and Oja's (JRSS B, 2009,
            <doi:10.1111/j.1467-9868.2009.00706.x>) and Oja, Sirkia and Eriksson's
            (AJS, 2006, <https://www.ajs.or.at/index.php/ajs/article/view/vol35,%20no2%263%20-%207>) method of two different
            scatter matrices to obtain an invariant coordinate system or independent
            components, depending on the underlying assumptions.
Implementation of tandem clustering with invariant coordinate 
              selection with different scatter matrices and several choices for the 
              selection of components as described in Alfons, A., Archimbaud, A., Nordhausen, K.and Ruiz-Gazen, A. (2022) <arXiv:2212.06108>.
Implements the Interval-Censored Sequence Kernel Association (ICSKAT) test for testing the association between interval-censored time-to-event outcomes and groups of single nucleotide polymorphisms (SNPs). Interval-censored time-to-event data occur when the event time is not known exactly but can be deduced to fall within a given interval. For example, some medical conditions like bone mineral density deficiency are generally only diagnosed at clinical visits. If a patient goes for clinical checkups yearly and is diagnosed at, say, age 30, then the onset of the deficiency is only known to fall between the date of their age 29 checkup and the date of the age 30 checkup. Interval-censored data include right- and left-censored data as special cases. This package also implements the interval-censored Burden test and the ICSKATO test, which is the optimal combination of the ICSKAT and Burden tests. Please see the vignette for a quickstart guide.
Tools for multivariate nonparametrics, as location tests based on marginal ranks, spatial median and spatial signs computation, Hotelling's T-test, estimates of shape are implemented.
Multivariate outlier detection is performed using invariant coordinates where the package offers different methods to choose the appropriate components. ICS is a general multivariate technique with many applications in multivariate analysis. ICSOutlier offers a selection of functions for automated detection of outliers in the data based on a fitted ICS object or by specifying the dataset and the scatters of interest. The current implementation targets data sets with only a small percentage of outliers.
The Iterative Cumulative Sum of Squares (ICSS) algorithm by Inclan/Tiao (1994) <https://www.jstor.org/stable/2290916> detects multiple change points, i.e. structural break points, in the variance of a sequence of independent observations. For series of moderate size (i.e. 200 observations and beyond), the ICSS algorithm offers results comparable to those obtained by a Bayesian approach or by likelihood ration tests, without the heavy computational burden required by these approaches.
Performs Invariant Coordinate Selection (ICS) (Tyler, Critchley, Duembgen and Oja (2009) <doi:10.1111/j.1467-9868.2009.00706.x>) and especially ICS for multivariate outlier detection with application to quality control (Archimbaud, Nordhausen, Ruiz-Gazen (2018) <doi:10.1016/j.csda.2018.06.011>) using a shiny app.
We construct the explicit form of clamped cubic interpolating spline (both uniform - knots are equidistant and non-uniform - knots are arbitrary). Using this form, we propose a linear regression model suitable for real data smoothing.
Currently using the proportional hazards (PH) model. More methods under other semiparametric regression models will be included in later versions.
For different linear dimension reduction methods like principal components analysis (PCA), independent components analysis (ICA) and supervised linear dimension reduction tests and estimates for the number of interesting components (ICs) are provided.
Functions for computing the global and local Gaussian density estimates based on the ICV bandwidth. See the article of Savchuk, O.Y., Hart, J.D., Sheather, S.J. (2010). Indirect cross-validation for density estimation. Journal of the American Statistical Association, 105(489), 415-423 <doi:10.1198/jasa.2010.tm08532>.
Functions for converting time series of spatial abundance or density 
    data in raster format to vector fields of population movement using the digital 
    image correlation technique. More specifically, the functions in the package 
    compute cross-covariance using discrete fast Fourier transforms for computational 
    efficiency. Vectors in vector fields point in the direction of highest two 
    dimensional cross-covariance. The package has a novel implementation of the 
    digital image correlation algorithm that is designed to detect persistent 
    directional movement when image time series extend beyond a sequence of 
    two raster images.
Computes and tests individual (species, phylogenetic and functional) diversity-area relationships, i.e., how species-, phylogenetic- and functional-diversity varies with spatial scale around the individuals of some species in a community. See applications of these methods in Wiegand et al. (2007) <doi:10.1073/pnas.0705621104> or Chacon-Labella et al. (2016) <doi:10.1007/s00442-016-3547-z>.
Provides datasets and functions for the class "Modelling and Data Analysis for Pharmaceutical Sciences". 
             The datasets can be used to present various methods of data analysis and statistical modeling.
             Functions for data visualization are also implemented.
Use R to make requests to the US Census Bureau's International Data Base API.
             Results are returned as R data frames.  For more information about the IDB API, visit
             <https://www.census.gov/data/developers/data-sets/international-database.html>.
The digits of the old version (before 2000 year) of 'Chinese ID Card Number' is 15, this package aims to update to the current version of 18 digits. Besides, this package can help check whether the given 'ID' is right or not.
Provides access to the 
    Idea Data Center (IDC) application for conducting 
    nonresponse bias analysis (NRBA). The IDC NRBA app is an
    interactive, browser-based Shiny application that can be used to 
    analyze survey data with respect to response rates,
    representativeness, and nonresponse bias. This app provides a user-friendly
    interface to statistical methods implemented by the 'nrba' package.
    Krenzke, Van de Kerckhove, and Mohadjer (2005) 
    <http://www.asasrms.org/Proceedings/y2005/files/JSM2005-000572.pdf>
    and Lohr and Riddles (2016) 
    <https://www150.statcan.gc.ca/n1/en/pub/12-001-x/2016002/article/14677-eng.pdf?st=q7PyNsGR>
    provide an overview of the statistical methods implemented in the application.
The Integro-Difference Equation model is a linear, dynamical model used to model
   phenomena that evolve in space and in time; see, for example, Cressie and Wikle (2011,
   ISBN:978-0-471-69274-4) or Dewar et al. (2009) <doi:10.1109/TSP.2008.2005091>. At the
   heart of the model is the kernel, which dictates how the process evolves from one time
   point to the next. Both process and parameter reduction are used to facilitate computation,
   and spatially-varying kernels are allowed. Data used to estimate the parameters are assumed
   to be readings of the process corrupted by Gaussian measurement error. Parameters are fitted
   by maximum likelihood, and estimation is carried out using an evolution algorithm.
When added to an existing shiny app, users may subset any
    developer-chosen R data.frame on the fly. That is, users are empowered to
    slice & dice data by applying multiple (order specific) filters using the
    AND (&) operator between each, and getting real-time updates on the number
    of rows effected/available along the way. Thus, any downstream processes
    that leverage this data source (like tables, plots, or statistical procedures)
    will re-render after new filters are applied. The shiny module’s user interface has
    a 'minimalist' aesthetic so that the focus can be on the data &
    other visuals. In addition to returning a reactive (filtered) data.frame,
    'IDEAFilter' as also returns 'dplyr' filter statements used to actually slice
    the data.
Time series plain text conversion and data visualization. It allows
    to transform IDEAM (Instituto de Hidrologia, Meteorologia y Estudios Ambientales)
    daily series from plain text to CSV files or data frames in R. Additionally,
    it is possible to obtain exploratory graphs from times series. IDEAM’s data
    is freely delivered under formal request through the official web page
    <http://www.ideam.gov.co/solicitud-de-informacion>.
A suite of convenient tools for social network analysis geared toward students, entry-level users, and non-expert practitioners. ‘ideanet’ features unique functions for the processing and measurement of sociocentric and egocentric network data. These functions automatically generate node- and system-level measures commonly used in the analysis of these types of networks. Outputs from these functions maximize the ability of novice users to employ network measurements in further analyses while making all users less prone to common data analytic errors. Additionally, ‘ideanet’ features an R Shiny graphic user interface that allows novices to explore network data with minimal need for coding.
Collection of tools to automate the processing of data collected though the IDEA4 method (see Zahm et al. (2018) <doi:10.1051/cagri/2019004> ). Starting from the original data collecting files this packages provides functions to compute IDEA indicators, draw modern and aesthetic plots, and produce a wide range of reporting materials.
Generates efficient designs for discrete choice experiments based on
              the multinomial logit model, and individually adapted designs for the mixed 
              multinomial logit model. The generated designs can be presented on screen
              and choice data can be gathered using a shiny application. Traets F, Sanchez G, 
              and Vandebroek M (2020) <doi:10.18637/jss.v096.i03>.
Interactive dendrogram that enables the user to select and
    color clusters, to zoom and pan the dendrogram, and to visualize
    the clustered data not only in a built-in heat map, but also in
    'GGobi' interactive plots and user-supplied plots. 
    This is a backport of Qt-based 'idendro' 
    (<https://github.com/tsieger/idendro>) to base R graphics and 
    Tcl/Tk GUI.
An implementation of various methods for estimating intrinsic
    dimension of vector-valued dataset or distance matrix. Most methods implemented
    are based on different notion of fractal dimension such as the capacity
    dimension, the box-counting dimension, and the information dimension.
Provides efficient implementation of the Isolate-Detect
    methodology for the consistent estimation of the number and location of multiple 
    change-points in one-dimensional data sequences from the "deterministic 
    + noise" model. For details on the Isolate-Detect methodology, please see Anastasiou and
    Fryzlewicz (2018) <https://docs.wixstatic.com/ugd/24cdcc_6a0866c574654163b8255e272bc0001b.pdf>.
    Currently implemented scenarios are: piecewise-constant signal with Gaussian
    noise, piecewise-constant signal with heavy-tailed noise, continuous piecewise-linear 
    signal with Gaussian noise, continuous piecewise-linear signal with heavy-tailed noise.
Intensity-duration-frequency (IDF) curves are a widely used analysis-tool
              in hydrology to assess extreme values of precipitation
              [e.g. Mailhot et al., 2007, <doi:10.1016/j.jhydrol.2007.09.019>].
              The package 'IDF' provides functions to estimate IDF parameters for given
              precipitation time series on the basis of a duration-dependent
              generalized extreme value distribution
              [Koutsoyiannis et al., 1998, <doi:10.1016/S0022-1694(98)00097-3>].
A joint mixture model has been developed by Majumdar et al. (2025) <doi:10.48550/arXiv.2412.17511> that integrates information from gene expression data and methylation data at the modelling stage to capture their inherent dependency structure, enabling simultaneous identification of differentially methylated cytosine-guanine dinucleotide (CpG) sites and differentially expressed genes. The model leverages a joint likelihood function that accounts for the nested structure in the data, with parameter estimation performed using an expectation-maximisation algorithm.
Fits covariate dependent partial correlation matrices for integrative models to identify differential networks between two groups. The methods are described in Class et. al., (2018) <doi:10.1093/bioinformatics/btx750> and Ha et. al., (2015) <doi:10.1093/bioinformatics/btv406>.
Plot idiograms of karyotypes, plasmids, circular chr. having a set of data.frames for chromosome data and optionally mark data. Two styles of chromosomes can be used: without or with visible chromatids. Supports micrometers, cM and Mb or any unit. Three styles of centromeres are available: triangle, rounded and inProtein; and six styles of marks are available: square (squareLeft), dots, cM (cMLeft), cenStyle, upArrow (downArrow), exProtein (inProtein); its legend (label) can be drawn inline or to the right of karyotypes. Idiograms can also be plotted in concentric circles. It is possible to calculate chromosome indices by Levan et al. (1964) <doi:10.1111/j.1601-5223.1964.tb01953.x>, karyotype indices of Watanabe et al. (1999) <doi:10.1007/PL00013869> and Romero-Zarco (1986) <doi:10.2307/1221906> and classify chromosomes by morphology Guerra (1986) and Levan et al. (1964).
Carry out comparative authorship analysis of disputed and undisputed texts within the Likelihood Ratio Framework for expressing evidence in forensic science. This package contains implementations of well-known algorithms for comparative authorship analysis, such as Smith and Aldridge's (2011) Cosine Delta <doi:10.1080/09296174.2011.533591> or Koppel and Winter's (2014) Impostors Method <doi:10.1002/asi.22954>, as well as functions to measure their performance and to calibrate their outputs into Log-Likelihood Ratios.
A personalized dynamic latent factor model (Zhang et al. (2024) <doi:10.1093/biomet/asae015>) for irregular multi-resolution time series data, to interpolate unsampled measurements from low-resolution time series.
Incremental Multiple Correspondence Analysis and Principal
    Component Analysis.
Interpreting the differences between mean scale scores across various
    forms of an assessment can be challenging. This difficulty arises from different
    mappings between raw scores and scale scores, complex mathematical relationships,
    adjustments based on judgmental procedures, and diverse equating functions applied
    to different assessment forms. An alternative method involves running simulations
    to explore the effect of incrementing raw scores on mean scale scores. The
    'idmact' package provides an implementation of this approach based on the
    algorithm detailed in Schiel (1998)
    <https://www.act.org/content/dam/act/unsecured/documents/ACT_RR98-01.pdf> which
    was developed to help interpret differences between mean scale scores on the
    American College Testing (ACT) assessment. The function idmact_subj() within
    the package offers a framework for running simulations on subject-level scores.
    In contrast, the idmact_comp() function provides a framework for conducting
    simulations on composite scores.
Utilities to work with data from the Internal Displacement
    Monitoring Centre (IDMC) (<https://www.internal-displacement.org/>),
    with convenient functions for loading events data from the IDMC API
    and transforming events data to daily displacement estimates.
Provides tools for assessment and quantification of individual identity information in animal signals. This package accompanies a research article by Linhart et al. (2019) <doi:10.1101/546143>: "Measuring individual identity information in animal signals: Overview and performance of available identity metrics".
Contains techniques for mining large and high-dimensional data
    sets by using the concept of Intrinsic Dimension (ID). Here the ID is
    not necessarily an integer. It is extended to fractal dimensions. And
    the Morisita estimator is used for the ID estimation, but other
    tools are included as well.
A systematic biology tool was developed to identify dysregulated miRNAs via a miRNA-miRNA interaction network. 'IDMIR' first constructed a weighted miRNA interaction network through integrating miRNA-target interaction information, molecular function data from Gene Ontology (GO) database and gene transcriptomic data in specific-disease context, and then, it used a network propagation algorithm on the network to identify significantly dysregulated miRNAs.
Most existing approaches for network reconstruction can only infer an overall network 
	and, also, fail to capture a complete set of network properties. To address these issues, 
	a new model has been developed, which converts static data into their 'dynamic' form. 
	'idopNetwork' is an 'R' interface to this model, it can inferring informative, dynamic, 
	omnidirectional and personalized networks. For more information on functional 
	clustering part, see Kim et al. (2008) <doi:10.1534/genetics.108.093690>, 
	Wang et al. (2011) <doi:10.1093/bib/bbr032>. For more information on our model, 
	see Chen et al. (2019) <doi:10.1038/s41540-019-0116-1>, and Cao et al. (2022) 
	<doi:10.1080/19490976.2022.2106103>.
A method to integrate molecular profiles of cancer patients (gene copy number and mRNA abundance) to 
	identify candidate gain of function alterations. These candidate alterations can be subsequently further tested  
	to discover cancer driver alterations. Briefly, this method tests of genomic correlates of mRNA dysregulation and prioritise 
	those where DNA gains/amplifications are associated with elevated mRNA expression of the same gene. For details see,
	Haider S et al. (2016) "Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia", Genome Biology, <https://pubmed.ncbi.nlm.nih.gov/27358048/>.
Implements a nonparametric maximum likelihood method for assessing 
  potentially time-varying vaccine efficacy (VE) against SARS-CoV-2 infection 
  under staggered enrollment and time-varying community transmission, allowing 
  crossover of placebo volunteers to the vaccine arm. 
  Lin, D. Y., Gu, Y., Zeng, D., Janes, H. E., and Gilbert, P. B. (2021) 
  <doi:10.1093/cid/ciab630>.
Different high-level graphics functions for displaying large datasets, displaying circular data in a very flexible way, finding local maxima, brewing color ramps, drawing nice arrows, zooming 2D-plots, creating figures with differently colored margin and plot region.  In addition, the package contains auxiliary functions for data manipulation like omitting observations with irregular values or selecting data by logical vectors, which include NAs. Other functions are especially useful in spectroscopy and analyses of environmental data: robust baseline fitting, finding peaks in spectra, converting humidity measures.
Functions to perform robust
		 nonparametric survival analysis with right censored 
		 data using a prior near-ignorant Dirichlet Process.
		 Mangili, F., Benavoli, A., de Campos, C.P., Zaffalon, M. (2015) <doi:10.1002/bimj.201500062>.
This is a package for estimating the copula mixture model and plotting correspondence curves. Details are in "Measuring reproducibility of high-throughput experiments" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779, by Li, Brown, Huang, and Bickel.
Generate random or human readable and pronounceable identifiers.
A fragmentation spectra detection pipeline for high-throughput LC/HRMS data processing using peaklists generated by the 'IDSL.IPA' workflow <doi:10.1021/acs.jproteome.2c00120>. The 'IDSL.CSA' package can deconvolute fragmentation spectra from Composite Spectra Analysis (CSA), Data Dependent Acquisition (DDA) analysis, and various Data-Independent Acquisition (DIA) methods such as MS^E, All-Ion Fragmentation (AIF) and SWATH-MS analysis. The 'IDSL.CSA' package was introduced in <doi:10.1021/acs.analchem.3c00376>.
The 'IDSL.FSA' package was designed to annotate standard .msp (mass spectra format) and .mgf (Mascot generic format) files using mass spectral entropy similarity, dot product (cosine) similarity, and normalized Euclidean mass error (NEME) followed by intelligent pre-filtering steps for rapid spectra searches. 'IDSL.FSA' also provides a number of modules to convert and manipulate .msp and .mgf files. The 'IDSL.FSA' workflow was integrated in the 'IDSL.CSA' and 'IDSL.NPA' packages introduced in <doi:10.1021/acs.analchem.3c00376>.
A multi-layered untargeted pipeline for high-throughput LC/HRMS data processing to extract signals of organic small molecules. The package performs ion pairing, peak detection, peak table alignment, retention time correction, aligned peak table gap filling, peak annotation and visualization of extracted ion chromatograms (EICs) and total ion chromatograms (TICs). The 'IDSL.IPA' package was introduced in <doi:10.1021/acs.jproteome.2c00120> .
A tiny parser to extract mass spectra data and metadata table of mass spectrometry acquisition properties from mzML, mzXML and netCDF files introduced in <doi:10.1021/acs.jproteome.2c00120>.
A pipeline to process nominal mass spectrometry data to create .msp files for untargeted analyses.
A simplified version of the 'IDSL.UFA' package to calculate isotopic profiles and adduct formulas from molecular formulas with no dependency on other R packages for online tools and educational mass spectrometry courses. The 'IDSL.SUFA' package also provides an ancillary module to process user-defined adduct formulas.
A pipeline to annotate chromatography peaks from the 'IDSL.IPA' workflow <doi:10.1021/acs.jproteome.2c00120> with molecular formulas of a prioritized chemical space using an isotopic profile matching approach. The 'IDSL.UFA' workflow only requires mass spectrometry level 1 (MS1) data for formula annotation. The 'IDSL.UFA' methods was described in <doi:10.1021/acs.analchem.2c00563> .
A pipeline to annotate a number of peaks from the 'IDSL.IPA' peaklists using an exhaustive chemical enumeration-based approach. This package can perform elemental composition calculations using the following 15 elements : C, B, Br, Cl, K, S, Si, N, H, As, F, I, Na, O, and P.
Implements various novel and standard clustering statistics and
  other analyses useful for understanding the spread of infectious disease.
Convert files to and from IDX format to vectors, matrices and arrays.
    IDX is a very simple file format designed for storing vectors and multidimensional matrices in
    binary format. The format is described on the website from Yann LeCun
    <http://yann.lecun.com/exdb/mnist/>.
A collection of Irucka Embry's miscellaneous USGS functions
    (processing .exp and .psf files, statistical error functions,
    "+" dyadic operator for use with NA, creating ADAPS and QW
    spreadsheet files, calculating saturated enthalpy). Irucka created these
    functions while a Cherokee Nation Technology Solutions (CNTS) United States
    Geological Survey (USGS) Contractor and/or USGS employee.
A collection of Irucka Embry's miscellaneous USGS data sets (USGS
    Parameter codes with fixed values, USGS global time zone codes, and US Air
    Force Global Engineering Weather Data). Irucka created these data sets
    while a Cherokee Nation Technology Solutions (CNTS) United States
    Geological Survey (USGS) Contractor and/or USGS employee.
A pair of functions for getting and setting the IEEE rounding 
  mode for floating point computations.
Integrated toolbox supporting common file formats used for intracranial 
    Electroencephalography (iEEG) and deep-brain stimulation (DBS) study.
An eclectic collection of short stories and poetry with topics on
    climate strange, connecting the geopolitical dots, the myth of us versus
    them, and the idiocy of war. Please refer to the COPYRIGHTS file and the
    text_citation.cff file for the reference copyright information and for the
    complete citations of the reference sources, respectively.
Computes characteristics of independent rainfall events (duration, total rainfall depth, and intensity) 
  extracted from a sub-daily rainfall time series based on the inter-event time definition (IETD) method. To have a 
  reference value of IETD, it also analyzes/computes IETD values through three methods: autocorrelation analysis, the 
  average annual number of events analysis, and coefficient of variation analysis. Ideal for analyzing the sensitivity 
  of IETD to characteristics of independent rainfall events.
  Adams B, Papa F (2000) <ISBN: 978-0-471-33217-6>.
  Joo J et al. (2014) <doi:10.3390/w6010045>.
  Restrepo-Posada P, Eagleson P (1982) <doi:10.1016/0022-1694(82)90136-6>.
Used in testing if the indirect effect from linear regression mediation analysis is equal to 0. Includes established methods such as the Sobel Test, Joint Significant test (maxP), and tests based off the distribution of the Product or Normal Random Variables. Additionally, this package adds more powerful tests based on Intersection-Union theory. These tests are the S-Test, the ps-test, and the ascending squares test. These new methods are uniformly more powerful than maxP, which is more powerful than Sobel and less anti-conservative than the Product of Normal Random Variables. These methods are explored by Kidd and Lin, (2024) <doi:10.1007/s12561-023-09386-6> and Kidd et al., (2025) <doi:10.1007/s10260-024-00777-7>.
Interface to the 'OpenGWAS' database API <https://api.opengwas.io/api/>. Includes a wrapper
    to make generic calls to the API, plus convenience functions for
    specific queries.
Tools, tutorials, and demos of Item Factor Analysis using 'OpenMx'.
    This software is described in Pritikin & Falk (2020) <doi:10.1177/0146621620929431>.
Contains several tools to treat imaging flow cytometry data from 'ImageStream®' and 'FlowSight®' cytometers ('Amnis®' 'Cytek®'). Provides an easy and simple way to read and write .fcs, .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved for each single cell. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize, manipulate and export 'IFC' data. Toy data example can be installed through the 'IFCdata' package of approximately 32 MB, which is available in a 'drat' repository <https://gitdemont.github.io/IFCdata/>. See file 'COPYRIGHTS' and file 'AUTHORS' for a list of copyright holders and authors.
Automatically detects Copy Number Variations (CNV) from Next Generation Sequencing data using a machine learning algorithm, Isolation forest. More details about the method can be found in the paper by Cabello-Aguilar (2022) <doi:10.1101/2022.01.03.474771>.
Provides utility functions to deal with Italian fiscal
    code ('codice fiscale').
Implements an S7 class for estimates based on influence functions. 
  Standard arithmetic operations are defined for the class.
Implementation of two multi-criteria decision making methods (MCDM): Intuitionistic Fuzzy Synthetic Measure (IFSM) and Intuitionistic Fuzzy Technique for Order of Preference by Similarity to Ideal Solution (IFTOPSIS) for intuitionistic fuzzy data sets for multi-criteria decision making problems. References describing the methods: Jefmański (2020) <doi:10.1007/978-3-030-52348-0_4>; Jefmański, Roszkowska, Kusterka-Jefmańska (2021) <doi:10.3390/e23121636>.
Download ifo business survey data and more time series from
    ifo institute <https://www.ifo.de/en/ifo-time-series>.
Compute onestep and multistep time series forecasts for machine learning models.
A suite for identifying causal models using relative concordances and identifying causal polymorphisms in case-control genetic association data, especially with large controls re-sequenced data.
Imputation of missing values using the last observation carried forward technique on Indonesia food prices data that is time series data. Also, this technique applies imputation to data whose dates do not appear directly. So that the series assumptions in the time series data are met.
Iterated Function Systems Estimator as in Iacus and La Torre (2005) <doi:10.1155/JAMDS.2005.33>.
This function predicts item response probabilities and item 
  responses using the item-focused tree model. The item-focused tree model
  combines logistic regression with recursive partitioning to detect 
  Differential Item Functioning in dichotomous items. The model applies 
  partitioning rules to the data, splitting it into homogeneous subgroups, and 
  uses logistic regression within each subgroup to explain the data. 
  Differential Item Functioning detection is achieved by examining potential 
  group differences in item response patterns. This method is useful for 
  understanding how different predictors, such as demographic or psychological 
  factors, influence item responses across subgroups.
Implements the "Smith-Pittman" community detection algorithm  
    for network analysis using 'igraph' objects. This algorithm combines node 
    degree and betweenness centrality measures to identify communities within 
    networks, with a gradient evident in social partitioning. The package 
    provides functions for community detection, visualization, and analysis of 
    the resulting community structure. Methods are based on results from Smith, 
    Pittman and Xu (2024) <doi:10.48550/arXiv.2411.01394>.
A dataset of the top colours of photos from Instagram 
 taken in 2014 in the city of Vancouver, British Columbia, Canada.
 It consists of: top colour and counts data. This data was
 obtained using the Instagram API. Instagram is a web photo 
 sharing service. It can be found at: <https://instagram.com>.
 The Instagram API is documented at: <https://instagram.com/developer/>.
Provides functions and a user-friendly console-based interface for the
    efficient use of the main function of the R package 'gapfill' to fill missing values of satellite
    images subsets. In addition to the R package documentation, the 'gapfill' methods are introduced in 
    Gerber et al. (2018) <doi:10.1109/TGRS.2017.2785240>.
Functions to calculate indices used to score immunoglobulin A (IgA) binding of bacteria in IgA sequencing (IgA-Seq) experiments.
  This includes the original Kau and Palm indices and more recent methods as described in Jackson et al. (2020) <doi:10.1101/2020.08.19.257501>.
  Additionally the package contains a function to simulate IgA-Seq data and an example experimental data set for method testing.
A collection of statistical tests for genetic association studies and summary data based Mendelian randomization.
An implementation of the initial guided analytics for parameter testing and
    controlband extraction framework. Functions are available for continuous and 
    categorical target variables as well as for generating standardized reports of the
    conducted analysis. See <https://github.com/stefan-stein/igate> for more information
    on the technology.
Develops a General Equilibrium (GE) Model, which estimates key variables such as wages, the number of residents and workers, the prices of the floor space, and its distribution between commercial and residential use, as in Ahlfeldt et al., (2015) <doi:10.3982/ECTA10876>. By doing so, the model allows understanding the economic influence of different urban policies.
Compute distributional quantities for an
    Integrated Gamma (IG) or Integrated Gamma Limit (IGL) copula, such
    as a cdf and density. Compute corresponding conditional quantities
    such as the cdf and quantiles. Generate
    data from an IG or IGL copula. See the vignette for formulas,
    or for a derivation, see Coia, V (2017) "Forecasting of Nonlinear 
    Extreme Quantiles Using Copula Models." PhD Dissertation, 
    The University of British Columbia.
Implements a wide range of metrics for measuring glucose control and glucose variability based on continuous glucose monitoring data. The list of implemented metrics is summarized in Rodbard (2009) <doi:10.1089/dia.2009.0015>. Additional visualization tools include time-series plots, lasagna plots and ambulatory glucose profile report.
Tools to extract information from the Intergovernmental
    Organizations ('IGO') Database , version 3, provided by the Correlates
    of War Project <https://correlatesofwar.org/>. See also Pevehouse, J.
    C. et al. (2020).  Version 3 includes information from 1815 to 2014.
Provides function to read data from the 'Igor Pro' data analysis
    program by 'Wavemetrics'. The data formats supported are 'Igor' packed 
    experiment format ('pxp') and 'Igor' binary wave ('ibw'). See: 
    <https://www.wavemetrics.com/> for details. Also includes functions to load 
    special 'pxp' files produced by the 'Igor Pro' 'Neuromatic' and 'Nclamp' 
    packages for recording and analysing neuronal data. See 
    <https://github.com/SilverLabUCL/NeuroMatic> for details.
Launches a shiny application generating code to
    view tables in several ways,
    import/export tables,
    modify tables,
    make some basic graphics.
  'IGoR' is a graphic user interface designed to help beginners
  using simple functions around table management and exploration.
  Inspired by 'Rcmdr', 'IGoR' is a code generator that, with simple inputs under a Shiny application,
  provides R code mainly built around the 'tidyverse' or some packages in the direct line of the Mosaic project:
  the 'rio' and 'ggformula' packages.
  The generated code doesn't depend on IGoR and can be manually modified by the user or copied elsewhere.
Convert between Irish grid references and Irish Grid coordinates. Irish grid 
    references can also be converted to or from an 'sf' object in any coordinate reference 
    system. Precisions from 1 m to 100 km including 2 km (tetrads) are supported, as are 
    datasets with mixed precision. Conversion to 'sf' polygons is precision-aware.
Routines for simple graphs and network analysis. It can
    handle large graphs very well and provides functions for generating
    random and regular graphs, graph visualization, centrality methods and
    much more.
A small collection of various network data sets,
    to use with the 'igraph' package: the Enron email network, various food webs,
    interactions in the immunoglobulin protein, the karate club network,
    Koenigsberg's bridges, visuotactile brain areas of the macaque monkey,
    UK faculty friendship network, domestic US flights network, etc.
Using 'shiny' to demo 'igraph' package makes learning graph theory easy and fun.
Versatile tools and data for graph matching analysis with various forms of prior information
    that supports working with 'igraph' objects, matrix objects, or lists of either.
This program facilitates exporting igraph graphs to the
        SoNIA file format
Interesting 'igraph' datasets from Melanie Walsh's sample social network datasets repository <https://github.com/melaniewalsh/sample-social-network-datasets>.
The 14th generation International Geomagnetic Reference Field (IGRF).
 A standard spherical harmonic representation of the Earth's main field.
To integrate multiple GSEA studies, we propose a hybrid strategy,
    iGSEA-AT, for choosing random effects (RE) versus fixed effect (FE) models,
    with an attempt to achieve the potential maximum statistical efficiency as 
    well as stability in performance in various practical situations. In addition
    to iGSEA-AT, this package also provides options to perform integrative GSEA
    with testing based on a FE model (iGSEA-FE) and testing based on a RE model
    (iGSEA-RE). The approaches account for different set sizes when testing a
    database of gene sets. The function is easy to use, and the three approaches
    can be applied to both binary and continuous phenotypes.
Mining informative genes with certain biological meanings are important for clinical diagnosis of disease and discovery of disease mechanisms in plants and animals. This process involves identification of relevant genes and removal of redundant genes as much as possible from a whole gene set. This package selects the informative genes related to a specific trait using gene expression dataset. These trait specific genes are considered as informative genes. This package returns the informative gene set from the high dimensional gene expression data using a combination of methods SVM and MRMR (for feature selection) with bootstrapping procedure.
Provides a set of tools to
  i) identify geographic areas with significant change over time in drug utilization, and 
  ii) characterize common change over time patterns among the time series for multiple geographic areas.
  For reference, see below:
    1. Song, J., Carey, M., Zhu, H., Miao, H., Ram´ırez, J. C., & Wu, H. (2018) <doi:10.1504/IJCBDD.2018.10011910>
    2. Wu, S., Wu, H. (2013) <doi:10.1186/1471-2105-14-6>
    3. Carey, M., Wu, S., Gan, G. & Wu, H. (2016) <doi:10.1016/j.idm.2016.07.001>.
Make complex, interactive heatmaps. 'iheatmapr' includes a modular 
    system for iteratively building up complex heatmaps, as well as the 
    iheatmap() function for making relatively standard heatmaps.
A set of tools for writing documents
    according to Geneva Graduate Institute conventions and regulations.
    The most common use is for writing and compiling theses or thesis
    chapters, as drafts or for examination with correct preamble formatting. 
    However, the package also offers users to create HTML presentation
    slides with 'xaringan', complete problem sets, format posters, and, 
    for course instructors, prepare a syllabus.
    The package includes additional functions for institutional color palettes,
    an institutional 'ggplot' theme, a function for counting manuscript words,
    and a bibliographical analysis toolkit.
Web scraping the <https://www.dallasfed.org> for
    up-to-date data on international house prices and exuberance
    indicators. Download data in tidy format.
Simulate an inhomogeneous self-exciting process (IHSEP), or Hawkes process, with a given (possibly time-varying) baseline intensity and an excitation function. Calculate the likelihood of an IHSEP with given baseline intensity and excitation functions for an (increasing) sequence of event times. Calculate the point process residuals (integral transforms of the original event times). Calculate the mean intensity process.
A novel machine learning method for plant viruses diagnostic using 
    genome sequencing data. This package includes three different machine 
    learning models, random forest, XGBoost, and elastic net, to train and 
    predict mapped genome samples. Mappability profile and unreliable regions 
    are introduced to the algorithm, and users can build a mappability profile 
    from scratch with functions included in the package. Plotting mapped sample 
    coverage information is provided.
Computes individual contributions to the overall Gini and 
    Theil's T and Theil's L measures and their decompositions by groups 
    such as race, gender, national origin, with the three functions of 
    iGini(), iTheiT(), and iTheilL(). For details, see Tim F. Liao (2019)
    <doi:10.1177/0049124119875961>.
The Importance Index (I.I.) can determine the loss and solution sources for a system in certain knowledge areas (e.g., agronomy), when production (e.g., fruits) is known (Demolin-Leite, 2021). Events (e.g., agricultural pest) can have different magnitudes (numerical measurements), frequencies, and distributions (aggregate, random, or regular) of event occurrence, and I.I. bases in this triplet (Demolin-Leite, 2021) <https://cjascience.com/index.php/CJAS/article/view/1009/1319>. Usually, the higher the magnitude and frequency of aggregated distribution, the greater the problem or the solution (e.g., natural enemies versus pests) for the system (Demolin-Leite, 2021). However, the final production of the system is not always known or is difficult to determine (e.g., degraded area recovery). A derivation of the I.I. is the percentage of Importance Index-Production Unknown (% I.I.-PU) that can detect the loss or solution sources, when production is unknown for the system (Demolin-Leite, 2024) <DOI:10.1590/1519-6984.253218>.
These datasets and functions accompany Wolfe and Schneider (2017) - Intuitive Introductory Statistics (ISBN:  978-3-319-56070-0) <doi:10.1007/978-3-319-56072-4>. They are used in the examples throughout the text and in the end-of-chapter exercises. The datasets are meant to cover a broad range of topics in order to appeal to the diverse set of interests and backgrounds typically present in an introductory Statistics class.
Time parceling method and Bayesian variability modeling methods for modeling within individual variability indicators as predictors.For more details, see <https://github.com/xliu12/IIVpredicitor>.
Provides a function to calculate infinite-jackknife-based
    standard errors for fixed effects parameters in 'brms' models, handling
    both clustered and independent data. 
    References: Ji et al. (2024) <doi:10.48550/arXiv.2407.09772>; Giordano et al. (2024) <doi:10.48550/arXiv.2305.06466>.
General purpose TIFF file I/O for R users.  Currently the
    only such package with read and write support for TIFF files with
    floating point (real-numbered) pixels, and the only package that can
    correctly import TIFF files that were saved from 'ImageJ' and write
    TIFF files than can be correctly read by 'ImageJ'
    <https://imagej.net/ij/>. Also supports text image I/O.
Simple handling of survey data. Smart handling of meta-information like e.g. variable-labels value-labels and scale-levels. Easy access and validation of meta-information. Useage of value labels and values respectively for subsetting and recoding data.
Convert irregularly spaced longitudinal data into regular intervals for further analysis, 
             and perform clustering using advanced machine learning techniques. 
             The package is designed for handling complex longitudinal datasets, 
             optimizing them for research in healthcare, demography, and other fields 
             requiring temporal data modeling.
It performs interlaboratory studies (ILS) to detect those
    laboratories that provide non-consistent results when comparing to others. It
    permits to work simultaneously with various testing materials, from standard
    univariate, and functional data analysis (FDA) perspectives. The univariate
    approach based on ASTM E691-08 consist of estimating the Mandel's h and
    k statistics to identify those laboratories that provide more significant
    different results, testing also the presence of outliers by Cochran and Grubbs
    tests, Analysis of variance (ANOVA) techniques are provided (F and Tuckey
    tests) to test differences in means corresponding to different laboratories per
    each material. Taking into account the functional nature of data retrieved in
    analytical chemistry, applied physics and engineering (spectra, thermograms,
    etc.). ILS package provides a FDA approach for finding the Mandel's k and h
    statistics distribution by smoothing bootstrap resampling.
Merges and downloads 'SPSS' data from different International Large-Scale Assessments (ILSA), including: Trends in International Mathematics and Science Study (TIMSS), Progress in International Reading Literacy Study (PIRLS), and others.
Calculates point estimates and standard errors using replicate weights and plausible values for International Large-Scale Assessments (ILSA), including: means, proportions, quantiles, correlations, singlelevel regressions, and multilevel regressions.
Linear regression when covariates include missing values by embedding the 
    correlation information between covariates. Especially for block missing data,
    it works well. 'ILSE' conducts imputation and regression simultaneously and iteratively. 
    More details can be referred to 
    Huazhen Lin, Wei Liu and Wei Lan. (2021) <doi:10.1080/07350015.2019.1635486>.
In view of the analysis of the structural characteristics of the multilayer network has been complete, however, there is still a lack of a unified operation that can quickly obtain the corresponding characteristics of the multilayer network. 
    To solve this insufficiency, 'ILSM' was designed for supporting calculating such metrics of multilayer networks by functions of this R package.
Provides functionality to perform a likelihood-free method for estimating the parameters of complex models
    that results in a simulated sample from the posterior distribution of model parameters given targets. The method begins
    with a accept/reject approximate bayes computation (ABC) step applied to a sample of points from the prior distribution
    of model parameters. Accepted points result in model predictions that are within the initially specified tolerance
    intervals around the target points. The sample is iteratively updated by drawing additional points from a mixture of
    multivariate normal distributions, accepting points within tolerance intervals. As the algorithm proceeds, the
    acceptance intervals are narrowed. The algorithm returns a set of points and sampling weights that account for the
    adaptive sampling scheme. For more details see Rutter, Ozik, DeYoreo, and Collier (2018) <arXiv:1804.02090>.
Improve optical character recognition by binarizing images. The package focuses primarily on local adaptive thresholding algorithms. 
    In English, this means that it has the ability to turn a color or gray scale image into a black and white image. This is particularly useful
    as a preprocessing step for optical character recognition or handwritten text recognition.
An implementation of the Canny Edge Detector for detecting edges in images. The package provides an interface to the algorithm available at <https://github.com/Neseb/canny>.
An implementation of the Unsupervised Smooth Contour Detection algorithm for digital images as described in the paper: "Unsupervised Smooth Contour Detection" by Rafael Grompone von Gioi, and Gregory Randall (2016). 
    The algorithm is explained at <doi:10.5201/ipol.2016.175>.
An implementation of the "FAST-9" corner detection algorithm explained in the paper 'FASTER and better: A machine learning approach to corner detection' by Rosten E., Porter R. and Drummond T. (2008), available at <arXiv:0810.2434>.
    The package allows to detect corners in digital images.
An implementation of the Harris Corner Detection as described in the paper "An Analysis and Implementation of the Harris Corner Detector" by Sánchez J. et al (2018) available at <doi:10.5201/ipol.2018.229>. 
    The package allows to detect relevant points in images which are characteristic to the digital image.
An open source library for face detection in images. 
    Provides a pretrained convolutional neural network based on <https://github.com/ShiqiYu/libfacedetection> which can be used to detect faces which have size greater than 10x10 pixels.
An implementation of the Line Segment Detector on digital images described in the paper: "LSD: A Fast Line Segment Detector with a False Detection Control" by Rafael Grompone von Gioi et al (2012). 
    The algorithm is explained at <doi:10.5201/ipol.2012.gjmr-lsd>.
An implementation of the Otsu's Image Segmentation Method described in the paper: "A C++ Implementation of Otsu's Image Segmentation Method". The algorithm is explained at <doi:10.5201/ipol.2016.158>.
The goal of 'image2data' is to extract images and return
    them into a data set, 
    especially for teaching data manipulation and data visualization. 
    Basically, the eponymous function takes an 
    image file ('png', 'tiff', 'jpeg', 'bmp') and turn it into a data set,
    pixels being rows (subjects) and columns (variables) being their coordinate positions (x- and y-axis) and their respective color (in hex codes). 
    The function can return a complete image or a range of color (i.e., contour, silhouette).
    The data can then be manipulated as would any data set by either creating other related variables (to hide the image) or as a genuine toy data set.
Note that 'imageData' has been superseded by 'growthPheno'. 
    The package 'growthPheno' incorporates all the functionality of 
    'imageData' and has functionality not available in 'imageData', 
    but some 'imageData' functions have been renamed.  
    The 'imageData' package is no longer maintained, but is retained 
    for legacy purposes.
Get image statistics based on processing fluency theory. The
    functions provide scores for several basic aesthetic principles that
    facilitate fluent cognitive processing of images: contrast,
    complexity / simplicity, self-similarity, symmetry, and typicality.
    See Mayer & Landwehr (2018) <doi:10.1037/aca0000187> and Mayer & Landwehr
    (2018) <doi:10.31219/osf.io/gtbhw> for the theoretical background of the methods.
Synthesize images into characteristic features for time-series analysis or machine learning applications.  The package was originally intended for monitoring volcanic eruptions in video data by highlighting and extracting regions above the vent associated with plume activity.  However, the functions within are general and have wide applications for image processing, analyzing, filtering, and plotting.
Fast image processing for images in up to 4 dimensions (two spatial
    dimensions, one time/depth dimension, one colour dimension). Provides most
    traditional image processing tools (filtering, morphology, transformations,
    etc.) as well as various functions for easily analysing image data using R. The
    package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image
    processing.
Provides advanced functions for image processing based on the package 'imager'.
Tools for manipulating, visualizing, and exporting raster images in R.
 Designed as an educational resource for students learning the basics of remote sensing,
 the package provides user-friendly functions to apply color ramps, export RGB composites,
 and create multi-frame visualizations. Built on top of the 'terra' and 'ggplot2' packages.
 See <https://github.com/ducciorocchini/imageRy> for more details and examples.
A general-purpose workflow for image segmentation using TensorFlow models based on the U-Net architecture by Ronneberger et al. (2015) <arXiv:1505.04597> and the U-Net++ architecture by Zhou et al. (2018) <arXiv:1807.10165>. We provide pre-trained models for assessing canopy density and understory vegetation density from vegetation photos. In addition, the package provides a workflow for easily creating model input and model architectures for general-purpose image segmentation based on grayscale or color images, both for binary and multi-class image segmentation.
Display a 2D-matrix data as a interactive zoomable gray-scale image viewer, providing tools for manual data inspection. The viewer window shows cursor guiding lines and a corresponding data slices for both axes at the current cursor position. A tool-bar allows adjusting image display brightness/contrast through WebGL filters and performing basic high-pass/low-pass filtering.
Simulate general insurance policies, losses and loss emergence. The functions contemplate 
  deterministic and stochastic policy retention and growth scenarios. Retention and growth rates are percentages relative
  to the expiring portfolio. Claims are simulated for each policy. This is accomplished either be assuming a frequency
  distribution per development lag or by generating random wait times until claim emergence and settlement. Loss simulation 
  uses standard loss distributions for claim amounts.
Provides fast application of image filters to data matrices,
    using R and C++ algorithms.
This is an Automatic Item Generator for Psychological Assessment. Items created with the 'IMak' package should not be used in applied settings as part of the working protocol without ensuring first that the items meet the required psychometric quality standards (see Blum & Holling, 2018) <DOI:10.3389/fpsyg.2018.01286>.
A model that provides researchers with a powerful tool for the classification
    and study of native corn by aiding in the identification of racial complexes
    which are fundamental to Mexico's agriculture and culture. This package has been
    developed based on data collected by "Proyecto Global de Maíces Nativos México",
    which has conducted exhaustive surveys across the country to document the
    qualitative and quantitative characteristics of different types of native maize.
    The trained model uses a robust and diverse dataset, enabling it to achieve an
    80% accuracy in classifying maize racial complexes. The characteristics included
    in the analysis comprise geographic location, grain and cob colors, as well as
    various physical measurements, such as lengths and widths.
Class imbalance usually damages the performance of classifiers. Thus, it is
             important to treat data before applying a classifier algorithm. This package
             includes recent resampling algorithms in the literature: (Barua et al. 2014)
             <doi:10.1109/tkde.2012.232>; (Das et al. 2015) <doi:10.1109/tkde.2014.2324567>,
             (Zhang et al. 2014) <doi:10.1016/j.inffus.2013.12.003>; (Gao et al. 2014)
             <doi:10.1016/j.neucom.2014.02.006>; (Almogahed et al. 2014)
             <doi:10.1007/s00500-014-1484-5>. It also includes an useful interface to
             perform oversampling.
Relocates oversampled data from a specific oversampling method to
    cover area determined by pure and proper class cover catch digraphs (PCCCD). 
    It prevents any data to be generated in class overlapping area.
    For more details, see the corresponding publication: 
    F. Sağlam (2025) <doi:10.1007/s10994-025-06755-8>.
Provides a set of fast, chainable image-processing operations
             which are applicable to images of two, three or four dimensions,
             particularly medical images.
Containerizes cytometry data and allows for S4 class structure to extend slots related to cell morphology, spatial coordinates, phenotype network information, and unique cellular labeling.
Cluster sampling is a valuable approach when constructing a comprehensive list of individual units is challenging. It provides operational and cost advantages. This package is designed to test the efficiency of cluster sampling in terms cluster variance and design effect in context to crop surveys. This package has been developed using the algorithm of Iqbal et al. (2018) <doi:10.19080/BBOAJ.2018.05.555673>.
Index of Multiple Deprivation for UK nations at various 
    geographical levels. In England, deprivation data is for Lower Layer Super
    Output Areas, Middle Layer Super Output Areas, Wards, and Local Authorities
    based on data from <https://www.gov.uk/government/statistics/english-indices-of-deprivation-2019>.
    In Wales, deprivation data is for Lower Layer Super Output Areas, Middle 
    Layer Super Output Areas, Wards, and Local Authorities based on data from
    <https://gov.wales/welsh-index-multiple-deprivation-full-index-update-ranks-2019>.
    In Scotland, deprivation data is for Data Zones, Intermediate Zones, and 
    Council Areas based on data from <https://simd.scot>. In Northern Ireland,
    deprivation data is for Super Output Areas and Local Government Districts
    based on data from <https://www.nisra.gov.uk/statistics/deprivation/northern-ireland-multiple-deprivation-measure-2017-nimdm2017>.
    The 'IMD' package also provides the composite UK index developed by
    <https://github.com/mysociety/composite_uk_imd>.
Provides API access to the <http://imdbapi.net> which maintains metadata
             about movies, games and television shows through a public API.
Theories are one of the most important tools of science. Although psychologists discussed problems of theory in their discipline for a long time, weak theories are still widespread in most subfields. 
    One possible reason for this is that psychologists lack the tools to systematically assess the quality of their theories. 
    Previously a computational model for formal theory evaluation based on the concept of explanatory coherence was developed (Thagard, 1989, <doi:10.1017/S0140525X00057046>). 
    However, there are possible improvements to this model and it is not available in software that psychologists typically use. 
    Therefore, a new implementation of explanatory coherence based on the Ising model is available in this R-package.
Implements likelihood based methods for mediation analysis.
A straightforward interface for accessing the IMF 
    (International Monetary Fund) data JSON API, 
    available at <https://data.imf.org/>. This package offers direct access to 
    the primary API endpoints: Dataflow, DataStructure, and CompactData. 
    And, it provides an intuitive interface for exploring available 
    dimensions and attributes, as well as querying individual time-series datasets. 
    Additionally, the package implements a rate limit on API calls to reduce the 
    chances of exceeding service limits (limited to 10 calls every 5 seconds) 
    and encountering response errors.
Tree height is an important dendrometric variable and forms the basis of vertical structure of a forest stand. This package will help to fit and validate various non-linear height diameter models for assessing the underlying relationship that exists between tree height and diameter at breast height in case of conifer trees. This package has been implemented on Naslund, Curtis, Michailoff, Meyer, Power, Michaelis-Menten and Wykoff non linear models using algorithm of  Huang et al.  (1992) <doi:10.1139/x92-172> and Zeide et al. (1993) <doi:10.1093/forestscience/39.3.594>.
Provides ability to create color palettes from image files. It 
    offers control over the type of color palette to derive from an image 
    (qualitative, sequential or divergent) and other palette properties.
    Quantiles of an image color distribution can be trimmed. Near-black or 
    near-white colors can be trimmed in RGB color space independent of trimming 
    brightness or saturation distributions in HSV color space. Creating 
    sequential palettes also offers control over the order of HSV color 
    dimensions to sort by. This package differs from other related packages 
    like 'RImagePalette' in approaches to quantizing and extracting colors in 
    images to assemble color palettes and the level of user control over 
    palettes construction.
Provides an interface for image recognition using the 'Google Vision API' <https://cloud.google.com/vision/> .  Converts API data for features such as object detection and optical character recognition to data frames. The package also includes functions for analyzing image annotations.
Estimating height of forest plant is one of the key challenges of recent times. This package will help to fit and validate AI (Artificial Intelligence) based machine learning algorithms for estimation of height of conifer trees based on diameter at breast height as explanatory variable using algorithm of Paul et al. (2022) <doi:10.1371/journal.pone.0270553>..
Provides flexible Bayesian estimation of Infinite Mixtures of Infinite Factor Analysers and related models, for nonparametrically clustering high-dimensional data, introduced by Murphy et al. (2020) <doi:10.1214/19-BA1179>. The IMIFA model conducts Bayesian nonparametric model-based clustering with factor analytic covariance structures without recourse to model selection criteria to choose the number of clusters or cluster-specific latent factors, mostly via efficient Gibbs updates. Model-specific diagnostic tools are also provided, as well as many options for plotting results, conducting posterior inference on parameters of interest, posterior predictive checking, and quantifying uncertainty.
A multivariate Gaussian mixture model framework to integrate multiple types of genomic data and allow modeling of inter-data-type correlations for association analysis. 'IMIX' can be implemented to test whether a disease is associated with genes in multiple genomic data types, such as DNA methylation, copy number variation, gene expression, etc. It can also study the integration of multiple pathways. 'IMIX' uses the summary statistics of association test outputs and conduct integration analysis for two or three types of genomics data. 'IMIX' features statistically-principled model selection, global FDR control and computational efficiency. Details are described in Ziqiao Wang and Peng Wei (2020) <doi:10.1093/bioinformatics/btaa1001>.
Interpretability methods to analyze the behavior and
    predictions of any machine learning model.  Implemented methods are:
    Feature importance described by Fisher et al. (2018)
    <doi:10.48550/arxiv.1801.01489>, accumulated local effects plots described by Apley
    (2018) <doi:10.48550/arxiv.1612.08468>, partial dependence plots described by
    Friedman (2001) <www.jstor.org/stable/2699986>, individual conditional
    expectation ('ice') plots described by Goldstein et al.  (2013)
    <doi:10.1080/10618600.2014.907095>, local models (variant of 'lime')
    described by Ribeiro et. al (2016) <doi:10.48550/arXiv.1602.04938>, the Shapley
    Value described by Strumbelj et. al (2014)
    <doi:10.1007/s10115-013-0679-x>, feature interactions described by
    Friedman et. al <doi:10.1214/07-AOAS148> and tree surrogate models.
Send emails using the 'mailgun' api. To use this package you will need an account from <https://www.mailgun.com> .
Toolkit for Poly-pharmacology Research of Traditional Chinese Medicine. Based on the
    biological descriptors and drug-disease interaction networks, it can
    analyze the potential poly-pharmacological mechanisms of Traditional Chinese Medicine and be
    used for drug-repositioning in Traditional Chinese Medicine.
Implements some item response models for multiple
    ratings, including the hierarchical rater model, 
    conditional maximum likelihood estimation of linear 
    logistic partial credit model and a wrapper function
    to the commercial FACETS program. See Robitzsch and
    Steinfeld (2018) for a description of the functionality
    of the package. 
    See Wang, Su and Qiu (2014; <doi:10.1111/jedm.12045>)
    for an overview of modeling alternatives.
Based on large margin principle, this package performs feature selection methods: "IM4E"(Iterative Margin-Maximization under Max-Min Entropy Algorithm); "Immigrate"(Iterative Max-Min Entropy Margin-Maximization with Interaction Terms Algorithm); "BIM"(Boosted version of IMMIGRATE algorithm); "Simba"(Iterative Search Margin Based Algorithm); "LFE"(Local Feature Extraction Algorithm). This package also performs prediction for the above feature selection methods.
Fitting and validation of machine learning algorithms
             for volume prediction of trees, currently for conifer trees based on
			 diameter at breast height and height as explanatory variables.
A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell
    T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and
    visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq)
    and single-cell sequencing (scRNAseq). Immunarch implements most of the widely used AIRR analysis methods,
    such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes
    and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor
    databases and clonotype tracking in vaccination and cancer studies. A successor to our
    previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.
Used for analyzing immune responses and predicting vaccine efficacy using machine learning and advanced data processing techniques. 'Immunaut' integrates both unsupervised and supervised learning methods, managing outliers and capturing immune response variability. It performs multiple rounds of predictive model testing to identify robust immunogenicity signatures that can predict vaccine responsiveness. The platform is designed to handle high-dimensional immune data, enabling researchers to uncover immune predictors and refine personalized vaccination strategies across diverse populations.
Provides a unified data layer for single-cell, spatial and bulk
 T-cell and B-cell immune receptor repertoire data, integrating diverse 
 data formats such as AIRR and raw sequencing files. Includes utilities for 
 receptor aggregation, metadata normalization, and clonotype filtering.
A comprehensive toolkit for clinical Human Leukocyte Antigen (HLA) informatics, built on 'tidyverse' <https://tidyverse.tidyverse.org/> principles and making use of genotype list string (GL string, Mack et al. (2023) <doi:10.1111/tan.15126>) for storing and computing HLA genotype data.  Specific functionalities include: coercion of HLA data in tabular format to and from GL string; calculation of matching and mismatching in all directions, with multiple output formats; automatic formatting of HLA data for searching within a GL string; truncation of molecular HLA data to a specific number of fields; and reading HLA genotypes in HML files and extracting the GL string.
It offers a sophisticated and versatile tool for creating and evaluating artificial intelligence based neural network models tailored for regression analysis on datasets with continuous target variables. Leveraging the power of neural networks, it allows users to experiment with various hidden neuron configurations across two layers, optimizing model performance through "5 fold"" or "10 fold"" cross validation. The package normalizes input data to ensure efficient training and assesses model accuracy using key metrics such as R squared (R2), Root Mean Square Error (RMSE), Mean Absolute Error (MAE), and Percentage Error (PER). By storing and visualizing the best performing models, it provides a comprehensive solution for precise and efficient regression modeling making it an invaluable tool for data scientists and researchers aiming to harness AI for predictive analytics.
Neural network has potential in forestry modelling. This package is designed to create and assess Artificial Intelligence based Neural Networks with varying architectures for prediction of volume of forest trees using two input features: height and diameter at breast height, as they are the key factors in predicting volume, therefore development and validation of efficient volume prediction neural network model is necessary. This package has been developed using the algorithm of Tabassum et al. (2022) <doi:10.18805/ag.D-5555>.
Allows easy creation of CSS layouts (grid and flexbox)
  directly from R without added CSS.
Contains functions for evaluating & comparing the performance of Binary classification models. Functions can be called either statically or interactively (as Shiny Apps).
Functions to analyse missing value mechanisms and to impute data sets in the context of bottom-up MS-based proteomics.
Implement a multivariate analysis of the impact of items to identify a bias in the questionnaire validation of Likert-type scale variables. The items requires considering a null value (category doesn't have tendency). Offering frequency, importance and impact of the items.
A non-parametric effect size measure capturing changes in central tendency or shape of data distributions. The package provides the necessary functions to calculate and plot the Impact effect size measure between two groups.
Implements the compartment model from Tokars (2018) 
  <doi:10.1016/j.vaccine.2018.10.026>. This enables quantification of 
  population-wide impact of vaccination against vaccine-preventable 
  diseases such as influenza.
Functions to read, process and analyse accelerometer
    data related to mechanical loading variables. This package is
    developed and tested for use with raw accelerometer data from
    triaxial 'ActiGraph' <https://theactigraph.com> accelerometers.
Imputing blockwise missing data by imprecise imputation,
    featuring a domain-based, variable-wise, and case-wise strategy. 
    Furthermore, the estimation of lower and upper bounds for 
    unconditional and conditional probabilities based on the obtained
    imprecise data is implemented.
    Additionally, two utility functions are supplied: one to check 
    whether variables in a data set contain set-valued observations;
    and another to merge two already imprecisely imputed data. 
    The method is described in a technical report by Endres, Fink and
    Augustin (2018, <doi:10.5282/ubm/epub.42423>).
Support for implicit expansion of arrays in operations involving
    arrays of mismatching sizes. This pattern is known as "broadcasting" in
    'Python' and  "implicit expansion" in 'Matlab' and is explained for example in
    the article "Array programming with NumPy" by C. R. Harris et al. (2020)
    <doi:10.1038/s41586-020-2649-2>.
A tool for computing the scores for the Implicit Association Test 
    (IAT; Greenwald, McGhee & Schwartz (1998) <doi:10.1037/0022-3514.74.6.1464>) 
    and the Single Category-IAT (SC-IAT: Karpinski & Steinman 
    (2006) <doi:10.1037/0022-3514.91.1.16>). Functions for preparing the data 
    (both for the IAT and the SC-IAT), plotting the results, and obtaining a 
    table with the scores of implicit measures descriptive statistics are 
    provided.
Convert between bookmaker odds and probabilities. Eight different
    algorithms are available, including basic normalization, Shin's method 
    (Hyun Song Shin, (1992) <doi:10.2307/2234526>), and others.
'SQL' back-end to 'dplyr' for Apache Impala, the massively
    parallel processing query engine for Apache 'Hadoop'. Impala enables
    low-latency 'SQL' queries on data stored in the 'Hadoop' Distributed
    File System '(HDFS)', Apache 'HBase', Apache 'Kudu', Amazon Simple 
    Storage Service '(S3)', Microsoft Azure Data Lake Store '(ADLS)', 
    and Dell 'EMC' 'Isilon'. See <https://impala.apache.org> for more
    information about Impala.
Alternative mechanism for importing objects from packages
    and R modules. The syntax allows for importing multiple objects with a single
    command in an expressive way. The import package bridges some of the gap
    between using library (or require) and direct (single-object) imports.
    Furthermore the imported objects are not placed in the current environment.
The Percentage of Importance Indice (Percentage_I.I.) bases in magnitudes, frequencies, and distributions of occurrence of an event (DEMOLIN-LEITE, 2021) <http://cjascience.com/index.php/CJAS/article/view/1009/1350>. This index can detect the key loss sources (L.S) and solution sources (S.S.), classifying them according to their importance in terms of loss or income gain, on the productive system. The Percentage_I.I. = [(ks1 x c1 x ds1)/SUM (ks1 x c1 x ds1) + (ks2 x c2 x ds2) + (ksn x cn x dsn)] x 100. key source (ks) is obtained using simple regression analysis and magnitude (abundance). Constancy (c) is SUM of occurrence of L.S. or S.S. on the samples (absence = 0 or presence = 1), and distribution source (ds) is obtained using chi-square test. This index has derivations: i.e., i) Loss estimates and solutions effectiveness and ii) Attention and non-attention levels (DEMOLIN-LEITE,2024) <DOI: 10.1590/1519-6984.253215>.
Enables 'Python'-like importing/loading of packages or functions
    with aliasing to prevent namespace conflicts.
Import and export data from the most common statistical formats by using 
	     R functions that guarantee the least loss of the data information, giving special
	     attention to the date variables and the labelled ones.
Download and manage data sets of statistical projects and geographic data created by Instituto Nacional de Estadistica y Geografia (INEGI). See <https://www.inegi.org.mx/>.
An imprecise inference presented in the study of Walley (1996) <doi:10.1111/j.2517-6161.1996.tb02065.x> is one of the statistical reasoning methods when prior information is unavailable. Functions and utils needed for illustrating this inferential paradigm are implemented for classroom teaching and further comprehensive research. Two imprecise models are demonstrated using multinomial data and 2x2 contingency table data. The concepts of prior ignorance and imprecision are discussed in lower and upper probabilities. Representation invariance principle, hypothesis testing, decision-making, and further generalization are also illustrated.
Provides color palettes from Impressionism and post-Impressionism artworks. This package allows to select colors combinations while looking at the original paintings where colors were sampled from.
Reconstruct birth-year specific probabilities of immune imprinting to influenza A, using the methods of Gostic et al. (2016) <doi:10.1126/science.aag1322>. Plot, save, or export the calculated probabilities for use in your own research. By default, the package calculates subtype-specific imprinting probabilities, but with user-provided frequency data, it is possible to calculate probabilities for arbitrary kinds of primary exposure to influenza A, including primary vaccination and exposure to specific clades, strains, etc.
A variety of improved shrinkage estimators in the area of statistical analysis: unrestricted; restricted; preliminary test; improved preliminary test; Stein; and positive-rule Stein. More details can be found in chapter 7 of Saleh, A. K. Md. E. (2006) <ISBN: 978-0-471-56375-4>.
Creation of imprecise classification trees. They rely on
    probability estimation within each node by means of either the
    imprecise Dirichlet model or the nonparametric predictive
    inference approach. The splitting variable is selected by the
    strategy presented in Fink and Crossman (2013)
    <http://www.sipta.org/isipta13/index.php?id=paper&paper=014.html>,
    but also the original imprecise information gain of Abellan and
    Moral (2003) <doi:10.1002/int.10143> is covered.
Missing values often occur in financial data due to a variety 
    of reasons (errors in the collection process or in the processing stage, 
    lack of asset liquidity, lack of reporting of funds, etc.). However, 
    most data analysis methods expect complete data and cannot be employed 
    with missing values. One convenient way to deal with this issue without 
    having to redesign the data analysis method is to impute the missing 
    values. This package provides an efficient way to impute the missing 
    values based on modeling the time series with a random walk or an 
    autoregressive (AR) model, convenient to model log-prices and log-volumes 
    in financial data. In the current version, the imputation is 
    univariate-based (so no asset correlation is used). In addition,
    outliers can be detected and removed.
    The package is based on the paper:
    J. Liu, S. Kumar, and D. P. Palomar (2019). Parameter Estimation of 
    Heavy-Tailed AR Model With Missing Data Via Stochastic EM. IEEE Trans. on 
    Signal Processing, vol. 67, no. 8, pp. 2159-2172. <doi:10.1109/TSP.2019.2899816>.
The general workflow of most imputation methods is quite
    similar. The aim of this package is to provide parts of this general
    workflow to make the implementation of imputation methods easier. The
    heart of an imputation method is normally the used model. These models
    can be defined using the 'parsnip' package or customized
    specifications. The rest of an imputation method are more technical
    specification e.g. which columns and rows should be used for
    imputation and in which order. These technical specifications can be
    set inside the imputation functions.
A collection of functions for left-censored missing data imputation. Left-censoring is a special case of missing not at random (MNAR)  mechanism that generates non-responses in proteomics experiments. The package also contains functions to artificially generate peptide/protein expression data (log-transformed) as random draws from a multivariate Gaussian distribution as well as a function to generate missing data (both randomly and non-randomly). For comparison reasons, the package also contains several wrapper functions for the imputation of non-responses that are missing at random. * New functionality has been added: a hybrid method that allows the imputation of missing values in a more complex scenario where the missing data are both MAR and MNAR.
Imputation of longitudinal categorical covariates. We use a methodological framework which ensures that the plausibility of transitions is preserved, overfitting and colinearity issues are resolved, and confounders can be utilized. See Mamouris (2023) <doi:10.1002/sim.9919> for an overview.
Compute missing values on a training data set and impute them on a new data set. Current available options are median/mode and random forest.
Implements imputation methods using EM and Data Augmentation for
    multinomial data following the work of Schafer 1997 <ISBN: 978-0-412-04061-0>.
Multivariate Expectation-Maximization (EM) based imputation framework that offers several different algorithms. These include regularisation methods like Lasso and Ridge regression, tree-based models and dimensionality reduction methods like PCA and PLS.
Set of functions to impute missing rare earth data, calculate La 
    and Pr concentrations and Ce anomalies in zircons based on the
    Chondrite-Onuma and Chondrite-Lattice of Carrasco-Godoy and 
    Campbell (2023) <doi:10.1007/s00410-023-02025-9> and the Logarithmic regression from  
    Zhong et al. (2019) <doi:10.1007/s00710-019-00682-y>.
Provides new imputation methods for the 'mice' package based on generalized additive models for location, scale, and shape (GAMLSS) as described in de Jong, van Buuren and Spiess <doi:10.1080/03610918.2014.911894>.
Provides a test bench for the comparison of missing data imputation 
    methods in uni-variate time series. Imputation methods are compared using 
    different error metrics. Proposed imputation methods and alternative error 
    metrics can be used.
Imputation (replacement) of missing values 
             in univariate time series. 
             Offers several imputation functions
             and missing data plots. 
             Available imputation algorithms include: 
            'Mean', 'LOCF', 'Interpolation', 
            'Moving Average', 'Seasonal Decomposition', 
            'Kalman Smoothing on Structural Time Series models',
            'Kalman Smoothing on ARIMA models'. Published in Moritz and Bartz-Beielstein (2017) 
            <doi:10.32614/RJ-2017-009>.
This software does Multi-Reader, Multi-Case (MRMC) analyses of data from imaging studies where clinicians (readers) evaluate patient images (cases). What does this mean? ... Many imaging studies are designed so that every reader reads every case in all modalities, a fully-crossed study. In this case, the data is cross-correlated, and we consider the readers and cases to be cross-correlated random effects. An MRMC analysis accounts for the variability and correlations from the readers and cases when estimating variances, confidence intervals, and p-values. The functions in this package can treat arbitrary study designs and studies with missing data, not just fully-crossed study designs. An overview of this software, including references presenting details on the methods, can be found here: <https://www.fda.gov/medical-devices/science-and-research-medical-devices/imrmc-software-do-multi-reader-multi-case-statistical-analysis-reader-studies>.
Estimate the relative abundance of tissue-infiltrating immune subpopulations abundances using gene expression data.
A toolkit for causal inference in experimental and observational 
    studies. Implements various simple Bayesian models including linear, 
    negative binomial, and logistic regression for impact estimation. 
    Provides functionality for randomization and checking baseline equivalence 
    in experimental designs. The package aims to simplify the process of 
    impact measurement for researchers and analysts across different fields. 
    Examples and detailed usage instructions are available at 
    <https://book.martinez.fyi>.
Implementation of the information matrix test for generalized partial credit models.
Estimate the orientation of an inertial measurement unit 
    (IMU) with a 3-axis accelerometer and a 3-axis gyroscope using a 
    complementary filter. 'imuf' takes an IMU's accelerometer and gyroscope 
    readings, time duration, its initial orientation, and a gain factor as 
    inputs, and returns an estimate of the IMU's final orientation.
Volume prediction is one of challenging task in forestry research. This package is a comprehensive toolset designed for the fitting and validation of various linear and nonlinear allometric equations (Linear, Log-Linear, Inverse, Quadratic, Cubic, Compound, Power and Exponential) used in the prediction of conifer tree volume. This package is particularly useful for forestry professionals, researchers, and resource managers engaged in assessing and estimating the volume of coniferous trees. This package has been developed using the algorithm of Sharma et al. (2017) <doi:10.13140/RG.2.2.33786.62407>.
Partitioning clustering algorithms divide data sets into k subsets or partitions so-called clusters. They require some initialization procedures for starting the algorithms. Initialization of cluster prototypes is one of such kind of procedures for most of the partitioning algorithms. Cluster prototypes are the centers of clusters, i.e. centroids or medoids, representing the clusters in a data set. In order to initialize cluster prototypes, the package 'inaparc' contains a set of the functions that are the implementations of several linear time-complexity and loglinear time-complexity methods in addition to some novel techniques. Initialization of fuzzy membership degrees matrices is another important task for starting the probabilistic and possibilistic partitioning algorithms. In order to initialize membership degrees matrices required by these algorithms, a number of functions based on some traditional and novel initialization techniques are also available in the package 'inaparc'.
A framework for analysing inbreeding and heterozygosity-fitness
    correlations (HFCs) based on microsatellite and SNP markers.
Specific functions are provided for rounding real weights to integers and performing an integer programming algorithm for calibration problems. These functions are useful for census-weights adjustments, survey calibration, or for performing linear regression with integer parameters <https://www.nass.usda.gov/Education_and_Outreach/Reports,_Presentations_and_Conferences/reports/New_Integer_Calibration_%20Procedure_2016.pdf>. This research was supported in part by the U.S. Department of Agriculture, National Agriculture Statistics Service. The findings and conclusions in this publication are those of the authors and should not be construed to represent any official USDA, or US Government determination or policy.
Offers a pipe-friendly alternative to the 'dplyr' functions
    case_when() and if_else(), as well as a number of user-friendly
    simplifications for common use cases.  These functions accept a vector
    as an optional first argument, allowing conditional statements to be
    built using the 'magrittr' dot operator.  The functions also coerce
    all outputs to the same type, meaning you no longer have to worry
    about using specific typed variants of NA or explicitly declaring
    integer outputs, and evaluate outputs somewhat lazily, so you don't
    waste time on long operations that won't be used.
The Dynamic Time Warping (DTW) distance measure for time series allows non-linear alignments of time series to match  similar patterns in time series of different lengths and or different speeds. IncDTW is characterized by (1) the incremental calculation of DTW (reduces runtime complexity to a linear level for updating the DTW distance) - especially for life data streams or subsequence matching, (2) the vector based implementation of DTW which is faster because no matrices are allocated (reduces the space complexity from a quadratic to a linear level in the number of observations) - for all runtime intensive DTW computations, (3) the subsequence matching algorithm runDTW, that efficiently finds the k-NN to a query pattern in a long time series, and (4) C++ in the heart. For details about DTW see the original paper "Dynamic programming algorithm optimization for spoken word recognition" by Sakoe and Chiba (1978) <DOI:10.1109/TASSP.1978.1163055>. For details about this package, Dynamic Time Warping and Incremental Dynamic Time Warping please see "IncDTW: An R Package for Incremental Calculation of Dynamic Time Warping" by Leodolter et al. (2021) <doi:10.18637/jss.v099.i09>.
An efficient and incremental approach for calculating 
    the differences in orbit counts when performing single edge modifications 
    in a network. Calculating the differences in orbit counts is much more efficient than
    recalculating all orbit counts from scratch for each time point.
Provides functions and classes to compute, handle and visualise
  incidence from dated events for a defined time interval. Dates can be provided
  in various standard formats. The class 'incidence' is used to store computed
  incidence and can be easily manipulated, subsetted, and plotted. In addition,
  log-linear models can be fitted to 'incidence' objects using 'fit'. This
  package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit
  for outbreak analysis.
Provides functions and classes to compute, handle and visualise 
  incidence from dated events for a defined time interval. Dates can be 
  provided in various standard formats. The class 'incidence2' is used to store
  computed incidence and can be easily manipulated, subsetted, and plotted.
Calculate incidence and prevalence using data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model. Incidence and prevalence can be estimated for the total population in a database or for a stratification cohort.
Make empirical Bayes incidence curves from reported case data using a specified delay distribution.
Functions to generate incidence matrices and bipartite graphs that have (1) a fixed fill rate, (2) given marginal sums, (3) marginal sums that follow given distributions, or (4) represent bill sponsorships in the US Congress <doi:10.31219/osf.io/ectms>. It can also generate an incidence matrix from an adjacency matrix, or bipartite graph from a unipartite graph, via a social process mirroring team, group, or organization formation <doi:10.48550/arXiv.2204.13670>.
Implements a variety of nonparametric and parametric methods that are commonly used when the data set is a mixture of paired observations and independent samples. The package also calculates and returns values of different tests with their corresponding p-values.
    Bhoj, D. S. (1991) <doi:10.1002/bimj.4710330108> "Testing equality of means in the presence of correlation and missing data".
    Dubnicka, S. R., Blair, R. C., and Hettmansperger, T. P. (2002) <doi:10.22237/jmasm/1020254460> "Rank-based procedures for mixed paired and two-sample designs".
    Einsporn, R. L. and Habtzghi, D. (2013) <https://pdfs.semanticscholar.org/89a3/90bafeb2bc41ed4414533cfd5ab84a6b54b6.pdf> "Combining paired and two-sample data using a permutation test".
    Ekbohm, G. (1976) <doi:10.1093/biomet/63.2.299> "On comparing means in the paired case with incomplete data on both responses".
    Lin, P. E. and Stivers, L. E. (1974) <doi:10.1093/biomet/61.2.325> On difference of means with incomplete data".
    Maritz, J. S. (1995) <doi:10.1111/j.1467-842x.1995.tb00649.x> "A permutation paired test allowing for missing values".
Suite of functions to study animal incubation.
    At the core of incR 
    lies an algorithm that allows for the scoring of 
    incubation behaviour. Additionally, several functions 
    extract biologically relevant metrics of incubation such as off-bout number 
    and off-bout duration - for a review of avian incubation studies, 
    see Nests, Eggs, and Incubation: New ideas about avian reproduction (2015) 
    edited by D. Charles Deeming and S. James Reynolds <doi:10.1093/acprof:oso/9780198718666.001.0001>.
Tools for estimating incidence from biomarker data in cross-
    sectional surveys, and for calibrating tests for recent infection. 
    Implements and extends the method of Kassanjee et al. (2012)
    <doi:10.1097/EDE.0b013e3182576c07>.
Fit parametric models for time-to-event data that show an initial
    'incubation period', i.e., a variable delay phase where the hazard is zero. The
    delayed Weibull distribution serves as foundational data model. The
    specific method of 'MPSE' (maximum product of spacings estimation) and MLE-based methods are used for parameter
    estimation. Bootstrap confidence intervals for parameters and significance
    tests in a two group setting are provided.
A 'shiny' app that supports both dual and bulk RNA-seq, with the dual
    RNA-seq functionality offering the flexibility to perform either a
    sequential approach (where reads are mapped separately to each genome)
    or a combined approach (where reads are aligned to a single merged
    genome). The user-friendly interface automates the analysis process,
    providing step-by-step guidance, making it easy for users to navigate
    between different analysis steps, and download intermediate results
    and publication-ready plots.
Genome-wide gene insertion and deletion rates can be modelled in a maximum 
    likelihood framework with the additional flexibility of modelling potential missing 
    data using the models included within. These models simultaneously estimate insertion 
    and deletion (indel) rates of gene families and proportions of "missing" data for 
    (multiple) taxa of interest. The likelihood framework is utilized for parameter 
    estimation. A phylogenetic tree of the taxa and gene presence/absence patterns 
    (with data ordered by the tips of the tree) are required. See Dang et al.
    (2016) <doi:10.1534/genetics.116.191973> for more details.
Estimates weights to make a continuous-valued exposure statistically independent of a vector of pre-treatment covariates using the method proposed in Huling, Greifer, and Chen (2021) <arxiv:2107.07086>.
Implementations of the weighted Kozachenko-Leonenko entropy estimator and independence tests based on this estimator, (Kozachenko and Leonenko (1987) <http://mi.mathnet.ru/eng/ppi797>). Also includes a goodness-of-fit test for a linear model which is an independence test between covariates and errors.
Extract and replace elements using indices that start from zero (rather than one), as is common in mathematical notation and other programming languages.
Derivation of indexes for benchmarking purposes. A methodology with flexible number of constituents is implemented. Also functions for market capitalization and volume weighted indexes with fixed number of constituents are available. The main function of the package, indexComp(), provides the derived index, suitable for analysis purposes. The functions indexUpdate(), indexMemberSelection() and indexMembersUpdate() are components of indexComp() and enable one to construct and continuously update an index, e.g. for display on a website. The methodology behind the functions provided gets introduced in Trimborn and Haerdle (2018) <doi:10.1016/j.jempfin.2018.08.004>.
We provide an R tool for teaching in Social Sciences. It allows the computation of index numbers. It is a measure of the evolution of a fixed magnitude for only a product of for several products. It is very useful in Social Sciences. Among others, we obtain simple index numbers (in chain or in serie), index numbers for not only a product or weighted index numbers as the Laspeyres index (Laspeyres, 1864), the Paasche index (Paasche, 1874) or the Fisher index (Lapedes, 1978).
A set of utilities for manipulating index numbers series including chain-linking, re-referencing, and computing growth rates.
Computes bilateral and multilateral index numbers. 
    It has support for many standard bilateral indexes as well as
    multilateral index number methods such as GEKS, GEKS-Tornqvist 
    (or CCDI), Geary-Khamis and the weighted time product dummy
    (for details on these methods see Diewert and Fox (2020) 
    <doi:10.1080/07350015.2020.1816176>). 
    It also supports updating of multilateral indexes using 
    several splicing methods.
Helps with the thoughtful saving, reading, and management of result
  files (using 'rds' files). The core functions take a list of parameters that are
  used to generate a unique hash to save results under. Then, the same
  parameter list can be used to read those results back in. This
  is helpful to avoid clunky file naming when running a large number of
  simulations. Additionally, helper functions are available for compiling a flat
  file of parameters of saved results, monitoring result usage, and cleaning up
  unwanted or unused results. For more information, visit the 'indexr' homepage 
  <https://lharris421.github.io/indexr/>.
Quick indexation of any type of vector or of any combination of those. Indexation turns a vector into an integer vector going from 1 to the number of unique elements. Indexes are important building blocks for many algorithms. The method is described at <https://github.com/lrberge/indexthis/>.
Allows the construction selection indices based on estimated breeding values in animal and plant breeding and to calculate several analytic measures around to assess its impact on genetic and phenotypic progress. The methodology thereby allows to analyze genetic gain of traits in the breeding goal which are not part of the actual index and automatically computes several analytic measures. It further allows to retrospectively derive realized economic weights from observed genetic trends. The framework is described in Simianer, H., Heise, J., Rensing, S., Pook, T. Geibel, J. and Reimer, C. (2023) <doi:10.1186/s12711-023-00807-0>.
Computation of test statistics of independence between  (continuous) innovations of time series. They can be used with stochastic volatility models and Hidden Markov Models (HMM). This improves the results in Duchesne, Ghoudi & Remillard (2012) <doi:10.1002/cjs.11141>.
Set of routines for influence diagnostics by using case-deletion in ordinary least 
    squares, nonlinear regression [Ross (1987). <doi:10.2307/3315198>], ridge estimation [Walker and Birch (1988). <doi:10.1080/00401706.1988.10488370>] 
    and least absolute deviations (LAD) regression [Sun and Wei (2004). <doi:10.1016/j.spl.2003.08.018>].
Different functions includes constructing composite indicators, imputing missing data, and evaluating imputation techniques. Additionally, different tools for data normalization. Detailed methodologies of  'Indicator' package are: OECD/European Union/EC-JRC (2008), "Handbook on Constructing Composite Indicators: Methodology and User Guide", OECD Publishing, Paris, <DOI:10.1787/533411815016>, Matteo Mazziotta & Adriano Pareto, (2018) "Measuring Well-Being Over Time: The Adjusted Mazziotta–Pareto Index Versus Other Non-compensatory Indices" <DOI:10.1007/s11205-017-1577-5> and De Muro P., Mazziotta M., Pareto A. (2011), "Composite Indices  of Development and Poverty: An Application to MDGs" <DOI:10.1007/s11205-010-9727-z>.
Functions to assess the strength and statistical significance of the relationship between species occurrence/abundance and groups of sites [De Caceres & Legendre (2009) <doi:10.1890/08-1823.1>]. Also includes functions to measure species niche breadth using resource categories [De Caceres et al. (2011) <doi:10.1111/J.1600-0706.2011.19679.x>].
Simplifies the generation of customized R Markdown PDF templates.
    A template may include an individual logo, typography, geometry or color
    scheme. The package provides a skeleton with detailed instructions for
    customizations. The skeleton can be modified by changing defaults in the
    'YAML' header, by adding additional 'LaTeX' commands or by applying dynamic
    adjustments in R. Individual corporate design elements, such as a title page, can be added as R functions that produce 'LaTeX' code.
Functions are provided to facilitate prior elicitation for Bayesian generalised linear models using independent conditional means priors. The package supports the elicitation of multivariate normal priors for generalised linear models. The approach can be applied to indirect elicitation for a generalised linear model that is linear in the parameters. The package is designed such that the facilitator executes functions within the R console during the elicitation session to provide graphical and numerical feedback at each design point. Various methodologies for eliciting fractiles (equivalently, percentiles or quantiles) are supported, including versions of the approach of Hosack et al. (2017) <doi:10.1016/j.ress.2017.06.011>. For example, experts may be asked to provide central credible intervals that correspond to a certain probability. Or experts may be allowed to vary the probability allocated to the central credible interval for each design point. Additionally, a median may or may not be elicited.
It provides a general framework to analyse dependence between point processes in time. It includes parametric and non-parametric tests to study independence,  and functions for generating and analysing  different types of dependence.
Companion package to the book "industRial data science", 
    J.Ramalho (2021) <https://j-ramalho.github.io/industRial/>. 
    Provides data sets and functions to complete the case studies and contains 
    the book original Rmd files and tutorials.
Provides access to granular socioeconomic indicators from the
    Spanish Statistical Office (INE) Household Income Distribution Atlas.
    The package downloads and processes data from a companion 'GitHub'
    repository (<https://github.com/pablogguz/ineAtlas.data/>) which contains
    processed versions of the official INE Atlas data. Functions are
    provided to fetch data at multiple geographic levels (municipalities,
    districts, and census tracts), including income indicators,
    demographic characteristics, and inequality metrics. The data
    repository is updated every year when new releases are published by
    INE.
It provides multiple functions that are useful for ecological research and teaching statistics to ecologists. It is based on data analysis courses offered at the Instituto de Ecología AC (INECOL). For references and published evidence see, Manrique-Ascencio, et al (2024) <doi:10.1111/gcb.17282>, Manrique-Ascencio et al (2024) <doi:10.1111/plb.13683>, Ruiz-Guerra et al(2017) <doi:10.17129/botsci.812>, Juarez-Fragoso et al (2024) <doi:10.1007/s10980-024-01809-z>, Papaqui-Bello et al (2024) <doi:10.13102/sociobiology.v71i2.10503>.
Provides functions to download and parse information from INEGI
    (Official Mexican statistics agency). To learn more about the API, see <https://www.inegi.org.mx/servicios/api_indicadores.html>.
Inequality, concentration, and poverty measures. Lorenz curves (empirical and theoretical).
Decomposition of income inequality by groups formed of individuals 
    possessing similar characteristics (e.g., sex, education, age) and their 
    income sources at the same time.
    Decomposition of the Theil index is based on Giammatteo, M. (2007) 
    <https://www.lisdatacenter.org/wps/liswps/466.pdf>.
    Decomposition of the squared coefficient of variation is based on
    Garcia-Penalosa, C., & Orgiazzi, E. (2013) <doi:10.1111/roiw.12054>.
Computes and decomposes Gini, Bonferroni and Zenga 2007 point and synthetic concentration indexes. Decompositions are intended: by sources, by subpopulations and by sources and subpopulations jointly. References, Zenga M. M.(2007) <doi:10.1400/209575> Zenga M. (2015) <doi:10.1400/246627> Zenga M., Valli I. (2017) <doi:10.26350/999999_000005> Zenga M., Valli I. (2018) <doi:10.26350/999999_000011>.
Performs inference with the lasso in Gaussian Graphical Models. The package consists of wrappers for functions from the 'hdi' package.
It constructs a Consensus Network which identifies the general information of all the layers and Specific Networks for each layer with the information present only in that layer and not in all the others.The method is described in Policastro et al. (2024) "INet for network integration" <doi:10.1007/s00180-024-01536-8>.
Provides simple functions to compute and plot two types 
    (sample-size- and coverage-based) rarefaction and extrapolation curves for species
    diversity (Hill numbers) based on individual-based abundance data or sampling-unit-
    based incidence data; see Chao and others (2014, Ecological Monographs) for pertinent
    theory and methodologies, and Hsieh, Ma and Chao (2016, Methods in Ecology and Evolution)
    for an introduction of the R package.
Biodiversity is a multifaceted concept covering different levels of organization from
            genes to ecosystems. 'iNEXT.3D' extends 'iNEXT' to include three dimensions (3D) 
            of biodiversity, i.e., taxonomic diversity (TD), phylogenetic diversity (PD) and functional 
            diversity (FD). This package provides functions to compute standardized 3D diversity estimates 
            with a common sample size or sample coverage. A unified framework based on Hill numbers 
            and their generalizations (Hill-Chao numbers) are used to quantify 3D. All 3D estimates 
            are in the same units of species/lineage equivalents and can be meaningfully compared. 
            The package features size- and coverage-based rarefaction and extrapolation sampling 
            curves to facilitate rigorous comparison of 3D diversity across individual assemblages. 
            Asymptotic 3D diversity estimates are also provided. See Chao et al. (2021) 
            <doi:10.1111/2041-210X.13682> for more details.
Expands 'iNEXT' to include the estimation of sample completeness and evenness. The package provides simple functions to perform the following four-step biodiversity analysis:
       STEP 1: Assessment of sample completeness profiles.
       STEP 2a: Analysis of size-based rarefaction and extrapolation sampling curves to 
       determine whether the asymptotic diversity can be accurately estimated. 
       STEP 2b: Comparison of the observed and the estimated asymptotic diversity profiles. 
       STEP 3: Analysis of non-asymptotic coverage-based rarefaction and extrapolation sampling curves.
       STEP 4: Assessment of evenness profiles. 
       The analyses in STEPs 2a, 2b and STEP 3 are mainly based on the previous 'iNEXT' package. Refer to the 'iNEXT' package for details. This package is mainly focusing on the computation for STEPs 1 and 4. See Chao et al. (2020) <doi:10.1111/1440-1703.12102> for statistical background.
As a sequel to 'iNEXT', the 'iNEXT.beta3D' package provides functions to compute 
              standardized taxonomic, phylogenetic, and functional diversity (3D) estimates 
              with a common sample size (for alpha and gamma diversity) or sample coverage 
              (for alpha, beta, gamma diversity as well as dissimilarity or turnover indices). 
              Hill numbers and their generalizations are used to quantify 3D and to make 
              multiplicative decomposition (gamma = alpha x beta). The package also features 
              size- and coverage-based rarefaction and extrapolation sampling curves to 
              facilitate rigorous comparison of beta diversity across datasets.  
              See Chao et al. (2023) <doi:10.1002/ecm.1588> for more details.
Provides functions to access real-time infectious disease data from the 'disease.sh API',
    including COVID-19 global, US states, continent, and country statistics, vaccination coverage,
    influenza-like illness data from Centers for Disease Control and Prevention (CDC), and more. Also includes curated datasets on a variety
    of infectious diseases such as influenza, measles, dengue, Ebola, tuberculosis, meningitis,
    AIDS, and others. The package supports epidemiological research and data analysis by
    combining API access with high-quality historical and survey datasets on infectious diseases. For more details on the 'disease.sh API', see <https://disease.sh/>.
The objective of this package is to perform inference using
    an expressive statistical grammar that coheres with the tidy design
    framework.
An R package for inferring cell-type specific gene regulatory network from single-cell RNA data.
Functions to make inference about the 
        standardized mortality ratio (SMR) when evaluating the
        effect of a screening program. The package is
        based on methods described in Sasieni (2003) 
        <doi: 10.1097/00001648-200301000-00026> and 
        Talbot et al. (2011) <doi: 10.1002/sim.4334>.
Provides methods for estimating causal effects in the presence of interference described in  B. Saul and M. Hugdens (2017) <doi:10.18637/jss.v082.i02>. Currently it implements the inverse-probability weighted (IPW) estimators proposed by E.J. Tchetgen Tchetgen and T.J. Vanderweele (2012) <doi:10.1177/0962280210386779>.
Select set of parametric and non-parametric statistical tests. 'inferr' builds upon the solid set of
    statistical tests provided in 'stats' package by including additional data types as inputs, expanding and
    restructuring the test results. The tests included are t tests, variance tests, proportion tests, chi square tests, Levene's test, McNemar Test, Cochran's Q test and Runs test.
A set of functions for the modeling of data derived from the
    Minidisc Infiltrometer device.  It calculates cumulative infiltration
    and square root of time. Also, it calculates the A parameter based on
    soil physical properties.
Sampler and post-processing functions for semi-parametric Bayesian infinite factor models, motivated by the Multiplicative Gamma Shrinkage Prior of Bhattacharya and Dunson (2011) <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419391/>. Contains component C++ functions for building samplers for linear and 2-way interaction factor models using the multiplicative gamma and Dirichlet-Laplace shrinkage priors. The package also contains post processing functions to return matrices that display rotational ambiguity to identifiability through successive application of orthogonalization procedures and resolution of column label and sign switching. This package was developed with the support of the National Institute of Environmental Health Sciences grant 1R01ES028804-01.
The proportion of cancer cells in solid tumor sample, known as the tumor purity, has adverse impact on a variety of data analyses if not properly accounted for. We develop 'InfiniumPurify', which is a comprehensive R package for estimating and accounting for tumor purity based on DNA methylation Infinium 450k array data. 'InfiniumPurify' provides functionalities for tumor purity estimation. In addition, it can perform differential methylation detection and tumor sample clustering with the consideration of tumor purities.
Contains a number of infix binary operators that may be useful in day to day practices.
Infix functions in R are those that comes between its
  arguments such as %in%, +, and *. These are useful in R 
  programming when manipulating data, performing logical operations, 
  and making new functions. 'infixit' extends the infix functions 
  found in R to simplify frequent tasks, such as finding elements
  that are NOT in a set, in-line text concatenation, augmented assignment
  operations, additional logical and control flow operators, and 
  identifying if a number or date lies between two others.
Provides access to core inflation functions. Four different core inflation 
 functions are provided. The well known trimmed means, exclusion and double weighing methods, 
 alongside the new Triple Filter method introduced in Ferreira et al. (2016) <https://goo.gl/UYLhcj>.
Implementation of methods Extremum Surface Estimator (ESE) and 
   Extremum Distance Estimator (EDE) to identify the inflection point of a curve .
   Christopoulos, DT (2014) <doi:10.48550/arXiv.1206.5478> .
   Christopoulos, DT (2016) <https://demovtu.veltech.edu.in/wp-content/uploads/2016/04/Paper-04-2016.pdf> .
   Christopoulos, DT (2016) <doi:10.2139/ssrn.3043076> .
Analyzes raw abundance data from a cellular thermal shift experiment and calculates melt temperatures and melt shifts for each protein in the experiment. 
    McCracken (2022) <doi:10.1101/2022.12.30.522131>.
Provides a collection of tools for
        detecting influential cases in generalized mixed effects
        models. It analyses models that were estimated using 'lme4'. The
        basic rationale behind identifying influential data is that
        when single units are omitted from the data, models
        based on these data should not produce substantially different
        estimates. To standardize the assessment of how influential a
        (single group of) observation(s) is, several measures of
        influence are common practice, such as Cook's Distance. 
        In addition, we provide a measure of percentage change of the fixed point 
        estimates and a simple procedure to detect changing levels of significance.
A set of tools for evaluating several measures of case influence for structural equation models.
Ke, B. S., Chiang, A. J., & Chang, Y. C. I. (2018) <doi:10.1080/10543406.2017.1377728> provide two theoretical methods (influence function and local influence) based on the area under the receiver operating characteristic curve (AUC) to quantify the numerical impact of each observation to the overall AUC. Alternative graphical tools, cumulative lift charts, are proposed to reveal the existences and approximate locations of those influential observations through data visualization.
Provides functionality to compute various node centrality measures on networks.
    Included are functions to compute betweenness centrality (by utilizing Madduri and Bader's
    SNAP library), implementations of constraint and effective network size by Burt (2000) <doi:10.1016/S0191-3085(00)22009-1>; algorithm 
    to identify key players by Borgatti (2006) <doi:10.1007/s10588-006-7084-x>; and the 
    bridging algorithm by Valente and Fujimoto (2010) <doi:10.1016/j.socnet.2010.03.003>. 
    On Unix systems, the betweenness, Key Players, and
    bridging implementations are parallelized with OpenMP, which may run
    faster on systems which have OpenMP configured.
Contains functions for the classification and ranking of top candidate features, reconstruction of networks from
    adjacency matrices and data frames, analysis of the topology of the network 
    and calculation of centrality measures, and identification of the most
    influential nodes. Also, a function is provided for running SIRIR model, which 
    is the combination of leave-one-out cross validation technique and the conventional SIR model, on a network to unsupervisedly rank the true influence of vertices. Additionally, some functions have been provided for the assessment 
    of dependence and correlation of two network centrality measures as well as 
    the conditional probability of deviation from their corresponding means in opposite direction.
    Fred Viole and David Nawrocki (2013, ISBN:1490523995).
    Csardi G, Nepusz T (2006). "The igraph software package for complex network research." InterJournal, Complex Systems, 1695.
    Adopted algorithms and sources are referenced in function document.
'InfluxDB' 2.x time-series database client. Supports both 'InfluxDB' OSS (<https://portal.influxdata.com/downloads/>) and Cloud (<https://cloud2.influxdata.com/>) version.
An R interface to the InfluxDB time series database <https://www.influxdata.com>. This package allows you to fetch and write time series data from/to an InfluxDB server. Additionally, handy wrappers for the Influx Query Language (IQL) to manage and explore a remote database are provided.
The main purpose of this package is to generate the structure of the analysis of variance 
            (ANOVA) table of the two-phase experiments. The user only need to input the design and the 
              relationships of the random and fixed factors using the Wilkinson-Rogers' syntax, 
              this package can then quickly generate the structure of the ANOVA table with the 
              coefficients of the variance components for the expected mean squares.
              Thus, the balanced incomplete block design and provides the efficiency
              factors of the fixed effects can also be studied and compared much easily.
Performs exploratory data analysis and variable screening for
    binary classification models using weight-of-evidence (WOE) and information
    value (IV). In order to make the package as efficient as possible, aggregations
    are done in data.table and creation of WOE vectors can be distributed across
    multiple cores. The package also supports exploration for uplift models (NWOE
    and NIV).
Multiple Imputation for Informative Censoring.
    This package implements two methods. Gamma Imputation
    described in <DOI:10.1002/sim.6274> and Risk Score Imputation
    described in <DOI:10.1002/sim.3480>.
Calculation of informative simultaneous confidence intervals
    for graphical described multiple test procedures and given information
    weights. Bretz et al. (2009) <doi:10.1002/sim.3495> and Brannath et
    al. (2024) <doi:10.48550/arXiv.2402.13719>. Furthermore, exploration of the
    behavior of the informative bounds in dependence of the information
    weights.  Comparisons with compatible bounds are possible.
    Strassburger and Bretz (2008) <doi:10.1002/sim.3338>.
After testing for biased treatment assignment in an observational study using an unaffected outcome, the sensitivity analysis is constrained to be compatible with that test.  The package uses the optimization software gurobi obtainable from <https://www.gurobi.com/>, together with its associated R package, also called gurobi; see: <https://www.gurobi.com/documentation/7.0/refman/installing_the_r_package.html>.  The method is a substantial computational and practical enhancement of a concept introduced in Rosenbaum (1992) Detecting bias with confidence in observational studies Biometrika, 79(2), 367-374  <doi:10.1093/biomet/79.2.367>.
Estimation of the most-left informative set of gross returns 
             (i.e., the informative set).
             The procedure to compute the informative set adjusts the method 
             proposed by 
             Mariani et al. (2022a) <doi:10.1007/s11205-020-02440-6> 
             and 
             Mariani et al. (2022b) <doi:10.1007/s10287-022-00422-2> 
             to gross returns of financial assets. 
             This is accomplished through an adaptive algorithm
             that identifies sub-groups of gross returns in 
             each iteration by approximating their distribution with a
             sequence of two-component log-normal mixtures. 
             These sub-groups emerge when a significant change
             in the distribution occurs below the median of the 
             financial returns, with their boundary termed as
             the “change point" of the mixture. 
             The process concludes when no further change points are detected.
             The outcome encompasses parameters of the leftmost mixture 
             distributions and change points of the
             analyzed financial time series.
             The functionalities of the INFOSET package include: (i) modelling asset distribution
             detecting the parameters which describe left tail behaviour (infoset function), (ii) clustering, (iii) labeling of the financial
             series for predictive and classification purposes through a Left Risk measure based on the first change point (LR_cp function)
             (iv) portfolio construction (ptf_construction function).
             The package also provide a specific function to construct rolling windows of different length size and overlapping time.
Implements various measures of information theory based on several entropy estimators.
Estimates the probability of informed trading (PIN) initially introduced by Easley et. al. (1996) <doi:10.1111/j.1540-6261.1996.tb04074.x> . Contribution of the package is that it uses likelihood factorizations of Easley et. al. (2010) <doi:10.1017/S0022109010000074> (EHO factorization) and Lin and Ke (2011) <doi:10.1016/j.finmar.2011.03.001> (LK factorization). Moreover, the package uses different estimation algorithms. Specifically, the grid-search algorithm proposed by Yan and Zhang (2012) <doi:10.1016/j.jbankfin.2011.08.003> , hierarchical agglomerative clustering approach proposed by Gan et. al. (2015) <doi:10.1080/14697688.2015.1023336> and later extended by Ersan and Alici (2016) <doi:10.1016/j.intfin.2016.04.001> .
Facilitates the generation of input files for infraFDTD and processes snapshot output. infraFDTD is a finite-difference model written by Keehoon Kim for simulating infrasound that considers topography and a 1-D atmosphere (see Kim et al., 2015 <doi:10.1002/2015GL064466>).
Implements functions for simulation-based inference. In particular, implements functions to perform likelihood inference from data summaries whose distributions are simulated, as first described in Rousset et al. (2017) <doi:10.1111/1755-0998.12627>. The package implements more advanced methods described in Rousset et al. (2025) <doi:10.1101/2024.09.30.615940>.
Collection of tools for assessment of feature importance and feature effects.
    Key functions are:
    feature_importance() for assessment of global level feature importance,
    ceteris_paribus() for calculation of the what-if plots,
    partial_dependence() for partial dependence plots,
    conditional_dependence() for conditional dependence plots,
    accumulated_dependence() for accumulated local effects plots,
    aggregate_profiles() and cluster_profiles() for aggregation of ceteris paribus profiles,
    generic print() and plot() for better usability of selected explainers,
    generic plotD3() for interactive, D3 based explanations, and
    generic describe() for explanations in natural language.
    The package 'ingredients' is a part of the 'DrWhy.AI' universe (Biecek 2018) <arXiv:1806.08915>.
Parse simple '.ini' configuration files to an structured list. Users
  can manipulate this resulting list with lapply() functions. This same
  structured list can be used to write back to file after modifications.
R dependency injection framework. Dependency injection allows
    a program design to follow the dependency inversion principle. The user
    delegates to external code (the injector) the responsibility of providing its
    dependencies. This separates the responsibilities of use and construction.
Calculate the injury severity score (ISS)
    based on the dictionary in 'ICDPIC' from <https://ideas.repec.org/c/boc/bocode/s457028.html>. The original code was written in 
    'STATA 11'. The original 'STATA' code was written by David Clark, 
    Turner Osler and David Hahn. I implement the same logic for easier access.
    Ref: David E. Clark & Turner M. Osler & David R. Hahn, 2009. 
    "ICDPIC: Stata module to provide methods for translating International 
    Classification of Diseases (Ninth Revision) diagnosis codes into standard injury 
    categories and/or scores," Statistical Software Components S457028, 
    Boston College Department of Economics, revised 29 Oct 2010.
Sports Injury Data analysis aims to identify and describe the
  magnitude of the injury problem, and to gain more insights (e.g. determine
  potential risk factors) by statistical modelling approaches. The 'injurytools'
  package provides standardized routines and utilities that simplify such
  analyses. It offers functions for data preparation, informative visualizations 
  and descriptive and model-based analyses.
Fit Spatial Econometrics models using Bayesian model averaging 
  on models fitted with INLA. The INLA package can be obtained from 
  <https://www.r-inla.org>.
Facilitates spatial and general latent Gaussian modeling using
  integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>).
  Additionally, extends the GAM-like model class to more general nonlinear predictor
  expressions, and implements a log Gaussian Cox process likelihood for 
  modeling univariate and spatial point processes based on ecological survey data.
  Model components are specified with general inputs and mapping methods to the
  latent variables, and the predictors are specified via general R expressions,
  with separate expressions for each observation likelihood model in
  multi-likelihood models. A prediction method based on fast Monte Carlo sampling
  allows posterior prediction of general expressions of the latent variables.
  Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019)
  <doi:10.1111/2041-210X.13168>.
Estimation of joint models for multivariate longitudinal markers (with various distributions available) and survival outcomes (possibly accounting for competing risks) with Integrated Nested Laplace Approximations (INLA). The flexible and user friendly function joint() facilitates the use of the fast and reliable inference technique implemented in the 'INLA' package for joint modeling. More details are given in the help page of the joint() function (accessible via ?joint in the R console) and the vignette associated to the joint() function (accessible via vignette("INLAjoint") in the R console).
Facilitates fitting measurement error and missing data imputation models using integrated nested Laplace approximations, according to the method described in Skarstein, Martino and Muff (2023) <doi:10.1002/bimj.202300078>. See Skarstein and Muff (2024) <doi:10.48550/arXiv.2406.08172> for details on using the package.
Prepare objects to implement models over spatial and 
  spacetime domains with the 'INLA' package (<https://www.r-inla.org>).
  These objects contain data to for the 'cgeneric' interface in
  'INLA', enabling fast parallel computations.
  We implemented the spatial barrier model, see Bakka et. al. (2019) 
  <doi:10.1016/j.spasta.2019.01.002>, and some of the spatio-temporal 
  models proposed in Lindgren et. al. (2023) 
  <https://www.idescat.cat/sort/sort481/48.1.1.Lindgren-etal.pdf>. 
  Details are provided in the available vignettes and from the URL bellow.
Contain code to work with latent Gaussian
  Markov random field (GMRF) models. Queries for the 
  'cgeneric' interface, specified as a way to implement
  new GMRF models to be fitted as model components
  in the 'INLA' package (<https://www.r-inla.org>).
  The implemented functionalities leverage the use 
  of 'cgeneric' models and provide a way to debug 
  the code as well to work with the prior for the 
  model parameters and to sample from it. 
  A Kronecker product method is also implemented to 
  work with the four possible combinations between 
  a 'cgeneric' and a 'rgeneric' model.
A collection of functions for creating color schemes.
    Used to support packages and scripts written
    by researchers at the United States Geological Survey (USGS)
    Idaho National Laboratory Project Office.
A collection of analysis-ready datasets for the
    U.S. Geological Survey - Idaho National Laboratory (USGS-INL)
    groundwater and surface-water monitoring networks, administered by the
    USGS-INL Project Office in cooperation with the U.S. Department of Energy.
    The data collected from wells and surface-water stations at the
    Idaho National Laboratory and surrounding areas have been used to describe
    the effects of waste disposal on water contained in the
    eastern Snake River Plain aquifer, located in the southeastern part of
    Idaho, and the availability of water for long-term consumptive and
    industrial use. The package includes long-term monitoring records dating
    back to measurements from 1922. Geospatial data describing the areas from
    which samples were collected or observations were made are also included in
    the package. Bundling this data into a single package significantly reduces
    the magnitude of data processing for researchers and provides a way to
    distribute the data along with its documentation in a standard format.
    Geospatial datasets are made available in a common projection and datum, and
    geohydrologic data have been structured to facilitate analysis.
Functionality to dynamically define R functions and S4 methods
 with 'inlined' C, C++ or Fortran code supporting the .C and .Call calling
 conventions.
Generates Rd files from R source code with comments.
 The main features of the default syntax are that
 (1) docs are defined in comments near the relevant code,
 (2) function argument names are not repeated in comments, and
 (3) examples are defined in R code, not comments.
 It is also easy to define a new syntax.
Contains bibliographic information for the U.S. Geological Survey
    (USGS) Idaho National Laboratory (INL) Project Office.
Interpretation methods for analyzing the behavior and individual
    predictions of modern neural networks in a three-step procedure: Converting 
    the model, running the interpretation method, and visualizing the results. 
    Implemented methods are, e.g., 'Connection Weights' described by Olden et al. (2004)
    <doi:10.1016/j.ecolmodel.2004.03.013>, layer-wise relevance
    propagation ('LRP') described by Bach et al. (2015)
    <doi:10.1371/journal.pone.0130140>, deep learning important features
    ('DeepLIFT') described by Shrikumar et al.  (2017) <doi:10.48550/arXiv.1704.02685>
    and gradient-based methods like 'SmoothGrad' described by Smilkov et
    al. (2017) <doi:10.48550/arXiv.1706.03825>, 'Gradient x Input' 
    or 'Vanilla Gradient'.
    Details can be found in the accompanying scientific paper: Koenen & Wright 
    (2024, Journal of Statistical Software, <doi:10.18637/jss.v111.i08>).
Analysis of the initialization for numerical optimization of 
    real-valued functions, particularly likelihood functions of statistical 
    models. See <https://loelschlaeger.de/ino/> for more details.
Infix operators to detect, subset, and replace the elements matched by a given condition.
  The functions have several variants of operator types, including subsets, ranges, regular expressions and others.
  Implemented operators work on vectors, matrices, and lists.
A set of functions to analyse and compare texts, using classical 
  text mining	functions, as well as those from theoretical ecology.
It provides in-place operators for R 
    that are equivalent to '+=', '-=', '*=', '/=' in C++. 
    Those can be applied on integer|double vectors|matrices.
    You have also access to sweep operations (in-place).
Non-parametric resampling-based inference tests for ExPosition.
Collection of functions for quality control (QC) of climatological daily time series (e.g. the ECA&D station data).
For environmental chemists, ecologists, researchers and agricultural scientists to understand the dissipation kinetics, calculate the half-life periods and rate constants of compounds, pesticides, contaminants in different matrices.
A user-friendly interface, using Shiny, to analyse glucose-stimulated insulin secretion (GSIS) 
    assays in pancreatic beta cells or islets.
    The package allows the user to import several sets of experiments from different spreadsheets 
    and to perform subsequent steps: summarise in a tidy format, visualise data quality 
    and compare experimental conditions without omitting to account for technical confounders 
    such as the date of the experiment or the technician.
    Together, insane is a comprehensive method that optimises pre-processing and analyses of 
    GSIS experiments in a friendly-user interface.
    The Shiny App was initially designed for EndoC-betaH1 cell line following method described 
    in Ndiaye et al., 2017 (<doi:10.1016/j.molmet.2017.03.011>).
Provides tools for probabilistic taxon assignment with informatic sequence classification trees. See Wilkinson et al (2018) <doi:10.7287/peerj.preprints.26812v1>.
Using embedded sdmx queries, get the data of more than 150 000 insee series from 'bdm' macroeconomic database.
A tool to provide an easy, intuitive and consistent
    access to information contained in various R models, like model
    formulas, model terms, information about random effects, data that was
    used to fit the model or data from response variables. 'insight'
    mainly revolves around two types of functions: Functions that find
    (the names of) information, starting with 'find_', and functions that
    get the underlying data, starting with 'get_'. The package has a
    consistent syntax and works with many different model objects, where
    otherwise functions to access these information are missing.
Computes individual causes of death and population cause-specific mortality fractions using the 'InSilicoVA' algorithm from McCormick et al. (2016) <DOI:10.1080/01621459.2016.1152191>. It uses data derived from verbal autopsy (VA) interviews, in a format similar to the input of the widely used 'InterVA' method. This package provides general model fitting and customization for 'InSilicoVA' algorithm and basic graphical visualization of the output.
Provides a data-driven projection-based method for estimating changepoints in high-dimensional time series. Multiple changepoints are estimated using a (wild) binary segmentation scheme.
A collection of utilities for columnwise summary, comparison and visualisation of data frames.  Functions report missingness, categorical levels, numeric distribution, correlation, column types and memory usage.
A 'shiny' application to assist in phytosanitary inspections. It generates a diagram of pallets in a lot, highlights the units to be sampled, and documents them based on the selected sampling method (simple random or systematic sampling).
Utility functions that implement and automate common sets of validation tasks. 
    These functions are particularly useful to validate inputs, intermediate objects and output 
    values in user-defined functions, resulting in tidier and less verbose functions.
This is a shiny app used for the statistical classifying and analysing
    pre-clinical tumour responses.
Collect  marketing data from Instagram Ads using the 'Windsor.ai' API <https://windsor.ai/api-fields/>.
The function 'install_load' checks the local R library(ies) to see
    if the required package(s) is/are installed or not. If the package(s)
    is/are not installed, then the package(s) will be installed along with
    the required dependency(ies). This function pulls source or
    binary packages from the Posit/RStudio-sponsored CRAN mirror. Lastly, the
    chosen package(s) is/are loaded. The function 'load_package' simply loads
    the provided package(s). If this package does not fit your needs, then you
    may want to consider these other R packages: 'needs', 'easypackages',
    'pacman', 'pak', 'anyLib', and/or 'librarian'.
R is great for installing software.  Through the 'installr'
    package you can automate the updating of R (on Windows, using updateR())
    and install new software. Software installation is initiated through a
    GUI (just run installr()), or through functions such as: install.Rtools(),
    install.pandoc(), install.git(), and many more. The updateR() command
    performs the following: finding the latest R version, downloading it,
    running the installer, deleting the installation file, copy and updating
    old packages to the new R installation.
Similar to 'rstantools' for 'rstan',
  the 'instantiate' package builds pre-compiled
  'CmdStan' models into CRAN-ready statistical modeling R packages.
  The models compile once during installation,
  the executables live inside the file systems of their respective packages,
  and users have the full power and convenience of
  'cmdstanr' without any additional compilation after package installation.
  This approach saves time and helps R package developers
  migrate from 'rstan' to the more modern 'cmdstanr'.
  Packages 'rstantools', 'cmdstanr', 'stannis', and
  'stanapi' are similar Stan clients with different objectives.
Provides an interface to the Instagram API <https://instagram.com/
    developer/>, which allows R users to download public pictures filtered by
    hashtag, popularity, user or location, and to access public users' profile data.
Insurance datasets, which are often used in claims severity and claims frequency modelling. It helps testing new regression models in those problems, such as GLM, GLMM, HGLM, non-linear mixed models etc. Most of the data sets are applied in the project "Mixed models in ratemaking" supported by grant NN 111461540 from Polish National Science Center.
Functions to build, evaluate, and visualize insurance rating 
    models. It simplifies the process of modeling premiums, and allows to 
    analyze insurance risk factors effectively. The package employs a 
    data-driven strategy for constructing insurance tariff classes, drawing on 
    the work of Antonio and Valdez (2012) <doi:10.1007/s10182-011-0152-7>.
It facilitates the calculation of 40 different insulin sensitivity indices based on fasting, oral glucose tolerance test (OGTT), lipid (adipose), and tracer (palmitate and glycerol rate) and dxa (fat mass) measurement values. It enables easy and accurate assessment of insulin sensitivity, critical for understanding and managing metabolic disorders like diabetes and obesity. Indices calculated are described in Gastaldelli (2022). <doi:10.1002/oby.23503> and Lorenzo (2010). <doi:10.1210/jc.2010-1144>.
Geostatistical interpolation has traditionally been done by manually fitting a variogram and then interpolating. Here, we introduce classes and methods that can do this interpolation automatically. Pebesma et al (2010) gives an overview of the methods behind and possible usage <doi:10.1016/j.cageo.2010.03.019>.
The IntCal20 radiocarbon calibration curves (Reimer et al. 2020 <doi:10.1017/RDC.2020.68>) are provided here in a single data package, together with previous IntCal curves (IntCal13, IntCal09, IntCal04, IntCal98) and postbomb curves. Also provided are functions to copy the curves into memory, and to plot the curves and their underlying data, as well as functions to calibrate radiocarbon dates.
Semiparametric regression models on the cumulative incidence function for interval-censored competing risks data as described in Bakoyannis, Yu, & Yiannoutsos (2017) /doi{10.1002/sim.7350} and the models with missing event types as described in Park, Bakoyannis, Zhang, & Yiannoutsos (2021) \doi{10.1093/biostatistics/kxaa052}. The proportional subdistribution hazards model (Fine-Gray model), the proportional odds model, and other models that belong to the class of semiparametric generalized odds rate transformation models.
The kernel of this 'Rcpp' based package is an efficient implementation of the generalized gradient projection method for spline function based constrained maximum likelihood estimator for interval censored survival data (Wu, Yuan; Zhang, Ying. Partially monotone tensor spline estimation of the joint distribution function with bivariate current status data. Ann. Statist. 40, 2012, 1609-1636 <doi:10.1214/12-AOS1016>). The key function computes the density function of the joint distribution of event time and the marker and returns the receiver operating characteristic (ROC) curve for the interval censored survival data as well as area under the curve (AUC).
Provides a systematic framework for
 integrating multiple modalities of assays profiled on the same set of
 samples. The goal is to identify genes that are altered in cancer
 either marginally or consistently across different assays. The
 heterogeneity among different platforms and different samples are
 automatically adjusted so that the overall alteration magnitude can
 be accurately inferred. See Tong and Coombes (2012) 
 <doi:10.1093/bioinformatics/bts561>.
Generates a 'Graphviz' graph of the most significant 3-way 
    interaction gains (i.e. conditional information gains) based on a provided 
    discrete data frame. Various output formats are supported ('Graphviz', SVG, 
    PNG, PDF, PS). For references, see the webpage of Aleks Jakulin 
    <http://stat.columbia.edu/~jakulin/Int/>.
Offers modeling the association between gene-expression and bioassay data, taking care of the effect due to a fingerprint feature and helps with several plots to better understand the analysis.
Four datasets are provided here from the 'Intendo' game
    'Super Jetroid'. It is data from the 2015 year of operation and it comprises
    a revenue table ('all_revenue'), a daily users table ('users_daily'), a user
    summary table ('user_summary'), and a table with data on all user sessions
    ('all_sessions'). These core datasets come in different sizes, and, each of
    them has a variant that was intentionally made faulty (totally riddled with
    errors and inconsistencies). This suite of tables is useful for testing with
    packages that focus on data validation and data documentation.
Electricity is not made equal and it vary in its carbon footprint (or carbon intensity) 
    depending on its source. This package enables to access and query data provided by the 
    Carbon Intensity API (<https://carbonintensity.org.uk/>). National Grid’s Carbon Intensity API 
    provides an indicative trend of regional carbon intensity of the electricity system in Great Britain.
Tools to analyze point patterns in space occurring over planar network structures derived from graph-related intensity measures for undirected, directed, and mixed networks. 
    This package is based on the following research: Eckardt and Mateu (2018) <doi:10.1080/10618600.2017.1391695>. Eckardt and Mateu (2021) <doi:10.1007/s11749-020-00720-4>.
Power analysis for regression models which test the interaction of
    two or three independent variables on a single dependent variable. Includes options 
    for correlated interacting variables and specifying variable reliability. 
    Two-way interactions can include continuous, binary, or ordinal variables.
    Power analyses can be done either analytically or via simulation.  Includes 
    tools for simulating single data sets and visualizing power analysis results.
    The primary functions are power_interaction_r2() and power_interaction() for two-way
    interactions, and power_interaction_3way_r2() for three-way interactions. 
    Please cite as: Baranger DAA, Finsaas MC, Goldstein BL, Vize CE, Lynam DR,
    Olino TM (2023). "Tutorial: Power analyses for interaction effects in 
    cross-sectional regressions." <doi:10.1177/25152459231187531>.
Produces a publication-ready table that includes all effect estimates necessary for full reporting effect modification and interaction analysis as recommended by Knol and Vanderweele (2012) [<doi:10.1093/ije/dyr218>]. It also estimates confidence interval for the trio of additive interaction measures using the delta method (see Hosmer and Lemeshow (1992), [<doi:10.1097/00001648-199209000-00012>]), variance recovery method (see Zou (2008), [<doi:10.1093/aje/kwn104>]), or percentile bootstrapping (see Assmann et al. (1996), [<doi:10.1097/00001648-199605000-00012>]).
A tool to calculate and plot estimates from models 
    in which an interaction between the main predictor and a continuous covariate has been specified.
    Methods used in the package refer to Harrell Jr FE (2015, ISBN:9783319330396); 
    Durrleman S, Simon R. (1989) <doi:10.1002/sim.4780080504>; Greenland S. (1995) <doi:10.1097/00001648-199507000-00005>.
A suite of functions for conducting and interpreting analysis 
  of statistical interaction in regression models that was formerly part of the 
  'jtools' package. Functionality includes visualization of two- and three-way
  interactions among continuous and/or categorical variables as well as 
  calculation of "simple slopes" and Johnson-Neyman intervals (see e.g., 
  Bauer & Curran, 2005 <doi:10.1207/s15327906mbr4003_5>). These
  capabilities are implemented for generalized linear models in addition to the 
  standard linear regression context.
Implements the procedures suggested in Esarey and Sumner (2017) <http://justinesarey.com/interaction-overconfidence.pdf> for controlling the false discovery rate when constructing marginal effects plots for models with interaction terms.
Chi-square tests are computed with corrections.
Various functions and a Shiny app to enrich the results of Multiple Correspondence Analysis with interpretive axes and planes (see Moschidis, Markos, and Thanopoulos, 2022; <doi:10.1108/ACI-07-2022-0191>).
Extensive penalized variable selection methods have been developed in the past two decades for analyzing high dimensional omics data, such as gene expressions, single nucleotide polymorphisms (SNPs), copy number variations (CNVs) and others. However, lipidomics data have been rarely investigated by using high dimensional variable selection methods. This package incorporates our recently developed penalization procedures to conduct interaction analysis for high dimensional lipidomics data with repeated measurements. The core module of this package is developed in C++. The development of this software package and the associated statistical methods have been partially supported by an Innovative Research Award from Johnson Cancer Research Center, Kansas State University.
Provides a runtime type system, allowing users to define and implement interfaces, enums, typed data.frame/data.table, as well as typed functions. This package enables stricter type checking and validation, improving code structure, robustness and reliability.
Graphical User Interface allowing to determine the concentration in the sample in CFU per mL or in number of copies per mL provided to qPCR results after with or without PMA treatment. This package is simply to use because no knowledge in R commands is necessary. A graphic represents the standard curve, and a table containing the result for each sample is created.
A dataframe validation framework for package builders who use
  dataframes as function parameters. It performs checks on column names, coerces
  data-types, and checks grouping to make sure user inputs conform to a
  specification provided by the package author. It provides a mechanism for
  package authors to automatically document supported dataframe inputs and
  selectively dispatch to functions depending on the format of a dataframe much
  like S3 does for classes. It also contains some developer tools to make
  working with and documenting dataframe specifications easier. It helps package
  developers to improve their documentation and simplifies parameter validation
  where dataframes are used as function parameters.
Performs diagnostic tests of multiplicative interaction models and plots non-linear marginal effects of a treatment on an outcome across different values of a moderator.
Functions implemented in this package allow to coerce (i.e.
	convert) network data between classes provided by other R packages.
	Currently supported classes are those defined in packages: network and
	igraph.
Allows the simulation of the recruitment and both the event and treatment phase of a clinical trial. Based on these simulations, the timing of interim analyses can be assessed.
Allows an interactive assessment of the timing of interim analyses. The algorithm simulates both the recruitment and treatment/event phase of a clinical trial based on the package 'interim'.
Converts matrices and lists of matrices into a single vector by interleaving 
    their values. That is, each element of the result vector is filled from the input 
    matrices one row at a time. This is the same as transposing a matrix, then removing the 
    dimension attribute, but is designed to operate on matrices in nested list structures.
Interlinearized glossed texts (IGT) are used in descriptive linguistics for
 representing a morphological analysis of a text through a morpheme-by-morpheme gloss.
 'InterlineaR' provide a set of functions that targets several popular formats of IGT
 ('SIL Toolbox', 'EMELD XML') and that turns an IGT into a set of data frames following
 a relational model (the tables represent the different linguistic units: texts,
 sentences, word, morphems).
 The same pieces of software ('SIL FLEX', 'SIL Toolbox') typically produce dictionaries
 of the morphemes used in the glosses. 'InterlineaR' provide a function for turning
 the LIFT XML dictionary format into a set of data frames following a relational model
 in order to represent the dictionary entries, the sense(s) attached to the entries,
 the example(s) attached to senses, etc.
Intervention analysis is used to investigate structural changes in data resulting from external events. Traditional time series intervention models, viz. Autoregressive Integrated Moving Average model with exogeneous variables (ARIMA-X) and Artificial Neural Networks with exogeneous variables (ANN-X), rely on linear intervention functions such as step or ramp functions, or their combinations. In this package, the Gompertz, Logistic, Monomolecular, Richard and Hoerl function have been used as non-linear intervention function. The equation of the above models are represented as: Gompertz: A * exp(-B * exp(-k * t)); Logistic: K / (1 + ((K - N0) / N0) * exp(-r * t)); Monomolecular: A * exp(-k * t); Richard: A + (K - A) / (1 + exp(-B * (C - t)))^(1/beta) and Hoerl: a*(b^t)*(t^c).This package introduced algorithm for time series intervention analysis employing ARIMA and ANN models with a non-linear intervention function. This package has been developed using algorithm of Yeasin et al. <doi:10.1016/j.hazadv.2023.100325> and Paul and Yeasin <doi:10.1371/journal.pone.0272999>.
Bivariate data interpolation on regular and irregular
  grids, either linear or using splines are the main part of this
  package.  It is intended to provide FOSS replacement functions for
  the ACM licensed akima::interp and tripack::tri.mesh functions.
  Linear interpolation is implemented in 
  interp::interp(..., method="linear"), this corresponds to the call 
  akima::interp(..., linear=TRUE) which is the default setting and 
  covers most of akima::interp use cases in depending packages.  
  A re-implementation of Akimas irregular grid spline
  interpolation (akima::interp(..., linear=FALSE)) is now also
  available via interp::interp(..., method="akima").
  Estimators for partial derivatives are now also available in 
  interp::locpoly(), these are a prerequisite for the spline interpolation.  
  The basic part is a GPLed triangulation algorithm (sweep hull 
  algorithm by David Sinclair) providing the starting point for the
  irregular grid interpolator. As side effect this algorithm is also
  used to provide replacements for almost all functions of the tripack
  package which also suffers from the same ACM license restrictions.  
  All functions are designed to be backward compatible with their 
  akima / tripack counterparts.
Computational topology, which enables topological data analysis
    (TDA), makes pervasive use of abstract mathematical objects called
    simplicial complexes; see Edelsbrunner and Harer (2010)
    <doi:10.1090/mbk/069>.
    Several R packages and other software libraries used through an R interface
    construct and use data structures that represent simplicial complexes,
    including mathematical graphs viewed as 1-dimensional complexes.
    This package provides coercers (converters) between these data structures.
    Currently supported structures are complete lists of simplices as used by
    'TDA'; the simplex trees of Boissonnat and Maria (2014)
    <doi:10.1007/s00453-014-9887-3> as implemented in 'simplextree' and in
    Python GUDHI (by way of 'reticulate'); and the graph classes of 'igraph' and
    'network', by way of the 'intergraph' package.
Plots the conditional coefficients ("marginal effects") of
    variables included in multiplicative interaction terms.
Spatial interpolation toolkit designed for environmental and geospatial applications. It includes a range of methods, from traditional techniques to advanced machine learning approaches, ensuring accurate and efficient estimation of values in unobserved locations.
Provides two different methods, linear and nonlinear, to
    interpolate a bivariate function, scalar-valued or vector-valued. 
    The interpolated data are not necessarily gridded. The algorithms 
    are performed by the 'C++' library 'CGAL' (<https://www.cgal.org/>).
Some interpolation methods taken from 'Boost': barycentric
    rational interpolation, modified Akima interpolation, PCHIP (piecewise
    cubic Hermite interpolating polynomial) interpolation, and Catmull-Rom
    splines.
Package for training interpretable machine learning models. Historically, the most interpretable machine learning models were not very accurate, and the most accurate models were not very interpretable. Microsoft Research has developed an algorithm called the Explainable Boosting Machine (EBM) which has both high accuracy and interpretable characteristics. EBM uses machine learning techniques like bagging and boosting to breathe new life into traditional GAMs (Generalized Additive Models). This makes them as accurate as random forests and gradient boosted trees, and also enhances their intelligibility and editability. Details on the EBM algorithm can be found in the paper by Rich Caruana, Yin Lou, Johannes Gehrke, Paul Koch, Marc Sturm, and Noemie Elhadad (2015, <doi:10.1145/2783258.2788613>).
Estimate confidence intervals for mean, proportion, mean difference 
   for unpaired and paired samples and proportion difference. Plot the confidence 
   intervals. Generate documents explaining the statistical result step by step.
High resolution mass spectrometry yields often large data sets of 
    spectra from compounds which are not present in available libraries. These 
    spectra need to be annotated and interpreted.
    'InterpretMSSpectrum' provides a set of functions to perform such tasks for 
    Electrospray-Ionization and Atmospheric-Pressure-Chemical-Ionization derived 
    data in positive and negative ionization mode.
Compute permutation- based performance measures and create partial
    dependence plots for (cross-validated) 'randomForest' and 'ada' models.
Provides access to low-level operating system mechanisms for
    performing atomic operations on shared data structures. Mutexes provide
    shared and exclusive locks. Semaphores act as counters. Message queues
    move text strings from one process to another. All these interprocess
    communication (IPC) tools can optionally block with or without a timeout.
    Implemented using the cross-platform 'boost' 'C++' library
    <https://www.boost.org/doc/libs/release/libs/interprocess/>.
A set of functions to estimate interactions flexibly in the face of possibly many controls. Implements the procedures described in Blackwell and Olson (2022) <doi:10.1017/pan.2021.19>.
Generates three inter-related genomic datasets: methylation, gene expression and protein expression having user specified cluster patterns. The simulation utilizes the realistic inter- and intra- relationships from real DNA methylation, mRNA expression and protein expression data from the TCGA ovarian cancer study, Chalise (2016) <doi:10.1016/j.cmpb.2016.02.011>.
Provides an R version of the 'InterVA4' software (<http://www.interva.net>) for coding cause of death from verbal autopsies. It also provides simple graphical representation of individual and population level statistics.
Provides an R version of the 'InterVA5' software (<http://www.byass.uk/interva/>) for coding cause of death from verbal autopsies. It also provides simple graphical representation of individual and population level statistics.
Functions to fit nonparametric survival curves, plot them, and perform logrank or Wilcoxon type tests [see Fay and Shaw <doi:10.18637/jss.v036.i02>].
Perform fast and memory efficient time-weighted averaging of values 
    measured over intervals into new arbitrary intervals. 
	This package is useful in the context of data measured or represented
	as constant values over intervals on a one-dimensional discrete axis 
	(e.g. time-integrated averages of a curve over defined periods). 
	This package was written specifically to deal with air 
	pollution data recorded or predicted as averages over sampling periods. 
	Data in this format often needs to be shifted to non-aligned periods 
	or averaged up to periods of longer duration (e.g. averaging data measured over 
	sequential non-overlapping periods to calendar years).
Implements the Interval Consensus Model (ICM) for analyzing continuous bounded interval-valued responses in psychometrics using 'Stan' for 'Bayesian' estimation. Provides functions for transforming interval data to simplex representations, fitting item response theory (IRT) models with isometric log-ratio (ILR) and sum log-ratio (SLR) link functions, and visualizing results. The package enables aggregation and analysis of interval-valued response data commonly found in psychological measurement and related disciplines. Based on Kloft et al. (2024) <doi:10.31234/osf.io/dzvw2>.
A user-friendly toolbox for doing the statistical analysis of
  interval-valued responses in questionnaires measuring intrinsically
  imprecise human attributes or features (attitudes, perceptions, opinions,
  feelings, etc.). In particular, this package provides S4 classes, methods,
  and functions in order to compute basic arithmetic and statistical operations
  with interval-valued data; prepare customized plots; associate each
  interval-valued response to its equivalent Likert-type and visual analogue
  scales answers through the minimum theta-distance and the mid-point criteria;
  analyze the reliability of respondents' answers from the internal consistency
  point of view by means of Cronbach's alpha coefficient; and simulate
  interval-valued responses in this type of questionnaires. The package also
  incorporates some real-life data that can be used to illustrate its working
  with several non-trivial reproducible examples. The methodology used in this
  package is based in many theoretical and applied publications from
  SMIRE+CoDiRE (Statistical Methods with Imprecise Random Elements and
  Comparison of Distributions of Random Elements) Research Group
  (<https://bellman.ciencias.uniovi.es/smire+codire/>)
  from the University of Oviedo (Spain).
Tools for working with and comparing sets of points and intervals.
Manipulate integer-bounded intervals including finding overlaps, piling and merging.
Performs hypothesis testing
    using the interval estimates (e.g., confidence intervals). The
    non-overlapping interval estimates indicates the statistical
    significance. References to these procedures can be found at
    Noguchi and Marmolejo-Ramos (2016) <doi:10.1080/00031305.2016.1200487>,
    Bonett and Seier (2003) <doi:10.1198/0003130032323>, and
    Lemm (2006) <doi:10.1300/J082v51n02_05>.
Creation of tables of summary statistics or counts for clinical data (for 'TLFs'). 
  These tables can be exported as in-text table (with the 'flextable' package) for a Clinical Study Report 
  (Word format) or a 'topline' presentation (PowerPoint format), 
  or as interactive table (with the 'DT' package) to an html document for clinical data review.
The 'inti' package is part of the 'inkaverse' project for developing 
    different procedures and tools used in plant science and experimental designs. 
    The mean aim of the package is to support researchers during the planning of
    experiments and data collection (tarpuy()), data analysis and graphics (yupana())
    , and technical writing. 
    Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
An interval-valued extension of ordinary and simple kriging.
    Optimization of the function is based on a generalized interval distance.
    This creates a non-differentiable cost function that requires a
    differentiable approximation to the absolute value function. This
    differentiable approximation is optimized using a Newton-Raphson algorithm
    with a penalty function to impose the constraints. Analyses in the package
    are driven by the 'intsp' and 'intgrd' 
    classes, 
    which are interval-valued extensions of
    'SpatialPointsDataFrame' and 'SpatialPixelsDataFrame' respectively. 
    The package includes several wrappers to functions in the 
    'gstat' and 'sp' packages.
Provides a key-value store data structure. The keys are
    integers and the values can be any R object. This is like a list but
    indexed by a set of integers, not necessarily contiguous and possibly
    negative. The implementation uses a 'R6' class. These containers are 
    not faster than lists but their usage can be more convenient for 
    certain situations.
Implementing the interventional effects for mediation analysis for up to 3 mediators.
    The methods used are based on VanderWeele, Vansteelandt and Robins (2014) <doi:10.1097/ede.0000000000000034>, 
    Vansteelandt and Daniel (2017) <doi:10.1097/ede.0000000000000596> and Chan and Leung (2020; unpublished manuscript, available on request from the author of this package).
    Linear regression, logistic regression and Poisson regression are used for continuous, binary 
    and count mediator/outcome variables respectively.
Carries out integrative clustering analysis using multiple types of genomic dataset using integrative Non-negative Matrix factorization.
Models, analyzes, and forecasts financial intraday signals. This package
    currently supports a univariate state-space model for intraday trading volume provided
    by Chen (2016) <doi:10.2139/ssrn.3101695>.
For tree ensembles such as random forests, regularized random forests and gradient boosted trees, this package provides functions for: extracting, measuring and pruning rules; selecting a compact rule set; summarizing rules into a learner; calculating frequent variable interactions; formatting rules in latex code.  Reference: Interpreting tree ensembles with inTrees (Houtao Deng, 2019, <doi:10.1007/s41060-018-0144-8>).
Performs Goodness of Fit for regression models 
  using Integrated Regression method. Works for several 
  different fitting techniques.
Estimate the proportions of the null and the reproducibility and
    non-reproducibility of the signal group for the input data set. The Bayes factor
    calculation and EM (Expectation Maximization) algorithm procedures are also
    included.
Provides functions to estimate the intrinsic dimension of a dataset 
  via likelihood-based approaches. Specifically, the package implements the 
  'TWO-NN' and 'Gride' estimators and the 'Hidalgo' Bayesian mixture model. 
  In addition, the first reference contains an extended vignette on the usage of 
  the 'TWO-NN' and 'Hidalgo' models. References: 
    Denti (2023, <doi:10.18637/jss.v106.i09>); 
    Allegra et al. (2020, <doi:10.1038/s41598-020-72222-0>); 
    Denti et al. (2022, <doi:10.1038/s41598-022-20991-1>);
    Facco et al. (2017, <doi:10.1038/s41598-017-11873-y>); 
    Santos-Fernandez et al. (2021, <doi:10.1038/s41598-022-20991-1>).
A variety of methods for estimating intrinsic dimension of data sets (i.e the manifold or Hausdorff dimension of the support of the distribution that generated the data) as reviewed in Johnsson, K. (2016, ISBN:978-91-7623-921-6) and Johnsson, K., Soneson, C. and Fontes, M. (2015) <doi:10.1109/TPAMI.2014.2343220>. Furthermore, to evaluate the performance of these estimators, functions for generating data sets with given intrinsic dimensions are provided.
Functions for evaluating and testing asset pricing models, including
    estimation and testing of factor risk premia, selection of "strong" risk 
    factors (factors having nonzero population correlation with test asset
    returns), heteroskedasticity and autocorrelation robust covariance matrix
    estimation and testing for model misspecification and identification. 
    The functions for estimating and testing factor risk 
    premia implement the Fama-MachBeth (1973) <doi:10.1086/260061> two-pass 
    approach, the misspecification-robust approaches of Kan-Robotti-Shanken (2013) 
    <doi:10.1111/jofi.12035>, and the approaches based on tradable factor risk
    premia of Quaini-Trojani-Yuan (2023) <doi:10.2139/ssrn.4574683>. The 
    functions for selecting the "strong" risk factors are based on the Oracle
    estimator of Quaini-Trojani-Yuan (2023) <doi:10.2139/ssrn.4574683> and the 
    factor screening procedure of Gospodinov-Kan-Robotti (2014) <doi:10.2139/ssrn.2579821>. 
    The functions for evaluating model misspecification implement the HJ
    model misspecification distance of Kan-Robotti (2008) <doi:10.1016/j.jempfin.2008.03.003>,
    which is a modification of the prominent Hansen-Jagannathan (1997)
    <doi:10.1111/j.1540-6261.1997.tb04813.x> distance.
    The functions for testing model identification 
    specialize the Kleibergen-Paap (2006) <doi:10.1016/j.jeconom.2005.02.011> 
    and the Chen-Fang (2019) <doi:10.1111/j.1540-6261.1997.tb04813.x> rank test 
    to the regression coefficient matrix of test asset returns on risk factors.
    Finally, the function for heteroskedasticity and autocorrelation robust 
    covariance estimation implements the Newey-West (1994) <doi:10.2307/2297912>
    covariance estimator.
Kappa statistics is one of the most used methods to evaluate the effectiveness of inpsections based on attribute assessments in industry. However, its estimation by available methods does not provide its "real" or "intrinstic" value. This package provides functions for the computation of the intrinsic kappa value as it is described in: Rafael Sanchez-Marquez, Frank Gerhorst and David Schindler (2023) "Effectiveness of quality inspections of attributive characteristics – A novel and practical method for estimating the “intrinsic” value of kappa based on alpha and beta statistics." <doi:10.1016/j.cie.2023.109006>.
Evaluating if values
  of vectors are within different open/closed intervals
  (`x %[]% c(a, b)`), or if two closed
  intervals overlap (`c(a1, b1) %[]o[]% c(a2, b2)`).
  Operators for negation and directional relations also implemented.
Calculates event rates and compares means and variances of groups of interval data corrected for missed arrival observations.
Integration of disparate datasets is needed in order to make efficient use of all available data and thereby address the issues currently threatening biodiversity.
   Data integration is a powerful modeling framework which allows us to combine these datasets together into a single model, yet retain the strengths of each individual dataset.
   We therefore introduce the package, 'intSDM': an R package designed to help ecologists develop a reproducible workflow of integrated species distribution models, using data both provided from the user as well as data obtained freely online.
   An introduction to data integration methods is discussed in Issac, Jarzyna, Keil, Dambly, Boersch-Supan, Browning, Freeman, Golding, Guillera-Arroita, Henrys, Jarvis, Lahoz-Monfort, Pagel, Pescott, Schmucki, Simmonds and O’Hara (2020) <doi:10.1016/j.tree.2019.08.006>.
Contains implementations of
    integrative survival analysis routines, including
    regular Cox cure rate model proposed by
    Kuk and Chen (1992) <doi:10.1093/biomet/79.3.531>
    via an EM algorithm proposed by
    Sy and Taylor (2000) <doi:10.1111/j.0006-341X.2000.00227.x>,
    regularized Cox cure rate model with elastic net penalty following
    Masud et al. (2018) <doi:10.1177/0962280216677748>, and
    Zou and Hastie (2005) <doi:10.1111/j.1467-9868.2005.00503.x>, and
    weighted concordance index for cure models proposed by
    Asano and Hirakawa (2017) <doi:10.1080/10543406.2017.1293082>.
Provides tools for importing, merging, and analysing data from 
  international assessment studies (TIMSS, PIRLS, PISA, ICILS, and PIAAC).
Enum-type representation of vectors and representation
  of intervals, including a method of coercing variables in data frames.
Provides an up-to-date version of the 'InvaCost' database 
    (<doi:10.6084/m9.figshare.12668570>) in R, and
    several functions to analyse the costs of invasive alien species 
    (<doi:10.1111/2041-210X.13929>).
Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
The correction is achieved under the assumption that non-migrating cells of the essay approximately form a quadratic flow profile due to frictional effects, compare law of Hagen-Poiseuille for flow in a tube. The script fits a conical plane to give xyz-coordinates of the cells. It outputs the number of migrated cells and the new corrected coordinates.
Vector operations between grapes: An infix-only package! The 'invctr' functions perform common and less common operations on vectors, data frames matrices and list objects:
    - Extracting a value (range), or, finding the indices of a value (range).
    - Trimming, or padding a vector with a value of your choice.
    - Simple polynomial regression.
    - Set and membership operations.
    - General check & replace function for NAs, Inf and other values.
Simulate inventory policies with and without forecasting, facilitate inventory analysis calculations such as  stock levels and re-order points,pricing and promotions calculations. 
  The package includes calculations of inventory metrics, stock-out calculations and ABC analysis calculations.
    The package includes revenue management techniques such as Multi-product optimization,logit and polynomial model optimization.
  The functions are referenced from :
  1-Harris, Ford W. (1913). "How many parts to make at once". Factory, The Magazine of Management. 
  2- Nahmias, S. Production and Operations Analysis. McGraw-Hill International Edition.
  3-Silver, E.A., Pyke, D.F., Peterson, R. Inventory Management and Production Planning and Scheduling. 
  4-Ballou, R.H. Business Logistics Management. 
  5-MIT Micromasters Program. 
  6- Columbia University  course for supply and demand analysis.
  8- Price Elasticity of Demand MATH 104,Mark Mac Lean (with assistance from Patrick Chan) 2011W
  For further details or correspondence :<www.linkedin.com/in/haythamomar>, <www.rescaleanalytics.com>.
Reverse engineer a regular expression pattern for the characters
    contained in an R object. Individual characters can be categorised into
    digits, letters, punctuation or spaces and encoded into run-lengths. This
    can be used to summarise the structure of a dataset or identify non-standard
    entries. Many non-character inputs such as numeric vectors and data frames
    are supported.
Provides composable invertible transforms for
    (sparse) matrices.
Functions to facilitate inverse estimation (e.g., calibration) in
    linear, generalized linear, nonlinear, and (linear) mixed-effects models. A
    generic function is also provided for plotting fitted regression models with
    or without confidence/prediction bands that may be of use to the general
    user. For a general overview of these methods, see Greenwell and Schubert 
    Kabban (2014) <doi:10.32614/RJ-2014-009>.
Light weight implementation of the standard distribution
  functions for the inverse gamma distribution, wrapping those for the gamma
  distribution in the stats package.
Computes the log likelihood for an inverse gamma stochastic volatility model using a closed form expression of the likelihood. The details of the computation of this closed form expression are given in Gonzalez and Majoni (2023) <http://rcea.org/RePEc/pdf/wp23-11.pdf> .  
    The closed form expression is obtained for a stationary inverse gamma stochastic volatility model by marginalising out the volatility. This allows the user to obtain the maximum likelihood estimator for this non linear non Gaussian state space model. In addition, the user can obtain the estimates of the smoothed volatility using the exact smoothing distributions.
Fits the (randomized drift) inverse Gaussian distribution to survival data. The model is described in Aalen OO, Borgan O, Gjessing HK. Survival and Event History Analysis. A Process Point of View. Springer, 2008. It is based on describing time to event as the barrier hitting time of a Wiener process, where drift towards the barrier has been randomized with a Gaussian distribution. The model allows covariates to influence starting values of the Wiener process and/or average drift towards a barrier, with a user-defined choice of link functions.
Takes in vivo toxicokinetic concentration-time data and fits
    parameters of 1-compartment and 2-compartment models for each
    chemical. These methods are described in detail in "Informatics for Toxicokinetics" (submitted).
Contains functions that allow Bayesian inference on a parameter of some widely-used exponential models. The functions can generate independent samples from the closed-form posterior distribution using the inverse stable prior. Inverse stable is a non-conjugate prior for a parameter of an exponential subclass of discrete and continuous data distributions (e.g. Poisson, exponential, inverse gamma, double exponential (Laplace), half-normal/half-Gaussian, etc.). The prior class provides flexibility in capturing a wide array of prior beliefs (right-skewed and left-skewed) as modulated by a parameter that is bounded in (0,1). The generated samples can be used to simulate the prior and posterior predictive distributions. More details can be found in Cahoy and Sedransk (2019)  <doi:10.1007/s42519-018-0027-2>. The package can also be used as a teaching demo for introductory Bayesian courses.
Interaction and analysis of multiple response data,
    along with other tools for analysing these types of data including
    missing value analysis and calculation of standard errors for
    a range of covariance matrix results (proportions, multinomial,
    independent samples, and multiple response).
Simple plotting function(s) for exploratory data analysis with flexible options allowing for easy plot customisation. The goal is to make it easy for beginners to start exploring a dataset through simple R function calls, as well as provide a similar interface to summary statistics and inference information. Includes functionality to generate interactive HTML-driven graphs. Used by 'iNZight', a graphical user interface providing easy exploration and visualisation of data for students of statistics, available in both desktop and online versions.
Provides a suite of functions to use with regression models, including summaries, residual plots, and factor comparisons. Used as part of the Model Fitting module of 'iNZight', a graphical user interface providing easy exploration and visualisation of data for students of statistics, available in both desktop and online versions.
Provides a collection of wrapper functions for common variable and dataset manipulation workflows primarily used by 'iNZight', a graphical user interface providing easy exploration and visualisation of data for students of statistics, available in both desktop and online versions. Additionally, many of the functions return the 'tidyverse' code used to obtain the result in an effort to bridge the gap between GUI and coding.
Provides a collection of functions for working with time series data, including functions for drawing, decomposing, and forecasting. Includes capabilities to compare multiple series and fit both additive and multiplicative models. Used by 'iNZight', a graphical user interface providing easy exploration and visualisation of data for students of statistics, available in both desktop and online versions. Holt (1957) <doi:10.1016/j.ijforecast.2003.09.015>, Winters (1960) <doi:10.1287/mnsc.6.3.324>, Cleveland, Cleveland, & Terpenning (1990) "STL: A Seasonal-Trend Decomposition Procedure Based on Loess".
One function to read files. One function to write files. One
    function to direct plots to screen or file. Automatic file format inference
    and directory structure creation.
Calculates fundamental IO matrices (Leontief, Wassily W. (1951) <doi:10.1038/scientificamerican1051-15>); within period analysis via various rankings and coefficients (Sonis and Hewings (2006) <doi:10.1080/09535319200000013>, Blair and Miller (2009) <ISBN:978-0-521-73902-3>, Antras et al (2012) <doi:10.3386/w17819>, Hummels, Ishii, and Yi (2001) <doi:10.1016/S0022-1996(00)00093-3>); across period analysis with impact analysis (Dietzenbacher, van der Linden, and Steenge (2006) <doi:10.1080/09535319300000017>, Sonis, Hewings, and Guo (2006) <doi:10.1080/09535319600000002>); and a variety of table operators.
The data analysis module for the Iterative Optimization Heuristics
    Profiler ('IOHprofiler'). This module provides statistical analysis methods for the 
    benchmark data generated by optimization heuristics, which can be visualized through a 
    web-based interface. The benchmark data is usually generated by the 
    experimentation module, called 'IOHexperimenter'. 'IOHanalyzer' also supports
    the widely used 'COCO' (Comparing Continuous Optimisers) data format for benchmarking.
Addresses the 'log of zero' by developing a new family of 
    estimators called iterated Ordinary Least Squares. 
    This family nests standard approaches such as log-linear and 
    Poisson regressions, offers several computational advantages, 
    and corresponds to the correct way to perform the popular 
    log(Y + 1) transformation. For more details about how to use it, 
    see the notebook at: <https://www.davidbenatia.com/>.
Method for the calculation of copy numbers and calling of copy number alterations. The algorithm uses coverage data from amplicon sequencing of a sample cohort as input. The method includes significance assessment, correction for multiple testing and does not depend on normal DNA controls. Budczies (2016 Mar 15) <doi:10.18632/oncotarget.7451>.
Network functionalities specialized for data generated from input-output tables.
Collection of functions for IO Psychologists.
Density, spectral density, and regression estimation using infinite
    order flat-top kernels.
Pre-processing and basic analytical tasks related to working
    with Eurostat's symmetric input-output tables and provide basic
    input-output economics calculations. The package is part of rOpenGov
    <http://ropengov.github.io/> to open source open government initiatives.
Routines and tools for assessing the quality of content
    analysis on the basis of the Iota Reliability Concept. The concept is
    inspired by item response theory and can be applied to any kind of
    content analysis which uses a standardized coding scheme and discrete
    categories.  It is also applicable for content analysis conducted by
    artificial intelligence.  The package provides reliability measures
    for a complete scale as well as for every single category. Analysis of
    subgroup-invariance and error corrections are implemented. This
    information can support the development process of a coding scheme and
    allows a detailed inspection of the quality of the generated data.
    Equations and formulas working in this package are part of Berding et
    al. (2022)<doi:10.3389/feduc.2022.818365> and Berding and Pargmann
    (2022) <doi:10.30819/5581>.
Basic I/O tools for streaming and data parsing.
Provides S4 classes for Internet Protocol (IP) versions 4 and 6 addresses and efficient methods for 'IP' addresses comparison, arithmetic, bit manipulation and lookup. Both 'IPv4' and 'IPv6' arbitrary ranges are also supported as well as internationalized ('IDN') domain lookup with and 'whois' query.
Enables the user to find the country, region, district, city, coordinates, zip code, time zone, ISP, domain name, connection type, area code, weather, Mobile Country Code, Mobile Network Code, mobile brand name, elevation, usage type, address type, IAB category and Autonomous system information that any IP address or hostname originates from. Supported IPv4 and IPv6.
        Please visit <https://www.ip2location.com> to learn more. You may also want to visit <https://lite.ip2location.com> for free database download.
        This package requires 'IP2Location Python' module. At the terminal, please run 'pip install IP2Location' to install the module.
A system for submitting multiple IP information queries to 'IP2Location.io'’s IP Geolocation API and storing the resulting data in a dataframe. You provide a vector of IP addresses and your 'IP2Location.io' API key. The package returns a dataframe with one row per IP address and a column for each available data field (data fields not included in your API plan will contain NAs). This is the second submission of the package to CRAN.
Query for enriched data such as country, region, city, latitude & longitude, ZIP code, time zone, Autonomous System, Internet Service Provider, domain, net speed, International direct dialing (IDD) code, area code, weather station data, mobile data, elevation, usage type, address type, advertisement category, fraud score, and proxy data with an IP address. You can also query a list of hosted domain names for the IP address too.
    This package uses the 'IP2Location.io' API to query this data. To get started with a free API key, sign up here <https://www.ip2location.io/sign-up?ref=1>.
Enable user to find the IP addresses which are used as VPN anonymizer, open proxies, web proxies and Tor exits.
    The package lookup the proxy IP address from IP2Proxy BIN Data file. You may visit <https://lite.ip2location.com> for free database download.
Easily implement the checking of 'WHOIS' information for a particular domain. 'IP2WHOIS' supports the query for 1113 Top-level Domains(TLDs) and 634 Country Code Top-level Domains(ccTLDs).
    To get started with a free API key, you may sign up at here <https://www.ip2whois.com/register>.
Converts character vectors between phonetic
    representations.  Supports IPA (International Phonetic Alphabet),
    X-SAMPA (Extended Speech Assessment Methods Phonetic Alphabet), and
    ARPABET (used by the CMU Pronouncing Dictionary).
Classes and functions for working with IP (Internet Protocol)
    addresses and networks, inspired by the Python 'ipaddress' module.
    Offers full support for both IPv4 and IPv6 (Internet Protocol versions
    4 and 6) address spaces. It is specifically designed to work well with
    the 'tidyverse'.
A data clustering package based on admixture ratios (Q matrix) of population structure. The framework is based on iterative Pruning procedure that performs data clustering by splitting a given population into subclusters until meeting the condition of stopping criteria the same as ipPCA, iNJclust, and IPCAPS frameworks. The package also provides a function to retrieve phylogeny tree that construct a neighbor-joining tree based on a similar matrix between clusters. By given multiple Q matrices with varying a number of ancestors (K), the framework define a similar value between clusters i,j as a minimum number K* that makes majority of members of two clusters are in the different clusters. This K* reflexes a minimum number of ancestors we need to splitting cluster i,j into different clusters if we assign K* clusters based on maximum admixture ratio of individuals. The publication of this package is at Chainarong Amornbunchornvej, Pongsakorn Wangkumhang, and Sissades Tongsima (2020) <doi:10.1101/2020.03.21.001206>.
Read data from 'LimeSurvey'
    (<https://www.limesurvey.org/>)
    in a comfortable way.
    Heavily inspired by 'limer'
    (<https://github.com/cloudyr/limer/>),
    which lacked a few comfort features for me.
An R client for the 'ipbase.com' IP Geolocation 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://ipbase.com/docs> .
Provides tools for passing messages between R processes. 
    Shiny examples are provided showing how to perform useful tasks such as: 
    updating reactive values from within a future, progress bars for long running 
    async tasks, and interrupting async tasks based on user input.
We propose the inverse probability-of-censoring weighted (IPCW) Kendall's tau to measure the association of the survival trait with biomarkers and Kendall's partial correlation to reflect the relationship of the survival trait with interaction variable conditional on main effects, as described in Wang and Chen (2020) <doi:10.1093/bioinformatics/btaa017>.
Performs valid statistical inference on predicted data (IPD) using recent methods, where for a subset of the data, the outcomes have been predicted by an algorithm. Provides a wrapper function with specified defaults for the type of model and method to be used for estimation and inference. Further provides methods for tidying and summarizing results. Salerno et al., (2024) <doi:10.48550/arXiv.2410.09665>.
An implementation to reconstruct individual patient data from Kaplan-Meier (K-M) survival curves, visualize and assess the accuracy of the reconstruction, then perform secondary analysis on the reconstructed data. We involve a simple function to extract the coordinates form the published K-M curves. The function is developed based on Poisot T. ’s digitize package (2011)  <doi:10.32614/RJ-2011-004> . For more complex and tangled together graphs, digitizing software, such as 'DigitizeIt' (for MAC or windows) or 'ScanIt'(for windows) can be used to get the coordinates. Additional information should also be involved to increase the accuracy, like numbers of patients at risk (often reported at 5-10 time points under the x-axis of the K-M graph), total number of patients, and total number of events. The package implements the modified iterative K-M estimation algorithm (modified-iKM) improved upon the approach proposed by Guyot (2012) <doi:10.1186/1471-2288-12-9> with some modifications.
Functions are provided to interpolate geo-referenced point data via
    Inverse Path Distance Weighting. Useful for coastal marine applications where
    barriers in the landscape preclude interpolation with Euclidean distances.
Allows direct access to the macroeconomic, 
             financial and regional database maintained by 
             Brazilian Institute for Applied Economic Research ('Ipea').
             This R package uses the 'Ipeadata' API. For more information, 
             see <http://www.ipeadata.gov.br/>.
Convenient functions to create 'ggplot2' graphics following the 
             editorial guidelines of the  Institute for Applied Economic 
             Research (Ipea).
Calculates the RMS intrinsic and parameter-effects curvatures of a nonlinear regression model. The curvatures are global measures of assessing whether a model/data set combination is close-to-linear or not. See Bates and Watts (1980) <doi:10.1002/9780470316757> and Ratkowsky and Reddy (2017) <doi:10.1093/aesa/saw098> for details.
Contains data on Post-Secondary Institution Statistics in 2020 <https://nces.ed.gov/ipeds/use-the-data>. The package allows easy access to a wide variety of information regarding Post-secondary Institutions, its students, faculty, and their demographics, financial aid, educational and recreational offerings, and completions. This package can be used by students, college counselors, or involved parents interested in pursuing higher education, considering their options, and securing admission into their school of choice.
Starting from user-supplied institutional data, these scripts 
    transform, aggregate, and reshape the information to produce 
    key-value pair data files that are able to be uploaded to IPEDS (Integrated Postsecondary Education Data System) 
    through their submission portal <https://surveys.nces.ed.gov/ipeds/>. Starting data specifications can be found in the vignettes.  
    Final files are saved locally to a location of the user's choice. 
    User-friendly readable files can also be produced for purposes of data review and validation.
A tool to calculate the performance of a time series in a specific date or period. It is more intended for data analysis in the fields of finance, banking, telecommunications or operational marketing.
The core of the package is cvr2.ipflasso(), an extension of glmnet to be used when the (large) set of available predictors is partitioned into several modalities which potentially differ with respect to their information content in terms of prediction. For example, in biomedical applications patient outcome such as survival time or response to therapy may have to be predicted based on, say, mRNA data, miRNA data, methylation data, CNV data, clinical data, etc. The clinical predictors are on average often much more important for outcome prediction than the mRNA data. The ipflasso method takes this problem into account by using different penalty parameters for predictors from different modalities. The ratio between the different penalty parameters can be chosen from a set of optional candidates by cross-validation or alternatively generated from the input data.
A fast (C) implementation of the iterative proportional fitting
    procedure.
Performs iterative proportional updating given a seed table and
  an arbitrary number of marginal distributions. This is commonly used in
  population synthesis, survey raking, matrix rebalancing, and other
  applications. For example, a household survey may be weighted to match the
  known distribution of households by size from the census. An origin/
  destination trip matrix might be balanced to match traffic counts.
  The approach used by this package is based on a paper from
  Arizona State University (Ye, Xin, et. al. (2009)
  <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.537.723&rep=rep1&type=pdf>).
  Some enhancements have been made to their work including primary and 
  secondary target balance/importance, general marginal agreement, and weight 
  restriction.
Algorithms and utility functions for indoor positioning using fingerprinting techniques. 
    These functions are designed for manipulation of RSSI (Received Signal Strength Intensity) data 
    sets, estimation of positions,comparison of the performance of different models, and graphical 
    visualization of data. Machine learning algorithms and methods such as k-nearest neighbors or
    probabilistic fingerprinting are implemented in this package to perform analysis
    and estimations over RSSI data sets.
When you want to install R package or download file from GitHub, 
    but you can't access GitHub, this package helps you install R packages or 
    download file from GitHub via the proxy website <https://gh-proxy.com/> 
    or <https://ghfast.top/>, which is in real-time sync with GitHub.
Combining genomic prediction with Monte Carlo simulation, three different 
    strategies are implemented to select parental lines for multiple traits in plant 
    breeding. The selection strategies include (i) GEBV-O considers only genomic 
    estimated breeding values (GEBVs) of the candidate individuals; (ii) GD-O 
    considers only genomic diversity (GD) of the candidate individuals; and (iii) 
    GEBV-GD considers both GEBV and GD. The above method can be seen in Chung PY, 
    Liao CT (2020) <doi:10.1371/journal.pone.0243159>. Multi-trait genomic best 
    linear unbiased prediction (MT-GBLUP) model is used to simultaneously estimate 
    GEBVs of the target traits, and then a selection index is adopted to evaluate 
    the composite performance of an individual.
An R client for the 'iplookupapi.com' IP Lookup 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://iplookupapi.com/docs> .
Provides functions and data sets to accompany the  book 'Integrated Population Models: Theory and Ecological Applications with R and JAGS' by Michael Schaub and Marc Kéry (ISBN: 9780128205648).
Flexibly implements Integral Projection Models using a
  mathematical(ish) syntax. This package will not help with the vital rate
  modeling process, but will help convert those regression models into an
  IPM. 'ipmr' handles density dependence and environmental stochasticity, with a
  couple of options for implementing the latter. In addition, provides functions
  to avoid unintentional eviction of individuals from models. Additionally, 
  provides model diagnostic tools, plotting functionality, 
  stochastic/deterministic simulations, and analysis tools.
  Integral projection models are described in depth by Easterling et al. (2000) 
  <doi:10.1890/0012-9658(2000)081[0694:SSSAAN]2.0.CO;2>, Merow et al. (2013) 
  <doi:10.1111/2041-210X.12146>, Rees et al. (2014) <doi:10.1111/1365-2656.12178>,
  and Metcalf et al. (2015) <doi:10.1111/2041-210X.12405>. 
  Williams et al. (2012) <doi:10.1890/11-2147.1> discuss the problem of 
  unintentional eviction.
Calculation of key bacterial growth curve parameters using fourth degree polynomial functions. 
    Six growth curve parameters are provided including peak growth rate, doubling time, lag time, maximum growth, and etc.
    'ipolygrowth' takes time series data from individual biological samples (with technical replicates) or multiple samples.
Generates random numbers corresponding to the events on a Poisson point process with changing event rates. This includes the possibility to incorporate additional information such as the number of events occurring or the location of an already known event. It can also generate the probability density functions of specific events in the cases where additional information is available. Based on Hohmann (2019) <arXiv:1901.10754>.
Let us consider a sample of patients who can suffer from several diseases simultaneously, in a given set of diseases. The goal of the implemented algorithm is to estimate the individual average cost of each disease, starting from the global health costs available for each patient.
Improved predictive models by indirect classification and
  bagging for classification, regression and survival problems 
  as well as resampling based estimators of prediction error.
Provides methods to perform and analyse I-prior regression models.
    Estimation is done either via direct optimisation of the log-likelihood or 
    an EM algorithm.
Immunotherapy has revolutionized cancer treatment, but predicting patient
    response remains challenging. Here, we presented Intelligent Predicting
    Response to cancer Immunotherapy through Systematic Modeling (iPRISM), a
    novel network-based model that integrates multiple data types to predict
    immunotherapy outcomes. It incorporates gene expression, biological
    functional network, tumor microenvironment characteristics, immune-related
    pathways, and clinical data to provide a comprehensive view of factors
    influencing immunotherapy efficacy. By identifying key genetic and
    immunological factors, it provides an insight for more personalized
    treatment strategies and combination therapies to overcome resistance
    mechanisms.
Functions that wrap popular phylogenetic software for sequence
    alignment, masking of sequence alignments, and estimation of phylogenies and
    ancestral character states.
Estimates the density of a spatially distributed animal population 
  sampled with an array of passive detectors, such as traps. Models incorporating 
  distance-dependent detection are fitted by simulation and inverse prediction 
  as proposed by Efford (2004) <doi:10.1111/j.0030-1299.2004.13043.x>.
Advanced fuzzy logic based techniques are implemented to compute the similarity among different objects or items. Typically, application areas consist of transforming raw data into the corresponding advanced fuzzy logic representation and determining the similarity between two objects using advanced fuzzy similarity techniques in various fields of research, such as text classification, pattern recognition, software projects, decision-making, medical diagnosis, and market prediction. Functions are designed to compute the membership, non-membership, hesitant-membership, indeterminacy-membership, and refusal-membership for the input matrices. Furthermore, it also includes a large number of advanced fuzzy logic based similarity measure functions to compute the Intuitionistic fuzzy similarity (IFS), Pythagorean fuzzy similarity (PFS), and Spherical fuzzy similarity (SFS) between two objects or items based on their fuzzy relationships. It also includes working examples for each function with sample data sets.
Contains data sets, programmes and illustrations 
    discussed in the book, "Introduction to Probability, Statistics and R:
    Foundations for Data-Based Sciences."  Sahu (2024, isbn:9783031378645)
    describes the methods in detail.
An easy way to work with census, survey, and geographic data
    provided by IPUMS in R. Generate and download data through the IPUMS
    API and load IPUMS files into R with their associated metadata to
    make analysis easier. IPUMS data describing 1.4 billion individuals
    drawn from over 750 censuses and surveys is available free of charge
    from the IPUMS website <https://www.ipums.org>.
Generate plots based on the Item Pool Visualization concept for
    latent constructs. Item Pool Visualizations are used to display the
    conceptual structure of a set of items (self-report or psychometric).
    Dantlgraber, Stieger, & Reips (2019) <doi:10.1177/2059799119884283>.
Functions to estimate the probability to receive the observed treatment, based on
    individual characteristics. The inverse of these probabilities can be used as weights when
	estimating causal effects from observational data via marginal structural models. Both point
	treatment situations and longitudinal studies can be analysed. The same functions can be used to
	correct for informative censoring.
Boxplots adapted to the happenstance of missing observations where drop-out probabilities can be given by the practitioner or  modelled  using auxiliary covariates. The paper of "Zhang, Z., Chen, Z., Troendle, J. F. and Zhang, J.(2012) <doi:10.1111/j.1541-0420.2011.01712.x>", proposes estimators of marginal quantiles based on the Inverse Probability Weighting method.
An implementation of corrected sandwich variance (CSV) estimation method for making inference of marginal hazard ratios (HR) in inverse probability weighted (IPW) Cox model without and with clustered data, proposed by Shu, Young, Toh, and Wang (2019) in their paper under revision for Biometrics. Both conventional inverse probability weights and stabilized weights are implemented. Logistic regression model is assumed for propensity score model.
An implementation of the correction methods proposed by Shu and Yi (2017) <doi:10.1177/0962280217743777> for the inverse probability weighted (IPW) estimation of average treatment effect (ATE) with misclassified binary outcomes. Logistic regression model is assumed for treatment model for all implemented correction methods, and is assumed for the outcome model for the implemented doubly robust correction method. Misclassification probability given a true value of the outcome is assumed to be the same for all individuals.
An implementation of the MaxLFQ algorithm by
    Cox et al. (2014) <doi:10.1074/mcp.M113.031591> in a comprehensive
    pipeline for processing proteomics data in data-independent acquisition mode
    (Pham et al. 2020 <doi:10.1093/bioinformatics/btz961>).
    It offers additional options for protein quantification using
    the N most intense fragment ions, using all fragment ions, and
    a wrapper for the median polish algorithm by Tukey (1977, ISBN:0201076160).
    In general, the tool can be used to integrate multiple 
    proportional observations into a single quantitative value.
Builds statistical control charts with exact limits for
        univariate and multivariate cases.
Functions to import and handle infrared spectra (import from '.csv' and
  Thermo Galactic's '.spc', baseline correction, binning, clipping,
  interpolating, smoothing, averaging, adding, subtracting, dividing, 
  multiplying, atmospheric correction, 'tidyverse' methods, plotting).
Iterated race is an extension of the Iterated F-race method for
             the automatic configuration of optimization algorithms, that is,
             (offline) tuning their parameters by finding the most appropriate
             settings given a set of instances of an optimization problem.
             M. López-Ibáñez, J. Dubois-Lacoste, L. Pérez Cáceres, T. Stützle,
             and M. Birattari (2016) <doi:10.1016/j.orp.2016.09.002>.
Graphical visualization tools for analyzing the data produced by 'irace'. The 'iraceplot' package enables users to analyze the performance and the parameter space data sampled by the configuration during the search process. It provides a set of functions that generate different plots to visualize the configurations sampled during the execution of 'irace' and their performance. The functions just require the log file generated by 'irace' and, in some cases, they can be used with user-provided data.
Fit a predictive model using iteratively reweighted boosting (IRBoost) to minimize robust loss functions within the CC-family (concave-convex). This constitutes an application of iteratively reweighted convex optimization (IRCO), where convex optimization is performed using the functional descent boosting algorithm. IRBoost assigns weights to facilitate outlier identification. Applications include robust generalized linear models and robust accelerated failure time models. Wang (2025) <doi:10.6339/24-JDS1138>.
Provides implementation of various correlation coefficients of common use in
  Information Retrieval. In particular, it includes Kendall (1970, isbn:0852641990) tau coefficient
  as well as tau_a and tau_b for the treatment of ties. It also includes Yilmaz et al. (2008)
  <doi:10.1145/1390334.1390435> tauAP correlation coefficient, and versions tauAP_a and tauAP_b
  developed by Urbano and Marrero (2017) <doi:10.1145/3121050.3121106> to cope with ties.
An interface to the rich display capabilities of 'Jupyter' front-ends (e.g. 'Jupyter Notebook') <https://jupyter.org>.
    Designed to be used from a running 'IRkernel' session <https://irkernel.github.io>.
Contains some important regression methods for interval-valued variables. For each method, it is available the fitted values, residuals and some goodness-of-fit measures.
Calculates intraclass correlation coefficient (ICC) for assessing reproducibility of interval-censored data with two repeated measurements (Kovacic and Varnai (2014) <doi:10.1097/EDE.0000000000000139>). ICC is estimated by maximum likelihood from model with one fixed and one random effect (both intercepts). Help in model checking (normality of subjects' means and residuals) is provided.
Provides a scaling method to obtain a standardized Moran's I measure. Moran's I is a measure for the spatial autocorrelation of a data set, it gives a measure of similarity between data and its surrounding. The range of this value must be [-1,1], but this does not happen in practice. This package scale the Moran's I value and map it into the theoretical range of [-1,1]. Once the Moran's I value is rescaled, it facilitates the comparison between projects, for instance, a researcher can calculate Moran's I in a city in China, with a sample size of n1 and area of interest a1. Another researcher runs a similar experiment in a city in Mexico with different sample size, n2, and an area of interest a2. Due to the differences between the conditions, it is not possible to compare Moran's I in a straightforward way. In this version of the package, the spatial autocorrelation Moran's I is calculated as proposed in Chen(2013) <arXiv:1606.03658>.
Provides examples of code for analyzing data or accomplishing tasks that may be useful to institutional or educational researchers.
A comprehensive suite of tools for managing, processing, and analyzing data from the IFCB. I R FlowCytobot ('iRfcb') supports quality control, geospatial analysis, and preparation of IFCB data for publication in databases like <https://www.gbif.org>, <https://www.obis.org>, <https://emodnet.ec.europa.eu/en>, <https://shark.smhi.se/>, and <https://www.ecotaxa.org>. The package integrates with the MATLAB 'ifcb-analysis' tool, which is described in Sosik and Olson (2007) <doi:10.4319/lom.2007.5.204>, and provides features for working with raw, manually classified, and machine learning–classified image datasets. Key functionalities include image extraction, particle size distribution analysis, taxonomic data handling, and biomass concentration calculations, essential for plankton research.
Fits a double logistic function to NDVI time series and calculates 
             instantaneous rate of green (IRG) according to methods described
             in Bischoff et al. (2012) <doi:10.1086/667590>.
Provides the dataset and an implementation of the method illustrated in Friel, N., Rastelli, R., Wyse, J. and Raftery, A.E. (2016) <DOI:10.1073/pnas.1606295113>.
Classes and functions for metrics calculation as part of the
             'EarthScope MUSTANG' project. The functionality in this package 
             builds upon the base classes of the 'IRISSeismic' package.
             Metrics include basic statistics as well as higher level
             'health' metrics that can help identify problematic seismometers.
Provides classes and methods for seismic data analysis. The
             base classes and methods are inspired by the python code found in
             the 'ObsPy' python toolbox <https://github.com/obspy/obspy>. Additional classes and 
             methods support data returned by web services provided by the 'IRIS DMC'
             <http://service.iris.edu/>.
The R kernel for the 'Jupyter' environment executes R code which the front-end
    ('Jupyter Notebook' or other front-ends) submits to the kernel via the network.
Fast and memory efficient methods for truncated singular value
    decomposition and principal components analysis of large sparse and dense
    matrices.
The Row-column designs are widely recommended for experimental situations when there are two well-identified factors that are cross-classified representing known sources of variability. These designs are expected to result a gain in accuracy of estimating treatment comparisons in an experiment as they eliminate the effects of the row and column factors. However, these designs are not readily available when the number of treatments is more than the levels of row and column blocking factors. This package named 'iRoCoDe' generates row-column designs with incomplete rows and columns, by amalgamating two incomplete block designs (D1 and D2). The selection of D1 and D2 (the input designs) can be done from the available incomplete block designs, viz., balanced incomplete block designs/ partially balanced incomplete block designs/ t-designs. (Mcsorley, J.P., Phillips, N.C., Wallis, W.D. and Yucas, J.L. (2005).<doi:10.1007/s10623-003-6149-9>).
Imbalanced domain learning has almost exclusively focused on solving 
    classification tasks, where the objective is to predict cases labelled with a 
    rare class accurately. Such a well-defined approach for regression tasks lacked 
    due to two main factors. First, standard regression tasks assume that each value 
    is equally important to the user. Second, standard evaluation metrics focus on 
    assessing the performance of the model on the most common cases. This package 
    contains methods to tackle imbalanced domain learning problems in regression 
    tasks, where the objective is to predict extreme (rare) values.
    The methods contained in this package are: 1) an automatic and non-parametric 
    method to obtain such relevance functions; 2) visualisation tools; 3) suite of 
    evaluation measures for optimisation/validation processes; 4) the squared-error 
    relevance area measure, an evaluation metric tailored for imbalanced regression tasks.
    More information can be found in Ribeiro and Moniz (2020) <doi:10.1007/s10994-020-05900-9>.
A procedure for seeding R's built in random number
    generators using a variable-length sequence of values.
    Accumulates input entropy into a 256-bit hash digest or "ironseed"
    and is able to generate a variable-length sequence of output seeds
    from an ironseed.
Coefficients of Interrater Reliability and Agreement for
        quantitative, ordinal and nominal data: ICC, Finn-Coefficient,
        Robinson's A, Kendall's W, Cohen's Kappa, ...
Implements a 'Shiny Item Analysis' module and functions for computing false positive rate 
  and other binary classification metrics from inter-rater reliability based on Bartoš & Martinková (2024) 
   <doi:10.1111/bmsp.12343>.
Calculates various chance-corrected agreement coefficients (CAC) among 2 or more raters are provided. 
	Among the CAC coefficients covered are Cohen's kappa, Conger's kappa, Fleiss' kappa, Brennan-Prediger coefficient, Gwet's AC1/AC2 
	coefficients, and Krippendorff's alpha. Multiple sets of weights are proposed for computing weighted analyses. All of these statistical 
	procedures are described in details in Gwet, K.L. (2014,ISBN:978-0970806284): "Handbook of Inter-Rater Reliability," 4th edition, 
	Advanced Analytics, LLC.
Functions to help with analysis of longitudinal data featuring irregular observation times, where the observation times may be associated with the outcome process. There are functions to quantify the degree of irregularity, fit inverse-intensity weighted Generalized Estimating Equations (Lin H, Scharfstein DO, Rosenheck RA (2004) <doi:10.1111/j.1467-9868.2004.b5543.x>), perform multiple outputation (Pullenayegum EM (2016) <doi:10.1002/sim.6829>) and fit semi-parametric joint models (Liang Y (2009) <doi: 10.1111/j.1541-0420.2008.01104.x>).
Calculates various intraclass correlation coefficients used to quantify 
  inter-rater and intra-rater reliability.  The assumption here is that the raters produced quantitative ratings. Most of the statistical procedures implemented
  in this package are described in details in Gwet, K.L. (2014, ISBN:978-0970806284): "Handbook of Inter-Rater Reliability," 4th edition, 
  Advanced Analytics, LLC.
Provides coefficients of interrater reliability that are generalized to cope with randomly incomplete (i.e. unbalanced) datasets without any imputation of missing values or any (row-wise or column-wise) omissions of actually available data. Applied to complete (balanced) datasets, these generalizations yield the same results as the common procedures, namely the Intraclass Correlation according to McGraw & Wong (1996) \doi{10.1037/1082-989X.1.1.30} and the Coefficient of Concordance according to Kendall & Babington Smith (1939) \doi{10.1214/aoms/1177732186}.
A collection of Item Response Theory (IRT) and Computerized 
     Adaptive Testing (CAT) functions that are used in psychometrics.
Dichotomous and polytomous data analysis and their scoring using the unidimensional Item Response Theory model (Chalmers (2012) <doi:10.18637/jss.v048.i06>) with user-friendly graphic User Interface. Suitable for beginners who are learning item response theory.
Applying the family of the Bayesian Expectation-Maximization-Maximization (BEMM) algorithm to estimate: (1) Three parameter logistic (3PL) model proposed by Birnbaum (1968, ISBN:9780201043105); (2) four parameter logistic (4PL) model proposed by Barton & Lord (1981) <doi:10.1002/j.2333-8504.1981.tb01255.x>; (3) one parameter logistic guessing (1PLG) and (4) one parameter logistic ability-based guessing (1PLAG) models proposed by San Martín et al (2006) <doi:10.1177/0146621605282773>. The BEMM family includes (1) the BEMM algorithm for 3PL model proposed by Guo & Zheng (2019) <doi:10.3389/fpsyg.2019.01175>; (2) the BEMM algorithm for 1PLG model and (3) the BEMM algorithm for 1PLAG model proposed by Guo, Wu, Zheng, & Chen (2021) <doi:10.1177/0146621621990761>; (4) the BEMM algorithm for 4PL model proposed by Zheng, Guo, & Kern (2021) <doi:10.1177/21582440211052556>; and (5) their maximum likelihood estimation versions proposed by Zheng, Meng, Guo, & Liu (2018) <doi:10.3389/fpsyg.2017.02302>. Thus, both Bayesian modal estimates and maximum likelihood estimates are available.
Includes a collection of shiny applications to demonstrate
  or to explore fundamental item response theory (IRT) concepts
  such as estimation, scoring, and multidimensional IRT models.
Item response theory (IRT) parameter estimation using marginal maximum likelihood and expectation-maximization algorithm 
    (Bock & Aitkin, 1981 <doi:10.1007/BF02293801>). 
    Within parameter estimation algorithm, several methods for latent distribution estimation are available.
    Reflecting some features of the true latent distribution, these latent distribution estimation methods can possibly enhance the estimation accuracy and free the normality assumption on the latent distribution.
Performing Item Response Theory analysis such as parameter estimation, ability estimation, data generation, item and model fit analyse, local independence assumption, dimensionality assumption, wright map, characteristic and information curves under various models with a user-friendly Graphic User Interface.
IRT-M is a semi-supervised approach based on Bayesian Item Response Theory
    that produces theoretically identified underlying dimensions from input data
    and a constraints matrix. The methodology is fully described in 'Morucci et al. (2024),
    "Measurement That Matches Theory: Theory-Driven Identification in Item Response Theory Models"'. 
    Details are available at <https://www.cambridge.org/core/journals/american-political-science-review/article/measurement-that-matches-theory-theorydriven-identification-in-item-response-theory-models/395DA1DFE3DCD7B866DC053D7554A30B>.
A collection of functions useful in learning and practicing IRT,
    which can be combined into larger programs. Provides basic CTT analysis,
    a simple common interface to the estimation of item
    parameters in IRT models for binary responses with three different programs
    (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME, EAP, WLE, plausible 
    values), item and person fit statistics, scaling methods (MM, MS, Stocking-Lord,
    and the complete Hebaera method), and a rich array of parametric and 
    non-parametric (kernel) plots. Estimates and plots Haberman's interaction model
    when all items are dichotomously scored.
Implementation of analytical and sampling-based power analyses for
    the Wald, likelihood ratio (LR), score, and gradient tests. Can be applied
    to item response theory (IRT) models that are fitted using marginal maximum
    likelihood estimation. The methods are described in our paper
    (Zimmer et al. (2022) <doi:10.1007/s11336-022-09883-5>).
Fit unidimensional item response theory (IRT) models to test
    data, which includes both dichotomous and polytomous items, calibrate 
    pretest item parameters, estimate examinees' abilities, and examine 
    the IRT model-data fit on item-level in different ways as well as provide 
    useful functions related to IRT analyses such as IRT model-data fit 
    evaluation and differential item functioning analysis. 
    The bring.flexmirt() and write.flexmirt() functions were written by modifying 
    the read.flexmirt() function (Pritikin & Falk (2022) <doi:10.1177/0146621620929431>).
    The bring.bilog() and bring.parscale() functions were written by modifying the read.bilog() 
    and read.parscale() functions, respectively (Weeks (2010) <doi:10.18637/jss.v035.i12>).
    The bisection() function was written by modifying the bisection() function 
    (Howard (2017, ISBN:9780367657918)). The code of the inverse test characteristic curve 
    scoring in the est_score() function was written by modifying the irt.eq.tse() function 
    (González (2014) <doi:10.18637/jss.v059.i07>). In est_score() function, the code of weighted 
    likelihood estimation method was written by referring to the Pi(), Ji(), and Ii() functions
    of the catR package (Magis & Barrada (2017) <doi:10.18637/jss.v076.c01>).
Helper functions and example data sets to facilitate the estimation of IRTree models from data with different shape and using different software.
Estimation of reliability coefficients for ability estimates and sum scores from item response theory models as defined in Cheng, Y., Yuan, K.-H. and Liu, C. (2012) <doi:10.1177/0013164411407315> and Kim, S. and Feldt, L. S. (2010) <doi:10.1007/s12564-009-9062-8>. The package supports the 3-PL and generalized partial credit models and includes estimates of the standard errors of the reliability coefficient estimators, derived in Andersson, B. and Xin, T. (2018) <doi:10.1177/0013164417713570>.
Interactive shiny application for running Item Response Theory
    analysis. Provides graphics for characteristic and information curves.
The ISA is a biclustering algorithm that finds modules 
  in an input matrix. A module or bicluster is a block of the
  reordered input matrix.
We provide data sets used in the textbook "Introduction to Sports Analytics using R" by Elmore and Urbaczweski (2025).
These are data and functions to support quantitative peace science
    research. The data are important state-year information on democracy and
    wealth, which require periodic updates and regular maintenance. The
    functions permit some exploratory and diagnostic assessment of the kinds of
    data in demand by the community, but do not impose many dependencies on the
    user.
Reads the output of the 'PerkinElmer InForm' software <http://www.perkinelmer.com/product/inform-cell-analysis-one-seat-cls135781>. In addition to cell-density count, it can derive statistics of intercellular spatial distance for each cell-type.
ISA is a metadata framework to manage an increasingly diverse set 
    of life science, environmental and biomedical experiments. In isatabr 
    methods for reading, modifying and writing of files in the ISA-Tab format
    are implemented. It also contains methods for processing assay data.
The Inductive Subgroup Comparison Approach ('ISCA') offers a way to compare groups that are internally differentiated and heterogeneous. It starts by identifying the social structure of a reference group against which a minority or another group is to be compared, yielding empirical subgroups to which minority members are then matched based on how similar they are. The modelling of specific outcomes then occurs within specific subgroups in which majority and minority members are matched. 'ISCA' is characterized by its data-driven, probabilistic, and iterative approach and combines fuzzy clustering, Monte Carlo simulation, and regression analysis. ISCA_random_assignments() assigns subjects probabilistically to subgroups. ISCA_clustertable() provides summary statistics of each cluster across iterations. ISCA_modeling() provides Ordinary Least Squares regression results for each cluster across iterations. For further details please see Drouhot (2021) <doi:10.1086/712804>.
Implementation of functions to assign corresponding common job prestige scores (SIOPS, ISEI), the official job or group title and the ISCO-88 code to given ISCO-08 codes. ISCO-08 is the latest version of the International Standard Classification of Occupations which is used to organise information on labour and jobs.
Implementation of a KL-based scoring rule to assess the quality of different missing value imputations in the broad sense as introduced in Michel et al. (2021)  <arXiv:2106.03742>.
Provides datasets for the book "Introduction to Statistical Data Analysis for the Life Sciences, Second edition" by Ekstrøm and Sørensen (2014).
Tools for parsing 'NOAA' Integrated Surface Data ('ISD') files,
    described at <https://www.ncdc.noaa.gov/isd>. Data includes for example,
    wind speed and direction, temperature, cloud data, sea level pressure,
    and more. Includes data from approximately 35,000 stations worldwide,
    though best coverage is in North America/Europe/Australia. Data is stored
    as variable length ASCII character strings, with most fields optional.
    Included are tools for parsing entire files, or individual lines of data.
Characterisation and calibration of single or multiple Ion Selective Electrodes (ISEs); 
    activity estimation of experimental samples. Implements methods described in:
	Dillingham, P.W., Radu, T., Diamond, D., Radu, A. and McGraw, C.M. (2012) <doi:10.1002/elan.201100510>,  
	Dillingham, P.W., Alsaedi, B.S.O. and McGraw, C.M. (2017) <doi:10.1109/ICSENS.2017.8233898>,
	Dillingham, P.W., Alsaedi, B.S.O., Radu, A., and McGraw, C.M. (2019) <doi:10.3390/s19204544>, and
	Dillingham, P.W., Alsaedi, B.S.O., Granados-Focil, S., Radu, A., and McGraw, C.M. (2020)  <doi:10.1021/acssensors.9b02133>.
The implement of integrative analysis methods based on a two-part penalization, which realizes dimension reduction analysis and mining the heterogeneity and association of multiple studies with compatible designs. The software package provides the integrative analysis methods including integrative sparse principal component analysis (Fang et al., 2018), integrative sparse partial least squares (Liang et al., 2021) and integrative sparse canonical correlation analysis, as well as corresponding individual analysis and meta-analysis versions. References: (1) Fang, K., Fan, X., Zhang, Q., and Ma, S. (2018). Integrative sparse principal component analysis. Journal of Multivariate Analysis, <doi:10.1016/j.jmva.2018.02.002>. (2) Liang, W., Ma, S., Zhang, Q., and Zhu, T. (2021). Integrative sparse partial least squares. Statistics in Medicine, <doi:10.1002/sim.8900>.
This network estimation procedure eLasso, which is based on the Ising model, combines l1-regularized logistic regression with model selection based on the Extended Bayesian Information Criterion (EBIC). EBIC is a fit measure that identifies relevant relationships between variables. The resulting network consists of variables as nodes and relevant relationships as edges. Can deal with binary data.
A toolbox for constructing potential landscapes for Ising
    networks. The parameters of the networks can be directly supplied by
    users or estimated by the 'IsingFit' package by van Borkulo and
    Epskamp (2016) <https://CRAN.R-project.org/package=IsingFit> from
    empirical data. The Ising model's Boltzmann distribution is preserved
    for the potential landscape function. The landscape functions can be
    used for quantifying and visualizing the stability of network states,
    as well as visualizing the simulation process.
Classical Ising Model is a land mark system in statistical physics.The model explains the physics of spin glasses and magnetic materials, and cooperative phenomenon in general, for example phase transitions and neural networks.This package provides utilities to simulate one dimensional Ising Model with Metropolis and Glauber Monte Carlo with single flip dynamics in periodic boundary conditions. Utility functions for exact solutions are provided.
Sample states from the Ising model and compute the probability of states. Sampling can be done for any number of nodes, but due to the intractibility of the Ising model the distribution can only be computed up to ~10 nodes.
Develops stochastic models based on the Theory of Island
    Biogeography (TIB) of MacArthur and Wilson (1967) <doi:10.1023/A:1016393430551>
    and extensions. It implements methods to estimate colonization and
    extinction rates (including environmental variables) given presence-absence
    data, simulates community assembly, and performs model selection.
An implementation of the induced smoothing (IS) idea to lasso regularization models to allow estimation and inference on the model coefficients (currently hypothesis testing only). Linear, logistic, Poisson and gamma regressions with several link functions are implemented. The algorithm is described in the original paper; see <doi:10.1177/0962280219842890> and discussed in a tutorial <doi:10.13140/RG.2.2.16360.11521>.
We provide the collection of data-sets used in the book 'An Introduction to Statistical Learning with Applications in R'.
We provide the collection of data-sets used in the book 'An Introduction to Statistical Learning with Applications in R, Second Edition'. These include many data-sets that we used in the first edition (some with minor changes), and some new datasets.
The development of ISM was made by Warfield in 1974. 
      ISM is the process of collaborating distinct or related essentials into a simplified and an organized format. Hence, ISM is a methodology that seeks the interrelationships among the various elements considered and endows with a hierarchical and multilevel structure.
      To run this package user needs to provide a matrix (VAXO) converted into 0's and 1's.
      Warfield,J.N. (1974) <doi:10.1109/TSMC.1974.5408524>
      Warfield,J.N. (1974, E-ISSN:2168-2909).
Functions to support the computations carried out in
  `An Introduction to Statistical Modeling of Extreme Values' by
  Stuart Coles. The functions may be divided into the following 
  groups; maxima/minima, order statistics, peaks over thresholds
  and point processes.
Paquete creado con el fin de facilitar el cálculo y distribución del índice Socio Material Territorial (ISMT), elaborado por el Observatorio de Ciudades UC. La metodología completa está disponible en "ISMT" (<https://ideocuc-ocuc.hub.arcgis.com/datasets/6ed956450cfc4293b7d90df3ce3474e4/about>) [Observatorio de Ciudades UC (2019)]. || Package created to facilitate the calculation and distribution of the Socio-Material Territorial Index by Observatorio de Ciudades UC. The full methodology is available at "ISMT" (<https://ideocuc-ocuc.hub.arcgis.com/datasets/6ed956450cfc4293b7d90df3ce3474e4/about>) [Observatorio de Ciudades UC (2019)].
The current version provides functions to compute, print and summarize the Index of Sensitivity to Nonignorability (ISNI) in the generalized linear model for independent data, and in the marginal multivariate Gaussian model and the mixed-effects models for continuous and binary longitudinal/clustered data. It allows for arbitrary patterns of missingness in the regression outcomes  caused by dropout and/or intermittent missingness. One can compute the sensitivity index without estimating any nonignorable models or positing specific magnitude of nonignorability. Thus ISNI provides a simple quantitative assessment of how robust the standard estimates assuming missing at random  is with respect to the assumption of ignorability. For a tutorial, download at <https://huixie.people.uic.edu/Research/ISNI_R_tutorial.pdf>.	For more details, see Troxel Ma and Heitjan (2004) and Xie and Heitjan (2004) <doi:10.1191/1740774504cn005oa> and Ma Troxel and Heitjan (2005) <doi:10.1002/sim.2107> and  Xie (2008) <doi:10.1002/sim.3117> and  Xie (2012) <doi:10.1016/j.csda.2010.11.021> and Xie and Qian (2012) <doi:10.1002/jae.1157>.
Check if an 'externalptr' is a null pointer.
    R does currently not have a native function for that purpose.
    This package contains a C function that returns TRUE in case of a null pointer.
Linear order and unimodal order (univariate)
	     isotonic regression; bivariate isotonic regression
	     with linear order on both variables.
Some tools to assist with converting International Organization for Standardization (ISO) standard 11784 (ISO11784) animal ID codes between 4 recognised formats commonly displayed on Passive Integrated Transponder (PIT) tag readers.
    The most common formats are 15 digit decimal, e.g., 999123456789012, and 13 character hexadecimal 'dot' format, e.g., 3E7.1CBE991A14. These are referred
    to in this package as isodecimal and isodothex. The other two formats are the raw hexadecimal representation of the ISO11784 binary
    structure (see <https://en.wikipedia.org/wiki/ISO_11784_and_ISO_11785>). There are two 'flavours' of this format, a left and a right variation. Which flavour
    a reader happens to output depends on if the developers decided to reverse the binary number or not before converting to hexadecimal, a decision based on 
    the fact that the PIT tags will transmit their binary code Least Significant Bit (LSB) first, or backwards basically.
Functions to parse strings with ISO8601 dates, times, and
    date-times into R-objects.  Additionally, there are functions to determine
    the type of ISO8601 string and to standardise ISO8601 strings.
A fast C++ implementation to generate contour lines
    (isolines) and contour polygons (isobands) from regularly spaced grids
    containing elevation data.
In classification problems a monotone relation between some
  predictors and the classes may be assumed. In this package 'isoboost' 
  we propose new boosting algorithms, based on LogitBoost, that 
  incorporate this isotonicity information, yielding more accurate 
  and easily interpretable rules.
A set of functions to run simple and composite box-models to describe the 
    dynamic or static distribution of stable isotopes in open 
    or closed systems. The package also allows the sweeping of many 
    parameters in both static and dynamic conditions.
    The mathematical models used in this package are derived from Albarede, 1995, 
    Introduction to Geochemical Modelling, Cambridge University Press,
    Cambridge <doi:10.1017/CBO9780511622960>.
Perform common calculations based on published stable isotope theory, such as calculating carbon isotope discrimination and intrinsic water use efficiency from wood or leaf carbon isotope composition. See Mathias and Hudiburg (2022) in Global Change Biology <doi:10.1111/gcb.16407>.
This resource provides tools to create, compare, and post-process 
    spatial isotope assignment models of animal origin. It generates 
    probability-of-origin maps for individuals based on user-provided tissue and 
    environment isotope values (e.g., as generated by IsoMAP, Bowen et al. [2013] 
    <doi:10.1111/2041-210X.12147>) using the framework established in Bowen et al.
    (2010) <doi:10.1146/annurev-earth-040809-152429>). The package 'isocat' can then 
    quantitatively compare and cluster these maps to group individuals by 
    similar origin. It also includes techniques for applying four approaches 
    (cumulative sum, odds ratio, quantile only, and quantile simulation) with 
    which users can summarize geographic origins and probable distance traveled 
    by individuals. Campbell et al. [2020] establishes several of the functions
    included in this package <doi:10.1515/ami-2020-0004>.
A bunch of functions to deal with circular data under order restrictions.
ISO language, territory, currency, script and character codes.
  Provides ISO 639 language codes, ISO 3166 territory codes, ISO 4217
  currency codes, ISO 15924 script codes, and the ISO 8859 character codes
  as well as the UN M.49 area codes.
Analyzing Inductively Coupled Plasma - Mass Spectrometry (ICP-MS) 
    measurement data to evaluate isotope ratios (IRs) is a complex process. 
    The 'IsoCor' package facilitates this process and renders it reproducible 
    by providing a function to run a 'Shiny'-App locally in any web browser. 
    In this App the user can upload data files of various formats, select ion 
    traces, apply peak detection and perform calculation of IRs and delta 
    values. Results are provided as figures and tables and can be exported. 
    The App, therefore, facilitates data processing of ICP-MS experiments to 
    quickly obtain optimal processing parameters compared to traditional 'Excel'
    worksheet based approaches. A more detailed description can be found in the 
    corresponding article <doi:10.1039/D2JA00208F>. The most recent version 
    of 'IsoCor' can be tested online at <https://apps.bam.de/shn00/IsoCor/>.
ISO 3166-1 country codes and ISO 4217 currency codes provided
    by the International Organization for Standardization.
Distributional regression under stochastic order restrictions for
    numeric and binary response variables and partially ordered covariates. See
    Henzi, Ziegel, Gneiting (2020) <arXiv:1909.03725>.
This toolbox makes working with oxygen,
    carbon, and clumped isotope data reproducible and straightforward.
    Use it to quickly calculate isotope fractionation factors,
    and apply paleothermometry equations.
Implementation of Isolation kernel (Qin et al. (2019) <doi:10.1609/aaai.v33i01.33014755>).
API wrapper that contains functions to retrieve data from the 'IsoMemo' partnership databases. Web services for API: <https://isomemodb.com/api/v1/iso-data>.
Read and process isotopocule data from an Orbitrap Isotope Solutions mass spectrometer. Citation: Kantnerova et al. (Nature Protocols, 2024).
Clustering algorithm developed for use with plot inventories of species. It groups plots by subsets of diagnostic species rather than overall species composition. There is an unsupervised and a supervised mode, the latter accepting suggestions for species with greater weight and cluster medoids.
Ternary plots made simple. This package allows to create
    ternary plots using 'graphics'. It provides functions to display the
    data in the ternary space, to add or tune graphical elements and to
    display statistical summaries. It also includes common ternary
    diagrams which are useful for the archaeologist (e.g. soil texture
    charts, ceramic phase diagram).
Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington', 'Ludwig' and Omnivariant Generalised Least-Squares ('OGLS') approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, Th-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isochrons as well as 230Th-U evolution plots.
Provides a graphical user interface to the 'IsoplotR' package for radiometric geochronology. The GUI runs in an internet browser and can either be used offline, or hosted on a server to provide online access to the 'IsoplotR' toolbox.
Deconvolution of mixed tumour profiles into normal and cancer for each patient, using 
	the ISOpure algorithm in Quon et al. Genome Medicine, 2013 5:29. Deconvolution requires 
	mixed tumour profiles and a set of unmatched "basis" normal profiles.
Building isoscapes using mixed models and inferring the geographic
  origin of samples based on their isotopic ratios. This package is essentially a
  simplified interface to several other packages which implements a new
  statistical framework based on mixed models. It uses 'spaMM' for fitting and
  predicting isoscapes, and assigning an organism's origin depending on its
  isotopic ratio. 'IsoriX' also relies heavily on the package 'rasterVis' for
  plotting the maps produced with 'terra' using 'lattice'.
IsoSpec is a fine structure calculator used for obtaining the most
    probable masses of a chemical compound given the frequencies of the composing
    isotopes and their masses. It finds the smallest set of isotopologues with
    a given probability. The probability is assumed to be that of the product of
    multinomial distributions, each corresponding to one particular element and
    parametrized by the frequencies of finding these elements in nature. These
    numbers are supplied by IUPAC - the International Union of Pure and Applied
    Chemistry. See: Lacki, Valkenborg, Startek (2020) <DOI:10.1021/acs.analchem.0c00959>
    and Lacki, Startek, Valkenborg, Gambin (2017) <DOI:10.1021/acs.analchem.6b01459>
    for the description of the algorithms used.
Nonparametric estimation on survival analysis under order-restrictions.
Contains two main functions: one for
        solving general isotone regression problems using the
        pool-adjacent-violators algorithm (PAVA); another one provides
        a framework for active set methods for isotone optimization
        problems with arbitrary order restrictions. Various types of
        loss functions are prespecified.
Given a response y and a one- or two-dimensional predictor, the isotonic regression estimator is calculated with the usual orderings.
Implements Bayesian models to analyze data from tracer addition
    experiments. The implemented method was originally described in the article
    "A New Method to Reconstruct Quantitative Food Webs and Nutrient Flows from
    Isotope Tracer Addition Experiments" by López-Sepulcre et al. (2020)
    <doi:10.1086/708546>.
Fast and multi-threaded implementation of
	isolation forest (Liu, Ting, Zhou (2008) <doi:10.1109/ICDM.2008.17>),
	extended isolation forest (Hariri, Kind, Brunner (2018) <doi:10.48550/arXiv.1811.02141>),
	SCiForest (Liu, Ting, Zhou (2010) <doi:10.1007/978-3-642-15883-4_18>),
	fair-cut forest (Cortes (2021) <doi:10.48550/arXiv.2110.13402>),
	robust random-cut forest (Guha, Mishra, Roy, Schrijvers (2016) <http://proceedings.mlr.press/v48/guha16.html>),
	and customizable variations of them, for isolation-based outlier detection, clustered outlier detection,
	distance or similarity approximation (Cortes (2019) <doi:10.48550/arXiv.1910.12362>),
	isolation kernel calculation (Ting, Zhu, Zhou (2018) <doi:10.1145/3219819.3219990>),
	and imputation of missing values (Cortes (2019) <doi:10.48550/arXiv.1911.06646>),
	based on random or guided decision tree splitting, and providing different metrics for
	scoring anomalies based on isolation depth or density (Cortes (2021) <doi:10.48550/arXiv.2111.11639>).
	Provides simple heuristics for fitting the model to categorical columns and handling missing data,
	and offers options for varying between random and guided splits, and for using different splitting criteria.
The wiDB...() functions provide an interface to the public API 
    of the wiDB <https://github.com/SPATIAL-Lab/isoWater/blob/master/Protocol.md>: 
    build, check and submit queries, and receive and 
    unpack responses. Data analysis functions support Bayesian 
    inference of the source and source isotope composition of water 
    samples that may have experienced evaporation. Algorithms 
    adapted from Bowen et al. (2018, <doi:10.1007/s00442-018-4192-5>).
This is an substitute for the %V and %u formats which are
        not implemented on Windows. In addition, the package offers
        functions to convert from standard calender format yyyy-mm-dd
        to and from ISO 8601 week format yyyy-Www-d.
A collection of several functions related to construction and analysis of incomplete split-plot designs. The package contains functions to obtain  and analyze incomplete split-plot designs for three kinds of situations namely (i) when blocks are complete with respect to main plot treatments and main plots are incomplete with respect to subplot treatments, (ii) when blocks are  incomplete with respect to main plot treatments and main plots are complete with respect to subplot treatments and (iii) when blocks are incomplete with respect to main plot treatments and main plots are incomplete with respect to subplot treatments.
Allows access to data from the Rio de Janeiro Public Security Institute (ISP), such as criminal statistics, data on gun seizures and femicide. The package also contains the spatial data of Pacifying Police Units (UPPs) and Integrated Public Safety Regions, Areas and Circumscriptions.
We use the  ISR to handle with PCA-based missing data with high  correlation,  and the DISR to handle with distributed PCA-based missing data.  The philosophy of the package is described in Guo G. (2024)  <doi:10.1080/03610918.2022.2091779>.
This is the central location for data and tools for the development,
    maintenance, analysis, and deployment of the International Soil Radiocarbon Database
    (ISRaD). ISRaD was developed as a collaboration between the U.S. Geological Survey
    Powell Center and the Max Planck Institute for Biogeochemistry. This R package provides
    tools for accessing and manipulating ISRaD data, compiling local data using the ISRaD
    data structure, and simple query and reporting functions for ISRaD. For more detailed
    information visit the ISRaD website at: <https://soilradiocarbon.org/>.
Methodology for subgroup selection in the context of isotonic regression including methods for sub-Gaussian errors, classification, homoscedastic Gaussian errors and quantile regression. See the documentation of ISS(). Details can be found in the paper by Müller, Reeve, Cannings and Samworth (2023) <arXiv:2305.04852v2>.
Manage a 'GitHub' problem using R: wrangle issues, labels and
    milestones. It includes functions for storing, prioritizing (sorting),
    displaying, adding, deleting, and selecting (filtering) issues based
    on qualitative and quantitative information. Issues (labels and
    milestones) are written in lists and categorized into the S3 class to
    be easily manipulated as datasets in R.
You can access to open data published in Instituto Canario De Estadistica (ISTAC) APIs at <https://datos.canarias.es/api/estadisticas/>.
Download data from Istat (Italian Institute of Statistics) database, both old and new provider (respectively, <http://dati.istat.it/> and <https://esploradati.istat.it/databrowser/>). Additional functions for manipulating data are provided. Moreover, a 'shiny' application called 'shinyIstat' can be used to search, download and filter datasets in an easier way.
Launches a 'shiny' based application for Nuclear Magnetic Resonance (NMR)data importation and Statistical TOtal Correlation SpectroscopY (STOCSY) analyses in a full interactive approach. The theoretical background and applications of STOCSY method could be found at Cloarec, O., Dumas, M. E., Craig, A., Barton, R. H., Trygg, J., Hudson, J., Blancher, C., Gauguier, D., Lindon, J. C., Holmes, E. & Nicholson, J. (2005) <doi:10.1021/ac048630x>.
Multi-data type subtyping, which is data type agnostic and accepts missing data. Subtyping is performed using intermediary assessments created with autoencoders and similarity calculations.
Independent Surrogate Variable Analysis is an algorithm
        for feature selection in the presence of potential confounding
        factors (see Teschendorff AE et al 2011, <doi: 10.1093/bioinformatics/btr171>).
Data sets and scripts for text examples and exercises in 
  P. Dalgaard (2008), `Introductory Statistics with R', 2nd ed., Springer Verlag, ISBN 978-0387790534.
Provides two record linkage data sets on the Italian Survey on Household and Wealth, 2008 and 2010, a sample survey conducted by the Bank of Italy every two years. The 2010 survey covered 13,702 individuals, while the 2008 survey covered 13,734 individuals. The following categorical variables are included in this data set: year of birth, working status, employment status, branch of activity, town size, geographical area of birth, sex, whether or not Italian national, and highest educational level obtained. Unique identifiers are available to assess the accuracy of one’s method. Please see Steorts (2015) <DOI:10.1214/15-BA965SI> to find more details about the data set.
Functions for analyzing multiple choice items. These analyses include
  the convertion of student response into binaty data (correct/incorrect),
  the computation of the number of corrected responses and grade for each subject,
  the calculation of item difficulty and discrimination, the computation of the
  frecuency and point-biserial correlation for each distractor and the graphical
  analysis of each item.
Three methods for Individual Tree Crowns (ITCs) delineation on remote sensing data: one is based on LiDAR data in x,y,z format and one on imagery data in raster format.
The itdr() routine allows  for the estimation of sufficient dimension reduction subspaces in univariate regression such as the central mean subspace or central subspace in regression. This is achieved using Fourier transformation methods proposed by Zhu and Zeng (2006) <doi:10.1198/016214506000000140>, convolution transformation methods proposed by Zeng and Zhu (2010) <doi:10.1016/j.jmva.2009.08.004>, and iterative Hessian transformation methods proposed by Cook and Li (2002) <doi:10.1214/aos/1021379861>. Additionally, mitdr() function provides optimal estimators for sufficient dimension reduction subspaces in multivariate regression by optimizing a discrepancy function using a Fourier transform approach proposed by Weng and Yin (2022) <doi:10.5705/ss.202020.0312>, and selects the sufficient variables using Fourier transform sparse inverse regression estimators proposed by Weng (2022) <doi:10.1016/j.csda.2021.107380>.
Runs classical item analysis for multiple-choice test items and polytomous items (e.g., rating scales). The statistics reported in this package can be found in any measurement textbook such as Crocker and Algina (2006, ISBN:9780495395911).
Some functions for performing ICA, MICA, Group ICA, and Multilinear ICA are implemented.
    ICA, MICA/Group ICA, and Multilinear ICA extract statistically independent components from single matrix, multiple matrices, and single tensor, respectively.
    For the details of these methods, see the reference section of GitHub README.md <https://github.com/rikenbit/iTensor>.
Fits large-scale regression models with a penalty that 
  restricts the maximum number of non-zero regression coefficients
  to a prespecified value.  While Chu et al (2020) <doi:10.1093/gigascience/giaa044>
  describe the basic algorithm, this package uses Cyclops for an efficient implementation.
Know which loop iteration the code execution is up to by including
    a single, convenient function call inside the loop.
Support for iterators, which allow a programmer to traverse
    through all the elements of a vector, list, or other collection of data.
The iterLap (iterated Laplace approximation) algorithm approximates a
             general (possibly non-normalized) probability density on R^p, by repeated
             Laplace approximations to the difference between current approximation 
             and true density (on log scale). The final approximation is a mixture of
             multivariate normal distributions and might be used for example as a
             proposal distribution for importance sampling (eg in Bayesian applications). 
             The algorithm can be seen as a computational generalization of the Laplace 
             approximation suitable for skew or multimodal densities.
A fresh take on iterators in R. Designed to be cross-compatible with the 'iterators' package, but using the 'nextOr' method will offer better performance as well as more compact code. With batteries included: includes a collection of iterator constructors and combinators ported and refined from the 'iterators', 'itertools', and 'itertools2' packages.
Iterator for generating permutations and combinations. They
    can be either drawn with or without replacement, or with distinct/ non-distinct 
    items (multiset). The generated sequences are in lexicographical order 
    (dictionary order). The algorithms to generate permutations and combinations are 
    memory efficient. These iterative algorithms enable users to process all sequences 
    without putting all results in the memory at the same time. 
    The algorithms are written in C/C++ for faster performance. Note: 'iterpc' is no longer
    being maintained. Users are recommended to switch to 'arrangements'.
Various tools for creating iterators, many patterned after
        functions in the Python itertools module, and others patterned
        after functions in the 'snow' package.
A port of Python's excellent itertools module to R for efficient
    looping.
Leveraging information-theoretic measures like mutual information and v-measure to quantify spatial associations between patterns (Nowosad and Stepinski (2018) <doi:10.1080/13658816.2018.1511794>; Bai, H. et al. (2023) <doi:10.1080/24694452.2023.2223700>).
Functions to clean and process international trade data into an international trade network (ITN) are provided. It then provides a set a functions to undertake analysis and plots of the ITN (extract the backbone, centrality, blockmodels, clustering). Examining the key players in the ITN and regional trade patterns.
The 'Interactive Tree Of Life' <https://itol.embl.de/> online server can 
    edit and annotate trees interactively. The 'itol.toolkit' package can 
    support all types of annotation templates.
Infers a topology of relationships between different datasets, such as multi-omics and phenotypic data recorded on the same samples. We based this methodology on the RV coefficient (Robert & Escoufier, 1976, <doi:10.2307/2347233>), a measure of matrix correlation, which we have extended for partial matrix correlations and binary data (Aben et al., 2018, <doi:10.1101/293993>).
Supplements for a book, "iTOS" = "Introduction to the Theory of Observational Studies."  Data sets are 'aHDL' from Rosenbaum (2023a) <doi:10.1111/biom.13558> and 'bingeM' from Rosenbaum (2023b) <doi:10.1111/biom.13921>.  The function makematch() uses two-criteria matching from Zhang et al. (2023) <doi:10.1080/01621459.2021.1981337> to create the matched data 'bingeM' from 'binge'.  The makematch() function also implements optimal matching (Rosenbaum (1989) <doi:10.2307/2290079>) and matching with fine or near-fine balance (Rosenbaum et al. (2007) <doi:10.1198/016214506000001059> and Yang et al (2012) <doi:10.1111/j.1541-0420.2011.01691.x>).  The book makes use of two other R packages, 'weightedRank' and 'tightenBlock'.
Implements the Interpolate, Truncate, Project (ITP) root-finding 
    algorithm developed by Oliveira and Takahashi (2021) <doi:10.1145/3423597>.
    The user provides the function, from the real numbers to the real numbers, 
    and an interval with the property that the values of the function at its 
    endpoints have different signs. If the function is continuous over this 
    interval then the ITP method estimates the value at which the function is 
    equal to zero. If the function is discontinuous then a point of 
    discontinuity at which the function changes sign may be found. 
    The function can be supplied using either an R function or an external 
    pointer to a C++ function. Tuning parameters of the ITP algorithm can be 
    set by the user. Default values are set based on arguments in Oliveira and 
    Takahashi (2021).
Parse, trim, join, visualise and analyse data from Itrax sediment core multi-parameter 
    scanners manufactured by Cox Analytical Systems, Sweden. Functions are provided for parsing 
    XRF-peak area files, line-scan optical images, and radiographic images, alongside accompanying metadata. 
    A variety of data wrangling tasks like trimming, joining and reducing XRF-peak area data are simplified. 
    Multivariate methods are implemented with appropriate data transformation.
The improved trimmed weighted Hochberg procedure provides increased statistical power and relaxes the dependence assumptions for familywise error rate control compared to the original weighted Hochberg procedure. This package computes the boundaries required for implementing the proposed methodology and includes sample size optimization methods.
    See Gou, J., Chang, Y., Li, T., and Zhang, F.(2025). Improved trimmed weighted Hochberg procedures with two endpoints and sample size optimization. Technical Report.
Two functions for running and then post-estimating an Interrupted Time Series Analysis model. This is a solution for running time series analyses on temporally short data. See English (2019) 'The its.analysis R package - Modelling short time series data' <https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3398189> for an overview of the method.
GAMM (Generalized Additive Mixed Modeling; Lin & Zhang, 1999)
    as implemented in the R package 'mgcv' (Wood, S.N., 2006; 2011) is a nonlinear
    regression analysis which is particularly useful for time course data such as
    EEG, pupil dilation, gaze data (eye tracking), and articulography recordings,
    but also for behavioral data such as reaction times and response data. As time
    course measures are sensitive to autocorrelation problems, GAMMs implements
    methods to reduce the autocorrelation problems. This package includes functions
    for the evaluation of GAMM models (e.g., model comparisons, determining regions
    of significance, inspection of autocorrelational structure in residuals)
    and interpreting of GAMMs (e.g., visualization of complex interactions, and
    contrasts).
Provides a wrapper around the same API <https://app.americansocceranalysis.com/api/v1/__docs__/>
    that powers the American Soccer Analysis app.
Collection of R functions to do purely presence-only species
    distribution modeling with isolation forest (iForest) and its
    variations such as Extended isolation forest and SCiForest. See the
    details of these methods in references: Liu, F.T., Ting, K.M. and
    Zhou, Z.H. (2008) <doi:10.1109/ICDM.2008.17>, Hariri, S., Kind, M.C.
    and Brunner, R.J. (2019) <doi:10.1109/TKDE.2019.2947676>, Liu, F.T.,
    Ting, K.M. and Zhou, Z.H. (2010) <doi:10.1007/978-3-642-15883-4_18>,
    Guha, S., Mishra, N., Roy, G. and Schrijvers, O. (2016)
    <https://proceedings.mlr.press/v48/guha16.html>, Cortes, D. (2021)
    <doi:10.48550/arXiv.2110.13402>. 
    Additionally, Shapley values are used to explain
    model inputs and outputs. See details in references: Shapley, L.S.
    (1953) <doi:10.1515/9781400881970-018>, Lundberg, S.M. and Lee, S.I.
    (2017) <https://dm-gatech.github.io/CS8803-Fall2018-DML-Papers/shapley.pdf>, Molnar,
    C.  (2020) <ISBN:978-0-244-76852-2>, Štrumbelj, E. and Kononenko, I.
    (2014) <doi:10.1007/s10115-013-0679-x>. itsdm also provides functions
    to diagnose variable response, analyze variable importance, draw
    spatial dependence of variables and examine variable contribution. As
    utilities, the package includes a few functions to download
    bioclimatic variables including 'WorldClim' version 2.0 (see Fick,
    S.E. and Hijmans, R.J. (2017) <doi:10.1002/joc.5086>) and
    'CMCC-BioClimInd' (see Noce, S., Caporaso, L. and Santini, M. (2020)
    <doi:10.1038/s41597-020-00726-5>.
Provides functions for modeling and forecasting time series data. Forecasting is based on the innovations algorithm. A description of the innovations algorithm can be found in the textbook "Introduction to Time Series and Forecasting" by Peter J. Brockwell and Richard A. Davis.
Facilitates access to the International Union for Conservation of Nature (IUCN) Red List of Threatened Species, a comprehensive global inventory of species at risk of extinction. This package streamlines the process of determining conservation status by matching species names with Red List data, providing tools to easily query and retrieve conservation statuses. Designed to support biodiversity research and conservation planning, this package relies on data from the 'iucnrdata' package, available on GitHub <https://github.com/PaulESantos/iucnrdata>. To install the data package, use pak::pak('PaulESantos/iucnrdata').
Independent vector analysis (IVA) is a blind source separation (BSS) model where several datasets are jointly unmixed. This package provides several methods for the unmixing together with some performance measures. For details, see Anderson et al. (2011) <doi:10.1109/TSP.2011.2181836> and Lee et al. (2007) <doi:10.1016/j.sigpro.2007.01.010>.
A integrated variance correlation is proposed to measure the dependence between a categorical or continuous random variable and a continuous random variable or vector.
    This package is designed to estimate the new correlation coefficient with parametric and nonparametric approaches. 
    Test of independence for different problems can also be implemented via the new correlation coefficient with this package.
Estimating the mean and variance of a covariate for the complier, never-taker and always-taker subpopulation in the context of instrumental variable estimation. This package implements the method described in Marbach and Hangartner (2020) <doi:10.1017/pan.2019.48> and Hangartner, Marbach, Henckel, Maathuis, Kelz and Keele (2021) <doi:10.48550/arXiv.2103.06328>.
An implementation of randomization-based hypothesis 
    testing for three different estimands in a cluster-randomized 
    encouragement experiment. The three estimands include (1) testing
    a cluster-level constant proportional treatment effect (Fisher's
    sharp null hypothesis), (2) pooled effect ratio, and (3) average 
    cluster effect ratio. To test the third estimand, user needs to install
    'Gurobi' (>= 9.0.1) optimizer via its R API. Please refer to 
    <https://www.gurobi.com/documentation/9.0/refman/ins_the_r_package.html>.
Estimation and diagnostic tools for instrumental variables designs, which implements the guidelines proposed in Lal et al. (2023) <arXiv:2303.11399>, including bootstrapped confidence intervals, effective F-statistic, Anderson-Rubin test, valid-t ratio test, and local-to-zero tests.
Instrumental variable (IV) estimators for homogeneous and
    heterogeneous treatment effects with efficient machine learning instruments.
    The estimators are based on double/debiased machine learning allowing for
    nonlinear and potentially high-dimensional control variables. Details can 
    be found in Scheidegger, Guo and Bühlmann (2025) "Inference for 
    heterogeneous treatment effects with efficient instruments and machine 
    learning" <doi:10.48550/arXiv.2503.03530>.
Uses data and researcher's beliefs on measurement error and
    instrumental variable (IV) endogeneity to generate the space of consistent 
    beliefs across measurement error, instrument endogeneity, and instrumental 
    relevance for IV regressions. 
    Package based on DiTraglia and Garcia-Jimeno (2020) <doi:10.1080/07350015.2020.1753528>.
Provides facilities of general to specific model selection for
    exogenous regressors in 2SLS models. Furthermore, indicator saturation
    methods can be used to detect outliers and structural breaks in the sample.
A method that estimates
    an IV-optimal individualized treatment rule. An individualized
    treatment rule is said to be IV-optimal if it minimizes the 
    maximum risk with respect to the putative IV and the set of
    IV identification assumptions. Please refer to 
    <arXiv:2002.02579> for more details on the methodology and 
    some theory underpinning the method. Function IV-PILE() uses
    functions in the package 'locClass'. Package 'locClass' can be
    accessed and installed from the 'R-Forge' repository via the following link: 
    <https://r-forge.r-project.org/projects/locclass/>.
    Alternatively, one can install the package by entering the following in R:
    'install.packages("locClass", repos="<http://R-Forge.R-project.org>")'.
Carries out instrumental variable
    estimation of causal effects, including power analysis, sensitivity analysis,
    and diagnostics. See Kang, Jiang, Zhao, and Small (2020) <http://pages.cs.wisc.edu/~hyunseung/> for details.
The marginal treatment effect was introduced by Heckman and
    Vytlacil (2005) <doi:10.1111/j.1468-0262.2005.00594.x> to provide a
    choice-theoretic interpretation to instrumental variables models that
    maintain the monotonicity condition of Imbens and Angrist (1994)
    <doi:10.2307/2951620>. This interpretation can be used to extrapolate from
    the compliers to estimate treatment effects for other subpopulations. This
    package provides a flexible set of methods for conducting this
    extrapolation. It allows for parametric or nonparametric sieve estimation,
    and allows the user to maintain shape restrictions such as monotonicity. The
    package operates in the general framework developed by Mogstad, Santos and
    Torgovitsky (2018) <doi:10.3982/ECTA15463>, and accommodates either point
    identification or partial identification (bounds). In the partially
    identified case, bounds are computed using either linear programming
    or quadratically constrained quadratic programming. Support for
    four solvers is provided. Gurobi and the Gurobi R API
    can be obtained from <http://www.gurobi.com/index>. CPLEX can be obtained
    from <https://www.ibm.com/analytics/cplex-optimizer>. CPLEX R APIs 'Rcplex'
    and 'cplexAPI' are available from CRAN. MOSEK and the MOSEK R API can be
    obtained from <https://www.mosek.com/>. The lp_solve library is freely
    available from <http://lpsolve.sourceforge.net/5.5/>, and is included when
    installing its API 'lpSolveAPI', which is available from CRAN.
Nicely formatted frequency tables and contingency tables (1-way, 2-way, 3-way and 4-way tables), that can easily be exported to HTML or 'Office' documents. Designed to work with pipes.
An implementation of the Invariance Partial Pruning (IVPP) approach 
  described in Du, X., Johnson, S. U., Epskamp, S. (2025) The Invariance Partial 
  Pruning Approach to The Network Comparison in Longitudinal Data. IVPP is a 
  two-step method that first test for global network structural difference with 
  invariance test and then inspect specific edge difference with partial pruning.
Instrumental variable estimation for linear models by two-stage least-squares (2SLS) regression or by robust-regression via M-estimation (2SM) or MM-estimation (2SMM). The main ivreg() model-fitting function is designed to provide a workflow as similar as possible to standard lm() regression. A wide range of methods is provided for fitted ivreg model objects, including extensive functionality for computing and graphing regression diagnostics in addition to other standard model tools.
Provides a library for generic interval manipulations using a
    new interval vector class. Capabilities include: locating various
    kinds of relationships between two interval vectors, merging overlaps
    within a single interval vector, splitting an interval vector on its
    overlapping endpoints, and applying set theoretical operations on
    interval vectors. Many of the operations in this package were inspired
    by James Allen's interval algebra, Allen (1983)
    <doi:10.1145/182.358434>.
An instrumental variable estimator under structural cumulative additive intensity model is fitted, that leverages initial randomization as the IV. The estimator can be used to fit an additive hazards model under time to event data which handles treatment switching (treatment crossover) correctly. We also provide a consistent variance estimate.
Contains tools for instrumental variables estimation. Currently, non-parametric bounds, two-stage estimation and G-estimation are implemented. Balke, A. and Pearl, J. (1997) <doi:10.2307/2965583>, Vansteelandt S., Bowden J., Babanezhad M., Goetghebeur E. (2011) <doi:10.1214/11-STS360>.
Drawing statistical inference on the coefficients
    of a short- or long-horizon predictive regression with persistent
    regressors by using the IVX method of Magdalinos and Phillips (2009)
    <doi:10.1017/S0266466608090154> and Kostakis, Magdalinos and
    Stamatogiannis (2015) <doi:10.1093/rfs/hhu139>.
For a single variable, the IVY Plot stacks tied values in the form of leaflets. Five leaflets join to form a leaf. 
    Leaves are stacked vertically. At most twenty leaves are shown; For high frequency, each leaflet may represent more than 
    one observation with multiplicity declared in the subtitle.
Calculates irrigation water quality ratios and has functions that could be used to plot several popular diagrams for irrigation water quality classification.
Improved methods based on inverse probability weighting
        and outcome regression for causal inference and missing data
        problems.
Create and view tickets in 'gitea', a self-hosted git service <https://gitea.io>, using an 'RStudio' addin, and use helper functions to publish documentation and use git.
Code to specify, run, and then visualize and analyze the results of 
    Ixodidae (hard-bodied ticks) population and infection dynamics models. Such 
    models exist in the literature, but the source code to run them is not 
    always available. 'IxPopDyMod' provides an easy way for these models to be 
    written and shared.
Computes bootstrapped Monte Carlo estimate of p value of Kolmogorov-Smirnov (KS) test and 
    likelihood ratio test for zero-inflated count data, based on the work of Aldirawi et al. (2019) 
    <doi:10.1109/BHI.2019.8834661>. With the package, user can also find tools to simulate 
    random deviates from zero inflated or hurdle models and obtain  maximum likelihood estimate
    of unknown parameters in these models.
Call the data wrappers for Izmir Metropolitan Municipality's Open Data Portal. This will return all datasets formatted as Excel files (.csv or .xlsx), as well as datasets that require an API key.
An estimation method that can use computer simulations to
    approximate maximum-likelihood estimates even when the likelihood function can not
    be evaluated directly. It can be applied whenever it is feasible to conduct many
    simulations, but works best when the data is approximately Poisson distributed.
    It was originally designed for demographic inference in evolutionary
    biology (Naduvilezhath et al., 2011 <doi:10.1111/j.1365-294X.2011.05131.x>,
    Mathew et al., 2013 <doi:10.1002/ece3.722>).
    It has optional support for conducting coalescent simulation using
    the 'coala' package.
Provides data about the possible adverse events/reactions
    resulting from being injected with a vaccine/experimental gene therapy.
    Currently, this data set only includes information from six reference
    sources. Refer to the CITATION.cff file for the complete citations of
    the reference sources. For information about vaccination$/immunization$
    hazards, visit <https://www.questionuniverse.com/rethink.html#vaccine>,
    <https://www.ecoccs.com/healing.html#vaccines>,
    <https://www.questionuniverse.com/rethink_current_crisis.html#cov_vaccin>,
    and <https://www.questionuniverse.com/vaccination.html>.
Calculate statistical significance of Jaccard/Tanimoto similarity
    coefficients for binary data.
Schur polynomials appear in combinatorics and zonal
    polynomials appear in random matrix theory. They are particular cases
    of Jack polynomials. This package allows to compute these polynomials
    and other symmetric multivariate polynomials: flagged Schur
    polynomials, factorial Schur polynomials, t-Schur polynomials,
    Hall-Littlewood polynomials, Macdonald polynomials, and modified
    Macdonald polynomials. In addition, it can compute the Kostka-Jack
    numbers, the Kostka-Foulkes polynomials, the Kostka-Macdonald
    polynomials, and the Hall polynomials.  Mainly based on Demmel &
    Koev's paper (2006) <doi:10.1090/S0025-5718-05-01780-1> and
    Macdonald's book (1995) <doi:10.1093/oso/9780198534891.003.0001>.
Simply and efficiently
    simulates (i) variants from reference genomes and (ii) reads from both Illumina 
    <https://www.illumina.com/>
    and Pacific Biosciences (PacBio) <https://www.pacb.com/> platforms. 
    It can either read reference genomes from FASTA files or simulate new ones.
    Genomic variants can be simulated using summary statistics, phylogenies, 
    Variant Call Format (VCF) files, and coalescent simulations—the latter of which
    can include selection, recombination, and demographic fluctuations.
    'jackalope' can simulate single, paired-end, or mate-pair Illumina reads, 
    as well as PacBio reads.
    These simulations include sequencing errors, mapping qualities, multiplexing,
    and optical/polymerase chain reaction (PCR) duplicates.
    Simulating Illumina sequencing is based on ART
    by Huang et al. (2012) <doi:10.1093/bioinformatics/btr708>.
    PacBio sequencing simulation is based on 
    SimLoRD  by Stöcker et al. (2016) <doi:10.1093/bioinformatics/btw286>.
    All outputs can be written to standard file formats.
Implements delete-d jackknife resampling for robust statistical estimation. 
    The package provides both weighted (HC3-adjusted) and unweighted versions of 
    jackknife estimation, with parallel computation support. Suitable for biomedical 
    research and other fields requiring robust variance estimation.
Provides method used to check whether data have outlier in efficiency measurement 
  of big samples with data envelopment analysis (DEA). In this jackstrap method, the package 
  provides two criteria to define outliers: heaviside and k-s test. The technique was developed 
  by Sousa and Stosic (2005) "Technical Efficiency of the Brazilian Municipalities: Correcting 
  Nonparametric Frontier Measurements for Outliers." <doi:10.1007/s11123-005-4702-4>.
Test for association between the observed data and their estimated latent variables. The jackstraw package provides a resampling strategy and testing scheme to estimate statistical significance of association between the observed data and their latent variables. Depending on the data type and the analysis aim, the latent variables may be estimated by principal component analysis (PCA), factor analysis (FA), K-means clustering, and related unsupervised learning algorithms. The jackstraw methods learn over-fitting characteristics inherent in this circular analysis, where the observed data are used to estimate the latent variables and used again to test against that estimated latent variables. When latent variables are estimated by PCA, the jackstraw enables statistical testing for association between observed variables and latent variables, as estimated by low-dimensional principal components (PCs). This essentially leads to identifying variables that are significantly associated with PCs. Similarly, unsupervised clustering, such as K-means clustering, partition around medoids (PAM), and others, finds coherent groups in high-dimensional data. The jackstraw estimates statistical significance of cluster membership, by testing association between data and cluster centers. Clustering membership can be improved by using the resulting jackstraw p-values and posterior inclusion probabilities (PIPs), with an application to unsupervised evaluation of cell identities in single cell RNA-seq (scRNA-seq).
Evaluation of the Jacobi theta functions and related
    functions: Weierstrass elliptic function, Weierstrass sigma function,
    Weierstrass zeta function, Klein j-function, Dedekind eta function,
    lambda modular function, Jacobi elliptic functions, Neville theta
    functions, Eisenstein series, lemniscate elliptic functions, elliptic 
    alpha function, Rogers-Ramanujan continued fractions, and Dixon 
    elliptic functions. Complex values of the variable are supported.
Implements the classical Jacobi algorithm for the
    eigenvalues and eigenvectors of a real symmetric matrix, both in 
    pure 'R' and in 'C++' using 'Rcpp'. Mainly as a programming example 
    for teaching purposes.
Uses the Jaccard similarity index to account for population
    structure in sequencing studies. This method was specifically
    designed to detect population stratification based on rare variants, hence it
    will be especially useful in rare variant analysis.
Contains procedures to estimate the nine condensed Jacquard genetic identity coefficients
              (Jacquard, 1974) <doi:10.1007/978-3-642-88415-3> by constrained least squares
              (Graffelman et al., 2024) <doi:10.1101/2024.03.25.586682> and by the method of moments
	      (Csuros, 2014) <doi:10.1016/j.tpb.2013.11.001>. These procedures require previous estimation of the
	      allele frequencies. Functions are supplied that estimate relationship parameters that derive from the Jacquard
	      coefficients, such as individual inbreeding coefficients and kinship coefficients.
Cardoso's JADE algorithm as well as his functions for joint diagonalization are ported to R. Also several other blind source separation (BSS) methods, like AMUSE and SOBI, and some criteria for performance evaluation of BSS algorithms, are given. The package is described in Miettinen, Nordhausen and Taskinen (2017) <doi:10.18637/jss.v076.i02>.
Jade Lizard and Reverse Jade Lizard Option Strategies are presented here through their Graphs. The graphic indicators, strategies, calculations, functions and all the discussions are for academic, research, and educational purposes only and should not be construed as investment advice and come with absolutely no Liability.
    Russell A. Stultz (“The option strategy desk reference: an essential reference for option traders (First edition.)”, 2019, ISBN: 9781949443912).
Bayesian methods for estimating developmental age from ordinal dental data. For an explanation of the model used, see Konigsberg (2015) <doi:10.3109/03014460.2015.1045430>. For details on the conditional correlation correction, see Sgheiza (2022) <doi:10.1016/j.forsciint.2021.111135>. Dental scoring is based on Moorrees, Fanning, and Hunt (1963) <doi:10.1177/00220345630420062701>.
All the data and functions used to produce the book. We do not expect
    most people to use the package for any other reason than to get simple access to the
    'JAGS' model files, the data, and perhaps run some of the simple examples.
    The authors of the book are David Lucy (now sadly deceased) and James Curran. It is 
    anticipated that a manuscript will be provided to Taylor and Francis around February 2020, with
    bibliographic details to follow at that point. Until such time, further information
    can be obtained by emailing James Curran.
Tools are provided to streamline Bayesian analyses in 'JAGS' using 
    the 'jagsUI' package.  Included are functions for extracting output in 
    simpler format, functions for streamlining assessment of convergence, and 
    functions for producing summary plots of output.  Also included is a 
    function that provides a simple template for running 'JAGS' from 'R'.
    Referenced materials can be found at <DOI:10.1214/ss/1177011136>.
Bayesian data analysis usually incurs long runtimes
  and cumbersome custom code.
  A pipeline toolkit tailored to Bayesian statisticians,
  the 'jagstargets' R package is leverages
  'targets' and 'R2jags' to ease this burden.
  'jagstargets' makes it super easy to set up scalable
  JAGS pipelines that automatically parallelize the computation
  and skip expensive steps when the results are already up to date.
  Minimal custom code is required, and there is no need to manually
  configure branching, so usage is much easier than 'targets' alone.
  For the underlying methodology, please refer
  to the documentation of 'targets' <doi:10.21105/joss.02959> and 'JAGS'
  (Plummer 2003) <https://www.r-project.org/conferences/DSC-2003/Proceedings/Plummer.pdf>.
A set of wrappers around 'rjags' functions to run Bayesian analyses in 'JAGS' (specifically, via 'libjags').  A single function call can control adaptive, burn-in, and sampling MCMC phases, with MCMC chains run in sequence or in parallel. Posterior distributions are automatically summarized (with the ability to exclude some monitored nodes if desired) and functions are available to generate figures based on the posteriors (e.g., predictive check plots, traceplots). Function inputs, argument syntax, and output format are nearly identical to the 'R2WinBUGS'/'R2OpenBUGS' packages to allow easy switching between MCMC samplers.
The Jalaali calendar, also known as the Persian or Solar Hijri 
    calendar, is the official calendar of Iran and Afghanistan. It starts on 
    Nowruz, the spring equinox, and follows an astronomical system for 
    determining leap years. Each year consists of 365 or 366 days, divided into 
    12 months. This package provides functions for converting dates between the 
    Jalaali and Gregorian calendars. The conversion calculations are based on 
    the work of Kazimierz M. Borkowski (1996) (<doi:10.1007/BF00055188>), who 
    used an analytical model of Earth's motion to compute equinoxes from AD 550 
    to 3800 and determine leap years based on Tehran time.
Just analysis methods ('jam') base functions
    focused on bioinformatics.
    Version- and gene-centric alphanumeric sort,
    unique name and version assignment, colorized console and 'HTML' output,
    color ramp and palette manipulation,
    'Rmarkdown' cache import, styled 'Excel' worksheet import and export,
    interpolated raster output from smooth scatter and image plots,
    list to delimited vector, efficient list tools.
Provides an interface to 'Jamendo' API <https://developer.jamendo.com/v3.0>.
              Pull audio, features and other information for a given 
              'Jamendo' user (including yourself!) or enter an artist's -, album's -, 
              or track's name and retrieve the available information in seconds.
Fit latent space network cluster models using an expectation-maximization algorithm. Enables flexible modeling of unweighted or weighted network data (with or without noise edges), supporting both directed and undirected networks (with or without degree heterogeneity). Designed to handle large networks efficiently, it allows users to explore network structure through latent space representations, identify clusters (i.e., community detection) within network data, and simulate networks with varying clustering, connectivity patterns, and noise edges. Methodology for the implementation is described in Arakkal and Sewell (2025) <doi:10.1016/j.csda.2025.108228>.
Full texts for Jane Austen's 6 completed novels, ready for
    text analysis. These novels are "Sense and Sensibility", "Pride and
    Prejudice", "Mansfield Park", "Emma", "Northanger Abbey", and
    "Persuasion".
The main janitor functions can: perfectly format data.frame column
    names; provide quick counts of variable combinations (i.e., frequency
    tables and crosstabs); and explore duplicate records. Other janitor functions
    nicely format the tabulation results. These tabulate-and-report functions
    approximate popular features of SPSS and Microsoft Excel. This package
    follows the principles of the "tidyverse" and works well with the pipe function
    %>%. janitor was built with beginning-to-intermediate R users in mind and is
    optimized for user-friendliness.
Proposes a coarse-to-fine optimization of a recommending system based on deep-neural networks using 'tensorflow'.
Provides tools for using the API of 'e-Stat' (<https://www.e-stat.go.jp/>), a portal site for Japanese government statistics.
    Includes functions for automatic query generation, data collection and formatting.
Provides a function collection to extract metadata, sectioned text and study characteristics from scientific articles in 'NISO-JATS' format. Articles in PDF format can be converted to 'NISO-JATS' with the 'Content ExtRactor and MINEr' ('CERMINE', <https://github.com/CeON/CERMINE>). For convenience, two functions bundle the extraction heuristics: JATSdecoder() converts 'NISO-JATS'-tagged XML files to a structured list with elements title, author, journal, history, 'DOI', abstract, sectioned text and reference list. study.character() extracts multiple study characteristics like number of included studies, statistical methods used, alpha error, power, statistical results, correction method for multiple testing, software used. An estimation of the involved sample size is performed based on reports within the abstract and the reported degrees of freedom within statistical results. In addition, the package contains some useful functions to process text (text2sentences(), text2num(), ngram(), strsplit2(), grep2()). See Böschen, I. (2021) <doi:10.1007/s11192-021-04162-z> Böschen, I. (2021) <doi:10.1038/s41598-021-98782-3> and Böschen, I (2023) <doi:10.1038/s41598-022-27085-y>.
Graphics device routing all graphics commands to a Java
	     program. The actual functionality of the JavaGD depends
	     on the Java-side implementation. Simple AWT and Swing
	     implementations are included.
Simplifies the process of estimating above ground biomass components for teak trees using a few basic inputs, based on the equations taken from the journal "Allometric equations for estimating above ground biomass and leaf area of planted teak (Tectona grandis) forests under agroforestry management in East Java, Indonesia" (Purwanto & Shiba, 2006) <doi:10.60409/forestresearch.76.0_1>. This function is most reliable when applied to trees from the same region where the equations were developed, specifically East Java, Indonesia. This function help to estimate the stem diameter at the lowest major living branch (DB) using the stem diameter at breast height with R^2 = 0.969. Estimate the branch dry weight (WB) using the stem diameter at breast height and tree height (R^2 = 0.979). Estimate the stem weight (WS) using the stem diameter at breast height and tree height (R^2 = 0.997. Also estimate the leaf dry weight (WL) using the stem diameter at the lowest major living branch (R^2 = 0.996).
An implementation of the Jaya optimization algorithm for both 
    single-objective and multi-objective problems. Jaya is a population-based, 
    gradient-free optimization algorithm capable of solving constrained and 
    unconstrained optimization problems without hyperparameters. This package 
    includes features such as multi-objective Pareto optimization, adaptive 
    population adjustment, and early stopping. For further details, see 
    R.V. Rao (2016) <doi:10.5267/j.ijiec.2015.8.004>.
Provides an R interface to the JBrowse 2 genome browser.
    Enables embedding a JB2 genome browser in a Shiny app or R Markdown
    document. The browser can also be launched from an interactive R console.
    The browser can be loaded with a variety of common genomics data types,
    and can be used with a custom theme.
This is a set of simple utility functions to perform mutual conversion between the current Japanese calendar system that Wareki, the old Japanese calendar system that the Kyureki calendar and the Julian and Gregorian calendar.
    To calculate each calendar method, it converts to the Julian Day Number.
Provides a gridded classification of weather types by applying the Jenkinson and Collison classification. For a given region (it can be either local region or the whole map),it computes at each grid the 11 weather 
             types during the period considered for the analysis. See Otero et al., (2017) <doi:10.1007/s00382-017-3705-y> for more information.
Contains a selection of color palettes and 'ggplot2' themes designed by the package author.
Procedures for joint detection of changes in both expectation and variance in univariate sequences. Performs a statistical test of the null hypothesis of the absence of change points. In case of rejection performs an algorithm for change point detection. Reference - Bivariate change point detection - joint detection of changes in expectation and variance, Scandinavian Journal of Statistics, DOI 10.1111/sjos.12547.
The Impact Factor of a journal reported by Journal Citation Reports ('JCR') of  'Clarivate' 'Analytics' is provided. The impact factor is available for those journals only that were included Journal Citation Reports 'JCR'.
A calculation tool to obtain the 10-year risk of cardiovascular disease from various risk models (Hisayama, Suita, EPOCH Japan).
Tool for generating quality reports from cruncher outputs
    (and calculating series scores). The latest version of the cruncher
    can be downloaded here:
    <https://github.com/jdemetra/jwsacruncher/releases>.
A Wrapper for the Node.js 'Jdenticon' <https://jdenticon.com/> Library. Uses 'esbuild' <https://esbuild.github.io/> to reduce user dependencies.
Option is a one of the financial derivatives and its pricing is an important problem in practice. The process of stock prices are represented as Geometric Brownian motion [Black (1973) <doi:10.1086/260062>] or jump diffusion processes [Kou (2002) <doi:10.1287/mnsc.48.8.1086.166>]. In this package, algorithms and visualizations are implemented by Monte Carlo method in order to calculate European option price for three equations by Geometric Brownian motion and jump diffusion processes and furthermore a model that presents jumps among companies affect each other.
Customized R Markdown templates for authoring articles
    for Journal of Data Science.
Provides a fast and scalable joint estimator for integrating additional knowledge in learning multiple related sparse Gaussian Graphical Models (JEEK). The JEEK algorithm can be used to fast estimate multiple related precision matrices in a large-scale. For instance, it can identify multiple gene networks from multi-context gene expression datasets. By performing data-driven network inference from high-dimensional and heterogeneous data sets, this tool can help users effectively translate aggregated data into knowledge that take the form of graphs among entities. Please run demo(jeek) to learn the basic functions provided by this package. For further details, please read the original paper: Beilun Wang, Arshdeep Sekhon, Yanjun Qi "A Fast and Scalable Joint Estimator for Integrating Additional Knowledge in Learning Multiple Related Sparse Gaussian Graphical Models" (ICML 2018) <arXiv:1806.00548>.
Generates interactive Jellyfish plots to visualize spatiotemporal tumor
    evolution by integrating sample and phylogenetic trees into a unified plot.
    This approach provides an intuitive way to analyze tumor heterogeneity and
    evolution over time and across anatomical locations. The Jellyfish plot
    visualization design was first introduced by Lahtinen, Lavikka, et al.
    (2023, <doi:10.1016/j.ccell.2023.04.017>).
    This package also supports visualizing ClonEvol results, a tool developed
    by Dang, et al. (2017, <doi:10.1093/annonc/mdx517>), for analyzing clonal
    evolution from multi-sample sequencing data. The 'clonevol' package is not
    available on CRAN but can be installed from its GitHub
    repository (<https://github.com/hdng/clonevol>).
Fast extrapolation of univariate and multivariate time features using K-Nearest Neighbors. The compact set of hyper-parameters is tuned via grid or random search.
Manage project dependencies from your DESCRIPTION file. Create a reproducible virtual environment with minimal additional files in your project. Provides tools to add, remove, and update dependencies as well as install existing dependencies with a single function.
On Affymetrix gene expression microarrays, a single gene may be measured by multiple probe sets. This can present a mild conundrum when attempting to evaluate a gene "signature" that is defined by gene names rather than by specific probe sets. This package provides a one-to-one mapping from gene to "best" probe set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a, hgu133plus2, and u133x3p. This package also includes the pre-calculated probe set quality scores that were used to define the mapping.
The goal of 'jetty' is to execute R functions and code
    snippets in an isolated R subprocess within a 'Docker' container
    and return the evaluated results to the local R session. 'jetty'
    can install necessary packages at runtime and seamlessly propagates
    errors and outputs from the 'Docker' subprocess back to the main
    session. 'jetty' is primarily designed for sandboxed testing and
    quick execution of example code.
Estimates networks of conditional dependencies (Gaussian graphical models) from multiple classes of data (similar but not exactly, i.e. measurements on different equipment, in different locations or for various sub-types). Package also allows to generate simulation data and evaluate the performance. Implementation of the method described in Angelini, De Canditiis and Plaksienko (2022) <doi:10.3390/math10213983>.
Provides statistical methods for auditing as implemented in JASP
    for Audit (Derks et al., 2021 <doi:10.21105/joss.02733>). First, the package
    makes it easy for an auditor to plan a statistical sample, select the sample
    from the population, and evaluate the misstatement in the sample compliant
    with international auditing standards. Second, the package provides
    statistical methods for auditing data, including tests of digit
    distributions and repeated values. Finally, the package includes methods for
    auditing algorithms on the aspect of fairness and bias. Next to classical
    statistical methodology, the package implements Bayesian equivalents of
    these methods whose statistical underpinnings are described in Derks et al.
    (2021) <doi:10.1111/ijau.12240>, Derks et al. (2024)
    <doi:10.2308/AJPT-2021-086>, Derks et al. (2022) <doi:10.31234/osf.io/8nf3e>
    Derks et al. (2024) <doi:10.31234/osf.io/tgq5z>, and Derks et al. (2025)
    <doi:10.31234/osf.io/b8tu2>.
Offer procedures to download financial-economic time series data and enhanced procedures for computing the investment performance indices of Bacon (2004) <DOI:10.1002/9781119206309>.
Provides functions to extract joint planes from 3D triangular mesh derived
             from point cloud and makes data available for structural analysis.
Java GUI for R - cross-platform, universal and unified Graphical User Interface for R. For full functionality on Windows and Mac OS X JGR requires a start application which depends on your OS.
All datasets and functions used in the german book "Statistik mit R und RStudio" by grosse Schlarmann (2010-2024) <https://www.produnis.de/R/>.
An R package that implements the JICO algorithm [Wang, P., Wang, H., Li, Q., Shen, D., & Liu, Y. (2024). <Journal of Computational and Graphical Statistics, 33(3), 763-773>]. 
        It aims at solving the multi-group regression problem. The algorithm decomposes the responses from multiple groups into shared and group-specific
        components, which are driven by low-rank approximations of joint and individual structures from the covariates respectively.
Template engine powered by the 'inja' C++ library. Users
    write a template document, using syntax inspired by the 'Jinja' Python
    package, and then render the final document by passing data from R.
    The template syntax supports features such as variables, loops,
    conditions and inheritance.
Approximate joint-inclusion probabilities in Unequal Probability Sampling, or compute Monte Carlo approximations of the first and second-order inclusion probabilities of a general sampling design as in Fattorini (2006) <doi:10.1093/biomet/93.2.269>.
Set of common functions used for manipulating colors,
    detecting and interacting with 'RStudio', modeling, formatting, determining
    users' operating system, feature scaling, and more!
An implementation of fast cluster-based permutation analysis
    (CPA) for densely-sampled time data developed in Maris & Oostenveld,
    2007 <doi:10.1016/j.jneumeth.2007.03.024>. Supports (generalized,
    mixed-effects) regression models for the calculation of timewise
    statistics. Provides both a wholesale and a piecemeal interface to the
    CPA procedure with an emphasis on interpretability and diagnostics.
    Integrates 'Julia' libraries 'MixedModels.jl' and 'GLM.jl' for
    performance improvements, with additional functionalities for
    interfacing with 'Julia' from 'R' powered by the 'JuliaConnectoR'
    package.
Estimation of extended joint models with shared random effects. Longitudinal data are handled in latent process models for continuous (Gaussian or curvilinear) and ordinal outcomes while proportional hazard models are used for the survival part. We propose a frequentist approach using maximum likelihood estimation. See Saulnier et al, 2022 <doi:10.1016/j.ymeth.2022.03.003>.
Shared parameter models for the joint modeling of longitudinal and time-to-event data.
Provides features that allow users to download 
  weather data published by the Japan Meteorological Agency (JMA) website 
  (<https://www.jma.go.jp/jma/index.html>). The data includes information 
  dating back to 1976 and aligns with the categories available on the website. 
  Additionally, users can process the best track data of typhoons and easily 
  handle earthquake record files.
A mainly instrumental package meant to allow other packages whose core is written in 'C++' to read, write
        and manipulate matrices in a binary format so that the memory used for them is no more than strictly needed. Its functionality
        is already inside 'parallelpam' and 'scellpam', so if you have installed any of these, you do not need to install 'jmatrix'.
        Using just the needed memory is not always true with 'R' matrices or vectors, since by default they are of double type. Trials
        like the 'float' package have been done, but to use them you have to coerce a matrix already loaded in 'R' memory to a float matrix,
        and then you can delete it. The problem comes when your computer has not memory enough to hold the matrix in the first place, so
        you are forced to load it by chunks. This is the problem this package tries to address (with partial success, but this is a
        difficult problem since 'R' is not a strictly typed language, which is anyway quite hard to get in an interpreted language).
	This package allows the creation and manipulation of full, sparse and symmetric matrices of any standard data type.
Shared parameter models for the joint modeling of longitudinal and time-to-event data using MCMC; Dimitris Rizopoulos (2016) <doi:10.18637/jss.v072.i07>.
Fit joint models for longitudinal and time-to-event data under the Bayesian approach. Multiple longitudinal outcomes of mixed type (continuous/categorical) and multiple event times (competing risks and multi-state processes) are accommodated. Rizopoulos (2012, ISBN:9781439872864).
Provides model fitting, prediction, and plotting for joint models of longitudinal and multiple time-to-event data, including methods from Rizopoulos (2012) <doi:10.1201/b12208>. Useful for handling complex survival and longitudinal data in clinical research.
Provides analysis tools for big data where the sample size is very large. It offers
             a suite of functions for fitting and predicting joint models, which allow for the simultaneous
             analysis of longitudinal and time-to-event data. This statistical methodology is particularly 
             useful in medical research where there is often interest in understanding the relationship 
             between a longitudinal biomarker and a clinical outcome, such as survival or disease progression.
             This can be particularly useful in a clinical setting where it is important to be able to predict 
             how a patient's health status may change over time. Overall, this package provides a 
             comprehensive set of tools for joint modeling of BIG data obtained as survival and 
             longitudinal outcomes with both Bayesian and non-Bayesian approaches. Its versatility
             and flexibility make it a valuable resource for researchers in many different fields,
             particularly in the medical and health sciences.
Fit joint mean-covariance models for longitudinal data. The models
    and their components are represented using S4 classes and methods. The core
    computational algorithms are implemented using the 'Armadillo' C++ library
    for numerical linear algebra and 'RcppArmadillo' glue.
Joint mean and dispersion effects models fit the mean and dispersion parameters of a response variable by two separate linear models, the mean and dispersion submodels, simultaneously. It also allows the users to choose either the deviance or the Pearson residuals as the response variable of the dispersion submodel. Furthermore, the package provides the possibility to nest the submodels in one another, if one of the parameters has significant explanatory power on the other. Wu & Li (2016) <doi:10.1016/j.csda.2016.04.015>.
Performs power calculations for joint modeling of longitudinal 
  and survival data with k-th order trajectories when the variance-covariance 
  matrix, Sigma_theta, is unknown.
The main purpose of this package is to make it easy for userR's to interact with 'jMetrik' an open source application for psychometric analysis. For example it allows useR's to write data frames to file in a format that can be used by 'jMetrik'. It also allows useR's to read *.jmetrik files (e.g. output from an analysis) for follow-up analysis in R. The *.jmetrik format is a flat file that includes a multiline header and the data as comma separated values. The header includes metadata about the file and one row per variable with the following information in each row: variable name, data type, item scoring, special data codes, and variable label.
Maximum likelihood estimation for the semi-parametric joint modeling of competing risks and longitudinal data in the presence of heterogeneous within-subject variability, proposed by Li and colleagues (2023) <arXiv:2301.06584>.
             The proposed method models the within-subject variability of the biomarker and associates it with the risk of the competing risks event. The time-to-event data is modeled using a (cause-specific) Cox proportional hazards regression model with time-fixed covariates. 
             The longitudinal outcome is modeled using a mixed-effects location and scale model. The association is captured by shared random effects. The model 
             is estimated using an Expectation Maximization algorithm.
Computes the Jackknife Mutual Information (JMI) between two random vectors and provides the p-value for dependence tests. See Zeng, X., Xia, Y. and Tong, H. (2018) <doi:10.1073/pnas.1715593115>.
Implements time series z-normalization, SAX, HOT-SAX, VSM, SAX-VSM, RePair, and RRA
    algorithms facilitating time series motif (i.e., recurrent pattern), discord (i.e., anomaly),
    and characteristic pattern discovery along with interpretable time series classification.
Performs a permutation test on the difference between two location parameters, a permutation correlation test, a permutation F-test, the Siegel-Tukey test, a ratio mean deviance test.  Also performs some graphing techniques, such as for confidence intervals, vector addition, and Fourier analysis; and includes functions related to the Laplace (double exponential) and triangular distributions.  Performs power calculations for the binomial test.
A suite of common statistical methods such as descriptives,
    t-tests, ANOVAs, regression, correlation matrices, proportion tests,
    contingency tables, and factor analysis. This package is also useable from
    the 'jamovi' statistical spreadsheet (see <https://www.jamovi.org> for more
    information).
Methods to access data sets from the 'jamovi' statistical
  spreadsheet (see <https://www.jamovi.org> for more information) from R.
A framework for creating rich interactive analyses for the jamovi
    platform (see <https://www.jamovi.org> for more information).
The free and open a statistical spreadsheet 'jamovi'
    (<https://www.jamovi.org>) aims to make statistical analyses easy and
    intuitive. 'jamovi' produces syntax that can directly be used in R (in
    connection with the R-package 'jmv'). Having import / export routines for
    the data files 'jamovi' produces ('.omv') permits an easy transfer of
    data and analyses between 'jamovi' and R.
Aids in the calculation and visualization of regions of non-significance using the 'Johnson-Neyman' technique and its extensions as described by Bauer and Curran (2005) <doi:10.1207/s15327906mbr4003_5> to assess the influence of categorical and continuous moderators. Allows correcting for phylogenetic relatedness.
Call job::job({<code here>}) to run R code as an RStudio job and keep your console free in the meantime. This allows for a productive workflow while testing (multiple) long-running chunks of code. It can also be used to organize results using the RStudio Jobs GUI or to test code in a clean environment. Two RStudio Addins can be used to run selected code as a job.
Takes an R expression and returns a job object with a $stop() method
    which can be called to terminate the background job. Also provides timeouts
    and other mechanisms for automatically terminating a background job. The
    result of the expression is available synchronously via $result or
    asynchronously with callbacks or through the 'promises' package framework.
Computing and plotting joint confidence regions and intervals. Regions include classical ellipsoids, minimum-volume or minimum-length regions, and an empirical Bayes region. Intervals include the TOST procedure with ordinary or expanded intervals and a fixed-sequence procedure. Such regions and intervals are useful e.g., for the assessment of multi-parameter (bio-)equivalence. Joint confidence regions for the mean and variance of a normal distribution are available as well.
In a typical experiment for the intuitive judgment of frequencies (JoF) different stimuli with different frequencies are presented. The participants consider these stimuli with a constant duration and give a judgment of frequency. These judgments can be simulated by formal models: PASS 1 and PASS 2 based on Sedlmeier (2002, ISBN:978-0198508632), MINERVA 2 baesd on Hintzman (1984) <doi:10.3758/BF03202365> and TODAM 2 based on Murdock, Smith & Bai (2001) <doi:10.1006/jmps.2000.1339>. The package provides an assessment of the frequency by determining the core aspects of these four models (attention, decay, and presented frequency) that can be compared to empirical results.
Analysis of repeated measurements and time-to-event data via random
    effects joint models. Fits the joint models proposed by Henderson and colleagues
    <doi:10.1093/biostatistics/1.4.465> (single event time) and by Williamson and
    colleagues (2008) <doi:10.1002/sim.3451> (competing risks events time) to a
    single continuous repeated measure. The time-to-event data is modelled using a 
    (cause-specific) Cox proportional hazards regression model with time-varying 
    covariates. The longitudinal outcome is modelled using a linear mixed effects
    model. The association is captured by a latent Gaussian process. The model is 
    estimated using am Expectation Maximization algorithm. Some plotting functions 
    and the variogram are also included. This project is funded by the Medical 
    Research Council (Grant numbers G0400615 and MR/M013227/1).
Fits the joint model proposed by Henderson and colleagues (2000) 
    <doi:10.1093/biostatistics/1.4.465>, but extended to the case of multiple 
    continuous longitudinal measures. The time-to-event data is modelled using a 
    Cox proportional hazards regression model with time-varying covariates. The 
    multiple longitudinal outcomes are modelled using a multivariate version of the 
    Laird and Ware linear mixed model. The association is captured by a multivariate
    latent Gaussian process. The model is estimated using a Monte Carlo Expectation 
    Maximization algorithm. This project was funded by the Medical Research Council 
    (Grant number MR/M013227/1).
Implements penalised multivariate regression (i.e., for multiple outcomes and many features) by stacked generalisation (<doi:10.1093/bioinformatics/btab576>). For positively correlated outcomes, a single multivariate regression is typically more predictive than multiple univariate regressions. Includes functions for model fitting, extracting coefficients, outcome prediction, and performance measurement. For optional comparisons, install 'remMap' from GitHub (<https://github.com/cran/remMap>).
Fit survival data and perform dynamic prediction under joint frailty-copula models for tumour progression and death.
 Likelihood-based methods are employed for estimating model parameters, where the baseline hazard functions are modeled by the cubic M-spline or the Weibull model.
 The methods are applicable for meta-analytic data containing individual-patient information from several studies.
 Survival outcomes need information on both terminal event time (e.g., time-to-death) and non-terminal event time (e.g., time-to-tumour progression).
 Methodologies were published in
 Emura et al. (2017) <doi:10.1177/0962280215604510>, Emura et al. (2018) <doi:10.1177/0962280216688032>,
 Emura et al. (2020) <doi:10.1177/0962280219892295>, Shinohara et al. (2020) <doi:10.1080/03610918.2020.1855449>,
 Wu et al. (2020) <doi:10.1007/s00180-020-00977-1>, and Emura et al. (2021) <doi:10.1177/09622802211046390>.
 See also the book of Emura et al. (2019) <doi:10.1007/978-981-13-3516-7>.
 Survival data from ovarian cancer patients are also available.
Joint analysis and imputation of incomplete data in the Bayesian
    framework, using (generalized) linear (mixed) models and extensions there of,
    survival models, or joint models for longitudinal and survival data, as
    described in Erler, Rizopoulos and Lesaffre (2021) <doi:10.18637/jss.v100.i20>.
    Incomplete covariates, if present, are automatically imputed.
    The package performs some preprocessing of the data and creates a 'JAGS'
    model, which will then automatically be passed to 'JAGS' 
    <https://mcmc-jags.sourceforge.io/> with the help of 
    the package 'rjags'.
A small package containing functions to perform a joint calibration of totals and quantiles. The calibration for totals is based on Deville and Särndal (1992) <doi:10.1080/01621459.1992.10475217>, the calibration for quantiles is based on Harms and Duchesne (2006) <https://www150.statcan.gc.ca/n1/en/catalogue/12-001-X20060019255>. The package uses standard calibration via the 'survey', 'sampling' or 'laeken' packages. In addition, entropy balancing via the 'ebal' package and empirical likelihood based on codes from Wu (2005) <https://www150.statcan.gc.ca/n1/pub/12-001-x/2005002/article/9051-eng.pdf> can be used. See the paper by Beręsewicz and Szymkowiak (2023) for details <arXiv:2308.13281>.
Different algorithms to perform approximate joint diagonalization
	of a finite set of square matrices. Depending on the algorithm,
	orthogonal or non-orthogonal diagonalizer is found. These algorithms
	are particularly useful in the context of blind source separation. 
	Original publications of the algorithms can be found in 
	Ziehe et al. (2004), Pham and Cardoso (2001) <doi:10.1109/78.942614>, 
	Souloumiac (2009) <doi:10.1109/TSP.2009.2016997>, 
	Vollgraff and Obermayer <doi:10.1109/TSP.2006.877673>. An example of 
	application in the context of Brain-Computer Interfaces EEG denoising
	can be found in Gouy-Pailler et al (2010) <doi:10.1109/TBME.2009.2032162>.
Runs resampling-based tests jointly, e.g., sign-flip score tests from Hemerik et al., (2020) <doi:10.1111/rssb.12369>, to allow for multivariate testing, i.e., weak and strong control of the Familywise Error Rate or True Discovery Proportion.
Implementation of a parametric joint model for modelling recurrent
  and competing event processes using generalised survival models as described in
  Entrop et al., (2005) <doi:10.1002/bimj.70038>. The joint  model can 
  subsequently be used to predict the mean number of events in the
  presence of competing risks at different time points. Comparisons of the mean
  number of event functions, e.g. the differences in mean number of events
  between two exposure groups, are also available.
Jointly estimates two-group means and covariances
    for matrix-variate data and calculates test statistics.  
    This package implements the algorithms defined in 
    Hornstein, Fan, Shedden, and Zhou (2018) 
    <doi:10.1080/01621459.2018.1429275>.
Fits univariate and joint N-mixture models for data on two unmarked site-associated species. Includes functions to estimate latent abundances through empirical Bayes methods.
Estimate risk caused by two extreme and dependent forcing variables using bivariate extreme value models as described in Zheng, Westra, and Sisson (2013) <doi:10.1016/j.jhydrol.2013.09.054>; Zheng, Westra and Leonard (2014) <doi:10.1002/2013WR014616>; Zheng, Leonard and Westra (2015) <doi:10.2166/hydro.2015.052>.
Methods for fast segmentation of multivariate
    signals into piecewise constant profiles and for generating realistic
    copy-number profiles. A typical application is the joint segmentation of total
    DNA copy numbers and allelic ratios obtained from Single Nucleotide Polymorphism
    (SNP) microarrays in cancer studies. The methods are described in Pierre-Jean, 
    Rigaill and Neuvial (2015) <doi:10.1093/bib/bbu026>.
In the observational study design stage, matching/weighting methods are
    conducted. However, when many background variables are present, the decision as to 
    which variables to prioritize for matching/weighting is not trivial. Thus, the 
    joint treatment-outcome variable importance plots are created to guide variable
    selection. The joint variable importance plots enhance variable comparisons via
    unadjusted bias curves derived under the omitted variable bias framework. The 
    plots translate variable importance into recommended values for tuning parameters 
    in existing methods. Post-matching and/or weighting plots can also be used to 
    visualize and assess the quality of the observational study design. The method 
    motivation and derivation is presented in "Prioritizing Variables for Observational 
    Study Design using the Joint Variable Importance Plot" by Liao et al. (2024) 
    <doi:10.1080/00031305.2024.2303419>. See the package paper by Liao and Pimentel 
    (2024) <doi:10.21105/joss.06093> for a beginner friendly user introduction.
Performs Joins and Minus Queries on 'Excel' Files
    fulljoinXL() Merges all rows of 2 'Excel' files based upon a common column in the files.
    innerjoinXL() Merges all rows from base file and join file when the join condition is met.
    leftjoinXL() Merges all rows from the base file, and all rows from the join file
    if the join condition is met.
    rightjoinXL() Merges all rows from the join file, and all rows from the base file if the join
    condition is met.
    minusXL() Performs 2 operations source-minus-target and target-minus-source
    If the files are identical all output files will be empty.
    Choose two 'Excel' files via a dialog box, and then follow prompts at the console to
    choose a base or source file and columns to merge or minus on.
Implements an S4 distribution system and estimation methods for
    parameters of common distribution families. The common d, p, q, r function
    family for each distribution is enriched with the ll, e, and v counterparts,
    computing the log-likelihood, performing estimation, and calculating the
    asymptotic variance - covariance matrix, respectively. Parameter estimation
    is performed analytically whenever possible.
Similarly to package 'pan', 'jomo' is a package for multilevel joint modelling multiple imputation (Carpenter and Kenward, 2013) <doi:10.1002/9781119942283>.
 Novel aspects of 'jomo' are the possibility of handling binary and categorical data through latent normal variables, the option to use cluster-specific covariance matrices and to impute compatibly with the substantive model.
Functions and data to reproduce all plots in the book "Practical Smoothing. 
 The Joys of P-splines" by Paul H.C. Eilers and Brian D. Marx (2021, ISBN:978-1108482950).
A Jordan algebra is an algebraic object originally
   designed to study observables in quantum mechanics.  Jordan
   algebras are commutative but non-associative; they satisfy the
   Jordan identity.  The package follows the ideas and notation of
   K. McCrimmon (2004, ISBN:0-387-95447-3) "A Taste of Jordan
   Algebras".  To cite the package in publications, please use
   Hankin (2023) <doi:10.48550/arXiv.2303.06062>.
Implementation of some unit and area level EBLUP estimators as well as the estimators of their MSE also under heteroscedasticity. The package further documents the publications Breidenbach and Astrup (2012) <DOI:10.1007/s10342-012-0596-7>, Breidenbach et al. (2016) <DOI:10.1016/j.rse.2015.07.026> and Breidenbach et al. (2018 in press). The vignette further explains the use of the implemented functions.
Josa in Korean is often determined by judging the previous word. 
            When writing reports using Rmd, a function that prints the 
            appropriate investigation for each case is helpful. 
            The 'josaplay' package then evaluates the previous word 
            to determine which josa is appropriate.
Read and write JSON Web Keys (JWK, rfc7517), generate and verify JSON
    Web Signatures (JWS, rfc7515) and encode/decode JSON Web Tokens (JWT, rfc7519)
    <https://datatracker.ietf.org/wg/jose/documents/>. These standards provide 
    modern signing and encryption formats that are natively supported by browsers
    via the JavaScript WebCryptoAPI <https://www.w3.org/TR/WebCryptoAPI/#jose>, 
    and used by services like OAuth 2.0, LetsEncrypt, and Github Apps.
Reproducible work requires a record of where every statistic originated.
    When writing reports, some data is too big to load in the same environment and some statistics take a while to compute.
    This package offers a way to keep notes on statistics, simple functions, and small objects.
    Notepads can be locked to avoid accidental updates.
    Notepads keep track of who added the notes and when the notes were added.
    A simple text representation is used to allow for clear version histories.
Since the reference management software (such as 'Zotero', 'Mendeley') exports Bib file journal abbreviation is not detailed enough, the 'journalabbr' package only abbreviates the journal field of Bib file, and then outputs a new Bib file for generating reference format with journal abbreviation on other software (such as 'texstudio'). The abbreviation table is from 'JabRef'. At the same time, 'Shiny' application is provided to generate 'thebibliography', a reference format that can be directly used for latex paper writing based on 'Rmd' files.
Implements under/oversampling for probability estimation.  To be
    used with machine learning methods such as AdaBoost, random forests, etc.
Tool for diagnosing table joins. It combines the speed of `collapse`
     and `data.table`, the flexibility of `dplyr`, and the diagnosis and features 
     of the `merge` command in `Stata`.
Read Japanese city codes (<https://www.e-stat.go.jp/municipalities/cities>) 
    to get city and prefecture names, or convert to city codes at different 
    points in time. In addition, it merges or splits wards of designated cities
    and gets all city codes at a specific point in time.
This package provides an easy and simple way to read, write and display bitmap images stored in the JPEG format. It can read and write both files and in-memory raw vectors.
A Joint PENalty Estimation of Covariance and Inverse Covariance Matrices.
Provides functions for grid square codes in Japan
    (<https://www.stat.go.jp/english/data/mesh/index.html>).
    Generates the grid square codes from longitude/latitude, geometries, and 
    the grid square codes of different scales, and vice versa.
Download and post process the infectious disease case data 
              from Japan Institute for Health Security. Also the package included 
              ready-to-analyse datasets. See the data source website for further details
              <https://id-info.jihs.go.jp/>.
Helpful functions for using mesh code (80km to 100m) data in Japan. Visualize mesh code using 'ggplot2' and 'leaflet', etc.
Provides tools to use API such as 'e-Stat' (<https://www.e-stat.go.jp/>), 
    the portal site for Japanese government statistics, and 
    'RESAS' (Regional Economy and Society Analyzing System, <https://resas.go.jp>).
Contains functions for fitting a joinpoint proportional hazards model to relative survival or cause-specific survival data, including estimates of joinpoint years at which survival trends have changed and trend measures in the hazard and cumulative survival scale. See Yu et al.(2009) <doi:10.1111/j.1467-985X.2009.00580.x>.
A highly configurable 'jQuery' plugin offering a simple
    interface to create complex queries/filters in 'Shiny'. The outputted
    rules can easily be parsed into a set of 'R' and/or 'SQL' queries and
    used to filter data. Custom parsing of the rules is also supported.
    For more information about 'jQuery QueryBuilder' see
    <https://querybuilder.js.org/>.
We provide tools to estimate the individualized interval-valued dose rule (I2DR) that maximizes the expected beneficial clinical outcome for each individual and returns an optimal interval-valued dose, by using the jump Q-learning (JQL) method. The jump Q-learning method directly models the conditional mean of the response given the dose level and the baseline covariates via jump penalized least squares regression under the framework of Q learning. We develop a searching algorithm by dynamic programming in order to find the optimal I2DR with the time complexity O(n2) and spatial complexity O(n). To alleviate the effects of misspecification of the Q-function, a residual jump Q-learning is further proposed to estimate the optimal I2DR. The outcome of interest includes the best partition of the entire dosage of interest, the regression coefficients of each partition, and the value function under the estimated I2DR as well as the Wald-type confidence interval of value function constructed through the Bootstrap.
Client for 'jq', a 'JSON' processor (<https://jqlang.github.io/jq/>), 
    written in C. 'jq' allows the following with 'JSON' data: index into, parse, 
    do calculations, cut up and filter, change key names and values, perform 
    conditionals and comparisons, and more.
Obtain any major version of 'jQuery' (<https://code.jquery.com/>) and use it in any webpage generated by 'htmltools' (e.g. 'shiny', 'htmlwidgets', and 'rmarkdown').
    Most R users don't need to use this package directly, but other R packages (e.g. 'shiny', 'rmarkdown', etc.) depend on this package to avoid bundling redundant copies of 'jQuery'.
An 'httpuv' based bridge between R and 'JavaScript'. Provides an easy way to exchange commands and data between a web page and a currently running R session.
These functions calculate the taxonomic measures presented in Miranda-Esquivel (2016). 
   The package introduces Jack-knife resampling in evolutionary distinctiveness prioritization analysis, 
   as a way to evaluate the support of the ranking in area prioritization, and the persistence of a given area 
   in a conservation analysis.
   The algorithm is described in: Miranda-Esquivel, D (2016) <DOI:10.1007/978-3-319-22461-9_11>.
Methods to perform Joint graph Regularized Single-Cell Kullback-Leibler Sparse Non-negative Matrix Factorization ('jrSiCKLSNMF', pronounced "junior sickles NMF") on quality controlled single-cell multimodal omics count data. 'jrSiCKLSNMF' specifically deals with dual-assay scRNA-seq and scATAC-seq data. This package contains functions to extract meaningful latent factors that are shared across omics modalities. These factors enable accurate cell-type clustering and facilitate visualizations. Methods for pre-processing, clustering, and mini-batch updates and other adaptations for larger datasets are also included. For further details on the methods used in this package please see Ellis, Roy, and Datta (2023) <doi:10.3389/fgene.2023.1179439>.
Psychometric analysis and scoring of judgment data using polytomous Item-Response Theory (IRT) models, as described in Myszkowski and Storme (2019) <doi:10.1037/aca0000225> and Myszkowski (2021) <doi:10.1037/aca0000287>. A function is used to automatically compare and select models, as well as to present a variety of model-based statistics. Plotting functions are used to present category curves, as well as information, reliability and standard error functions.
Implements the basic financial analysis
    functions similar to (but not identical to) what
    is available in most spreadsheet software. This
    includes finding the IRR and NPV of regularly
    spaced cash flows and annuities. Bond pricing and
    YTM calculations are included. In addition, Black
    Scholes option pricing and Greeks are also
    provided.
A set of utilities for working with JavaScript syntax in R.
    Includes tools to parse, tokenize, compile, validate, reformat, optimize 
    and analyze JavaScript code.
Provides a 'RStudio' addin to send some 'JavaScript' code to the 'V8' console. The user can send an entire 'JavaScript' file or only some selected lines. This is useful to test the code.
The jscore() function in the package calculates the J-Score metric between two clustering
    assignments. The score is designed to address some problems with existing common metrics such 
    as problem of matching. The details of J-score is described in Ahmadinejad and Liu. (2021) <arXiv:2109.01306>.
Fits joint species distribution models ('jSDM')
    in a hierarchical Bayesian framework (Warton and al. 2015
    <doi:10.1016/j.tree.2015.09.007>). The Gibbs sampler is written
    in 'C++'. It uses 'Rcpp', 'Armadillo' and 'GSL' to maximize computation
    efficiency.
The age is estimated by calculating the Dirichlet Normal Energy (DNE) on the whole auricular surface and the apex of the auricular surface. It involves three estimation methods: principal component discriminant analysis (PCQDA), and principal component logistic regression analysis (PCLR) methods, principal component regression analysis with Southeast Asian (A_PCR), and principal component regression analysis with multipopulation (M_PCR). The package is created with the data from the Louis Lopes Collection in Lisbon, the 21st Century Identified Human Remains Collection in Coimbra, and the CAL Milano Cemetery Skeletal Collection in Milan, and  the skeletal collection at Khon Kaen University (KKU) Human Skeletal Research Centre (HSRC), housed in the Department of Anatomy in the Faculty of Medicine at KKU in Khon Kaen.
Allow to run 'jshint' on 'JavaScript' files with a 'R'
    command or a 'RStudio' addin. The report appears in the 'RStudio'
    viewer pane.
The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Maximum likelihood estimation for the semiparametric joint modeling of survival and longitudinal data. Refer to the Journal of Statistical Software article: <doi:10.18637/jss.v093.i02>.
A set of helper functions to conduct joint-significance tests
    for mediation analysis, as recommended by Yzerbyt, Muller, Batailler,
    & Judd. (2018) <doi:10.1037/pspa0000132>.
'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
The function get_parameters() is intended to be used within a docker container to read keyword arguments from a .json file automagically. A tool.yaml file contains specifications on these keyword arguments, which are then passed as input to containerized R tools in the [tool-runner framework](<https://github.com/hydrocode-de/tool-runner>). A template for a containerized R tool, which can be used as a basis for developing new tools, is available at the following URL: <https://github.com/VForWaTer/tool_template_r>.
Encode/Decode 'base64', with support for JSON format, using two functions: j_encode() and j_decode().    'Base64' is a group of similar binary-to-text encoding schemes that represent binary data in an ASCII string format by translating it into a radix-64 representation, used when there is a need to encode binary data that needs to be stored and transferred over media that are designed to deal with textual data, ensuring that the data will remain intact and without modification during transport. <https://developer.mozilla.org/en-US/docs/Web/API/WindowBase64/Base64_encoding_and_decoding>    On the other side, JSON (JavaScript Object Notation) is a lightweight data-interchange format. Easy to read, write, parse and generate. It is based on a subset of the JavaScript Programming Language. JSON is a text format that is completely language independent but uses conventions that are familiar to programmers of the C-family of languages, including C, C++, C#, Java, JavaScript, Perl, Python, and many others. JSON structure is built around name:value pairs and ordered list of values. <https://www.json.org>    The first function, j_encode(), let you transform a data.frame or list to a 'base64' encoded JSON (or JSON string).    The j_decode() function takes a 'base64' string (could be an encoded JSON) and transform it to a data.frame (or list, depending of the JSON structure).
Conversions between 'R' objects and Javascript Object Notation (JSON) using 
    the 'rapidjsonr' library <https://CRAN.R-project.org/package=rapidjsonr>.
JSON-LD <https://www.w3.org/TR/json-ld/> is a light-weight syntax for 
    expressing linked data. It is primarily intended for web-based programming
    environments, interoperable web services and for storing linked data in 
    JSON-based databases. This package provides bindings to the JavaScript 
    library for converting, expanding and compacting JSON-LD documents.
A reasonably fast JSON parser and generator, optimized for statistical 
    data and the web. Offers simple, flexible tools for working with JSON in R, and
    is particularly powerful for building pipelines and interacting with a web API. 
    The implementation is based on the mapping described in the vignette (Ooms, 2014).
    In addition to converting JSON data from/to R objects, 'jsonlite' contains 
    functions to stream, validate, and prettify JSON data. The unit tests included 
    with the package verify that all edge cases are encoded and decoded consistently 
    for use with dynamic data in systems and applications.
Provides a function allowing to normalize a 'JSON' string,
    for example by adding double quotes around the keys when they are
    missing. Also provides 'RStudio' addins for the same purpose.
Interface to 'JSON-stat' <https://json-stat.org/>,
  a simple lightweight 'JSON' format for data dissemination.
Uses the node library 'is-my-json-valid' or 'ajv' to
    validate 'JSON' against a 'JSON' schema.  Drafts 04, 06 and 07 of
    'JSON' schema are supported.
Implementation of joint sparse optimization (JSparO) to infer the gene regulatory network for cell fate conversion. The proximal gradient method is implemented to solve different low-order regularization models for JSparO.
Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Provides tools to access the J-STAGE WebAPI and retrieve 
    information published on J-STAGE 
    <https://www.jstage.jst.go.jp/browse/-char/ja>.
Functions and helpers to import metadata, ngrams and full-texts 
    delivered by Data for Research by JSTOR.
Create and customize interactive trees using the
       'jQuery' 'jsTree' <https://www.jstree.com/> plugin
       library and the 'htmlwidgets' package. These trees can
       be used directly from the R console, from 'RStudio', in
       Shiny apps and R Markdown documents.
Creates interactive trees that can be included in 'Shiny'
    apps and R markdown documents. A tree allows to represent hierarchical
    data (e.g. the contents of a directory). Similar to the 'shinyTree'
    package but offers more features and options, such as the grid
    extension, restricting the drag-and-drop behavior, and settings for
    the search functionality. It is possible to attach some data to the
    nodes of a tree and then to get these data in 'Shiny' when a node is
    selected. Also provides a 'Shiny' gadget allowing to manipulate one or
    more folders, and a 'Shiny' module allowing to navigate in the server
    side file system.
Uses least squares optimisation to estimate the parameters of the best-fitting JohnsonSU distribution for a given dataset, with the possibility of the distributions corresponding to the limiting cases of the JohnsonSU distribution. The code for the Golden Section Search used in the optimisation has been adapted from E. Cai. This package has been created as an extension of my Master's thesis. E. Cai (2013, "Scripts and Functions: Using R to Implement the Golden Section Search Method for Numerical Optimization", <https://chemicalstatistician.wordpress.com/2013/04/22/using-r-to-implement-the-golden-bisection-method/>).
Fitting and analyzing a Joint Trait Distribution Model. The Joint Trait Distribution Model is implemented in the Bayesian framework using conjugate priors and posteriors, thus guaranteeing fast inference. In particular the package computes joint probabilities and multivariate confidence intervals, and enables the investigation of how they depend on the environment through partial response curves. The method implemented by the package is described in Poggiato et al. (2023) <doi:10.1111/geb.13706>.
Minimal and memory efficient implementation of the junction tree
	     algorithm using the Lauritzen-Spiegelhalter scheme;
	     S. L. Lauritzen and D. J. Spiegelhalter (1988) 
	     <https://www.jstor.org/stable/2345762?seq=1>. The jti package is
	     part of the paper <doi:10.18637/jss.v111.i02>.
This is a collection of tools for more efficiently understanding 
  and sharing the results of (primarily) regression analyses. There are also a
  number of miscellaneous functions for statistical and programming purposes. 
  Support for models produced by the survey and lme4 packages are points of 
  emphasis.
A long-term forecast model called "Jubilee-Tectonic model" is implemented to forecast future returns of the U.S. stock market, Treasury yield, and gold price. The five-factor model forecasts the 10-year and 20-year future equity returns with high R-squared above 80 percent. It is based on linear growth and mean reversion characteristics in the U.S. stock market. This model also enhances the CAPE model by introducing the hypothesis that there are fault lines in the historical CAPE, which can be calibrated and corrected through statistical learning. In addition, it contains a module for business cycles, optimal interest rate, and recession forecasts.
A convenience tool to create 'HTML' with inline styles using 
  'juicyjuice' and 'markdown' packages. It is particularly useful when working 
  on a content management system (CMS) whose code editor eliminates style and 
  link tags. The main use case of the package is the learning management system, 
  'Moodle'. Additional helper functions for teaching purposes are provided. Learn 
  more about 'juicedown' at <https://kenjisato.github.io/juicedown/>.
Provides a GUI interface for automating data extraction from 
  multiple images containing scatter and bar plots, semi-automated tools to tinker 
  with extraction attempts, and a fully-loaded point-and-click manual extractor 
  with image zoom, calibrator, and classifier. Also provides detailed and 
  R-independent extraction reports as fully-embedded .html records.
There are occasions where you need a piece of HTML with integrated
    styles. A prime example of this is HTML email. This transformation
    involves moving the CSS and associated formatting instructions from the
    style block in the head of your document into the body of the HTML. Many
    prominent email clients require integrated styles in HTML email; otherwise a
    received HTML email will be displayed without any styling. This package will
    quickly and precisely perform these CSS transformations when given HTML text
    and it does so by using the JavaScript 'juice' library.
Generates image data for fractals (Julia and Mandelbrot sets) on the complex plane in the given region and resolution. Benoit B Mandelbrot (1982).
Provides an R interface to 'Julia',
    which is a high-level, high-performance dynamic programming language
    for numerical computing, see <https://julialang.org/> for more information.
    It provides a high-level interface as well as a low-level interface.
    Using the high level interface, you could call any 'Julia' function just like
    any R function with automatic type conversion. Using the low level interface,
    you could deal with C-level SEXP directly while enjoying the convenience of
    using a high-level programming language like 'Julia'.
Allows to import functions and whole packages from 'Julia' in R.
    Imported 'Julia' functions can directly be called as R functions.
    Data structures can be translated between 'Julia' and R.
    More details can also be found in the corresponding article
    <doi:10.18637/jss.v101.i06>.
Metaprogramming utilities for converting R regression model
    formulae to equivalents in 'Julia' <doi:10.1137/141000671>, via
    modifications to the abstract syntax tree. Supports translations in
    zero correlation random effects syntax, protection of expressions to
    be evaluated as-is, interaction terms, and more. Accepts strings or R
    formula objects and returns modified R formula objects where
    possible (or a modified string, if not a valid formula in R).
Implementing a computationally scalable false discovery rate control procedure for replicability analysis based on maximum of p-values. Please cite the manuscript corresponding to this package [Lyu, P. et al., (2023), <doi:10.1093/bioinformatics/btad366>].
A set of functions to compute the Hodrick-Prescott (HP)
    filter with automatically selected jumps. The original
    HP filter extracts a smooth trend from a time series, and our version
    allows for a small number of automatically identified jumps.
    See Maranzano and Pelagatti (2024) <doi:10.2139/ssrn.4896170> for details.
Structure and formatting requirements for clinical trial table and listing outputs
    vary between pharmaceutical companies. 'junco' provides additional tooling for use alongside
    the 'rtables', 'rlistings' and 'tern' packages when creating table and listing outputs. While
    motivated by the specifics of Johnson and Johnson Clinical and Statistical Programming's
    table and listing shells, 'junco' provides functionality that is general and reusable.
    Major features include a) alternative and extended statistical analyses beyond what 'tern'
    supports for use in standard safety and efficacy tables, b) a robust production-grade
    Rich Text Format (RTF) exporter for both tables and listings, c) structural support
    for spanning column headers and risk difference columns in tables, and d) robust
    font-aware automatic column width algorithms for both listings and tables.
Individual based simulations of hybridizing populations,
    where the accumulation of junctions is tracked. Furthermore,
    mathematical equations are provided to verify simulation outcomes.
    Both simulations and mathematical equations are based on Janzen
    (2018, <doi:10.1101/058107>) and Janzen (2022,
    <doi:10.1111/1755-0998.13519>).
Install packages without attaching them. If a package it is already installed, it will be skipped.
Leverages the 'yum' package to
             implement a 'YAML' ('YAML Ain't Markup Language', a human
             friendly standard for data serialization; see <https:yaml.org>)
             standard for documenting justifications, such as for decisions
             taken during the planning, execution and analysis of a study
             or during the development of a behavior change intervention
             as illustrated by Marques & Peters (2019)
             <doi:10.17605/osf.io/ndxha>. These justifications are both
             human- and machine-readable, facilitating efficient extraction
             and organisation.
Functions to justify alpha levels for statistical hypothesis tests by avoiding Lindley's paradox, or by minimizing or balancing error rates. For more information about the package please read the following: Maier & Lakens (2021) <doi:10.31234/osf.io/ts4r6>).
Provides functions to standardize and whiten data, and to perform
  Principal Component Analysis (PCA).  The main advantage of this
  package over alternatives like prcomp() is, that jvcoords makes it
  easy to convert (additional) data between the original and the
  transformed coordinates.  The package also provides a class coords,
  which can represent affine coordinate transformations.  This class
  forms the basis of the transformations provided by the package, but
  can also be used independently.  The implementation has been
  optimized to be of comparable speed (and sometimes even faster) than
  existing alternatives.
Miscellaneous tools and functions,
    including: generate descriptive statistics tables,
    format output, visualize relations among variables or check
    distributions, and generic functions for residual and
    model diagnostics.
Quality of life functions for interactive programming.
    Shortcuts for common combinations of functions or different default
    arguments. Not to be used in production level scripts, but useful for
    exploring and quickly manipulating data for easy analysis. Also
    imports a variety of packages to facilitate the installation of those
    imported packages on the host machine.
Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr' 
    and the piping syntax from 'magrittr'. Function 'kable()' is a light weight 
    table generator coming from 'knitr'. This package simplifies the way to 
    manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows 
    users to construct complex tables and customize styles using a readable 
    syntax.
Implementation of various kernel adaptive methods in nonparametric curve
    estimation like density estimation as introduced in Stute and Srihera (2011)
    <doi:10.1016/j.spl.2011.01.013> and Eichner and Stute (2013)
    <doi:10.1016/j.jspi.2012.03.011> for pointwise estimation, and like regression
    as described in Eichner and Stute (2012) <doi:10.1080/10485252.2012.760737>.
Search and download data from the API for Japanese Diet Proceedings (see the reference at <https://kokkai.ndl.go.jp/api.html>).
A toolkit for absolute and relative dating and analysis of
    chronological patterns. This package includes functions for
    chronological modeling and dating of archaeological assemblages from
    count data. It provides methods for matrix seriation. It also allows
    to compute time point estimates and density estimates of the
    occupation and duration of an archaeological site.
'Rcpp' implementation of the multivariate Kalman filter for state space models that can handle missing values and exogenous data in the observation and state equations. There is also a function to handle time varying parameters.
  Kim, Chang-Jin and Charles R. Nelson (1999) "State-Space Models with Regime Switching: Classical and Gibbs-Sampling Approaches with Applications" <doi:10.7551/mitpress/6444.001.0001><http://econ.korea.ac.kr/~cjkim/>.
Implements methods for clustering mixed-type data,
  specifically combinations of continuous and nominal data. Special attention
  is paid to the often-overlooked problem of equitably balancing the
  contribution of the continuous and categorical variables. This package
  implements KAMILA clustering, a novel method for clustering
  mixed-type data in the spirit of k-means clustering. It does not require
  dummy coding of variables, and is efficient enough to scale to rather large
  data sets. Also implemented is Modha-Spangler clustering, which uses a
  brute-force strategy to maximize the cluster separation simultaneously in the
  continuous and categorical variables. For more information, see Foss, Markatou,
  Ray, & Heching (2016) <doi:10.1007/s10994-016-5575-7> and Foss & Markatou
  (2018) <doi:10.18637/jss.v083.i13>.
Methods to extract information on pathways, genes and various single-nucleotid polymorphisms (SNPs) from online databases. It provides functions for data preparation and evaluation of genetic influence on a binary outcome using the logistic kernel machine test (LKMT). Three different kernel functions are offered to analyze genotype information in this variance component test: A linear kernel, a size-adjusted kernel and a network-based kernel).
Various tools and data sets that support the study of kanji, including their morphology, decomposition and concepts of distance and similarity between them.
One-way and two-way analysis of variance for replicated point
	patterns, grouped by one or two classification factors, on the
	basis of the corresponding K-functions.
Computes the Kantorovich distance between two probability
    measures on a finite set. The Kantorovich distance is also known as
    the Monge-Kantorovich distance or the first Wasserstein distance.
Sequences encoding by using the chaos game representation.
    Löchel et al. (2019) <doi:10.1093/bioinformatics/btz493>.
Tests the homogeneity of intraclass kappa statistics obtained from independent studies or a stratified study with binary results. It is desired to compare the kappa statistics obtained in multi-center studies or in a single stratified study to give a common or summary kappa using all available information. If the homogeneity test of these kappa statistics is not rejected, then it is possible to make inferences over a single kappa statistic that summarizes all the studies. Muammer Albayrak, Kemal Turhan, Yasemin Yavuz, Zeliha Aydin Kasap (2019) <doi:10.1080/03610918.2018.1538457> Jun-mo Nam (2003) <doi:10.1111/j.0006-341X.2003.00118.x> Jun-mo Nam (2005) <doi:10.1002/sim.2321>Mousumi Banerjee, Michelle Capozzoli, Laura McSweeney,Debajyoti Sinha (1999) <doi:10.2307/3315487> Allan Donner, Michael Eliasziw, Neil Klar (1996) <doi:10.2307/2533154>.
Estimate agreement of a group of raters with a gold standard rating
    on a nominal scale. For a single gold standard rater the average pairwise
    agreement of raters with this gold standard is provided. For a group of (gold
    standard) raters the approach of S. Vanbelle, A. Albert (2009)
    <doi:10.1007/s11336-009-9116-1> is implemented. Bias and standard error are
    estimated via delete-1 jackknife.
Offers a graphical user interface for the evaluation of inter-rater agreement with Cohen's and Fleiss' Kappa. The calculation of kappa statistics is done using the R package 'irr', so that 'KappaGUI' is essentially a Shiny front-end for 'irr'.
S4 tool box for capacity (or non-additive measure, fuzzy measure) and integral manipulation in a finite setting. It contains routines for handling various types of set functions such as games or capacities. It can be used to compute several non-additive integrals: the Choquet integral, the Sugeno integral, and the symmetric and asymmetric Choquet integrals. An analysis of capacities in terms of decision behavior can be performed through the computation of various indices such as the Shapley value, the interaction index, the orness degree, etc. The well-known Möbius transform, as well as other equivalent representations of set functions can also be computed. Kappalab further contains seven capacity identification routines: three least squares based approaches, a method based on linear programming, a maximum entropy like method based on variance minimization, a minimum distance approach and an unsupervised approach based on parametric entropies. The functions contained in Kappalab can for instance be used in the framework of multicriteria decision making or cooperative game theory.
Contains basic tools for sample size estimation in studies of interobserver/interrater agreement (reliability).  Includes functions for both the power-based and confidence interval-based methods, with binary or multinomial outcomes and two through six raters.
Attempts to remove vocals from a stereo '.wav' recording of a song.
This is a stochastic framework that combines biochemical reaction networks with extended Kalman filter and Rauch-Tung-Striebel smoothing. 
  This framework allows to investigate the dynamics of cell differentiation from high-dimensional clonal tracking data subject to measurement noise, false negative errors, and systematically unobserved cell types. 
  Our tool can provide statistical support to biologists in gene therapy clonal tracking studies for a deeper understanding of clonal reconstitution dynamics. Further details on the methods can be found in L. Del Core et al., (2022) <doi:10.1101/2022.07.08.499353>.
Real-time quantitative polymerase chain reaction (qPCR) data
    sets by Karlen et al. (2007) <doi:10.1186/1471-2105-8-131>. Provides one
    single tabular tidy data set in long format, encompassing 32
    dilution series, for seven PCR targets and four biological samples. The
    targeted amplicons are within the murine genes: Cav1, Ccn2, Eln, Fn1, Rpl27,
    Hspg2, and Serpine1, respectively. Dilution series: scheme 1 (Cav1, Eln,
    Hspg2, Serpine1): 1-fold, 10-fold, 50-fold, and 100-fold; scheme 2 (Ccn2,
    Rpl27, Fn1): 1-fold, 10-fold, 50-fold, 100-fold and 1000-fold.
    For each concentration there are five replicates, except for the 1000-fold
    concentration, where only two replicates were performed. Each amplification
    curve is 40 cycles long. Original raw data file is Additional file 2 from
    "Statistical significance of quantitative PCR" by Y. Karlen, A. McNair,
    S. Perseguers, C. Mazza, and N. Mermod (2007)
    <https://static-content.springer.com/esm/art%3A10.1186%2F1471-2105-8-131/MediaObjects/12859_2006_1503_MOESM2_ESM.ZIP>.
An R code with a GUI for microclimate time series, with an emphasis on underground environments. 'KarsTS' provides linear and nonlinear methods, including recurrence analysis (Marwan et al. (2007) <doi:10.1016/j.physrep.2006.11.001>) and filling methods (Moffat et al. (2007) <doi:10.1016/j.agrformet.2007.08.011>), as well as tools to manipulate easily time series and gap sets.
Analysis of DNA copy number in single cells using 
    custom genome-wide targeted DNA sequencing panels for the Mission Bio 
    Tapestri platform. Users can easily parse, manipulate, and visualize 
    datasets produced from the automated 'Tapestri Pipeline', with support for 
    normalization, clustering, and copy number calling. Functions are also 
    available to deconvolute multiplexed samples by genotype and parsing 
    barcoded reads from exogenous lentiviral constructs.
Convert latex math expressions to HTML and 'MathML' for use in 
    markdown documents or package manual pages. The rendering is done in 
    R using the V8 engine (i.e. server-side), which eliminates the need 
    for embedding the 'MathJax' library into your web pages. In addition
    a 'math-to-rd' wrapper is provided to automatically render beautiful
    math in R documentation files.
Provides data for Kaya identity variables (population, gross 
             domestic product, primary energy consumption, and energy-related 
             CO2 emissions) for the world and for individual nations, and 
             utility functions for looking up data,  plotting trends of 
             Kaya variables, and plotting the fuel mix for a given country
             or region. The Kaya identity (Yoichi Kaya and Keiichi Yokobori, 
             "Environment, Energy, and Economy: Strategies for Sustainability" 
             (United Nations University Press, 1998) and 
             <https://en.wikipedia.org/wiki/Kaya_identity>) expresses a nation's 
             or region's greenhouse gas emissions in terms of its population, 
             per-capita Gross Domestic Product, the energy intensity of its 
             economy, and the carbon-intensity of its energy supply.
Many data science problems reduce to operations on very tall,
    skinny matrices.  However, sometimes these matrices can be so tall that they
    are difficult to work with, or do not even fit into main memory.  One
    strategy to deal with such objects is to distribute their rows across
    several processors.  To this end, we offer an 'S4' class for tall, skinny,
    distributed matrices, called the 'shaq'.  We also provide many useful
    numerical methods and statistics operations for operating on these
    distributed objects.  The naming is a bit "tongue-in-cheek", with the class
    a play on the fact that 'Shaquille' 'ONeal' ('Shaq') is very tall, and he
    starred in the film 'Kazaam'.
Provides a weighting approach that employs kernels to make one group have a similar distribution to another group on covariates. This method matches not only means or marginal distributions but also higher-order transformations implied by the choice of kernel. 'kbal' is applicable to both treatment effect estimation and survey reweighting problems. Based on Hazlett, C. (2020) "Kernel Balancing: A flexible non-parametric weighting procedure for estimating causal effects." Statistica Sinica. <https://www.researchgate.net/publication/299013953_Kernel_Balancing_A_flexible_non-parametric_weighting_procedure_for_estimating_causal_effects>.
Computes Khattree-Bahuguna's univariate and multivariate skewness, principal-component-based Khattree-Bahuguna's multivariate skewness. It also provides several measures of univariate or multivariate skewnesses including, Pearson’s coefficient of skewness, Bowley’s univariate skewness and Mardia's multivariate skewness. See Khattree, R. and Bahuguna, M. (2019) <doi: 10.1007/s41060-018-0106-1>.
Implementation of the KCMeans regression estimator studied by 
    Wiemann (2023) <arXiv:2311.17021> for expectation function estimation conditional on 
    categorical variables. Computation leverages the unconditional KMeans 
    implementation in one dimension using dynamic programming algorithm of
    Wang and Song (2011) <doi:10.32614/RJ-2011-015>, allowing for global solutions in time polynomial in 
    the number of observed categories.
Implements approaches of non-parametric smooth test to 
            compare simultaneously K(K>1) copulas and non-parametric clustering 
            of multivariate populations with arbitrary sizes. 
            See Yves I. Ngounou Bakam and Denys Pommeret (2022) <arXiv:2112.05623> and
            Yves I. Ngounou Bakam and Denys Pommeret (2022) <arXiv:2211.06338>.
The running statistics of interest is first extracted using a time window which is slid across the time series, and in each window, the running statistics value is computed. KCP (Kernel Change Point) detection proposed by Arlot et al. (2012) <arXiv:1202.3878> is then implemented to flag the change points on the running statistics (Cabrieto et al., 2018, <doi:10.1016/j.ins.2018.03.010>). Change points are located by minimizing a variance criterion based on the pairwise similarities between running statistics which are computed via the Gaussian kernel. KCP can locate change points for a given k number of change points. To determine the optimal k, the KCP permutation test is first carried out by comparing the variance of the running statistics extracted from the original data to that of permuted data. If this test is significant, then there is sufficient evidence for at least one change point in the data. Model selection is then used to determine the optimal k>0.
It predicts any attribute (categorical) given a set of input numeric predictor values. Note that only numeric input predictors should be given.
             The k value can be chosen according to accuracies provided. The attribute to be predicted can be selected from the dropdown provided (select categorical attribute).
             This is because categorical attributes cannot be given as inputs here. A 'handsontable' is also provided to enter the input predictor values.
Predicts any variable in any categorical dataset for given values of predictor variables.
    If a dataset contains 4 variables, then any variable can be predicted based on the values of the other three variables given by the user. 
    The user can upload their own datasets and select what variable they want to predict.
    A 'handsontable' is provided to enter the predictor values and also accuracy of the prediction is also shown.
Provides an efficient implementation of univariate local polynomial
    kernel density estimators that can handle bounded and discrete data. See 
    Geenens (2014) <doi:10.48550/arXiv.1303.4121>, 
    Geenens and Wang (2018) <doi:10.48550/arXiv.1602.04862>, 
    Nagler (2018a) <doi:10.48550/arXiv.1704.07457>, 
    Nagler (2018b) <doi:10.48550/arXiv.1705.05431>.
Provides fast implementations of kernel smoothing techniques for
    bivariate copula densities, in particular density estimation and resampling,
    see Nagler (2018) <doi:10.18637/jss.v084.i07>.
Provides methods for selecting the optimal bandwidth in kernel density estimation for dependent samples, such as those generated by Markov chain Monte Carlo (MCMC). Implements a modified biased cross-validation (mBCV) approach that accounts for sample dependence, improving the accuracy of estimated density functions.
Handles univariate non-parametric density estimation with 
    parametric starts and asymmetric kernels in a simple and flexible way. 
    Kernel density estimation with parametric starts involves fitting a
    parametric density to the data before making a correction with kernel 
    density estimation, see Hjort & Glad (1995) <doi:10.1214/aos/1176324627>.
    Asymmetric kernels make kernel density estimation more efficient on bounded
    intervals such as (0, 1) and the positive half-line. Supported asymmetric 
    kernels are the gamma kernel of Chen (2000) <doi:10.1023/A:1004165218295>,
    the beta kernel of Chen (1999) <doi:10.1016/S0167-9473(99)00010-9>, and the
    copula kernel of Jones & Henderson (2007) <doi:10.1093/biomet/asm068>.
    User-supplied kernels, parametric starts, and bandwidths are supported.
Implements the vine copula based kernel density estimator of
    Nagler and Czado (2016) <doi:10.1016/j.jmva.2016.07.003>. The estimator does
    not suffer from the curse of dimensionality and is therefore well suited for
    high-dimensional applications.
Provide routines for filtering and smoothing, forecasting, sampling and Bayesian analysis of Dynamic Generalized Linear Models using the methodology described in Alves et al. (2024)<doi:10.48550/arXiv.2201.05387> and dos Santos Jr. et al. (2024)<doi:10.48550/arXiv.2403.13069>.
Density, distribution function, quantile function and random generation
             for the K-distribution. A plotting function that plots data on Weibull
             paper and another function to draw additional lines. See results from package in T Lamont-Smith (2018), submitted J. R. Stat. Soc.
Distance metrics for mixed-type data consisting of continuous, nominal, and ordinal variables. This methodology uses additive and product kernels to calculate similarity functions and metrics, and selects variables relevant to the underlying distance through bandwidth selection via maximum similarity cross-validation. These methods can be used in any distance-based algorithm, such as distance-based clustering. For further details, we refer the reader to Ghashti and Thompson (2024) <doi:10.1007/s00357-024-09493-z> for dkps() methodology, and Ghashti (2024) <doi:10.14288/1.0443975> for dkss() methodology.
A phenotype-aware algorithm for resolving cryptic relatedness in genetic studies. It removes related individuals based on kinship or identity-by-descent (IBD) scores while prioritizing subjects with phenotypes of interest. This approach helps maximize the retention of informative subjects, particularly for rare or valuable traits, and improves statistical power in genetic and epidemiological studies. KDPS supports both categorical and quantitative phenotypes, composite scoring, and customizable pruning strategies using a fuzziness parameter. Benchmark results show improved phenotype retention and high computational efficiency on large-scale datasets like the UK Biobank. Methods used include Manichaikul et al. (2010) <doi:10.1093/bioinformatics/btq559> for kinship estimation, Purcell et al. (2007) <doi:10.1086/519795> for IBD estimation, and Bycroft et al. (2018) <doi:10.1038/s41586-018-0579-z> for UK Biobank data reference.
A collection of personal helper functions to avoid redundancy
    in the spirit of the "Don't repeat yourself" principle of software
    development (<https://en.wikipedia.org/wiki/Don%27t_repeat_yourself>).
Smoothing techniques and computing bandwidth selectors of the nth derivative of a probability density for one-dimensional data (described in Arsalane Chouaib Guidoum (2020) <arXiv:2012.06102> [stat.CO]).
Provides arrays with flexible control over dimension dropping when subscripting.
Collection of utility functions used in the KEHRA project (see http://www.brunel.ac.uk/ife/britishcouncil). It refers to the multidimensional analysis of air pollution, weather and health data.
Uses Bessel functions to calculate the
    fundamental and complementary analytic solutions to the
    Kelvin differential equation.
Computes the Kendall rank correlation and Mann-Kendall
        trend test. See documentation for use of block bootstrap when
        there is autocorrelation.
The computational complexity of the implemented algorithm for
    Kendall's correlation is O(n log(n)), which is faster than the base R
    implementation with a computational complexity of O(n^2). For small vectors
    (i.e., less than 100 observations), the time difference is negligible.
    However, for larger vectors, the speed difference can be substantial and the
    numerical difference is minimal. The references are
    Knight (1966) <doi:10.2307/2282833>,
    Abrevaya (1999) <doi:10.1016/S0165-1765(98)00255-9>,
    Christensen (2005) <doi:10.1007/BF02736122> and
    Emara (2024) <https://learningcpp.org/>.
    This implementation is described in
    Vargas Sepulveda (2024) <doi:10.48550/arXiv.2408.09618>.
Kendall random walks are a continuous-space Markov chains generated
             by the Kendall generalized convolution. This package provides tools
             for simulating these random walks and studying distributions
             related to them. For more information about Kendall random walks see Jasiulis-Gołdyn (2014) <arXiv:1412.0220>.
Miscellaneous functions and data used in psychological research and teaching. Keng 
    currently has a built-in dataset depress, and could (1) scale a vector; (2) compute the cut-off 
    values of Pearson's r with known sample size; (3) test the significance and compute the post-hoc
    power for Pearson's r with known sample size; (4) conduct prior power analysis and plan the 
    sample size for Pearson's r; (5) compare lm()'s fitted outputs using R-squared, f_squared, 
    post-hoc power, and PRE (Proportional Reduction in Error, also called partial R-squared or 
    partial Eta-squared); (6) calculate PRE from partial correlation, Cohen's f, or f_squared; 
    (7) conduct prior power analysis and plan the sample size for one or a set of predictors in 
    regression analysis; (8) conduct post-hoc power analysis for one or a set of predictors in 
    regression analysis with known sample size.
Demo and dataset accompaying the books :
	De l'analyse des réseaux expérimentaux à la méta-analyse: Méthodes et applications avec le logiciel R pour les sciences agronomiques et environnementales (Published 2018-06-28, Quae, for french version) by David Makowski, Francois Piraux and Francois Brun - <https://www.quae.com/produit/1514/9782759228164/de-l-analyse-des-reseaux-experimentaux-a-la-meta-analyse>
	Knowledge Synthesis in Agriculture : from Experimental Network to Meta-Analysis (in preparation for 2018-06, Springer , for English version) by David Makowski, Francois Piraux and Francois Brun
	A full description of all the material is in both books.
	ACKNOWLEDGMENTS : The French network "RMT modeling and data analysis for agriculture" (<http://www.modelia.org>) have contributed to the development of this R package. This project and network are lead by ACTA (French Technical Institute for Agriculture) and was funded by a grant from the Ministry of Agriculture and Fishing of France.
Provides an implementation of a kernel-embedding of probability test for elliptical distribution. This is an asymptotic test for elliptical distribution under general alternatives, and the location and shape parameters are assumed to be unknown. Some side-products are posted, including the transformation between rectangular and polar coordinates and two product-type kernel functions. See Tang and Li (2024) <doi:10.48550/arXiv.2306.10594> for details.
Implements the kernel method of test equating as defined in von Davier, A. A., Holland, P. W. and Thayer, D. T. (2004) <doi:10.1007/b97446> and Andersson, B. and Wiberg, M. (2017) <doi:10.1007/s11336-016-9528-7> using the CB, EG, SG, NEAT CE/PSE and NEC designs, supporting Gaussian, logistic and uniform kernels and unsmoothed and pre-smoothed input data.
Interface to 'Keras' <https://keras.io>, a high-level neural
  networks 'API'. 'Keras' was developed with a focus on enabling fast experimentation,
  supports both convolution based networks and recurrent networks (as well as
  combinations of the two), and runs seamlessly on both 'CPU' and 'GPU' devices.
Interface to 'Keras' <https://keras.io>, a high-level neural
  networks API. 'Keras' was developed with a focus on enabling fast experimentation,
  supports both convolution based networks and recurrent networks (as well as
  combinations of the two), and runs seamlessly on both CPU and GPU devices.
'Keras Tuner' <https://keras-team.github.io/keras-tuner/> is a hypertuning framework made for humans. 
             It aims at making the life of AI practitioners, hypertuner 
             algorithm creators and model designers as simple as possible by 
             providing them with a clean and easy to use API for hypertuning. 
             'Keras Tuner' makes moving from a base model to a hypertuned one quick and 
             easy by only requiring you to change a few lines of code.
A new practical method to evaluate whether relationships between two sets of high-dimensional variables are different or not across two conditions.
    Song, H. and Wu, M.C. (2023) 
    <arXiv:2307.15268>.
Nonparametric kernel distribution function estimation is performed. Three bandwidth selectors are implemented: the plug-in selectors of Altman and Leger and of Polansky and Baker, and the cross-validation selector of Bowman, Hall and Prvan. The exceedance function, the mean return period and the return level are also computed. For details, see Quintela-del-Río and Estévez-Pérez (2012) <doi:10.18637/jss.v050.i08>.
An efficient algorithm inspired by majorization-minimization principle for solving the entire solution path of a flexible nonparametric expectile regression estimator constructed in a reproducing kernel Hilbert space.
Gaussian process regression with an emphasis on kernels.
    Quantitative and qualitative inputs are accepted. Some pre-defined
    kernels are available, such as radial or tensor-sum for
    quantitative inputs, and compound symmetry, low rank, group kernel
    for qualitative inputs. The user can define new kernels and
    composite kernels through a formula mechanism. Useful methods
    include parameter estimation by maximum likelihood, simulation,
    prediction and leave-one-out validation.
A novel implementation that solves the linear distance weighted discrimination and the kernel distance weighted discrimination. Reference: Wang and Zou (2018) <doi:10.1111/rssb.12244>.
Smoothed bootstrap and functions for random generation from
             univariate and multivariate kernel densities. It does not
             estimate kernel densities.
Binary classification based on an ensemble of kernel machines ("Ballings, M. and Van den Poel, D. (2013), Kernel Factory: An Ensemble of Kernel Machines. Expert Systems With Applications, 40(8), 2904-2913"). Kernel factory is an ensemble method where each base classifier (random forest) is fit on the kernel matrix of a subset of the training data.
In self-reported or anonymised data the user often encounters
    heaped data, i.e. data which are rounded (to a possibly different degree
    of coarseness). While this is mostly a minor problem in parametric density
    estimation the bias can be very large for non-parametric methods such as kernel
    density estimation. This package implements a partly Bayesian algorithm treating
    the true unknown values as additional parameters and estimates the rounding
    parameters to give a corrected kernel density estimate. It supports various
    standard bandwidth selection methods. Varying rounding probabilities (depending
    on the true value) and asymmetric rounding is estimable as well: Gross, M. and Rendtel, U. (2016) (<doi:10.1093/jssam/smw011>).
    Additionally, bivariate non-parametric density estimation for rounded data, Gross, M. et al. (2016) (<doi:10.1111/rssa.12179>),
    as well as data aggregated on areas is supported.
Extends the simple k-nearest neighbors algorithm by incorporating numerous kernel functions and a variety of distance metrics. The package takes advantage of 'RcppArmadillo' to speed up the calculation of distances between observations.
Efficient implementation of Kernel SHAP (Lundberg and Lee,
    2017, <doi:10.48550/arXiv.1705.07874>) permutation SHAP, and additive
    SHAP for model interpretability.  For Kernel SHAP and permutation
    SHAP, if the number of features is too large for exact calculations,
    the algorithms iterate until the SHAP values are sufficiently precise
    in terms of their standard errors.  The package integrates smoothly
    with meta-learning packages such as 'tidymodels', 'caret' or 'mlr3'.
    It supports multi-output models, case weights, and parallel
    computations.  Visualizations can be done using the R package
    'shapviz'.
Producing kernel estimates of the unconditional and conditional hazard
        function for right-censored data including methods of bandwidth selection.
Kernel-based machine learning methods for classification,
        regression, clustering, novelty detection, quantile regression
        and dimensionality reduction.  Among other methods 'kernlab'
        includes Support Vector Machines, Spectral Clustering, Kernel
        PCA, Gaussian Processes and a QP solver.
Implementation of Discrete Symmetric Optimal Kernel for estimating count data distributions, as described by T. Senga Kiessé and G. Durrieu (2024) <doi:10.1016/j.spl.2024.110078>.The nonparametric estimator using the discrete symmetric optimal kernel was illustrated on simulated data sets and a real-word data set included in the package, in comparison with two other discrete symmetric kernels.
Provides wind energy practitioners with an effective machine learning-based
    tool that estimates a multivariate power curve and predicts the wind power output
    for a specific environmental condition.
Kernel Machine Score Test for Pathway Analysis in the Presence of 
    Semi-Competing Risks. Method is detailed in: Neykov, Hejblum & Sinnott (2018) 
    <doi: 10.1177/0962280216653427>.
Functions for kernel smoothing (and density estimation)
  corresponding to the book: 
  Wand, M.P. and Jones, M.C. (1995) "Kernel Smoothing".
Fits nonparametric item and option characteristic curves using kernel smoothing. It allows for optimal selection of the smoothing bandwidth using cross-validation and a variety of exploratory plotting tools. The kernel smoothing is based on methods described in Silverman, B.W. (1986). Density Estimation for Statistics and Data Analysis. Chapman & Hall, London.
Adaptive estimation of the first-order intensity function of a spatio-temporal point process using kernels and variable bandwidths. The methodology used for estimation is presented in González and Moraga (2022). <doi:10.48550/arXiv.2208.12026>.
Kernel functions for diverse types of data (including, but not
    restricted to: nonnegative and real vectors, real matrices, categorical
    and ordinal variables, sets, strings), plus other utilities like kernel
    similarity, kernel Principal Components Analysis (PCA) and features'
    importance for Support Vector Machines (SVMs), which expand other 'R'
    packages like 'kernlab'.
New kernel-based test and fast tests for detecting change-points or changed-intervals where the distributions abruptly change. They work well particularly for high-dimensional data.
    Song, H. and Chen, H. (2022)
    <arXiv:2206.01853>.
New kernel-based test and fast tests for testing whether two samples are from the same distribution. They work well particularly for high-dimensional data.
      Song, H. and Chen, H. (2023) 
      <arXiv:2011.06127>.
A shiny app to visualize the knowledge networks for the code concepts. Using co-occurrence matrices of EHR codes from Veterans Affairs (VA) and Massachusetts General Brigham (MGB), the knowledge extraction via sparse embedding regression (KESER) algorithm was used to construct knowledge networks for the code concepts. Background and details about the method can be found at Chuan et al. (2021) <doi:10.1038/s41746-021-00519-z>.
Fits keyword assisted topic models (keyATM) using collapsed Gibbs samplers. The keyATM combines the latent dirichlet allocation (LDA) models with a small number of keywords selected by researchers in order to improve the interpretability and topic classification of the LDA. The keyATM can also incorporate covariates and directly model time trends. The keyATM is proposed in Eshima, Imai, and Sasaki (2024) <doi:10.1111/ajps.12779>.
We developed a package 'Keyboard' for designing single-agent, drug-combination, or phase I/II dose-finding clinical trials. The 'Keyboard' designs are novel early phase trial designs that can be implemented simply and transparently, similar to the 3+3 design, but yield excellent performance, comparable to those of more-complicated, model-based designs (Yan F, Mandrekar SJ, Yuan Y (2017) <doi:10.1158/1078-0432.CCR-17-0220>, Li DH, Whitmore JB, Guo W, Ji Y. (2017) <doi:10.1158/1078-0432.CCR-16-1125>,  Liu S, Johnson VE (2016) <doi:10.1093/biostatistics/kxv040>, Zhou Y, Lee JJ, Yuan Y (2019) <doi:10.1002/sim.8475>, Pan H, Lin R, Yuan Y (2020) <doi:10.1016/j.cct.2020.105972>). The 'Keyboard' package provides tools for designing, conducting, and analyzing single-agent, drug-combination, and phase I/II dose-finding clinical trials. For more details about how to use this packge, please refer to Li C, Sun H, Cheng C, Tang L, and Pan H. (2022) "A software tool for both the maximum tolerated dose and the optimal biological dose finding trials in early phase designs". Manuscript submitted for publication.
Control your keyboard and mouse with R code by simulating key presses and mouse clicks. The input simulation is implemented with the Windows API.
A fast and computationally efficient algorithm designed to enable researchers to efficiently and quickly extract semantically-related keywords using a fitted embedding model. For more details about the methods applied, see Chester (2025). <doi:10.17605/OSF.IO/5B7RQ>.
Tools for keeping track of information, named
    "keys", about rows of data frame like objects. This is done by
    creating special attribute "keys" which is updated after every change
    in rows (subsetting, ordering, etc.).  This package is designed to
    work tightly with 'dplyr' package.
Efficient implementation of permutation tests for keyword analysis in corpus linguistics as described in Mildenberger (2023) <arXiv:2308.13383>.
Computes group centrality scores and identifies the most central group of players in a network.
Wait for a single key press at the 'R' prompt.
    This works in terminals, but does not currently work
    in the 'Windows' 'GUI', the 'OS X' 'GUI' ('R.app'),
    in 'Emacs' 'ESS', in an 'Emacs' shell buffer or in
    'R Studio'. In these cases 'keypress' stops with an
    error message.
Platform independent 'API' to access the operating system's
    credential store. Currently supports: 'Keychain' on 'macOS',
    Credential Store on 'Windows', the Secret Service 'API' on 'Linux',
    and simple, platform independent stores implemented with environment
    variables or encrypted files.  Additional storage back-ends can be
    added easily.
Decrypts passwords stored in the Gnome Keyring, macOS Keychain and
    strings encrypted with the Windows Data Protection API.
Assign and listen to keyboard shortcuts in 'shiny' using the 
  'Mousetrap' Javascript library.
Convert keys and other values to memorable phrases. 
  Includes some methods to build lists of words.
Provides functions to identify plausible and replicable factor
  structures for a set of variables via k-fold cross validation. The process
  combines the exploratory and confirmatory factor analytic approach to scale
  development (Flora & Flake, 2017) <doi:10.1037/cbs0000069> with a cross validation
  technique that maximizes the available data (Hastie, Tibshirani, & Friedman, 2009)
  <isbn:978-0-387-21606-5>. Also available are functions to determine k by drawing 
  on power analytic techniques for covariance structures (MacCallum, Browne, &
  Sugawara, 1996) <doi:10.1037/1082-989X.1.2.130>, generate model syntax, and
  summarize results in a report.
State space modelling is an efficient and flexible framework for 
    statistical inference of a broad class of time series and other data. KFAS 
    includes computationally efficient functions for Kalman filtering, smoothing, 
    forecasting, and simulation of multivariate exponential family state space models, 
    with observations from Gaussian, Poisson, binomial, negative binomial, and gamma 
    distributions. See the paper by Helske (2017) <doi:10.18637/jss.v078.i10> for details.
Kernel Fisher Discriminant Analysis (KFDA) is performed using Kernel Principal Component Analysis (KPCA) and Fisher Discriminant Analysis (FDA).
    There are some similar packages. First, 'lfda' is a package that performs Local Fisher Discriminant Analysis (LFDA) and performs other functions.
    In particular, 'lfda' seems to be impossible to test because it needs the label information of the data in the function argument. Also, the 'ks' package has a limited dimension, which makes it difficult to analyze properly.
    This package is a simple and practical package for KFDA based on the paper of Yang, J., Jin, Z., Yang, J. Y., Zhang, D., and Frangi, A. F. (2004) <DOI:10.1016/j.patcog.2003.10.015>.
A streamlined cross-referencing system for R Markdown documents
    generated with 'knitr'. R Markdown is  an authoring format for generating
    dynamic content from R. 'kfigr' provides a hook for anchoring code
    chunks and a function to cross-reference document elements generated from
    said chunks, e.g. figures and tables.
A method for detecting outliers with a Kalman filter on impulsed 
  noised outliers and prediction on cleaned data. 'kfino' is a robust 
  sequential algorithm allowing to filter data with a large number of outliers. 
  This algorithm is based on simple latent linear Gaussian processes as in the 
  Kalman Filter method and is devoted to detect impulse-noised outliers. These 
  are data points that differ significantly from other observations. 'ML' 
  (Maximization Likelihood) and 'EM' (Expectation-Maximization algorithm) 
  algorithms were implemented in 'kfino'. The method is described in full 
  details in the following arXiv e-Print: <arXiv:2208.00961>.
Implementation for Kendall functional principal component analysis. Kendall functional principal component analysis is a robust functional principal component analysis technique for non-Gaussian functional/longitudinal data. The crucial function of this package is KFPCA() and KFPCA_reg(). Moreover, least square estimates of functional principal component scores are also provided. Refer to Rou Zhong, Shishi Liu, Haocheng Li, Jingxiao Zhang. (2021) <arXiv:2102.01286>. Rou Zhong, Shishi Liu, Haocheng Li, Jingxiao Zhang. (2021) <doi:10.1016/j.jmva.2021.104864>.
Implementation for kernel functional partial least squares (KFPLS) method. KFPLS method is developed for functional nonlinear models, and the method does not require strict constraints for the nonlinear structures. The crucial function of this package is KFPLS().
Aids in identifying the Koeppen-Geiger (KG) climatic zone for 
    a given location. The Koeppen-Geiger climate zones were first published in 1884, as a system
    to classify regions of the earth by their relative heat and humidity through the year, for 
    the benefit of human health, plant and agriculture and other human activity [1]. This climate
    zone classification system, applicable to all of the earths surface, has continued to be 
    developed by scientists up to the present day.  Recently one of use (FZ) has published updated,
    higher accuracy KG climate zone definitions [2]. In this package we use these updated 
    high-resolution maps as the data source [3]. We provide functions that return the KG climate zone 
    for a given longitude and lattitude, or for a given United States zip code. In addition
    the CZUncertainty() function will check climate zones nearby to check if the given location
    is near a climate zone boundary. In addition an interactive shiny app is provided to define 
    the KG climate zone for a given longitude and lattitude, or United States zip code. 
    Digital data, as well as animated maps, showing the shift of the climate zones are provided 
    on the following website <http://koeppen-geiger.vu-wien.ac.at>.
    This work was supported by the DOE-EERE SunShot award DE-EE-0007140.
     [1] W. Koeppen, (2011) <doi:10.1127/0941-2948/2011/105>.
     [2] F. Rubel and M. Kottek, (2010) <doi:10.1127/0941-2948/2010/0430>.
     [3] F. Rubel, K. Brugger, K. Haslinger, and I. Auer, (2016) <doi:10.1127/metz/2016/0816>.
A unified software package simultaneously implemented in 'Python', 'R', and 'Matlab' providing a uniform and internally-consistent way of calculating stoichiometric equilibrium constants in modern and palaeo seawater as a function of temperature, salinity, pressure and the concentration of magnesium, calcium, sulphate, and fluorine.
The kernel ridge regression and the gradient matching algorithm proposed in Niu et al. (2016) <https://proceedings.mlr.press/v48/niu16.html> and the warping algorithm proposed in Niu et al. (2017) <DOI:10.1007/s00180-017-0753-z> are implemented for parameter inference in differential equations. Four schemes are provided for improving parameter estimation in odes by using the odes regularisation and warping.
Metadata about populations and data about samples from the 1000 Genomes Project, including the 2,504 samples sequenced for the Phase 3 release and the expanded collection of 3,202 samples with 602 additional trios. The data is described in Auton et al. (2015) <doi:10.1038/nature15393> and Byrska-Bishop et al. (2022) <doi:10.1016/j.cell.2022.08.004>, and raw data is available at <http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/>. See Turner (2022) <doi:10.48550/arXiv.2210.00539> for more details.
Training and evaluating k-gram language models in R, 
        supporting several probability smoothing techniques, 
        perplexity computations, random text generation and more.
Knowledge graphs enable to efficiently visualize and gain insights into large-scale data analysis results, as p-values from multiple studies or embedding data matrices. The usual workflow is a user providing a data frame of association studies results and specifying target nodes, e.g. phenotypes, to visualize. The knowledge graph then shows all the features which are significantly associated with the phenotype, with the edges being proportional to the association scores. As the user adds several target nodes and grouping information about the nodes such as biological pathways, the construction of such graphs soon becomes complex. The 'kgraph' package aims to enable users to easily build such knowledge graphs, and provides two main features: first, to enable building a knowledge graph based on a data frame of concepts relationships, be it p-values or cosine similarities; second, to enable determining an appropriate cut-off on cosine similarities from a complete embedding matrix, to enable the building of a knowledge graph directly from an embedding matrix. The 'kgraph' package provides several display, layout and cut-off options, and has already proven useful to researchers to enable them to visualize large sets of p-value associations with various phenotypes, and to quickly be able to visualize embedding results. Two example datasets are provided to demonstrate these behaviors, and several live 'shiny' applications are hosted by the CELEHS laboratory and Parse Health, as the KESER Mental Health application <https://keser-mental-health.parse-health.org/> based on Hong C. (2021) <doi:10.1038/s41746-021-00519-z>.
Restore underlining numeric data from rating history graph of 
    KGS (an online platform of the game of go, <http://www.gokgs.com/>). 
    A shiny application is also provided.
Provides a user-friendly interface for interacting with the District Health 
    Information Software 2 (DHIS2) instance. It streamlines data retrieval, 
    empowering researchers, analysts, and healthcare professionals to obtain and 
    utilize data efficiently.
The King's Health Questionnaire (KHQ) is a disease-specific, 
  self-administered questionnaire designed specific to assess the impact of 
  Urinary Incontinence (UI) on Quality of Life. The questionnaire was developed 
  by Kelleher and collaborators (1997) <doi:10.1111/j.1471-0528.1997.tb11006.x>. 
  It is a simple, acceptable and reliable measure to use in the clinical setting 
  and a research tool that is useful in evaluating UI treatment outcomes. 
  The KHQ five dimensions (KHQ5D) is a condition-specific preference-based 
  measure developed by Brazier and collaborators (2008) <doi:10.1177/0272989X07301820>. 
  Although not as popular as the SF6D <doi:10.1016/S0895-4356(98)00103-6> and 
  EQ-5D <https://euroqol.org/>, the KHQ5D measures health-related quality of 
  life (HRQoL) specifically for UI, not general conditions like the others 
  two instruments mentioned. The KHQ5D ca be used in the clinical and economic 
  evaluation of health care. The subject self-rates their health in terms of 
  five dimensions: Role Limitation (RL), Physical Limitations (PL), Social 
  Limitations (SL), Emotions (E), and Sleep (S). Frequently the states 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. This package provides 
  methods to calculate scores for each dimension of the KHQ; converts KHQ item 
  scores to KHQ5D scores; and also calculates the utility index of the KHQ5D.
Color schemes ready for each type of data (qualitative,
    diverging or sequential), with colors that are distinct for all
    people, including color-blind readers. This package provides an
    implementation of Paul Tol (2018) and Fabio Crameri (2018)
    <doi:10.5194/gmd-11-2541-2018> color schemes for use with 'graphics'
    or 'ggplot2'. It provides tools to simulate color-blindness and to
    test how well the colors of any palette are identifiable. Several
    scientific thematic schemes (geologic timescale, land cover, FAO
    soils, etc.) are also implemented.
Contains kidney care oriented functions.
			 Current version contains functions for calculation of:
			 - Estimated glomerular filtration rate by CKD-EPI (2021 and 2009), MDRD, CKiD, FAS, EKFC, etc.
			 - Kidney Donor Risk Index and Kidney Donor Profile Index for kidney transplant donors.
			 - Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, <https://Scientific-Tools.Org>.  <doi:10.32614/CRAN.package.kidney.epi>.
Caches and then connects to a 'sqlite' database containing half a million pediatric drug safety signals. 
    The database is part of a family of resources catalogued at <https://nsides.io>. The database
    contains 17 tables where the description table provides a map between the fields the field's details. 
    The database was created by Nicholas Giangreco during his PhD thesis which you can read in Giangreco (2022) <doi:10.7916/d8-5d9b-6738>. 
    The observations are from the Food and Drug Administration's Adverse Event Reporting System. Generalized additive models estimated
    drug effects across child development stages for the occurrence of an adverse event when exposed to a drug compared to other drugs.
    Read more at the methods detailed in Giangreco (2022) <doi:10.1016/j.medj.2022.06.001>.
Optimized for handling complex datasets in environmental and ecological 
    research, this package offers functionality that is not fully met by 
    general-purpose packages. It provides two key functions, 'summarize_data()', 
    which summarizes datasets, and 'plot_means()', which creates plots with 
    error bars. The 'plot_means()' function incorporates error bars by default, 
    allowing quick visualization of uncertainties, crucial in ecological 
    studies. It also streamlines workflows for grouped datasets (e.g., 
    by species or treatment), making it particularly user-friendly and reducing 
    the complexity and time required for data summarization and visualization.
A collection of functions for analyzing data typically collected 
    or used by behavioral scientists. Examples of the functions include
    a function that compares groups in a factorial experimental design,
    a function that conducts two-way analysis of variance (ANOVA),
    and a function that cleans a data set generated by Qualtrics surveys.
    Some of the functions will require installing additional package(s).
    Such packages and other references are cited within the section
    describing the relevant functions. Many functions in this package
    rely heavily on these two popular R packages:
    Dowle et al. (2021) <https://CRAN.R-project.org/package=data.table>.
    Wickham et al. (2021) <https://CRAN.R-project.org/package=ggplot2>.
'Rcpp' implementation of the multivariate Kim filter, which combines the Kalman and Hamilton filters for state probability inference. 
  The filter is designed for state space models and can handle missing values and exogenous data in the observation and state equations.
  Kim, Chang-Jin and Charles R. Nelson (1999) "State-Space Models with Regime Switching: Classical and Gibbs-Sampling Approaches with Applications" <doi:10.7551/mitpress/6444.001.0001><http://econ.korea.ac.kr/~cjkim/>.
A collection of useful functions not found anywhere else,
    mainly for programming: Pretty intervals, generalized lagged
    differences, checking containment in an interval, and an alternative
    interface to assign().
Analysis of kin-cohort studies. kin.cohort provides estimates of age-specific 
 cumulative risk of a disease for carriers and noncarriers of a mutation. The cohorts are
 retrospectively built from relatives of probands for whom the genotype is known. Currently 
 the method of moments and marginal maximum likelihood are implemented. Confidence intervals 
 are calculated from bootstrap samples.
 Most of the code is a translation from previous 'MATLAB' code by N. Chatterjee.
Functions for simulating and estimating kinship-related dispersal. Based
    on the methods described in M. Jasper, T.L. Schmidt., N.W. Ahmad, S.P. Sinkins & A.A. 
    Hoffmann (2019) <doi:10.1111/1755-0998.13043> "A genomic approach to inferring kinship 
    reveals limited intergenerational dispersal in the yellow fever mosquito".
    Assumes an additive variance model of dispersal in two dimensions, compatible with 
    Wright's neighbourhood area. Simple and composite dispersal simulations are supplied, 
    as well as the functions needed to estimate parent-offspring dispersal for simulated or 
    empirical data, and to undertake sampling design for future field studies of dispersal. 
    For ease of use an integrated Shiny app is also included.
Allows analyzing time series representing two-dimensional movements.
    It accepts a data frame with a time (t), horizontal (x) and vertical (y) coordinate as columns,
    and returns several dynamical properties such as speed, acceleration or curvature.
A collection of 'shiny' applications for the 'tesselle'
    packages <https://www.tesselle.org/>. This package provides
    applications for archaeological data analysis and visualization. These
    mainly, but not exclusively, include applications for chronological
    modelling (e.g. matrix seriation, aoristic analysis) and count data
    analysis (e.g. diversity measures, compositional data analysis).
Data on houses in and around Seattle WA are included. Basic 
    characteristics are given along with sale prices.
Methods for inference about/under complex relationships using
  peak height data from DNA mixtures: the most basic example would be testing whether a contributor to 
  a mixture is the father of a child of known genotype. This provides most of the functionality
  of the 'KinMix' package, but with some loss of efficiency and restriction on problem size,
  as the latter uses 'RHugin' as the Bayes net engine, while this package uses 'gRain'.
  The package implements the methods introduced in 
  Green, P. J. and Mortera, J. (2017) <doi:10.1016/j.fsigen.2017.02.001> and 
  Green, P. J. and Mortera, J. (2021) <doi:10.1111/rssc.12498>.
Routines to handle family data with a pedigree object. The initial purpose
	     was to create correlation structures that describe family relationships such 
	     as kinship and identity-by-descent, which can be used to model family data 
	     in mixed effects models, such as in the coxme function. Also includes a tool
	     for pedigree drawing which is focused on producing compact layouts without 
	     intervention. Recent additions include utilities to trim the pedigree object
	     with various criteria, and kinship for the X chromosome.
Evaluate specific panels in different aspects: i) Simulation tools related to pedigree researches; ii) calculation for systemic effectiveness indicators, such as probability of exclusion (PE).
Machine learning, containing several algorithms for supervised and unsupervised classification, in addition to a function that plots the Receiver Operating Characteristic (ROC) and Precision-Recall (PRC) curve graphs, and also a function that returns several metrics used for model evaluation, the latter can be used in ranking results from other packs.
Multi-modal magnetic resonance imaging ('MRI')
    data from the 'Kirby21' 'reproducibility' study
    <https://www.nitrc.org/projects/multimodal/>, including functional
    and structural imaging.
Functional magnetic resonance imaging ('fMRI')
       data from the 'Kirby21' 'reproducibility' study
       <doi:10.1016/j.neuroimage.2010.11.047>.
Structural T1 magnetic resonance imaging ('MRI')
       data from the 'Kirby21' 'reproducibility' study
       <doi:10.1016/j.neuroimage.2010.11.047>.
API Wrapper to use Korea Investment & Securities (KIS) trading 
             system that provides various financial services like stock price 
             check, orders and balance check 
             <https://apiportal.koreainvestment.com/>.
Simulating species migration and range dynamics under stable or changing environmental conditions based on a simple, raster-based, deterministic or stochastic migration model. Kissmig runs on binary or quantitative suitability maps, which are pre-calculated with niche-based habitat suitability models (also called ecological niche models (ENMs) or species distribution models (SDMs)). Nobis & Normand (2014), <doi:10.1111/ecog.00930>.
Basic functions, implemented in C, for large data manipulation. Fast vectorised ifelse()/nested if()/switch() functions, psum()/pprod() functions equivalent to pmin()/pmax() plus others which are missing from base R. Most of these functions are callable at C level.
Provides tools to calculate the theoretical hydrodynamic response
    of an aquifer undergoing harmonic straining or pressurization, or analyze
    measured responses. There are
    two classes of models here, designed for use with confined
    aquifers: (1) for sealed wells, based on the model of 
    Kitagawa et al (2011, <doi:10.1029/2010JB007794>), 
    and (2) for open wells, based on the models of
    Cooper et al (1965, <doi:10.1029/JZ070i016p03915>), 
    Hsieh et al (1987, <doi:10.1029/WR023i010p01824>), 
    Rojstaczer (1988, <doi:10.1029/JB093iB11p13619>), 
    Liu et al (1989, <doi:10.1029/JB094iB07p09453>), and
    Wang et al (2018, <doi:10.1029/2018WR022793>). Wang's 
    solution is a special exception which
    allows for leakage out of the aquifer 
    (semi-confined); it is equivalent to Hsieh's model
    when there is no leakage (the confined case).
    These models treat strain (or aquifer head) as an input to the
    physical system, and fluid-pressure (or water height) as the output. The
    applicable frequency band of these models is characteristic of seismic
    waves, atmospheric pressure fluctuations, and solid earth tides.
Create a kite-square plot for contingency tables using 'ggplot2', to display their relevant quantities in a single figure (marginal, conditional, expected, observed, chi-squared). The plot resembles a flying kite inside a square if the variables are independent, and deviates from this the more dependence exists.
A wrapper for querying 'WISKI' databases via the 'KiWIS' 'REST' API. 'WISKI' is an 'SQL' relational database 
  used for the collection and storage of water data developed by KISTERS and 'KiWIS' is a 'REST' service that provides
  access to 'WISKI' databases via HTTP requests (<https://www.kisters.eu/water-weather-and-environment/>). 
  Contains a list of default databases (called 'hubs') and also allows users to provide their own 'KiWIS' URL. 
  Supports the entire query process- from metadata to specific time series values. All data is returned as tidy tibbles.
Weighted k-Nearest Neighbors for Classification, Regression
    and Clustering.
A variable selection procedure, dubbed KKO, for nonparametric additive model with finite-sample false discovery rate control guarantee. The method integrates three key components: knockoffs, subsampling for stability, and random feature mapping for nonparametric function approximation. For more information, see the accompanying paper: Dai, X., Lyu, X., & Li, L. (2021). “Kernel Knockoffs Selection for Nonparametric Additive Models”. arXiv preprint <arXiv:2105.11659>.
Miscellaneous functions for classification and visualization,
     e.g. regularized discriminant analysis, sknn() kernel-density naive Bayes, 
     an interface to 'svmlight' and stepclass() wrapper variable selection 
     for supervised classification, partimat() visualization of classification rules 
         and shardsplot() of cluster results as well as kmodes() clustering for categorical data, 
     corclust() variable clustering, variable extraction from different variable clustering models 
         and weight of evidence preprocessing.
Functions to search, retrieve, apply and update classifications 
  and codelists using Statistics Norway's API <https://www.ssb.no/klass> 
  from the system 'KLASS'. Retrieves classifications by date with options 
  to choose language, hierarchical level and formatting.
A set of functions designed to quickly generate results of a multiple choice
          test. Generates detailed global results, lists for anonymous feedback and
          personalised result feedback (in LaTeX and/or PDF format), as well as item
          statistics like Cronbach's alpha or disciminatory power. 'klausuR' also
          includes a plugin for the R GUI and IDE RKWard, providing graphical dialogs for
          its basic features. The respective R package 'rkward' cannot be installed
          directly from a repository, as it is a part of RKWard. To make full use of this
          feature, please install RKWard from <https://rkward.kde.org> (plugins are
          detected automatically). Due to some restrictions on CRAN, the full package
          sources are only available from the project homepage.
Estimation algorithms for Kullback-Leibler divergence between two probability
    distributions, based on one or two samples, and including uncertainty quantification.
    Distributions can be uni- or multivariate and continuous, discrete or mixed.
Most importantly, calculates Kullback-Leibler Divergence (KLD), Turing's perspective estimator
 and their confidence intervals.
Provides the function to calculate the kernel-lasso expansion, Z-score, and max-min-scale standardization.It can increase the dimension of existed dataset and remove abundant features by lasso. Z Dai, L Jiayi, T Gong, C Wang (2021) <doi:10.1088/1742-6596/1955/1/012047>.
Kernel Learning Integrative Clustering (KLIC) is an algorithm that allows to combine multiple kernels, each representing a different measure of the similarity between a set of observations. The contribution of each kernel on the final clustering is weighted according to the amount of information carried by it. As well as providing the functions required to perform the kernel-based clustering, this package also allows the user to simply give the data as input: the kernels are then built using consensus clustering. Different strategies to choose the best number of clusters are also available. For further details please see Cabassi and Kirk (2020) <doi:10.1093/bioinformatics/btaa593>.
A 'shiny' application for forensic kinship testing, based on
    the 'pedsuite' R packages. 'KLINK' is closely aligned with the (non-R)
    software 'Familias' and 'FamLink', but offers several unique features,
    including visualisations and automated report generation. The
    calculation of likelihood ratios supports pairs of linked markers, and
    all common mutation models.
A comprehensive set of geostatistical, visual,
    and analytical methods, in conjunction with the expanded version of the
    acclaimed J.E. Klovan's mining dataset, are included in 'klovan'. This makes the
    package an excellent learning resource for Principal Component Analysis (PCA),
    Factor Analysis (FA), kriging, and other geostatistical techniques. Originally
    published in the 1976 book 'Geological Factor Analysis', the included mining
    dataset was assembled by Professor J. E. Klovan of the University of Calgary.
    Being one of the first applications of FA in the geosciences, this dataset has
    significant historical importance. As a well-regarded and published dataset, it
    is an excellent resource for demonstrating the capabilities of PCA, FA, kriging,
    and other geostatistical techniques in geosciences. For those interested in
    these methods, the 'klovan' datasets provide a valuable and illustrative resource.
    Note that some methods require the 'RGeostats' package. Please refer to the
    README or Additional_repositories for installation instructions. This material is
    based upon research in the Materials Data Science for Stockpile Stewardship Center
    of Excellence (MDS3-COE), and supported by the Department of Energy's National
    Nuclear Security Administration under Award Number DE-NA0004104.
An implementation of the blocking algorithm KLSH in Steorts, Ventura, Sadinle, Fienberg (2014) <DOI:10.1007/978-3-319-11257-2_20>, which is a k-means variant of locality sensitive hashing. The method is illustrated with examples and a vignette.
Used to create dynamic, interactive 'D3.js' 
  based parallel coordinates and principal component plots in 'R'.
  The plots make visualizing k-means or other clusters simple and informative.
Computes various confidence intervals for the Kaplan-Meier
        estimator, namely: Peto's CI, Rothman CI, CI's based on
        Greenwood's variance, Thomas and Grunkemeier CI and the
        simultaneous confidence bands by Nair and Hall and Wellner.
Implements k-means like blockmodeling of one-mode and linked networks as presented in Žiberna (2020) <doi:10.1016/j.socnet.2019.10.006>. The development of this package is financially supported by the Slovenian Research Agency (<https://www.arrs.si/>) within the research programs P5-0168 and the research projects J7-8279 (Blockmodeling multilevel and temporal networks) and J5-2557 (Comparison and evaluation of different approaches to blockmodeling dynamic networks by simulations with application to Slovenian co-authorship networks).
Given constraints for right censored data, we use a recursive computational algorithm to calculate the the "constrained" Kaplan-Meier estimator. The constraint is assumed given in linear estimating equations or mean functions. We also illustrate how this leads to the empirical likelihood ratio test with right censored data and accelerated failure time model with given coefficients. EM algorithm from emplik package is used to get the initial value. The properties and performance of the EM algorithm is discussed in Mai Zhou and Yifan Yang (2015)<doi: 10.1007/s00180-015-0567-9> and Mai Zhou and Yifan Yang (2017) <doi: 10.1002/wics.1400>. More applications could be found in Mai Zhou (2015) <doi: 10.1201/b18598>.
Implementations of the kernel measure of multi-sample dissimilarity (KMD) between
    several samples using K-nearest neighbor graphs and minimum spanning trees. The KMD 
    measures the dissimilarity between multiple samples, based on the observations from them.
    It converges to the population quantity (depending on the kernel) which is between 0 and 1.
    A small value indicates the multiple samples are from the same distribution, and a large value
    indicates the corresponding distributions are different. The population quantity is 0 if and only
    if all distributions are the same, and 1 if and only if all distributions are mutually singular.
    The package also implements the tests based on KMD for H0: the M distributions are equal
    against H1: not all the distributions are equal. Both permutation test and asymptotic test are
    available. These tests are consistent against all alternatives where at least two samples have
    different distributions. For more details on KMD and the associated tests, see Huang, Z. and
    B. Sen (2022) <arXiv:2210.00634>.
Implementation of Kmeans clustering algorithm and a supervised KNN (K Nearest Neighbors) learning method. It allows users to perform unsupervised clustering and supervised classification on their datasets. Additional features include data normalization, imputation of missing values, and the choice of distance metric. The package also provides functions to determine the optimal number of clusters for Kmeans and the best k-value for KNN: knn_Function(), find_Knn_best_k(), KMEANS_FUNCTION(), and find_Kmeans_best_k().
Algorithms of distance-based k-medoids clustering: simple and fast 
  k-medoids, ranked k-medoids, and increasing number of clusters in k-medoids. 
  Calculate distances for mixed variable data such as Gower, Podani, Wishart, 
  Huang, Harikumar-PV, and Ahmad-Dey. Cluster validation applies internal and 
  relative criteria. The internal criteria includes silhouette index and shadow 
  values. The relative criterium applies bootstrap procedure producing a heatmap 
  with a flexible reordering matrix algorithm such as complete, ward, or average 
  linkages. The cluster result can be plotted in a marked barplot or pca biplot.
Online, Semi-online, and Offline K-medians algorithms are
    given. For both methods, the algorithms can be initialized
    randomly or with the help of a robust hierarchical
    clustering. The number of clusters can be selected with the
    help of a penalized criterion. We provide functions to provide
    robust clustering. Function gen_K() enables to generate a sample
    of data following a contaminated Gaussian mixture.
    Functions Kmedians() and Kmeans() consists in a K-median and a
    K-means algorithms while Kplot() enables to produce graph for both
    methods. 
    Cardot, H., Cenac, P. and Zitt, P-A. (2013). "Efficient and fast estimation of the geometric median in Hilbert spaces with an averaged stochastic gradient algorithm". Bernoulli, 19, 18-43. <doi:10.3150/11-BEJ390>.
    Cardot, H. and Godichon-Baggioni, A. (2017). "Fast Estimation of the Median Covariation Matrix with Application to Online Robust Principal Components Analysis". Test, 26(3), 461-480 <doi:10.1007/s11749-016-0519-x>.
    Godichon-Baggioni, A. and Surendran, S. "A penalized criterion for selecting the number of clusters for K-medians"     <arXiv:2209.03597> 
    Vardi, Y. and Zhang, C.-H. (2000). "The multivariate L1-median and associated data depth". Proc. Natl. Acad. Sci. USA, 97(4):1423-1426. <doi:10.1073/pnas.97.4.1423>.
Contains tools for rapidly computing distance matrices 
    and clustering large sequence datasets using fast alignment-free 
    k-mer counting and recursive k-means partitioning. 
    See Vinga and Almeida (2003) <doi:10.1093/bioinformatics/btg005> 
    for a review of k-mer counting methods and applications for 
    biological sequence analysis.
A multi-purpose and flexible k-meric enrichment analysis software. 
    'kmeRtone' measures the enrichment of k-mers by comparing the population of 
    k-mers in the case loci with a carefully devised internal negative control 
    group, consisting of k-mers from regions close to, yet sufficiently distant 
    from, the case loci to mitigate any potential sequencing bias. This method 
    effectively captures both the local sequencing variations and broader 
    sequence influences, while also correcting for potential biases, thereby 
    ensuring more accurate analysis. The core functionality of 'kmeRtone' is 
    the SCORE() function, which calculates the susceptibility scores for k-mers in 
    case and control regions. Case regions are defined by the genomic coordinates 
    provided in a file by the user and the control regions can be constructed 
    relative to the case regions or provided directly. The k-meric susceptibility 
    scores are calculated by using a one-proportion z-statistic. 'kmeRtone' is 
    highly flexible by allowing users to also specify their target k-mer patterns
    and quantify the corresponding k-mer enrichment scores in the context of 
    these patterns, allowing for a more comprehensive approach to understanding 
    the functional implications of specific DNA sequences on a genomic scale
    (e.g., CT motifs upon UV radiation damage).
    Adib A. Abdullah, Patrick Pflughaupt, Claudia Feng, Aleksandr B. Sahakyan (2024) Bioinformatics (submitted).
Performs a Kaplan-Meier multiple imputation to recover the missing potential censoring information from competing risks events, so that standard right-censored methods could be applied to the imputed data sets to perform analyses of the cumulative incidence functions (Allignol and Beyersmann, 2010 <doi:10.1093/biostatistics/kxq018>).
An implementation of k-means specifically design
        to cluster longitudinal data. It provides facilities to deal with missing
        value, compute several quality criterion (Calinski and Harabatz,
        Ray and Turie, Davies and Bouldin, BIC, ...) and propose a graphical
        interface for choosing the 'best' number of clusters.
An implementation of k-means specifically design
        to cluster joint trajectories (longitudinal data on
        several variable-trajectories).
        Like 'kml', it provides facilities to deal with missing
        value, compute several quality criterion (Calinski and Harabatz,
        Ray and Turie, Davies and Bouldin, BIC,...) and propose a graphical
        interface for choosing the 'best' number of clusters. In addition, the 3D graph
        representing the mean joint-trajectories of each cluster can be exported through
        LaTeX in a 3D dynamic rotating PDF graph.
The developed function is designed to facilitate the seamless conversion of KML (Keyhole Markup Language)
             files to Shapefiles while preserving attribute values. It provides a straightforward interface for users
             to effortlessly import KML data, extract relevant attributes, and export them into the widely compatible
             Shapefile format. The package ensures accurate representation of spatial data while maintaining the integrity
             of associated attribute information. For details see, Flores, G. (2021). <DOI:10.1007/978-3-030-63665-4_15>.
             Whether for spatial analysis, visualization, or data interoperability, it simplifies the conversion process and 
             empowers users to seamlessly work with geospatial datasets.
An implementation of the 'k-means--' algorithm proposed
    by Chawla and Gionis, 2013 in their paper,
    "k-means-- : A unified approach to clustering and outlier detection.
    SIAM International Conference on Data Mining (SDM13)",
    <doi:10.1137/1.9781611972832.21>
    and using 'ordering' described by Howe, 2013 in the thesis,
    Clustering and anomaly detection in tropical cyclones".
    Useful for creating (potentially) tighter clusters than
    standard k-means and simultaneously finding outliers inexpensively
    in multidimensional space.
Datasets and functions for Klein and Moeschberger (1997),
        "Survival Analysis, Techniques for Censored and Truncated
        Data", Springer.
Produce Kaplan–Meier plots in the style recommended
    following the KMunicate study by Morris et al. (2019)
    <doi:10.1136/bmjopen-2019-030215>. The KMunicate style consists of
    Kaplan-Meier curves with confidence intervals to quantify uncertainty
    and an extended risk table (per treatment arm) depicting the number of
    study subjects at risk, events, and censored observations over time.
    The resulting plots are built using 'ggplot2' and can be further
    customised to a certain extent, including themes, fonts, and colour
    scales.
The sampl.mcmc function creates samples of the feasible region of a knapsack problem with both equalities and inequalities constraints.
Given a set of points around a knee curve,
    analyzes first and second derivatives to find knee points.
Provides the ability to create dynamic citations
    in which the bibliographic information is pulled from the web rather
    than having to be entered into a local database such as 'bibtex' ahead of
    time. The package is primarily aimed at authoring in the R 'markdown'
    format, and can provide outputs for web-based authoring such as linked
    text for inline citations.  Cite using a 'DOI', URL, or
    'bibtex' file key.  See the package URL for details.
Provides several helper functions for working with 'knitr' and 'LaTeX'.
  It includes 'xTab' for creating traditional 'LaTeX' tables, 'lTab' for generating
  'longtable' environments, and 'sTab' for generating a 'supertabular' environment.
  Additionally, this package contains a knitr_setup() function which fixes a
  well-known bug in 'knitr', which distorts the 'results="asis"' command when used
  in conjunction with user-defined commands; and a com command (<<com=TRUE>>=)
  which renders the output from 'knitr' as a 'LaTeX' command.
Provides a general-purpose tool for dynamic report generation in R
    using Literate Programming techniques.
A framework to create Bootstrap <https://getbootstrap.com/> HTML reports from 'knitr'
    'rmarkdown'.
Implements a data language engine for incorporating data directly in 
    'rmarkdown' documents so that they can be made completely standalone.
Provides a progress bar similar to 'dplyr' that can write progress out to a 
    variety of locations, including stdout(), stderr(), or from file(). Useful when using 'knitr' or 'rmarkdown',
    and you still want to see progress of calculations in the terminal.
Convert an R Markdown documents into an '.xlsx' spreadsheet reports
    with the knitxl() function, which works similarly to knit() from the 
    'knitr' package. The generated report can be opened in 'Excel' or similar
    software for further analysis and presentation.
Similarly to the 'FNN' package, this package allows calculation of the k nearest neighbors (kNN) of a data matrix.
    The implementation is based on cover trees introduced by
    Alina Beygelzimer, Sham Kakade, and John Langford (2006) <doi:10.1145/1143844.1143857>.
This is a 'C++' mutual information (MI) library based on the k-nearest 
    neighbor (KNN) algorithm. There are three functions provided for computing MI 
    for continuous values, mixed continuous and discrete values, and conditional MI 
    for continuous values. They are based on algorithms by A. Kraskov, et. al. (2004) <doi:10.1103/PhysRevE.69.066138>, 
    BC Ross (2014)<doi:10.1371/journal.pone.0087357>, 
    and A. Tsimpiris (2012) <doi:10.1016/j.eswa.2012.05.014>, respectively.
Two main functionalities are provided. One of them is predicting values with 
    k-nearest neighbors algorithm and the other is optimizing the parameters k and d of the algorithm.
    These are carried out in parallel using multiple threads.
An interactive document on  the topic of K-nearest neighbour (KNN) using 'rmarkdown' and 'shiny' packages. Runtime examples are provided in the package function as well as at  <https://kartikeyabolar.shinyapps.io/KNNShiny/>.
k Nearest Neighbors with variable selection, combine grid search and forward selection to achieve variable selection in order to improve k Nearest Neighbors predictive performance.
Functions to implement K Nearest Neighbor forecasting using a weighted similarity metric tailored to the problem of forecasting univariate time series where recent observations, seasonal patterns, and exogenous predictors are all relevant in predicting future observations of the series in question. For more information on the formulation of this similarity metric please see Trupiano (2021) <arXiv:2112.06266>.
Application of a Known Biomass Production Model (KBPM): (1) the fitting of KBPM to each stock; (2) the estimation of the effects of environmental variability; (3) the retrospective analysis to identify regime shifts; (4) the estimation of forecasts. For more details see Schaefer (1954) <https://www.iattc.org/GetAttachment/62d510ee-13d0-40f2-847b-0fde415476b8/Vol-1-No-2-1954-SCHAEFER,-MILNER-B-_Some-aspects-of-the-dynamics-of-populations-important-to-the-management-of-the-commercial-marine-fisheries.pdf>, Pella and Tomlinson (1969) <https://www.iattc.org/GetAttachment/9865079c-6ee7-40e2-9e30-c4523ff81ddf/Vol-13-No-3-1969-PELLA,-JEROME-J-,-and-PATRICK-K-TOMLINSON_A-generalized-stock-production-model.pdf> and MacCall (2002) <doi:10.1577/1548-8675(2002)022%3C0272:UOKBPM%3E2.0.CO;2>.
The knockoff filter is a general procedure for controlling the false discovery rate (FDR)
  when performing variable selection. 
  For more information, see the website below and the accompanying paper: Candes et al., 
  "Panning for gold: model-X knockoffs for high-dimensional controlled variable selection", 
  J. R. Statist. Soc. B (2018) 80, 3, pp. 551-577.
Identification of putative causal variants in genome-wide association studies using hybrid analysis of both the trio and population designs. The package implements the method in the paper: Yang, Y., Wang, Q., Wang, C., Buxbaum, J., & Ionita-Laza, I. (2024). KnockoffHybrid: A knockoff framework for hybrid analysis of trio and population designs in genome-wide association studies. The American Journal of Human Genetics, in press.
Functions for identification of putative causal loci in whole-genome sequencing data. The functions allow genome-wide association scan. It also includes an efficient knockoff generator for genetic data.
Identification of putative causal variants in genome-wide association studies with trio and duo families. The package calculates the W feature statistics from KnockoffTrio and p-values from the family-based association test (FBAT) using trio and/or duo data. Compared to previous versions, a significant improvement has been made in Version 1.1.0 to allow the package to be applied not only to trio families but also to duo families. The package implements the methods in the paper: "Yang, Y., Wang, C., Liu, L., Buxbaum, J., He, Z., & Ionita-Laza, I. (2022). KnockoffTrio: A knockoff framework for the identification of putative causal variants in genome-wide association studies with trio design. The American Journal of Human Genetics, 109(10), 1761-1776."
Makes visually pleasing diagrams of knot projections using optimized Bezier curves.
It uses species accumulation curves and diverse estimators to assess, at the same time, the levels of survey coverage in multiple geographic cells of a size defined by the user or polygons. It also enables the geographical depiction of observed species richness, survey effort and completeness values including a background with administrative areas.
Retrieve data from 'kintone' (<https://www.kintone.com/>) via its API.
    'kintone' is an enterprise application platform.
Wrapper for 'Kobotoolbox' APIs ver 2 mentioned at <https://support.kobotoolbox.org/api.html>, to download data from 'Kobotoolbox' to R. Small and simple package that adds immense convenience for the data professionals using 'Kobotoolbox'.
A self-guided, weakly supervised learning algorithm for feature extraction from noisy and 
  high-dimensional data. It facilitates the identification of patterns that reflect underlying group 
  structures across all samples in a dataset. The method incorporates a novel strategy to integrate 
  spatial information, improving the interpretability of results in spatially resolved data.
Read Swiss time series data from the 'KOF Data' API, <https://datenservice.kof.ethz.ch>. The API provides macro economic time series data mostly about Switzerland. The package itself is a set of wrappers around the 'KOF Datenservice' API. The 'kofdata' package is able to consume public information as well as data that requires an API token.
To test if a tensor time series following a Tucker-decomposition factor model has a Kronecker product structure. Supplementary functions for tensor reshape and its reversal are also included.
Provides a function that uses a genetic algorithm to search for a subset
 of size k from the integers 1:n, such that a user-supplied objective function 
 is minimized at that subset.  The selection step is done by tournament selection 
 based on ranks, and elitism may be used to retain a portion of the best solutions 
 from one generation to the next. Population objective function values may 
 optionally be evaluated in parallel.
Rank-based tests for enrichment of KOG (euKaryotic Orthologous Groups) classes with up- or down-regulated genes based on a continuous measure. The meta-analysis is based on correlation of KOG delta-ranks across datasets (delta-rank is the difference between mean rank of genes belonging to a KOG class and mean rank of all other genes). With binary measure (1 or 0 to indicate significant and non-significant genes), one-tailed Fisher's exact test for over-representation of each KOG class among significant genes will be performed.
Functions to train self-organising maps (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.
Provides utilities for 'Kokudo Suuchi', the GIS data service of the Japanese government.
    See <https://nlftp.mlit.go.jp/index.html> for more information.
Assists researchers in choosing Key Opinion Leaders (KOLs) in a network to help disseminate or encourage adoption of an innovation by other network members. Potential KOL teams are evaluated using the ABCDE framework (Neal et al., 2025 <doi:10.31219/osf.io/3vxy9_v1>). This framework which considers: (1) the team members' Availability, (2) the Breadth of the team's network coverage, (3) the Cost of recruiting a team of a given size, and (4) the Diversity of the team's members, (5) which are pooled into a single Evaluation score.
Functions for analysing eye tracking data, including event detection, visualizations and area of interest (AOI) based analyses. 
  The package includes implementations of the IV-T, I-DT, adaptive velocity threshold, and Identification by two means clustering (I2MC) algorithms.
  See separate documentation for each function. The principles underlying I-VT and I-DT algorithms are described in   Salvucci & Goldberg (2000,\doi{10.1145/355017.355028}). 
  Two-means clustering is described in Hessels et al. (2017, \doi{10.3758/s13428-016-0822-1}). 
  The adaptive velocity threshold algorithm is described in Nyström & Holmqvist (2010,\doi{10.3758/BRM.42.1.188}).
  See a demonstration in the URL.
Write beautiful yet customizable letters in R Markdown and
  directly obtain the finished PDF. Smooth generation of PDFs is realized by
  'rmarkdown', the 'pandoc-letter' template and the 'KOMA-Script' letter class.
  'KOMA-Script' provides enhanced replacements for the standard 'LaTeX' classes
  with emphasis on typography and versatility. 'KOMA-Script' is particularly
  useful for international writers as it handles various paper formats well, 
  provides layouts for many common window envelope types (e.g. German, US, 
  French, Japanese) and lets you define your own layouts. The package comes 
  with a default letter layout based on 'DIN 5008B'.
Statistical methods that quantify the conditions necessary to
    alter inferences, also known as sensitivity analysis, are becoming
    increasingly important to a variety of quantitative sciences. A series
    of recent works, including Frank (2000)
    <doi:10.1177/0049124100029002001> and Frank et al. (2013)
    <doi:10.3102/0162373713493129> extend previous sensitivity analyses by
    considering the characteristics of omitted variables or unobserved
    cases that would change an inference if such variables or cases were
    observed. These analyses generate statements such as "an omitted
    variable would have to be correlated at xx with the predictor of
    interest (e.g., the treatment) and outcome to invalidate an inference of a
    treatment effect". Or "one would have to replace pp percent of the
    observed data with nor which the treatment had no effect to invalidate the 
    inference".
    We implement these recent developments of sensitivity analysis and
    provide modules to calculate these two robustness indices and generate
    such statements in R. In particular, the functions konfound(),
    pkonfound() and mkonfound() allow users to calculate the robustness of
    inferences for a user's own model, a single published study and
    multiple studies respectively.
The K-sample omnibus non-proportional hazards (KONP) tests are powerful non-parametric tests for comparing K (>=2) hazard functions based on right-censored data (Gorfine, Schlesinger and Hsu, 2020, <doi:10.1177/0962280220907355>). These tests are consistent against any differences between the hazard functions of the groups. The KONP tests are often more powerful than other existing tests, especially under non-proportional hazard functions.
Matches a data set with semi-structured address data, 
 e.g., street and house number as a concatenated string,
 wrongly spelled street names or non-existing house numbers to a 
 reference index. The methods are specifically designed for German 
 municipalities ('KOR'-community) and German address schemes.
A set of tools to analyze texts. Includes, amongst others, functions for
          automatic language detection, hyphenation, several indices of lexical diversity
          (e.g., type token ratio, HD-D/vocd-D, MTLD) and readability (e.g., Flesch,
          SMOG, LIX, Dale-Chall). Basic import functions for language corpora are also
          provided, to enable frequency analyses (supports Celex and Leipzig Corpora
          Collection file formats) and measures like tf-idf. Note: For full functionality
          a local installation of TreeTagger is recommended. It is also recommended to
          not load this package directly, but by loading one of the available language
          support packages from the 'l10n' repository
          <https://undocumeantit.github.io/repos/l10n/>. 'koRpus' also includes a plugin
          for the R GUI and IDE RKWard, providing graphical dialogs for its basic
          features. The respective R package 'rkward' cannot be installed directly from a
          repository, as it is a part of RKWard. To make full use of this feature, please
          install RKWard from <https://rkward.kde.org> (plugins are detected
          automatically). Due to some restrictions on CRAN, the full package sources are
          only available from the project homepage. To ask for help, report bugs, request
          features, or discuss the development of the package, please subscribe to the
          koRpus-dev mailing list (<https://korpusml.reaktanz.de>).
Adds support for the English language to the 'koRpus' package. To ask for help, report bugs, suggest feature improvements, or discuss the global development of the
                    package, please consider subscribing to the koRpus-dev mailing list (<https://korpusml.reaktanz.de>).
Performs variable selection for many types of L1-regularised regressions using the revisited knockoffs procedure. This procedure uses a matrix of knockoffs of the covariates independent from the response variable Y. The idea is to determine if a covariate belongs to the model depending on whether it enters the model before or after its knockoff. The procedure suits for a wide range of regressions with various types of response variables. Regression models available are exported from the R packages 'glmnet' and 'ordinalNet'. Based on the paper linked to via the URL below: Gegout A., Gueudin A., Karmann C. (2019) <arXiv:1907.03153>.
API wrapper to download statistical information from the
             Korean Statistical Information Service (KOSIS)
             <https://kosis.kr/openapi/index/index.jsp>.
Cubic spline fitting along with knot selection, includes support for additional variables.
Implementations of two empirical versions the kernel partial correlation (KPC) coefficient
    and the associated variable selection algorithms. KPC is a measure of the strength of conditional
    association between Y and Z given X, with X, Y, Z being random variables taking values in
    general topological spaces. As the name suggests, KPC is defined in terms of kernels on
    reproducing kernel Hilbert spaces (RKHSs). The population KPC is a deterministic number
    between 0 and 1; it is 0 if and only if Y is conditionally independent of Z given X, and it is 1 if
    and only if Y is a measurable function of Z and X. One empirical KPC estimator is based on
    geometric graphs, such as K-nearest neighbor graphs and minimum spanning trees, and is
    consistent under very weak conditions. The other empirical estimator, defined using conditional
    mean embeddings (CMEs) as used in the RKHS literature, is also consistent under suitable
    conditions. Using KPC, a stepwise forward variable selection algorithm KFOCI (using the graph
    based estimator of KPC) is provided, as well as a similar stepwise forward selection algorithm
    based on the RKHS based estimator. For more details on KPC, its empirical estimators and its
    application on variable selection, see Huang, Z., N. Deb, and B. Sen (2022). “Kernel partial
    correlation coefficient – a measure of conditional dependence” (URL listed below). When X is
    empty, KPC measures the unconditional dependence between Y and Z, which has been described
    in Deb, N., P. Ghosal, and B. Sen (2020), “Measuring association on topological spaces using
    kernels and geometric graphs” <arXiv:2010.01768>, and it is implemented in the functions
    KMAc() and Klin() in this package. The latter can be computed in near linear time.
The kernelized version of principal component analysis (KPCA) has proven to be a valid nonlinear alternative for tackling the nonlinearity of biological sample spaces. However, it poses new challenges in terms of the interpretability of the original variables. 'kpcaIG' aims to provide a tool to select the most relevant variables based on the kernel PCA representation of the data as in Briscik et al. (2023) <doi:10.1186/s12859-023-05404-y>. It also includes functions for 2D and 3D visualization of the original variables (as arrows) into the kernel principal components axes, highlighting the contribution of the most important ones.
The number of clusters (k) is needed to start all the partitioning clustering algorithms. An optimal value of this input argument is widely determined by using some internal validity indices. Since most of the existing internal indices suggest a k value which is computed from the clustering results after several runs of a clustering algorithm they are computationally expensive. On the contrary,  the package 'kpeaks' enables to estimate k before running any clustering algorithm. It is based on a simple novel technique using the descriptive statistics of peak counts of the features in a data set.
Provides an easy way to create interactive KPI (key performance indicator) widgets for 'Quarto' dashboards using 'Crosstalk'. The package enables visualization of key metrics in a structured format, supporting interactive filtering and linking with other 'Crosstalk'-enabled components. Designed for use in 'Quarto' Dashboards.
Software for k-means clustering of partially 
    observed data from Chi, Chi, and Baraniuk (2016) <doi:10.1080/00031305.2015.1086685>.
A comprehensive R interface to access data from the Kraken cryptocurrency exchange REST API <https://docs.kraken.com/api/>.
  It allows users to retrieve various market data, such as asset information, trading pairs, and price data.
  The package is designed to facilitate efficient data access for analysis, strategy development, and monitoring of cryptocurrency market trends.
Implements a quantified approach to the Kraljic Matrix (Kraljic, 1983, <https://hbr.org/1983/09/purchasing-must-become-supply-management>)
    for strategically analyzing a firm’s purchasing portfolio. It combines multi-objective decision analysis to measure purchasing characteristics and
    uses this information to place products and services within the Kraljic Matrix.
Provides basic functions for Continuation-Passing Style development.
Estimates kriging models for geographical point-referenced data. Method is described in Gill (2020) <doi:10.1177/1532440020930197>.
An implementation of a simple and highly optimized ordinary kriging algorithm to plot geographical data.
Criteria and algorithms for sequentially estimating level sets of a multivariate numerical function, possibly observed with noise.
Provides tools for applying Krippendorff's Alpha methodology <DOI:10.1080/19312450709336664>. Both the customary methodology and Hughes' methodology <DOI:10.48550/arXiv.2210.13265> are supported, the former being preferred for larger datasets, the latter for smaller datasets. The framework supports common and user-defined distance functions, and can accommodate any number of units, any number of coders, and missingness. Interval estimation can be done in parallel for either methodology.
Provides useful functions which are needed for bioinformatic analysis such as calculating linear principal components from numeric data and Single-nucleotide polymorphism (SNP) dataset, calculating fixation index (Fst) using Hudson method, creating scatter plots in 3 views, handling with PLINK binary file format, detecting rough structures and outliers using unsupervised clustering, and calculating matrix multiplication in the faster way for big data.
Package implements Kernel-based Regularized Least Squares (KRLS), a machine learning method to fit multidimensional functions y=f(x) for regression and classification problems without relying on linearity or additivity assumptions. KRLS finds the best fitting function by minimizing the squared loss of a Tikhonov regularization problem, using Gaussian kernels as radial basis functions. For further details see Hainmueller and Hazlett (2014).
Implements several methods for testing the variance component parameter in regression models that contain kernel-based random effects, including a maximum of adjusted scores test. Several kernels are supported, including a profile hidden Markov model mutual information kernel for protein sequence. This package is described in Fong et al. (2015) <DOI:10.1093/biostatistics/kxu056>.
Solves kernel ridge regression, within the the mixed model framework, for the linear, polynomial, Gaussian, Laplacian and ANOVA kernels. The model components (i.e. fixed and random effects) and variance parameters are estimated using the expectation-maximization (EM) algorithm. All the estimated components and parameters, e.g. BLUP of dual variables and BLUP of random predictor effects for the linear kernel (also known as RR-BLUP), are available. The kernel ridge mixed model (KRMM) is described in Jacquin L, Cao T-V and Ahmadi N (2016) A Unified and Comprehensible View of Parametric and Kernel Methods for Genomic Prediction with Application to Rice. Front. Genet. 7:145. <doi:10.3389/fgene.2016.00145>.
The goal of 'kronos' is to provide an easy-to-use framework to analyse circadian or otherwise rhythmic data using the familiar R linear modelling syntax, while taking care of the trigonometry under the hood.
Kernel smoothers for univariate and multivariate data, with comprehensive visualisation and bandwidth selection capabilities, including for densities, density derivatives, cumulative distributions, clustering, classification, density ridges, significant modal regions, and two-sample hypothesis tests. Chacon & Duong (2018) <doi:10.1201/9780429485572>.
The Retained Component Criterion for Principal Component Analysis (RCC_PCA) is a tool to determine the optimal number of components to retain in PCA.
Compares k samples using the Anderson-Darling test, Kruskal-Wallis type tests 
	with different rank score criteria, Steel's multiple comparison test, and the 
        Jonckheere-Terpstra (JT) test. It computes asymptotic, simulated or (limited) exact 
        P-values, all valid under randomization, with or without ties, or conditionally 
        under random sampling from populations, given the observed tie pattern.  Except for 
        Steel's test and the JT test it also combines these tests across several blocks of 
	samples.  Also analyzed are 2 x t contingency tables and their blocked combinations 
	using the Kruskal-Wallis criterion.  Steel's test is inverted to provide simultaneous 
	confidence bounds for shift parameters.  A plotting function compares tail probabilities
	obtained under asymptotic approximation with those obtained via simulation or exact 
	calculations.
Implements the Lilliefors-corrected Kolmogorov-Smirnov test for use
    in goodness-of-fit tests, suitable when population parameters are unknown and
    must be estimated by sample statistics. P-values are estimated by simulation.
    Can be used with a variety of continuous distributions, including normal,
    lognormal, univariate mixtures of normals, uniform, loguniform, exponential,
    gamma, and Weibull distributions. Functions to generate random numbers and
    calculate density, distribution, and quantile functions are provided for use
    with the log uniform and mixture distributions.
An adaptation of Kernelized Stein Discrepancy, this package provides a goodness-of-fit test of whether a given i.i.d. sample is drawn from a given distribution. It works for any distribution once its score function (the derivative of log-density) can be provided. This method is based on "A Kernelized Stein Discrepancy for Goodness-of-fit Tests and Model Evaluation" by Liu, Lee, and Jordan, available at <arXiv:1602.03253>.
Infers relative kinase activity from phosphoproteomics data
    using the method described by Casado et al. (2013) <doi:10.1126/scisignal.2003573>.
Selection of k in k-means clustering based on Pham et al. paper
    ``Selection of k in k-means clustering''.
Contains functions to compute p-values for the one-sample and two-sample Kolmogorov-Smirnov (KS) tests and the two-sample Kuiper test for any fixed critical level and arbitrary (possibly very large) sample sizes. For the one-sample KS test, this package implements a novel, accurate and efficient method named Exact-KS-FFT, which allows the pre-specified cumulative distribution function under the null hypothesis to be continuous, purely discrete or mixed. In the two-sample case, it is assumed that both samples come from an unspecified (unknown) continuous, purely discrete or mixed distribution, i.e. ties (repeated observations) are allowed, and exact p-values of the KS and the Kuiper tests are computed. Note, the two-sample Kuiper test is often used when data samples are on the line or on the circle (circular data). To cite this package in publication: (for the use of the one-sample KS test) Dimitrina S. Dimitrova, Vladimir K. Kaishev, and Senren Tan. Computing the Kolmogorov-Smirnov Distribution When the Underlying CDF is Purely Discrete, Mixed, or Continuous. Journal of Statistical Software. 2020; 95(10): 1--42.  <doi:10.18637/jss.v095.i10>. (for the use of the two-sample KS and Kuiper tests) Dimitrina S. Dimitrova, Yun Jia and Vladimir K. Kaishev (2024). The R functions KS2sample and Kuiper2sample: Efficient Exact Calculation of P-values of the Two-sample Kolmogorov-Smirnov and Kuiper Tests. submitted.
Clustering typically assigns data points into discrete groups, but the clusters can sometimes be indistinct. Cluster sharpening adjusts an existing clustering to create contrast between groups. This package provides a general interface for cluster sharpening along with several implementations based on different excision criteria.
Prediction with k* nearest neighbor algorithm 
    based on a publication by Anava and Levy (2016) <arXiv:1701.07266>.
To fit the kernel semi-parametric model and its extensions. It allows multiple kernels and unlimited interactions in the same model. Coefficients are estimated by maximizing a penalized log-likelihood; penalization terms and hyperparameters are estimated by minimizing leave-one-out error. It includes predictions with confidence/prediction intervals, statistical tests for the significance of each kernel, a procedure for variable selection and graphical tools for diagnostics and interpretation of covariate effects. Currently it is implemented for continuous dependent variables. The package is based on the paper of Liu et al. (2007), <doi:10.1111/j.1541-0420.2007.00799.x>.
Using this package you can combine known kinase substrate relationships with experimental data and determine active kinases and their substrates.
Implements the Known Sub-Sequence Algorithm <doi:10.1016/j.aaf.2021.12.013>, which helps to automatically identify and validate the best method for missing data imputation in a time series. Supports the comparison of multiple state-of-the-art algorithms.
Knowledge space theory by Doignon and Falmagne (1999) 
   <doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
   framework, which proposes mathematical formalisms to operationalize 
   knowledge structures in a particular domain. The 'kst' package provides 
   basic functionalities to generate, handle, and manipulate knowledge 
   structures and knowledge spaces.
Tools for estimate (joint) cumulants and (joint) products of cumulants of a random sample using (multivariate) k-statistics and (multivariate) polykays, unbiased estimators with minimum variance. Tools for generating univariate and multivariate Faa di Bruno's formula and related polynomials, such as Bell polynomials, generalized complete Bell polynomials, partition polynomials and generalized partition polynomials. For more details see Di Nardo E., Guarino G., Senato D. (2009) <arXiv:0807.5008>, <arXiv:1012.6008>.
Knowledge space theory by Doignon and Falmagne (1999) 
   <doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
   framework which proposes mathematical formalisms to operationalize 
   knowledge structures in a particular domain.  The 'kstIO' package 
   provides basic functionalities to read and write KST data from/to 
   files to be used together with the 'kst', 'kstMatrix', 'CDSS', 'pks', or 
   'DAKS' packages.
Knowledge space theory by Doignon and Falmagne (1999)
   <doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
   framework, which proposes mathematical formalisms to operationalize
   knowledge structures in a particular domain. The 'kstMatrix' package 
   provides basic functionalities to generate, handle, and manipulate 
   knowledge structures and knowledge spaces. Opposed to the 'kst'
   package, 'kstMatrix' uses matrix representations for knowledge
   structures. Furthermore, 'kstMatrix' contains several knowledge spaces
   developed by the research group around Cornelia Dowling through
   querying experts.
A clustering algorithm similar to K-Means is implemented, it has two main advantages, 
    namely (a) The estimator is resistant to outliers, that means that results of estimator are still correct when
    there are atypical values in the sample and (b) The estimator is efficient, roughly speaking, 
    if there are no outliers in the sample, results will be similar to those obtained by a classic algorithm (K-Means).
    Clustering procedure is carried out by minimizing the overall robust scale so-called tau scale.
    (see Gonzalez, Yohai and Zamar (2019) <arxiv:1906.08198>).
Provides a function called COTUCKER3() (Co-Inertia Analysis
    + Tucker3 method) which performs a Co-Tucker3 analysis of two sequences of
    matrices, as well as other functions called PCA() (Principal Component Analysis)
    and BGA() (Between-Groups Analysis), which perform analysis of one matrix,
    COIA() (Co-Inertia Analysis), which performs analysis of two matrices, PTA()
    (Partial Triadic Analysis), STATIS(), STATISDUAL() and TUCKER3(), which perform analysis of a sequence
    of matrices, and BGCOIA() (Between-Groups Co-Inertia Analysis), STATICO()
    (STATIS method + Co-Inertia Analysis), COSTATIS() (Co-Inertia Analysis + STATIS
    method), which also perform analysis of two sequences of matrices.
This is designed for use with an arbitrary set of equations with
 an arbitrary set of unknowns.
 The user selects "fixed" values for enough unknowns to leave as many variables as
 there are equations, which in most cases means the system is properly
 defined and a unique solution exists. The function, the fixed values
 and initial values for the remaining unknowns are fed to a nonlinear backsolver.  
 The original version of "TK!Solver" , now a product of Universal Technical Systems (<https://www.uts.com>) was the inspiration for this function.
Kernel-based 'Tweedie' compound Poisson gamma model using high-dimensional predictors for the analyses of zero-inflated response variables. The package features built-in estimation, prediction and cross-validation tools and supports choice of different kernel functions. For more details, please see Yi Lian, Archer Yi Yang, Boxiang Wang, Peng Shi & Robert William Platt (2023) <doi:10.1080/00401706.2022.2156615>.
This function performs the two-sample Kuiper test to assess the anomaly of continuous, one-dimensional probability distributions. References used for this method are (1). Kuiper, N. H. (1960). <DOI:10.1016/S1385-7258(60)50006-0> and (2). Paltani, S. (2004). <DOI:10.1051/0004-6361:20034220>.
Computes measures of multivariate kurtosis, matrices of fourth-order moments and cumulants, kurtosis-based projection pursuit.
             Franceschini, C. and Loperfido, N. (2018, ISBN:978-3-319-73905-2). "An Algorithm for Finding Projections with Extreme Kurtosis".
             Loperfido, N. (2017,ISSN:0024-3795). "A New Kurtosis Matrix, with Statistical Applications".
Tools for data importation, recoding, and inspection.
    There are functions to create new project
    folders, R code templates, create uniquely named output
    directories, and to quickly obtain a visual summary for each
    variable in a data frame.  The main feature here is the systematic
    implementation of the "variable key" framework for data
    importation and recoding.  We are eager to have community feedback
    about the variable key and the vignette about it. In version 1.7,
    the function 'semTable' is removed. It was deprecated since 1.67.
    That is provided in a separate package, 'semTable'.
The format KVH is a lightweight format that can be read/written both by humans and machines.
   It can be useful in situations where XML or alike formats seem to be an overkill.
   We provide an ability to parse KVH files in R pretty fast due to 'Rcpp' use.
Access business registration data from the Dutch Chamber of
    Commerce (Kamer van Koophandel, KvK) through their official API
    <https://developers.kvk.nl/>. Search for companies by name, location,
    or registration number. Retrieve detailed business profiles,
    establishment information, and company name histories. Built on
    'httr2' for robust API interaction with automatic pagination, error
    handling, and usage tracking.
Helper functions for creating formatted summary of regression models, writing publication-ready tables to latex files, and running Monte Carlo experiments.
Time Series Analysis including break detection, spectral analysis, KZ Fourier Transforms.
A spatial smoothing algorithm based on convolutions of finite rectangular kernels that provides sharp resolution in the presence of high levels of noise.
An efficient procedure for feature selection for generalized linear models with L0 penalty, including linear, logistic, Poisson, gamma, inverse Gaussian regression. Adaptive ridge algorithms are used to fit the models.
Highly optimized toolkit for approximately solving L0-regularized learning problems (a.k.a. best subset selection).
    The algorithms are based on coordinate descent and local combinatorial search.
    For more details, check the paper by Hazimeh and Mazumder (2020) <doi:10.1287/opre.2019.1919>.
Trend filtering is a widely used nonparametric method for knot detection. This package provides an efficient solution for L0 trend filtering, avoiding the traditional methods of using Lagrange duality or Alternating Direction Method of Multipliers  algorithms. It employ a splicing approach that minimizes L0-regularized sparse approximation by transforming the L0 trend filtering problem. The package excels in both efficiency and accuracy of trend estimation and changepoint detection in segmented functions. References: Wen et al. (2020) <doi:10.18637/jss.v094.i04>; Zhu et al. (2020)<doi:10.1073/pnas.2014241117>; Wen et al. (2023) <doi:10.1287/ijoc.2021.0313>.
Provides function for the l1-ball prior on high-dimensional regression. The main function, l1ball(), yields posterior samples for linear regression, as introduced by Xu and Duan (2020) <arXiv:2006.01340>.
Analyze graph/network data using L1 centrality and prestige. Functions for deriving global, local, and group L1 centrality/prestige are provided. Routines for visual inspection of a graph/network are also provided. Details are in Kang and Oh (2024a) <doi:10.48550/arXiv.2404.13233> and Kang and Oh (2024b) <doi:10.48550/arXiv.2408.12078>.
LINCS L1000 is a high-throughput technology that allows the gene expression measurement in a large number of assays. However, to fit the measurements of ~1000 genes in the ~500 color channels of LINCS L1000, every two landmark genes are designed to share a single channel. Thus, a deconvolution step is required to infer the expression values of each gene. Any errors in this step can be propagated adversely to the downstream analyses. We present a LINCS L1000 data peak calling R package l1kdeconv based on a new outlier detection method and an aggregate Gaussian mixture model. Upon the remove of outliers and the borrowing information among similar samples, l1kdeconv shows more stable and better performance than methods commonly used in LINCS L1000 data deconvolution.
L1 estimation for linear regression using Barrodale and Roberts' method
    <doi:10.1145/355616.361024> and the EM algorithm <doi:10.1023/A:1020759012226>.
    Estimation of mean and covariance matrix using the multivariate Laplace distribution,
    density, distribution function, quantile function and random number generation
    for univariate and multivariate Laplace distribution <doi:10.1080/03610929808832115>.
    Implementation of Naik and Plungpongpun <doi:10.1007/0-8176-4487-3_7> for the 
    Generalized spatial median estimator is included.
Simplify the loading matrix in factor models using the l1 criterion as proposed in Freyaldenhoven (2025) <doi:10.21799/frbp.wp.2020.25>. Given a data matrix, find the rotation of the loading matrix with the smallest l1-norm and/or test for the presence of local factors with main function local_factors().
Provides an l1-version of the spectral clustering algorithm devoted to robustly clustering highly perturbed graphs using l1-penalty. This algorithm is described with more details in the preprint C. Champion, M. Champion, M. Blazère, R. Burcelin and J.M. Loubes, "l1-spectral clustering algorithm: a spectral clustering method using l1-regularization" (2022).
Efficient implementation of Friedman's boosting algorithm with
    l2-loss function and coordinate direction (design matrix columns) basis
    functions.
Provides functions for the implementation of a density goodness-of-fit test, based on piecewise approximation of the L2 distance.
An implementation of a computational framework for performing robust structured regression with the L2 criterion 
             from Chi and Chi (2021+). Improvements using the majorization-minimization (MM) principle from Liu, Chi, and 
             Lange (2022+) added in Version 2.0.
Provides a method for detecting multiple change points in high-dimensional time
    series, targeting dense or spatially clustered signals. See Li et al. (2023) 
    "L2 Inference for Change Points in High-Dimensional Time Series via a Two-Way MOSUM". 
    arXiv preprint <arXiv:2208.13074>.
Contains Lioness Algorithm (LA) for finding optimal designs over continuous design space, optimal Latin hypercube designs, and optimal order-of-addition designs. LA is a brand new nature-inspired meta-heuristic optimization algorithm. Detailed methodologies of LA and its implementation on numerical simulations can be found at Hongzhi Wang, Qian Xiao and Abhyuday Mandal (2021) <doi:10.48550/arXiv.2010.09154>.
Navigating the shift of clinical laboratory data from primary everyday clinical use to secondary research purposes presents a significant challenge. Given the substantial time and expertise required for lab data pre-processing and cleaning and the lack of all-in-one tools tailored for this need, we developed our algorithm 'lab2clean' as an open-source R-package. 'lab2clean' package is set to automate and standardize the intricate process of cleaning clinical laboratory results. With a keen focus on improving the data quality of laboratory result values, our goal is to equip researchers with a straightforward, plug-and-play tool, making it smoother for them to unlock the true potential of clinical laboratory data in clinical research and clinical machine learning (ML) model development. Version 1.0 of the algorithm is described in detail in 'Zayed et al. (2024)' <doi:10.1186/s12911-024-02652-7>.
Miscellaneous scripts, e.g. functionality to make and plot factor diagrams for the statistical design.
A variety of ordination and community analyses
   useful in analysis of data sets in community ecology.  
   Includes many of the common ordination methods, with 
   graphical routines to facilitate their interpretation, 
   as well as several novel analyses.
The Bayesian estimation of mixture models (and more general hidden Markov models) suffers from the label switching phenomenon, making the MCMC output non-identifiable. This package can be used in order to deal with this problem using various relabelling algorithms.
Create custom labels, badges, certificates
  and other documents. Automate the production of potentially large 
  numbers of herbarium and collection labels, accreditation badges, 
  attendance and participation certificates, etc, and deliver them automatically.
  Documents are generated in PDF format, which requires a working 
  installation of 'LaTeX', such as 'TinyTeX'.
Functions which provide a range of axis labeling algorithms.
Work with labelled data imported from 'SPSS'
    or 'Stata' with 'haven' or 'foreign'. This package
    provides useful functions to deal with "haven_labelled" and
    "haven_labelled_spss" classes introduced by 'haven' package.
Assign meaningful labels to data frame columns.
    'labelmachine' manages your label assignment rules in 'yaml' files
    and makes it easy to use the same labels in multiple projects.
Create and use data frame labels for data frame objects (frame labels), their columns (name labels), and individual values of a column (value labels). Value labels include one-to-one and many-to-one labels for nominal and ordinal variables, as well as numerical range-based value labels for continuous variables. Convert value-labeled variables so each value is replaced by its corresponding value label. Add values-converted-to-labels columns to a value-labeled data frame while preserving parent columns. Filter and subset a value-labeled data frame using labels, while returning results in terms of values. Overlay labels in place of values in common R commands to increase interpretability. Generate tables of value frequencies, with categories expressed as raw values or as labels. Access data frames that show value-to-label mappings for easy reference.
Labels are a common construct in statistical software providing a 
  human readable description of a variable. While variable names are succinct,
  quick to type, and follow a language's naming conventions, labels may 
  be more illustrative and may use plain text and spaces. R does not provide
  native support for labels. Some packages, however, have made this feature
  available.  Most notably, the 'Hmisc' package provides labelling methods
  for a number of different object. Due to design decisions, these methods
  are not all exported, and so are unavailable for use in package development.
  The 'labelVector' package supports labels for atomic vectors in a light-weight
  design that is suitable for use in other packages.
Imports a data frame containing a single time resolved laser ablation mass spectrometry analysis of a foraminifera (or other carbonate shell), then detects when the laser has burnt through the foraminifera test as a function of change in signal over time.
Provides functions for normalizing standard laboratory measurements (e.g. hemoglobin, cholesterol levels) according to age and sex, based on the algorithms described in "Personalized lab test models to quantify disease potentials in healthy individuals" (Netta Mendelson Cohen, Omer Schwartzman, Ram Jaschek, Aviezer Lifshitz, Michael Hoichman, Ran Balicer, Liran I. Shlush, Gabi Barbash & Amos Tanay, <doi:10.1038/s41591-021-01468-6>). Allows users to easily obtain normalized values for standard lab results, and to visualize their distributions. See more at <https://tanaylab.weizmann.ac.il/labs/>.
Produces Labour Market Areas from commuting flows available at elementary territorial units. It provides tools for automatic tuning based on spatial contiguity. It also allows for statistical analyses and visualisation of the new functional geography.
Dati, scripts e funzioni per il libro "Ricerca sociale con R. Concetti e funzioni base per la ricerca sociale" (Datasets, scripts and functions to support the book "Ricerca sociale con R. Concetti e funzioni base per la ricerca sociale").
Simplex optimization algorithms as firstly proposed by Spendley
    et al. (1962) <doi:10.1080/00401706.1962.10490033> and later modified by 
    Nelder and Mead (1965) <doi:10.1093/comjnl/7.4.308> for laboratory and 
    manufacturing processes. The package also provides tools for graphical 
    representation of the simplexes and some example response surfaces that 
    are useful in illustrating the optimization process.
Insieme di funzioni di supporto al volume "Laboratorio di
        Statistica con R", Iacus-Masarotto, MacGraw-Hill Italia, 2006.
        This package contains sets of functions defined in "Laboratorio
        di Statistica con R", Iacus-Masarotto, MacGraw-Hill Italia,
        2006. Function names and docs are in italian as well.
Contains data sets to accompany the book: Lazic SE
    (2016). "Experimental Design for Laboratory Biologists: Maximising Information
    and Improving Reproducibility". Cambridge University Press.
Perform pairwise likelihood inference in latent autoregressive count models. See Pedeli and Varin (2020) for details.
Connect to the 'Less Annoying CRM' API with ease to get your crm data in a clean and tidy format. 'Less Annoying CRM' is a simple CRM built for small businesses, more information is available on their website <https://www.lessannoyingcrm.com/>.
Set of tools for analyzing lactate thresholds from a step incremental test to exhaustion. Easily analyze
    the methods Log-log, Onset of Blood Lactate Accumulation (OBLA), Baseline plus (Bsln+), Dmax, Lactate Turning Point (LTP),
    and Lactate / Intensity ratio (LTratio) in cycling, running, or swimming.
    Beaver WL, Wasserman K, Whipp BJ (1985) <doi:10.1152/jappl.1985.59.6.1936>.
    Heck H, Mader A, Hess G, Mücke S, Müller R, Hollmann W (1985) <doi:10.1055/s-2008-1025824>.
    Kindermann W, Simon G, Keul J (1979) <doi:10.1007/BF00421101>.
    Skinner JS, Mclellan TH (1980) <doi:10.1080/02701367.1980.10609285>.
    Berg A, Jakob E, Lehmann M, Dickhuth HH, Huber G, Keul J (1990) PMID 2408033.
    Zoladz JA, Rademaker AC, Sargeant AJ (1995) <doi:10.1113/jphysiol.1995.sp020959>.
    Cheng B, Kuipers H, Snyder A, Keizer H, Jeukendrup A, Hesselink M (1992) <doi:10.1055/s-2007-1021309>.
    Bishop D, Jenkins DG, Mackinnon LT (1998) <doi:10.1097/00005768-199808000-00014>.
    Hughson RL, Weisiger KH, Swanson GD (1987) <doi:10.1152/jappl.1987.62.5.1975>.
    Jamnick NA, Botella J, Pyne DB, Bishop DJ (2018) <doi:10.1371/journal.pone.0199794>.
    Hofmann P, Tschakert G (2017) <doi:10.3389/fphys.2017.00337>.
    Hofmann P, Pokan R, von Duvillard SP, Seibert FJ, Zweiker R, Schmid P (1997) <doi:10.1097/00005768-199706000-00005>.
    Pokan R, Hofmann P, Von Duvillard SP, et al. (1997) <doi:10.1097/00005768-199708000-00009>.
    Dickhuth H-H, Yin L, Niess A, et al. (1999) <doi:10.1055/s-2007-971105>.
Functions for estimating the gliding box lacunarity (GBL),
    covariance, and pair-correlation of a random closed set (RACS) in 2D
    from a binary coverage map (e.g. presence-absence land cover maps).
    Contains a number of newly-developed covariance-based estimators of
    GBL (Hingee et al., 2019) <doi:10.1007/s13253-019-00351-9> and
    balanced estimators, proposed by Picka (2000)
    <http://www.jstor.org/stable/1428408>, for covariance, centred
    covariance, and pair-correlation.  Also contains methods for
    estimating contagion-like properties of RACS and simulating 2D Boolean
    models.  Binary coverage maps are usually represented as raster images
    with pixel values of TRUE, FALSE or NA, with NA representing
    unobserved pixels.  A demo for extracting such a binary map from a
    geospatial data format is provided.  Binary maps may also be
    represented using polygonal sets as the foreground, however for most
    computations such maps are converted into raster images.  The package
    is based on research conducted during the author's PhD studies.
Calculates 3D lacunarity from voxel data. It is designed for use
    with point clouds generated from Light Detection And Ranging (LiDAR) scans
    in order to measure the spatial heterogeneity of 3-dimensional structures
    such as forest stands. It provides fast 'C++' functions to efficiently bin
    point cloud data into voxels and calculate lacunarity using different
    variants of the gliding-box algorithm originated by Allain & Cloitre (1991)
    <doi:10.1103/PhysRevA.44.3552>.
Calculate mean statistics and leaf angle distribution type from measured leaf inclination angles. LAD distribution is fitted using a two-parameters (mu, nu) Beta distribution and compared with six theoretical LAD distributions. Additional information is provided in Chianucci and Cesaretti (2022) <doi:10.1101/2022.10.28.513998>.
Create tables from within R directly on Google Slides
    presentations.  Currently supports matrix, data.frame and 'flextable'
    objects.
Set of tools for analyzing vertical fuel continuity at the tree level using Airborne Laser Scanning data. The workflow consisted of: 1) calculating the vertical height profiles of each segmented tree; 2) identifying gaps and fuel layers; 3) estimating the distance between fuel layers; and 4) retrieving the fuel layers base height and depth. Additionally, other functions recalculate previous metrics after considering distances greater than certain threshold. Moreover, the package calculates: i) the percentage of Leaf Area Density comprised in each fuel layer, ii) remove fuel layers with Leaf Area Density (LAD) percentage less than 10, and iii) recalculate the distances among the reminder ones. On the other hand, it identifies the crown base height (CBH) based on different criteria: the fuel layer with the highest LAD percentage and the fuel layers located at the largest- and at the last-distance. When there is only one fuel layer, it also identifies the CBH performing a segmented linear regression (breaking points) on the cumulative sum of LAD as a function of height. Finally, a collection of plotting functions is developed to represent: i) the initial gaps and fuel layers; ii) the fuels base height, depths and gaps with distances greater than certain threshold and, iii) the CBH based on different criteria. The methods implemented in this package are original and have not been published elsewhere.
Estimation of indicators on social exclusion and poverty, as well
    as Pareto tail modeling for empirical income distributions.
Methods for fast access to large ASCII files.  Currently the
    following file formats are supported: comma separated format (CSV) and fixed
    width format. It is assumed that the files are too large to fit into memory,
    although the package can also be used to efficiently access files that do
    fit into memory. Methods are provided to access and process files blockwise.
    Furthermore, an opened file can be accessed as one would an ordinary
    data.frame. The LaF vignette gives an overview of the functionality
    provided.
Provides classes and methods for objects, whose indexing
      naturally starts from zero. Subsetting, indexing and mathematical
      operations are defined naturally between lagged objects and lagged
      and base R objects. Recycling is not used, except for singletons.
      The single bracket operator doesn't drop dimensions by default.
Client for programmatic access to the Lake
    Multi-scaled Geospatial and Temporal database <https://lagoslakes.org>, with functions
    for accessing lake water quality and ecological context data for the US.
Performs approximate GP regression for large computer experiments and spatial datasets.  The approximation is based on finding small local designs for prediction (independently) at particular inputs. OpenMP and SNOW parallelization are supported for prediction over a vast out-of-sample testing set; GPU acceleration is also supported for an important subroutine.  OpenMP and GPU features may require special compilation.  An interface to lower-level (full) GP inference and prediction is provided. Wrapper routines for blackbox optimization under mixed equality and inequality constraints via an augmented Lagrangian scheme, and for large scale computer model calibration, are also provided.  For details and tutorial, see Gramacy (2016 <doi:10.18637/jss.v072.i01>.
Model-based linear model trees adjusting for spatial correlation using a
             simultaneous autoregressive spatial lag, Wagner and Zeileis (2019)
	     <doi:10.1111/geer.12146>.
Lag-sequential analysis is a method of assessing of patterns (what tends to 
        follow what?) in sequences of codes. The codes are typically for discrete 
        behaviors or states. The functions in this package read a stream of codes,
        or a frequency transition matrix, and produce a variety of lag sequential  
        statistics, including transitional frequencies, expected transitional frequencies, 
        transitional probabilities, z values, adjusted residuals, Yule's Q values, 
        likelihood ratio tests of stationarity across time and homogeneity across groups 
        or segments, transformed kappas for unidirectional dependence, bidirectional 
        dependence, parallel and nonparallel dominance, and significance levels based on 
        both parametric and randomization tests. The methods are described in
  Bakeman & Quera (2011) <doi:10.1017/CBO9781139017343>,
  O'Connor (1999) <doi:10.3758/BF03200753>,
  Wampold & Margolin (1982) <doi:10.1037/0033-2909.92.3.755>, and
  Wampold (1995, ISBN:0-89391-919-5).
Provides the tables from the 'Sean Lahman Baseball Database' as
    a set of R data.frames. It uses the data on pitching, hitting and fielding
    performance and other tables from 1871 through 2023, as recorded in the 2024
    version of the database. Documentation examples show how many baseball
    questions can be investigated.
Convert Leaf Area Index (LAI) from the Normalized Difference Vegetation Index (NDVI) using available equations from literature. 
    Detailed description of conversion equations in Bajocco et al. 2022 <doi:10.3390/rs14153554>.
A collection of tools for the calculation of freewater metabolism
    from in situ time series of dissolved oxygen, water temperature, and,
    optionally, additional environmental variables. LakeMetabolizer implements
    5 different metabolism models with diverse statistical underpinnings:
    bookkeeping, ordinary least squares, maximum likelihood, Kalman filter,
    and Bayesian. Each of these 5 metabolism models can be combined with
    1 of 7 models for computing the coefficient of gas exchange across the
    air–water interface (k). LakeMetabolizer also features a variety of
    supporting functions that compute conversions and implement calculations
    commonly applied to raw data prior to estimating metabolism (e.g., oxygen
    saturation and optical conversion models).
Lake morphometry metrics are used by limnologists to understand,
    among other things, the ecological processes in a lake. Traditionally, these
    metrics are calculated by hand, with planimeters, and increasingly with
    commercial GIS products. All of these methods work; however, they are either
    outdated, difficult to reproduce, or require expensive licenses to use. The
    'lakemorpho' package provides the tools to calculate a typical suite
    of these metrics from an input elevation model and lake polygon. The metrics
    currently supported are: fetch, major axis, minor axis, major/minor axis 
    ratio, maximum length, maximum width, mean width, maximum depth, mean depth, 
    shoreline development, shoreline length, surface area, and volume.
Lake temperature records, metadata, and climate drivers for 291 global lakes during the time period 1985-2009. Temperature observations were collected using satellite and in situ methods. Climatic drivers and geomorphometric characteristics were also compiled and are included for each lake. Data are part of the associated publication from the Global Lake Temperature Collaboration project (http://www.laketemperature.org). See citation('laketemps') for dataset attribution.
Determining consensus seriations for binary incidence matrices, using a two-step process of Procrustes-fit correspondence analysis for heuristic selection of partial seriations and iterative regression to establish a single consensus. Contains the Lakhesis Calculator, a graphical platform for identifying seriated sequences. Collins-Elliott (2024) <https://volweb.utk.edu/~scolli46/sceLakhesis.pdf>.
Includes some procedures for latent variable modeling with a 
    particular focus on multilevel data.
    The 'LAM' package contains mean and covariance structure modelling
    for multivariate normally distributed data (mlnormal(); Longford, 1987;
    <doi:10.1093/biomet/74.4.817>), a general Metropolis-Hastings algorithm 
    (amh(); Roberts & Rosenthal, 2001, <doi:10.1214/ss/1015346320>) and 
    penalized maximum likelihood estimation (pmle(); Cole, Chu & Greenland, 
    2014; <doi:10.1093/aje/kwt245>).
A variety of latent Markov models, including hidden Markov models, hidden semi-Markov models, 
  state-space models and continuous-time variants can be formulated and estimated within the same framework via directly maximising the likelihood function using the so-called forward algorithm. 
  Applied researchers often need custom models that standard software does not easily support. 
  Writing tailored 'R' code offers flexibility but suffers from slow estimation speeds. 
  We address these issues by providing easy-to-use functions (written in 'C++' for speed) for common tasks like the forward algorithm. 
  These functions can be combined into custom models in a Lego-type approach, offering up to 10-20 times faster estimation via standard numerical optimisers. 
  To aid in building fully custom likelihood functions, several vignettes are included that show how to simulate data from and estimate all the above model classes.
A language extension to efficiently write functional programs in R. Syntax extensions include multi-part function definitions, pattern matching, guard statements, built-in (optional) type safety.
Time series analysis based on lambda transformer and variational seq2seq, built on 'Torch'.
Runtime for serving containers that can execute R code on the 
    'AWS Lambda' serverless compute service <https://aws.amazon.com/lambda/>.
    Provides the necessary functionality for handling the various endpoints
    required for accepting new input and sending responses.
Lambert W x F distributions are a generalized framework to analyze
    skewed, heavy-tailed data. It is based on an input/output system, where the
    output random variable (RV) Y is a non-linearly transformed version of an input
    RV X ~ F with similar properties as X, but slightly skewed (heavy-tailed).
    The transformed RV Y has a Lambert W x F distribution. This package contains
    functions to model and analyze skewed, heavy-tailed data the Lambert Way:
    simulate random samples, estimate parameters, compute quantiles, and plot/
    print results nicely. The most useful function is 'Gaussianize',
    which works similarly to 'scale', but actually makes the data Gaussian.
    A do-it-yourself toolkit allows users to define their own Lambert W x
    'MyFavoriteDistribution' and use it in their analysis right away.
Interact with 'LaminDB'. 'LaminDB' is an open-source data
    framework for biology. This package allows you to query and download
    data from 'LaminDB' instances.
Approximate marginal maximum likelihood estimation of multidimensional
	latent variable models via adaptive quadrature or Laplace approximations to the 
	integrals in the likelihood function, as presented for confirmatory factor 
	analysis models in Jin, S., Noh, M., and Lee, Y. (2018) 
	<doi:10.1080/10705511.2017.1403287>, for item response theory models in 
	Andersson, B., and Xin, T. (2021) <doi:10.3102/1076998620945199>, and for 
	generalized linear latent variable models in Andersson, B., Jin, S., and 
	Zhang, M. (2023) <doi:10.1016/j.csda.2023.107710>. Models implemented include
	the generalized	partial credit model, the graded response model, and generalized 
	linear latent variable models for Poisson, negative-binomial and normal 
	distributions. Supports a combination of binary, ordinal, count and continuous 
	observed variables and multiple	group models.
Log-analytic methods intended for testing multiplicative effects.
Implements both real-valued branches of the Lambert-W function
    (Corless et al, 1996) <doi:10.1007/BF02124750> without the need for
    installing the entire GSL.
Implementation of the methods described in Holzmann, Klar (2024) 
    <doi:10.48550/arXiv.2303.17872>. Lancaster correlation is a correlation coefficient 
    which equals the absolute value of the Pearson correlation for the bivariate 
    normal distribution, and is equal to or slightly less than the maximum 
    correlation coefficient for a variety of bivariate distributions. Rank and 
    moment-based estimators and corresponding confidence intervals are 
    implemented, as well as independence tests based on these statistics.
Changes of landscape diversity and structure can be detected
    soon if relying on landscape class combinations and analysing patterns
    at multiple scales. 'LandComp' provides such an opportunity, based on
    Juhász-Nagy's functions (Juhász-Nagy P, Podani J 1983
    <doi:10.1007/BF00129432>). Functions can handle multilayered data.
    Requirements of the input: binary data contained by a regular square
    or hexagonal grid, and the grid should have projected coordinates.
Provides functions to estimate survival and a treatment effect using a landmark estimation approach.
Provides a function for classifying a landscape into different categories based on the Topographic Position Index (TPI) and slope. It offers two types of classifications: Slope Position Classification, and Landform Classification. The function internally calculates the TPI for the given landscape and then uses it along with the slope to perform the classification. Optionally, descriptive statistics for every class are calculated and plotted. The classifications are useful for identifying the position of a location on a slope and for identifying broader landform types.
The landmark approach allows survival predictions to be
	updated dynamically as new measurements from an individual are recorded.
	The idea is to set predefined time points, known as "landmark times",
	and form a model at each landmark time using only the individuals in the
	risk set. This package allows the longitudinal data to be modelled
	either using the last observation carried forward or linear mixed
	effects modelling. There is also the option to model competing risks,
	either through cause-specific Cox regression or Fine-Gray regression.
	To find out more about the methods in this package, please see 
	<https://isobelbarrott.github.io/Landmarking/articles/Landmarking>.
Non-parametric prediction of survival outcomes for mixture data that incorporates covariates and a landmark time. Details are described in Garcia (2021) <doi:10.1093/biostatistics/kxz052>.
Contains functions for a flexible varying-coefficient landmark model by incorporating multiple short-term events into the prediction of long-term survival probability. For more information about landmark prediction please see Li, W., Ning, J., Zhang, J., Li, Z., Savitz, S.I., Tahanan, A., Rahbar.M.H., (2023+). "Enhancing Long-term Survival Prediction with Multiple Short-term Events: Landmarking with A Flexible Varying Coefficient Model".
Provides functions for landmark prediction of a survival outcome incorporating covariate and short-term event information. For more information about landmark prediction please see: Parast, Layla, Su-Chun Cheng, and Tianxi Cai. Incorporating short-term outcome information to predict long-term survival with discrete markers. Biometrical Journal 53.2 (2011): 294-307, <doi:10.1002/bimj.201000150>.
Processing of Landsat or other multispectral satellite imagery. Includes relative normalization, image-based radiometric correction, and topographic correction options. The original package description was published as Goslee (2011) <doi:10.18637/jss.v043.i04>, and details of the topographic corrections in Goslee (2012) <doi:10.14358/PERS.78.9.973>.
Calculates landscape metrics for categorical landscape patterns in 
    a tidy workflow. 'landscapemetrics' reimplements the most common metrics from
    'FRAGSTATS' (<https://www.fragstats.org/>) and new ones from the current 
    literature on landscape metrics. This package supports 'terra' SpatRaster objects 
    as input arguments. It further provides utility functions to visualize patches, 
    select metrics and building blocks to develop new metrics.
Simulates categorical maps on actual geographical realms, starting from either empty landscapes or landscapes provided by the user (e.g. land use maps). Allows to tweak or create landscapes while retaining a high degree of control on its features, without the hassle of specifying each location attribute. In this it differs from other tools which generate null or neutral landscapes in a theoretical space. The basic algorithm currently implemented uses a simple agent style/cellular automata growth model, with no rules (apart from areas of exclusion) and von Neumann neighbourhood (four cells, aka Rook case). Outputs are raster dataset exportable to any common GIS format.
A stochastic, spatially-explicit, demo-genetic model simulating the spread and evolution 
    of a plant pathogen in a heterogeneous landscape to assess resistance deployment strategies. 
    It is based on a spatial geometry for describing the landscape and allocation of different cultivars, 
    a dispersal kernel for the dissemination of the pathogen, and a SEIR 
    ('Susceptible-Exposed-Infectious-Removed’) structure with a discrete time step.
    It provides a useful tool to assess the performance of a wide range of deployment options with 
    respect to their epidemiological, evolutionary and economic outcomes.
    Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G Barrett, 
    Peter H Thrall (2018) <doi:10.1371/journal.pcbi.1006067>.
Estimate drift and diffusion functions from time series and
    generate synthetic time series from given drift and diffusion coefficients.
An HTML widget that randomly tours 2D projections of numerical data. A random walk through projections of the data is shown. The user can manipulate the plot to use specified axes, or turn on Guided Tour mode to find an informative projection of the data. Groups within the data can be hidden or shown, as can particular axes. Points can be brushed, and the selection can be linked to other widgets using crosstalk. The underlying method to produce the random walk and projection pursuit uses Langevin dynamics. The widget can be used from within R, or included in a self-contained R Markdown or Quarto document or presentation, or used in a Shiny app.
Improve your text analysis with languagelayer
        <https://languagelayer.com>, a powerful language detection
        API.
Data sets exemplifying statistical methods, and some
        facilitatory utility functions used in ``Analyzing Linguistic
        Data: A practical introduction to statistics using R'',
        Cambridge University Press, 2008.
An implementation of the Language Server Protocol
    for R. The Language Server protocol is used by an editor client to
    integrate features like auto completion. See
    <https://microsoft.github.io/language-server-protocol/> for details.
Allows to install the R 'languageserver' with all dependencies
    into a separate library and use that independent installation
    automatically when R is instantiated as a language server process.
    Useful for making language server seamless to use without
    running into package version conflicts.
R interface for working with nanometer scale secondary ion mass 
    spectrometry (NanoSIMS) data exported from Look at NanoSIMS.
Provides a complete environment for Bayesian inference using a variety of different samplers (see ?LaplacesDemon for an overview).
Auxiliary package for better/faster analytics, visualization, data mining, and machine
    learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling,
    Marketing Mix Modeling (Robyn), Exploratory, API, and Scrapper, it helps the analyst or 
    data scientist to get quick and robust results, without the need of repetitive coding or 
    advanced R programming skills.
Useful 'shiny' production-ready modules and helpers such as login window and visualization tools.
Provides instrumental variable estimation of treatment effects when both the endogenous treatment and its instrument are binary. Applicable to both binary and continuous outcomes.
Conducts a cointegration test for high-dimensional vector autoregressions (VARs) of order k based on the large N,T asymptotics of Bykhovskaya and Gorin, 2022 (<doi:10.48550/arXiv.2202.07150>). The implemented test is a modification of the Johansen likelihood ratio test. In the absence of cointegration the test converges to the partial sum of the Airy-1 point process. This package contains simulated quantiles of the first ten partial sums of the Airy-1 point process that are precise up to the first three digits.
Compute lifetime attributable risk of 
    radiation-induced cancer reveals that it can be helpful with 
    enhancement of the flexibility in research with fast calculation 
    and various options. Important reference papers include
    Berrington de Gonzalez et al. (2012) <doi:10.1088/0952-4746/32/3/205>,
    National Research Council (2006, ISBN:978-0-309-09156-5).
Efficient procedures for fitting an entire lasso
		sequence with the cost of a single least squares
		fit. Least angle regression and infinitesimal forward
		stagewise regression are related to the lasso, as
		described in the paper below.
Implementation of the algorithm introduced in Shah, R. D.
    (2016) <https://www.jmlr.org/papers/volume17/13-515/13-515.pdf>.
    Data with thousands of predictors can be handled. The algorithm
    performs sequential Lasso fits on design matrices containing
    increasing sets of candidate interactions. Previous fits are used to greatly
    speed up subsequent fits, so the algorithm is very efficient.
Fits generalized estimating equations with L1 regularization to longitudinal data with high dimensional covariates. Use a efficient iterative composite gradient descent algorithm.
Contains functions to estimate a penalized regression model using 3CoSE algorithm, see Weber, Striaukas, Schumacher Binder (2018) <doi:10.2139/ssrn.3211163>.
Estimate the p-values for predictors x against target variable y in lasso regression, using the regularization strength when each predictor enters the active set of regularization path for the first time as the statistic. This is based on the assumption that predictors (of the same variance) that (first) become active earlier tend to be more significant. Three null distributions are supported: normal and spherical, which are computed separately for each predictor and analytically under approximation, which aims at efficiency and accuracy for small p-values.
Estimate the sufficient dimension reduction space using sparsed sliced inverse regression via Lasso (Lasso-SIR) introduced in Lin, Zhao, and Liu (2019) <doi:10.1080/01621459.2018.1520115>. The Lasso-SIR is consistent and achieve the optimal convergence rate under certain sparsity conditions for the multiple index models.
Various opportunities to evaluate the effects of including one or more control variable(s) in structural equation models onto model-implied variances, covariances, and parameter estimates. The derivation of the methodology employed in this package can be obtained from Blötner (2023) <doi:10.31234/osf.io/dy79z>.
A graph
  proposed by Rosenbaum is useful
  for checking some properties of various
  sorts of latent scale, this program generates commands
  to obtain the graph using 'dot' from 'graphviz'.
Estimating causal parameters in the presence of treatment spillover is of great interest in statistics.
    This package provides tools for instrumental variables estimation of average causal effects under network interference of unknown form.
    The target parameters are the local average direct effect, the local average indirect effect, the local average overall effect, and the local average spillover effect.
    The methods are developed by Hoshino and Yanagi (2023) <doi:10.48550/arXiv.2108.07455>.
Effectively simulates the discretization process inherent to
    Likert scales while minimizing distortion.  It converts continuous
    latent variables into ordinal categories to generate Likert scale item
    responses.  Particularly useful for accurately modeling and analyzing
    survey data that use Likert scales, especially when applying
    statistical techniques that require metric data.
Bayesian model averaging (BMA) algorithms for univariate link latent Gaussian models (ULLGMs). For detailed information, refer to Steel M.F.J. & Zens G. (2024) "Model Uncertainty in Latent Gaussian Models with Univariate Link Function" <doi:10.48550/arXiv.2406.17318>. The package supports various g-priors and a beta-binomial prior on the model space. It also includes auxiliary functions for visualizing and tabulating BMA results. Currently, it offers an out-of-the-box solution for model averaging of Poisson log-normal (PLN) and binomial logistic-normal (BiL) models. The codebase is designed to be easily extendable to other likelihoods, priors, and link functions.
The first stand-alone R package for computation of latent correlation that takes into account all variable types (continuous/binary/ordinal/zero-inflated),
             comes with an optimized memory footprint, and is computationally efficient, essentially making latent correlation estimation almost as fast as rank-based correlation estimation.
             The estimation is based on latent copula Gaussian models.
             For continuous/binary types, see Fan, J., Liu, H., Ning, Y., and Zou, H. (2017).
             For ternary type, see Quan X., Booth J.G. and Wells M.T. (2018) <arXiv:1809.06255>.
             For truncated type or zero-inflated type, see Yoon G., Carroll R.J. and Gaynanova I. (2020) <doi:10.1093/biomet/asaa007>.
             For approximation method of computation, see Yoon G., Müller C.L. and Gaynanova I. (2021) <doi:10.1080/10618600.2021.1882468>. The latter method uses multi-linear interpolation originally implemented in the R package <https://cran.r-project.org/package=chebpol>.
Generates data based on latent factor models. Data can be continuous, polytomous, dichotomous, or mixed. Skews, cross-loadings, wording effects, population errors, and local dependencies can be added. All parameters can be manipulated. Data categorization is based on Garrido, Abad, and Ponsoda (2011) <doi:10.1177/0013164410389489>.
Three methods are provided to estimate graphical models with latent variables: (1) Jin, Y., Ning, Y., and Tan, K. M. (2020) (preprint available); (2) Chandrasekaran, V., Parrilo, P. A. & Willsky, A. S. (2012) <doi:10.1214/11-AOS949>; (3) Tan, K. M., Ning, Y., Witten, D. M. & Liu, H. (2016) <doi:10.1093/biomet/asw050>.
Fit and simulate latent position and cluster models for statistical networks. See Krivitsky and Handcock (2008) <doi:10.18637/jss.v024.i05> and Krivitsky, Handcock, Raftery, and Hoff (2009) <doi:10.1016/j.socnet.2009.04.001>.
Executes arbitrary R or C functions some time after the current
    time, after the R execution stack has emptied. The functions are scheduled
    in an event loop.
Calculates and plots Handedness index (HI), absolute HI, mean HI and z-score which are commonly used indexes for the study of hand preference (laterality) in non-human primates.
Implements the Linear Approach to Threshold with Ergodic Rate 
    (LATER) model, which predicts distributions of reaction times and 
    summarises them with as little as two free parameters. Allows for easy 
    visualisation and comparison of datasets, along with fitting of datasets 
    using the LATER model.
Parses and converts LaTeX math formulas to R's plotmath
    expressions, used to enter mathematical formulas and symbols to be rendered as
    text, axis labels, etc. throughout R's plotting system.
Produces a PDF diff of two 'rmarkdown', 'quarto', Sweave or TeX 
  files, using the external 'latexdiff' utility.
Converts table-like objects to stand-alone PDF or PNG.
 Can be used to embed tables and arbitrary content in PDF or Word
 documents. Provides a low-level R interface for creating 'LaTeX'
 code, e.g. command() and a high-level interface for creating PDF
 documents, e.g. as.pdf.data.frame(). Extensive customization is
 available via mid-level functions, e.g. as.tabular(). See also 
 'package?latexpdf'. Support for PNG is experimental; see
 'as.png.data.frame'. Adapted from 'metrumrg' 
 <https://r-forge.r-project.org/R/?group_id=1215>.
 Requires a compatible installation of 'pdflatex',
 e.g. <https://miktex.org/>.
Build complex 'LaTeX' mathematical expressions using intuitive 'R' functions. Replace error-prone 'LaTeX' syntax with readable, modular functions that make mathematical typesetting straightforward and maintainable.
A framework for clustering longitudinal datasets in a standardized way. 
    The package provides an interface to existing R packages for clustering longitudinal univariate trajectories, facilitating reproducible and transparent analyses. 
    Additionally, standard tools are provided to support cluster analyses, including repeated estimation, model validation, and model assessment. 
    The interface enables users to compare results between methods, and to implement and evaluate new methods with ease.
    The 'akmedoids' package is available from <https://github.com/MAnalytics/akmedoids>.
Back-end connections to 'LattE' (<https://www.math.ucdavis.edu/~latte/>) 
	for counting lattice points and integration inside convex polytopes and 
	'4ti2' (<http://www.4ti2.de/>) for algebraic, geometric, and combinatorial 
	problems on linear spaces and front-end tools facilitating their use in the 
	'R' ecosystem.
A powerful and elegant high-level data visualization
  system inspired by Trellis graphics, with an emphasis on
  multivariate data. Lattice is sufficient for typical graphics needs,
  and is also flexible enough to handle most nonstandard requirements.
  See ?Lattice for an introduction.
Lattice-based space-filling designs with fill or separation distance properties including 
	interleaved lattice-based minimax distance designs proposed in Xu He (2017) 
	<doi:10.1093/biomet/asx036>, interleaved lattice-based maximin distance designs proposed in 
	Xu He (2018) <doi:10.1093/biomet/asy069>, interleaved lattice-based designs with low fill and 
	high separation distance properties proposed in Xu He (2024) <doi:10.1137/23M156940X>, 
	rotated sphere packing designs proposed in Xu He (2017) 
	<doi:10.1080/01621459.2016.1222289>, sliced rotated sphere packing designs proposed in 
	Xu He (2019) <doi:10.1080/00401706.2018.1458655>, 
	and densest packing-based maximum projections designs proposed in Xu He (2021) 
	<doi:10.1093/biomet/asaa057> and Xu He (2018) <doi:10.48550/arXiv.1709.02062>.
Building on the infrastructure provided by the lattice
	     package, this package provides several new high-level
	     functions and methods, as well as additional utilities
	     such as panel and axis annotation functions.
A general implementation of Structural Equation Models
	with latent variables (MLE, 2SLS, and composite likelihood
	estimators) with both continuous, censored, and ordinal
	outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>).
	Mixture latent variable models and non-linear latent variable models
	(Holst and Budtz-Joergensen (2020) <doi:10.1093/biostatistics/kxy082>).
	The package also provides methods for graph exploration (d-separation,
	back-door criterion), simulation of general non-linear latent variable
	models, and estimation of influence functions for a broad range of
	statistical models.
Fit a variety of latent variable models, including confirmatory
   factor analysis, structural equation modeling and latent growth curve models.
The primary purpose of 'lavaan.mi' is to extend the functionality 
     of the R package 'lavaan', which implements structural equation modeling
     (SEM).  When incomplete data have been multiply imputed, the imputed data
     sets can be analyzed by 'lavaan' using complete-data estimation methods,
     but results must be pooled across imputations (Rubin, 1987, <doi:10.1002/9780470316696>).
     The 'lavaan.mi' package automates the pooling of point and standard-error
     estimates, as well as a variety of test statistics, using a familiar interface
     that allows users to fit an SEM to multiple imputations as they would to a
     single data set using the 'lavaan' package.
Helpers for customizing selected outputs from
  'lavaan' by Rosseel (2012) <doi:10.18637/jss.v048.i02>
  and print them. The functions are intended to be used
  by package developers in their packages and so are not
  designed to be user-friendly. They are designed to be
  let developers customize the tables by other
  functions. Currently the parameter estimates tables of a
  fitted object are supported.
Interactive shiny application for working with different kinds of
    latent variable analysis, with the 'lavaan' package. Graphical output for models
    are provided and different estimators are supported.
Affords an alternative, vector-based syntax to 'lavaan', as well as other 
             convenience functions such as naming paths and defining indirect
             links automatically, in addition to convenience formatting optimized
             for a publication and script sharing workflow.
Provides a graphical user interface with an 
    integrated diagrammer for latent variables from the 'lavaan' package. 
    It offers two core functions:  first, lavaangui() launches a web application
    that allows users to specify models by drawing path diagrams, fitting them, 
    assessing model fit, and more; second, plot_lavaan() creates 
    interactive path diagrams from models specified in 'lavaan'. 
    Karch (2024) <doi: 10.31234/osf.io/f4ary> contains a tutorial.
Plots path diagrams from models in 'lavaan' using the plotting
    functionality from the 'DiagrammeR' package. 'DiagrammeR' provides nice path diagrams 
    via 'Graphviz', and these functions make it easy to generate these diagrams from a
    'lavaan' path model without having to write the DOT language graph specification.
Estimation of a multi-group count regression models (i.e., Poisson, 
    negative binomial) with latent covariates. This packages provides two extensions
    compared to ordinary count regression models based on a generalized linear model:
    First, measurement models for the predictors can be specified allowing to account 
    for measurement error. Second, the count regression can be simultaneously estimated 
    in multiple groups with stochastic group weights. The marginal maximum likelihood 
    estimation is described in Kiefer & Mayer (2020) <doi:10.1080/00273171.2020.1751027>.
Tools for model specification in the latent variable framework
    (add-on to the 'lava' package). The package contains three main functionalities:
    Wald tests/F-tests with improved control of the type 1 error in small samples,
    adjustment for multiple comparisons when searching for local dependencies,
    and adjustment for multiple comparisons when doing inference for multiple latent variable models.
A variety of models to analyze latent variables based on Bayesian learning: the partially CFA (Chen, Guo, Zhang, & Pan, 2020) <DOI: 10.1037/met0000293>; generalized PCFA; partially confirmatory IRM (Chen, 2020) <DOI: 10.1007/s11336-020-09724-3>; Bayesian regularized EFA <DOI: 10.1080/10705511.2020.1854763>; Fully and partially EFA.
Statistical tests widely utilized in biostatistics, public policy, and law. Along with the well-known tests for equality of means and variances, randomness, and measures of relative variability, the package contains new robust tests of symmetry, omnibus and directional tests of normality, and their graphical counterparts such as robust QQ plot, robust trend tests for variances, etc. All implemented tests and methods are illustrated by simulations and real-life examples from legal statistics, economics, and biostatistics.
Performs adjusted inferences based on model objects fitted, using 
    maximum likelihood estimation, by the extreme value analysis packages
    'eva' <https://cran.r-project.org/package=eva>, 
    'evd' <https://cran.r-project.org/package=evd>, 
    'evir' <https://cran.r-project.org/package=evir>, 
    'extRemes' <https://cran.r-project.org/package=extRemes>, 
    'fExtremes' <https://cran.r-project.org/package=fExtremes>, 
    'ismev' <https://cran.r-project.org/package=ismev>, 
    'mev' <https://cran.r-project.org/package=mev>, 
    'POT' <https://cran.r-project.org/package=POT> and
    'texmex' <https://cran.r-project.org/package=texmex>. 
    Adjusted standard errors and an adjusted loglikelihood are provided, using    
    the 'chandwich' package <https://cran.r-project.org/package=chandwich>
    and the object-oriented features of the 'sandwich' package 
    <https://cran.r-project.org/package=sandwich>. The adjustment is based on a 
    robust sandwich estimator of the parameter covariance matrix, based on the 
    methodology in Chandler and Bate (2007) <doi:10.1093/biomet/asm015>. This 
    can be used for cluster correlated data when interest lies in the 
    parameters of the marginal distributions, or for performing inferences that 
    are robust to certain types of model misspecification.  Univariate extreme 
    value models, including regression models, are supported.
Creating efficiently new column(s) in a data frame (including tibble) by applying a function one row at a time.
Simplifies the whole process of creating stacked tilted maps,
    that are often used in scientific publications to show different
    environmental layers for a geographical region. Tilting maps and
    layering them allows to easily draw visual correlations between these
    environmental layers.
By combining constant, linear, and quadratic local models,
        lazy estimates the value of an unknown multivariate function on
        the basis of a set of possibly noisy samples of the function
        itself.  This implementation of lazy learning automatically
        adjusts the bandwidth on a query-by-query basis through a
        leave-one-out cross-validation.
Multi-threaded serialization of compressed array that 
    fully utilizes modern solid state drives. It allows 
    to store and load extremely large data on demand within seconds
    without occupying too much memories. With data stored on hard drive, 
    a lazy-array data can be loaded, shared across multiple R sessions.
    For arrays with partition mode on, multiple R sessions can write to 
    a same array simultaneously along the last dimension (partition). 
    The internal storage format is provided by 'fstcore' package geared by 
    'LZ4' and 'ZSTD' compressors.
A simple progress bar showing estimated remaining time. 
    Multiple forecast methods and user defined forecast method for 
    the remaining time are supported.
Supplies a LazyData facility for packages which have data
		sets but do not provide LazyData: true.  A single function is
		is included, requireData, which is a drop-in replacement for
		base::require, but carrying the additional
		functionality. By default, it suppresses package
		startup messages as well.  See argument 'reallyQuitely'.
An alternative approach to non-standard evaluation using
    formulas. Provides a full implementation of LISP style 'quasiquotation',
    making it easier to generate code with other code.
Lazy read for drawings. A 'dplyr' back end for data sources supported by 
    'GDAL' vector drivers, that allows working with local or remote sources as if they 
    are in-memory data frames. Basic features works with any drawing format ('GDAL vector 
    data source') supported by the 'sf' package.
Helper functions to build SQL statements
    for dbGetQuery or dbSendQuery under program control.
    They are intended to increase speed of coding and
    to reduce coding errors. Arguments are carefully checked,
    in particular SQL identifiers such as names of tables or columns.
    More patterns will be added as required.
Provide sets of functions and methods to learn and practice data science using idea of algorithmic trading.
    Main goal is to process information within "Decision Support System" to come up with analysis or predictions.
    There are several utilities such as dynamic and adaptive risk management using reinforcement learning
    and even functions to generate predictions of price changes using pattern recognition deep regression learning.
    Summary of Methods used: Awesome H2O tutorials: <https://github.com/h2oai/awesome-h2o>, 
    Market Type research of Van Tharp Institute: <https://vantharp.com/>,
    Reinforcement Learning R package: <https://CRAN.R-project.org/package=ReinforcementLearning>.
Provides the functionality to write LaTeX code from within R
    without having to learn LaTeX.  Functionality also exists to create HTML
    and Markdown code.  While the functionality still exists to write
    complete documents with lazyWeave, it is generally easier to do so with
    with markdown and knitr.  lazyWeave's main strength now is the ability
    to design custom and complex tables for reporting results.
Latent budget analysis is a method for the analysis of a two-way
    contingency table with an exploratory variable and a response variable. It is
    specially designed for compositional data.
A suite of tools for literature-based discovery in biomedical research. 
    Provides functions for retrieving scientific articles from 'PubMed' and 
    other NCBI databases, extracting biomedical entities (diseases, drugs, genes, etc.), 
    building co-occurrence networks, and applying various discovery models 
    including 'ABC', 'AnC', 'LSI', and 'BITOLA'. The package also includes 
    visualization tools for exploring discovered connections.
A wrapper built around the libLBFGS optimization library by Naoaki Okazaki. The lbfgs package implements both the Limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) and the Orthant-Wise Quasi-Newton Limited-Memory (OWL-QN) optimization algorithms. The L-BFGS algorithm solves the problem of minimizing an objective, given its gradient, by iteratively computing approximations of the inverse Hessian matrix. The OWL-QN algorithm finds the optimum of an objective plus the L1-norm of the problem's parameters. The package offers a fast and memory-efficient implementation of these optimization routines, which is particularly suited for high-dimensional problems.
Interfacing to Nocedal et al. L-BFGS-B.3.0
        (See <http://users.iems.northwestern.edu/~nocedal/lbfgsb.html>)
        limited memory BFGS minimizer with bounds on parameters.
        This is a fork of 'lbfgsb3'.
	This registers a 'R' compatible 'C' interface to L-BFGS-B.3.0 that uses the same
	function types and optimization as the optim() function (see writing 'R' extensions
        and source for details).  This package also adds more stopping criteria as well
        as allowing the adjustment of more tolerances.
Maximum likelihood estimation and likelihood ratio test are essential for modern statistics. This package supports in calculating likelihood based inference.
             Reference: Pawitan Y. (2001, ISBN:0-19-850765-8).
Fit the log binomial regression model (LBM) by Exact method. Limited parameter space of 
    LBM causes trouble to find admissible estimates and fail to converge when MLE is close to or on 
    the boundary of space. Exact method utilizes the property of boundary vectors to re-parametrize 
    the model without losing any information, and fits the model on the standard fitting algorithm 
    with no convergence issues.
Implements a logistic box-cox model. This model is fully described in Xing, L. et al. (2021) <doi:10.1002/cjs.11587>.
The Length-Biased Power Garima distribution for computes the probability density,
    the cumulative density distribution and the quantile function of the distribution, 
    and generates sample values with random variables based on Kittipong and Sirinapa(2021)<DOI: 10.14456/sjst-psu.2021.89>.
Maximum likelihood estimation of log-binomial regression with special functionality when the MLE is on the boundary of the parameter space.
Simulate expected equilibrium length composition, yield-per-recruit, and
    the spawning potential ratio (SPR) using the length-based SPR (LBSPR) model. Fit the LBSPR
    model to length data to estimate  selectivity, relative apical fishing mortality, and
    the spawning potential ratio for data-limited fisheries.
    See Hordyk et al (2016) <doi:10.1139/cjfas-2015-0422> for more information about the
    LBSPR assessment method.
Performs model fitting and significance estimation for Localised Co-Dependency between pairs of features of a numeric dataset.
Latent Class Analysis of
        phenotypic measurements in pedigrees and model selection
        based on one of two methods: likelihood-based cross-validation
        and Bayesian Information Criterion. Computation of individual
        and triplet child-parents weights in a pedigree is performed using an
        upward-downward algorithm. The model takes into account the familial
        dependence defined by the pedigree structure by considering
        that a class of a child depends on his parents classes via
        triplet-transition probabilities of the classes. The package
        handles the case where measurements are available on all
        subjects and the case where measurements are available only on
        symptomatic (i.e. affected) subjects. Distributions for
        discrete (or ordinal) and continuous data are currently
        implemented. The package can deal with missing data.
Provides Shiny widgets and theme that support a 'Library Computer Access/Retrieval System' (LCARS) aesthetic for Shiny apps. 
    The package also includes functions for adding a minimal LCARS theme to static 'ggplot2' graphs. 
    More details about LCARS can be found at <https://en.wikipedia.org/wiki/LCARS>.
Estimates the longitudinal concordance correlation to access the longitudinal agreement profile. The estimation approach implemented is variance components approach based on polynomial mixed effects regression model, as proposed by Oliveira, Hinde and Zocchi (2018) <doi:10.1007/s13253-018-0321-1>.  In addition, non-parametric confidence intervals were implemented using percentile method or normal-approximation based on Fisher Z-transformation.
Estimation of latent class models with individual covariates for capture-recapture data. See Bartolucci, F. and Forcina, A. (2022), Estimating the size of a closed population by modeling latent and observed heterogeneity, Biometrics, 80(2), ujae017.
Providing a method for Local Discrimination via Latent Class Models. The approach is described in <https://www.r-project.org/conferences/useR-2009/abstracts/pdf/Bucker.pdf>.
This package contains (1) event-related brain potential data recorded from 10 participants at electrodes Fz, Cz, Pz, and Oz (0--300 ms) in the context of Antoine Tremblay's PhD thesis (Tremblay, 2009); (2) ERP amplitudes at electrode Fz restricted to the 100 to 175 millisecond time window; and (3) plotting data generated from a linear mixed-effects model.
A joint latent class model where a hierarchical structure exists, with an interaction between female and male partners of a couple. A Bayesian perspective to inference and Markov chain Monte Carlo algorithms to obtain posterior estimates of model parameters. The reference paper is: Beom Seuk Hwang, Zhen Chen, Germaine M.Buck Louis, Paul S. Albert, (2018) "A Bayesian multi-dimensional couple-based latent risk model with an application to infertility". Biometrics, 75, 315-325. <doi:10.1111/biom.12972>.
Bayesian population size estimation using non parametric latent-class models.
Estimation of various extensions of the mixed models including latent class mixed models, joint latent class mixed models, mixed models for curvilinear outcomes, mixed models for multivariate longitudinal outcomes using a maximum likelihood estimation method (Proust-Lima, Philipps, Liquet (2017) <doi:10.18637/jss.v078.i02>).
The goal of 'LCMSQA' is to make it easy to check the quality of
             liquid chromatograph/mass spectrometry (LC/MS) experiments using a
             'shiny' application. This package provides interactive data
             visualizations for quality control (QC) samples, including total
             ion current chromatogram (TIC), base peak chromatogram (BPC), mass
             spectrum, extracted ion chromatogram (XIC), and feature detection
             results from internal standards or known metabolites.
Provides functions to upload vectorial data and derive landscape
    connectivity metrics in habitat or matrix systems. Additionally, includes an 
    approach to assess individual patch contribution to the overall landscape 
    connectivity, enabling the prioritization of habitat patches. The computation
    of landscape connectivity and patch importance are very useful in Landscape 
    Ecology research. The metrics available are: number of components, number of 
    links, size of the largest component, mean size of components, class coincidence
    probability, landscape coincidence probability, characteristic path length, 
    expected cluster size, area-weighted flux and integral index of connectivity.
    Pascual-Hortal, L., and Saura, S. (2006) <doi:10.1007/s10980-006-0013-z>
    Urban, D., and Keitt, T. (2001) <doi:10.2307/2679983>
    Laita, A., Kotiaho, J., Monkkonen, M. (2011) <doi:10.1007/s10980-011-9620-4>.
Collections of functions allowing random number generations and
    estimation of 'Liouville' copulas, as described in Belzile and Neslehova (2017) <doi:10.1016/j.jmva.2017.05.008>.
An implementation of the Log Cumulative Probability Model (LCPM) 
  and Proportional Probability Model (PPM) for which the Maximum Likelihood Estimates are determined using constrained optimization. 
  This implementation accounts for the implicit constraints on the parameter space. Other 
  features such as standard errors, z tests and p-values use standard methods adapted from the results based on constrained optimization.
For fitting Bayesian joint latent class and regression models using
    Gibbs sampling. See the documentation for the model.
    The technical details of the model implemented here are described in Elliott,
    Michael R., Zhao, Zhangchen, Mukherjee, Bhramar, Kanaya, Alka, Needham,
    Belinda L., "Methods to account for uncertainty in latent class assignments when
    using latent classes as predictors in regression models, with application to
    acculturation strategy measures" (2020) In press at Epidemiology
    <doi:10.1097/EDE.0000000000001139>.
Helper functions to implement univariate and bivariate latent change score models in R using the 'lavaan' package.
  For details about Latent Change Score Modeling (LCSM) see McArdle (2009) <doi:10.1146/annurev.psych.60.110707.163612> and Grimm, An, McArdle, Zonderman and Resnick (2012) <doi:10.1080/10705511.2012.659627>.
  The package automatically generates 'lavaan' syntax for different model specifications and varying timepoints.
  The 'lavaan' syntax generated by this package can be returned and further specifications can be added manually.
  Longitudinal plots as well as simplified path diagrams can be created to visualise data and model specifications.
  Estimated model parameters and fit statistics can be extracted as data frames.
  Data for different univariate and bivariate LCSM can be simulated by specifying estimates for model parameters to explore their effects.
  This package combines the strengths of other R packages like 'lavaan', 'broom', and 'semPlot' by generating 'lavaan' syntax that helps these packages work together.
Provides researchers and educators with easy-to-learn user friendly tools for calculating 
    key spatial statistics and to apply simple as well as advanced methods of spatial analysis in real data. 
    These include: Local Pearson and Geographically Weighted Pearson Correlation Coefficients, 
    Spatial Inequality Measures (Gini, Spatial Gini, LQ, Focal LQ), Spatial Autocorrelation 
    (Global and Local Moran's I), several Geographically Weighted Regression techniques and other 
    Spatial Analysis tools (other geographically weighted statistics). This package also contains functions for 
    measuring the significance of each statistic calculated, mainly based on Monte Carlo simulations.
Analysis of stock data ups and downs trend, the stock technical analysis indicators function have trend line, reversal pattern and market trend.
Implements latent Dirichlet allocation (LDA)
	     and related models.  This includes (but is not limited
	     to) sLDA, corrLDA, and the mixed-membership stochastic
	     blockmodel.  Inference for all of these models is
	     implemented via a fast collapsed Gibbs sampler written
	     in C.  Utility functions for reading/writing data
	     typically used in topic models, as well as tools for
	     examining posterior distributions are also included.
Computation of linkage disequilibrium of ancestry (LDA) and linkage disequilibrium of ancestry score (LDAS). LDA calculates the pairwise linkage disequilibrium of ancestry between single nucleotide polymorphisms (SNPs). LDAS calculates the LDA score of SNPs. The methods are described in Barrie W, Yang Y, Irving-Pease E.K, et al (2024) <doi:10.1038/s41586-023-06618-z>.
Cellular cooperation compromises the established method of
	calculating clonogenic activity from limiting dilution assay (LDA) data.
	This tool provides functions that enable robust analysis in presence or
	absence of cellular cooperation. The implemented method incorporates the
	same cooperativity module to model the non-linearity associated with
	cellular cooperation as known from the colony formation assay (Brix et al.
	(2021) <doi:10.1038/s41596-021-00615-0>: "Analysis of clonogenic growth in
	vitro." Nature protocols).
Select statistically similar research groups by backward selection using various robust algorithms, including a heuristic based on linear discriminant analysis, multiple heuristics based on the test statistic, and parallelized exhaustive search.
Determine a Prototype from a number of runs of Latent Dirichlet Allocation (LDA) measuring its similarities with S-CLOP: A procedure to select the LDA run with highest mean pairwise similarity, which is measured by S-CLOP (Similarity of multiple sets by Clustering with Local Pruning), to all other runs. LDA runs are specified by its assignments leading to estimators for distribution parameters. Repeated runs lead to different results, which we encounter by choosing the most representative LDA run as prototype.
A classification tree method that uses Uncorrelated Linear Discriminant Analysis (ULDA) for variable selection, split determination, and model fitting in terminal nodes.  It automatically handles missing values and offers visualization tools. For more details, see Wang (2024) <doi:10.48550/arXiv.2410.23147>.
Combines Latent Dirichlet Allocation (LDA) and Bayesian multinomial time series methods in a two-stage analysis to quantify dynamics in high-dimensional temporal data. LDA decomposes multivariate data into lower-dimension latent groupings, whose relative proportions are modeled using generalized Bayesian time series models that include abrupt changepoints and smooth dynamics. The methods are described in Blei et al. (2003) <doi:10.1162/jmlr.2003.3.4-5.993>, Western and Kleykamp (2004) <doi:10.1093/pan/mph023>, Venables and Ripley (2002, ISBN-13:978-0387954578), and Christensen et al. (2018) <doi:10.1002/ecy.2373>.
Tools to create an interactive web-based visualization of a
    topic model that has been fit to a corpus of text data using
    Latent Dirichlet Allocation (LDA). Given the estimated parameters of
    the topic model, it computes various summary statistics as input to
    an interactive visualization built with D3.js that is accessed via
    a browser. The goal is to help users interpret the topics in their
    LDA topic model.
Flexible procedures to compute local density-based outlier scores for ranking outliers.
  Both exact and approximate nearest neighbor search can be implemented, while also accommodating
  multiple neighborhood sizes and four different local density-based methods. It allows for
  referencing a random subsample of the input data or a user specified reference data set
  to compute outlier scores against, so both unsupervised and semi-supervised outlier
  detection can be implemented.
Computations related to group sequential boundaries.
    Includes calculation of bounds using the Lan-DeMets
    alpha spending function approach. Based on FORTRAN
        program ld98 implemented by Reboussin, et al. (2000) <doi:10.1016/s0197-2456(00)00057-x>.
Four measures of linkage disequilibrium are provided: the usual r^2
        measure, the r^2_S measure (r^2 corrected by the structure
        sample), the r^2_V (r^2 corrected by the relatedness of
        genotyped individuals), the r^2_VS measure (r^2 corrected by
        both the relatedness of genotyped individuals and the structure
        of the sample).
Implementation of the drift-diffusion mixed model for category learning as described in Paulon et al. (2021) <doi:10.1080/01621459.2020.1801448>.
Hidden Markov Model (HMM) based on symmetric lambda distribution
    framework is implemented for the study of return time-series in the financial
    market. Major features in the S&P500 index, such as regime identification,
    volatility clustering, and anti-correlation between return and volatility,
    can be extracted from HMM cleanly. Univariate symmetric lambda distribution
    is essentially a location-scale family of exponential power distribution.
    Such distribution is suitable for describing highly leptokurtic time series
    obtained from the financial market. It provides a theoretically solid foundation
    to explore such data where the normal distribution is not adequate. The HMM
    implementation follows closely the book: "Hidden Markov Models for Time Series",
    by Zucchini, MacDonald, Langrock (2016).
Provides access to the 'LDlink' API (<https://ldlink.nih.gov/?tab=apiaccess>)
    using the R console.  This programmatic access facilitates researchers who are 
    interested in performing batch queries in 1000 Genomes Project (2015) <doi:10.1038/nature15393> 
    data using 'LDlink'. 'LDlink' is an interactive and powerful suite of web-based tools for querying 
    germline variants in human population groups of interest. For more details, please see 
    Machiela et al. (2015) <doi:10.1093/bioinformatics/btv402>.
A single analysis path that includes distance-based ordination, global tests of any effect of the microbiome, and tests of the effects of individual taxa with false-discovery-rate (FDR) control. It accommodates both continuous and discrete covariates as well as interaction terms to be tested either singly or in combination, allows for adjustment of confounding covariates, and uses permutation-based p-values that can control for sample correlations. It can be applied to transformed data, and an omnibus test can combine results from analyses conducted on different transformation scales. It can also be used for testing presence-absence associations based on infinite number of rarefaction replicates, testing mediation effects of the microbiome, analyzing censored time-to-event outcomes, and for compositional analysis by fitting linear models to centered-log-ratio taxa count data.
A suite of tools for estimating, assessing model fit, simulating from, and visualizing location dependent marked point processes characterized by regularity in the pattern.
    You provide a reference marked point process, a set of raster images containing location specific covariates, and select the estimation algorithm and type of mark model.
    'ldmppr' estimates the process and mark models and allows you to check the appropriateness of the model using a variety of diagnostic tools.
    Once a satisfactory model fit is obtained, you can simulate from the model and visualize the results.
    Documentation for the package 'ldmppr' is available in the form of a vignette.
This is a Neural Network regression model implementation using 'Keras', consisting of 10 Long Short-Term Memory layers that are fully connected along with the rest of the inputs.
Linear dimension reduction subspaces can be uniquely defined using orthogonal projection matrices. This package provides tools to compute distances between such subspaces and to compute the average subspace. For details see Liski, E.Nordhausen K., Oja H., Ruiz-Gazen A. (2016) Combining Linear Dimension Reduction Subspaces <doi:10.1007/978-81-322-3643-6_7>.
Estimate haplotypic or composite pairwise linkage disequilibrium
    (LD) in polyploids, using either genotypes or genotype likelihoods. 
    Support is provided to estimate the popular measures of LD: the LD 
    coefficient D, the standardized LD coefficient D', and the Pearson 
    correlation coefficient r. All estimates are returned with corresponding 
    standard errors. These estimates and standard errors can then be used
    for shrinkage estimation. The main functions are ldfast(), ldest(), mldest(),
    sldest(), plot.lddf(), format_lddf(), and ldshrink(). Details of the methods
    are available in Gerard (2021a) <doi:10.1111/1755-0998.13349>
    and Gerard (2021b) <doi:10.1038/s41437-021-00462-5>.
Streamflow (and climate) reconstruction using Linear Dynamical Systems. 
    The advantage of this method is the additional state trajectory which can reveal more information 
    about the catchment or climate system. For details of the method please refer to Nguyen and Galelli 
    (2018) <doi:10.1002/2017WR022114>.
Methods and tools for model selection and multi-model inference (Burnham and Anderson (2002) <doi:10.1007/b97636>, among others). 
             'SUR' (for parameter estimation), 'logit'/'probit' (for binary classification), and 'VARMA' (for time-series forecasting) are implemented.
             Evaluations are both in-sample and out-of-sample. 
             It is designed to be efficient in terms of CPU usage and memory consumption.
The leader clustering algorithm provides
 a means for clustering a set of data points. Unlike many other clustering
 algorithms it does not require the user to specify the number of clusters,
 but instead requires the approximate radius of a cluster as its primary
 tuning parameter. The package provides a fast implementation of this
 algorithm in n-dimensions using Lp-distances (with special cases for p=1,2,
 and infinity) as well as for spatial data using the Haversine
 formula, which takes latitude/longitude pairs as inputs and clusters
 based on great circle distances.
Extracts and creates an analysis pipeline for the JSON data files from Brain Sense sessions using Medtronic's Deep Brain Stimulation surgery electrode implants.
An interface for the image processing program 'ImageJ', which
    allows a rapid digital image analysis for particle sizes. This package includes
    function to write an 'ImageJ' macro which is optimized for a leaf area analysis by
    default.
Provides drill down functionality for 'leaflet' choropleths in 'shiny' apps.
Provides extensions for packages 'leaflet' & 'mapdeck', 
    many of which are used by package 'mapview'. 
    Focus is on functionality readily available in 
    Geographic Information Systems such as 'Quantum GIS'. Includes functions
    to display coordinates of mouse pointer position, query image values via 
    mouse pointer and zoom-to-layer buttons. Additionally, provides a feature 
    type agnostic function to add points, lines, polygons to a map.
Provides bindings to the 'Leaflet.glify' JavaScript library which extends the 'leaflet' JavaScript library to render large data in the browser using 'WebGl'.
Provides extensions to the 'leaflet' package to 
    customize legends with images, text styling, orientation, sizing,
    and symbology and functions to create symbols to plot on maps.
Create and customize interactive maps using the 'Leaflet'
    JavaScript library and the 'htmlwidgets' package. These maps can be
    used directly from the R console, from 'RStudio', in Shiny
    applications and R Markdown documents.
The 'leaflet' JavaScript library provides many plugins some of which
    are available in the core 'leaflet' package, but there are many more. It is not
    possible to support them all in the core 'leaflet' package. This package serves
    as an add-on to the 'leaflet' package by providing extra functionality via 'leaflet'
    plugins.
Several 'leaflet' plugins are integrated, which are available as extension to the 'leaflet' package.
Add and modify small charts on an interactive map created with 
    package 'leaflet'. These charts can be used to represent at same time multiple 
    variables on a single map.
Contains third-party map tile provider information from
    'Leaflet.js', <https://github.com/leaflet-extras/leaflet-providers>,
    to be used with the 'leaflet' R package. Additionally,
    'leaflet.providers' enables users to retrieve up-to-date provider
    information between package updates.
Provides 'sf' data for Chinese provinces and cities,
  methods for plotting shape maps of Chinese provinces and cities,
  Convert Coordinates Between Different Systems,
  and a layer for 'leaflet' with Gaode tiles.
  It is designed to facilitate geographical data visualization in China.
A collection of tools for interactive manipulation of (spatial) data 
    layers on leaflet web maps. Tools include editing of existing layers, creation 
    of new layers through drawing of shapes (points, lines, polygons), deletion 
    of shapes as well as cutting holes into existing shapes. Provides control over 
    options to e.g. prevent self-intersection of polygons and lines or to enable/disable 
    snapping to align shapes.
Creates 'HTML' strings to embed tables, images or graphs in pop-ups
  of interactive maps created with packages like 'leaflet' or 'mapview'. Handles
  local images located on the file system or via remote URL. Handles graphs created 
  with 'lattice' or 'ggplot2' as well as interactive plots created with 'htmlwidgets'.
A set of functions for analyzing the structure 
  of forests based on the leaf area density (LAD) and leaf area index (LAI) measures 
  calculated from Airborne Laser Scanning (ALS), i.e., scanning lidar (Light Detection 
  and Ranging) data. The methodology is discussed and described in 
  Almeida et al. (2019) <doi:10.3390/rs11010092> and 
  Stark et al. (2012) <doi:10.1111/j.1461-0248.2012.01864.x>.
Implementation of trigonometric functions to calculate the exposure of flat, tilted surfaces, such as leaves and slopes, to direct solar radiation. It implements the equations in A.G. Escribano-Rocafort, A. Ventre-Lespiaucq, C. Granado-Yela, et al. (2014) <doi:10.1111/2041-210X.12141> in a few user-friendly R functions. All functions handle data obtained with 'Ahmes' 1.0 for Android, as well as more traditional data sources (compass, protractor, inclinometer). The main function (star()) calculates the potential exposure of flat, tilted surfaces to direct solar radiation (silhouette to area ratio, STAR). It is equivalent to the ratio of the leaf projected area to total leaf area, but instead of using area data it uses spatial position angles, such as pitch, roll and course, and information on the geographical coordinates, hour, and date. The package includes additional functions to recalculate STAR with custom settings of location and time, to calculate the tilt angle of a surface, and the minimum angle between two non-orthogonal planes.
Create small multiples of several leaflet web maps with (optional) 
    synchronised panning and zooming control. When syncing is enabled all maps 
    respond to mouse actions on one map. This allows side-by-side comparisons
    of different attributes of the same geometries. Syncing can be adjusted
    so that any combination of maps can be synchronised.
Use the 'leaflet-timeline' plugin with a leaflet widget to add an
    interactive slider with play, pause, and step buttons to explore temporal
    geographic spatial data changes.
Instrumental variables (IVs) are a popular and powerful tool for 
  estimating causal effects in the presence of unobserved confounding. However, 
  classical methods rely on strong assumptions such as the exclusion criterion,
  which states that instrumental effects must be entirely mediated by 
  treatments. In the so-called "leaky" IV setting, candidate instruments are 
  allowed to have some direct influence on outcomes, rendering the average 
  treatment effect (ATE) unidentifiable. But with limits on the amount of 
  information leakage, we may still recover sharp bounds on the ATE, providing 
  partial identification. This package implements methods for ATE bounding in 
  the leaky IV setting with linear structural equations. For details, see Watson
  et al. (2024) <doi:10.48550/arXiv.2404.04446>.
Provides access to the 'Leanpub' API
    <https://leanpub.com/help/api> for gathering information about 
    publications and submissions to the 'Leanpub' platform.
An emulator designed for rapid sequential emulation (e.g., Markov chain Monte Carlo applications). Works via extension of the 'laGP' approach by Gramacy and Apley (2015 <doi:10.1080/10618600.2014.914442>). Details are given in Rumsey et al. (2023 <doi:10.1002/sta4.576>).
These functions take a gene expression value matrix, a
        primary covariate vector, an additional known covariates
        matrix.  A two stage analysis is applied to counter the effects
        of latent variables on the rankings of hypotheses.  The
        estimation and adjustment of latent effects are proposed by
        Sun, Zhang and Owen (2011).  "leapp" is developed in the
        context of microarray experiments, but may be used as a general
        tool for high throughput data sets where dependence may be
        involved.
Regression subset selection, including exhaustive search.
Provides methods for estimating borders of uniform distribution on
  the interval (one-dimensional) and on the elliptical domain (two-dimensional)
  under measurement errors. For one-dimensional case, it also estimates the
  length of underlying uniform domain and tests the hypothesized length against
  two-sided or one-sided alternatives. For two-dimensional case, it estimates
  the area of underlying uniform domain. It works with numerical inputs as well
  as with pictures in JPG format.
A collection of functions helpful in learning the basic tenets of Bayesian statistical inference.  It contains functions for summarizing basic one and two parameter posterior distributions and predictive distributions.  It contains MCMC algorithms for summarizing posterior distributions defined by the user.  It also contains functions for regression models, hierarchical models, Bayesian tests, and illustrations of Gibbs sampling.
Classical hierarchical clustering algorithms, agglomerative and divisive clustering. Algorithms are implemented as a theoretical way, step by step.
  It includes some detailed functions that explain each step. Every function allows options to get different results using different techniques. 
  The package explains non expert users how hierarchical clustering algorithms work.
Implements transfer learning methods for low-rank matrix 
    estimation. These methods leverage similarity in the latent row and column 
    spaces between the source and target populations to improve estimation in 
    the target population. The methods include the LatEnt spAce-based tRaNsfer 
    lEaRning (LEARNER) method and the direct projection LEARNER (D-LEARNER) 
    method described by McGrath et al. (2024) <doi:10.48550/arXiv.2412.20605>.
Contains some functions to learn and teach basic plane Geometry at undergraduate level with the aim of being helpful to young students with little programming skills.
Crabs in the English channel, deer skulls, English
    monarchs, half-caste Manga characters, Jamaican cities,
    Shakespeare's The Tempest, drugged up cyclists and sexually
    transmitted diseases.
Aids in learning statistical functions incorporating the result of calculus done with each function and how they are obtained, that is, which equation and variables are used. Also for all these equations and their related variables detailed explanations and interactive exercises are also included. All these characteristics allow to the package user to improve the learning of statistics basics by means of their use.
Provides tools to teach students elemental statistics. The main topics covered are descriptive statistics, probability models (discrete and continuous variables) and statistical inference (confidence intervals and hypothesis tests). One of the main advantages of this package is that allows the user to read quite a variety of types of data files with one unique command. Moreover it includes shortcuts to simple but up-to-now not in R descriptive features such a complete frequency table or an histogram with the optimal number of intervals. Related to model distributions (both discrete and continuous), the package allows the student to easy plot the mass/density function, distribution function and quantile function just detailing as input arguments the known population parameters. The inference related tools are basically confidence interval and hypothesis testing. Having defined independent commands for these two tools makes it easier for the student to understand what the software is performing, and it also helps the student to have a better knowledge on which specific tool they need to use in each situation. Moreover, the hypothesis testing commands provide not only the numeric result on the screen but also a very intuitive graph (which includes the statistic distribution, the observed value of the statistic, the rejection area and the p-value) that is very useful for the student to visualise the process. The regression section includes up to now, a simple linear model, with one single command the student can obtain the numeric summary as well as the corresponding diagram with the adjusted regression model and a legend with basic information (formula of the adjusted model and R-squared).
The Programme for International Student Assessment (PISA) is a global study conducted by the Organization for Economic Cooperation and Development (OECD) in member and non-member countries to assess educational systems by assessing 15-year-old school students academic performance in mathematics, science, and reading. This datasets contains information on their scores and other socioeconomic characteristics, information about their school and its infrastructure, as well as the countries that are taking part in the program.
Implements non-parametric tests from Higgins (2004, ISBN:0534387756), including tests for one sample, two samples, k samples, paired comparisons, blocked designs, trends and association. Built with 'Rcpp' for efficiency and 'R6' for flexible, object-oriented design, the package provides a unified framework for performing or creating custom permutation tests.
Principal component analysis (PCA) is one of the most widely used data analysis techniques.  This package provides a series of vignettes explaining PCA starting from basic concepts. The primary purpose is to serve as a self-study resource for anyone wishing to understand PCA better. A few convenience functions are provided as well.
Conducts various numerical analyses and simulations in population genetics and evolutionary theory, primarily for the purpose of teaching (and learning about) key concepts in population & quantitative genetics, and evolutionary theory.
Create interactive tutorials using R Markdown. Use a
    combination of narrative, figures, videos, exercises, and quizzes to
    create self-paced tutorials for learning about R and R packages.
Data, scripts and code from chunks used as examples in the book 
   "Learn R: As a Language" 1ed and 2ed by Pedro J. Aphalo.
   ISBN 9780367182533 (pbk 1ed); ISBN 9780367182557 (hbk 1ed); ISBN 9780429060342 (ebk 1ed).
Supervised classification methods, which (if asked) can provide
    step-by-step explanations of the algorithms used, as described in
    PK Josephine et. al., (2021) <doi:10.59176/kjcs.v1i1.1259>; and datasets to
    test them on, which highlight the strengths and weaknesses of each technique.
Summarizes characteristics of linear mixed effects models without 
    data or a fitted model by converting code for fitting lmer() from 'lme4' 
    and lme() from 'nlme' into tables, equations, and visuals. Outputs can be 
    used to learn how to fit linear mixed effects models in 'R' and to 
    communicate about these models in presentations, manuscripts, and analysis 
    plans.
Calculates cost surfaces based on slope to be used when modelling pathways and movement potential within a landscape (Lewis, 2021) <doi:10.1007/s10816-021-09522-w>.
Utilities for querying plain text accounting files from 'Ledger', 'HLedger', and 'Beancount'.
An educational package for teaching statistics and mathematics in both primary and higher education. The objective is to assist in the teaching/learning process, both for student study planning and teacher teaching strategies. The leem package aims to provide, in a simple yet in-depth manner, knowledge of statistics and mathematics to anyone who wants to study these areas of knowledge.
Complete analytical environment for the construction and analysis
             of matrix population models and integral projection models.
             Includes the ability to construct historical matrices, which are
             2d matrices comprising 3 consecutive times of demographic
             information. Estimates both raw and function-based forms of
             historical and standard ahistorical matrices. It also estimates
             function-based age-by-stage matrices and raw and function-based
             Leslie matrices.
A 'ggplot2' extension that focusses on expanding the
    plotter's arsenal of guides. Guides in 'ggplot2' include axes and
    legends. 'legendry' offers new axes and annotation options, as well as
    new legends and colour displays.
Functions implementing multivariate state space models for purposes of time series analysis and forecasting.
             The focus of the package is on multivariate models, such as Vector Exponential Smoothing,
             Vector ETS (Error-Trend-Seasonal model) etc. It currently includes Vector Exponential
             Smoothing (VES, de Silva et al., 2010, <doi:10.1177/1471082X0901000401>), Vector ETS (Svetunkov et al., 2023,
             <doi:10.1016/j.ejor.2022.04.040>) and simulation function for VES.
Facilitates access to the Comparative Legislators Database (CLD). The CLD includes political, sociodemographic, career, online presence, public attention, and visual information for over 67,000 contemporary and historical politicians from 16 countries.
Constructs genotype x environment interaction (GxE) models where
    G is a weighted sum of genetic variants (genetic score) and E is a weighted
    sum of environments (environmental score) using the alternating optimization algorithm 
    by Jolicoeur-Martineau et al. (2017) <arXiv:1703.08111>. This approach has greatly 
    enhanced predictive power over traditional GxE models which include only a single 
    genetic variant and a single environmental exposure. Although this approach was 
    originally made for GxE modelling, it is flexible and does not require the use of 
    genetic and environmental variables. It can also handle more than 2 latent variables 
    (rather than just G and E) and 3-way interactions or more. The LEGIT model produces 
    highly interpretable results and is very parameter-efficient thus it can even be 
    used with small sample sizes (n < 250). Tools to determine the type of interaction
    (vantage sensitivity, diathesis-stress or differential susceptibility), with any 
    number of genetic variants or environments, are available <arXiv:1712.04058>. The 
    software can now produce mixed-effects LEGIT models through the lme4 package.
Provides a dataset containing several color naming conventions established by multiple sources, along with associated color metadata.
    The package also provides related helper functions for mapping among the different Lego color naming conventions and between Lego colors, hex colors, and 'R' color names, 
    making it easy to convert any color palette to one based on existing Lego colors while keeping as close to the original color palette as possible.
    The functions use nearest color matching based on Euclidean distance in RGB space. 
    Naming conventions for color mapping include those from 'BrickLink' (<https://www.bricklink.com>), 'The Lego Group' (<https://www.lego.com>), 'LDraw' (<https://www.ldraw.org/>), and 'Peeron' (<http://www.peeron.com/>).
Designed to query Longitudinal Employer-Household Dynamics (LEHD) 
    workplace/residential association and origin-destination flat files and 
    optionally aggregate Census block-level data to block group, tract, county, 
    or state. Data comes from the LODES FTP server <https://lehd.ces.census.gov/data/lodes/LODES8/>.
Miscellaneous R functions (for graphics, data import, 
    data transformation, and general utilities) and templates (for exploratory 
    analysis, Bayesian modeling, and crafting scientific manuscripts).
Implements the 'Python leidenalg' module to be called in R.
    Enables clustering using the leiden algorithm for partition a graph into communities.
    See the 'Python' repository for more details: <https://github.com/vtraag/leidenalg>
    Traag et al (2018) From Louvain to Leiden: guaranteeing well-connected communities. <arXiv:1810.08473>.
An R interface to the Leiden algorithm, an iterative community detection algorithm on networks. The algorithm is designed to converge to a partition in which all subsets of all communities are locally optimally assigned, yielding communities guaranteed to be connected. The implementation proves to be fast, scales well, and can be run on graphs of millions of nodes (as long as they can fit in memory). The original implementation was constructed as a python interface "leidenalg" found here: <https://github.com/vtraag/leidenalg>. The algorithm was originally described in Traag, V.A., Waltman, L. & van Eck, N.J. "From Louvain to Leiden: guaranteeing well-connected communities". Sci Rep 9, 5233 (2019) <doi:10.1038/s41598-019-41695-z>.
An R to C/C++ interface that runs the Leiden community
    detection algorithm to find a basic partition (). It runs the
    equivalent of the 'leidenalg' find_partition() function, which is
    given in the 'leidenalg' distribution file
    'leiden/src/functions.py'. This package includes the
    required source code files from the official 'leidenalg'
    distribution and functions from the R 'igraph'
    package.  The 'leidenalg' distribution is available from
    <https://github.com/vtraag/leidenalg/>
    and the R 'igraph' package is available from
    <https://igraph.org/r/>.
    The Leiden algorithm is described in the article by
    Traag et al. (2019) <doi:10.1038/s41598-019-41695-z>.
    Leidenbase includes code from the packages:
       igraph version 0.9.8 with license GPL (>= 2),
       leidenalg version 0.8.10 with license GPL 3.
Estimate the slope and intercept of a bivariate
	linear relationship by calculating a posterior density
	that is invariant to interchange and scaling of the
	coordinates.
Set up, run and explore the outputs of the Length-based Multi-species model (LeMans; Hall et al. 2006 <doi:10.1139/f06-039>), focused on the marine environment.
The reference implementation of model equations and default
    parameters for the toxicokinetic-toxicodynamic (TKTD) model of the Lemna
    (duckweed) aquatic plant. Lemna is a standard test macrophyte used in ecotox
    effect studies. The model was described and published by the SETAC Europe
    Interest Group Effect Modeling. It is a refined description of the Lemna
    TKTD model published by Schmitt et al. (2013)
    <doi:10.1016/j.ecolmodel.2013.01.017>.
Functions for working with legends and axis lines of 'ggplot2',
    facets that repeat axis lines on all panels, and some 'knitr' extensions.
Convenient aliases for common ways of misspelling the base R function length(). These include every permutation of the final three letters.
Provides tools for creating and using lenses to simplify data manipulation. Lenses are composable getter/setter pairs for working with data in a purely functional way. Inspired by the 'Haskell' library 'lens' (Kmett, 2012) <https://hackage.haskell.org/package/lens>. For a fairly comprehensive (and highly technical) history of lenses please see the 'lens' wiki <https://github.com/ekmett/lens/wiki/History-of-Lenses>.
An implementation of the Input-Output model developed by
    Wassily Leontief that represents the interdependencies between different 
    sectors of a national economy or different regional economies.
A collection of colour palettes inspired by some of our
    dearest butterfly species.  This package provides continuous and
    categorical palettes, including some colour blind friendly options.
Code generator for robust dependency-free 'Shiny' 
    applications in the form of packages. It includes numerous
    convenience functions to create modules, include utility 
    functions to create common 'Bootstrap' elements, setup a
    project from the ground-up, and much more.
A way to fit Parsimonious Finite Mixtures of Multivariate Elliptical Leptokurtic-Normals. Two methods of estimation are implemented.
Generates quotes from 'Lero Lero', a database for meaningless sentences filled with corporate buzzwords, intended to be used as corporate lorem ipsum (see <http://www.lerolero.com/> for more information). Unfortunately, quotes are currently portuguese-only.
"Learning with Subset Stacking" is a supervised learning algorithm that is based on training many local estimators on subsets of a given dataset, and then passing their predictions to a global estimator. You can find the details about LESS in our manuscript at <arXiv:2112.06251>.
Each function replaces multiple standard R functions. For example, two function calls, Read() and CountAll(), generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for summary statistics via pivot tables, a comprehensive regression analysis, ANOVA and t-test, visualizations including the Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, time series with aggregation and forecasting, color themes, and Trellis (facet) graphics. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, generation and rendering of regression instructions for interpretative output, and interactive visualizations.
Provides regularized structural equation modeling 
  (regularized SEM) with non-smooth penalty functions (e.g., lasso) building 
  on 'lavaan'. The package is heavily inspired by the 
  ['regsem'](<https://github.com/Rjacobucci/regsem>) and 
  ['lslx'](<https://github.com/psyphh/lslx>) packages.
Functions for vectorised conditional recoding of
    variables. case_when() enables you to vectorise multiple if and else
    statements (like 'CASE WHEN' in 'SQL'). if_else() is a stricter and
    more predictable version of ifelse() in 'base' that preserves
    attributes. These functions are forked from 'dplyr' with all package
    dependencies removed and behave identically to the originals.
Some simple objects and functions to do 
             statistics using linear models and a Bayesian framework.
Provides tools to retrieve and summarize taxonomic information and synonymy data for reptile species using data scraped from The Reptile Database website (<https://reptile-database.reptarium.cz/>). Outputs include clean and structured data frames useful for ecological, evolutionary, and conservation research.
Handling, processing, and analyzing geographic
    data on species' distributions and environmental variables. 
    Read Vilela & Villalobos (2015) <doi:10.1111/2041-210X.12401> for details.
Letter Values for the course Exploratory Data Analysis at Federal University of Bahia (Brazil). The approach implemented in the package is presented in the textbook of Tukey  (1977) <ISBN: 978-0201076165>.
Provides string similarity calculations inspired by the
    Python 'thefuzz' package. Compare strings by edit distance, similarity
    ratio, best matching substring, ordered token matching and set-based
    token matching. A range of edit distance measures are available thanks
    to the 'stringdist' package.
Implements code to identify lexical competitors in a given list
  of words. We include many of the standard competitor types used in spoken word
  recognition research, such as functions to find cohorts, neighbors, and
  rhymes, amongst many others. The package includes documentation for using a
  variety of lexicon files, including those with form codes made up of multiple
  letters (i.e., phoneme codes) and also basic orthographies. Importantly, the
  code makes use of multiple CPU cores and vectorization when possible, making
  it extremely fast and able to handle large lexicons. Additionally, the package
  contains documentation for users to easily write new functions, allowing
  researchers to examine other relationships within a lexicon. 
  Preprint: <https://osf.io/preprints/psyarxiv/8dyru/>. Open access: <doi:10.3758/s13428-021-01667-6>. 
  Citation: Li, Z., Crinnion, A.M. & Magnuson, J.S. (2021). 
  <doi:10.3758/s13428-021-01667-6>.
A collection of lexical hash tables, dictionaries, and word lists.
Provides easy access for sentiment lexicons for those who want to do text analysis in Portuguese texts.
    As of now, two Portuguese lexicons are available: 'SentiLex-PT02' and 'OpLexicon' (v2.1 and v3.0).
My PhD supervisor once told me that everyone doing newspaper
    analysis starts by writing code to read in files from the 'LexisNexis' newspaper
    archive (retrieved e.g., from <https://www.lexisnexis.com/> or any of the partner
    sites). However, while this is a nice exercise I do recommend, not everyone has
    the time. This package takes files downloaded from the newspaper archive of
    'LexisNexis', reads them into R and offers functions for further processing.
Plots empty Lexis grids, adds lifelines and highlights certain areas of the grid, like cohorts and age groups.
An R implementation of the LexRank algorithm described by G. Erkan and D. R. Radev (2004) <DOI:10.1613/jair.1523>.
Provides an extension to factors called 'lfactor' that are similar
    to factors but allows users to refer to 'lfactor' levels by either the level or
    the label.
Shiny apps for the quantitative analysis of images from lateral flow assays (LFAs). The images are segmented and background corrected and color intensities are extracted. The apps can be used to import and export intensity data and to calibrate LFAs by means of linear, loess, or gam models. The calibration models can further be saved and applied to intensity data from new images for determining concentrations.
Ratios of count data such as obtained from RNA-seq are modelled
    using Bayesian statistics to derive posteriors for effects sizes. This
    approach is described in Erhard & Zimmer (2015) <doi:10.1093/nar/gkv696> 
    and Erhard (2018) <doi:10.1093/bioinformatics/bty471>.
Functions for performing and visualizing Local Fisher Discriminant
    Analysis(LFDA), Kernel Fisher Discriminant Analysis(KLFDA), and Semi-supervised
    Local Fisher Discriminant Analysis(SELF).
Suite of R functions for the estimation of the local false discovery rate (LFDR) using Type II maximum likelihood estimation (MLE).
Estimation of the local false discovery rate using the method of moments.
New empirical Bayes methods aiming at analyzing the association of single nucleotide polymorphisms (SNPs) to some particular disease are implemented in this package. The package uses local false discovery rate (LFDR) estimates of SNPs within a sample population defined as a  "reference class" and discovers if SNPs are associated with the corresponding disease. Although SNPs are used throughout this document, other biological data such as protein data and other gene data can be used. Karimnezhad, Ali and Bickel, D. R. (2016) <http://hdl.handle.net/10393/34889>.
Transforms away factors with many levels prior to doing an OLS.
  Useful for estimating linear models with multiple group fixed effects, and for
  estimating linear models which uses factors with many levels as pure control variables. See Gaure (2013) <doi:10.1016/j.csda.2013.03.024>
  Includes support for instrumental variables, conditional F statistics for weak instruments,
  robust and multi-way clustered standard errors, as well as limited mobility bias correction (Gaure 2014 <doi:10.1002/sta4.68>).
  Since version 3.0, it provides dedicated functions to estimate Poisson models.
Various algorithms related to linguistic fuzzy logic: mining for linguistic fuzzy association
    rules, composition of fuzzy relations, performing perception-based logical deduction (PbLD), 
    and forecasting time-series using fuzzy rule-based ensemble (FRBE). The package also contains basic
    fuzzy-related algebraic functions capable of handling missing values in different styles (Bochvar,
    Sobocinski, Kleene etc.), computation of Sugeno integrals and fuzzy transform.
Enables the generation of Laplace factor models across diverse Laplace distributions and facilitates the application of Sparse Online Principal Component (SOPC), Incremental Principal Component (IPC), Perturbation Principal Component (PPC), Stochastic Approximation Principal Component (SAPC), Sparse Principal Component (SPC) and other PC methods and Farm Test methods to these models. Evaluates the efficacy of these methods within the context of Laplace factor models by scrutinizing parameter estimation accuracy, mean square error, and the degree of sparsity.
Fast and accurate inference of 
             gene-environment associations (GEA) in genome-wide studies 
             (Caye et al., 2019, <doi:10.1093/molbev/msz008>). 
             We developed a least-squares estimation approach for confounder and effect sizes 
             estimation that provides a unique framework for several categories of genomic data, 
             not restricted to genotypes. 
             The speed of the new algorithm is several times faster than the existing GEA approaches, 
             then our previous version of the 'LFMM' program present in the 'LEA' package 
             (Frichot and Francois, 2015, <doi:10.1111/2041-210X.12382>).
Label-free bottom-up proteomics expression data is often affected by data heterogeneity and missing values. Normalization and missing value imputation are commonly used techniques to address these issues and make the dataset suitable for further downstream analysis. This package provides an optimal combination of normalization and imputation methods for the dataset. The package utilizes three normalization methods and three imputation methods.The statistical evaluation measures named pooled co-efficient of variance, pooled estimate of variance and pooled median absolute deviation are used for selecting the best combination of normalization and imputation method for the given dataset. The user can also visualize the results by using various plots available in this package. The user can also perform the differential expression  analysis between two sample groups with the function included in this package. The chosen three normalization methods, three imputation methods and three evaluation measures were chosen for this study based on the research papers published by	Välikangas et al. (2016) <doi:10.1093/bib/bbw095>, Jin et al. (2021) <doi:10.1038/s41598-021-81279-4> and Srivastava et al. (2023) <doi:10.2174/1574893618666230223150253>.This work has published by Sakthivel et al. (2025) <doi:10.1021/acs.jproteome.4c00552>.
The "Manual on Low-flow Estimation and Prediction" (Gustard & Demuth (2009, ISBN:978-92-63-11029-9)), published by the World Meteorological Organisation, gives a comprehensive summary on how to analyse stream flow data focusing on low-flows. This packages provides functions to compute the described statistics and produces plots similar to the ones in the manual.
An implementation of locally Gaussian distributions. It provides methods for
    implementing locally Gaussian multivariate density estimation, conditional density 
    estimation, various independence tests for iid and time series data, a test for conditional 
    independence and a test for financial contagion.
Simulation and estimation of univariate and multivariate log-GARCH models. The main functions of the package are: lgarchSim(), mlgarchSim(), lgarch() and mlgarch(). The first two functions simulate from a univariate and a multivariate log-GARCH model, respectively, whereas the latter two estimate a univariate and multivariate log-GARCH model, respectively.
Spatial and spatio-temporal modelling of point patterns using the
    log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal,
    multivariate and aggregated point processes using Markov chain Monte Carlo. See Benjamin M. Taylor, Tilman M. Davies, Barry S. Rowlingson, Peter J. Diggle (2015) <doi:10.18637/jss.v063.i07>.
Implements Cumulative Sum (CUSUM) control charts specifically
 designed for monitoring processes following a Gamma distribution. Provides
 functions to estimate distribution parameters, simulate control limits, and
 apply cautious learning schemes for adaptive thresholding. It supports
 upward and downward monitoring with guaranteed performance evaluated via
 Monte Carlo simulations. It is useful for quality control applications in
 industries where data follows a Gamma distribution. Methods are based on
 Madrid-Alvarez et al. (2024) <doi:10.1002/qre.3464> and Madrid-Alvarez et
 al. (2024) <doi:10.1080/08982112.2024.2440368>.
The goal of this package is to cover the most common steps in Loss Given Default (LGD) rating model development.
             The main procedures available are those that refer to bivariate and multivariate analysis. In particular two statistical methods for 
             multivariate analysis are currently implemented – OLS regression and fractional logistic regression.
             Both methods are also available within different blockwise model designs and both have customized stepwise algorithms. 
             Descriptions of these customized designs are available in Siddiqi (2016) <doi:10.1002/9781119282396.ch10> and 
             Anderson, R.A. (2021) <doi:10.1093/oso/9780192844194.001.0001>. 
             Although they are explained for PD model, the same designs are applicable for LGD model with different underlying regression methods 
             (OLS and fractional logistic regression). To cover other important steps for LGD model development, it is recommended to use 
             'LGDtoolkit' package along with 'PDtoolkit', and 'monobin' (or 'monobinShiny') packages.
             Additionally, 'LGDtoolkit' provides set of procedures handy for initial and periodical model validation.
Functions for genome-wide association studies (GWAS)/gene-environment-wide interaction studies (GEWIS) with longitudinal outcomes and exposures. He et al. (2017) "Set-Based Tests for Gene-Environment Interaction in Longitudinal Studies" and He et al. (2017) "Rare-variant association tests in longitudinal studies, with an application to the Multi-Ethnic Study of Atherosclerosis (MESA)".
For high-dimensional correlated observations, this package carries out the L_1 penalized maximum likelihood 
            estimation of the precision matrix (network) and the correlation parameters. The correlated data can be 
            longitudinal data (may be irregularly spaced) with dampening correlation or clustered data with uniform correlation.  
            For the details of the algorithms, please see the paper Jie Zhou et al. Identifying Microbial Interaction Networks Based on Irregularly Spaced 
            Longitudinal 16S rRNA sequence data <doi:10.1101/2021.11.26.470159>.
Interpretable nonparametric modeling of longitudinal data
    using additive Gaussian process regression. Contains functionality
    for inferring covariate effects and assessing covariate relevances.
    Models are specified using a convenient formula syntax, and can include
    shared, group-specific, non-stationary, heterogeneous and temporally
    uncertain effects. Bayesian inference for model parameters is performed
    using 'Stan'. The modeling approach and methods are described in detail in
    Timonen et al. (2021) <doi:10.1093/bioinformatics/btab021>.
A flexible, feature-rich yet light-weight logging
    framework based on 'R6' classes. It supports hierarchical loggers,
    custom log levels, arbitrary data fields in log events, logging to
    plaintext, 'JSON', (rotating) files, memory buffers. For extra
    appenders that support logging to databases, email and push
    notifications see the the package lgr.app.
A largish collection of example datasets, including several classics. Many of
    these datasets are well suited for regression, classification, and visualization.
Additional appenders for the logging package 'lgr' that
    support logging to databases, email and push notifications.
Functions for the longitudinal genetic random field method (He et al., 2015, <doi:10.1111/biom.12310>) to test the association between a longitudinally measured quantitative outcome and a set of genetic variants in a gene/region.
Implements Lagrangian multiplier smoothing splines for flexible
    nonparametric regression and function estimation. Provides tools for fitting,
    prediction, and inference using a constrained optimization approach to 
    enforce smoothness.
    Supports generalized linear models, Weibull accelerated failure time (AFT) models, 
    quadratic programming problems, and customizable arbitrary correlation structures. 
    Options for fitting in parallel are provided. The method builds upon the framework described 
    by Ezhov et al. (2018) <doi:10.1515/jag-2017-0029> using Lagrangian multipliers 
    to fit cubic splines. For more information on correlation structure estimation, 
    see Searle et al. (2009) <ISBN:978-0470009598>. For quadratic programming and 
    constrained optimization in general, see Nocedal & Wright (2006) <doi:10.1007/978-0-387-40065-5>. 
    For a comprehensive background on smoothing splines, see Wahba (1990) 
    <doi:10.1137/1.9781611970128> and Wood (2006) <ISBN:978-1584884743> 
    "Generalized Additive Models: An Introduction with R".
A very simple implementation of a class for 
	     longitudinal data.
Contains different algorithms and construction methods for optimal Latin hypercube designs (LHDs) with flexible sizes. Our package is comprehensive since it is capable of generating maximin distance LHDs, maximum projection LHDs, and orthogonal and nearly orthogonal LHDs. Detailed comparisons and summary of all the algorithms and construction methods in this package can be found at Hongzhi Wang, Qian Xiao and Abhyuday Mandal (2021) <doi:10.48550/arXiv.2010.09154>. This package is particularly useful in the area of Design and Analysis of Experiments (DAE). More specifically, design of computer experiments.
Fits sex-specific life-history models for fish and other taxa where some of the individuals have unknown sex.
Provides a number of methods for creating and augmenting Latin Hypercube Samples and Orthogonal Array Latin Hypercube Samples.
Provides functions for validating and normalizing bibliographic
   codes such as ISBN, ISSN, and LCCN. Also includes functions to communicate
   with the WorldCat API, translate Call numbers (Library of Congress and
   Dewey Decimal) to their subject classifications or subclassifications,
   and provides various loadable data files such call number / subject
   crosswalks and code tables.
Basic infrastructure for linear test statistics and permutation
  inference in the framework of Strasser and Weber (1999) <https://epub.wu.ac.at/102/>.
  This package must not be used by end-users. CRAN package 'coin' implements all
  user interfaces and is ready to be used by anyone.
Whole-buffer DEFLATE-based compression and 
    decompression of raw vectors using the 'libdeflate' library 
    (see <https://github.com/ebiggers/libdeflate>). Provides the user with additional 
    control over the speed and the quality of DEFLATE compression 
    compared to the fixed level of compression offered in R's 
    'memCompress()' function. Also provides the 'libdeflate' static library and 
    'C' headers along with a 'CMake' target and 'package‑config' file that 
    ease linking of 'libdeflate' in packages that compile and statically link 
    bundled libraries using 'CMake'.
Provides the Open Source Geometry Engine ('GEOS') as a
  C API that can be used to write high-performance C and C++
  geometry operations using R as an interface. Headers are provided
  to make linking to and using these functions from C++ code as
  easy and as safe as possible. This package contains an internal
  copy of the 'GEOS' library to guarantee the best possible
  consistency on multiple platforms.
Provides a static library for 'Imath' 
        (see <https://github.com/AcademySoftwareFoundation/Imath>),
        a library for functions and data types common in computer graphics
        applications, including a 16-bit floating-point type.
A wrapper around the LIBLINEAR C/C++ library for machine
        learning (available at
        <https://www.csie.ntu.edu.tw/~cjlin/liblinear/>). LIBLINEAR is
        a simple library for solving large-scale regularized linear
        classification and regression. It currently supports
        L2-regularized classification (such as logistic regression,
        L2-loss linear SVM and L1-loss linear SVM) as well as
        L1-regularized classification (such as L2-loss linear SVM and
        logistic regression) and L2-regularized support vector
        regression (with L1- or L2-loss). The main features of
        LiblineaR include multi-class classification (one-vs-the rest,
        and Crammer & Singer method), cross validation for model
        selection, probability estimates (logistic regression only) or
        weights for unbalanced data. The estimation of the models is
        particularly fast as compared to other libraries.
Contains a set of functions to create data libraries,
    generate data dictionaries, and simulate a data step.
    The libname() function will load a directory of data into 
    a library in one line of code.  The dictionary() function
    will generate data dictionaries for individual
    data frames or an entire library.  And the datestep() function
    will perform row-by-row data processing.
Efficient procedures for fitting the regularization path
    for linear, binomial, multinomial, Ising and Potts models with lasso,
    group lasso or column lasso(only for multinomial) penalty.
    The package uses Linearized Bregman Algorithm to solve the
    regularization path through iterations. Bregman Inverse Scale Space Differential
    Inclusion solver is also provided for linear model with lasso penalty.
Automatically install, update, and load 'CRAN', 'GitHub', and 'Bioconductor' 
    packages in a single function call. By accepting bare unquoted names for packages, 
    it's easy to add or remove packages from the list.
Generate a local library copy with relevant packages. 
    All packages currently found within the search path - except base packages - 
    will be copied to the directory provided and can be used later on with the 
    .libPaths() function.
Tools for fast and accurate evaluation of skew stable distributions 
  (CDF, PDF and quantile functions), random number generation, and parameter 
  estimation.  This is 'libstableR' as per Royuela del Val, Simmross-Wattenberg, 
  and Alberola López (2017) <doi:10.18637/jss.v078.i01> under a new maintainer.
The LIC criterion is to determine the most informative subsets so that the subset can retain most of the information contained in the complete data. The philosophy of the package is described in Guo G. (2022) <doi:10.1080/02664763.2022.2053949>.
Reads raw files from Li-COR gas analyzers and produces a dataframe that can directly be used with 'fluxible' <https://cran.r-project.org/package=fluxible>.
Provides functions for forest objects detection, structure metrics 
    computation, model calibration and mapping with airborne laser scanning:
    co-registration of field plots (Monnet and Mermin (2014) 
    <doi:10.3390/f5092307>); tree detection (method 1 in Eysn et al. (2015) 
    <doi:10.3390/f6051721>) and segmentation; forest parameters estimation with 
    the area-based approach: model calibration with ground reference, and maps 
    export (Aussenac et al. (2023) <doi:10.12688/openreseurope.15373.2>); 
    extraction of both physical (gaps, edges, trees) and statistical 
    features useful for e.g. habitat suitability modeling (Glad et al. (2020) 
    <doi:10.1002/rse2.117>) and forest maturity mapping (Fuhr et al. (2022) 
    <doi:10.1002/rse2.274>).
Airborne LiDAR (Light Detection and Ranging) interface for data
    manipulation and visualization. Read/write 'las' and 'laz' files, computation
    of metrics in area based approach, point filtering, artificial point reduction,
    classification from geographic data, normalization, individual tree segmentation
    and other manipulations.
Real-time quantitative polymerase chain reaction (qPCR) data
    sets by Lievens et al. (2012) <doi:10.1093/nar/gkr775>. Provides one
    single tabular tidy data set in long format, encompassing three
    dilution series, targeted against the soybean Lectin endogene. Each dilution
    series was assayed in one of the following PCR-efficiency-modifying
    conditions: no PCR inhibition, inhibition by isopropanol and inhibition by
    tannic acid. The inhibitors were co-diluted along with the dilution series.
    The co-dilution series consists of a five-point, five-fold serial dilution.
    For each concentration there are 18 replicates. Each amplification
    curve is 60 cycles long. Original raw data file is available at the 
    Supplementary Data section at Nucleic Acids Research Online <doi:10.1093/nar/gkr775>.
Classes and methods that allow the user to manage life table,
    actuarial tables (also multiple decrements tables). Moreover, functions to easily
    perform demographic, financial and actuarial mathematics on life contingencies
    insurances calculations are contained therein. See Spedicato (2013)	<doi:10.18637/jss.v055.i10>.
Provides in built datasets and three functions.
  These functions are mobility_index, nonStanTest and linkedLives.  The mobility_index
  function facilitates the calculation of lifecourse fluidity, whilst the nonStanTest and the 
  linkedLives functions allow the user to determine the probability that the observed sequence data 
  was due to chance.  The linkedLives function acknowledges the fact that some individuals may
  have identical sequences.
  The datasets available provide sequence data on marital status(maritalData) 
  and mobility (mydata) for a selected group of individuals from the British Household Panel Study
  (BHPS).  In addition, personal and house ID's for 100 individuals are provided in a 
  third dataset (myHouseID) from the BHPS.
Manage the life cycle of your exported functions with shared
    conventions, documentation badges, and user-friendly deprecation
    warnings.
Likelihood-based estimation of individual growth and sexual maturity models for organisms, usually fish and invertebrates. It includes methods for data organization, plotting standard exploratory and analytical plots, predictions.
Use of this package is deprecated.  It has been renamed to 'LifeInsureR'.
R6 classes to model traditional life insurance
    contracts like annuities, whole life insurances or endowments. Such life
    insurance contracts provide a guaranteed interest and are not directly linked
    to the performance of a particular investment vehicle, but they typically
    provide (discretionary) profit participation. This package provides a framework
    to model such contracts in a very generic (cash-flow-based) way and includes
    modelling profit participation schemes, dynamic increases or more general
    contract layers, as well as contract changes (like sum increases or premium
    waivers). All relevant quantities like premium decomposition, reserves and 
    benefits over the whole contract period are calculated and potentially 
    exported to 'Excel'. Mortality rates are given using the 'MortalityTables' package.
Allow to visualise data on the NCBI phylogenetic tree as presented in Lifemap <https://lifemap.cnrs.fr/>. It takes as input a dataframe with at least a "taxid" column containing NCBI format TaxIds and allows to draw multiple layers with different visualisation tools.
Calculates insurance reserves and equivalence premiums using advanced numerical methods, including the Runge-Kutta algorithm and product integrals for transition probabilities. This package is useful for actuarial analyses and life insurance modeling, facilitating accurate financial projections.
A suite of tools to use the 'eBird' database 
    (<https://ebird.org/home/>) and APIs to compare users' species lists to 
    recent observations and create a report of the top sites to visit to see 
    new species.
Life and Fertility Tables are appropriate to study the dynamics of 
    arthropods populations. This package provides utilities for constructing
    Life Tables and Fertility Tables, related demographic parameters, and some
    simple graphs of interest. It also offers functions to transform the
    obtained data into a known format for better manipulation. This document is
    based on the article by Maia, Luiz, and Campanhola "Statistical Inference on
    Associated Fertility Life Table Parameters Using Jackknife Technique
    Computational Aspects" (April 2000, Journal of Economic Entomology, Volume
    93, Issue 2) <doi:10.1603/0022-0493-93.2.511>.
Implementations of Hurst exponent estimators based on the relationship between wavelet lifting scales and wavelet energy of Knight et al (2017) <doi:10.1007/s11222-016-9698-2>.
Persistent reproducible reporting by containerization of R Markdown documents.
A bootstrap proportion test for Brand Lift Testing to quantify the effectiveness of online advertising. Methods of the bootstrap proportion test are presented in
    Liu, Yu, Mao, Wu, Dyer (2023) <doi:10.1145/3583780.3615021>.
Allows you to read and change the state of 'LIFX' smart light bulbs via the 'LIFX' developer api <https://api.developer.lifx.com/>.
    Covers most 'LIFX' api endpoints, including changing light color and brightness, selecting lights by id, group or location as well as activating effects.
Fast calculation of Area Under Curve (AUC) metric of a
             Receiver Operating Characteristic (ROC) curve, using the algorithm
             of Fawcett (2006) <doi:10.1016/j.patrec.2005.10.010>. Therefore it
             is appropriate for large-scale AUC metric calculations.
Tree based algorithms can be improved by introducing boosting frameworks.
    'LightGBM' is one such framework, based on Ke, Guolin et al. (2017) <https://papers.nips.cc/paper/6907-lightgbm-a-highly-efficient-gradient-boosting-decision>.
    This package offers an R interface to work with it.
    It is designed to be distributed and efficient with the following advantages:
        1. Faster training speed and higher efficiency.
        2. Lower memory usage.
        3. Better accuracy.
        4. Parallel learning supported.
        5. Capable of handling large-scale data.
    In recognition of these advantages, 'LightGBM' has been widely-used in many winning solutions of machine learning competitions.
    Comparison experiments on public datasets suggest that 'LightGBM' can outperform existing boosting frameworks on both efficiency and accuracy, with significantly lower memory consumption. In addition, parallel experiments suggest that in certain circumstances, 'LightGBM' can achieve a linear speed-up in training time by using multiple machines.
Import, processing, validation, and visualization of personal light exposure measurement data from wearable devices. The package implements features such as the import of data and metadata files, conversion of common file formats, validation of light logging data, verification of crucial metadata, calculation of common parameters, and semi-automated analysis and visualization.
Split your 'rmarkdown' or 'quarto' files by sections into a
    tibble: titles, text, chunks. Rebuild the file from the tibble.
Parse various reflectance/transmittance/absorbance spectra file
    formats to extract spectral data and metadata, as described in Gruson, White
    & Maia (2019) <doi:10.21105/joss.01857>. Among other formats, it can import
    files from 'Avantes' <https://www.avantes.com/>, 'CRAIC'
    <https://www.microspectra.com/>, and 'OceanOptics'/'OceanInsight'
    <https://www.oceanoptics.com/> brands.
Lights Out is a puzzle game consisting of a grid of lights
    that are either on or off. Pressing any light will toggle it and its
    adjacent lights. The goal of the game is to switch all the lights off. This
    package provides an interface to play the game on different board sizes,
    both through the command line or with a visual application. Puzzles can
    also be solved using the automatic solver included. View a demo
    online at <https://daattali.com/shiny/lightsout/>.
Tools for maximum likelihood estimation of parameters 
  of scientific models. Based on Goffe et al (1994) <doi:10.1016/0304-4076(94)90038-8>.
Functions for computing the r and r* statistics for inference on an arbitrary scalar function of model parameters, plus some code for the (modified) profile likelihood.
Provides likelihood functions as defined by Fisher (1922)
    <doi:10.1098/rsta.1922.0009> and a function that creates likelihood 
    functions from density functions. The functions are meant to aid in 
    education of likelihood based methods.
A collection of functions that calculate the log likelihood 
    (support) for a range of statistical tests. Where possible the likelihood 
    function and likelihood interval for the observed data are displayed. The 
    evidential approach used here is based on the book "Likelihood" by A.W.F. 
    Edwards (1992, ISBN-13 : 978-0801844430), "Statistical Evidence" by R. 
    Royall (1997, ISBN-13 : 978-0412044113), S.N. Goodman & R. Royall 
    (2011) <doi:10.2105/AJPH.78.12.1568>, "Understanding 
    Psychology as a Science" by Z. Dienes (2008, ISBN-13 : 978-0230542310), 
    S. Glover & P. Dixon <doi:10.3758/BF03196706> 
    and others. This package accompanies "Evidence-Based Statistics" by 
    P. Cahusac (2020, ISBN-13 : 978-1119549802) 
    <doi:10.1002/9781119549833>.
Managing and exploring parameter estimation results derived from Maximum Likelihood Estimation (MLE) using the 'likelihood' package. It provides functions for organizing, visualizing, and summarizing MLE outcomes, streamlining statistical analysis workflows. By improving interpretation and facilitating model evaluation, it helps users gain deeper insights into parameter estimation and model fitting, making MLE result exploration more efficient and accessible. See Goffe et al. (1994) <doi:10.1016/0304-4076(94)90038-8> for details on MLE, and Canham and Uriarte (2006) <doi:10.1890/04-0657> for application of MLE using 'likelihood'.
An approach to analyzing Likert response items, with an emphasis on visualizations. 
    The stacked bar plot is the preferred method for presenting Likert results. Tabular results
    are also implemented along with density plots to assist researchers in determining whether 
    Likert responses can be used quantitatively instead of qualitatively. See the likert(), 
    summary.likert(), and plot.likert() functions to get started.
Provides functions for summarizing, visualizing, and analyzing 
    Likert-scale survey data. Includes support for computing descriptive statistics, 
    Relative Importance Index (RII), reliability analysis (Cronbach's Alpha), 
    and response distribution plots.
Generate and correlate synthetic Likert and rating-scale data
    with predefined means, standard deviations, Cronbach's Alpha, Factor
    Loading table, and other summary statistics.  Worked examples and
    documentation are available in the package vignettes, accessible via
    browseVignettes("LikertMakeR").
A comprehensive analysis tool for metabolomics data.  It consists a variety of functional modules, including several new modules: a pre-processing module for normalization and imputation, an exploratory data analysis module for dimension reduction and source of variation analysis, a classification module with the new deep-learning method and other machine-learning methods, a prognosis module with cox-PH and neural-network based Cox-nnet methods, and pathway analysis module to visualize the pathway and interpret metabolite-pathway relationships. References: H. Paul Benton <http://www.metabolomics-forum.com/index.php?topic=281.0> Jeff Xia <https://github.com/cangfengzhe/Metabo/blob/master/MetaboAnalyst/website/name_match.R> Travers Ching, Xun Zhu, Lana X. Garmire (2018) <doi:10.1371/journal.pcbi.1006076>.
Estimation of life expectancy and
    Life Years Lost (LYL, or lillies for short) for a given population, for 
    example those with a given disease or condition. In addition, the package 
    can be used to compare estimates from different populations, or to estimate 
    confidence intervals. Technical details of the method are available in
    Plana-Ripoll et al. (2020) <doi:10.1371/journal.pone.0228073> and Andersen
    (2017) <doi:10.1002/sim.7357>.
This is for code management functions, NLP tools, a Monty Hall simulator, and for implementing my own variable reduction technique called Feed Reduction. The Feed Reduction technique is not yet published, but is merely a tool for implementing a series of binary neural networks meant for reducing data into N dimensions, where N is the number of possible values of the response variable.
When building complex models, it is often difficult to explain why
    the model should be trusted. While global measures such as accuracy are
    useful, they cannot be used for explaining why a model made a specific
    prediction. 'lime' (a port of the 'lime' 'Python' package) is a method for
    explaining the outcome of black box models by fitting a local model around
    the point in question an perturbations of this point. The approach is
    described in more detail in the article by Ribeiro et al. (2016) 
    <arXiv:1602.04938>.
Provides an interface to the financial data platform <https://datahub.limex.com/>., enabling users to retrieve real-time and historical financial data. Functions within the package allow access to instruments, candlestick charts, fundamentals, news, events, models, and trading signals. Authentication is managed through user-specific API tokens, which are securely handled via environment variables.
Palettes generated from limnology based field and laboratory photos. Palettes can be used to generate color values to be used in any functions that calls for a color (i.e. ggplot(), plot(), flextable(), etc.).
'LimeSurvey' is Free/Libre Open Source Software for
  the development and administrations of online studies, using
  sophisticated tailoring capabilities to support multiple study
  designs (see <https://www.limesurvey.org>). This package supports
  programmatic creation of surveys that can then be imported into
  'LimeSurvey', as well as user friendly import of responses from
  'LimeSurvey' studies.
A flexible approach, inspired by cosinor regression, for
  differential analysis of rhythmic transcriptome data. See Singer and Hughey
  (2018) <doi:10.1177/0748730418813785>.
Fit linear models based on periodic splines, moderate model
  coefficients using multivariate adaptive shrinkage, then compute properties of
  the moderated curves.
Functions that (1) find the minimum/maximum of a linear or quadratic function:
  min or max (f(x)), where f(x) = ||Ax-b||^2 or f(x) = sum(a_i*x_i)
  subject to equality constraints Ex=f and/or inequality constraints Gx>=h,
  (2) sample an underdetermined- or overdetermined system Ex=f subject to Gx>=h, and if applicable Ax~=b,      
  (3) solve a linear system Ax=B for the unknown x. It includes banded and tridiagonal linear systems.
Evaluates whether the relationship between two vectors is linear or nonlinear. Performs a test to determine how well a linear model fits the data compared to higher order polynomial models. Jhang et al. (2004) <doi:10.1043/1543-2165(2004)128%3C44:EOLITC%3E2.0.CO;2>.
Short for 'linear binning', the linbin package provides functions
    for manipulating, binning, and plotting linearly referenced data. Although
    developed for data collected on river networks, it can be used with any interval
    or point data referenced to a 1-dimensional coordinate system. Flexible bin
    generation and batch processing makes it easy to compute and visualize variables
    at multiple scales, useful for identifying patterns within and between variables
    and investigating the influence of scale of observation on data interpretation.
Estimate and confidence/credible intervals for an unknown
    regressor x0 given an observed y0.
Perform two linear combination methods for biomarkers: (1) Empirical performance optimization for specificity (or sensitivity) at a controlled sensitivity (or specificity) level of Huang and Sanda (2022) <doi:10.1214/22-aos2210>, and (2) weighted maximum score estimator with empirical minimization of averaged false positive rate and false negative rate. Both adopt the algorithms of Huang and Sanda (2022) <doi:10.1214/22-aos2210>. 'MOSEK' solver is used and needs to be installed; an academic license for 'MOSEK' is free.
Sample truncated multivariate Normal distribution following Gessner, A., Kanjilal, O., & Hennig, P. (2019). Integrals over Gaussians under Linear Domain Constraints. 108. <arxiv:1910.09328>.
L-systems or Lindenmayer systems are parallel rewriting systems which can
    be used to simulate biological forms and certain kinds of fractals.
    Briefly, in an L-system a series of symbols in a string are replaced
    iteratively according to rules to give a more complex string. Eventually,
    the symbols are translated into turtle graphics for plotting. Wikipedia has
    a very good introduction: en.wikipedia.org/wiki/L-system This package
    provides basic functions for exploring L-systems.
Provides a set of streamlined functions that allow
    easy generation of linear regression diagnostic plots necessarily 
    for checking linear model assumptions.
    This package is meant for easy scheming of linear 
    regression diagnostics, while preserving merits of 
    "The Grammar of Graphics" as implemented in 'ggplot2'.
    See the 'ggplot2' website for more information regarding the
    specific capability of graphics.
Computes the probability density function, the cumulative distribution function, the hazard rate function, the quantile function and random generation for Lindley Power Series distributions, see Nadarajah and Si (2018) <doi:10.1007/s13171-018-0150-x>.
Functions to access and test results from a linear model.
Consider linear regression model Y = Xb + error where the distribution function of errors is unknown, but errors are independent and symmetrically distributed. The package contains a function named LRMDE which takes Y and X as input and returns minimum distance estimator of parameter b in the model.
Tests whether the linear hypothesis of a model
    is correct specified using Dominguez-Lobato test. Also Ramsey's RESET (Regression Equation 
    Specification Error Test) test is implemented and Wald tests can be carried out. 
    Although RESET test is widely used to 
    test the linear hypothesis of a model, Dominguez and Lobato (2019) proposed a novel 
    approach that generalizes well known specification tests such as Ramsey's. This test 
    relies on wild-bootstrap; this package implements this approach to be 
    usable with any function that fits linear models and is compatible with 
    the update() function such as 'stats'::lm(), 'lfe'::felm() and 'forecast'::Arima(), 
    for ARMA (autoregressive–moving-average) models. 
    Also the package can handle custom statistics such as Cramer von Mises and Kolmogorov 
    Smirnov, described by the authors, and custom distributions such as Mammen (discrete 
    and continuous) and Rademacher.
    Manuel A. Dominguez & Ignacio N. Lobato (2019) <doi:10.1080/07474938.2019.1687116>.
Provides tools to help storing and handling case line list data. The 'linelist' class adds a tagging system to classical 'data.frame' objects to identify key epidemiological data such as dates of symptom onset, epidemiological case definition, age, gender or disease outcome. Once tagged, these variables can be seamlessly used in downstream analyses, making data pipelines more robust and reliable.
Provides tools for performing Bayesian inference on epidemiological 
  data to estimate the time-varying reproductive number and other related metrics.
  These methods were published in Li and White (2021) <doi:10.1371/journal.pcbi.1009210>.
  This package supports analyses based on aggregated case count data and individual line list 
  data, facilitating enhanced surveillance and intervention planning for infectious 
  diseases like COVID-19.
Create maps made of lines. The package contains one function:
    linemap(). linemap() displays a map made of lines using a
    raster or gridded data.
Fits a linear excess relative risk model by maximum likelihood, possibly including several variables and allowing for lagged exposures.
Tools for detecting and correcting sample mix-ups between two sets
    of measurements, such as between gene expression data on two tissues.
    Broman et al. (2015) <doi:10.1534/g3.115.019778>.
Tools for detecting and correcting sample mix-ups between two sets
    of measurements, such as between gene expression data on two
    tissues. This is a revised version of the 'lineup' package, to be
    more general and not tied to the 'qtl' package.
'LineUp' is an interactive technique designed to create, visualize and explore rankings of items based on a set of heterogeneous attributes.
  This is a 'htmlwidget' wrapper around the JavaScript library 'LineUp.js'.
  It is designed to be used in 'R Shiny' apps and 'R Markddown' files.
  Due to an outdated 'webkit' version of 'RStudio' it won't work in the integrated viewer.
Create interactive time series visualizations.
    'linevis' includes an extensive API to manipulate time series after creation,
    and supports getting data out of the visualization. Based on the
    'timevis' package and the 'vis.js' Timeline 'JavaScript' library <https://visjs.github.io/vis-timeline/docs/graph2d/>.
A fast generalized edit distance and string alignment computation mainly for linguistic aims. As a generalization to the classic edit distance algorithms, the package allows users to define custom cost for every symbol's insertion, deletion, and substitution. The package also allows character combinations in any length to be seen as a single symbol which is very useful for International Phonetic Alphabet (IPA) transcriptions with diacritics. In addition to edit distance result, users can get detailed alignment information such as all possible alignment scenarios between two strings which is useful for testing, illustration or any further usage. Either the distance matrix or its long table form can be obtained and tools to do such conversions are provided. All functions in the package are implemented in 'C++' and the distance matrix computation is parallelized leveraging the 'RcppThread' package.
Helps to render interlinear glossed linguistic examples in html 
    'rmarkdown' documents and then semi-automatically compiles the list of
    glosses at the end of the document. It also provides a database of linguistic
    glosses.
Measure similarity between texts. Offers a variety of processing
  tools and similarity metrics to facilitate flexible representation of texts and matching.
  Implements forms of Language Style Matching (Ireland & Pennebaker, 2010) <doi:10.1037/a0020386>
  and Latent Semantic Analysis (Landauer & Dumais, 1997) <doi:10.1037/0033-295X.104.2.211>.
Provides R with the Glottolog database <https://glottolog.org/> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <https://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://docs.ropensci.org/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and some others and to create your own database website.
Provides 'Shiny gadgets' to search, type, and insert IPA symbols
    into documents or scripts, requiring only knowledge about phonetics or 
    'X-SAMPA'. Also provides functions to facilitate the rendering of IPA
    symbols in 'LaTeX' and PDF format, making IPA symbols properly rendered
    in all output formats. A minimal R Markdown template for authoring 
    Linguistics related documents is also bundled with the package. Some
    helper functions to facilitate authoring with R Markdown is also provided.
Automatic detection of hyperlinks for packages and calls in the text
    of 'rmarkdown' or 'quarto' documents.
Functions and tools for using open GIS and remote sensing command-line interfaces in a reproducible environment.
It allows to cluster communication networks using the Stochastic
  Topic Block Model <doi:10.1007/s11222-016-9713-7> by posting jobs through 
  the API of the linkage.fr server, which implements the clustering method.
  The package also allows to visualize the clustering results returned by the server.
Produces high resolution, publication ready linkage maps
    and quantitative trait loci maps. Input can be output from 'R/qtl',
    simple text or comma delimited files. Output is currently
    a portable document file.
Prototypes for construction of a Gaussian Stochastic Process emulator (GASP) of a computer model. This is done within the objective Bayesian implementation of the GASP. The package allows for construction of a linked GASP of the composite computer model. Computational implementation follows the mathematical exposition given in publication: Ksenia N. Kyzyurova, James O. Berger, Robert L. Wolpert. Coupling computer models through linking their statistical emulators. SIAM/ASA Journal on Uncertainty Quantification, 6(3): 1151-1171, (2018).<DOI:10.1137/17M1157702>.
Collect  marketing data from 'LinkedIn' Ads using the 'Windsor.ai' API <https://windsor.ai/api-fields/>.
A class that links matrix-like objects (nodes) by rows or by
    columns while behaving similarly to a base R matrix. Very large matrices
    are supported if the nodes are file-backed matrices.
Implementations of most of the existing proximity-based methods of 
  link prediction in graphs. Among the 20 implemented methods are e.g.:
  Adamic L. and Adar E. (2003) <doi:10.1016/S0378-8733(03)00009-1>,
  Leicht E., Holme P., Newman M. (2006) <doi:10.1103/PhysRevE.73.026120>,
  Zhou T. and Zhang Y (2009) <doi:10.1140/epjb/e2009-00335-8>, and
  Fouss F., Pirotte A., Renders J., and Saerens M. (2007) <doi:10.1109/TKDE.2007.46>.
Compute and visualize using the 'visNetwork' package all the bivariate correlations of a dataframe.
  Several and different types of correlation coefficients (Pearson's r, Spearman's rho, Kendall's tau,
  distance correlation, maximal information coefficient and 
  equal-freq discretization-based maximal normalized mutual information) are used according to 
  the variable couple type (quantitative vs categorical, quantitative vs quantitative, categorical vs categorical).
A 'LaTeX' Letter class for 'rmarkdown', using the
 'pandoc-letter' template adapted for use with 'markdown'.
Conveniently generate 'CSS' using R code.
Generate concentration-time profiles from linear pharmacokinetic
  (PK) systems, possibly with first-order absorption or zero-order infusion,
  possibly with one or more peripheral compartments, and possibly under
  steady-state conditions. Single or multiple doses may be specified. Secondary
  (derived) PK parameters (e.g. Cmax, Ctrough, AUC, Tmax, half-life, etc.) are
  computed.
Can be used to solve Linear Programming / Linear
   Optimization problems by using the simplex algorithm.
Interactive visualization of effects, response functions 
    and marginal effects for different kinds of regression models. In this version 
    linear regression models, generalized linear models, generalized additive
    models and linear mixed-effects models are supported.  
    Major features are the interactive approach and the handling of the effects of categorical covariates: 
    if two or more factors are used as covariates every combination of the levels of each 
    factor is treated separately. The automatic calculation of 
    marginal effects and a number of possibilities to customize the graphical output 
    are useful features as well.
Estimate the mean of a Gaussian vector, by choosing among a large collection of estimators,
  following the method developed by Y. Baraud, C. Giraud and S. Huet (2014) <doi:10.1214/13-AIHP539>.
  In particular it solves the problem of variable selection by choosing the best predictor among predictors emanating from different methods as lasso,
  elastic-net, adaptive lasso, pls, randomForest. Moreover, it can be applied for choosing the tuning parameter in a Gauss-lasso procedure.
Variable elimination (Gaussian elimination, Fourier-Motzkin elimination), 
    Moore-Penrose pseudoinverse, reduction to reduced row echelon form, value substitution,  
    projecting a vector on the convex polytope described by a system of (in)equations, 
    simplify systems by removing spurious columns and rows and collapse implied equalities, 
    test if a matrix is totally unimodular, compute variable ranges implied by linear
    (in)equalities.
Checks adherence to a given style, syntax errors and possible
    semantic issues.  Supports on the fly checking of R code edited with
    'RStudio IDE', 'Emacs', 'Vim', 'Sublime Text', 'Atom' and 'Visual
    Studio Code'.
Extends the functionality of the 'tourr' package by an interactive
             graphical user interface. The interactivity allows users to
             effortlessly refine their 'tourr' results by manual intervention,
             which allows for integration of expert knowledge and aids the
             interpretation of results. For more information on 'tourr' see
             Wickham et. al (2011) <doi:10.18637/jss.v040.i02> or
             <https://github.com/ggobi/tourr>.
Lipid Maps Rest service. Researchers can access the Lipid Maps Rest
  service programmatically and conveniently integrate it into the current workflow
  or packages.
Lipid annotation in untargeted LC-MS lipidomics based on fragmentation rules. Alcoriza-Balaguer MI, Garcia-Canaveras JC, Lopez A, Conde I, Juan O, Carretero J, Lahoz A (2019) <doi:10.1021/acs.analchem.8b03409>.
Create lipidome-wide heatmaps of statistics with the 'lipidomeR'.
    The 'lipidomeR' provides a streamlined pipeline for the systematic 
    interpretation of the lipidome through publication-ready visualizations 
    of regression models fitted on lipidomics data. 
    With 'lipidomeR', associations between covariates and the lipidome 
    can be interpreted systematically and intuitively through heatmaps, where 
    lipids are categorized by the lipid class and are presented on 
    two-dimensional maps organized by the lipid size and level of saturation. 
    This way, the 'lipidomeR' helps you gain an immediate understanding of 
    the multivariate patterns in the lipidome already at first glance.
    You can create lipidome-wide heatmaps of statistical associations, changes, 
    differences, variation, or other lipid-specific values.  
    The heatmaps are provided with publication-ready quality and the results 
    behind the visualizations are based on rigorous statistical models.
An elegant tool for processing and visualizing lipidomics data generated by mass spectrometry. 'LipidomicsR' simplifies channel and replicate handling while providing thorough lipid species annotation. Its visualization capabilities encompass principal components analysis plots, heatmaps, volcano plots, and radar plots, enabling concise data summarization and quality assessment. Additionally, it can generate bar plots and line plots to visualize the abundance of each lipid species.
This computes Lipinski Rule of Five parameters and offers visualization for drug discovery. It analyzes molecular properties like molecular weight, hydrogen bond donors, acceptors, and ALogP, providing histograms and pass/fail status plots for efficient compound evaluation, aiding in drug development.
Provides three classes: Queue, PriorityQueue and Stack. Queue is just a
    "plain vanilla" FIFO queue; PriorityQueue orders items according to priority. Stack implements LIFO.
Performs Bayesian linear regression and forecasting in astronomy. The method accounts for heteroscedastic errors in both the independent and the dependent variables, intrinsic scatters (in both variables) and scatter correlation, time evolution of slopes, normalization, scatters, Malmquist and Eddington bias, upper limits and break of linearity. The posterior distribution of the regression parameters is sampled with a Gibbs method exploiting the JAGS library.
Contains 128 palettes from Color Lisa. All palettes are based on 
    masterpieces from the worlds greatest artists. For more information, see 
    <http://colorlisa.com/>.
This is an unofficial package aimed at automating the import of LISREL output in R. 
				This package or its maintainer is not in any way affiliated with the creators of LISREL and SSI, Inc.
Allows researchers to conduct multivariate
    statistical analyses of survey data with list experiments. This
    survey methodology is also known as the item count technique or
    the unmatched count technique and is an alternative to the commonly
    used randomized response method. The package implements the methods
    developed by Imai (2011) <doi:10.1198/jasa.2011.ap10415>, 
    Blair and Imai (2012) <doi:10.1093/pan/mpr048>, 
    Blair, Imai, and Lyall (2013) <doi:10.1111/ajps.12086>, 
    Imai, Park, and Greene (2014) <doi:10.1093/pan/mpu017>,
    Aronow, Coppock, Crawford, and Green (2015) <doi:10.1093/jssam/smu023>, 
    Chou, Imai, and Rosenfeld (2017) <doi:10.1177/0049124117729711>, and 
    Blair, Chou, and Imai (2018) <https://imai.fas.harvard.edu/research/files/listerror.pdf>. 
    This includes a Bayesian MCMC implementation of regression for the 
    standard and multiple sensitive item list experiment designs and a 
    random effects setup, a Bayesian MCMC hierarchical regression model 
    with up to three hierarchical groups, the combined list experiment 
    and endorsement experiment regression model, a joint model of the 
    list experiment that enables the analysis of the list experiment as 
    a predictor in outcome regression models, a method for combining 
    list experiments with direct questions, and methods for diagnosing and
    adjusting for response error. In addition, the package implements the 
    statistical test that is designed to detect certain failures of list 
    experiments, and a placebo test for the list experiment using data from 
    direct questions.
The aim of the package is to create data objects which allow for accesses like x["test"] and x["test","test"].
A toolbox for R arrays. Flexibly split, bind, reshape, modify, 
    subset and name arrays.
An implementation of list comprehensions as purely syntactic
  sugar with a minor runtime overhead. It constructs nested for-loops and
  executes the byte-compiled loops to collect the results.
Syntactic shortcuts for creating synthetic lists, vectors, 
    data frames, and matrices using list comprehension.
Programmatically create R Markdown documents from lists.
List environments are environments that have list-like properties.  For instance, the elements of a list environment are ordered and can be accessed and iterated over using index subsetting, e.g. 'x <- listenv(a = 1, b = 2); for (i in seq_along(x)) x[[i]] <- x[[i]] ^ 2; y <- as.list(x)'.
Tools for common operations on lists. Provided are short-cuts to
    operations like selecting and merging data stored in lists. The functions in
    this package are designed to be used with pipes.
R lists, especially nested lists, can be very difficult to
    visualize or represent. Sometimes 'str()' is not enough, so this suite of
    htmlwidgets is designed to help see, understand, and maybe even modify your R
    lists.  The function 'reactjson()' requires a package
    'reactR' that can be installed from CRAN or <https://github.com/timelyportfolio/reactR>.
Provides a function that, as an alternative to base::list, allows
    default values to be inherited from another list.
Identifying latent genetic interactions in genome-wide association studies
    using the Latent Interaction Testing (LIT) framework.
    LIT is a flexible kernel-based approach that leverages information across
    multiple traits to detect latent genetic interactions without specifying or
    observing the interacting variable (e.g., environment). LIT accepts
    standard PLINK files as inputs to analyze large genome-wide association studies.
Performs likelihood-based inference for stationary time series 
    extremes.  The general approach follows Fawcett and Walshaw (2012)
    <doi:10.1002/env.2133>.  Marginal extreme value inferences are adjusted for 
    cluster dependence in the data using the methodology in Chandler and Bate 
    (2007) <doi:10.1093/biomet/asm015>, producing an adjusted log-likelihood 
    for the model parameters.  A log-likelihood for the extremal index is 
    produced using the K-gaps model of Suveges and Davison (2010) 
    <doi:10.1214/09-AOAS292>. These log-likelihoods are combined to make 
    inferences about extreme values. Both maximum likelihood and Bayesian 
    approaches are available.
Render R Markdown to Markdown (without using 'knitr'), and Markdown
    to lightweight HTML or 'LaTeX' documents with the 'commonmark' package (instead
    of 'Pandoc'). Some missing Markdown features in 'commonmark' are also
    supported, such as raw HTML or 'LaTeX' blocks, 'LaTeX' math, superscripts,
    subscripts, footnotes, element attributes, and appendices,
    but not all 'Pandoc' Markdown features are (or will be) supported. With
    additional JavaScript and CSS, you can also create HTML slides and articles.
    This package can be viewed as a trimmed-down version of R Markdown and
    'knitr'. It does not aim at rich Markdown features or a large variety of
    output formats (the primary formats are HTML and 'LaTeX'). Book and website
    projects of multiple input documents are also supported.
Temporary and permanent message queues for R. Built on top of
    'SQLite' databases. 'SQLite' provides locking, and makes it possible
    to detect crashed consumers. Crashed jobs can be automatically marked
    as "failed", or put in the queue again, potentially a limited number of times.
An updated implementation of R package 'ranger' by Wright et al,
    (2017) <doi:10.18637/jss.v077.i01> for training and predicting from random
    forests, particularly suited to high-dimensional data, and for embedding in
    'Multiple Imputation by Chained Equations' (MICE) by van Buuren (2007)
    <doi:10.1177/0962280206074463>. Ensembles of classification and regression
    trees are currently supported. Sparse data of class 'dgCMatrix' (R package
    'Matrix') can be directly analyzed. Conventional bagged predictions are
    available alongside an efficient prediction for MICE via the algorithm
    proposed by Doove et al (2014) <doi:10.1016/j.csda.2013.10.025>. Trained
    forests can be written to and read from storage. Survival and probability
    forests are not supported in the update, nor is data of class 'gwaa.data'
    (R package 'GenABEL'); use the original 'ranger' package for these analyses.
Dataset and functions to explore quality of literary novels. The package is a part of the Riddle of Literary Quality project, and it contains the data of a reader survey about fiction in Dutch, a description of the novels the readers rated, and the results of stylistic measurements of the novels. The package also contains functions to combine, analyze, and visualize these data. For more details, see: Eder M, van Zundert J, Lensink S, van Dalen-Oskam K (2022). Replicating The Riddle of Literary Quality: The litRiddle package for R. In _Digital Humanities 2022: Conference Abstracts_, 636-637.
Data sets on various litter types like beach litter, riverain
    litter, floating litter, and seafloor litter are rapidly growing. This 
    package offers a simple user interface to analyse these litter data in
    a consistent and reproducible way. It also provides functions to 
    facilitate several kinds of litter analysis, e.g., trend analysis, 
    power analysis, and baseline analysis. Under the hood, these functions 
    are also used by the user interface. See Schulz et al. (2019)
    <doi:10.1016/j.envpol.2019.02.030> for details. MS-Windows users are
    advised to run 'litteR' in 'RStudio'. See our vignette: Installation manual 
    for 'RStudio' and 'litteR'.
There is a long tradition of studying the flux of carbon from the biosphere to the atmosphere by following a particular cohort of litter (wood, leaves, roots, or other organic material) through time.  The resulting data are mass remaining and time. A variety of functional forms may be used to fit the resulting data. Some work better empirically. Some are better connected to a process-based understanding.  Some have a small number of free parameters; others have more. This package matches decomposition data to a family of these curves using likelihood--based fitting. This package is based on published research by Cornwell & Weedon (2013) <doi:10.1111/2041-210X.12138>.
A scripting and command-line front-end
 is provided by 'r' (aka 'littler') as a lightweight binary wrapper around
 the GNU R language and environment for statistical computing and graphics.
 While R can be used in batch mode, the r binary adds full support for
 both 'shebang'-style scripting (i.e. using a  hash-mark-exclamation-path
 expression as the first line in scripts) as well as command-line use in
 standard Unix pipelines. In other words, r provides the R language without
 the environment.
Linear Liu regression coefficient's estimation and testing with different Liu related measures such as MSE, R-squared etc.
  REFERENCES
  i.   Akdeniz and Kaciranlar (1995) <doi:10.1080/03610929508831585>
  ii.  Druilhet and Mom (2008) <doi:10.1016/j.jmva.2006.06.011>
  iii. Imdadullah, Aslam, and Saima (2017)
  iv.  Liu (1993) <doi:10.1080/03610929308831027>
  v.   Liu (2001) <doi:10.1016/j.jspi.2010.05.030>.
Interpretability of complex machine learning models is a growing concern.
    This package helps to understand key factors that drive the 
    decision made by complicated predictive model (so called black box model). 
    This is achieved through local approximations that are either based on 
    additive regression like model or CART like model that allows for 
    higher interactions. The methodology is based on Tulio Ribeiro, Singh, Guestrin (2016) <doi:10.1145/2939672.2939778>.
    More details can be found in Staniak, Biecek (2018) <doi:10.32614/RJ-2018-072>.
Provides a suite of helper functions and a collection of datasets used in the book <https://uncovering-data-science.netlify.app>. It is designed to make data science techniques accessible to individuals with minimal coding experience. Inspired by an ancient Persian idiom, the package likens this learning process to "eating the liver of data science," symbolizing deep and immersive engagement with the field.
Extracts 'zip' files, converts 'Word', 'Excel', and 'html'/'htm' files to 'pdf' format. 'Word' and 'Excel' conversion uses 'VBScript', while 'html'/'htm' conversion uses 'webshot' and 'PhantomJS'. Additionally, the package merges 'pdf' files into a single document. This package is only supported on 'Windows' due to 'VBScript' dependencies.
Converts video files to 'mp3', merges multiple audio files and trims audio files using 'FFmpeg', which is dynamically downloaded to avoid bundling any third-party binaries. Users must ensure compliance with the license terms of 'FFmpeg' when using the package. See <https://github.com/BtbN/FFmpeg-Builds/releases/download/latest/ffmpeg-master-latest-win64-gpl.zip> for details.
Fits and tests logistic joinpoint models.
Computes Logistic Knowledge Tracing ('LKT') which is a general method for tracking human learning in an educational software system. Please see Pavlik, Eglington, and Harrel-Williams (2021) <https://ieeexplore.ieee.org/document/9616435>. 'LKT' is a method to compute features of student data that are used as predictors of subsequent performance. 'LKT' allows great flexibility in the choice of predictive components and features computed for these predictive components. The system is built on top of 'LiblineaR', which enables extremely fast solutions compared to base glm() in R.
Provides functionality to train and evaluate algorithm selection models for portfolios.
R functions and data sets for the work Paz, R.F., Balakrishnan, N and Bazán, J.L. (2018). L-logistic regression models: Prior sensitivity analysis, robustness to outliers and applications. Brazilian Journal of Probability and Statistics, <https://www.imstat.org/wp-content/uploads/2018/05/BJPS397.pdf>.
Performs likelihood criterion analysis using the Laplace regression model to determine its optimal subset of variables. The methodology is based on Guo et al. (2023), LIC criterion for optimal subset selection in distributed interval estimation <doi:10.1080/02331888.2020.1823979>.
Fits the Logit Leaf Model, makes predictions and visualizes the output. (De Caigny et al., (2018) <DOI:10.1016/j.ejor.2018.02.009>).
Provides modular, graph-based agents powered by large language models (LLMs) for intelligent task execution in R. 
      Supports structured workflows for tasks such as forecasting, data visualization, feature engineering, data wrangling, data cleaning, 'SQL', code generation, weather reporting, and research-driven question answering. 
      Each agent performs iterative reasoning: recommending steps, generating R code, executing, debugging, and explaining results. 
      Includes built-in support for packages such as 'tidymodels', 'modeltime', 'plotly', 'ggplot2', and 'prophet'. Designed for analysts, developers, and teams building intelligent, reproducible AI workflows in R. 
      Compatible with LLM providers such as 'OpenAI', 'Anthropic', 'Groq', and 'Ollama'. Inspired by the Python package 'langagent'.
Provides a unified interface to interact with multiple Large Language Model (LLM) APIs. The package supports text generation, embeddings, parallelization, as well as tidyverse integration.  Users can switch between different LLM providers seamlessly within R workflows, or call multiple models in parallel. The package enables creation of LLM agents for automated tasks and provides consistent error handling across all supported APIs. APIs include 'OpenAI' (see <https://platform.openai.com/docs> for details), 'Anthropic' (see <https://docs.anthropic.com/en/api/getting-started> for details), 'Groq' (see <https://console.groq.com/docs/api-reference> for details), 'Together AI' (see <https://docs.together.ai/docs/quickstart> for details), 'DeepSeek' (see <https://api-docs.deepseek.com> for details), 'Gemini' (see <https://aistudio.google.com> for details), 'xAI' (see <https://docs.x.ai/> for details), and 'Voyage AI' (see <https://docs.voyageai.com/docs/introduction> for details).
Density, distribution function, quantile function and random generation for the L-Logistic distribution with parameters m and phi. The parameter m is the median of the distribution.
Originally design to characterise Aqueous Two Phase Systems, LLSR provide a simple way to analyse experimental data and obtain phase diagram parameters, among other properties, systematically. The package will include (every other update) new functions in order to comprise useful tools in liquid-liquid extraction research.
Adds standardized regression coefficients to objects created by 'lm'. Also extends the S3 methods 'print', 'summary' and 'coef' with additional boolean argument 'standardized' and provides 'xtable'-support.
Exact significance tests for a changepoint in linear or multiple linear regression.  
  Confidence regions with exact coverage probabilities for the changepoint.  Based on 
  Knowles, Siegmund and Zhang (1991) <doi:10.1093/biomet/78.1.15>.
Set of tools for mapping of categorical response variables based on principal component analysis (pca) and multidimensional unfolding (mdu).
Various efficient and robust bootstrap methods are implemented for 
    linear models with least squares estimation.  Functions within this package 
    allow users to create bootstrap sampling distributions for model parameters, 
    test hypotheses about parameters, and visualize the bootstrap sampling or null 
    distributions.  Methods implemented for linear models include the wild bootstrap by 
    Wu (1986) <doi:10.1214/aos/1176350142>, the residual and paired bootstraps by
    Efron (1979, ISBN:978-1-4612-4380-9), the delete-1 jackknife by 
    Quenouille (1956) <doi:10.2307/2332914>, and the Bayesian bootstrap by 
    Rubin (1981) <doi:10.1214/aos/1176345338>.
Local Mean Decomposition is an iterative and self-adaptive approach for demodulating, processing, and analyzing multi-component amplitude modulated and frequency modulated signals. This R package is based on the approach suggested by Smith (2005) <doi:10.1098/rsif.2005.0058> and the 'Python' library 'PyLMD'.
Several service functions to be used to analyse datasets obtained from diallel experiments within the frame of linear models in R, as described in  Onofri et al (2020) <DOI:10.1007/s00122-020-03716-8>.
A fast dimensionality reduction method scaleable to large numbers of samples.
  Landmark Multi-Dimensional Scaling (LMDS) is an extension of classical Torgerson MDS,
  but rather than calculating a complete distance matrix between all pairs of samples,
  only the distances between a set of landmarks and the samples are calculated.
Fit linear and generalized linear mixed-effects models.
    The models and their components are represented using S4 classes and
    methods.  The core computational algorithms are implemented using the
    'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Fit relationship-based and customized mixed-effects models with complex variance-covariance structures using the 'lme4' machinery. The core computational algorithms are implemented using the
    'Eigen' 'C++' library for numerical linear algebra and 'RcppEigen' 'glue'.
Flexible functions that use 'lme4' as computational engine for 
             fitting models used in Genomic Selection (GS). GS is a technology used for genetic 
             improvement, and it has many advantages over phenotype-based selection. There 
             are several statistical models that adequately approach the statistical 
             challenges in GS, such as in linear mixed models (LMMs). The 'lme4' is the 
             standard package for fitting linear and generalized LMMs in the R-package, 
             but its use for genetic analysis is limited because it does not allow the 
             correlation between individuals or groups of individuals to be defined. The 
             'lme4GS' package is focused on fitting LMMs with covariance structures defined 
             by the user, bandwidth selection, and genomic prediction. The new package is 
             focused on genomic prediction of the models used in GS and can fit LMMs using
             different variance-covariance matrices. Several examples of GS models are 
             presented using this package as well as the analysis using real data. For more
             details see Caamal-Pat et.al. (2021) <doi:10.3389/fgene.2021.680569>.
Provides analytic derivatives and information matrices for
    fitted linear mixed effects (lme) models and generalized least squares (gls) models
    estimated using lme() (from package 'nlme') and gls() (from package 'nlme'), respectively.
    The package includes functions for estimating the sampling variance-covariance of variance
    component parameters using the inverse Fisher information. The variance components include
    the parameters of the random effects structure (for lme models), the variance structure,
    and the correlation structure. The expected and average forms of the Fisher information matrix
    are used in the calculations, and models estimated by full maximum likelihood or
    restricted maximum likelihood are supported. The package also includes a function for estimating
    standardized mean difference effect sizes (Pustejovsky, Hedges, and Shadish (2014) <DOI:10.3102/1076998614547577>)
    based on fitted lme or gls models.
The main function of the package is to perform backward selection of fixed effects, forward fitting of the random effects, and post-hoc analysis using parallel capabilities. Other functionality includes the computation of ANOVAs with upper- or lower-bound p-values and R-squared values for each model term, model criticism plots, data trimming on model residuals, and data visualization. The data to run examples is contained in package LCF_data.
Bootstrap routines for nested linear mixed effects models fit using
    either 'lme4' or 'nlme'. The provided 'bootstrap()' function implements the
    parametric, residual, cases, random effect block (REB), and wild bootstrap 
    procedures. An overview of these procedures can be found 
    in Van der Leeden et al. (2008) <doi: 10.1007/978-0-387-73186-5_11>, 
    Carpenter, Goldstein & Rasbash (2003) <doi: 10.1111/1467-9876.00415>,
    and Chambers & Chandra (2013) <doi: 10.1080/10618600.2012.681216>.
We provide a solution for performing permutation tests on linear and mixed linear regression models. It
             allows users to obtain accurate p-values without making distributional assumptions about the data. By 
             generating a null distribution of the test statistics through repeated permutations of the response variable,
             permutation tests provide a powerful alternative to traditional parameter tests (Holt et al. (2023) 
             <doi:10.1007/s10683-023-09799-6>). In this early version, we focus on the permutation tests over observed 
             t values of beta coefficients, i.e.original t values generated by parameter tests. After generating a null 
             distribution of the test statistic through repeated permutations of the response variable, each observed t 
             values would be compared to the null distribution to generate a p-value. To improve the efficiency,a stop 
             criterion (Anscombe (1953) <doi:10.1111/j.2517-6161.1953.tb00121.x>) is adopted to force permutation to stop 
             if the estimated standard deviation of the value falls below a fraction of the estimated p-value. By doing so,
             we avoid the need for massive calculations in exact permutation methods while still generating stable and accurate 
             p-values.
Provides p-values in type I, II or III anova and summary tables
    for lmer model fits (cf. lme4) via Satterthwaite's degrees of freedom method. A
    Kenward-Roger method is also available via the pbkrtest package. Model selection
    methods include step, drop1 and anova-like tables for random effects (ranova).
    Methods for Least-Square means (LS-means) and tests of linear contrasts of fixed
    effects are also available.
Adds smoothing spline modelling capability to nlme. Fits
        smoothing spline terms in Gaussian linear and nonlinear
        mixed-effects models.
Latent Markov models for longitudinal continuous and categorical data. See Bartolucci, Pandolfi, Pennoni (2017)<doi:10.18637/jss.v081.i04>.
Provides methods for estimation and statistical
               inference on directional and fluctuating selection in age-structured
               populations.
We present a method based on filtering algorithms to estimate the parameters of linear, i.e. the coefficients and the variance of the error term. The proposed algorithms make use of Particle Filters following Ristic, B., Arulampalam, S., Gordon, N. (2004, ISBN: 158053631X) resampling methods. Parameters of logistic regression models are also estimated using an evolutionary particle filter method.
Functions for different purposes related to forest biometrics, including illustrative graphics, numerical computation, modeling height-diameter relationships, prediction of tree volumes, modelling of diameter distributions and estimation off stand density using ITD. Several empirical datasets are also included.
Introduces in-sample, out-of-sample, pseudo out-of-sample, and
    benchmark model forecast tests and a new class for working with forecast data, Forecast.
A collection of helper functions for multiple
  regression models fitted by lm(). Most of them are simple
  functions for simple tasks which can be done with coding,
  but may not be easy for occasional users of R. Most of
  the tasks addressed are those sometimes needed when
  using the 'manymome' package (Cheung and Cheung, 2023,
  <doi:10.3758/s13428-023-02224-z>) and 'stdmod' package
  (Cheung, Cheung, Lau, Hui, and Vong, 2022,
  <doi:10.1037/hea0001188>). However, they can also be used
  in other scenarios.
The Gaussian location-scale regression model is a multi-predictor
    model with explanatory variables for the mean (= location) and the standard
    deviation (= scale) of a response variable. This package implements maximum
    likelihood and Markov chain Monte Carlo (MCMC) inference (using algorithms
    from Girolami and Calderhead (2011) <doi:10.1111/j.1467-9868.2010.00765.x>
    and Nesterov (2009) <doi:10.1007/s10107-007-0149-x>), a parametric
    bootstrap algorithm, and diagnostic plots for the model class.
It implements Expectation/Conditional Maximization Either (ECME)
             and rapidly converging algorithms as well as
             Bayesian inference for linear mixed models, 
             which is described in Schafer, J.L. (1998)
             "Some improved procedures for linear mixed models".
             Dept. of Statistics, The Pennsylvania State University.
In addition to modeling the expectation (location) of an outcome, mixed effects location scale models (MELSMs) include submodels on the variance components (scales) directly. This allows models on the within-group variance with mixed effects, and between-group variances with fixed effects. The MELSM can be used to model volatility, intraindividual variance, uncertainty, measurement error variance, and more. Multivariate MELSMs (MMELSMs) extend the model to include multiple correlated outcomes, and therefore multiple locations and scales. The latent multivariate MELSM (LMMELSM) further includes multiple correlated latent variables as outcomes. This package implements two-level mixed effects location scale models on multiple observed or latent outcomes, and between-group variance modeling. Williams, Martin, Liu, and Rast (2020) <doi:10.1027/1015-5759/a000624>. Hedeker, Mermelstein, and Demirtas (2008) <doi:10.1111/j.1541-0420.2007.00924.x>.
Fit right censored Multiple Ordinal Tobit (MOT) model.
Embarrassingly Parallel Linear Mixed Model calculations spread across local cores which repeat until convergence.
An efficient and flexible system to solve sparse mixed model
    equations. Important applications are the use of splines to model spatial or temporal
    trends as described in Boer (2023). (<doi:10.1177/1471082X231178591>).
Companion R package for the course "Statistical analysis of correlated and repeated measurements for health science researchers"
	     taught by the section of Biostatistics of the University of Copenhagen.
	     It implements linear mixed models where the model for the variance-covariance of the residuals is specified via patterns (compound symmetry, toeplitz, unstructured, ...).
	     Statistical inference for mean, variance, and correlation parameters is performed based on the observed information and a Satterthwaite approximation of the degrees of freedom.
	     Normalized residuals are provided to assess model misspecification.
	     Statistical inference can be performed for arbitrary linear or non-linear combination(s) of model coefficients.
	     Predictions can be computed conditional to covariates only or also to outcome values.
Efficient Frequentist profiling and Bayesian marginalization of parameters for which the conditional likelihood is that of a multivariate linear regression model.  Arbitrary inter-observation error correlations are supported, with optimized calculations provided for independent-heteroskedastic and stationary dependence structures.
Computes model II simple linear regression using ordinary
 least squares (OLS), major axis (MA), standard major axis (SMA), and
 ranged major axis (RMA).
A complete framework for frequency analysis is provided by 'LMoFit'. It has functions related to the determination of sample L-moments as in Hosking, J.R.M. (1990) <doi:10.1111/j.2517-6161.1990.tb01775.x>, the fitting of various distributions as in Zaghloul et al. (2020) <doi:10.1016/j.advwatres.2020.103720> and Hosking, J.R.M. (2019) <https://CRAN.R-project.org/package=lmom>, besides plotting and manipulating L-space diagrams as in Papalexiou, S.M. & Koutsoyiannis, D. (2016) <doi:10.1016/j.advwatres.2016.05.005> for two-shape parametric distributions on the L-moment ratio diagram. Additionally, the quantile, probability density, and cumulative probability functions of various distributions are provided in a user-friendly manner.
Functions related to L-moments: computation of L-moments
  and trimmed L-moments of distributions and data samples; parameter
  estimation; L-moment ratio diagram; plot vs. quantiles of an
  extreme-value distribution.
Extensive functions for Lmoments (LMs) and probability-weighted moments (PWMs),
  distribution parameter estimation, LMs for distributions, LM ratio diagrams, multivariate
  Lcomoments, and asymmetric (asy) trimmed LMs (TLMs). Maximum likelihood and
  maximum product spacings estimation are available. Right-tail and left-tail LM censoring
  by threshold or indicator variable are available. LMs of residual (resid) and reversed
  (rev) residual life are implemented along with 13 quantile operators for reliability analyses.
  Exact analytical bootstrap estimates of order statistics, LMs, and LM var-covars are available.
  Harri-Coble Tau34-squared Normality Test is available. Distributions with L, TL, and added
  (+) support for right-tail censoring (RC) encompass: Asy Exponential (Exp) Power [L],
  Asy Triangular [L], Cauchy [TL], Eta-Mu [L], Exp. [L], Gamma [L], Generalized (Gen) Exp
  Poisson [L], Gen Extreme Value [L], Gen Lambda [L, TL], Gen Logistic [L], Gen Normal [L],
  Gen Pareto [L+RC, TL], Govindarajulu [L], Gumbel [L], Kappa [L], Kappa-Mu [L],
  Kumaraswamy [L], Laplace [L], Linear Mean Residual Quantile Function [L], Normal [L],
  3p log-Normal [L], Pearson Type III [L], Polynomial Density-Quantile 3 and 4 [L],
  Rayleigh [L], Rev-Gumbel [L+RC], Rice [L], Singh Maddala [L], Slash [TL], 3p Student t [L],
  Truncated Exponential [L], Wakeby [L], and Weibull [L].
Contains functions to estimate
        L-moments and trimmed L-moments from the data. Also
        contains functions to estimate the parameters of the normal
        polynomial quantile mixture and the Cauchy polynomial quantile
        mixture from L-moments and trimmed L-moments.
It is an extension of 'lmom' R package: 'pel...()','cdf...()',qua...()' function
    families are lumped and called from one function per each family respectively in order to
    create robust automatic tools to fit data  with different probability
    distributions and then to estimate probability values and return periods.  The implemented functions are able to manage time series with constant and/or missing values without stopping
    the execution with error messages. The package also contains tools to  calculate several  indices based on variability (e.g. 'SPI' , Standardized
    Precipitation Index, see <https://climatedataguide.ucar.edu/climate-data/standardized-precipitation-index-spi> and <http://spei.csic.es/>) for multiple time series or spatially gridded values.
Functions for regional frequency analysis
  using the methods of J. R. M. Hosking and J. R. Wallis (1997),
  "Regional frequency analysis: an approach based on L-moments".
European Commission's Labour Market Policy (LMP) database
  (<https://webgate.ec.europa.eu/empl/redisstat/databrowser/explore/all/lmp?lang=en&display=card&sort=category>)
  provides information on labour market interventions, which are government
  actions to help and support the unemployed and other disadvantaged groups in
  the transition from unemployment or inactivity to work. It covers the EU
  countries and Norway. This package provides functions for downloading and
  importing the LMP data and metadata (codelists).
Linear model functions using permutation tests.
Implementation based on Zhang, Jie & Huang, Kun (2014) <doi:10.4137/CIN.S14021> Normalized ImQCM: An Algorithm for Detecting Weak Quasi-Cliques in Weighted Graph with Applications in Gene Co-Expression Module Discovery in Cancers. Cancer informatics, 13, CIN-S14021.
Linear ridge regression coefficient's estimation and testing with different ridge related measures such as MSE, R-squared etc.
  REFERENCES
  i.   Hoerl and Kennard (1970) <doi:10.1080/00401706.1970.10488634>,
  ii.  Halawa and El-Bassiouni (2000) <doi:10.1080/00949650008812006>,
  iii. Imdadullah, Aslam, and Saima (2017),
  iv.  Marquardt (1970) <doi:10.2307/1267205>.
Exact and approximation algorithms for variable-subset
  selection in ordinary linear regression models.  Either compute all
  submodels with the lowest residual sum of squares, or determine the
  single-best submodel according to a pre-determined statistical
  criterion.  Hofmann et al. (2020) <doi:10.18637/jss.v093.i03>.
A collection of tests, data sets, and examples
 for diagnostic checking in linear regression models. Furthermore,
 some generic tools for inference in parametric models are provided.
Robust test(s) for model diagnostics in regression. The current version contains a robust test for functional specification (linearity). The test is based on the robust bounded-influence test by Heritier and Ronchetti (1994) <doi:10.1080/01621459.1994.10476822>.
Non-parametric estimators for casual effects based on longitudinal modified treatment 
  policies as described in Diaz, Williams, Hoffman, and Schenck <doi:10.1080/01621459.2021.1955691>, traditional point treatment, 
  and traditional longitudinal effects. Continuous, binary, categorical treatments, and multivariate treatments are allowed as well are 
  censored outcomes. The treatment mechanism is estimated via a density ratio classification procedure 
  irrespective of treatment variable type. For both continuous and binary outcomes, additive treatment effects 
  can be calculated and relative risks and odds ratios may be calculated for binary outcomes. 
  Supports survival outcomes with competing risks (Diaz, Hoffman, and Hejazi; <doi:10.1007/s10985-023-09606-7>).
Contains a suite of shiny applications
    meant to explore linear model inference feature through simulation
    and games.
Computes the implied weights of linear regression models for estimating
     average causal effects and provides diagnostics based on these weights. These
     diagnostics rely on the analyses in Chattopadhyay and Zubizarreta (2023)
     <doi:10.1093/biomet/asac058> where
     several regression estimators are represented as weighting estimators, in connection
     to inverse probability weighting. 'lmw' provides tools to diagnose
     representativeness, balance, extrapolation, and influence for these models,
     clarifying the target population of inference. Tools are also available to
     simplify estimating treatment effects for specific target populations of interest.
We developed an approach to detect differential expression features in long non-coding RNA low counts, using generalized linear model with zero-inflated exponential quasi likelihood ratio test. Methods implemented in this package are described in Li (2019) <doi:10.1186/s12864-019-5926-4>.
Long non-coding RNAs identification and analysis. Default models are trained with human, mouse and wheat datasets by employing SVM. Features are based on intrinsic composition of sequence, EIIP value (electron-ion interaction pseudopotential), and secondary structure. This package can also extract other classic features and build new classifiers. Reference: Han S., et al. (2019) <doi:10.1093/bib/bby065>.
Allows the simultaneous analysis of responses and response times in an Item Response Theory (IRT) modelling framework. Supports variable person speed functions (intercept, trend, quadratic), and covariates for item and person (random) parameters. Data missing-by-design can be specified. Parameter estimation is done with a MCMC algorithm. LNIRT replaces the package CIRT, which was written by Rinke Klein Entink. For reference, see the paper by Fox, Klein Entink and Van der Linden (2007), "Modeling of Responses and Response Times with the Package cirt", Journal of Statistical Software, <doi:10.18637/jss.v020.i07>.
An implementation of logistic normal multinomial (LNM) clustering. It is an extension of LNM mixture model proposed by Fang and Subedi (2020) <arXiv:2011.06682>, and is designed for clustering compositional data. The package includes 3 extended models: LNM Factor Analyzer (LNM-FA), LNM Bicluster Mixture Model (LNM-BMM) and Penalized LNM Factor Analyzer (LNM-FA). There are several advantages of LNM models: 1. LNM provides more flexible covariance structure; 2. Factor analyzer can reduce the number of parameters to estimate; 3. Bicluster can simultaneously cluster subjects and taxa, and provides significant biological insights; 4. Penalty term allows sparse estimation in the covariance matrix. Details for model assumptions and interpretation can be found in papers: Tu and Subedi (2021) <arXiv:2101.01871> and Tu and Subedi (2022) <doi:10.1002/sam.11555>.
Bayesian Survival models via the mixture of Log-Normal distribution extends the well-known survival models and accommodates different behaviour over time and considers higher censored survival times. The proposal combines mixture distributions Fruhwirth-Schnatter(2006) <doi:10.1007/s11336-009-9121-4>, and data augmentation techniques Tanner and Wong (1987) <doi:10.1080/01621459.1987.10478458>.
Estimates a lognormal-Pareto mixture by means of the Expectation-Conditional-Maximization-Either algorithm and by maximizing the profile likelihood function. A likelihood ratio test for discriminating between lognormal and Pareto tail is also implemented. See Bee, M. (2022) <doi:10.1007/s11634-022-00497-4>.
Various plots and functions that make use of the lattice/trellis plotting framework. 
   The plots, which include loaPlot(), loaMapPlot() and trianglePlot(), and use panelPal(), a function that 
   extends 'lattice' and 'hexbin' package methods to automate plot subscript and panel-to-panel 
   and panel-to-key synchronization/management.
Provides a framework to load text and excel files through a 'shiny' graphical interface. It allows renaming, transforming, ordering and removing variables. It includes basic exploratory methods such as the mean, median, mode, normality test, histogram and correlation.
Computing statistical hypothesis testing for loading in principal component analysis (PCA) (Yamamoto, H. et al. (2014) <doi:10.1186/1471-2105-15-51>), orthogonal smoothed PCA (OS-PCA) (Yamamoto, H. et al. (2021) <doi:10.3390/metabo11030149>), one-sided kernel PCA (Yamamoto, H. (2023) <doi:10.51094/jxiv.262>), partial least squares (PLS) and PLS discriminant analysis (PLS-DA) (Yamamoto, H. et al. (2009) <doi:10.1016/j.chemolab.2009.05.006>), PLS with rank order of groups (PLS-ROG) (Yamamoto, H. (2017) <doi:10.1002/cem.2883>), regularized canonical correlation analysis discriminant analysis (RCCA-DA) (Yamamoto, H. et al. (2008) <doi:10.1016/j.bej.2007.12.009>), multiset PLS and PLS-ROG (Yamamoto, H. (2022) <doi:10.1101/2022.08.30.505949>).
Modifying a load shape to match specific peak and 
  load factor is a fundamental component for various power system 
  planning and operation studies. This package is an efficient tool 
  to modify a reference load shape while matching the desired peak
  and load factor. The package offers both linear and non-linear method,
  described in <https://rpubs.com/riazakhan94/load_shape_match_peak_energy>. 
  The user can control the shape of the final load shape by regulating 
  certain parameters. The package provides validation metrics for 
  assessing the derived load shape in terms of preserving time series 
  properties. It also offers powerful graphics, that allows the user to
  visually assess the derived load shape.
Automated analysis and modeling of longitudinal 'omics' data (e.g. breath 'metabolomics') using generalized spline mixed effect models. Including automated filtering of noise parameters and determination of breakpoints.
Simulate lobster catch process in a trap fishery. Factors such as lobster density on ocean floor, their movement, trap saturation and bait shrinkage rate can be modeled. Details of the methods for modeling those processes can be found in: Addison and Bell (1997) <doi:10.1071/MF97169>.
A set of tools for inspecting and understanding R data
    structures inspired by str(). Includes ast() for visualizing abstract
    syntax trees, ref() for showing shared references, cst() for showing
    call stack trees, and obj_size() for computing object sizes.
Network analysis usually requires estimating the uncertainty of
    graph statistics. Through this package, we provide tools to bootstrap 
    various networks via local bootstrap procedure. Additionally, it includes 
    functions for generating probability matrices, creating network adjacency 
    matrices from probability matrices, and plotting network structures. 
    The reference will be updated soon.
Implements novel nonparametric approaches to address
    biases and confounding when comparing treatments or exposures in
    observational studies of outcomes. While designed and appropriate for use
    in studies involving medicine and the life sciences, the package can be
    used in other situations involving outcomes with multiple confounders.
    The package implements a family of methods for non-parametric bias correction
    when comparing treatments in observational studies, including survival
    analysis settings, where competing risks and/or censoring may be present.
    The approach extends to bias-corrected personalized predictions of treatment
    outcome differences, and analysis of heterogeneity of treatment effect-sizes
    across patient subgroups. For further details, please see: 
    Lauve NR, Nelson SJ, Young SS, Obenchain RL, Lambert CG. LocalControl:
    An R Package for Comparative Safety and Effectiveness Research.
    Journal of Statistical Software. 2020. p. 1–32. Available from <doi:10.18637/jss.v096.i04>.
Implements a local likelihood estimator for the dependence parameter in bivariate conditional copula models.  Copula family and local likelihood bandwidth parameters are selected by leave-one-out cross-validation.  The models are implemented in 'TMB', meaning that the local score function is efficiently calculated via automated differentiation (AD), such that quasi-Newton algorithms may be used for parameter estimation.
Implementation of a theoretically supported alternative to k-nearest neighbors for functional data 
  to solve problems of estimating unobserved segments of a partially observed functional data sample, 
  functional classification and outlier detection. The approximating neighbor curves are piecewise functions built from a functional sample. 
  Instead of a distance on a function space we use a locally defined distance function that satisfies stabilization criteria. 
  The package allows the implementation of the methodology and the replication of the results in Elías, A., Jiménez, R. and Yukich, J. (2020) <arXiv:2007.16059>.
Computational routines for estimating local Gaussian parameters. Local Gaussian parameters are useful for characterizing and testing for non-linear dependence within bivariate data. See e.g. Tjostheim and Hufthammer, Local Gaussian correlation: A new measure of dependence, Journal of Econometrics, 2013, Volume 172 (1), pages 33-48 <DOI:10.1016/j.jeconom.2012.08.001>.
Local Individual Conditional Expectation ('localICE') is a local explanation approach from the field of eXplainable Artificial Intelligence (XAI). localICE is a model-agnostic XAI approach which provides three-dimensional local explanations for particular data instances. The approach is proposed in the master thesis of Martin Walter as an extension to ICE (see Reference). The three dimensions are the two features at the horizontal and vertical axes as well as the target represented by different colors. The approach is applicable for classification and regression problems to explain interactions of two features towards the target. For classification models, the number of classes can be more than two and each class is added as a different color to the plot. The given instance is added to the plot as two dotted lines according to the feature values. The localICE-package can explain features of type factor and numeric of any machine learning model. Automatically supported machine learning packages are 'mlr', 'randomForest', 'caret' or all other with an S3 predict function. For further model types from other libraries, a predict function has to be provided as an argument in order to get access to the model. Reference to the ICE approach: Alex Goldstein, Adam Kapelner, Justin Bleich, Emil Pitkin (2013) <arXiv:1309.6392>.
In the generalized Roy model, the marginal treatment effect (MTE) can be used as
  a building block for constructing conventional causal parameters such as the average treatment
  effect (ATE) and the average treatment effect on the treated (ATT). Given a treatment selection
  equation and an outcome equation, the function mte() estimates the MTE via the semiparametric
  local instrumental variables method or the normal selection model. The function mte_at() evaluates
  MTE at different values of the latent resistance u with a given X = x, and the function mte_tilde_at()
  evaluates MTE projected onto the estimated propensity score. The function ace() estimates
  population-level average causal effects such as ATE, ATT, or the marginal policy relevant
  treatment effect.
Local explanations of machine learning models describe, how features contributed to a single prediction. 
    This package implements an explanation method based on LIME 
    (Local Interpretable Model-agnostic Explanations, 
    see Tulio Ribeiro, Singh, Guestrin (2016) <doi:10.1145/2939672.2939778>) in which interpretable
    inputs are created based on local rather than global behaviour of each original feature.
Functionalities for calculating the local score and calculating statistical relevance (p-value) to find a local Score in a sequence of given distribution (S. Mercier and J.-J. Daudin (2001) <https://hal.science/hal-00714174/>) ; S. Karlin and S. Altschul (1990) <https://pmc.ncbi.nlm.nih.gov/articles/PMC53667/>  ; S. Mercier, D. Cellier and F. Charlot (2003) <https://hal.science/hal-00937529v1/> ; A. Lagnoux, S. Mercier and P. Valois (2017) <doi:10.1093/bioinformatics/btw699> ).
The package converts R data onto input and data for LocalSolver,
    executes optimization and exposes optimization results as R data.
    LocalSolver (http://www.localsolver.com/) is an optimization engine
    developed by Innovation24 (http://www.innovation24.fr/). It is designed to
    solve large-scale mixed-variable non-convex optimization problems.  The
    localsolver package is developed and maintained by WLOG Solutions
    (http://www.wlogsolutions.com/en/) in collaboration with Decision Support
    and Analysis Division at Warsaw School of Economics
    (http://www.sgh.waw.pl/en/).
Implements a local indicator of stratified power to analyze local spatial stratified association and demonstrate how spatial stratified association changes spatially and in local regions, as outlined in Hu et al. (2024) <doi:10.1080/13658816.2024.2437811>.
A set of functions and tools to conduct acoustic source localization, as well as organize and check localization data and results. The localization functions implement the modified steered response power algorithm described by Cobos et al. (2010) <doi:10.1109/LSP.2010.2091502>.
Download Internet Protocol (IP) address location and more from the 'ip-api' application programming interface (API) <https://ip-api.com/>. The package makes it easy to get the latitude, longitude, country, region, and organisation associated to the provided IP address. The information is conveniently returned in a rectangular format.
A set of functions to locate some programs 
 available on the user machine. The package provides functions to locate 
 'Node.js', 'npm', 'LibreOffice', 'Microsoft Word', 'Microsoft PowerPoint', 
 'Microsoft Excel', 'Python', 'pip', 'Mozilla Firefox' and 'Google Chrome'.
 User can test the availability of a program with eventually a version 
 and call it with function system2() or system(). This allows the use of 
 a single function to retrieve the path to a program regardless of the 
 operating system and its configuration.
Identification of equilibrium locations in location games (Hotelling (1929) 
    <doi:10.2307/2224214>). In these games, two competing actors place
    customer-serving units in two locations simultaneously. Customers make the 
    decision to visit the location that is closest to them. The functions in 
    this package include Prim algorithm (Prim (1957) 
    <doi:10.1002/j.1538-7305.1957.tb01515.x>) to find the minimum spanning tree 
    connecting all network vertices, an implementation of Dijkstra algorithm 
    (Dijkstra (1959) <doi:10.1007/BF01386390>) to find the shortest distance and 
    path between any two vertices, a self-developed algorithm using elimination 
    of purely dominated strategies to find the equilibrium, and several plotting 
    functions.
A bioinformatics pipeline for performing taxonomic
    assignment of DNA metabarcoding sequence data while considering
    geographic location. A detailed tutorial is available at
    <https://urodelan.github.io/Local_Taxa_Tool_Tutorial/>.
    A manuscript describing these methods is in preparation.
Computation of local false discovery rates.
Local regression, likelihood and density estimation methods as described in the 1999 book by Loader.
Provides test of second-order stationarity for time
	series (for dyadic and arbitrary-n length data). Provides
	localized autocovariance, with confidence intervals,
	for locally stationary (nonstationary) time series.
	See Nason, G P (2013) "A test for second-order stationarity and
	approximate confidence intervals for localized autocovariance
	for locally stationary time series." Journal of the Royal Statistical
	Society, Series B, 75, 879-904.  <doi:10.1111/rssb.12015>.
Datasets for the third edition of "Statistics: Unlocking the Power of Data" by Lock^5
    Includes version of datasets from earlier editions.
Locally sparse estimator of generalized varying coefficient model for asynchronous longitudinal data by kernel-weighted estimating equation.
Computes local polynomial estimators for 
  the regression and also density. It comprises several 
  different utilities to handle kernel estimators.
Fast implementations to compute the genetic covariance matrix, the Jaccard similarity matrix, the s-matrix (the weighted Jaccard similarity matrix), and the (classic or robust) genomic relationship matrix of a (dense or sparse) input matrix (see Hahn, Lutz, Hecker, Prokopenko, Cho, Silverman, Weiss, and Lange (2020) <doi:10.1002/gepi.22356>). Full support for sparse matrices from the R-package 'Matrix'. Additionally, an implementation of the power method (von Mises iteration) to compute the largest eigenvector of a matrix is included, a function to perform an automated full run of global and local correlations in population stratification data, a function to compute sliding windows, and a function to invert minor alleles and to select those variants/loci exceeding a minimal cutoff value. New functionality in locStra allows one to extract the k leading eigenvectors of the genetic covariance matrix, Jaccard similarity matrix, s-matrix, and genomic relationship matrix via fast PCA without actually computing the similarity matrices. The fast PCA to compute the k leading eigenvectors can now also be run directly from 'bed'+'bim'+'fam' files.
To decompose symmetric matrices such as brain connectivity matrices so that one can extract sparse latent component matrices and also estimate mixing coefficients, a blind source separation (BSS) method named LOCUS was proposed in Wang and Guo (2023) <arXiv:2008.08915>. For brain connectivity matrices, the outputs correspond to sparse latent connectivity traits and individual-level trait loadings.
Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots <doi:10.1093/bioadv/vbaf006>.
Read and write access to PNG image files using the LodePNG
    library. The package has no external dependencies.
Genome-wide association (GWAS) analyses
  of a biomarker that account for the limit of detection.
Impute observed values below the limit of detection (LOD) via
    censored likelihood multiple imputation (CLMI) in single-pollutant
    models, developed by Boss et al (2019) <doi:10.1097/EDE.0000000000001052>.
    CLMI handles exposure detection limits that may change throughout the course
    of exposure assessment. 'lodi' provides functions for imputing and
    pooling for this method.
Tools to fit linear regression model to data while taking into account covariates with lower limit of detection (LOD).
Data sets for Chirok Han (2022, ISBN:979-11-303-1497-6,
  "Lectures on Econometrics"). Students, teachers, and self-learners will
  find the data sets essential for replicating the results in the book.
Estimate model parameters to determine whether two compounds have synergy, antagonism, or Loewe's Additivity.
Alternate font rendering is useful when rendering text to novel
   graphics outputs where modern font rendering is not available or 
   where bespoke text positioning is required. Bitmap and vector fonts allow for 
   custom layout and rendering using pixel coordinates and line drawing.  
   Formatted text is created as a data.frame of pixel coordinates (for bitmap fonts)
   or stroke coordinates (for vector fonts).  All text can be easily 
   previewed as a matrix or raster image.  
   A selection of fonts is included with this package.
Logger to keep track of informational events and errors useful for debugging.
The log4r package is meant to provide a fast, lightweight,
  object-oriented approach to logging in R based on the widely-emulated
  'log4j' system and etymology.
Enables users to handle the dataset cleaning for conducting
    specific analyses with the log files from two international educational
    assessments: the Programme for International Student Assessment (PISA,
    <https://www.oecd.org/pisa/>) and the Programme for the International
    Assessment of Adult Competencies (PIAAC,
    <https://www.oecd.org/skills/piaac/>). An illustration of the analyses can be
    found on the LOGAN Shiny app (<https://loganpackage.shinyapps.io/shiny/>) on
    your browser.
Methods for fitting log-link GLMs and GAMs to binomial data,
    including EM-type algorithms with more stable convergence properties than standard methods.
Software for computing a log-concave (maximum likelihood) estimator for independent and identically distributed data in any number of dimensions. For a detailed description of the method see Cule, Samworth and Stewart (2010, Journal of Royal Statistical Society Series B, <doi:10.1111/j.1467-9868.2010.00753.x>).
Based on right or interval censored data, compute the maximum likelihood estimator of a (sub)probability density under the assumption that it is log-concave. For further information see Duembgen, Rufibach and Schuhmacher (2014) <doi:10.1214/14-EJS930>.
Given independent and identically distributed observations X(1), ..., X(n), compute the maximum likelihood estimator (MLE) of a density as well as a smoothed version of it under the assumption that the density is log-concave, see Rufibach (2007) and Duembgen and Rufibach (2009). The main function of the package is 'logConDens' that allows computation of the log-concave MLE and its smoothed version. In addition, we provide functions to compute (1) the value of the density and distribution function estimates (MLE and smoothed) at a given point (2) the characterizing functions of the estimator, (3) to sample from the estimated distribution, (5) to compute a two-sample permutation test based on log-concave densities, (6) the ROC curve based on log-concave estimates within cases and controls, including confidence intervals for given values of false positive fractions (7) computation of a confidence interval for the value of the true density at a fixed point. Finally, three datasets that have been used to illustrate log-concave density estimation are made available.
Given independent and identically distributed observations X(1), ..., X(n), allows to compute the maximum likelihood estimator (MLE) of probability mass function (pmf) under the assumption that it is log-concave, see Weyermann (2007) and Balabdaoui, Jankowski, Rufibach, and Pavlides (2012). The main functions of the package are 'logConDiscrMLE' that allows computation of the log-concave MLE, 'logConDiscrCI' that computes pointwise confidence bands for the MLE, and 'kInflatedLogConDiscr' that computes a mixture of a log-concave PMF and a point mass at k.
Inspired by the the 'futile.logger' R package and 'logging'
    Python module, this utility provides a flexible and extensible way of
    formatting and delivering log messages with low overhead.
Pure R implementation of the ubiquitous log4j package. It offers hierarchic 
  loggers, multiple handlers per logger, level based filtering, space handling in messages 
  and custom formatting.
An effortless 'ndjson' (newline-delimited 'JSON') logger, with two primary
    log-writing interfaces. It provides a set of wrappings for base R's
    message(), warning(), and stop() functions that maintain identical
    functionality, but also log the handler message to an 'ndjson' log file.
    'loggit' also exports its internal 'loggit()' function for powerful and
    configurable custom logging. No change in existing code is necessary to use
    this package, and should only require additions to fully leverage the power
    of the logging system. 'loggit' also provides a log reader for reading an
    'ndjson' log file into a data frame, log rotation, and live echo of the
    'ndjson' log messages to terminal 'stdout' for log capture by external
    systems (like containers). 'loggit' is ideal for Shiny apps, data pipelines,
    modeling work flows, and more. Please see the vignettes for detailed example
    use cases.
An easy-to-use 'ndjson' (newline-delimited 'JSON') logger.
    It provides a set of wrappers for base R's message(), warning(), and
    stop() functions that maintain identical functionality, but also log
    the handler message to an 'ndjson' log file.
    No change in existing code is necessary to use this package, 
    and only a few additional adjustments are needed to fully 
    utilize its potential.
Implementation of the Swiss Confederation's standard analysis
    model for salary analyses
    <https://www.ebg.admin.ch/en/equal-pay-analysis-with-logib> in R. The
    analysis is run at company-level and the model is intended for
    medium-sized and large companies. It can technically be used with 50
    or more employees (apprentices, trainees/interns and expats are not
    included in the analysis). Employees with at least 100 employees are
    required by the Gender Equality Act to conduct an equal pay analysis.
    This package allows users to run the equal salary analysis in R,
    providing additional transparency with respect to the methodology and
    simple automation possibilities.
Fast binning of multiple variables using parallel processing. A summary of all the variables binned is generated which provides the information value, entropy, an indicator of whether the variable follows a monotonic trend or not, etc. It supports rebinning of variables to force a monotonic trend as well as manual binning based on pre specified cuts. The cut points of the bins are based on conditional inference trees as implemented in the partykit package. The conditional inference framework is described by Hothorn T, Hornik K, Zeileis A (2006) <doi:10.1198/106186006X133933>.
A statistical learning method that tries to find the best set
  of predictors and interactions between predictors for modeling binary or
  quantitative response data in a decision tree. Several search algorithms
  and ensembling techniques are implemented allowing for finetuning the
  method to the specific problem. Interactions with quantitative
  covariables can be properly taken into account by fitting local
  regression models. Moreover, a variable importance measure for assessing
  marginal and interaction effects is provided. Implements the
  procedures proposed by Lau et al. (2024, <doi:10.1007/s10994-023-06488-6>).
Logic Forest is an ensemble machine learning method that identifies important and interpretable combinations of binary predictors using logic regression trees to model complex relationships with an outcome. Wolf, B.J., Slate, E.H., Hill, E.G. (2010) <doi:10.1093/bioinformatics/btq354>.
Routines for fitting Logic Regression models. Logic Regression is described
	in Ruczinski, Kooperberg, and LeBlanc (2003) <DOI:10.1198/1061860032238>. Monte
        Carlo Logic Regression is described in and Kooperberg and Ruczinski (2005)
        <DOI:10.1002/gepi.20042>.
Provides histograms, boxplots and dotplots as alternatives to scatterplots of data when plotting fitted logistic regressions.
Framework for adding authentication to 'shiny' applications.
    Provides flexibility as compared to other options for where user
    credentials are saved, allows users to create their own accounts, and
    password reset functionality. Bryer (2024)
    <doi:10.5281/zenodo.10987876>.
Fit a logistic regression model using Firth's bias reduction method, equivalent to penalization of the log-likelihood by the Jeffreys 
	prior. Confidence intervals for regression coefficients can be computed by penalized profile likelihood. Firth's method was proposed as ideal
	solution to the problem of separation in logistic regression, see Heinze and Schemper (2002) <doi:10.1002/sim.1047>. If needed, the bias reduction can be turned off such that ordinary
	maximum likelihood logistic regression is obtained. Two new modifications of Firth's method, FLIC and FLAC, lead to unbiased predictions and are now available
	in the package as well, see Puhr et al (2017) <doi:10.1002/sim.7273>.
Error in a binary dependent variable, also known as misclassification, has not drawn much attention in psychology. Ignoring misclassification in logistic regression can result in misleading parameter estimates and statistical inference. This package conducts logistic regression analysis with misspecification in outcome variables.
An implementation of a method of extending a logistic regression
    model beyond linear effects of the co-variates. The extension in is
    constructed by first equating the logistic regression model to a naive Bayes
    model where all the margins are specified to follow natural exponential 
    distributions conditional on Y, that is, a model for Y given X that is
    specified through the distribution of X given Y, where the columns of X are
    assumed to be mutually independent conditional on Y. Subsequently, the
    model is expanded by adding vine - copulas to relax the assumption of
    mutual independence, where pair-copulas are added in a stage-wise, forward
    selection manner. Some heuristics are employed during the process of
    selecting edges, as well as the families of pair-copula models. After each
    component is added, the parameters are updated by a (smaller) number of
    gradient steps to maximise the likelihood. When the algorithm has stopped
    adding edges, based the criterion that a new edge should improve the
    likelihood more than k times the number new parameters, the parameters are
    updated with a larger number of gradient steps, or until convergence.
A system for fitting Logistic Curve by Rhodes Method. Method for fitting logistic curve by Rhodes Method is described in A.M.Gun,M.K.Gupta and B.Dasgupta(2019,ISBN:81-87567-81-3).
Automatically returns 36 logistic models including 23 individual models and 13 ensembles of models of logistic data. The package also returns 10 plots, 5 tables, and a summary report. The package automatically
    builds all 36 models, reports all results, and provides graphics to show how the models performed. This can be used for a wide range of data sets. The package includes medical data (the Pima Indians data set), and
    information about the performance of Lebron James. The package can be used to analyze many other examples, such as stock market data. The package automatically returns many values for each model, such as
    True Positive Rate, True Negative Rate, False Positive Rate, False Negative Rate, Positive Predictive Value, Negative Predictive Value, F1 Score, Area Under the Curve. The package also returns 36 Receiver
    Operating Characteristic (ROC) curves for each of the 36 models.
Dimensionality reduction techniques for binary data including
    logistic PCA.
Here we provide an implementation of the linear and logistic regression-based Reliable Change Index (RCI), to be used with lm and binomial glm model objects, respectively, following Moral et al. <https://psyarxiv.com/gq7az/>. The RCI function returns a score assumed to be approximately normally distributed, which is helpful to detect patients that may present cognitive decline.
Adjusted odds ratio conditional on potential confounders can be directly obtained from logistic regression. However, those adjusted odds ratios have been widely incorrectly interpreted as a relative risk. As relative risk is often of interest in public health, we provide a simple code to return adjusted relative risks from logistic regression model under potential confounders.
Functions for fitting a functional principal components logit regression model
	in four different situations: ordinary and filtered functional principal components
	of functional predictors, included in the model according to their variability
	explanation power, and according to their prediction ability by stepwise methods. The
	proposed methods were developed in Escabias et al (2004) 
	<doi:10.1080/10485250310001624738> and Escabias et al (2005)
	<doi:10.1016/j.csda.2005.03.011>.
Density, distribution, quantile and random generation function for the logitnormal distribution. Estimation of the mode and the first two moments. Estimation of distribution parameters.
Fast estimation of multinomial (MNL) and mixed logit (MXL) models in R. Models can be estimated using "Preference" space or "Willingness-to-pay" (WTP) space utility parameterizations. Weighted models can also be estimated. An option is available to run a parallelized multistart optimization loop with random starting points in each iteration, which is useful for non-convex problems like MXL models or models with WTP space utility parameterizations. The main optimization loop uses the 'nloptr' package to minimize the negative log-likelihood function. Additional functions are available for computing and comparing WTP from both preference space and WTP space models and for predicting expected choices and choice probabilities for sets of alternatives based on an estimated model. Mixed logit models can include uncorrelated or correlated heterogeneity covariances and are estimated using maximum simulated likelihood based on the algorithms in Train (2009) <doi:10.1017/CBO9780511805271>. More details can be found in Helveston (2023) <doi:10.18637/jss.v105.i10>.
Computes log-transformed kernel density estimates for positive data using a variety of kernels. It follows the methods described in Jones, Nguyen and McLachlan (2018) <doi:10.21105/joss.00870>.
Functions to sample from the double log normal distribution and calculate the density, distribution and quantile functions.
Functions to fit log-multiplicative models using 'gnm', with
  support for convenient printing, plots, and jackknife/bootstrap
  standard errors. For complex survey data, models can be fitted from
  design objects from the 'survey' package. Currently supported models
  include UNIDIFF (Erikson & Goldthorpe, 1992),
  a.k.a. log-multiplicative layer effect model (Xie, 1992)
  <doi:10.2307/2096242>, and several association models:
  Goodman (1979) <doi:10.2307/2286971>
  row-column association models of the RC(M) and RC(M)-L families
  with one or several dimensions; two skew-symmetric association
  models proposed by Yamaguchi (1990) <doi:10.2307/271086>
  and by van der Heijden & Mooijaart (1995) <doi:10.1177/0049124195024001002>
  Functions allow computing the intrinsic association coefficient
  (see Bouchet-Valat (2022) <doi:10.1177/0049124119852389>)
  and the Altham (1970) index <doi:10.1111/j.2517-6161.1970.tb00816.x>,
  including via the Bayes shrinkage estimator proposed
  by Zhou (2015) <doi:10.1177/0081175015570097>;
  and the RAS/IPF/Deming-Stephan algorithm.
Estimation of a lognormal - Generalized Pareto mixture via the Expectation-Maximization algorithm. Computation of bootstrap standard errors is supported and performed via parallel computing. Functions for random number simulation and density evaluation are also available. For more details see Bee and Santi (2025) <doi:10.48550/arXiv.2505.22507>.
The lognormal distribution  
  (Limpert et al. (2001) <doi:10.1641/0006-3568(2001)051%5B0341:lndats%5D2.0.co;2>)
  can characterize uncertainty that is bounded by zero.
  This package provides estimation of distribution parameters, computation of
  moments and other basic statistics, and an approximation of the distribution
  of the sum of several correlated lognormally distributed variables 
  (Lo 2013 <doi:10.12988/ams.2013.39511>) and the approximation of the 
  difference of two correlated lognormally distributed variables
  (Lo 2012 <doi:10.1155/2012/838397>).
Functions to fits simple linear regression models with log normal errors 
		and identity link, i.e. taking the responses on the original scale. See
		Muggeo (2018) <doi:10.13140/RG.2.2.18118.16965>.
Uses approximations to compute the natural logarithm of the Gamma
    function for large values.
Access to the Greek New Testament (27 books) and the Old Testament (39 books) and allow users to do textual analysis on the data. The New and Old Testament have been provided in their original languages, Greek and Hebrew, respectively. Additionally, the Revised American Standard Bible is also provided for users who'd rather use a word–for–word modern English translation.
Contains functions to help create log files.  The 
    package aims to overcome the difficulty of the base R sink() command.  The
    log_print() function will print to both the console and the file log, 
    without interfering in other write operations.
Tools for assessing equivalence of similar Logistic Regression models.
A utility to facilitate the logging and review of R programs in clinical trial programming workflows.
This is an extension package to 'logrx', which is a log creation 
  program focused on Clinical Reporting within the Pharma Industry.  This package 
  enables a simple 'shiny-based' Add-in that provides a point and click interface 
  to produce a log for a single program.
Contains routines for logspline density estimation.
	The function oldlogspline() uses the same algorithm as the logspline package
	version 1.0.x; i.e. the Kooperberg and Stone (1992) 
	algorithm (with an improved interface).  The recommended routine logspline()
	uses an algorithm from Stone et al (1997)  <DOI:10.1214/aos/1031594728>.
Kernel regression smoothing with adaptive local or global plug-in
	     bandwidth selection.
Draw lolliplot using GRanges objects. this package was designed 
  only for drawing lolliplot. So, it's faster than 'trackViewer', but un-related 
  functions has been derived.
Estimation of Latent Order Logistic (LOLOG) Models for Networks.
    LOLOGs are a flexible and fully general class of statistical graph models. 
    This package provides functions for performing MOM, GMM and variational 
    inference. Visual diagnostics and goodness of fit metrics are provided. 
    See Fellows (2018) <arXiv:1804.04583> for a detailed description of the methods.
Supervised learning techniques designed for the situation when the dimensionality exceeds the sample size have a tendency to overfit as the dimensionality of the data increases. To remedy this High dimensionality; low sample size (HDLSS) situation, we attempt to learn a lower-dimensional representation of the data before learning a classifier. That is, we project the data to a situation where the dimensionality is more manageable, and then are able to better apply standard classification or clustering techniques since we will have fewer dimensions to overfit. A number of previous works have focused on how to strategically reduce dimensionality in the unsupervised case, yet in the supervised HDLSS regime, few works have attempted to devise dimensionality reduction techniques that leverage the labels associated with the data. In this package and the associated manuscript Vogelstein et al. (2017) <arXiv:1709.01233>, we provide several methods for feature extraction, some utilizing labels and some not, along with easily extensible utilities to simplify cross-validative efforts to identify the best feature extraction method. Additionally, we include a series of adaptable benchmark simulations to serve as a standard for future investigative efforts into supervised HDLSS. Finally, we produce a comprehensive comparison of the included algorithms across a range of benchmark simulations and real data applications.
Read, register and compare point sets from single molecule localization microscopy.
Computes the Lomb-Scargle Periodogram and actogram for evenly or unevenly sampled time series. Includes a randomization procedure to obtain exact p-values. Partially based on C original by Press et al. (Numerical Recipes) and the Python module Astropy. For more information see Ruf, T. (1999). The Lomb-Scargle periodogram in biological rhythm research: analysis of incomplete and unequally spaced time-series. Biological Rhythm Research, 30(2), 178-201.
An easy tool to transform 2D longitudinal data into 3D arrays suitable for 
  Long short-term memory neural networks training. The array output can be
  used by the 'keras' package. Long short-term memory neural networks are described
  in: Hochreiter, S., & Schmidhuber, J. (1997) <doi:10.1162/neco.1997.9.8.1735>.
Constructs tree for continuous longitudinal data and survival data using baseline covariates as partitioning variables according to the 'LongCART' and 'SurvCART' algorithm, respectively. Later also included functions to calculate conditional power and predictive power of success based on interim results and probability of success for a prospective trial.
Clustering or classification of longitudinal data based on a mixture of multivariate t or Gaussian distributions with a Cholesky-decomposed covariance structure. Details in McNicholas and Murphy (2010) <doi:10.1002/cjs.10047> and McNicholas and Subedi (2012) <doi:10.1016/j.jspi.2011.11.026>.
This tool takes longitudinal dataset as input and analyzes if there is significant 
             change of the features over time (a proxy for treatments), while detects and controls 
             for 'covariates' simultaneously. 'LongDat' is able to take in several data types as input, 
             including count, proportion, binary, ordinal and continuous data. The output table contains 
              p values, effect sizes and 'covariates' of each feature, making the downstream analysis easy.
Provides tools to decompose differences in cohort health expectancy (HE)
    by age and cause using longitudinal data. The package implements a novel
    longitudinal attribution method based on a semiparametric additive hazards
    model with time-dependent covariates, specifically designed to address interval
    censoring and semi-competing risks via a copula framework. The resulting
    age-cause-specific contributions to disability prevalence and death probability
    can be used to quantify and decompose differences in cohort HE between groups.
    The package supports stepwise replacement decomposition algorithms and is
    applicable to cohort-based health disparity research across diverse populations.
    Related methods include
    Sun et al. (2023) <doi:10.1177/09622802221133552>.
A collection of parametric and nonparametric methods for the analysis of survival data. Parametric families implemented include Gompertz-Makeham, exponential and generalized Pareto models and extended models. The package includes an implementation of the nonparametric maximum likelihood estimator for arbitrary truncation and censoring pattern based on Turnbull (1976) <doi:10.1111/j.2517-6161.1976.tb01597.x>, along with graphical goodness-of-fit diagnostics. Parametric models for positive random variables and peaks over threshold models based on extreme value theory are described in Rootzén and Zholud (2017) <doi:10.1007/s10687-017-0305-5>; Belzile et al. (2021) <doi:10.1098/rsos.202097> and Belzile et al. (2022) <doi:10.1146/annurev-statistics-040120-025426>.
High dimensional longitudinal data analysis with Markov Chain Monte Carlo(MCMC). 
             Currently support mixed effect regression with or without missing observations by considering 
             covariance structures. It provides estimates by missing at random and missing not at random assumptions.
             In this R package, we present Bayesian approaches that statisticians and clinical 
             researchers can easily use. The functions' methodology is based on the book "Bayesian Approaches in Oncology Using R and OpenBUGS" by 
             Bhattacharjee A (2020) <doi:10.1201/9780429329449-14>.
Contains general data structures and
  functions for longitudinal data with multiple variables, 
  repeated measurements, and irregularly spaced time points.
  Also implements a shrinkage estimator of dynamical correlation
  and dynamical covariance.
Regression analysis of mixed sparse synchronous and asynchronous longitudinal covariates. Please cite the manuscripts corresponding to this package: Sun, Z. et al. (2023) <arXiv:2305.17715>  and  Liu, C. et al. (2023) <arXiv:2305.17662>.
Creates a series of sets of graphics and statistics related to the longitudinal cascade, all included in a single object. The longitudinal cascade inputs longitudinal data to identify gaps in the HIV and related cascades by observing differences using time to event and survival methods. The stage definitions are set by the user, with default standard options. Outputs include graphics, datasets, and formal statistical tests.
Tools for longitudinal data and joint longitudinal data (used by packages kml and kml3d).
Random forests are a statistical learning method widely used in many areas of scientific research essentially for its ability to learn complex relationships between input and output variables and also its capacity to handle high-dimensional data. However, current random forests approaches are not flexible enough to handle longitudinal data.  In this package, we propose a general approach of random forests for high-dimensional longitudinal data. It includes a flexible stochastic model which allows the covariance structure to vary over time. Furthermore, we introduce a new method which takes intra-individual covariance into consideration to build random forests. The method is fully detailled in Capitaine et.al. (2020) <doi:10.1177/0962280220946080> Random forests for high-dimensional longitudinal data.
The proposed method aims at predicting the longitudinal mean response trajectory by a 
              kernel-based estimator. The kernel estimator is constructed by imposing weights based on 
              subject-wise similarity on L2 metric space between predictor trajectories as well as time proximity. 
              Users could also perform variable selections to derive functional predictors with predictive significance
              by the proposed multiplicative model with multivariate Gaussian kernels.
Datasets and Functionality from
  'Jan Beran' (1994). Statistics for Long-Memory Processes; Chapman & Hall.
  Estimation of Hurst (and more) parameters for fractional Gaussian noise,
  'fARIMA' and 'FEXP' models.
An adaption of the consensus clustering approach from
    'ConsensusClusterPlus' for longitudinal data. The longitudinal data is
    clustered with flexible mixture models from 'flexmix', while the consensus
    matrices are hierarchically clustered as in 'ConsensusClusterPlus'. By using
    the flexibility from 'flexmix' and 'FactoMineR', one can use mixed data
    types for the clustering.
Compute power and sample size for linear models of longitudinal
    data. Supported models include mixed-effects models and models fit by
    generalized least squares and generalized estimating equations. The package
    is described in Iddi and Donohue (2022) <DOI:10.32614/RJ-2022-022>. Relevant
    formulas are derived by Liu and Liang (1997) <DOI:10.2307/2533554>, 
    Diggle et al (2002) <ISBN:9780199676750>, and Lu, Luo, and Chen (2008)
    <DOI:10.2202/1557-4679.1098>.
Performs variety of viral quasispecies diversity analyses [see Pamornchainavakul et al. (2024) <doi:10.21203/rs.3.rs-4637890/v1>] based on long-read sequence alignment. Main functions include 1) sequencing error and other noise minimization and read sampling, 2) Single nucleotide variant (SNV) profiles comparison, and 3) viral quasispecies profiles comparison and visualization.
Time-dependent Receiver Operating Characteristic curves, Area Under the Curve, and Net Reclassification Indexes for repeated measures. It is based on methods in Barbati and Farcomeni (2017) <doi:10.1007/s10260-017-0410-2>.
Performs recursive partitioning of linear and nonlinear mixed effects models,
    specifically for longitudinal data. The package is an
    extension of the original 'longRPart' package by 
    Stewart and Abdolell (2013) <https://cran.r-project.org/package=longRPart>.
Assess the proportion of treatment effect explained by a longitudinal surrogate marker as described in Agniel D and Parast L (2021) <doi:10.1111/biom.13310>.
Tools are provided to expand vectors of short URLs into long 'URLs'. 
    No 'API' services are used, which may mean that this operates more slowly than 
    'API' services do (since they usually cache results of expansions that every 
    user of the service requests). You can setup your own caching layer with the 
    'memoise' package if you wish to have a speedup during single sessions or add 
    larger dependencies, such as 'Redis', to gain a longer-term performance boost 
    at the expense of added complexity.
Efficient approximate leave-one-out cross-validation (LOO)
    for Bayesian models fit using Markov chain Monte Carlo, as 
    described in Vehtari, Gelman, and Gabry (2017) 
    <doi:10.1007/s11222-016-9696-4>. 
    The approximation uses Pareto smoothed importance sampling (PSIS), 
    a new procedure for regularizing importance weights. 
    As a byproduct of the calculations, we also obtain approximate 
    standard errors for estimated predictive errors and for the comparison 
    of predictive errors between models. The package also provides methods 
    for using stacking and other model weighting techniques to average 
    Bayesian predictive distributions.
Outlier detection using leave-one-out kernel density estimates and
    extreme value theory. The bandwidth for kernel density estimates is computed 
    using persistent homology, a technique in topological data analysis. Using 
    peak-over-threshold method, a generalized Pareto distribution is fitted to
    the log of leave-one-out kde values to identify outliers.
Simple functions to lookup items in key-value pairs. See
    Mehta (2021) <doi:10.1007/978-1-4842-6613-7_6>.
Fits look-up tables by filling entries with the mean or median values of observations
            fall in partitions of the feature space. Partitions can be determined by user of the
            package using input argument feature.boundaries, and dimensions of the feature space
            can be any combination of continuous and categorical features provided by the data set.
            A Predict function directly fetches corresponding entry value, and a default value is
            defined as the mean or median of all available observations.
            The table and other components are represented using the S4 class lookupTable.
An extendable toolkit for interactive data visualization and exploration.
Data used as examples in the 'loon' package.
Provides a bridge between the 'loon' and  'ggplot2' packages.  Extends the grammar of ggplot to add clauses to create interactive 'loon' plots. Existing ggplot(s) can be turned into interactive 'loon' plots and 'loon' plots into static ggplot(s); the function 'loon.ggplot()' is the bridge from one plot structure to the other.
Package 'shiny' provides interactive web applications in R. Package 'loon' is an interactive toolkit engaged in open-ended, creative and unscripted data exploration. The 'loon.shiny' package can take 'loon' widgets and display a selfsame 'shiny' app.
Implement tour algorithms in interactive graphical system 'loon'.
Performs Levins' loop analysis of qualitatively-specified complex causal systems. Loop analysis makes qualitative predictions of variable change in a system of causally interdependent variables, where "qualitative" means direct causal relationships and indirect causal effects are coded as sign only (i.e. increases, decreases, no change, and ambiguous). This implementation includes output support for graphs in .dot file format for use with visualization software such as 'graphviz' (<https://graphviz.org>). 'LoopAnalyst' provides tools for the construction and output of community matrices, computation and output of community effect matrices, tables of correlations, adjoint, absolute feedback, weighted feedback and weighted prediction matrices, change in life expectancy matrices, and feedback, path and loop enumeration tools.
Detect feedback loops (cycles, circuits) between species (nodes) in ordinary differential equation (ODE) models. Feedback loops are paths from a node to itself without visiting any other node twice, and they have important regulatory functions. Loops are reported with their order of participating nodes and their length, and whether the loop is a positive or a negative feedback loop. An upper limit of the number of feedback loops limits runtime (which scales with feedback loop count). Model parametrizations and values of the modelled variables are accounted for. Computation uses the characteristics of the Jacobian matrix as described e.g. in Thomas and Kaufman (2002) <doi:10.1016/s1631-0691(02)01452-x>. Input can be the Jacobian matrix of the ODE model or the ODE function definition; in the latter case, the Jacobian matrix is determined using 'numDeriv'. Graph-based algorithms from 'igraph' are employed for path detection.
Performs extreme value analysis at multiple locations using functions from the 'evd' package. Supports both point-based and gridded input data using the 'terra' package, enabling flexible looping across spatial datasets for batch processing of generalised extreme value, Gumbel fits.
Common coordinate-based workflows involving processed chromatin loop and genomic element data are considered and packaged into appropriate customizable functions. Includes methods for linking element sets via chromatin loops and creating consensus loop datasets.
Change-point detection algorithm with
 label constraints and a penalty for each change outside of labels.
 Read TD Hocking, A Srivastava (2023) <doi:10.1007/s00180-022-01238-z>
 for details.
Estimates marginal likelihood from a posterior sample using the method described in Wang et al. (2023) <doi:10.1093/sysbio/syad007>, which does not require evaluation of any additional points and requires only the log of the unnormalized posterior density for each sampled parameter vector.
Performs analysis of Differential Item Functioning (DIF) for
        dichotomous and polytomous items using an iterative hybrid of
        ordinal logistic regression and item response theory (IRT) according to 
        Choi, Gibbons, and Crane (2011) <doi:10.18637/jss.v039.i08>.
Estimate covariance matrices that contain low rank and sparse components
Quickly generate lorem ipsum placeholder text. Easy to
    integrate in RMarkdown documents. Includes an RStudio addin to insert
    lorem ipsum into the current document.
The Lorentz transform in special relativity; also the
    gyrogroup structure of three-velocities.  Performs active and
    passive transforms and has the ability to use units in which the
    speed of light is not unity.  Includes some experimental
    functionality for celerity and rapidity.  For general relativity,
    see the 'schwarzschild' package.
Provides two methods of estimating income inequality statistics from binned income data, such as the income data provided in the Census.
  These methods use different interpolation techniques to infer the distribution of incomes within income bins.  One method is an implementation of 
  Jargowsky and Wheeler's mean-constrained integration over brackets (MCIB).  The other method is based on a new technique, Lorenz interpolation, 
  which estimates income inequality by constructing an interpolated Lorenz curve based on the binned income data.  These methods can be used to 
  estimate three income inequality measures: the Gini (the default measure returned), the Theil, and the Atkinson's index.  
  Jargowsky and Wheeler (2018) <doi:10.1177/0081175018782579>.
Inference for the Lorenz and penalized Lorenz regressions. More broadly, the package proposes functions to assess inequality and graphically represent it. The Lorenz Regression procedure is introduced in Heuchenne and Jacquemain (2022) <doi:10.1016/j.csda.2021.107347> and in Jacquemain, A., C. Heuchenne, and E. Pircalabelu (2024) <doi:10.1214/23-EJS2200>.
Analysis, imputation, and multiple imputation of count data using covariates. LORI uses a log-linear Poisson model where main row and column effects, as well as effects of known covariates and interaction terms can be fitted. The estimation procedure is based on the convex optimization of the Poisson loss penalized by a Lasso type penalty and a nuclear norm. LORI returns estimates of main effects, covariate effects and interactions, as well as an imputed count table. The package also contains a multiple imputation procedure. The methods are described in Robin, Josse, Moulines and Sardy (2019) <doi:10.1016/j.jmva.2019.04.004>.
Provides a robust collection of functions tailored for microbial ecology analysis, encompassing both data analysis and visualization. It introduces an encapsulation feature that streamlines the process into a summary object. With the initial configuration of this summary object, users can execute a wide range of analyses with a single line of code, requiring only two essential parameters for setup. The package delivers comprehensive outputs including analysis objects, statistical outcomes, and visualization-ready data, enhancing the efficiency of research workflows. Designed with user-friendliness in mind, it caters to both novices and seasoned researchers, offering an intuitive interface coupled with adaptable customization options to meet diverse analytical needs.
Functions for simulating missing morphometric
	data randomly, with taxonomic bias and with anatomical bias. LOST also 
	includes functions for estimating linear and geometric morphometric data.
Provides a simple mechanism to specify a symmetric block
    diagonal matrices (often used for covariance matrices).  This is based
    on the domain specific language implemented in 'nlmixr2' but expanded
    to create matrices in R generally instead of specifying parts of
    matrices to estimate. It has expanded to include some matrix manipulation
    functions that are generally useful for 'rxode2' and 'nlmixr2'.
Implementation of the LoTTA (Local Trimmed Taylor Approximation) model 
    described in "Bayesian Regression Discontinuity Design with Unknown Cutoff" 
    by Kowalska, van de Wiel, van der Pas (2024) <doi:10.48550/arXiv.2406.11585>.
A curated collection of Howard Phillips 
    Lovecraft's complete stories, collected for the purpose of text 
    analysis.
Performs the trimmed k-means clustering algorithm with lower memory use. It also provides a number of utility functions such as BIC calculations.
Creates lowpass filters which are commonly used in ion channel recordings. It supports generation of random numbers that are filtered, i.e. follow a model for ion channel recordings, see <doi:10.1109/TNB.2018.2845126>. Furthermore, time continuous convolutions of piecewise constant signals with the kernel of lowpass filters can be computed.
Solves quadratic programming problems where the Hessian is represented as the product of two matrices. Thanks to Greg Hunt for helping getting this version back on CRAN. The methods in this package are described in: Ormerod, Wand and Koch (2008) "Penalised spline support vector classifiers: computational issues" <doi:10.1007/s00180-007-0102-8>.
Implementation of Low Walsh Figure of Merit (WAFOM) sequence
        based on Niederreiter-Xing sequence <DOI:10.1007/978-3-642-56046-0_30>.
Implementation of Low Walsh Figure of Merit (WAFOM) sequence
        based on Sobol sequence.
Provides the method for computing the local partial autocorrelation function for locally stationary wavelet time series from Killick, Knight, Nason, Eckley (2020) <doi:10.1214/20-EJS1748>.
Given a postulated model and a set of data, the comparison density is estimated and the deviance test is implemented in order to assess if the data distribution deviates significantly from the postulated model. Finally, the results are summarized in a CD-plot as described in Algeri S. (2019) <arXiv:1906.06615>.
Implements the LPC method of Witten&Tibshirani(Annals of Applied Statistics 2008) for identification of significant genes in a microarray experiment.
Tools for estimation and inference of conditional densities, derivatives and functions. This is the companion software for Cattaneo, Chandak, Jansson and Ma (2024) <doi:10.3150/23-BEJ1711>.
Fitting multivariate data patterns with local principal curves, including tools for data compression (projection) and measuring goodness-of-fit; with some additional functions for mean shift clustering.  See Einbeck, Tutz and Evers (2005) <doi:10.1007/s11222-005-4073-8> and Ameijeiras-Alonso and Einbeck (2023) <doi:10.1007/s11634-023-00575-1>.
Classification method obtained through linear programming.
    It is advantageous with respect to the classical developments when the distribution of the variables
    involved is unknown or when the number of variables is much greater than the number of individuals.
    Mathematical details behind the method are published in Nueda, et al. (2022) "LPDA: A new classification method based on linear programming".
    <doi:10.1371/journal.pone.0270403>.
Without imposing stringent distributional assumptions or shape restrictions, nonparametric estimation has been popular in economics and other social sciences for counterfactual analysis, program evaluation, and policy recommendations. This package implements a novel density (and derivatives) estimator based on local polynomial regressions, documented in Cattaneo, Jansson and Ma (2022) <doi:10.18637/jss.v101.i02>: lpdensity() to construct local polynomial based density (and derivatives) estimator, and lpbwdensity() to perform data-driven bandwidth selection.
It uses 'phenological' and productivity-related variables derived from time series of vegetation 
    indexes, such as the Normalized Difference Vegetation Index, to assess ecosystem dynamics and change, which 
    eventually might drive to land degradation. The final result of the Land Productivity Dynamics indicator 
    is a categorical map with 5 classes of land productivity dynamics, ranging from declining to increasing 
    productivity. See www.sciencedirect.com/science/article/pii/S1470160X21010517/ for a description 
    of the methods used in the package to calculate the indicator.
A nonparametric method to approximate Laplacian graph spectra of a network with 
    ordered vertices. This provides a computationally efficient algorithm for obtaining an 
	accurate and smooth estimate of the graph Laplacian basis. The approximation results can 
	then be used for tasks like change point detection, k-sample testing, and so on. The 
	primary reference is Mukhopadhyay, S. and Wang, K. (2018, Technical Report).
Provides a bunch of algorithms based on linear programming for estimating, under 
    the homogeneity hypothesis, RxC ecological contingency tables (or vote transition matrices) 
    using mainly aggregate data (from voting units). 
    References: 
    Pavía and Romero (2024) <doi:10.1177/00491241221092725>.
    Pavía and Romero (2024) <doi:10.1093/jrsssa/qnae013>.
    Pavía (2023) <doi:10.1007/s43545-023-00658-y>.
    Pavía (2024) <doi:10.1080/0022250X.2024.2423943>.
    Pavía (2024) <doi:10.1177/07591063241277064>.
    Pavía and Penadés (2024). A bottom-up approach for ecological inference.
    Romero, Pavía, Martín and Romero (2020) <doi:10.1080/02664763.2020.1804842>.
    Acknowledgements:
    The authors wish to thank Consellería de Educación, Universidades y Empleo, Generalitat Valenciana (grants AICO/2021/257, CIAICO/2023/031) and Ministerio de Economía e Innovación (grant PID2021-128228NB-I00) for supporting this research.
Functions to estimate the intensity function and its derivative of a given order of a multiplicative counting process using the local polynomial method.
Provides functions to estimate and visualize linear as well as nonlinear impulse 
             responses based on local projections by Jordà (2005) <doi:10.1257/0002828053828518>.
             The methods and the package are explained in detail in Adämmer (2019) <doi:10.32614/RJ-2019-052>.
LP nonparametric high-dimensional K-sample comparison method that includes 
    (i) confirmatory test, (ii) exploratory analysis, and (iii) options to output a 
	data-driven LP-transformed matrix for classification. The primary reference is 
	Mukhopadhyay, S. and Wang, K. (2020, Biometrika); <arXiv:1810.01724>.
Local partial likelihood estimation by Fan, Lin and Zhou(2006)<doi:10.1214/009053605000000796> and simultaneous confidence band is a set of tools to test the covariates-biomarker interaction for survival data. Test for the covariates-biomarker interaction using the bootstrap method and the asymptotic method with simultaneous confidence band (Liu, Jiang and Chen (2015)<doi:10.1002/sim.6563>).
Apply Univariate Long Memory Models,
    Apply Multivariate Short Memory Models To Hydrological Dataset,
    Estimate Intensity Duration Frequency curve to rainfall series.
    NEW -- Calculate the monthly water requirement for herbaceous and arboreal 
    plants.
Creates a consensus genetic map by merging linkage maps from different populations.  The software uses linear programming (LP) to efficiently minimize the mean absolute error between the consensus map and the linkage maps.  This minimization is performed subject to linear inequality constraints that ensure the ordering of the markers in the linkage maps is preserved.  When marker order is inconsistent between linkage maps, a minimum set of ordinal constraints is deleted to resolve the conflicts.
Computes power, or sample size or the detectable difference for a repeated measures model with attrition. It requires the variance covariance matrix of the observations but can compute this matrix for several common random effects models. See Diggle, P, Liang, KY and Zeger, SL (1994, ISBN:9780198522843).
Provide methods to perform customized inference at individual level by taking 
	contextual covariates into account. Three main functions are provided 
	in this package: (i) LASER(): it generates specially-designed artificial relevant 
	samples for a given case; (ii) g2l.proc(): computes customized fdr(z|x); and (iii) 
	rEB.proc(): performs empirical Bayes inference based on LASERs. The details can be 
	found in Mukhopadhyay, S., and Wang, K (2021, <arXiv:2004.09588>).
Local Polynomial Regression with Ridging.
Classical tests of goodness-of-fit aim to validate the conformity of a postulated model to the data under study. In their standard formulation, however, they do not allow exploring how the hypothesized model deviates from the truth nor do they provide any insight into how the rejected model could be improved to better fit the data. To overcome these shortcomings, we establish a comprehensive framework for goodness-of-fit which naturally integrates modeling, estimation, inference and graphics. In this package, the deviance tests and comparison density plots are performed to conduct the LP smoothed inference, where the letter L denotes nonparametric methods based on quantiles and P stands for polynomials. Simulations methods are used to perform variance estimation, inference and post-selection adjustments. Algeri S. and Zhang X. (2020) <arXiv:2005.13011>.
Lp_solve is freely available (under LGPL 2) software for
        solving linear, integer and mixed integer programs. In this
        implementation we supply a "wrapper" function in C and some R
        functions that solve general linear/integer problems,
        assignment problems, and transportation problems. This version
        calls lp_solve version 5.5.
The lpSolveAPI package provides an R interface to 'lp_solve',
    a Mixed Integer Linear Programming (MILP) solver with support for pure
    linear, (mixed) integer/binary, semi-continuous and special ordered sets
    (SOS) models.
Produces a group screening procedure that is based on maximum Lq-likelihood estimation, to simultaneously account for the group structure and data contamination in variable screening. The methods are described in Li, Y., Li, R., Qin, Y., Lin, C., & Yang, Y. (2021) Robust Group Variable Screening Based on Maximum Lq-likelihood Estimation. Statistics in Medicine, 40:6818-6834.<doi:10.1002/sim.9212>.
Estimate linear quantile mixtures based on Time-Constant (TC) and/or Time-Varying (TV), discrete, random coefficients.
Functions to fit quantile regression models for hierarchical
    data (2-level nested designs) as described in Geraci and
    Bottai (2014, Statistics and Computing) <doi:10.1007/s11222-013-9381-9>.
    A vignette is given in Geraci (2014, Journal of Statistical Software)
    <doi:10.18637/jss.v057.i13> and included in the package documents.
    The packages also provides functions to fit quantile models for
    independent	data and for count responses.
It fits a robust linear quantile regression model using a new family of zero-quantile distributions for the error term. Missing values and censored observations can be handled as well. This family of distribution includes skewed versions of the Normal, Student's t, Laplace, Slash and Contaminated Normal distribution. It also performs logistic quantile regression for bounded responses as shown in Galarza et.al.(2020) <doi:10.1007/s13571-020-00231-0>. It provides estimates and full inference. It also provides envelopes plots for assessing the fit and confidences bands when several quantiles are provided simultaneously.
Lexical response data is a package that 
    can be used for processing cued-recall, free-recall, 
    and sentence responses from memory experiments.
The programs were developed for estimation of parameters and testing exponential versus Pareto distribution during our work on hydrologic extremes. See Kozubowski, T.J., A.K. Panorska, F. Qeadan, and A. Gershunov (2007) <doi:10.1080/03610910802439121>, and Panorska, A.K., A. Gershunov, and T.J. Kozubowski (2007) <doi:10.1007/978-0-387-34918-3_26>.
In the fashion of 'node.js' <https://nodejs.org/>, requires a file,
  sourcing into the current environment only the variables explicitly specified
  in the module.exports or exports list variable. If the file was already sourced,
  the result of the earlier sourcing is returned to the caller.
Implements a Gibbs sampler to do linear regression with multiple covariates, multiple responses, Gaussian measurement errors on covariates and responses, Gaussian intrinsic scatter, and a covariate prior distribution which is given by either a Gaussian mixture of specified size or a Dirichlet process with a Gaussian base distribution. Described further in Mantz (2016) <DOI:10.1093/mnras/stv3008>.
Provides S3 classes to represent low rank matrix
    decompositions.
Performs power and sample size calculation for non-proportional hazards model using the Fleming-Harrington family of weighted log-rank tests. The sequentially calculated log-rank test score statistics are assumed to have independent increments as characterized in Anastasios A. Tsiatis (1982) <doi:10.1080/01621459.1982.10477898>. The mean and variance of log-rank test score statistics are calculated based on Kaifeng Lu (2021) <doi:10.1002/pst.2069>. The boundary crossing probabilities are calculated using the recursive integration algorithm described in Christopher Jennison and Bruce W. Turnbull (2000, ISBN:0849303168). The package can also be used for continuous, binary, and count data. For continuous data, it can handle missing data through mixed-model for repeated measures (MMRM). In crossover designs, it can estimate direct treatment effects while accounting for carryover effects. For binary data, it can design Simon's 2-stage, modified toxicity probability-2 (mTPI-2), and Bayesian optimal interval (BOIN) trials. For count data, it can design group sequential trials for negative binomial endpoints with censoring. Additionally, it facilitates group sequential equivalence trials for all supported data types. Moreover, it can design adaptive group sequential trials for changes in sample size, error spending function, number and spacing or future looks. Finally, it offers various options for adjusted p-values, including graphical and gatekeeping procedures.
A collection of hypothesis tests and confidence intervals based on the likelihood ratio
    <https://en.wikipedia.org/wiki/Likelihood-ratio_test>.
Estimates two-dimensional local wavelet spectra.
Wavelet-based methods for testing stationarity and quadtree segmenting of images, see Taylor et al (2014) <doi:10.1080/00401706.2013.823890>.
The basic idea of latent semantic analysis (LSA) is, 
  that text do have a higher order (=latent semantic) structure which, 
  however, is obscured by word usage (e.g. through the use of synonyms 
  or polysemy). By using conceptual indices that are derived statistically 
  via a truncated singular value decomposition (a two-mode factor analysis) 
  over a given document-term matrix, this variability problem can be overcome.
Provides functions that allow for convenient working with vector space models of semantics/distributional semantic models/word embeddings. 
	Originally built for LSA models (hence the name), but can be used for all such vector-based models. 
	For actually building a vector semantic space, use the package 'lsa' or other specialized software. 
	Downloadable semantic spaces can be found at <https://sites.google.com/site/fritzgntr/software-resources>.
Provides a lasso-based method for building mechanistic models using the SAMBA algorithm (Stochastic Approximation for Model Building Algorithm) (M Prague, M  Lavielle (2022) <doi:10.1002/psp4.12742>). The package extends the 'Rsmlx' package (version 2024.1.0) to better handle high-dimensional data. It relies on the 'Monolix' software (version 2024R1; see (<https://monolixsuite.slp-software.com/monolix/2024R1/>), which must be installed beforehand.
Dieses R-Paket stellt Zusatzmaterial in Form von Daten, Funktionen
             und R-Hilfe-Seiten für den Herausgeberband Breit, S. und Schreiner, 
             C. (Hrsg.). (2016). "Large-Scale Assessment mit R: Methodische Grundlagen 
             der österreichischen Bildungsstandardüberprüfung." Wien: facultas. 
             (ISBN: 978-3-7089-1343-8, <https://www.iqs.gv.at/themen/bildungsforschung/publikationen/veroeffentlichte-publikationen>) zur 
             Verfügung.
Provides functions to simulate data from large-scale educational
  assessments, including background questionnaire data and cognitive item
  responses that adhere to a multiple-matrix sampled design. The theoretical
  foundation can be found on
  Matta, T.H., Rutkowski, L., Rutkowski, D. et al. (2018)
  <doi:10.1186/s40536-018-0068-8>.
Bandwidth selection for kernel density estimators of 2-d
    level sets and highest density regions. It applies a plug-in
    strategy to estimate the asymptotic risk function and minimize to
    get the optimal bandwidth matrix. See Doss and Weng (2018)
    <arXiv:1806.00731> for more detail.
Create lots of colorful plots in a plethora of variations. Try the LSD demotour().
Implementation of Locally Scaled Density Based Clustering (LSDBC) algorithm proposed by Bicici and Yuret (2007) <doi:10.1007/978-3-540-71618-1_82>. This package also contains some supporting functions such as betaCV() function and get_spectral() function.
Interfaces R with LSD simulation models. Reads object-oriented data in results files (.res[.gz]) produced by LSD and creates appropriate multi-dimensional arrays in R. Supports multiple core parallel threads of multi-file data reading for increased performance. Also provides functions to extract basic information and statistics from data files. LSD (Laboratory for Simulation Development) is free software developed by Marco Valente and Marcelo C. Pereira (documentation and downloads available at <https://www.labsimdev.org/>).
Performing impulse-response function (IRF) analysis of relevant variables of agent-based simulation models, in particular for models described in 'LSD' format. Based on the data produced by the simulation model, it performs both linear and state-dependent IRF analysis, providing the tools required by the Counterfactual Monte Carlo (CMC) methodology (Amendola and Pereira (2024) <doi:10.2139/ssrn.4740360>), including state identification and sensitivity. CMC proposes retrieving the causal effect of shocks by exploiting the opportunity to directly observe the counterfactual in a fully controlled experimental setup. 'LSD' (Laboratory for Simulation Development) is free software available at <https://www.labsimdev.org/>).
Tools for sensitivity analysis of LSD simulation models. Reads object-oriented data produced by LSD simulation models and performs screening and global sensitivity analysis (Sobol decomposition method, Saltelli et al. (2008) ISBN:9780470725177). A Kriging or polynomial meta-model (Kleijnen (2009) <doi:10.1016/j.ejor.2007.10.013>) is estimated using the simulation data to provide the data required by the Sobol decomposition. LSD (Laboratory for Simulation Development) is free software developed by Marco Valente and Marcelo C. Pereira (documentation and downloads available at <https://www.labsimdev.org/>).
The solution of equality constrained least squares problem (LSE) is
    given through four analytics methods (Generalized QR Factorization, Lagrange 
    Multipliers, Direct Elimination and Null Space method). We expose the 
    orthogonal decomposition called Generalized QR Factorization (GQR) and also RQ 
    factorization. Finally some codes for the solution of LSE applied in 
    quaternions.
Implements bootstrap methods for linear regression models with errors following a time-varying process, focusing on approximating the distribution of the least-squares estimator for regression models with locally stationary errors. It enables the construction of bootstrap and classical confidence intervals for regression coefficients, leveraging intensive simulation studies and real data analysis.
It contains functions that solve least squares linear
	     regression problems under linear equality/inequality
	     constraints. Functions for solving quadratic programming
	     problems are also available, which transform such problems
	     into least squares ones first. It is developed based on the
	     'Fortran' program of Lawson and Hanson (1974, 1995), which is
	     public domain and available at
	     <http://www.netlib.org/lawson-hanson/>.
Analysis of dichotomous and continuous response data using latent factor by both 1PL LSIRM and 2PL LSIRM as described in Jeon et al. (2021) <doi:10.1007/s11336-021-09762-5>. It includes original 1PL LSIRM and 2PL LSIRM provided for binary response data and its extension for continuous response data. Bayesian model selection with spike-and-slab prior and method for dealing data with missing value under missing at random, missing completely at random are also supported. Various diagnostic plots are available to inspect the latent space and summary of estimated parameters.
Fits structural equation modeling via penalized likelihood.
Fits semi-confirmatory structural equation modeling (SEM) via penalized likelihood (PL) or penalized least squares (PLS). For details, please see Huang (2020) <doi:10.18637/jss.v093.i07>.
When the values of the outcome variable Y are either 0 or 1,
      the function lsm() calculates the estimation of the log likelihood 
      in the saturated model. 
      This model is characterized by Llinas (2006, ISSN:2389-8976) in section 2.3 
      through the assumptions 1 and 2. 
      The function LogLik() works (almost perfectly) when the number of independent
      variables K is high, but for small K it calculates wrong values in some cases.
      For this reason, when Y is dichotomous and the data are grouped in J populations,
      it is recommended to use the function lsm() because it works very well for all K.
Obtain least-squares means for linear, generalized linear, 
    and mixed models. Compute contrasts or linear functions of 
    least-squares means, and comparisons of slopes. 
    Plots and compact letter displays. Least-squares means were proposed in
    Harvey, W (1960) "Least-squares analysis of data with unequal subclass numbers",
    Tech Report ARS-20-8, USDA National Agricultural Library, and discussed
    further 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>.
    NOTE: lsmeans now relies primarily on code in the 'emmeans' package.
    'lsmeans' will be archived in the near future.
The package compiles functions for calculating prices of American put options with Least Squares Monte Carlo method. The option types are plain vanilla American put, Asian American put, and Quanto American put. The pricing algorithms include variance reduction techniques such as Antithetic Variates and Control Variates. Additional functions are given to derive "price surfaces" at different volatilities and strikes, create 3-D plots, quickly generate Geometric Brownian motion, and calculate prices of European options with Black & Scholes analytical solution.
The least-squares Monte Carlo (LSM) simulation method is a popular method for the approximation of the value of early and multiple exercise options. 'LSMRealOptions' provides implementations of the LSM simulation method to value American option products and capital investment projects through real options analysis. 'LSMRealOptions' values capital investment projects with cash flows dependent upon underlying state variables that are stochastically evolving, providing analysis into the timing and critical values at which investment is optimal. 'LSMRealOptions' provides flexibility in the stochastic processes followed by underlying assets, the number of state variables, basis functions and underlying asset characteristics to allow a broad range of assets to be valued through the LSM simulation method. Real options projects are further able to be valued whilst considering construction periods, time-varying initial capital expenditures and path-dependent operational flexibility including the ability to temporarily shutdown or permanently abandon projects after initial investment has occurred. The LSM simulation method was first presented in the prolific work of Longstaff and Schwartz (2001) <doi:10.1093/rfs/14.1.113>.
A 'C++' header library for using the 'libsoda-cxx' library with R. The 'C++' header reimplements the 'lsoda' function from the 'ODEPACK' library for solving initial value problems for first order ordinary differential equations (Hindmarsh, 1982; <https://computing.llnl.gov/sites/default/files/ODEPACK_pub1_u88007.pdf>). The 'C++' header can be used by other R packages by linking against this package. The 'C++' functions can be called inline using 'Rcpp'. Finally, the package provides an 'ode' function to call from R.
Tools for statistical analysis using partitioning-based least squares regression as described in Cattaneo, Farrell and Feng (2020a, <doi:10.48550/arXiv.1804.04916>) and Cattaneo, Farrell and Feng (2020b, <doi:10.48550/arXiv.1906.00202>): lsprobust() for nonparametric point estimation of regression functions and their derivatives and for robust bias-corrected (pointwise and uniform) inference; lspkselect() for data-driven selection of the IMSE-optimal number of knots; lsprobust.plot() for regression plots with robust confidence intervals and confidence bands; lsplincom() for estimation and inference for linear combinations of regression functions from different groups.
Creates plots of peptides from shotgun proteomics analysis of secretome and lysate samples. These plots contain associated protein features and scores for potential secretion and truncation.
Linear splines with convenient parametrisations such that 
  (1) coefficients are slopes of consecutive segments or (2) coefficients are 
  slope changes at consecutive knots. Knots can be set manually or at break points
  of equal-frequency or equal-width intervals covering the range of 'x'.
  The implementation follows Greene (2003), chapter 7.2.5.
Implements the LS-PLS (least squares - partial least squares)
  method described in for instance Jørgensen, K., Segtnan, V. H., Thyholt, K.,
  Næs, T. (2004)  "A Comparison of Methods for Analysing Regression Models with
  Both Spectral and Designed Variables"
  Journal of Chemometrics, 18(10), 451--464, <doi:10.1002/cem.890>.
A collection of tools intended to make introductory 
    statistics easier to teach, including wrappers for common 
    hypothesis tests and basic data manipulation. It accompanies 
    Navarro, D. J. (2015). Learning Statistics with R: A Tutorial 
    for Psychology Students and Other Beginners, Version 0.6.
Rapid satellite data streams in operational applications
    have clear benefits for monitoring land cover, 
    especially when information can be delivered as fast as changing
    surface conditions. Over the past decade,
    remote sensing has become a key tool for monitoring and predicting
    environmental variables by using satellite data. 
    This package presents the main applications in remote sensing for 
    land surface monitoring and land cover mapping (soil, vegetation, water...).
     Tomlinson, C.J., Chapman, L., Thornes, E., Baker, C (2011) <doi:10.1002/met.287>.
Due to lack of proper inference procedure and software,
        the ordinary linear regression model is seldom used in practice
        for the analysis of right censored data. This paper presents an
        S-Plus/R program that implements a recently developed inference
        procedure (Jin, Lin and Ying, 2006) <doi:10.1093/biomet/93.1.147> 
        for the accelerated failure time model based on the least-squares
        principle.
Calculates Land Surface Temperature from Landsat band 10 and 11.
  Revision of the Single-Channel Algorithm for Land Surface Temperature Retrieval From Landsat Thermal-Infrared Data. Jimenez-Munoz JC, Cristobal J, Sobrino JA, et al (2009). <doi: 10.1109/TGRS.2008.2007125>.
  Land surface temperature retrieval from LANDSAT TM 5. Sobrino JA, Jiménez-Muñoz JC, Paolini L (2004). <doi:10.1016/j.rse.2004.02.003>.
  Surface temperature estimation in Singhbhum Shear Zone of India using Landsat-7 ETM+ thermal infrared data. Srivastava PK, Majumdar TJ, Bhattacharya AK (2009). <doi: 10.1016/j.asr.2009.01.023>.
  Mapping land surface emissivity from NDVI: Application to European, African, and South American areas. Valor E (1996). <doi:10.1016/0034-4257(96)00039-9>.
  On the relationship between thermal emissivity and the normalized difference vegetation index for natural surfaces. Van de Griend AA, Owe M (1993). <doi:10.1080/01431169308904400>.
  Land Surface Temperature Retrieval from Landsat 8 TIRS—Comparison between Radiative Transfer Equation-Based Method, Split Window Algorithm and Single Channel Method. Yu X, Guo X, Wu Z (2014). <doi:10.3390/rs6109829>.
  Calibration and Validation of land surface temperature for Landsat8-TIRS sensor. Land product validation and evolution. Skoković D, Sobrino JA, Jimenez-Munoz JC, Soria G, Julien Y, Mattar C, Cristóbal J. (2014).
"Lessons in Statistical Thinking" D.T. Kaplan (2014) 
    <https://dtkaplan.github.io/Lessons-in-statistical-thinking/> 
    is a textbook for a first or second course in statistics that embraces 
    data wrangling, causal reasoning, modeling, statistical adjustment, 
    and simulation. 'LSTbook' supports the student-centered, tidy, 
    pipeline-oriented computing style featured in the book.
A method for factor retention using a pre-trained Long Short Term Memory (LSTM) Network, 
             which is originally developed by 
             Hochreiter and Schmidhuber (1997) <doi:10.1162/neco.1997.9.8.1735>, is provided. 
             The sample size of the dataset used to train the LSTM model is 1,000,000. 
             Each sample is a batch of simulated response data with a specific latent factor structure. 
             The eigenvalues of these response data will be used as sequential data to train the LSTM. 
             The pre-trained LSTM is capable of factor retention for real response data with a 
             true latent factor number ranging from 1 to 10, that is, determining the number of factors.
A set of functions that allow stationary analysis and locally stationary time series analysis.
Implementations of estimation algorithm of low rank plus sparse structured VAR model by using Fast Iterative Shrinkage-Thresholding Algorithm (FISTA). It relates to the algorithm in Sumanta, Li, and Michailidis (2019) <doi:10.1109/TSP.2018.2887401>.
Library of functions for the statistical analysis and simulation of Locally Stationary Wavelet Packet (LSWP) processes.  The methods implemented by this library are described in Cardinali and Nason (2017) <doi:10.1111/jtsa.12230>.
A word embeddings-based semi-supervised model for document scaling Watanabe (2020) <doi:10.1080/19312458.2020.1832976>.
    LSS allows users to analyze large and complex corpora on arbitrary dimensions with seed words exploiting efficiency of word embeddings (SVD, Glove).
    It can generate word vectors on a users-provided corpus or incorporate a pre-trained word vectors.
Constructs tables of counts and proportions out of data sets with possibility to insert tables to Excel, Word, HTML, and PDF documents. Transforms tables to data suitable for modelling. Features Gibbs sampling based log-linear (NB2) and power analyses (original by Oleksandr Ocheredko <doi:10.35566/isdsa2019c5>) for tabulated data.
A suite of functions for reading in a rate file in XML format, 
    stratify a cohort, and calculate 'SMRs' from the stratified cohort and rate file.
Implementation of the three-step approach of latent transition cognitive diagnosis model (CDM) with covariates. This approach can be used to assess changes in attribute mastery status and to evaluate the covariate effects on both the initial states and transition probabilities over time using latent logistic regression. Because stepwise approaches often yield biased estimates, correction for classification error probabilities (CEPs) is considered in this approach. The three-step approach for latent transition CDM with covariates involves the following steps: (1) fitting a CDM to the response data without covariates at each time point separately, (2) assigning examinees to latent states at each time point and computing the associated CEPs, and (3) estimating the latent transition CDM with the known CEPs and computing the regression coefficients. The method was proposed in Liang et al. (2023) <doi:10.3102/10769986231163320> and demonstrated using mental health data in Liang et al. (in press; annotated R code and data utilized in this example are available in Mendeley data) <doi:10.17632/kpjp3gnwbt.1>.
Curated datasets from US Long Term Ecological Research sites.
Allows identification of palettes derived from LTER (Long Term Ecological Research) 
   photographs based on user criteria.
   Also facilitates extraction of palettes from users' photos directly.
Set of the data science tools created by various members of the Long Term 
    Ecological Research (LTER) community. These functions were initially written largely 
    as standalone operations and have later been aggregated into this package.
Implementation of several phenotype-based family genetic risk scores 
  with unified input data and data preparation functions to help facilitate
  the required data preparation and management. The implemented family genetic
  risk scores are the extended liability threshold model conditional on family history (LT-FH++)
  from Pedersen (2022) <doi:10.1016/j.ajhg.2022.01.009> and Pedersen (2023)  <https://www.nature.com/articles/s41467-023-41210-z>,
  Pearson-Aitken Family Genetic Risk Scores (PA-FGRS) from Krebs (2024) <doi:10.1016/j.ajhg.2024.09.009>,
  and family genetic risk score by Kendler (2021) <doi:10.1001/jamapsychiatry.2021.0336>.
Implementation of LT-FH++, an extension of
    the liability threshold family history (LT-FH) model.
    LT-FH++ uses a Gibbs sampler for sampling from the truncated 
    multivariate normal distribution and allows for 
    flexible family structures. LT-FH++ was first described in 
    Pedersen, Emil M., et al. (2022) 
    <doi:10.1016/j.ajhg.2022.01.009> 
    as an extension to LT-FH with more flexible family structures, 
    and again as the age-dependent liability threshold (ADuLT) model
    Pedersen, Emil M., et al. (2023) 
    <https://www.nature.com/articles/s41467-023-41210-z> 
    as an alternative to traditional time-to-event genome-wide
    association studies, where family history was not considered.
Analysis of multivariate dichotomous and polytomous data using latent trait models under the Item Response Theory approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's Three-Parameter, the Graded Response, and the Generalized Partial Credit Models.
Mixture modelling of one-dimensional data using combinations of left-truncated Gamma, Weibull, and Lognormal Distributions. Blostein, Martin & Miljkovic, Tatjana. (2019) <doi:10.1016/j.insmatheco.2018.12.001>.
Targeted Maximum Likelihood Estimation ('TMLE') of
    treatment/censoring specific mean outcome or marginal structural model for
    point-treatment and longitudinal data.
Calculation of rectifying LTPD and AOQL plans for sampling inspection by variables which minimize mean inspection cost per lot of process average quality.
Recursive partition algorithms designed for fitting survival trees with left-truncated and right-censored (LTRC) data, as well as interval-censored data.
    The LTRC trees can also be used to fit survival trees with time-varying covariates.
Methods of developing linear time series modelling.
 Methods are given for loglikelihood computation, forecasting
  and simulation.
Implements local spatial and local spatiotemporal Kriging based on local spatial and local spatiotemporal variograms, respectively. The method is documented in Kumar et al (2013) <https://www.nature.com/articles/jes201352)>.
Implementation of robust and sparse PCA algorithm of Wang and Van Aelst (2019) <DOI:10.1080/00401706.2019.1671234>.
Sparklines are small plots (about one line of text high),
  made popular by Edward Tufte.  This package is the interface from R
  to the LaTeX package sparklines by Andreas Loeffer and Dan Luecking
  (<http://www.ctan.org/pkg/sparklines>).  It can work with Sweave or
  knitr or other engines that produce TeX.  The package can be used to
  plot vectors, matrices, data frames, time series (in ts or zoo format).
An interface to 'LuaJIT' <https://luajit.org>, a just-in-time 
    compiler for the 'Lua' scripting language <https://www.lua.org>. Allows 
    users to run 'Lua' code from 'R'.
Functions to work with date-times and time-spans: fast and
    user friendly parsing of date-time data, extraction and updating of
    components of a date-time (years, months, days, hours, minutes, and
    seconds), algebraic manipulation on date-time and time-span objects.
    The 'lubridate' package has a consistent and memorable syntax that
    makes working with dates easy and fun.
Provides a set of tools designed to enhance transparency and understanding of date-time manipulation functions from the 'lubridate' package. 
        It provides detailed feedback about the operations performed by 'lubridate' functions, allowing users to better comprehend and debug their code. 
        These insights serve as both a learning tool for newcomers and a debugging aid for programmers working with date-time data.
Reproduces the harmonized DB of the ESTAT survey of the same name. The survey data is served as separate spreadsheets with noticeable differences in the collected attributes. The tool here presented carries out a series of instructions that harmonize the attributes in terms of name, meaning, and occurrence, while also introducing a series of new variables, instrumental to adding value to the product. Outputs include one harmonized table with all the years, and three separate geometries, corresponding to the theoretical point, the gps location where the measurement was made and the 250m east-facing transect.
Print vectors (and data frames) of floating point numbers
    using a non-scientific format optimized for human readers.  Vectors of
    numbers are rounded using significant digits, aligned at the decimal
    point, and all zeros trailing the decimal point are dropped.  See:
    Wright (2016). Lucid: An R Package for Pretty-Printing Floating Point
    Numbers. In JSM Proceedings, Statistical Computing Section.
    Alexandria, VA: American Statistical Association. 2270-2279.
An implementation of estimating the Latent Unknown Clusters By Integrating Multi-omics Data (LUCID) model (Peng (2019) <doi:10.1093/bioinformatics/btz667>). LUCID conducts integrated clustering using exposures, omics information (and outcome information as an option). This package implements three different integration strategies for multi-omics data analysis within the LUCID framework: LUCID early integration (the original LUCID model), LUCID in parallel (intermediate integration), and LUCID in serial (late integration). Automated model selection for each LUCID model is available to obtain the optimal number of latent clusters, and an integrated imputation approach is implemented to handle sporadic and list-wise missingness in multi-omics data. Lasso-type regularity for exposure and omics features were added. S3 methods for summary and plotting functions were fixed. Fixed minor bugs.
Probabilistic record linkage without direct identifiers using only 
    diagnosis codes. Method is detailed in: Hejblum, Weber, Liao, Palmer, 
    Churchill, Szolovits, Murphy, Kohane & Cai (2019) <doi: 10.1038/sdata.2018.298> ;
    Zhang, Hejblum, Weber, Palmer, Churchill, Szolovits, Murphy, Liao, Kohane 
    & Cai (2021) <doi: 10.1101/2021.05.02.21256490>.
Contains LUE_BIOMASS(),LUE_BIOMASS_VPD(), LUE_YIELD() and LUE_YIELD_VPD() to estimate aboveground biomass and crop yield firstly by calculating the Absorbed Photosynthetically Active Radiation (APAR) and secondly the actual values of light use efficiency with and without vapour presure deficit Shi et al.(2007) <doi:10.2134/agronj2006.0260>.
Miscellaneous functions commonly used by LuLab. This package aims to help more researchers on epidemiology to perform data management and visualization more efficiently.
Classes and methods for spatially explicit land use change
    modelling in R.
A framework that allows for easy logging of changes in data.
    Main features: start tracking changes by adding a single line of code to 
    an existing script. Track changes in multiple datasets, using multiple 
    loggers. Add custom-built loggers or use loggers offered by other 
    packages. <doi:10.18637/jss.v098.i01>.
A collection of various R functions for the purpose of Luminescence
    dating data analysis. This includes, amongst others, data import, export,
    application of age models, curve deconvolution, sequence analysis and
    plotting of equivalent dose distributions.
Provides functions to calculate lunar and other related
    environmental covariates.
Input latitude and longitude values or an 'sf/sfc' POINT 
    object and get back the time zone in which they exist. Two methods are implemented. 
    One is very fast and uses 'Rcpp' in conjunction with data from the 'Javascript' library
    (<https://github.com/darkskyapp/tz-lookup-oss/>). This method also works outside of countries' 
    borders and in international waters, however speed comes at the cost of accuracy - near time 
    zone borders away from populated centres there is a chance that it will return the incorrect
    time zone. The other method is slower but more accurate - it uses the 'sf' package to intersect 
    points with a detailed map of time zones from here: 
    <https://github.com/evansiroky/timezone-boundary-builder/>. The package also 
    contains several utility functions for helping to understand and visualize 
    time zones, such as listing of world time zones, including information about 
    daylight savings times and their offsets from UTC. You can also plot a 
    time zone to visualize the UTC offset over a year and when daylight savings 
    times are in effect.
A high level interface for 'torch' providing utilities to reduce the
    the amount of code needed for common tasks, abstract away torch details and 
    make the same code work on both the 'CPU' and 'GPU'. It's flexible enough to
    support expressing a large range of models. It's heavily inspired by 'fastai' by 
    Howard et al. (2020) <arXiv:2002.04688>, 'Keras' by Chollet et al. (2015) and 
    'PyTorch Lightning' by Falcon et al. (2019) <doi:10.5281/zenodo.3828935>.
Provides flexible but lightweight logging facilities for R scripts.
    Supports priority levels for logs and messages, flagging messages, capturing
    script output, switching logs, and logging to files or connections.
Fit response surfaces for datasets with latent-variable Gaussian process modeling, predict responses for new inputs, and plot latent variables locations in the latent space (only 1D or 2D).
    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 is done using a successive approximation/relaxation algorithm similar to another GP modeling package "GPM".
    The modeling method is published in "A Latent Variable Approach to Gaussian Process Modeling with Qualitative and Quantitative Factors"
    by Yichi Zhang, Siyu Tao, Wei Chen, and Daniel W. Apley (2018) <arXiv:1806.07504>. The package is developed in IDEAL of Northwestern University.
Provides stochastic EM algorithms for latent variable models
    with a high-dimensional latent space. So far, we provide functions for confirmatory item
    factor analysis based on the multidimensional two parameter logistic (M2PL) model and the 
    generalized multidimensional partial credit model. These functions scale well for problems
    with many latent traits (e.g., thirty or even more) and are virtually tuning-free.
    The computation is facilitated by multiprocessing 'OpenMP' API.
    For more information, please refer to:
    Zhang, S., Chen, Y., & Liu, Y. (2018). An Improved Stochastic EM Algorithm for Large-scale
    Full-information Item Factor Analysis. British Journal of Mathematical and Statistical
    Psychology. <doi:10.1111/bmsp.12153>.
Contains a collection of useful
    functions for basic data computation and manipulation,
    wrapper functions for generating 'ggplot2' graphics,
    including statistical model diagnostic plots, methods
    for computing statistical models quality measures (such
    as AIC, BIC, r squared, root mean squared error) and
    general utilities.
Estimate, fit and compare Structural Equation Models (SEM) and network models (Gaussian Graphical Models; GGM) using OpenMx. Allows for two possible generalizations to include GGMs in SEM: GGMs can be used between latent variables (latent network modeling; LNM) or between residuals (residual network modeling; RNM). For details, see Epskamp, Rhemtulla and Borsboom (2017) <doi:10.1007/s11336-017-9557-x>.
Implements the letter value 'boxplot' which extends the
    standard 'boxplot' to deal with both larger and smaller number of data
    points by dynamically selecting the appropriate number of letter
    values to display.
Generates the Langa-Weir classification of cognitive function for 
    the 2022 Health and Retirement Study (HRS) cognition data. It is 
    particularly useful for researchers studying cognitive aging who wish to 
    work with the most recent release of HRS data. The package provides 
    user-friendly functions for data preprocessing, scoring, and classification
    allowing users to easily apply the Langa-Weir classification system. 
    For details regarding the;
    HRS <https://hrsdata.isr.umich.edu/> and
    Langa-Weir classifications <https://hrsdata.isr.umich.edu/data-products/langa-weir-classification-cognitive-function-1995-2020>.
Provides a flexible and easy-to use interface for the soil vegetation 
    atmosphere transport (SVAT) model LWF-BROOK90, written in Fortran.
    The model simulates daily transpiration, interception, soil and snow evaporation, 
    streamflow and soil water fluxes through a soil profile covered with vegetation, 
    as described in Hammel & Kennel (2001, ISBN:978-3-933506-16-0) and Federer et al. (2003) 
    <doi:10.1175/1525-7541(2003)004%3C1276:SOAETS%3E2.0.CO;2>. A set of high-level functions
    for model set up, execution and parallelization provides easy access to plot-level SVAT 
    simulations, as well as multi-run and large-scale applications.
Access to selected functions found in 'liblwgeom' <https://github.com/postgis/postgis/tree/master/liblwgeom>, the light-weight geometry library used by 'PostGIS' <http://postgis.net/>.
Wrapper functions for the implementation of lagged weighted quantile sum regression, as per 'Gennings et al' (2020) <doi:10.1016/j.envres.2020.109529>.
An implementation of algorithms described in Jewell and Witten (2017) <arXiv:1703.08644>.
Provide access to  the 'lz-string' 
    <http://pieroxy.net/blog/pages/lz-string/index.html> 'C++' library for 
    Lempel-Ziv (LZ) based compression and decompression of strings.
Prediction of behaviour from movement 
	characteristics using observation and random forest for the analyses of movement
	data in ecology.
	From movement information (speed, bearing...) the model predicts the
	observed behaviour (movement, foraging...) using random forest. The
	model can then extrapolate behavioural information to movement data
	without direct observation of behaviours.
	The specificity of this method relies on the derivation of multiple predictor variables from the
	movement data over a range of temporal windows. This procedure allows to capture
	as much information as possible on the changes and variations of movement and
	ensures the use of the random forest algorithm to its best capacity. The method
	is very generic, applicable to any set of data providing movement data together with
	observation of behaviour.
Persistent interface to 'Macaulay2' <https://www.macaulay2.com>
    and front-end tools facilitating its use in the 'R' ecosystem. For details see 
    Kahle et. al. (2020) <doi:10.18637/jss.v093.i09>.
A new method to implement clustering from multiple modality data of certain samples, 
    the function M2SMF() jointly factorizes multiple similarity matrices into a shared sub-matrix 
    and several modality private sub-matrices, which is further used for clustering. Along with 
    this method, we also provide function to calculate the similarity matrix and function to 
    evaluate the best cluster number from the original data.
A new method to implement clustering from multiple modality data of certain samples, 
    the function M2SMjF() jointly factorizes multiple similarity matrices into a shared sub-matrix 
    and several modality private sub-matrices, which is further used for clustering. Along with 
    this method, we also provide function to calculate the similarity matrix and function to 
    evaluate the best cluster number from the original data.
Provides functions to read in and manipulate air quality model output from Models3-formatted files.  This format is used by the Community Multiscale Air Quality (CMAQ) model.
Multi modality data matrices are factorized conjointly into the multiplication of a shared sub-matrix and multiple modality specific sub-matrices, group sparse constraint is applied to the shared sub-matrix to capture the homogeneous and heterogeneous information, respectively. Then the samples are classified by clustering the shared sub-matrix with kmeanspp(), a new version of kmeans() developed here to obtain concordant results. The package also provides the cluster number estimation by rotation cost. Moreover, cluster specific features could be retrieved using hypergeometric tests.
Data manipulation in one package and in base R.
  Minimal. No dependencies.
  'dplyr' and 'tidyr'-like in one place.
  Nothing else than base R to build the package.
A computational method developed for model-based analysis of alternative polyadenylation (APA) using 3' end-linked reads. It accurately assigns 3' RNA-seq reads to polyA sites through statistical modeling, and generates multiple statistics for APA analysis. Please also see Li WV, Zheng D, Wang R, Tian B (2021) <doi:10.1186/s13059-021-02429-5>.
Provides an extension of the shadow-test approach to computerized adaptive
    testing (CAT) implemented in the 'TestDesign' package for the assessment framework
    involving multiple tests administered periodically throughout the year. This framework
    is referred to as the Multiple Administrations Adaptive Testing (MAAT) and supports
    multiple item pools vertically scaled and multiple phases (stages) of CAT within each test.
    Between phases and tests, transitioning from one item pool (and associated constraints)
    to another is allowed as deemed necessary to enhance the quality of measurement.
Easy implementation of the MABAC multi-criteria decision method, that was introduced by Pamučar and Ćirović in the work entitled: "The selection of transport and handling resources in logistics centers using Multi-Attributive Border Approximation area Comparison (MABAC)" - <doi:10.1016/j.eswa.2014.11.057> - which aimed to choose implements for logistics centers. This package receives data, preferably in a spreadsheet, reads it and applies the mathematical algorithms inherent to the MABAC method to generate a ranking with the optimal solution according to the established criteria, weights and type of criteria. The data will be normalized, weighted by the weights, the border area will be determined, the distances to this border area will be calculated and finally a ranking with the optimal option will be generated.
Fit data from a continuous population with a smooth density on finite interval by an approximate Bernstein polynomial model which is a mixture of certain beta distributions and find maximum approximate Bernstein likelihood estimator of the unknown coefficients. Consequently, maximum likelihood estimates of the unknown density, distribution functions, and more can be obtained. If the support of the density is not the unit interval then transformation can be applied. This is an implementation of the methods proposed by the author of this package published in the Journal of Nonparametric Statistics: Guan (2016) <doi:10.1080/10485252.2016.1163349> and Guan (2017) <doi:10.1080/10485252.2017.1374384>. For data with covariates, under some semiparametric regression models such as Cox proportional hazards model and the accelerated failure time model, the baseline survival function can be estimated smoothly based on general interval censored data.
Conducts and simulates the MABOUST design, including making interim decisions to stop a treatment for inferiority or stop the trial early for superiority or equivalency.
Efficient way to design and conduct psychological experiments for testing the performance of large language models. It simplifies the process of setting up experiments and data collection via language models’ API, facilitating a smooth workflow for researchers in the field of machine behaviour.
To assist biological researchers in assembling taxonomically and marker focused molecular sequence data sets. 'MACER' accepts a list of genera as a user input and uses NCBI-GenBank and BOLD as resources to download and assemble molecular sequence datasets. These datasets are then assembled by marker, aligned, trimmed, and cleaned. The use of this package allows the publication of specific parameters to ensure reproducibility. The 'MACER' package has four core functions and an example run through using all of these functions can be found in the associated repository <https://github.com/rgyoung6/MACER_example>.
Meta-package for statistical and machine learning with a unified
    interface for model fitting, prediction, performance assessment, and
    presentation of results.  Approaches for model fitting and prediction of
    numerical, categorical, or censored time-to-event outcomes include
    traditional regression models, regularization methods, tree-based methods,
    support vector machines, neural networks, ensembles, data preprocessing,
    filtering, and model tuning and selection.  Performance metrics are provided
    for model assessment and can be estimated with independent test sets, split
    sampling, cross-validation, or bootstrap resampling.  Resample estimation
    can be executed in parallel for faster processing and nested in cases of
    model tuning and selection.  Modeling results can be summarized with
    descriptive statistics; calibration curves; variable importance; partial
    dependence plots; confusion matrices; and ROC, lift, and other performance
    curves.
Download data from the Ada and Archibald MacLeish Field 
    Station in Whately, MA. The Ada 
    and Archibald MacLeish Field Station is a 260-acre patchwork of 
    forest and farmland located in West Whately, MA that provides opportunities 
    for faculty and students to pursue environmental research, outdoor 
    education, and low-impact recreation 
    (see <https://www.smith.edu/about-smith/sustainable-smith/macleish> for more information). 
    This package contains 
    weather data over several years, and spatial data on various man-made and 
    natural structures.
Following the common types of measures of uncertainty for parameter estimation, two measures of uncertainty were proposed for model selection, see Liu, Li and Jiang (2020) <doi:10.1007/s11749-020-00737-9>. The first measure is a kind of model confidence set that relates to the variation of model selection, called Mac. The second measure focuses on error of model selection, called LogP. They are all computed via bootstrapping. This package provides functions to compute these two measures. Furthermore, a similar model confidence set adapted from Bayesian Model Averaging can also be computed using this package.
Procedures for simulating biomes by equilibrium vegetation 
  models, with a special focus on paleoenvironmental applications.
  Three widely used equilibrium biome models are currently implemented in 
  the package: the Holdridge Life Zone (HLZ) system (Holdridge 1947, 
  <doi:10.1126/science.105.2727.367>), the Köppen-Geiger classification 
  (KGC) system (Köppen 1936, 
  <https://koeppen-geiger.vu-wien.ac.at/pdf/Koppen_1936.pdf>) and the 
  BIOME model (Prentice et al. 1992, <doi:10.2307/2845499>). Three 
  climatic forest-steppe models are also implemented.
  An approach for estimating monthly time series of relative sunshine 
  duration from temperature and precipitation data (Yin 1999, 
  <doi:10.1007/s007040050111>) is also adapted, allowing 
  process-based biome models to be combined with high-resolution 
  paleoclimate simulation datasets (e.g., CHELSA-TraCE21k v1.0 dataset: 
  <https://chelsa-climate.org/chelsa-trace21k/>).
This repository aims to contribute to the econometric models' production
	with Colombian data, by providing a set of web-scrapping functions 
	of some of the main macro-financial indicators. All the sources are public and
	free, but the advantage of these functions is that they directly download 
	and harmonize the information in R's environment. No need to import or download
	additional files. You only need an internet connection!
Use standard genomics file format (BED) and a table of orthologs to 
 illustrate synteny conservation at the genome-wide scale. 
 Significantly conserved linkage groups are identified as described in Simakov et al. (2020) <doi:10.1038/s41559-020-1156-z> 
 and displayed on an Oxford Grid (Edwards (1991) <doi:10.1111/j.1469-1809.1991.tb00394.x>) or a chord diagram as in Simakov et al. (2022) <doi:10.1126/sciadv.abi5884>. 
 The package provides a function that uses a network-based greedy algorithm to find communities (Clauset et al. (2004) <doi:10.1103/PhysRevE.70.066111>) 
 and so automatically order the chromosomes on the plot to improve interpretability.
Includes functions  for calculating basic indices of macrozoobenthos for water quality and is designed to provide researchers and environmental professionals with a comprehensive tool for evaluating the ecological health of aquatic ecosystems.The package is based on the following references: Paisley, M. F., Trigg, D. J. and Walley, W. J. (2014)<doi:10.1002/rra.2686>. Arslan, N., Salur, A., Kalyoncu, H. et al.(2016)  <doi:10.1515/biolog-2016-0005>. Hilsenhoff W.L. (1987). Hilsenhoff. W.L. (1988)  Barbour, M.T., Gerritsen, J., Snyder, B.D., and Stribling, J.B. (1999).
Provides methods and classes for adding m-activation ("multiplicative activation") layers to MLR or multivariate logistic regression models.  M-activation layers created in this library detect and add input interaction (polynomial) effects into a predictive model.  M-activation can detect high-order interactions -- a traditionally non-trivial challenge.  Details concerning application, methodology, and relevant survey literature can be found in this library's vignette, "About."
Performs causal mediation analysis for count and zero-inflated
    count data without or with a post-treatment confounder; calculates power
    to detect prespecified causal mediation effects, direct effects, and 
    total effects; performs sensitivity analysis when there is a treatment-
    induced mediator-outcome confounder as described by Cheng, J., Cheng, N.F., 
    Guo, Z., Gregorich, S., Ismail, A.I., Gansky, S.A. (2018) 
    <doi:10.1177/0962280216686131>. Implements Instrumental Variable (IV) 
    method to estimate the controlled (natural) direct and mediation effects, 
    and compute the bootstrap Confidence Intervals as described by Guo, Z., 
    Small, D.S., Gansky, S.A., Cheng, J. (2018) <doi:10.1111/rssc.12233>. This 
    software was made possible by Grant R03DE028410 from the National 
    Institute of Dental and Craniofacial Research, a component of the National 
    Institutes of Health.
A collection of functions for conducting a meta-analysis with mean differences data.  It uses recommended procedures as	described in The 	Handbook of Research Synthesis and Meta-Analysis	(Cooper, Hedges, & Valentine, 2009).
Provides functions for diagnostic meta-analysis. Next to basic analysis and visualization the bivariate Model of Reitsma et al. (2005) that is equivalent to the HSROC of Rutter & Gatsonis (2001) can be fitted. A new approach based to diagnostic meta-analysis of Holling et al. (2012) is also available. Standard methods like summary, plot and so on are provided.
This is an open-source software designed specifically for text mining in the Persian language. It allows users to examine word frequencies, download data for analysis, and generate word clouds. This tool is particularly useful for researchers and analysts working with Persian language data.
    This package mainly makes use of the 'PersianStemmer' (Safshekan, R., et al. (2019). <https://CRAN.R-project.org/package=PersianStemmer>),
    'udpipe' (Wijffels, J., et al. (2023). <https://CRAN.R-project.org/package=udpipe>),
    and 'shiny' (Chang, W., et al. (2023). <https://CRAN.R-project.org/package=shiny>) packages.
Provides an extension to 'MadanText' for creating and analyzing co-occurrence networks in Persian text data.
             This package mainly makes use of the 'PersianStemmer' (Safshekan, R., et al. (2019). <https://CRAN.R-project.org/package=PersianStemmer>),
             'udpipe' (Wijffels, J., et al. (2023). <https://CRAN.R-project.org/package=udpipe>),
             and 'shiny' (Chang, W., et al. (2023). <https://CRAN.R-project.org/package=shiny>) packages.
Contains the Maddison Project 2018 database, which provides 
    estimates of GDP per capita for all countries in the world between AD 1 and
    2016. See <https://www.rug.nl/ggdc/historicaldevelopment/maddison/> for more information.
A Momentumized, Adaptive, Dual Averaged Gradient Method for Stochastic 
  Optimization algorithm. MADGRAD is a 'best-of-both-worlds' optimizer with the 
  generalization performance of stochastic gradient descent and at least as fast 
  convergence as that of Adam, often faster. A drop-in optim_madgrad() implementation
  is provided based on Defazio et al (2020) <arxiv:2101.11075>.
Provides pipe-style interface for 'data.table'. Package preserves all 'data.table' features without
              significant impact on performance. 'let' and 'take' functions are simplified interfaces for most common data
              manipulation tasks. For example, you can write 'take(mtcars, mean(mpg), by = am)' for aggregation or 
              'let(mtcars, hp_wt = hp/wt, hp_wt_mpg = hp_wt/mpg)' for modification. Use 'take_if/let_if' for conditional
              aggregation/modification. Additionally there are some conveniences such as automatic 'data.frame' 
              conversion to 'data.table'.
This system allows one to model a multi-variate, multi-response
    problem with interaction effects. It combines the usual squared error loss
    for the multi-response problem with some penalty terms to encourage
    responses that correlate to form groups and also allow for modeling main and
    interaction effects that exit within the covariates.
    The optimization method employed is the Alternating Direction Method of
    Multipliers (ADMM). The implementation is based on the methodology
    presented on Quachie Asenso, T., & Zucknick, M. (2023)
    <doi:10.48550/arXiv.2303.11155>.
An object that supports automatic differentiation
    of matrix- and multidimensional-valued functions with 
    respect to multidimensional independent variables. 
    Automatic differentiation is via 'forward accumulation'.
Tools for the analysis of population differences
    using the Major Histocompatibility Complex (MHC) genotypes of samples
    having a variable number of alleles (1-4) recorded for each
    individual.  A hierarchical Dirichlet-Multinomial model on the
    genotype counts is used to pool small samples from multiple
    populations for pairwise tests of equality.  Bayesian inference is
    implemented via the 'rstan' package.  Bootstrapped and posterior
    p-values are provided for chi-squared and likelihood ratio tests of
    equal genotype probabilities.
Estimates average treatment effects using model average double robust (MA-DR) estimation. The MA-DR estimator is defined as weighted average of double robust estimators, where each double robust estimator corresponds to a specific choice of the outcome model and the propensity score model. The MA-DR estimator extend the desirable double robustness property by achieving consistency under the much weaker assumption that either the true propensity score model or the true outcome model be within a specified, possibly large, class of models.
Provides a framework which should improve reproducibility and
    transparency in data processing. It provides functionality such as
    automatic meta data creation and management, rudimentary quality
    management, data caching, work-flow management and data aggregation.
    * The title is a wish not a promise. By no means we expect this
    package to deliver everything what is needed to achieve full
    reproducibility and transparency, but we believe that it supports
    efforts in this direction.
Functions to support data cleaning, evaluation, and description, 
     developed for integration with Maelstrom Research software tools. 'madshapR' 
     provides functions primarily to evaluate and manipulate datasets and 
     data dictionaries in preparation for data harmonization with the package 
     'Rmonize' and to facilitate integration and transfer between RStudio servers 
     and secure Opal environments. 'madshapR' functions can be used independently
     but are optimized in conjunction with ‘Rmonize’ functions for streamlined 
     and coherent harmonization processing.
This function allows to generate two biological conditions synthetic 
             microarray dataset which has similar behavior to those currently 
             observed with common platforms. User provides a subset of parameters.
             Available default parameters settings can be modified.
Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
A bundle of functions for modifying MAESTRA/MAESPA input files,reading output files, and visualizing the stand in 3D. Handy for running sensitivity analyses, scenario analyses, etc.
Interfaces the Python library 'zuko' implementing Masked Autoregressive Flows. See Rozet, Divo and Schnake (2023) <doi:10.5281/zenodo.7625672> and Papamakarios, Pavlakou and Murray (2017) <doi:10.48550/arXiv.1705.07057>.
Data class for increased interoperability working with
    spatial-temporal data together with corresponding functions and
    methods (conversions, basic calculations and basic data manipulation).
    The class distinguishes between spatial, temporal and other dimensions
    to facilitate the development and interoperability of tools build for
    it. Additional features are name-based addressing of data and internal
    consistency checks (e.g. checking for the right data order in
    calculations).
Use a 'glmmkin' class object (GMMAT package) from the null model to perform generalized linear mixed model-based single-variant and variant set main effect tests, gene-environment interaction tests, and joint tests for association, as proposed in Wang et al. (2020) <DOI:10.1002/gepi.22351>.
Provides fast and accurate inference for the parameter estimation problem in Ordinary Differential
    Equations, including the case when there are unobserved system components. Implements the MAGI method
    (MAnifold-constrained Gaussian process Inference) of Yang, Wong, and Kou (2021) <doi:10.1073/pnas.2020397118>.
    A user guide is provided by the accompanying software paper Wong, Yang, and Kou (2024) <doi:10.18637/jss.v109.i04>.
A collection of functions for the manipulation and
 analysis of arbitrarily dimensioned arrays.  The original motivation
 for the package was the development of efficient, vectorized
 algorithms for the creation and investigation of magic squares and
 high-dimensional magic hypercubes.
Functions to make useful (and pretty) plots for scientific plotting. Additional plotting features are added for base plotting, with particular emphasis on making attractive log axis plots.
Magic functions to obtain results from for loops.
Bindings to 'ImageMagick': the most comprehensive open-source image
    processing library available. Supports many common formats (png, jpeg, tiff,
    pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc).
    All operations are vectorized via the Magick++ STL meaning they operate either
    on a single frame or a series of frames for working with layers, collages,
    or animation. In RStudio images are automatically previewed when printed to
    the console, resulting in an interactive editing environment. The latest 
    version of the package includes a native graphics device for creating 
    in-memory graphics or drawing onto images using pixel coordinates.
Enables us to use the functions of the package 'magick' interactively.
Set of utility functions to interact with 'WeMo Switch', a smart 
    plug that can be remotely controlled via wifi. The provided functions make 
    it possible to turn one or more 'WeMo Switch' plugs on and off in a 
    scriptable fashion. More information about 'WeMo Switch' can be found at 
    <http://www.belkin.com/us/p/P-F7C027/>.
Balancing quasi-experimental field research for effects of covariates is fundamental for drawing causal inference. Propensity Score Matching deals with this issue but current
    techniques are restricted to binary treatment variables. Moreover, they provide several solutions without providing a comprehensive framework on choosing the best model. The
    MAGMA R-package addresses these restrictions by offering nearest neighbor matching for two to four groups. It also includes the option to match data of a 2x2 design. In addition, 
    MAGMA includes a framework for evaluating the post-matching balance. The package includes functions for the matching process and matching reporting. We provide a tutorial on 
    MAGMA as vignette. More information on MAGMA can be found in Feuchter, M. D., Urban, J., Scherrer V., Breit, M. L., and Preckel F. (2022) <https://osf.io/p47nc/>.
An implementation for the multi-task Gaussian processes with common 
    mean framework. Two main algorithms, called 'Magma' and 'MagmaClust', 
    are available to perform predictions for supervised learning problems, in
    particular for time series or any functional/continuous data applications.
    The corresponding articles has been respectively proposed by Arthur Leroy, 
    Pierre Latouche, Benjamin Guedj and Servane Gey (2022) 
    <doi:10.1007/s10994-022-06172-1>, and Arthur Leroy, Pierre Latouche, 
    Benjamin Guedj and Servane Gey (2023) <https://jmlr.org/papers/v24/20-1321.html>.
    Theses approaches leverage the learning of cluster-specific mean processes,
    which are common across similar tasks, to provide enhanced prediction
    performances (even far from data) at a linear computational cost (in
    the number of tasks).  'MagmaClust' is a generalisation of 'Magma'
    where the tasks are simultaneously clustered into groups, each being
    associated to a specific mean process.  User-oriented functions in the
    package are decomposed into training, prediction and plotting
    functions. Some basic features (classic kernels, training, prediction) of
    standard Gaussian processes are also implemented.
A client for interacting with 'magma', the data warehouse of the
    'UCSF Data Library'. 'magmaR' includes functions for querying and
    downloading data from 'magma', in order to enable working with such data in
    R, as well as for uploading local data to 'magma'.
Correlates variation within the meta-genome to target species
    phenotype variations in meta-genome with association studies. Follows
    the pipeline described in Chaston, J.M. et al. (2014) <doi:10.1128/mBio.01631-14>.
Implements an interface to the legacy Fortran code from O'Connell and Dobson (1984) <DOI:10.2307/2531148>. Implements Fortran 77 code for the methods developed by Schouten (1982) <DOI:10.1111/j.1467-9574.1982.tb00774.x>. Includes estimates of average agreement for each observer and average agreement for each subject.
Provides a mechanism for chaining commands with a new
    forward-pipe operator, %>%. This operator will forward a value, or the
    result of an expression, into the next function call/expression.
    There is flexible support for the type of right-hand side expressions.
    For more information, see package vignette.  To quote Rene Magritte,
    "Ceci n'est pas un pipe."
Provides a comprehensive graphical user interface for analysis of Affymetrix, Agilent, Illumina, Nimblegen and other microarray data. It can perform miscellaneous tasks such as gene set enrichment and test analyses, identifying gene symbols and building co-expression network. It can also estimate sample size for atleast two-fold expression change. The current version is its slenderized form for compatable and flexible implementation.