Packages Installed on ITS machines

Bruce Dudek

Fall Semester 2020

ITS classrooms have R/RStudio installed on Windows machines. This document contains a list of all packages available in those installations. Users who wish to have additional packages installed can contact bdudek at albany dot edu and the installation can happen rapidly. Pls note that the base system R packages are listed at the bottom of the table, below the zoo package.

PackageName PackageTitle abd The Analysis of Biological Data abind Combine Multidimensional Arrays ACCLMA ACC & LMA Graph Plotting acepack ACE and AVAS for Selecting Multiple Regression Transformations ada The Ada for Stochastic Boosting addinmanager RStudio ’addin’ Manager additivityTests Additivity Tests in the Two Way Anova with Single Sub-class Numbers ade4 Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences ade4TkGUI ’ade4’ Tcl/Tk Graphical User Interface adegenet Exploratory Analysis of Genetic and Genomic Data adegraphics An S4 Lattice-Based Package for the Representation of Multivariate Data adehabitat Analysis of Habitat Selection by Animals adehabitatLT Analysis of Animal Movements adehabitatMA Tools to Deal with Raster Maps adephylo Exploratory Analyses for the Phylogenetic Comparative Method ads Spatial Point Patterns Analysis AED What the package does (short line) AER Applied Econometrics with R afex Analysis of Factorial Experiments agricolae Statistical Procedures for Agricultural Research airports Data on Airports akima Interpolation of Irregularly and Regularly Spaced Data AlgDesign Algorithmic Experimental Design alphahull Generalization of the Convex Hull of a Sample of Points in the Plane alr3 Data to Accompany Applied Linear Regression 3rd Edition alr4 Data to Accompany Applied Linear Regression 4th Edition amap Another Multidimensional Analysis Package AMCP A Model Comparison Perspective Amelia A Program for Missing Data anacor Simple and Canonical Correspondence Analysis animation A Gallery of Animations in Statistics and Utilities to Create Animations AnnotationDbi Annotation Database Interface ape Analyses of Phylogenetics and Evolution aplpack Another Plot Package: ’Bagplots’, ’Iconplots’, ’Summaryplots’, Slider Functions and Others argparse Command Line Optional and Positional Argument Parser

1 arm Data Analysis Using Regression and Multilevel/Hierarchical Models arules Mining Association Rules and Frequent Itemsets arulesViz Visualizing Association Rules and Frequent Itemsets asbio A Collection of Statistical Tools for Biologists ascii Export R objects to several markup languages ash David Scott’s ASH Routines askpass Safe Password Entry for R, Git, and SSH aspace A collection of functions for estimating centrographic statistics and computational geometries for spatial point patterns assertthat Easy Pre and Post Assertions AUC Threshold independent performance measures for probabilistic classifiers. automap Automatic interpolation package av Working with Audio and Video in R backports Reimplementations of Functions Introduced Since R-3.0.0 barcode Barcode distribution plots base64 Base64 Encoder and Decoder base64enc Tools for base64 encoding BayesFactor Computation of Bayes Factors for Common Designs bayesm Bayesian Inference for Marketing/Micro-Econometrics bayesplot Plotting for Bayesian Models bayestestR Understand and Describe Bayesian Models and Posterior Distributions BayesX R Utilities Accompanying the Package BayesX BaylorEdPsych R Package for Baylor University Educational Psychology Quantitative Courses BB Solving and Optimizing Large-Scale Nonlinear Systems bbmle Tools for General Maximum Likelihood Estimation bcdstats A collection of functions to support B. Dudek’s APSY510/511 classes BDgraph Bayesian Structure Learning in Graphical Models using Birth-Death MCMC bdsmatrix Routines for Block Diagonal Symmetric Matrices beeswarm The Bee Swarm Plot, an Alternative to Stripchart benchmark Benchmark Experiments Toolbox BEST Bayesian Estimation Supersedes the t-Test bestglm Best Subset GLM and Regression Utilities bestNormalize Normalizing Transformation Functions betareg Beta Regression BH Boost ++ Header Files BiasedUrn Biased Urn Model Distributions bibtex Bibtex Parser biclust BiCluster Algorithms BIFIEsurvey Tools for Survey Statistics in Educational Assessment bigassertr Assertion and Message Functions biglm bounded memory linear and generalized linear models bigmemory Manage Massive Matrices with Shared Memory and Memory-Mapped Files bigmemory.sri A shared resource interface for Bigmemory Project packages bigparallelr Easy Parallel Tools bigutilsr Utility Functions for Large-scale Data bindr Parametrized Active Bindings bindrcpp An ’Rcpp’ Interface to Active Bindings binGroup Evaluation and Experimental Design for Binomial Group Testing binom Binomial Confidence Intervals For Several Parameterizations Biobase Biobase: Base functions for Bioconductor BiocGenerics S4 generic functions for Bioconductor BiocInstaller Install/Update Bioconductor, CRAN, and Packages BiocManager Access the Bioconductor Project Package Repository BiocVersion Set the appropriate version of Bioconductor packages bit A Class for Vectors of 1-Bit Booleans

2 bit64 A S3 Class for Vectors of 64bit Integers bitops Bitwise Operations blme Bayesian Linear Mixed-Effects Models blob A Simple S3 Class for Representing Vectors of Binary Data (’BLOBS’) blockTools Block, Assign, and Diagnose Potential Interference in Randomized Experiments BMA Bayesian Model Averaging bold Interface to Bold Systems API bookdown Authoring Books and Technical Documents with R boot Bootstrap Functions (Originally by Angelo Canty for S) BootPR Bootstrap Prediction Intervals and Bias-Corrected Forecasting bootRes Bootstrapped Response and Correlation Functions bootruin A Bootstrap Test for the Probability of Ruin in the Classical Risk Process bootspecdens Testing equality of spectral densities bootStepAIC Bootstrap stepAIC bootstrap Functions for the Book "An Introduction to the Bootstrap" BradleyTerry2 Bradley-Terry Models brew Templating Framework for Report Generation brglm Bias Reduction in Binomial-Response Generalized Linear Models bridgesampling Bridge Sampling for Marginal Likelihoods and Bayes Factors brms Bayesian Regression Models using ’’ Brobdingnag Very Large Numbers in R broom Convert Statistical Objects into Tidy Tibbles BRugs Interface to the ’OpenBUGS’ MCMC Software BSDA Basic Statistics and Data Analysis btergm Temporal Exponential Random Graph Models by Bootstrapped Pseudolikelihood Cairo R Graphics Device using Cairo Graphics Library for Creating High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG, PostScript) and Display (X11 and Win32) Output cairoDevice Embeddable Cairo Graphics Device Driver callr Call R from R car Companion to Applied Regression CARBayes Spatial Generalised Linear Mixed Models for Areal Unit Data CARBayesdata Data Used in the Vignettes Accompanying the CARBayes and CARBayesST Packages carData Companion to Applied Regression Data Sets caret Classification and Regression Training catdata Categorical Data caTools Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc cba Clustering for Business Analytics CDM Cognitive Diagnosis Modeling cellranger Translate Spreadsheet Cell Ranges to Rows and Columns changepoint Methods for Changepoint Detection checkmate Fast and Versatile Argument Checks chemometrics Multivariate Statistical Analysis in Chemometrics cherryblossom Cherry Blossom Run Race Results chron Chronological Objects which can Handle Dates and Times CircStats Circular Statistics, from "Topics in Circular Statistics" (2001) Ckmeans.1d.dp Optimal, Fast, and Reproducible Univariate Clustering class Functions for Classification classifly Explore classification models in high dimensions classInt Choose Univariate Class Intervals cli Helpers for Developing Command Line Interfaces cliapp Create Rich Command Line Applications clipr Read and Write from the System Clipboard clisymbols Symbols at the R Prompt cluster "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et al. clv Cluster Validation Techniques

3 cmprsk Subdistribution Analysis of Competing Risks cobs Constrained B-Splines (Sparse Matrix Based) coda Output Analysis and Diagnostics for MCMC codetools Code Analysis Tools for R coin Conditional Inference Procedures in a Permutation Test Framework colorspace A Toolbox for Manipulating and Assessing Colors and Palettes colourpicker A Colour Picker Tool for Shiny and for Selecting Colours in Plots colourvalues Assigns Colours to Values combinat combinatorics utilities CommonJavaJars Useful Libraries for Building a Java Based GUI under R commonmark High Performance CommonMark and Github Markdown Rendering in R CompQuadForm Distribution Function of Quadratic Forms in Normal Variables CompRandFld Composite-Likelihood Based Analysis of Random Fields conditionz Control How Many Times Conditions are Thrown conquer Convolution-Type Smoothed Quantile Regression contfrac Continued Fractions contrast A Collection of Contrast Methods copBasic General Bivariate Copula Theory and Many Utility Functions corpcor Efficient Estimation of Covariance and (Partial) Correlation corrgram Plot a Correlogram corrplot Visualization of a Correlation Matrix covr Test Coverage for Packages cowplot Streamlined Plot Theme and Plot Annotations for ’’ coxme Mixed Effects Cox Models cplm Compound Poisson Linear Models crayon Colored Output crossdes Construction of Crossover Designs crosstalk Inter-Widget Interactivity for HTML Widgets crsmeta Extract Coordinate System Metadata crul HTTP Client cshapes The CShapes Dataset and Utilities csvy Import and Export CSV Data with a YAML Metadata Header ctv CRAN Task Views cubature Adaptive Multivariate Integration over Hypercubes Cubist Rule- And Instance-Based Regression Modeling curl A Modern and Flexible Web Client for R CVST Fast Cross-Validation via Sequential Testing cvTools Cross-validation tools for regression models cyclocomp Cyclomatic Complexity of R Code d3Network Tools for creating D3 JavaScript network, tree, dendrogram, and Sankey graphs from R DAAG Data Analysis and Graphics Data and Functions data.table Extension of ‘data.frame‘ data.tree General Purpose Hierarchical Data Structure date Functions for Handling Dates DBI R Database Interface dbplyr A ’’ Back End for Databases dbscan Density Based Clustering of Applications with Noise (DBSCAN) and Related Algorithms DCluster Functions for the Detection of Spatial Clusters of Diseases dcurver Utility Functions for Davidian Curves ddalpha Depth-Based Classification and Calculation of Data Depth debugme Debug R Packages degreenet Models for Skewed Count Distributions Relevant to Networks deldir Delaunay Triangulation and Dirichlet (Voronoi) Tessellation dendextend Extending ’dendrogram’ Functionality in R

4 denstrip Density Strips and Other Methods for Compactly Illustrating Distributions DEoptimR Differential Evolution Optimization in Pure R depthTools Depth Tools Package Deriv Symbolic Differentiation desc Manipulate DESCRIPTION Files descr Descriptive Statistics DescTools Tools for Descriptive Statistics deSolve Solvers for Initial Value Problems of Differential Equations (’ODE’, ’DAE’, ’DDE’) devEMF EMF Graphics Output Device Devore7 Data sets from Devore’s "Prob and Stat for Eng (7th ed)" devtools Tools to Make Developing R Packages Easier dfidx Indexed Data Frames dfoptim Derivative-Free Optimization diagram Functions for Visualising Simple Graphs (Networks), Plotting Flow Diagrams DiagrammeR Graph/Network Visualization dials Tools for Creating Tuning Parameter Values DiceDesign Designs of Computer Experiments dichromat Color Schemes for Dichromats diffobj Diffs for R Objects digest Create Compact Hash Digests of R Objects dimRed A Framework for Dimensionality Reduction diptest Hartigan’s Dip Test Statistic for Unimodality - Corrected directlabels Direct Labels for Multicolor Plots diseasemapping Modelling Spatial Variation in Disease Risk for Areal Data dismo Species Distribution Modeling distr Object Oriented Implementation of Distributions distrEx Extensions of Package ’distr’ divagis Provides tools for quality checks of georeferenced plant species accessions. dlm Bayesian and Likelihood Analysis of Dynamic Linear Models doBy Groupwise Statistics, LSmeans, Linear Contrasts, Utilities doParallel Foreach Parallel Adaptor for the ’parallel’ Package doRNG Generic Reproducible Parallel Backend for ’foreach’ Loops dotCall64 Enhanced Foreign Function Interface Supporting Long Vectors downloader Download Files over HTTP and HTTPS dplR Dendrochronology Program Library in R dplyr A Grammar of Data Manipulation dreamerr Error Handling Made Easy DRR Dimensionality Reduction via Regression DSpat Spatial Modelling for Distance Sampling Data DT A Wrapper of the JavaScript Library ’DataTables’ DTK Dunnett-Tukey-Kramer Pairwise Multiple Comparison Test Adjusted for Unequal Variances and Unequal Sample Sizes dtw Dynamic Time Warping Algorithms dunn.test Dunn’s Test of Multiple Comparisons Using Rank Sums dygraphs Interface to ’Dygraphs’ Interactive Time Series Charting Library DynamicDistribution Dynamically visualized probability distributions and their moments dynlm Dynamic Linear Regression e1071 Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien earth Multivariate Adaptive Regression Splines Ecdat Data Sets for Econometrics ecespa Functions for Spatial Point Pattern Analysis Ecfun Functions for Ecdat EDR Estimation of the Effective Dimension Reduction (’EDR’) Space eeptools Convenience Functions for Education Data effects Effect Displays for Linear, Generalized Linear, and Other Models

5 effectsize Indices of Effect Size and Standardized Parameters effsize Efficient Effect Size Computation ElemStatLearn Data Sets, Functions and Examples from the Book: "The Elements of Statistical Learning, Data Mining, Inference, and Prediction" by Trevor Hastie, Robert Tibshirani and Jerome Friedman ellipse Functions for Drawing Ellipses and Ellipse-Like Confidence Regions ellipsis Tools for Working with ... elliptic Weierstrass and Jacobi Elliptic Functions emdbook Support Functions and Data for "Ecological Models and Data" emmeans Estimated Marginal Means, aka Least-Squares Means EMT Exact Multinomial Test: Goodness-of-Fit Test for Discrete Multivariate data energy E-Statistics: Multivariate Inference via the Energy of Data Epi A Package for Statistical Analysis in Epidemiology EpiModel Mathematical Modeling of Infectious Disease Dynamics epitools Epidemiology Tools ergm Fit, Simulate and Diagnose Exponential-Family Models for Networks ergm.count Fit, Simulate and Diagnose Exponential-Family Models for Networks with Count Edges ergmharris Local Health Department network data set es.dif Compute Effect Sizes of the Difference estimability Tools for Assessing Estimability of Linear Predictions etm Empirical Transition Matrix evaluate Parsing and Evaluation Tools that Provide More Details than the Default evd Functions for Extreme Value Distributions Exact Unconditional Exact Test excel.link Convenient Data Exchange with Excel expm Matrix Exponential, Log, ’etc’ expsmooth Data Sets from "Forecasting with Exponential Smoothing" extrafont Tools for using extrafontdb Package for holding the database for the extrafont package ez Easy Analysis and Visualization of Factorial Experiments FactoMineR Multivariate Exploratory Data Analysis and Data Mining fANCOVA Nonparametric Analysis of Covariance fansi ANSI Control Sequence Aware String Functions faraway Functions and Datasets for Books by Julian Faraway farver High Performance Colour Space Manipulation fastcluster Fast Hierarchical Clustering Routines for R and ’Python’ fastICA FastICA Algorithms to Perform ICA and Projection Pursuit fastmap Fast Implementation of a Key-Value Store fastmatch Fast match() function fastR Foundations and Applications of Statistics Using R fBasics - Markets and Basic Statistics fda Functional Data Analysis fdrtool Estimation of (Local) False Discovery Rates and Higher Criticism feather R Bindings to the Feather ’API’ ff Memory-Efficient Storage of Large Data on Disk and Fast Access Functions ffbase Basic Statistical Functions for Package ’ff’ fGarch Rmetrics - Autoregressive Conditional Heteroskedastic Modelling fields Tools for Spatial Data FieldSim Random Fields (and Bridges) Simulations filehash Simple Key-Value Database fImport Rmetrics - Importing Economic and Financial Data findpython Functions to Find an Acceptable Python Binary fishmethods Fishery Science Methods and Models fit.models Compare Fitted Models fixest Fast -Effects Estimations flashClust Implementation of optimal hierarchical clustering

6 flexclust Flexible Cluster Algorithms flexmix Flexible Mixture Modeling flexsurv Flexible Parametric Survival and Multi-State Models float 32-Bit Floats flock Process Synchronization Using File Locks fma Data Sets from "Forecasting: Methods and Applications" by Makridakis, Wheelwright & Hyndman (1998) FME A Flexible Modelling Environment for Inverse Modelling, Sensitivity, Identifiability and Monte Carlo Analysis FNN Fast Nearest Neighbor Search Algorithms and Applications fontBitstreamVera Fonts with ’ Fonts’ License fontcm for use with extrafont package fontLiberation Liberation Fonts fontquiver Set of Installed Fonts forcats Tools for Working with Categorical Variables (Factors) foreach Provides Foreach Looping Construct forecast Forecasting Functions for Time Series and Linear Models foreign Read Data Stored by ’’, ’S’, ’SAS’, ’SPSS’, ’’, ’Systat’, ’’, ’dBase’, ... formatR Format R Code Automatically Formula Extended Model Formulas fortunes R Fortunes fpc Flexible Procedures for Clustering fpp Data for "Forecasting: principles and practice" fracdiff Fractionally Differenced ARIMA aka ARFIMA(P,d,q) Models freetypeharfbuzz Deterministic Computation of Text Box Metrics fs Cross-Platform File System Operations Based on ’libuv’ FSA Simple Fisheries Stock Assessment Methods FSAdata Data to Support Fish Stock Assessment (’FSA’) Package fTrading Rmetrics - Trading and Rebalancing Financial Instruments fts R Interface to ’tslib’ (a Time Series Library in C++) furrr Apply Mapping Functions in Parallel using Futures futile.logger A Logging Utility for R futile.options Futile Options Management future Unified Parallel and Distributed Processing in R for Everyone future.apply Apply Function to Elements in Parallel using Futures GA Genetic Algorithms gam Generalized Additive Models gamair Data for ’GAMs: An Introduction with R’ gamlss Generalised Additive Models for Location Scale and Shape gamlss.data GAMLSS Data gamlss.dist Distributions for Generalized Additive Models for Location Scale and Shape gamm4 Generalized Additive Mixed Models using ’mgcv’ and ’lme4’ gapminder Data from Gapminder gargle Utilities for Working with APIs gbm Generalized Boosted Regression Models gbRd Utilities for processing Rd objects and files gclus Clustering Graphics gdata Various R Programming Tools for Data Manipulation gdtools Utilities for Graphical Rendering gee Generalized Estimation Equation Solver geepack Generalized Estimating Equation Package generics Common S3 Generics not Provided by Base R Methods Related to Model Fitting GenKern Functions for generating and manipulating binned kernel density estimates GenSA Generalized Simulated Annealing geodist Fast, Dependency-Free Geodesic Distance Calculations geojsonsf GeoJSON to Simple Feature Converter

7 GEOmap Topographic and Geologic Mapping geomapdata Data for topographic and Geologic Mapping geometry Mesh Generation and Surface Tessellation geonames Interface to the "Geonames" Spatial Query Web Service geoR Analysis of Geostatistical Data geoRglm A Package for Generalised Linear Spatial Models geosphere Spherical Trigonometry geostatsp Geostatistical Modelling with Likelihood and Bayes GeoXp Interactive exploratory spatial data analysis GERGM Estimation and Fit Diagnostics for Generalized Exponential Random Graph Models getopt C-Like ’getopt’ Behavior GGally Extension to ’ggplot2’ ggbeeswarm Categorical Scatter (Violin Point) Plots ggbiplot A ggplot2 based biplot ggdendro Create Dendrograms and Tree Diagrams Using ’ggplot2’ ggeffects Create Tidy Data Frames of Marginal Effects for ’ggplot’ from Model Outputs ggExtra Add Marginal Histograms to ’ggplot2’, and More ’ggplot2’ Enhancements ggforce Accelerating ’ggplot2’ ggformula Formula Interface to the Grammar of Graphics ggfortify Data Visualization Tools for Statistical Analysis Results ggm Graphical Markov Models with Mixed Graphs ggmap Spatial Visualization with ggplot2 ggplot2 Create Elegant Data Visualisations Using the Grammar of Graphics ggplot2movies Movies Data ggpol Visualizing Social Science Data with ’ggplot2’ ggpubr ’ggplot2’ Based Publication Ready Plots ggraph An Implementation of Grammar of Graphics for Graphs and Networks ggrepel Automatically Position Non-Overlapping Text Labels with ’ggplot2’ ggridges Ridgeline Plots in ’ggplot2’ ggsci Scientific Journal and Sci-Fi Themed Color Palettes for ’ggplot2’ ggsignif Significance Brackets for ’ggplot2’ ggstance Horizontal ’ggplot2’ Components ggthemes Extra Themes, Scales and Geoms for ’ggplot2’ GGUM Generalized Graded Unfolding Model ggvis Interactive Grammar of Graphics gh ’GitHub’ ’API’ gifski Highest Quality GIF Encoder git2r Provides Access to Git Repositories glasso Graphical Lasso: Estimation of Gaussian Graphical Models glmmBUGS Generalised Linear Mixed Models with BUGS and JAGS glmmTMB Generalized Linear Mixed Models using Template Model Builder glmnet Lasso and Elastic-Net Regularized Generalized Linear Models globals Identify Global Objects in R Expressions glue Interpreted String Literals gmm Generalized Method of Moments and Generalized Empirical Likelihood gmodels Various R Programming Tools for Model Fitting gmp Multiple Precision Arithmetic gmt Interface Between GMT Map-Making Software and R gnm Generalized Nonlinear Models gof Model Diagnostics Based on Cumulative Residuals goftest Classical Goodness-of-Fit Tests for Univariate Distributions googledrive An Interface to googlePolylines Encoding Coordinates into ’Google’ Polylines googlesheets Manage Google Spreadsheets from R

8 googlesheets4 Access Google Sheets using the Sheets API V4 googleVis R Interface to Google Charts gower Gower’s Distance gpairs The Generalized Pairs Plot GPArotation GPA Factor Rotation gpclib General Polygon Clipping Library for R GPfit Gaussian Processes Modeling gplots Various R Programming Tools for Plotting Data granova Graphical Analysis of Variance granovaGG Graphical Analysis of Variance Using ggplot2 graph graph: A package to handle graph data structures graphlayouts Additional Layout Algorithms for Network Visualizations GREA Gotta Read ’Em All gridBase Integration of base and grid graphics gridExtra Miscellaneous Functions for "Grid" Graphics gridGraphics Redraw Base Graphics Using ’grid’ Graphics grouped Regression Analysis of Grouped and Coarse Data grpreg Regularization Paths for Regression Models with Grouped Covariates gsl Wrapper for the Gnu Scientific Library gss General Smoothing Splines gstat Spatial and Spatio-Temporal Geostatistical Modelling, Prediction and Simulation gt Easily Create Presentation-Ready Display Tables gtable Arrange ’Grobs’ in Tables gtheory Apply Generalizability Theory with R gtools Various R Programming Tools Guerry Maps, Data and Methods Related to Guerry (1833) "Moral Statistics of France" gvlma Global Validation of Linear Models Assumptions gWidgets gWidgets API for Building Toolkit-Independent, Interactive GUIs gWidgets2 Rewrite of gWidgets API for Simplified GUI Construction gWidgets2tcltk Toolkit Implementation of gWidgets2 for tcltk gWidgetsRGtk2 Toolkit Implementation of gWidgets for RGtk2 gWidgetstcltk Toolkit implementation of gWidgets for tcltk package HandTill2001 Multiple Class Area under ROC Curve hardhat Construct Modeling Packages haven Import and Export ’SPSS’, ’Stata’ and ’SAS’ Files hdeco Hierarchical DECOmposition of Entropy for Categorical Map Comparisons hdi High-Dimensional Inference HDInterval Highest (Posterior) Density Intervals hdrcde Highest Density Regions and Conditional Density Estimation heplots Visualizing Hypothesis Tests in Multivariate Linear Models here A Simpler Way to Find Your Files hexbin Hexagonal Binning Routines HH Statistical Analysis and Data Display: Heiberger and Holland highlight Syntax Highlighter highr Syntax Highlighting for R Source Code HistData Data Sets from the History of Statistics and Data Visualization hmeasure The H-Measure and Other Scalar Classification Performance Metrics Hmisc Harrell Miscellaneous hms Pretty Time of Day hrbrmisc What the Package Does (one line, title case) hrbrthemes Additional Themes, Theme Components and Utilities for ’ggplot2’ HSAUR A Handbook of Statistical Analyses Using R (1st Edition) HSAUR2 A Handbook of Statistical Analyses Using R (2nd Edition) htmlTable Advanced Tables for Markdown/HTML

9 htmltools Tools for HTML htmlwidgets HTML Widgets for R httpcode ’HTTP’ Status Code Helper httpuv HTTP and WebSocket Server Library httr Tools for Working with URLs and HTTP huge High-Dimensional Undirected Graph Estimation hunspell High-Performance Stemmer, Tokenizer, and Spell Checker hwriter HTML Writer - Outputs R objects in HTML format hypergeo The Gauss Hypergeometric Function ic.infer Inequality Constrained Inference in Linear Normal Situations ICC Facilitating Estimation of the Intraclass Correlation Coefficient ICS Tools for Exploring Multivariate Data via ICS/ICA ICSNP Tools for Multivariate Nonparametrics ICSOutlier Outlier Detection Using Invariant Coordinate Selection ids Generate Random Identifiers igraph Network Analysis and Visualization igraphdata A Collection of Network Data Sets for the ’igraph’ Package indicspecies Relationship Between Species and Groups of Sites ineq Measuring Inequality, Concentration, and Poverty infer Tidy Statistical Inference influenceR Software Tools to Quantify Structural Importance of Nodes in a Network ini Read and Write ’.ini’ Files inline Functions to Inline C, C++, Function Calls from R inlinedocs Convert Inline Comments to Documentation inlmisc Miscellaneous Functions for the USGS INL Project Office insight Easy Access to Model Information for Various Model Objects installr Using R to Install Stuff on Windows OS (Such As: R, ’Rtools’, ’RStudio’, ’Git’, and More!) intamap Procedures for Automated Interpolation intamapInteractive Interactive Add-on Functionality for ’intamap’ intergraph Coercion Routines for Network Data Objects intervals Tools for Working with Points and Intervals inum Interval and Enum-Type Representation of Vectors invgamma The Inverse Gamma Distribution iplots iPlots - interactive graphics for R ipred Improved Predictors IRanges Infrastructure for manipulating intervals on sequences IRdisplay ’Jupyter’ Display Machinery irlba Fast Truncated Singular Value Decomposition and Principal Components Analysis for Large Dense and Sparse Matrices isoband Generate Isolines and Isobands from Regularly Spaced Elevation Grids ISOcodes Selected ISO Codes ISwR Introductory Statistics with R iterators Provides Iterator Construct itertools Iterator Tools its Irregular Time Series janeaustenr Jane Austen’s Complete Novels JavaGD Java Graphics Device JGR Java GUI for R joineRML Joint Modelling of Multivariate Longitudinal Data and Time-to-Event Outcomes jomo Multilevel Joint Modelling Multiple Imputation jpeg Read and write JPEG images jsonify Convert Between ’R’ Objects and Javascript Object Notation (JSON) jsonlite A Robust, High Performance JSON Parser and Generator for R jtools Analysis and Presentation of Social Scientific Data kableExtra Construct Complex Table with ’kable’ and Pipe Syntax

10 kappalab Non-Additive Measure and Integral Manipulation Functions Kendall Kendall rank correlation and Mann-Kendall trend test kernlab Kernel-Based Machine Learning Lab KernSmooth Functions for Kernel Smoothing Supporting Wand & Jones (1995) KFAS Kalman Filter and Smoother for Exponential Family State Space Models klaR Classification and Visualization km.ci Confidence intervals for the Kaplan-Meier estimator A General-Purpose Package for Dynamic Report Generation in R koRpus An R Package for Text Analysis ks Kernel Smoothing KScorrect Lilliefors-Corrected Kolmogorov-Smirnov Goodness-of-Fit Tests kutils Project Management Tools labdsv Ordination and Multivariate Analysis for Ecology labeling Axis Labeling labelled Manipulating Labelled Data laeken Estimation of Indicators on Social Exclusion and Poverty Lahman Sean ’Lahman’ Baseball Database lambda.r Modeling Data with Functional Programming LambertW Probabilistic Models to Analyze and Gaussianize Heavy-Tailed, Skewed Data lamW Lambert-W Function languageR Analyzing Linguistic Data: A Practical Introduction to Statistics lars Least Angle Regression, Lasso and Forward Stagewise latentnet Latent Position and Cluster Models for Statistical Networks later Utilities for Scheduling Functions to Execute Later with Event Loops lattice Trellis Graphics for R latticeExtra Extra Graphical Utilities Based on Lattice lava Latent Variable Models lavaan Latent Variable Analysis lavaan.survey Complex Survey Structural Equation Modeling (SEM) lawstat Tools for Biostatistics, Public Policy, and Law lazyeval Lazy (Non-Standard) Evaluation leafem ’leaflet’ Extensions for ’mapview’ leaflet Create Interactive Web Maps with the JavaScript ’Leaflet’ Library leaflet.providers Leaflet Providers leafpop Include Tables, Images and Graphs in Leaflet Pop-Ups leafsync Small Multiples for Leaflet Web Maps leaps Regression Subset Selection LearnBayes Functions for Learning Bayesian Inference LearnEDA Functions for Learning Exploratory Data Analysis lessR Less Code, More Results lfda Local Fisher Discriminant Analysis lfe Linear Group Fixed Effects lgr A Fully Featured Logging Framework lhs Latin Hypercube Samples libcoin Linear Test Statistics for Permutation Inference lifecycle Manage the Life Cycle of your Package Functions likert Analysis and Visualization Likert Items linprog Linear Programming / Optimization lintr A ’Linter’ for R Code lisrelToR Import output from LISREL into R listenv Environments Behaving (Almost) as Lists lmboot Bootstrap in Linear Models lme4 Linear Mixed-Effects Models using ’Eigen’ and S4 lmerTest Tests in Linear Mixed Effects Models

11 lmodel2 Model II Regression lmomco L-Moments, Censored L-Moments, Trimmed L-Moments, L-Comoments, and Many Distributions Lmoments L-Moments and Quantile Mixtures lmPerm Permutation Tests for Linear Models lmtest Testing Linear Regression Models loa Lattice Options and Add-Ins locfit Local Regression, Likelihood and Density Estimation logcondens Estimate a Log-Concave Probability Density from Iid Observations logspline Routines for Logspline Density Estimation longmemo Statistics for Long-Memory Processes (Book Jan Beran), and Related Functionality loo Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models lpSolve Interface to ’Lp_solve’ v. 5.5 to Solve Linear/Integer Programs lpSolveAPI R Interface to ’lp_solve’ Version 5.5.2.0 LSD Lots of Superior Depictions lsmeans Least-Squares Means lsr Companion to "Learning Statistics with R" ltm Latent Trait Models under IRT lubridate Make Dealing with Dates a Little Easier lwgeom Bindings to Selected ’liblwgeom’ Functions for Simple Features MAd Meta-Analysis with Mean Differences magic Create and Investigate Magic Squares magick Advanced Graphics and Image-Processing in R magrittr A Forward-Pipe Operator for R mail Sending Email Notifications from R manipulate Interactive Plots for RStudio manipulateWidget Add Even More Interactivity to Interactive Charts mapdata Extra Map Databases mapdeck Interactive Maps Using ’Mapbox GL JS’ and ’Deck.gl’ mapmisc Utilities for Producing Maps mapproj Map Projections maps Draw Geographical Maps maptools Tools for Handling Spatial Objects maptree Mapping, pruning, and graphing tree models mapview Interactive Viewing of Spatial Data in R markdown Render Markdown with the C Library ’Sundown’ marked Mark-Recapture Analysis for Survival and Abundance Estimation MASS Support Functions and Datasets for Venables and Ripley’s MASS Matching Multivariate and Propensity Score Matching with Balance Optimization MatchIt Nonparametric Preprocessing for Parametric Causal Inference matrixcalc Collection of functions for matrix calculations MatrixModels Modelling with Sparse And Dense Matrices matrixStats Functions that Apply to Rows and Columns of Matrices (and to Vectors) maxent Low-memory Multinomial Logistic Regression with Support for Text Classification maxLik Maximum Likelihood Estimation and Related Tools MBA Multilevel B-Spline Approximation MBESS The MBESS R Package mboost Model-Based Boosting mc2d Tools for Two-Dimensional Monte-Carlo Simulations mclust Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation mcmc MCMCglmm MCMC Generalised Linear Mixed Models MCMCpack Markov Chain Monte Carlo (MCMC) Package mcplR Multiple Cue Probability Learning in R mda Mixture and Flexible Discriminant Analysis

12 mediation Causal Mediation Analysis memisc Management of Survey Data and Presentation of Analysis Results memoise Memoisation of Functions MEMSS Data Sets from Mixed-Effects Models in S metafor Meta-Analysis Package for R mets Analysis of Multivariate Event Times mgcv Mixed GAM Computation Vehicle with Automatic Smoothness Estimation mi Missing Data Imputation and Model Checking mice Multivariate Imputation by Chained Equations miceadds Some Additional Multiple Imputation Functions, Especially for ’mice’ microbenchmark Accurate Timing Functions mime Map Filenames to MIME Types miniUI Shiny UI Widgets for Small Screens minpack.lm R Interface to the Levenberg-Marquardt Nonlinear Least-Squares Algorithm Found in MINPACK, Plus Support for Bounds minqa Derivative-free optimization algorithms by quadratic approximation mirt Multidimensional Item Response Theory misc3d Miscellaneous 3D Plots miscTools Miscellaneous Tools and Utilities missMDA Handling Missing Values with Multivariate Data Analysis mitml Tools for Multiple Imputation in Multilevel Modeling mitools Tools for Multiple Imputation of Missing Data mix Estimation/Multiple Imputation for Mixed Categorical and Continuous Data mlbench Machine Learning Benchmark Problems mlmRev Examples from Multilevel Modelling Software Review mlogit Multinomial Logit Models MNM Multivariate Nonparametric Methods. An Approach Based on Spatial Signs and Ranks mnormt The Multivariate Normal and t Distributions, and Their Truncated Versions modelbased Estimation of Model-Based Predictions, Contrasts and Means modeldata Data Sets Used Useful for Modeling Packages ModelMap Modeling and Map Production using Random Forest and Related Stochastic Models ModelMetrics Rapid Calculation of Model Metrics modelr Modelling Functions that Work with the Pipe modeltools Tools and Classes for Statistical Models moments Moments, cumulants, skewness, kurtosis and related tests mondate Keep track of dates in terms of months mosaic Project MOSAIC Statistics and Mathematics Teaching Utilities mosaicCalc Function-Based Numerical and Symbolic Differentiation and Antidifferentiation mosaicCore Common Utilities for Other MOSAIC-Family Packages mosaicData Project MOSAIC Data Sets MPV Data Sets from Montgomery, Peck and Vining mratios Ratios of Coefficients in the General Linear Model msm Multi-State Markov and Hidden Markov Models in Continuous Time mstate Data Preparation, Estimation and Prediction in Multi-State Models MSwM Fitting Markov Switching Models muhaz Hazard Function Estimation in Survival Analysis multcomp Simultaneous Inference in General Parametric Models multcompView Visualizations of Paired Comparisons multicool Permutations of Multisets in Cool-Lex Order multilevel Multilevel Functions multiwayvcov Multi-Way Standard Error Clustering multtest Resampling-based multiple hypothesis testing munsell Utilities for Using Munsell Colours mutoss Unified Multiple Testing Procedures mutossGUI A Graphical User Interface for the MuToss Project

13 MVN Multivariate Normality Tests mvnfast Fast Multivariate Normal and Student’s t Methods mvoutlier Multivariate Outlier Detection Based on Robust Methods mvtnorm Multivariate Normal and t Distributions nabor Wraps ’libnabo’, a Fast K Nearest Neighbour Library for Low Dimensions NADA Nondetects and Data Analysis for Environmental Data natserv ’NatureServe’ Interface ncdf Interface to Unidata netCDF Data Files ncdf4 Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files ncf Spatial Covariance Functions ndtv Network Dynamic Temporal Visualizations network Classes for Relational Data networkDynamic Dynamic Extensions for Network Objects networksis Simulate Bipartite Graphs with Fixed Marginals Through Sequential Importance Sampling neuralnet Training of Neural Networks nFactors Parallel Analysis and Other Non Graphical Solutions to the Cattell Scree Test NHANES Data from the US National Health and Nutrition Examination Study nleqslv Solve Systems of Nonlinear Equations nlme Linear and Nonlinear Mixed Effects Models nloptr R Interface to NLopt NLP Natural Language Processing Infrastructure nlstools Tools for Nonlinear Regression Analysis NMF Algorithms and Framework for Nonnegative Matrix Factorization (NMF) nnet Feed-Forward Neural Networks and Multinomial Log-Linear Models nnls The Lawson-Hanson algorithm for non-negative least squares (NNLS) nor1mix Normal aka Gaussian (1-d) Mixture Models (S3 Classes and Methods) normalp Routines for Exponential Power Distribution normtest Tests for Normality nortest Tests for Normality np Nonparametric Kernel Smoothing Methods for Mixed Data Types NSM3 Functions and Datasets to Accompany Hollander, Wolfe, and Chicken - Nonparametric Statistical Methods, Third Edition numDeriv Accurate Numerical Derivatives nycflights13 Flights that Departed NYC in 2013 odbc Connect to ODBC Compatible Databases (using the DBI Interface) odfWeave processing of Open Document Format (ODF) files officer Manipulation of Microsoft Word and PowerPoint Documents olsrr Tools for Building OLS Regression Models openintro Data Sets and Supplemental Functions from ’OpenIntro’ Textbooks and Labs OpenMx Extended Structural Equation Modelling openssl Toolkit for Encryption, Signatures and Certificates Based on OpenSSL openxlsx Read, Write and Edit xlsx Files optextras Tools to Support Optimization Possibly with Bounds and Masks optimx Expanded Replacement and Extension of the ’optim’ Function optpart Optimal Partitioning of Similarity Relations orcutt Estimate Procedure in Case of First Order Autocorrelation ordinal Regression Models for Ordinal Data ore An R Interface to the Onigmo Regular Expression Library orientlib Support for Orientation Data orloca Operations Research LOCational Analysis Models orloca.es Spanish version of orloca package. Modelos de localizacion en investigacion operativa orthopolynom Collection of functions for orthogonal and orthonormal polynomials outliers Tests for outliers oz Plot the Australian Coastline and States packrat A Dependency Management System for Projects and their R Package Dependencies

14 pairsD3 D3 Scatterplot Matrices pamm Power Analysis for Random Effects in Mixed Models pamr Pam: Prediction Analysis for Microarrays pan Multiple Imputation for Multivariate Panel or Clustered Data pander An R ’Pandoc’ Writer parameters Processing of Model Parameters parsedate Recognize and Parse Dates in Various Formats, Including All ISO 8601 Formats parsnip A Common API to Modeling and Analysis Functions partitions Additive Partitions of Integers party A Laboratory for Recursive Partytioning partykit A Toolkit for Recursive Partytioning pastecs Package for Analysis of Space-Time Ecological Series pbapply Adding Progress Bar to ’*apply’ Functions pbivnorm Vectorized Bivariate Normal CDF pbkrtest Parametric Bootstrap and Kenward Roger Based Methods for Mixed Model Comparison PBSmapping Mapping Fisheries Data and Spatial Analysis Tools pbv Probabilities for Bivariate Normal Distribution pcaPP Robust PCA by Projection Pursuit pdftools Text Extraction, Rendering and Converting of PDF Documents pequod Moderated Regression Package performance Assessment of Regression Models Performance PerformanceAnalytics Econometric Tools for Performance and Risk Analysis permtest Permutation test to compare variability within and distance between two groups permuco Permutation Tests for Regression, (Repeated Measures) ANOVA/ANCOVA and Comparison of Signals permute Functions for Generating Restricted Permutations of Data pgirmess Spatial Analysis and Data Mining for Field Ecologists phangorn Phylogenetic Reconstruction and Analysis phia Post-Hoc Interaction Analysis phylobase Base Package for Phylogenetic Structures and Comparative Data pillar Coloured Formatting for Columns pingr Check if a Remote Computer is Up pixmap Bitmap Images (“Pixel Maps”) pkgbuild Find Tools Needed to Build R Packages pkgconfig Private Configuration for ’R’ Packages pkgdown Make Static HTML Documentation for a Package pkgKitten Create Simple Packages Which Do not Upset R Package Checks pkgload Simulate Package Installation and Attach pkgmaker Development Utilities for R Packages PKI Public Key Infrastucture for R Based on the X.509 Standard PKPDmodels Pharmacokinetic/pharmacodynamic models playwith A GUI for interactive plots using GTK+ plm Linear Models for Panel Data plogr The ’plog’ C++ Logging Library plot3D Plotting Multi-Dimensional Data plot3Drgl Plotting Multi-Dimensional Data - Using ’rgl’ plotly Create Interactive Web Graphics via ’plotly.js’ plotmo Plot a Model’s Residuals, Response, and Partial Dependence Plots plotrix Various Plotting Functions pls Partial Least Squares and Principal Component Regression plyr Tools for Splitting, Applying and Combining Data pmg Poor Man’s GUI pmml Generate PMML for Various Models pmmlTransformations Transforms Input Data from a PMML Perspective png Read and write PNG images

15 poLCA Polytomous variable Latent Class Analysis polspline Polynomial Spline Routines polyclip Polygon Clipping polycor Polychoric and Polyserial Correlations polynom A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations pool Object Pooling portfolio Analysing Equity Portfolios ppcor Partial and Semi-Partial (Part) Correlation pps Functions for PPS sampling prabclus Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data pracma Practical Numerical Math Functions praise Praise Users prediction Tidy, Type-Safe ’prediction()’ Methods prefmod Utilities to Fit Paired Comparison Models for Preferences PresenceAbsence Presence-Absence Model Evaluation. prettycode Pretty Print R Code in the Terminal prettyR Pretty Descriptive Stats prettyunits Pretty, Human Readable Formatting of Quantities pROC Display and Analyze ROC Curves processx Execute and Control System Processes prodlim Product-Limit Estimation for Censored Event History Analysis profileModel Profiling Inference Functions for Various Model Classes progress Terminal Progress Bars PROJ Generic Coordinate System Transformations Using ’PROJ’ proj4 A simple interface to the PROJ.4 cartographic projections library promises Abstractions for Promise-Based Asynchronous Programming proto Prototype Object-Based Programming proxy Distance and Similarity Measures pryr Tools for Computing on the Language ps List, Query, Manipulate System Processes pscl Political Science Computational Laboratory psgp Projected Spatial Gaussian Process Methods pso Particle Swarm Optimization psy Various procedures used in psychometry psych Procedures for Psychological, Psychometric, and Personality Research psychometric Applied Psychometric Theory psychotools Psychometric Modeling Infrastructure psyphy Functions for analyzing psychophysical data in R purrr Functional Programming Tools pwr Basic Functions for Power Analysis qap Heuristics for the Quadratic Assignment Problem (QAP) qcc Quality Control Charts qgraph Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation qpdf Split, Combine and Compress PDF Files quadprog Functions to Solve Quadratic Programming Problems quantmod Quantitative Financial Modelling Framework QuantPsyc Quantitative Psychology Tools quantreg Quantile Regression questionr Functions to Make Surveys Processing Easier qvcalc Quasi Variances for Factor Effects in Statistical Models R.cache Fast and Light-Weight Caching (Memoization) of Objects and Results to Speed Up Computations R.devices Unified Handling of Graphics Devices R. Read and Write MAT Files and Call MATLAB from Within R R.methodsS3 S3 Methods Simplified

16 R.oo R Object-Oriented Programming with or without References R.rsp Dynamic Generation of Scientific Reports R.utils Various Programming Utilities R2admb ’ADMB’ to R Interface Functions R2HTML HTML Exportation for R Objects R2wd Write MS-Word documents from R R2WinBUGS Running ’WinBUGS’ and ’OpenBUGS’ from ’R’ / ’S-PLUS’ R6 Encapsulated Classes with Reference Semantics ramps Bayesian Geostatistical Modeling with RAMPS randomcoloR Generate Attractive Random Colors RandomFields Simulation and Analysis of Random Fields RandomFieldsUtils Utilities for the Simulation and Analysis of Random Fields randomForest Breiman and Cutler’s Random Forests for Classification and Regression randomForestSRC Fast Unified Random Forests for Survival, Regression, and Classification (RF-SRC) randomizr Easy-to-Use Tools for Common Forms of Random Assignment and Sampling randtoolbox Toolbox for Pseudo and Quasi Random Number Generation and Random Generator Tests ranger A Fast Implementation of Random Forests RANN Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric rapidjsonr ’Rapidjson’ C++ Header Files rappdirs Application Directories: Determine Where to Save Data, Caches, and Logs RArcInfo Functions to import data from Arc/Info V7.x binary coverages rARPACK Solvers for Large Scale Eigenvalue and SVD Problems raster Geographic Data Analysis and Modeling rasterVis Visualization Methods for Raster Data rattle Graphical User Interface for Data Science in R rbenchmark Benchmarking routine for R Rcapture Loglinear Models for Capture-Recapture Experiments rcartocolor ’CARTOColors’ Palettes Rcgmin Conjugate Gradient Minimization of Nonlinear Functions rcmdcheck Run ’R CMD check’ from ’R’ and Capture Results Rcmdr RcmdrMisc R Commander Miscellaneous Functions RcmdrPlugin.coin Rcmdr Coin Plug-In RcmdrPlugin.depthTools R commander Depth Tools Plug-In RcmdrPlugin.epack Rcmdr plugin for time series RcmdrPlugin.Export Export R Output to LaTeX or HTML RcmdrPlugin.FactoMineR Graphical User Interface for FactoMineR RcmdrPlugin.HH Rcmdr Support for the HH Package RcmdrPlugin.IPSUR An IPSUR Plugin for the R Commander RcmdrPlugin.orloca A GUI for Planar Location Problems RcmdrPlugin.qcc Rcmdr qcc Plug-In RcmdrPlugin.qual Rcmdr plugin for quality control course RcmdrPlugin.sampling Tools for sampling in Official Statistical Surveys RcmdrPlugin.survival R Commander Plug-in for the ’survival’ Package RcmdrPlugin.SurvivalT Rcmdr Survival Plug-In RcmdrPlugin.TeachingDemos Rcmdr Teaching Demos Plug-in RColorBrewer ColorBrewer Palettes rcompanion Functions to Support Extension Education Program Evaluation Rcpp Seamless R and C++ Integration RcppArmadillo ’Rcpp’ Integration for the ’Armadillo’ Templated Linear Algebra Library RcppEigen ’Rcpp’ Integration for the ’Eigen’ Templated Linear Algebra Library RcppParallel Parallel Programming Tools for ’Rcpp’ RcppProgress An Interruptible Progress Bar with OpenMP Support for C++ in R Packages RcppRoll Efficient Rolling / Windowed Operations

17 Rcsdp R Interface to the CSDP Semidefinite Programming Library RCurl General Network (HTTP/FTP/...) Client Interface for R Rd2roxygen Convert Rd to ’Roxygen’ Documentation Rdpack Update and Manipulate Rd Documentation Objects readODS Read and Write ODS Files readr Read Rectangular Text Data readstata13 Import ’Stata’ Data Files readxl Read Excel Files recipes Preprocessing Tools to Create Design Matrices registry Infrastructure for R Package Registries regress Gaussian Linear Models with Linear Covariance Structure regsem Regularized Structural Equation Modeling rela Item Analysis Package with Standard Errors relaimpo Relative Importance of Regressors in Linear Models relations Data Structures and Algorithms for Relations relevent Relational Event Models relimp Relative Contribution of Effects in a Regression Model rem Relational Event Models (REM) rematch Match Regular Expressions with a Nicer ’API’ rematch2 Tidy Output from Regular Expression Matching remotes R Package Installation from Remote Repositories, Including ’GitHub’ rentrez ’Entrez’ in R repmis Miscellaneous Tools for Reproducible Research reportr A General Message and Error Reporting System repr Serializable Representations reprex Prepare Reproducible Example Code via the Clipboard reproj Coordinate System Transformations for Generic Map Data resample Resampling Functions reshape Flexibly Reshape Data reshape2 Flexibly Reshape Data: A Reboot of the Reshape Package reticulate Interface to ’Python’ rex Friendly Regular Expressions Rfit Rank-Based Estimation for Linear Models RFOC Graphics for Spherical Distributions and Earthquake Focal Mechanisms rgdal Bindings for the ’Geospatial’ Data Abstraction Library rgenoud R Version of GENetic Optimization Using Derivatives rgeos Interface to Geometry Engine - Open Source (’GEOS’) rgexf Build, Import and Export GEXF Graph Files rggobi Interface Between R and ’GGobi’ rgl 3D Visualization Using OpenGL rglwidget ’rgl’ in ’htmlwidgets’ Framework RgoogleMaps Overlays on Static Maps Rgraphviz Provides plotting capabilities for R graph objects RGtk2 R Bindings for Gtk 2.8.0 and Above RGtk2Extras Data frame editor and dialog making wrapper for RGtk2 rhandsontable Interface to the ’Handsontable.js’ Library RhpcBLASctl Control the Number of Threads on ’BLAS’ rio A Swiss-Army Knife for Data I/O ritis Integrated Taxonomic Information System Client rjags Bayesian Graphical Models using MCMC rJava Low-Level R to Java Interface rjson JSON for R RJSONIO Serialize R Objects to JSON, JavaScript Object Notation rlang Functions for Base Types and Core R and ’’ Features

18 RMark R Code for Mark Analysis rmarkdown Dynamic Documents for R rmeta Meta-Analysis Rmpfr R MPFR - Multiple Precision Floating-Point Reliable Rmpi Interface (Wrapper) to MPI (Message-Passing Interface) rms Regression Modeling Strategies RMySQL Database Interface and ’MySQL’ Driver for R rncl An Interface to the Nexus Class Library RNeXML Semantically Rich I/O for the ’NeXML’ Format rngtools Utility Functions for Working with Random Number Generators rngWELL Toolbox for WELL Random Number Generators robCompositions Compositional Data Analysis robust Port of the S+ "Robust Library" robustbase Basic Robust Statistics rockchalk Regression Estimation and Presentation ROCR Visualizing the Performance of Scoring Classifiers RODBC ODBC Database Access Rook Rook - a web server interface for R rootSolve Nonlinear Root Finding, Equilibrium and Steady-State Analysis of Ordinary Differential Equations rotl Interface to the ’Open Tree of Life’ API roxygen in R roxygen2 In-Line Documentation for R rpanel Simple Interactive Controls for R using the ’tcltk’ Package rpart Recursive Partitioning and Regression Trees rpart.plot Plot ’rpart’ Models: An Enhanced Version of ’plot.rpart’ rpf Response Probability Functions RPMG Graphical User Interface (GUI) for Interactive R Analysis Sessions RPostgres ’Rcpp’ Interface to ’PostgreSQL’ RPostgreSQL R Interface to the ’PostgreSQL’ Database System rprojroot Finding Files in Project Subdirectories RPyGeo ArcGIS Geoprocessing via Python rrcov Scalable Robust Estimators with High Breakdown Point rredlist ’IUCN’ Red List Client RSAGA SAGA Geoprocessing and Terrain Analysis rsample General Resampling Infrastructure rsconnect Deployment Interface for R Markdown Documents and Shiny Applications rscproxy statconn: provides portable C-style interface to R (StatConnector) RSEIS Seismic Time Series Analysis Tools RSiena Siena - Simulation Investigation for Empirical Network Analysis Rsolnp General Non-Linear Optimization RSpectra Solvers for Large-Scale Eigenvalue and SVD Problems RSQLite ’SQLite’ Interface for R rstan R Interface to Stan rstanarm Bayesian Applied Regression Modeling via Stan rstantools Tools for Developing R Packages Interfacing with ’Stan’ rstatix Pipe-Friendly Framework for Basic Statistical Tests Rstem Interface to Snowball implementation of Porter’s word stemming algorithm. rstudioapi Safely Access the RStudio API RStudioConsoleRender RStudio addin for rendering an Rmarkdown document in the console RSurvey Geographic Information System Application rsvg Render SVG Images into PDF, PNG, PostScript, or Bitmap Arrays RSVGTipsDevice An R SVG Graphics Device with Dynamic Tips and Hyperlinks rtiff Read and Write TIFF Files Rtsne T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation

19 Rttf2pt1 ’ttf2pt1’ Program RUnit R Unit Test Framework rversions Query ’R’ Versions, Including ’r-release’ and ’r-oldrel’ rvest Easily Harvest (Scrape) Web Pages Rvmmin Variable Metric Nonlinear Function Minimization Rwave Time-Frequency Analysis of 1-D Signals RWiener Wiener Process Distribution Functions rworldmap Mapping Global Data rworldxtra Country boundaries at high resolution. S4Vectors S4 implementation of vector-like and list-like objects sampleSelection Sample Selection Models samplesize Sample Size Calculation for Various t-Tests and Wilcoxon-Test SampleSizeMeans Sample size calculations for normal means SampleSizeProportions Calculating sample size requirements when estimating the difference between two binomial proportions sampling Survey Sampling samplingbook Survey Sampling Procedures sandwich Robust Covariance Matrix Estimators sas7bdat SAS Database Reader (experimental) SASmixed Data sets from "SAS System for Mixed Models" sass Syntactically Awesome Style Sheets (’Sass’) satellite Handling and Manipulating Remote Sensing Data scagnostics Compute scagnostics - scatterplot diagnostics scales Scale Functions for Visualization scalreg Scaled Sparse Linear Regression scatterplot3d 3D Scatter Plot scholar Analyse Citation Data from Google Scholar scico Colour Palettes Based on the Scientific Colour-Maps sciplot Scientific Graphing Functions for Factorial Designs SCRT Single-Case Randomization Tests see Visualisation Toolbox for ’easystats’ and Extra Geoms, Themes and Color Palettes for ’ggplot2’ segmented Regression Models with Break-Points / Change-Points Estimation selectr Translate CSS Selectors to XPath Expressions sem Structural Equation Models SemiPar Semiparametic Regression semPlot Path Diagrams and Visual Analysis of Various SEM Packages’ Output semTools Useful Tools for Structural Equation Modeling sendplot Tool for sending interactive plots with tool-tip content. SensoMineR Sensory Data Analysis seqinr Biological Sequences Retrieval and Analysis seriation Infrastructure for Ordering Objects Using Seriation servr A Simple HTTP Server to Serve Static Files or Dynamic Documents sessioninfo R Session Information setRNG Set (Normal) Random Number Generator and Seed sets Sets, Generalized Sets, Customizable Sets and Intervals sf Simple Features for R sfheaders Converts Between R Objects and Simple Feature Objects sfsmisc Utilities from ’Seminar fuer Statistik’ ETH Zurich sgeostat An Object-Oriented Framework for Geostatistical Modeling in S+ shape Functions for Plotting Graphical Shapes, Colors shapefiles Read and Write ESRI Shapefiles shiny Framework for R shinyBS Twitter Bootstrap Components for Shiny shinybusy Busy Indicator for ’Shiny’ Applications shinyjs Easily Improve the User Experience of Your Shiny Apps in Seconds

20 shinyRGL Shiny Wrappers for RGL shinysky A set of Shiny UI components/widgets. shinystan Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models shinytest Test Shiny Apps shinythemes Themes for Shiny showimage Show an Image on an ’R’ Graphics Device signal Signal Processing SimComp Simultaneous Comparisons for Multiple Endpoints simecol Simulation of Ecological (and Other) Dynamic Systems simpleboot Simple Bootstrap Routines simstudy Simulation of Study Data SingleCaseES A Calculator for Single-Case Effect Sizes sirt Supplementary Item Response Theory Models sjlabelled Labelled Data Utility Functions sjmisc Data and Variable Transformation Functions sjPlot Data Visualization for Statistics in Social Science sjstats Collection of Convenient Functions for Common Statistical Computations slackr Send Messages, Images, R Objects and Files to ’Slack’ Channels/Users slam Sparse Lightweight Arrays and Matrices sm Smoothing Methods for Nonparametric Regression and Density Estimation sn The Skew-Normal and Related Distributions Such as the Skew-t sna Tools for Social Network Analysis snakecase Convert Strings into any Case snow Simple Network of Workstations SnowballC Snowball Stemmers Based on the C ’libstemmer’ UTF-8 Library snowfall Easier cluster computing (based on snow). socviz Utility Functions and Data Sets for Data Visualization solitude An Implementation of Isolation Forest solrium General Purpose R Interface to ’Solr’ som Self-Organizing Map soma General-Purpose Optimisation With the Self-Organising Migrating Algorithm sos Search Contributed R Packages, Sort by Package sourcetools Tools for Reading, Tokenizing and Parsing R Code sp Classes and Methods for Spatial Data spacetime Classes and Methods for Spatio-Temporal Data spam SPArse Matrix sparr Spatial and Spatiotemporal Relative Risk SparseM Sparse Linear Algebra spatcounts Spatial count regression spatgraphs Graph Edge Computations for Spatial Point Patterns spatial Functions for Kriging and Point Pattern Analysis spatialCovariance Computation of Spatial Covariance Matrices for Data on Rectangles SpatialEpi Methods and Data for Spatial Epidemiology SpatialExtremes Modelling Spatial Extremes spatialkernel Non-Parametric Estimation of Spatial Segregation in a Multivariate Point Process SpatialNP Multivariate Nonparametric Methods Based on Spatial Signs and Ranks spatialsegregation Segregation Measures for Multitype Spatial Point Patterns spatialwidget Formats Spatial Data for Use in Htmlwidgets spatstat Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests spatstat.data Datasets for ’spatstat’ spatstat.utils Utility Functions for ’spatstat’ spBayes Univariate and Multivariate Spatial-Temporal Modeling spc Statistical Process Control – Calculation of ARL and Other Control Chart Performance Measures spcosa Spatial Coverage Sampling and Random Sampling from Compact Geographical Strata

21 spData Datasets for Spatial Analysis spdep Spatial Dependence: Weighting Schemes, Statistics spe Stochastic Proximity Embedding speedglm Fitting Linear and Generalized Linear Models to Large Data Sets speff2trial Semiparametric efficient estimation for a two-sample treatment effect spelling Tools for Spell Checking in R spgrass6 Interface Between GRASS 6+ Geographical Information System and R spgwr Geographically Weighted Regression SpherWave Spherical Wavelets and SW-based Spatially Adaptive Methods sphet Estimation of Spatial Autoregressive Models with and without Heteroscedasticity splancs Spatial and Space-Time Point Pattern Analysis spls Sparse Partial Least Squares (SPLS) Regression and Classification spsurvey Spatial Survey Design and Analysis spuRs Functions and Datasets for "Introduction to Scientific Programming and Simulation Using R" SQUAREM Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms sROC Nonparametric Smooth ROC Curves for Continuous Data SSDforR Functions to Analyze Single System Data stabledist Stable Distribution Functions stabs Stability Selection with Error Control StanHeaders C++ Header Files for Stan stars Spatiotemporal Arrays, Raster and Vector Data Cubes startupmsg Utilities for Start-Up Messages statmod Statistical Modeling statnet Software Tools for the Statistical Analysis of Network Data statnet.common Common R Scripts and Utilities Used by the Statnet Project Software Stem Spatio-temporal models in R stopwords Multilingual Stopword Lists stringdist Approximate String Matching, Fuzzy Text Search, and String Distance Functions stringi Character String Processing Facilities stringr Simple, Consistent Wrappers for Common String Operations strucchange Testing, Monitoring, and Dating Structural Changes styler Non-Invasive Pretty Printing of R Code subselect Selecting Variable Subsets superpc Supervised principal components SuppDists Supplementary Distributions survey Analysis of Complex Survey Samples survival Survival Analysis survPresmooth Presmoothed Estimation in Survival Analysis svDialogs ’SciViews’ - Standard Dialog Boxes for Windows, MacOS and Linuxes svglite An ’SVG’ Graphics Device svGUI SciViews - Manage GUIs in R svIDE Functions to Ease Interactions Between R and IDE or Code Editors svMisc SciViews - Miscellaneous Functions svSocket ’SciViews’ - Socket Server svUnit ’SciViews’ - Unit, Integration and System Testing svWidgets Management of GUI Widgets, Windows, and Other GUI Resources SweaveListingUtils Utilities for Sweave Together with TeX ’listings’ Package sylly Hyphenation and Syllable Counting for Text Analysis sys Powerful and Reliable Tools for Running System Commands in R systemfit Estimating Systems of Simultaneous Equations systemfonts System Native Font Finding tables Formula-Driven Table Generation TAM Test Analysis Modules tau Text Analysis Utilities

22 taxize Taxonomic Information from Around the Web tcltk2 Tcl/Tk Additions TDA Statistical Tools for Topological Data Analysis TDAmapper Analyze High-Dimensional Data Using Discrete Morse Theory TeachingDemos Demonstrations for Teaching and Learning tensor Tensor product of arrays tensorA Advanced Tensor Arithmetic with Named Indices tergm Fit, Simulate and Diagnose Models for Network Evolution Based on Exponential-Family Random Graph Models tesseract Open Source OCR Engine testit A Simple Package for Testing R Packages testthat Unit Testing for R texreg Conversion of R Regression Output to LaTeX or HTML Tables tgp Bayesian Treed Gaussian Process Models TH.data TH’s Data Archive threejs Interactive 3D Scatter Plots, Networks and Globes tibble Simple Data Frames tidygraph A Tidy API for Graph Manipulation tidymodels Easily Install and Load the ’Tidymodels’ Packages tidyposterior Bayesian Analysis to Compare Models using Resampling Statistics tidypredict Run Predictions Inside the Database tidyr Tidy Messy Data tidyselect Select from a Set of Strings tidytext Text Mining using ’dplyr’, ’ggplot2’, and Other Tidy Tools tidyverse Easily Install and Load the ’Tidyverse’ tigerstats R Functions for Elementary Statistics tikzDevice R Graphics Output in LaTeX Format timeDate Rmetrics - Chronological and Calendar Objects timereg Flexible Regression Models for Survival Data timeSeries Financial Time Series Objects (Rmetrics) TinnR Resources of Tinn-R GUI/Editor for R Environment tinytex Helper Functions to Install and Maintain ’TeX Live’, and Compile ’LaTeX’ Documents tis Time Indexes and Time Indexed Series tkrplot TK Rplot tm Text Mining Package tmap Thematic Maps tmaptools Thematic Map Tools TMB Template Model Builder: A General Random Effect Tool Inspired by ’ADMB’ tmvnsim Truncated Multivariate Normal Simulation tnam Temporal Network Autocorrelation Models (TNAM) tnet Weighted, Two-Mode, and Longitudinal Networks Analysis tokenizers Fast, Consistent Tokenization of Natural Language Text traipse Shared Tools for Tracking Data tree Classification and Regression Trees treemap Treemap Visualization triangle Provides the Standard Distribution Functions for the Triangle Distribution triebeard ’Radix’ Trees in ’Rcpp’ trimcluster Cluster Analysis with Trimming trip Tools for the Analysis of Animal Track Data tripack Triangulation of Irregularly Spaced Data tripEstimation Metropolis Sampler and Supporting Functions for Estimating Animal Movement from Archival Tags and Satellite Fixes truncdist Truncated Random Variables truncnorm Truncated Normal Distribution truncreg Truncated Gaussian Regression Models trust Trust Region Optimization

23 TSA Time Series Analysis tseries Time Series Analysis and Computational Finance tsna Tools for Temporal Social Network Analysis TSP Traveling Salesperson Problem (TSP) TTR Technical Trading Rules tufte Tufte’s Styles for R Markdown Documents tune Tidy Tuning Tools tweedie Evaluation of Tweedie Exponential Family Models tweenr Interpolate Data for Smooth Animations ucminf General-Purpose Unconstrained Non-Linear Optimization ufs Quantitative Analysis Made Accessible units Measurement Units for R Vectors urca Unit Root and Cointegration Tests for Time Series Data urltools Vectorised Tools for URL Handling and Parsing uroot Unit Root Tests for Seasonal Time Series UScensus2000cdp US Census 2000 Designated Places Shapefiles and Additional Demographic Data UScensus2000tract US Census 2000 Tract Level Shapefiles and Additional Demographic Data UScensus2010 US Census 2010 Suite of R Packages usdata Data on the States and Counties of the United States userfriendlyscience Quantitative Analysis Made Accessible usethis Automate Package and Project Setup UsingR Data Sets, Etc. for the Text "Using R for Introductory Statistics", Second Edition utf8 Unicode Text Processing uuid Tools for Generating and Handling of UUIDs V8 Embedded JavaScript and WebAssembly Engine for R vardiag Variogram Diagnostics vars VAR Modelling vcd Visualizing Categorical Data vctrs Vector Helpers vdiffr Visual Regression Testing and Graphical Diffing vegan Community Ecology Package vegdata Access Vegetation Databases and Treat Taxonomy VennDiagram Generate High-Resolution Venn and Plots verification Weather Forecast Verification Utilities VGAM Vector Generalized Linear and Additive Models VGAMdata Data Supporting the ’VGAM’ Package VIM Visualization and Imputation of Missing Values vioplot Violin Plot vipor Plot Categorical Data Using Quasirandom Noise and Density Estimates viridis Default Color Maps from ’matplotlib’ viridisLite Default Color Maps from ’matplotlib’ (Lite Version) visNetwork Network Visualization using ’vis.js’ Library visreg Visualization of Regression Models waffle Create Waffle Chart Visualizations in R waveslim Basic Wavelet Routines for One-, Two-, and Three-Dimensional Signal Processing webdriver ’WebDriver’ Client for ’PhantomJS’ webp A New Format for Lossless and Lossy Image Compression webshot Take Screenshots of Web Pages wesanderson A Wes Anderson Palette Generator whisker {{mustache}} for R, Logicless Templating whoami Username, Full Name, Email Address, ’GitHub’ Username of the Current User widgetframe ’Htmlwidgets’ in Responsive ’iframes’ WikidataR API Client Library for ’Wikidata’ WikipediR A MediaWiki API Wrapper

24 wikitaxa Taxonomic Information from ’Wikipedia’ withr Run Code ’With’ Temporarily Modified Global State wordcloud Word Clouds workflows Modeling Workflows worrms World Register of Marine Species (WoRMS) Client WrightMap IRT Item-Person Map with ’ConQuest’ Integration WriteXLS Cross-Platform Perl Based R Function to Create Excel 2003 (XLS) and Excel 2007 (XLSX) Files WRS2 A Collection of Robust Statistical Methods wskm Weighted k-Means Clustering xergm Extensions of Exponential Random Graph Models xergm.common Common Infrastructure for Extensions of Exponential Random Graph Models xfun Miscellaneous Functions by ’’ xgboost Extreme Gradient Boosting XLConnect Excel Connector for R XLConnectJars JAR Dependencies for the XLConnect Package xlsx Read, Write, Format Excel 2007 and Excel 97/2000/XP/2003 Files xlsxjars Package required POI jars for the xlsx package XML Tools for Parsing and Generating XML Within R and S-Plus xml2 Parse XML xmlparsedata Parse Data of ’R’ Code as an ’XML’ Tree xopen Open System Files, ’URLs’, Anything xsplines ** No title available ** xtable Export Tables to LaTeX or HTML xts eXtensible Time Series yacca Yet Another Canonical Correlation Analysis Package YaleToolkit Data exploration tools from Yale University. yaml Methods to Convert R Data to YAML and Back yardstick Tidy Characterizations of Model Performance yhat Interpreting Regression Effects zCompositions Treatment of Zeros, Left-Censored and Missing Values in Compositional Data Sets zeallot Multiple, Unpacking, and Destructuring Assignment Zelig Everyone’s Statistical Software zip Cross-Platform ’zip’ Compression zipcode U.S. ZIP Code database for geocoding zipfR Statistical Models for Word Frequency Distributions zoo S3 Infrastructure for Regular and Irregular Time Series (Z’s Ordered Observations) base The R Base Package boot Bootstrap Functions (Originally by Angelo Canty for S) class Functions for Classification cluster "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et al. codetools Code Analysis Tools for R compiler The R Compiler Package datasets The R Datasets Package foreign Read Data Stored by ’Minitab’, ’S’, ’SAS’, ’SPSS’, ’Stata’, ’Systat’, ’Weka’, ’dBase’, ... graphics The R Graphics Package grDevices The R Graphics Devices and Support for Colours and Fonts grid The Grid Graphics Package KernSmooth Functions for Kernel Smoothing Supporting Wand & Jones (1995) lattice Trellis Graphics for R MASS Support Functions and Datasets for Venables and Ripley’s MASS Matrix Sparse and Dense Matrix Classes and Methods methods Formal Methods and Classes mgcv Mixed GAM Computation Vehicle with Automatic Smoothness Estimation nlme Linear and Nonlinear Mixed Effects Models

25 nnet Feed-Forward Neural Networks and Multinomial Log-Linear Models parallel Support for Parallel computation in R rpart Recursive Partitioning and Regression Trees spatial Functions for Kriging and Point Pattern Analysis splines Regression Spline Functions and Classes stats The R Stats Package stats4 Statistical Functions using S4 Classes survival Survival Analysis tcltk Tcl/Tk Interface tools Tools for Package Development translations The R Translations Package utils The R Utils Package

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