R 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 R Package 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 Software 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 C++ 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 github 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 Markdown 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 ’Stan’ 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 Unicode 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 ’ggplot2’ coxme Mixed Effects Cox Models cplm Compound Poisson Linear Models crayon Colored Terminal Output crossdes Construction of Crossover Designs crosstalk