R-3.4.3-foss-2016b-fh1

Package List

• ADGofTest-0.3 Anderson-Darling GoF test
• ASCAT 2.4.3
• AUC-0.3.0 Threshold independent performance measures for probabilistic<U+000a>classifiers.
• AlgDesign-1.1-7.3 Algorithmic Experimental Design
• BB-2014.10-1 Solving and Optimizing Large-Scale Nonlinear Systems
• BBmisc-1.11 Miscellaneous Helper Functions for B. Bischl
• BDgraph-2.43 Bayesian Structure Learning in Graphical Models using Birth-Death MCMC
• BH-1.65.0-1 Boost C++ Header Files
• BatchJobs-1.7 Batch Computing with R
• Bhat-0.9-10 General likelihood exploration
• BiasedUrn-1.07 Biased Urn Model Distributions
• BivarP-1.0 Estimating the Parameters of Some Bivariate Distributions
• Bolstad-0.2-34 Functions for Elementary Bayesian Inference
• Bolstad2-1.0-28 Bolstad functions
• BradleyTerry2-1.0-8 Bradley-Terry Models
• Brobdingnag-1.2-4 Very Large Numbers in R
• CVST-0.2-1 Fast Cross-Validation via Sequential Testing
• Cairo-1.5-9 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
• CompQuadForm-1.4.3 Distribution Function of Quadratic Forms in Normal Variables
• DAAG-1.22 Data Analysis and Graphics Data and Functions
• DBI-0.7 R Database Interface
• DEoptimR-1.0-8 Differential Evolution Optimization in Pure R
• DRR-0.0.2 Dimensionality Reduction via Regression
• DT-0.2 A Wrapper of the JavaScript Library ‘DataTables’
• Deriv-3.8.3 Symbolic Differentiation
• DiagrammeR-0.9.2 Graph/Network Visualization
• DiscriMiner-0.1-29 Tools of the Trade for Discriminant Analysis
• EasyABC-1.5 Efficient Approximate Bayesian Computation Sampling Schemes
• EpiModel-1.5.0 Mathematical Modeling of Infectious Disease Dynamics
• FNN-1.1 Fast Nearest Neighbor Search Algorithms and Applications
• FactoMineR-1.39 Multivariate Exploratory Data Analysis and Data Mining
• Formula-1.2-2 Extended Model Formulas
• GGally-1.3.2 Extension to ‘ggplot2’
• GSA-1.03 Gene set analysis
• GWASExactHW-1.01 Exact Hardy-Weinburg testing for Genome Wide Association Studies
• GeneNet-1.2.13 Modeling and Inferring Gene Networks
• HaploSim-1.8.4 Functions to simulate haplotypes
• Hmisc-4.0-3 Harrell Miscellaneous
• IDPmisc-1.1.17 Utilities of Institute of Data Analyses and Process Design<U+000a>(www.idp.zhaw.ch)
• IRdisplay-0.4.4 ‘Jupyter’ Display Machinery
• Iso-0.0-17 Functions to Perform Isotonic Regression
• KernSmooth-2.23-15 Functions for Kernel Smoothing Supporting Wand & Jones (1995)
• LearnBayes-2.15 Functions for Learning Bayesian Inference
• Lmoments-1.2-3 L-Moments and Quantile Mixtures
• LogicReg-1.5.9 Logic Regression
• MASS-7.3-47 Support Functions and Datasets for Venables and Ripley’s MASS
• MCMCglmm-2.25 MCMC Generalised Linear Mixed Models
• MPV-1.38 Data Sets from Montgomery, Peck and Vining
• Matrix-1.2-12 Sparse and Dense Matrix Classes and Methods
• MatrixModels-0.4-1 Modelling with Sparse And Dense Matrices
• ModelMetrics-1.1.0 Rapid Calculation of Model Metrics
• NLP-0.1-11 Natural Language Processing Infrastructure
• NMF-0.20.6 Algorithms and Framework for Nonnegative Matrix Factorization (NMF)
• PBSddesolve-1.12.2 Solver for Delay Differential Equations
• ParamHelpers-1.10 Helpers for Parameters in Black-Box Optimization, Tuning and Machine Learning
• PolynomF-1.0-1 Polynomials in R
• R.matlab-3.6.1 Read and Write MAT Files and Call MATLAB from Within R
• R.methodsS3-1.7.1 S3 Methods Simplified
• R.oo-1.21.0 R Object-Oriented Programming with or without References
• R.utils-2.6.0 Various Programming Utilities
• R2WinBUGS-2.1-21 Running ‘WinBUGS’ and ‘OpenBUGS’ from ‘R’ / ‘S-PLUS’
• R2jags-0.5-7 Using R to Run ‘JAGS’
• R6-2.2.2 Classes with Reference Semantics
• RANN-2.5.1 Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric
• RCircos-1.2.0 Circos 2D Track Plot
• RColorBrewer-1.1-2 ColorBrewer Palettes
• RCurl-1.95-4.8 General Network (HTTP/FTP/…) Client Interface for R
• REDCapR-0.9.8 Interaction Between R and REDCap
• RGCCA-2.1.2 Regularized and Sparse Generalized Canonical Correlation Analysis for Multiblock Data
• RJSONIO-1.3-0 Serialize R objects to JSON, JavaScript Object Notation
• RMTstat-0.3 Distributions, Statistics and Tests derived from Random Matrix<U+000a>Theory
• RMySQL-0.10.13 Database Interface and ‘MySQL’ Driver for R
• RNeXML-2.0.8 Semantically Rich I/O for the ‘NeXML’ Format
• ROCR-1.0-7 Visualizing the Performance of Scoring Classifiers
• RODBC-1.3-15 ODBC Database Access
• RPostgreSQL-0.6-2 R Interface to the ‘PostgreSQL’ Database System
• RSNNS-0.4-9 Neural Networks using the Stuttgart Neural Network Simulator (SNNS)
• RSQLite-2.0 ‘SQLite’ Interface for R
• RSclient-0.7-3 Client for Rserve
• RUnit-0.4.31 R Unit Test Framework
• RWeka-0.4-36 R/Weka Interface
• RWekajars-3.9.1-5 R/Weka Interface Jars
• Rcpp-0.12.14 Seamless R and C++ Integration
• RcppArmadillo-0.8.300.1.0 ‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra Library
• RcppEigen-0.3.3.3.1 ‘Rcpp’ Integration for the ‘Eigen’ Templated Linear Algebra Library
• RcppParallel-4.3.20 Parallel Programming Tools for ‘Rcpp’
• RcppRoll-0.2.2 Efficient Rolling / Windowed Operations
• Rglpk-0.6-3 R/GNU Linear Programming Kit Interface
• Rhpc-0.15-244 Permits *apply() Style Dispatch for ‘HPC’
• Rlabkey-2.1.136 Data Exchange Between R and ‘LabKey’ Server
• Rmpi-0.6-6 Interface (Wrapper) to MPI (Message-Passing Interface)
• Rook-1.1-1 Rook - a web server interface for R
• Rttf2pt1-1.3.5 ‘ttf2pt1’ Program
• SparseM-1.77 Sparse Linear Algebra
• StanHeaders-2.16.0-1 C++ Header Files for Stan
• SuperLearner-2.0-22 Super Learner Prediction
• SuppDists-1.1-9.4 Supplementary Distributions
• TH.data-1.0-8 TH’s Data Archive
• TTR-0.23-2 Technical Trading Rules
• TeachingDemos-2.10 Demonstrations for Teaching and Learning
• TraMineR-2.0-7 Trajectory Miner: a Toolbox for Exploring and Rendering Sequences
• VGAM-1.0-4 Vector Generalized Linear and Additive Models
• VennDiagram-1.6.18 Generate High-Resolution Venn and Euler Plots
• WikidataR-1.4.0 API Client Library for ‘Wikidata’
• WikipediR-1.5.0 A MediaWiki API Wrapper
• XML-3.98-1.9 Tools for Parsing and Generating XML Within R and S-Plus
• abc-2.1 Tools for Approximate Bayesian Computation (ABC)
• abc.data-1.0 Data Only: Tools for Approximate Bayesian Computation (ABC)
• abind-1.4-5 Combine Multidimensional Arrays
• acepack-1.4.1 ACE and AVAS for Selecting Multiple Regression Transformations
• adabag-4.1 Applies Multiclass AdaBoost.M1, SAMME and Bagging
• ade4-1.7-8 Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
• adegenet-2.1.0 Exploratory Analysis of Genetic and Genomic Data
• adephylo-1.1-10 Exploratory Analyses for the Phylogenetic Comparative Method
• akima-0.6-2 Interpolation of Irregularly and Regularly Spaced Data
• alr3-2.0.5 Data to Accompany Applied Linear Regression 3rd Edition
• animation-2.5 A Gallery of Animations in Statistics and Utilities to Create Animations
• ape-5.0 Analyses of Phylogenetics and Evolution
• argparser-0.4 Command-Line Argument Parser
• arm-1.9-3 Data Analysis Using Regression and Multilevel/Hierarchical Models
• assertthat-0.2.0 Easy Pre and Post Assertions
• aws.ec2metadata-0.1.2 Get EC2 Instance Metadata
• aws.s3-0.3.3 ‘AWS S3’ Client Package
• aws.signature-0.3.5 Amazon Web Services Request Signatures
• backports-1.1.1 Reimplementations of Functions Introduced Since R-3.0.0
• base built in
• base64-2.0 Base64 Encoder and Decoder
• base64enc-0.1-3 Tools for base64 encoding
• bdsmatrix-1.3-2 Routines for Block Diagonal Symmetric Matrices
• beanplot-1.2 Visualization via Beanplots (like Boxplot/Stripchart/Violin<U+000a>Plot)
• benchmark-0.3-6 Benchmark Experiments Toolbox
• biglm-0.9-1 bounded memory linear and generalized linear models
• bigmemory-4.5.31 Manage Massive Matrices with Shared Memory and Memory-Mapped Files
• bigmemory.sri-0.1.3 A shared resource interface for Bigmemory Project packages
• bindr-0.1 Parametrized Active Bindings
• bindrcpp-0.2 An ‘Rcpp’ Interface to Active Bindings
• bio3d-2.3-3 Biological Structure Analysis
• biom-0.3.12 An interface package (beta) for the BIOM file format.
• bit-1.1-12 A Class for Vectors of 1-Bit Booleans
• bit64-0.9-7 A S3 Class for Vectors of 64bit Integers
• bitops-1.0-6 Bitwise Operations
• blob-1.1.0 A Simple S3 Class for Representing Vectors of Binary Data (‘BLOBS’)
• bnlearn-4.2 Bayesian Network Structure Learning, Parameter Learning and Inference
• bold-0.5.0 Interface to Bold Systems API
• boot-1.3-20 Bootstrap Functions (Originally by Angelo Canty for S)
• bootstrap-2017.2 Functions for the Book “An Introduction to the Bootstrap”
• brew-1.0-6 Templating Framework for Report Generation
• brglm-0.6.1 Bias Reduction in Binomial-Response Generalized Linear Models
• broom-0.4.3 Convert Statistical Analysis Objects into Tidy Data Frames
• caTools-1.17.1 Tools: moving window statistics, GIF, Base64, ROC AUC, etc.
• calibrate-1.7.2 Calibration of Scatterplot and Biplot Axes
• car-2.1-6 Companion to Applied Regression
• caret-6.0-77 Classification and Regression Training
• catdata-1.2.1 Categorical Data
• cellranger-1.1.0 Translate Spreadsheet Cell Ranges to Rows and Columns
• cgdsr-1.2.6 R-Based API for Accessing the MSKCC Cancer Genomics Data Server (CGDS)
• checkmate-1.8.5 Fast and Versatile Argument Checks
• chemometrics-1.4.2 Multivariate Statistical Analysis in Chemometrics
• chron-2.3-51 Chronological Objects which can Handle Dates and Times
• clValid-0.6-6 Validation of Clustering Results
• class-7.3-14 Functions for Classification
• cluster-2.0.6 “Finding Groups in Data”: Cluster Analysis Extended Rousseeuw et al.
• clusterGeneration-1.3.4 Random Cluster Generation (with Specified Degree of Separation)
• clusterRepro-0.5-1.1 Reproducibility of gene expression clusters
• coda-0.19-1 Output Analysis and Diagnostics for MCMC
• codetools-0.2-15 Code Analysis Tools for R
• coin-1.2-2 Conditional Inference Procedures in a Permutation Test Framework
• colorspace-1.3-2 Color Space Manipulation
• combinat-0.0-8 combinatorics utilities
• commonmark-1.4 High Performance CommonMark and Github Markdown Rendering in R
• compare-0.2-6 Comparing Objects for Differences
• compiler built in
• config-0.2 Manage Environment Specific Configuration Values
• copula-0.999-18 Multivariate Dependence with Copulas
• corpcor-1.6.9 Efficient Estimation of Covariance and (Partial) Correlation
• coxme-2.2-5 Mixed Effects Cox Models
• crayon-1.3.4 Colored Terminal Output
• crosstalk-1.0.0 Inter-Widget Interactivity for HTML Widgets
• crul-0.4.0 HTTP Client
• cubature-1.3-11 Adaptive Multivariate Integration over Hypercubes
• curl-3.0 A Modern and Flexible Web Client for R
• cvAUC-1.1.0 Cross-Validated Area Under the ROC Curve Confidence Intervals
• d3Network-0.5.2.1 Tools for creating D3 JavaScript network, tree, dendrogram, and<U+000a>Sankey graphs from R
• data.table-1.10.4-3 Extension of data.frame
• datasets built in
• dbplyr-1.1.0 A ‘dplyr’ Back End for Databases
• ddalpha-1.3.1 Depth-Based Classification and Calculation of Data Depth
• deSolve-1.20 Solvers for Initial Value Problems of Differential Equations (‘ODE’, ‘DAE’, ‘DDE’)
• deal-1.2-37 Learning Bayesian Networks with Mixed Variables
• degreenet-1.3-1 Models for Skewed Count Distributions Relevant to Networks
• deldir-0.1-14 Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
• desc-1.1.1 Manipulate DESCRIPTION Files
• devtools-1.13.4 Tools to Make Developing R Packages Easier
• dfoptim-2016.7-1 Derivative-Free Optimization
• diamonds-1.0-5 Analysis and sampling grids from diamond partitions
• dichromat-2.0-0 Color Schemes for Dichromats
• digest-0.6.12 Create Compact Hash Digests of R Objects
• dimRed-0.1.0 A Framework for Dimensionality Reduction
• diptest-0.75-7 Hartigan’s Dip Test Statistic for Unimodality - Corrected
• dismo-1.1-4 Species Distribution Modeling
• distillery-1.0-4 Method Functions for Confidence Intervals and to Distill Information from an Object
• diveRsity-1.9.90 A Comprehensive, General Purpose Population Genetics Analysis Package
• doAzureParallel 0.5.0
• doMC-1.3.4 Foreach Parallel Adaptor for ‘parallel’
• doMPI-0.2.2 Foreach Parallel Adaptor for the Rmpi Package
• doParallel-1.0.11 Foreach Parallel Adaptor for the ‘parallel’ Package
• doRNG-1.6.6 Generic Reproducible Parallel Backend for ‘foreach’ Loops
• doSNOW-1.0.15 Foreach Parallel Adaptor for the ‘snow’ Package
• dotCall64-0.9-04 Enhanced Foreign Function Interface Supporting Long Vectors
• downloader-0.4 Download Files over HTTP and HTTPS
• dplyr-0.7.4 A Grammar of Data Manipulation
• dummies-1.5.6 Create dummy/indicator variables flexibly and efficiently
• e1071-1.6-8 Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien
• elasticnet-1.1 Elastic-Net for Sparse Estimation and Sparse PCA
• ellipse-0.3-8 Functions for Drawing Ellipses and Ellipse-Like Confidence Regions
• ergm-3.8.0 Fit, Simulate and Diagnose Exponential-Family Models for Networks
• ergm.count-3.2.2 Fit, Simulate and Diagnose Exponential-Family Models for Networks with Count Edges
• evaluate-0.10.1 Parsing and Evaluation Tools that Provide More Details than the Default
• expm-0.999-2 Matrix Exponential, Log, ‘etc’
• expsmooth-2.3 Data Sets from “Forecasting with Exponential Smoothing”
• extRemes-2.0-8 Extreme Value Analysis
• extrafont-0.17 Tools for using fonts
• extrafontdb-1.0 Package for holding the database for the extrafont package
• fail-1.3 File Abstraction Interface Layer (FAIL)
• fastICA-1.2-1 FastICA Algorithms to Perform ICA and Projection Pursuit
• fastcluster-1.1.24 Fast Hierarchical Clustering Routines for R and ‘Python’
• fastmatch-1.1-0 Fast match() function
• fasttime-1.0-2 Fast Utility Function for Time Parsing and Conversion
• fda-2.4.7 Functional Data Analysis
• fdrtool-1.2.15 Estimation of (Local) False Discovery Rates and Higher Criticism
• ff-2.2-13 Memory-Efficient Storage of Large Data on Disk and Fast Access Functions
• ffbase-0.12.3 Basic Statistical Functions for Package ‘ff’
• fftw-1.0-4 Fast FFT and DCT Based on the FFTW Library
• fftwtools-0.9-8 Wrapper for ‘FFTW3’ Includes: One-Dimensional Univariate, One-Dimensional Multivariate, and Two-Dimensional Transform
• fields-9.0 Tools for Spatial Data
• filehash-2.4-1 Simple Key-Value Database
• fit.models-0.5-14 Compare Fitted Models
• flashClust-1.01-2 Implementation of optimal hierarchical clustering
• flexclust-1.3-4 Flexible Cluster Algorithms
• flexmix-2.3-14 Flexible Mixture Modeling
• fma-2.3 Data Sets from “Forecasting: Methods and Applications” by Makridakis, Wheelwright & Hyndman (1998)
• foreach-1.4.3 Provides Foreach Looping Construct for R
• forecast-8.2 Forecasting Functions for Time Series and Linear Models
• foreign-0.8-69 Read Data Stored by ‘Minitab’, ‘S’, ‘SAS’, ‘SPSS’, ‘Stata’, ‘Systat’, ‘Weka’, ‘dBase’, …
• formatR-1.5 Format R Code Automatically
• fossil-0.3.7 Palaeoecological and Palaeogeographical Analysis Tools
• fpc-2.1-10 Flexible Procedures for Clustering
• fpp-0.5 Data for “Forecasting: principles and practice”
• fracdiff-1.4-2 Fractionally differenced ARIMA aka ARFIMA(p,d,q) models
• fts-0.9.9 R interface to tslib (a time series library in c++)
• futile.logger-1.4.3 A Logging Utility for R
• futile.options-1.0.0 Futile Options Management
• gam-1.14-4 Generalized Additive Models
• gamlss.data-5.0-0 GAMLSS Data
• gamlss.dist-5.0-3 Distributions for Generalized Additive Models for Location Scale and Shape
• gap-1.1-20 Genetic Analysis Package
• gbm-2.1.3 Generalized Boosted Regression Models
• gclus-1.3.1 Clustering Graphics
• gdata-2.18.0 Various R Programming Tools for Data Manipulation
• geepack-1.2-1 Generalized Estimating Equation Package
• geiger-2.0.6 Analysis of Evolutionary Diversification
• geometry-0.3-6 Mesh Generation and Surface Tesselation
• getopt-1.20.1 C-Like ‘getopt’ Behavior
• ggm-2.3 Functions for graphical Markov models
• ggplot2-2.2.1 Create Elegant Data Visualisations Using the Grammar of Graphics
• ggvis-0.4.3 Interactive Grammar of Graphics
• git2r-0.19.0 Provides Access to Git Repositories
• glasso-1.8 Graphical lasso- estimation of Gaussian graphical models
• glmnet-2.0-13 Lasso and Elastic-Net Regularized Generalized Linear Models
• glmpath-0.97 L1 Regularization Path for Generalized Linear Models and Cox Proportional Hazards Model
• glue-1.2.0 Interpreted String Literals
• gmm-1.6-1 Generalized Method of Moments and Generalized Empirical Likelihood
• gmodels-2.16.2 Various R Programming Tools for Model Fitting
• goftest-1.1-1 Classical Goodness-of-Fit Tests for Univariate Distributions
• gower-0.1.2 Gower’s Distance
• gplots-3.0.1 Various R Programming Tools for Plotting Data
• grDevices built in
• graphics built in
• grid built in
• gridBase-0.4-7 Integration of base and grid graphics
• gridExtra-2.3 Miscellaneous Functions for “Grid” Graphics
• gsalib-2.1 Utility Functions For GATK
• gsl-1.9-10.3 Wrapper for the Gnu Scientific Library
• gsubfn-0.6-6 Utilities for Strings and Function Arguments
• gtable-0.2.0 Arrange ‘Grobs’ in Tables
• gtools-3.5.0 Various R Programming Tools
• hapassoc-1.2-8 Inference of Trait Associations with SNP Haplotypes and Other Attributes using the EM Algorithm
• haplo.stats-1.7.7 Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous
• hexbin-1.27.1 Hexagonal Binning Routines
• highr-0.6 Syntax Highlighting for R Source Code
• hms-0.4.0 Pretty Time of Day
• htmlTable-1.11.0 Advanced Tables for Markdown/HTML
• htmltools-0.3.6 Tools for HTML
• htmlwidgets-0.9 HTML Widgets for R
• httpcode-0.2.0 ‘HTTP’ Status Code Helper
• httpuv-1.3.5 HTTP and WebSocket Server Library
• httr-1.3.1 Tools for Working with URLs and HTTP
• huge-1.2.7 High-Dimensional Undirected Graph Estimation
• hwriter-1.3.2 HTML Writer - Outputs R objects in HTML format
• ichorCNA 0.1.0
• idr-1.2 Irreproducible discovery rate
• igraph-1.1.2 Network Analysis and Visualization
• igraphdata-1.0.1 A Collection of Network Data Sets for the ‘igraph’ Package
• inferference-1.0.0 Methods for Causal Inference with Interference
• influenceR-0.1.0 Software Tools to Quantify Structural Importance of Nodes in a Network
• infotheo-1.2.0 Information-Theoretic Measures
• inline-0.3.14 Functions to Inline C, C++, Fortran Function Calls from R
• interpretR-0.2.4 Binary Classifier and Regression Model Interpretation Functions
• ipred-0.9-6 Improved Predictors
• irace-2.4 Iterated Racing for Automatic Algorithm Configuration
• irlba-2.3.1 Fast Truncated Singular Value Decomposition and Principal Components Analysis for Large Dense and Sparse Matrices
• iterators-1.0.8 Provides Iterator Construct for R
• itertools-0.1-3 Iterator Tools
• its-1.1.8 Irregular Time Series
• jpeg-0.1-8 Read and write JPEG images
• jsonlite-1.5 A Robust, High Performance JSON Parser and Generator for R
• kernlab-0.9-25 Kernel-Based Machine Learning Lab
• kin.cohort-0.7 Analysis of Kin-Cohort Studies
• kinship2-1.6.4 Pedigree Functions
• klaR-0.6-12 Classification and Visualization
• knitr-1.17 A General-Purpose Package for Dynamic Report Generation in R
• kohonen-3.0.4 Supervised and Unsupervised Self-Organising Maps
• ks-1.10.7 Kernel Smoothing
• kyotil-2017.10-31 Utility Functions for Statistical Analysis Report Generation and Monte Carlo Studies
• labdsv-1.8-0 Ordination and Multivariate Analysis for Ecology
• labeling-0.3 Axis Labeling
• lambda.r-1.2 Modeling Data with Functional Programming
• lars-1.2 Least Angle Regression, Lasso and Forward Stagewise
• lasso2-1.2-19 L1 constrained estimation aka `lasso’
• latentnet-2.8.0 Latent Position and Cluster Models for Statistical Networks
• lattice-0.20-35 Trellis Graphics for R
• latticeExtra-0.6-28 Extra Graphical Utilities Based on Lattice
• lava-1.5.1 Latent Variable Models
• lavaan-0.5-23.1097 Latent Variable Analysis
• lazy-1.2-15 Lazy Learning for Local Regression
• lazyeval-0.2.1 Lazy (Non-Standard) Evaluation
• leaps-3.0 Regression Subset Selection
• lhs-0.14 Latin Hypercube Samples
• lintr-1.0.2 A ‘Linter’ for R Code
• lme4-1.1-14 Linear Mixed-Effects Models using ‘Eigen’ and S4
• lmtest-0.9-35 Testing Linear Regression Models
• locfit-1.5-9.1 Local Regression, Likelihood and Density Estimation.
• logcondens-2.1.5 Estimate a Log-Concave Probability Density from Iid Observations
• logistf-1.22 Firth’s Bias-Reduced Logistic Regression
• logspline-2.1.9 Routines for Logspline Density Estimation
• lokern-1.1-8 Kernel Regression Smoothing with Local or Global Plug-in Bandwidth
• longitudinal-1.1.12 Analysis of Multiple Time Course Data
• longmemo-1.0-0 Statistics for Long-Memory Processes (Jan Beran) – Data and<U+000a>Functions
• lpSolve-5.6.13 Interface to ‘Lp_solve’ v. 5.5 to Solve Linear/Integer Programs
• lpridge-1.0-7 Local Polynomial (Ridge) Regression
• lubridate-1.7.1 Make Dealing with Dates a Little Easier
• magic-1.5-6 Create and Investigate Magic Squares
• magrittr-1.5 A Forward-Pipe Operator for R
• mapdata-2.2-6 Extra Map Databases
• mapproj-1.2-5 Map Projections
• maps-3.2.0 Draw Geographical Maps
• maptools-0.9-2 Tools for Reading and Handling Spatial Objects
• markdown-0.8 ‘Markdown’ Rendering for R
• matrixStats-0.52.2 Functions that Apply to Rows and Columns of Matrices (and to Vectors)
• matrixcalc-1.0-3 Collection of functions for matrix calculations
• maxLik-1.3-4 Maximum Likelihood Estimation and Related Tools
• mboost-2.8-1 Model-Based Boosting
• mclust-5.4 Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation
• mediation-4.4.6 Causal Mediation Analysis
• memoise-1.1.0 Memoisation of Functions
• methods built in
• mets-1.2.2 Analysis of Multivariate Event Times
• mgcv-1.8-22 Mixed GAM Computation Vehicle with Automatic Smoothness Estimation
• mi-1.0 Missing Data Imputation and Model Checking
• mice-2.46.0 Multivariate Imputation by Chained Equations
• mime-0.5 Map Filenames to MIME Types
• minqa-1.2.4 Derivative-free optimization algorithms by quadratic<U+000a>approximation
• misc3d-0.8-4 Miscellaneous 3D Plots
• miscTools-0.6-22 Miscellaneous Tools and Utilities
• mixtools-1.1.0 Tools for Analyzing Finite Mixture Models
• mlbench-2.1-1 Machine Learning Benchmark Problems
• mlogit-0.2-4 Multinomial Logit Models
• mlr-2.11 Machine Learning in R
• mnormt-1.5-5 The Multivariate Normal and t Distributions
• modeltools-0.2-21 Tools and Classes for Statistical Models
• mondate-0.10.01.02 Keep track of dates in terms of months
• mongolite-1.2 Fast and Simple ‘MongoDB’ Client for R
• msm-1.6.5 Multi-State Markov and Hidden Markov Models in Continuous Time
• multcomp-1.4-8 Simultaneous Inference in General Parametric Models
• multicool-0.1-10 Permutations of Multisets in Cool-Lex Order
• munsell-0.4.3 Utilities for Using Munsell Colours
• mvtnorm-1.0-6 Multivariate Normal and t Distributions
• natserv-0.1.4 ‘NatureServe’ Interface
• ncbit-2013.03.29 retrieve and build NBCI taxonomic data
• ncdf4-1.16 Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files
• ndtv-0.10.0 Network Dynamic Temporal Visualizations
• network-1.13.0 Classes for Relational Data
• networkDynamic-0.9.0 Dynamic Extensions for Network Objects
• networksis-2.1-3 Simulate Bipartite Graphs with Fixed Marginals Through Sequential Importance Sampling
• neuRosim-0.2-12 Functions to Generate fMRI Data Including Activated Data, Noise Data and Resting State Data
• nleqslv-3.3.1 Solve Systems of Nonlinear Equations
• nlme-3.1-131 Linear and Nonlinear Mixed Effects Models
• nloptr-1.0.4 R interface to NLopt
• nnet-7.3-12 Feed-Forward Neural Networks and Multinomial Log-Linear Models
• nnls-1.4 The Lawson-Hanson algorithm for non-negative least squares<U+000a>(NNLS)
• nor1mix-1.2-3 Normal (1-d) Mixture Models (S3 Classes and Methods)
• np-0.60-4 Nonparametric Kernel Smoothing Methods for Mixed Data Types
• numDeriv-2016.8-1 Accurate Numerical Derivatives
• nws-1.7.0.1 R functions for NetWorkSpaces and Sleigh
• openssl-0.9.9 Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
• openxlsx-4.0.17 Read, Write and Edit XLSX Files
• optparse-1.4.4 Command Line Option Parser
• pROC-1.10.0 Display and Analyze ROC Curves
• parallelMap-1.3 Unified Interface to Parallelization Back-Ends
• partools-1.1.6 Tools for the ‘Parallel’ Package
• party-1.2-3 A Laboratory for Recursive Partytioning
• pbivnorm-0.6.0 Vectorized Bivariate Normal CDF
• pbkrtest-0.4-7 Parametric Bootstrap and Kenward Roger Based Methods for Mixed Model Comparison
• pcaPP-1.9-72 Robust PCA by Projection Pursuit
• pdist-1.2 Partitioned Distance Function
• pedigree-1.4 Pedigree functions
• pedigreemm-0.3-3 Pedigree-based mixed-effects models
• penalized-0.9-50 L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation in GLMs and in the Cox Model
• perm-1.0-0.0 Exact or Asymptotic permutation tests
• permute-0.9-4 Functions for Generating Restricted Permutations of Data
• phangorn-2.3.1 Phylogenetic Reconstruction and Analysis
• pheatmap-1.0.8 Pretty Heatmaps
• phylobase-0.8.4 Base Package for Phylogenetic Structures and Comparative Data
• pim-2.0.1 Fit Probabilistic Index Models
• pixmap-0.4-11 Bitmap Images (``Pixel Maps’’)
• pkgconfig-2.0.1 Private Configuration for ‘R’ Packages
• pkgmaker-0.22 Development Utilities for R Packages
• plogr-0.1-1 The ‘plog’ C++ Logging Library
• plotly-4.7.1 Create Interactive Web Graphics via ‘plotly.js’
• plotrix-3.6-6 Various Plotting Functions
• pls-2.6-0 Partial Least Squares and Principal Component Regression
• plyr-1.8.4 Tools for Splitting, Applying and Combining Data
• png-0.1-7 Read and write PNG images
• polspline-1.1.12 Polynomial Spline Routines
• polyclip-1.6-1 Polygon Clipping
• polynom-1.3-9 A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations
• prabclus-2.2-6 Functions for Clustering of Presence-Absence, Abundance and Multilocus Genetic Data
• pracma-2.1.1 Practical Numerical Math Functions
• praise-1.0.0 Praise Users
• prettyunits-1.0.2 Pretty, Human Readable Formatting of Quantities
• prodlim-1.6.1 Product-Limit Estimation for Censored Event History Analysis
• profileModel-0.5-9 Tools for profiling inference functions for various model<U+000a>classes
• progress-1.1.2 Terminal Progress Bars
• proto-1.0.0 Prototype Object-Based Programming
• pscl-1.5.2 Political Science Computational Laboratory
• pspline-1.0-18 Penalized Smoothing Splines
• psych-1.7.8 Procedures for Psychological, Psychometric, and Personality Research
• psychotools-0.4-2 Psychometric Modeling Infrastructure
• purrr-0.2.4 Functional Programming Tools
• pvclust-2.0-0 Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling
• qgraph-1.4.4 Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation
• qtl-1.41-6 Tools for Analyzing QTL Experiments
• quadprog-1.5-5 Functions to solve Quadratic Programming Problems.
• quantmod-0.4-11 Quantitative Financial Modelling Framework
• quantreg-5.34 Quantile Regression
• qvcalc-0.9-1 Quasi Variances for Factor Effects in Statistical Models
• rAzureBatch 0.5.1
• rJava-0.9-9 Low-Level R to Java Interface
• randomForest-4.6-12 Breiman and Cutler’s Random Forests for Classification and Regression
• randomForestSRC-2.5.1 Random Forests for Survival, Regression, and Classification (RF-SRC)
• rappdirs-0.3.1 Application Directories: Determine Where to Save Data, Caches, and Logs
• raster-2.6-7 Geographic Data Analysis and Modeling
• readr-1.1.1 Read Rectangular Text Data
• readxl-1.0.0 Read Excel Files
• recipes-0.1.1 Preprocessing Tools to Create Design Matrices
• registry-0.5 Infrastructure for R Package Registries
• regress-1.3-15 Gaussian Linear Models with Linear Covariance Structure
• regtools-1.0.1 Regression Tools
• relations-0.6-7 Data Structures and Algorithms for Relations
• relevent-1.0-4 Relational Event Models
• rematch-1.0.1 Match Regular Expressions with a Nicer ‘API’
• rentrez-1.1.0 ‘Entrez’ in R
• repr-0.12.0 Serializable Representations
• reshape-0.8.7 Flexibly Reshape Data
• reshape2-1.4.2 Flexibly Reshape Data: A Reboot of the Reshape Package
• rex-1.1.2 Friendly Regular Expressions
• rgenoud-5.8-1.0 R Version of GENetic Optimization Using Derivatives
• rgexf-0.15.3 Build, Import and Export GEXF Graph Files
• rgl-0.98.1 3D Visualization Using OpenGL
• ritis-0.7.0 Integrated Taxonomic Information System Client
• rjags-4-6 Bayesian Graphical Models using MCMC
• rjson-0.2.15 JSON for R
• rlang-0.1.4 Functions for Base Types and Core R and ‘Tidyverse’ Features
• rlecuyer-0.3-4 R Interface to RNG with Multiple Streams
• rmarkdown-1.8 Dynamic Documents for R
• rmeta-2.16 Meta-Analysis
• rms-5.1-1 Regression Modeling Strategies
• rncl-0.8.2 An Interface to the Nexus Class Library
• rngtools-1.2.4 Utility Functions for Working with Random Number Generators
• robustbase-0.92-8 Basic Robust Statistics
• rootSolve-1.7 Nonlinear Root Finding, Equilibrium and Steady-State Analysis of Ordinary Differential Equations
• rotl-3.0.3 Interface to the ‘Open Tree of Life’ API
• roxygen2-6.0.1 In-Line Documentation for R
• rpart-4.1-11 Recursive Partitioning and Regression Trees
• rprojroot-1.2 Finding Files in Project Subdirectories
• rrcov-1.4-3 Scalable Robust Estimators with High Breakdown Point
• rredlist-0.4.0 ‘IUCN’ Red List Client
• rslurm-0.4.0 Submit R Calculations to a Slurm Cluster
• rstan-2.16.2 R Interface to Stan
• rstudioapi-0.7 Safely Access the RStudio API
• rversions-1.0.3 Query ‘R’ Versions, Including ‘r-release’ and ‘r-oldrel’
• rzmq-0.9.3 R Bindings for ‘ZeroMQ’
• sandwich-2.4-0 Robust Covariance Matrix Estimators
• scales-0.5.0 Scale Functions for Visualization
• scatterplot3d-0.3-40 3D Scatter Plot
• scidb-2.0.0 An R Interface to SciDB
• segmented-0.5-3.0 Regression Models with Break-Points / Change-Points Estimation
• sem-3.1-9 Structural Equation Models
• sendmailR-1.2-1 send email using R
• seqinr-3.4-5 Biological Sequences Retrieval and Analysis
• sets-1.0-17 Sets, Generalized Sets, Customizable Sets and Intervals
• sfsmisc-1.1-1 Utilities from ‘Seminar fuer Statistik’ ETH Zurich
• shape-1.4.3 Functions for Plotting Graphical Shapes, Colors
• shapefiles-0.7 Read and Write ESRI Shapefiles
• shiny-1.0.5 Web Application Framework for R
• shinycssloaders-0.2.0 Add CSS Loading Animations to ‘shiny’ Outputs
• shinydashboard-0.6.1 Create Dashboards with ‘Shiny’
• slam-0.1-40 Sparse Lightweight Arrays and Matrices
• sm-2.2-5.4 Smoothing Methods for Nonparametric Regression and Density Estimation
• sna-2.4 Tools for Social Network Analysis
• snow-0.4-2 Simple Network of Workstations
• snowfall-1.84-6.1 Easier cluster computing (based on snow).
• solrium-1.0.0 General Purpose R Interface to ‘Solr’
• som-0.3-5.1 Self-Organizing Map
• sourcetools-0.1.6 Tools for Reading, Tokenizing and Parsing R Code
• sp-1.2-5 Classes and Methods for Spatial Data
• spData-0.2.6.7 Datasets for Spatial Analysis
• spam-2.1-1 SPArse Matrix
• sparklyr-0.6.4 R Interface to Apache Spark
• spatial-7.3-11 Functions for Kriging and Point Pattern Analysis
• spatstat-1.54-0 Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
• spatstat.data-1.2-0 Datasets for ‘spatstat’
• spatstat.utils-1.8-0 Utility Functions for ‘spatstat’
• spdep-0.7-4 Spatial Dependence: Weighting Schemes, Statistics and Models
• splines built in
• sqldf-0.4-11 Manipulate R Data Frames Using SQL
• stabledist-0.7-1 Stable Distribution Functions
• stabs-0.6-3 Stability Selection with Error Control
• statmod-1.4.30 Statistical Modeling
• statnet-2016.9 Software Tools for the Statistical Analysis of Network Data
• statnet.common-4.0.0 Common R Scripts and Utilities Used by the Statnet Project Software
• stats built in
• stats4 built in
• stringdist-0.9.4.6 Approximate String Matching and String Distance Functions
• stringi-1.1.6 Character String Processing Facilities
• stringr-1.2.0 Simple, Consistent Wrappers for Common String Operations
• strucchange-1.5-1 Testing, Monitoring, and Dating Structural Changes
• subplex-1.4-1 Unconstrained Optimization using the Subplex Algorithm
• survey-3.32-1 Analysis of Complex Survey Samples
• survival-2.41-3 Survival Analysis
• survivalROC-1.0.3 Time-dependent ROC curve estimation from censored survival data
• synapseClient 1.13-4
• tables-0.8.3 Formula-Driven Table Generation
• taxize-0.9.0 Taxonomic Information from Around the Web
• tensor-1.5 Tensor product of arrays
• tensorA-0.36 Advanced tensors arithmetic with named indices
• tergm-3.4.1 Fit, Simulate and Diagnose Models for Network Evolution Based on Exponential-Family Random Graph Models
• testthat-1.0.2 Unit Testing for R
• tibble-1.3.4 Simple Data Frames
• tidyr-0.7.2 Easily Tidy Data with ‘spread()’ and ‘gather()’ Functions
• tidyselect-0.2.3 Select from a Set of Strings
• tiff-0.1-5 Read and write TIFF images
• timeDate-3042.101 Rmetrics - Chronological and Calendar Objects
• timeSeries-3042.102 Rmetrics - Financial Time Series Objects
• timereg-1.9.1 Flexible Regression Models for Survival Data
• tkrplot-0.0-23 TK Rplot
• tm-0.7-2 Text Mining Package
• tmvtnorm-1.4-10 Truncated Multivariate Normal and Student t Distribution
• tools built in
• tree-1.0-37 Classification and Regression Trees
• triebeard-0.3.0 ‘Radix’ Trees in ‘Rcpp’
• trimcluster-0.1-2 Cluster analysis with trimming
• tripack-1.3-8 Triangulation of Irregularly Spaced Data
• trust-0.1-7 Trust Region Optimization
• tseries-0.10-42 Time Series Analysis and Computational Finance
• tseriesChaos-0.1-13 Analysis of nonlinear time series
• udunits2-0.13 Udunits-2 Bindings for R
• unbalanced-2.0 Racing for Unbalanced Methods Selection
• urca-1.3-0 Unit Root and Cointegration Tests for Time Series Data
• urltools-1.6.0 Vectorised Tools for URL Handling and Parsing
• utils built in
• uuid-0.1-2 Tools for generating and handling of UUIDs
• vcd-1.4-4 Visualizing Categorical Data
• vegan-2.4-5 Community Ecology Package
• vioplot-0.2 Violin plot
• viridis-0.4.0 Default Color Maps from ‘matplotlib’
• viridisLite-0.2.0 Default Color Maps from ‘matplotlib’ (Lite Version)
• visNetwork-2.0.1 Network Visualization using ‘vis.js’ Library
• waveslim-1.7.5 Basic wavelet routines for one-, two- and three-dimensional<U+000a>signal processing
• wavethresh-4.6.8 Wavelets Statistics and Transforms
• whisker-0.3-2 for R, logicless templating
• wikitaxa-0.1.4 Taxonomic Information from ‘Wikipedia’
• withr-2.1.0 Run Code ‘With’ Temporarily Modified Global State
• worrms-0.2.0 World Register of Marine Species (WoRMS) Client
• xlsx-0.5.7 Read, Write, Format Excel 2007 and Excel 97/2000/XP/2003 Files
• xlsxjars-0.6.1 Package required POI jars for the xlsx package
• xml2-1.1.1 Parse XML
• xtable-1.8-2 Export Tables to LaTeX or HTML
• xts-0.10-0 eXtensible Time Series
• yaml-2.1.15 Methods to Convert R Data to YAML and Back
• zoo-1.8-0 S3 Infrastructure for Regular and Irregular Time Series (Z’s Ordered Observations)