Difference between revisions of "R"
Moskalenko (talk | contribs) m (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==") |
Moskalenko (talk | contribs) |
||
Line 34: | Line 34: | ||
R is a free software environment for statistical computing and graphics. | R is a free software environment for statistical computing and graphics. | ||
− | |||
'''Note: File a [http://support.hpc.ufl.edu support ticket] to request installation of additional libraries.''' | '''Note: File a [http://support.hpc.ufl.edu support ticket] to request installation of additional libraries.''' | ||
− | + | <!--Modules--> | |
− | |||
− | |||
− | |||
− | <!-- --> | ||
{{#if: {{#var: mod}}|==Execution Environment and Modules== | {{#if: {{#var: mod}}|==Execution Environment and Modules== | ||
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} |
Revision as of 02:44, 10 August 2012
Contents
Description
R is a free software environment for statistical computing and graphics.
Note: File a support ticket to request installation of additional libraries.
Execution Environment and Modules
To use R with the environment modules system at HPC the following commands are available:
Get module information for r:
$module spider R
Load the default application module:
$module load R
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_R_DIR - directory where R is located.
- HPC_R_BIN - executable directory
- HPC_R_LIB - library directory
- HPC_R_INCLUDE - includes directory
To use the version of R built for parallel execution with MPI via the Rmpi library load the following modules:
module load intel/11.1 openmpi/1.4.3 R
Installed Libraries
Note: Many of the packages in the R library shown below are installed as a part of Bioconductor meta-library. The list is generated from the default R version.
Name | Description |
---|---|
a4Core | Automated Affymetrix Array Analysis Core Package |
a4Preproc | Automated Affymetrix Array Analysis Preprocessing Package |
abind | Combine Multidimensional Arrays |
acepack | ACE and AVAS for Selecting Multiple Regression Transformations |
adabag | Applies Multiclass AdaBoost.M1 |
adagio | Discrete and Global Optimization Routines |
ade4 | Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences |
adegenet | Exploratory Analysis of Genetic and Genomic Data |
AdhereR | Adherence to Medications |
adnuts | No-U-Turn MCMC Sampling for 'ADMB' and 'TMB' Models |
affxparser | Affymetrix File Parsing SDK |
affy | Methods for Affymetrix Oligonucleotide Arrays |
affyio | Tools for parsing Affymetrix data files |
affyPLM | Methods for fitting probe-level models |
AGHmatrix | Relationship matrices for diploid and autopolyploid species |
agricolae | Statistical Procedures for Agricultural Research |
akima | Interpolation of Irregularly and Regularly Spaced Data |
ALDEx2 | Analysis Of Differential Abundance Taking Sample Variation Into Account |
AlgDesign | Algorithmic Experimental Design |
amap | Another Multidimensional Analysis Package |
Amelia | A Program for Missing Data |
animation | A Gallery of Animations in Statistics and Utilities to Create Animations |
annaffy | Annotation tools for Affymetrix biological metadata |
annotate | Annotation for microarrays |
AnnotationDbi | Annotation Database Interface |
AnnotationFilter | Facilities for Filtering Bioconductor Annotation Resources |
AnnotationHub | Client to access AnnotationHub resources |
annotSnpStats | Annotated SnpMatrix objects |
apcluster | Affinity Propagation Clustering |
ape | Analyses of Phylogenetics and Evolution |
arm | Data Analysis Using Regression and Multilevel/Hierarchical Models |
aroma.light | Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types |
arrayQualityMetrics | Quality metrics report for microarray data sets |
assertive | Readable Check Functions to Ensure Code Integrity |
assertive.base | A Lightweight Core of the 'assertive' Package |
assertive.code | Assertions to Check Properties of Code |
assertive.data | Assertions to Check Properties of Data |
assertive.data.uk | Assertions to Check Properties of Strings |
assertive.data.us | Assertions to Check Properties of Strings |
assertive.datetimes | Assertions to Check Properties of Dates and Times |
assertive.files | Assertions to Check Properties of Files |
assertive.matrices | Assertions to Check Properties of Matrices |
assertive.models | Assertions to Check Properties of Models |
assertive.numbers | Assertions to Check Properties of Numbers |
assertive.properties | Assertions to Check Properties of Variables |
assertive.reflection | Assertions for Checking the State of R |
assertive.sets | Assertions to Check Properties of Sets |
assertive.strings | Assertions to Check Properties of Strings |
assertive.types | Assertions to Check Types of Variables |
assertthat | Easy Pre and Post Assertions |
automap | Automatic interpolation package |
backports | Reimplementations of Functions Introduced Since R-3.0.0 |
ballgown | Flexible |
BAMMtools | Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees |
base64 | Base64 Encoder and Decoder |
base64enc | Tools for base64 encoding |
baseline | Baseline Correction of Spectra |
bayesm | Bayesian Inference for Marketing/Micro-Econometrics |
bayesplot | Plotting for Bayesian Models |
bazar | Miscellaneous Basic Functions |
BB | Solving and Optimizing Large-Scale Nonlinear Systems |
bbmle | Tools for General Maximum Likelihood Estimation |
bdsmatrix | Routines for Block Diagonal Symmetric Matrices |
beadarray | Quality assessment and low-level analysis for Illumina BeadArray data |
BeadDataPackR | Compression of Illumina BeadArray data |
beanplot | Visualization via Beanplots (like Boxplot/Stripchart/Violin Plot) |
BEDMatrix | Extract Genotypes from a PLINK .bed File |
bestglm | Best Subset GLM and Regression Utilities |
BGData | A Suite of Packages for Analysis of Big Genomic Data |
BGLR | Bayesian Generalized Linear Regression |
BH | Boost C++ Header Files |
BiasedUrn | Biased Urn Model Distributions |
bibtex | Bibtex Parser |
biganalytics | Utilities for 'big.matrix' Objects from Package 'bigmemory' |
big.char | Provides Very Large Vectors of Character Strings |
big.data.frame | Extend big.char and bigmemory's big.matrix to support larger-than-RAM data.frame-like objects in R. |
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 |
BigVAR | Dimension Reduction Methods for Multivariate Time Series |
bindr | Parametrized Active Bindings |
bindrcpp | An 'Rcpp' Interface to Active Bindings |
Biobase | Biobase: Base functions for Bioconductor |
BiocGenerics | S4 generic functions for Bioconductor |
BiocInstaller | Install/Update Bioconductor |
BiocParallel | Bioconductor facilities for parallel evaluation |
BioGeoBEARS | BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts |
biomaRt | Interface to BioMart databases (e.g. Ensembl |
biomformat | An interface package for the BIOM file format |
Biostrings | Efficient manipulation of biological strings |
biovizBase | Basic graphic utilities for visualization of genomic data. |
bipartite | Visualising Bipartite Networks and Calculating Some (Ecological) Indices |
bit | A Class for Vectors of 1-Bit Booleans |
bit64 | A S3 Class for Vectors of 64bit Integers |
bitops | Bitwise Operations |
blob | A Simple S3 Class for Representing Vectors of Binary Data ('BLOBS') |
blockmodeling | Generalized and Classical Blockmodeling of Valued Networks |
bold | Interface to Bold Systems API |
Boom | Bayesian Object Oriented Modeling |
BoomSpikeSlab | MCMC for Spike and Slab Regression |
boot | Bootstrap Functions (Originally by Angelo Canty for S) |
brew | Templating Framework for Report Generation |
broom | Convert Statistical Analysis Objects into Tidy Data Frames |
BSgenome | Software infrastructure for efficient representation of full genomes and their SNPs |
BSgenome.Hsapiens.UCSC.hg19 | Full genome sequences for Homo sapiens (UCSC version hg19) |
bsts | Bayesian Structural Time Series |
bumphunter | Bump Hunter |
BurStFin | Burns Statistics Financial |
Cairo | R graphics device using cairo graphics library for creating high-quality bitmap (PNG |
calibrate | Calibration of Scatterplot and Biplot Axes |
callr | Call R from R |
CAMERA | Collection of annotation related methods for mass spectrometry data |
car | Companion to Applied Regression |
carData | Companion to Applied Regression Data Sets |
caret | Classification and Regression Training |
caTools | Tools: moving window statistics |
CCA | Canonical correlation analysis |
cccrm | Concordance Correlation Coefficient for Repeated (and Non-Repeated) Measures |
ccdrAlgorithm | CCDr Algorithm for Learning Sparse Gaussian Bayesian Networks |
cellranger | Translate Spreadsheet Cell Ranges to Rows and Columns |
checkmate | Fast and Versatile Argument Checks |
ChemoSpec | Exploratory Chemometrics for Spectroscopy |
chopsticks | The snp.matrix and X.snp.matrix classes |
chron | Chronological Objects which can Handle Dates and Times |
circlize | Circular Visualization |
cladoRcpp | C++ implementations of phylogenetic cladogenesis calculations |
class | Functions for Classification |
classInt | Choose Univariate Class Intervals |
cleangeo | Cleaning Geometries from Spatial Objects |
cli | Helpers for Developing Command Line Interfaces |
clipr | Read and Write from the System Clipboard |
clue | Cluster Ensembles |
cluster | Finding Groups in Data: Cluster Analysis Extended Rousseeuw et al. |
clusterGeneration | Random Cluster Generation (with Specified Degree of Separation) |
clusterProfiler | statistical analysis and visualization of functional profiles for genes and gene clusters |
cnv | Detection of Copy Number Variation by Sequencing |
coda | Output Analysis and Diagnostics for MCMC |
codetools | Code Analysis Tools for R |
coin | Conditional Inference Procedures in a Permutation Test Framework |
colorspace | Color Space Manipulation |
colourpicker | A Colour Picker Tool for Shiny and for Selecting Colours in Plots |
combinat | combinatorics utilities |
commonmark | High Performance CommonMark and Github Markdown Rendering in R |
compare | Comparing Objects for Differences |
ComplexHeatmap | Making Complex Heatmaps |
compositions | Compositional Data Analysis |
CompRandFld | Composite-Likelihood Based Analysis of Random Fields |
concaveman | A Very Fast 2D Concave Hull Algorithm |
CondReg | Condition Number Regularized Covariance Estimation |
config | Manage Environment Specific Configuration Values |
corpcor | Efficient Estimation of Covariance and (Partial) Correlation |
covr | Test Coverage for Packages |
cowplot | Streamlined Plot Theme and Plot Annotations for 'ggplot2' |
CpGassoc | Association Between Methylation and a Phenotype of Interest |
crayon | Colored Terminal Output |
crch | Censored Regression with Conditional Heteroscedasticity |
crmn | CCMN and other noRMalizatioN methods for metabolomics data |
crochet | Implementation Helper for [ and [<- Of Custom Matrix-Like Types |
crosstalk | Inter-Widget Interactivity for HTML Widgets |
crul | HTTP Client |
cubature | Adaptive Multivariate Integration over Hypercubes |
curl | A Modern and Flexible Web Client for R |
CVST | Fast Cross-Validation via Sequential Testing |
cvTools | Cross-validation tools for regression models |
dagitty | Graphical Analysis of Structural Causal Models |
DASTool | DAS Tool - Dereplication Aggregation and Scoring Tool for genome-resolved metagenomics |
DatABEL | File-Based Access to Large Matrices Stored on HDD in Binary Format |
data.table | Extension of `data.frame` |
date | Functions for Handling Dates |
DBI | R Database Interface |
dbplyr | A 'dplyr' Back End for Databases |
dcurver | Utility Functions for Davidian Curves |
ddalpha | Depth-Based Classification and Calculation of Data Depth |
debugme | Debug R Packages |
DelayedArray | Delayed operations on array-like objects |
deldir | Delaunay Triangulation and Dirichlet (Voronoi) Tessellation |
denstrip | Density Strips and Other Methods for Compactly Illustrating Distributions |
DEoptimR | Differential Evolution Optimization in Pure R |
depmixS4 | Dependent Mixture Models - Hidden Markov Models of GLMs and Other Distributions in S4 |
Deriv | Symbolic Differentiation |
desc | Manipulate DESCRIPTION Files |
DESeq | Differential gene expression analysis based on the negative binomial distribution |
DESeq2 | Differential gene expression analysis based on the negative binomial distribution |
deSolve | Solvers for Initial Value Problems of Differential Equations ('ODE' |
devtools | Tools to Make Developing R Packages Easier |
dfoptim | Derivative-Free Optimization |
dichromat | Color Schemes for Dichromats |
diffusionMap | Diffusion map |
digest | Create Compact Hash Digests of R Objects |
dimRed | A Framework for Dimensionality Reduction |
diptest | Hartigan's Dip Test Statistic for Unimodality - Corrected |
discretecdAlgorithm | Coordinate-Descent Algorithm for Learning Sparse Discrete Bayesian Networks |
dismo | Species Distribution Modeling |
diversitree | Comparative 'Phylogenetic' Analyses of Diversification |
dlm | Bayesian and Likelihood Analysis of Dynamic Linear Models |
doBy | Groupwise Statistics |
DO.db | A set of annotation maps describing the entire Disease Ontology |
doMC | Foreach Parallel Adaptor for 'parallel' |
doParallel | Foreach Parallel Adaptor for the 'parallel' Package |
doRNG | Generic Reproducible Parallel Backend for 'foreach' Loops |
DOSE | Disease Ontology Semantic and Enrichment analysis |
doSNOW | Foreach Parallel Adaptor for the 'snow' Package |
dotCall64 | Enhanced Foreign Function Interface Supporting Long Vectors |
dplyr | A Grammar of Data Manipulation |
DRR | Dimensionality Reduction via Regression |
DT | A Wrapper of the JavaScript Library 'DataTables' |
dtw | Dynamic Time Warping Algorithms |
dupRadar | Assessment of duplication rates in RNA-Seq datasets |
dygraphs | Interface to 'Dygraphs' Interactive Time Series Charting Library |
dynamicTreeCut | Methods for Detection of Clusters in Hierarchical Clustering Dendrograms |
e1071 | Misc Functions of the Department of Statistics |
earth | Multivariate Adaptive Regression Splines |
EbayesThresh | Empirical Bayes Thresholding and Related Methods |
EBImage | Image processing and analysis toolbox for R |
EBSeq | An R package for gene and isoform differential expression analysis of RNA-seq data |
edgeR | Empirical Analysis of Digital Gene Expression Data in R |
eDNAoccupancy | Multi-scale Occupancy Modeling of Environmental DNA Data |
egg | Extensions for 'ggplot2': Custom Geom |
ellipse | Functions for Drawing Ellipses and Ellipse-Like Confidence Regions |
emdbook | Support Functions and Data for "Ecological Models and Data" |
emulator | Bayesian Emulation of Computer Programs |
energy | E-Statistics: Multivariate Inference via the Energy of Data |
EnsDb.Hsapiens.v75 | Ensembl based annotation package |
ensembldb | Utilities to create and use Ensembl-based annotation databases |
equateIRT | IRT Equating Methods |
estimability | Tools for Assessing Estimability of Linear Predictions |
EthSEQ | Ethnicity Annotation from Whole Exome Sequencing Data |
evaluate | Parsing and Evaluation Tools that Provide More Details than the Default |
evd | Functions for Extreme Value Distributions |
expm | Matrix Exponential |
fastAdaboost | a Fast Implementation of Adaboost |
fastcluster | Fast Hierarchical Clustering Routines for R and 'Python' |
fastICA | FastICA Algorithms to Perform ICA and Projection Pursuit |
fastmatch | Fast match() function |
fastseg | fastseg - a fast segmentation algorithm |
fBasics | Rmetrics - Markets and Basic Statistics |
FD | Measuring functional diversity (FD) from multiple traits |
fda | Functional Data Analysis |
FDb.InfiniumMethylation.hg19 | Annotation package for Illumina Infinium DNA methylation probes |
fdth | Frequency Distribution Tables |
ff | Memory-Efficient Storage of Large Data on Disk and Fast Access Functions |
fftwtools | Wrapper for 'FFTW3' Includes: One-Dimensional Univariate |
fGarch | Rmetrics - Autoregressive Conditional Heteroskedastic Modelling |
FGN | Fractional Gaussian Noise and power law decay time series model fitting |
fgsea | Fast Gene Set Enrichment Analysis |
fields | Tools for Spatial Data |
FinTS | Companion to Tsay (2005) Analysis of Financial Time Series |
fitdistrplus | Help to Fit of a Parametric Distribution to Non-Censored or Censored Data |
fit.models | Compare Fitted Models |
flare | Family of Lasso Regression |
flexmix | Flexible Mixture Modeling |
FNN | Fast Nearest Neighbor Search Algorithms and Applications |
forcats | Tools for Working with Categorical Variables (Factors) |
foreach | Provides Foreach Looping Construct for R |
forecast | Forecasting Functions for Time Series and Linear Models |
foreign | Read Data Stored by 'Minitab' |
formatR | Format R Code Automatically |
Formula | Extended Model Formulas |
fpc | Flexible Procedures for Clustering |
fracdiff | Fractionally differenced ARIMA aka ARFIMA(p |
fst | Lightning Fast Serialization of Data Frames for R |
futile.logger | A Logging Utility for R |
futile.matrix | Random Matrix Generation and Manipulation |
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 |
GAabbreviate | Abbreviating Items Measures using Genetic Algorithms |
gap | Genetic Analysis Package |
gapminder | Data from Gapminder |
gbm | Generalized Boosted Regression Models |
gcrma | Background Adjustment Using Sequence Information |
gdalUtils | Wrappers for the Geospatial Data Abstraction Library (GDAL) Utilities |
gdata | Various R Programming Tools for Data Manipulation |
gdmp | Genomic Data Management |
gdsfmt | R Interface to CoreArray Genomic Data Structure (GDS) Files |
gdtools | Utilities for Graphical Rendering |
geeM | Solve Generalized Estimating Equations |
geepack | Generalized Estimating Equation Package |
geigen | Calculate Generalized Eigenvalues |
geiger | Analysis of Evolutionary Diversification |
GenABEL | genome-wide SNP association analysis |
GenABEL.data | Package contains data which is used by GenABEL example and test functions |
gender | Predict Gender from Names Using Historical Data |
genefilter | genefilter: methods for filtering genes from high-throughput experiments |
geneplotter | Graphics related functions for Bioconductor |
GeneSelector | Stability and Aggregation of ranked gene lists |
genetics | Population Genetics |
genlasso | Path algorithm for generalized lasso problems |
GenomeInfoDb | Utilities for manipulating chromosome and other 'seqname' identifiers |
GenomeInfoDbData | Species and taxonomy ID look up tables used by GenomeInfoDb |
GenomicAlignments | Representation and manipulation of short genomic alignments |
GenomicFeatures | Tools for making and manipulating transcript centric annotations |
GenomicRanges | Representation and manipulation of genomic intervals and variables defined along a genome |
geometry | Mesh Generation and Surface Tesselation |
GEOquery | Get data from NCBI Gene Expression Omnibus (GEO) |
geosphere | Spherical Trigonometry |
getopt | C-Like 'getopt' Behavior |
GetoptLong | Parsing Command-Line Arguments and Variable Interpolation |
GGally | Extension to 'ggplot2' |
ggbio | Visualization tools for genomic data |
ggdendro | Create Dendrograms and Tree Diagrams Using 'ggplot2' |
ggjoy | Joyplots in 'ggplot2' |
ggm | Functions for graphical Markov models |
ggplot2 | Create Elegant Data Visualisations Using the Grammar of Graphics |
ggplot2movies | Movies Data |
ggpubr | 'ggplot2' Based Publication Ready Plots |
ggRandomForests | Visually Exploring Random Forests |
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' |
ggtree | an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data |
ggvis | Interactive Grammar of Graphics |
GIGrvg | Random Variate Generator for the GIG Distribution |
git2r | Provides Access to Git Repositories |
glasso | Graphical lasso- estimation of Gaussian graphical models |
glm2 | Fitting Generalized Linear Models |
glmmLasso | Variable Selection for Generalized Linear Mixed Models by L1-Penalized Estimation |
glmnet | Lasso and Elastic-Net Regularized Generalized Linear Models |
GlobalOptions | Generate Functions to Get or Set Global Options |
globals | Identify Global Objects in R Expressions |
glue | Interpreted String Literals |
gmailr | Access the Gmail RESTful API |
gmodels | Various R Programming Tools for Model Fitting |
gmp | Multiple Precision Arithmetic |
GO.db | A set of annotation maps describing the entire Gene Ontology |
GOSemSim | GO-terms Semantic Similarity Measures |
gower | Gower's Distance |
GPArotation | GPA Factor Rotation |
gplots | Various R Programming Tools for Plotting Data |
graph | graph: A package to handle graph data structures |
gridBase | Integration of base and grid graphics |
gridExtra | Miscellaneous Functions for "Grid" Graphics |
gridSVG | Export 'grid' Graphics as SVG |
grplasso | Fitting user specified models with Group Lasso penalty |
grpreg | Regularization Paths for Regression Models with Grouped Covariates |
gss | General Smoothing Splines |
gstat | Spatial and Spatio-Temporal Geostatistical Modelling |
gsubfn | Utilities for Strings and Function Arguments |
gtable | Arrange 'Grobs' in Tables |
gtools | Various R Programming Tools |
GUESSFM | Using GUESS for Fine Mapping |
hashmap | The Faster Hash Map |
haven | Import and Export 'SPSS' |
hdf5r | Interface to the 'HDF5' Binary Data Format |
HDMD | Statistical Analysis Tools for High Dimension Molecular Data (HDMD) |
hexbin | Hexagonal Binning Routines |
highr | Syntax Highlighting for R Source Code |
HKprocess | Hurst-Kolmogorov Process |
Hmisc | Harrell Miscellaneous |
hms | Pretty Time of Day |
horseshoe | Implementation of the Horseshoe Prior |
hpar | Human Protein Atlas in R |
htmlTable | Advanced Tables for Markdown/HTML |
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 |
hwriter | HTML Writer - Outputs R objects in HTML format |
hydroGOF | Goodness-of-Fit Functions for Comparison of Simulated and Observed Hydrological Time Series |
hydroTSM | Time Series Management |
hyperSpec | Work with Hyperspectral Data |
ica | Independent Component Analysis |
igraph | Network Analysis and Visualization |
illuminaio | Parsing Illumina Microarray Output Files |
impute | impute: Imputation for microarray data |
indicspecies | Relationship Between Species and Groups of Sites |
inline | Functions to Inline C |
intansv | Integrative analysis of structural variations |
interactiveDisplayBase | Base package for enabling powerful shiny web displays of Bioconductor objects |
intervals | Tools for Working with Points and Intervals |
IONiseR | Quality Assessment Tools for Oxford Nanopore MinION data |
IPO | Automated Optimization of XCMS Data Processing parameters |
ipred | Improved Predictors |
ipw | Estimate Inverse Probability Weights |
IRanges | Infrastructure for manipulating intervals on sequences |
IRdisplay | 'Jupyter' Display Machinery |
IRkernel | Native R Kernel for the 'Jupyter Notebook' |
irlba | Fast Truncated Singular Value Decomposition and Principal Components Analysis for Large Dense and Sparse Matrices |
itcSegment | Individual Tree Crowns Segmentation |
iterators | Provides Iterator Construct for R |
itertools | Iterator Tools |
jagsUI | A Wrapper Around 'rjags' to Streamline 'JAGS' Analyses |
jomo | Multilevel Joint Modelling Multiple Imputation |
jpeg | Read and write JPEG images |
jsonlite | A Robust |
kebabs | Kernel-Based Analysis Of Biological Sequences |
KEGG.db | A set of annotation maps for KEGG |
KEGGgraph | KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor |
KEGGprofile | An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathway |
KEGGREST | Client-side REST access to KEGG |
keras | R Interface to 'Keras' |
kerasR | R Interface to the Keras Deep Learning Library |
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 |
kimisc | Kirill's Miscellaneous Functions |
kinship2 | Pedigree Functions |
klaR | Classification and Visualization |
knitr | A General-Purpose Package for Dynamic Report Generation in R |
labeling | Axis Labeling |
labelled | Manipulating Labelled Data |
lambda.r | Modeling Data with Functional Programming |
lambda.tools | Tools for Modeling Data with Functional Programming |
lars | Least Angle Regression |
lassoshooting | L1 regularized regression (Lasso) solver using the Cyclic Coordinate Descent algorithm aka Lasso Shooting |
later | Utilities for Delaying Function Execution |
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) |
lazyeval | Lazy (Non-Standard) Evaluation |
LDcorSV | Linkage Disequilibrium Corrected by the Structure and the Relatedness |
LDheatmap | Graphical Display of Pairwise Linkage Disequilibria Between SNPs |
leaflet | Create Interactive Web Maps with the JavaScript 'Leaflet' Library |
leaflet.extras | Extra Functionality for 'leaflet' Package |
leaps | Regression Subset Selection |
LearnBayes | Functions for Learning Bayesian Inference |
lfmm | Latent Factor Mixed Models |
LiblineaR | Linear Predictive Models Based on the 'LIBLINEAR' C/C++ Library |
lidR | Airborne LiDAR Data Manipulation and Visualization for Forestry Applications |
limma | Linear Models for Microarray Data |
limSolve | Solving Linear Inverse Models |
LinkedMatrix | Column-Linked and Row-Linked Matrices |
lintr | A 'Linter' for R Code |
listenv | Environments Behaving (Almost) as Lists |
lme4 | Linear Mixed-Effects Models using 'Eigen' and S4 |
lmmen | Linear Mixed Model Elastic Net |
lmmlasso | Linear mixed-effects models with Lasso |
lmtest | Testing Linear Regression Models |
locfit | Local Regression |
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 |
lsgl | Linear Multiple Output Sparse Group Lasso |
lsmeans | Least-Squares Means |
ltsa | Linear Time Series Analysis |
lubridate | Make Dealing with Dates a Little Easier |
magic | Create and Investigate Magic Squares |
magrittr | A Forward-Pipe Operator for R |
MAIT | Statistical Analysis of Metabolomic Data |
MALDIquant | Quantitative Analysis of Mass Spectrometry Data |
manipulate | Interactive Plots for RStudio |
manipulateWidget | Add Even More Interactivity to Interactive Charts |
mapdata | Extra Map Databases |
mapedit | Interactive Editing of Spatial Data in R |
mapproj | Map Projections |
maps | Draw Geographical Maps |
maptools | Tools for Reading and Handling Spatial Objects |
mapview | Interactive Viewing of Spatial Data in R |
markdown | 'Markdown' Rendering for R |
MARSS | Multivariate Autoregressive State-Space Modeling |
MASS | Support Functions and Datasets for Venables and Ripley's MASS |
MassSpecWavelet | Mass spectrum processing by wavelet-based algorithms |
Matrix | Sparse and Dense Matrix Classes and Methods |
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) |
MaxentVariableSelection | Selecting the Best Set of Relevant Environmental Variables along with the Optimal Regularization Multiplier for Maxent Niche Modeling |
mclust | Gaussian Mixture Modelling for Model-Based Clustering |
mcmc | Markov Chain Monte Carlo |
MCMCpack | Markov Chain Monte Carlo (MCMC) Package |
mcmcplots | Create Plots from MCMC Output |
mda | Mixture and Flexible Discriminant Analysis |
mdatools | Multivariate Data Analysis for Chemometrics |
memoise | Memoisation of Functions |
memuse | Memory Estimation Utilities |
MESS | Miscellaneous Esoteric Statistical Scripts |
metabolomics | Analysis of Metabolomics Data |
MetaboSignal | MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways |
metap | Meta-Analysis of Significance Values |
methylKit | DNA methylation analysis from high-throughput bisulfite sequencing results |
methylumi | Handle Illumina methylation data |
Metrics | Evaluation Metrics for Machine Learning |
mgcv | Mixed GAM Computation Vehicle with Automatic Smoothness Estimation |
mice | Multivariate Imputation by Chained Equations |
micropan | Microbial Pan-Genome Analysis |
microseq | Basic Biological Sequence Handling |
mime | Map Filenames to MIME Types |
minfi | Analyze Illumina Infinium DNA methylation arrays |
miniUI | Shiny UI Widgets for Small Screens |
minpack.lm | R Interface to the Levenberg-Marquardt Nonlinear Least-Squares Algorithm Found in MINPACK |
minqa | Derivative-free optimization algorithms by quadratic approximation |
mirt | Multidimensional Item Response Theory |
misc3d | Miscellaneous 3D Plots |
miscTools | Miscellaneous Tools and Utilities |
missForest | Nonparametric Missing Value Imputation using Random Forest |
mitml | Tools for Multiple Imputation in Multilevel Modeling |
mitools | Tools for multiple imputation of missing data |
mixOmics | Omics Data Integration Project |
mixtools | Tools for Analyzing Finite Mixture Models |
mlbench | Machine Learning Benchmark Problems |
mnormt | The Multivariate Normal and t Distributions |
ModelMetrics | Rapid Calculation of Model Metrics |
modelr | Modelling Functions that Work with the Pipe |
modeltools | Tools and Classes for Statistical Models |
mpm | Multivariate Projection Methods |
mpoly | Symbolic Computation and More with Multivariate Polynomials |
msm | Multi-State Markov and Hidden Markov Models in Continuous Time |
MSnbase | Base Functions and Classes for Mass Spectrometry and Proteomics |
MTS | All-Purpose Toolkit for Analyzing Multivariate Time Series (MTS) and Estimating Multivariate Volatility Models |
multcomp | Simultaneous Inference in General Parametric Models |
multispatialCCM | Multispatial Convergent Cross Mapping |
multiwayvcov | Multi-Way Standard Error Clustering |
multtest | Resampling-based multiple hypothesis testing |
munsell | Utilities for Using Munsell Colours |
mvtnorm | Multivariate Normal and t Distributions |
MWASTools | MWASTools: an integrated pipeline to perform metabolome-wide association studies |
mygene | Access MyGene.Info_ services |
mzID | An mzIdentML parser for R |
mzR | parser for netCDF |
NADA | Nondetects and Data Analysis for Environmental Data |
natserv | 'NatureServe' Interface |
ncbit | retrieve and build NBCI taxonomic data |
ncvreg | Regularization Paths for SCAD and MCP Penalized Regression Models |
neldermead | R Port of the 'Scilab' Neldermead Module |
network | Classes for Relational Data |
neuralnet | Training of Neural Networks |
nleqslv | Solve Systems of Nonlinear Equations |
nlme | Linear and Nonlinear Mixed Effects Models |
nloptr | R interface to NLopt |
NLP | Natural Language Processing Infrastructure |
NMF | Algorithms and Framework for Nonnegative Matrix Factorization (NMF) |
nnet | Feed-Forward Neural Networks and Multinomial Log-Linear Models |
NOISeq | Exploratory analysis and differential expression for RNA-seq data |
nor1mix | Normal (1-d) Mixture Models (S3 Classes and Methods) |
np | Nonparametric Kernel Smoothing Methods for Mixed Data Types |
numDeriv | Accurate Numerical Derivatives |
oligo | Preprocessing tools for oligonucleotide arrays |
oligoClasses | Classes for high-throughput arrays supported by oligo and crlmm |
openNLP | Apache OpenNLP Tools Interface |
openNLPdata | Apache OpenNLP Jars and Basic English Language Models |
openssl | Toolkit for Encryption |
openxlsx | Read |
optextras | Tools to Support Optimization Possibly with Bounds and Masks |
optimbase | R port of the Scilab optimbase module |
optimsimplex | R Port of the 'Scilab' Optimsimplex Module |
optimx | A Replacement and Extension of the optim() Function |
optparse | Command Line Option Parser |
ordinal | Regression Models for Ordinal Data |
ordinationDuality | Performs orthogonal decomposition |
OrganismDbi | Software to enable the smooth interfacing of different database packages |
org.Hs.eg.db | Genome wide annotation for Human |
orthopolynom | Collection of functions for orthogonal and orthonormal polynomials |
packrat | A Dependency Management System for Projects and their R Package Dependencies |
pamr | Pam: prediction analysis for microarrays |
pan | Multiple Imputation for Multivariate Panel or Clustered Data |
parallelDist | Parallel Distance Matrix Computation using Multiple Threads |
partitions | Additive Partitions of Integers |
pbapply | Adding Progress Bar to '*apply' Functions |
pbdZMQ | Programming with Big Data -- Interface to 'ZeroMQ' |
pbivnorm | Vectorized Bivariate Normal CDF |
pbkrtest | Parametric Bootstrap and Kenward Roger Based Methods for Mixed Model Comparison |
pbmcapply | Tracking the Progress of Mc*pply with Progress Bar |
pcalg | Methods for Graphical Models and Causal Inference |
pcaMethods | A collection of PCA methods |
pcaPP | Robust PCA by Projection Pursuit |
pegas | Population and Evolutionary Genetics Analysis System |
penalized | L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation in GLMs and in the Cox Model |
PerformanceAnalytics | Econometric Tools for Performance and Risk Analysis |
permute | Functions for Generating Restricted Permutations of Data |
phangorn | Phylogenetic Reconstruction and Analysis |
pheatmap | Pretty Heatmaps |
phylobase | Base Package for Phylogenetic Structures and Comparative Data |
phylolm | Phylogenetic Linear Regression |
phylomap | Phylogenetic Stochastic Mapping |
phyloseq | Handling and analysis of high-throughput microbiome census data |
phytools | Phylogenetic Tools for Comparative Biology (and Other Things) |
picasso | Pathwise Calibrated Sparse Shooting Algorithm |
pillar | Coloured Formatting for Columns |
pinfsc50 | Sequence ('FASTA') |
pixmap | Bitmap Images (``Pixel Maps) |
pkgconfig | Private Configuration for 'R' Packages |
pkgmaker | Development Utilities for R Packages |
PKI | Public Key Infrastucture for R Based on the X.509 Standard |
plogr | The 'plog' C++ Logging Library |
plot3D | Plotting Multi-Dimensional Data |
plotly | Create Interactive Web Graphics via 'plotly.js' |
plotmo | Plot a Model's Residuals |
plotrix | Various Plotting Functions |
pls | Partial Least Squares and Principal Component Regression |
plsgenomics | PLS Analyses for Genomics |
plsRglm | Partial Least Squares Regression for Generalized Linear Models |
plyr | Tools for Splitting |
png | Read and write PNG images |
polynom | A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations |
PopGenome | An Efficient Swiss Army Knife for Population Genomic Analyses |
pophelper | Tabulate |
poRe | An R package to enable organisation and visualisation of nanopore sequencing data |
poweRlaw | Analysis of Heavy Tailed Distributions |
ppcor | Partial and Semi-Partial (Part) Correlation |
prabclus | Functions for Clustering of Presence-Absence |
pracma | Practical Numerical Math Functions |
praise | Praise Users |
preprocessCore | A collection of pre-processing functions |
PresenceAbsence | Presence-Absence Model Evaluation. |
prettyunits | Pretty |
pROC | Display and Analyze ROC Curves |
processx | Execute and Control System Processes |
prodlim | Product-Limit Estimation for Censored Event History Analysis |
progress | Terminal Progress Bars |
proj4 | A simple interface to the PROJ.4 cartographic projections library |
promises | Abstractions for Promise-Based Asynchronous Programming |
propr | Calculating Proportionality Between Vectors of Compositional Data |
ProtGenerics | S4 generic functions for Bioconductor proteomics infrastructure |
proto | Prototype Object-Based Programming |
proxy | Distance and Similarity Measures |
pryr | Tools for Computing on the Language |
pscl | Political Science Computational Laboratory |
psych | Procedures for Psychological |
purrr | Functional Programming Tools |
purrrlyr | Tools at the Intersection of 'purrr' and 'dplyr' |
qdap | Bridging the Gap Between Qualitative Data and Quantitative Analysis |
qdapDictionaries | Dictionaries and Word Lists for the 'qdap' Package |
qdapRegex | Regular Expression Removal |
qdapTools | Tools for the 'qdap' Package |
qpcR | Modelling and Analysis of Real-Time PCR Data |
qqman | Q-Q and Manhattan Plots for GWAS Data |
qtl | Tools for Analyzing QTL Experiments |
quadprog | Functions to solve Quadratic Programming Problems. |
quantmod | Quantitative Financial Modelling Framework |
quantreg | Quantile Regression |
questionr | Functions to Make Surveys Processing Easier |
qvalue | Q-value estimation for false discovery rate control |
R2admb | 'ADMB' to R Interface Functions |
R2GUESS | Wrapper Functions for GUESS |
R2HTML | HTML Exportation for R Objects |
R2jags | Using R to Run 'JAGS' |
R2WinBUGS | Running 'WinBUGS' and 'OpenBUGS' from 'R' / 'S-PLUS' |
R6 | Classes with Reference Semantics |
radiator | RADseq Data Exploration |
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 | Random Forests for Survival |
randtoolbox | Toolbox for Pseudo and Quasi Random Number Generation and RNG Tests |
ranger | A Fast Implementation of Random Forests |
RANN | Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric |
rARPACK | Solvers for Large Scale Eigenvalue and SVD Problems |
raster | Geographic Data Analysis and Modeling |
rasterVis | Visualization Methods for Raster Data |
R.basic | [R] Class Library - Stand-alone basic functions [DEPRECATED] |
RBGL | An interface to the BOOST graph library |
Rcgmin | Conjugate Gradient Minimization of Nonlinear Functions |
RColorBrewer | ColorBrewer Palettes |
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 |
RcppGSL | 'Rcpp' Integration for 'GNU GSL' Vectors and Matrices |
RcppParallel | Parallel Programming Tools for 'Rcpp' |
RcppProgress | An Interruptible Progress Bar with OpenMP Support for C++ in R Packages |
RcppRoll | Efficient Rolling / Windowed Operations |
RcppZiggurat | 'Rcpp' Integration of Different "Ziggurat" Normal RNG Implementations |
RCurl | General Network (HTTP/FTP/...) Client Interface for R |
rda | Shrunken Centroids Regularized Discriminant Analysis |
R.devices | Unified Handling of Graphics Devices |
readr | Read Rectangular Text Data |
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 |
rematch | Match Regular Expressions with a Nicer 'API' |
rentrez | 'Entrez' in R |
reports | Assist the Workflow of Writing Academic Articles and Other Reports |
repr | Serializable Representations |
reprex | Prepare Reproducible Example Code via the Clipboard |
reshape | Flexibly Reshape Data |
reshape2 | Flexibly Reshape Data: A Reboot of the Reshape Package |
ResourceSelection | Resource Selection (Probability) Functions for Use-Availability Data |
reticulate | Interface to 'Python' |
rex | Friendly Regular Expressions |
rexpokit | R Wrappers for EXPOKIT; Other Matrix Functions |
rgdal | Bindings for the 'Geospatial' Data Abstraction Library |
rgeos | Interface to Geometry Engine - Open Source ('GEOS') |
rgl | 3D Visualization Using OpenGL |
Rgraphviz | Provides plotting capabilities for R graph objects |
rhdf5 | HDF5 interface to R |
rhierbaps | rhierbaps |
RhpcBLASctl | Control the Number of Threads on 'BLAS' |
Rhtslib | HTSlib high-throughput sequencing library as an R package |
RInside | C++ Classes to Embed R in C++ Applications |
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 |
rlang | Functions for Base Types and Core R and 'Tidyverse' Features |
rlas | Read and Write 'las' and 'laz' Binary File Formats Used for Remote Sensing Data |
rlecuyer | R Interface to RNG with Multiple Streams |
rmarkdown | Dynamic Documents for R |
R.methodsS3 | S3 Methods Simplified |
Rmisc | Rmisc: Ryan Miscellaneous |
RMTstat | Distributions |
RMySQL | Database Interface and 'MySQL' Driver for R |
RnBeads | RnBeads |
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 |
robust | Port of the S+ "Robust Library" |
robustbase | Basic Robust Statistics |
ROC | utilities for ROC |
ROCR | Visualizing the Performance of Scoring Classifiers |
R.oo | R Object-Oriented Programming with or without References |
rotl | Interface to the 'Open Tree of Life' API |
roxygen2 | In-Line Documentation for R |
rpart | Recursive Partitioning and Regression Trees |
RPMM | Recursively Partitioned Mixture Model |
RPostgreSQL | R Interface to the 'PostgreSQL' Database System |
rprojroot | Finding Files in Project Subdirectories |
rrBLUP | Ridge Regression and Other Kernels for Genomic Selection |
rrcov | Scalable Robust Estimators with High Breakdown Point |
rredlist | 'IUCN' Red List Client |
rrpack | Reduced-Rank Regression |
Rsamtools | Binary alignment (BAM) |
rsconnect | Deployment Interface for R Markdown Documents and Shiny Applications |
RSkittleBrewer | Fun with R Colors |
rslurm | Submit R Calculations to a Slurm Cluster |
rsm | Response-Surface 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' |
rstudioapi | Safely Access the RStudio API |
Rsubread | Subread sequence alignment for R |
rtracklayer | R interface to genome annotation files and the UCSC genome browser |
Rtsne | T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation |
RUnit | R Unit Test Framework |
R.utils | Various Programming Utilities |
ruv | Detect and Remove Unwanted Variation using Negative Controls |
rvcheck | R/Package Version Check |
rversions | Query 'R' Versions |
rvest | Easily Harvest (Scrape) Web Pages |
Rvmmin | Variable Metric Nonlinear Function Minimization |
rworldmap | Mapping Global Data |
S4Vectors | S4 implementation of vector-like and list-like objects |
SALES | Elastic Net and (Adaptive) Lasso Penalized Sparse Asymmetric Least Squares (SALES) and Coupled Sparse Asymmetric Least Squares (COSALES) using Coordinate Descent and Proximal Gradient Algorithms |
samr | SAM: Significance Analysis of Microarrays |
sandwich | Robust Covariance Matrix Estimators |
satellite | Handling and Manipulating Remote Sensing Data |
scales | Scale Functions for Visualization |
scatterplot3d | 3D Scatter Plot |
scoringRules | Scoring Rules for Parametric and Simulated Distribution Forecasts |
SDMTools | Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises |
seegSDM | Streamlined Functions for Species Distribution Modelling in the SEEG Research Group |
segmented | Regression Models with Break-Points / Change-Points Estimation |
selectr | Translate CSS Selectors to XPath Expressions |
sensitivity | Global Sensitivity Analysis of Model Outputs |
seqinr | Biological Sequences Retrieval and Analysis |
setRNG | Set (Normal) Random Number Generator and Seed |
settings | Software Option Settings Manager for R |
Seurat | Tools for Single Cell Genomics |
sf | Simple Features for R |
sfsmisc | Utilities from 'Seminar fuer Statistik' ETH Zurich |
sglOptim | Generic Sparse Group Lasso Solver |
shape | Functions for Plotting Graphical Shapes |
shiny | Web Application Framework for R |
shinyjs | Easily Improve the User Experience of Your Shiny Apps in Seconds |
shinystan | Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models |
shinythemes | Themes for Shiny |
ShortRead | FASTQ input and manipulation |
siggenes | Multiple testing using SAM and Efron's empirical Bayes approaches |
SimCorMultRes | Simulates Correlated Multinomial Responses |
SKAT | SNP-Set (Sequence) Kernel Association Test |
slam | Sparse Lightweight Arrays and Matrices |
sleuth | Tools for investigating RNA-Seq |
sn | The Skew-Normal and Related Distributions Such as the Skew-t |
sna | Tools for Social Network Analysis |
snow | Simple Network of Workstations |
snowfall | Easier cluster computing (based on snow). |
snpReady | Preparing Genotypic Datasets in Order to Run Genomic Analysis |
SNPRelate | Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data |
snpStats | SnpMatrix and XSnpMatrix classes and methods |
solrium | General Purpose R Interface to 'Solr' |
sommer | Solving Mixed Model Equations in R |
sourcetools | Tools for Reading |
sp | Classes and Methods for Spatial Data |
spacetime | Classes and Methods for Spatio-Temporal Data |
spam | SPArse Matrix |
sparsebn | Learning Sparse Bayesian Networks from High-Dimensional Data |
sparsebnUtils | Utilities for Learning Sparse Bayesian Networks |
SparseM | Sparse Linear Algebra |
sparsevar | A Package for Sparse VAR/VECM Estimation |
spatial | Functions for Kriging and Point Pattern Analysis |
SpatioTemporal | Spatio-Temporal Model Estimation |
spData | Datasets for Spatial Analysis |
spDataLarge | Large datasets for spatial analysis |
spdep | Spatial Dependence: Weighting Schemes |
speedglm | Fitting Linear and Generalized Linear Models to Large Data Sets |
SpiecEasi | Sparse Inverse Covariance for Ecological Statistical Inference |
splancs | Spatial and Space-Time Point Pattern Analysis |
splitstackshape | Stack and Reshape Datasets After Splitting Concatenated Values |
spls | Sparse Partial Least Squares (SPLS) Regression and Classification |
sqldf | Manipulate R Data Frames Using SQL |
SQUAREM | Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms |
stabledist | Stable Distribution Functions |
StanHeaders | C++ Header Files for Stan |
statip | Statistical Functions for Probability Distributions |
statmod | Statistical Modeling |
statnet.common | Common R Scripts and Utilities Used by the Statnet Project Software |
stringdist | Approximate String Matching and String Distance Functions |
stringi | Character String Processing Facilities |
stringr | Simple |
strucchange | Testing |
subplex | Unconstrained Optimization using the Subplex Algorithm |
SummarizedExperiment | SummarizedExperiment container |
survey | Analysis of Complex Survey Samples |
survival | Survival Analysis |
sva | Surrogate Variable Analysis |
svDialogs | 'SciViews' - Standard Dialog Boxes for Windows |
SVGAnnotation | Tools for post-processing SVG plots created in R |
svglite | An 'SVG' Graphics Device |
svGUI | SciViews - Manage GUIs in R |
svUnit | SciViews GUI API - Unit testing |
symDMatrix | Partitioned Symmetric Matrices |
synbreed | Framework for the Analysis of Genomic Prediction Data using R |
targetSeqView | View alignments over candidate structural variant loci |
tawny | Clean Covariance Matrices Using Random Matrix Theory and Shrinkage Estimators for Portfolio Optimization |
tawny.types | Common Types for Tawny |
taxize | Taxonomic Information from Around the Web |
tclust | Robust Trimmed Clustering |
TeachingDemos | Demonstrations for Teaching and Learning |
tensorA | Advanced tensors arithmetic with named indices |
tensorflow | R Interface to 'TensorFlow' |
testthat | Unit Testing for R |
tfruns | Training Run Tools for 'TensorFlow' |
TH.data | TH's Data Archive |
threejs | Interactive 3D Scatter Plots |
tibble | Simple Data Frames |
tidyr | Easily Tidy Data with 'spread()' and 'gather()' Functions |
tidyselect | Select from a Set of Strings |
tidyverse | Easily Install and Load the 'Tidyverse' |
tiff | Read and write TIFF images |
timeDate | Rmetrics - Chronological and Calendar Objects |
timeSeries | Rmetrics - Financial Time Series Objects |
tinytex | Helper Functions to Install and Maintain 'TeX Live' |
tm | Text Mining Package |
treeio | Base Classes and Functions for Phylogenetic Tree Input and Output |
triebeard | 'Radix' Trees in 'Rcpp' |
trimcluster | Cluster analysis with trimming |
truncnorm | Truncated Normal Distribution |
tseries | Time Series Analysis and Computational Finance |
tseriesChaos | Analysis of nonlinear time series |
tsne | T-Distributed Stochastic Neighbor Embedding for R (t-SNE) |
TTR | Technical Trading Rules |
twang | Toolkit for Weighting and Analysis of Nonequivalent Groups |
TxDb.Hsapiens.UCSC.hg19.knownGene | Annotation package for TxDb object(s) |
ucminf | General-Purpose Unconstrained Non-Linear Optimization |
udunits2 | Udunits-2 Bindings for R |
units | Measurement Units for R Vectors |
UpSetR | A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets |
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 |
utf8 | Unicode Text Processing |
uuid | Tools for generating and handling of UUIDs |
V8 | Embedded JavaScript Engine for R |
VariantAnnotation | Annotation of Genetic Variants |
vars | VAR Modelling |
varSelRF | Variable Selection using Random Forests |
vcd | Visualizing Categorical Data |
vcfR | Manipulate and Visualize VCF Data |
vegan | Community Ecology Package |
VEGAWES | A package to perform vartiational-based copy number segmentation on WES data |
VennDiagram | Generate High-Resolution Venn and Euler Plots |
venneuler | Venn and Euler Diagrams |
VGAM | Vector Generalized Linear and Additive Models |
viridis | Default Color Maps from 'matplotlib' |
viridisLite | Default Color Maps from 'matplotlib' (Lite Version) |
vsn | Variance stabilization and calibration for microarray data |
wavelets | A package of functions for computing wavelet filters |
waveslim | Basic wavelet routines for one- |
wavethresh | Wavelets Statistics and Transforms |
wbs | Wild Binary Segmentation for Multiple Change-Point Detection |
webshot | Take Screenshots of Web Pages |
WGCNA | Weighted Correlation Network Analysis |
whisker | {{mustache}} for R |
WikidataR | API Client Library for 'Wikidata' |
WikipediR | A MediaWiki API Wrapper |
wikitaxa | Taxonomic Information from 'Wikipedia' |
withr | Run Code 'With' Temporarily Modified Global State |
wordcloud | Word Clouds |
worrms | World Register of Marine Species (WoRMS) Client |
xcms | LC/MS and GC/MS Data Analysis |
xgboost | Extreme Gradient Boosting |
xlsx | Read |
xlsxjars | Package required POI jars for the xlsx package |
XML | Tools for Parsing and Generating XML Within R and S-Plus |
xml2 | Parse XML |
xtable | Export Tables to LaTeX or HTML |
xts | eXtensible Time Series |
XVector | Representation and manipulation of external sequences |
yaml | Methods to Convert R Data to YAML and Back |
zCompositions | Treatment of Zeros and Nondetects in Compositional Data Sets |
zeallot | Multiple |
zip | Cross-Platform 'zip' Compression |
zlibbioc | An R packaged zlib-1.2.5 |
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' |
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 |
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 |
utils | The R Utils Package |
FAQ
- Q: When I submit the job with N=1 and M=1 it runs and R allocates the 10 slaves that I want. Is this the OK?
- A: In short, no. This is bad since you are lying to the scheduler about the resources you intend to run. We have scripts that will kill your job if they catch it and we tend to suspend accounts of users who make a practice of it. :)
- Q: The actual job I want to run is much larger. Anywhere from 31 to 93 processors are desired. Is it ok to request this many processors.
- A: That depends on the level of investment from your PI. If you ask for processors than your groups core allocation, which depends on the investment level, you will be essentially borrowing cores from other groups and may wait an extended period of time in the queue before your job runs. Groups are allowed to run on up to 10x their core allocation provided the resources are available. If you ask for more than 10x your groups core allocation, the job will be blocked indefinitely.
- Q: Do I need the number of nodes requested to be correct or can I just have R go grab slaves after the job is submitted with N=1 and M=1?
- A: Your resource request must be consistent with what you actually intend to use as noted above.
- Q: Is it better to request a large number of nodes for a shorter period of time or less nodes for longer period of time (concretely, say 8 nodes for 40 hours versus 16 nodes for 20 hours) in terms of getting through the queue?
- A: Do not confuse "nodes" with "cores/processors". Each "node" is a physical machine with between 4 and 48 cores. Your MPI threads will run on "cores" which may all be in the same "node" or spread among multiple nodes. You should ask for the number of cores you need and spread them among as few nodes as possible unless you have a good reason to do otherwise. Thus you should generally ask for things like
#PBS -l nodes=1:ppn=8 (we have lots of 8p nodes) #PBS -l nodes=1:ppn=12 (we have a number of 12p also)
Multiples of the above work as well so you might ask for nodes=3:ppn=8 if you want to run 24 threads on 24 different cores. It looks like in the R model there is a master/slave paradigm so you really need one master thread to manage the "slave" threads. It is likely that the master thread accumulates little CPU time so you could neglect it. In other words tell the scheduler that you want nodes=3:ppn=8 and tell R to spawn 24 children. This is a white lie which will do little harm. However, if it turns out that the master accumulates significant CPU time and your job gets killed by our rogue process killer, you can ask for the resources as follows
#PBS -l nodes=1:ppn=1infiniband+3:ppn=8:infiniband
This will allocate 1 thread on a separate node (the master thread) and then the slave threads will be allocated on 3 additional nodes with at least 8 cores each.
- A: Do not confuse "nodes" with "cores/processors". Each "node" is a physical machine with between 4 and 48 cores. Your MPI threads will run on "cores" which may all be in the same "node" or spread among multiple nodes. You should ask for the number of cores you need and spread them among as few nodes as possible unless you have a good reason to do otherwise. Thus you should generally ask for things like
Rmpi Example
Example of using the parallel module to run MPI jobs under R 2.14.1+
{{#fileAnchor: rmpi_test.R}} Download raw source of the [{{#fileLink: rmpi_test.R}} rmpi_test.R] file.
# Load the R MPI package if it is not already loaded.
if (!is.loaded("mpi_initialize")) {
library("Rmpi")
}
# Spawn as many slaves as possible
mpi.spawn.Rslaves()
# In case R exits unexpectedly, have it automatically clean up
# resources taken up by Rmpi (slaves, memory, etc...)
.Last <- function(){
if (is.loaded("mpi_initialize")){
if (mpi.comm.size(1) > 0){
print("Please use mpi.close.Rslaves() to close slaves.")
mpi.close.Rslaves()
}
print("Please use mpi.quit() to quit R")
.Call("mpi_finalize")
}
}
# Tell all slaves to return a message identifying themselves
mpi.remote.exec(paste("I am",mpi.comm.rank(),"of",mpi.comm.size()))
# Tell all slaves to close down, and exit the program
mpi.close.Rslaves()
mpi.quit()