[]

• My directory of R packages for data analysis and visualization, Bayesian statistics, mapping, GIS, climate, Species Distribution Modelling, ecology, biogeography, evolution, reproducible science…
• Data sources
• Data management
• General statistics
  • Ordination & Multivariate Analysis
  • Survival analysis
  • Regression tools
  • Bayesian/MCMC
• Plotting & Visualisation
  • GGPLOT2
  • Colour
• Reproducible Research - Report generation
• Parallelisation & Big Data
• Niche & Species Distribution Modelling
  • Occupancy modelling
• Remote Sensing
• Climate
• GIS/spatial functionality
• Spatial Analysis
• Networks
• Phylogenetics, phylogeography & comparative analysis
• Palaeoecology
• Dendrochronology
• Ecological analyses (miscellaneous)
• Miscellaneous
• R programming

My directory of R packages for data analysis and visualization, Bayesian statistics, mapping, GIS, climate, Species Distribution Modelling, ecology, biogeography, evolution, reproducible science…

F. Rodriguez-Sanchez

Updated 2019-10-03

These are packages that I often use or, alternatively, I need only rarely but don’t want to forget about. Of course, there are many other useful packages out there (e.g. at CRAN or GitHub. Check also CRAN task views.

Data sources

Check CRAN Task View on Web technologies.

Data management

Check out this great cheatsheet: Data wrangling with dplyr and tidyr

• rio A Swiss-Army Knife for Data I/O
• tidyr Reshape data
• reshape2 Reshape data from long to wide format and vice versa
• dplyr Data wrangling
• data.table Tools for managing data frames
• gdata Data manipulation
• Hmisc Frank Harrell’s miscellaneous tools
• Kmisc Data reshaping, table and plot generation from RMarkdown
• lubridate Dates and times
• multitable Manipulate multiple arrays
• datacheck Tools for checking data consistency
• tabplot Large datasets viz.
• tabplotd3 Interactive
• tableplot
• taRifx Useful functions
• DescTools Many useful functions
• summarytools Quickly summarize dataframes (inc. markdown output)

General statistics

Ordination & Multivariate Analysis

Check also Environmetrics and Multivariate CRAN Task Views.

• vegan
• ade4 Multivariate data analysis and display
• dave Data Analysis in Vegetation Ecology
• ecodist Dissimilarity-based analysis (ordination, Mantel tests…)
• labdsv Includes plotting functions
• mvabund Analysing multivariate data (upscaling from individual species models)
• boral Bayesian ordination and regression analysis
• eigenprcomp Computes confidence intervals for the proportion explained by the first 1,2,k principal components

Survival analysis

• survival
• survMisc
• coxme Mixed-effects cox regression
• rawr Plotting functions: kmplot & ggsurv

Regression tools

• aod Analysis of Overdispersed data
• AICcmodavg Model selection and multimodel inference
• arm Gelman’s package: includes bayesglm, sim, coefplot…
• bbmle Tools for MLE
• binomTools Diagnostics for binomial regression
• car Regression tools
• coefplot Plot model coefficients
• confReg Estimating confidence of individual regression predictions
• COUNT Regression models for count data (Poisson, Negative Binomial)
• DAAG Some regression tools from the book ‘Data Analysis and Graphics using R’
• dhglm Hierarchical GLMs with random effects in both the mean and dispersion components
• dynlm Dynamic linear models and time series regression
• earth Multivariate Adaptive Regression Splines
• effects Displays effects estimated from regression models
• emdbook Tools from ‘Ecological Models and Data’ (inc. several plotting functions)
• fit.models Compare results from different models
• FME Modelling tools
• gam Generalised Additive Models (GAMs)
• gamm4 GAMMs
• gbm Generalised Boosted regression models
• gee Generalized Estimating Equations
• glm2 To fit GLMs with convergence problems
• MuMIn Model selection and averaging
• glmulti Model selection and multimodel inference
• gnm Generalized nonlinear models
• heatmapFit Checking logistic regression goodness of fit
• hier.part Variance partitioning to assess ‘importance’ of predictors. See also relaimpo.
• relaimpo Relative importance of predictors
• nlme Mixed models
• lme4 Mixed models
• pamm Power analysis for mixed models
• odprism Power analysis for mixed models
• likelihood Maximum Likelihood Estimation
• lmtest Diagnostic checks for linear regression
• MARSS Multivariate Autoregressive State-Space Modeling
• MCMCglmm Mixed models fitted by MCMC
• mgcv GAM fitting
• miscF Multivariate Normal regression, spatial Bayesian mixed models, piecewise regression…
• mlogit Multinomial regression
• mvinfluence Influence Measures and Diagnostic Plots for Multivariate Linear Models
• msm Multi-state Markov and hidden Markov models in continuous time
• PCovR Principal Covariates Regression (Reducing collinear predictor variables to a few components and regressing on them)
• HLMdiag Diagnostic tools for hierarchical models (fitted with lme4)
• stremo Learning Structural Equation Models
• rockchalk Regression Estimation and Presentation
• R2STATS GUI for fitting and comparing GLM and GLMM in R
• LMERConvenienceFunctions
• R2admb
• rms Regression modeling strategies
• Zelig

Bayesian/MCMC

Check also Bayesian CRAN Task View.

• rstanarm
• blme Bayesian multilevel models
• BMA Model averaging
• dclone Data cloning and MCMC tools (inc. JAGS functions)
• dcmle Hierarchical models through data cloning
• dlm Dynamic models and MCMC tools
• dlmodeler State-space modelling
• sspir State-space models
• MCMCglmm Mixed models fitted by MCMC
• RSGHB Hierarchical Bayes models
• bayespref Analysis of count data
• predcomps Average Predictive Comparisons

Generic MCMC samplers

• adaptMCMC Generic MCMC sampler
• BRugs Interface to OpenBUGS
• BayesX Structured Additive Regression
• R2BayesX
• rjags
• runjags
• R2jags
• jagsUI
• R2OpenBUGS
• R2WinBUGS
• rstan
• filzbach
• iBUGS Interface to BUGS/JAGS
• rube
• INLA Integrated Nested Laplace Approximation
• LaplacesDemon
• LearnBayes
• MCMCpack MCMC samplers
• MHAdative MCMC sampler
• glmmBUGS
• mcmc
• datalist

MCMC diagnostics & plotting

• coda MCMC output analysis
• boa Analyses of MCMC output (like coda)
• ggmcmc Graphic analysis of MCMC output
• mcmcmplots Plot MCMC output
• plotMCMC Diagnostic plots
• bmk MCMC diagnostics
• superdiag testing MCMC noncovergence
• shinyStan
• MCMCvis
• rwty
• dMCMC
• bayesplot

Spatial Bayes

• CARBayes Spatial models with CAR
• spBayes spatial Bayes
• geoCount generalized linear spatial models

ABC

• abc Approximate Bayesian Computation
• easyABC Approximate Bayesian Computation

Plotting & Visualisation

Check also CRAN Task View on Graphics.

• denstrip Plotting distributions (w uncertainty)
• visualize Graph Probability Distributions
• fanplot Visualise sequential probability distributions
• diagram Networks, flow diagrams, etc
• beanplot Bean plots
• vioplot Violin plots
• viopoints 1-D Scatter Plots with Jitter Using Kernel Density Estimates
• dagR Directed Acyclic graphs (DAGs)
• effects Displays effects estimated from regression models
• coefplot Plot model coefficients
• plotmo Plot model responses
• corrgram Plot correlation matrix
• gclus Clustering graphics
• vcd Viz categorical data
• extracat Viz categorical data
• plot3d Plotting multi-dimensional data
• VizOR visualization tools for complex observational data
• GrapheR GUI for base plots

GGPLOT2

• ggplot2

• GGally extension to ggplot

• ggsubplot Embedding subplots within plots

• ggthemes Extra themes, scales and geoms for ggplot

• gplot2bdc

• ggtern Ternary diagrams

• ggthemr Extra themes for ggplot2

• plotly R interface to plotly

• googleVis Using google chart tools

• rCharts Interactive charts

• lattice Multivariate plots

• manipulate Interactive plots

• misc3d 3D plots

• mvtsplot Multivariate time series plot

• pca3d Three dimensional PCA plots

• longCatEDA Plot Categorical Longitudinal and Time-Series Data

• squash Color-based plots for multivariate visualization

• tourr

• latticist GUI for graphic exploratory data analysis using lattice

• tfplot Plot time series

• pathdiagram

• RIGHT Interactive graphics via HTML

• clickme Interactive plots

• animation Create animations

• calibrate Axes calibration

• labeling Axis labeling

• directlabels Labels for multicolor plots. See also Hmisc:::labcurve.

• gplots Useful plotting tools

• magicaxis Pretty scientific plots (e.g. log scales)

• PlotRegionHighlighter Creates an envelope that surrounds a set of points

• compactr Plots with compact axis notation

• plotflow Useful plotting functions

• sendplot Interactive plots with tool-tip content

• zoom Allow to zoom/navigate in any plot.

• Hmisc

• epade Easy plots

• prettyGraphs Publication-quality graphics.

• scagnostics Scatterplot diagnostics

Colour

• colorRamps Colour palettes

• RColorBrewer

• colorspace HCL (perceptually-based) palettes

• colortools

• plotKML Colour palettes for mapping

• gplots Rich.colors palettes

• dataview

• tabplot Large datasets viz.

• tabplotd3 Interactive

• R2SWF Convert R graphics to Flash

• sendplot Send interactive plots with tooltip content

• sjPlot

• squash Color-based plots for multivariate visualization

Reproducible Research - Report generation

Check also CRAN Task View on Reproducible Research.

• brew
• knitr Dynamic report generation
• knitrBootstrap create bootstrap styled HTML reports from Rmarkdown
• reports writing reports and presentations
• repmis
• rapport report templating system
• pander Exploits pandoc to convert among multiple formats
• stargazer Easily create tables with regression outputs (directly from model objects)
• rtf Produce Rich Text Format documents from R
• R2HTML HTML reports from R
• xtable Export R objects to HTML tables
• R2wd Write MS-Word documents from R
• rmarkdown
• sjPlot
• Rgitbook
• table1xls Summary tables in Excel format.
• DescTools
• rctrack

Parallelisation & Big Data

Check also CRAN Task View on High Performance Computing.

• ff Big data management. See also package ffbase
• batch Batching routines in parallel
• bigdata

Niche & Species Distribution Modelling

• rgbif Access to GBIF data
• spocc Species occurrence data retrieval and mapping
• dismo Distribution modelling
• SDMTools
• adehabitatHS
• biomod2 SDM ensembles
• hSDM Bayesian SDM
• maxlike SDM for presence-only data
• MigClim Implements dispersal in SDMs
• GRaF SDM using latent Gaussian random fields
• SightabilityModel
• EnvNicheR
• RinSp Ecological niche metrics to measure individual specialization
• bdvis Biodiversity data visualization
• phyloclim Includes functions for calculating niche overlap
• phylospacer Phyloclimates and phylomorphospaces
• PresenceAbsence
• mboost Decomposing environmental, spatial, and spatiotemporal components of species distributions (Hothorn et al. 2011 Ecol Monogr)
• usdm Uncertainty analysis for species distribution models, esp. focused on positional uncertainty
• ModelMap Random Forest and Stochastic Gradient Boosting Models
• modEVA
• rangemapper
• comclim Community climate statistics
• hypervolume Modeling hypervolumes (species’ niches)
• ppmlasso Point process models
• sdmvspecies Create virtual species for SDM
• virtualspecies Create virtual species
• coenocline Simulate species presence and abundance along environmental gradients
• ecospat Many useful functions for niche & SDM (by A. Guisan’s group)
• comclim
• Metadata
• ENiRG

Occupancy modelling

• detect Occupancy modelling
• marked
• unmarked
• stocc Occupancy modeling
• hierarchicalDS hierarchical analysis of distance sampling data

Remote Sensing

• RStoolbox
• moveVis
• earthEngineGrabR
• rsMove
• satellite
• satelliteTools
• uavRst
• fieldRS
• cropPhenology
• rTIMESAT
• luna
• rabbiTS
• theiaR
• sentinel2
• getSpatialData
• sen2r
• S2utils
• SentinelAPI
• RGISTools

Climate

• BerkeleyEarth Climate data from Berkeley Earth database
• climates Tools for climate data (bioclim, downscaling, interpolation…)
• climatol Homogenisation of climate time series
• climstats Tools for climate data
• RMAWGEN Generate daily time series from monthly mean values
• climdex.pcic Computation of climate indices
• ClimClass Climate Classification according to various indices
• RClimMAWGEN generate time series of climate indices
• chillR Climate and phenology analysis
• rWBclimate Lots of historical data and future projections
• rnoaa
• rghcnV3 GHCN
• RNCEP weather data
• sirad Evapotranspiration etc
• SPEI Calculates Standardised Precipitation-Evaporation Index
• SPI
• weathermetrics
• raincpc Rainfall data
• Evapotranspiration
• GhcnDaily
• crn Get data from Climate Reference Network
• iki.dataclim
• FedData
• stationaRy Hourly data worldwide
• tempcyclesdata Temperature data for ca. 8000 stations 1975-2013

GIS/spatial functionality

Check also CRAN Task View on Spatial and Spatiotemporal data. Check also CRAN Task View on Web technologies for access to many GIS data.

• sp

• spacetime

• spatial

• rgeos

• rgdal

• raster

• rasterVis

• rts Raster time series

• spatial.tools Functions for raster processing, including parallel processing

• maptools Reading and manipulating geographic data

• PBSmapping

• taRifx.geo Useful spatial functions

• climstats Tools for climate and raster analyses

• countrycode Converts country codes

• cshapes Dataset of country boundaries

• gdistance Calculate distances and routes on grids

• geometry Mesh generation and surface tesselation

• geosphere Several GIS tools, esp. aimed at large scales (global)

• geonames

• mapproj Converts lat-lon data into projected coordinates

• geospacom Generates distance matrices from shape files and represents spatially weighted multilevel analysis results

• dismo

• fossil

• ggmap Plotting on Google Maps and OpenStreetMap

• GISTools Some further GIS tools (e.g. cloropleth maps)

• mapplots Data visualisation on maps

• maps Mapping tools

• OpenStreetMap Access to OpenStreetMap and Bing images

• osmar

• plotGoogleMaps

• RgoogleMaps

• R2G2 Plot anything in Google Earth

• rCarto useful functions for mapping

• marmap working with bathymetric and topographic data

• plotKML Visualization of spatial and spatio-temporal objects in Google Earth

• MODISTools

• spGoogle Interacting R with Google maps

• rMaps Interactive maps

• leafletR

• GEOmap

• rworldmap

• choroplethr

• mapmisc Utilities for producing maps

• sinkr Some GIS functions and colour palettes

• rlandscape Generates spatial landscapes

• RSAGA

• spgrass6

• spsextante

• RPyGeo

Spatial Analysis

Check also CRAN Task View on Spatial and Spatiotemporal data.

• akima Interpolation
• automap Automatic interpolation (kriging)
• ecespa Point pattern analysis
• fields Splines, kriging, etc
• geoR Geostatistical analysis
• geoRglm Spatial GLMs
• geospt Geostatistics
• GeoXP Interactive exploratory analysis of spatial data
• gstat Geostatistics (variograms, kriging)
• intamap Automatic spatial interpolation
• geostatsp Geostatistics using SpatialPoints and rasters
• spatstat
• spBayes
• spdep Modeling spatial dependence
• stpp Point patterns
• rtop Spatial interpolation of data

Networks

• bipartite
• igraph Network analysis and visualization
• enaR
• qgraph

Phylogenetics, phylogeography & comparative analysis

Check also Phylogenetics CRAN task view.

• ape
• adephylo Exploratory analysis
• Treesim Tree simulation. See also treesimGM
• cladoRcpp Phylogenetic analysis of geographic ranges
• caper Comparative analysis
• PVR Phylogenetic Eigenvector Regression
• BEDASSLE Disentangles the effects of geographic and ecological isolation on genetic differentiation
• geiger
• geoscale Geological timescale
• phangorn
• phytools
• pegas
• picante
• stratigraph
• treebase
• MCMCglmm

Palaeoecology

• Bchron Bayesian chronologies
• Bclim Palaeoclimate reconstruction

Dendrochronology

• dplR Dendrochronology
• measuRing Measuring ring width from scanned images.
• TRADER Tree Ring Analysis of Disturbance Events
• dendrobox Interactive Tree-Ring Data Exploration Tool
• treeclim Modeling tree-climate relationships.
• bootRes Bootstrapped response functions.
• rwtocore convert tree-ring measurements to drawings of cores (Ruby).
• triforce read the TRiDaS dendrochronological standard and communicate with Tellervo servers.
• pointRes Calculate and plot pointer years
• BIOdry Multilevel Modeling of Dendroclimatical Fluctuations
• sclero Measure Growth Patterns and Align Sampling Spots in Photographs
• dendrometeR Analyzing Dendrometer Data.
• wvtool Image Tools for Automated Wood Identification
• DendroSync Calculating Spatial Synchrony Between Tree-Ring Chronologies
• iadf Analysis of Intra Annual Density Fluctuations
• dendroExtra Finds the optimal sequence of days that are linearly or nonlinearly related to one or more tree-ring proxy records.

Ecological analyses (miscellaneous)

Check also Environmetrics CRAN Task View.

• betapart Beta diversity
• BiodiversityR GUI for biodiversity, suitability and community ecology analyses
• cheddar Analysis and visualisation of community data
• coexist Modelling species coexistence
• DSpat Distance Sampling
• fossil Species richness, species-area curves, beta-diversity
• indicspecies Assess associations between different species and sites (e.g. indicator species)
• IPMpack Integral Projection Models
• marked Mark-recapture analysis
• MBI Multiple Beta Diversity indices
• rmeta Meta-analysis
• neighlikeli Neighborhood models
• earlywarnings
• MAR1 Multivariate Autoregressive Modeling for Analysis of Community Time-Series Data
• ncbit retrieve NBCI taxonomic data
• spacodiR Spatial and Phylogenetic Analysis of Community Diversity
• Reol Interface to Encyclopedia of Life
• SPECIES Species richness and diversity analysis
• BayesComm Bayesian multivariate binary regression models for analysis of ecological communities
• pom Patch occupancy models
• capwire Population size estimation from non-invasive sampling
• vegclust Fuzzy clustering of vegetation data
• popbio
• demoniche Spatially-explicit demographic modelling
• BEDASSLE Disentangles the effects of geographic and ecological isolation on genetic differentiation.
• rphylopic Organisms silhouettes
• GSIF Global Soil Information
• Rarity Rarity indices
• taxize Taxonomy etc.
• Taxonstand
• sExtinct Extinction analysis based on sightings
• BEDASSLE Disentangles the effects of geographic and ecological isolation on genetic differentiation
• ecomodtools Simulation models (inc. dispersal)
• comclim Community climate statistics
• kernelPop Spatially explicit population genetic simulations
• siplab spatially explicit individual-based vegetation models.

Miscellaneous

• digitize Extract data from plots
• downloader Download files from internet
• hwriter Outputs R objects in HTML format
• installr Automatically update R
• mail Send email notifications from R
• sendmailR
• mosaic
• audiolyzR Creates audio representations of common plots
• WebDevelopR Web development
• ProjectTemplate
• gpk Datasets for educational uses
• NCmisc
• PubMedWordcloud Create wordcloud with abstracts.
• alm Altmetrics
• rAltmetric Retrieves data from altmetrics.com
• RMendeley
• rcrossref
• RefManageR Bibliography Management.
• refnet Reads and works with data from ISI Web of Knowledge
• scholar
• slidify
• sos Search R packages
• source.gist
• twitteR
• DescTools

R programming

• codetools Code analysis tools
• compiler Compile R code (e.g. a function) to speed it up
• devtools
• formatR Format and tidy R code
• gtools Useful functions (e.g. mixedsort)
• inline Define functions in C code within R
• iterators Tools for iteration on many different types of objects (see also itertools)
• Kmisc Data reshaping, table and plot generation from RMarkdown
• operators Additional operators
• simFrame A framework to work with simulations
• simSummary
• staticdocs Create webpage with package documentation
• testit Testing R packages
• testthat Testing R code
• tester Test characteristics of R objects
• assertthat.
• httr Working with URLs and HTTP
• RCurl HTTP interface
• stringr
• Rd2Roxygen
• Rxoygen2
• scrapeR
• aprof Profiling code and visualizing results to evaluate where is best to focus code optimization.
• regex Regular expressions made easier.