├── .gitignore ├── README.Rmd ├── README.md ├── add_CRAN_links_auto.R └── render.R /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | Rpackages_dir.Rproj 5 | -------------------------------------------------------------------------------- /README.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | output: 3 | github_document: 4 | toc: yes 5 | --- 6 | 7 | ## My directory of R packages for data analysis and visualization, Bayesian statistics, mapping, GIS, climate, Species Distribution Modelling, ecology, biogeography, evolution, reproducible science... 8 | 9 | [F. Rodriguez-Sanchez](http://bit.ly/frod_san) 10 | 11 | Updated `r as.character(Sys.Date())` 12 | 13 | 14 | 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](http://cran.r-project.org/web/packages/available_packages_by_name.html) or [GitHub](https://github.com/search?q=package&type=Repositories&ref=advsearch&l=R). Check also [CRAN task views](http://cran.r-project.org/web/views/). 15 | 16 | 17 | 18 | 19 | 20 | 21 | ## Data sources 22 | 23 | Check [CRAN Task View on Web technologies](http://cran.r-project.org/web/views/WebTechnologies.html). 24 | 25 | 26 | ## Data management 27 | 28 | Check out this great cheatsheet: [Data wrangling with dplyr and tidyr](http://www.rstudio.com/wp-content/uploads/2015/02/data-wrangling-cheatsheet.pdf) 29 | 30 | 31 | * [rio](https://cran.r-project.org/package=rio) A Swiss-Army Knife for Data I/O 32 | * [tidyr](https://cran.r-project.org/package=tidyr) Reshape data 33 | * [reshape2](https://cran.r-project.org/package=reshape2) Reshape data from long to wide format and vice versa 34 | * [dplyr](https://cran.r-project.org/package=dplyr) Data wrangling 35 | * [data.table](https://cran.r-project.org/package=data.table) Tools for managing data frames 36 | * [gdata](https://cran.r-project.org/package=gdata) Data manipulation 37 | * [Hmisc](https://cran.r-project.org/package=Hmisc) Frank Harrell's miscellaneous tools 38 | * [Kmisc](https://cran.r-project.org/package=Kmisc) Data reshaping, table and plot generation from RMarkdown 39 | * [lubridate](https://cran.r-project.org/package=lubridate) Dates and times 40 | * [multitable](https://cran.r-project.org/package=multitable) Manipulate multiple arrays 41 | * [datacheck](https://cran.r-project.org/package=datacheck) Tools for checking data consistency 42 | * [tabplot](https://cran.r-project.org/package=tabplot) Large datasets viz. 43 | * [tabplotd3](https://cran.r-project.org/package=tabplotd3) Interactive 44 | * [tableplot](https://cran.r-project.org/package=tableplot) 45 | * [taRifx](http://cran.r-project.org/web/packages/taRifx/index.html) Useful functions 46 | * [DescTools](http://cran.r-project.org/web/packages/DescTools/index.html) Many useful functions 47 | * [summarytools](https://cran.r-project.org/package=summarytools) Quickly summarize dataframes (inc. markdown output) 48 | 49 | 50 | 51 | 52 | ## General statistics 53 | 54 | 55 | 56 | 57 | ### Ordination & Multivariate Analysis 58 | 59 | 60 | Check also [Environmetrics](http://cran.r-project.org/web/views/Environmetrics.html) and [Multivariate](http://cran.r-project.org/web/views/Multivariate.html) CRAN Task Views. 61 | 62 | 63 | * [vegan](https://cran.r-project.org/package=vegan) 64 | * [ade4](http://cran.r-project.org/web/packages/ade4/index.html) Multivariate data analysis and display 65 | * [dave](https://cran.r-project.org/package=dave) Data Analysis in Vegetation Ecology 66 | * [ecodist](https://cran.r-project.org/package=ecodist) Dissimilarity-based analysis (ordination, Mantel tests...) 67 | * [labdsv](https://cran.r-project.org/package=labdsv) Includes plotting functions 68 | * [mvabund](https://cran.r-project.org/package=mvabund) Analysing multivariate data (upscaling from individual species models) 69 | * [boral](https://cran.r-project.org/package=boral) Bayesian ordination and regression analysis 70 | * [eigenprcomp](http://cran.r-project.org/web/packages/eigenprcomp/) Computes confidence intervals for the proportion explained by the first 1,2,k principal components 71 | 72 | 73 | 74 | ### Survival analysis 75 | 76 | 77 | * [survival](https://cran.r-project.org/package=survival) 78 | * [survMisc](https://cran.r-project.org/package=survMisc) 79 | * [coxme](https://cran.r-project.org/package=coxme) Mixed-effects cox regression 80 | * [rawr](https://cran.r-project.org/package=rawr) Plotting functions: kmplot & ggsurv 81 | 82 | 83 | ### Regression tools 84 | 85 | 86 | * [aod](https://cran.r-project.org/package=aod) Analysis of Overdispersed data 87 | * [AICcmodavg](http://cran.r-project.org/web/packages/AICcmodavg/index.html) Model selection and multimodel inference 88 | * [arm](https://cran.r-project.org/package=arm) Gelman's package: includes bayesglm, sim, coefplot... 89 | * [bbmle](https://cran.r-project.org/package=bbmle) Tools for MLE 90 | * [binomTools](https://cran.r-project.org/package=binomTools) Diagnostics for binomial regression 91 | * [car](https://cran.r-project.org/package=car) Regression tools 92 | * [coefplot](https://cran.r-project.org/package=coefplot) Plot model coefficients 93 | * [confReg](https://cran.r-project.org/package=confReg) Estimating confidence of individual regression predictions 94 | * [COUNT](https://cran.r-project.org/package=COUNT) Regression models for count data (Poisson, Negative Binomial) 95 | * [DAAG](https://cran.r-project.org/package=DAAG) Some regression tools from the book 'Data Analysis and Graphics using R' 96 | * [dhglm](https://cran.r-project.org/package=dhglm) Hierarchical GLMs with random effects in both the mean and dispersion components 97 | * [dynlm](https://cran.r-project.org/package=dynlm) Dynamic linear models and time series regression 98 | * [earth](https://cran.r-project.org/package=earth) Multivariate Adaptive Regression Splines 99 | * [effects](https://cran.r-project.org/package=effects) Displays effects estimated from regression models 100 | * [emdbook](https://cran.r-project.org/package=emdbook) Tools from 'Ecological Models and Data' (inc. several plotting functions) 101 | * [fit.models](https://cran.r-project.org/package=fit.models) Compare results from different models 102 | * [FME](https://cran.r-project.org/package=FME) Modelling tools 103 | * [gam](https://cran.r-project.org/package=gam) Generalised Additive Models (GAMs) 104 | * [gamm4](https://cran.r-project.org/package=gamm4) GAMMs 105 | * [gbm](https://cran.r-project.org/package=gbm) Generalised Boosted regression models 106 | * [gee](https://cran.r-project.org/package=gee) Generalized Estimating Equations 107 | * [glm2](https://cran.r-project.org/package=glm2) To fit GLMs with convergence problems 108 | * [MuMIn](https://cran.r-project.org/package=MuMIn) Model selection and averaging 109 | * [glmulti](https://cran.r-project.org/package=glmulti) Model selection and multimodel inference 110 | * [gnm](https://cran.r-project.org/package=gnm) Generalized nonlinear models 111 | * [heatmapFit](https://cran.r-project.org/package=heatmapFit) Checking logistic regression goodness of fit 112 | * [hier.part](https://cran.r-project.org/package=hier.part) Variance partitioning to assess 'importance' of predictors. See also `relaimpo`. 113 | * [relaimpo](https://cran.r-project.org/package=relaimpo) Relative importance of predictors 114 | * [nlme](https://cran.r-project.org/package=nlme) Mixed models 115 | * [lme4](https://cran.r-project.org/package=lme4) Mixed models 116 | * [pamm](https://cran.r-project.org/package=pamm) Power analysis for mixed models 117 | * [odprism](https://cran.r-project.org/package=odprism) Power analysis for mixed models 118 | * [likelihood](https://cran.r-project.org/package=likelihood) Maximum Likelihood Estimation 119 | * [lmtest](https://cran.r-project.org/package=lmtest) Diagnostic checks for linear regression 120 | * [MARSS](https://cran.r-project.org/package=MARSS) Multivariate Autoregressive State-Space Modeling 121 | * [MCMCglmm](https://cran.r-project.org/package=MCMCglmm) Mixed models fitted by MCMC 122 | * [mgcv](https://cran.r-project.org/package=mgcv) GAM fitting 123 | * [miscF](https://cran.r-project.org/package=miscF) Multivariate Normal regression, spatial Bayesian mixed models, piecewise regression... 124 | * [mlogit](https://cran.r-project.org/package=mlogit) Multinomial regression 125 | * [mvinfluence](https://cran.r-project.org/package=mvinfluence) Influence Measures and Diagnostic Plots for Multivariate Linear Models 126 | * [msm](https://cran.r-project.org/package=msm) Multi-state Markov and hidden Markov models in continuous time 127 | * [PCovR](https://cran.r-project.org/package=PCovR) Principal Covariates Regression (Reducing collinear predictor variables to a few components and regressing on them) 128 | * [HLMdiag](https://cran.r-project.org/package=HLMdiag) Diagnostic tools for hierarchical models (fitted with lme4) 129 | * [stremo](https://cran.r-project.org/package=stremo) Learning Structural Equation Models 130 | * [rockchalk](https://cran.r-project.org/package=rockchalk) Regression Estimation and Presentation 131 | * [R2STATS](https://cran.r-project.org/package=R2STATS) GUI for fitting and comparing GLM and GLMM in R 132 | * [LMERConvenienceFunctions](https://cran.r-project.org/package=LMERConvenienceFunctions) 133 | * [R2admb](https://cran.r-project.org/package=R2admb) 134 | * [rms](https://cran.r-project.org/package=rms) Regression modeling strategies 135 | * [Zelig](https://cran.r-project.org/package=Zelig) 136 | 137 | 138 | 139 | 140 | 141 | ### Bayesian/MCMC 142 | 143 | 144 | Check also [Bayesian CRAN Task View](http://cran.r-project.org/web/views/Bayesian.html). 145 | 146 | * [rstanarm](https://cran.r-project.org/package=rstanarm) 147 | * [blme](https://cran.r-project.org/package=blme) Bayesian multilevel models 148 | * [BMA](https://cran.r-project.org/package=BMA) Model averaging 149 | * [dclone](https://cran.r-project.org/package=dclone) Data cloning and MCMC tools (inc. JAGS functions) 150 | * [dcmle](https://cran.r-project.org/package=dcmle) Hierarchical models through data cloning 151 | * [dlm](https://cran.r-project.org/package=dlm) Dynamic models and MCMC tools 152 | * [dlmodeler](https://cran.r-project.org/package=dlmodeler) State-space modelling 153 | * [sspir](https://cran.r-project.org/package=sspir) State-space models 154 | * [MCMCglmm](https://cran.r-project.org/package=MCMCglmm) Mixed models fitted by MCMC 155 | * [RSGHB](https://cran.r-project.org/package=RSGHB) Hierarchical Bayes models 156 | * [bayespref](https://cran.r-project.org/package=bayespref) Analysis of count data 157 | * [predcomps](https://github.com/dchudz/predcomps) Average Predictive Comparisons 158 | 159 | 160 | 161 | #### Generic MCMC samplers 162 | 163 | * [adaptMCMC](http://cran.r-project.org/web/packages/adaptMCMC/index.html) Generic MCMC sampler 164 | * [BRugs](https://cran.r-project.org/package=BRugs) Interface to OpenBUGS 165 | * [BayesX](https://cran.r-project.org/package=BayesX) Structured Additive Regression 166 | * [R2BayesX](https://cran.r-project.org/package=R2BayesX) 167 | * [rjags](https://cran.r-project.org/package=rjags) 168 | * [runjags](https://cran.r-project.org/package=runjags) 169 | * [R2jags](https://cran.r-project.org/package=R2jags) 170 | * [jagsUI](https://cran.r-project.org/package=jagsUI) 171 | * [R2OpenBUGS](https://cran.r-project.org/package=R2OpenBUGS) 172 | * [R2WinBUGS](https://cran.r-project.org/package=R2WinBUGS) 173 | * [rstan](https://cran.r-project.org/package=rstan) 174 | * [filzbach](https://cran.r-project.org/package=filzbach) 175 | * [iBUGS](https://cran.r-project.org/package=iBUGS) Interface to BUGS/JAGS 176 | * [rube](http://stat.cmu.edu/~hseltman/rube/) 177 | * [INLA](https://cran.r-project.org/package=INLA) Integrated Nested Laplace Approximation 178 | * [LaplacesDemon](https://cran.r-project.org/package=LaplacesDemon) 179 | * [LearnBayes](https://cran.r-project.org/package=LearnBayes) 180 | * [MCMCpack](https://cran.r-project.org/package=MCMCpack) MCMC samplers 181 | * [MHAdative](https://cran.r-project.org/package=MHAdative) MCMC sampler 182 | * [glmmBUGS](https://cran.r-project.org/package=glmmBUGS) 183 | * [mcmc](https://cran.r-project.org/package=mcmc) 184 | * [datalist](http://cran.r-project.org/web/packages/datalist/index.html) 185 | 186 | 187 | 188 | 189 | #### MCMC diagnostics & plotting 190 | 191 | * [coda](https://cran.r-project.org/package=coda) MCMC output analysis 192 | * [boa](https://cran.r-project.org/package=boa) Analyses of MCMC output (like `coda`) 193 | * [ggmcmc](https://cran.r-project.org/package=ggmcmc) Graphic analysis of MCMC output 194 | * [mcmcmplots](https://cran.r-project.org/package=mcmcplots) Plot MCMC output 195 | * [plotMCMC](https://cran.r-project.org/package=plotMCMC) Diagnostic plots 196 | * [bmk](https://cran.r-project.org/package=bmk) MCMC diagnostics 197 | * [superdiag](https://cran.r-project.org/package=superdiag) testing MCMC noncovergence 198 | * [shinyStan](https://cran.r-project.org/package=shinyStan) 199 | * [MCMCvis](https://cran.r-project.org/package=MCMCvis) 200 | * [rwty](https://cran.r-project.org/package=rwty) 201 | * [dMCMC](https://github.com/MarcoDVisser/dMCMC) 202 | * [bayesplot](https://github.com/stan-dev/bayesplot) 203 | 204 | 205 | 206 | 207 | 208 | #### Spatial Bayes 209 | 210 | * [CARBayes](https://cran.r-project.org/package=CARBayes) Spatial models with CAR 211 | * [spBayes](https://cran.r-project.org/package=spBayes) spatial Bayes 212 | * [geoCount](http://cran.r-project.org/web/packages/geoCount/index.html) generalized linear spatial models 213 | 214 | 215 | #### ABC 216 | 217 | * [abc](http://cran.r-project.org/web/packages/abc/index.html) Approximate Bayesian Computation 218 | * [easyABC](https://cran.r-project.org/package=easyABC) Approximate Bayesian Computation 219 | 220 | 221 | 222 | 223 | 224 | ## Plotting & Visualisation 225 | 226 | 227 | Check also [CRAN Task View on Graphics](http://cran.r-project.org/web/views/Graphics.html). 228 | 229 | * [denstrip](https://cran.r-project.org/package=denstrip) Plotting distributions (w uncertainty) 230 | * [visualize](https://cran.r-project.org/package=visualize) Graph Probability Distributions 231 | * [fanplot](https://cran.r-project.org/package=fanplot) Visualise sequential probability distributions 232 | * [diagram](https://cran.r-project.org/package=diagram) Networks, flow diagrams, etc 233 | * [beanplot](https://cran.r-project.org/package=beanplot) Bean plots 234 | * [vioplot](https://cran.r-project.org/package=vioplot) Violin plots 235 | * [viopoints](https://cran.r-project.org/package=viopoints) 1-D Scatter Plots with Jitter Using Kernel Density Estimates 236 | * [dagR](https://cran.r-project.org/package=dagR) Directed Acyclic graphs (DAGs) 237 | * [effects](https://cran.r-project.org/package=effects) Displays effects estimated from regression models 238 | * [coefplot](https://cran.r-project.org/package=coefplot) Plot model coefficients 239 | * [plotmo](https://cran.r-project.org/package=plotmo) Plot model responses 240 | * [corrgram](https://cran.r-project.org/package=corrgram) Plot correlation matrix 241 | * [gclus](https://cran.r-project.org/package=gclus) Clustering graphics 242 | * [vcd](https://cran.r-project.org/package=vcd) Viz categorical data 243 | * [extracat](https://cran.r-project.org/package=extracat) Viz categorical data 244 | * [plot3d](http://cran.r-project.org/web/packages/plot3D/index.html) Plotting multi-dimensional data 245 | * [VizOR](http://cran.r-project.org/web/packages/VizOR/index.html) visualization tools for complex observational data 246 | * [GrapheR](https://cran.r-project.org/package=GrapheR) GUI for base plots 247 | 248 | 249 | ### GGPLOT2 250 | 251 | * [ggplot2](https://cran.r-project.org/package=ggplot2) 252 | * [GGally](https://cran.r-project.org/package=GGally) extension to ggplot 253 | * [ggsubplot](https://cran.r-project.org/package=ggsubplot) Embedding subplots within plots 254 | * [ggthemes](https://cran.r-project.org/package=ggthemes) Extra themes, scales and geoms for ggplot 255 | * [gplot2bdc](https://github.com/briandconnelly/ggplot2bdc) 256 | * [ggtern](http://www.ggtern.com/) Ternary diagrams 257 | * [ggthemr](https://github.com/cttobin/ggthemr) Extra themes for ggplot2 258 | 259 | 260 | 261 | * [plotly](https://github.com/ropensci/plotly) R interface to plotly 262 | * [googleVis](https://cran.r-project.org/package=googleVis) Using google chart tools 263 | * [rCharts](https://cran.r-project.org/package=rCharts) Interactive charts 264 | * [lattice](https://cran.r-project.org/package=lattice) Multivariate plots 265 | 266 | * [manipulate](https://cran.r-project.org/package=manipulate) Interactive plots 267 | * [misc3d](https://cran.r-project.org/package=misc3d) 3D plots 268 | * [mvtsplot](https://cran.r-project.org/package=mvtsplot) Multivariate time series plot 269 | * [pca3d](https://cran.r-project.org/package=pca3d) Three dimensional PCA plots 270 | * [longCatEDA](https://cran.r-project.org/package=longCatEDA) Plot Categorical Longitudinal and Time-Series Data 271 | * [squash](https://cran.r-project.org/package=squash) Color-based plots for multivariate visualization 272 | * [tourr](https://cran.r-project.org/package=tourr) 273 | * [latticist](https://cran.r-project.org/package=latticist) GUI for graphic exploratory data analysis using lattice 274 | * [tfplot](https://cran.r-project.org/package=tfplot) Plot time series 275 | * [pathdiagram](http://cran.r-project.org/web/packages/pathdiagram/) 276 | * [RIGHT](https://cran.r-project.org/package=RIGHT) Interactive graphics via HTML 277 | * [clickme](https://github.com/nachocab/clickme) Interactive plots 278 | 279 | * [animation](https://cran.r-project.org/package=animation) Create animations 280 | 281 | * [calibrate](https://cran.r-project.org/package=calibrate) Axes calibration 282 | * [labeling](https://cran.r-project.org/package=labeling) Axis labeling 283 | * [directlabels](https://cran.r-project.org/package=directlabels) Labels for multicolor plots. See also `Hmisc:::labcurve`. 284 | * [gplots](https://cran.r-project.org/package=gplots) Useful plotting tools 285 | * [magicaxis](https://cran.r-project.org/package=magicaxis) Pretty scientific plots (e.g. log scales) 286 | * [PlotRegionHighlighter](https://cran.r-project.org/package=PlotRegionHighlighter) Creates an envelope that surrounds a set of points 287 | * [compactr](http://cran.us.r-project.org/web/packages/compactr/index.html) Plots with compact axis notation 288 | * [plotflow](https://github.com/trinker/plotflow) Useful plotting functions 289 | * [sendplot](https://cran.r-project.org/package=sendplot) Interactive plots with tool-tip content 290 | * [zoom](https://cran.r-project.org/package=zoom) Allow to zoom/navigate in any plot. 291 | * [Hmisc](https://cran.r-project.org/package=Hmisc) 292 | * [epade](https://cran.r-project.org/package=epade) Easy plots 293 | * [prettyGraphs](https://cran.r-project.org/package=prettyGraphs) Publication-quality graphics. 294 | * [scagnostics](https://cran.r-project.org/package=scagnostics) Scatterplot diagnostics 295 | 296 | 297 | 298 | ### Colour 299 | 300 | * [colorRamps](https://cran.r-project.org/package=colorRamps) Colour palettes 301 | * [RColorBrewer](https://cran.r-project.org/package=RColorBrewer) 302 | * [colorspace](https://cran.r-project.org/package=colorspace) HCL (perceptually-based) palettes 303 | * [colortools](https://cran.r-project.org/package=colortools) 304 | * [plotKML](https://cran.r-project.org/package=plotKML) Colour palettes for mapping 305 | * [gplots](https://cran.r-project.org/package=gplots) Rich.colors palettes 306 | 307 | 308 | 309 | * [dataview](https://cran.r-project.org/package=dataview) 310 | * [tabplot](https://cran.r-project.org/package=tabplot) Large datasets viz. 311 | * [tabplotd3](https://cran.r-project.org/package=tabplotd3) Interactive 312 | * [R2SWF](https://cran.r-project.org/package=R2SWF) Convert R graphics to Flash 313 | * [sendplot](https://cran.r-project.org/package=sendplot) Send interactive plots with tooltip content 314 | * [sjPlot](https://cran.r-project.org/package=sjPlot) 315 | * [squash](https://cran.r-project.org/package=squash) Color-based plots for multivariate visualization 316 | 317 | 318 | 319 | 320 | 321 | ## Reproducible Research - Report generation 322 | 323 | 324 | Check also CRAN Task View on [Reproducible Research](http://cran.r-project.org/web/views/ReproducibleResearch.html). 325 | 326 | * [brew](https://cran.r-project.org/package=brew) 327 | * [knitr](https://cran.r-project.org/package=knitr) Dynamic report generation 328 | * [knitrBootstrap](https://github.com/jimhester/knitrBootstrap) create bootstrap styled HTML reports from Rmarkdown 329 | * [reports](https://cran.r-project.org/package=reports) writing reports and presentations 330 | * [repmis](https://cran.r-project.org/package=repmis) 331 | * [rapport](http://cran.r-project.org/web/packages/rapport/index.html) report templating system 332 | * [pander](https://cran.r-project.org/package=pander) Exploits pandoc to convert among multiple formats 333 | * [stargazer](https://cran.r-project.org/package=stargazer) Easily create tables with regression outputs (directly from model objects) 334 | * [rtf](http://cran.r-project.org/web/packages/rtf/index.html) Produce Rich Text Format documents from R 335 | * [R2HTML](http://cran.r-project.org/web/packages/R2HTML/index.html) HTML reports from R 336 | * [xtable](http://cran.r-project.org/web/packages/xtable/index.html) Export R objects to HTML tables 337 | * [R2wd](https://cran.r-project.org/package=R2wd) Write MS-Word documents from R 338 | * [rmarkdown](https://cran.r-project.org/package=rmarkdown) 339 | * [sjPlot](https://cran.r-project.org/package=sjPlot) 340 | * [Rgitbook](https://github.com/jbryer/Rgitbook) 341 | * [table1xls](http://cran.r-project.org/web/packages/table1xls/index.html) Summary tables in Excel format. 342 | * [DescTools](http://cran.r-project.org/web/packages/DescTools/index.html) 343 | * [rctrack](http://www.stjuderesearch.org/site/depts/biostats/rctrack) 344 | 345 | 346 | 347 | 348 | ## Parallelisation & Big Data 349 | 350 | 351 | Check also [CRAN Task View on High Performance Computing](http://cran.r-project.org/web/views/HighPerformanceComputing.html). 352 | 353 | * [ff](https://cran.r-project.org/package=ff) Big data management. See also package `ffbase` 354 | * [batch](https://cran.r-project.org/package=batch) Batching routines in parallel 355 | * [bigdata](https://cran.r-project.org/package=bigdata) 356 | 357 | 358 | 359 | ## Niche & Species Distribution Modelling 360 | 361 | 362 | * [rgbif](https://cran.r-project.org/package=rgbif) Access to GBIF data 363 | * [spocc](https://cran.r-project.org/package=spocc) Species occurrence data retrieval and mapping 364 | * [dismo](https://cran.r-project.org/package=dismo) Distribution modelling 365 | * [SDMTools](http://www.rdocumentation.org/packages/SDMTools) 366 | * [adehabitatHS](http://cran.r-project.org/web/packages/adehabitatHS/index.html) 367 | * [biomod2](https://cran.r-project.org/package=biomod2) SDM ensembles 368 | * [hSDM](https://cran.r-project.org/package=hSDM) Bayesian SDM 369 | * [maxlike](https://cran.r-project.org/package=maxlike) SDM for presence-only data 370 | * [MigClim](https://cran.r-project.org/package=MigClim) Implements dispersal in SDMs 371 | * [GRaF](https://cran.r-project.org/package=GRaF) SDM using latent Gaussian random fields 372 | * [SightabilityModel](https://cran.r-project.org/package=SightabilityModel) 373 | * [EnvNicheR](https://cran.r-project.org/package=EnvNicheR) 374 | * [RinSp](http://cran.r-project.org/web/packages/RInSp/) Ecological niche metrics to measure individual specialization 375 | * [bdvis](https://github.com/vijaybarve/bdvis) Biodiversity data visualization 376 | * [phyloclim](https://cran.r-project.org/package=phyloclim) Includes functions for calculating niche overlap 377 | * [phylospacer](https://cran.r-project.org/package=phylospacer) Phyloclimates and phylomorphospaces 378 | * [PresenceAbsence](https://cran.r-project.org/package=PresenceAbsence) 379 | * [mboost](https://cran.r-project.org/package=mboost) Decomposing environmental, spatial, and spatiotemporal components of species distributions (Hothorn et al. 2011 Ecol Monogr) 380 | * [usdm](http://www.rdocumentation.org/packages/usdm) Uncertainty analysis for species distribution models, esp. focused on positional uncertainty 381 | * [ModelMap](http://cran.r-project.org/web/packages/ModelMap/) Random Forest and Stochastic Gradient Boosting Models 382 | * [modEVA](http://modtools.wordpress.com) 383 | * [rangemapper](https://cran.r-project.org/package=rangemapper) 384 | * [comclim](http://cran.r-project.org/web/packages/comclim/index.html) Community climate statistics 385 | * [hypervolume](http://cran.r-project.org/web/packages/hypervolume/index.html) Modeling hypervolumes (species' niches) 386 | * [ppmlasso](https://cran.r-project.org/package=ppmlasso) Point process models 387 | * [sdmvspecies](https://cran.r-project.org/package=sdmvspecies) Create virtual species for SDM 388 | * [virtualspecies](http://borisleroy.com/virtualspecies/) Create virtual species 389 | * [coenocline](https://cran.r-project.org/package=coenocline) Simulate species presence and abundance along environmental gradients 390 | * [ecospat](http://cran.r-project.org/web/packages/ecospat/index.html) Many useful functions for niche & SDM (by A. Guisan's group) 391 | * [comclim](https://cran.r-project.org/package=comclim) 392 | * [Metadata](https://cran.r-project.org/package=Metadata) 393 | * [ENiRG](http://cran.r-project.org/web/packages/ENiRG/index.html) 394 | 395 | 396 | 397 | ### Occupancy modelling 398 | 399 | * [detect](https://cran.r-project.org/package=detect) Occupancy modelling 400 | * [marked](https://cran.r-project.org/package=marked) 401 | * [unmarked](https://cran.r-project.org/package=unmarked) 402 | * [stocc](https://cran.r-project.org/package=stocc) Occupancy modeling 403 | * [hierarchicalDS](https://cran.r-project.org/package=hierarchicalDS) hierarchical analysis of distance sampling data 404 | 405 | 406 | 407 | ## Remote Sensing 408 | 409 | * [RStoolbox](https://github.com/bleutner/RStoolbox) 410 | * [moveVis](https://github.com/16EAGLE/moveVis) 411 | * [earthEngineGrabR](https://github.com/JesJehle/earthEngineGrabR) 412 | * [rsMove](https://github.com/RRemelgado/rsMove) 413 | * [satellite](https://github.com/environmentalinformatics-marburg/satellite) 414 | * [satelliteTools](https://github.com/environmentalinformatics-marburg/satelliteTools) 415 | * [uavRst](https://github.com/gisma/uavRst) 416 | * [fieldRS](https://github.com/RRemelgado/fieldRS) 417 | * [cropPhenology](https://github.com/SofanitAraya/CropPhenology) 418 | * [rTIMESAT](https://github.com/kongdd/rTIMESAT) 419 | * [luna](https://github.com/rspatial/luna) 420 | * [rabbiTS](https://github.com/16EAGLE/rabbiTS) 421 | * [theiaR](https://github.com/norival/theiaR) 422 | * [sentinel2](https://github.com/IVFL-BOKU/sentinel2) 423 | * [getSpatialData](https://github.com/16EAGLE/getSpatialData) 424 | * [sen2r](https://github.com/ranghetti/sen2r) 425 | * [S2utils](https://github.com/bbrede/S2utils) 426 | * [SentinelAPI](https://github.com/mattjbayly/SentinelAPI) 427 | * [RGISTools](https://github.com/spatialstatisticsupna/RGISTools) 428 | 429 | 430 | 431 | 432 | 433 | 434 | ## Climate 435 | 436 | 437 | 438 | * [BerkeleyEarth](http://cran.r-project.org/web/packages/BerkeleyEarth/index.html) Climate data from Berkeley Earth database 439 | * [climates](https://cran.r-project.org/package=climates) Tools for climate data (bioclim, downscaling, interpolation...) 440 | * [climatol](https://cran.r-project.org/package=climatol) Homogenisation of climate time series 441 | * [climstats](https://cran.r-project.org/package=climstats) Tools for climate data 442 | * [RMAWGEN](https://cran.r-project.org/package=RMAWGEN) Generate daily time series from monthly mean values 443 | * [climdex.pcic](https://cran.r-project.org/package=climdex.pcic) Computation of climate indices 444 | * [ClimClass](http://cran.r-project.org/web/packages/ClimClass/index.html) Climate Classification according to various indices 445 | * [RClimMAWGEN](https://cran.r-project.org/package=RClimMAWGEN) generate time series of climate indices 446 | * [chillR](https://cran.r-project.org/package=chillR) Climate and phenology analysis 447 | * [rWBclimate](https://cran.r-project.org/package=rWBclimate) Lots of historical data and future projections 448 | * [rnoaa](https://cran.r-project.org/package=rnoaa) 449 | * [rghcnV3](https://cran.r-project.org/package=rghcnV3) GHCN 450 | * [RNCEP](https://cran.r-project.org/package=RNCEP) weather data 451 | * [sirad](https://cran.r-project.org/package=sirad) Evapotranspiration etc 452 | * [SPEI](https://cran.r-project.org/package=SPEI) Calculates Standardised Precipitation-Evaporation Index 453 | * [SPI](https://cran.r-project.org/package=SPI) 454 | * [weathermetrics](https://cran.r-project.org/package=weathermetrics) 455 | * [raincpc](https://cran.r-project.org/package=raincpc) Rainfall data 456 | * [Evapotranspiration](http://cran.r-project.org/web/packages/Evapotranspiration/index.html) 457 | * [GhcnDaily](http://cran.r-project.org/web/packages/GhcnDaily/index.html) 458 | * [crn](http://cran.r-project.org/web/packages/crn/index.html) Get data from Climate Reference Network 459 | * [iki.dataclim](http://cran.r-project.org/web/packages/iki.dataclim/index.html) 460 | * [FedData](http://cran.r-project.org/web/packages/FedData/index.html) 461 | * [stationaRy](https://github.com/rich-iannone/stationaRy) Hourly data worldwide 462 | * [tempcyclesdata](https://cran.r-project.org/web/packages/tempcyclesdata/index.html) Temperature data for ca. 8000 stations 1975-2013 463 | 464 | 465 | ## GIS/spatial functionality 466 | 467 | 468 | 469 | Check also CRAN Task View on [Spatial](http://cran.r-project.org/web/views/Spatial.html) and [Spatiotemporal](http://cran.r-project.org/web/views/SpatioTemporal.html) data. 470 | Check also CRAN Task View on [Web technologies](http://cran.r-project.org/web/views/WebTechnologies.html) for access to many GIS data. 471 | 472 | 473 | * [sp](https://cran.r-project.org/package=sp) 474 | * [spacetime](https://cran.r-project.org/package=spacetime) 475 | * [spatial](https://cran.r-project.org/package=spatial) 476 | * [rgeos](https://cran.r-project.org/package=rgeos) 477 | * [rgdal](https://cran.r-project.org/package=rgdal) 478 | * [raster](https://cran.r-project.org/package=raster) 479 | * [rasterVis](https://cran.r-project.org/package=rasterVis) 480 | * [rts](https://cran.r-project.org/package=rts) Raster time series 481 | * [spatial.tools](https://cran.r-project.org/package=spatial.tools) Functions for raster processing, including parallel processing 482 | * [maptools](https://cran.r-project.org/package=maptools) Reading and manipulating geographic data 483 | * [PBSmapping](https://cran.r-project.org/package=PBSmapping) 484 | * [taRifx.geo](https://cran.r-project.org/package=taRifx.geo) Useful spatial functions 485 | 486 | * [climstats](https://cran.r-project.org/package=climstats) Tools for climate and raster analyses 487 | 488 | * [countrycode](https://cran.r-project.org/package=countrycode) Converts country codes 489 | * [cshapes](https://cran.r-project.org/package=cshapes) Dataset of country boundaries 490 | * [gdistance](https://cran.r-project.org/package=gdistance) Calculate distances and routes on grids 491 | * [geometry](https://cran.r-project.org/package=geometry) Mesh generation and surface tesselation 492 | * [geosphere](https://cran.r-project.org/package=geosphere) Several GIS tools, esp. aimed at large scales (global) 493 | * [geonames](https://cran.r-project.org/package=geonames) 494 | * [mapproj](https://cran.r-project.org/package=mapproj) Converts lat-lon data into projected coordinates 495 | * [geospacom](https://cran.r-project.org/package=geospacom) Generates distance matrices from shape files and represents spatially weighted multilevel analysis results 496 | 497 | * [dismo](https://cran.r-project.org/package=dismo) 498 | * [fossil](https://cran.r-project.org/package=fossil) 499 | 500 | * [ggmap](https://cran.r-project.org/package=ggmap) Plotting on Google Maps and OpenStreetMap 501 | * [GISTools](https://cran.r-project.org/package=GISTools) Some further GIS tools (e.g. cloropleth maps) 502 | * [mapplots](https://cran.r-project.org/package=mapplots) Data visualisation on maps 503 | * [maps](https://cran.r-project.org/package=maps) Mapping tools 504 | * [OpenStreetMap](https://cran.r-project.org/package=OpenStreetMap) Access to OpenStreetMap and Bing images 505 | * [osmar](https://cran.r-project.org/package=osmar) 506 | * [plotGoogleMaps](https://cran.r-project.org/package=plotGoogleMaps) 507 | * [RgoogleMaps](https://cran.r-project.org/package=RgoogleMaps) 508 | * [R2G2](https://cran.r-project.org/package=R2G2) Plot anything in Google Earth 509 | * [rCarto](https://cran.r-project.org/package=rCarto) useful functions for mapping 510 | * [marmap](https://cran.r-project.org/package=marmap) working with bathymetric and topographic data 511 | * [plotKML](https://cran.r-project.org/package=plotKML) Visualization of spatial and spatio-temporal objects in Google Earth 512 | * [MODISTools](http://cran.r-project.org/web/packages/MODISTools/) 513 | * [spGoogle](http://cran.r-project.org/web/packages/spGoogle) Interacting R with Google maps 514 | * [rMaps](https://cran.r-project.org/package=rMaps) Interactive maps 515 | * [leafletR](https://cran.r-project.org/package=leafletR) 516 | * [GEOmap](https://cran.r-project.org/package=GEOmap) 517 | * [rworldmap](https://cran.r-project.org/package=rworldmap) 518 | * [choroplethr](https://cran.r-project.org/package=choroplethr) 519 | * [mapmisc](http://cran.r-project.org/web/packages/mapmisc/index.html) Utilities for producing maps 520 | * [sinkr](https://github.com/menugget/sinkr) Some GIS functions and colour palettes 521 | 522 | * [rlandscape](https://cran.r-project.org/package=rlandscape) Generates spatial landscapes 523 | 524 | * [RSAGA](https://cran.r-project.org/package=RSAGA) 525 | * [spgrass6](https://cran.r-project.org/package=spgrass6) 526 | * [spsextante](https://cran.r-project.org/package=spsextante) 527 | * [RPyGeo](https://cran.r-project.org/package=RPyGeo) 528 | 529 | 530 | 531 | 532 | 533 | ## Spatial Analysis 534 | 535 | 536 | Check also CRAN Task View on [Spatial](http://cran.r-project.org/web/views/Spatial.html) and [Spatiotemporal](http://cran.r-project.org/web/views/SpatioTemporal.html) data. 537 | 538 | * [akima](https://cran.r-project.org/package=akima) Interpolation 539 | * [automap](https://cran.r-project.org/package=automap) Automatic interpolation (kriging) 540 | * [ecespa](https://cran.r-project.org/package=ecespa) Point pattern analysis 541 | * [fields](https://cran.r-project.org/package=fields) Splines, kriging, etc 542 | * [geoR](https://cran.r-project.org/package=geoR) Geostatistical analysis 543 | * [geoRglm](https://cran.r-project.org/package=geoRglm) Spatial GLMs 544 | * [geospt](https://cran.r-project.org/package=geospt) Geostatistics 545 | * [GeoXP](https://cran.r-project.org/package=GeoXP) Interactive exploratory analysis of spatial data 546 | * [gstat](https://cran.r-project.org/package=gstat) Geostatistics (variograms, kriging) 547 | * [intamap](https://cran.r-project.org/package=intamap) Automatic spatial interpolation 548 | * [geostatsp](https://cran.r-project.org/package=geostatsp) Geostatistics using SpatialPoints and rasters 549 | * [spatstat](https://cran.r-project.org/package=spatstat) 550 | * [spBayes](https://cran.r-project.org/package=spBayes) 551 | * [spdep](https://cran.r-project.org/package=spdep) Modeling spatial dependence 552 | * [stpp](https://cran.r-project.org/package=stpp) Point patterns 553 | * [rtop](https://cran.r-project.org/package=rtop) Spatial interpolation of data 554 | 555 | 556 | 557 | ## Networks 558 | 559 | * [bipartite](https://cran.r-project.org/package=bipartite) 560 | * [igraph](https://cran.r-project.org/package=igraph) Network analysis and visualization 561 | * [enaR](https://cran.r-project.org/package=enaR) 562 | * [qgraph](https://cran.r-project.org/package=qgraph) 563 | 564 | 565 | 566 | 567 | ## Phylogenetics, phylogeography & comparative analysis 568 | 569 | 570 | Check also [Phylogenetics CRAN task view](http://cran.r-project.org/web/views/Phylogenetics.html). 571 | 572 | * [ape](https://cran.r-project.org/package=ape) 573 | * [adephylo](http://cran.r-project.org/web/packages/adephylo/index.html) Exploratory analysis 574 | * [Treesim]() Tree simulation. See also [treesimGM](https://cran.r-project.org/package=Treesim]() Tree simulation. See also [treesimGM) 575 | * [cladoRcpp](https://cran.r-project.org/package=cladoRcpp) Phylogenetic analysis of geographic ranges 576 | * [caper](https://cran.r-project.org/package=caper) Comparative analysis 577 | * [PVR](https://cran.r-project.org/package=PVR) Phylogenetic Eigenvector Regression 578 | * [BEDASSLE](http://cran.r-project.org/web/packages/BEDASSLE/) Disentangles the effects of geographic and ecological isolation on genetic differentiation 579 | * [geiger](https://cran.r-project.org/package=geiger) 580 | * [geoscale](https://cran.r-project.org/package=geoscale) Geological timescale 581 | * [phangorn](https://cran.r-project.org/package=phangorn) 582 | * [phytools](https://cran.r-project.org/package=phytools) 583 | * [pegas](https://cran.r-project.org/package=pegas) 584 | * [picante](https://cran.r-project.org/package=picante) 585 | * [stratigraph](https://cran.r-project.org/package=stratigraph) 586 | * [treebase](https://cran.r-project.org/package=treebase) 587 | * [MCMCglmm](https://cran.r-project.org/package=MCMCglmm) 588 | 589 | 590 | 591 | 592 | 593 | ## Palaeoecology 594 | 595 | * [Bchron](https://cran.r-project.org/web/packages/Bchron/index.html) Bayesian chronologies 596 | * [Bclim](https://cran.r-project.org/web/packages/Bclim/index.html) Palaeoclimate reconstruction 597 | 598 | 599 | 600 | ## Dendrochronology 601 | 602 | * [dplR](https://github.com/cran/dplR) Dendrochronology 603 | * [measuRing](https://github.com/cran/measuRing) Measuring ring width from scanned images. 604 | * [TRADER](https://github.com/pavel-fibich/TRADER) Tree Ring Analysis of Disturbance Events 605 | * [dendrobox](https://github.com/cszang/dendrobox) Interactive Tree-Ring Data Exploration Tool 606 | * [treeclim](https://github.com/cszang/treeclim) Modeling tree-climate relationships. 607 | * [bootRes](https://github.com/cszang/bootRes) Bootstrapped response functions. 608 | * [rwtocore](https://github.com/ltrr-arizona-edu/rwtocore) convert tree-ring measurements to drawings of cores (Ruby). 609 | * [triforce](https://github.com/ltrr-arizona-edu/triforce) read the TRiDaS dendrochronological standard and communicate with Tellervo servers. 610 | * [pointRes](https://cran.r-project.org/web/packages/pointRes/index.html) Calculate and plot pointer years 611 | * [BIOdry](https://cran.r-project.org/web/packages/BIOdry/index.html) Multilevel Modeling of Dendroclimatical Fluctuations 612 | * [sclero](https://cran.r-project.org/web/packages/sclero/) Measure Growth Patterns and Align Sampling Spots in Photographs 613 | * [dendrometeR](https://cran.r-project.org/web/packages/dendrometeR/) Analyzing Dendrometer Data. 614 | * [wvtool](https://cran.r-project.org/package=wvtool) Image Tools for Automated Wood Identification 615 | * [DendroSync](https://cran.r-project.org/web/packages/DendroSync/index.html) Calculating Spatial Synchrony Between Tree-Ring Chronologies 616 | * [iadf](https://cran.r-project.org/web/packages/iadf/index.html) Analysis of Intra Annual Density Fluctuations 617 | * [dendroExtra](https://cran.r-project.org/package=dendroExtra) Finds the optimal sequence of days that are linearly or nonlinearly related to one or more tree-ring proxy records. 618 | 619 | 620 | 621 | 622 | 623 | ## Ecological analyses (miscellaneous) 624 | 625 | Check also [Environmetrics CRAN Task View](http://cran.r-project.org/web/views/Environmetrics.html). 626 | 627 | 628 | * [betapart](https://cran.r-project.org/package=betapart) Beta diversity 629 | * [BiodiversityR](https://cran.r-project.org/package=BiodiversityR) GUI for biodiversity, suitability and community ecology analyses 630 | * [cheddar](https://cran.r-project.org/package=cheddar) Analysis and visualisation of community data 631 | * [coexist](https://cran.r-project.org/package=coexist) Modelling species coexistence 632 | * [DSpat](https://cran.r-project.org/package=DSpat) Distance Sampling 633 | * [fossil](https://cran.r-project.org/package=fossil) Species richness, species-area curves, beta-diversity 634 | * [indicspecies](https://cran.r-project.org/package=indicspecies) Assess associations between different species and sites (e.g. indicator species) 635 | * [IPMpack](https://cran.r-project.org/package=IPMpack) Integral Projection Models 636 | * [marked](https://cran.r-project.org/package=marked) Mark-recapture analysis 637 | * [MBI](https://cran.r-project.org/package=MBI) Multiple Beta Diversity indices 638 | * [rmeta](https://cran.r-project.org/package=rmeta) Meta-analysis 639 | * [neighlikeli](https://cran.r-project.org/package=neighlikeli) Neighborhood models 640 | * [earlywarnings](https://cran.r-project.org/package=earlywarnings) 641 | * [MAR1](https://cran.r-project.org/package=MAR1) Multivariate Autoregressive Modeling for Analysis of Community Time-Series Data 642 | * [ncbit](https://cran.r-project.org/package=ncbit) retrieve NBCI taxonomic data 643 | * [spacodiR](https://cran.r-project.org/package=spacodiR) Spatial and Phylogenetic Analysis of Community Diversity 644 | * [Reol](http://cran.r-project.org/web/packages/Reol/) Interface to Encyclopedia of Life 645 | * [SPECIES](https://cran.r-project.org/package=SPECIES) Species richness and diversity analysis 646 | * [BayesComm](https://cran.r-project.org/package=BayesComm) Bayesian multivariate binary regression models for analysis of ecological communities 647 | * [pom](https://cran.r-project.org/package=pom) Patch occupancy models 648 | * [capwire](https://cran.r-project.org/package=capwire) Population size estimation from non-invasive sampling 649 | * [vegclust](https://cran.r-project.org/package=vegclust) Fuzzy clustering of vegetation data 650 | * [popbio](https://cran.r-project.org/package=popbio) 651 | * [demoniche](http://demoniche.r-forge.r-project.org/) Spatially-explicit demographic modelling 652 | * [BEDASSLE](https://cran.r-project.org/package=BEDASSLE) Disentangles the effects of geographic and ecological isolation on genetic differentiation. 653 | * [rphylopic](https://github.com/sckott/rphylopic) Organisms silhouettes 654 | * [GSIF](https://cran.r-project.org/package=GSIF) Global Soil Information 655 | * [Rarity](https://cran.r-project.org/package=Rarity) Rarity indices 656 | * [taxize](https://cran.r-project.org/package=taxize) Taxonomy etc. 657 | * [Taxonstand](https://cran.r-project.org/package=Taxonstand) 658 | * [sExtinct](https://cran.r-project.org/package=sExtinct) Extinction analysis based on sightings 659 | * [BEDASSLE](http://cran.r-project.org/web/packages/BEDASSLE/) Disentangles the effects of geographic and ecological isolation on genetic differentiation 660 | * [ecomodtools](https://cran.r-project.org/package=ecomodtools) Simulation models (inc. dispersal) 661 | * [comclim](http://cran.r-project.org/web/packages/comclim/index.html) Community climate statistics 662 | * [kernelPop](http://cran.r-project.org/web/packages/kernelPop/index.html) Spatially explicit population genetic simulations 663 | * [siplab](http://cran.r-project.org/web/packages/siplab/index.html) spatially explicit individual-based vegetation models. 664 | 665 | 666 | ## Miscellaneous 667 | 668 | 669 | * [digitize](https://cran.r-project.org/package=digitize) Extract data from plots 670 | * [downloader](https://cran.r-project.org/package=downloader) Download files from internet 671 | * [hwriter](https://cran.r-project.org/package=hwriter) Outputs R objects in HTML format 672 | * [installr](https://cran.r-project.org/package=installr) Automatically update R 673 | * [mail](https://cran.r-project.org/package=mail) Send email notifications from R 674 | * [sendmailR](https://cran.r-project.org/package=sendmailR) 675 | * [mosaic](https://cran.r-project.org/package=mosaic) 676 | * [audiolyzR](https://cran.r-project.org/package=audiolyzR) Creates audio representations of common plots 677 | * [WebDevelopR](https://cran.r-project.org/package=WebDevelopR) Web development 678 | * [ProjectTemplate](https://cran.r-project.org/package=ProjectTemplate) 679 | * [gpk](https://cran.r-project.org/package=gpk) Datasets for educational uses 680 | * [NCmisc](http://cran.r-project.org/web/packages/NCmisc/) 681 | * [PubMedWordcloud](https://cran.r-project.org/package=PubMedWordcloud) Create wordcloud with abstracts. 682 | * [alm](https://cran.r-project.org/package=alm) Altmetrics 683 | * [rAltmetric](https://cran.r-project.org/package=rAltmetric) Retrieves data from altmetrics.com 684 | * [RMendeley](https://cran.r-project.org/package=RMendeley) 685 | * [rcrossref](https://cran.r-project.org/package=rcrossref) 686 | * [RefManageR](https://cran.r-project.org/package=RefManageR) Bibliography Management. 687 | * [refnet](https://cran.r-project.org/package=refnet) Reads and works with data from ISI Web of Knowledge 688 | * [scholar](https://cran.r-project.org/package=scholar) 689 | * [slidify](https://cran.r-project.org/package=slidify) 690 | * [sos](https://cran.r-project.org/package=sos) Search R packages 691 | * [source.gist](https://cran.r-project.org/package=source.gist) 692 | * [twitteR](https://cran.r-project.org/package=twitteR) 693 | * [DescTools](http://cran.r-project.org/web/packages/DescTools/index.html) 694 | 695 | 696 | 697 | ## R programming 698 | 699 | 700 | * [codetools](https://cran.r-project.org/package=codetools) Code analysis tools 701 | * [compiler](https://cran.r-project.org/package=compiler) Compile R code (e.g. a function) to speed it up 702 | * [devtools](https://cran.r-project.org/package=devtools) 703 | * [formatR](https://cran.r-project.org/package=formatR) Format and tidy R code 704 | * [gtools](https://cran.r-project.org/package=gtools) Useful functions (e.g. mixedsort) 705 | * [inline](https://cran.r-project.org/package=inline) Define functions in C code within R 706 | * [iterators](https://cran.r-project.org/package=iterators) Tools for iteration on many different types of objects (see also `itertools`) 707 | * [Kmisc](https://cran.r-project.org/package=Kmisc) Data reshaping, table and plot generation from RMarkdown 708 | * [operators](https://cran.r-project.org/package=operators) Additional operators 709 | * [simFrame](https://cran.r-project.org/package=simFrame) A framework to work with simulations 710 | * [simSummary](https://cran.r-project.org/package=simSummary) 711 | * [staticdocs](https://cran.r-project.org/package=staticdocs) Create webpage with package documentation 712 | * [testit](https://cran.r-project.org/package=testit) Testing R packages 713 | * [testthat](https://cran.r-project.org/package=testthat) Testing R code 714 | * [tester](https://cran.r-project.org/package=tester) Test characteristics of R objects 715 | * [assertthat](https://cran.r-project.org/package=assertthat). 716 | * [httr](https://cran.r-project.org/package=httr) Working with URLs and HTTP 717 | * [RCurl](https://cran.r-project.org/package=RCurl) HTTP interface 718 | * [stringr](https://cran.r-project.org/package=stringr) 719 | * [Rd2Roxygen](https://cran.r-project.org/package=Rd2Roxygen) 720 | * [Rxoygen2](https://cran.r-project.org/package=Rxoygen2) 721 | * [scrapeR](https://cran.r-project.org/package=scrapeR) 722 | * [aprof](http://cran.r-project.org/web/packages/aprof/index.html) Profiling code and visualizing results to evaluate where is best to focus code optimization. 723 | * [regex](https://github.com/richierocks/regex) Regular expressions made easier. 724 | 725 | 726 | 727 | 728 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | [] 2 | - [My directory of R packages for data analysis and visualization, 3 | Bayesian statistics, mapping, GIS, climate, Species Distribution 4 | Modelling, ecology, biogeography, evolution, reproducible 5 | science…](#my-directory-of-r-packages-for-data-analysis-and-visualization-bayesian-statistics-mapping-gis-climate-species-distribution-modelling-ecology-biogeography-evolution-reproducible-science) 6 | - [Data sources](#data-sources) 7 | - [Data management](#data-management) 8 | - [General statistics](#general-statistics) 9 | - [Ordination & Multivariate 10 | Analysis](#ordination-multivariate-analysis) 11 | - [Survival analysis](#survival-analysis) 12 | - [Regression tools](#regression-tools) 13 | - [Bayesian/MCMC](#bayesianmcmc) 14 | - [Plotting & Visualisation](#plotting-visualisation) 15 | - [GGPLOT2](#ggplot2) 16 | - [Colour](#colour) 17 | - [Reproducible Research - Report 18 | generation](#reproducible-research---report-generation) 19 | - [Parallelisation & Big Data](#parallelisation-big-data) 20 | - [Niche & Species Distribution 21 | Modelling](#niche-species-distribution-modelling) 22 | - [Occupancy modelling](#occupancy-modelling) 23 | - [Remote Sensing](#remote-sensing) 24 | - [Climate](#climate) 25 | - [GIS/spatial functionality](#gisspatial-functionality) 26 | - [Spatial Analysis](#spatial-analysis) 27 | - [Networks](#networks) 28 | - [Phylogenetics, phylogeography & comparative 29 | analysis](#phylogenetics-phylogeography-comparative-analysis) 30 | - [Palaeoecology](#palaeoecology) 31 | - [Dendrochronology](#dendrochronology) 32 | - [Ecological analyses 33 | (miscellaneous)](#ecological-analyses-miscellaneous) 34 | - [Miscellaneous](#miscellaneous) 35 | - [R programming](#r-programming) 36 | 37 | ## My directory of R packages for data analysis and visualization, Bayesian statistics, mapping, GIS, climate, Species Distribution Modelling, ecology, biogeography, evolution, reproducible science… 38 | 39 | [F. Rodriguez-Sanchez](http://bit.ly/frod_san) 40 | 41 | Updated 2019-10-03 42 | 43 | These are packages that I often use or, alternatively, I need only 44 | rarely but don’t want to forget about. Of course, there are many other 45 | useful packages out there (e.g. at 46 | [CRAN](http://cran.r-project.org/web/packages/available_packages_by_name.html) 47 | or 48 | [GitHub](https://github.com/search?q=package&type=Repositories&ref=advsearch&l=R). 49 | Check also [CRAN task views](http://cran.r-project.org/web/views/). 50 | 51 | ## Data sources 52 | 53 | Check [CRAN Task View on Web 54 | technologies](http://cran.r-project.org/web/views/WebTechnologies.html). 55 | 56 | ## Data management 57 | 58 | Check out this great cheatsheet: [Data wrangling with dplyr and 59 | tidyr](http://www.rstudio.com/wp-content/uploads/2015/02/data-wrangling-cheatsheet.pdf) 60 | 61 | - [rio](https://cran.r-project.org/package=rio) A Swiss-Army Knife for 62 | Data I/O 63 | - [tidyr](https://cran.r-project.org/package=tidyr) Reshape data 64 | - [reshape2](https://cran.r-project.org/package=reshape2) Reshape data 65 | from long to wide format and vice versa 66 | - [dplyr](https://cran.r-project.org/package=dplyr) Data wrangling 67 | - [data.table](https://cran.r-project.org/package=data.table) Tools 68 | for managing data frames 69 | - [gdata](https://cran.r-project.org/package=gdata) Data manipulation 70 | - [Hmisc](https://cran.r-project.org/package=Hmisc) Frank Harrell’s 71 | miscellaneous tools 72 | - [Kmisc](https://cran.r-project.org/package=Kmisc) Data reshaping, 73 | table and plot generation from RMarkdown 74 | - [lubridate](https://cran.r-project.org/package=lubridate) Dates and 75 | times 76 | - [multitable](https://cran.r-project.org/package=multitable) 77 | Manipulate multiple arrays 78 | - [datacheck](https://cran.r-project.org/package=datacheck) Tools for 79 | checking data consistency 80 | - [tabplot](https://cran.r-project.org/package=tabplot) Large datasets 81 | viz. 82 | - [tabplotd3](https://cran.r-project.org/package=tabplotd3) 83 | Interactive 84 | - [tableplot](https://cran.r-project.org/package=tableplot) 85 | - [taRifx](http://cran.r-project.org/web/packages/taRifx/index.html) 86 | Useful 87 | functions 88 | - [DescTools](http://cran.r-project.org/web/packages/DescTools/index.html) 89 | Many useful functions 90 | - [summarytools](https://cran.r-project.org/package=summarytools) 91 | Quickly summarize dataframes (inc. markdown output) 92 | 93 | ## General statistics 94 | 95 | ### Ordination & Multivariate Analysis 96 | 97 | Check also 98 | [Environmetrics](http://cran.r-project.org/web/views/Environmetrics.html) 99 | and 100 | [Multivariate](http://cran.r-project.org/web/views/Multivariate.html) 101 | CRAN Task Views. 102 | 103 | - [vegan](https://cran.r-project.org/package=vegan) 104 | - [ade4](http://cran.r-project.org/web/packages/ade4/index.html) 105 | Multivariate data analysis and display 106 | - [dave](https://cran.r-project.org/package=dave) Data Analysis in 107 | Vegetation Ecology 108 | - [ecodist](https://cran.r-project.org/package=ecodist) 109 | Dissimilarity-based analysis (ordination, Mantel tests…) 110 | - [labdsv](https://cran.r-project.org/package=labdsv) Includes 111 | plotting functions 112 | - [mvabund](https://cran.r-project.org/package=mvabund) Analysing 113 | multivariate data (upscaling from individual species models) 114 | - [boral](https://cran.r-project.org/package=boral) Bayesian 115 | ordination and regression analysis 116 | - [eigenprcomp](http://cran.r-project.org/web/packages/eigenprcomp/) 117 | Computes confidence intervals for the proportion explained by the 118 | first 1,2,k principal components 119 | 120 | ### Survival analysis 121 | 122 | - [survival](https://cran.r-project.org/package=survival) 123 | - [survMisc](https://cran.r-project.org/package=survMisc) 124 | - [coxme](https://cran.r-project.org/package=coxme) Mixed-effects cox 125 | regression 126 | - [rawr](https://cran.r-project.org/package=rawr) Plotting functions: 127 | kmplot & ggsurv 128 | 129 | ### Regression tools 130 | 131 | - [aod](https://cran.r-project.org/package=aod) Analysis of 132 | Overdispersed 133 | data 134 | - [AICcmodavg](http://cran.r-project.org/web/packages/AICcmodavg/index.html) 135 | Model selection and multimodel inference 136 | - [arm](https://cran.r-project.org/package=arm) Gelman’s package: 137 | includes bayesglm, sim, coefplot… 138 | - [bbmle](https://cran.r-project.org/package=bbmle) Tools for MLE 139 | - [binomTools](https://cran.r-project.org/package=binomTools) 140 | Diagnostics for binomial regression 141 | - [car](https://cran.r-project.org/package=car) Regression tools 142 | - [coefplot](https://cran.r-project.org/package=coefplot) Plot model 143 | coefficients 144 | - [confReg](https://cran.r-project.org/package=confReg) Estimating 145 | confidence of individual regression predictions 146 | - [COUNT](https://cran.r-project.org/package=COUNT) Regression models 147 | for count data (Poisson, Negative Binomial) 148 | - [DAAG](https://cran.r-project.org/package=DAAG) Some regression 149 | tools from the book ‘Data Analysis and Graphics using R’ 150 | - [dhglm](https://cran.r-project.org/package=dhglm) Hierarchical GLMs 151 | with random effects in both the mean and dispersion components 152 | - [dynlm](https://cran.r-project.org/package=dynlm) Dynamic linear 153 | models and time series regression 154 | - [earth](https://cran.r-project.org/package=earth) Multivariate 155 | Adaptive Regression Splines 156 | - [effects](https://cran.r-project.org/package=effects) Displays 157 | effects estimated from regression models 158 | - [emdbook](https://cran.r-project.org/package=emdbook) Tools from 159 | ‘Ecological Models and Data’ (inc. several plotting functions) 160 | - [fit.models](https://cran.r-project.org/package=fit.models) Compare 161 | results from different models 162 | - [FME](https://cran.r-project.org/package=FME) Modelling tools 163 | - [gam](https://cran.r-project.org/package=gam) Generalised Additive 164 | Models (GAMs) 165 | - [gamm4](https://cran.r-project.org/package=gamm4) GAMMs 166 | - [gbm](https://cran.r-project.org/package=gbm) Generalised Boosted 167 | regression models 168 | - [gee](https://cran.r-project.org/package=gee) Generalized Estimating 169 | Equations 170 | - [glm2](https://cran.r-project.org/package=glm2) To fit GLMs with 171 | convergence problems 172 | - [MuMIn](https://cran.r-project.org/package=MuMIn) Model selection 173 | and averaging 174 | - [glmulti](https://cran.r-project.org/package=glmulti) Model 175 | selection and multimodel inference 176 | - [gnm](https://cran.r-project.org/package=gnm) Generalized nonlinear 177 | models 178 | - [heatmapFit](https://cran.r-project.org/package=heatmapFit) Checking 179 | logistic regression goodness of fit 180 | - [hier.part](https://cran.r-project.org/package=hier.part) Variance 181 | partitioning to assess ‘importance’ of predictors. See also 182 | `relaimpo`. 183 | - [relaimpo](https://cran.r-project.org/package=relaimpo) Relative 184 | importance of predictors 185 | - [nlme](https://cran.r-project.org/package=nlme) Mixed models 186 | - [lme4](https://cran.r-project.org/package=lme4) Mixed models 187 | - [pamm](https://cran.r-project.org/package=pamm) Power analysis for 188 | mixed models 189 | - [odprism](https://cran.r-project.org/package=odprism) Power analysis 190 | for mixed models 191 | - [likelihood](https://cran.r-project.org/package=likelihood) Maximum 192 | Likelihood Estimation 193 | - [lmtest](https://cran.r-project.org/package=lmtest) Diagnostic 194 | checks for linear regression 195 | - [MARSS](https://cran.r-project.org/package=MARSS) Multivariate 196 | Autoregressive State-Space Modeling 197 | - [MCMCglmm](https://cran.r-project.org/package=MCMCglmm) Mixed models 198 | fitted by MCMC 199 | - [mgcv](https://cran.r-project.org/package=mgcv) GAM fitting 200 | - [miscF](https://cran.r-project.org/package=miscF) Multivariate 201 | Normal regression, spatial Bayesian mixed models, piecewise 202 | regression… 203 | - [mlogit](https://cran.r-project.org/package=mlogit) Multinomial 204 | regression 205 | - [mvinfluence](https://cran.r-project.org/package=mvinfluence) 206 | Influence Measures and Diagnostic Plots for Multivariate Linear 207 | Models 208 | - [msm](https://cran.r-project.org/package=msm) Multi-state Markov and 209 | hidden Markov models in continuous time 210 | - [PCovR](https://cran.r-project.org/package=PCovR) Principal 211 | Covariates Regression (Reducing collinear predictor variables to a 212 | few components and regressing on them) 213 | - [HLMdiag](https://cran.r-project.org/package=HLMdiag) Diagnostic 214 | tools for hierarchical models (fitted with lme4) 215 | - [stremo](https://cran.r-project.org/package=stremo) Learning 216 | Structural Equation Models 217 | - [rockchalk](https://cran.r-project.org/package=rockchalk) Regression 218 | Estimation and Presentation 219 | - [R2STATS](https://cran.r-project.org/package=R2STATS) GUI for 220 | fitting and comparing GLM and GLMM in 221 | R 222 | - [LMERConvenienceFunctions](https://cran.r-project.org/package=LMERConvenienceFunctions) 223 | - [R2admb](https://cran.r-project.org/package=R2admb) 224 | - [rms](https://cran.r-project.org/package=rms) Regression modeling 225 | strategies 226 | - [Zelig](https://cran.r-project.org/package=Zelig) 227 | 228 | ### Bayesian/MCMC 229 | 230 | Check also [Bayesian CRAN Task 231 | View](http://cran.r-project.org/web/views/Bayesian.html). 232 | 233 | - [rstanarm](https://cran.r-project.org/package=rstanarm) 234 | - [blme](https://cran.r-project.org/package=blme) Bayesian multilevel 235 | models 236 | - [BMA](https://cran.r-project.org/package=BMA) Model averaging 237 | - [dclone](https://cran.r-project.org/package=dclone) Data cloning and 238 | MCMC tools (inc. JAGS functions) 239 | - [dcmle](https://cran.r-project.org/package=dcmle) Hierarchical 240 | models through data cloning 241 | - [dlm](https://cran.r-project.org/package=dlm) Dynamic models and 242 | MCMC tools 243 | - [dlmodeler](https://cran.r-project.org/package=dlmodeler) 244 | State-space modelling 245 | - [sspir](https://cran.r-project.org/package=sspir) State-space models 246 | - [MCMCglmm](https://cran.r-project.org/package=MCMCglmm) Mixed models 247 | fitted by MCMC 248 | - [RSGHB](https://cran.r-project.org/package=RSGHB) Hierarchical Bayes 249 | models 250 | - [bayespref](https://cran.r-project.org/package=bayespref) Analysis 251 | of count data 252 | - [predcomps](https://github.com/dchudz/predcomps) Average Predictive 253 | Comparisons 254 | 255 | #### Generic MCMC samplers 256 | 257 | - [adaptMCMC](http://cran.r-project.org/web/packages/adaptMCMC/index.html) 258 | Generic MCMC sampler 259 | - [BRugs](https://cran.r-project.org/package=BRugs) Interface to 260 | OpenBUGS 261 | - [BayesX](https://cran.r-project.org/package=BayesX) Structured 262 | Additive Regression 263 | - [R2BayesX](https://cran.r-project.org/package=R2BayesX) 264 | - [rjags](https://cran.r-project.org/package=rjags) 265 | - [runjags](https://cran.r-project.org/package=runjags) 266 | - [R2jags](https://cran.r-project.org/package=R2jags) 267 | - [jagsUI](https://cran.r-project.org/package=jagsUI) 268 | - [R2OpenBUGS](https://cran.r-project.org/package=R2OpenBUGS) 269 | - [R2WinBUGS](https://cran.r-project.org/package=R2WinBUGS) 270 | - [rstan](https://cran.r-project.org/package=rstan) 271 | - [filzbach](https://cran.r-project.org/package=filzbach) 272 | - [iBUGS](https://cran.r-project.org/package=iBUGS) Interface to 273 | BUGS/JAGS 274 | - [rube](http://stat.cmu.edu/~hseltman/rube/) 275 | - [INLA](https://cran.r-project.org/package=INLA) Integrated Nested 276 | Laplace Approximation 277 | - [LaplacesDemon](https://cran.r-project.org/package=LaplacesDemon) 278 | - [LearnBayes](https://cran.r-project.org/package=LearnBayes) 279 | - [MCMCpack](https://cran.r-project.org/package=MCMCpack) MCMC 280 | samplers 281 | - [MHAdative](https://cran.r-project.org/package=MHAdative) MCMC 282 | sampler 283 | - [glmmBUGS](https://cran.r-project.org/package=glmmBUGS) 284 | - [mcmc](https://cran.r-project.org/package=mcmc) 285 | - [datalist](http://cran.r-project.org/web/packages/datalist/index.html) 286 | 287 | #### MCMC diagnostics & plotting 288 | 289 | - [coda](https://cran.r-project.org/package=coda) MCMC output analysis 290 | - [boa](https://cran.r-project.org/package=boa) Analyses of MCMC 291 | output (like `coda`) 292 | - [ggmcmc](https://cran.r-project.org/package=ggmcmc) Graphic analysis 293 | of MCMC output 294 | - [mcmcmplots](https://cran.r-project.org/package=mcmcplots) Plot MCMC 295 | output 296 | - [plotMCMC](https://cran.r-project.org/package=plotMCMC) Diagnostic 297 | plots 298 | - [bmk](https://cran.r-project.org/package=bmk) MCMC diagnostics 299 | - [superdiag](https://cran.r-project.org/package=superdiag) testing 300 | MCMC noncovergence 301 | - [shinyStan](https://cran.r-project.org/package=shinyStan) 302 | - [MCMCvis](https://cran.r-project.org/package=MCMCvis) 303 | - [rwty](https://cran.r-project.org/package=rwty) 304 | - [dMCMC](https://github.com/MarcoDVisser/dMCMC) 305 | - [bayesplot](https://github.com/stan-dev/bayesplot) 306 | 307 | #### Spatial Bayes 308 | 309 | - [CARBayes](https://cran.r-project.org/package=CARBayes) Spatial 310 | models with CAR 311 | - [spBayes](https://cran.r-project.org/package=spBayes) spatial 312 | Bayes 313 | - [geoCount](http://cran.r-project.org/web/packages/geoCount/index.html) 314 | generalized linear spatial models 315 | 316 | #### ABC 317 | 318 | - [abc](http://cran.r-project.org/web/packages/abc/index.html) 319 | Approximate Bayesian Computation 320 | - [easyABC](https://cran.r-project.org/package=easyABC) Approximate 321 | Bayesian Computation 322 | 323 | ## Plotting & Visualisation 324 | 325 | Check also [CRAN Task View on 326 | Graphics](http://cran.r-project.org/web/views/Graphics.html). 327 | 328 | - [denstrip](https://cran.r-project.org/package=denstrip) Plotting 329 | distributions (w uncertainty) 330 | - [visualize](https://cran.r-project.org/package=visualize) Graph 331 | Probability Distributions 332 | - [fanplot](https://cran.r-project.org/package=fanplot) Visualise 333 | sequential probability distributions 334 | - [diagram](https://cran.r-project.org/package=diagram) Networks, flow 335 | diagrams, etc 336 | - [beanplot](https://cran.r-project.org/package=beanplot) Bean plots 337 | - [vioplot](https://cran.r-project.org/package=vioplot) Violin plots 338 | - [viopoints](https://cran.r-project.org/package=viopoints) 1-D 339 | Scatter Plots with Jitter Using Kernel Density Estimates 340 | - [dagR](https://cran.r-project.org/package=dagR) Directed Acyclic 341 | graphs (DAGs) 342 | - [effects](https://cran.r-project.org/package=effects) Displays 343 | effects estimated from regression models 344 | - [coefplot](https://cran.r-project.org/package=coefplot) Plot model 345 | coefficients 346 | - [plotmo](https://cran.r-project.org/package=plotmo) Plot model 347 | responses 348 | - [corrgram](https://cran.r-project.org/package=corrgram) Plot 349 | correlation matrix 350 | - [gclus](https://cran.r-project.org/package=gclus) Clustering 351 | graphics 352 | - [vcd](https://cran.r-project.org/package=vcd) Viz categorical data 353 | - [extracat](https://cran.r-project.org/package=extracat) Viz 354 | categorical data 355 | - [plot3d](http://cran.r-project.org/web/packages/plot3D/index.html) 356 | Plotting multi-dimensional data 357 | - [VizOR](http://cran.r-project.org/web/packages/VizOR/index.html) 358 | visualization tools for complex observational data 359 | - [GrapheR](https://cran.r-project.org/package=GrapheR) GUI for base 360 | plots 361 | 362 | ### GGPLOT2 363 | 364 | - [ggplot2](https://cran.r-project.org/package=ggplot2) 365 | 366 | - [GGally](https://cran.r-project.org/package=GGally) extension to 367 | ggplot 368 | 369 | - [ggsubplot](https://cran.r-project.org/package=ggsubplot) Embedding 370 | subplots within plots 371 | 372 | - [ggthemes](https://cran.r-project.org/package=ggthemes) Extra 373 | themes, scales and geoms for ggplot 374 | 375 | - [gplot2bdc](https://github.com/briandconnelly/ggplot2bdc) 376 | 377 | - [ggtern](http://www.ggtern.com/) Ternary diagrams 378 | 379 | - [ggthemr](https://github.com/cttobin/ggthemr) Extra themes for 380 | ggplot2 381 | 382 | - [plotly](https://github.com/ropensci/plotly) R interface to plotly 383 | 384 | - [googleVis](https://cran.r-project.org/package=googleVis) Using 385 | google chart tools 386 | 387 | - [rCharts](https://cran.r-project.org/package=rCharts) Interactive 388 | charts 389 | 390 | - [lattice](https://cran.r-project.org/package=lattice) Multivariate 391 | plots 392 | 393 | - [manipulate](https://cran.r-project.org/package=manipulate) 394 | Interactive plots 395 | 396 | - [misc3d](https://cran.r-project.org/package=misc3d) 3D plots 397 | 398 | - [mvtsplot](https://cran.r-project.org/package=mvtsplot) Multivariate 399 | time series plot 400 | 401 | - [pca3d](https://cran.r-project.org/package=pca3d) Three dimensional 402 | PCA plots 403 | 404 | - [longCatEDA](https://cran.r-project.org/package=longCatEDA) Plot 405 | Categorical Longitudinal and Time-Series Data 406 | 407 | - [squash](https://cran.r-project.org/package=squash) Color-based 408 | plots for multivariate visualization 409 | 410 | - [tourr](https://cran.r-project.org/package=tourr) 411 | 412 | - [latticist](https://cran.r-project.org/package=latticist) GUI for 413 | graphic exploratory data analysis using lattice 414 | 415 | - [tfplot](https://cran.r-project.org/package=tfplot) Plot time series 416 | 417 | - [pathdiagram](http://cran.r-project.org/web/packages/pathdiagram/) 418 | 419 | - [RIGHT](https://cran.r-project.org/package=RIGHT) Interactive 420 | graphics via HTML 421 | 422 | - [clickme](https://github.com/nachocab/clickme) Interactive plots 423 | 424 | - [animation](https://cran.r-project.org/package=animation) Create 425 | animations 426 | 427 | - [calibrate](https://cran.r-project.org/package=calibrate) Axes 428 | calibration 429 | 430 | - [labeling](https://cran.r-project.org/package=labeling) Axis 431 | labeling 432 | 433 | - [directlabels](https://cran.r-project.org/package=directlabels) 434 | Labels for multicolor plots. See also `Hmisc:::labcurve`. 435 | 436 | - [gplots](https://cran.r-project.org/package=gplots) Useful plotting 437 | tools 438 | 439 | - [magicaxis](https://cran.r-project.org/package=magicaxis) Pretty 440 | scientific plots (e.g. log 441 | scales) 442 | 443 | - [PlotRegionHighlighter](https://cran.r-project.org/package=PlotRegionHighlighter) 444 | Creates an envelope that surrounds a set of 445 | points 446 | 447 | - [compactr](http://cran.us.r-project.org/web/packages/compactr/index.html) 448 | Plots with compact axis notation 449 | 450 | - [plotflow](https://github.com/trinker/plotflow) Useful plotting 451 | functions 452 | 453 | - [sendplot](https://cran.r-project.org/package=sendplot) Interactive 454 | plots with tool-tip content 455 | 456 | - [zoom](https://cran.r-project.org/package=zoom) Allow to 457 | zoom/navigate in any plot. 458 | 459 | - [Hmisc](https://cran.r-project.org/package=Hmisc) 460 | 461 | - [epade](https://cran.r-project.org/package=epade) Easy plots 462 | 463 | - [prettyGraphs](https://cran.r-project.org/package=prettyGraphs) 464 | Publication-quality graphics. 465 | 466 | - [scagnostics](https://cran.r-project.org/package=scagnostics) 467 | Scatterplot diagnostics 468 | 469 | ### Colour 470 | 471 | - [colorRamps](https://cran.r-project.org/package=colorRamps) Colour 472 | palettes 473 | 474 | - [RColorBrewer](https://cran.r-project.org/package=RColorBrewer) 475 | 476 | - [colorspace](https://cran.r-project.org/package=colorspace) HCL 477 | (perceptually-based) palettes 478 | 479 | - [colortools](https://cran.r-project.org/package=colortools) 480 | 481 | - [plotKML](https://cran.r-project.org/package=plotKML) Colour 482 | palettes for mapping 483 | 484 | - [gplots](https://cran.r-project.org/package=gplots) Rich.colors 485 | palettes 486 | 487 | - [dataview](https://cran.r-project.org/package=dataview) 488 | 489 | - [tabplot](https://cran.r-project.org/package=tabplot) Large datasets 490 | viz. 491 | 492 | - [tabplotd3](https://cran.r-project.org/package=tabplotd3) 493 | Interactive 494 | 495 | - [R2SWF](https://cran.r-project.org/package=R2SWF) Convert R graphics 496 | to Flash 497 | 498 | - [sendplot](https://cran.r-project.org/package=sendplot) Send 499 | interactive plots with tooltip content 500 | 501 | - [sjPlot](https://cran.r-project.org/package=sjPlot) 502 | 503 | - [squash](https://cran.r-project.org/package=squash) Color-based 504 | plots for multivariate visualization 505 | 506 | ## Reproducible Research - Report generation 507 | 508 | Check also CRAN Task View on [Reproducible 509 | Research](http://cran.r-project.org/web/views/ReproducibleResearch.html). 510 | 511 | - [brew](https://cran.r-project.org/package=brew) 512 | - [knitr](https://cran.r-project.org/package=knitr) Dynamic report 513 | generation 514 | - [knitrBootstrap](https://github.com/jimhester/knitrBootstrap) create 515 | bootstrap styled HTML reports from Rmarkdown 516 | - [reports](https://cran.r-project.org/package=reports) writing 517 | reports and presentations 518 | - [repmis](https://cran.r-project.org/package=repmis) 519 | - [rapport](http://cran.r-project.org/web/packages/rapport/index.html) 520 | report templating system 521 | - [pander](https://cran.r-project.org/package=pander) Exploits pandoc 522 | to convert among multiple formats 523 | - [stargazer](https://cran.r-project.org/package=stargazer) Easily 524 | create tables with regression outputs (directly from model objects) 525 | - [rtf](http://cran.r-project.org/web/packages/rtf/index.html) Produce 526 | Rich Text Format documents from R 527 | - [R2HTML](http://cran.r-project.org/web/packages/R2HTML/index.html) 528 | HTML reports from R 529 | - [xtable](http://cran.r-project.org/web/packages/xtable/index.html) 530 | Export R objects to HTML tables 531 | - [R2wd](https://cran.r-project.org/package=R2wd) Write MS-Word 532 | documents from 533 | R 534 | - [rmarkdown](https://cran.r-project.org/package=rmarkdown) 535 | - [sjPlot](https://cran.r-project.org/package=sjPlot) 536 | - [Rgitbook](https://github.com/jbryer/Rgitbook) 537 | - [table1xls](http://cran.r-project.org/web/packages/table1xls/index.html) 538 | Summary tables in Excel 539 | format. 540 | - [DescTools](http://cran.r-project.org/web/packages/DescTools/index.html) 541 | - [rctrack](http://www.stjuderesearch.org/site/depts/biostats/rctrack) 542 | 543 | ## Parallelisation & Big Data 544 | 545 | Check also [CRAN Task View on High Performance 546 | Computing](http://cran.r-project.org/web/views/HighPerformanceComputing.html). 547 | 548 | - [ff](https://cran.r-project.org/package=ff) Big data management. See 549 | also package `ffbase` 550 | - [batch](https://cran.r-project.org/package=batch) Batching routines 551 | in parallel 552 | - [bigdata](https://cran.r-project.org/package=bigdata) 553 | 554 | ## Niche & Species Distribution Modelling 555 | 556 | - [rgbif](https://cran.r-project.org/package=rgbif) Access to GBIF 557 | data 558 | - [spocc](https://cran.r-project.org/package=spocc) Species occurrence 559 | data retrieval and mapping 560 | - [dismo](https://cran.r-project.org/package=dismo) Distribution 561 | modelling 562 | - [SDMTools](http://www.rdocumentation.org/packages/SDMTools) 563 | - [adehabitatHS](http://cran.r-project.org/web/packages/adehabitatHS/index.html) 564 | - [biomod2](https://cran.r-project.org/package=biomod2) SDM ensembles 565 | - [hSDM](https://cran.r-project.org/package=hSDM) Bayesian SDM 566 | - [maxlike](https://cran.r-project.org/package=maxlike) SDM for 567 | presence-only data 568 | - [MigClim](https://cran.r-project.org/package=MigClim) Implements 569 | dispersal in SDMs 570 | - [GRaF](https://cran.r-project.org/package=GRaF) SDM using latent 571 | Gaussian random 572 | fields 573 | - [SightabilityModel](https://cran.r-project.org/package=SightabilityModel) 574 | - [EnvNicheR](https://cran.r-project.org/package=EnvNicheR) 575 | - [RinSp](http://cran.r-project.org/web/packages/RInSp/) Ecological 576 | niche metrics to measure individual specialization 577 | - [bdvis](https://github.com/vijaybarve/bdvis) Biodiversity data 578 | visualization 579 | - [phyloclim](https://cran.r-project.org/package=phyloclim) Includes 580 | functions for calculating niche overlap 581 | - [phylospacer](https://cran.r-project.org/package=phylospacer) 582 | Phyloclimates and 583 | phylomorphospaces 584 | - [PresenceAbsence](https://cran.r-project.org/package=PresenceAbsence) 585 | - [mboost](https://cran.r-project.org/package=mboost) Decomposing 586 | environmental, spatial, and spatiotemporal components of species 587 | distributions (Hothorn et al. 2011 Ecol Monogr) 588 | - [usdm](http://www.rdocumentation.org/packages/usdm) Uncertainty 589 | analysis for species distribution models, esp. focused on positional 590 | uncertainty 591 | - [ModelMap](http://cran.r-project.org/web/packages/ModelMap/) Random 592 | Forest and Stochastic Gradient Boosting Models 593 | - [modEVA](http://modtools.wordpress.com) 594 | - [rangemapper](https://cran.r-project.org/package=rangemapper) 595 | - [comclim](http://cran.r-project.org/web/packages/comclim/index.html) 596 | Community climate 597 | statistics 598 | - [hypervolume](http://cran.r-project.org/web/packages/hypervolume/index.html) 599 | Modeling hypervolumes (species’ niches) 600 | - [ppmlasso](https://cran.r-project.org/package=ppmlasso) Point 601 | process models 602 | - [sdmvspecies](https://cran.r-project.org/package=sdmvspecies) Create 603 | virtual species for SDM 604 | - [virtualspecies](http://borisleroy.com/virtualspecies/) Create 605 | virtual species 606 | - [coenocline](https://cran.r-project.org/package=coenocline) Simulate 607 | species presence and abundance along environmental gradients 608 | - [ecospat](http://cran.r-project.org/web/packages/ecospat/index.html) 609 | Many useful functions for niche & SDM (by A. Guisan’s group) 610 | - [comclim](https://cran.r-project.org/package=comclim) 611 | - [Metadata](https://cran.r-project.org/package=Metadata) 612 | - [ENiRG](http://cran.r-project.org/web/packages/ENiRG/index.html) 613 | 614 | ### Occupancy modelling 615 | 616 | - [detect](https://cran.r-project.org/package=detect) Occupancy 617 | modelling 618 | - [marked](https://cran.r-project.org/package=marked) 619 | - [unmarked](https://cran.r-project.org/package=unmarked) 620 | - [stocc](https://cran.r-project.org/package=stocc) Occupancy modeling 621 | - [hierarchicalDS](https://cran.r-project.org/package=hierarchicalDS) 622 | hierarchical analysis of distance sampling 623 | data 624 | 625 | ## Remote Sensing 626 | 627 | - [RStoolbox](https://github.com/bleutner/RStoolbox) 628 | - [moveVis](https://github.com/16EAGLE/moveVis) 629 | - [earthEngineGrabR](https://github.com/JesJehle/earthEngineGrabR) 630 | - [rsMove](https://github.com/RRemelgado/rsMove) 631 | - [satellite](https://github.com/environmentalinformatics-marburg/satellite) 632 | - [satelliteTools](https://github.com/environmentalinformatics-marburg/satelliteTools) 633 | - [uavRst](https://github.com/gisma/uavRst) 634 | - [fieldRS](https://github.com/RRemelgado/fieldRS) 635 | - [cropPhenology](https://github.com/SofanitAraya/CropPhenology) 636 | - [rTIMESAT](https://github.com/kongdd/rTIMESAT) 637 | - [luna](https://github.com/rspatial/luna) 638 | - [rabbiTS](https://github.com/16EAGLE/rabbiTS) 639 | - [theiaR](https://github.com/norival/theiaR) 640 | - [sentinel2](https://github.com/IVFL-BOKU/sentinel2) 641 | - [getSpatialData](https://github.com/16EAGLE/getSpatialData) 642 | - [sen2r](https://github.com/ranghetti/sen2r) 643 | - [S2utils](https://github.com/bbrede/S2utils) 644 | - [SentinelAPI](https://github.com/mattjbayly/SentinelAPI) 645 | - [RGISTools](https://github.com/spatialstatisticsupna/RGISTools) 646 | 647 | ## Climate 648 | 649 | - [BerkeleyEarth](http://cran.r-project.org/web/packages/BerkeleyEarth/index.html) 650 | Climate data from Berkeley Earth database 651 | - [climates](https://cran.r-project.org/package=climates) Tools for 652 | climate data (bioclim, downscaling, interpolation…) 653 | - [climatol](https://cran.r-project.org/package=climatol) 654 | Homogenisation of climate time series 655 | - [climstats](https://cran.r-project.org/package=climstats) Tools for 656 | climate data 657 | - [RMAWGEN](https://cran.r-project.org/package=RMAWGEN) Generate daily 658 | time series from monthly mean values 659 | - [climdex.pcic](https://cran.r-project.org/package=climdex.pcic) 660 | Computation of climate 661 | indices 662 | - [ClimClass](http://cran.r-project.org/web/packages/ClimClass/index.html) 663 | Climate Classification according to various indices 664 | - [RClimMAWGEN](https://cran.r-project.org/package=RClimMAWGEN) 665 | generate time series of climate indices 666 | - [chillR](https://cran.r-project.org/package=chillR) Climate and 667 | phenology analysis 668 | - [rWBclimate](https://cran.r-project.org/package=rWBclimate) Lots of 669 | historical data and future projections 670 | - [rnoaa](https://cran.r-project.org/package=rnoaa) 671 | - [rghcnV3](https://cran.r-project.org/package=rghcnV3) GHCN 672 | - [RNCEP](https://cran.r-project.org/package=RNCEP) weather data 673 | - [sirad](https://cran.r-project.org/package=sirad) Evapotranspiration 674 | etc 675 | - [SPEI](https://cran.r-project.org/package=SPEI) Calculates 676 | Standardised Precipitation-Evaporation Index 677 | - [SPI](https://cran.r-project.org/package=SPI) 678 | - [weathermetrics](https://cran.r-project.org/package=weathermetrics) 679 | - [raincpc](https://cran.r-project.org/package=raincpc) Rainfall 680 | data 681 | - [Evapotranspiration](http://cran.r-project.org/web/packages/Evapotranspiration/index.html) 682 | - [GhcnDaily](http://cran.r-project.org/web/packages/GhcnDaily/index.html) 683 | - [crn](http://cran.r-project.org/web/packages/crn/index.html) Get 684 | data from Climate Reference 685 | Network 686 | - [iki.dataclim](http://cran.r-project.org/web/packages/iki.dataclim/index.html) 687 | - [FedData](http://cran.r-project.org/web/packages/FedData/index.html) 688 | - [stationaRy](https://github.com/rich-iannone/stationaRy) Hourly data 689 | worldwide 690 | - [tempcyclesdata](https://cran.r-project.org/web/packages/tempcyclesdata/index.html) 691 | Temperature data for ca. 8000 stations 1975-2013 692 | 693 | ## GIS/spatial functionality 694 | 695 | Check also CRAN Task View on 696 | [Spatial](http://cran.r-project.org/web/views/Spatial.html) and 697 | [Spatiotemporal](http://cran.r-project.org/web/views/SpatioTemporal.html) 698 | data. Check also CRAN Task View on [Web 699 | technologies](http://cran.r-project.org/web/views/WebTechnologies.html) 700 | for access to many GIS data. 701 | 702 | - [sp](https://cran.r-project.org/package=sp) 703 | 704 | - [spacetime](https://cran.r-project.org/package=spacetime) 705 | 706 | - [spatial](https://cran.r-project.org/package=spatial) 707 | 708 | - [rgeos](https://cran.r-project.org/package=rgeos) 709 | 710 | - [rgdal](https://cran.r-project.org/package=rgdal) 711 | 712 | - [raster](https://cran.r-project.org/package=raster) 713 | 714 | - [rasterVis](https://cran.r-project.org/package=rasterVis) 715 | 716 | - [rts](https://cran.r-project.org/package=rts) Raster time series 717 | 718 | - [spatial.tools](https://cran.r-project.org/package=spatial.tools) 719 | Functions for raster processing, including parallel processing 720 | 721 | - [maptools](https://cran.r-project.org/package=maptools) Reading and 722 | manipulating geographic data 723 | 724 | - [PBSmapping](https://cran.r-project.org/package=PBSmapping) 725 | 726 | - [taRifx.geo](https://cran.r-project.org/package=taRifx.geo) Useful 727 | spatial functions 728 | 729 | - [climstats](https://cran.r-project.org/package=climstats) Tools for 730 | climate and raster analyses 731 | 732 | - [countrycode](https://cran.r-project.org/package=countrycode) 733 | Converts country codes 734 | 735 | - [cshapes](https://cran.r-project.org/package=cshapes) Dataset of 736 | country boundaries 737 | 738 | - [gdistance](https://cran.r-project.org/package=gdistance) Calculate 739 | distances and routes on grids 740 | 741 | - [geometry](https://cran.r-project.org/package=geometry) Mesh 742 | generation and surface tesselation 743 | 744 | - [geosphere](https://cran.r-project.org/package=geosphere) Several 745 | GIS tools, esp. aimed at large scales (global) 746 | 747 | - [geonames](https://cran.r-project.org/package=geonames) 748 | 749 | - [mapproj](https://cran.r-project.org/package=mapproj) Converts 750 | lat-lon data into projected coordinates 751 | 752 | - [geospacom](https://cran.r-project.org/package=geospacom) Generates 753 | distance matrices from shape files and represents spatially weighted 754 | multilevel analysis results 755 | 756 | - [dismo](https://cran.r-project.org/package=dismo) 757 | 758 | - [fossil](https://cran.r-project.org/package=fossil) 759 | 760 | - [ggmap](https://cran.r-project.org/package=ggmap) Plotting on Google 761 | Maps and OpenStreetMap 762 | 763 | - [GISTools](https://cran.r-project.org/package=GISTools) Some further 764 | GIS tools (e.g. cloropleth maps) 765 | 766 | - [mapplots](https://cran.r-project.org/package=mapplots) Data 767 | visualisation on maps 768 | 769 | - [maps](https://cran.r-project.org/package=maps) Mapping tools 770 | 771 | - [OpenStreetMap](https://cran.r-project.org/package=OpenStreetMap) 772 | Access to OpenStreetMap and Bing images 773 | 774 | - [osmar](https://cran.r-project.org/package=osmar) 775 | 776 | - [plotGoogleMaps](https://cran.r-project.org/package=plotGoogleMaps) 777 | 778 | - [RgoogleMaps](https://cran.r-project.org/package=RgoogleMaps) 779 | 780 | - [R2G2](https://cran.r-project.org/package=R2G2) Plot anything in 781 | Google Earth 782 | 783 | - [rCarto](https://cran.r-project.org/package=rCarto) useful functions 784 | for mapping 785 | 786 | - [marmap](https://cran.r-project.org/package=marmap) working with 787 | bathymetric and topographic data 788 | 789 | - [plotKML](https://cran.r-project.org/package=plotKML) Visualization 790 | of spatial and spatio-temporal objects in Google Earth 791 | 792 | - [MODISTools](http://cran.r-project.org/web/packages/MODISTools/) 793 | 794 | - [spGoogle](http://cran.r-project.org/web/packages/spGoogle) 795 | Interacting R with Google maps 796 | 797 | - [rMaps](https://cran.r-project.org/package=rMaps) Interactive maps 798 | 799 | - [leafletR](https://cran.r-project.org/package=leafletR) 800 | 801 | - [GEOmap](https://cran.r-project.org/package=GEOmap) 802 | 803 | - [rworldmap](https://cran.r-project.org/package=rworldmap) 804 | 805 | - [choroplethr](https://cran.r-project.org/package=choroplethr) 806 | 807 | - [mapmisc](http://cran.r-project.org/web/packages/mapmisc/index.html) 808 | Utilities for producing maps 809 | 810 | - [sinkr](https://github.com/menugget/sinkr) Some GIS functions and 811 | colour palettes 812 | 813 | - [rlandscape](https://cran.r-project.org/package=rlandscape) 814 | Generates spatial landscapes 815 | 816 | - [RSAGA](https://cran.r-project.org/package=RSAGA) 817 | 818 | - [spgrass6](https://cran.r-project.org/package=spgrass6) 819 | 820 | - [spsextante](https://cran.r-project.org/package=spsextante) 821 | 822 | - [RPyGeo](https://cran.r-project.org/package=RPyGeo) 823 | 824 | ## Spatial Analysis 825 | 826 | Check also CRAN Task View on 827 | [Spatial](http://cran.r-project.org/web/views/Spatial.html) and 828 | [Spatiotemporal](http://cran.r-project.org/web/views/SpatioTemporal.html) 829 | data. 830 | 831 | - [akima](https://cran.r-project.org/package=akima) Interpolation 832 | - [automap](https://cran.r-project.org/package=automap) Automatic 833 | interpolation (kriging) 834 | - [ecespa](https://cran.r-project.org/package=ecespa) Point pattern 835 | analysis 836 | - [fields](https://cran.r-project.org/package=fields) Splines, 837 | kriging, etc 838 | - [geoR](https://cran.r-project.org/package=geoR) Geostatistical 839 | analysis 840 | - [geoRglm](https://cran.r-project.org/package=geoRglm) Spatial GLMs 841 | - [geospt](https://cran.r-project.org/package=geospt) Geostatistics 842 | - [GeoXP](https://cran.r-project.org/package=GeoXP) Interactive 843 | exploratory analysis of spatial data 844 | - [gstat](https://cran.r-project.org/package=gstat) Geostatistics 845 | (variograms, kriging) 846 | - [intamap](https://cran.r-project.org/package=intamap) Automatic 847 | spatial interpolation 848 | - [geostatsp](https://cran.r-project.org/package=geostatsp) 849 | Geostatistics using SpatialPoints and rasters 850 | - [spatstat](https://cran.r-project.org/package=spatstat) 851 | - [spBayes](https://cran.r-project.org/package=spBayes) 852 | - [spdep](https://cran.r-project.org/package=spdep) Modeling spatial 853 | dependence 854 | - [stpp](https://cran.r-project.org/package=stpp) Point patterns 855 | - [rtop](https://cran.r-project.org/package=rtop) Spatial 856 | interpolation of data 857 | 858 | ## Networks 859 | 860 | - [bipartite](https://cran.r-project.org/package=bipartite) 861 | - [igraph](https://cran.r-project.org/package=igraph) Network analysis 862 | and visualization 863 | - [enaR](https://cran.r-project.org/package=enaR) 864 | - [qgraph](https://cran.r-project.org/package=qgraph) 865 | 866 | ## Phylogenetics, phylogeography & comparative analysis 867 | 868 | Check also [Phylogenetics CRAN task 869 | view](http://cran.r-project.org/web/views/Phylogenetics.html). 870 | 871 | - [ape](https://cran.r-project.org/package=ape) 872 | - [adephylo](http://cran.r-project.org/web/packages/adephylo/index.html) 873 | Exploratory analysis 874 | - [Treesim]() Tree simulation. See also 875 | [treesimGM](https://cran.r-project.org/package=Treesim%5D\(\)%20Tree%20simulation.%20See%20also%20%5BtreesimGM) 876 | - [cladoRcpp](https://cran.r-project.org/package=cladoRcpp) 877 | Phylogenetic analysis of geographic ranges 878 | - [caper](https://cran.r-project.org/package=caper) Comparative 879 | analysis 880 | - [PVR](https://cran.r-project.org/package=PVR) Phylogenetic 881 | Eigenvector Regression 882 | - [BEDASSLE](http://cran.r-project.org/web/packages/BEDASSLE/) 883 | Disentangles the effects of geographic and ecological isolation on 884 | genetic differentiation 885 | - [geiger](https://cran.r-project.org/package=geiger) 886 | - [geoscale](https://cran.r-project.org/package=geoscale) Geological 887 | timescale 888 | - [phangorn](https://cran.r-project.org/package=phangorn) 889 | - [phytools](https://cran.r-project.org/package=phytools) 890 | - [pegas](https://cran.r-project.org/package=pegas) 891 | - [picante](https://cran.r-project.org/package=picante) 892 | - [stratigraph](https://cran.r-project.org/package=stratigraph) 893 | - [treebase](https://cran.r-project.org/package=treebase) 894 | - [MCMCglmm](https://cran.r-project.org/package=MCMCglmm) 895 | 896 | ## Palaeoecology 897 | 898 | - [Bchron](https://cran.r-project.org/web/packages/Bchron/index.html) 899 | Bayesian chronologies 900 | - [Bclim](https://cran.r-project.org/web/packages/Bclim/index.html) 901 | Palaeoclimate reconstruction 902 | 903 | ## Dendrochronology 904 | 905 | - [dplR](https://github.com/cran/dplR) Dendrochronology 906 | - [measuRing](https://github.com/cran/measuRing) Measuring ring width 907 | from scanned images. 908 | - [TRADER](https://github.com/pavel-fibich/TRADER) Tree Ring Analysis 909 | of Disturbance Events 910 | - [dendrobox](https://github.com/cszang/dendrobox) Interactive 911 | Tree-Ring Data Exploration Tool 912 | - [treeclim](https://github.com/cszang/treeclim) Modeling tree-climate 913 | relationships. 914 | - [bootRes](https://github.com/cszang/bootRes) Bootstrapped response 915 | functions. 916 | - [rwtocore](https://github.com/ltrr-arizona-edu/rwtocore) convert 917 | tree-ring measurements to drawings of cores (Ruby). 918 | - [triforce](https://github.com/ltrr-arizona-edu/triforce) read the 919 | TRiDaS dendrochronological standard and communicate with Tellervo 920 | servers. 921 | - [pointRes](https://cran.r-project.org/web/packages/pointRes/index.html) 922 | Calculate and plot pointer years 923 | - [BIOdry](https://cran.r-project.org/web/packages/BIOdry/index.html) 924 | Multilevel Modeling of Dendroclimatical Fluctuations 925 | - [sclero](https://cran.r-project.org/web/packages/sclero/) Measure 926 | Growth Patterns and Align Sampling Spots in Photographs 927 | - [dendrometeR](https://cran.r-project.org/web/packages/dendrometeR/) 928 | Analyzing Dendrometer Data. 929 | - [wvtool](https://cran.r-project.org/package=wvtool) Image Tools for 930 | Automated Wood 931 | Identification 932 | - [DendroSync](https://cran.r-project.org/web/packages/DendroSync/index.html) 933 | Calculating Spatial Synchrony Between Tree-Ring Chronologies 934 | - [iadf](https://cran.r-project.org/web/packages/iadf/index.html) 935 | Analysis of Intra Annual Density Fluctuations 936 | - [dendroExtra](https://cran.r-project.org/package=dendroExtra) Finds 937 | the optimal sequence of days that are linearly or nonlinearly 938 | related to one or more tree-ring proxy records. 939 | 940 | ## Ecological analyses (miscellaneous) 941 | 942 | Check also [Environmetrics CRAN Task 943 | View](http://cran.r-project.org/web/views/Environmetrics.html). 944 | 945 | - [betapart](https://cran.r-project.org/package=betapart) Beta 946 | diversity 947 | - [BiodiversityR](https://cran.r-project.org/package=BiodiversityR) 948 | GUI for biodiversity, suitability and community ecology analyses 949 | - [cheddar](https://cran.r-project.org/package=cheddar) Analysis and 950 | visualisation of community data 951 | - [coexist](https://cran.r-project.org/package=coexist) Modelling 952 | species coexistence 953 | - [DSpat](https://cran.r-project.org/package=DSpat) Distance Sampling 954 | - [fossil](https://cran.r-project.org/package=fossil) Species 955 | richness, species-area curves, beta-diversity 956 | - [indicspecies](https://cran.r-project.org/package=indicspecies) 957 | Assess associations between different species and sites 958 | (e.g. indicator species) 959 | - [IPMpack](https://cran.r-project.org/package=IPMpack) Integral 960 | Projection Models 961 | - [marked](https://cran.r-project.org/package=marked) Mark-recapture 962 | analysis 963 | - [MBI](https://cran.r-project.org/package=MBI) Multiple Beta 964 | Diversity indices 965 | - [rmeta](https://cran.r-project.org/package=rmeta) Meta-analysis 966 | - [neighlikeli](https://cran.r-project.org/package=neighlikeli) 967 | Neighborhood models 968 | - [earlywarnings](https://cran.r-project.org/package=earlywarnings) 969 | - [MAR1](https://cran.r-project.org/package=MAR1) Multivariate 970 | Autoregressive Modeling for Analysis of Community Time-Series Data 971 | - [ncbit](https://cran.r-project.org/package=ncbit) retrieve NBCI 972 | taxonomic data 973 | - [spacodiR](https://cran.r-project.org/package=spacodiR) Spatial and 974 | Phylogenetic Analysis of Community Diversity 975 | - [Reol](http://cran.r-project.org/web/packages/Reol/) Interface to 976 | Encyclopedia of Life 977 | - [SPECIES](https://cran.r-project.org/package=SPECIES) Species 978 | richness and diversity analysis 979 | - [BayesComm](https://cran.r-project.org/package=BayesComm) Bayesian 980 | multivariate binary regression models for analysis of ecological 981 | communities 982 | - [pom](https://cran.r-project.org/package=pom) Patch occupancy models 983 | - [capwire](https://cran.r-project.org/package=capwire) Population 984 | size estimation from non-invasive sampling 985 | - [vegclust](https://cran.r-project.org/package=vegclust) Fuzzy 986 | clustering of vegetation data 987 | - [popbio](https://cran.r-project.org/package=popbio) 988 | - [demoniche](http://demoniche.r-forge.r-project.org/) 989 | Spatially-explicit demographic modelling 990 | - [BEDASSLE](https://cran.r-project.org/package=BEDASSLE) Disentangles 991 | the effects of geographic and ecological isolation on genetic 992 | differentiation. 993 | - [rphylopic](https://github.com/sckott/rphylopic) Organisms 994 | silhouettes 995 | - [GSIF](https://cran.r-project.org/package=GSIF) Global Soil 996 | Information 997 | - [Rarity](https://cran.r-project.org/package=Rarity) Rarity indices 998 | - [taxize](https://cran.r-project.org/package=taxize) Taxonomy etc. 999 | - [Taxonstand](https://cran.r-project.org/package=Taxonstand) 1000 | - [sExtinct](https://cran.r-project.org/package=sExtinct) Extinction 1001 | analysis based on sightings 1002 | - [BEDASSLE](http://cran.r-project.org/web/packages/BEDASSLE/) 1003 | Disentangles the effects of geographic and ecological isolation on 1004 | genetic differentiation 1005 | - [ecomodtools](https://cran.r-project.org/package=ecomodtools) 1006 | Simulation models (inc. dispersal) 1007 | - [comclim](http://cran.r-project.org/web/packages/comclim/index.html) 1008 | Community climate 1009 | statistics 1010 | - [kernelPop](http://cran.r-project.org/web/packages/kernelPop/index.html) 1011 | Spatially explicit population genetic simulations 1012 | - [siplab](http://cran.r-project.org/web/packages/siplab/index.html) 1013 | spatially explicit individual-based vegetation models. 1014 | 1015 | ## Miscellaneous 1016 | 1017 | - [digitize](https://cran.r-project.org/package=digitize) Extract data 1018 | from plots 1019 | - [downloader](https://cran.r-project.org/package=downloader) Download 1020 | files from internet 1021 | - [hwriter](https://cran.r-project.org/package=hwriter) Outputs R 1022 | objects in HTML format 1023 | - [installr](https://cran.r-project.org/package=installr) 1024 | Automatically update R 1025 | - [mail](https://cran.r-project.org/package=mail) Send email 1026 | notifications from R 1027 | - [sendmailR](https://cran.r-project.org/package=sendmailR) 1028 | - [mosaic](https://cran.r-project.org/package=mosaic) 1029 | - [audiolyzR](https://cran.r-project.org/package=audiolyzR) Creates 1030 | audio representations of common plots 1031 | - [WebDevelopR](https://cran.r-project.org/package=WebDevelopR) Web 1032 | development 1033 | - [ProjectTemplate](https://cran.r-project.org/package=ProjectTemplate) 1034 | - [gpk](https://cran.r-project.org/package=gpk) Datasets for 1035 | educational 1036 | uses 1037 | - [NCmisc](http://cran.r-project.org/web/packages/NCmisc/) 1038 | - [PubMedWordcloud](https://cran.r-project.org/package=PubMedWordcloud) 1039 | Create wordcloud with abstracts. 1040 | - [alm](https://cran.r-project.org/package=alm) Altmetrics 1041 | - [rAltmetric](https://cran.r-project.org/package=rAltmetric) 1042 | Retrieves data from altmetrics.com 1043 | - [RMendeley](https://cran.r-project.org/package=RMendeley) 1044 | - [rcrossref](https://cran.r-project.org/package=rcrossref) 1045 | - [RefManageR](https://cran.r-project.org/package=RefManageR) 1046 | Bibliography Management. 1047 | - [refnet](https://cran.r-project.org/package=refnet) Reads and works 1048 | with data from ISI Web of Knowledge 1049 | - [scholar](https://cran.r-project.org/package=scholar) 1050 | - [slidify](https://cran.r-project.org/package=slidify) 1051 | - [sos](https://cran.r-project.org/package=sos) Search R 1052 | packages 1053 | - [source.gist](https://cran.r-project.org/package=source.gist) 1054 | - [twitteR](https://cran.r-project.org/package=twitteR) 1055 | - [DescTools](http://cran.r-project.org/web/packages/DescTools/index.html) 1056 | 1057 | ## R programming 1058 | 1059 | - [codetools](https://cran.r-project.org/package=codetools) Code 1060 | analysis tools 1061 | - [compiler](https://cran.r-project.org/package=compiler) Compile R 1062 | code (e.g. a function) to speed it up 1063 | - [devtools](https://cran.r-project.org/package=devtools) 1064 | - [formatR](https://cran.r-project.org/package=formatR) Format and 1065 | tidy R code 1066 | - [gtools](https://cran.r-project.org/package=gtools) Useful functions 1067 | (e.g. mixedsort) 1068 | - [inline](https://cran.r-project.org/package=inline) Define functions 1069 | in C code within R 1070 | - [iterators](https://cran.r-project.org/package=iterators) Tools for 1071 | iteration on many different types of objects (see also `itertools`) 1072 | - [Kmisc](https://cran.r-project.org/package=Kmisc) Data reshaping, 1073 | table and plot generation from RMarkdown 1074 | - [operators](https://cran.r-project.org/package=operators) Additional 1075 | operators 1076 | - [simFrame](https://cran.r-project.org/package=simFrame) A framework 1077 | to work with simulations 1078 | - [simSummary](https://cran.r-project.org/package=simSummary) 1079 | - [staticdocs](https://cran.r-project.org/package=staticdocs) Create 1080 | webpage with package documentation 1081 | - [testit](https://cran.r-project.org/package=testit) Testing R 1082 | packages 1083 | - [testthat](https://cran.r-project.org/package=testthat) Testing R 1084 | code 1085 | - [tester](https://cran.r-project.org/package=tester) Test 1086 | characteristics of R objects 1087 | - [assertthat](https://cran.r-project.org/package=assertthat). 1088 | - [httr](https://cran.r-project.org/package=httr) Working with URLs 1089 | and HTTP 1090 | - [RCurl](https://cran.r-project.org/package=RCurl) HTTP interface 1091 | - [stringr](https://cran.r-project.org/package=stringr) 1092 | - [Rd2Roxygen](https://cran.r-project.org/package=Rd2Roxygen) 1093 | - [Rxoygen2](https://cran.r-project.org/package=Rxoygen2) 1094 | - [scrapeR](https://cran.r-project.org/package=scrapeR) 1095 | - [aprof](http://cran.r-project.org/web/packages/aprof/index.html) 1096 | Profiling code and visualizing results to evaluate where is best to 1097 | focus code optimization. 1098 | - [regex](https://github.com/richierocks/regex) Regular expressions 1099 | made easier. -------------------------------------------------------------------------------- /add_CRAN_links_auto.R: -------------------------------------------------------------------------------- 1 | path <- paste0(getwd(), "/README.Rmd") 2 | 3 | rmd <- readLines(paste0(getwd(), "/README.Rmd")) 4 | 5 | rmd2 <- gsub("\\* \\[(.+)]\\(\\)", "\\* \\[\\1]\\(https://cran.r-project.org/package=\\1\\)", rmd) 6 | 7 | cat(paste(rmd2, collapse = "\n"), file = path) 8 | -------------------------------------------------------------------------------- /render.R: -------------------------------------------------------------------------------- 1 | # From Tyler Rinker: https://github.com/trinker/testing_Rmd 2 | 3 | rmarkdown::render("README.Rmd", "all") 4 | 5 | md_toc <- function(path = paste0(getwd(), "/README.md")){ 6 | x <- suppressWarnings(readLines(path)) 7 | inds <- 1:(which(!grepl("^\\s*-", x))[1] - 1) 8 | temp <- gsub("(^[ -]+)(.+)", "\\1", x[inds]) 9 | content <- gsub("^[ -]+", "", x[inds]) 10 | x[inds] <- sprintf("%s[%s]", temp, content, gsub("\\s", "-", tolower(content))) 11 | cat(paste(x, collapse = "\n"), file = path) 12 | } 13 | 14 | md_toc() 15 | --------------------------------------------------------------------------------