{"id":14063190,"url":"https://github.com/dirmeier/essential-R","last_synced_at":"2025-07-29T14:32:23.982Z","repository":{"id":133195346,"uuid":"118235336","full_name":"dirmeier/essential-R","owner":"dirmeier","description":" :blue_book: Essential tools and libraries for programming in R","archived":false,"fork":false,"pushed_at":"2020-08-13T19:03:25.000Z","size":19807,"stargazers_count":19,"open_issues_count":1,"forks_count":1,"subscribers_count":4,"default_branch":"master","last_synced_at":"2024-11-23T14:51:25.506Z","etag":null,"topics":["awesome-r","essential-packages","r"],"latest_commit_sha":null,"homepage":"https://dirmeier.github.io/essential-R","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dirmeier.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-01-20T11:09:38.000Z","updated_at":"2024-10-06T00:58:53.000Z","dependencies_parsed_at":"2023-07-04T09:02:37.225Z","dependency_job_id":null,"html_url":"https://github.com/dirmeier/essential-R","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dirmeier%2Fessential-R","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dirmeier%2Fessential-R/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dirmeier%2Fessential-R/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dirmeier%2Fessential-R/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dirmeier","download_url":"https://codeload.github.com/dirmeier/essential-R/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":228023097,"owners_count":17857593,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["awesome-r","essential-packages","r"],"created_at":"2024-08-13T07:03:07.732Z","updated_at":"2024-12-04T00:31:27.600Z","avatar_url":"https://github.com/dirmeier.png","language":null,"funding_links":[],"categories":["Others"],"sub_categories":[],"readme":"# Essential R\n\n[![Project Status](http://www.repostatus.org/badges/latest/concept.svg)](http://www.repostatus.org/#concept)\n\n:rocket: Essential tools and libraries for programming in R\n\n## About\n\nThis document serves as a personal list of\n\n* tools for package development,\n* good practices for programming,\n* and most frequently used packages\n\nwith an emphasis on data science, Bayesian stats and probabilistic ML.\n\n## R package development\n\nA minimum `R`-package stack at least consists of the following packages of tools:\n\n- [`goodpractice`](https://github.com/MangoTheCat/goodpractice) for advice on writing R packages\n- [`devtools`](https://github.com/r-lib/devtools) for general package development\n- [`testthat`](https://github.com/r-lib/testthat) for unit testing\n- [`roxygen2`](https://github.com/r-lib/testthat) for method documentation\n- [`covr`](https://github.com/r-lib/covr) to generate coverage reports\n- [`lintr`](https://github.com/jimhester/lintr) for static code analysis\n- [`styler`](https://github.com/r-lib/styler) to automatically format code\n- [`usethis`](https://github.com/r-lib/usethis) for automation of repetitive tasks during development\n- [`remotes`](https://github.com/r-lib/remotes) to install R packages from Git repositories, CRAN and Bioconductor\n- [`pkgdown`](https://github.com/r-lib/pkgdown) to generate websites of your package\n- [`rcmdcheck`](https://github.com/r-lib/pkgdown) to check your package within R\n- [`profvis`](https://github.com/rstudio/profvis) to visualize profiling data\n- [`bench`](https://github.com/r-lib/bench) to time R expressions\n- [`microbenchmark`](https://github.com/r-lib/bench) to also time R expressions\n- [`lobstr`](https://github.com/r-lib/lobstr) to pry open R\n- [`here`](https://github.com/r-lib/here) to find files and folders\n\nMany more can be find on github at [r-lib](https://github.com/r-lib) or [rstudio](https://github.com/rstudio/).\n\n## Programming\n\n- [`purrr`](https://github.com/tidyverse/purrr) for functional programming\n- [`magrittr`](https://github.com/tidyverse/magrittr) for pipeing function calls\n- [`R6`](https://github.com/r-lib/R6) for object-oriented programming with encapsulation\n- [`Rcpp`](https://github.com/RcppCore/Rcpp) (with `RcppArmadillo`, `RcppEigen` and `BH`) for integration of C++ code\n- [`reticulate`](https://github.com/rstudio/reticulate) for interfacing to Python\n- [`cpp11`](https://github.com/r-lib/cpp11) as alternative (and complement) to Rcpp\n- `compiler`, `doParallel`, `parallel`, `foreach` for speeding up R\n- [`rlang`](https://github.com/dirmeier/datastructures) as low-level API for programming in R\n\n### C++\n\n- [`meson`](https://mesonbuild.com/) as modern build system and [`autotools`](https://www.gnu.org/software/automake/manual/html_node/Autotools-Introduction.html) since R is old\n- [`VTune`](https://software.intel.com/content/www/us/en/develop/tools/vtune-profiler.html) and the Parallel Studio to profile code\n- [`Callgrind`](https://valgrind.org/docs/manual/cl-manual.html) as an alternative to the above\n- [`gdb`](https://www.gnu.org/software/gdb/) and [`lldb`](https://lldb.llvm.org/) for debugging C++\n- [`sanitizers`](https://gcc.gnu.org/onlinedocs/gcc/Instrumentation-Options.html) to detect memory leaks, etc.\n- [`cppcheck`](http://cppcheck.sourceforge.net/) for static code analysis\n- [`cpplint`](https://github.com/cpplint/cpplint) to check C++ style\n- [`clang-format`](https://clang.llvm.org/docs/ClangFormat.html) to format C++ files\n- [`doxygen`](http://cppcheck.sourceforge.net/) for code documentation\n- [`boost`](https://www.boost.org/) for unit tests, data structures and basically everything you ever need\n\nFurthermore, some good reading:\n\n- Scott Meyers: Effective C++\n- Scott Meyers: Effective Modern C++\n- Scott Meyers: Effective STL\n- Kurt Guntheroth: Optimized C++\n- David Vandevoorde: C++ Templates - the compete guide\n- Nicolai Josuttis: C++17 - the complete guide\n\n## Working with data\n\n- [`tidyverse`](https://github.com/tidyverse/tidyverse) (`dplyr`, `tidyr`, ...) for working with data in general\n- [`data.table`](https://github.com/Rdatatable/data.table) as a fast alternative to R`s native data frame\n- [`datastructures`](https://github.com/dirmeier/datastructures) for advanced data structures\n- [`dbplyr`](https://github.com/tidyverse/dbplyr/) to work with data bases\n- [`RSQLite`](https://db.rstudio.com/databases/sqlite/) to work with SQLite data bases\n\n## Machine learning and Bayesian statistics \n\n- [`rstan`](https://github.com/stan-dev/rstan) to fit Bayesian models\n- [`cmdstanr`](https://github.com/stan-dev/cmdstanr) as light-weight interface to `cmdstan`\n- [`rstanarm`](https://github.com/stan-dev/rstanarm) for applied regression modeling\n- [`brms`](https://github.com/paul-buerkner/brms) for  multilevel models\n- [`bayesplot`](https://github.com/stan-dev/bayesplot) to visualize Bayesian inferences\n- [`loo`](https://github.com/stan-dev/loo) for approximate LOO-CV and PSIS\n- [`projpred`](https://github.com/stan-dev/projpred) for projection predictive variable selection \n- [`rstantools`](https://github.com/stan-dev/rstantools) for developing R Packages interfacing with Stan \n- [`posterior`](https://github.com/stan-dev/posterior) for working with output from Bayesian models\n- [`coda`](https://cran.r-project.org/web/packages/coda/index.html) for summarizing and working with MCMC output\n- [`MCMCpack`](https://cran.r-project.org/web/packages/MCMCpack/index.html) provides some utility functions\n- [`LaplacesDemon`](https://github.com/LaplacesDemonR/LaplacesDemon) for even more Bayes utility\n- [`mgcv`](https://cran.r-project.org/web/packages/mgcv/index.html) for generalized additive mixed models\n- [`tensorflow`](https://github.com/rstudio/tensorflow) for numerical computation\n- [`tfprobability`](https://cran.r-project.org/web/packages/mgcv/index.html) for statistical computation and probabilistic modeling\n- [`keras`](https://github.com/rstudio/tensorflow) to work with neural networks\n- [`sparklyr`](https://github.com/sparklyr/sparklyr) for big data processing\n- [`kernlab`](https://cran.r-project.org/web/packages/kernlab/index.html) for kernel-based machine learning\n\n## Graphical models and causal inference\n\n- [`bnlearn`](https://cran.r-project.org/web/packages/bnlearn/) for BN structure learning\n- [`pcalg`](https://cran.r-project.org/web/packages/pcalg/) for causal inference using graphical models\n- [`ggdag`](https://github.com/malcolmbarrett/ggdag) for visualizing DAGs\n- [`dagitty`](https://github.com/jtextor/dagitty) for analysis of structural equation models\n\n## Optimization\n\n- [`nloptr`](https://cran.r-project.org/web/packages/nloptr/index.html) for non-linear optimization\n- [`cvxr`](https://github.com/cvxgrp/CVXR) for disciplined convec optimization\n\n## Visualization\n\n- [`ggplot2`](https://github.com/tidyverse/ggplot2) as base package for visualization\n- [`paletteer`](https://github.com/EmilHvitfeldt/paletteer) for all the palettes\n- [`vapoRwave`](https://github.com/moldach/vapoRwave) for even more palettes\n- [`gpubr`](https://github.com/kassambara/ggpubr) for publication ready visualization\n- [`ggthemes`](https://github.com/jrnold/ggthemes) for additional themes and scales for ggplot2\n- [`hrbrthemes`](https://github.com/hrbrmstr/hrbrthemes) for even more themes\n- [`ggsci`](https://github.com/nanxstats/ggsci) for sci-fi themes\n- [`ggthemr`](https://github.com/cttobin/ggthemr) for even mroe themes\n- [`colourlovers`](https://github.com/andrewheiss/colourlovers) for access to the COLOURlovers API \n- [`patchwork`](https://github.com/thomasp85/patchwork) to easily compose plots\n- [`colorspace`](https://cran.r-project.org/web/packages/colorspace/index.html) for color manipulation\n- [`cowplot`](https://github.com/wilkelab/cowplot) for plot annotations\n- [`scales`](https://github.com/r-lib/scales) and [`swatches`](https://github.com/hrbrmstr/swatches) \n- [`plotly`](https://github.com/ropensci/plotly) for interactive plots\n- [`ggraph`](https://github.com/thomasp85/ggraph) to visualize graphs\n- [`gganimate`](https://github.com/thomasp85/gganimate) to animate plots\n- [`DiagrammeR`](https://github.com/rich-iannone/DiagrammeR) for diagrammes, graphs and networks\n- [`highcharter`](https://github.com/jbkunst/highcharter) as alternative to `plotly`\n- [`tidybayes`](https://github.com/mjskay/tidybayes) for geoms for Bayesian models\n- [`scico`](https://github.com/thomasp85/scico) for more color palettes\n- [`ggnetwork`](https://github.com/briatte/ggnetwork) for geoms for networks\n- [`tweenr`](https://github.com/thomasp85/tweenr) to interpolate data\n- [`magick`](https://github.com/ropensci/magick) to work with images\n- [`imager`](https://github.com/dahtah/imager) as complement to `magick`\n- [`r2d3`](https://github.com/rstudio/r2d3) to interface to [`d3`](https://d3js.org/)\n\n# Reporting\n\n- [`shiny`](https://github.com/rstudio/shiny) for interactive web applications\n- [`rmarkdown`](https://rmarkdown.rstudio.com/index.html) to generate websites, pdf documents, etc from markdown files\n- [`bookdown`](https://github.com/rstudio/bookdown) for authoring books\n- [`tufte`](https://github.com/rstudio/tufte) for Tufte-style documents\n- [`xaringan`](https://github.com/yihui/xaringan) for HTML presentations\n\n## Other\n\n- [`igraph`](https://github.com/igraph/igraph) to work with graphs\n- [`drake`](https://github.com/ropensci/drake) for building pipelines\n\n## Author\n\nSimon Dirmeier \u003ca href=\"mailto:simon.dirmeier@web.de\"\u003esimon.dirmeier@web.de\u003c/a\u003e\n\n## License\n\n\u003ca rel=\"license\" href=\"http://creativecommons.org/licenses/by-nc/4.0/\"\u003e\u003cimg alt=\"Creative Commons License\" style=\"border-width:0\" src=\"https://i.creativecommons.org/l/by-nc/4.0/88x31.png\" /\u003e\u003c/a\u003e\u003cbr /\u003eThis work by Simon Dirmeier is licensed under a \u003ca rel=\"license\" href=\"http://creativecommons.org/licenses/by-nc/4.0/\"\u003eCreative Commons Attribution-NonCommercial 4.0 International License\u003c/a\u003e.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdirmeier%2Fessential-R","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdirmeier%2Fessential-R","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdirmeier%2Fessential-R/lists"}