diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 423 |
1 files changed, 404 insertions, 19 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 62dc6a9bd7..108650d19a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2017 Roel Janssen <roel@gnu.org> ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr> ;;; @@ -95,13 +95,13 @@ error stream.") (define-public r-rcpp (package (name "r-rcpp") - (version "0.12.14") + (version "0.12.15") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "0qvyxggddyg87lza45hjl0a2prabdyshkqzkz418vi777zygqa6s")))) + (base32 "1pnv6sl4vdn69ygmgrb1b3gsigfdcfb56wnzikic93l8gkvdsvxv")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ integration") @@ -206,14 +206,14 @@ on (non-orthogonal) variable vectors in scatterplots and biplots.") (define-public r-shape (package (name "r-shape") - (version "1.4.3") + (version "1.4.4") (source (origin (method url-fetch) (uri (cran-uri "shape" version)) (sha256 (base32 - "1v9xp60p813rnx41vchkh32qmcb4z2zp9l7r1a8a6f8aqylnq3vj")))) + "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/shape") (synopsis "Functions for plotting graphical shapes") @@ -321,14 +321,14 @@ rows, dropping names) to see if the modified versions are identical.") (define-public r-dendextend (package (name "r-dendextend") - (version "1.6.0") + (version "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "dendextend" version)) (sha256 (base32 - "0pichh08zi12lpxzc061dmv4smj6lizygd1xymln8wfz18sf7923")))) + "1krvqadnnh53xx5ql7bwzxaif6a317jzbs1m00gnc6jnj03rfl5d")))) (build-system r-build-system) (propagated-inputs `(("r-fpc" ,r-fpc) @@ -542,14 +542,14 @@ plot networks.") (define-public r-proxy (package (name "r-proxy") - (version "0.4-20") + (version "0.4-21") (source (origin (method url-fetch) (uri (cran-uri "proxy" version)) (sha256 (base32 - "15g6dacdmlbkcnimblscghl23aj732cn6qwbs583r4im9v5nvbla")))) + "1vih8gsfzv97h5c8ixd1qjnn02i7fzla2p9fdj2wpisqhx0p0xv0")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/proxy") (synopsis "Distance and similarity measures") @@ -562,14 +562,14 @@ most popular ones.") (define-public r-sp (package (name "r-sp") - (version "1.2-5") + (version "1.2-7") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 (base32 - "09yydnacp33yx0kn537k96fjlbf75fjafqfknpa5gvci4l888bqd")))) + "0q04yfgyjannsrzl0ppwcv0simrxrrbx2iz5mzaafc5x38zf0q3d")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -989,20 +989,44 @@ testing framework of Wald are generic and can therefore also be used in other contexts.") (license license:gpl2+))) +(define-public r-squarem + (package + (name "r-squarem") + (version "2017.10-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "SQUAREM" version)) + (sha256 + (base32 + "10xj26x7qjyvzndnbjl5krr9wabnb9cbrnp3m7xg673g8ddr12cv")))) + (properties `((upstream-name . "SQUAREM"))) + (build-system r-build-system) + (home-page "http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html") + (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms") + (description + "This package provides algorithms for accelerating the convergence of +slow, monotone sequences from smooth, contraction mapping such as the EM +algorithm. It can be used to accelerate any smooth, linearly convergent +acceleration scheme. A tutorial style introduction to this package is +available in a vignette.") + (license license:gpl2+))) + (define-public r-lava (package (name "r-lava") - (version "1.5.1") + (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 - "1vcm04h9i39gmf2prl5d4j4il4gs6skzr6y2fvl1vn4hklna87f4")))) + "02xf5d968raz9gnq5ywy04wz29xpdyca1hm79vbbg1mcxvzdl1dz")))) (build-system r-build-system) (propagated-inputs `(("r-numderiv" ,r-numderiv) + ("r-squarem" ,r-squarem) ("r-survival" ,r-survival))) (home-page "https://github.com/kkholst/lava") (synopsis "Latent variable models") @@ -1014,14 +1038,14 @@ variable models.") (define-public r-drr (package (name "r-drr") - (version "0.0.2") + (version "0.0.3") (source (origin (method url-fetch) (uri (cran-uri "DRR" version)) (sha256 (base32 - "1scfwp6ry6apxzqjclsmn2frxp9qfw6zxsxn5w0j0q3sz42hz1h2")))) + "1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl")))) (properties `((upstream-name . "DRR"))) (build-system r-build-system) (propagated-inputs @@ -1106,14 +1130,14 @@ calendar objects.") (define-public r-ddalpha (package (name "r-ddalpha") - (version "1.3.1") + (version "1.3.1.1") (source (origin (method url-fetch) (uri (cran-uri "ddalpha" version)) (sha256 (base32 - "0pczw9543y7f92m7gyk7rxcjn8vsjaldc5vl0r56ywip9i374zbh")))) + "13w8ir5rd80rka4mq343zd4wn93vfw870lzfqrd3cxgwb1bwcw7y")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) @@ -1279,14 +1303,14 @@ provides a one-row summary of model-level statistics.") (define-public r-recipes (package (name "r-recipes") - (version "0.1.1") + (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "recipes" version)) (sha256 (base32 - "0id46c7iaf49miw4kxpidsbg3hdywav43n1lh2zd1vg5946bzg04")))) + "1car3a3mqn87pz049cbgkaayz86970mvkapk6al2k7jjw76306l9")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -1840,3 +1864,364 @@ plots in @code{ggplot2}.") attractive command line interfaces (CLIs). It includes tools for drawing rules, boxes, trees, and Unicode symbols with ASCII alternatives.") (license license:expat))) + +(define-public r-argparser + (package + (name "r-argparser") + (version "0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "argparser" version)) + (sha256 + (base32 + "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9")))) + (build-system r-build-system) + (home-page "https://bitbucket.org/djhshih/argparser") + (synopsis "Command-line argument parser") + (description + "This package provides a cross-platform command-line argument parser +written purely in R with no external dependencies. It is useful with the +Rscript front-end and facilitates turning an R script into an executable +script.") + (license license:gpl3+))) + +(define-public r-debugme + (package + (name "r-debugme") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "debugme" version)) + (sha256 + (base32 + "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd")))) + (build-system r-build-system) + (propagated-inputs `(("r-crayon" ,r-crayon))) + (home-page "https://github.com/r-lib/debugme#readme") + (synopsis "Debug R packages") + (description + "This package allows the user to specify debug messages as special string +constants, and control debugging of packages via environment variables.") + (license license:expat))) + +(define-public r-processx + (package + (name "r-processx") + (version "2.0.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "processx" version)) + (sha256 + (base32 + "0yw23lp9xjvbpswzghkmjiayw7p19hbvmgv58k3i6b8g5nav4qcg")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-crayon" ,r-crayon) + ("r-debugme" ,r-debugme) + ("r-r6" ,r-r6))) + (home-page "https://github.com/r-lib/processx3") + (synopsis "Execute and control system processes") + (description + "This package provides portable tools to run system processes in the +background. It can check if a background process is running; wait on a +background process to finish; get the exit status of finished processes; kill +background processes and their children; restart processes. It can read the +standard output and error of the processes, using non-blocking connections. +@code{processx} can poll a process for standard output or error, with a +timeout. It can also poll several processes at once.") + (license license:expat))) + +(define-public r-tsp + (package + (name "r-tsp") + (version "1.1-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "TSP" version)) + (sha256 + (base32 + "03xxfr5kk4zhzpb1q1pwncdp0dhchm9b48wzhvvxn2dxf3mnby2w")))) + (properties `((upstream-name . "TSP"))) + (build-system r-build-system) + (propagated-inputs `(("r-foreach" ,r-foreach))) + (home-page "https://cran.r-project.org/web/packages/TSP/") + (synopsis "Traveling salesperson problem (TSP)") + (description "This package provides basic infrastructure and some +algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the +traveling salesman problem).") + (license license:gpl3))) + +(define-public r-qap + (package + (name "r-qap") + (version "0.1-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "qap" version)) + (sha256 + (base32 + "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "http://cran.r-project.org/web/packages/qap/") + (synopsis "Heuristics for the quadratic assignment problem (QAP)") + (description "This package implements heuristics for the @dfn{quadratic +assignment problem} (QAP). Currently only a simulated annealing heuristic is +available.") + (license license:gpl3))) + +(define-public r-gclus + (package + (name "r-gclus") + (version "1.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "gclus" version)) + (sha256 + (base32 + "02ba6zj9bjwrzykamjp40ajynx9xjx9h2i85n0ym0r5lcki4x6fn")))) + (build-system r-build-system) + (propagated-inputs `(("r-cluster" ,r-cluster))) + (home-page "http://cran.r-project.org/web/packages/gclus/") + (synopsis "Clustering graphics") + (description "This package orders panels in scatterplot matrices and +parallel coordinate displays by some merit index. It contains various indices +of merit, ordering functions, and enhanced versions of @code{pairs} and +@code{parcoord} which color panels according to their merit level.") + (license license:gpl2+))) + +(define-public r-webshot + (package + (name "r-webshot") + (version "0.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "webshot" version)) + (sha256 + (base32 + "07r71zzmggp4jf92x4ws4wg6v1x98vaj01lsar85bnb30n5vx8gh")))) + (build-system r-build-system) + (propagated-inputs + `(("r-jsonlite" ,r-jsonlite) + ("r-magrittr" ,r-magrittr) + ("r-processx" ,r-processx) + ("r-withr" ,r-withr))) + (home-page "https://github.com/wch/webshot/") + (synopsis "Take screenshots of web pages") + (description + "Webshot makes it easy to take screenshots of web pages from within R. +It can also run Shiny applications locally and take screenshots of the +application; and it can render and screenshot static as well as interactive R +Markdown documents.") + (license license:gpl2))) + +(define-public r-seriation + (package + (name "r-seriation") + (version "1.2-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "seriation" version)) + (sha256 + (base32 + "1q6hw4hjw224b4y0dc0j630v2pgj6sn455nwkilb70w8k31hpk92")))) + (build-system r-build-system) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-colorspace" ,r-colorspace) + ("r-dendextend" ,r-dendextend) + ("r-gclus" ,r-gclus) + ("r-gplots" ,r-gplots) + ("r-mass" ,r-mass) + ("r-qap" ,r-qap) + ("r-registry" ,r-registry) + ("r-tsp" ,r-tsp))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "http://s2.smu.edu/IDA/seriation/") + (synopsis "Infrastructure for ordering objects using seriation") + (description + "This package provides infrastructure for seriation with an +implementation of several seriation/sequencing techniques to reorder matrices, +dissimilarity matrices, and dendrograms. It also provides (optimally) +reordered heatmaps, color images and clustering visualizations like +dissimilarity plots, and visual assessment of cluster tendency plots (VAT and +iVAT).") + (license license:gpl3))) + +(define-public r-heatmaply + (package + (name "r-heatmaply") + (version "0.14.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "heatmaply" version)) + (sha256 + (base32 + "03p2caclhfgqgpx3wwck5h06jy3mxgs05gjmwkb7hmwghkjh41jc")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-colorspace" ,r-colorspace) + ("r-dendextend" ,r-dendextend) + ("r-ggplot2" ,r-ggplot2) + ("r-gplots" ,r-gplots) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-magrittr" ,r-magrittr) + ("r-plotly" ,r-plotly) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-reshape2" ,r-reshape2) + ("r-scales" ,r-scales) + ("r-seriation" ,r-seriation) + ("r-viridis" ,r-viridis) + ("r-webshot" ,r-webshot))) + (home-page "https://cran.r-project.org/package=heatmaply") + (synopsis "Interactive cluster heat maps using plotly") + (description "Heatmaps are used in many fields for visualizing +observations, correlations, missing values patterns, and more. Interactive +heatmaps allow the inspection of specific value by hovering the mouse over a +cell, as well as zooming into a region of the heatmap by dragging a rectangle +around the relevant area. This work is based on the @code{ggplot2} and +@code{plotly.js} engine. It produces similar heatmaps as @code{heatmap.2} or +@code{d3heatmap}, with the advantage of speed, the ability to zoom from the +dendrogram panes, and the placing of factor variables in the sides of the +heatmap.") + (license (list license:gpl2 license:gpl3)))) + +(define-public r-xfun + (package + (name "r-xfun") + (version "0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "xfun" version)) + (sha256 + (base32 + "1sm51gmwgw876d6d1q8smxmfgfh6zsnykfx8qp8z6jmh0fvd89pj")))) + (build-system r-build-system) + (home-page "https://github.com/yihui/xfun") + (synopsis "Miscellaneous functions") + (description + "This package provides miscellaneous functions commonly used in other +packages maintained by Yihui Xie.") + (license license:expat))) + +(define-public r-utf8 + (package + (name "r-utf8") + (version "1.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "utf8" version)) + (sha256 + (base32 + "03s4j6059q0nly68vpk6wy3p3f5ypakw93fj35kzd82b4z1r9cs3")))) + (build-system r-build-system) + (home-page "https://github.com/patperry/r-utf8") + (synopsis "Unicode text processing") + (description + "This package provides tools to process and print UTF-8 encoded +international text (Unicode). Input, validate, normalize, encode, format, and +display.") + (license license:asl2.0))) + +(define-public r-pillar + (package + (name "r-pillar") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "pillar" version)) + (sha256 + (base32 + "1gh3j2pbbf5y4d5nyqnlr0x27jjyvjjspcccmw61airs1n6rx8jq")))) + (build-system r-build-system) + (propagated-inputs + `(("r-cli" ,r-cli) + ("r-crayon" ,r-crayon) + ("r-rlang" ,r-rlang) + ("r-utf8" ,r-utf8))) + (home-page "https://github.com/r-lib/pillar") + (synopsis "Coloured formatting for columns") + (description + "This package provides a @code{pillar} generic designed for formatting +columns of data using the full range of colours provided by modern +terminals.") + (license license:gpl3))) + +(define-public r-uuid + (package + (name "r-uuid") + (version "0.1-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "uuid" version)) + (sha256 + (base32 + "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx")))) + (build-system r-build-system) + (home-page "http://www.rforge.net/uuid") + (synopsis "Tools for generating and handling of UUIDs") + (description + "This package provides tools for generating and handling of +@dfn{Universally Unique Identifiers} (UUIDs).") + (license license:expat))) + +(define-public r-tinytex + (package + (name "r-tinytex") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "tinytex" version)) + (sha256 + (base32 + "0mhxlr4709mca9jshnah5i7yjyy6k12s933619p7p9c8nbqj39cn")))) + (build-system r-build-system) + (home-page "https://github.com/yihui/tinytex") + (synopsis "Helper functions for TeX Live and compiling LaTeX documents") + (description + "This package provides helper functions to install and maintain the LaTeX +distribution named TinyTeX, a lightweight, cross-platform, portable, and +easy-to-maintain version of TeX Live. This package also contains helper +functions to compile LaTeX documents, and install missing LaTeX packages +automatically.") + (license license:expat))) + +(define-public r-metap + (package + (name "r-metap") + (version "0.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "metap" version)) + (sha256 + (base32 + "06ny9zkilawdy0s8yiwhnygs3yppw89bbyf76zgdavykbzscz5lh")))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice))) + (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") + (synopsis "Meta-analysis of significance values") + (description + "The canonical way to perform meta-analysis involves using effect sizes. +When they are not available this package provides a number of methods for +meta-analysis of significance values including the methods of Edgington, +Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate +published results; and a routine for graphical display.") + (license license:gpl2))) |