diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 403 |
1 files changed, 320 insertions, 83 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 36f1889efa..db1a6871ad 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2016 Roel Janssen <roel@gnu.org> ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> +;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -101,7 +102,7 @@ be output in text, PostScript, PDF or HTML.") (define-public r (package (name "r") - (version "3.3.1") + (version "3.3.2") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -109,7 +110,7 @@ be output in text, PostScript, PDF or HTML.") version ".tar.gz")) (sha256 (base32 - "1qm9znh8akfy9fkzzi6f1vz2w1dd0chsr6qn7kw80lqzhgjrmi9x")))) + "0k2i9qdd83g09fcpls2198q4ykxkii5skczb514gnx7mx4hsv56j")))) (build-system gnu-build-system) (arguments `(#:make-flags @@ -205,16 +206,63 @@ publication-quality data plots. A large amount of 3rd-party packages are available, greatly increasing its breadth and scope.") (license license:gpl3+))) +(define-public r-bit + (package + (name "r-bit") + (version "1.1-12") + (source + (origin + (method url-fetch) + (uri (cran-uri "bit" version)) + (sha256 + (base32 + "0a6ig6nnjzq80r2ll4hc74za3xwzbzig6wlyb4dby0knzf3iqa6f")))) + (build-system r-build-system) + (home-page "http://ff.r-forge.r-project.org") + (synopsis "Class for vectors of 1-bit booleans") + (description + "This package provides bitmapped vectors of booleans (no @code{NA}s), +coercion from and to logicals, integers and integer subscripts, fast boolean +operators and fast summary statistics. With @code{bit} class vectors of true +binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.") + (license license:gpl2))) + +(define-public r-bit64 + (package + (name "r-bit64") + (version "0.9-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "bit64" version)) + (sha256 + (base32 + "0fz5m3fhvxgwjl76maag7yn0zdw24rx34gy6v77378fajag9yllg")))) + (build-system r-build-system) + (propagated-inputs + `(("r-bit" ,r-bit))) + (home-page "http://ff.r-forge.r-project.org/") + (synopsis "S3 class for vectors of 64 bit integers") + (description + "The bit64 package provides serializable S3 atomic 64 bit (signed) +integers that can be used in vectors, matrices, arrays and @code{data.frames}. +Methods are available for coercion from and to logicals, integers, doubles, +characters and factors as well as many elementwise and summary functions. +Many fast algorithmic operations such as @code{match} and @code{order} support +interactive data exploration and manipulation and optionally leverage +caching.") + (license license:gpl2))) + (define-public r-colorspace (package (name "r-colorspace") - (version "1.2-7") + (version "1.3-2") (source (origin (method url-fetch) (uri (cran-uri "colorspace" version)) (sha256 - (base32 "0flw97iwwpkxy6si9cn982jhl61wb1rxi3r0nz2xxf0c3fzw18d5")))) + (base32 "0d1ya7hx4y58n5ivwmdmq2zgh0g2sbv7ykh13n85c1355csd57yx")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/colorspace") (synopsis "Color space manipulation") @@ -276,13 +324,13 @@ OpenSSL should be used.") (define-public r-estimability (package (name "r-estimability") - (version "1.1-1") + (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "estimability" version)) (sha256 (base32 - "049adh8i0ad0m0qln2ylqdxcs5v2q9zfignn2a50r5f93ip2ay6w")))) + "13b80bpnbrarazjvnpnk91ljjsqgfm2fm3gy66aj09cmmsmv199h")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/estimability") (synopsis "Tools for assessing estimability of linear predictions") @@ -394,13 +442,13 @@ Munsell colour system.") (define-public r-rcpp (package (name "r-rcpp") - (version "0.12.7") + (version "0.12.8") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "1ipid4yfqp1k5c70f7bz7izzq63srmrcxhiqrnyilk2wgrvd7ypb")))) + (base32 "0is1vql1q82g7yakad4skx707ip0fx3rgdwv9a8mi8259gly2qji")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ Integration") @@ -440,14 +488,14 @@ and operations on them using LAPACK and SuiteSparse.") (define-public r-mgcv (package (name "r-mgcv") - (version "1.8-15") + (version "1.8-16") (source (origin (method url-fetch) (uri (cran-uri "mgcv" version)) (sha256 (base32 - "05xzmsx51y92c0r0yihac8m9d3v1sqnn8ahcgm3q75j8z6zybsjs")))) + "0pj31gdwra7nv8spys4pfcbmsik99q1y1d0d2g37ywc3sz5s0rlj")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/mgcv") (synopsis "Mixed generalised additive model computation") @@ -638,13 +686,13 @@ using just two functions: melt and dcast (or acast).") (define-public r-scales (package (name "r-scales") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "scales" version)) (sha256 - (base32 "19y6q4j8vpmc73dnn4ncp5wj44gri7m77ys3z2rn3crrcc9zc7l5")))) + (base32 "1lqccfmqdwrw0cjyqvw2zvgpk2jvnqrfb303l1raqyyf3zxqhav4")))) (build-system r-build-system) (propagated-inputs `(("r-dichromat" ,r-dichromat) @@ -664,22 +712,22 @@ legends.") (define-public r-ggplot2 (package (name "r-ggplot2") - (version "2.1.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "ggplot2" version)) (sha256 - (base32 "0s9rvp0f736ji6p9xpxq54agxf95pjkql4sj7ag0hv2xhnp27hzj")))) + (base32 "0543782ddv2hp6s0l702mnxfg8n7a6qlbm8bm55x22hnqgz8kg2z")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) ("r-gtable" ,r-gtable) ("r-plyr" ,r-plyr) - ("r-proto" ,r-proto) + ("r-lazyeval" ,r-lazyeval) + ("r-tibble" ,r-tibble) ("r-reshape2" ,r-reshape2) - ("r-scales" ,r-scales) - ("r-svglite" ,r-svglite))) + ("r-scales" ,r-scales))) (home-page "http://ggplot2.org") (synopsis "An implementation of the grammar of graphics") (description @@ -694,14 +742,14 @@ aesthetic attributes.") (define-public r-gdtools (package (name "r-gdtools") - (version "0.1.1") + (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "gdtools" version)) (sha256 (base32 - "1l9d759x9s4ddz51sls8kcjps2i9kwfbc72dnagrdavh82h0al8n")))) + "1prh814lw3qkgnf0760cvpic1k68jhlkpcxlksv8chjkvsrnnf09")))) (build-system r-build-system) (native-inputs `(("r-rcpp" ,r-rcpp) @@ -720,14 +768,14 @@ and to generate base64 encoded string from raster matrix.") (define-public r-svglite (package (name "r-svglite") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "svglite" version)) (sha256 (base32 - "11ryicjglfi6jvkk4jgg5kra42qbs5z2zid7jjhlslpjcljfwc70")))) + "1s1gvmlmmna5y4jsn9h6438pg5b86fl4nwfvkgm6n4h6ljfgqyx3")))) (build-system r-build-system) (native-inputs `(("r-rcpp" ,r-rcpp))) (propagated-inputs @@ -803,13 +851,13 @@ R/DBMS implementations.") (define-public r-bh (package (name "r-bh") - (version "1.60.0-2") + (version "1.62.0-1") (source (origin (method url-fetch) (uri (cran-uri "BH" version)) (sha256 (base32 - "136497fng9bcvrf8favpj8inz96pxdwp1rrb2k00sxjxjbgawhg4")))) + "01vfdpfznd4ynqql33z238xr262mvy3i80lyi8l3a3p3hi0a262p")))) (build-system r-build-system) (home-page "https://github.com/eddelbuettel/bh") (synopsis "R package providing subset of Boost headers") @@ -926,13 +974,13 @@ syntax that can be converted to XHTML or other formats.") (define-public r-yaml (package (name "r-yaml") - (version "2.1.13") + (version "2.1.14") (source (origin (method url-fetch) (uri (cran-uri "yaml" version)) (sha256 (base32 - "18kz5mfn7qpif5pn91w4vbrc5bkycsj85vwm5wxwzjlb02i9mxi6")))) + "0x88xicrf7vwp77xgan27mnpdljhpkn0pz5kphnwqi3ddy25k9a1")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/yaml/") (synopsis "Methods to convert R data to YAML and back") @@ -944,18 +992,17 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.14") + (version "1.15.1") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "1v0s0knb294p7a2xkwy35bhg0w8p3qcgyphd748sj86hh8a30vds")))) + "1pbxd3k7kv5sa1a5gxm0zc2bhjxdgx2nfch9xap5k85djmgsfqc1")))) (build-system r-build-system) (propagated-inputs `(("r-evaluate" ,r-evaluate) ("r-digest" ,r-digest) - ("r-formatr" ,r-formatr) ("r-highr" ,r-highr) ("r-markdown" ,r-markdown) ("r-stringr" ,r-stringr) @@ -1323,13 +1370,13 @@ and density estimation.") (define-public r-chron (package (name "r-chron") - (version "2.3-47") + (version "2.3-48") (source (origin (method url-fetch) (uri (cran-uri "chron" version)) (sha256 (base32 - "1xj50kk8b8mbjpszp8i0wbripb5a4b36jcscwlbyap8n4487g34s")))) + "1q1d0p2wq19w3mpfqnrg8nmspxqmhv4ap52r393s6y3abl36ccac")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/chron") (synopsis "Chronological R objects which can handle dates and times") @@ -1341,16 +1388,14 @@ times.") (define-public r-data-table (package (name "r-data-table") - (version "1.9.6") + (version "1.10.0") (source (origin (method url-fetch) (uri (cran-uri "data.table" version)) (sha256 (base32 - "0vi3zplpxqbg78z9ifjfs1kl2i8qhkqxr7l9ysp2663kq54w6x3g")))) + "1168arn4wjd1jj7kgr4sb8xd52hr8p8iqp85g5jwp3mkz4p76qfg")))) (build-system r-build-system) - (propagated-inputs - `(("r-chron" ,r-chron))) (home-page "https://github.com/Rdatatable/data.table/wiki") (synopsis "Enhanced version of data.frame R object") (description @@ -1483,16 +1528,14 @@ inference for statistical models.") (define-public r-coda (package (name "r-coda") - (version "0.18-1") + (version "0.19-1") (source (origin (method url-fetch) (uri (cran-uri "coda" version)) (sha256 (base32 - "03sc780734zj2kqcm8lkyvf76fql0jbfhkblpn8l58zmb6cqi958")))) + "14a4a8df4ygj05h37chmdn8kzcqs07fpbflxfrq530563mrza7yl")))) (build-system r-build-system) - (propagated-inputs - `(("r-lattice" ,r-lattice))) (home-page "http://cran.r-project.org/web/packages/coda") (synopsis "This is a package for Output Analysis and Diagnostics for MCMC") (description "This package provides functions for summarizing and plotting @@ -1504,14 +1547,14 @@ chain.") (define-public r-ade4 (package (name "r-ade4") - (version "1.7-4") + (version "1.7-5") (source (origin (method url-fetch) (uri (cran-uri "ade4" version)) (sha256 (base32 - "17sbicash7z4b63dlrbaf8xx2pbwh62vykzvhdjs43h8jkl881y7")))) + "0aaqbnydm5fb37nrvqj4bx6hxax7255j426cwh2lh88nyvznbq37")))) (build-system r-build-system) (home-page "http://pbil.univ-lyon1.fr/ADE-4") (synopsis "Multivariate data analysis and graphical display") @@ -1776,14 +1819,14 @@ collation, and NAMESPACE files.") (define-public r-openssl (package (name "r-openssl") - (version "0.9.5") + (version "0.9.6") (source (origin (method url-fetch) (uri (cran-uri "openssl" version)) (sha256 (base32 - "1lal8mmcwjhhln10mfi96ipv3d364k0wiviiln220wvhddcpr9pp")))) + "0ffwllii8xl6sa2v66134g0fwaw1y3zn3mvaa4nrc120vv5d3mkd")))) (build-system r-build-system) (inputs `(("openssl" ,openssl))) @@ -1833,13 +1876,13 @@ functions make it easy to control additional request components.") (define-public r-git2r (package (name "r-git2r") - (version "0.15.0") + (version "0.18.0") (source (origin (method url-fetch) (uri (cran-uri "git2r" version)) (sha256 (base32 - "1rpdf85wy9fp456ypvbhl3p9whkb7kgl0n7rkqxd2bhvyzkvjak8")))) + "0bgzdsdi9n6l8pchivs6a2g4ksa56qs8hygpyv2c0ndqmx4jxcwi")))) (build-system r-build-system) ;; This R package contains modified sources of libgit2. This modified ;; version of libgit2 is built as the package is built. Hence libgit2 is @@ -1926,14 +1969,14 @@ were originally a part of the r-devtools package.") (define-public r-hms (package (name "r-hms") - (version "0.2") + (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "hms" version)) (sha256 (base32 - "0ln1dc26mkl5pc26vvyf01d35x75q6cjaj39cccxp67chbwbdlds")))) + "127znf522r5mn3k6frhdd7pqh063bs3l85gn9h7cx50hpjf2as4k")))) (build-system r-build-system) (home-page "https://github.com/rstats-db/hms") (synopsis "Pretty time of day") @@ -1970,13 +2013,13 @@ disk (or a connection).") (define-public r-plotrix (package (name "r-plotrix") - (version "3.6-3") + (version "3.6-4") (source (origin (method url-fetch) (uri (cran-uri "plotrix" version)) (sha256 (base32 - "0h97jra8zqssi9j4i0psa6c7ya49ya8jd2qc18lc61a4s2yn8w91")))) + "1wxzjnzvkl3aga51ad2xhv4s7v46kvnp4z0nz4cb9cn10057sfw8")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/plotrix") (synopsis "Various plotting functions") @@ -2049,13 +2092,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.7.500.0.0") + (version "0.7.600.1.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "06qb6877c5qd8lvnc4b27z8fwb5r5pyylkj0g6kj1rn868zkh5ps")) + "0k1wniip184j0ckcg9kcjy2q4mcfj5jpd1nkk4l0ab75ad8znywv")) (modules '((guix build utils))) ;; Remove bundled armadillo sources (snippet @@ -2130,27 +2173,50 @@ ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off-error-free sum and cumsum, etc.") (license license:gpl3+))) +(define-public r-rprojroot + (package + (name "r-rprojroot") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "rprojroot" version)) + (sha256 + (base32 + "04ywfpar4d2hyi4rh4fbixrbzd665gpa2jhx67g8857cr70pp0nh")))) + (build-system r-build-system) + (propagated-inputs + `(("r-backports" ,r-backports))) + (home-page "https://github.com/krlmlr/rprojroot") + (synopsis "Finding files in project subdirectories") + (description + "This package helps accessing files relative to a project root. It +provides helpers for robust, reliable and flexible paths to files below a +project root. The root of a project is defined as a directory that matches a +certain criterion, e.g., it contains a certain regular file.") + (license license:gpl3))) + (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "1.1") + (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 (base32 - "1czvkaz1ji3jyj6qrvbswisqs9d05ljqc4vjkfdrf6hygix7azd0")))) + "1vvxyf3zhyxx6k697lia299456hryp8nh3zr0fc27f3107a8mcjf")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs `(("r-catools" ,r-catools) ("r-evaluate" ,r-evaluate) - ("r-tibble" ,r-tibble) ("r-htmltools" ,r-htmltools) ("r-jsonlite" ,r-jsonlite) ("r-base64enc" ,r-base64enc) ("r-knitr" ,r-knitr) + ("r-rprojroot" ,r-rprojroot) ("r-yaml" ,r-yaml) ("ghc-pandoc" ,ghc-pandoc))) (home-page "http://rmarkdown.rstudio.com") @@ -2203,20 +2269,44 @@ grobs.") and draw tables.") (license license:gpl2+))) +(define-public r-plogr + (package + (name "r-plogr") + (version "0.1-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "plogr" version)) + (sha256 + (base32 + "13zliqlbkl8b04k9ga0sx5jsh7k867gracgl84l2a9kcqy9mqx92")))) + (build-system r-build-system) + (home-page "https://github.com/krlmlr/plogr") + (synopsis "R bindings for the plog C++ logging library") + (description + "This package provides the header files for a stripped-down version of +the plog header-only C++ logging library, and a method to log to R's standard +error stream.") + (license license:expat))) + (define-public r-rsqlite (package (name "r-rsqlite") - (version "1.0.0") + (version "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "RSQLite" version)) (sha256 (base32 - "08b1syv8z887gxiw8i09dpqh0zisfb6ihq6qqr01zipvkahzq34f")))) + "11vnzds5gidgakdmsbdn0bvnsz064ym1savwb7l6gc1bjn7xa2k4")))) (properties `((upstream-name . "RSQLite"))) (build-system r-build-system) (propagated-inputs - `(("r-dbi" ,r-dbi))) + `(("r-dbi" ,r-dbi) + ("r-bh" ,r-bh) + ("r-memoise" ,r-memoise) + ("r-plogr" ,r-plogr) + ("r-rcpp" ,r-rcpp))) (home-page "https://github.com/rstats-db/RSQLite") (synopsis "SQLite interface for R") (description @@ -2259,20 +2349,18 @@ ldap, and also supports cookies, redirects, authentication, etc.") (define-public r-xml (package (name "r-xml") - (version "3.98-1.4") + (version "3.98-1.5") (source (origin (method url-fetch) (uri (cran-uri "XML" version)) (sha256 (base32 - "09hiy5a875v2fhsgrsfymrwccn9249wnnsr6ck2slrig65svq2lw")))) + "0dcdj7ryn8lm7wmv4hqhh9jxa5k97l6ad8xyvb932yfkwj1g1byy")))) (properties `((upstream-name . "XML"))) (build-system r-build-system) (inputs `(("libxml2" ,libxml2))) - (propagated-inputs - `(("r-rcurl" ,r-rcurl))) (home-page "http://www.omegahat.org/RSXML") (synopsis "Tools for parsing and generating XML within R") (description @@ -2420,13 +2508,13 @@ worker processes and collect and return the results on the master.") (define-public r-sparsem (package (name "r-sparsem") - (version "1.72") + (version "1.74") (source (origin (method url-fetch) (uri (cran-uri "SparseM" version)) (sha256 (base32 - "0zpb1swn9xjkb22sky10ixff7vqfiz9m36nkbc1qqbm9frcldnka")))) + "1fpfhld887y5lyb8jydprmv5krqm1fk6n53z942b4g4z1v4g04j7")))) (properties `((upstream-name . "SparseM"))) (inputs @@ -2954,13 +3042,13 @@ maintenance for package developers.") (define-public r-r-utils (package (name "r-r-utils") - (version "2.4.0") + (version "2.5.0") (source (origin (method url-fetch) (uri (cran-uri "R.utils" version)) (sha256 (base32 - "0cn0wlmgwclmqak05825wrk9q894xa4qjqa7rn0i9p4ss7k6vifj")))) + "17q3w5dlly5xl2srrzsmf9s7vs5d576vqbcs6sr2p5x4qvqa1q8s")))) (properties `((upstream-name . "R.utils"))) (build-system r-build-system) (propagated-inputs @@ -3002,13 +3090,13 @@ persistent (on the file system).") (define-public r-r-rsp (package (name "r-r-rsp") - (version "0.30.0") + (version "0.40.0") (source (origin (method url-fetch) (uri (cran-uri "R.rsp" version)) (sha256 (base32 - "1ssykygqkxzx9qblxhavxlf2z6r5bhk0s47yw1dllfiyc8zy7jv2")))) + "1hz5fnxz30m3cc7x7ha1swx4pn8c2244z6ka6v9m3l5lpdgc1367")))) (properties `((upstream-name . "R.rsp"))) (build-system r-build-system) (propagated-inputs @@ -3204,13 +3292,13 @@ features present in other programming languages.") (define-public r-plotly (package (name "r-plotly") - (version "4.5.2") + (version "4.5.6") (source (origin (method url-fetch) (uri (cran-uri "plotly" version)) (sha256 (base32 - "08shs0qhy9js0fpj3d4rzfbwmw11ki3z5vg8jszfm6m69mfkgzw1")))) + "09yw977yxlcxv57kni3q899zrxyxa6pznr06cylr9lqkyr7llfhx")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -3421,40 +3509,59 @@ definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.") (license license:lgpl2.0+))) +(define-public r-base64 + (package + (name "r-base64") + (version "2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "base64" version)) + (sha256 + (base32 + "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf")))) + (build-system r-build-system) + (propagated-inputs + `(("r-openssl" ,r-openssl))) + (home-page "http://cran.r-project.org/web/packages/base64") + (synopsis "Base64 encoder and decoder") + (description + "This package is a compatibility wrapper to replace the orphaned package +by Romain Francois. New applications should use the openssl or base64enc +package instead.") + (license license:expat))) + (define-public r-hmisc (package (name "r-hmisc") - (version "4.0-0") + (version "4.0-2") (source (origin (method url-fetch) (uri (cran-uri "Hmisc" version)) (sha256 (base32 - "0azxmg9h9c456biydc0wpi9xhljmd37m8bv0zaadbvc93g7x0l4b")))) + "1lg9k0kj803wsm3h0a991q9l2lrgsqryzfv2z79b88kjbfapqpqr")))) (properties `((upstream-name . "Hmisc"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (propagated-inputs `(("r-acepack" ,r-acepack) - ("r-cluster" ,r-cluster) + ("r-base64" ,r-base64) + ("r-base64enc" ,r-base64enc) ("r-data-table" ,r-data-table) - ("r-foreign" ,r-foreign) ("r-formula" ,r-formula) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-gtable" ,r-gtable) - ("r-lattice" ,r-lattice) ;; Hmisc needs survival >= 2.40.1, so it cannot use the survival - ;; package that comes with R 3.3.1. + ;; package that comes with R 3.3.2. ("r-survival" ,r-survival) ("r-latticeextra" ,r-latticeextra) ("r-htmltable" ,r-htmltable) ("r-htmltools" ,r-htmltools) - ("r-viridis" ,r-viridis) - ("r-nnet" ,r-nnet) - ("r-rpart" ,r-rpart))) + ("r-viridis" ,r-viridis))) (home-page "http://biostat.mc.vanderbilt.edu/Hmisc") (synopsis "Miscellaneous data analysis and graphics functions") (description @@ -3530,14 +3637,14 @@ routines.") (define-public r-fastcluster (package (name "r-fastcluster") - (version "1.1.20") + (version "1.1.22") (source (origin (method url-fetch) (uri (cran-uri "fastcluster" version)) (sha256 (base32 - "0rlbxhh894znf10x0xgkv9dzpibgq9jw5aqpgviccdnxc2c5hwid")))) + "006k9isra5biyavqwci61avladw19mhp6kmkjj3777rl1r4r8b9z")))) (build-system r-build-system) (home-page "http://danifold.net/fastcluster.html") (synopsis "Fast hierarchical clustering routines") @@ -3730,16 +3837,14 @@ estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) (define-public r-zoo (package (name "r-zoo") - (version "1.7-13") + (version "1.7-14") (source (origin (method url-fetch) (uri (cran-uri "zoo" version)) (sha256 (base32 - "0m67bnrg7r1jxvs9p7rpa430szp5qfp65r056yb8bivpc16jd98c")))) + "167m142rwwfy8b9hnfc3fi28dcsdjk61g1crqhll6sh5xmgnfn28")))) (build-system r-build-system) - (propagated-inputs - `(("r-lattice" ,r-lattice))) (home-page "http://zoo.R-Forge.R-project.org/") (synopsis "S3 infrastructure for regular and irregular time series") (description "This package contains an S3 class with methods for totally @@ -3767,3 +3872,135 @@ with alternating row colors) in LaTeX and HTML formats easily from @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and @code{cbind.mytable} objects.") (license license:gpl2+))) + +(define-public r-vipor + (package + (name "r-vipor") + (version "0.4.4") + (source (origin + (method url-fetch) + (uri (cran-uri "vipor" version)) + (sha256 + (base32 + "0p1z9a3fazl78pj8a1i2n62v8hrs8cinq82j9wpawhmfkn3dggss")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/vipor") + (synopsis "Plot categorical data using noise and density estimates") + (description + "This package provides tools to generate a violin point plot, a +combination of a violin/histogram plot and a scatter plot by offsetting points +within a category based on their density using quasirandom noise.") + (license license:gpl2+))) + +(define-public r-beeswarm + (package + (name "r-beeswarm") + (version "0.2.3") + (source (origin + (method url-fetch) + (uri (cran-uri "beeswarm" version)) + (sha256 + (base32 + "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581")))) + (build-system r-build-system) + (home-page "http://www.cbs.dtu.dk/~eklund/beeswarm/") + (synopsis "Implementation of bee swarm plots") + (description + "This package provides an implementation of bee swarm plots. The bee +swarm plot is a one-dimensional scatter plot like stripchart, but with +closely-packed, non-overlapping points.") + (license license:artistic2.0))) + +(define-public r-sourcetools + (package + (name "r-sourcetools") + (version "0.1.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "sourcetools" version)) + (sha256 + (base32 + "0jx6kslygfqaic3cmjwag3dy98q1a2dw20cz7z8agsknmmbk6dy2")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/sourcetools") + (synopsis "Tools for reading, tokenizing and parsing R code") + (description + "The sourcetools package provides both an R and C++ interface for the +tokenization of R code, and helpers for interacting with the tokenized +representation of R code.") + (license license:expat))) + +(define-public r-ggbeeswarm + (package + (name "r-ggbeeswarm") + (version "0.5.3") + (source (origin + (method url-fetch) + (uri (cran-uri "ggbeeswarm" version)) + (sha256 + (base32 + "1jgp55rvmzc4agcrlsjn8m5lk85di9c4wj94xzikqkql4lvq3qpd")))) + (build-system r-build-system) + (propagated-inputs + `(("r-beeswarm" ,r-beeswarm) + ("r-ggplot2" ,r-ggplot2) + ("r-vipor" ,r-vipor))) + (home-page "https://github.com/eclarke/ggbeeswarm") + (synopsis "Categorical scatter (violin point) plots") + (description + "This package provides two methods of plotting categorical scatter plots +such that the arrangement of points within a category reflects the density of +data at that region, and avoids over-plotting.") + (license license:gpl2+))) + +(define-public r-ggthemes + (package + (name "r-ggthemes") + (version "3.3.0") + (source (origin + (method url-fetch) + (uri (cran-uri "ggthemes" version)) + (sha256 + (base32 + "1qdxg2siwsiq32fmgcxn4vihgxad9v8q0aqigl7a94c26bwxs7y2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-colorspace" ,r-colorspace) + ("r-ggplot2" ,r-ggplot2) + ("r-scales" ,r-scales))) + (home-page "https://cran.rstudio.com/web/packages/ggthemes") + (synopsis "Extra themes, scales and geoms for @code{ggplot2}") + (description "This package provides extra themes and scales for +@code{ggplot2} that replicate the look of plots by Edward Tufte and +Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The +Wall Street Journal, among others. This package also provides +@code{geoms} for Tufte's box plot and range frame.") + (license license:gpl2))) + +(define-public r-statmod + (package + (name "r-statmod") + (version "1.4.27") + (source (origin + (method url-fetch) + (uri (cran-uri "statmod" version)) + (sha256 + (base32 + "14yilq9d3z20hig4rs8bjqyydw3dfx90mhmzvw9w8p16h0s595sn")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/statmod") + (native-inputs + `(("gfortran" ,gfortran))) + (synopsis "Statistical modeling") + (description + "This package provides a collection of algorithms and functions to aid +statistical modeling. It includes growth curve comparisons, limiting dilution +analysis (aka ELDA), mixed linear models, heteroscedastic regression, +inverse-Gaussian probability calculations, Gauss quadrature and a secure +convergence algorithm for nonlinear models. It also includes advanced +generalized linear model functions that implement secure convergence, +dispersion modeling and Tweedie power-law families.") + ;; Statmod is distributed under either license + (license (list license:gpl2 license:gpl3)))) |