diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 589 |
1 files changed, 515 insertions, 74 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 9c197f4977..3d0faf7572 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -40,6 +40,7 @@ #:use-module (gnu packages image) #:use-module (gnu packages java) #:use-module (gnu packages maths) + #:use-module (gnu packages multiprecision) #:use-module (gnu packages pcre) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) @@ -97,7 +98,7 @@ be output in text, PostScript, PDF or HTML.") (define-public r (package (name "r") - (version "3.2.3") + (version "3.2.5") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -105,7 +106,7 @@ be output in text, PostScript, PDF or HTML.") version ".tar.gz")) (sha256 (base32 - "1hdnv77ralzcx5k5b88jq1r8l6zqnywpq00g2qs949rqh63psfxr")))) + "1dc0iybjk9kr1nghz3fpir6mb9hb9rnrz9bgh00w5pg5vir5cx30")))) (build-system gnu-build-system) (arguments `(#:make-flags @@ -224,14 +225,19 @@ effects of different types of color-blindness.") (define-public r-digest (package (name "r-digest") - (version "0.6.8") + (version "0.6.9") (source (origin (method url-fetch) (uri (cran-uri "digest" version)) (sha256 - (base32 "0m9grqv67hhf51lz10whymhw0g0d98466ka694kya5x95hn44qih")))) + (base32 "0ixy1mb7kfl20lkckqiilpw03g1ip4ibihs03gicz7w625hc7zcm")))) (build-system r-build-system) + ;; Vignettes require r-knitr, which requires r-digest, so we have to + ;; disable them and the tests. + (arguments + `(#:tests? #f + #:configure-flags (list "--no-build-vignettes"))) (home-page "http://dirk.eddelbuettel.com/code/digest.html") (synopsis "Create cryptographic hash digests of R objects") (description @@ -305,13 +311,13 @@ see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"") (define-public r-munsell (package (name "r-munsell") - (version "0.4.2") + (version "0.4.3") (source (origin (method url-fetch) (uri (cran-uri "munsell" version)) (sha256 - (base32 "1bi5yi0i80778bbzx2rm4f0glpc34kvh24pwwfhm4v32izsqgrw4")))) + (base32 "0jdxlbjslkzaqgp058da1cgm85qvqi09wpcgpvp4hvwnmy83qz1r")))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace))) @@ -325,13 +331,13 @@ Munsell colour system.") (define-public r-rcpp (package (name "r-rcpp") - (version "0.12.0") + (version "0.12.4") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "182109z0yc1snqgd833ssl2cix6cbq83bcxmy5344b15ym820y38")))) + (base32 "1lyhyaxrnb5w4igi3l1p378s4jblcnrv6h7h5ym42ljm54mm44w3")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ Integration") @@ -408,14 +414,14 @@ designed by Cynthia Brewer as described at http://colorbrewer2.org") (define-public r-stringi (package (name "r-stringi") - (version "0.5-5") + (version "1.0-1") (source (origin (method url-fetch) (uri (cran-uri "stringi" version)) (sha256 (base32 - "183wrrjhpgl1wbnn9lhghyvhz7l2mc64mpcmzplckal7y9j7pmhw")))) + "1ld38536sswyywp6pyys3v8vkngbk5cksrhdxp8jyr6bz7qf8j77")))) (build-system r-build-system) (inputs `(("icu4c" ,icu4c))) (native-inputs `(("pkg-config" ,pkg-config))) @@ -480,13 +486,13 @@ using just two functions: melt and dcast (or acast).") (define-public r-scales (package (name "r-scales") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "scales" version)) (sha256 - (base32 "1kkgpqzb0a6lnpblhcprr4qzyfk5lhicdv4639xs5cq16n7bkqgl")))) + (base32 "19y6q4j8vpmc73dnn4ncp5wj44gri7m77ys3z2rn3crrcc9zc7l5")))) (build-system r-build-system) (propagated-inputs `(("r-dichromat" ,r-dichromat) @@ -506,13 +512,13 @@ legends.") (define-public r-ggplot2 (package (name "r-ggplot2") - (version "2.0.0") + (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "ggplot2" version)) (sha256 - (base32 "07r5zw0ccv4sf1mdxcz9wa86p2c6j61cnnq18qdjrh3zhhcbmdp2")))) + (base32 "0s9rvp0f736ji6p9xpxq54agxf95pjkql4sj7ag0hv2xhnp27hzj")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -593,13 +599,13 @@ R/DBMS implementations.") (define-public r-bh (package (name "r-bh") - (version "1.58.0-1") + (version "1.60.0-1") (source (origin (method url-fetch) (uri (cran-uri "BH" version)) (sha256 (base32 - "17rnwyw9ib2pvm60iixzkbz7ff4fslpifp1nlx4czp42hy67kqpf")))) + "08gc3b0irgvpjl59irdxs8jhlbky4yp4fvs3zi4pq0wdwj43cfsk")))) (build-system r-build-system) (home-page "https://github.com/eddelbuettel/bh") (synopsis "R package providing subset of Boost headers") @@ -611,13 +617,13 @@ for template use among CRAN packages.") (define-public r-evaluate (package (name "r-evaluate") - (version "0.8") + (version "0.8.3") (source (origin (method url-fetch) (uri (cran-uri "evaluate" version)) (sha256 (base32 - "137gc35jlizhqnx19mxim3llrkm403abj8ghb2b7v5ls9rvd40pq")))) + "08d6164m9wqf9qq6yh1s9a0qxwqzqpsq7312hilzy79gxf9gixzr")))) (build-system r-build-system) (propagated-inputs `(("r-stringr" ,r-stringr))) @@ -633,13 +639,13 @@ adapted for other output formats, such as HTML or LaTeX.") (define-public r-formatr (package (name "r-formatr") - (version "1.2.1") + (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "formatR" version)) (sha256 (base32 - "0f4cv2zv5wayyqx99ybfyl0p83kgjvnsv8dhcwa4s49kw6jsx1lr")))) + "09fsd0z6nhksc1h921h8q28f87hr6d1q8d6dmpxphjylb9r5xmj4")))) (build-system r-build-system) (home-page "http://yihui.name/formatR") (synopsis "Format R code automatically") @@ -734,13 +740,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.11") + (version "1.12.3") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "1ikjla0hnpjfkdbydqhhqypc0aiizbi4nyn8c694sdk9ca4jasdd")))) + "1v3rzv6wq8mvpdrljsaqk4z3f8323jnv385js24wmn4fglqly6dz")))) (build-system r-build-system) (propagated-inputs `(("r-evaluate" ,r-evaluate) @@ -763,13 +769,13 @@ generation in R using Literate Programming techniques.") (define-public r-microbenchmark (package (name "r-microbenchmark") - (version "1.4-2") + (version "1.4-2.1") (source (origin (method url-fetch) (uri (cran-uri "microbenchmark" version)) (sha256 (base32 - "05yxvdnkxr2ll94h6f2m5sn3gg7vrlm9nbdxgmj2g8cp8gfxpfkg")))) + "0qn5r1a6qidghcisc2hpbdmj62pnixc3zz6p4ipk8mvakf0hdsvg")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) @@ -822,13 +828,13 @@ understand the language at a deeper level.") (define-public r-memoise (package (name "r-memoise") - (version "0.2.1") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "memoise" version)) (sha256 (base32 - "19wm4b3kq6xva43kga3xydnl7ybl5mq7b4y2fczgzzjz63jd75y4")))) + "0sq2dhpvxy17v1baj256r0jnygdy3m5a8x4zh6vhv29957qnq6zx")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest))) @@ -862,20 +868,42 @@ New styles can also be created easily. This package was inspired by the \"chalk\" JavaScript project.") (license license:expat))) +(define-public r-praise + (package + (name "r-praise") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "praise" version)) + (sha256 + (base32 + "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw")))) + (build-system r-build-system) + (home-page "https://github.com/gaborcsardi/praise") + (synopsis "Functions to praise users") + (description + "This package provides template functions to assist in building friendly +R packages that praise their users.") + (license license:expat))) + (define-public r-testthat (package (name "r-testthat") - (version "0.10.0") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "testthat" version)) (sha256 (base32 - "0b3akwcx5mv9dmi8vssbk91hr3yrrdxd2fm6zhr31fnyz8kjx4pw")))) + "1ci1y54kaz7g4di79fcibp0m0wkkxn2glchhs6v8jfg6374ka410")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) - ("r-crayon" ,r-crayon))) + ("r-crayon" ,r-crayon) + ("r-magrittr" ,r-magrittr) + ("r-praise" ,r-praise) + ("r-r6" ,r-r6))) (home-page "https://github.com/hadley/testthat") (synopsis "Unit testing for R") (description @@ -886,21 +914,14 @@ flexible and easy to set up.") (define-public r-r6 (package (name "r-r6") - (version "2.1.1") + (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "R6" version)) (sha256 (base32 - "16qq35bgxgswf989yvsqkb6fv7srpf8n8dv2s2c0z9n6zgmwq66m")))) + "0yad91i9p4r8bbz6nq8zny39y767n9an7ak5p275ynx8km6v3yqv")))) (build-system r-build-system) - (propagated-inputs - `(("r-knitr" ,r-knitr) - ("r-microbenchmark" ,r-microbenchmark) - ("r-pryr" ,r-pryr) - ("r-testthat" ,r-testthat) - ("r-ggplot2" ,r-ggplot2) - ("r-scales" ,r-scales))) (home-page "https://github.com/wch/R6/") (synopsis "Classes with reference semantics in R") (description @@ -944,6 +965,110 @@ matter where it is stored, whether in a data frame, a data table or database.") (license license:expat))) +(define-public r-acepack + (package + (name "r-acepack") + (version "1.3-3.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "acepack" version)) + (sha256 + (base32 + "13ry3vyys12iplb14jfhmkrl9g5fxg3iijiggq4s4zb5m5436b1y")))) + (build-system r-build-system) + (inputs + `(("gfortran" ,gfortran))) + (home-page "http://cran.r-project.org/web/packages/acepack") + (synopsis "Functions for regression transformations") + (description + "This package provides ACE and AVAS methods for choosing regression +transformations.") + (license license:expat))) + +(define-public r-cluster + (package + (name "r-cluster") + (version "2.0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "cluster" version)) + (sha256 + (base32 + "1r669aaaia05i8sv8hxiig1ddah7hm8qw869wgig5i0zzk22bnfl")))) + (build-system r-build-system) + (inputs + `(("gfortran" ,gfortran))) + (home-page "http://cran.r-project.org/web/packages/cluster") + (synopsis "Methods for data cluster analysis") + (description + "This package provides tools that are useful in finding groups in data. +It is based on the methods described in Kaufman and Rousseeuw (1990) \"Finding +Groups in Data\".") + (license license:gpl2+))) + +(define-public r-foreign + (package + (name "r-foreign") + (version "0.8-66") + (source + (origin + (method url-fetch) + (uri (cran-uri "foreign" version)) + (sha256 + (base32 + "19278jm85728zb20800w6hq9q8jy8ywdn81mgmlnxkmrr9giwh6p")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/foreign") + (synopsis "Read data stored by other statistics software in R") + (description + "This package provides functions for reading and writing data stored by +some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka, and +for reading and writing some dBase files.") + (license license:gpl2+))) + +(define-public r-formula + (package + (name "r-formula") + (version "1.2-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "Formula" version)) + (sha256 + (base32 + "02in5325zzrqbhlygx6s0dinj6ymw845q70y56frqacv25ayzcax")))) + (properties `((upstream-name . "Formula"))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/Formula") + (synopsis "Extended model formulas") + (description + "This package provides a new class @code{Formula}, which extends the base +class @code{formula}. It supports extended formulas with multiple parts of +regressors on the right-hand side and/or multiple responses on the left-hand +side.") + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-locfit + (package + (name "r-locfit") + (version "1.5-9.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "locfit" version)) + (sha256 + (base32 + "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/locfit") + (synopsis "Local regression, likelihood and density estimation") + (description + "This package provides functions used for local regression, likelihood +and density estimation.") + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-chron (package (name "r-chron") @@ -984,6 +1109,26 @@ fast ordered joins, fast add/modify/delete of columns by group, column listing and fast file reading.") (license license:gpl3+))) +(define-public r-xtable + (package + (name "r-xtable") + (version "1.8-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "xtable" version)) + (sha256 + (base32 + "0398qkpvlw3dv0myz4mjcyqwpwc2m31l127r8vdzwc71wb6s28qn")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "http://xtable.r-forge.r-project.org/") + (synopsis "Export R tables to LaTeX or HTML") + (description + "This package provides tools to export R data as LaTeX and HTML tables.") + (license license:gpl2+))) + (define-public python-patsy (package (name "python-patsy") @@ -1180,13 +1325,13 @@ module, Java Server Pages, and Python's psp module.") (define-public r-roxygen2 (package (name "r-roxygen2") - (version "5.0.0") + (version "5.0.1") (source (origin (method url-fetch) (uri (cran-uri "roxygen2" version)) (sha256 (base32 - "0xjdphjs7l1v71lylmqgp76cbcxzvm9z1a40jgkdwvz072nn08vr")))) + "19gblyrrn29msbpawcb1hn5m1rshiqwxy0lby0vf92rm13fmsxcz")))) (build-system r-build-system) (propagated-inputs `(("r-brew" ,r-brew) @@ -1201,21 +1346,51 @@ module, Java Server Pages, and Python's psp module.") collation, and NAMESPACE files.") (license license:gpl2+))) +(define-public r-openssl + (package + (name "r-openssl") + (version "0.9.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "openssl" version)) + (sha256 + (base32 + "1dbsaciz39zvsmcyxkmpfm5yxzrpw2iv2nb86525wn80q0cyv0cb")))) + (build-system r-build-system) + (inputs + `(("openssl" ,openssl))) + (home-page "https://github.com/jeroenooms/openssl") + (synopsis "Toolkit for encryption, signatures and certificates") + (description + "This package provides R bindings to OpenSSL libssl and libcrypto, plus +custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384 +and P-521. Cryptographic signatures can either be created and verified +manually or via x509 certificates. AES block cipher is used in CBC mode for +symmetric encryption; RSA for asymmetric (public key) encryption. High-level +envelope functions combine RSA and AES for encrypting arbitrary sized data. +Other utilities include key generators, hash functions (md5, sha1, sha256, +etc), base64 encoder, a secure random number generator, and @code{bignum} math +methods for manually performing crypto calculations on large multibyte +integers.") + (license license:expat))) + (define-public r-httr (package (name "r-httr") - (version "1.0.0") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "httr" version)) (sha256 (base32 - "1yprw8p4g8026jhravgg1hdwj1g51cpdgycyr5a58jwm4i5f79cq")))) + "08sq34pknsfcy8lm06nydi12mbaxpqpgb025ahr33v9d3g0wvh6p")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) ("r-digest" ,r-digest) ("r-jsonlite" ,r-jsonlite) + ("r-openssl" ,r-openssl) ("r-mime" ,r-mime) ("r-r6" ,r-r6) ("r-stringr" ,r-stringr))) @@ -1231,13 +1406,13 @@ functions make it easy to control additional request components.") (define-public r-git2r (package (name "r-git2r") - (version "0.11.0") + (version "0.14.0") (source (origin (method url-fetch) (uri (cran-uri "git2r" version)) (sha256 (base32 - "1h5ag8sm512jsn2sp4yhiqspc7hjq5y8z0kqz24sdznxa3b7rpn9")))) + "0jkkrggffpflaaw0gn2hnm1wz83xs31amriim481g73zf30g2bpr")))) (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 @@ -1257,13 +1432,13 @@ pure C implementation of the Git core methods.") (define-public r-rstudioapi (package (name "r-rstudioapi") - (version "0.3.1") + (version "0.5") (source (origin (method url-fetch) (uri (cran-uri "rstudioapi" version)) (sha256 (base32 - "0q7671d924nzqsqhs8d9p7l907bcam56wjwm7vvz44xgj0saj8bs")))) + "0sgnqfx0m3hzh57k10s7ndrbw7yqjjjcgfikafya98jcc7wmpwym")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/rstudioapi") (synopsis "Safely access the RStudio API") @@ -1275,13 +1450,13 @@ informative error messages when it's not available.") (define-public r-devtools (package (name "r-devtools") - (version "1.10.0") + (version "1.11.0") (source (origin (method url-fetch) (uri (cran-uri "devtools" version)) (sha256 (base32 - "11x51bqhjwypbxv5sfnrnxx06b92k8kzmmx7zrwk3537r072b6pa")))) + "101j15d0f9107pnmdpdwqyvk2ncykq48336rl8lnqp6idiq8id2q")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) @@ -1346,13 +1521,13 @@ disk (or a connection).") (define-public r-plotrix (package (name "r-plotrix") - (version "3.6") + (version "3.6-1") (source (origin (method url-fetch) (uri (cran-uri "plotrix" version)) (sha256 (base32 - "0zn6k8azh40v0lg7q9yd4sy30a26bcc0fjvndn4z7k36avlw4i25")))) + "1y8xnlpy4zba70af9lwj2sshvfdfcmfdh92wamyzj8z9gciailfr")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/plotrix") (synopsis "Various plotting functions") @@ -1398,16 +1573,40 @@ multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to handle most nonstandard requirements.") (license license:gpl2+))) +(define-public r-latticeextra + (package + (name "r-latticeextra") + (version "0.6-28") + (source + (origin + (method url-fetch) + (uri (cran-uri "latticeExtra" version)) + (sha256 + (base32 + "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq")))) + (properties `((upstream-name . "latticeExtra"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice) + ("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page "http://latticeextra.r-forge.r-project.org/") + (synopsis "Extra graphical utilities based on lattice") + (description + "Building on the infrastructure provided by the lattice package, this +package provides several new high-level graphics functions and methods, as +well as additional utilities such as panel and axis annotation functions.") + (license license:gpl2+))) + (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.6.200.2.0") + (version "0.6.700.3.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "137wqqga776yj6synx5awhrzgkz7mmqnvgmggh9l4k6d99vwp9gj")) + "1mc62b6my568ni18w4clgs6l6ggqrwzsm3lgx0c1prf4rap69s8w")) (modules '((guix build utils))) ;; Remove bundled armadillo sources (snippet @@ -1485,14 +1684,14 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "0.8.1") + (version "0.9.5") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 (base32 - "07q5g9dvac5j3vnf4sjc60mnkij1k6y7vnzjz6anf499rwdwbxza")))) + "1zz98jxvw3lzva5kkj1n37gbhjwqd96gjs04y6h37pqy6qmkhk8c")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs @@ -1511,13 +1710,13 @@ variety of formats.") (define-public r-gtable (package (name "r-gtable") - (version "0.1.2") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "gtable" version)) (sha256 (base32 - "0k9hfj6r5y238gqh92s3cbdn34biczx3zfh79ix5xq0c5vkai2xh")))) + "0vz7073m0a2q12qzzihrfh5c2kx5jqi5l7z470fxmwqghdllh7l0")))) (properties `((upstream-name . "gtable"))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/gtable") @@ -1530,13 +1729,13 @@ grobs.") (define-public r-gridextra (package (name "r-gridextra") - (version "2.0.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "gridExtra" version)) (sha256 (base32 - "19yyrfd37c5hxlavb9lca9l26wjhc80rlqhgmfj9k3xhbvvpdp17")))) + "0638ihwl00j76ivaxxhxvi8z573lwy1jym3srr78mx6dbdd4bzj4")))) (properties `((upstream-name . "gridExtra"))) (build-system r-build-system) (propagated-inputs @@ -1607,13 +1806,13 @@ ldap, and also supports cookies, redirects, authentication, etc.") (define-public r-xml (package (name "r-xml") - (version "3.98-1.3") + (version "3.98-1.4") (source (origin (method url-fetch) (uri (cran-uri "XML" version)) (sha256 (base32 - "0j9ayp8a35g0227a4zd8nbmvnbfnj5w687jal6qvj4lbhi3va7sy")))) + "09hiy5a875v2fhsgrsfymrwccn9249wnnsr6ck2slrig65svq2lw")))) (properties `((upstream-name . "XML"))) (build-system r-build-system) @@ -1629,6 +1828,34 @@ documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an XPath \"interpreter\".") (license license:bsd-2))) +(define-public r-xnomial + (package + (name "r-xnomial") + (version "1.0.4") + (source + (origin (method url-fetch) + (uri (cran-uri "XNomial" version)) + (sha256 + (base32 + "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6")))) + (properties (quasiquote ((upstream-name . "XNomial")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/XNomial") + (synopsis "Goodness-of-Fit test for multinomial data") + (description + "This package provides an exact Goodness-of-Fit test for +multinomial data with fixed probabilities. It can be used to +determine whether a set of counts fits a given expected ratio. To see +whether a set of observed counts fits an expectation, one can examine +all possible outcomes with @code{xmulti()} or a random sample of them +with @code{xmonte()} and find the probability of an observation +deviating from the expectation by at least as much as the observed. +As a measure of deviation from the expected, one can use the +log-likelihood ratio, the multinomial probability, or the classic +chi-square statistic. A histogram of the test statistic can also be +plotted and compared with the asymptotic curve.") + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-lambda-r (package (name "r-lambda-r") @@ -1881,16 +2108,175 @@ The 'DataTables' library has been included in this R package.") flexible than the orphaned \"base64\" package.") (license license:gpl2+))) +(define-public r-irlba + (package + (name "r-irlba") + (version "2.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "irlba" version)) + (sha256 + (base32 + "1gms3rxrm24ri4vjvnpl4v47m7bx0zk63z8y85rbhsvx230xdy0m")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/irlba") + (synopsis "Methods for eigendecomposition of large matrices") + (description + "This package provides fast and memory efficient methods for truncated +singular and eigenvalue decompositions, as well as for principal component +analysis of large sparse or dense matrices.") + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-pkgmaker + (package + (name "r-pkgmaker") + (version "0.22") + (source + (origin + (method url-fetch) + (uri (cran-uri "pkgmaker" version)) + (sha256 + (base32 + "0vrqnd3kg6liqvpbd969jjsdx0f0rvmmxgdbwwrp6xfmdg0pib8r")))) + (build-system r-build-system) + (propagated-inputs + `(("r-codetools" ,r-codetools) + ("r-digest" ,r-digest) + ("r-registry" ,r-registry) + ("r-stringr" ,r-stringr) + ("r-xtable" ,r-xtable))) + (home-page "https://renozao.github.io/pkgmaker") + (synopsis "Package development utilities") + (description + "This package provides some low-level utilities to use for R package +development. It currently provides managers for multiple package specific +options and registries, vignette, unit test and bibtex related utilities.") + (license license:gpl2+))) + + (define-public r-registry + (package + (name "r-registry") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "registry" version)) + (sha256 + (base32 + "0c7lscfxncwwd8zp46h2xfw9gw14dypqv6m2kx85xjhjh0xw99aq")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/registry") + (synopsis "Infrastructure for R package registries") + (description + "This package provides a generic infrastructure for creating and using R +package registries.") + (license license:gpl2+))) + +(define-public r-rngtools + (package + (name "r-rngtools") + (version "1.2.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "rngtools" version)) + (sha256 + (base32 + "1fcgfqrrb48z37xgy8sffx91p9irp39yqzxv7nqp1x2hnwsrh097")))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-pkgmaker" ,r-pkgmaker) + ("r-stringr" ,r-stringr))) + (home-page "https://renozao.github.io/rngtools") + (synopsis "Utility functions for working with random number generators") + (description + "This package contains a set of functions for working with Random Number +Generators (RNGs). In particular, it defines a generic S4 framework for +getting/setting the current RNG, or RNG data that are embedded into objects +for reproducibility. Notably, convenient default methods greatly facilitate +the way current RNG settings can be changed.") + (license license:gpl3+))) + +(define-public r-nmf + (package + (name "r-nmf") + (version "0.20.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "NMF" version)) + (sha256 + (base32 + "0mmh9bz0zjwd8h9jplz4rq3g94npaqj8s4px51vcv47csssd9k6z")))) + (properties `((upstream-name . "NMF"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-colorspace" ,r-colorspace) + ("r-digest" ,r-digest) + ("r-doparallel" ,r-doparallel) + ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) + ("r-gridbase" ,r-gridbase) + ("r-pkgmaker" ,r-pkgmaker) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-registry" ,r-registry) + ("r-reshape2" ,r-reshape2) + ("r-rngtools" ,r-rngtools) + ("r-stringr" ,r-stringr))) + (home-page "http://renozao.github.io/NMF") + (synopsis "Algorithms and framework for nonnegative matrix factorization") + (description + "This package provides a framework to perform Non-negative Matrix +Factorization (NMF). The package implements a set of already published +algorithms and seeding methods, and provides a framework to test, develop and +plug new or custom algorithms. Most of the built-in algorithms have been +optimized in C++, and the main interface function provides an easy way of +performing parallel computations on multicore machines.") + (license license:gpl2+))) + +(define-public r-igraph + (package + (name "r-igraph") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "igraph" version)) + (sha256 + (base32 + "00jnm8v3kvxpxav5klld2z2nnkcpj4sdwv4ksipddy5mp04ysr6w")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (inputs + `(("gmp" ,gmp) + ("libxml2" ,libxml2))) + (propagated-inputs + `(("r-irlba" ,r-irlba) + ("r-magrittr" ,r-magrittr) + ("r-nmf" ,r-nmf))) + (home-page "http://igraph.org") + (synopsis "Network analysis and visualization") + (description + "This package provides routines for simple graphs and network analysis. +It can handle large graphs very well and provides functions for generating +random and regular graphs, graph visualization, centrality methods and much +more.") + (license license:gpl2+))) + (define-public r-r-methodss3 (package (name "r-r-methodss3") - (version "1.7.0") + (version "1.7.1") (source (origin (method url-fetch) (uri (cran-uri "R.methodsS3" version)) (sha256 (base32 - "1dg4bbrwr8jcsqisjrrwxs942mrjq72zw8yvl2br4djdm0md8zz5")))) + "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24")))) (properties `((upstream-name . "R.methodsS3"))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/R.methodsS3") @@ -1908,13 +2294,13 @@ want to migrate to S4.") (define-public r-r-oo (package (name "r-r-oo") - (version "1.19.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (cran-uri "R.oo" version)) (sha256 (base32 - "15rm1qb9a212bqazhcpk7m48hcp7jq8rh4yhd9c6zfyvdqszfmsb")))) + "1l1x4r69mdchjyi6sq52p580fz3b3bqv6dpn1706y9n4vq47qx24")))) (properties `((upstream-name . "R.oo"))) (build-system r-build-system) (propagated-inputs @@ -1931,13 +2317,13 @@ maintenance for package developers.") (define-public r-r-utils (package (name "r-r-utils") - (version "2.1.0") + (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "R.utils" version)) (sha256 (base32 - "03pi6pkcsq65fv7cn4x74cj050dc8x5d4xyg930p6f7flk788xaz")))) + "0f4z7ka1wb7bgxc5wyqihqxsnqwgyyzbglwvfwmx0gn8i0wzi647")))) (properties `((upstream-name . "R.utils"))) (build-system r-build-system) (propagated-inputs @@ -1979,13 +2365,13 @@ persistent (on the file system).") (define-public r-r-rsp (package (name "r-r-rsp") - (version "0.20.0") + (version "0.21.0") (source (origin (method url-fetch) (uri (cran-uri "R.rsp" version)) (sha256 (base32 - "06vq9qq5hdz3hqc99q82622mab6ix7jwap20h4za6ap6gnwqs0fv")))) + "0snc6ps75s3ci6sy8mil1wg2i9xmlr1ygh9n244y1brdvp43dfsw")))) (properties `((upstream-name . "R.rsp"))) (build-system r-build-system) (propagated-inputs @@ -2010,13 +2396,13 @@ vignettes.") (define-public r-matrixstats (package (name "r-matrixstats") - (version "0.15.0") + (version "0.50.1") (source (origin (method url-fetch) (uri (cran-uri "matrixStats" version)) (sha256 (base32 - "1068k85s6rlwfzlszw790c2rndydvrsw7rpck6k6z17896m8drfa")))) + "08l32abp7dfnsc49ca4hzznh934y60n5z01x5ga2ixky5961s57c")))) (properties `((upstream-name . "matrixStats"))) (build-system r-build-system) (native-inputs @@ -2034,13 +2420,13 @@ memory usage.") (define-public r-viridis (package (name "r-viridis") - (version "0.3.1") + (version "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "viridis" version)) (sha256 (base32 - "0zz9i874s1fwhl9bcbiprlzaz7zsy1rj6c729zn3k525d63qbnj7")))) + "1a9hqn2pccpc51vh8ghw698ni6xzdnp8v0n8kgjh51nlz5hhc87j")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -2057,26 +2443,81 @@ black-and-white. They are also designed to be perceived by readers with the most common form of color blindness.") (license license:x11))) +(define-public r-tidyr + (package + (name "r-tidyr") + (version "0.4.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "tidyr" version)) + (sha256 + (base32 + "0xp6lyr2l4ix2mrilx4qmca7wm5qmbhvi24m4nf7qsgwp54gnv2h")))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-lazyeval" ,r-lazyeval) + ("r-magrittr" ,r-magrittr) + ("r-rcpp" ,r-rcpp) + ("r-stringi" ,r-stringi))) + (home-page "https://github.com/hadley/tidyr") + (synopsis "Tidy data with `spread()` and `gather()` functions") + (description + "tidyr is a reframing of the reshape2 package designed to accompany the +tidy data framework, and to work hand-in-hand with magrittr and dplyr to build +a solid pipeline for data analysis. It is designed specifically for tidying +data, not the general reshaping that reshape2 does, or the general aggregation +that reshape did. In particular, built-in methods only work for data frames, +and tidyr provides no margins or aggregation.") + (license license:expat))) + +(define-public r-hexbin + (package + (name "r-hexbin") + (version "1.27.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "hexbin" version)) + (sha256 + (base32 + "0xi6fbf1fvyn2gffr052n3viibqzpr3603sgi4xaminbzja4syjh")))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "http://github.com/edzer/hexbin") + (synopsis "Hexagonal binning routines") + (description + "This package provides binning and plotting functions for hexagonal bins. +It uses and relies on grid graphics and formal (S4) classes and methods.") + (license license:gpl2+))) + (define-public r-plotly (package (name "r-plotly") - (version "2.0.3") + (version "3.4.13") (source (origin (method url-fetch) (uri (cran-uri "plotly" version)) (sha256 (base32 - "16pqycns8qf0y1j21n009qf242lv0izwyidlx40zv88izxhg1vs0")))) + "1pfl9w35iwin8a1hfwcihajyps2ngjbyrmvi61b9lspcdbk39lf8")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-digest" ,r-digest) ("r-ggplot2" ,r-ggplot2) + ("r-hexbin" ,r-hexbin) ("r-htmlwidgets" ,r-htmlwidgets) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) ("r-magrittr" ,r-magrittr) ("r-plyr" ,r-plyr) + ("r-scales" ,r-scales) + ("r-tidyr" ,r-tidyr) ("r-viridis" ,r-viridis))) (home-page "https://plot.ly/r") (synopsis "Create interactive web graphics") |