diff options
author | Marius Bakke <mbakke@fastmail.com> | 2020-03-02 23:49:10 +0100 |
---|---|---|
committer | Marius Bakke <mbakke@fastmail.com> | 2020-03-02 23:49:10 +0100 |
commit | fb98351621a6b311d4ff9593d6c22d40a3b3fe8f (patch) | |
tree | 05fb46c92657a70cad6923c64b63540a88555bb4 /gnu/packages/cran.scm | |
parent | d614f0bba90c86c836131eea3ebb9cbd30f19abf (diff) | |
parent | 15a6805751309452616999933492f1fb9da8bcec (diff) | |
download | guix-fb98351621a6b311d4ff9593d6c22d40a3b3fe8f.tar.gz |
Merge branch 'master' into staging
Diffstat (limited to 'gnu/packages/cran.scm')
-rw-r--r-- | gnu/packages/cran.scm | 253 |
1 files changed, 191 insertions, 62 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7ff282bde1..9d154c030a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -195,14 +195,14 @@ functions are simplified but can be faster or have other advantages.") (define-public r-matrix-utils (package (name "r-matrix-utils") - (version "0.9.7") + (version "0.9.8") (source (origin (method url-fetch) (uri (cran-uri "Matrix.utils" version)) (sha256 (base32 - "1x64r4aj3gy1dzjjysyrk1j9jq3qsnyrqws8i6bs7q8pf6gvr7va")))) + "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb")))) (properties `((upstream-name . "Matrix.utils"))) (build-system r-build-system) (propagated-inputs @@ -473,14 +473,14 @@ the embedded @code{RapidXML} C++ library.") (define-public r-modelr (package (name "r-modelr") - (version "0.1.5") + (version "0.1.6") (source (origin (method url-fetch) (uri (cran-uri "modelr" version)) (sha256 (base32 - "0nnfhlzz75ihs8azy963cc4cwg1kx81rybk4z3wm98bbghwfxfs5")))) + "1x2m34m4qirb401krmgc5wg3g7ndbcglfab2l0655rmky3fz7rfp")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -489,7 +489,8 @@ the embedded @code{RapidXML} C++ library.") ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + ("r-tidyr" ,r-tidyr) + ("r-tidyselect" ,r-tidyselect))) (home-page "https://github.com/tidyverse/modelr") (synopsis "Helper functions for modelling in pipelines") (description @@ -1916,14 +1917,14 @@ rows, dropping names) to see if the modified versions are identical.") (define-public r-dendextend (package (name "r-dendextend") - (version "1.13.3") + (version "1.13.4") (source (origin (method url-fetch) (uri (cran-uri "dendextend" version)) (sha256 (base32 - "1gx6blw644sx2c4s90672scrwl4bv5xlgnfwbcalkh6nff2sai0h")))) + "1pjbz6sb4pgh3d5pm53vmf3q8y6lq3hrgjd6547xxs3m63sb8mn4")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -2157,13 +2158,13 @@ most popular ones.") (define-public r-sp (package (name "r-sp") - (version "1.4-0") + (version "1.4-1") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 - (base32 "0mgjrlviv6qapgpiqdjcbsygzfs8bf5c64krh2rk555vf5njmnh7")))) + (base32 "0fbh865r4py89g6ln8bslig2vbxxwa642p5k5g02rskyhajg35lg")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -3066,14 +3067,14 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "0.5.4") + (version "0.5.5") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "1w35v1qrg8d0bm7a4gsdqkmrl9nmymsvmamy48vc046a1axzgzq1")))) + "0n7zd64263kfavdi28rl2bxrsa00c3m4vjhhjdrfwvvmrcxj39fx")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -3791,14 +3792,14 @@ plots in @code{ggplot2}.") (define-public r-cli (package (name "r-cli") - (version "2.0.1") + (version "2.0.2") (source (origin (method url-fetch) (uri (cran-uri "cli" version)) (sha256 (base32 - "0x28i7kj4qndk6mnn99qn9w2nfldv8csjnsn0n8phfnxq5hnmp5y")))) + "1dhkah6jvr96k4h4agcc2rfls75bpjb0j58fzaz3dc0fp3jk8229")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -4127,14 +4128,14 @@ terminals.") (define-public r-uuid (package (name "r-uuid") - (version "0.1-2") + (version "0.1-4") (source (origin (method url-fetch) (uri (cran-uri "uuid" version)) (sha256 (base32 - "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx")))) + "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q")))) (build-system r-build-system) (home-page "http://www.rforge.net/uuid") (synopsis "Tools for generating and handling of UUIDs") @@ -4146,14 +4147,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.19") + (version "0.20") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "0jlcrvcqcbkimg7w40z5vhlnakb829vfgqpspm3pfl8karwzgqp6")))) + "0n8v8inpsc99r0snvqbjhqlc6nm9hxjsw120hrxc2mw03pa5fvkg")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) @@ -5935,14 +5936,14 @@ clustering.") (define-public r-factominer (package (name "r-factominer") - (version "2.2") + (version "2.3") (source (origin (method url-fetch) (uri (cran-uri "FactoMineR" version)) (sha256 (base32 - "1hcas9iby95y6xcrf231yrd44s799aaaggb9jd1dcb5nd5vfpzw0")))) + "0ldgf3daksh6lpblhqys67m4mxqx3q9s9n5plfam6dwshfik0ky6")))) (properties `((upstream-name . "FactoMineR"))) (build-system r-build-system) (propagated-inputs @@ -6191,23 +6192,19 @@ references and Rd files.") (define-public r-officer (package (name "r-officer") - (version "0.3.6") + (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 - "1i6jmnbkx7gd0qyf6akhizmxp7y1dh3h7a886mcbmrzka9d60zh4")))) + "1zyrcf0xxm67bskynjac8dhil2as7rb0mmqaq30zp9lrgfwiycpz")))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-digest" ,r-digest) - ("r-htmltools" ,r-htmltools) + `(("r-digest" ,r-digest) ("r-magrittr" ,r-magrittr) ("r-r6" ,r-r6) - ("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang) ("r-uuid" ,r-uuid) ("r-xml2" ,r-xml2) ("r-zip" ,r-zip))) @@ -6959,13 +6956,13 @@ based on index arrays and simple triplet representations, respectively.") (define-public r-manipulatewidget (package (name "r-manipulatewidget") - (version "0.10.0") + (version "0.10.1") (source (origin (method url-fetch) (uri (cran-uri "manipulateWidget" version)) (sha256 - (base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x")))) + (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx")))) (properties `((upstream-name . "manipulateWidget"))) (build-system r-build-system) @@ -8554,14 +8551,14 @@ results using @code{ggplot2}.") (define-public r-effectsize (package (name "r-effectsize") - (version "0.1.1") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 - "0dd7nbkg8kmash9zh2gg08m7hbpsqwpkvkdhinfqkbg5d0jinhq8")))) + "1liix8rf8xq3hzi7684bl0s20iflsq6g5mxr5k59wp2qwn1i6aww")))) (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs @@ -8895,14 +8892,14 @@ ways.") (define-public r-summarytools (package (name "r-summarytools") - (version "0.9.5") + (version "0.9.6") (source (origin (method url-fetch) (uri (cran-uri "summarytools" version)) (sha256 (base32 - "0iv5237478y2ggbqln3cppm0crnqk3myrkf6ydkhwsd1z5q538pd")))) + "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -9047,14 +9044,14 @@ the interfaces between R and C++.") (define-public r-mvabund (package (name "r-mvabund") - (version "4.0.1") + (version "4.1.3") (source (origin (method url-fetch) (uri (cran-uri "mvabund" version)) (sha256 (base32 - "0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k")))) + "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -9187,14 +9184,14 @@ address a bug.") (define-public r-rcppannoy (package (name "r-rcppannoy") - (version "0.0.14") + (version "0.0.15") (source (origin (method url-fetch) (uri (cran-uri "RcppAnnoy" version)) (sha256 (base32 - "1wiigx5g5788j6lyc3f6bs1rsvc4alyc3052g35hxl1giinxmhn4")))) + "1rlw6npwwcp066midvkhnzf0xmmfkkdf6f581j3j1s2naqss3fvl")))) (properties `((upstream-name . "RcppAnnoy"))) (build-system r-build-system) (propagated-inputs @@ -9846,13 +9843,13 @@ manipulate tree data.") (define-public r-rvcheck (package (name "r-rvcheck") - (version "0.1.7") + (version "0.1.8") (source (origin (method url-fetch) (uri (cran-uri "rvcheck" version)) (sha256 - (base32 "1a3xlzi4n1rqiapfa180aif7n7nws8pbg8k3nk7ccaczvmni38aw")))) + (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac")))) (build-system r-build-system) (propagated-inputs `(("r-biocmanager" ,r-biocmanager) @@ -11386,14 +11383,14 @@ library.") (define-public r-protviz (package (name "r-protviz") - (version "0.6.0") + (version "0.6.3") (source (origin (method url-fetch) (uri (cran-uri "protViz" version)) (sha256 (base32 - "165bh2m6rrcmr0pc2drj6hdg6xfx8k02lznxzj1fmsswsrlfhn3v")))) + "1ldciqh3f43xr9663yyhd9r6qwrg4c4vmkprlcancbnd460wakg7")))) (properties `((upstream-name . "protViz"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) @@ -13649,14 +13646,14 @@ that accept short and long options.") (define-public r-wgcna (package (name "r-wgcna") - (version "1.68") + (version "1.69") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 - "1s7gy5vd7x67hpgli8r7ba2z99w3psiyv5hqmrh94zw141dg210a")))) + "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs @@ -13669,7 +13666,6 @@ that accept short and long options.") ("r-hmisc" ,r-hmisc) ("r-impute" ,r-impute) ("r-rcpp" ,r-rcpp) - ("r-robust" ,r-robust) ("r-survival" ,r-survival) ("r-matrixstats" ,r-matrixstats) ("r-preprocesscore" ,r-preprocesscore))) @@ -14027,14 +14023,14 @@ yeast.") (define-public r-gridgraphics (package (name "r-gridgraphics") - (version "0.4-1") + (version "0.5-0") (source (origin (method url-fetch) (uri (cran-uri "gridGraphics" version)) (sha256 (base32 - "1kr3p54bkv2q7agxrva30y9bkwkiq1k2cfl5z1kvyjv6f5xi4w5p")))) + "0rlyc3xk8kfrfzbfd8n4javq3yxqd7lsfmi4q5n6s61srnrl6c1r")))) (properties `((upstream-name . "gridGraphics"))) (build-system r-build-system) (home-page "https://github.com/pmur002/gridgraphics") @@ -14931,14 +14927,14 @@ batch correction, and data correction.") (define-public r-styler (package (name "r-styler") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "styler" version)) (sha256 (base32 - "14vfw1w22b9kbbgz72dcg814ycjvrd91ziva42jmmzqbspfxjvmw")))) + "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -15137,14 +15133,14 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.") (define-public r-dalex (package (name "r-dalex") - (version "1.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 - "0fcyk1zhpw5yyppyw45rplx8603mrbp4vxq8398h2lswgy1nmls4")))) + "1jbyn57vn6d281a5y15h5d8ljin8cdb9lr7lbgggc950blyfv4g0")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) @@ -16068,14 +16064,14 @@ porting.") (define-public r-subplex (package (name "r-subplex") - (version "1.5-4") + (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "subplex" version)) (sha256 (base32 - "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z")))) + "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -17866,14 +17862,14 @@ allowed.") (define-public r-gdina (package (name "r-gdina") - (version "2.7.8") + (version "2.7.9") (source (origin (method url-fetch) (uri (cran-uri "GDINA" version)) (sha256 (base32 - "1aj2ssd7vpszl7p22srkkkpx4a7gkc38vrv3bq7j1zr32096y4zj")))) + "13pmj069r04h38hg61ibyn1ab15zdy9m0qv60vi25ahgsmg6ccvx")))) (properties `((upstream-name . "GDINA"))) (build-system r-build-system) (propagated-inputs @@ -19453,14 +19449,14 @@ Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.") (define-public r-quanteda (package (name "r-quanteda") - (version "1.5.2") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "quanteda" version)) (sha256 (base32 - "0iv25rpx5cl9ansazjs0qb97pniajrxf4mqsnb5q98y2hil9ipd3")))) + "0snr610vahbdqkmma0zy5mg5qbb6n1b8sgsclqb2sccn1gg38vyy")))) (properties `((upstream-name . "quanteda"))) (build-system r-build-system) (propagated-inputs @@ -19469,7 +19465,7 @@ Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.") ("r-fastmatch" ,r-fastmatch) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) - ("r-lubridate" ,r-lubridate) + ("r-jsonlite" ,r-jsonlite) ("r-magrittr" ,r-magrittr) ("r-matrix" ,r-matrix) ("r-network" ,r-network) @@ -19477,10 +19473,8 @@ Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.") ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rcppparallel" ,r-rcppparallel) - ("r-rspectra" ,r-rspectra) ("r-sna" ,r-sna) ("r-snowballc" ,r-snowballc) - ("r-spacyr" ,r-spacyr) ("r-stopwords" ,r-stopwords) ("r-stringi" ,r-stringi) ("r-xml2" ,r-xml2) @@ -19803,14 +19797,14 @@ and analyze Stan models.") (define-public r-rpf (package (name "r-rpf") - (version "1.0.2") + (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "rpf" version)) (sha256 (base32 - "0j1229qc1mg0vy3msk3yzrpk2r64b8zvnk4rj8q27s38pgz9mix3")))) + "1i2kqd7nx55nn35qnw89xmnqk23x9c8xhkh736c2xg7k2ai84ybl")))) (properties `((upstream-name . "rpf"))) (build-system r-build-system) (propagated-inputs @@ -19831,14 +19825,14 @@ Complete access to optimized C functions is made available with (define-public r-openmx (package (name "r-openmx") - (version "2.17.2") + (version "2.17.3") (source (origin (method url-fetch) (uri (cran-uri "OpenMx" version)) (sha256 (base32 - "092xbwgi72ihxv45qmzm6lv0470rsrqsn7l2jh61jnkx95n72zbb")))) + "1s2pcg281ag3qz2wz8yi826f2d3kj3qg916js7zz0nsrljcyv5bc")))) (properties `((upstream-name . "OpenMx"))) (build-system r-build-system) (propagated-inputs @@ -20561,3 +20555,138 @@ need to derive the partial derivatives.") for Bayesian estimation. Users specify models via the customary R syntax with a formula and @code{data.frame} plus some additional arguments for priors.") (license license:gpl3+))) + +(define-public r-kendall + (package + (name "r-kendall") + (version "2.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "Kendall" version)) + (sha256 + (base32 + "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn")))) + (properties `((upstream-name . "Kendall"))) + (build-system r-build-system) + (propagated-inputs + `(("r-boot" ,r-boot))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/Kendall/") + (synopsis "Kendall rank correlation and Mann-Kendall trend test") + (description + "This package computes the Kendall rank correlation and Mann-Kendall +trend test.") + (license license:gpl2+))) + +(define-public r-zyp + (package + (name "r-zyp") + (version "0.10-1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "zyp" version)) + (sha256 + (base32 + "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9")))) + (properties `((upstream-name . "zyp"))) + (build-system r-build-system) + (propagated-inputs + `(("r-kendall" ,r-kendall))) + (home-page "https://cran.r-project.org/web/packages/zyp/") + (synopsis "Zhang + Yue-Pilon Trends Package") + (description + "This package contains an efficient implementation of Sen's slope +method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and +Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in +climate data.") + (license license:lgpl2.1))) + +(define-public r-zvcv + (package + (name "r-zvcv") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ZVCV" version)) + (sha256 + (base32 + "1npw836q2skx54843lgxvb0rfwafckjc8k8dljykm60ad3z7zak8")))) + (properties `((upstream-name . "ZVCV"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-glmnet" ,r-glmnet) + ("r-mvtnorm" ,r-mvtnorm) + ("r-partitions" ,r-partitions) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (home-page "https://cran.r-project.org/web/packages/ZVCV/") + (synopsis "Zero-Variance Control Variates") + (description + "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method +to reduce the variance of Monte Carlo estimators of expectations using the +derivatives of the log target. Once the derivatives are available, the only +additional computational effort is in solving a linear regression problem. +This method has been extended to higher dimensions using regularisation. This +package can be used to easily perform ZV-CV or regularised ZV-CV when a set of +samples, derivatives and function evaluations are available. Additional +functions for applying ZV-CV to two estimators for the normalising constant of +the posterior distribution in Bayesian statistics are also supplied.") + (license license:gpl2+))) + +(define-public r-ztype + (package + (name "r-ztype") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ztype" version)) + (sha256 + (base32 + "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx")))) + (properties `((upstream-name . "ztype"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-lubridate" ,r-lubridate) + ("r-magrittr" ,r-magrittr) + ("r-rvest" ,r-rvest) + ("r-stringr" ,r-stringr))) + (home-page "https://cran.r-project.org/web/packages/ztype/") + (synopsis "Run a Ztype game loaded with R functions") + (description + "How fast can you type R functions on your keyboard? Find out by running +a @code{zty.pe} game: export R functions as instructions to type to destroy +opponents' vessels.") + (license license:gpl3))) + +(define-public r-zseq + (package + (name "r-zseq") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "Zseq" version)) + (sha256 + (base32 + "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi")))) + (properties `((upstream-name . "Zseq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-gmp" ,r-gmp))) + (home-page "https://cran.r-project.org/web/packages/Zseq/") + (synopsis "Integer sequence generator") + (description + "This package generates well-known integer sequences. The @code{gmp} +package is adopted for computing with arbitrarily large numbers. Every +function has a hyperlink to its corresponding item in the @dfn{On-Line +Encyclopedia of Integer Sequences} (OEIS) in the function help page.") + (license license:gpl3+))) |