diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 247 |
1 files changed, 188 insertions, 59 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 199bc69c03..4229fc2cea 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -926,6 +926,27 @@ differential abundance analysis of zero-inflated high-dimensional compositional data.") (license license:gpl3))) +(define-public r-gwasexacthw + (package + (name "r-gwasexacthw") + (version "1.01") + (source (origin + (method url-fetch) + (uri (cran-uri "GWASExactHW" version)) + (sha256 + (base32 + "19qmk8h7kxmn9kzw0x4xns5p3qqz27xkqq4q6zmh4jzizd0fsl78")))) + (properties `((upstream-name . "GWASExactHW"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=GWASExactHW") + (synopsis + "Exact Hardy-Weinburg testing for Genome Wide Association Studies") + (description + "This package contains a function to do exact Hardy-Weinburg +testing (using Fisher's test) for SNP genotypes as typically obtained in a +@dfn{Genome Wide Association Study} (GWAS).") + (license license:gpl3))) + (define-public r-gwidgets2 (package (name "r-gwidgets2") @@ -1255,13 +1276,13 @@ for authoring journal articles and conference submissions.") (define-public r-babelwhale (package (name "r-babelwhale") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "babelwhale" version)) (sha256 - (base32 "01l8vwyz3bx0iks6cjs5y9ifdsnc1p1yqp4i0kzqd1gjhycizv6y")))) + (base32 "0m5q83ykz5w1fsjsk2vyrnv21cg4n075kbvfvw4k22c61p78shdl")))) (properties `((upstream-name . "babelwhale"))) (build-system r-build-system) (propagated-inputs @@ -1871,14 +1892,14 @@ variables.") (define-public r-ggpp (package (name "r-ggpp") - (version "0.5.2") + (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "ggpp" version)) (sha256 (base32 - "0w93427hyiihddsdr6q962gfl01b06yxchi3x3dinfb8mf1m5qmk")))) + "1shcjplw2w8jbfbp0flpxhb7jfy7v79vhjv1qlh6lmam2fziydcc")))) (properties `((upstream-name . "ggpp"))) (build-system r-build-system) (propagated-inputs @@ -3997,14 +4018,14 @@ conditionals and comparisons, and more.") (define-public r-sass (package (name "r-sass") - (version "0.4.6") + (version "0.4.7") (source (origin (method url-fetch) (uri (cran-uri "sass" version)) (sha256 (base32 - "06f0279ljg6mbcimmfx4rp18zxb9yc24sdp2yxwfxzdp17kjrs1f")))) + "1vp9qnhkvz4shhvwrwbwcy1xnrgry0rmqxsg96ggv90m6sv0hyki")))) (properties `((upstream-name . "sass"))) (build-system r-build-system) (propagated-inputs @@ -5013,13 +5034,13 @@ coordinates.") (define-public r-gensa (package (name "r-gensa") - (version "1.1.8") + (version "1.1.9") (source (origin (method url-fetch) (uri (cran-uri "GenSA" version)) (sha256 (base32 - "05m2xjaf4202jzzn5l7i7k80kzr8vihv7jpw99c9ic5n3ra8fpip")))) + "10qm0467r2rbcck1w7dijng5j676314vsyxsr0p8l843xz7s66rq")))) (properties `((upstream-name . "GenSA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=GenSA") @@ -5616,13 +5637,13 @@ factorization and divisive clustering for large sparse and dense matrices.") (define-public r-rcppspdlog (package (name "r-rcppspdlog") - (version "0.0.13") + (version "0.0.14") (source (origin (method url-fetch) (uri (cran-uri "RcppSpdlog" version)) (sha256 - (base32 "1149kh047301hrp15479ikcmrix968pwqw3jza7mp7bsxhrjrp3k")))) + (base32 "1n63mz2rr63kz3v7mg6n4cvw2lrw1ffk7xvln1j1005argvzvd4c")))) (properties `((upstream-name . "RcppSpdlog"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -5881,18 +5902,19 @@ graphics packages that comes with the base installation.") (define-public r-ctrdata (package (name "r-ctrdata") - (version "1.13.3") + (version "1.14.0") (source (origin (method url-fetch) (uri (cran-uri "ctrdata" version)) (sha256 (base32 - "15vs8b2jxap5ya59n6pdby1p89hd0y0b4say72q6icxsjzzj979z")))) + "0x5dpph62s7dwfs0y4gd73zzbil9cr1y5q8mpn9m7z2gdr67wk1c")))) (properties `((upstream-name . "ctrdata"))) (build-system r-build-system) (propagated-inputs (list r-clipr r-curl + r-dplyr r-httr r-jqr r-jsonlite @@ -7987,6 +8009,28 @@ can be computed between character vectors while taking proper care of encoding or between integer vectors representing generic sequences.") (license license:gpl3+))) +(define-public r-uchardet + (package + (name "r-uchardet") + (version "1.1.1") + (source (origin + (method url-fetch) + (uri (cran-uri "uchardet" version)) + (sha256 + (base32 + "0m3xy807smqdxhkhd9cwrcf3ljlyvfmnkd7831qzpgcadam2jcdj")))) + (properties `((upstream-name . "uchardet"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://artemklevtsov.gitlab.io/uchardet") + (synopsis "Universal character encoding detector") + (description + "This package provides R bindings to the uchardet encoding detector +library from Mozilla. It takes a sequence of bytes in an unknown character +encoding without any additional information, and attempts to get the encoding +of the text. All return names of the encodings are iconv-compatible.") + (license license:gpl2))) + (define-public r-ucminf (package (name "r-ucminf") @@ -11224,6 +11268,28 @@ package covers Models, Completions, Chat, Edits, Images, Embeddings, Audio, Files, Fine-tunes, Moderations, and legacy Engines endpoints.") (license license:expat))) +(define-public r-operator-tools + (package + (name "r-operator-tools") + (version "1.6.3") + (source (origin + (method url-fetch) + (uri (cran-uri "operator.tools" version)) + (sha256 + (base32 + "1v4dg7xhz24dnp0zxn815x1405ig64ibii6y40la1gvmzcc41dz5")))) + (properties `((upstream-name . "operator.tools"))) + (build-system r-build-system) + (home-page "https://github.com/decisionpatterns/operator.tools") + (synopsis "Utilities for working with R's operators") + (description + "This package provides a collection of utilities that allow programming +with R's operators. Routines allow classifying operators, translating to and +from an operator and its underlying function, and inverting some +operators (e.g. comparison operators), etc. All methods can be extended to +custom infix operators.") + (license license:gpl2))) + (define-public r-openxlsx (package (name "r-openxlsx") @@ -13274,14 +13340,14 @@ the work.") (define-public r-doby (package (name "r-doby") - (version "4.6.16") + (version "4.6.17") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 - "1rxvxhb572n29mbvkh6xmi7cnwc6c8g2xzw1wp10nfr9gnspx4ym")))) + "02jb1z19rsmbvzwapgfx7m8lfnlcx9dqf6gkr9fmgcl77d5992n5")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs @@ -16571,13 +16637,13 @@ address a bug.") (define-public r-rcppalgos (package (name "r-rcppalgos") - (version "2.7.2") + (version "2.8.0") (source (origin (method url-fetch) (uri (cran-uri "RcppAlgos" version)) (sha256 (base32 - "1wfwwbv9wrs2vbk0c36zcwcl9yyzz2h1mw36mpq7lz56xxhy0wf5")))) + "1f9wxwqzv03bgr22s3hnj7mg9qlbap1dsg6vj1blgjl6xpfvz5bn")))) (properties `((upstream-name . "RcppAlgos"))) (build-system r-build-system) (inputs (list gmp)) @@ -17547,13 +17613,13 @@ maps.") (define-public r-tidytree (package (name "r-tidytree") - (version "0.4.2") + (version "0.4.4") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 - (base32 "0phmvbpsxx85fvw4000d160qh8njrgmzpr3ja0gy59dgv1k1m0yb")))) + (base32 "196c7j3pgapwh8j8jdhsz078wl24xcf5jkrbbsr2s7xg32j0lmi1")))) (build-system r-build-system) (propagated-inputs (list r-ape @@ -19377,16 +19443,47 @@ hierarchic loggers, multiple handlers per logger, level based filtering, space handling in messages and custom formatting.") (license license:gpl3))) +(define-public r-logistf + (package + (name "r-logistf") + (version "1.25.0") + (source (origin + (method url-fetch) + (uri (cran-uri "logistf" version)) + (sha256 + (base32 + "0w78jsynw5jh3l9r3ssjs8rza6givgrxzwnb5jwazcm8637d6gix")))) + (properties `((upstream-name . "logistf"))) + (build-system r-build-system) + (propagated-inputs (list r-formula-tools r-matrix r-mgcv r-mice)) + (home-page + "https://cemsiis.meduniwien.ac.at/en/kb/science-research\ +/software/statistical-software/firth-correction/") + (synopsis "Firth's bias-reduced logistic regression") + (description + "Fit a logistic regression model using Firth's bias reduction method, +equivalent to penalization of the log-likelihood by the Jeffreys prior. +Confidence intervals for regression coefficients can be computed by penalized +profile likelihood. Firth's method was proposed as ideal solution to the +problem of separation in logistic regression, see Heinze and Schemper (2002) +<doi:10.1002/sim.1047>. If needed, the bias reduction can be turned off such +that ordinary maximum likelihood logistic regression is obtained. Two new +modifications of Firth's method, FLIC and FLAC, lead to unbiased predictions +and are now available in the package as well, see Puhr et al (2017) +<doi:10.1002/sim.7273>.") + ;; Any version of the GPL + (license license:gpl3+))) + (define-public r-longdat (package (name "r-longdat") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "LongDat" version)) (sha256 (base32 - "1k8rl6jv4xzsm620wf373ds6l8fbb5ff07rgbp0bgqrymvwdf1jc")))) + "1rzkb7byd32jqvhf75zyvy0dlkq79aicz8j0x7lk821qiq4dfv6l")))) (properties `((upstream-name . "LongDat"))) (build-system r-build-system) (propagated-inputs (list r-bestnormalize @@ -21606,17 +21703,25 @@ information about geometries.") (define-public r-sf (package (name "r-sf") - (version "1.0-13") + (version "1.0-14") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 - "11lcc57vqip1zj8hi09mnisl9jiqqxwx6b06jl752dayxi2109br")))) + "1xrrqd91601lcd83zzwksb4ampy1j8vf8f6941csk89psm45clwb")))) (build-system r-build-system) (inputs - (list gdal geos proj sqlite)) + (list curl + gdal + geos + openssh + openssl + pcre2 + proj + sqlite + zlib)) (propagated-inputs (list r-classint r-dbi @@ -24044,13 +24149,13 @@ code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.") (define-public r-sccore (package (name "r-sccore") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "sccore" version)) (sha256 - (base32 "1bvqbqh8pkiljy7s3mc67wsr1jlxb19rhd95160xparmrbffpxqb")))) + (base32 "11l7xl1ylzmda4i2p1b08a43pvciin2i2sas2n3cj1gmamflkji3")))) (properties `((upstream-name . "sccore"))) (build-system r-build-system) (propagated-inputs @@ -27288,14 +27393,14 @@ transcription, ...") (define-public r-seewave (package (name "r-seewave") - (version "2.2.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "seewave" version)) (sha256 (base32 - "0bi1l47l3846c18k6h2vrv0xp9xh00n544a578jrndahzrj1hfwl")))) + "0whfanh3949162575ddw5y6s5ydq9v24l929gwdd1jv16xzlnp9h")))) (properties `((upstream-name . "seewave"))) (build-system r-build-system) (inputs @@ -29551,6 +29656,30 @@ to improve the readability of data presented in tabular form rendered in web pages.") (license license:expat))) +(define-public r-formula-tools + (package + (name "r-formula-tools") + (version "1.7.1") + (source (origin + (method url-fetch) + (uri (cran-uri "formula.tools" version)) + (sha256 + (base32 + "15d3ikfmsh9zszfgfkrxb3jkipl41inm7n6bhs73kwlnklnygq2g")))) + (properties `((upstream-name . "formula.tools"))) + (build-system r-build-system) + (propagated-inputs (list r-operator-tools)) + (home-page "https://github.com/decisionpatterns/formula.tools") + (synopsis + "Utilities for manipulating formulas, calls, assignments and other R objects") + (description + "These utilities facilitate the programmatic manipulations of formulas, +expressions, calls, assignments and other R language objects. These objects +all share the same structure: a left-hand side, operator and right-hand side. +This packages provides methods for accessing and modifying this structures as +well as extracting and replacing names and symbols from these objects.") + (license license:gpl2))) + (define-public r-xmisc (package (name "r-xmisc") @@ -36170,40 +36299,40 @@ package online.") (name "r-prereg") (version "0.6.0") (source - (origin - (method url-fetch) - (uri (cran-uri "prereg" version)) - (sha256 - (base32 - "039nrl5cirsx1ysh214dr6xnn1h6h3f90im6k9dgmzfksxdqigpw")))) + (origin + (method url-fetch) + (uri (cran-uri "prereg" version)) + (sha256 + (base32 + "039nrl5cirsx1ysh214dr6xnn1h6h3f90im6k9dgmzfksxdqigpw")))) (properties `((upstream-name . "prereg"))) (build-system r-build-system) (propagated-inputs - (list r-rmarkdown - ;; The package provides a custom LaTex template in - ;; inst/rmd/prereg_form.tex, which depends on these packages: - texlive-amsmath - texlive-booktabs - texlive-etoolbox - texlive-iftex - texlive-fancyhdr - texlive-fancyvrb - texlive-latex-geometry - texlive-graphics - texlive-latex-threeparttable - texlive-titlesec - texlive-latex-upquote - texlive-listings - texlive-polyglossia - texlive-titling - texlive-tools - texlive-ulem - (texlive-updmap.cfg (list texlive-amsfonts texlive-lm)))) + (list r-rmarkdown + ;; The package provides a custom LaTex template in + ;; inst/rmd/prereg_form.tex, which depends on these packages: + texlive-amsmath + texlive-booktabs + texlive-etoolbox + texlive-fancyhdr + texlive-fancyvrb + texlive-geometry + texlive-graphics + texlive-iftex + texlive-listings + texlive-polyglossia + texlive-threeparttable + texlive-titlesec + texlive-titling + texlive-tools + texlive-ulem + texlive-upquote + (texlive-updmap.cfg (list texlive-lm)))) (home-page "https://github.com/crsh/prereg") (synopsis - "R Markdown Templates to preregister Scientific Studies") + "R Markdown Templates to preregister Scientific Studies") (description - "This package provides a collection of templates to author + "This package provides a collection of templates to author preregistration documents for scientific studies in PDF format.") (license license:gpl3))) @@ -36800,14 +36929,14 @@ light-weight geometry library used by @url{http://postgis.net/,PostGIS}.") (define-public r-stars (package (name "r-stars") - (version "0.6-1") + (version "0.6-2") (source (origin (method url-fetch) (uri (cran-uri "stars" version)) (sha256 (base32 - "19q44bs2w12lyim8gzfpgxfkp2cdf29cav4cv74vzsxrv8xdny0z")))) + "0prip06c28d72wa7h8h8p2y7rw7jnh2h2yhnygbaipc8cbzlvi7x")))) (properties `((upstream-name . "stars"))) (build-system r-build-system) (propagated-inputs @@ -39211,14 +39340,14 @@ be efficient and easy to use.") (define-public r-ggh4x (package (name "r-ggh4x") - (version "0.2.4") + (version "0.2.5") (source (origin (method url-fetch) (uri (cran-uri "ggh4x" version)) (sha256 (base32 - "15b2agnk5dsinrxkbq5bmqgckssvlrkwarj2pi7xi8lxsqqrpw3w")))) + "0xj4nlxrpmwzdlj4q3vnhwy7gd1634ff7yjsnaf609ap0q23mxb1")))) (properties `((upstream-name . "ggh4x"))) (build-system r-build-system) (propagated-inputs |