diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 860 |
1 files changed, 678 insertions, 182 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4fe257e6c1..73098ba11e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -258,14 +258,14 @@ projects via a flexible, declarative dependency loading syntax.") (define-public r-brio (package (name "r-brio") - (version "1.1.4") + (version "1.1.5") (source (origin (method url-fetch) (uri (cran-uri "brio" version)) (sha256 (base32 - "1s0q1qk3w3fwf7gn4xfwhf8i8yqqb6z096x6xqsj8av8924z7fqc")))) + "1f6hh7mck4bb1caivcvr6ms2pyqzzzawqyxjbgi9s0rrx8sj7wm9")))) (properties `((upstream-name . "brio"))) (build-system r-build-system) (home-page "https://github.com/r-lib/brio") @@ -537,13 +537,13 @@ labels on the node can also be achieved.") (define-public r-collapse (package (name "r-collapse") - (version "2.0.12") + (version "2.0.13") (source (origin (method url-fetch) (uri (cran-uri "collapse" version)) (sha256 - (base32 "0dplfsj4lqafw0zkrqhph9sk22qpkm5i753pgwf9w9cq5d17f537")))) + (base32 "11i1zw9c9fp5rnhd14b8ivqas38v8qywmmh9w4iaxrb02s77qwz5")))) (properties `((upstream-name . "collapse"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -1680,6 +1680,26 @@ ROCit package provides flexibility to easily evaluate threshold-bound metrics.") (license license:gpl3))) +(define-public r-roi-plugin-lpsolve + (package + (name "r-roi-plugin-lpsolve") + (version "1.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "ROI.plugin.lpsolve" version)) + (sha256 + (base32 "0xgg1fzq5sba3yvvrci3iw97p31walpnhv4zwnd39gw8v5z6f9dj")))) + (properties `((upstream-name . "ROI.plugin.lpsolve"))) + (build-system r-build-system) + (propagated-inputs (list r-lpsolveapi r-roi)) + (home-page "https://roigrp.gitlab.io") + (synopsis "Plugin of lp_solve for the R optimization infrastructure") + (description + "This package enhances the @acronym{ROI, R Optimization Infrastructure} with +the lp_solve solver.") + (license license:gpl3))) + (define-public r-rorcid (package (name "r-rorcid") @@ -2469,14 +2489,14 @@ variables.") (define-public r-ggpp (package (name "r-ggpp") - (version "0.5.6") + (version "0.5.7") (source (origin (method url-fetch) (uri (cran-uri "ggpp" version)) (sha256 (base32 - "0xnjbxd1lkg85c2hsx7cgxqsqb3dc0pma8jwdlqfgg7d519d60xa")))) + "0gd8dbcja4qjwjh414mp2xf8hnjlrp4zm4ac8j59kqxzpwxv8n04")))) (properties `((upstream-name . "ggpp"))) (build-system r-build-system) (propagated-inputs @@ -2492,6 +2512,7 @@ variables.") r-scales r-stringr r-tibble + r-vctrs r-xts r-zoo)) (native-inputs @@ -2672,13 +2693,13 @@ axis} (SMA), and @dfn{ranged major axis} (RMA).") (define-public r-ggpmisc (package (name "r-ggpmisc") - (version "0.5.5") + (version "0.5.6") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 - "1j49q1fbihxir5q5llqwyga111j3lggifzjk3cvq8lphim4c3jia")))) + "0w514js5q6xchbbw2x3085d7parwa8nqaj4fvjplhpfah6rya2dv")))) (build-system r-build-system) (propagated-inputs (list r-confintr @@ -2837,13 +2858,13 @@ higher.") (define-public r-oompadata (package (name "r-oompadata") - (version "3.1.3") + (version "3.1.4") (source (origin (method url-fetch) (uri (cran-uri "oompaData" version)) (sha256 (base32 - "0gdp7bghgpz3q0h06w8r926x7wkpcvkpyf0v5qfi1qixbpvk5fdf")))) + "0g9d551djqa67y2l9nmajnsgf7kys4jcvgi3yx7az7jgm44j8986")))) (properties `((upstream-name . "oompaData"))) (build-system r-build-system) (home-page "https://oompa.r-forge.r-project.org/") @@ -2930,6 +2951,28 @@ provides methods for automatically determining breaks and labels for axes and legends.") (license license:expat))) +(define-public r-skat + (package + (name "r-skat") + (version "2.2.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "SKAT" version)) + (sha256 + (base32 "1x2iyvzc66lmzwjdr8hy5gf3nxc7ik5vhbs40w00d2m7nr3glh8l")))) + (properties `((upstream-name . "SKAT"))) + (build-system r-build-system) + (propagated-inputs (list r-matrix r-rspectra r-spatest)) + (home-page "https://cran.r-project.org/package=SKAT") + (synopsis "SNP-Set (Sequence) kernel association test") + (description + "This package provides functions for kernel-regression-based association +tests including Burden test, SKAT and SKAT-O. These methods aggregate +individual SNP score statistics in a SNP set and efficiently compute SNP-set +level p-values.") + (license license:gpl2+))) + (define-public r-swagger (package (name "r-swagger") @@ -3578,13 +3621,13 @@ similar to OLS.") (define-public r-mboost (package (name "r-mboost") - (version "2.9-9") + (version "2.9-10") (source (origin (method url-fetch) (uri (cran-uri "mboost" version)) (sha256 (base32 - "1apcd90xsr9hl5f1szhyibdx61zi4p6s9bvag8bdk2yj4kqq6fmz")))) + "13dhs3q9gf5n6kwf6j3b29gvwxnkycfkpsw5fr4lnhllm9zs84z7")))) (build-system r-build-system) (propagated-inputs (list r-lattice @@ -3996,13 +4039,13 @@ scraping tasks, inspired by libraries like @code{BeautifulSoup}.") (define-public r-secretbase (package (name "r-secretbase") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "secretbase" version)) (sha256 - (base32 "0b05js4vh6pkkiqms2qmipy5pq96q1i5grb951skk0h953cmwf11")))) + (base32 "04xxjz4b9lpixgpa547rb9y2d370rs6jy1vyr6z24zkia1fmybg4")))) (properties `((upstream-name . "secretbase"))) (build-system r-build-system) (home-page "https://shikokuchuo.net/secretbase/") @@ -4211,6 +4254,38 @@ categorical and continuous (time series) data, otherwise known as dependent mixture models.") (license license:gpl2+))) +(define-public r-detectseparation + (package + (name "r-detectseparation") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "detectseparation" version)) + (sha256 + (base32 "05z3p1z5mhmdj5qdknz1b8f6fwbghzckl88pv79v59cfwpbvgmz8")))) + (properties `((upstream-name . "detectseparation"))) + (build-system r-build-system) + (propagated-inputs (list r-lpsolveapi r-pkgload r-roi r-roi-plugin-lpsolve)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/ikosmidis/detectseparation") + (synopsis + "Detect and check for separation and infinite maximum likelihood estimates") + (description + "This package provides pre-fit and post-fit methods for detecting separation +and infinite maximum likelihood estimates in generalized linear models with +categorical responses. The pre-fit methods apply on binomial-response generalized +liner models such as logit, probit and cloglog regression, and can be directly +supplied as fitting methods to the @code{glm()} function. The post-fit methods +apply to models with categorical responses, including binomial-response +generalized linear models and multinomial-response models, such as baseline +category logits and adjacent category logits models; for example, the models +implemented in the brglm2 package. The post-fit methods successively refit the +model with increasing number of iteratively reweighted least squares iterations, +and monitor the ratio of the estimated standard error for each parameter to what +it has been in the first iteration.") + (license license:gpl3))) + (define-public r-readxl (package (name "r-readxl") @@ -4237,6 +4312,35 @@ the embedded @code{RapidXML} C++ library.") ;; 'rapidxml' which is Boost. (license (list license:gpl3 license:bsd-2 license:boost1.0)))) +(define-public r-rearrr + (package + (name "r-rearrr") + (version "0.3.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "rearrr" version)) + (sha256 + (base32 "1inx1gikiqxaf6a8g10b02l1qs2y0zxs2yrxn6dyx9n6xlra3rnr")))) + (properties `((upstream-name . "rearrr"))) + (build-system r-build-system) + (propagated-inputs (list r-checkmate + r-dplyr + r-lifecycle + r-plyr + r-purrr + r-r6 + r-rlang + r-tibble)) + (home-page "https://github.com/ludvigolsen/rearrr") + (synopsis "Rearranging data by a set of methods") + (description + "This package arranges data by a set of methods. It uses rearrangers to +reorder data points and mutators to change their values. From basic utilities, +to centering the greatest value, to swirling in 3-dimensional space, rearrr +enables creativity when plotting and experimenting with data.") + (license license:expat))) + (define-public r-model4you (package (name "r-model4you") @@ -4510,13 +4614,13 @@ in Miettinen, Nordhausen and Taskinen (2017) <doi:10.18637/jss.v076.i02>.") (define-public r-job (package (name "r-job") - (version "0.3.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "job" version)) (sha256 - (base32 "0d7pw3q5lqlgmav1vx63y8l6gdav96656bg378wj001rx5gx052h")))) + (base32 "14i0ljq2wp9k8112fr27sz0bc0zi2a68kls8vw5h3qa5n40v27cc")))) (properties `((upstream-name . "job"))) (build-system r-build-system) (propagated-inputs (list r-digest r-rstudioapi)) @@ -4578,6 +4682,28 @@ all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.") (license license:expat))) +(define-public r-jsonvalidate + (package + (name "r-jsonvalidate") + (version "1.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "jsonvalidate" version)) + (sha256 + (base32 "0myvm93azl6mj60l8fp91qa3ln3nnwj4p48xli8k215sm6zhhv1b")))) + (properties `((upstream-name . "jsonvalidate"))) + (build-system r-build-system) + (propagated-inputs (list r-v8)) + (native-inputs (list r-knitr)) + (home-page "https://docs.ropensci.org/jsonvalidate/") + (synopsis "Validate JSON schema") + (description + "This package uses the node library @code{is-my-json-valid} or @code{ajv} +to validate JSON against a JSON schema. Drafts 04, 06 and 07 of JSON schema +are supported.") + (license license:expat))) + (define-public r-servr (package (name "r-servr") @@ -6279,14 +6405,14 @@ component analysis (with robust methods, and parallelized functions).") (define-public r-ape (package (name "r-ape") - (version "5.7-1") + (version "5.8") (source (origin (method url-fetch) (uri (cran-uri "ape" version)) (sha256 (base32 - "0yh5wl7nydhwwc82h6yr8wcacc2f791pp05w8fg65anq309cf2cb")))) + "092dx0x763r6ch6pp4c4fkmnq5alrq0527p72w1wdg71g6cp5ki4")))) (build-system r-build-system) (propagated-inputs (list r-digest r-lattice r-nlme r-rcpp)) @@ -6756,13 +6882,13 @@ factorization and divisive clustering for large sparse and dense matrices.") (define-public r-rcppspdlog (package (name "r-rcppspdlog") - (version "0.0.16") + (version "0.0.17") (source (origin (method url-fetch) (uri (cran-uri "RcppSpdlog" version)) (sha256 - (base32 "12xryg2mp00nxmpchf0lki43c13c1vsda14pcc4dcfplamwkhlza")))) + (base32 "0f1s0c32kid910p2q08d77rwprlxx3cq3ngy0kfgfpy13cvm34aa")))) (properties `((upstream-name . "RcppSpdlog"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -7390,13 +7516,13 @@ curve to a data matrix in arbitrary dimensions.") (define-public r-prismatic (package (name "r-prismatic") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "prismatic" version)) (sha256 (base32 - "013i0mq4n8s2zbzvfrz1vjcn2a6l98bamslkcv1a3cn70gpphja9")))) + "0qg2f5d7sz6q0ijrrdmjhp1msx9n77wndphrqqhjkdf9six5pgxs")))) (properties `((upstream-name . "prismatic"))) (build-system r-build-system) (propagated-inputs (list r-farver)) @@ -7431,13 +7557,13 @@ way.") (define-public r-restrserve (package (name "r-restrserve") - (version "1.2.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "RestRserve" version)) (sha256 - (base32 "1xfcp0y9l31815g1jk33mnkb6z68qpjl0gb4fj7f4578kx3v1c8p")))) + (base32 "0jbzalk17jg4qm99005q69pyk76c0wjvdwzjp25npzcvlbsxa194")))) (build-system r-build-system) (propagated-inputs (list r-checkmate @@ -7544,13 +7670,13 @@ most popular ones.") (define-public r-sp (package (name "r-sp") - (version "2.1-3") + (version "2.1-4") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 - (base32 "0m44qr2l8xmqbgi95h200bwy9ca8jihiqzfarws1p09lwmr954zs")))) + (base32 "02lz8wcx16ay3zdqhdb57847i9qg2wzajrfp1z2xpmyjc7xyg1g1")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) @@ -7814,13 +7940,13 @@ which should be seen for details.") (define-public r-evd (package (name "r-evd") - (version "2.3-6.1") + (version "2.3-7") (source (origin (method url-fetch) (uri (cran-uri "evd" version)) (sha256 - (base32 "0wc95hfj0gwkyghipdrhwd3s6q2agh9x2wy6y7dr6mjw7wnmjb36")))) + (base32 "0j2nnprzww1akin6mnj619wp6ihbd7jgbr2daj6lmgirbpqrv2aa")))) (properties `((upstream-name . "evd"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=evd") @@ -8169,6 +8295,26 @@ functions that solve general linear/integer problems, assignment problems, and transportation problems.") (license license:lgpl2.0))) +(define-public r-lpsolveapi + (package + (name "r-lpsolveapi") + (version "5.5.2.0-17.11") + (source + (origin + (method url-fetch) + (uri (cran-uri "lpSolveAPI" version)) + (sha256 + (base32 "191zjgyap3kcsvh8fygqqyr9p0agbzm160fzynnpaxf19yp6r3dh")))) + (properties `((upstream-name . "lpSolveAPI"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=lpSolveAPI") + (synopsis "Interface to lp_solve") + (description + "The lpSolveAPI package provides an R interface to lp_solve, a @acronym{MILP, +Mixed Integer Linear Programming}, solver with support for pure linear, (mixed) +integer/binary, semi-continuous and @acronym{SOS, special ordered sets} models.") + (license license:lgpl2.0))) + (define-public r-limsolve (package (name "r-limsolve") @@ -9952,7 +10098,18 @@ training models for classification or ranking.") (uri (cran-uri "xts" version)) (sha256 (base32 - "1yqx1x395hvdav1fvmpwrfm8sir398ky1bi0x5zsm7acbkv91maa")))) + "1yqx1x395hvdav1fvmpwrfm8sir398ky1bi0x5zsm7acbkv91maa")) + (modules '((guix build utils))) + (snippet + '(with-directory-excursion "inst/doc" + ;; These files are generated from Rnw files. + (for-each delete-file + (list "xts-faq.R" + "xts-faq.Rnw" + "xts-faq.pdf" + "xts.R" + "xts.Rnw" + "xts.pdf")))))) (build-system r-build-system) (propagated-inputs (list r-zoo)) (home-page "https://github.com/joshuaulrich/xts") @@ -10121,16 +10278,16 @@ of Eigenmatrices} (JADE).") (define-public r-ips (package (name "r-ips") - (version "0.0.11") + (version "0.0.12") (source (origin (method url-fetch) (uri (cran-uri "ips" version)) (sha256 (base32 - "02jxanfhsjrabj33nwjv71vdc87hiyzikyqrfdj9ix6dky6lm199")))) + "0vnsalm94vzagksqv4ph6x7vdwhd1lq278sak30pr4m9bc9xxchw")))) (properties `((upstream-name . "ips"))) (build-system r-build-system) - (propagated-inputs (list r-ape r-phangorn r-plyr r-seqinr r-xml)) + (propagated-inputs (list r-ape r-data-table r-phangorn r-plyr r-xml)) (home-page "https://cran.r-project.org/package=ips") (synopsis "Interfaces to phylogenetic software in R") (description @@ -10361,14 +10518,14 @@ functions and used in the data analysis.") (define-public r-debugme (package (name "r-debugme") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "debugme" version)) (sha256 (base32 - "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd")))) + "16ghf60rj0l8ypm0hxjp23zxdi2ndq8ii74cilq61m107fnha9mj")))) (build-system r-build-system) (propagated-inputs (list r-crayon)) (home-page "https://github.com/r-lib/debugme#readme") @@ -10547,14 +10704,14 @@ Markdown documents.") (define-public r-seriation (package (name "r-seriation") - (version "1.5.4") + (version "1.5.5") (source (origin (method url-fetch) (uri (cran-uri "seriation" version)) (sha256 (base32 - "17rk4674r5knfgqyik9gbz6yj42qv6h79j2prw79glc1ym99qcyj")))) + "0v84pic838rpbcmrz8ip466aagz57vmzlgfk0vkhlcv8zn34r0zp")))) (build-system r-build-system) (propagated-inputs (list r-ca @@ -10816,14 +10973,14 @@ vectors.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.50") + (version "0.51") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "11k0pl073b4k4wmpxkw4a071jbpvhr1g3cwm9v99rw3gh6p6x15l")))) + "1sn8fkmz01x0igsh7ynkqsl5h50ccl4xf8025a87i3mmni8kn4dv")))) (build-system r-build-system) (propagated-inputs (list r-xfun)) @@ -12169,6 +12326,26 @@ facilitate data exploration.") experimental designs and random samples for common sampling designs.") (license license:expat))) +(define-public r-roi + (package + (name "r-roi") + (version "1.0-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ROI" version)) + (sha256 + (base32 "05hnj9fskfm2klz7zv97lb0r60akjq4a1cay8p62whpi0hri9zyl")))) + (properties `((upstream-name . "ROI"))) + (build-system r-build-system) + (propagated-inputs (list r-checkmate r-registry r-slam)) + (home-page "https://roi.r-forge.r-project.org/") + (synopsis "R optimization infrastructure") + (description + "The @acronym{ROI, R Optimization Infrastructure} is a framework for handling +optimization problems in R.") + (license license:gpl3))) + (define-public r-roptim (package (name "r-roptim") @@ -13484,13 +13661,13 @@ the source data frame.") (define-public r-rapiclient (package (name "r-rapiclient") - (version "0.1.3") + (version "0.1.4") (source (origin (method url-fetch) (uri (cran-uri "rapiclient" version)) (sha256 (base32 - "1pm4kdga2nz1cpmchdb0ad8gr3bqfm84b1kl32cyc0x3x5rr2syz")))) + "0k92557f90mrmsbfsyvjv377qi04zdh6lqhgnqx51z95f5198kd8")))) (properties `((upstream-name . "rapiclient"))) (build-system r-build-system) (propagated-inputs @@ -13583,14 +13760,14 @@ those searches and pull data into their R sessions.") (define-public r-renv (package (name "r-renv") - (version "1.0.5") + (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 - "07y1xqnx5jkgk0cqgf8c4p5vm3qy87zjl31zv6s0jssy3v7amq4p")))) + "01s5g4w96s0jz9xa1gdj8y4pfvz8cf3gg0kz2smh6f3l4f5baq3v")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (native-inputs @@ -13706,14 +13883,14 @@ always locate the files relative to your project root.") (define-public r-reticulate (package (name "r-reticulate") - (version "1.35.0") + (version "1.36.1") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "0693gzb7ihx4qzsr07k664k5r8vygcinwbdiiccmq9lshl1g64sy")))) + "0c6x6fm8pqw4dj5x2xn12l01piaday0fv588hx903mw3lks3fzbw")))) (build-system r-build-system) (arguments (list @@ -14022,14 +14199,14 @@ clustering.") (define-public r-factominer (package (name "r-factominer") - (version "2.10") + (version "2.11") (source (origin (method url-fetch) (uri (cran-uri "FactoMineR" version)) (sha256 (base32 - "1kjb0hk7zck8702inw9ayxrpbi8raq3rldxsq848lk15z3wg9r6w")))) + "0qzhfjcz0kahqf214g4xs7gfpqx05xbfiwa5r2ldgn2drd16phij")))) (properties `((upstream-name . "FactoMineR"))) (build-system r-build-system) (propagated-inputs @@ -14390,14 +14567,14 @@ references and Rd files.") (define-public r-officer (package (name "r-officer") - (version "0.6.5") + (version "0.6.6") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 - "1lzpabpdrwx3331b9qn43376r25bzgph1j9gbxzqjhzr1h871cpb")))) + "04mlmq64gjdicdlai78iy28n8z64p3k4mnk4k381znlrj9x3zz7i")))) (build-system r-build-system) (propagated-inputs (list r-openssl r-r6 r-ragg r-uuid r-xml2 r-zip)) @@ -14585,14 +14762,14 @@ parse and convert strings into cases like snake or camel among others.") (define-public r-prediction (package (name "r-prediction") - (version "0.3.14") + (version "0.3.17") (source (origin (method url-fetch) (uri (cran-uri "prediction" version)) (sha256 (base32 - "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx")))) + "09fwg3cv7s5mzlcnwp4a04h0ps9m5qlb533p1cpqlinwl72lj4dq")))) (build-system r-build-system) (propagated-inputs (list r-data-table)) @@ -14629,14 +14806,14 @@ Decomposition in R (Beaton et al 2014) <doi:10.1016/j.csda.2013.11.006>.") (define-public r-insight (package (name "r-insight") - (version "0.19.10") + (version "0.19.11") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "0sh7pwnrlggizzpi0smpdq9fds2v8ql3bwdg4yxa2z2apaq3xk6y")))) + "0za6f3bvkybd84jyazg1n03lhzl1w3mpca5c0qsygkgbbyhiddbj")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -14795,14 +14972,14 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.9.5") + (version "0.9.6") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "14mq27k7998405qwpdpxa1csbf5pdgzj9s892xm95bd4chnshdvw")))) + "0acjiwrm0qn0i0v4p0n279ldvlknqhb43mcar9c5s6r3xh5habi3")))) (build-system r-build-system) (propagated-inputs (list r-data-table @@ -15021,14 +15198,14 @@ matches version and feature constraints.") (define-public r-argparse (package (name "r-argparse") - (version "2.2.2") + (version "2.2.3") (source (origin (method url-fetch) (uri (cran-uri "argparse" version)) (sha256 (base32 - "0vc59854fxnznjcrzy5kdmnbyk602ml92jk15rxgndfawvsrnb5n")))) + "0x16zp6jh9asyval1kwkxzavwjhx3a47xzlc593kw1hz4bhw8355")))) (build-system r-build-system) (inputs (list python)) (propagated-inputs @@ -15115,27 +15292,31 @@ the work.") (define-public r-doby (package (name "r-doby") - (version "4.6.20") + (version "4.6.21") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 - "08nsl9xzyi2k7xkwa9mn91fn77ji0z9z5lm388pfdmydbfmpy2ks")))) + "01s9kls9j1nvygh0cc2bfd6n5sjccaalvfw3zx8sv7r2p4clgsij")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs - (list r-broom + (list r-boot + r-broom + r-cowplot r-deriv r-dplyr r-ggplot2 - r-magrittr r-mass r-matrix r-microbenchmark + r-modelr r-pbkrtest - r-tibble)) + r-rlang + r-tibble + r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://people.math.aau.dk/~sorenh/software/doBy/") @@ -15918,14 +16099,14 @@ subsequence} (LCS) using a dynamic programming algorithm.") (define-public r-labelled (package (name "r-labelled") - (version "2.12.0") + (version "2.13.0") (source (origin (method url-fetch) (uri (cran-uri "labelled" version)) (sha256 (base32 - "1f6jh1mrbwb3v1kc49pb65sf5ffqs0h9vizpig4r5rhhv4n3q17y")))) + "0dx2zwympwlys8ndyfz2qki3xywz7sqxfkbd8y52zdj34fj84bly")))) (properties `((upstream-name . "labelled"))) (build-system r-build-system) (propagated-inputs @@ -15935,6 +16116,7 @@ subsequence} (LCS) using a dynamic programming algorithm.") r-rlang r-stringr r-tidyr + r-tidyselect r-vctrs)) (native-inputs (list r-knitr)) @@ -16753,19 +16935,19 @@ handle data from simple random samples as well as complex surveys.") (define-public r-tarchetypes (package (name "r-tarchetypes") - (version "0.8.0") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "tarchetypes" version)) (sha256 (base32 - "18vn2mx5nqlib0by5v7493g8gsbzcdbg0dn92cpbf713r69v1lbk")))) + "0lb5y3rlm369szabmamhq8rrjh7ybngmd3av0jisi84bwdvrwhxk")))) (properties `((upstream-name . "tarchetypes"))) (build-system r-build-system) - (propagated-inputs (list r-digest - r-dplyr + (propagated-inputs (list r-dplyr r-fs r-rlang + r-secretbase r-targets r-tibble r-tidyselect @@ -16787,13 +16969,13 @@ were influenced by the drake R package by Will Landau (2018) (define-public r-targets (package (name "r-targets") - (version "1.6.0") + (version "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "targets" version)) (sha256 (base32 - "1ddpbhvdydxm62k6ay7hpqjh8kh2isjpcdh3gygzcdrghx6d7x65")))) + "1h939mvyxd1wjakcbxjxcmn6a7i23ya1kc89aqwarizsj00hdjil")))) (properties `((upstream-name . "targets"))) (build-system r-build-system) (propagated-inputs (list r-base64url @@ -16801,7 +16983,6 @@ were influenced by the drake R package by Will Landau (2018) r-cli r-codetools r-data-table - r-digest r-igraph r-knitr r-ps @@ -17527,14 +17708,14 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "1.5.1") + (version "1.5.2") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "07a23lkj5v98hnqn3qiaxw6rijh6dg5g7kzp7vnsq4mkkm3hsicw")))) + "1f5ralb5fkcv2rflsl0y9lgwdmx6zzv3s1087lql9x5vjd1hkvcg")))) (build-system r-build-system) (propagated-inputs (list r-insight)) @@ -17555,14 +17736,14 @@ results using @code{ggplot2}.") (define-public r-effectsize (package (name "r-effectsize") - (version "0.8.7") + (version "0.8.8") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 - "07lfa0pvqhanjyyx9hs6gdqw1zyi1y21k539jgvgnrvixfilfkb2")))) + "1dx83xv98iny4pzphrr64fv277k70cgmia1s18bh7fix2h3md45k")))) (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs @@ -17756,14 +17937,14 @@ repositories.") (define-public r-fs (package (name "r-fs") - (version "1.6.3") + (version "1.6.4") (source (origin (method url-fetch) (uri (cran-uri "fs" version)) (sha256 (base32 - "0wgrq0vgaf9czjyzlxdmpy7swxcyd4mryks0gr5xk96pa0g0d0ps")))) + "1j2sx9zxz0qcgvim8mvvjrl0z2qbn2j4idsivx7zadmy5l7jj1ky")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -17956,14 +18137,14 @@ the code was copied over from @code{devtools}.") (define-public r-xopen (package (name "r-xopen") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "xopen" version)) (sha256 (base32 - "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2")))) + "1v4sna4md4cpqwi7802m4mfflgi506fxh78la0kam894qfw7icp3")))) (build-system r-build-system) (propagated-inputs (list r-processx)) @@ -18658,13 +18839,13 @@ simulation of correlated data, and more.") (define-public r-biocmanager (package (name "r-biocmanager") - (version "1.30.22") + (version "1.30.23") (source (origin (method url-fetch) (uri (cran-uri "BiocManager" version)) (sha256 - (base32 "0dg86nbh9h77ypaarsd79df24j0vnlm2df4zcmbhfasnsv0ck2ak")))) + (base32 "0k7kv06wksy3lkp37yf0kfnsbwf6fbac2vmrqip2wyy996y5vd7p")))) (properties `((upstream-name . "BiocManager"))) (build-system r-build-system) (native-inputs @@ -19351,14 +19532,14 @@ Processing.") (define-public r-tm (package (name "r-tm") - (version "0.7-12") + (version "0.7-13") (source (origin (method url-fetch) (uri (cran-uri "tm" version)) (sha256 (base32 - "1z0zpz6jgzg34cz07cdpya2zwwsvywrd8xgwahhlz15vnaij7j3y")))) + "1d0xczmmfsj82183nygvb4f9h1qbydz763b3jlzxb6ns8pi6q9p5")))) (properties `((upstream-name . "tm"))) (build-system r-build-system) (propagated-inputs @@ -19697,18 +19878,19 @@ large datasets (> 100,000 samples) very efficiently.") (define-public r-qlcmatrix (package (name "r-qlcmatrix") - (version "0.9.7") + (version "0.9.8") (source (origin (method url-fetch) (uri (cran-uri "qlcMatrix" version)) (sha256 (base32 - "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y")))) + "0d38jb653787s05g8syc9wgaljaifmkviijwz5rzcd881glgs8sv")))) (properties `((upstream-name . "qlcMatrix"))) (build-system r-build-system) (propagated-inputs (list r-docopt r-matrix r-slam r-sparsesvd)) + (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://cran.r-project.org/web/packages/qlcMatrix") (synopsis "Sparse matrix functions for quantitative language comparison") (description @@ -20195,13 +20377,13 @@ handling.") (define-public r-gridpattern (package (name "r-gridpattern") - (version "1.1.1") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "gridpattern" version)) (sha256 - (base32 "1v7xfgbnrr4v3arr7nm0663aywn47xb89sd0rn9s9dcz7r50aa2i")))) + (base32 "0rkhwk3h5rd3z52dnjc5rq1gbay17r208zfqbkh9gj9kn8rb2wb8")))) (properties `((upstream-name . "gridpattern"))) (build-system r-build-system) (propagated-inputs @@ -20489,14 +20671,14 @@ Emphasis is always given to methods for visualizing the data.") (define-public r-pixmap (package (name "r-pixmap") - (version "0.4-12") + (version "0.4-13") (source (origin (method url-fetch) (uri (cran-uri "pixmap" version)) (sha256 (base32 - "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9")))) + "04g74v8g9r0f3czzk4r3n0wxyg7ldgfdlh21bas7axa9l10wdnz3")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pixmap") (synopsis "Tools for bitmap images") @@ -22707,14 +22889,14 @@ latent growth curve models.") (define-public r-nonnest2 (package (name "r-nonnest2") - (version "0.5-6") + (version "0.5-7") (source (origin (method url-fetch) (uri (cran-uri "nonnest2" version)) (sha256 (base32 - "1s31a03c148azvc20ihmz8vhzgs7a3r0nxzf806zsr5j1zsl94dm")))) + "0gnv538wskgyp6v08b0grz76mfpc1qlbp0r5w19b9lrv9d3c4h74")))) (build-system r-build-system) (propagated-inputs (list r-compquadform r-lavaan r-mvtnorm r-sandwich)) @@ -22971,14 +23153,14 @@ network.") (define-public r-apcluster (package (name "r-apcluster") - (version "1.4.11") + (version "1.4.13") (source (origin (method url-fetch) (uri (cran-uri "apcluster" version)) (sha256 (base32 - "0crk7skivcmlvr0njsbd8dksj5wa6qlvdp99ay5b2b40cs3xm5s4")))) + "19x1sma5pli5jl0v92c6x7jbqkigz7waaghaxi29kvvx8am5p5sy")))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp)) @@ -23860,13 +24042,13 @@ either PDF/EPS files.") (define-public r-polspline (package (name "r-polspline") - (version "1.1.24") + (version "1.1.25") (source (origin (method url-fetch) (uri (cran-uri "polspline" version)) (sha256 - (base32 "0mal78f79jl6cj02xabv9vqf88m4iiadmgiv3qliv117cxkc6hb6")))) + (base32 "18wv3v76y4xdlrz7qdp6amr0ynhyqbja1rjqmbz0lc12v56gqhr9")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/polspline/") @@ -24127,13 +24309,13 @@ SELECT or UPDATE queries to an end-point.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.38") + (version "0.39") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "1i0z75sxvy3cb582siz544az6b9bs3vk2kyij9zx5jdpc1247fgd")) + "1brfv50lq92m7d4d18n92ywhfr28lrbq02naf0bwdsmd0ngasxrm")) ;; TODO: there is one more file to replace: ;; inst/resources/gitbook/js/app.min.js (snippet @@ -24221,13 +24403,13 @@ authoring books and technical documents with R Markdown.") (define-public r-options (package (name "r-options") - (version "0.1.0") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "options" version)) (sha256 - (base32 "0pprbp2pxvgh120f8dahswws44gpdm4f4nlq3h3nvqrlhnspwnb8")))) + (base32 "02qnbipdmnw01f40300pg1ycrcbnr37f8yiqbabm6jznf6r4ihm9")))) (properties `((upstream-name . "options"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -24242,14 +24424,14 @@ global options, defining default values and more.") (define-public r-optparse (package (name "r-optparse") - (version "1.7.4") + (version "1.7.5") (source (origin (method url-fetch) (uri (cran-uri "optparse" version)) (sha256 (base32 - "122x490161f836l7mmd021dpylz50qrqdhjcgvkd8wpsjijxd8lk")))) + "04jp85jik1zkbb08w44m2h0hqyzd80w4pjnfp1lnwy40ax81gj8c")))) (build-system r-build-system) (propagated-inputs (list r-getopt)) @@ -24676,14 +24858,14 @@ consists of @code{grid} grobs and viewports that can then be manipulated with (define-public r-farver (package (name "r-farver") - (version "2.1.1") + (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "farver" version)) (sha256 (base32 - "1klnr73fhm7n46q85in1v9gi99y6rcdzzg4h4wvnbx23lxndmkqd")))) + "09gy2wmm3jp2k3q6zbmjl6z55a974221q7vi6xhmdd5abnwj722j")))) (build-system r-build-system) (home-page "https://github.com/thomasp85/farver") (synopsis "Vectorized color conversion and comparison") @@ -25074,14 +25256,14 @@ proteomics applications).") (define-public r-pamr (package (name "r-pamr") - (version "1.56.1") + (version "1.56.2") (source (origin (method url-fetch) (uri (cran-uri "pamr" version)) (sha256 (base32 - "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh")))) + "0n7wpgzdadngj44ddsg3171wap4qhiaap75ndr6g768r3mv6q119")))) (build-system r-build-system) (propagated-inputs (list r-cluster r-survival)) @@ -25287,14 +25469,14 @@ using the three.js visualization library.") (define-public r-mlbench (package (name "r-mlbench") - (version "2.1-3.1") + (version "2.1-5") (source (origin (method url-fetch) (uri (cran-uri "mlbench" version)) (sha256 (base32 - "1w2w7nkrp69c0di0lss82jf4fbxdpqwxzqa2lrp55av8i7awdzks")))) + "0vz7r4f0d0k7i9dx3r7gz8i7rs9f7b96qfjdajphqz6smm9ddgsd")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/mlbench/") (synopsis "Machine learning benchmark problems") @@ -26623,14 +26805,14 @@ versions. A Shiny application implementing the functions is also included.") (define-public r-ggfortify (package (name "r-ggfortify") - (version "0.4.16") + (version "0.4.17") (source (origin (method url-fetch) (uri (cran-uri "ggfortify" version)) (sha256 (base32 - "05h3a4ycain0y621anjpjphsjlhpayb2nnd6n70rlymrbilfw6xv")))) + "1ygbvk3b99mabwqc9hh5lz3adj1i05ym7i8b6kbgid8cgrbaaxag")))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -26774,14 +26956,14 @@ in R, including a translation of the original algorithm into R.") (define-public r-uwot (package (name "r-uwot") - (version "0.1.16") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "uwot" version)) (sha256 (base32 - "0j4f7vnb3mwf6p4nhg2limy7i32qrcj2gxbs8wsq9c6xxpcs0qsz")))) + "1lbckamb2hk24qxcvchdfid982cvcz64j9hvdnrx8c4ms91qr4yr")))) (build-system r-build-system) (propagated-inputs (list r-dqrng @@ -26790,7 +26972,9 @@ in R, including a translation of the original algorithm into R.") r-matrix r-rcpp r-rcppannoy - r-rcppprogress)) + r-rcppprogress + r-rspectra)) + (native-inputs (list r-knitr)) (home-page "https://github.com/jlmelville/uwot") (synopsis "Uniform manifold approximation and projection") (description @@ -27067,14 +27251,14 @@ OpenMP.") (define-public r-lda (package (name "r-lda") - (version "1.4.2") + (version "1.5.2") (source (origin (method url-fetch) (uri (cran-uri "lda" version)) (sha256 (base32 - "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn")))) + "1m0g2mz7rhjsp6pm784qjngzrb6kp69zjb85fflm48q0drw59lwm")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/lda/") (synopsis "Collapsed Gibbs sampling methods for topic models") @@ -28700,6 +28884,28 @@ Components. The Lasso solution paths can be computed by the same function.") and mixture of Gaussian models.") (license license:gpl2+))) +(define-public r-spatest + (package + (name "r-spatest") + (version "3.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "SPAtest" version)) + (sha256 + (base32 "1x5r4a6jnizhhazxywb2cf2jj2rx6rfynl6xcscmlix6n394xmxk")))) + (properties `((upstream-name . "SPAtest"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=SPAtest") + (synopsis + "Score test and meta-analysis based on Saddlepoint approximation") + (description + "This package performs score test using saddlepoint approximation to +estimate the null distribution. It also prepares summary statistics for +meta-analysis and performs meta-analysis to combine multiple association +results.") + (license license:gpl2+))) + (define-public r-accsda (package (name "r-accsda") @@ -29311,14 +29517,14 @@ provided as well.") (define-public r-tuner (package (name "r-tuner") - (version "1.4.6") + (version "1.4.7") (source (origin (method url-fetch) (uri (cran-uri "tuneR" version)) (sha256 (base32 - "1l270rk1m3967fvgpshrbd71l7ns74wdhivbmavayk68dnsiyi65")))) + "02lnnsh2r22qg54ygdjjpd6986gqr5r3qbzxxrz34lq98jh58h9n")))) (properties `((upstream-name . "tuneR"))) (build-system r-build-system) (propagated-inputs (list r-signal)) @@ -29499,13 +29705,13 @@ classes into dummy/indicator variables.") (define-public r-dunn-test (package (name "r-dunn-test") - (version "1.3.5") + (version "1.3.6") (source (origin (method url-fetch) (uri (cran-uri "dunn.test" version)) (sha256 (base32 - "0lqwvyl3pyygfc73nf81gzw3zl3w43r7ki0yw2dgrzhkpb2iji4a")))) + "0z3qyq0lnflmsx41dbkr5lwgiqf3z8rn5wy54c93fwmahva0lqs9")))) (properties `((upstream-name . "dunn.test"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=dunn.test") @@ -30311,14 +30517,14 @@ number embedded in the file rather than the file extension.") (define-public r-imager (package (name "r-imager") - (version "0.45.8") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "imager" version)) (sha256 (base32 - "0vrv7m9b9w8xjqa9w17xvrmpl403476zr0l9wqdp9ir6ssvnaf2f")))) + "0sjn3ig5p020gml200cy5bdbrbql7qv1fqhhzjpcbmhprf39113w")))) (properties `((upstream-name . "imager"))) (build-system r-build-system) (inputs @@ -30515,18 +30721,18 @@ used in outliers detection.") (define-public r-tolerance (package (name "r-tolerance") - (version "2.0.0") + (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "tolerance" version)) (sha256 (base32 - "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd")))) + "0pk75i0qmfrpm02jm4c0vvryq3f2drmj9dzj1q0zr3sbmp9w6mpf")))) (properties `((upstream-name . "tolerance"))) (build-system r-build-system) (propagated-inputs - (list r-mass r-rgl)) + (list r-mass r-plotly)) (home-page "https://cran.r-project.org/web/packages/tolerance/") (synopsis "Statistical tolerance intervals and regions") (description @@ -30627,14 +30833,14 @@ Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.") (define-public r-flexclust (package (name "r-flexclust") - (version "1.4-1") + (version "1.4-2") (source (origin (method url-fetch) (uri (cran-uri "flexclust" version)) (sha256 (base32 - "13akk3w6a76jpws5v9108c3hdmb8i6gm0sc06lr2hqly0pgpfyfn")))) + "0massgyn8vdzp40dz5l02qqzjynw1lgyw9psvb792q73j7b20iqc")))) (properties `((upstream-name . "flexclust"))) (build-system r-build-system) (propagated-inputs @@ -31767,14 +31973,14 @@ Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.") (define-public r-quanteda (package (name "r-quanteda") - (version "4.0.1") + (version "4.0.2") (source (origin (method url-fetch) (uri (cran-uri "quanteda" version)) (sha256 (base32 - "0m0iw7vm9v7dcrh9yd56kr0vagas1czqgbn2ybyxg86nwcrl73qq")))) + "1s046p3bnf36z2mqh5ijirq7jygqj5clal3r0l3f89gr0466a75j")))) (properties `((upstream-name . "quanteda"))) (build-system r-build-system) (propagated-inputs @@ -32108,14 +32314,14 @@ perform @dfn{exploratory mediation} (XMed).") (define-public r-stanheaders (package (name "r-stanheaders") - (version "2.32.6") + (version "2.32.7") (source (origin (method url-fetch) (uri (cran-uri "StanHeaders" version)) (sha256 (base32 - "18p1rch5ipj0f4jdvr8mnlk8pg1l4njjj4cgbp7ni7kcngsn3049")))) + "1dlgq0laz5j4ryiz589xhd97fk89q63255wkdbddixfg6cq02ypf")))) (properties `((upstream-name . "StanHeaders"))) (build-system r-build-system) (inputs (list pandoc)) @@ -32326,13 +32532,13 @@ league, the Bundesliga. It contains data from 1964 to 2016.") (define-public r-butcher (package (name "r-butcher") - (version "0.3.3") + (version "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "butcher" version)) (sha256 (base32 - "14zf732rcy0f1n0l7km9jx74i0dwqdf864v2510lwpkfblgnw4s7")))) + "027j48n0izwzlg63gml5wkx19kpmd5crbdkmg7p366lpbhhvbs0d")))) (properties `((upstream-name . "butcher"))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -34633,14 +34839,14 @@ simple interface for all functions.") (define-public r-iml (package (name "r-iml") - (version "0.11.2") + (version "0.11.3") (source (origin (method url-fetch) (uri (cran-uri "iml" version)) (sha256 (base32 - "1sjv0cj50iivjlb2hri401z78rmidxxh6q5akscd42k98jyw2r30")))) + "1d0p41byqpw7niyyyqcj00y43dmhqrm2csmbarcy8mz7n0i1842b")))) (properties `((upstream-name . "iml"))) (build-system r-build-system) (propagated-inputs @@ -35452,14 +35658,14 @@ censored data.") (define-public r-flexsurv (package (name "r-flexsurv") - (version "2.2.2") + (version "2.3") (source (origin (method url-fetch) (uri (cran-uri "flexsurv" version)) (sha256 (base32 - "1qshsii5fqpx4l113vr4lx9ijxhcr8494lx3ixjdbzy58077adb6")))) + "1y31ghfn02fcpss3aliy5r7kk0a7h0h2krnj665h13y8jgqkc6j7")))) (properties `((upstream-name . "flexsurv"))) (build-system r-build-system) (propagated-inputs @@ -36216,14 +36422,14 @@ for creating, simulating, or validating values for such parameters.") (define-public r-tune (package (name "r-tune") - (version "1.2.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "tune" version)) (sha256 (base32 - "1z5id7mp9yknxz4lbb0304wn47ii61zmds3grffc4q84v3d9gb76")))) + "1qb4ncadq10pzy8xhkpgg06raahbv6n8002wdjdh4jlv73hsk6ki")))) (properties `((upstream-name . "tune"))) (build-system r-build-system) (propagated-inputs @@ -36507,14 +36713,14 @@ vignettes in all common formats.") (define-public r-tidytext (package (name "r-tidytext") - (version "0.4.1") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "tidytext" version)) (sha256 (base32 - "05f8209qx1rvddnkl0h05yig09xahs8lqgq9w5dvdiwarji50rsj")))) + "0m1dxlrmkany4pjbr2p2m9hzn59gldmznyvs6dcb3zdr5861ix0c")))) (properties `((upstream-name . "tidytext"))) (build-system r-build-system) (propagated-inputs @@ -36825,6 +37031,28 @@ meta-analyses accounting for known correlation structures (e.g. due to phylogenetic relatedness) can also be conducted.") (license license:gpl2+))) +(define-public r-metaskat + (package + (name "r-metaskat") + (version "0.82") + (source + (origin + (method url-fetch) + (uri (cran-uri "MetaSKAT" version)) + (sha256 + (base32 "0cbj3xfsnwn4ibqqs12sqyhhaj24ydjpyl1p1gy1dl5405j58ncl")))) + (properties `((upstream-name . "MetaSKAT"))) + (build-system r-build-system) + (propagated-inputs (list r-skat)) + (home-page "https://cran.r-project.org/package=MetaSKAT") + (synopsis "Meta analysis for SNP-Set (Sequence) kernel association test") + (description + "This package provides functions for Meta-analysis Burden Test, Sequence +Kernel Association Test (SKAT) and Optimal SKAT (SKAT-O) by Lee et al. (2013) +<doi:10.1016/j.ajhg.2013.05.010>. These methods use summary-level score +statistics to carry out gene-based meta-analysis for rare variants.") + (license license:gpl2+))) + (define-public r-altmeta (package (name "r-altmeta") @@ -37008,14 +37236,14 @@ data to rasters. It speeds up plotting of data with millions of points.") (define-public r-seuratobject (package (name "r-seuratobject") - (version "5.0.1") + (version "5.0.2") (source (origin (method url-fetch) (uri (cran-uri "SeuratObject" version)) (sha256 (base32 - "0hgrymldcqja40prr23gwx1c7lvwjjwcla3dld6x8wzkzqh1gkjs")))) + "1kx0icqzjck7vynxj5962sz9zlassia4j32azr9y7ds5yhhhvlyy")))) (properties `((upstream-name . "SeuratObject"))) (build-system r-build-system) (propagated-inputs @@ -37074,13 +37302,13 @@ other R users.") (define-public r-seurat (package (name "r-seurat") - (version "5.0.3") + (version "5.1.0") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "08r5l6sk8i134izd29ydfm7hva7a9b3lfglmgngc9w73qs9dzwz4")))) + "0nad49g13v5zg4rr2099m1cl1qcmmj1a0m09gam5xiccg8yv9kxd")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs @@ -37680,6 +37908,182 @@ visualization, and logging. Its modular implementation allows easy customization by the user.") (license license:bsd-2))) +(define-public r-mlr3cluster + (package + (name "r-mlr3cluster") + (version "0.1.9") + (source + (origin + (method url-fetch) + (uri (cran-uri "mlr3cluster" version)) + (sha256 + (base32 "09fsw2b43f9m7clv1qwylimyz622snhn9ykq3xwbiric7zr4ca91")))) + (properties `((upstream-name . "mlr3cluster"))) + (build-system r-build-system) + (propagated-inputs (list r-backports + r-checkmate + r-clue + r-cluster + r-data-table + r-fpc + r-mlr3 + r-mlr3misc + r-paradox + r-r6)) + (home-page "https://mlr3cluster.mlr-org.com") + (synopsis "Cluster extension for mlr3") + (description + "This package extends the mlr3 package with cluster analysis.") + (license license:lgpl3))) + +(define-public r-mlr3data + (package + (name "r-mlr3data") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "mlr3data" version)) + (sha256 + (base32 "04hwmj8cdszwgd845va26pgzdw0k4cm025zjrmp3fr7ypp73mirg")))) + (properties `((upstream-name . "mlr3data"))) + (build-system r-build-system) + (home-page "https://github.com/mlr-org/mlr3data") + (synopsis "Collection of machine learning data Sets for mlr3") + (description + "This package provides a small collection of interesting and educational +machine learning data sets which are used as examples in the mlr3 book Applied +machine learning using mlr3 in R @url{https://mlr3book.mlr-org.com}, the use case +gallery @url{https://mlr3gallery.mlr-org.com}, or in other examples. All data +sets are properly preprocessed and ready to be analyzed by most machine learning +algorithms. Data sets are automatically added to the dictionary of tasks if +mlr3 is loaded.") + (license license:lgpl3))) + +(define-public r-mlr3filters + (package + (name "r-mlr3filters") + (version "0.8.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "mlr3filters" version)) + (sha256 + (base32 "16z359bc2li7f35xk4g08np3r2a3127avv0ak6bn9bywcs13z6bl")))) + (properties `((upstream-name . "mlr3filters"))) + (build-system r-build-system) + (propagated-inputs (list r-backports + r-checkmate + r-data-table + r-mlr3 + r-mlr3misc + r-paradox + r-r6)) + (home-page "https://mlr3filters.mlr-org.com") + (synopsis "Filter based feature selection for mlr3") + (description + "This package extends mlr3 with filter methods for feature selection. Besides +standalone filter methods built-in methods of any machine-learning algorithm are +supported. Partial scoring of multivariate filter methods is supported.") + (license license:lgpl3))) + +(define-public r-mlr3fselect + (package + (name "r-mlr3fselect") + (version "0.12.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "mlr3fselect" version)) + (sha256 + (base32 "1f18y4ahnjzlwk9pfs87i80kb6z84hgyc5cdlj3mafawq790hg1h")))) + (properties `((upstream-name . "mlr3fselect"))) + (build-system r-build-system) + (propagated-inputs (list r-bbotk + r-checkmate + r-data-table + r-lgr + r-mlr3 + r-mlr3misc + r-paradox + r-r6)) + (home-page "https://mlr3fselect.mlr-org.com") + (synopsis "Feature selection for mlr3") + (description + "This package is a feature selection package of the mlr3 ecosystem. It +selects the optimal feature set for any mlr3 learner. The package works with +several optimization algorithms e.g. random search, Recursive feature elimination, +and genetic search. Moreover, it can automatically optimize learners and estimate +the performance of optimized feature sets with nested resampling.") + (license license:lgpl3))) + +(define-public r-mlr3hyperband + (package + (name "r-mlr3hyperband") + (version "0.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "mlr3hyperband" version)) + (sha256 + (base32 "1x6vfhadxlb4c9q61d5qv957mkyfwdwchzbg3flfd0j28b4bck1p")))) + (properties `((upstream-name . "mlr3hyperband"))) + (build-system r-build-system) + (propagated-inputs (list r-bbotk + r-checkmate + r-data-table + r-lgr + r-mlr3 + r-mlr3misc + r-mlr3tuning + r-paradox + r-r6)) + (home-page "https://mlr3hyperband.mlr-org.com") + (synopsis "Hyperband for mlr3") + (description + "This package implements a successive halving and hyperband optimization +algorithm for the mlr3 ecosystem. The implementation in mlr3hyperband features +improved scheduling and parallelizes the evaluation of configurations. The package +includes tuners for hyperparameter optimization in mlr3tuning and optimizers for +black-box optimization in bbotk.") + (license license:lgpl3))) + +(define-public r-mlr3mbo + (package + (name "r-mlr3mbo") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "mlr3mbo" version)) + (sha256 + (base32 "0jdj5dx6jb7n0g950h0j8jhafdj5mcalv5vxfiyf07myr6mjipri")))) + (properties `((upstream-name . "mlr3mbo"))) + (build-system r-build-system) + (propagated-inputs (list r-bbotk + r-checkmate + r-data-table + r-lgr + r-mlr3 + r-mlr3misc + r-mlr3tuning + r-paradox + r-r6 + r-spacefillr)) + (native-inputs (list r-knitr)) + (home-page "https://mlr3mbo.mlr-org.com") + (synopsis "Flexible Bayesian optimization") + (description + "This package provides a flexible approach to Bayesian optimization / model +based optimization building on the bbotk package. The mlr3mbo is a toolbox +providing both ready-to-use optimization algorithms as well as their fundamental +building blocks allowing for straightforward implementation of custom algorithms. +Single- and multi-objective optimization is supported as well as mixed continuous, +categorical and conditional search spaces. Moreover, using mlr3mbo for +hyperparameter optimization of machine learning models within the mlr3 ecosystem +is straightforward via mlr3tuning.") + (license license:lgpl3))) + (define-public r-mlr3measures (package (name "r-mlr3measures") @@ -37705,13 +38109,13 @@ are.") (define-public r-mlr3misc (package (name "r-mlr3misc") - (version "0.14.0") + (version "0.15.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3misc" version)) (sha256 (base32 - "19q20ld2phplrg6jqg849rjpi8yl3j5v1d8bgzagyyhka3nxn4fx")))) + "1l40l0sx1dgs2rdblx7pd9nk93flad6y1mvppzg7qf4cyn8gfc3x")))) (build-system r-build-system) (propagated-inputs (list r-backports r-checkmate r-data-table r-digest r-r6)) @@ -37727,13 +38131,13 @@ package also supersedes the package @code{BBmisc}.") (define-public r-mlr3pipelines (package (name "r-mlr3pipelines") - (version "0.5.1") + (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "mlr3pipelines" version)) (sha256 (base32 - "1brsvzn519yc5vq2sax0q5xwvs0180ykn6ljk2wy502aabrcxzmg")))) + "1glp4z5wnvcsil37gzvbvazn73088vilks9c5limnwhz8f454147")))) (build-system r-build-system) (propagated-inputs (list r-backports @@ -37788,6 +38192,98 @@ resampled, benchmarked, and tuned.") performing ordinal regression.") (license license:expat)))) +(define-public r-mlr3tuningspaces + (package + (name "r-mlr3tuningspaces") + (version "0.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "mlr3tuningspaces" version)) + (sha256 + (base32 "1snrd7xq388mvqh0ydaxvx8k9iwp40g06c3irp0m718jw3wsz5vm")))) + (properties `((upstream-name . "mlr3tuningspaces"))) + (build-system r-build-system) + (propagated-inputs (list r-checkmate + r-data-table + r-mlr3 + r-mlr3misc + r-mlr3tuning + r-paradox + r-r6)) + (home-page "https://mlr3tuningspaces.mlr-org.com") + (synopsis "Search spaces for mlr3") + (description + "This package is a collection of search spaces for hyperparameter optimization +in the mlr3 ecosystem. It features ready-to-use search spaces for many popular +machine learning algorithms. The search spaces are from scientific articles and +work for a wide range of data sets.") + (license license:lgpl3))) + +(define-public r-mlr3verse + (package + (name "r-mlr3verse") + (version "0.2.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "mlr3verse" version)) + (sha256 + (base32 "0ld4vch1qdq3gh8vhj38s2wz7acn5z7f8hxmnwnrq22g44gckd8s")))) + (properties `((upstream-name . "mlr3verse"))) + (build-system r-build-system) + (propagated-inputs (list r-bbotk + r-data-table + r-mlr3 + r-mlr3cluster + r-mlr3data + r-mlr3filters + r-mlr3fselect + r-mlr3hyperband + r-mlr3learners + r-mlr3mbo + r-mlr3misc + r-mlr3pipelines + r-mlr3tuning + r-mlr3tuningspaces + r-mlr3viz + r-paradox)) + (home-page "https://mlr3verse.mlr-org.com") + (synopsis "Easily install and load of the mlr3 package family") + (description + "The mlr3 package family is a set of packages for machine-learning purposes +built in a modular fashion. This wrapper package is aimed to simplify the +installation and loading of the core mlr3 packages.") + (license license:lgpl3))) + +(define-public r-mlr3viz + (package + (name "r-mlr3viz") + (version "0.8.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "mlr3viz" version)) + (sha256 + (base32 "1m2f54yqhk1bd4c30vd1z509yblz6y4i8qkwhg73aa1sflnsycvf")))) + (properties `((upstream-name . "mlr3viz"))) + (build-system r-build-system) + (propagated-inputs (list r-checkmate + r-data-table + r-ggplot2 + r-mlr3misc + r-scales + r-viridis)) + (home-page "https://mlr3viz.mlr-org.com") + (synopsis "Visualizations for mlr3") + (description + "This package offers features plots for mlr3 objects such as tasks, learners, +predictions, benchmark results, tuning instances and filters via the +@code{autoplot()} generic of ggplot2. The mlr3viz package draws plots with +the viridis color palette and applies the minimal theme. Visualizations include +barplots, boxplots, histograms, ROC curves, and precision-recall curves.") + (license license:lgpl3))) + (define-public r-paradox (package (name "r-paradox") @@ -37812,13 +38308,13 @@ implemented as @code{R6} classes.") (define-public r-mlr3 (package (name "r-mlr3") - (version "0.18.0") + (version "0.19.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3" version)) (sha256 (base32 - "0v83lwigpm227dqr8hz5x1khcjqf3q0glqvz812sckbcf74ibhdz")))) + "0dgik4lfrw5m2sqxp33kzkdp7ihlcm27y5p5g5b9wah7h7ramiqs")))) (build-system r-build-system) (propagated-inputs (list r-backports @@ -38201,14 +38697,14 @@ the font tool-set provided by the @code{systemfonts} package.") (define-public r-ragg (package (name "r-ragg") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "ragg" version)) (sha256 (base32 - "1chlas4i6p8gigx02x1y7nanmz9jbv1h4fa145zk223bbg9j931j")))) + "1p3bhbcgkllgmby9rdc1hillb5qgmc22blpmvdhd5j9ndywv2h0w")))) (properties `((upstream-name . "ragg"))) (build-system r-build-system) (inputs @@ -38263,14 +38759,14 @@ in output to the equivalent HTML.") (define-public r-pkgdown (package (name "r-pkgdown") - (version "2.0.7") + (version "2.0.9") (source (origin (method url-fetch) (uri (cran-uri "pkgdown" version)) (sha256 (base32 - "0sim3fwayf4mpxqi8y9v7clnkzs56amhxsc75lc1k0zskn374f7k")))) + "186xzilh4079a6xjig3j4pdn99ipg4d5s5q1k75qclivq0b24m3f")))) (properties `((upstream-name . "pkgdown"))) (build-system r-build-system) (inputs (list pandoc)) @@ -39262,14 +39758,14 @@ join the effort of providing interesting text visualisations.") (define-public r-gsa (package (name "r-gsa") - (version "1.03.2") + (version "1.03.3") (source (origin (method url-fetch) (uri (cran-uri "GSA" version)) (sha256 (base32 - "1f1mrxxdbdlnibgav6nsvbpniz2x3km2svc0hf43spb4zicn0z8p")))) + "0b18b8n6dh3yx9vp5b7ym25590x9qrcbprs5vjnkj0zlj1hphnal")))) (properties `((upstream-name . "GSA"))) (build-system r-build-system) (home-page "https://statweb.stanford.edu/~tibs/GSA/") @@ -39825,14 +40321,14 @@ C API for topology operations on geometries.") (define-public r-tfruns (package (name "r-tfruns") - (version "1.5.2") + (version "1.5.3") (source (origin (method url-fetch) (uri (cran-uri "tfruns" version)) (sha256 (base32 - "1iw80r31jddngby48wf53ayjhvvx77kas4hvvp7j65klvx337aqw")))) + "0z0cbw4fr374s82ds0vdxmd37bbd6yrixwgby26qzkjr7dvzsbmy")))) (properties `((upstream-name . "tfruns"))) (build-system r-build-system) (propagated-inputs @@ -39882,14 +40378,14 @@ Tensorflow graphs.") (define-public r-tensorflow (package (name "r-tensorflow") - (version "2.15.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (cran-uri "tensorflow" version)) (sha256 (base32 - "16650x0skqi4nyd2zmgdfj574gnw98k00d13rap7n95cv7sv9abw")))) + "113ikbg2k56zigxwgxy242vxpikxkfkv150wn21zyfn9885wgbzm")))) (properties `((upstream-name . "tensorflow"))) (build-system r-build-system) (propagated-inputs @@ -39913,14 +40409,14 @@ between them.") (define-public r-keras (package (name "r-keras") - (version "2.13.0") + (version "2.15.0") (source (origin (method url-fetch) (uri (cran-uri "keras" version)) (sha256 (base32 - "1xjmkrz06rh8767pfqi81fgkljkyb4i7bzllahw7b62b9s2wp38l")))) + "0xahkgww3dzp8vjz0456sn6ihz0w0q0dz1gnmx07r2vx81isirvc")))) (properties `((upstream-name . "keras"))) (build-system r-build-system) (propagated-inputs @@ -40214,14 +40710,14 @@ fully reproducible.") (define-public r-paws-common (package (name "r-paws-common") - (version "0.7.1") + (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "paws.common" version)) (sha256 (base32 - "1mjbyykav3f5yv59hnaihqsqhinvrlhphp93ks9xp756w6abciqf")))) + "0d1gj8z3c592cadngfhp8w8m6nd1ffb8k0wj8r2w1bldniq5yx70")))) (properties `((upstream-name . "paws.common"))) (build-system r-build-system) (propagated-inputs @@ -40245,14 +40741,14 @@ Service (S3).") (define-public r-paws-customer-engagement (package (name "r-paws-customer-engagement") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "paws.customer.engagement" version)) (sha256 (base32 - "1380waqavwga17fvdzfpag4snzynkykh3pnia5bi73476y7myj5h")))) + "1akwx39xmkms9zpsb7i5wx2hzvhhkmi0xlxag13cf9gjpg822361")))) (properties `((upstream-name . "paws.customer.engagement"))) (build-system r-build-system) @@ -40293,13 +40789,13 @@ more.") (define-public r-paws-developer-tools (package (name "r-paws-developer-tools") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "paws.developer.tools" version)) (sha256 - (base32 "177q7x8l9asyidpc7j20xwpyk0bd9x9m20cy4qzlnnmr14anyvjm")))) + (base32 "1cj9k005267wpd9pblvhk0sdy2ll2n0wcq4ch5wjwkz9kgl02jjr")))) (properties `((upstream-name . "paws.developer.tools"))) (build-system r-build-system) (propagated-inputs @@ -40315,13 +40811,13 @@ deployment, and more.") (define-public r-paws-end-user-computing (package (name "r-paws-end-user-computing") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "paws.end.user.computing" version)) (sha256 - (base32 "0qz5kps9819yfqjdqjmv7wx70ll7xayfxmd5dc867k14i41f91cm")))) + (base32 "17550n93d0lndhfk9r8zdh2yif4hw3m4wn7wzgj53akgqy1jg10y")))) (properties `((upstream-name . "paws.end.user.computing"))) (build-system r-build-system) (propagated-inputs @@ -40337,14 +40833,14 @@ and more.") (define-public r-paws-application-integration (package (name "r-paws-application-integration") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "paws.application.integration" version)) (sha256 (base32 - "1sgzp0yr1jsmbyzyk26m762rhpxb89wrwqqvrrw3xr1ib0cg06ah")))) + "0wmkxnrjmaf88bw1xypj7n41klxxhf538krsk0xrnwjb14v7lqla")))) (properties `((upstream-name . "paws.application.integration"))) (build-system r-build-system) @@ -40386,14 +40882,14 @@ more.") (define-public r-paws-analytics (package (name "r-paws-analytics") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "paws.analytics" version)) (sha256 (base32 - "07nwa39mn749a9rqb683wf19kd8si7ksws87annbldmd57r072l8")))) + "0w65f4bmcybp30zas20b90f1cmw1znhpjhcsf8xnq7x4s2lnpy3d")))) (properties `((upstream-name . "paws.analytics"))) (build-system r-build-system) @@ -40410,14 +40906,14 @@ Elasticsearch search engine, and more.") (define-public r-paws-machine-learning (package (name "r-paws-machine-learning") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "paws.machine.learning" version)) (sha256 (base32 - "0zcw758xsw2360571dj215gyd1amaxx07i58h1r6r5zys940lxis")))) + "1l2gy9bzibbjwqxb5x72dpfaylxa999c3zyb3y3359ckqkxsqgpy")))) (properties `((upstream-name . "paws.machine.learning"))) (build-system r-build-system) @@ -40458,14 +40954,14 @@ monitoring, Auto Scaling for automatically scaling resources, and more.") (define-public r-paws-networking (package (name "r-paws-networking") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "paws.networking" version)) (sha256 (base32 - "0qs6bp0vlbazxir9jmdcnazh90yrvhrw6k9046id73hw1j7h5zaf")))) + "1lfkll2gb83vw9zfb7bnmlg4alncqhp48s1w046fkh9qlg8hc7j6")))) (properties `((upstream-name . "paws.networking"))) (build-system r-build-system) @@ -40482,14 +40978,14 @@ CloudFront content delivery, load balancing, and more.") (define-public r-paws-database (package (name "r-paws-database") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "paws.database" version)) (sha256 (base32 - "0nlkbnyxd3znmvqxqb3w43sznacmikq32d9fihyc1dx7ghvmf61z")))) + "0jm3cwl2scfc4jgxzlwnax195xlii2b3p9kjmid48p8zx6h68hb9")))) (properties `((upstream-name . "paws.database"))) (build-system r-build-system) (propagated-inputs @@ -40506,14 +41002,14 @@ database, and more.") (define-public r-paws-storage (package (name "r-paws-storage") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "paws.storage" version)) (sha256 (base32 - "0v2g1shv9m4h2fz2lvjad479g3nmxc92wlyrxj4s7fifzzs2pd97")))) + "1mngxy88r94n1zwbvimj71hw4w9myk5kgqpgyj0m3spwv7338rfd")))) (properties `((upstream-name . "paws.storage"))) (build-system r-build-system) (propagated-inputs @@ -40881,14 +41377,14 @@ neighborhood graphs, and relatives.") (define-public r-crul (package (name "r-crul") - (version "1.4.0") + (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "crul" version)) (sha256 (base32 - "18n9ga0ah628k83qin75ys0wipc9dgc25xnafcj400jp85g42l4f")))) + "0is164bbdk5zy1gxrliiqzlmj47nvzsjym05ijzzs3zkj7qpfp20")))) (properties `((upstream-name . "crul"))) (build-system r-build-system) (propagated-inputs |