diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 1275 |
1 files changed, 902 insertions, 373 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 98f7fc46fd..80e2ca9021 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com> @@ -31,7 +31,7 @@ ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net> ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com> -;;; Copyright © 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com> +;;; Copyright © 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com> ;;; Copyright © 2021 Marcel Schilling <marcel.schilling@uni-luebeck.de> ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net> @@ -114,14 +114,14 @@ (define-public r-brio (package (name "r-brio") - (version "1.1.2") + (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "brio" version)) (sha256 (base32 - "1vviykwx1z71yhk1xl87riaygj8sq0sj7ixyig1irqsi66aydpa2")))) + "1inwzvlf6zj6gi47gd0byzqv02qajb3l475z8pjvx2b1hm0r1a7a")))) (properties `((upstream-name . "brio"))) (build-system r-build-system) (home-page "https://github.com/r-lib/brio") @@ -187,14 +187,14 @@ etc.") (define-public r-datawizard (package (name "r-datawizard") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "datawizard" version)) (sha256 (base32 - "062phzfcvn79npn4s58gz1m5ignyvr4q2zlqnyxla4p7l760djl9")))) + "0sd0blrczf9qz5kd0jg112fag2w401kkbw1gp9wi5pgffgwp6va3")))) (properties `((upstream-name . "datawizard"))) (build-system r-build-system) (propagated-inputs @@ -378,14 +378,14 @@ easier.") (define-public r-rticles (package (name "r-rticles") - (version "0.21") + (version "0.22") (source (origin (method url-fetch) (uri (cran-uri "rticles" version)) (sha256 (base32 - "0xk0xz97k8r8srmniihn3y4dkxddxf97yjbsljcxlgcq8f0zcc2s")))) + "0jgsmqwwqzvsxcbsm9fx0rp724mn3ipi70883bhvm7n9i8mq877m")))) (properties `((upstream-name . "rticles"))) (build-system r-build-system) (propagated-inputs @@ -463,17 +463,40 @@ The package provides functions for point generation, arc length estimation, degree elevation and curve fitting.") (license license:gpl2+))) +(define-public r-bwstest + (package + (name "r-bwstest") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "BWStest" version)) + (sha256 + (base32 "02amzlfprmw5pyis0dg0kg0x8xqh50a4vfdcxxmklrzik3b1vzzs")))) + (properties `((upstream-name . "BWStest"))) + (build-system r-build-system) + (propagated-inputs (list r-memoise r-rcpp)) + (home-page "https://github.com/shabbychef/BWStest") + (synopsis "Baumgartner Weiss Schindler Test of equal distributions") + (description + "This package performs the Baumgartner-Weiss-Schindler two-sample test of +equal probability distributions (doi:10.2307/2533862). It also performs +similar rank-based tests for equal probability distributions due to Neuhauser +(doi:10.1080/10485250108832874) and Murakami +(doi:10.1080/00949655.2010.551516).") + (license license:lgpl3))) + (define-public r-v8 (package (name "r-v8") - (version "3.6.0") + (version "4.0.0") (source (origin (method url-fetch) (uri (cran-uri "V8" version)) (sha256 (base32 - "0xqk4rcv255r2wll2jpzf9ix8j6hbhw0vbhg2g9i6z2apyc9i5m3")))) + "1j5vknhq12kfzda46y7nwiqdzqipzgympqzjq9d8ckr6f6v4qshl")))) (properties `((upstream-name . "V8"))) (build-system r-build-system) (arguments @@ -484,19 +507,17 @@ degree elevation and curve fitting.") (substitute* "configure" (("^PKG_LIBS=.*") (string-append "PKG_LIBS=" - (assoc-ref inputs "node") + (assoc-ref inputs "libnode") "/lib/libnode.so.64\n"))) (setenv "INCLUDE_DIR" (string-append - (assoc-ref inputs "node") + (assoc-ref inputs "libnode") "/include/node")) (setenv "LIB_DIR" (string-append - (assoc-ref inputs "node") "/lib")) - #t))))) + (assoc-ref inputs "libnode") "/lib"))))))) (inputs - `(("node" ,libnode) - ("zlib" ,zlib))) + (list libnode zlib)) (propagated-inputs (list r-curl r-jsonlite r-rcpp)) (native-inputs @@ -677,14 +698,14 @@ variables.") (define-public r-ggpp (package (name "r-ggpp") - (version "0.4.2") + (version "0.4.3") (source (origin (method url-fetch) (uri (cran-uri "ggpp" version)) (sha256 (base32 - "0m2wq9kqlxqxlzyx9fd0c4iw6qb7kpjrq7fqqa2kvwyj79vx6ahj")))) + "175mk5zcnhwr8hvs1567x0k0vmq7g2qnq250pnxlwnv1wpmvrqhz")))) (properties `((upstream-name . "ggpp"))) (build-system r-build-system) (propagated-inputs @@ -744,13 +765,13 @@ axis} (SMA), and @dfn{ranged major axis} (RMA).") (define-public r-ggpmisc (package (name "r-ggpmisc") - (version "0.4.4") + (version "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 - "01dnr2a33zmgi0gjsxlcz4hp68b18xsi8z1lkhgcla5im59qf9xi")))) + "036y3zhl9ndj5wlqy2nkp95vi7pjfpvf63ndsigramzad0fz0c98")))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -1084,13 +1105,13 @@ high-dimensional data.") (define-public r-shadowtext (package (name "r-shadowtext") - (version "0.0.9") + (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "shadowtext" version)) (sha256 (base32 - "1g6mgnfnzf2c17yzqk3zybfc5y62p5ndrbikxb3xcm2hiljiiqna")))) + "01h0w3b02r8snjkx5sxkf2x8xm4gd0r8jm27xqz9cv6hgqfmh1pb")))) (properties `((upstream-name . "shadowtext"))) (build-system r-build-system) (propagated-inputs @@ -1556,13 +1577,13 @@ Zucchini.") (define-public r-httpuv (package (name "r-httpuv") - (version "1.6.3") + (version "1.6.5") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 - "0xh8y05k4jxdwp9xh4x478y3scnv80q05l9gxk2ni6f0dk43iqxz")) + "0mlilxh2mlrsbbrncla2rg02crr8nnajv649d8whx7ayr8lkdxpm")) ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv ;; only contains fixes for building on Solaris. (patches (search-patches "r-httpuv-1.5.5-unvendor-libuv.patch")) @@ -1603,13 +1624,13 @@ particularly easy to create complete web applications using httpuv alone.") (define-public r-jsonlite (package (name "r-jsonlite") - (version "1.7.2") + (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "jsonlite" version)) (sha256 (base32 - "1lhzcpz9clwq04i5m6jzkvw9x03pwlqrixv4l9xzchjr8d84nd86")))) + "0n65x9ifxjssb000g7psgh9pgl374ax2ni1if9kp3sx56rg0n2kj")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -1715,13 +1736,13 @@ applications.") (define-public r-htmltable (package (name "r-htmltable") - (version "2.3.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (cran-uri "htmlTable" version)) (sha256 - (base32 "0xx5fza40six81mkfjsja6a8j6cg1mlzg0cxfgv084riyq79l387")))) + (base32 "17csp0ry4iy4m5xy271dn5wd81v4p03l79swmvlfxkvpdmhvb8jc")))) (properties `((upstream-name . "htmlTable"))) (build-system r-build-system) (propagated-inputs @@ -1775,8 +1796,7 @@ const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\"); if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); } " m)))))))) (inputs - `(("libcurl" ,curl) - ("zlib" ,zlib))) + (list curl zlib)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/jeroenooms/curl") @@ -1813,14 +1833,14 @@ objects in HTML format.") (define-public r-rjson (package (name "r-rjson") - (version "0.2.20") + (version "0.2.21") (source (origin (method url-fetch) (uri (cran-uri "rjson" version)) (sha256 (base32 - "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s")))) + "1qm27r1w677zg31gsiln60hcciszbymkw78cnaq7s36cbk9mcawq")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rjson") (synopsis "JSON library for R") @@ -2758,14 +2778,14 @@ Projection code and larger maps are in separate packages (@code{mapproj} and (define-public r-mapproj (package (name "r-mapproj") - (version "1.2.7") + (version "1.2.8") (source (origin (method url-fetch) (uri (cran-uri "mapproj" version)) (sha256 (base32 - "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h")))) + "10bpib827011fpgvzsmlv4j3i41s0r3cv1hvawwdlk753s7i0pw6")))) (build-system r-build-system) (propagated-inputs (list r-maps)) (home-page "https://cran.r-project.org/web/packages/mapproj") @@ -2947,14 +2967,14 @@ component analysis (with robust methods, and parallelized functions).") (define-public r-ape (package (name "r-ape") - (version "5.5") + (version "5.6-1") (source (origin (method url-fetch) (uri (cran-uri "ape" version)) (sha256 (base32 - "16i9sny7j90zi0k3znfff5lpnj5naxcy1142v73zxslr9g3h3am3")))) + "1xzpq3a4q5hmksc8nl530c9n31fdkj3nigqm1qhd3vkncl1iwh15")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-nlme r-rcpp)) @@ -3023,14 +3043,14 @@ colors are provided.") (define-public r-glue (package (name "r-glue") - (version "1.5.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (cran-uri "glue" version)) (sha256 (base32 - "1wjar579m46j1jnch34h7976sc1qbj6hzdyz5jm16nz1iw6z47jv")))) + "0f23dgnc7rv81vhmdhmiwk666mqwb602hxzai1hssyn4y9zg7gkp")))) (build-system r-build-system) ;; knitr depends on glue, so we can't add knitr here to build the ;; vignettes. @@ -3191,13 +3211,13 @@ processes. Most of its code is based on the @code{psutil} Python package.") (define-public r-pkgbuild (package (name "r-pkgbuild") - (version "1.2.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "pkgbuild" version)) (sha256 - (base32 "0qx920h2viwjg10va81nj0xja495d8ni6vcc25ggvzki6a6k069f")))) + (base32 "0j6v5nbp8kg1m3j999gd1qsbdmqcqm1mf28ngmm177miwv8q4skw")))) (build-system r-build-system) (propagated-inputs (list r-callr @@ -3219,14 +3239,14 @@ is configured appropriately so R can use them.") (define-public r-pkgload (package (name "r-pkgload") - (version "1.2.3") + (version "1.2.4") (source (origin (method url-fetch) (uri (cran-uri "pkgload" version)) (sha256 (base32 - "0jdkaj5cl0viy0i0hkcm4n2wlg1mfv3camr7f385njfararfanhh")))) + "03yr9mswx9nij27bp21q6c533zx310xwzhwm52dwr7554k42p4fn")))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -3267,13 +3287,13 @@ value for each cluster in a dendrogram.") (define-public r-rcpp (package (name "r-rcpp") - (version "1.0.7") + (version "1.0.8") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "07fwlgmx0ib4nziqbrylla2dlakw04vzny9w4qbfvnhn49rs9r8m")))) + (base32 "1vkqyqly6lzr1h3szaihmayvpjkzscxp4y258vnw8nh4pjb957w7")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ integration") @@ -4291,14 +4311,14 @@ statistics/methods are implemented.") (define-public r-suppdists (package (name "r-suppdists") - (version "1.1-9.5") + (version "1.1-9.7") (source (origin (method url-fetch) (uri (cran-uri "SuppDists" version)) (sha256 (base32 - "1i3iq12a5x5k49ac01mikzcrrq9gc148xq3m08h4xm07bha6f2v8")))) + "025b9nlxz62wk84295csyzbncpn80i3iby3sxdigf3swcgi2fmbb")))) (properties `((upstream-name . "SuppDists"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/SuppDists") @@ -4396,13 +4416,13 @@ available in a vignette.") (define-public r-progressr (package (name "r-progressr") - (version "0.9.0") + (version "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "progressr" version)) (sha256 - (base32 "03sk5cv8cywahlszjkd8pfqmhbj6cv0j54d3lassa7h44f20zryg")))) + (base32 "1p5s35rzh28n2id2lipgyqmh3wzib66m7x0pz9028y8cql8xr5ac")))) (properties `((upstream-name . "progressr"))) (build-system r-build-system) (propagated-inputs @@ -4488,18 +4508,20 @@ the Kaplan-Meier and Aalen-Johansen methods.") (define-public r-dimred (package (name "r-dimred") - (version "0.2.3") + (version "0.2.4") (source (origin (method url-fetch) (uri (cran-uri "dimRed" version)) (sha256 (base32 - "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6")))) + "1534axd5gcwma3nbglrn0l2an53n3yyya30fqkgb4d8l124ygb7j")))) (properties `((upstream-name . "dimRed"))) (build-system r-build-system) (propagated-inputs (list r-drr r-magrittr)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/gdkrmr/dimRed") (synopsis "Framework for dimensionality reduction") (description @@ -4555,14 +4577,14 @@ dimensioned arrays.") (define-public r-rmysql (package (name "r-rmysql") - (version "0.10.22") + (version "0.10.23") (source (origin (method url-fetch) (uri (cran-uri "RMySQL" version)) (sha256 (base32 - "05hiwqakhz11kra24yyxrss8b8n32wg7k39j7hwdnvhh1n96scnl")))) + "05aavyggyjv46awa7ggbxlfcy9707vak5kh7kj0ljdx8zga7xb7l")))) (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (inputs @@ -4816,14 +4838,14 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "0.7.10") + (version "0.7.11") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "0ks64xwkaqh5cinq8j56d89rn9kipm7cdipsgqmz9xxy7ajxb7qj")))) + "069fp8lscw59nmsm658w0164cpgfa36xx09s9j7jxisscg99jfcy")))) (build-system r-build-system) (propagated-inputs (list r-backports @@ -5142,14 +5164,14 @@ analysis of multiply imputed data sets.") (define-public r-mice (package (name "r-mice") - (version "3.13.0") + (version "3.14.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 - "11cpyqlilakan2pwjzacb9jjlazazsqdngy237nnrj8j6mky822i")))) + "01fnfrr7adp29s5kic95r9q0rdznkz2pjmziyimnrqzyicyvfyzq")))) (build-system r-build-system) (propagated-inputs (list r-broom @@ -5159,7 +5181,8 @@ analysis of multiply imputed data sets.") r-lattice r-rcpp r-rlang - r-tidyr)) + r-tidyr + r-withr)) (home-page "https://cran.r-project.org/web/packages/mice/") (synopsis "Multivariate imputation by chained equations") (description @@ -5223,18 +5246,18 @@ programming} (SQP) based solver).") (define-public r-hardyweinberg (package (name "r-hardyweinberg") - (version "1.7.3") + (version "1.7.4") (source (origin (method url-fetch) (uri (cran-uri "HardyWeinberg" version)) (sha256 (base32 - "0ppkzbhrb83dj796pm6gn5ypsf1ql8d9b3fv47w63i0snkhxfiv4")))) + "11y3zg8aqxk5xdzsv7i3bgqkky6a0wgf2n8saa3a4adq75k328ib")))) (properties `((upstream-name . "HardyWeinberg"))) (build-system r-build-system) (propagated-inputs - (list r-mice r-rcpp r-rsolnp)) + (list r-mice r-nnet r-rcpp r-rsolnp)) (home-page "https://cran.r-project.org/package=HardyWeinberg") (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium") (description @@ -5275,13 +5298,13 @@ and density estimation") (define-public r-venndiagram (package (name "r-venndiagram") - (version "1.7.0") + (version "1.7.1") (source (origin (method url-fetch) (uri (cran-uri "VennDiagram" version)) (sha256 (base32 - "1l9mmc8wwn885l2b13kshhrkz53pqigcw6d8gklvv92fx5m5cdvm")))) + "0yw54j9as0vf8ypnq4a3sl2w0lajri6s979f4y11hjzpgmr1m16b")))) (properties `((upstream-name . "VennDiagram"))) (build-system r-build-system) (propagated-inputs @@ -5609,14 +5632,14 @@ plots in @code{ggplot2}.") (define-public r-cli (package (name "r-cli") - (version "3.1.0") + (version "3.1.1") (source (origin (method url-fetch) (uri (cran-uri "cli" version)) (sha256 (base32 - "04ff3bgsahi736s8l6a26zlwwil8jw4shx7bb56ah1pp1f1n22n7")))) + "1kslrx22djrs3wnf5xyligwy7h4hzsn5awl946x961fn980ydcy8")))) (build-system r-build-system) (propagated-inputs (list r-glue)) @@ -5813,13 +5836,13 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.28") + (version "0.29") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 - (base32 "0civd050r94w2vwfx3xgz1w36wkwrkm5dscdv5kb3klbvqwy8nqb")))) + (base32 "1x2f49n3ak85nab937wq6q5sqi1mdlfzwbv8603kxl2k8rxvp1dz")))) (build-system r-build-system) ;; knitr itself depends on xfun #; @@ -5983,14 +6006,14 @@ packages that work with genomic data.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.35") + (version "0.36") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "04ng34kfds2isz4j9ch1xlii0dfclqay9fsc6wvr6sfifzv9fqyk")))) + "0y1vfq89yi302cwdcnassm02dk14j9ivk5vf83fp6rb8h6ww3rk5")))) (build-system r-build-system) (propagated-inputs (list r-xfun)) @@ -6205,14 +6228,14 @@ of these tests are also included.") (define-public r-ttr (package (name "r-ttr") - (version "0.24.2") + (version "0.24.3") (source (origin (method url-fetch) (uri (cran-uri "TTR" version)) (sha256 (base32 - "06vicgbhwpsww09hhha5mbcd0cwip6cvkfbhjjhp950rv64bk1r5")))) + "11xsmbvmxq2j119j2z58bx1fkkb2xlhmzc35z5fbwr3nchrfz6jd")))) (properties `((upstream-name . "TTR"))) (build-system r-build-system) (propagated-inputs @@ -6224,6 +6247,205 @@ of these tests are also included.") rules with R.") (license license:gpl2))) +(define-public r-leaflet-providers + (package + (name "r-leaflet-providers") + (version "1.9.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "leaflet.providers" version)) + (sha256 + (base32 "0yynrwv4xd5cdh49cwvfxm4ranarah9iiry2cd3b4fiihdfcg3wy")))) + (properties `((upstream-name . "leaflet.providers"))) + (build-system r-build-system) + (home-page "https://github.com/rstudio/leaflet.providers") + (synopsis "Leaflet map tile providers") + (description + "This package contains third-party map tile provider information from +Leaflet.js, to be used with the @code{leaflet} R package. Additionally, +@code{leaflet.providers} enables users to retrieve up-to-date provider +information between package updates.") + (license license:bsd-2))) + +;; This package contains a lot of minified JavaScript with unclear provenance. +;; When upgrading please make sure that all minified JavaScript files are +;; removed in a snippet and that the replacement sources correspond to the +;; original minified scripts. +(define-public r-leaflet + (package + (name "r-leaflet") + (version "2.0.4.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "leaflet" version)) + (sha256 + (base32 "07whi3zkz1lmbqx5ydpiya802ck22ny0s7gskwnx7r8xbwlkiw5h")) + (snippet + '(for-each + delete-file + (list "inst/htmlwidgets/lib/leaflet/leaflet.js" + "inst/htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js" + "inst/htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js" + "inst/htmlwidgets/lib/jquery/jquery.min.js" + "inst/htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js" + "inst/htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js" + "inst/htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js" + "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js" + "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js" + "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js" + "inst/legacy/www/leaflet.js"))))) + (properties `((upstream-name . "leaflet"))) + (build-system r-build-system) + (arguments + `(#:modules ((guix build utils) + (guix build r-build-system) + (srfi srfi-1)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + ;; The inst directory contains some minified JavaScript files. + ;; Regenerate them from sources. + (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-leaflet")) + (with-directory-excursion "inst/" + (call-with-values + (lambda () + (unzip2 + `(("/tmp/leaflet-src.js" + "htmlwidgets/lib/leaflet/leaflet.js") + (,(assoc-ref inputs "js-leaflet-measure") + "htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js") + (,(assoc-ref inputs "js-leaflet-omnivore") + "htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js") + (,(assoc-ref inputs "js-jquery") + "htmlwidgets/lib/jquery/jquery.min.js") + ("htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.js" + "htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js") + (,(assoc-ref inputs "js-bootstrap3") + "htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js") + ("htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.js" + "htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js") + (,(string-append (assoc-ref inputs "js-leaflet-markercluster") + "/dist/leaflet.markercluster-src.js") + "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js") + (,(assoc-ref inputs "js-leaflet-markercluster-freezable") + "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js") + (,(assoc-ref inputs "js-leaflet-markercluster-layersupport") + "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js") + (,(assoc-ref inputs "js-proj4leaflet") + "htmlwidgets/plugins/Proj4Leaflet/proj4.min.js") + ("legacy/www/leaflet-src.js" + "legacy/www/leaflet.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #true "Processing ~a --> ~a~%" + source target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))) + sources targets))))))))) + (native-inputs + `(("esbuild" ,esbuild) + ("unzip" ,unzip) + ("js-bootstrap3" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/twbs/bootstrap/v3.3.7/dist/js/bootstrap.js") + (sha256 + (base32 + "1j1qjagwj0m3q322z9wxxnpkd8zbk6g3kl047dsbmqad6gmqvgha")))) + ("js-jquery" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-1.12.4.js") + (sha256 + (base32 + "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3")))) + ("js-leaflet" + ,(origin + (method url-fetch) + (uri "http://cdn.leafletjs.com/leaflet/v1.3.1/leaflet.zip") + (sha256 + (base32 + "10phzd2vczy3zm1b64whp2nna69cf9hlj2bndc9yq47vf3ddqx8f")))) + ("js-leaflet-omnivore" + ,(origin + (method url-fetch) + (uri (string-append "https://api.tiles.mapbox.com/mapbox.js/plugins/" + "leaflet-omnivore/v0.3.1/leaflet-omnivore.js")) + (sha256 + (base32 + "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))) + ("js-leaflet-markercluster" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Leaflet/Leaflet.markercluster.git") + (commit "v1.1.0"))) + (file-name (git-file-name "js-leaflet-markercluster" "1.1.0")) + (sha256 + (base32 + "0ds8c7picqjmc86bm5n6hm8k71fwsa2cpgib19sbdamzr9hm0rs1")))) + ("js-leaflet-markercluster-freezable" + ,(origin + (method url-fetch) + (uri (string-append + "https://raw.githubusercontent.com/ghybs/Leaflet.MarkerCluster.Freezable/" + "9db80a3fba7dff4aee940e05d3d4dceaa1fffcf9/src/freezable.js")) + (file-name "leaflet-markercluster-freezable.js") + (sha256 + (base32 + "1k6sn5n0z2x3an91vwvkzmqq4b8ppswgk5hi5qrr79klas1hbx1k")))) + ("js-leaflet-markercluster-layersupport" + ,(origin + (method url-fetch) + (uri (string-append + "https://raw.githubusercontent.com/ghybs/Leaflet.MarkerCluster.LayerSupport/" + "87f3848b92e0516d9c98f6d4cd175f7b8a4e3805/src/layersupport.js")) + (file-name "leaflet-markercluster-layersupport.js") + (sha256 + (base32 + "15qa21xif94y762c65yxxysxykz3mma6y6agw3nxpr3s7wbb75ff")))) + ("js-leaflet-measure" + ,(origin + (method url-fetch) + (uri "https://unpkg.com/leaflet-measure@1.5.2/dist/leaflet-measure.js") + (file-name "js-leaflet-measure-1.5.2.js") + (sha256 + (base32 + "0ggg3ffmm7pj9ry4gssrh0a17pnad3p6gwi0dg98y819pmpqa7y0")))) + ("js-proj4leaflet" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/kartena/Proj4Leaflet/1.0.2/lib/proj4.js") + (file-name "js-proj4leaflet-1.0.2.js") + (sha256 + (base32 + "0vyrbf6gv2lyh4c2bzp5349ivwvvg28gpn87y52a7jdb13rlkpab")))))) + (propagated-inputs + (list r-base64enc + r-crosstalk + r-htmltools + r-htmlwidgets + r-leaflet-providers + r-magrittr + r-markdown + r-png + r-raster + r-rcolorbrewer + r-scales + r-sp + r-viridis)) + (home-page "https://rstudio.github.io/leaflet/") + (synopsis "Create interactive web maps with the JavaScript Leaflet library") + (description + "Create and customize interactive maps using the Leaflet JavaScript +library and the @code{htmlwidgets} package. These maps can be used directly +from the R console, from RStudio, in Shiny applications and R Markdown +documents.") + (license license:gpl3))) + (define-public r-leaps (package (name "r-leaps") @@ -7030,7 +7252,7 @@ It also includes interpolation functions.") (build-system r-build-system) (propagated-inputs (list r-proto)) (home-page "https://code.google.com/archive/p/gsubfn/") - (synopsis "Utilities for strings and function arguments.") + (synopsis "Utilities for strings and function arguments") (description "This package provides @code{gsubfn} which is like @code{gsub} but can take a replacement function or certain other objects instead of the @@ -7282,14 +7504,14 @@ evaluated by the @dfn{Akaike Information Criterion} (AIC).") (define-public r-arules (package (name "r-arules") - (version "1.7-1") + (version "1.7-3") (source (origin (method url-fetch) (uri (cran-uri "arules" version)) (sha256 (base32 - "0zzwr1mg92ha5l6razdb04da8ik3z3k74rm0rah44l1j2a6d30sk")))) + "05g6ik4z87g83nlicmb380331f84sqchvv1vch49zb7rq6v8gw6r")))) (build-system r-build-system) (propagated-inputs (list r-generics r-matrix)) @@ -7395,14 +7617,14 @@ additional external tools on any platform.") (define-public r-openxlsx (package (name "r-openxlsx") - (version "4.2.4") + (version "4.2.5") (source (origin (method url-fetch) (uri (cran-uri "openxlsx" version)) (sha256 (base32 - "0vn8ifxb7ccip6b1ijf5lpa6c0n5y5ll8fbabybsb8nfc0y1nmxg")))) + "0695b265g7jwiqk5c3vmmfkvagx82bkpwhvqzhqaqmmn34l6vl35")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-stringi r-zip)) @@ -7713,14 +7935,14 @@ finance, conversion from and to JSON, and many other applications.") (define-public r-dtplyr (package (name "r-dtplyr") - (version "1.1.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "dtplyr" version)) (sha256 (base32 - "0cn7vxn92dcxrnabccla6ppf5x7pxfz6pjlmamp0imfphmr1ns4r")))) + "1wyhhn16mvdj55k2xsh7vy489l7xk4mkz7pjrw16z87awk6yjh16")))) (properties `((upstream-name . "dtplyr"))) (build-system r-build-system) (propagated-inputs @@ -7876,14 +8098,14 @@ those searches and pull data into their R sessions.") (define-public r-renv (package (name "r-renv") - (version "0.14.0") + (version "0.15.1") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 - "194hcxikdnna526bvyz9y60ccmmm9fib5g0w9dqivrg0fld23lyh")))) + "0nwvdzwyjvqlvkwp1yhhvqm8b9pwimwng99s0m0j63zm9bgwis1n")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (native-inputs @@ -7993,14 +8215,14 @@ always locate the files relative to your project root.") (define-public r-reticulate (package (name "r-reticulate") - (version "1.22") + (version "1.23") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "0v7m2pv94lfqiw8rhz3c9g66vvz4qvih4vd29rhfk2phmcwpnvmh")))) + "1mindiw7k7pa33hpwrgq0g5808c8qs9hl0351n8z2w9wyczlm87y")))) (build-system r-build-system) (inputs (list python)) (propagated-inputs @@ -8010,6 +8232,7 @@ always locate the files relative to your project root.") r-png r-rappdirs r-rcpp + r-rcpptoml r-withr)) (native-inputs (list r-knitr)) @@ -8311,14 +8534,14 @@ steps and provides ggplot2-based elegant data visualization.") (define-public r-fansi (package (name "r-fansi") - (version "0.5.0") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "fansi" version)) (sha256 (base32 - "0kx5kjhr8dvqz1mq1zkijkgp29jv8b0irm1xplx1d74n2v1zh6wx")))) + "0mxm06png4lrl5gy5giws5dgig2faryang8y0wcvwfk120pczqni")))) (build-system r-build-system) (native-inputs (list r-knitr)) ; for vignettes @@ -8469,14 +8692,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rbibutils (package (name "r-rbibutils") - (version "2.2.4") + (version "2.2.7") (source (origin (method url-fetch) (uri (cran-uri "rbibutils" version)) (sha256 (base32 - "15yyihk0dgz3yyqz28r5nc6m99zcywpabnabf18phbs7rb87p7mv")))) + "1iamdbww3hvxy0bbywc307kyhiczx0bvfhw7nngsm33balcng7kw")))) (properties `((upstream-name . "rbibutils"))) (build-system r-build-system) (home-page "https://geobosh.github.io/rbibutils/") @@ -8491,14 +8714,14 @@ implemented in bibutils.") (define-public r-rdpack (package (name "r-rdpack") - (version "2.1.2") + (version "2.1.3") (source (origin (method url-fetch) (uri (cran-uri "Rdpack" version)) (sha256 (base32 - "0s51c5fw1ka75b8cxk5bh27h6wcy5169yl93sjlxji2k27n9fj3i")))) + "1f2m9pxm4s4gkrqh58jznkqj2fcw6f29c1l05k5mmkwsdf3ai0c3")))) (properties `((upstream-name . "Rdpack"))) (build-system r-build-system) (propagated-inputs @@ -8735,14 +8958,14 @@ other add-on packages.") (define-public r-insight (package (name "r-insight") - (version "0.14.5") + (version "0.15.0") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "10kc72g2hfsiipba4kalda1wxsb01nq2ax2yim386bkk0vjszwfx")))) + "1vizx515a24v5x4f5mzbigl0wl4gz75hp5gqw8lkijygw71li8fn")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -8789,14 +9012,14 @@ vice versa), or to deal with multiple declared missing values.") (define-public r-sjmisc (package (name "r-sjmisc") - (version "2.8.7") + (version "2.8.9") (source (origin (method url-fetch) (uri (cran-uri "sjmisc" version)) (sha256 (base32 - "17hcjb2j690qi2zrkwc14sr1wsid6dy6v7bfsf0bc94ql812k8g2")))) + "1gzkq95ckxr0vhrzggflzli9hs7zr8c0yym9zn1wf74yrr0mgc3q")))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -8840,23 +9063,23 @@ hypothesis of normality.") (define-public r-moonbook (package (name "r-moonbook") - (version "0.2.4") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "moonBook" version)) (sha256 (base32 - "0z78pzc8sr2g19xjdd9cmai4iqyifmh79gj8x40ddww6a27dalry")))) + "1ml4vvm0mvrprpyi0l50aw38brx18bk2qny4gybmkvlbakalz9bx")))) (properties `((upstream-name . "moonBook"))) (build-system r-build-system) (propagated-inputs - (list r-magrittr + (list r-crayon + r-magrittr r-nortest r-sjmisc r-stringr - r-survival - r-ztable)) + r-survival)) (native-inputs (list r-knitr)) (home-page "https://github.com/cardiomoon/moonBook") @@ -9020,14 +9243,14 @@ matches version and feature constraints.") (define-public r-argparse (package (name "r-argparse") - (version "2.1.2") + (version "2.1.3") (source (origin (method url-fetch) (uri (cran-uri "argparse" version)) (sha256 (base32 - "1cz5qlxw3v8smd5vb00wlzy02mx5i0infm5hnq55hnakffd3b5wr")))) + "0vm6nrzl6rsq2qw3km3i4s92kq9phs3cbxzv3i8hlyld9ajk3nmf")))) (build-system r-build-system) (inputs (list python)) (propagated-inputs @@ -9306,13 +9529,13 @@ the analyzed items.") (define-public r-slam (package (name "r-slam") - (version "0.1-49") + (version "0.1-50") (source (origin (method url-fetch) (uri (cran-uri "slam" version)) (sha256 - (base32 "044hnfqbx57v5zr64gl09b5arj45swn9ywqzrl9rsc8267ys0028")))) + (base32 "1ggqcf8l1z2hpi7qy4mg0d2ps48bjjb8z1y1xz6fq162cqrbz6bq")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/slam/") (synopsis "Sparse lightweight arrays and matrices") @@ -9426,14 +9649,14 @@ from the @code{stats} package (plus some extra parameters).") (define-public r-cmplot (package (name "r-cmplot") - (version "3.7.0") + (version "4.0.0") (source (origin (method url-fetch) (uri (cran-uri "CMplot" version)) (sha256 (base32 - "0d6ww8pdrawdg5acbhiyi2jpmapf2ghixy9mi4kmsq8yg36pksfh")))) + "0xyh75y0c84nnkrv6c8xrvla54w51phgdwn8a69799f2r87z7c81")))) (properties `((upstream-name . "CMplot"))) (build-system r-build-system) (home-page "https://github.com/YinLiLin/CMplot") @@ -9527,7 +9750,7 @@ through permutation testing.") (home-page "http://mbojan.github.io/intergraph") (synopsis "Coercion routines for network data objects") (description - "Functions implemented in this package allow to coerce (i.e. convert) + "Functions implemented in this package allow coercing (i.e. convert) network data between classes provided by other R packages. Currently supported classes are those defined in packages @code{network} and @code{igraph}.") @@ -9680,14 +9903,14 @@ ggplot2 package.") (define-public r-cvauc (package (name "r-cvauc") - (version "1.1.0") + (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "cvAUC" version)) (sha256 (base32 - "13bk97l5nn97h85iz93zxazhr63n21nwyrpnl856as9qp59yvn64")))) + "1m2y50a1yapf1c74km9a4r47ds2z2bfp4wwwkqin7swv9v1s7d28")))) (properties `((upstream-name . "cvAUC"))) (build-system r-build-system) (propagated-inputs @@ -9917,7 +10140,7 @@ subsequence} (LCS) using a dynamic programming algorithm.") (description "This package provides useful functions to deal with the @code{haven_labelled} and @code{haven_labelled_spss} classes introduced by the -haven package. ") +haven package.") (license license:gpl3))) (define-public r-ggformula @@ -9976,14 +10199,14 @@ used to teach mathematics, statistics, computation and modeling.") (define-public r-raster (package (name "r-raster") - (version "3.5-2") + (version "3.5-11") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 - "0wixw1ixnmcmkwczpj8m90c76727zira2rl4ighashggydkm2mlr")))) + "18v1vflq15915dwa3caf5sp1d1kp8w6plpaqk3z6a3164lwq5i76")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-sp r-terra)) @@ -10013,16 +10236,19 @@ Processing of very large files is supported.") r-ggformula r-ggplot2 r-ggrepel + r-ggridges + r-ggstance r-glue r-gridextra r-lattice r-latticeextra - r-lazyeval + r-leaflet r-mass r-matrix r-mosaiccore r-mosaicdata r-readr + r-rlang r-tidyr)) (native-inputs (list r-knitr)) @@ -10784,16 +11010,16 @@ estimation problem.") (define-public r-abundant (package (name "r-abundant") - (version "1.1") + (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "abundant" version)) (sha256 - (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7")))) + (base32 "15m3ngj5aipjg961yy5kvdg9xlfcpliw30dq6gchzxabhnfzcipd")))) (build-system r-build-system) (propagated-inputs - (list r-quic)) + (list r-glasso)) (home-page "https://cran.r-project.org/web/packages/abundant/") (synopsis "Abundant regression and high-dimensional principal fitted components") (description @@ -10970,14 +11196,14 @@ packages maintained by Torsten Hothorn.") (define-public r-multcomp (package (name "r-multcomp") - (version "1.4-17") + (version "1.4-18") (source (origin (method url-fetch) (uri (cran-uri "multcomp" version)) (sha256 (base32 - "02zv739mbmx672yrqqx8am229h7ps476wphig7jrrbfgay29sl21")))) + "01i8gjppyxl3xph1dw0kags8qbb7r06j91kk3lkqn5gzrxjmwyhh")))) (build-system r-build-system) (propagated-inputs (list r-codetools r-mvtnorm r-sandwich r-survival r-th-data)) @@ -10991,17 +11217,38 @@ analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz, Hothorn, Westfall, 2010, CRC Press).") (license license:gpl2))) +(define-public r-multcompview + (package + (name "r-multcompview") + (version "0.1-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "multcompView" version)) + (sha256 + (base32 "1rfq9wvvrghq0542ff40wy8vdmsyd8spzz6ihcywcvxdfa8m6g8j")))) + (properties `((upstream-name . "multcompView"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=multcompView") + (synopsis "Visualizations of paired comparisons") + (description + "Convert a logical vector or a vector of p-values or a correlation, +difference, or distance matrix into a display identifying the pairs for which +the differences were not significantly different.") + ;; Any version of the GPL. + (license license:gpl3+))) + (define-public r-emmeans (package (name "r-emmeans") - (version "1.7.0") + (version "1.7.2") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "1ig94mjifhhygznv2xv1gl8hdvk618w5fcmkaj1xmpwpc64m9dnl")))) + "1g112yvqvxi83x128hwz4qpifwihlm0y5szg82cdsx3c9cm1rrfk")))) (build-system r-build-system) (propagated-inputs (list r-estimability r-mvtnorm r-numderiv r-xtable)) @@ -11306,14 +11553,14 @@ results using @code{ggplot2}.") (define-public r-effectsize (package (name "r-effectsize") - (version "0.5") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 - "0w7m3hzmwral9cycpvknrkbdvgk230b3vg5sxbm84x72mw534hnh")))) + "0xhibc868sngkc8v9g385vlhqdqxzy6b4mj1jihjy6wvk9jw266s")))) (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs @@ -11332,13 +11579,13 @@ conversion of indices such as Cohen's d, r, odds, etc.") (define-public r-sjplot (package (name "r-sjplot") - (version "2.8.9") + (version "2.8.10") (source (origin (method url-fetch) (uri (cran-uri "sjPlot" version)) (sha256 - (base32 "07b9p5wbb6xmyapg9j6i4cdcj7j9wj9gi30gljj6j2lj1flgdd7q")))) + (base32 "1rnwhh271xj8xgvvlpqw9ain56mfz37fvl7f6jq9nzx9jxx95bjd")))) (properties `((upstream-name . "sjPlot"))) (build-system r-build-system) (propagated-inputs @@ -11445,14 +11692,14 @@ repositories.") (define-public r-fs (package (name "r-fs") - (version "1.5.0") + (version "1.5.2") (source (origin (method url-fetch) (uri (cran-uri "fs" version)) (sha256 (base32 - "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn")))) + "11qr3v0xn65vfhgcxl4l6yv48s4w0w3ldp3anpzc25vd3mwd3jim")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -11486,14 +11733,14 @@ terminals that do not support Unicode.") (define-public r-credentials (package (name "r-credentials") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "credentials" version)) (sha256 (base32 - "0q3s1bibwvw1p541k8a5cjx4dj1iabl4crg61fgjxkniclxag5c7")))) + "1f18j3zrq8c9kah57xwahmmljsjg5qphlgamvx507ynvpq8pryig")))) (properties `((upstream-name . "credentials"))) (build-system r-build-system) (arguments @@ -11502,10 +11749,9 @@ terminals that do not support Unicode.") (add-after 'unpack 'setenv-HOME (lambda _ ;; This is necessary because git looks for $HOME/.gitconfig - (setenv "HOME" "/tmp") - #t))))) + (setenv "HOME" "/tmp")))))) (inputs - `(("git" ,git-minimal))) + (list git-minimal)) (propagated-inputs (list r-askpass r-curl r-jsonlite r-openssl r-sys)) (native-inputs @@ -11526,14 +11772,14 @@ user credentials.") (define-public r-gert (package (name "r-gert") - (version "1.4.3") + (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "gert" version)) (sha256 (base32 - "06g3gy4260y4f43zgahamckisjs8dvl06rb0kyinrwlm675dqppm")))) + "1bm2fjyh527y6x0dr5cs8h31jgl1fkk09ljzj1h37d0c7f4k1hwz")))) (properties `((upstream-name . "gert"))) (build-system r-build-system) (inputs @@ -11560,14 +11806,14 @@ User credentials are shared with command line git through the (define-public r-usethis (package (name "r-usethis") - (version "2.1.3") + (version "2.1.5") (source (origin (method url-fetch) (uri (cran-uri "usethis" version)) (sha256 (base32 - "1gwvirp53pa0zychd7d47d56a2vfdzz7l3p61l8m9n270ac7bc1d")))) + "0lph2rxv7nq3h022gp8d50wbq5lwicnx85d2l5dx876wxhb9wlvx")))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -11601,14 +11847,14 @@ Rcpp, RStudio projects, and more.") (define-public r-sessioninfo (package (name "r-sessioninfo") - (version "1.2.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "sessioninfo" version)) (sha256 (base32 - "0w3vhp652524348a4cfyvvs8z9xpxkcznw8x406nvkwfh0gdyka2")))) + "1jy7n37qnrb4fgzmn8s8yf7kv29yw27x8zklwf8qdb2kgj2q6qpm")))) (build-system r-build-system) (propagated-inputs (list r-cli)) @@ -11623,14 +11869,14 @@ more information about packages, and where they were installed from.") (define-public r-remotes (package (name "r-remotes") - (version "2.4.1") + (version "2.4.2") (source (origin (method url-fetch) (uri (cran-uri "remotes" version)) (sha256 (base32 - "0xij8x4ga0r7rp2lxx9hw1zlzv48mfg56v8nf03gsw0dw6r7gmym")))) + "05m5dgv0nba5vhjbdkd8z5lbhpfxgkw31j58am7vz1d44igqgvzj")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -12154,14 +12400,14 @@ package provides a minimal R interface by relying on the Rcpp package.") (define-public r-rcppparallel (package (name "r-rcppparallel") - (version "5.1.4") + (version "5.1.5") (source (origin (method url-fetch) (uri (cran-uri "RcppParallel" version)) (sha256 (base32 - "10pa9vaz7p4m6hjca2cpy6vj7rvgly4zv0q1g2xfsmcchyk4bdbn")))) + "1sn211ajlb1p12sglxqns175rg078yvww268m8cp0vvd7cmk55k3")))) (properties `((upstream-name . "RcppParallel"))) (build-system r-build-system) (home-page "https://rcppcore.github.io/RcppParallel/") @@ -12177,14 +12423,14 @@ other values.") (define-public r-ncdf4 (package (name "r-ncdf4") - (version "1.17.1") + (version "1.19") (source (origin (method url-fetch) (uri (cran-uri "ncdf4" version)) (sha256 (base32 - "1fyjhp2zkvp7ls1sxn623far7473lpkfsqqvj3a1fczpmqs6iw4m")))) + "0qzvin2fjzcb7h2knlnw14s6043pwi1nm7yf6p27ax7w269173fb")))) (build-system r-build-system) (inputs (list netcdf zlib)) @@ -12305,13 +12551,13 @@ isosurfaces.") (define-public r-ks (package (name "r-ks") - (version "1.13.2") + (version "1.13.3") (source (origin (method url-fetch) (uri (cran-uri "ks" version)) (sha256 - (base32 "02gnpyjqdlj6dl2x9i7mmks4f5nrh85j3h0kfa0v1v6wi8blx7kw")))) + (base32 "0wyfdmhr753vpizns9kl7h7pfnnb16c7m7w9a4bpz62xcvgq1yyy")))) (build-system r-build-system) (propagated-inputs (list r-fnn @@ -12458,14 +12704,14 @@ for evolution along a phylogenetic tree.") (define-public r-fmsb (package (name "r-fmsb") - (version "0.7.1") + (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "fmsb" version)) (sha256 (base32 - "09pq7p7i6vkq9av7l7x9hicl9sqh7xn96f9pac117hy6z852jvi2")))) + "1ylwj4385wg7rymx0m3kayyvrbil89wxb7phdl0fvi0xq2krkzhb")))) (build-system r-build-system) (home-page "http://minato.sip21c.org/msb/") (synopsis "Functions for medical statistics book with demographic data") @@ -12539,6 +12785,31 @@ Anderson-Darling Distribution\".") ;; Any version of the GPL. (license license:gpl3+))) +(define-public r-admisc + (package + (name "r-admisc") + (version "0.22") + (source + (origin + (method url-fetch) + (uri (cran-uri "admisc" version)) + (sha256 + (base32 "1jwz9z3brq4lbnqrkxx40vrn47rknkkj4xfv2gi8kmf1mzc5aqcd")))) + (properties `((upstream-name . "admisc"))) + (build-system r-build-system) + (home-page "https://github.com/dusadrian/admisc") + (synopsis "Adrian Dusa's miscellaneous") + (description + "This package contains miscellaneous functions used to interpret and +translate, factorize and negate Sum of Products expressions, for both binary +and multi-value crisp sets, and to extract information (set names, set values) +from those expressions. Other functions perform various other checks if +possibly numeric (even if all numbers reside in a character vector) and coerce +to numeric, or check if the numbers are whole. It also offers, among many +others, a highly flexible recoding routine and a more flexible alternative to +the base function @code{with()}.") + (license license:gpl3+))) + (define-public r-sodium (package (name "r-sodium") @@ -12758,13 +13029,13 @@ maps.") (define-public r-tidytree (package (name "r-tidytree") - (version "0.3.6") + (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 - (base32 "1gnpm4zz0kvqng5s179301q0h5993ajynm8y0zbdz38qcmzfpsdk")))) + (base32 "1wp411lf3syf0g1czhx3ksb4mx5d6vaw6ppipv0s0k69ivag45kq")))) (build-system r-build-system) (propagated-inputs (list r-ape @@ -14138,13 +14409,13 @@ This makes it a convenient and fast interface to C/C++ and Fortran code.") (define-public r-spam (package (name "r-spam") - (version "2.7-0") + (version "2.8-0") (source (origin (method url-fetch) (uri (cran-uri "spam" version)) (sha256 - (base32 "03c50wfyrzcmrcv9mkgj8dmdg2cwkh4p4ys8gaclr8w7ym45qav3")))) + (base32 "1ann2a2ifr3z983fcg1c0pkgmbxz6a0ym5q1dmq1r382bd1pg0fr")))) (build-system r-build-system) (propagated-inputs (list r-dotcall64)) @@ -14420,13 +14691,13 @@ But it can also be used to do data analysis for small scale data sets.") (define-public r-cmprsk (package (name "r-cmprsk") - (version "2.2-10") + (version "2.2-11") (source (origin (method url-fetch) (uri (cran-uri "cmprsk" version)) (sha256 - (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8")))) + (base32 "050f24l5ab1ds9824c7yjahimf6pg8ih2k83jzpzfb0n5k5jfh44")))) (build-system r-build-system) (propagated-inputs (list r-survival)) @@ -14649,14 +14920,14 @@ them in distributed compute environments.") (define-public r-parallelly (package (name "r-parallelly") - (version "1.29.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (cran-uri "parallelly" version)) (sha256 (base32 - "0a84lr2jqqnvmdayb9v9kv7m8rffp65s4s1wcalr96sl3cxypyc7")))) + "0fwzkzw9vjblwk5rg56yl8qfn7irnbpm70405lmj7awvf35q1c5a")))) (properties `((upstream-name . "parallelly"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/parallelly") @@ -15057,14 +15328,14 @@ users of rARPACK are advised to switch to the RSpectra package.") (define-public r-compositions (package (name "r-compositions") - (version "2.0-2") + (version "2.0-4") (source (origin (method url-fetch) (uri (cran-uri "compositions" version)) (sha256 (base32 - "05pji62pzgfk9dyiybmr16q0h6mdzsmvyzxdni3hn0dvl4a7mr5m")))) + "1bqg0qqzsf92q0jb7hdjycr54bwv8rk7ajhvxgch5yslyqxpm73v")))) (build-system r-build-system) (propagated-inputs (list r-bayesm r-mass r-robustbase r-tensora)) @@ -15154,17 +15425,17 @@ transformation, respectively.") (define-public r-shinyjs (package (name "r-shinyjs") - (version "2.0.0") + (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "shinyjs" version)) (sha256 (base32 - "1zzq356dvd8ciajy6r5n4ybgx9xk7ydwv25j86xlcsqznkxdkkf2")))) + "1id9gsrkr28xl80a8794in17rxmmz06zqvd5hlns7mqz3fzhrhky")))) (build-system r-build-system) (propagated-inputs - (list r-digest r-htmltools r-jsonlite r-shiny)) + (list r-digest r-jsonlite r-shiny)) (native-inputs (list r-knitr)) (home-page "https://deanattali.com/shinyjs") @@ -15540,14 +15811,14 @@ compatible with @code{rzmq} are also provided.") (define-public r-repr (package (name "r-repr") - (version "1.1.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "repr" version)) (sha256 (base32 - "0qimllv9pn8wsl550bjkp5dkknbmr69j85mrwfbbq75m2ga466sk")))) + "0h3h14ybamcbwmm31ib66fx13v75vkzn4bn2v26n2h097sl9qybg")))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-htmltools r-jsonlite r-pillar)) @@ -15561,14 +15832,14 @@ several formats and MIME types.") (define-public r-irdisplay (package (name "r-irdisplay") - (version "1.0") + (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "IRdisplay" version)) (sha256 (base32 - "15jbjrihm1mk899357h9xb08iq3xyagds1xb40fmdpkfcmcfqrw9")))) + "0awdiv4rr93y8jb1d64sm1iy37ywyniqm7w98yv6qm0zz47h7sw3")))) (properties `((upstream-name . "IRdisplay"))) (build-system r-build-system) (propagated-inputs @@ -15584,14 +15855,14 @@ running IRkernel session.") (define-public r-irkernel (package (name "r-irkernel") - (version "1.2") + (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "IRkernel" version)) (sha256 (base32 - "14gz3790iv6gg6yi9wslk1yn0jq57yvhxgm840qh818xfkdxpd2z")))) + "00qrmsywpzw2hfp88020zjaijma7q4hqm9h2cz53rywdjzywnzss")))) (properties `((upstream-name . "IRkernel"))) (build-system r-build-system) (arguments @@ -15656,17 +15927,18 @@ network.") (define-public r-apcluster (package (name "r-apcluster") - (version "1.4.8") + (version "1.4.9") (source (origin (method url-fetch) (uri (cran-uri "apcluster" version)) (sha256 (base32 - "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj")))) + "0wnbb3kj9m7rfq63xr43jjf6n8jxm1r2wvvx6g0qkss0wvipbb1s")))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/apcluster/") (synopsis "Affinity propagation clustering") (description @@ -15677,37 +15949,6 @@ can also be used to join clusters obtained from affinity propagation. Various plotting functions are available for analyzing clustering results.") (license license:gpl2+))) -(define-public r-valr - (package - (name "r-valr") - (version "0.6.3") - (source - (origin - (method url-fetch) - (uri (cran-uri "valr" version)) - (sha256 - (base32 - "1lzdlw0mw06rymyjzwf4i8rx1z6zxpwxxqfsc9ggqlnhq6bfhy93")))) - (build-system r-build-system) - (propagated-inputs - (list r-broom - r-dplyr - r-ggplot2 - r-rcpp - r-readr - r-rlang - r-stringr - r-tibble)) - (native-inputs - (list r-knitr)) - (home-page "https://github.com/rnabioco/valr") - (synopsis "Genome interval arithmetic in R") - (description - "This package enables you to read and manipulate genome intervals and -signals. It provides functionality similar to command-line tool suites within -R, enabling interactive analysis and visualization of genome-scale data.") - (license license:expat))) - (define-public r-rematch2 (package (name "r-rematch2") @@ -15866,14 +16107,14 @@ additional utilities for genomic regions processing.") (define-public r-sets (package (name "r-sets") - (version "1.0-19") + (version "1.0-20") (source (origin (method url-fetch) (uri (cran-uri "sets" version)) (sha256 (base32 - "18185rm458nlifzrp73fjrjvksmm5dvn5ygs949kdzdln1myb4xf")))) + "1mkmqi3n1lh01k47yvkr0dlf4imqdi6d6bglx9bvrjmg816p4jr3")))) (properties `((upstream-name . "sets"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/sets") @@ -16073,14 +16314,14 @@ classes.") (define-public r-udunits2 (package (name "r-udunits2") - (version "0.13.1") + (version "0.13.2") (source (origin (method url-fetch) (uri (cran-uri "udunits2" version)) (sha256 (base32 - "1l889f8iy8qaacxfs6ll62d6hs8g8qsr5ynn24grpvp8dk8l888w")))) + "0sarkw5ciafiaq1haam8d8w0cmai63wrw2m4rcbjfa5k0648j07f")))) (properties `((upstream-name . "udunits2"))) (build-system r-build-system) (inputs @@ -16194,18 +16435,16 @@ tessellation.") (define-public r-wk (package (name "r-wk") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "wk" version)) (sha256 (base32 - "0fj2wzswv3dfninsyw9irf52fc2d0lag5b822x841vdfpvh01mbi")))) + "1xga4rrqsr190g55by39az4nimnn06bf5b6mcjgwqvba0lvjhb5g")))) (properties `((upstream-name . "wk"))) (build-system r-build-system) - (propagated-inputs - (list r-cpp11)) (home-page "https://paleolimbot.github.io/wk/") (synopsis "Lightweight well-known geometry parsing") (description @@ -16250,14 +16489,14 @@ information about geometries.") (define-public r-sf (package (name "r-sf") - (version "1.0-4") + (version "1.0-5") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 - "0dxln3ikqmwczz0ri63xwj05v09hkpljw2qvma6n03nzczyg2713")))) + "1i0s9839m9zffad2aq6zgcpz0d61g68caqh9wxaxaxx7bvx2h319")))) (build-system r-build-system) (inputs (list gdal geos proj sqlite zlib)) @@ -16283,38 +16522,28 @@ datum transformations.") (define-public r-spdep (package (name "r-spdep") - (version "1.1-12") + (version "1.2-1") (source (origin (method url-fetch) (uri (cran-uri "spdep" version)) (sha256 (base32 - "1dykhsk5djh62b3zcvpmvm3s87rn8ywzbwblhzivhln0y6pzk9hv")) + "1ya39bgmzagrk4k51zd96l4xvnbc2vzmvd0z9qprdfvg9s6pik78")) (snippet - '(for-each delete-file '("inst/doc/nb_igraph.html" - "inst/doc/nb_igraph.R" - "inst/doc/nb_igraph.Rmd" - "inst/doc/sids.html" - "inst/doc/sids.R" + '(for-each delete-file '("inst/doc/CO69.html" + "inst/doc/CO69.R" "inst/doc/nb.html" "inst/doc/nb.R" - "inst/doc/CO69.html" - "inst/doc/CO69.R" "inst/doc/nb_sf.html" "inst/doc/nb_sf.R" - "inst/doc/nb_sf.Rmd"))))) + "inst/doc/nb_sf.Rmd" + "inst/doc/sids.html" + "inst/doc/sids.R"))))) (build-system r-build-system) (propagated-inputs (list r-boot - r-coda r-deldir r-e1071 - r-expm - r-gmodels - r-learnbayes - r-mass - r-matrix - r-nlme r-s2 r-sf r-sp @@ -16373,16 +16602,16 @@ also provided to illustrate various methods.") (define-public r-pegas (package (name "r-pegas") - (version "1.0-1") + (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "pegas" version)) (sha256 - (base32 "0ykx84p7c8cad5d1mj8cm1d5cz2paacdjx4ll4qzmq827lcyycz1")))) + (base32 "0ngd0laqbs139ji9hm9kwsm9rm56agw2yyfcplxgqva936l93fl7")))) (build-system r-build-system) (propagated-inputs - (list r-adegenet r-ape)) + (list r-ape)) (home-page "http://ape-package.ird.fr/pegas.html") (synopsis "Population and evolutionary genetics analysis system") (description @@ -16908,14 +17137,14 @@ the corresponding outputs (tables and graphs).") (define-public r-rjava (package (name "r-rjava") - (version "1.0-5") + (version "1.0-6") (source (origin (method url-fetch) (uri (cran-uri "rJava" version)) (sha256 (base32 - "1pkgndppk498by44sai440l3i7vzndknbngn1q748cv39xvsbnrg")))) + "1ijqhvnb8ab38cp9pwdf7zq7xqqlm6x94gkrab2dd98p6d4x1472")))) (properties `((upstream-name . "rJava"))) (build-system r-build-system) (arguments @@ -17766,14 +17995,14 @@ function for computing a matrix of correlation p-values.") (define-public r-ggfun (package (name "r-ggfun") - (version "0.0.4") + (version "0.0.5") (source (origin (method url-fetch) (uri (cran-uri "ggfun" version)) (sha256 (base32 - "07njcjcj212zxanq8x3nkh7mgvqmym08rx5s41rz9flhk9gkc9jr")))) + "10spayf5jzmizhs6aassjplrjr9mr6bcww30pyxzyb1djfl41qxi")))) (properties `((upstream-name . "ggfun"))) (build-system r-build-system) (propagated-inputs @@ -18059,14 +18288,14 @@ external dependencies. This package has is implemented purely in R.") (define-public r-aplot (package (name "r-aplot") - (version "0.1.1") + (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "aplot" version)) (sha256 (base32 - "067yzy35spvs6jbccqpmvnjilglxzda6qqlqhjv311kfvnppzsyf")))) + "1w09flb6a4fxibfrm1z24pg672r80b7phgc0m7mv3vfw3l84v749")))) (properties `((upstream-name . "aplot"))) (build-system r-build-system) (propagated-inputs @@ -18170,14 +18399,14 @@ library.") (define-public r-rex (package (name "r-rex") - (version "1.2.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "rex" version)) (sha256 (base32 - "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06")))) + "1mmzlc3j7xa0rbjxa369f4sr0iw3gq58g8fmjjxbsjvfq14ychmg")))) (build-system r-build-system) (propagated-inputs (list r-lazyeval)) @@ -18248,14 +18477,14 @@ on, for a performance vs accuracy trade-off.") (define-public r-rsparse (package (name "r-rsparse") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "rsparse" version)) (sha256 (base32 - "1blg59gsidh0sn6yy761pisz2phml0hzgqc24s5s8q9q903rddr9")))) + "0d05h47j29zipyxbkv9cwzv2dzj894z6hh9dqfhwswwjbv6ciwpq")))) (properties `((upstream-name . "rsparse"))) (build-system r-build-system) (propagated-inputs @@ -18263,6 +18492,7 @@ on, for a performance vs accuracy trade-off.") r-float r-lgr r-matrix + r-matrixextra r-rcpp r-rcpparmadillo r-rhpcblasctl)) @@ -18422,26 +18652,29 @@ code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.") (define-public r-sctransform (package (name "r-sctransform") - (version "0.3.2") + (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "sctransform" version)) (sha256 (base32 - "1p3m6i28nlxh6r609syn88cwlbdpl3dw44dy3gsijk2ibq20mfsx")))) + "0aqbcarsvvzkh5h4i65f08y4b8dfcs3zi62hmvfy24gj81f15bw3")))) (build-system r-build-system) (propagated-inputs - (list r-future + (list r-dplyr + r-future r-future-apply r-ggplot2 r-gridextra + r-magrittr r-mass r-matrix r-matrixstats r-rcpp r-rcpparmadillo - r-reshape2)) + r-reshape2 + r-rlang)) (home-page "https://github.com/ChristophH/sctransform") (synopsis "Variance stabilizing transformations for Single Cell UMI Data") (description @@ -18849,14 +19082,14 @@ includes data sets from oceanography.") (define-public r-ggfortify (package (name "r-ggfortify") - (version "0.4.13") + (version "0.4.14") (source (origin (method url-fetch) (uri (cran-uri "ggfortify" version)) (sha256 (base32 - "0qls8pyndrlwx75wzlc0xmk04qq263d7065r3d6kvay7haa4nm40")))) + "038m74azpy43869ax1yi6wxbl1kr59iaxl8raiikjg749vcx6njw")))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -18999,14 +19232,14 @@ in R, including a translation of the original algorithm into R.") (define-public r-uwot (package (name "r-uwot") - (version "0.1.10") + (version "0.1.11") (source (origin (method url-fetch) (uri (cran-uri "uwot" version)) (sha256 (base32 - "08vxh085wnrxgwy35ksb4cr7ccjvd98pyr2zlgarqryfgc1bdqbf")))) + "06ylzxmdh8jipbrzgqaiivd2lnqmbcva41cyvc0iyals6vqr1ksg")))) (build-system r-build-system) (propagated-inputs (list r-dqrng @@ -19390,14 +19623,14 @@ be used further by e.g. graphic devices.") (define-public r-graphlayouts (package (name "r-graphlayouts") - (version "0.7.2") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "graphlayouts" version)) (sha256 (base32 - "0vncg1pfnwrfkjfwz5k86b0ir8vnjkbyd0kzpbgb0cpkdz7987pc")))) + "1l7gkn0r1ijllv3w7cbwcbi0jggs7wlkq9b2lykprng4g1kjc96p")))) (properties `((upstream-name . "graphlayouts"))) (build-system r-build-system) (propagated-inputs @@ -19415,14 +19648,14 @@ emphasize hidden group structures in networks or focus on specific nodes.") (define-public r-terra (package (name "r-terra") - (version "1.4-20") + (version "1.5-12") (source (origin (method url-fetch) (uri (cran-uri "terra" version)) (sha256 (base32 - "0c4nx113sfympixy5rkvgzc7pprcfflnadkbwhcpzjlky8gmmsk4")))) + "06fcjyzllw6dnzq0a7dc73v7rlpf250dyw41q0vr08y3x17c2p46")))) (properties `((upstream-name . "terra"))) (build-system r-build-system) (inputs @@ -19535,14 +19768,14 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.15.0") + (version "0.16.0") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "0f06bwlc1g0xdyhdqzx8plfx1jwk8a9j4lcbl91wjsil8wja0bkl")))) + "1i295d5nqjr3pvp9vz59wiasrxy9n78q518phcd15sxcjzcj0l27")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs @@ -19563,13 +19796,13 @@ effect size.") (define-public r-rgdal (package (name "r-rgdal") - (version "1.5-27") + (version "1.5-28") (source (origin (method url-fetch) (uri (cran-uri "rgdal" version)) (sha256 - (base32 "0mjpxs2dvbngbchlb0kfs0jcac7v88slwxmka81ds92lggnmb9b2")))) + (base32 "18k1w8cb77h4mw1m5b21r0fng40arb1md24fyriv83ccz8n46m3z")))) (properties `((upstream-name . "rgdal"))) (build-system r-build-system) (inputs @@ -19720,15 +19953,44 @@ from 1-D, 2-D and 3-D partial differential equations that have been converted to ODEs by numerical differencing.") (license license:gpl2+))) +(define-public r-pmcmrplus + (package + (name "r-pmcmrplus") + (version "1.9.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "PMCMRplus" version)) + (sha256 + (base32 "00sgk4c7vpmbfifrsbqd5gh7hwdpm8kymlpnnrdzlhvkymhbmfkn")))) + (properties `((upstream-name . "PMCMRplus"))) + (build-system r-build-system) + (inputs (list gmp)) + (propagated-inputs + (list r-bwstest + r-gmp + r-ksamples + r-mass + r-multcompview + r-mvtnorm + r-rmpfr + r-suppdists)) + (native-inputs (list gfortran r-knitr)) + (home-page "https://cran.r-project.org/package=PMCMRplus") + (synopsis "Calculate pairwise multiple comparisons of mean rank sums extended") + (description + "This package provides multiple pairwise tests.") + (license license:gpl3+))) + (define-public r-pracma (package (name "r-pracma") - (version "2.3.3") + (version "2.3.6") (source (origin (method url-fetch) (uri (cran-uri "pracma" version)) (sha256 - (base32 "0g5r5ir5k43ba0ngnsanp108k479l2dnsjd5w6idk1d34ivqs7yg")))) + (base32 "1pmqk7b6c600v6pn0s047p3msl13azwk611zvh05w5f993yq7b0p")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pracma/") (synopsis "Practical numerical math functions") @@ -19741,14 +20003,14 @@ porting.") (define-public r-subplex (package (name "r-subplex") - (version "1.6") + (version "1.7") (source (origin (method url-fetch) (uri (cran-uri "subplex" version)) (sha256 (base32 - "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d")))) + "11zqzydbj6ivgvlw1gv1r2yxra7misbc622g575p2vckhjjg9v6m")))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -20289,14 +20551,14 @@ included.") (define-public r-qgam (package (name "r-qgam") - (version "1.3.3") + (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "qgam" version)) (sha256 (base32 - "0vx2wf3rqc3j8i0870xrwxndkbgza0nnh7f0yxi8h67lfi7gws4s")))) + "1jyamamdffaks89rspyhmg18b4iik0nb1j0vgqzvfnm890514cvn")))) (properties `((upstream-name . "qgam"))) (build-system r-build-system) (propagated-inputs @@ -20319,14 +20581,14 @@ regression models.") (define-public r-abtest (package (name "r-abtest") - (version "0.2.2") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "abtest" version)) (sha256 (base32 - "1ak0m4jd1grriwg4pn3aqf1468qma6rjn5kqjh8izx7zl29jd07v")))) + "0jz2ry5364p8h8xlk5a5sycn8xlpxd1iasfg99bcr4jqzd92jfqg")))) (properties `((upstream-name . "abtest"))) (build-system r-build-system) (propagated-inputs @@ -20349,18 +20611,18 @@ elicitation options based on Kass and Vaidyanathan (1992) (define-public r-reldist (package (name "r-reldist") - (version "1.6-6") + (version "1.7-0") (source (origin (method url-fetch) (uri (cran-uri "reldist" version)) (sha256 (base32 - "09vips7spcz0fahrpy0bl15hk43zgnq74h189hmygyi41l95aywa")))) + "0i04d6w3r6fzm4bykz6lnnh6dngmd61v5wlpli70r3fzdzhi7fji")))) (properties `((upstream-name . "reldist"))) (build-system r-build-system) (propagated-inputs - (list r-hmisc r-mgcv)) + (list r-densestbayes r-hmisc r-mgcv)) (home-page "http://www.stat.ucla.edu/~handcock/RelDist") (synopsis "Relative distribution methods") (description @@ -21587,21 +21849,20 @@ allowed.") (define-public r-gdina (package (name "r-gdina") - (version "2.8.7") + (version "2.8.8") (source (origin (method url-fetch) (uri (cran-uri "GDINA" version)) (sha256 (base32 - "08cdjp4mqn81j3wa770v7n8zkslys9jqqb3d3c09dkfmgdk6hga4")))) + "1slq1npsq8s8aghnrpm6vvc6kxj4svz0kr2x0akblndrcr25wxjr")))) (properties `((upstream-name . "GDINA"))) (build-system r-build-system) (propagated-inputs (list r-alabama r-ggplot2 r-mass - r-nloptr r-numderiv r-rcpp r-rcpparmadillo @@ -22481,14 +22742,14 @@ Edition), John Wiley and Sons.") (define-public r-anthropometry (package (name "r-anthropometry") - (version "1.16") + (version "1.17") (source (origin (method url-fetch) (uri (cran-uri "Anthropometry" version)) (sha256 (base32 - "0iqlmp9vig4qdavs37kislqxwhk0c0pgsn1kwz3mm75nylxmpbp0")))) + "0vxjlzxv16bygw8n57f25msq5bd1dydg41my92ximah0nzzvbg41")))) (properties `((upstream-name . "Anthropometry"))) (build-system r-build-system) (propagated-inputs @@ -22513,6 +22774,29 @@ They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis.") (license license:gpl2+))) +(define-public r-anndata + (package + (name "r-anndata") + (version "0.7.5.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "anndata" version)) + (sha256 + (base32 "115v7gdilayd18hd519vzkixp2s6rvvrd1inc1i6amn7d0spy8r1")))) + (properties `((upstream-name . "anndata"))) + (build-system r-build-system) + (propagated-inputs (list r-assertthat r-matrix r-r6 r-reticulate)) + (native-inputs (list r-knitr)) + (home-page "https://anndata.dynverse.org") + (synopsis "Anndata for R") + (description + "This package provides a reticulate wrapper for the Python package +@code{anndata}. It provides a scalable way of keeping track of data and +learned annotations. It is used to read from and write to the h5ad file +format.") + (license license:expat))) + (define-public r-adamethods (package (name "r-adamethods") @@ -23058,14 +23342,14 @@ Raftery, Appl.Statistics, 1989); it includes inference and basic methods.") (define-public r-forecast (package (name "r-forecast") - (version "8.15") + (version "8.16") (source (origin (method url-fetch) (uri (cran-uri "forecast" version)) (sha256 (base32 - "0x4ij55sb45qnwba3bybs50vsvv82q3j8p47xmbv959h13nsnfn7")))) + "0zvn44k7npxai8kj0hgxaaqv1hgd8rxicnvj4cg7wfl8ba4yn0cz")))) (properties `((upstream-name . "forecast"))) (build-system r-build-system) (propagated-inputs @@ -23142,14 +23426,14 @@ programming} (OOP) using R Reference Class.") (define-public r-proxyc (package (name "r-proxyc") - (version "0.2.3") + (version "0.2.4") (source (origin (method url-fetch) (uri (cran-uri "proxyC" version)) (sha256 (base32 - "1g90d82rp82dkidlfykankprzpp94d7394s2b2qjlyiia3k0hlb3")))) + "1mcimswrx1cjjm7wsgkzfrgh3jpf4sncwfvdvg2f14fzfzy7afd6")))) (properties `((upstream-name . "proxyC"))) (build-system r-build-system) (propagated-inputs @@ -23167,14 +23451,14 @@ and Euclidean distance is particularly fast.") (define-public r-isocodes (package (name "r-isocodes") - (version "2021.02.24") + (version "2022.01.10") (source (origin (method url-fetch) (uri (cran-uri "ISOcodes" version)) (sha256 (base32 - "19irnn2yi1bzhf03g666la84kj8040f5913kfrmd16dfnjy6j9qm")))) + "0gy7n5bgxnl4rawry0pg078bkks9lzsbsrwjq8q5cvxl4k3dwpdj")))) (properties `((upstream-name . "ISOcodes"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=ISOcodes") @@ -23256,14 +23540,14 @@ Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.") (define-public r-quanteda (package (name "r-quanteda") - (version "3.1.0") + (version "3.2.0") (source (origin (method url-fetch) (uri (cran-uri "quanteda" version)) (sha256 (base32 - "0gafbb73gcxx2gq9q7bg88alyhymkr471lp394m5ydij6mdm4hb9")))) + "0q72jsc6zalnl35qq02z9niissnyax4zxzqzpfpjsmgmxpd797mw")))) (properties `((upstream-name . "quanteda"))) (build-system r-build-system) (propagated-inputs @@ -23355,18 +23639,18 @@ regressions.") (define-public r-polycor (package (name "r-polycor") - (version "0.7-10") + (version "0.8-1") (source (origin (method url-fetch) (uri (cran-uri "polycor" version)) (sha256 (base32 - "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna")))) + "0285rvx8238qp8dix0jq0cqq7ks8h6cjwsscbc7dx4n9nph56pzh")))) (properties `((upstream-name . "polycor"))) (build-system r-build-system) (propagated-inputs - (list r-matrix r-mvtnorm)) + (list r-admisc r-matrix r-mvtnorm)) (home-page "https://r-forge.r-project.org/projects/polycor/") (synopsis "Polychoric and polyserial correlations") (description @@ -23473,6 +23757,50 @@ additional functions that are comparable to APL functions which are useful for actuarial models such as pension mathematics.") (license license:gpl2+))) +(define-public r-matrixextra + (package + (name "r-matrixextra") + (version "0.1.9-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "MatrixExtra" version)) + (sha256 + (base32 "098apgqlncgxspa8mi4bx2nk5fbk3880whqiwkvydsfsqrbv1sj0")))) + (properties `((upstream-name . "MatrixExtra"))) + (build-system r-build-system) + (propagated-inputs + (list r-float r-matrix r-rcpp r-rhpcblasctl)) + (native-inputs + (list r-knitr)) + (home-page "https://github.com/david-cortes/MatrixExtra") + (synopsis "Extra methods for sparse matrices") + (description + "This package extends sparse matrix and vector classes from the Matrix +package by providing: + +@enumerate +@item Methods and operators that work natively on CSR formats (compressed + sparse row, a.k.a. @code{RsparseMatrix}) such as slicing/sub-setting, + assignment, @code{rbind()}, mathematical operators for CSR and COO such as + addition or @code{sqrt()}, and methods such as @code{diag()}; +@item Multi-threaded matrix multiplication and cross-product for many + @code{<sparse, dense>} types, including the @code{float32} type from + @code{float}; +@item Coercion methods between pairs of classes which are not present in + @code{Matrix}, such as from @code{dgCMatrix} to @code{ngRMatrix}, as well as + convenience conversion functions; +@item Utility functions for sparse matrices such as sorting the indices or + removing zero-valued entries; +@item Fast transposes that work by outputting in the opposite storage format; +@item Faster replacements for many @code{Matrix} methods for all sparse types, + such as slicing and elementwise multiplication. +@item Convenience functions for sparse objects, such as @code{mapSparse} or a + shorter @code{show} method. +@end enumerate +") + (license license:gpl2+))) + (define-public r-sem (package (name "r-sem") @@ -23614,14 +23942,14 @@ Complete access to optimized C functions is made available with (define-public r-openmx (package (name "r-openmx") - (version "2.19.8") + (version "2.20.0") (source (origin (method url-fetch) (uri (cran-uri "OpenMx" version)) (sha256 (base32 - "0q37mwxqhgdi05rwdfwfapgazfp541xsvw3yskf21lv11y2yjjyb")))) + "1flkm5nsvdnqhjayzajv80lsvjbh21v4zbm7ak09051x0giv3shj")))) (properties `((upstream-name . "OpenMx"))) (build-system r-build-system) (propagated-inputs @@ -23635,7 +23963,7 @@ Complete access to optimized C functions is made available with r-rcppparallel r-rpf r-stanheaders)) - (native-inputs (list gfortran)) + (native-inputs (list r-knitr gfortran)) (home-page "http://openmx.ssri.psu.edu") (synopsis "Extended structural equation modelling") (description @@ -24230,14 +24558,14 @@ techniques to average Bayesian predictive distributions.") (define-public r-rstan (package (name "r-rstan") - (version "2.21.2") + (version "2.21.3") (source (origin (method url-fetch) (uri (cran-uri "rstan" version)) (sha256 (base32 - "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3")))) + "1ccjdwh0xspna2c0m5p8as8y2b0lnhdyk9hfd3jh58j6n8fbzg3n")))) (properties `((upstream-name . "rstan"))) (build-system r-build-system) (arguments @@ -24262,9 +24590,7 @@ techniques to average Bayesian predictive distributions.") r-rcpp r-rcppeigen r-rcppparallel - r-stanheaders - r-v8 - r-withr)) + r-stanheaders)) (home-page "https://discourse.mc-stan.org/") (synopsis "R interface to Stan") (description @@ -24348,14 +24674,14 @@ trend test.") (define-public r-keyring (package (name "r-keyring") - (version "1.2.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "keyring" version)) (sha256 (base32 - "1rqz29ycsmfqixhnzhhfd89j9ivnmp7x2z3vxdla622zmakbcy4c")))) + "1j8l6nmh4dr70kwybiais8yh687fdwrj134xynq68igw1b1rm8ga")))) (properties `((upstream-name . "keyring"))) (build-system r-build-system) (propagated-inputs @@ -25231,14 +25557,14 @@ vignette for more information and examples.") (define-public r-distributional (package (name "r-distributional") - (version "0.2.2") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "distributional" version)) (sha256 (base32 - "0ps30ijlf0xwranxkq1z29d76d3zgy8drwxpnxp6ffmyma8mm3h2")))) + "1mji8xlhwrw8msih5wdpbzwv4g59kly0xkdklhn8yzb18rrnrczs")))) (properties `((upstream-name . "distributional"))) (build-system r-build-system) @@ -25268,14 +25594,14 @@ including means, variances, intervals, and highest density regions.") (define-public r-posterior (package (name "r-posterior") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "posterior" version)) (sha256 (base32 - "1lpldkkkxv94dr30q5wb5qr61qrgp9shqnskgwriigy1phnjdxpg")))) + "11j3jgk8mykicqi77a6frn0gck7fx0i6sl6g774sqj44m48ig81b")))) (properties `((upstream-name . "posterior"))) (build-system r-build-system) (propagated-inputs @@ -25315,14 +25641,14 @@ inference diagnostics. (define-public r-brms (package (name "r-brms") - (version "2.16.1") + (version "2.16.3") (source (origin (method url-fetch) (uri (cran-uri "brms" version)) (sha256 (base32 - "1i0vkkfziac29vncw4igja5m7a6rhw9rqwifrw3y47q6zgczp7kl")))) + "1q93z4cf3iy4rs6pgvph6z7hc8q05iwif76hcg8p4kr6nl82nc38")))) (properties `((upstream-name . "brms"))) (build-system r-build-system) (propagated-inputs @@ -25341,7 +25667,6 @@ inference diagnostics. r-nleqslv r-nlme r-posterior - r-projpred r-rcpp r-rstan r-rstantools @@ -25596,14 +25921,14 @@ input.") (define-public r-lightgbm (package (name "r-lightgbm") - (version "3.3.1") + (version "3.3.2") (source (origin (method url-fetch) (uri (cran-uri "lightgbm" version)) (sha256 (base32 - "0hvpwirskzcd7ww47f9gllgl3wjvpghnwj8a41glpppwwaaxa0z4")))) + "12hbvm1va6sb5yny564jvhhzrkcq4j33rcdhqhwxaac2m08cpi8s")))) (properties `((upstream-name . "lightgbm"))) (build-system r-build-system) (propagated-inputs @@ -25833,14 +26158,14 @@ coefficients are constructed using multiplier bootstrap.") (define-public r-fastshap (package (name "r-fastshap") - (version "0.0.5") + (version "0.0.7") (source (origin (method url-fetch) (uri (cran-uri "fastshap" version)) (sha256 (base32 - "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg")))) + "0gxch67i3bj6m8nb94m5hswq058w6n1q9war4dy2qnimlv7cmhdv")))) (properties `((upstream-name . "fastshap"))) (build-system r-build-system) (propagated-inputs @@ -25996,14 +26321,14 @@ diagonals. This package allows you to compute the tensor product of arrays.") (define-public r-spatstat-utils (package (name "r-spatstat-utils") - (version "2.2-0") + (version "2.3-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat.utils" version)) (sha256 (base32 - "1aypccpv0zavxwmqzvlka8981n9km7ml3jbmxz21sql58997xn2s")))) + "06nvn2ffyrskhzaavsy6lmdp0m8askkrp1fnwrhjsj01lbjnq2az")))) (properties `((upstream-name . "spatstat.utils"))) (build-system r-build-system) @@ -26017,14 +26342,14 @@ which may also be useful for other purposes.") (define-public r-spatstat-sparse (package (name "r-spatstat-sparse") - (version "2.0-0") + (version "2.1-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat.sparse" version)) (sha256 (base32 - "1iqrpazb88s4w208adf2qgm4ajwz3kwqck65k9g5l28zw9jcxyr7")))) + "148fxbxss569w73xaqpzwpz9rfjdgznh2ngf06gvm33631222680")))) (properties `((upstream-name . "spatstat.sparse"))) (build-system r-build-system) @@ -26041,14 +26366,14 @@ matrix calculations that are common in statistics, such as quadratic forms.") (define-public r-spatstat-data (package (name "r-spatstat-data") - (version "2.1-0") + (version "2.1-2") (source (origin (method url-fetch) (uri (cran-uri "spatstat.data" version)) (sha256 (base32 - "0csmz5vjaxnznkbsfah8qd3v8p0y56jvis01ialxzvf71snl160v")))) + "1r8s4xl25xr71h4g5qqi5y370h2ik3kz5fb4qyml2b6dwsl1ildv")))) (properties `((upstream-name . "spatstat.data"))) (build-system r-build-system) (propagated-inputs @@ -26063,14 +26388,14 @@ package.") (define-public r-spatstat-geom (package (name "r-spatstat-geom") - (version "2.3-0") + (version "2.3-1") (source (origin (method url-fetch) (uri (cran-uri "spatstat.geom" version)) (sha256 (base32 - "1iz9zi45nli5lf96ng6bqqbl4ix3zxzlfclkg4cdb9h98nj4c5vv")))) + "1h3ja45in7hnar2gwqp18jkz4rcqi99gllar6jqzlsvdbb85hgpj")))) (properties `((upstream-name . "spatstat.geom"))) (build-system r-build-system) (propagated-inputs @@ -26086,14 +26411,14 @@ for the geometry of linear networks.") (define-public r-spatstat-core (package (name "r-spatstat-core") - (version "2.3-1") + (version "2.3-2") (source (origin (method url-fetch) (uri (cran-uri "spatstat.core" version)) (sha256 (base32 - "1fq6ynds66d836drf758syqhfz0341fxif0r5hbf5lfkwp3a2wfk")))) + "0g7nj8nf9ywhdbc5irxlry6kzq6bwwbkk9cp22kyv1wigycnskbz")))) (properties `((upstream-name . "spatstat.core"))) (build-system r-build-system) (propagated-inputs @@ -26118,14 +26443,14 @@ user-level code from spatstat, except for the code for linear networks.") (define-public r-spatstat-linnet (package (name "r-spatstat-linnet") - (version "2.3-0") + (version "2.3-1") (source (origin (method url-fetch) (uri (cran-uri "spatstat.linnet" version)) (sha256 (base32 - "1yd2z629f7908xw9kyqiahk3qn9ajpl6qffbkv887zmq3p28kh7h")))) + "1hrqa2i6mp7d79jw4h56b8hk9590959s79vh9xcsj6k5vbisd6qi")))) (properties `((upstream-name . "spatstat.linnet"))) (build-system r-build-system) @@ -26146,14 +26471,14 @@ for spatial data on a linear network.") (define-public r-spatstat (package (name "r-spatstat") - (version "2.2-0") + (version "2.3-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat" version)) (sha256 (base32 - "0lz3sidn05xjswxaxhagal6jj5hra6aya0azxybjw7mgspl903wg")))) + "01jckks3j39854mhsarzyzn4rj82h1xrnyd2b6fyzizj48vl80ns")))) (properties `((upstream-name . "spatstat"))) (build-system r-build-system) (propagated-inputs @@ -26202,14 +26527,14 @@ for linear mixed models (AIREML).") (define-public r-cpp11 (package (name "r-cpp11") - (version "0.4.1") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "cpp11" version)) (sha256 (base32 - "1nk47xkab7i17h7917l4cfyfvnxf782dfq67wwxa6n0r4jqqxzz9")))) + "16cvjfkbc7c0ymdmbcqg9px6pjsqx6qhyfq5frqj739mhazy0g20")))) (properties `((upstream-name . "cpp11"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -26222,6 +26547,27 @@ jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with @code{ALTREP} vectors.") (license license:expat))) +(define-public r-rcpptoml + (package + (name "r-rcpptoml") + (version "0.1.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "RcppTOML" version)) + (sha256 + (base32 "0h8517ipwqhqkhcfiyqmvsb585g01p0ra0azbpzyxip6pq6g029g")))) + (properties `((upstream-name . "RcppTOML"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp)) + (home-page "http://dirk.eddelbuettel.com/code/rcpp.toml.html") + (synopsis "Rcpp bindings to TOML parser") + (description + "The TOML configuration format specifies an excellent format suitable for +both human editing as well as the common uses of a machine-readable format. +This package provides Rcpp bindings to a TOML parser.") + (license license:gpl2+))) + (define-public r-rcppziggurat (package (name "r-rcppziggurat") @@ -26253,14 +26599,14 @@ aggregation for comparing different implementations in order to provide a (define-public r-rfast (package (name "r-rfast") - (version "2.0.3") + (version "2.0.4") (source (origin (method url-fetch) (uri (cran-uri "Rfast" version)) (sha256 (base32 - "1bmhmli6q4kg8321595k0yy91w9cblk14s6qbc9wf8f05108rg15")))) + "1n9imwkkq14ickp0g34jyha4jkr180xj0ar8xh3hqqi4dvihg6cm")))) (properties `((upstream-name . "Rfast"))) (build-system r-build-system) (propagated-inputs @@ -26785,6 +27131,27 @@ adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian geometric models.") (license license:lgpl3+))) +(define-public r-add2ggplot + (package + (name "r-add2ggplot") + (version "0.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "add2ggplot" version)) + (sha256 + (base32 "0c94i1cfp2pvplvxmfvvz2fyj026r1jnax05mrzrc7ppnqzy25y0")))) + (properties `((upstream-name . "add2ggplot"))) + (build-system r-build-system) + (propagated-inputs + (list r-ggplot2 r-magick r-magrittr r-rcolorbrewer r-zeallot)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/JiaxiangBU/add2ggplot") + (synopsis "Extension for ggplot2") + (description "This packages provides tools to create themes and color +palettes for the package ggplot2.") + (license license:expat))) + (define-public r-diffusionmap (package (name "r-diffusionmap") @@ -26811,14 +27178,14 @@ model.") (define-public r-igraph (package (name "r-igraph") - (version "1.2.8") + (version "1.2.11") (source (origin (method url-fetch) (uri (cran-uri "igraph" version)) (sha256 (base32 - "01hvphaf5mx9xvwiazcw39kp6gc1lafqrbjwczy6f7hr145dn1pl")))) + "1ph042yinl8ig2x7laha5j1xr14fky9771l5ha87svhynrg732qw")))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -26931,14 +27298,14 @@ object sizes.") (define-public r-yardstick (package (name "r-yardstick") - (version "0.0.8") + (version "0.0.9") (source (origin (method url-fetch) (uri (cran-uri "yardstick" version)) (sha256 (base32 - "13b0lyj2k0r568mwlyz9yvp9156rzlj4jqnjazaffh9vwqh4whir")))) + "00hv4gk1ba4dab8i3dcq7lim4bll7l572rgc8km9x4ja8by95j8h")))) (properties `((upstream-name . "yardstick"))) (build-system r-build-system) (propagated-inputs @@ -26983,6 +27350,30 @@ used in further calculations that rely on a specific temporal spacing between observations.") (license license:expat))) +(define-public r-scico + (package + (name "r-scico") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "scico" version)) + (sha256 + (base32 "08grfbjd5s0vdw76ni37yjl2242rr8i2jy72sgpwgra282hpnji3")))) + (properties `((upstream-name . "scico"))) + (build-system r-build-system) + (propagated-inputs (list r-scales)) + (home-page "https://github.com/thomasp85/scico") + (synopsis "Colour Palettes Based on the Scientific Colour-Maps") + (description + "This package provides colour choice in information visualisation. It +important in order to avoid being mislead by inherent bias in the used colour +palette. This package provides access to the perceptually uniform and +colour-blindness friendly palettes developed by Fabio Crameri and released +under the \"Scientific Colour-Maps\" moniker. The package contains 24 +different palettes and includes both diverging and sequential types.") + (license license:expat))) + (define-public r-slider (package (name "r-slider") @@ -27008,6 +27399,28 @@ advanced usage, an index can be used as a secondary vector that defines how sliding windows are to be created.") (license license:expat))) +(define-public r-rlist + (package + (name "r-rlist") + (version "0.4.6.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "rlist" version)) + (sha256 + (base32 "15q99rhbbjq8zd976yjmfnny45dd5fg2p2dv1sljg2kwi66nbppb")))) + (properties `((upstream-name . "rlist"))) + (build-system r-build-system) + (propagated-inputs (list r-data-table r-jsonlite r-xml r-yaml)) + (home-page "https://renkun-ken.github.io/rlist/") + (synopsis "A Toolbox for Non-Tabular Data Manipulation") + (description + "This package provides a set of functions for data manipulation with +list objects, including mapping, filtering, grouping, sorting, updating, +searching, and other useful functions. Most functions are designed to be +pipeline friendly so that data processing with lists can be chained.") + (license license:expat))) + (define-public r-rsample (package (name "r-rsample") @@ -27469,14 +27882,14 @@ model-related packages.") (define-public r-conflicted (package (name "r-conflicted") - (version "1.0.4") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "conflicted" version)) (sha256 (base32 - "0xp04cdvmp3b1phazhmjqn0vmax1b2218xsb5854ffv43m7qvrra")))) + "1qg9ar114r98wm0pnf65mss4v2ksq3924rlpm13mqp4s3p6j9yi4")))) (properties `((upstream-name . "conflicted"))) (build-system r-build-system) (propagated-inputs @@ -27758,14 +28171,14 @@ data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") (define-public r-maldiquant (package (name "r-maldiquant") - (version "1.20") + (version "1.21") (source (origin (method url-fetch) (uri (cran-uri "MALDIquant" version)) (sha256 (base32 - "1h9i158czlzwbn5zakkqd2ggc9g90r73vdspmp6kgfcmy9frvwzz")))) + "1y1g3819ss06dry70kfhg2syddw71682qmzkcyppfsma6hhghw87")))) (properties `((upstream-name . "MALDIquant"))) (build-system r-build-system) (native-inputs @@ -27808,14 +28221,14 @@ data to rasters. It speeds up plotting of data with millions of points.") (define-public r-seuratobject (package (name "r-seuratobject") - (version "4.0.3") + (version "4.0.4") (source (origin (method url-fetch) (uri (cran-uri "SeuratObject" version)) (sha256 (base32 - "06gch6416hmwpfxa7bidw5izfp4yvkdka7mvxp6grmldnj5iqm6g")))) + "1308hjbs8br3gp9vwm65awgp6vimwgi2jyl1ryn96l84savn2ljq")))) (properties `((upstream-name . "SeuratObject"))) (build-system r-build-system) (propagated-inputs @@ -27833,13 +28246,13 @@ other R users.") (define-public r-seurat (package (name "r-seurat") - (version "4.0.5") + (version "4.1.0") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "18svlpfbgs5vdzw2jyg99kj0jacag6dwwhjdg1zpmrh0fm0praxg")))) + "0p9i3fnkqa3vranr7c7ckzp1kq42d7p0gcfi9ml4kr334yd84195")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs @@ -27979,14 +28392,14 @@ distributed as independent packages.") (define-public r-phangorn (package (name "r-phangorn") - (version "2.8.0") + (version "2.8.1") (source (origin (method url-fetch) (uri (cran-uri "phangorn" version)) (sha256 (base32 - "1pg5lfc5m4ccphswbfbihj91ppmqhf4084kbjlmfsrqxylsyy8ch")))) + "0xfwi7adl1pcfcwk72fj7lkwfm0wiip96ij7m4252xr9mq818ivd")))) (build-system r-build-system) (propagated-inputs (list r-ape @@ -28036,14 +28449,14 @@ rate speciation and extinction.") (define-public r-calculus (package (name "r-calculus") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "calculus" version)) (sha256 (base32 - "0m9cjc3bqv88vrrj51kd7c7xnczka5w9q0ln4l4nk514gvlr79bn")))) + "1x3bcdd422wqv9gk9r2m8g19qcga220sm5rxdp4bgfc6vlqzzz7y")))) (properties `((upstream-name . "calculus"))) (build-system r-build-system) (propagated-inputs @@ -28100,6 +28513,39 @@ estimation in measurement error models: The R package decon. Journal of Statistical Software, 39(10), 1-24.") (license license:gpl3+))) +(define-public r-densestbayes + (package + (name "r-densestbayes") + (version "1.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "densEstBayes" version)) + (sha256 + (base32 "16fb7vkic9q5p8s4f0f215zmb36fcizqr4r2vm9dxxj9rasrg2f3")))) + (properties `((upstream-name . "densEstBayes"))) + (build-system r-build-system) + (propagated-inputs + (list r-bh + r-mass + r-nlme + r-rcpp + r-rcpparmadillo + r-rcppeigen + r-rcppparallel + r-rstan + r-rstantools + r-stanheaders)) + (home-page "https://cran.r-project.org/package=densEstBayes") + (synopsis "Density estimation via Bayesian inference engines") + (description + "Bayesian density estimates for univariate continuous random samples are +provided using the Bayesian inference engine paradigm. The engine options +are: Hamiltonian Monte Carlo, the no U-turn sampler, semiparametric mean field +variational Bayes and slice sampling. The methodology is described in Wand +and Yu (2020), arXiv:2009.06182.") + (license license:gpl2+))) + (define-public r-locpol (package (name "r-locpol") @@ -28245,13 +28691,13 @@ well as email and push notifications.") (define-public r-mlr3measures (package (name "r-mlr3measures") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "mlr3measures" version)) (sha256 (base32 - "1qlqfan5akz42zwkcz3ncln6rd9c302dy4cyp7nx0jcafr5i459f")))) + "1kbw3xd7c9x65v9zzs8i5skmrvl0mf2wsbyssmiif0lvrbzfhcmb")))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-prroc)) @@ -28267,13 +28713,13 @@ are.") (define-public r-mlr3misc (package (name "r-mlr3misc") - (version "0.9.5") + (version "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3misc" version)) (sha256 (base32 - "1ax1mvnm8xjcskq12x63jkal766v1zwilpgrkdv6yawd7yrww4q9")))) + "1wnzyij1x67smkb3gjb9gpp7iy5andfl0s1c78xx4wylhycc6m11")))) (build-system r-build-system) (propagated-inputs (list r-backports r-checkmate r-data-table r-digest r-r6)) @@ -28286,6 +28732,69 @@ helper functions for functional programming, for printing, to work with package also supersedes the package @code{BBmisc}.") (license license:lgpl3))) +(define-public r-mlr3pipelines + (package + (name "r-mlr3pipelines") + (version "0.4.0") + (source (origin + (method url-fetch) + (uri (cran-uri "mlr3pipelines" version)) + (sha256 + (base32 + "0913f67c1r9bi68gxh1prsp0vch21bl6plahnvjrlbq8rrs1sr6p")))) + (build-system r-build-system) + (propagated-inputs + (list r-backports + r-checkmate + r-data-table + r-digest + r-lgr + r-mlr3 + r-mlr3misc + r-paradox + r-r6 + r-withr)) + (home-page "https://mlr3pipelines.mlr-org.com/") + (synopsis "Preprocessing Operators and Pipelines for @code{mlr3}") + (description "@code{mlr3pipelines} enriches @code{mlr3} with a diverse +set of pipelining operators (PipeOps) that can be composed into graphs. +Operations exist for data preprocessing, model fitting, and ensemble learning. +Graphs can themselves be treated as @code{mlr3} Learners and can therefore be +resampled, benchmarked, and tuned.") + (license license:lgpl3))) + +(define-public r-mlr3ordinal + (let ((commit "9febac983b11b7b1f477e5cf0212e5999cd2ed44") + (revision "0")) + (package + (name "r-mlr3ordinal") + (version (git-version "0.1.0-9000" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mlr-org/mlr3ordinal") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1icfhz1pjm0mlsn2y60gsrbk31b2p7xmpx3xsg7639rcgdb5f9gl")))) + (build-system r-build-system) + (propagated-inputs + (list r-checkmate + r-data-table + r-mlr3 + r-mlr3misc + r-mlr3pipelines + r-nloptr + r-ordinal + r-paradox + r-r6)) + (home-page "https://mlr3ordinal.mlr-org.com/") + (synopsis "Ordinal Regression for mlr3") + (description "This package extends @code{mlr3} with support for +performing ordinal regression.") + (license license:expat)))) + (define-public r-paradox (package (name "r-paradox") @@ -28310,13 +28819,13 @@ implemented as @code{R6} classes.") (define-public r-mlr3 (package (name "r-mlr3") - (version "0.13.0") + (version "0.13.1") (source (origin (method url-fetch) (uri (cran-uri "mlr3" version)) (sha256 (base32 - "1729wbdp62cjjk775qxrahyskp191s9qqnmqbxncfjrpdxphxk34")))) + "052685d08cfsrh3r31yn05ngwi6z3fmz26gwiy32z7cpcigz8jjs")))) (build-system r-build-system) (propagated-inputs (list r-r6 @@ -28373,14 +28882,14 @@ vector machines, and gradient boosting.") (define-public r-bbotk (package (name "r-bbotk") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "bbotk" version)) (sha256 (base32 - "09cw6z397laszsg5wsgpjh7jda74amqrcl2p25bgjg33ina2nvg7")))) + "15y1w3mi1g91p73786ql1mmqld011757vax17i1vq7zw1s51yzxz")))) (properties `((upstream-name . "bbotk"))) (build-system r-build-system) (propagated-inputs @@ -28403,19 +28912,18 @@ annealing.") (define-public r-mlr3tuning (package (name "r-mlr3tuning") - (version "0.9.0") + (version "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3tuning" version)) (sha256 (base32 - "0i428kdbak81j1wlwmdf9y40hqi63azhyny802ms2z04wl8lwnvs")))) + "0cqbqp53053v7lvi9ynpr860n8fm9w9842hai5z6xvmgzqdmjiyp")))) (build-system r-build-system) (propagated-inputs (list r-bbotk r-checkmate r-data-table - r-digest r-lgr r-mlr3 r-mlr3misc @@ -28696,14 +29204,14 @@ the font tool-set provided by the @code{systemfonts} package.") (define-public r-ragg (package (name "r-ragg") - (version "1.2.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "ragg" version)) (sha256 (base32 - "1wbk7vny8435ii3aak586imd0dgh4ri55kqypx5b10x6ygp32avb")))) + "08dknkibmmwllycga2cp2732idsi3jfkkl5ghh6r2g2wdli1n2y1")))) (properties `((upstream-name . "ragg"))) (build-system r-build-system) (inputs @@ -28757,31 +29265,31 @@ in output to the equivalent HTML.") (define-public r-pkgdown (package (name "r-pkgdown") - (version "1.6.1") + (version "2.0.2") (source (origin (method url-fetch) (uri (cran-uri "pkgdown" version)) (sha256 (base32 - "1k31biyvxkv3xjc1yy3nzb9wfza3vbx97fv17nly5a6vlv7zqbs4")))) + "11grx7a2rz6b4kwspm7c8crjav677c22hysnp4bkwh5g8kr5nm2h")))) (properties `((upstream-name . "pkgdown"))) (build-system r-build-system) (inputs (list pandoc)) (propagated-inputs - (list r-callr + (list r-bslib + r-callr r-crayon r-desc r-digest r-downlit r-fs r-httr + r-jsonlite r-magrittr r-memoise - r-openssl r-purrr r-ragg - r-rematch2 r-rlang r-rmarkdown r-tibble @@ -28803,14 +29311,14 @@ package online.") (define-public r-prereg (package (name "r-prereg") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "prereg" version)) (sha256 (base32 - "0bck13iiaxwpqh0rd45mp1s5d8z62ggg0wa7rmyi8a65aywiypsi")))) + "039nrl5cirsx1ysh214dr6xnn1h6h3f90im6k9dgmzfksxdqigpw")))) (properties `((upstream-name . "prereg"))) (build-system r-build-system) (propagated-inputs @@ -29371,14 +29879,14 @@ light-weight geometry library used by @url{http://postgis.net/,PostGIS}.") (define-public r-stars (package (name "r-stars") - (version "0.5-4") + (version "0.5-5") (source (origin (method url-fetch) (uri (cran-uri "stars" version)) (sha256 (base32 - "1h5fway2fk637mkglw0h3ajiyyx8saqcapg42xzsiwbk8lnaf9f4")))) + "0hcbzr8c7wk30qjwrvx6bflzwkjpms79pavaxawnq1h8kry5fngk")))) (properties `((upstream-name . "stars"))) (build-system r-build-system) (propagated-inputs @@ -29562,14 +30070,14 @@ BTM-WWW13.pdf}.") (define-public r-delaporte (package (name "r-delaporte") - (version "8.0.1") + (version "8.0.2") (source (origin (method url-fetch) (uri (cran-uri "Delaporte" version)) (sha256 (base32 - "0ijhmwclpg5czs2sl2vykcw8qj2pxy26xf6knh62rqq6p6sm43f4")))) + "10xsmms2jfw7x4hmgpd35dv4n4azpjzmfid6585kg6qfh2zg23g5")))) (properties `((upstream-name . "Delaporte"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -29877,14 +30385,14 @@ time zone manipulations.") (define-public r-vroom (package (name "r-vroom") - (version "1.5.6") + (version "1.5.7") (source (origin (method url-fetch) (uri (cran-uri "vroom" version)) (sha256 (base32 - "0b1lbi20gadwjwinw1v0az4g0y79vlcqfqyblphls601h3nnmn3p")))) + "1plz20x6s01gkkcac51lhx4r2s024pgh778ri7y25hkiiwacp1yh")))) (properties `((upstream-name . "vroom"))) (build-system r-build-system) (propagated-inputs @@ -29990,13 +30498,13 @@ reading and writing arbitrary protocol-buffer data in R.") (define-public r-opencpu (package (name "r-opencpu") - (version "2.2.5") + (version "2.2.6") (source (origin (method url-fetch) (uri (cran-uri "opencpu" version)) (sha256 - (base32 "1qlwx8iq30qfy2sh0v31pxg955bj4zs0r7v8yklbdwb3qw7kv30g")))) + (base32 "0cmjfhkbk4im3x8aas0q5pivlsxgqixf4f3jiindchki7g9nsw91")))) (properties `((upstream-name . "opencpu"))) (build-system r-build-system) (inputs @@ -30033,14 +30541,14 @@ Apache2.") (define-public r-exactextractr (package (name "r-exactextractr") - (version "0.7.1") + (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "exactextractr" version)) (sha256 (base32 - "1gc1p9pgazhblk8jgykxxjpblylbaq5r9hdlw3ilz5g45yjjwcnc")))) + "0n39dqgsfzybi9yvnpnfdyypl8c9fml80jq0wxssik2n47mvbcif")))) (properties `((upstream-name . "exactextractr"))) (build-system r-build-system) (inputs (list geos)) @@ -30059,14 +30567,14 @@ the @code{raster} package that is suitable for extracting raster values using (define-public r-stringfish (package (name "r-stringfish") - (version "0.15.4") + (version "0.15.5") (source (origin (method url-fetch) (uri (cran-uri "stringfish" version)) (sha256 (base32 - "1n67y9vgv8vb8qd091d1wm5sgbalcm2avh2fz0hd3mmglpkr83wf")))) + "0ac17wl0fcpmipbvhhg5nyccg055671fnlxvnjd5l3kilx313wlx")))) (properties `((upstream-name . "stringfish"))) (build-system r-build-system) (propagated-inputs @@ -30107,14 +30615,14 @@ package.") (define-public r-qs (package (name "r-qs") - (version "0.25.1.1") + (version "0.25.2") (source (origin (method url-fetch) (uri (cran-uri "qs" version)) (sha256 (base32 - "077i181vh0izvsdy2d4366yir0ajg531g6d1s7ab044ssbphg38x")))) + "1gswppmw8rhd7h50hffhss4c4niz0x54r9sc8pgqzy26vkjqlhpy")))) (properties `((upstream-name . "qs"))) (build-system r-build-system) (inputs (list zlib)) @@ -30132,14 +30640,14 @@ object to and from disk.") (define-public r-rgeos (package (name "r-rgeos") - (version "0.5-8") + (version "0.5-9") (source (origin (method url-fetch) (uri (cran-uri "rgeos" version)) (sha256 (base32 - "05539shf38slvq38pf92h9q57vmzn2vfqbirl3pbbvvc2j957cqd")))) + "1m73y0nwrdwsjrl48c4fg1kdqnh79835brnmxv9ak01ndbzcp45b")))) (properties `((upstream-name . "rgeos"))) (build-system r-build-system) (inputs @@ -30516,14 +31024,14 @@ fully reproducible.") (define-public r-paws-common (package (name "r-paws-common") - (version "0.3.14") + (version "0.3.15") (source (origin (method url-fetch) (uri (cran-uri "paws.common" version)) (sha256 (base32 - "013yiki3bjx0np577wy17ikfxdr2hiv6sd10anv281r108kldm1x")))) + "0kj5b4253j4rljkj0ibh21kh9r1yq9idz9vf1f4ag775ivsc2dk5")))) (properties `((upstream-name . "paws.common"))) (build-system r-build-system) (propagated-inputs @@ -31514,17 +32022,38 @@ data. This package provides functions that query the BIEN database by constructing and executing optimized SQL queries.") (license license:expat))) +(define-public r-varhandle + (package + (name "r-varhandle") + (version "2.0.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "varhandle" version)) + (sha256 + (base32 "1l42d0s6fbjjc9l28a2m3myxkrx2c0p0b9yj8wjjjgilw19yc3lv")))) + (properties `((upstream-name . "varhandle"))) + (build-system r-build-system) + (home-page "https://bitbucket.org/mehrad_mahmoudian/varhandle") + (synopsis "Functions for robust variable handling") + (description + "This package contains some functions to help users (especially data +explorers) to make more sense of their variables and take the most out of +variables and hardware resources. Functions in this package are supposed to +be efficient and easy to use.") + (license license:gpl2+))) + (define-public r-ggh4x (package (name "r-ggh4x") - (version "0.2.0") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "ggh4x" version)) (sha256 (base32 - "0gv9ckkdqbcjknzsv8h3955wnikawdfypr279v74hvwyq86af29r")))) + "1r49yfm5fqv5s7jb92ad6rf8hd9plcry6f500czjhnhhrp16cqfp")))) (properties `((upstream-name . "ggh4x"))) (build-system r-build-system) (propagated-inputs |