diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 637 |
1 files changed, 538 insertions, 99 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index cd586eab80..2db969f28f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -35,7 +35,8 @@ ;;; 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> -;;; Copyright © 2022 Navid Afkhami <navid.afkhami@mdc-berlin.de> +;;; Copyright © 2022 Navid Afkhami <navid.afkhami@mdc-berlin.de> +;;; Copyright © 2022 Greg Hogan <code@greghogan.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -1004,6 +1005,61 @@ variables.") ") (license license:gpl2+))) +(define-public r-ggprism + (package + (name "r-ggprism") + (version "1.0.3") + (source (origin + (method url-fetch) + (uri (cran-uri "ggprism" version)) + (sha256 + (base32 + "09dh0r8r5s61i5dbk6rswajc2vm7k8wvlqyvzq8wr160676lycjp")))) + (properties `((upstream-name . "ggprism"))) + (build-system r-build-system) + (propagated-inputs + (list r-digest + r-ggplot2 + r-glue + r-gtable + r-rlang + r-scales + r-tibble)) + (native-inputs (list r-knitr)) + (home-page "https://csdaw.github.io/ggprism/") + (synopsis "ggplot2 extension inspired by GraphPad Prism") + (description + "This package provides various themes, palettes, and other functions that are +used to customise ggplots to look like they were made in GraphPad Prism. The +Prism-look is achieved with @code{theme_prism()} and +@code{scale_fill|colour_prism()}, axes can be changed with custom guides like +@code{guide_prism_minor()}, and significance indicators added with +@code{add_pvalue()}.") + (license license:gpl3+))) + +(define-public r-ggrastr + (package + (name "r-ggrastr") + (version "1.0.1") + (source (origin + (method url-fetch) + (uri (cran-uri "ggrastr" version)) + (sha256 + (base32 + "07sx5wlawfyb0zy5am2q1ajhkdym5r9ih47p57l8bv4dlc7ykml2")))) + (properties `((upstream-name . "ggrastr"))) + (build-system r-build-system) + (propagated-inputs (list r-cairo r-ggbeeswarm r-ggplot2 r-png r-ragg)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/VPetukhov/ggrastr") + (synopsis "Rasterize layers for ggplot2") + (description + "Rasterize only specific layers of a ggplot2 plot while simultaneously keeping +all labels and text in vector format. This allows users to keep plots within +the reasonable size limit without losing vector properties of the +scale-sensitive information.") + (license license:expat))) + (define-public r-lmds (package (name "r-lmds") @@ -1051,13 +1107,13 @@ axis} (SMA), and @dfn{ranged major axis} (RMA).") (define-public r-ggpmisc (package (name "r-ggpmisc") - (version "0.4.6") + (version "0.4.7") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 - "1iq39rx4nj1lf37hnj4df0c7gbk9374d0mzcnhdr7aqpxaxgs3ys")))) + "1z1ncnlbhy38ml2rdq43jbw33z7fmy0b6xp7wcwwqxy44c7y34zx")))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -1839,16 +1895,16 @@ such as copy/paste from an R session.") (define-public r-reordercluster (package (name "r-reordercluster") - (version "1.0") + (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "ReorderCluster" version)) (sha256 (base32 - "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58")))) + "0zq143xvv2br7016f9b1501ymcpkjqm3al1dn5qfm21axyi2p1iq")))) (build-system r-build-system) (propagated-inputs - (list r-gplots r-rcpp)) + (list r-gplots r-gtools r-rcpp)) (home-page "https://cran.r-project.org/web/packages/ReorderCluster") (synopsis "Reordering the dendrogram according to the class labels") (description "This package provides tools for performing the leaf reordering @@ -2954,21 +3010,21 @@ Bootstrap themes, which are packaged for use with Shiny applications.") (uri "https://d3js.org/d3.v5.js") (sha256 (base32 - "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn")))) + "177ypw6mjrp2ch9lj6znibwacwrvm4ypjxflsxsnl2sigx5dcwic")))) ("d3.v6.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v6.js") (sha256 (base32 - "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9")))) + "13hick3glizzm442b9swlwz584rzwwvhpq9qvfbh3m5jay10wxw0")))) ("d3.v7.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v7.js") (sha256 (base32 - "0sd6vavxs8mx5xyb8xahlqghdiczqd284a7d5wravhqnrj0bw097")))))) + "1hif1phswlkkpvcf1hbqmfsxdb5s5gr5g2frcwbh0rh8g6nbkyqi")))))) (home-page "https://github.com/timelyportfolio/d3r") (synopsis "d3.js utilities for R") (description @@ -3643,6 +3699,28 @@ inspired by Python's Literal String Interpolation (PEP-0498) and Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.") (license license:expat))) +(define-public r-paletteer + (package + (name "r-paletteer") + (version "1.4.0") + (source (origin + (method url-fetch) + (uri (cran-uri "paletteer" version)) + (sha256 + (base32 + "1m0h1p0cbmmi0rk157qyrgcz57pw0syadskrnfa4vs7hm1rndp3m")))) + (properties `((upstream-name . "paletteer"))) + (build-system r-build-system) + (propagated-inputs (list r-prismatic r-rematch2 r-rlang r-rstudioapi)) + (home-page "https://github.com/EmilHvitfeldt/paletteer") + (synopsis "Comprehensive collection of color palettes") + (description + "The choices of color palettes in R can be quite overwhelming with palettes +spread over many packages with many different API's. This package aims to +collect all color palettes across the R ecosystem under the same package with +a streamlined API.") + (license license:gpl3))) + (define-public r-palmerpenguins (package (name "r-palmerpenguins") @@ -3691,13 +3769,13 @@ initiative to bring PASSTEC 2000 functionalities to R.") (define-public r-partykit (package (name "r-partykit") - (version "1.2-15") + (version "1.2-16") (source (origin (method url-fetch) (uri (cran-uri "partykit" version)) (sha256 (base32 - "1b73s5l19yicwginqsg5xr7fzb005x372n0wb34kk6jb5x5lbsdj")))) + "1cnx6qbw5svwh3nq40n5vr20179ihd3jgznm7mz4k50qkkid8hz6")))) (build-system r-build-system) (propagated-inputs (list r-formula @@ -3771,13 +3849,13 @@ print, summary, plot, update, etc. (define-public r-ps (package (name "r-ps") - (version "1.7.0") + (version "1.7.1") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 - (base32 "1qaj9gyz7q09aadlnj5al53k2pa4axmzjsbndf5r0b51qqrcy842")))) + (base32 "1waylmbrl23j62010r12c8xwzlvs1dys3cnh7hnrgk27glvqlicw")))) (build-system r-build-system) (home-page "https://ps.r-lib.org") (synopsis "List, query, and manipulate system processes") @@ -3817,22 +3895,23 @@ is configured appropriately so R can use them.") (define-public r-pkgload (package (name "r-pkgload") - (version "1.2.4") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "pkgload" version)) (sha256 (base32 - "03yr9mswx9nij27bp21q6c533zx310xwzhwm52dwr7554k42p4fn")))) + "0a22kxgm9a8ax1dw2q9v3338qhjmhfbcqw8r4b6608k6074m7xjs")))) (build-system r-build-system) (propagated-inputs (list r-cli r-crayon r-desc + r-fs + r-glue r-rlang r-rprojroot - r-rstudioapi r-withr)) (home-page "https://github.com/r-lib/pkgload") (synopsis "Simulate package installation and attach") @@ -4327,6 +4406,26 @@ quantities.") curve to a data matrix in arbitrary dimensions.") (license license:gpl2))) +(define-public r-prismatic + (package + (name "r-prismatic") + (version "1.1.0") + (source (origin + (method url-fetch) + (uri (cran-uri "prismatic" version)) + (sha256 + (base32 + "1f6k11hcll33g2wbadjhm91pm5h4khg4zd8g9fzs3m9xlqpfaywh")))) + (properties `((upstream-name . "prismatic"))) + (build-system r-build-system) + (propagated-inputs (list r-farver)) + (home-page "https://github.com/EmilHvitfeldt/prismatic") + (synopsis "Color manipulation tools") + (description + "Manipulate and visualize colors in a intuitive, low-dependency and functional +way.") + (license license:expat))) + (define-public r-reshape (package (name "r-reshape") @@ -4717,13 +4816,13 @@ tools for inference in parametric models are provided.") (define-public r-idr (package (name "r-idr") - (version "1.2") + (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "idr" version)) (sha256 (base32 - "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb")))) + "1r6icxf0c0y9wvihwmkk5xqscr1qhacqk3w2076kjm2993f10fbb")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/idr/") (synopsis "Irreproducible discovery rate") @@ -5507,14 +5606,14 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "0.8.0") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "16grzja9hz5mqpfzbp1r6zif1gp7swfadkm52340si9h8ifhk8b6")))) + "04hlwiqkj7c9cf357dgjfgg5a6mpicg6vzvwwcqjkq69nzbsr18n")))) (build-system r-build-system) (propagated-inputs (list r-backports @@ -6408,13 +6507,13 @@ constants, and control debugging of packages via environment variables.") (define-public r-processx (package (name "r-processx") - (version "3.6.0") + (version "3.6.1") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 - (base32 "0kx6hvkkj6lh8lrdh819hvkx8nyq5aac53mkvpqyskwkmmlnf63m")))) + (base32 "1xgjj37s304vdwp2a02rl999xl6dw7iw0ib9jyfpjrqyc1lmfw47")))) (build-system r-build-system) (propagated-inputs (list r-ps r-r6)) @@ -6454,14 +6553,14 @@ traveling salesman problem).") (define-public r-qap (package (name "r-qap") - (version "0.1-1") + (version "0.1-2") (source (origin (method url-fetch) (uri (cran-uri "qap" version)) (sha256 (base32 - "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0")))) + "19adb1bw46pcnmmhqz2jklr0vmma3llxajqp0j9mqfksmsisv927")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/qap/") @@ -6743,14 +6842,14 @@ packages that work with genomic data.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.39") + (version "0.40") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "1v95pjxdq0ma90jji5yqh8ihlcf35cmrqx9v0z649zh0q9vrnbpj")))) + "13fqhg0yrzc28b39hpr4jip9w0q9yzhzxrczlf0q2yh45kdplpiz")))) (build-system r-build-system) (propagated-inputs (list r-xfun)) @@ -7236,6 +7335,25 @@ provides some missing S-PLUS functionality in R.") (base32 "16a7rbvlym3bnfm93ikr5kl0l86ppk0s41fva6idvcx765g3fqkk")))) (build-system r-build-system) + (arguments + (list + #:phases + `(modify-phases %standard-phases + (add-after 'unpack 'compatibility + (lambda _ + ;; These definitions are no longer part of R since 4.2.0. See + ;; https://cran.r-project.org/doc/manuals/r-devel/NEWS.html for + ;; details. + (substitute* "inst/include/ut_RS.h" + (("#include \"R.h\"" m) + (string-append "\ +#define R_PROBLEM_BUFSIZE 4096 +#define PROBLEM {char R_problem_buf[R_PROBLEM_BUFSIZE];(sprintf)(R_problem_buf, +#define MESSAGE {char R_problem_buf[R_PROBLEM_BUFSIZE];(sprintf)(R_problem_buf, +#define ERROR ),error(R_problem_buf);} +#define WARNING(x) ),warning(R_problem_buf);} +#define WARN WARNING(NULL) +" m)))))))) (propagated-inputs (list r-mass r-splus2r)) (home-page "https://cran.r-project.org/web/packages/ifultools/") @@ -9499,13 +9617,13 @@ patterned after functions in the snow package.") (define-public r-itsadug (package (name "r-itsadug") - (version "2.4") + (version "2.4.1") (source (origin (method url-fetch) (uri (cran-uri "itsadug" version)) (sha256 - (base32 "0759l7hhvj05dp92pz59xwrxjm9s1iwkwrdhs68l0fq57550j70l")))) + (base32 "1sdqs279qxr3993hw08xg7b54yq03jw1597cqn6cf24sh9vpw9m1")))) (properties `((upstream-name . "itsadug"))) (build-system r-build-system) (propagated-inputs (list r-mgcv r-plotfunctions)) @@ -11132,14 +11250,14 @@ used to teach mathematics, statistics, computation and modeling.") (define-public r-raster (package (name "r-raster") - (version "3.5-15") + (version "3.5-21") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 - "11fnznymwavpph733dayklhcx4phpjgrijfxlaszi122sg2x7ir9")))) + "1alny43aw5ydlwc7157bf524r0dxp74bf5d0nkvm8qnni57z9bci")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-sp r-terra)) @@ -12082,14 +12200,29 @@ observation.") (define-public r-sandwich (package (name "r-sandwich") - (version "3.0-1") + (version "3.0-2") (source (origin (method url-fetch) (uri (cran-uri "sandwich" version)) (sha256 (base32 - "12aa5083k3sfrfq1jy3l94wffss9h0rga8j71jy3n8pkhiq4nn7n")))) + "1d72vwxidsyac9mbyxrm06qds63rzcr82nn4c05466gbajsvcc3f")) + (modules '((guix build utils))) + (snippet + '(with-directory-excursion "inst/doc" + ;; These files are generated from Rnw files. + (for-each delete-file + (list "sandwich-OOP.pdf" + "sandwich-OOP.R" + "sandwich-OOP.Rnw" + "sandwich-CL.R" + "sandwich-CL.Rnw" + "sandwich-CL.pdf" + "sim-CL.rda" + "sim-CL.R" + "sandwich.pdf" + "sandwich.R")))))) (build-system r-build-system) (propagated-inputs (list r-zoo)) @@ -12173,14 +12306,14 @@ the differences were not significantly different.") (define-public r-emmeans (package (name "r-emmeans") - (version "1.7.4-1") + (version "1.7.5") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "08g7ifqhwqa00hc850nwx03dp7isz0281ig6kvixc4xdahmkm8zp")))) + "04zy4fb5v3l5zi74bgch8l7mzf2zg16w303k6kp7hwqjlfzh6zms")))) (build-system r-build-system) (propagated-inputs (list r-estimability r-mvtnorm r-numderiv r-xtable)) @@ -12432,14 +12565,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.9.0") + (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "1znr4i1pjv6z3lj6qrma2i3l94rz1z29w92mrxxfy3ch0s71crww")))) + "0xiqy9z070v5xzf2iq4x01licabhkygji5x6qfy7l08n43z4agny")))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-datawizard r-insight)) @@ -13768,13 +13901,13 @@ Anderson-Darling Distribution\".") (define-public r-admisc (package (name "r-admisc") - (version "0.28") + (version "0.29") (source (origin (method url-fetch) (uri (cran-uri "admisc" version)) (sha256 - (base32 "0cfx4g64mybd69xm595zzv79j4fbzn7vihpvzcvicggs3immppha")))) + (base32 "02vl2k58ijqd30d7y01x0ap2b2vh1is3xg14g3cpvm5gflyxyinf")))) (properties `((upstream-name . "admisc"))) (build-system r-build-system) (home-page "https://github.com/dusadrian/admisc") @@ -13939,14 +14072,14 @@ Processing.") (define-public r-waveslim (package (name "r-waveslim") - (version "1.8.2") + (version "1.8.3") (source (origin (method url-fetch) (uri (cran-uri "waveslim" version)) (sha256 (base32 - "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k")))) + "0yxkwgdq1xqh027l2akwb4zji4li3sgpmyxlmfq1rhz15kjxr2wq")))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -14755,14 +14888,14 @@ decomposition is shared between datasets.") (define-public r-strucchange (package (name "r-strucchange") - (version "1.5-2") + (version "1.5-3") (source (origin (method url-fetch) (uri (cran-uri "strucchange" version)) (sha256 (base32 - "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x")))) + "11hgz64snlwhfqsmqajmkciflwkz1wficxr340wqvk38iw1b9ina")))) (build-system r-build-system) (propagated-inputs (list r-sandwich r-zoo)) @@ -15724,14 +15857,14 @@ model with finite state space using the Aalen-Johansen estimator.") (define-public r-epi (package (name "r-epi") - (version "2.46") + (version "2.47") (source (origin (method url-fetch) (uri (cran-uri "Epi" version)) (sha256 (base32 - "0s3ij0rya4wd7k97kc4s3pwj1d1ypaxl1s7zqr6sa07hp4a8fzz0")))) + "1dkdx000cvy2rgxq3w6ppl3j9h7mwmcqg5xqsqh5hr3aks845pwx")))) (properties `((upstream-name . "Epi"))) (build-system r-build-system) (propagated-inputs @@ -15881,14 +16014,14 @@ subsetting.") (define-public r-globals (package (name "r-globals") - (version "0.15.0") + (version "0.15.1") (source (origin (method url-fetch) (uri (cran-uri "globals" version)) (sha256 (base32 - "15llx4233ihj4w815k7inc17530w9ja0mi29n1i0s2sr42j8jdpq")))) + "0svsssf8swzsihng6c8wpmn33lxaj4f5xq975ywlr950svmjfz7f")))) (build-system r-build-system) (propagated-inputs (list r-codetools)) @@ -17163,17 +17296,17 @@ customizable sets, and intervals.") (define-public r-partitions (package (name "r-partitions") - (version "1.9-22") + (version "1.10-4") (source (origin (method url-fetch) (uri (cran-uri "partitions" version)) (sha256 (base32 - "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns")))) + "1ik7cj2yfybx4v847nvnjrbkd0k66pfqqv6lkygfnlrldi0r205i")))) (build-system r-build-system) (propagated-inputs - (list r-gmp r-polynom r-sets)) + (list r-gmp r-mathjaxr r-polynom r-sets)) (home-page "https://cran.r-project.org/web/packages/partitions") (synopsis "Additive partitions of integers") (description @@ -18002,13 +18135,13 @@ SELECT or UPDATE queries to an end-point.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.26") + (version "0.27") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "11din9h2sgzvg44627xc5is4psbq2b34km5sbiaprskjrf474866")))) + "08wzi7hh3x1dfpmzpxhphrv5zb6a3p7rziaazisfpp1zwsxllwif")))) (build-system r-build-system) (propagated-inputs (list r-htmltools @@ -18474,14 +18607,14 @@ package.") (define-public r-yulab-utils (package (name "r-yulab-utils") - (version "0.0.4") + (version "0.0.5") (source (origin (method url-fetch) (uri (cran-uri "yulab.utils" version)) (sha256 (base32 - "1bj93gnj7j4b7dgkbr5v22rsbwfcw5dvipl5irmidaakvrihd19q")))) + "0sq5wc0mp84h6fs4wa2smvf7dcn0p0xarzb2ljvqc3p4vb2lvkbf")))) (properties `((upstream-name . "yulab.utils"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=yulab.utils") @@ -18809,7 +18942,7 @@ microarrays.") (uri (cran-uri "rda" version)) (sha256 (base32 - "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639")))) + "17ll0idnms4bcpbl65xnl8zfnwsk9ww0rg5z8qqh4ahk5qdab8zf")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rda/") (synopsis "Shrunken centroids regularized discriminant analysis") @@ -19654,29 +19787,29 @@ provides tools to compute this metric.") (define-public r-lintr (package (name "r-lintr") - (version "2.0.1") + (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "lintr" version)) (sha256 (base32 - "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy")))) + "1d3pn6aarmpqyyzb2vawwcamrgrdvyqfdijk0ixp44c3fhld9cgf")))) (properties `((upstream-name . "lintr"))) (build-system r-build-system) (propagated-inputs - (list r-codetools + (list r-backports + r-codetools r-crayon r-cyclocomp r-digest - r-httr + r-glue r-jsonlite r-knitr r-rex - r-rstudioapi - r-testthat r-xml2 r-xmlparsedata)) + (native-inputs (list r-knitr)) (home-page "https://github.com/jimhester/lintr") (synopsis "Linter for R code") (description "This package checks adherence to a given style, syntax @@ -20041,14 +20174,14 @@ been used in the call to @code{aov}.") (define-public r-dalex (package (name "r-dalex") - (version "2.4.1") + (version "2.4.2") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 - "0mcdd2bd8zlsz7x174g87dp8vy4wc06w58dyr27f6lgv9shzya8j")))) + "1m19ibv8rpghqm4vr8nrvarrjkm9rxw6jx8xl3hzrqnnmf2xifqr")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs @@ -22379,14 +22512,14 @@ identify file sets and individual files.") (define-public r-r-devices (package (name "r-r-devices") - (version "2.17.0") + (version "2.17.1") (source (origin (method url-fetch) (uri (cran-uri "R.devices" version)) (sha256 (base32 - "1djz6vm1b7sjvx1q319dl47gbnz9kvipaxcz9i0spyp094lv3m62")))) + "02cwdhb9m97gxi4pki4kasc5j3a12r7yzsychzzk9h0ijc1mfziv")))) (properties `((upstream-name . "R.devices"))) (build-system r-build-system) (propagated-inputs @@ -23094,14 +23227,14 @@ variable observed over time.") (define-public r-fda (package (name "r-fda") - (version "6.0.3") + (version "6.0.4") (source (origin (method url-fetch) (uri (cran-uri "fda" version)) (sha256 (base32 - "1lvp4i4hqz650k27sa5flbdlkalihc79xy9128hfhr16h6wi8n10")))) + "0r2a1rsg904gz6vwcw5jrji7a7pspkfcxmnl9dswpglkn2dsans2")))) (properties `((upstream-name . "fda"))) (build-system r-build-system) (propagated-inputs @@ -23648,17 +23781,18 @@ also supports low-level tensor operations and GPU acceleration.") (define-public r-additivitytests (package (name "r-additivitytests") - (version "1.1-4") + (version "1.1-4.1") (source (origin (method url-fetch) (uri (cran-uri "additivityTests" version)) (sha256 (base32 - "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw")))) + "00kzfv86z6kk0gvbz9mg3p6xi5fb8cn74rhslr17rdpd02md0884")))) (properties `((upstream-name . "additivityTests"))) (build-system r-build-system) + (native-inputs (list r-knitr)) (home-page "https://github.com/simecek/additivityTests") (synopsis "Additivity tests in the two way Anova with single sub-class numbers") (description @@ -23940,6 +24074,35 @@ spectroscopy and analyses of environmental data: robust baseline fitting, finding peaks in spectra, converting humidity measures.") (license license:gpl3+))) +(define-public r-qqconf + (package + (name "r-qqconf") + (version "1.2.3") + (source (origin + (method url-fetch) + (uri (cran-uri "qqconf" version)) + (sha256 + (base32 + "0qnfzq2zb776kmvbwmyj9di4nlzx7dg0nz4097hfcllfx9160nwv")))) + (properties `((upstream-name . "qqconf"))) + (build-system r-build-system) + (inputs (list fftw)) + (propagated-inputs + (list r-dplyr + r-magrittr + r-mass + r-rcpp + r-rlang + r-robustbase)) + (native-inputs (list pkg-config r-knitr)) + (home-page "https://github.com/eweine/qqconf") + (synopsis "Create simultaneous testing bands for QQ-plots") + (description + "This package provides functionality for creating Quantile-Quantile (QQ) and +Probability-Probability (PP) plots with simultaneous testing bands to asses +significance of sample deviation from a reference distribution.") + (license license:gpl3))) + (define-public r-qqman (package (name "r-qqman") @@ -25444,14 +25607,14 @@ interesting features. iheatmapr uses the plotly library for interactivity.") (define-public r-packrat (package (name "r-packrat") - (version "0.8.0") + (version "0.8.1") (source (origin (method url-fetch) (uri (cran-uri "packrat" version)) (sha256 (base32 - "1vs4i19x6jdwl3jnanp127k4hk80h1mj56cjn07w1gkl542vj99h")))) + "1ni3xn51xifdb2bya5z54jn4nxgss6f23b3hn126j2kaz80h7ns5")))) (properties `((upstream-name . "packrat"))) (build-system r-build-system) (home-page "https://github.com/rstudio/packrat/") @@ -27001,14 +27164,14 @@ counting and recursive k-means partitioning.") (define-public r-hardhat (package (name "r-hardhat") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "hardhat" version)) (sha256 (base32 - "1cdl52lzv3wffq8fzrb6sk85i4i8lm8skgad1c8az3ifmzssjx03")))) + "0y5dxpd4gsrs365x1v4qf2vq7hq2qb6f6x50dyj29xmmn760wcpr")))) (properties `((upstream-name . "hardhat"))) (build-system r-build-system) (propagated-inputs @@ -27957,14 +28120,14 @@ censored data.") (define-public r-flexsurv (package (name "r-flexsurv") - (version "2.1") + (version "2.2") (source (origin (method url-fetch) (uri (cran-uri "flexsurv" version)) (sha256 (base32 - "0kwij9nkdvnsn1kn12fj3hjkd2qpgw7bdda4qad7basq5p6divlp")))) + "0244amsyf2izih6008n2535r3ddksgdnys8pyslrcb1c09spmjrw")))) (properties `((upstream-name . "flexsurv"))) (build-system r-build-system) (propagated-inputs @@ -27972,6 +28135,7 @@ censored data.") r-desolve r-dplyr r-generics + r-ggplot2 r-magrittr r-matrix r-mstate @@ -27983,6 +28147,7 @@ censored data.") r-rcpp r-rlang r-rstpm2 + r-statmod r-survival r-tibble r-tidyr @@ -28317,14 +28482,14 @@ model.") (define-public r-igraph (package (name "r-igraph") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "igraph" version)) (sha256 (base32 - "0khl87ncc9hkvx4f1kyzv7w7bg9zbyd1rk20ja3azkhpqjkjnnjh")))) + "0863gr9k7rvjrm7gz4l35q827jh8802m1q6f51ficgi21qc6cl0g")))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -28389,18 +28554,21 @@ workflow. The advantages are: (define-public r-lobstr (package (name "r-lobstr") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "lobstr" version)) (sha256 (base32 - "0vkif17825x33cz8r89j0qph4wj5l8fzfgl8nh2g7m2v140cxjdq")))) + "060p7b7i2qx09d7nf0kdl85r9j886fivrkrsl2bn10cggvnk7icv")))) (properties `((upstream-name . "lobstr"))) (build-system r-build-system) (propagated-inputs - (list r-crayon r-rcpp r-rlang)) + (list r-cpp11 + r-crayon + r-prettyunits + r-rlang)) (home-page "https://github.com/r-lib/lobstr") (synopsis "Visualize R data structures with trees") (description @@ -28562,14 +28730,14 @@ pipeline friendly so that data processing with lists can be chained.") (define-public r-rsample (package (name "r-rsample") - (version "0.1.1") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "rsample" version)) (sha256 (base32 - "01xwhj4zfvxbv9cjb6mbz3aphxqc3cnjjx1xy2yx2wd94fbka42z")))) + "0n3pzjxdb6s0cbpalhi1sjba6ifrvjjb448dczvryrqjk7pqvby5")))) (properties `((upstream-name . "rsample"))) (build-system r-build-system) (propagated-inputs @@ -28577,7 +28745,8 @@ pipeline friendly so that data processing with lists can be chained.") r-ellipsis r-furrr r-generics - r-lifecycle + r-glue + r-pillar r-purrr r-rlang r-slider @@ -28617,14 +28786,14 @@ Design} (SFD) and to test their quality.") (define-public r-dials (package (name "r-dials") - (version "0.1.1") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "dials" version)) (sha256 (base32 - "1h695g9vklqn0vd53j9k03s0989xjpjr11h5qhz3a0v6465fwm8a")))) + "0flpd7bxknsscv0gk6c7zz1aid9y3z6sibkvjp9zcyc5wnqldrvj")))) (properties `((upstream-name . "dials"))) (build-system r-build-system) (propagated-inputs @@ -28633,6 +28802,7 @@ Design} (SFD) and to test their quality.") r-glue r-hardhat r-lifecycle + r-pillar r-purrr r-rlang r-scales @@ -28737,14 +28907,14 @@ results.") (define-public r-tidyposterior (package (name "r-tidyposterior") - (version "0.1.0") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "tidyposterior" version)) (sha256 (base32 - "1h1664sjrg6akph6nrk8ynn2kjiswv6gshy35gamam1h4axf6wah")))) + "19cyyhh417i5xcchb8kq3iycaf4y7aznr7y9r004h2k2vk3svc86")))) (properties `((upstream-name . "tidyposterior"))) (build-system r-build-system) (propagated-inputs @@ -28829,6 +28999,46 @@ novels, ready for text analysis. These novels are \"Sense and Sensibility\", and \"Persuasion\".") (license license:expat))) +(define-public r-janitor + (package + (name "r-janitor") + (version "2.1.0") + (source (origin + (method url-fetch) + (uri (cran-uri "janitor" version)) + (sha256 + (base32 + "09nqm957m2f54y2l30619b58x4i7gxwvr2lwg5kly5xy1ya1a1nn")))) + (properties `((upstream-name . "janitor"))) + (build-system r-build-system) + (propagated-inputs + (list r-dplyr + r-lifecycle + r-lubridate + r-magrittr + r-purrr + r-rlang + r-snakecase + r-stringi + r-stringr + r-tidyr + r-tidyselect)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/sfirke/janitor") + (synopsis "Simple tools for examining and cleaning dirty data") + (description + "The main janitor functions can: perfectly format @code{data.frame column} +names; provide quick counts of variable combinations (i.e., frequency tables +and crosstabs); and isolate duplicate records. Other janitor functions nicely +format the tabulation results. These tabulate-and-report functions +approximate popular features of SPSS and Excel. This package follows the +principles of the \"tidyverse\" and works well with the pipe function +@code{%>%}. janitor was built with beginning-to-intermediate R users in mind +and is optimized for user-friendliness. Advanced R users can already do +everything covered here, but with janitor they can do it faster and save their +thinking for the fun stuff.") + (license license:expat))) + (define-public r-tokenizers (package (name "r-tokenizers") @@ -28931,14 +29141,14 @@ analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.") (define-public r-parsnip (package (name "r-parsnip") - (version "0.2.1") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "parsnip" version)) (sha256 (base32 - "195i4j38mljv9193yx8lmh65h85yhc52y9vc1mk8zvxi52ks1yln")))) + "0lwz95ff69arbl2mpmnkwjf24cgb866nr3frkb89va91gp1w9691")))) (properties `((upstream-name . "parsnip"))) (build-system r-build-system) (propagated-inputs @@ -28951,6 +29161,7 @@ analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.") r-hardhat r-lifecycle r-magrittr + r-pillar r-prettyunits r-purrr r-rlang @@ -29149,18 +29360,18 @@ package also provides functions to visualize the observed data and the MLE.") (define-public r-metafor (package (name "r-metafor") - (version "2.4-0") + (version "3.4-0") (source (origin (method url-fetch) (uri (cran-uri "metafor" version)) (sha256 (base32 - "1b599fxk7s0brkchmx698fr5k4g1kzkia2rnlvhg349ffs5nfjmn")))) + "0vn244xfgq7yxwl6ykvadb305z360ssc9vzva7kbcdfiqhhvrqcj")))) (properties `((upstream-name . "metafor"))) (build-system r-build-system) (propagated-inputs - (list r-matrix r-nlme)) + (list r-mathjaxr r-matrix r-metadat r-nlme r-pbapply)) (home-page "https://cran.r-project.org/web/packages/metafor/") (synopsis "Meta-analysis package for R") (description @@ -29543,18 +29754,19 @@ distributed as independent packages.") (define-public r-phangorn (package (name "r-phangorn") - (version "2.8.1") + (version "2.9.0") (source (origin (method url-fetch) (uri (cran-uri "phangorn" version)) (sha256 (base32 - "0xfwi7adl1pcfcwk72fj7lkwfm0wiip96ij7m4252xr9mq818ivd")))) + "08ys4vgmsp070v3119wzl1nrgx359427gb6lcxj67p5y0bhdnqij")))) (build-system r-build-system) (propagated-inputs (list r-ape r-fastmatch + r-generics r-igraph r-matrix r-quadprog @@ -30293,14 +30505,14 @@ chunks.") (define-public r-clustree (package (name "r-clustree") - (version "0.4.4") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "clustree" version)) (sha256 (base32 - "0vwmicajl7c0rmjdmf4f857fii0xrxz25vjkn888svlsikw00qbs")))) + "1haam13aifak8fladyxwa0gz56anj1zfczfjgs07gbw90kf6azx8")))) (properties `((upstream-name . "clustree"))) (build-system r-build-system) (propagated-inputs @@ -30384,14 +30596,14 @@ AGG to use as alternative to the raster devices provided through the (define-public r-downlit (package (name "r-downlit") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "downlit" version)) (sha256 (base32 - "10zvrqdpwavdy97h3q26bqh3k63z61fmc04w9vwsnvmnv8hnh3vl")))) + "1h9jjrrfm1k4lz7hlg9qvqny5s1qq3p4l9pzsy6vqg4zmh2nb85v")))) (properties `((upstream-name . "downlit"))) (build-system r-build-system) (propagated-inputs @@ -30403,6 +30615,7 @@ AGG to use as alternative to the raster devices provided through the r-memoise r-rlang r-vctrs + r-withr r-yaml)) (home-page "https://downlit.r-lib.org/") (synopsis "Syntax highlighting and automatic linking") @@ -30417,14 +30630,14 @@ in output to the equivalent HTML.") (define-public r-pkgdown (package (name "r-pkgdown") - (version "2.0.4") + (version "2.0.5") (source (origin (method url-fetch) (uri (cran-uri "pkgdown" version)) (sha256 (base32 - "02lwr53xvxybcsg8md8qbq1wq833ap7ssn5v92cd4qqay5iya374")))) + "1bk10jh01v4yqzmpvhs2iw9hwwj0nldskbm2942hjx3xf08y1q4i")))) (properties `((upstream-name . "pkgdown"))) (build-system r-build-system) (inputs (list pandoc)) @@ -33438,3 +33651,229 @@ jitterplot, or half violinplot and half dotplot.") coefficients or scattering amplitudes, for seismological P and S-waves at an interface.") (license license:gpl2+))) + +(define-public r-metadat + (package + (name "r-metadat") + (version "1.2-0") + (source (origin + (method url-fetch) + (uri (cran-uri "metadat" version)) + (sha256 + (base32 + "1f7mb3pw5d0akr09jjva06ay223izhpzbr21bapnw99x1kiybk7h")))) + (properties `((upstream-name . "metadat"))) + (build-system r-build-system) + (propagated-inputs (list r-mathjaxr)) + (home-page "https://github.com/wviechtb/metadat") + (synopsis "Meta-Analysis Datasets") + (description + "This package provides a collection of meta-analysis datasets for teaching +purposes, illustrating/testing meta-analytic methods, and validating published +analyses.") + (license license:gpl2+))) + +(define-public r-mathjaxr + (package + (name "r-mathjaxr") + (version "1.6-0") + (source (origin + (method url-fetch) + (uri (cran-uri "mathjaxr" version)) + (sha256 + (base32 + "0yf1sfkb2kjsplipl2v4k2gp20li9xzsynclg228sy0v243pdi7c")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "src/mathjax/es5/input") + (delete-file-recursively "src/mathjax/es5/output") + (delete-file "src/mathjax/es5/tex-chtml-full.js"))))) + (properties `((upstream-name . "mathjaxr"))) + (build-system r-build-system) + (arguments + (list + #:phases + `(modify-phases %standard-phases + (add-after 'unpack 'use-js-mathjax + (lambda* (#:key inputs #:allow-other-keys) + (symlink + (search-input-directory + inputs "/share/javascript/mathjax/es5/output") + "src/mathjax/es5/output") + (symlink + (search-input-directory + inputs "/share/javascript/mathjax/es5/input") + "src/mathjax/es5/input") + (symlink + (search-input-file + inputs "/share/javascript/mathjax/es5/tex-chtml-full.js") + "src/mathjax/es5/tex-chtml-full.js")))))) + (inputs + (list js-mathjax-for-r-mathjaxr)) + (home-page "https://github.com/wviechtb/mathjaxr") + (synopsis "Use Mathjax in Rd Files") + (description + "This package provides MathJax and macros to enable its use within Rd files +for rendering equations in the HTML help files.") + (license (list license:asl2.0 license:gpl3)))) + +(define-public r-spacetime + (package + (name "r-spacetime") + (version "1.2-8") + (source (origin + (method url-fetch) + (uri (cran-uri "spacetime" version)) + (sha256 + (base32 + "0nacy8a9mbxh22q248zxhnlcfrmgj9yslrgc3kj35zscmcks15s2")))) + (properties `((upstream-name . "spacetime"))) + (build-system r-build-system) + (propagated-inputs (list r-lattice r-sp r-zoo r-xts r-intervals)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/edzer/spacetime/") + (synopsis "Classes and methods for spatio-temporal data") + (description + "@command{spacetime} provides classes and methods for spatio-temporal +data, including space-time regular lattices, sparse lattices, irregular data, +and trajectories; utility functions for plotting data as map sequences (lattice +or animation) or multiple time series; methods for spatial and temporal +matching or aggregation, retrieving coordinates, print, summary, etc.") + (license license:gpl2+))) + +(define-public r-gstat + (package + (name "r-gstat") + (version "2.0-9") + (source (origin + (method url-fetch) + (uri (cran-uri "gstat" version)) + (sha256 + (base32 + "19m4zcj1qvg6gs8yjr5ijvd6rrv4av5yp5rmhnb88f0m5qn06b0j")))) + (properties `((upstream-name . "gstat"))) + (build-system r-build-system) + (propagated-inputs (list r-lattice r-sp r-zoo r-spacetime r-fnn)) + (home-page "https://github.com/r-spatial/gstat/") + (synopsis "Spatial and spatio-temporal geostatistical modelling, +prediction and simulation") + (description + "This package enables variogram modelling, including: simple, ordinary and +universal point or block (co)kriging; spatio-temporal kriging; and sequential +Gaussian or indicator (co)simulation. It includes variogram and variogram map +plotting utility functions, and supports @command{sf} and @command{stars}.") + (license license:gpl2+))) + +(define-public r-automap + (package + (name "r-automap") + (version "1.0-16") + (source (origin + (method url-fetch) + (uri (cran-uri "automap" version)) + (sha256 + (base32 + "0jz0p28gmx9cpzv4cz0xhbml3w1inf2nsd2ynbhmfxg5rm2f7dca")))) + (properties `((upstream-name . "automap"))) + (build-system r-build-system) + (propagated-inputs (list r-ggplot2 + r-gstat + r-lattice + r-maptools + r-reshape + r-sp)) + (home-page "https://cran.r-project.org/package=automap") + (synopsis "Automatic interpolation package") + (description + "@command{automap} performs an automatic interpolation by automatically +estimating the variogram and then calling @command{gstat}.") + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-cartogram + (package + (name "r-cartogram") + (version "0.2.2") + (source (origin + (method url-fetch) + (uri (cran-uri "cartogram" version)) + (sha256 + (base32 + "0kz8hwdr5n8llkylwaixnb66f4pzaxxniz57spxhqizmi6qay7yd")))) + (properties `((upstream-name . "cartogram"))) + (build-system r-build-system) + (propagated-inputs (list r-packcircles r-sf)) + (home-page "https://github.com/sjewo/cartogram/") + (synopsis "Create cartograms with R") + (description "This package enables construction of continuous and +non-contiguous area cartograms.") + (license license:gpl3))) + +(define-public r-measurements + (package + (name "r-measurements") + (version "1.4.0") + (source (origin + (method url-fetch) + (uri (cran-uri "measurements" version)) + (sha256 + (base32 + "1kihavs9vgxwqjm9z1zjjngkmcwfsv8dg7nn9nrv5r06k5hv8bz6")))) + (properties `((upstream-name . "measurements"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/measurements/") + (synopsis "Tools for units of measurement") + (description + "This package provides a collection of tools to make working with physical +measurements easier. One can convert between metric and imperial units, or +calculate a dimension's unknown value from other dimensions' measurements.") + (license license:gpl3))) + +(define-public r-sungeo + (package + (name "r-sungeo") + (version "0.2.288") + (source (origin + (method url-fetch) + (uri (cran-uri "SUNGEO" version)) + (sha256 + (base32 + "0c8y0ngx1020rw2v00rxmq8syd72f41ckik5sg7gigg7d80gi31w")) + (modules '((guix build utils))) + (snippet '(begin + ;; Fortunately, the package does not actually use + ;; rmapshaper, which has got a js/node dependency. + ;; The only occurrence is in R/point2poly_tess.R, + ;; where it is commented out. + (substitute* "DESCRIPTION" + (("rmapshaper,") "")) + (substitute* "NAMESPACE" + (("importFrom\\(rmapshaper,ms_dissolve\\) +") "")) + #t)))) + (properties `((upstream-name . "SUNGEO"))) + (build-system r-build-system) + (propagated-inputs (list r-automap + r-cartogram + r-data-table + r-dplyr + r-fasterize + r-httr + r-jsonlite + r-measurements + r-packcircles + r-purrr + r-rann + r-raster + r-rcpp + r-rcurl + r-rlang + r-sf + r-sp + r-spdep)) + (home-page "https://github.com/zhukovyuri/SUNGEO/") + (synopsis "Sub-National Geospatial Data Archive: Geoprocessing Toolkit") + (description + "Tools for integrating spatially-misaligned GIS datasets. Part of the +Sub-National Geospatial Data Archive System.") + (license license:gpl2))) |