X-Git-Url: https://git.hcoop.net/jackhill/guix/guix.git/blobdiff_plain/181e3c01282f9260a5ff868d15369521bedb3583..213d7e76492cf19ebbdd41a740086a15e371102e:/gnu/packages/cran.scm diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 37a13b4c1a..e94f44707d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -33,6 +33,7 @@ ;;; Copyright © 2020 Magali Lemes ;;; Copyright © 2020 Simon Tournier ;;; Copyright © 2020 Aniket Patil +;;; Copyright © 2021 Tim Howes ;;; ;;; This file is part of GNU Guix. ;;; @@ -155,14 +156,14 @@ automatically pruning objects to maintain the constraints.") (define-public r-diffobj (package (name "r-diffobj") - (version "0.3.3") + (version "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "diffobj" version)) (sha256 (base32 - "1x3d5sk8mk0s2d7dq8wxi1zv6krlx33n22ls2jwnb58b8xrmakj1")))) + "1z4yhfasjpi9rxl1lh9bny7yvs947a6hhc768azc1wwad748mk9q")))) (properties `((upstream-name . "diffobj"))) (build-system r-build-system) (propagated-inputs `(("r-crayon" ,r-crayon))) @@ -343,13 +344,13 @@ the system clipboards.") (define-public r-zoo (package (name "r-zoo") - (version "1.8-8") + (version "1.8-9") (source (origin (method url-fetch) (uri (cran-uri "zoo" version)) (sha256 (base32 - "1rrw431jwaxd9xljp73f15rhcxvwc0xlyrmr0ghi5fj7a03c932f")))) + "18vjywalpgzqyk66gajb8x1yp8avdaaf11ykynld9fd8cy82bgmp")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -392,13 +393,13 @@ variables.") (define-public r-ggpmisc (package (name "r-ggpmisc") - (version "0.3.8-1") + (version "0.3.9") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 - "0kcrh73nwha52vl6z35wafmqs5lsdh2p4nqvi2ir70cv1k5y46zf")))) + "0nb0lpwqph9334s9sq77mk3nd22icy9d9hywz4awhf6nvp5rcc2v")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -500,14 +501,14 @@ higher.") (define-public r-oenb (package (name "r-oenb") - (version "0.0.1") + (version "0.0.2") (source (origin (method url-fetch) (uri (cran-uri "oenb" version)) (sha256 (base32 - "1x1jlqp6r27c4gb7wafzpmh5rq6yq61a2d395r5lsmv2g5jb4biz")))) + "1jgxw7ycx2lcdzglg9nix8k08fs4r6i5jdsjzrd6w1dg6smsinl5")))) (properties `((upstream-name . "oenb"))) (build-system r-build-system) (propagated-inputs @@ -873,18 +874,21 @@ single step.") (define-public r-rvest (package (name "r-rvest") - (version "0.3.6") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "rvest" version)) (sha256 - (base32 "1yh2p429a0zr8pqmlw5rzf6m797j20j5w6xwxlqq0wrdbnif6bka")))) + (base32 "04spcv6nxlmx5bxncq0vybfqrs8jgjamzyrn6wmkdcwii8jvyn53")))) (build-system r-build-system) (propagated-inputs `(("r-httr" ,r-httr) + ("r-lifecycle" ,r-lifecycle) ("r-magrittr" ,r-magrittr) + ("r-rlang" ,r-rlang) ("r-selectr" ,r-selectr) + ("r-tibble" ,r-tibble) ("r-xml2" ,r-xml2))) (native-inputs `(("r-knitr" ,r-knitr))) @@ -923,14 +927,14 @@ package is a port of the Python package @code{cssselect}.") (define-public r-reprex (package (name "r-reprex") - (version "1.0.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "reprex" version)) (sha256 (base32 - "07nzx0fdl48jw95ipx17ql0l13q60yl3rjrkj1m375wrc7h1v5nx")))) + "1lcnxczy28n4g3rvph09va7svcznfyqa7zdggklqb924qvy7flwh")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) @@ -941,6 +945,7 @@ package is a port of the Python package @code{cssselect}.") ("r-knitr" ,r-knitr) ("r-rlang" ,r-rlang) ("r-rmarkdown" ,r-rmarkdown) + ("r-rstudioapi" ,r-rstudioapi) ("r-withr" ,r-withr))) (native-inputs `(("r-knitr" ,r-knitr))) @@ -979,14 +984,14 @@ same time tries to group instances from the same class together.") (define-public r-callr (package (name "r-callr") - (version "3.5.1") + (version "3.6.0") (source (origin (method url-fetch) (uri (cran-uri "callr" version)) (sha256 (base32 - "15l6ppsxdadlnl4fk0f8bvf327n8izk96px5d08m1ay9iij8qcyf")))) + "050s7l1ipi6snbj6xnk052l6acycnxjyzv84026adw5x8kki0yz6")))) (build-system r-build-system) (propagated-inputs `(("r-r6" ,r-r6) @@ -2835,31 +2840,6 @@ where the bound function accepts additional arguments.") bindings that call a C++ function.") (license license:expat))) -(define-public r-bisquerna - (package - (name "r-bisquerna") - (version "1.0.4") - (source (origin - (method url-fetch) - (uri (cran-uri "BisqueRNA" version)) - (sha256 - (base32 - "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2")))) - (properties `((upstream-name . "BisqueRNA"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-limsolve" ,r-limsolve))) - (home-page "https://www.biorxiv.org/content/10.1101/669911v1") - (synopsis "Decomposition of bulk expression with single-cell sequencing") - (description "This package provides tools to accurately estimate cell type -abundances from heterogeneous bulk expression. A reference-based method -utilizes single-cell information to generate a signature matrix and -transformation of bulk expression for accurate regression based estimates. -A marker-based method utilizes known cell-specific marker genes to measure -relative abundances across samples.") - (license license:gpl3))) - (define-public r-auc (package (name "r-auc") @@ -3789,7 +3769,7 @@ statistics/methods are implemented.") (uri (cran-uri "SuppDists" version)) (sha256 (base32 - "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak")))) + "1i3iq12a5x5k49ac01mikzcrrq9gc148xq3m08h4xm07bha6f2v8")))) (properties `((upstream-name . "SuppDists"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/SuppDists") @@ -3888,14 +3868,14 @@ available in a vignette.") (define-public r-lava (package (name "r-lava") - (version "1.6.8.1") + (version "1.6.9") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 - "1yiz8y3jhxkszgz9m9fialp9r27hy97xh0imfvs8ziv7dk43y93d")))) + "07difbrz8zmvdyns63958v0zw4hyv48956mcww8zh7064a564k83")))) (build-system r-build-system) (propagated-inputs `(("r-numderiv" ,r-numderiv) @@ -4216,14 +4196,14 @@ provided.") (define-public r-ipred (package (name "r-ipred") - (version "0.9-10") + (version "0.9-11") (source (origin (method url-fetch) (uri (cran-uri "ipred" version)) (sha256 (base32 - "0p9cd2v47h71jbz8q0z6xykkaqpcp0mkpsfmd2bn961n1hfgpa63")))) + "04hfg27c72v0fz4091w3rgbc2vd7g6yl78y9plvsvh0vjlx8ymmp")))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class) @@ -4243,19 +4223,21 @@ problems as well as resampling based estimators of prediction error.") (define-public r-psych (package (name "r-psych") - (version "2.0.12") + (version "2.1.3") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 - "0k5dw5nb7kx7f21b0z01dry99qcpnk7iaicv7xq9d35wv2hx8wca")))) + "1ibh1ivr280wpmk3qjgm715dk79wx0ikjl9jjjcqs03q6vz4wmdx")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) ("r-mnormt" ,r-mnormt) ("r-nlme" ,r-nlme))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/psych/") (synopsis "Procedures for psychological, psychometric, and personality research") (description @@ -4296,14 +4278,14 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "0.7.5") + (version "0.7.6") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "1qjyl5b100bsakm48w1vi3819lkpys7vb86n1sv9h4y2wr1c4jmw")))) + "1ljcl8mh0yqxw3qxzar482qwbxbcaim1x6y1wm82ws12pfdw0j8n")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -4786,14 +4768,14 @@ structure.") (define-public r-vioplot (package (name "r-vioplot") - (version "0.3.5") + (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "vioplot" version)) (sha256 (base32 - "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v")))) + "15vmrm9gwdhfg8mnq8rsg7m59kzc9h53cv96am4ds1dkm56w4n6p")))) (build-system r-build-system) (propagated-inputs `(("r-sm" ,r-sm) @@ -5069,18 +5051,17 @@ plots in @code{ggplot2}.") (define-public r-cli (package (name "r-cli") - (version "2.3.1") + (version "2.4.0") (source (origin (method url-fetch) (uri (cran-uri "cli" version)) (sha256 (base32 - "1jh64ixn6mg2ap1sx4azrxkjnlsyjbfxyc9zjkx8m9dlakgf4v2i")))) + "0l1s9yv23bc7mm0hfdlamgz4wjfrisv8aylr65ihjs98jsynrkg3")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-glue" ,r-glue))) + `(("r-glue" ,r-glue))) (home-page "https://github.com/r-lib/cli#readme") (synopsis "Helpers for developing command line interfaces") (description "This package provides a suite of tools designed to build @@ -5132,13 +5113,13 @@ constants, and control debugging of packages via environment variables.") (define-public r-processx (package (name "r-processx") - (version "3.4.5") + (version "3.5.1") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 - (base32 "055v2gdrgqsfy8s672wsq79bqr44b4jjmcbqivx4p2d6lqx10s73")))) + (base32 "1z7zag7g041xlhzhkdfl33y2phc877h1pwj9k69p69b967qi6p6k")))) (build-system r-build-system) (propagated-inputs `(("r-ps" ,r-ps) @@ -5279,13 +5260,13 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.21") + (version "0.22") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 - (base32 "18qjs81fn8q2d2drcan8gpgvrbgxgd0b659c92z19kg2h4c1g3k4")))) + (base32 "0ix3p0iw2c60whn5mvsflh0vhm4yixhw4s9d9v4023qhp077nw9y")))) (build-system r-build-system) ;; knitr itself depends on xfun #; @@ -5301,15 +5282,17 @@ packages maintained by Yihui Xie.") (define-public r-utf8 (package (name "r-utf8") - (version "1.1.4") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "utf8" version)) (sha256 (base32 - "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn")))) + "1yw7vjn3gpkqddc91rbfh4kk0zmn2kp0jycrd3066sissh01jhdk")))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/patperry/r-utf8") (synopsis "Unicode text processing") (description @@ -5342,18 +5325,17 @@ to variables on the left-hand side of the assignment.") (define-public r-vctrs (package (name "r-vctrs") - (version "0.3.6") + (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 - "09ddxgzyah7lw42hn6n8fynsixf43s10jamsf94d2aidky63czfz")))) + "03hyxk3x635xfdn2x707gygdb2xk0cayl1nl44zib9bwqyyb7nas")))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-ellipsis" ,r-ellipsis) + `(("r-ellipsis" ,r-ellipsis) ("r-glue" ,r-glue) ("r-rlang" ,r-rlang))) (native-inputs @@ -5431,14 +5413,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.30") + (version "0.31") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "0dk6mpszwh1m65b0wfwjlcvpzywmasf6p31niqiq53wnd92my0gw")))) + "04a3ncaxix30n9m73slpsn1idxv7j1f7fy3nhxpvkk514x9rgg0p")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) @@ -5746,14 +5728,14 @@ sapa R packages.") (define-public r-sapa (package (name "r-sapa") - (version "2.0-2") + (version "2.0-3") (source (origin (method url-fetch) (uri (cran-uri "sapa" version)) (sha256 (base32 - "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds")))) + "0kj681rd4c2lvqr926lb6f4qwp281x5274dg6vbk8pf5y7s0qlpc")))) (build-system r-build-system) (propagated-inputs `(("r-ifultools" ,r-ifultools) @@ -6725,14 +6707,14 @@ evaluated by the @dfn{Akaike Information Criterion} (AIC).") (define-public r-arules (package (name "r-arules") - (version "1.6-6") + (version "1.6-7") (source (origin (method url-fetch) (uri (cran-uri "arules" version)) (sha256 (base32 - "1pk3jjizn2m5rwi7qkdkbq9f07acgpy0qdzzqmx0agg47cwahlkm")))) + "0m80kndfbannw8h53nqdd5wl8h33q2z259aa1cp1nwadaxf9fc1q")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -6906,14 +6888,14 @@ simple method for converting between file types.") (define-public r-maptools (package (name "r-maptools") - (version "1.0-2") + (version "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "maptools" version)) (sha256 (base32 - "0jgf3wg47jdnznxb3ncv4is9ackwviy4lzcyggqwzw3wh6jnvb6s")))) + "0pn4gwh2rl6pfh2vbc7ln86kzlg22cfpd02z95j7zpjidz2mva8l")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) @@ -7250,14 +7232,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (define-public r-rastervis (package (name "r-rastervis") - (version "0.50") + (version "0.50.1") (source (origin (method url-fetch) (uri (cran-uri "rasterVis" version)) (sha256 (base32 - "0m7fjd53apxim0d0rjnyzc28vmfcg4spcrn0zbnk8llillxji1hi")))) + "1fkmyllydnmk3j2cmgf86r91wyxf2kh573x8bkck7wgkfniw4h7w")))) (properties `((upstream-name . "rasterVis"))) (build-system r-build-system) (propagated-inputs @@ -7309,14 +7291,14 @@ those searches and pull data into their R sessions.") (define-public r-renv (package (name "r-renv") - (version "0.13.0") + (version "0.13.2") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 - "16n2dz9jibc03f7q1wrzxss6l5jmaks7m2lnli9dz9anvcmxbdia")))) + "0jlsf6vfvqhr4i35xy3xf1ixkfillivzy3wbpl6ca9vyjpnhiwj1")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (native-inputs @@ -7880,14 +7862,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rbibutils (package (name "r-rbibutils") - (version "2.0") + (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "rbibutils" version)) (sha256 (base32 - "1vfg2188i4dyhrmvnwpsh2la8qkd4wkryz2fpj4cppi1wfz3ml83")))) + "13phw0dk3p3s1z45ff7dbqnn27zws1209mp3d4763zh7xnsdsl44")))) (properties `((upstream-name . "rbibutils"))) (build-system r-build-system) (home-page "https://geobosh.github.io/rbibutils/") @@ -7928,14 +7910,14 @@ references and Rd files.") (define-public r-officer (package (name "r-officer") - (version "0.3.17") + (version "0.3.18") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 - "1apg0dh1zfhrqcbbmm8318l40gyjbqc2l9sdvwxx7qi8mzc1mqvw")))) + "1j3bv4j8x5ijj0j447vpdsk4p8pl3ncwdwnns6n3plfrqgsf3vsg")))) (build-system r-build-system) (propagated-inputs `(("r-r6" ,r-r6) @@ -8189,14 +8171,14 @@ other add-on packages.") (define-public r-insight (package (name "r-insight") - (version "0.13.1") + (version "0.13.2") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "1la4yxzfl9fnknamnaziil6gvpdzl78z16lfzis9jgzg8r9q0y5l")))) + "03b7kd17h25mi1si40ibcp3jpasyqpj51mr8js0ywywyfw7909j1")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -8325,14 +8307,14 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.6.3") + (version "0.6.4") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "0as80m19lvajc0vzllq9d9p63zglsm2ph7vdfg3jgk90jp8j76dg")))) + "1ykjfnqhn8nd9f3l4jj8hf1bbjjckkna3p7fdsg0a73c05a17yma")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -8659,14 +8641,14 @@ procedures to speed up calculations in R.") (define-public r-blockfest (package (name "r-blockfest") - (version "1.8") + (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "BlockFeST" version)) (sha256 (base32 - "12cbrmgqszlj729zrn9d1d7drbr0iay43knnmrzcxs6v7lfszsx5")))) + "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65")))) (properties `((upstream-name . "BlockFeST"))) (build-system r-build-system) (propagated-inputs `(("r-basix" ,r-basix))) @@ -9686,14 +9668,14 @@ samples is large and the number of mixture components is not too large.") (define-public r-magick (package (name "r-magick") - (version "2.6.0") + (version "2.7.1") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 - "1k4fqhxh2ppynl56fs044wpn4wk6gbv6lwp2x4x7j67zwcv56n36")))) + "16svy84dq25g69axqgympsrh8dzssa1w3zz08zc8m6nprr3jqwqf")))) (build-system r-build-system) (inputs `(("imagemagick" ,imagemagick) @@ -10128,14 +10110,14 @@ Hothorn, Westfall, 2010, CRC Press).") (define-public r-emmeans (package (name "r-emmeans") - (version "1.5.4") + (version "1.5.5-1") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "1rbh3ls23fazrwpsam5llk3kqdzz2zvsms3i4f1cgn34ky3w8361")))) + "0l5dd71ihhs7zy6ygniy07iisgy7a1ai1w41hqf84swb0j3cl6iz")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) @@ -10418,14 +10400,14 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "1c5rvycaqp7zp1j6j17c84v8nlpi0w7bhfxmcha4n37m0snk1kgy")))) + "0qh8x8yi8gkb5x7zfxmb1c689k7bhc1f5947yymny34j7xdsb9s8")))) (build-system r-build-system) (propagated-inputs `(("r-insight" ,r-insight) @@ -10448,14 +10430,14 @@ results using @code{ggplot2}.") (define-public r-effectsize (package (name "r-effectsize") - (version "0.4.3") + (version "0.4.4-1") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 - "1hcrnax9wf0nwsb8nv15rxw8yy8w5dak16dw3w5bxi8xnf56lkz2")))) + "02rwf3lxnzgc8yh0wridsc6lqr9s6v0cqzbk4biwnr494rvs46zb")))) (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs @@ -10565,14 +10547,14 @@ repositories.") (define-public r-gh (package (name "r-gh") - (version "1.2.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "gh" version)) (sha256 (base32 - "1zvy3ylxvni10lhvmbm9h14mg4wlsbdbzbzviwf28jxss8749219")))) + "16xa1qb1r28f8yc6ybjrxiq2zigxj886dp9k29jpsn5091xbzkq0")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -10676,14 +10658,14 @@ user credentials.") (define-public r-gert (package (name "r-gert") - (version "1.2.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "gert" version)) (sha256 (base32 - "0ag2ia6cfb5drf3517lg5nhik1w0nv09a75wdy5jdciws1qra3d6")))) + "1fh72p92wj83yv1ch77jms6k1gjqfji8cmgw23vpxd0p8l9jj4h7")))) (properties `((upstream-name . "gert"))) (build-system r-build-system) (inputs @@ -10776,14 +10758,14 @@ more information about packages, and where they were installed from.") (define-public r-remotes (package (name "r-remotes") - (version "2.2.0") + (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "remotes" version)) (sha256 (base32 - "1f1kdw9j1wald3fs8b3n68x1kljy07j60g3aw1aarx26ikyk9whj")))) + "0f35648bdxhvplcfj80r4hfj5w21f1s01kcz6b29d098c1mnfzb7")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -10902,14 +10884,14 @@ ways.") (define-public r-summarytools (package (name "r-summarytools") - (version "0.9.8") + (version "0.9.9") (source (origin (method url-fetch) (uri (cran-uri "summarytools" version)) (sha256 (base32 - "0n7rad6bkfn9cb99wbfzbwl5qzch48r0gafhddfcqvyh4fbn2k0j")))) + "0ig7vgjvldbndwhky1bsi38zifr9ji8xvvfqbfffplac08llvrbr")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -11293,15 +11275,17 @@ netCDF files.") (define-public r-biocmanager (package (name "r-biocmanager") - (version "1.30.10") + (version "1.30.12") (source (origin (method url-fetch) (uri (cran-uri "BiocManager" version)) (sha256 - (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk")))) + (base32 "0c2anza01pc36manj3cvycbq8p57qpq18dsimk3y3gpks70hhqf3")))) (properties `((upstream-name . "BiocManager"))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/BiocManager/") (synopsis "Access the Bioconductor project package repository") (description @@ -11718,19 +11702,21 @@ redundant complex conjugate when the input is real data.") (define-public r-tiff (package (name "r-tiff") - (version "0.1-7") + (version "0.1-8") (source (origin (method url-fetch) (uri (cran-uri "tiff" version)) (sha256 (base32 - "101n6x70fr1dhcwx53g3s8q1j4wh93y0388v1s1316f8558rxqxh")))) + "18m17g5q3nz4v4wrqxnb129b1j02873g2vknddczkklf1pvq4x2b")))) (build-system r-build-system) (inputs `(("libtiff" ,libtiff) ("libjpeg" ,libjpeg-turbo) ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) (home-page "https://www.rforge.net/tiff/") (synopsis "Read and write TIFF images") (description @@ -12632,21 +12618,24 @@ and manipulating sets of ontological terms.") (define-public r-gargle (package (name "r-gargle") - (version "1.0.0") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "gargle" version)) (sha256 (base32 - "0hsqn4hf935wn6vk2pwym7la4sdvy271y4cashp38pg4hkpg9zph")))) + "03y29dzz54bw9px5k8a72vmc000lcyrkc5l0izkqcciyi9ijkr3w")))) (build-system r-build-system) (propagated-inputs - `(("r-fs" ,r-fs) + `(("r-cli" ,r-cli) + ("r-fs" ,r-fs) ("r-glue" ,r-glue) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) + ("r-rappdirs" ,r-rappdirs) ("r-rlang" ,r-rlang) + ("r-rstudioapi" ,r-rstudioapi) ("r-withr" ,r-withr))) (native-inputs `(("r-knitr" ,r-knitr))) @@ -12721,14 +12710,14 @@ limitations\" using the GNU Multiple Precision library.") (define-public r-rmpfr (package (name "r-rmpfr") - (version "0.8-2") + (version "0.8-3") (source (origin (method url-fetch) (uri (cran-uri "Rmpfr" version)) (sha256 (base32 - "007pc7fpzl2mcg3qxa2vfjip6m2dr314qjsnybkj3kdj70bszxkl")))) + "1m9wwwch9wg886147brr2zfih65yfdfs3vmfvim1w6jykycasc9a")))) (properties `((upstream-name . "Rmpfr"))) (build-system r-build-system) (inputs @@ -13696,14 +13685,14 @@ them in distributed compute environments.") (define-public r-parallelly (package (name "r-parallelly") - (version "1.23.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (cran-uri "parallelly" version)) (sha256 (base32 - "025whcz55wj9jd73dalkbxh4l2331mqn758glr6hlf472lwf4v1p")))) + "1x04pxcyyzmg1rl9mcd7mmxglzmxgy40fmbwpy7vf5y7z15rzrp6")))) (properties `((upstream-name . "parallelly"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/parallelly") @@ -14444,14 +14433,14 @@ probabilities from a standard bivariate normal CDF.") (define-public r-lavaan (package (name "r-lavaan") - (version "0.6-7") + (version "0.6-8") (source (origin (method url-fetch) (uri (cran-uri "lavaan" version)) (sha256 (base32 - "0ks62wrwghbm1brzmqvr92h5n1295dpc87m1g3xrfx0mkdaqdcdk")))) + "18l49f1v7nrngwra4v983ic8w1d4w23ws8xf36337dq0j6809qj0")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -15146,14 +15135,14 @@ utilities for sequence data management under the ACNUC system.") (define-public r-units (package (name "r-units") - (version "0.7-0") + (version "0.7-1") (source (origin (method url-fetch) (uri (cran-uri "units" version)) (sha256 (base32 - "0kwfcrrbcwl7s50n1wp33vswqzmprh91clvakbd1jpznqpg5m3js")))) + "0wwndzjjgqj795xvx1jwa86nwd8adfiwj0pn15yyzzk9baky2axw")))) (build-system r-build-system) (inputs `(("udunits" ,udunits))) @@ -15299,14 +15288,14 @@ tessellation.") (define-public r-sf (package (name "r-sf") - (version "0.9-7") + (version "0.9-8") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 - "175fmnnw11fjhfgjv9sn9b0jfjcqbybpgwsvv99d5yddigvw5jja")))) + "096gg2hbynn6mv3w8n69x987fklg5rrgd0d4nbqaw7vhg1jhlmqi")))) (build-system r-build-system) (inputs `(("gdal" ,gdal) @@ -15336,14 +15325,14 @@ datum transformations.") (define-public r-spdep (package (name "r-spdep") - (version "1.1-5") + (version "1.1-7") (source (origin (method url-fetch) (uri (cran-uri "spdep" version)) (sha256 (base32 - "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7")))) + "0sg417d95paww625663lgmk6jwhs88djqzc96gbs1hxazlf77qb1")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) @@ -15539,13 +15528,13 @@ lspec, polyclass, and polymars.") (define-public r-rms (package (name "r-rms") - (version "6.1-1") + (version "6.2-0") (source (origin (method url-fetch) (uri (cran-uri "rms" version)) (sha256 - (base32 "1zgfd60lzbakcv7x0i5k3lkw3s0xx5bzssjgangna5lq2j17cdli")))) + (base32 "1di4xvsx0rwkr77nfqiysbg4qf699199xqil70i39d4zwfzqrm8h")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) @@ -16283,14 +16272,14 @@ packages with Rcpp.") (define-public r-tweenr (package (name "r-tweenr") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "tweenr" version)) (sha256 (base32 - "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg")))) + "17znizh4yabh2zs9mzyr0sl6p0pw49961i61br7cl1b7v9sza18q")))) (build-system r-build-system) (propagated-inputs `(("r-farver" ,r-farver) @@ -16471,6 +16460,32 @@ visualizations and provides the same flexible approach to building up plots layer by layer.") (license license:gpl3))) +(define-public r-gkmsvm + (package + (name "r-gkmsvm") + (version "0.81.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "gkmSVM" version)) + (sha256 + (base32 + "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj")))) + (properties `((upstream-name . "gkmSVM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-kernlab" ,r-kernlab) + ("r-rcpp" ,r-rcpp) + ("r-rocr" ,r-rocr) + ("r-seqinr" ,r-seqinr))) + (home-page "https://cran.r-project.org/web/packages/gkmSVM") + (synopsis "Gapped-kmer support vector machine") + (description + "This R package provides tools for training gapped-kmer SVM classifiers +for DNA and protein sequences. This package supports several sequence +kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") + (license license:gpl2+))) + (define-public r-varselrf (package (name "r-varselrf") @@ -17171,14 +17186,14 @@ batch correction, and data correction.") (define-public r-styler (package (name "r-styler") - (version "1.3.2") + (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "styler" version)) (sha256 (base32 - "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz")))) + "10fj4cnazicb2z9djbv5pszcmrf7wbzagbjvksffqpdc5vbbbw5x")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -17192,6 +17207,8 @@ batch correction, and data correction.") ("r-tibble" ,r-tibble) ("r-withr" ,r-withr) ("r-xfun" ,r-xfun))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/r-lib/styler") (synopsis "Non-invasive pretty printing of R code") (description @@ -17445,14 +17462,14 @@ classification and regression models.") (define-public r-dae (package (name "r-dae") - (version "3.1-32") + (version "3.1-37") (source (origin (method url-fetch) (uri (cran-uri "dae" version)) (sha256 (base32 - "126w1lb9pz8mb2ajl2vz5dj798nbifp0dypnzfgcwixif5g5bpqi")))) + "102fgbdpn7yvm1zj180cv4sr1096sz35d4gndsv7w9kriqyi1c1l")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -17484,14 +17501,14 @@ been used in the call to @code{aov}.") (define-public r-dalex (package (name "r-dalex") - (version "2.1.1") + (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 - "1dnqsml94s648w8swsrq8spddnd4mj5pl3q6xxr917w6a1jxgyfz")))) + "1qnjbhilv4jfmwqxfi9xc5ysrh8gr84a2a5imjfci7d1n3zcnryn")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs @@ -19564,14 +19581,14 @@ discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.") (define-public r-gamlss-data (package (name "r-gamlss-data") - (version "5.1-4") + (version "6.0-1") (source (origin (method url-fetch) (uri (cran-uri "gamlss.data" version)) (sha256 (base32 - "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd")))) + "1cjb2n5i5mnhmb5qbqycdbfg65j7nxb9s74yihqs9kpa39byrzcq")))) (properties `((upstream-name . "gamlss.data"))) (build-system r-build-system) (home-page "http://www.gamlss.org/") @@ -19585,14 +19602,14 @@ models.") (define-public r-gamlss (package (name "r-gamlss") - (version "5.3-1") + (version "5.3-4") (source (origin (method url-fetch) (uri (cran-uri "gamlss" version)) (sha256 (base32 - "1ngf6g4zixwm6ni5r0fs0f6132xd2f2a6mlski9hlqnvvwb46iwr")))) + "06mh00jjxnqwknbv777hawjk0zm81ixrp35fg59mrlqz8y3p2w3j")))) (properties `((upstream-name . "gamlss"))) (build-system r-build-system) (propagated-inputs @@ -20796,14 +20813,14 @@ API; see the package vignette for details.") (define-public r-actuar (package (name "r-actuar") - (version "3.1-1") + (version "3.1-2") (source (origin (method url-fetch) (uri (cran-uri "actuar" version)) (sha256 (base32 - "0sxn1mskh7x164f1vbrqnadgxnq7y2p3a9mlmqc0sp6cqkw9lhp9")))) + "0gaqm8bkjly2b1jkr1nqnxlp5vqvfpj0a4jd70jv4f9ndlif676y")))) (properties `((upstream-name . "actuar"))) (build-system r-build-system) (propagated-inputs `(("r-expint" ,r-expint))) @@ -20873,14 +20890,14 @@ number embedded in the file rather than the file extension.") (define-public r-imager (package (name "r-imager") - (version "0.42.7") + (version "0.42.8") (source (origin (method url-fetch) (uri (cran-uri "imager" version)) (sha256 (base32 - "1dq0rblnrmnk689bcdmml179gk9lff8x92s2npkjllgjq5q2vfpd")))) + "1kzl93l6k9i4528bbycbqxdn28mj7hnx0fbxisva859xl1wys5c5")))) (properties `((upstream-name . "imager"))) (build-system r-build-system) (inputs @@ -21022,14 +21039,14 @@ functions.") (define-public r-univoutl (package (name "r-univoutl") - (version "0.2") + (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "univOutl" version)) (sha256 (base32 - "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v")))) + "1hhpxrpmp2wbrynx9xjndnp2sccirgky2x6ksd6yk6phmk0rbzjp")))) (properties `((upstream-name . "univOutl"))) (build-system r-build-system) (propagated-inputs @@ -21237,14 +21254,14 @@ different conceptual parts of the algorithm.") (define-public r-shapes (package (name "r-shapes") - (version "1.2.5") + (version "1.2.6") (source (origin (method url-fetch) (uri (cran-uri "shapes" version)) (sha256 (base32 - "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s")))) + "1p9fr95zk3q2v277c5ksb0nh26mcpzwjzjb2lmag51z6hck8cb66")))) (properties `((upstream-name . "shapes"))) (build-system r-build-system) (propagated-inputs @@ -21861,14 +21878,14 @@ Raftery, Appl.Statistics, 1989); it includes inference and basic methods.") (define-public r-forecast (package (name "r-forecast") - (version "8.13") + (version "8.14") (source (origin (method url-fetch) (uri (cran-uri "forecast" version)) (sha256 (base32 - "0vrql5d4v28890np2m6ws1nr1fcl6frs1bz74vfkihkixcmkl3j9")))) + "12bfw029xb1dndcjyn2r7a51i7hnkkbdilp69k97sz2v8b7v1y3s")))) (properties `((upstream-name . "forecast"))) (build-system r-build-system) (propagated-inputs @@ -22037,32 +22054,23 @@ Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.") (define-public r-quanteda (package (name "r-quanteda") - (version "2.1.2") + (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "quanteda" version)) (sha256 (base32 - "13rjwgmg5v1dbryrs9ifyy76s5ib6wrbrm2y5af44vhf1h6p9cvy")))) + "0b1jfkdhpsg5jhjz4p0nf4cmi9p8w40wv3i2f17jf2x1n1y2hjj8")))) (properties `((upstream-name . "quanteda"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-digest" ,r-digest) - ("r-extrafont" ,r-extrafont) - ("r-fastmatch" ,r-fastmatch) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-jsonlite" ,r-jsonlite) + `(("r-fastmatch" ,r-fastmatch) ("r-magrittr" ,r-magrittr) ("r-matrix" ,r-matrix) - ("r-network" ,r-network) - ("r-proxyc" ,r-proxyc) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rcppparallel" ,r-rcppparallel) - ("r-sna" ,r-sna) ("r-snowballc" ,r-snowballc) ("r-stopwords" ,r-stopwords) ("r-stringi" ,r-stringi) @@ -22831,14 +22839,14 @@ interesting features. iheatmapr uses the plotly library for interactivity.") (define-public r-packrat (package (name "r-packrat") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "packrat" version)) (sha256 (base32 - "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n")))) + "01cn2vf95nc8bh0hh8imkn030yra3hx64q1fb8jwsr52p9s397fr")))) (properties `((upstream-name . "packrat"))) (build-system r-build-system) (home-page "https://github.com/rstudio/packrat/") @@ -23507,17 +23515,19 @@ appropriate dog and cat images for many status codes.") (define-public r-latex2exp (package (name "r-latex2exp") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "latex2exp" version)) (sha256 (base32 - "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw")))) + "0qknpw7zwwbzsbry94j8fn48mq7kq5rc5448g9hybbisain3wfvg")))) (build-system r-build-system) (propagated-inputs `(("r-stringr" ,r-stringr) ("r-magrittr" ,r-magrittr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/stefano-meschiari/latex2exp/") (synopsis "Use LaTeX expressions in plots") (description "@code{latex2exp} parses and converts LaTeX math formulas to @@ -24087,14 +24097,14 @@ vignette for more information and examples.") (define-public r-brms (package (name "r-brms") - (version "2.14.4") + (version "2.15.0") (source (origin (method url-fetch) (uri (cran-uri "brms" version)) (sha256 (base32 - "0mzwihhgmn405l6zq11a180q4k3chggj9qj0j7q838b9vrszg59j")))) + "0byc3fyvf9qbvvgwf55ih5d4br1nnxlbaidq9fvr11bmv38h25y1")))) (properties `((upstream-name . "brms"))) (build-system r-build-system) (propagated-inputs @@ -24377,14 +24387,14 @@ input.") (define-public r-lightgbm (package (name "r-lightgbm") - (version "3.1.1") + (version "3.2.0") (source (origin (method url-fetch) (uri (cran-uri "lightgbm" version)) (sha256 (base32 - "1pwsh6j9ksahh58b15j5ij56bsc6syy3z4k4a5zhy5n7829rz555")))) + "0aw1zcrg7nhddfaif9544hn8g8qcylv6vzpkf8d3kl07nzvgxkvj")))) (properties `((upstream-name . "lightgbm"))) (build-system r-build-system) (propagated-inputs @@ -24413,14 +24423,14 @@ designed to be distributed and efficient with the following goals: (define-public r-shapforxgboost (package (name "r-shapforxgboost") - (version "0.1.0") + (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "SHAPforxgboost" version)) (sha256 (base32 - "0jgyss9bawl7sf4dwa75sn7ld3mvrrr0z2074lbkq3f5qb9gwsly")))) + "106nsf02b1w3yshb55lwnyw1rl1a60162v2wk8znjz3b4ln3mqj5")))) (properties `((upstream-name . "SHAPforxgboost"))) (build-system r-build-system) @@ -24431,9 +24441,10 @@ designed to be distributed and efficient with the following goals: ("r-ggforce" ,r-ggforce) ("r-ggplot2" ,r-ggplot2) ("r-ggpubr" ,r-ggpubr) - ("r-lightgbm" ,r-lightgbm) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-xgboost" ,r-xgboost))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/liuyanguu/SHAPforxgboost") (synopsis "SHAP Plots for XGBoost") (description @@ -24783,6 +24794,33 @@ diagonals. This package allows you to compute the tensor product of arrays.") which may also be useful for other purposes.") (license license:gpl2+))) +(define-public r-spatstat-sparse + (package + (name "r-spatstat-sparse") + (version "1.2-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "spatstat.sparse" version)) + (sha256 + (base32 + "1w312q7gxzchigxxzk9akscdsz66j5085lgjryamschjgp4f8yk2")))) + (properties + `((upstream-name . "spatstat.sparse"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-matrix" ,r-matrix) + ("r-spatstat-utils" ,r-spatstat-utils) + ("r-tensor" ,r-tensor))) + (home-page "http://spatstat.org/") + (synopsis "Sparse three-dimensional arrays and linear algebra utilities") + (description + "This package defines sparse three-dimensional arrays and supports +standard operations on them. The package also includes utility functions for +matrix calculations that are common in statistics, such as quadratic forms.") + (license license:gpl2+))) + (define-public r-spatstat-data (package (name "r-spatstat-data") @@ -24806,31 +24844,111 @@ which may also be useful for other purposes.") package.") (license license:gpl2+))) -(define-public r-spatstat +(define-public r-spatstat-geom (package - (name "r-spatstat") - (version "1.64-1") + (name "r-spatstat-geom") + (version "1.65-5") (source (origin (method url-fetch) - (uri (cran-uri "spatstat" version)) + (uri (cran-uri "spatstat.geom" version)) (sha256 (base32 - "06jmxfs9kz9qqi3ichfgn8dglwb87kq2nl578p83za5psv8cfgya")))) - (properties `((upstream-name . "spatstat"))) + "0g0m5b3nbzpyblbp77n56k6aiw3fn23jkk72h9fhqlg1ydn2fzpk")))) + (properties `((upstream-name . "spatstat.geom"))) + (build-system r-build-system) + (propagated-inputs + `(("r-deldir" ,r-deldir) + ("r-polyclip" ,r-polyclip) + ("r-spatstat-data" ,r-spatstat-data) + ("r-spatstat-sparse" ,r-spatstat-sparse) + ("r-spatstat-utils" ,r-spatstat-utils))) + (home-page "http://spatstat.org/") + (synopsis "Geometrical functionality of the spatstat package") + (description + "This is a subset of the original spatstat package, containing the +user-level code from spatstat which performs geometrical operations, except +for the geometry of linear networks.") + (license license:gpl2+))) + +(define-public r-spatstat-core + (package + (name "r-spatstat-core") + (version "1.65-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "spatstat.core" version)) + (sha256 + (base32 + "0wq61sd53hwyk3fzjdc2prrr66n67zbwb5i3ii7kvyhfwx0xikm3")))) + (properties `((upstream-name . "spatstat.core"))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) - ("r-deldir" ,r-deldir) ("r-goftest" ,r-goftest) ("r-matrix" ,r-matrix) ("r-mgcv" ,r-mgcv) ("r-nlme" ,r-nlme) - ("r-polyclip" ,r-polyclip) ("r-rpart" ,r-rpart) ("r-spatstat-data" ,r-spatstat-data) + ("r-spatstat-geom" ,r-spatstat-geom) + ("r-spatstat-sparse" ,r-spatstat-sparse) ("r-spatstat-utils" ,r-spatstat-utils) ("r-tensor" ,r-tensor))) + (home-page "http://spatstat.org/") + (synopsis "Core functionality of the spatstat package") + (description + "This is a subset of the original spatstat package, containing all of the +user-level code from spatstat, except for the code for linear networks.") + (license license:gpl2+))) + +(define-public r-spatstat-linnet + (package + (name "r-spatstat-linnet") + (version "1.65-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "spatstat.linnet" version)) + (sha256 + (base32 + "1y088r26h5yv006ydgcb4iwpvnc7ql857gky0hbi7xqqciqr8wdv")))) + (properties + `((upstream-name . "spatstat.linnet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-spatstat-core" ,r-spatstat-core) + ("r-spatstat-data" ,r-spatstat-data) + ("r-spatstat-geom" ,r-spatstat-geom) + ("r-spatstat-utils" ,r-spatstat-utils))) + (home-page "http://spatstat.org/") + (synopsis "Linear networks functionality of the spatstat package") + (description + "This is a subset of the spatstat package, containing its functionality +for spatial data on a linear network.") + (license license:gpl2+))) + +(define-public r-spatstat + (package + (name "r-spatstat") + (version "2.0-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "spatstat" version)) + (sha256 + (base32 + "1xq11ijc0d0lbixxb3wnvyr4gplfj2d2i64ynsa089xd525zzzbw")))) + (properties `((upstream-name . "spatstat"))) + (build-system r-build-system) + (propagated-inputs + `(("r-spatstat-core" ,r-spatstat-core) + ("r-spatstat-data" ,r-spatstat-data) + ("r-spatstat-geom" ,r-spatstat-geom) + ("r-spatstat-linnet" ,r-spatstat-linnet) + ("r-spatstat-utils" ,r-spatstat-utils))) (home-page "http://www.spatstat.org") (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests") (description @@ -25465,14 +25583,14 @@ more.") (define-public r-workflows (package (name "r-workflows") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "workflows" version)) (sha256 (base32 - "1mk0pnmpqlhf143mvj9rwvjrrshirz6s83s5hbfalhnyw7hzkfb9")))) + "19ipcxx4qfz28cjkgr1vny03yhmbd3m2v64v30gk5pf73nazvmaz")))) (properties `((upstream-name . "workflows"))) (build-system r-build-system) (propagated-inputs @@ -25483,7 +25601,8 @@ more.") ("r-hardhat" ,r-hardhat) ("r-parsnip" ,r-parsnip) ("r-rlang" ,r-rlang) - ("r-tidyselect" ,r-tidyselect))) + ("r-tidyselect" ,r-tidyselect) + ("r-vctrs" ,r-vctrs))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/tidymodels/workflows") @@ -25738,6 +25857,45 @@ for finding reasonable values of hyper-parameters in models, pre-processing methods, and post-processing steps.") (license license:expat))) +(define-public r-workflowsets + (package + (name "r-workflowsets") + (version "0.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "workflowsets" version)) + (sha256 + (base32 + "1q41isvj7hhbkx3y8k6kazpiygig92xannsz8dpklh0k3j9l3c2p")))) + (properties `((upstream-name . "workflowsets"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cli" ,r-cli) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-prettyunits" ,r-prettyunits) + ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) + ("r-rsample" ,r-rsample) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-tune" ,r-tune) + ("r-vctrs" ,r-vctrs) + ("r-withr" ,r-withr) + ("r-workflows" ,r-workflows))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/tidymodels/workflowsets") + (synopsis "Create a collection of tidymodels workflows") + (description + "A workflow is a combination of a model and preprocessors (e.g, a +formula, recipe, etc.). In order to try different combinations of these, an +object can be created that contains many workflows. There are functions to +create workflows en masse as well as training them and visualizing the +results.") + (license license:expat))) + (define-public r-tidyposterior (package (name "r-tidyposterior") @@ -26065,6 +26223,32 @@ statistical analysis that share the underlying design philosophy, grammar, and data structures of the tidyverse.") (license license:gpl3))) +(define-public r-lsa + (package + (name "r-lsa") + (version "0.73.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "lsa" version)) + (sha256 + (base32 + "1a33irqa6qvbc02z12rgbgv8kxq2gmahy7j5bg8b23lvvaxif06b")))) + (properties `((upstream-name . "lsa"))) + (build-system r-build-system) + (propagated-inputs + `(("r-snowballc" ,r-snowballc))) + (home-page "https://cran.r-project.org/package=lsa") + (synopsis "Latent semantic analysis") + (description + "The basic idea of latent semantic analysis (LSA) is, that text do have a +higher order (=latent semantic) structure which, however, is obscured by word +usage (e.g. through the use of synonyms or polysemy). By using conceptual +indices that are derived statistically via a truncated singular value +decomposition (a two-mode factor analysis) over a given document-term matrix, +this variability problem can be overcome.") + (license license:gpl2+))) + (define-public r-mlecens (package (name "r-mlecens") @@ -26343,13 +26527,13 @@ other R users.") (define-public r-seurat (package (name "r-seurat") - (version "4.0.0") + (version "4.0.1") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "1mp3py00bmzj4541d8ry5sfzkpfzvnl9dpa8n4qhakd13dl30xdn")))) + "17cmp9mimvykb8ny796dn1zwmvg0pwwjw1zcixyamc5q1lwnxi3p")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs @@ -26392,7 +26576,8 @@ other R users.") ("r-sctransform" ,r-sctransform) ("r-seuratobject" ,r-seuratobject) ("r-shiny" ,r-shiny) - ("r-spatstat" ,r-spatstat) + ("r-spatstat-core" ,r-spatstat-core) + ("r-spatstat-geom" ,r-spatstat-geom) ("r-tibble" ,r-tibble) ("r-uwot" ,r-uwot))) (home-page "http://www.satijalab.org/seurat") @@ -26465,33 +26650,6 @@ include Markov models of discrete and continuous trait evolution and constant rate speciation and extinction.") (license license:gpl2+))) -(define-public r-absfiltergsea - (package - (name "r-absfiltergsea") - (version "1.5.1") - (source - (origin - (method url-fetch) - (uri (cran-uri "AbsFilterGSEA" version)) - (sha256 - (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w")))) - (properties `((upstream-name . "AbsFilterGSEA"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-deseq" ,r-deseq) - ("r-limma" ,r-limma) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) - (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") - (synopsis "Improved false positive control of gene-permuting with absolute filtering") - (description - "This package provides a function that performs gene-permuting of a gene-set -enrichment analysis (GSEA) calculation with or without the absolute filtering. - Without filtering, users can perform (original) two-tailed or one-tailed -absolute GSEA.") - (license license:gpl2))) - (define-public r-calculus (package (name "r-calculus") @@ -26824,14 +26982,14 @@ vector machines, and gradient boosting.") (define-public r-bbotk (package (name "r-bbotk") - (version "0.3.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "bbotk" version)) (sha256 (base32 - "0kbjbwwq1fdfpl4xzy08hz4qvhjjchvz58icxq0dlbsmdyqwhwv0")))) + "1f29wxnxr73c4yp5afk05jqggpm7k1z8wiak8xsyw68h7xflq550")))) (properties `((upstream-name . "bbotk"))) (build-system r-build-system) (propagated-inputs @@ -26854,13 +27012,13 @@ annealing.") (define-public r-mlr3tuning (package (name "r-mlr3tuning") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3tuning" version)) (sha256 (base32 - "0xpq16qij05nsfwg0qnfziqjvgk5wn0dgl0sb5gg3qsp1cs6vfqj")))) + "16rvsf0jf06yvalydbs7zzn2994hvvyfw975ydiyv3wy1qzgr8bv")))) (build-system r-build-system) (propagated-inputs `(("r-bbotk" ,r-bbotk) @@ -27153,14 +27311,14 @@ clusterings as resolution increases.") (define-public r-textshaping (package (name "r-textshaping") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "textshaping" version)) (sha256 (base32 - "16y3amb9cxwq126q1mxssx7kswzalqf9n2437mi5n7q1nqby6wlq")))) + "0fqh4z505b2qriqcj70g2hhdgiawd3w2rs9rqxdwizz5vk8jjygx")))) (properties `((upstream-name . "textshaping"))) (build-system r-build-system) (inputs @@ -27423,7 +27581,7 @@ in same length matches).") `(("r-data-table" ,r-data-table) ("r-slam" ,r-slam) ("r-stringi" ,r-stringi))) - (home-page "http://github.com/trinker/textshape") + (home-page "https://github.com/trinker/textshape") (synopsis "Tools for Reshaping Text") (description "Tools that can be used to reshape and restructure text data.") @@ -27996,3 +28154,160 @@ supply the workflow to create thematic maps. This package also facilitates via @url{https://developer.twitter.com/en/docs,Twitter's REST and stream Application Program Interfaces (API)}.") (license license:expat))) + +(define-public r-intervals + (package + (name "r-intervals") + (version "0.15.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "intervals" version)) + (sha256 + (base32 + "0mvwfwc03ifb30a3dzbmkv9adwqb8ajxhcw24d8xip8px063plhb")))) + (properties `((upstream-name . "intervals"))) + (build-system r-build-system) + (home-page "https://github.com/edzer/intervals") + (synopsis + "Tools for Working with Points and Intervals") + (description + "Tools for working with and comparing sets of points and intervals.") + (license license:artistic2.0))) + +(define-public r-eyelinker + (package + (name "r-eyelinker") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "eyelinker" version)) + (sha256 + (base32 + "14rfcdxad9iazwd46q6bm8gg1ryh6s8kf7arj00hhb7xz3gvk9c2")))) + (properties `((upstream-name . "eyelinker"))) + (build-system r-build-system) + (propagated-inputs + `(("r-intervals" ,r-intervals) + ("r-readr" ,r-readr) + ("r-stringi" ,r-stringi) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page + "https://github.com/a-hurst/eyelinker") + (synopsis + "Import ASC Files from EyeLink Eye Trackers") + (description + "Imports plain-text ASC data files from EyeLink eye trackers into +(relatively) tidy data frames for analysis and visualization.") + (license license:gpl3))) + +(define-public r-btm + (package + (name "r-btm") + (version "0.3.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "BTM" version)) + (sha256 + (base32 + "1x6bncb7r97z8bdyxnn2frdi9kyawfy6c2041mv9f42zdrfzm6jb")))) + (properties `((upstream-name . "BTM"))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/bnosac/BTM") + (synopsis "Biterm Topic Models for Short Text") + (description + "Biterm Topic Models find topics in collections of short texts. It is a +word co-occurrence based topic model that learns topics by modeling word-word +co-occurrences patterns which are called biterms. This in contrast to +traditional topic models like Latent Dirichlet Allocation and Probabilistic +Latent Semantic Analysis which are word-document co-occurrence topic models. A +biterm consists of two words co-occurring in the same short text window. This +context window can for example be a twitter message, a short answer on a +survey, a sentence of a text or a document identifier. The techniques are +explained in detail in the paper 'A Biterm Topic Model For Short Text' by +Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013) +@url{https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/\ +BTM-WWW13.pdf}.") + (license license:asl2.0))) + +(define-public r-textplot + (package + (name "r-textplot") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "textplot" version)) + (sha256 + (base32 + "1sgkndy2cxk8c76h8hwajn6f78w5jj2n8vsmaxh9kj931crzn8cy")))) + (properties `((upstream-name . "textplot"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-lattice" ,r-lattice) + ("r-matrix" ,r-matrix))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/bnosac/textplot") + (synopsis "Text Plots") + (description + "Visualise complex relations in texts. This is done by providing +functionalities for displaying text co-occurrence networks, text correlation +networks, dependency relationships as well as text clustering. Feel free to +join the effort of providing interesting text visualisations.") + (license license:gpl2))) + +(define-public r-gsa + (package + (name "r-gsa") + (version "1.03.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "GSA" version)) + (sha256 + (base32 + "05x9wspah1cdznjpncqam1iawsxdiigyl8v2anyhss2k7wwd94p1")))) + (properties `((upstream-name . "GSA"))) + (build-system r-build-system) + (home-page "https://statweb.stanford.edu/~tibs/GSA/") + (synopsis "Gene set analysis") + (description "This package lets you determine the significance of +pre-defined sets of genes with respect to an outcome variable, such as a group +indicator, a quantitative variable or a survival time.") + ;; Any version of the LGPL + (license license:lgpl3+))) + +(define-public r-samr + (package + (name "r-samr") + (version "3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "samr" version)) + (sha256 + (base32 + "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15")))) + (properties `((upstream-name . "samr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-gsa" ,r-gsa) + ("r-impute" ,r-impute) + ("r-matrixstats" ,r-matrixstats) + ("r-openxlsx" ,r-openxlsx) + ("r-shiny" ,r-shiny) + ("r-shinyfiles" ,r-shinyfiles))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://statweb.stanford.edu/~tibs/SAM/") + (synopsis "Significance analysis of Microarrays") + (description + "This is a package for significance analysis of Microarrays for +differential expression analysis, RNAseq data and related problems.") + ;; Any version of the LGPL + (license license:lgpl3+)))