diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 3368 |
1 files changed, 2676 insertions, 692 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 87f19f2640..fa33165f0b 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, 2022 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015-2023 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> @@ -11,13 +11,13 @@ ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com> ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net> ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net> -;;; Copyright © 2018, 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> +;;; Copyright © 2018, 2020-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com> ;;; Copyright © 2018 Leo Famulari <leo@famulari.name> ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org> ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com> -;;; Copyright © 2019, 2020, 2021 Wiktor Żelazny <wzelazny@vurv.cz> +;;; Copyright © 2019, 2020, 2021, 2022 Wiktor Żelazny <wzelazny@vurv.cz> ;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de> ;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com> @@ -31,11 +31,11 @@ ;;; 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, 2022 Simon Tournier <zimon.toutoune@gmail.com> +;;; Copyright © 2020, 2021, 2022, 2023 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> -;;; Copyright © 2022 Navid Afkhami <navid.afkhami@mdc-berlin.de> +;;; Copyright © 2022, 2023 Navid Afkhami <navid.afkhami@mdc-berlin.de> ;;; Copyright © 2022 Greg Hogan <code@greghogan.com> ;;; ;;; This file is part of GNU Guix. @@ -213,6 +213,26 @@ functions always read and write UTF-8 (8-bit Unicode Transformation Format) files and provide more explicit control over line endings.") (license license:expat))) +(define-public r-ca + (package + (name "r-ca") + (version "0.71.1") + (source (origin + (method url-fetch) + (uri (cran-uri "ca" version)) + (sha256 + (base32 + "095lk7p2b9835hc3a03c4019wg0baf0dhz6c2vqpaq1m9k4jy304")))) + (properties `((upstream-name . "ca"))) + (build-system r-build-system) + (home-page "http://www.carme-n.org/") + (synopsis "Simple, multiple and joint correspondence analysis") + (description + "This is a package for computation and visualization of simple, +multiple and joint correspondence analysis.") + ;; Any version of the GPL + (license license:gpl3+))) + (define-public r-cachem (package (name "r-cachem") @@ -236,16 +256,43 @@ can limit either their total size or the age of the oldest object (or both), automatically pruning objects to maintain the constraints.") (license license:expat))) +(define-public r-castor + (package + (name "r-castor") + (version "1.7.6") + (source (origin + (method url-fetch) + (uri (cran-uri "castor" version)) + (sha256 + (base32 + "1qbndwmzzpkzgiah0hgid9z5f9iv2j53d515bjcci1591gx1fk36")))) + (properties `((upstream-name . "castor"))) + (build-system r-build-system) + (propagated-inputs (list r-matrix r-naturalsort r-rcpp r-rspectra)) + (home-page "https://cran.r-project.org/package=castor") + (synopsis "Efficient phylogenetics on large trees") + (description + "This tool supports analyses on massive phylogenies comprising up to +millions of tips. Functions include pruning, rerooting, calculation of +most-recent common ancestors, calculating distances from the tree root and +calculating pairwise distances. In addition, this tool takes care of +calculation of phylogenetic signal and mean trait depth (trait conservatism), +ancestral state reconstruction and hidden character prediction of discrete +characters, simulating and fitting models of trait evolution, fitting and +simulating diversification models, dating trees, comparing trees, and +reading/writing trees in Newick format.") + (license license:gpl2+))) + (define-public r-collections (package (name "r-collections") - (version "0.3.5") + (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "collections" version)) (sha256 - (base32 "053ig88pva78wxxwya3v7cz853k563dkpgxrf2xvd0l0d9fanxmz")))) + (base32 "003zlp5s2ilq3pq0imlp7p46jkfihwzg1hkkgk7378ikcbwnz17z")))) (properties `((upstream-name . "collections"))) (build-system r-build-system) (home-page "https://github.com/randy3k/collections") @@ -287,14 +334,14 @@ etc.") (define-public r-datawizard (package (name "r-datawizard") - (version "0.6.0") + (version "0.6.5") (source (origin (method url-fetch) (uri (cran-uri "datawizard" version)) (sha256 (base32 - "1r89h5npv8iwsvylkpazfpcadgh55zd336rz8hndbzp0w9dcmpli")))) + "0il98vmy8l4wrisqz9xli7iki2ajdlsxyhh4k4grrd28gzkj8lgb")))) (properties `((upstream-name . "datawizard"))) (build-system r-build-system) (propagated-inputs @@ -312,13 +359,13 @@ wrangling backend for the packages in the @code{easystats} ecosystem.") (define-public r-dbscan (package (name "r-dbscan") - (version "1.1-10") + (version "1.1-11") (source (origin (method url-fetch) (uri (cran-uri "dbscan" version)) (sha256 - (base32 "1h8x1v9kk5zmw5qd575cyr16yz8l226lsaq71n079l4i8crcrzg1")))) + (base32 "0bz66lvvg7290c5260ph92k4r7adgisbx3vml9096qhjwrkqwjgh")))) (properties `((upstream-name . "dbscan"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -379,6 +426,25 @@ visualization of their differences.") (description "This package implements Dirichlet regression models.") (license license:gpl2+))) +(define-public r-dirmult + (package + (name "r-dirmult") + (version "0.1.3-5") + (source (origin + (method url-fetch) + (uri (cran-uri "dirmult" version)) + (sha256 + (base32 + "05whzhl81nyag7321hw98xa63r440s9bgj1764346yvm9bvzjqi4")))) + (properties `((upstream-name . "dirmult"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=dirmult") + (synopsis "Estimation in Dirichlet-Multinomial distribution") + (description + "This package estimates the parameters in Dirichlet-Multinomial and +computes log-likelihoods.") + (license license:gpl2+))) + (define-public r-dixontest (package (name "r-dixontest") @@ -402,6 +468,36 @@ wrapper functions. The core applies McBane's Fortran functions that use Gaussian quadrature for a numerical solution.") (license license:gpl3))) +(define-public r-dmwr2 + (package + (name "r-dmwr2") + (version "0.0.2") + (source (origin + (method url-fetch) + (uri (cran-uri "DMwR2" version)) + (sha256 + (base32 + "1vzfbz2k05j8r2hpig3d2grb99rnnh2s1sviii3prcyqicxfh0i9")))) + (properties `((upstream-name . "DMwR2"))) + (build-system r-build-system) + (propagated-inputs + (list r-class + r-dbi + r-dplyr + r-quantmod + r-readr + r-rpart + r-xts + r-zoo)) + (home-page "https://github.com/ltorgo/DMwR2") + (synopsis + "Functions and data for the second edition of \"Data Mining with R\"") + (description + "This package provides functions and data accompanying the second +edition of the book \"Data Mining with R, learning with case studies\" +by Luis Torgo, published by CRC Press.") + (license license:gpl2+))) + (define-public r-emdist (package (name "r-emdist") @@ -549,6 +645,27 @@ Google. @code{googleVis} makes use of the internal R HTTP server to display the output locally.") (license license:gpl2+))) +(define-public r-gson + (package + (name "r-gson") + (version "0.0.9") + (source (origin + (method url-fetch) + (uri (cran-uri "gson" version)) + (sha256 + (base32 + "065ify3i7zqwi7h5jzr7kdgr358kwgw6xrkvvmrznbl7s9f7d57n")))) + (properties `((upstream-name . "gson"))) + (build-system r-build-system) + (propagated-inputs (list r-jsonlite r-rlang r-tidyr)) + (home-page "https://cran.r-project.org/package=gson") + (synopsis "Base Class and Methods for 'gson' Format") + (description + "This package proposes a new file format named @code{gson} for storing +gene set and related information, and provides read, write and other utilities +to process this file format.") + (license license:artistic2.0))) + (define-public r-guix-install (package (name "r-guix-install") @@ -577,6 +694,107 @@ from CRAN, but also from Bioconductor or even arbitrary git or mercurial repositories, replacing the need for installation via @code{devtools}.") (license license:gpl3+))) +(define-public r-gunifrac + (package + (name "r-gunifrac") + (version "1.7") + (source (origin + (method url-fetch) + (uri (cran-uri "GUniFrac" version)) + (sha256 + (base32 + "13qb5fw9km6p5x8li9x3liqbh833wf2v73npj8jl3msplzfk82vp")))) + (properties `((upstream-name . "GUniFrac"))) + (build-system r-build-system) + (propagated-inputs + (list r-ape + r-dirmult + r-foreach + r-ggplot2 + r-ggrepel + r-mass + r-matrix + r-matrixstats + r-modeest + r-rcpp + r-rmutil + r-statmod + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=GUniFrac") + (synopsis + "Generalized UniFrac distances and methods for microbiome data analysis") + (description + "This package provides a suite of methods for powerful and robust +microbiome data analysis, including data normalization, data simulation, +community-level association testing and differential abundance analysis. It +implements generalized UniFrac distances, @dfn{Geometric Mean of Pairwise +Ratios} (GMPR) normalization, semiparametric data simulator, distance-based +statistical methods, and feature- based statistical methods. The +distance-based statistical methods include three extensions of PERMANOVA: + +@itemize +@item PERMANOVA using the Freedman-Lane permutation scheme, +@item PERMANOVA omnibus test using multiple matrices, and +@item analytical approach to approximating PERMANOVA p-value. +@end itemize + +Feature-based statistical methods include linear model-based methods for +differential abundance analysis of zero-inflated high-dimensional +compositional data.") + (license license:gpl3))) + +(define-public r-gwidgets2 + (package + (name "r-gwidgets2") + (version "1.0-9") + (source (origin + (method url-fetch) + (uri (cran-uri "gWidgets2" version)) + (sha256 + (base32 + "1ifljpdazzmwf3mgkg9g76365n2cmw8dd3da161fpvw84xxyznfl")))) + (properties `((upstream-name . "gWidgets2"))) + (build-system r-build-system) + (propagated-inputs (list r-digest)) + (home-page "https://github.com/gWidgets3/gWidgets2") + (synopsis "Rewrite of gWidgets API for simplified GUI construction") + (description + "This package provides a re-implementation of the @code{gWidgets} API. +The API is defined in this package. A second, toolkit-specific package is +required to use it.") + (license license:gpl3+))) + +(define-public r-gwidgets2tcltk + (package + (name "r-gwidgets2tcltk") + (version "1.0-8") + (source (origin + (method url-fetch) + (uri (cran-uri "gWidgets2tcltk" version)) + (sha256 + (base32 + "02ic4avpa33dnqsnm1mzg7ci1psngk1p169pqf259szf6v39qf8h")))) + (properties `((upstream-name . "gWidgets2tcltk"))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'start-x-server + (lambda _ + ;; Tests require a running X server. + (system "Xvfb :1 +extension GLX &") + (setenv "DISPLAY" ":1")))))) + (propagated-inputs (list r-digest r-gwidgets2 r-memoise)) + (native-inputs + (list xorg-server-for-tests)) + (home-page "https://github.com/jverzani/gWidgets2tcltk") + (synopsis "Toolkit implementation of gWidgets2 for tcltk") + (description "This package is a port of the @code{gWidgets2} API for the +@code{tcltk} package.") + (license license:gpl2+))) + (define-public r-ids (package (name "r-ids") @@ -639,16 +857,16 @@ can read and write both the metadata and the cell data in a Sheet.") (define-public r-proj4 (package (name "r-proj4") - (version "1.0-11") + (version "1.0-12") (source (origin (method url-fetch) (uri (cran-uri "proj4" version)) (sha256 (base32 - "07fil52jswbg2h807cd82m2wlm5j2fb891ifri9ms037099qdwf5")))) + "1y3n6zjc4s78pagq5f2x9sdfjg5x5nwnhq67jd06fndlsma8mssa")))) (properties `((upstream-name . "proj4"))) (build-system r-build-system) - (inputs (list proj.4 zlib)) + (inputs (list proj-7 zlib)) (native-inputs (list pkg-config)) (home-page "http://www.rforge.net/proj4/") (synopsis "Simple interface to the PROJ.4 cartographic projections library") @@ -659,6 +877,33 @@ allows transformation of geographic coordinates from one projection and/or datum to another.") (license license:gpl2))) +(define-public r-rorcid + (package + (name "r-rorcid") + (version "0.7.0") + (source (origin + (method url-fetch) + (uri (cran-uri "rorcid" version)) + (sha256 + (base32 + "1d0s5w48ksyj152nc4xq5w0nsimab8jc5fgspdwnbas2g8a52igr")))) + (properties `((upstream-name . "rorcid"))) + (build-system r-build-system) + (propagated-inputs (list r-crul + r-data-table + r-fauxpas + r-httr + r-jsonlite + r-tibble + r-xml2)) + (home-page "https://github.com/ropensci/rorcid") + (synopsis "Interface to the @url{Orcid.org, https://orcid.org} API") + (description + "This package provides an API for @url{Orcid.org, https://orcid.org}. +Functions include searching for people, searching by DOI, or searching by +Orcid ID.") + (license license:expat))) + (define-public r-waldo (package (name "r-waldo") @@ -833,14 +1078,14 @@ similar rank-based tests for equal probability distributions due to Neuhauser (define-public r-v8 (package (name "r-v8") - (version "4.2.1") + (version "4.2.2") (source (origin (method url-fetch) (uri (cran-uri "V8" version)) (sha256 (base32 - "1w1zihmhrygn2i674wimbv7xqjnwlld4x3ndvh5dl4cdg7s1m24r")))) + "0friwpw3cbg40hfsqnlp8g3a6l4zhfag6lh005ya6dw634kkarah")))) (properties `((upstream-name . "V8"))) (build-system r-build-system) (arguments @@ -957,6 +1202,61 @@ isolated functions, also called crates, print to the console with their total size and can be easily tested locally before being sent to a remote.") (license license:gpl3))) +(define-public r-climaemet + (package + (name "r-climaemet") + (version "1.0.2") + (source (origin + (method url-fetch) + (uri (cran-uri "climaemet" version)) + (sha256 + (base32 + "1z0i8iz7f32kns8j1yb3sp2m0zhl4pgp4bf52aiqykjp9i791dqm")))) + (properties `((upstream-name . "climaemet"))) + (build-system r-build-system) + (propagated-inputs + (list r-dplyr + r-ggplot2 + r-httr + r-jsonlite + r-rappdirs + r-readr + r-rlang + r-tibble + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://ropenspain.github.io/climaemet/") + (synopsis "Climate AEMET Tools") + (description + "This package provides tools to download the climatic data of the Spanish +Meteorological Agency (AEMET) directly from R using their API and create +scientific graphs (climate charts, trend analysis of climate time series, +temperature and precipitation anomalies maps, warming stripes graphics, +climatograms, etc.).") + (license license:gpl3))) + +(define-public r-climatol + (package + (name "r-climatol") + (version "3.1.2") + (source (origin + (method url-fetch) + (uri (cran-uri "climatol" version)) + (sha256 + (base32 + "0p3nk4n7izj0cmmqd9apa1gix5lfdzp08ydy0n7rkl5kbkmrkb6n")))) + (properties `((upstream-name . "climatol"))) + (build-system r-build-system) + (propagated-inputs (list r-mapdata r-maps)) + (home-page "http://www.climatol.eu/") + (synopsis "Climate tools") + (description + "This package provides functions for the quality control, homogenization +and missing data infilling of climatological series, and to obtain +climatological summaries and grids from the results. Also functions to draw +wind-roses and Walter&Lieth climate diagrams are included.") + (license license:gpl2+))) + (define-public r-clipr (package (name "r-clipr") @@ -978,6 +1278,32 @@ size and can be easily tested locally before being sent to a remote.") the system clipboards.") (license license:gpl3))) +(define-public r-clock + (package + (name "r-clock") + (version "0.6.1") + (source (origin + (method url-fetch) + (uri (cran-uri "clock" version)) + (sha256 + (base32 + "00hp7k24d599dzkzhhb6xky2pj6xaggdfwgviyb3i592v1gkh37q")))) + (properties `((upstream-name . "clock"))) + (build-system r-build-system) + (propagated-inputs (list r-cpp11 r-rlang r-tzdb r-vctrs)) + (native-inputs (list r-knitr)) + (home-page "https://clock.r-lib.org") + (synopsis "Date-Time types and tools") + (description + "This package provides a comprehensive library for date-time +manipulations using a new family of orthogonal date-time +classes (durations, time points, zoned-times, and calendars) that +partition responsibilities so that the complexities of time zones are +only considered when they are really needed. Capabilities include: +date-time parsing, formatting, arithmetic, extraction and updating of +components, and rounding.") + (license license:expat))) + (define-public r-clvalid (package (name "r-clvalid") @@ -1003,13 +1329,13 @@ BSI. Further information can be found in Brock, G et al. (2008) <doi: (define-public r-dlm (package (name "r-dlm") - (version "1.1-5") + (version "1.1-6") (source (origin (method url-fetch) (uri (cran-uri "dlm" version)) (sha256 - (base32 "1aksm66sfa7ipl5xgs4j5giac7q2m744wjl40mva56xn6i674h4r")))) + (base32 "0mxfakryagyg2idjhw1ydp4xqk57s3z17cv69hj16lisx8q43pc9")))) (properties `((upstream-name . "dlm"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=dlm") @@ -1020,6 +1346,38 @@ and smoothing, and Bayesian analysis of Normal linear State Space models, also known as Dynamic Linear Models.") (license license:gpl2+))) +(define-public r-zcompositions + (package + (name "r-zcompositions") + (version "1.4.0-1") + (source (origin + (method url-fetch) + (uri (cran-uri "zCompositions" version)) + (sha256 + (base32 + "1rrhja9iaq123r2gqw1bzrn1ri0s3z4wzq8p0sfcr1yb6pv13vik")))) + (properties `((upstream-name . "zCompositions"))) + (build-system r-build-system) + (propagated-inputs + (list r-mass + r-nada + r-truncnorm)) + (home-page "https://github.com/Japal/zCompositions") + (synopsis + "Treatment of zeros, left-censored and missing values in compositional data") + (description + "This is an R package for the imputation of left-censored data +under a compositional approach. The implemented methods consider +aspects of relevance for a compositional approach such as scale +invariance, subcompositional coherence or preserving the multivariate +relative structure of the data. Based on solid statistical +frameworks, it comprises the ability to deal with single and varying +censoring thresholds, consistent treatment of closed and non-closed +data, exploratory tools, multiple imputation, @dfn{Markov Chain Monte +Carlo} (MCMC), robust and non-parametric alternatives, and recent +proposals for count data.") + (license license:gpl2+))) + (define-public r-zoo (package (name "r-zoo") @@ -1043,13 +1401,13 @@ series of numeric vectors/matrices and factors.") (define-public r-fontawesome (package (name "r-fontawesome") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "fontawesome" version)) (sha256 - (base32 "0c8sb8isiyn2gr3xfql75yyssf9wlb152cw67whq83aqsksgrvjd")))) + (base32 "0br4sjl2z5av5kf42mnp35sichk3syrz68xic08wxnqdnp2hn2kn")))) (properties `((upstream-name . "fontawesome"))) (build-system r-build-system) (propagated-inputs @@ -1144,14 +1502,14 @@ variables.") (define-public r-ggpp (package (name "r-ggpp") - (version "0.4.4") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "ggpp" version)) (sha256 (base32 - "0wcaczxjav5yg8h2197cf288mqk13p3iq675q0x0di9g8lnblvk1")))) + "0zmxnzsdmwv9v77fifgiknalwif59261kslq8848x1xch8f82l77")))) (properties `((upstream-name . "ggpp"))) (build-system r-build-system) (propagated-inputs @@ -1191,13 +1549,13 @@ variables.") (define-public r-ggprism (package (name "r-ggprism") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "ggprism" version)) (sha256 (base32 - "09dh0r8r5s61i5dbk6rswajc2vm7k8wvlqyvzq8wr160676lycjp")))) + "0ycklp7764cw65hqh9r61im8vqfd7sjayyw1gvprxzg7k217gnl3")))) (properties `((upstream-name . "ggprism"))) (build-system r-build-system) (propagated-inputs @@ -1349,13 +1707,13 @@ axis} (SMA), and @dfn{ranged major axis} (RMA).") (define-public r-ggpmisc (package (name "r-ggpmisc") - (version "0.5.0") + (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 - "1i7cfmhmgih3hn0zr5yn33ziznfa3a4j8hkn237bv7jckwzpklxw")))) + "1zvq580vi1h2afdgxaqabjhfsphvmdchwiaahqvvhljxmpmh82q6")))) (build-system r-build-system) (propagated-inputs (list r-confintr @@ -1384,13 +1742,13 @@ respecting the grammar of its graphics paradigm.") (define-public r-ggside (package (name "r-ggside") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "ggside" version)) (sha256 (base32 - "1vl7kzgmi5xxxsqvyg4cm4xwd3lfjgysay1lw6hri5vj22mnga5h")))) + "1z50z4xpxfpqdz26hja6xw3q403p00cr5qawjxl0qg4jixl7j65p")))) (properties `((upstream-name . "ggside"))) (build-system r-build-system) (propagated-inputs @@ -1399,7 +1757,8 @@ respecting the grammar of its graphics paradigm.") r-gtable r-rlang r-scales - r-tibble)) + r-tibble + r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=ggside") (synopsis "Side grammar graphics that extends @code{ggplot2}") @@ -1579,6 +1938,31 @@ consistent fashion. It seeks to combine functionality from lower level functions which can speed up workflow.") (license license:gpl2))) +(define-public r-pals + (package + (name "r-pals") + (version "1.7") + (source (origin + (method url-fetch) + (uri (cran-uri "pals" version)) + (sha256 + (base32 + "18pbivmqs9yqsb6p8anv42alny0njaq3dajibhzysax0b7rsk2js")))) + (properties `((upstream-name . "pals"))) + (build-system r-build-system) + (propagated-inputs + (list r-colorspace + r-dichromat + r-mapproj + r-maps)) + (native-inputs (list r-knitr)) + (home-page "https://kwstat.github.io/pals/") + (synopsis "Color palettes, color maps, and tools to evaluate them") + (description + "This package provides a comprehensive collection of color +palettes, color maps, and tools to evaluate them.") + (license license:gpl3))) + (define-public r-paralleldist (package (name "r-paralleldist") @@ -1628,13 +2012,13 @@ control over dimensions and appearance.") (define-public r-philentropy (package (name "r-philentropy") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "philentropy" version)) (sha256 (base32 - "1dpf4hfflp4mcql4na46wzcq1flabkipiwyycz9wj5xbxlmcz2hk")))) + "1dw46p2bk68hqbc44629lywg5r1mdaz37ahccgmsx07fg8rf4wnf")))) (properties `((upstream-name . "philentropy"))) (build-system r-build-system) (propagated-inputs (list r-kernsmooth r-poorman r-rcpp)) @@ -1767,6 +2151,30 @@ excellent candidate for labeling of a polygon.") @code{dplyr} and the wider @code{tidyverse} using only @code{base}.") (license license:expat))) +(define-public r-ecosolver + (package + (name "r-ecosolver") + (version "0.5.4") + (source (origin + (method url-fetch) + (uri (cran-uri "ECOSolveR" version)) + (sha256 + (base32 + "0973m346vakgddp92dzqlky0wa196hj341r9y7rz67bc2zl8jx2x")))) + (properties `((upstream-name . "ECOSolveR"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bnaras.github.io/ECOSolveR/") + (synopsis "Embedded conic solver in R") + (description + "This package provides an R interface to the @dfn{Embedded COnic +Solver} (ECOS), an efficient and robust C library for convex problems. +Conic and equality constraints can be specified in addition to integer +and boolean variable constraints for mixed-integer problems. This R +interface is inspired by the Python interface and has similar calling +conventions.") + (license license:gpl3+))) + (define-public r-ecp (package (name "r-ecp") @@ -1818,13 +2226,13 @@ are not used.") (define-public r-ga (package (name "r-ga") - (version "3.2.2") + (version "3.2.3") (source (origin (method url-fetch) (uri (cran-uri "GA" version)) (sha256 - (base32 "135z03lnbj44jihnk6dii5a684jmc666ncpdwyyi910vl4sccib2")))) + (base32 "0q0br75zklnp0g3j98x6lll5fhyayxqzaqs3hc2z39s2imwi2fpb")))) (properties `((upstream-name . "GA"))) (build-system r-build-system) (propagated-inputs @@ -1950,14 +2358,14 @@ These functions draw text grob with background shadow.") (define-public r-sys (package (name "r-sys") - (version "3.4") + (version "3.4.1") (source (origin (method url-fetch) (uri (cran-uri "sys" version)) (sha256 (base32 - "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p")))) + "0lng3ri17jxq06c6hhhmvsb65lazkiqpp1h4pii4w9jqvs7nskij")))) (build-system r-build-system) (home-page "https://github.com/jeroen/sys") (synopsis "Powerful and reliable tools for running system commands in R") @@ -2047,14 +2455,14 @@ Analysis Approach Using R. Chapman-Hall, 2019, (define-public r-vegan (package (name "r-vegan") - (version "2.6-2") + (version "2.6-4") (source (origin (method url-fetch) (uri (cran-uri "vegan" version)) (sha256 (base32 - "0nf0ny6jzfy135xiygzzkr0y55y8g27hrbk8c869plarr48d2xxb")))) + "01hxlb5sy0d28ajq993fqs4z0qjcyl610d0ahjyjpbkrpszd92jx")))) (build-system r-build-system) (native-inputs (list r-knitr ; needed for vignettes @@ -2238,14 +2646,14 @@ same time tries to group instances from the same class together.") (define-public r-callr (package (name "r-callr") - (version "3.7.2") + (version "3.7.3") (source (origin (method url-fetch) (uri (cran-uri "callr" version)) (sha256 (base32 - "01q3b0w1cbrryvv1dwvnyd3j1f09xmhnwg1wskc51r3r4qhqmnhj")))) + "0knh5yxhxwjz96kbjrq524w4j8cac10k6mghhmblq79s0zgzwysn")))) (build-system r-build-system) (propagated-inputs (list r-r6 r-processx)) @@ -2333,17 +2741,40 @@ supported for the trees and a test for parameter heterogeneity is provided for the personalised models.") (license license:gpl2+))) +(define-public r-modelenv + (package + (name "r-modelenv") + (version "0.1.0") + (source (origin + (method url-fetch) + (uri (cran-uri "modelenv" version)) + (sha256 + (base32 + "18wgl3hslvwq4z8ab91514p5nhzxzb727s61ccawvx3ixfjfrid4")))) + (properties `((upstream-name . "modelenv"))) + (build-system r-build-system) + (propagated-inputs (list r-glue r-rlang r-tibble r-vctrs)) + (home-page "https://github.com/tidymodels/modelenv") + (synopsis "Tools for registering models for use in tidymodels") + (description + "This is a developer-focused, low dependency package in +@code{tidymodels} that provides functions to register how models are +to be used. Functions to register models are complimented with +accessor functions to retrieve registered model information to aid in +model fitting and error handling.") + (license license:expat))) + (define-public r-modelr (package (name "r-modelr") - (version "0.1.9") + (version "0.1.10") (source (origin (method url-fetch) (uri (cran-uri "modelr" version)) (sha256 (base32 - "1jd9vxirj5ii4ac0ka07g0rcq1c8yqv06jg27nmvp5a6kvlgvs8h")))) + "0qqgdb7gpb1h9lf5zijg51gd0qmbzj8f37aykhv1w633cglacick")))) (build-system r-build-system) (propagated-inputs (list r-broom @@ -2405,13 +2836,13 @@ Zucchini.") (define-public r-httpuv (package (name "r-httpuv") - (version "1.6.6") + (version "1.6.7") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 - "14qjf7bpl7pay89b7vi2vccl342q8xs6101a9x6qijy54k9myfa1")) + "0jjb2w59x8a4k24j9rc4rjm37h1ccrfq1nzd40inbnd6kcqf3lkm")) ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv ;; only contains fixes for building on Solaris. (patches (search-patches "r-httpuv-1.6.6-unvendor-libuv.patch")) @@ -2449,16 +2880,48 @@ particularly easy to create complete web applications using httpuv alone.") ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE (license license:gpl3+))) +(define-public r-httr2 + (package + (name "r-httr2") + (version "0.2.2") + (source (origin + (method url-fetch) + (uri (cran-uri "httr2" version)) + (sha256 + (base32 + "1gzjsw3w7c3rsp3gb9rdbfmmnmd2sq09s3wza49730gp84jvc6jx")))) + (properties `((upstream-name . "httr2"))) + (build-system r-build-system) + (propagated-inputs + (list r-cli + r-curl + r-glue + r-magrittr + r-openssl + r-r6 + r-rappdirs + r-rlang + r-withr)) + (native-inputs (list r-knitr)) + (home-page "https://httr2.r-lib.org") + (synopsis "Perform HTTP requests and process the responses") + (description + "This package provides tools for creating and modifying HTTP requests, +then performing them and processing the results. @code{httr2} is a +re-imagining of @code{httr} that uses a pipe-based interface and solves more +of the problems that API wrapping packages face.") + (license license:expat))) + (define-public r-jsonlite (package (name "r-jsonlite") - (version "1.8.0") + (version "1.8.4") (source (origin (method url-fetch) (uri (cran-uri "jsonlite" version)) (sha256 (base32 - "0k6dal7gmm19jl5sjsry5gwbnhsbrnn00q3iixig8k6bxgpr463v")))) + "0y0jzf74c3q1sghgarvwmrkvxs7yahywd342m8c0jsr28bhapskr")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -2478,13 +2941,13 @@ in systems and applications.") (define-public r-servr (package (name "r-servr") - (version "0.24") + (version "0.25") (source (origin (method url-fetch) (uri (cran-uri "servr" version)) (sha256 (base32 - "11x0857m3xzdbzr4z0vx4fcdk36arfagyf2qgamvprich0qisknr")))) + "0g77lpyfjaibcpqb3z723z1p82msjdnc74f2n5l740z91560vbp6")))) (build-system r-build-system) (propagated-inputs (list r-httpuv r-jsonlite r-mime r-xfun)) @@ -2522,16 +2985,16 @@ a list of p-values.") (define-public r-htmltools (package (name "r-htmltools") - (version "0.5.3") + (version "0.5.4") (source (origin (method url-fetch) (uri (cran-uri "htmltools" version)) (sha256 (base32 - "0krjyz99q7zvdfg60b128c0zwr36h54gb05jw9c874d8kqv1ni9c")))) + "0zij9zrgsi82q5c65sf4pbidnzrkfr763g0n4ypdhf8dd6l2i0h0")))) (build-system r-build-system) (propagated-inputs - (list r-base64enc r-digest r-fastmap r-rlang)) + (list r-base64enc r-digest r-ellipsis r-fastmap r-rlang)) (home-page "https://cran.r-project.org/web/packages/htmltools") (synopsis "R tools for HTML") (description @@ -2541,16 +3004,18 @@ a list of p-values.") (define-public r-htmlwidgets (package (name "r-htmlwidgets") - (version "1.5.4") + (version "1.6.1") (source (origin (method url-fetch) (uri (cran-uri "htmlwidgets" version)) (sha256 (base32 - "1hgz8sx8xrvfcdwa4q15k942w4qsqg8lyxbbf7qyfzbi807wcgqs")))) + "0hqfjvfs3mcpqwim79vac1738k19ipr10zvdqrw5kzpwpsy3qls2")))) (build-system r-build-system) (propagated-inputs - (list r-htmltools r-jsonlite r-yaml)) + (list r-htmltools r-jsonlite + r-knitr r-rmarkdown + r-yaml)) (native-inputs (list r-knitr)) (home-page "https://github.com/ramnathv/htmlwidgets") @@ -2598,13 +3063,13 @@ LaTeX.") (define-public r-curl (package (name "r-curl") - (version "4.3.2") + (version "4.3.3") (source (origin (method url-fetch) (uri (cran-uri "curl" version)) (sha256 (base32 - "0s55022hy8shjm1pzax1dqzrg20bv4nvlwnjnddk3dp89g5zmcch")))) + "17kwc7njblfndnlij0m5a7a3jj42ag412xg0ry5ddnj0mnnbcrrm")))) (build-system r-build-system) (arguments `(#:phases @@ -2726,14 +3191,14 @@ rules and utility functions for adaptive GH quadrature.") (define-public r-rstpm2 (package (name "r-rstpm2") - (version "1.5.7") + (version "1.5.9") (source (origin (method url-fetch) (uri (cran-uri "rstpm2" version)) (sha256 (base32 - "1gsizffplj4m9x1ln82f76936psgxn9cii45m7658lpwf2nzwli2")))) + "1zl7z1l19s960mrhlzvpga07kzqfrhhq7qlkgln4wj0gcmhicyc6")))) (properties `((upstream-name . "rstpm2"))) (build-system r-build-system) (propagated-inputs @@ -2815,17 +3280,41 @@ rmarkdown, etc.) depend on this package to avoid bundling redundant copies of jQuery.") (license license:expat))) +(define-public r-jqr + (package + (name "r-jqr") + (version "1.2.3") + (source (origin + (method url-fetch) + (uri (cran-uri "jqr" version)) + (sha256 + (base32 + "1a91zcjxdilhqdyr2lipnwc35f90h0wyqlbg0vw9ay7sq6llxgs9")))) + (properties `((upstream-name . "jqr"))) + (build-system r-build-system) + (inputs (list jq)) + (propagated-inputs (list r-lazyeval r-magrittr)) + (native-inputs (list pkg-config)) + (home-page "https://docs.ropensci.org/jqr/") + (synopsis "R client for jq, a JSON Processor") + (description + "This package provides an R client for @command{jq}, a JSON processor. +@command{jq} allows the following with JSON data: index into, parse, do +calculations, cut up and filter, change key names and values, perform +conditionals and comparisons, and more.") + (license license:expat))) + (define-public r-sass (package (name "r-sass") - (version "0.4.2") + (version "0.4.4") (source (origin (method url-fetch) (uri (cran-uri "sass" version)) (sha256 (base32 - "0iln5ky6k1ix0gddlyw4rr2953kc499x66bcyi9yiyp91nfh82dl")))) + "0hk5svmpbhx9q3ni3qll2pa7q3pfc0zxv616kp62r6vakn1az16j")))) (properties `((upstream-name . "sass"))) (build-system r-build-system) (propagated-inputs @@ -2880,18 +3369,17 @@ expression estimates for all genes.") (define-public r-bslib (package (name "r-bslib") - (version "0.4.0") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "bslib" version)) (sha256 (base32 - "1hkmaj0mpygbf6qr1955biv9z4q3khflyqi5x0c3dwi6qz74xspv")) + "069ghbzp0bsmbw2nzw28cmbym65i3a90v50y7qksy2g4pfhvfh4s")) (snippet '(for-each delete-file '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js" - "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js" "inst/lib/bs3/assets/javascripts/bootstrap.min.js" "inst/lib/bs4/dist/js/bootstrap.bundle.min.js" "inst/lib/bs5/dist/js/bootstrap.bundle.min.js"))))) @@ -2927,11 +3415,13 @@ expression estimates for all genes.") (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs - (list r-cachem + (list r-base64enc + r-cachem r-htmltools r-jquerylib r-jsonlite r-memoise + r-mime r-rlang r-sass)) (native-inputs @@ -2946,10 +3436,10 @@ expression estimates for all genes.") ("js-bootstrap5-bundle" ,(origin (method url-fetch) - (uri "https://raw.githubusercontent.com/twbs/bootstrap/v5.1.3/dist/js/bootstrap.bundle.js") + (uri "https://raw.githubusercontent.com/twbs/bootstrap/v5.2.2/dist/js/bootstrap.bundle.js") (sha256 (base32 - "116979i2vr1y9i6g7n5iir19p85xwr642scbl9jcqdr0w9801nw6")))))) + "1ibfb1lwwm50did0b4fvxaqc7xyljmp20f3qb1ybdlvcy22mk8bg")))))) (home-page "https://rstudio.github.io/bslib/") (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown") (description @@ -3440,13 +3930,13 @@ in a ggplot2 plot.") (define-public r-mbess (package (name "r-mbess") - (version "4.9.1") + (version "4.9.2") (source (origin (method url-fetch) (uri (cran-uri "MBESS" version)) (sha256 - (base32 "18klyyjvmwggv4ma2x77jac3640yxbsbinl3s2rp1ik4n9phnjd0")))) + (base32 "0cq4z7nx361rcw42jflrrdjbqs2q5973dlvhcr7i2wbkj3gzkwla")))) (properties `((upstream-name . "MBESS"))) (build-system r-build-system) (propagated-inputs @@ -3496,13 +3986,13 @@ annotation data to keep updated.") (define-public r-ggtern (package (name "r-ggtern") - (version "3.3.5") + (version "3.4.1") (source (origin (method url-fetch) (uri (cran-uri "ggtern" version)) (sha256 - (base32 "15hhn8msy0l8zbq8ms0zvg1iajn1c28gd77v3hp6dvwwsla8zzbd")))) + (base32 "0w0kg6755kfpczqpaly251fgqv31js9gdzr17x734l2adycji3yr")))) (properties `((upstream-name . "ggtern"))) (build-system r-build-system) (propagated-inputs @@ -3651,14 +4141,14 @@ files). It currently supports linked brushing and filtering.") (define-public r-rook (package (name "r-rook") - (version "1.1-1") + (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "Rook" version)) (sha256 (base32 - "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00")))) + "0qjziszrrwsp1mbykps3yf5r98q83cyd4jzpgi7gvbsd2ssy96n7")))) (properties `((upstream-name . "Rook"))) (build-system r-build-system) (propagated-inputs (list r-brew)) @@ -3714,17 +4204,37 @@ work well on small screens.") data store designed for maximum speed.") (license license:asl2.0))) +(define-public r-mapdata + (package + (name "r-mapdata") + (version "2.3.1") + (source (origin + (method url-fetch) + (uri (cran-uri "mapdata" version)) + (sha256 + (base32 + "1m2r4c8f7fp900g3sdjbfxxnxjla86hn75jd8hi96ms188p0j8b0")))) + (properties `((upstream-name . "mapdata"))) + (build-system r-build-system) + (propagated-inputs (list r-maps)) + (home-page "https://cran.r-project.org/package=mapdata") + (synopsis "Extra map databases") + (description + "This is a supplement to the @code{maps} package providing the larger +and/or higher-resolution databases.") + (license license:gpl2))) + (define-public r-maps (package (name "r-maps") - (version "3.4.0") + (version "3.4.1") (source (origin (method url-fetch) (uri (cran-uri "maps" version)) (sha256 (base32 - "0ispkx1szgwxhr0zzhdzgqqwcgc6psg7vry4sj4rb89w76rcq63r")))) + "0034114pdakxcx480b45qy9j4vq1v5ss961ssy92w4nqiqhsb4z6")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/maps") (synopsis "Draw geographical maps") @@ -3736,14 +4246,14 @@ Projection code and larger maps are in separate packages (@code{mapproj} and (define-public r-mapproj (package (name "r-mapproj") - (version "1.2.8") + (version "1.2.9") (source (origin (method url-fetch) (uri (cran-uri "mapproj" version)) (sha256 (base32 - "10bpib827011fpgvzsmlv4j3i41s0r3cv1hvawwdlk753s7i0pw6")))) + "10nzfbyfkc545qxf51i33g0f8iiidcnhj971ylphnbh7j2sgla6s")))) (build-system r-build-system) (propagated-inputs (list r-maps)) (home-page "https://cran.r-project.org/web/packages/mapproj") @@ -3802,16 +4312,16 @@ complex non-linear objective function with a very large number of optima.") (define-public r-geosphere (package (name "r-geosphere") - (version "1.5-14") + (version "1.5-18") (source (origin (method url-fetch) (uri (cran-uri "geosphere" version)) (sha256 (base32 - "0bg4vfmrw140j2ax0p6bflvb77w03ir39wa87l96rj473jpa9hzj")))) + "1h6sqvxwxv22js6hz4s8sjk50ygw0y34icbbbdb2v36ca3q6zzwr")))) (build-system r-build-system) - (propagated-inputs (list r-sp)) + (propagated-inputs (list r-rcpp r-sp)) (home-page "https://cran.r-project.org/web/packages/geosphere") (synopsis "Spherical trigonometry") (description "This package computes spherical trigonometry for geographic @@ -3822,14 +4332,14 @@ applications. That is, compute distances and related measures for angular (define-public r-jpeg (package (name "r-jpeg") - (version "0.1-9") + (version "0.1-10") (source (origin (method url-fetch) (uri (cran-uri "jpeg" version)) (sha256 (base32 - "0wihj538wdnr71wdldym83qadb4kh68a6rkallwbh2f25r27b881")))) + "1jkqj58hj33ar9wyl7c1cnj3h42icq7crmjk93n933q8qc4zdnf8")))) (build-system r-build-system) (inputs (list libjpeg-turbo)) (home-page "https://www.rforge.net/jpeg/") @@ -3842,17 +4352,18 @@ files and in-memory raw vectors.") (define-public r-ggmap (package (name "r-ggmap") - (version "3.0.0") + (version "3.0.1") (source (origin (method url-fetch) (uri (cran-uri "ggmap" version)) (sha256 (base32 - "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln")))) + "0pg38zyxv1j6mwdwdqljynqrg7zjwqpsh65xdwmvbl0zgxa4p0pw")))) (build-system r-build-system) (propagated-inputs (list r-bitops + r-cli r-digest r-dplyr r-ggplot2 @@ -3864,7 +4375,7 @@ files and in-memory raw vectors.") r-png r-purrr r-rgooglemaps - r-rjson + r-rlang r-scales r-stringr r-tibble @@ -3929,13 +4440,13 @@ including functions for geolocation and routing.") (define-public r-amap (package (name "r-amap") - (version "0.8-18") + (version "0.8-19") (source (origin (method url-fetch) (uri (cran-uri "amap" version)) (sha256 (base32 - "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs")))) + "000r5705lq2mc15skin07dfxjf5816nbfy4gqkya1sv99dlfljbk")))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -4046,16 +4557,43 @@ 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-glmnetutils + (package + (name "r-glmnetutils") + (version "1.1.8") + (source (origin + (method url-fetch) + (uri (cran-uri "glmnetUtils" version)) + (sha256 + (base32 + "1k8ivzjgpkm2a948qxx3wmkhlppbk31qc76spv2pscmp24x0lxyn")))) + (properties `((upstream-name . "glmnetUtils"))) + (build-system r-build-system) + (propagated-inputs + (list r-glmnet + r-matrix)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/hongooi73/glmnetUtils") + (synopsis + "Streamline the process of fitting elastic net models with glmnet") + (description + "This package provides a collection of tools to streamline the +process of fitting elastic net models with @code{glmnet}. In addition +to providing a formula interface, it also features a function +@code{cva.glmnet} to do crossvalidation for both α and λ, as well as +some utility functions.") + (license license:gpl2))) + (define-public r-paletteer (package (name "r-paletteer") - (version "1.4.1") + (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "paletteer" version)) (sha256 (base32 - "0vj945cgpfhmbd98mcj167mgshghv32dxh8m4ngxs6i4q4y5blm7")))) + "1mm0k651356cjasv7wibscw82m1k8mwpp4xafpv66dsq24h28ikl")))) (properties `((upstream-name . "paletteer"))) (build-system r-build-system) (propagated-inputs (list r-prismatic r-rematch2 r-rlang r-rstudioapi)) @@ -4196,13 +4734,13 @@ print, summary, plot, update, etc. (define-public r-ps (package (name "r-ps") - (version "1.7.1") + (version "1.7.2") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 - (base32 "1waylmbrl23j62010r12c8xwzlvs1dys3cnh7hnrgk27glvqlicw")))) + (base32 "06mjwsn074195vd4yv7zzkmcf3sc124cw0cbnddj86swvggfn9cj")))) (build-system r-build-system) (home-page "https://ps.r-lib.org") (synopsis "List, query, and manipulate system processes") @@ -4214,13 +4752,13 @@ processes. Most of its code is based on the @code{psutil} Python package.") (define-public r-pkgbuild (package (name "r-pkgbuild") - (version "1.3.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "pkgbuild" version)) (sha256 - (base32 "0j6v5nbp8kg1m3j999gd1qsbdmqcqm1mf28ngmm177miwv8q4skw")))) + (base32 "1mjyln5njbvi0k97w8az2v5klmas6pqiz68mlylfll4nr503qzrm")))) (build-system r-build-system) (propagated-inputs (list r-callr @@ -4228,6 +4766,7 @@ processes. Most of its code is based on the @code{psutil} Python package.") r-crayon r-desc r-prettyunits + r-processx r-r6 r-rprojroot r-withr)) @@ -4242,14 +4781,14 @@ is configured appropriately so R can use them.") (define-public r-pkgload (package (name "r-pkgload") - (version "1.3.0") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "pkgload" version)) (sha256 (base32 - "0a22kxgm9a8ax1dw2q9v3338qhjmhfbcqw8r4b6608k6074m7xjs")))) + "0bvbnj98b1yaiksdmfi017g2w3229a5pcsnpjamzrvpy5c1rml9m")))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -4312,6 +4851,27 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see @code{citation(\"Rcpp\")} for details on these last two.") (license license:gpl2+))) +(define-public r-rcppde + (package + (name "r-rcppde") + (version "0.1.7") + (source (origin + (method url-fetch) + (uri (cran-uri "RcppDE" version)) + (sha256 + (base32 + "1846pl9gxikycdvwfgy1gw41z0fx4ycjp5p4295v8k2pgvlqw8sa")))) + (properties `((upstream-name . "RcppDE"))) + (build-system r-build-system) + (propagated-inputs + (list r-rcpp r-rcpparmadillo)) + (home-page "https://cran.r-project.org/package=RcppDE") + (synopsis "Global optimization by differential evolution in C++") + (description + "This package provides an iteration of the @code{DEoptim} function. It +performs global optimization by differential evolution.") + (license license:gpl2+))) + (define-public r-rcppml (package (name "r-rcppml") @@ -4575,6 +5135,33 @@ approach is used to estimate the lower cut-off for the scaling region.") ;; Any of these GPL versions. (license (list license:gpl2 license:gpl3)))) +(define-public r-ptw + (package + (name "r-ptw") + (version "1.9-16") + (source (origin + (method url-fetch) + (uri (cran-uri "ptw" version)) + (sha256 + (base32 + "0rma3h9ksc5qigdvk5vappb4ipd4rpk64wckzcxvxspakr5w71vy")))) + (properties `((upstream-name . "ptw"))) + (build-system r-build-system) + (propagated-inputs (list r-rcppde)) + (home-page "https://github.com/rwehrens/ptw") + (synopsis "Parametric time warping") + (description + "Parametric time warping aligns patterns. It aims to put corresponding +features at the same locations. The algorithm searches for an optimal +polynomial describing the warping. It is possible to align one sample to a +reference, several samples to the same reference, or several samples to +several references. One can choose between calculating individual warpings, +or one global warping for a set of samples and one reference. Two +optimization criteria are implemented: @acronym{RMS, Root Mean Square} error +and @acronym{WCC, Weighted Cross Correlation}. Both warping of peak profiles +and of peak lists are supported.") + (license license:gpl2+))) + (define-public r-compare (package (name "r-compare") @@ -4910,13 +5497,13 @@ most popular ones.") (define-public r-sp (package (name "r-sp") - (version "1.5-0") + (version "1.5-1") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 - (base32 "077q1wh9ihhcn1338xspnd90hy16ljxsav1xcrxdxj4fyynhd6lk")))) + (base32 "1pr9yb2wqapyizdfpi7zqd4a5b40q58czbfj6svvp2fkh6sfmfb9")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) @@ -5115,14 +5702,14 @@ spreadsheet software.") (define-public r-extremes (package (name "r-extremes") - (version "2.1-2") + (version "2.1-3") (source (origin (method url-fetch) (uri (cran-uri "extRemes" version)) (sha256 (base32 - "19q560prq02h3bwk01jb68693qb5bhsv8wiqhia7v5knm34qv8x7")))) + "0h1w177vz3z58vbqrfbiqapf9z2qsd7gcbv8fnbyn0i5akfz1k71")))) (properties `((upstream-name . "extRemes"))) (build-system r-build-system) (propagated-inputs @@ -5315,14 +5902,14 @@ topics for ecologists (ISBN 978-0-691-12522-0).") (define-public r-lpsolve (package (name "r-lpsolve") - (version "5.6.16") + (version "5.6.17") (source (origin (method url-fetch) (uri (cran-uri "lpSolve" version)) (sha256 (base32 - "0amvxki4l2sp60adcc6ra7kbqjrfv55gbn6kasq04klihi8ix88q")))) + "124jdjvxi1kqfd10jv85jqllvba1hi2z4j5g7n8wc1fwv4mq09gp")))) (properties `((upstream-name . "lpSolve"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/lpSolve") @@ -5398,14 +5985,14 @@ data). Weighted versions of MLE, MME and QME are available.") (define-public r-energy (package (name "r-energy") - (version "1.7-10") + (version "1.7-11") (source (origin (method url-fetch) (uri (cran-uri "energy" version)) (sha256 (base32 - "19xyw5bkyzfk22gly2ca2nsznqnrhaq4a77727kr1k26bj3y8gal")))) + "04b55ckmaqbnlpifg4w7smvly03kqycklvbg9x8d4yf902q8z7y2")))) (build-system r-build-system) (propagated-inputs (list r-boot r-gsl r-rcpp)) @@ -5505,6 +6092,43 @@ testing framework of Wald are generic and can therefore also be used in other contexts.") (license license:gpl2+))) +(define-public r-cvxr + (package + (name "r-cvxr") + (version "1.0-11") + (source (origin + (method url-fetch) + (uri (cran-uri "CVXR" version)) + (sha256 + (base32 + "0alp1g4bszxqcrjbn54bz1zswg8y10372fwwlbi0jjazycw9cap9")))) + (properties `((upstream-name . "CVXR"))) + (build-system r-build-system) + (propagated-inputs + (list r-bit64 + r-ecosolver + r-gmp + r-matrix + r-osqp + r-r6 + r-rcpp + r-rcppeigen + r-rmpfr + r-scs)) + (native-inputs (list r-knitr)) + (home-page "https://cvxr.rbind.io") + (synopsis "Disciplined convex optimization") + (description + "This package provides an object-oriented modeling language for +@dfn{disciplined convex programming} (DCP) as described in Fu, +Narasimhan, and Boyd (2020, <doi:10.18637/jss.v094.i14>). It allows +the user to formulate convex optimization problems in a natural way +following mathematical convention and DCP rules. The system analyzes +the problem, verifies its convexity, converts it into a canonical +form, and hands it off to an appropriate solver to obtain the +solution. Interfaces to solvers on CRAN and elsewhere are provided.") + (license license:asl2.0))) + (define-public r-squarem (package (name "r-squarem") @@ -5531,13 +6155,13 @@ available in a vignette.") (define-public r-progressr (package (name "r-progressr") - (version "0.11.0") + (version "0.12.0") (source (origin (method url-fetch) (uri (cran-uri "progressr" version)) (sha256 - (base32 "1nbc6vvsyqa1gvh1a1m4prnvng88wsa0r35i9fiwq84a6j18qrnq")))) + (base32 "0nahvfcnx45n0q24r4j9cjqmmgh302ra3207izs6fzfda7sqn25q")))) (properties `((upstream-name . "progressr"))) (build-system r-build-system) (propagated-inputs @@ -5556,14 +6180,14 @@ these progress updates.") (define-public r-lava (package (name "r-lava") - (version "1.6.10") + (version "1.7.1") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 - "0bi3c1aqwlq7jbz4raz6vga4r264w7lldi0i62xjlbl7hnlgi23s")))) + "0r7panw0pb9xi10navih9796r08yc5l6j914pfn8wzlm4mfwr7bs")))) (build-system r-build-system) (propagated-inputs (list r-future-apply r-numderiv r-progressr r-squarem r-survival)) @@ -5645,17 +6269,42 @@ techniques from R packages and provides a common interface for calling the methods.") (license license:gpl3))) +(define-public r-timechange + (package + (name "r-timechange") + (version "0.1.1") + (source (origin + (method url-fetch) + (uri (cran-uri "timechange" version)) + (sha256 + (base32 + "0w3zbmzhg3zr5d9aa83kmr6gyhk75l7jysa7zs0pnz9x4ffr20w5")))) + (properties `((upstream-name . "timechange"))) + (build-system r-build-system) + (propagated-inputs (list r-cpp11)) + (home-page "https://github.com/vspinu/timechange/") + (synopsis "Efficient manipulation of Date-Times") + (description + "This package provides efficient routines for manipulation of +date-time objects while accounting for time-zones and daylight saving +times. The package includes utilities for updating of date-time +components (year, month, day etc.), modification of time-zones, +rounding of date-times, period addition and subtraction etc. Parts of +the CCTZ source code, released under the Apache 2.0 License, are +included in this package.") + (license license:gpl3))) + (define-public r-timedate (package (name "r-timedate") - (version "4021.104") + (version "4022.108") (source (origin (method url-fetch) (uri (cran-uri "timeDate" version)) (sha256 (base32 - "03ncgbc9igiwl4s8pa94nj2v7aw3gw8ay51pwvv9gkv2f7l7dvh3")))) + "1vyfpz2ac43c0s6a4j4d0xfc430mwgw3syf03xszzggnw97rp555")))) (properties `((upstream-name . "timeDate"))) (build-system r-build-system) (home-page "https://www.rmetrics.org") @@ -5669,14 +6318,14 @@ calendar objects.") (define-public r-magic (package (name "r-magic") - (version "1.6-0") + (version "1.6-1") (source (origin (method url-fetch) (uri (cran-uri "magic" version)) (sha256 (base32 - "1gybia2aq80ldk1d845y5srncfzbbmpqhgl7vfaz7qqqjs6d85j5")))) + "0xkrrg5qk62pfqx0avijdjaljzslpwd0hv2m52qnqwrbx5xfqyfa")))) (build-system r-build-system) (propagated-inputs (list r-abind)) @@ -5692,14 +6341,14 @@ dimensioned arrays.") (define-public r-rmysql (package (name "r-rmysql") - (version "0.10.23") + (version "0.10.25") (source (origin (method url-fetch) (uri (cran-uri "RMySQL" version)) (sha256 (base32 - "05aavyggyjv46awa7ggbxlfcy9707vak5kh7kj0ljdx8zga7xb7l")))) + "1527ba5vqg4ss6rqxrkxa1a66r1m9h4zmdnv9xdzva8fv2dhy4zd")))) (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (inputs @@ -5741,6 +6390,38 @@ to access PostgreSQL database systems.") ;; under the PostgreSQL license. (license license:gpl2))) +(define-public r-rpostgres + (package + (name "r-rpostgres") + (version "1.4.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "RPostgres" version)) + (sha256 + (base32 + "1z6diaq4kwinl97d1v9cb96j8mrkj2s2v4ml1vykgy1jqi40dk69")))) + (properties `((upstream-name . "RPostgres"))) + (build-system r-build-system) + (inputs (list postgresql)) + (propagated-inputs + (list r-bit64 + r-blob + r-dbi + r-hms + r-lubridate + r-plogr + r-rcpp + r-withr)) + (native-inputs + (list pkg-config r-knitr)) + (home-page "https://rpostgres.r-dbi.org") + (synopsis "Rcpp Interface to PostgreSQL") + (description + "This package provides a fully @code{DBI}-compliant @code{Rcpp}-backed +interface to @code{PostgreSQL}, a relational database.") + (license license:gpl3))) + (define-public r-linprog (package (name "r-linprog") @@ -5829,14 +6510,14 @@ multivariate and 5 functional classification problems are included.") (define-public r-gower (package (name "r-gower") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "gower" version)) (sha256 (base32 - "0p9qx9aafkdm7wibfwk59jzw6vspsff6zwp84bc40lg0myxbf737")))) + "1z0mhfp8xp7rk9i820pkvspm6mwih24g6b5rqs63m37sbs79ssi9")))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/gower") (synopsis "Gower's distance") @@ -5900,14 +6581,14 @@ problems as well as resampling based estimators of prediction error.") (define-public r-psych (package (name "r-psych") - (version "2.2.5") + (version "2.2.9") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 - "08f3byqwabgkqcxwpjbsxdcjkdg012iraqinw0fzskfl1srzkhyw")))) + "0wamcwbwn2x5y91d5hv3l3sfc41k685hlsv9cx8gkzl7yfziimac")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-mnormt r-nlme)) @@ -5953,21 +6634,20 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "14i8729m38nxf5q344isgq4006p3b50wi3q8jgckxqphhnj5lpjb")))) + "13hj4y3ajrn7x8hvirp2vfh1c8j2pdrz3dnxc5f0dr7jyfhp4dcy")))) (build-system r-build-system) (propagated-inputs (list r-backports r-dplyr r-ellipsis r-generics - r-ggplot2 r-glue r-purrr r-rlang @@ -5992,17 +6672,18 @@ provides a one-row summary of model-level statistics.") (define-public r-recipes (package (name "r-recipes") - (version "1.0.1") + (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "recipes" version)) (sha256 (base32 - "1jav29biq13xf0vg9kj3k6khqb71hqak26kxxi0vy29l849f4fly")))) + "0pi7j1jj5dmc5kzx6zkm691xya7dw4fn8c8nb2x3gs8mp14spzhg")))) (build-system r-build-system) (propagated-inputs (list r-cli + r-clock r-dplyr r-ellipsis r-generics @@ -6062,14 +6743,14 @@ for certain use cases.") (define-public r-ggrepel (package (name "r-ggrepel") - (version "0.9.1") + (version "0.9.2") (source (origin (method url-fetch) (uri (cran-uri "ggrepel" version)) (sha256 (base32 - "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9")))) + "123lh86qs7w1i3v8i1a08jxlwx4sy32bpznyclm8wlkph728hc0a")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-rcpp r-rlang r-scales)) @@ -6132,16 +6813,69 @@ color labels, layout, etc.") ;; Any version of the GPL (license license:gpl2+))) +(define-public r-stable + (package + (name "r-stable") + (version "1.1.6") + (source (origin + (method url-fetch) + (uri (cran-uri "stable" version)) + (sha256 + (base32 + "194xsa291v5f0jya1c3aigbclg8cci427ffpb8brxamm6n57hf12")))) + (properties `((upstream-name . "stable"))) + (build-system r-build-system) + (propagated-inputs (list r-rmutil)) + (home-page "https://www.commanster.eu/rcode.html") + (synopsis + "Probability functions and regression models for stable distributions") + (description + "This package provides density, distribution, quantile and hazard +functions of a stable variate, as well as generalized regression models for +the parameters of a stable distribution.") + (license license:gpl2+))) + +(define-public r-statip + (package + (name "r-statip") + (version "0.2.3") + (source (origin + (method url-fetch) + (uri (cran-uri "statip" version)) + (sha256 + (base32 + "0kymc3ds1nx0h11ffmm3vmqr1w34gd0k788vf72x2v45h8c1ma2n")))) + (properties `((upstream-name . "statip"))) + (build-system r-build-system) + (propagated-inputs + (list r-clue r-rpart)) + (home-page "https://github.com/paulponcet/statip") + (synopsis "Statistical functions for probability distributions and regression") + (description + "This package provides a collection of miscellaneous statistical +functions for: +@itemize +@item probability distributions, +@item probability density estimation, +@item most frequent value estimation, +@item other statistical measures of location, +@item construction of histograms, +@item calculation of the Hellinger distance, +@item use of classical kernels, and +@item univariate piecewise-constant regression. +@end itemize") + (license license:gpl3))) + (define-public r-stringdist (package (name "r-stringdist") - (version "0.9.8") + (version "0.9.10") (source (origin (method url-fetch) (uri (cran-uri "stringdist" version)) (sha256 - (base32 "1fv1hbdlm8qwx57b2aj50mw0say5k48awzavx65mfk67qp6ddk7g")))) + (base32 "1s3cy2q6l4ppgslwfbfydi5f3kzshfhzkb25gz546n7jgw5jxm3g")))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/stringdist") (synopsis "Approximate string matching and string distance functions") @@ -6158,14 +6892,14 @@ or between integer vectors representing generic sequences.") (define-public r-ucminf (package (name "r-ucminf") - (version "1.1-4") + (version "1.1-4.1") (source (origin (method url-fetch) (uri (cran-uri "ucminf" version)) (sha256 (base32 - "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2")))) + "1cknk42allcflgk16i4gwi4a389idrxqz6y2w8i7s9mdfgrvd981")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ucminf/") @@ -6231,17 +6965,17 @@ response matrices.") (define-public r-ordinal (package (name "r-ordinal") - (version "2019.12-10") + (version "2022.11-16") (source (origin (method url-fetch) (uri (cran-uri "ordinal" version)) (sha256 (base32 - "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs")))) + "14yld28vjmvxbwz6mapfri4vrj3nsf9p73fn2z80j6jkz8fsv22l")))) (build-system r-build-system) (propagated-inputs - (list r-mass r-matrix r-numderiv r-ucminf)) + (list r-mass r-matrix r-nlme r-numderiv r-ucminf)) (home-page "https://github.com/runehaubo/ordinal") (synopsis "Regression models for ordinal data") (description @@ -6300,14 +7034,14 @@ clustered data.") (define-public r-mitml (package (name "r-mitml") - (version "0.4-3") + (version "0.4-4") (source (origin (method url-fetch) (uri (cran-uri "mitml" version)) (sha256 (base32 - "00i18nnvrdrg91crgcp2a431xs71cawaip3xkqk2myv0iav3xga9")))) + "12mgjvifpprzlpjbcybd08fkps0kdxim45saan4cng4lc4klh880")))) (build-system r-build-system) (propagated-inputs (list r-haven r-jomo r-pan)) @@ -6325,14 +7059,14 @@ analysis of multiply imputed data sets.") (define-public r-mice (package (name "r-mice") - (version "3.14.0") + (version "3.15.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 - "01fnfrr7adp29s5kic95r9q0rdznkz2pjmziyimnrqzyicyvfyzq")))) + "0yz88b40mpn24z40yfpxrkwrsxk362gwks3v5x69rkix1qkdsr1x")))) (build-system r-build-system) (propagated-inputs (list r-broom @@ -6342,8 +7076,7 @@ analysis of multiply imputed data sets.") r-lattice r-rcpp r-rlang - r-tidyr - r-withr)) + r-tidyr)) (home-page "https://cran.r-project.org/web/packages/mice/") (synopsis "Multivariate imputation by chained equations") (description @@ -6456,6 +7189,47 @@ University Press. It provides smoothing methods for nonparametric regression and density estimation") (license license:gpl2+))) +(define-public r-smurf + (package + (name "r-smurf") + (version "1.1.3") + (source (origin + (method url-fetch) + (uri (cran-uri "smurf" version)) + (sha256 + (base32 + "0n99dzsb17r0a6d8nkijfg6rdvvc2g4pard2dnmyjq0p69j3f3gb")))) + (properties `((upstream-name . "smurf"))) + (build-system r-build-system) + (propagated-inputs + (list r-catdata + r-glmnet + r-mass + r-matrix + r-mgcv + r-rcolorbrewer + r-rcpp + r-rcpparmadillo + r-speedglm)) + (native-inputs (list r-knitr)) + (home-page "https://gitlab.com/TReynkens/smurf") + (synopsis "Sparse multi-type regularized feature modeling") + (description + "The @code{smurf} package contains the implementation of the +@dfn{Sparse Multi-type Regularized Feature} (SMuRF) modeling algorithm +to fit @dfn{generalized linear models} (GLMs) with multiple types of +predictors via regularized maximum likelihood. Next to the fitting +procedure, following functionality is available: + +@itemize +@item Selection of the regularization tuning parameter lambda using + three different approaches: in-sample, out-of-sample or using + cross-validation. +@item S3 methods to handle the fitted object including visualization + of the coefficients and a model summary. +@end itemize") + (license license:gpl2+))) + (define-public r-venndiagram (package (name "r-venndiagram") @@ -6482,14 +7256,14 @@ structure.") (define-public r-vioplot (package (name "r-vioplot") - (version "0.3.7") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "vioplot" version)) (sha256 (base32 - "1dmdasp3jldc41233z6r08w3j76vyyp9m3jrj7n4ahk48yd5siq6")))) + "1db7g0378jbcd6ssb7afff4y4r0v472qnb625hfwixx4wf1v8aap")))) (build-system r-build-system) (propagated-inputs (list r-sm r-zoo)) @@ -6530,14 +7304,14 @@ training models for classification or ranking.") (define-public r-xts (package (name "r-xts") - (version "0.12.1") + (version "0.12.2") (source (origin (method url-fetch) (uri (cran-uri "xts" version)) (sha256 (base32 - "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n")))) + "0hx7vh8cm4c80rnhwqg78l5xb0snvf4adrkbb74z93vmxgm7qa4w")))) (build-system r-build-system) (propagated-inputs (list r-zoo)) (home-page "https://github.com/joshuaulrich/xts") @@ -6704,14 +7478,14 @@ phylogenies and ancestral character states.") (define-public r-dtw (package (name "r-dtw") - (version "1.22-3") + (version "1.23-1") (source (origin (method url-fetch) (uri (cran-uri "dtw" version)) (sha256 (base32 - "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z")))) + "0vc2is1hf1g0sw92kzl8mddck264qwiqgm5q2wkcwwz65fss7mkf")))) (build-system r-build-system) (propagated-inputs (list r-proxy)) (home-page "http://dtw.r-forge.r-project.org/") @@ -6769,17 +7543,17 @@ plotting. a three dimensional point cloud.") (define-public r-ggridges (package (name "r-ggridges") - (version "0.5.3") + (version "0.5.4") (source (origin (method url-fetch) (uri (cran-uri "ggridges" version)) (sha256 (base32 - "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm")))) + "0lfqx21g09s3fp74mld47qfx1nnav18xqj37griyqk406hh1rxrb")))) (build-system r-build-system) (propagated-inputs - (list r-ggplot2 r-plyr r-scales r-withr)) + (list r-ggplot2 r-scales r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/clauswilke/ggridges") @@ -6811,17 +7585,37 @@ distributions over time or space. This package enables the creation of such plots in @code{ggplot2}.") (license license:gpl2))) +(define-public r-gss + (package + (name "r-gss") + (version "2.2-3") + (source (origin + (method url-fetch) + (uri (cran-uri "gss" version)) + (sha256 + (base32 + "0jr45lkpcndg5nynjsfnxn1wwkh4gkhsgv4hlvw6jn2frw0n8c14")))) + (properties `((upstream-name . "gss"))) + (build-system r-build-system) + (native-inputs (list gfortran)) + (home-page "https://cran.r-project.org/package=gss") + (synopsis "General smoothing splines") + (description + "This package provides a comprehensive collection for structural +multivariate function estimation using smoothing splines.") + (license license:gpl2+))) + (define-public r-cli (package (name "r-cli") - (version "3.4.0") + (version "3.5.0") (source (origin (method url-fetch) (uri (cran-uri "cli" version)) (sha256 (base32 - "0mxsls49g8m5vrak64b9mpsgw3mh8hnb1xxn56skbn4qb1hppbff")))) + "1p3gzq30f7hpr3v2s555z18r0y57zq2h03kijv7rl48lqzbnrjwc")))) (build-system r-build-system) (home-page "https://github.com/r-lib/cli#readme") (synopsis "Helpers for developing command line interfaces") @@ -6854,13 +7648,13 @@ script.") (define-public r-aricode (package (name "r-aricode") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "aricode" version)) (sha256 (base32 - "0772l9gyrih48l1kymih0mb7szjqqnwcm4lzj0yzp4cs8l2mdf4f")))) + "1w5jnql49f0wd5h4b89l69s7qldp7qm90p4jm0j4kz9w0vvm2kjz")))) (properties `((upstream-name . "aricode"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp)) @@ -6875,6 +7669,31 @@ information} (NMI), @dfn{adjusted mutual information} (AMI), @dfn{normalized variation information} (NVI) and entropy.") (license license:gpl3+))) +(define-public r-attempt + (package + (name "r-attempt") + (version "0.3.1") + (source (origin + (method url-fetch) + (uri (cran-uri "attempt" version)) + (sha256 + (base32 + "1ylgg7jcp8wqmxgf1mydnvh26k0mr8jyjla4hw06730r40yrs58m")))) + (properties `((upstream-name . "attempt"))) + (build-system r-build-system) + (propagated-inputs (list r-rlang)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/ColinFay/attempt") + (synopsis "Tools for defensive programming") + (description + "This package provides tools for defensive programming. It is inspired +by @code{purrr} mappers and based on @code{rlang}. Attempt extends and +facilitates defensive programming by providing a consistent grammar, and a set +of functions for common tests and conditions. Attempt only depends on +@code{rlang}, and focuses on speed, so it can be integrated with other +functions and used in the data analysis.") + (license license:expat))) + (define-public r-debugme (package (name "r-debugme") @@ -6898,13 +7717,13 @@ constants, and control debugging of packages via environment variables.") (define-public r-processx (package (name "r-processx") - (version "3.7.0") + (version "3.8.0") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 - (base32 "1lsyspd3jak6g625sna5jdqrg5fw02qgdfiz0hsyqlzw6m0qssny")))) + (base32 "02zviyqk1ljvrdc3bgqxnkyb8mkmqlgmq6l0c881a523dk9djw4j")))) (build-system r-build-system) (propagated-inputs (list r-ps r-r6)) @@ -6920,6 +7739,28 @@ standard output and error of the processes, using non-blocking connections. timeout. It can also poll several processes at once.") (license license:expat))) +(define-public r-timeseries + (package + (name "r-timeseries") + (version "4021.105") + (source (origin + (method url-fetch) + (uri (cran-uri "timeSeries" version)) + (sha256 + (base32 + "1k6vihbs20m7zjrxh13y9mmsvnia3844c7j13p0b7m5i9fb6rqxz")))) + (properties `((upstream-name . "timeSeries"))) + (build-system r-build-system) + (propagated-inputs (list r-timedate)) + (home-page + "https://r-forge.r-project.org/scm/viewvc.php/pkg/timeSeries/?root=rmetrics") + (synopsis "Metrics for financial time series objects") + (description + "This package implements S4 classes and various tools for financial time +series. Basic functions such as scaling and sorting, subsetting, mathematical +operations and statistical functions are provided.") + (license license:gpl2+))) + (define-public r-tsp (package (name "r-tsp") @@ -6985,14 +7826,14 @@ of merit, ordering functions, and enhanced versions of @code{pairs} and (define-public r-webshot (package (name "r-webshot") - (version "0.5.3") + (version "0.5.4") (source (origin (method url-fetch) (uri (cran-uri "webshot" version)) (sha256 (base32 - "1h6v94zwq0ypgi4vf8xlhp5k13j7f9061hx908177i68c6zg5i5p")))) + "094ggb6yby5irf3hj45p6vp5wdy6rjwpc0h6xbgf2mbqxyxbkhix")))) (build-system r-build-system) (propagated-inputs (list r-callr r-jsonlite r-magrittr)) @@ -7008,17 +7849,18 @@ Markdown documents.") (define-public r-seriation (package (name "r-seriation") - (version "1.3.6") + (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "seriation" version)) (sha256 (base32 - "1i0bbfxbvzy2lwprliqrn97ww8lqr2s9klg0g3qqjyr8cdxs5fyc")))) + "1b8z7alav4d0i90251crzrq3yp3f11w0zlalh1f3b7si5yl2dkmr")))) (build-system r-build-system) (propagated-inputs - (list r-cluster + (list r-ca + r-cluster r-colorspace r-gclus r-mass @@ -7040,13 +7882,13 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.33") + (version "0.36") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 - (base32 "0v7f84gqsb94zff4x64478fssjg0sbis9m34vsxnjyw6ab9c5ys5")))) + (base32 "1vk930bn7rp2qp8yvmd9d3lgi10rgf20n62jr3lfwi6hf7jhs5x8")))) (build-system r-build-system) ;; knitr itself depends on xfun #; @@ -7105,13 +7947,13 @@ to variables on the left-hand side of the assignment.") (define-public r-zlog (package (name "r-zlog") - (version "1.0.0") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "zlog" version)) (sha256 (base32 - "1d5j31p0h3rrn230087h3ngpvwknlisjv0f1qdbicdj9m177spci")))) + "0fi9aqrmikdg5ibwhn82kslj4lxih03vm27jmi14m73h09yy4in5")))) (properties `((upstream-name . "zlog"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -7127,17 +7969,20 @@ estimated from a given sample.") (define-public r-vctrs (package (name "r-vctrs") - (version "0.4.1") + (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 - "1pb0wjpwix29q8d8p3wi72a9mp9mif7369pk31w238cs00g8hxln")))) + "01yv85rjpn9cz4473m768awrcaif51ffjh29p097c7pj2zvq4ya9")))) (build-system r-build-system) (propagated-inputs - (list r-cli r-glue r-rlang)) + (list r-cli r-glue r-lifecycle r-rlang)) + ;; We can't have r-knitr among the inputs here, because r-vctrs ends up + ;; being an eventual input to r-knitr. + #; (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/vctrs") @@ -7209,6 +8054,28 @@ annotation file. This package is intended to be used as example data for packages that work with genomic data.") (license license:gpl2+))) +(define-public r-piton + (package + (name "r-piton") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "piton" version)) + (sha256 + (base32 "1krf6zi238m275nxjlpyayv8y2drbgs2kg19dpkqm0lmlz5y5ar8")))) + (properties `((upstream-name . "piton"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp)) + (home-page "https://github.com/Ironholds/piton") + (synopsis "Parsing expression grammars in Rcpp") + (description + "This package provides a wrapper around the Parsing Expression Grammar +Template Library, a C++11 library for generating parsing expression grammars, +that makes it accessible within Rcpp. With this, developers can implement +their own grammars and easily expose them in R packages.") + (license license:expat))) + (define-public r-uuid (package (name "r-uuid") @@ -7231,14 +8098,14 @@ packages that work with genomic data.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.41") + (version "0.43") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "1fhnh53fg8l4qyignvgz0nk5nqmljyykn8gpvq82nr7c051rfqaz")))) + "01183i6z6jyyqmmxri3xmscn7k6hswi2q7r0b5ix0s7pd1cz57jq")))) (build-system r-build-system) (propagated-inputs (list r-xfun)) @@ -7290,14 +8157,14 @@ features: (define-public r-network (package (name "r-network") - (version "1.17.2") + (version "1.18.0") (source (origin (method url-fetch) (uri (cran-uri "network" version)) (sha256 (base32 - "1xrhzbci7ls4h05skdlirxl49jsvmylrqivz2kd6i33wh2ca324m")))) + "0nyf8i94lnqm4gfjz1szbwvl4c438xg3rjdkqr18fz68fh0v3x2r")))) (build-system r-build-system) (propagated-inputs (list r-magrittr r-statnet-common r-tibble)) @@ -7816,14 +8683,14 @@ financial trading strategies.") (define-public r-tseries (package (name "r-tseries") - (version "0.10-51") + (version "0.10-52") (source (origin (method url-fetch) (uri (cran-uri "tseries" version)) (sha256 (base32 - "0zr09ikaz96djcvnjbr8ah6waqzjy06f4yd4isshlwc391q20px5")))) + "0icgmng0dzvfkkn6dam74wvlz8g0cy46wkw57f5lpd5kxpdwi6ck")))) (build-system r-build-system) (propagated-inputs (list r-quadprog r-quantmod r-zoo)) @@ -7904,6 +8771,37 @@ functions and random generation functions for a large number of univariate and multivariate distributions.") (license license:gpl2))) +(define-public r-fbasics + (package + (name "r-fbasics") + (version "4021.93") + (source (origin + (method url-fetch) + (uri (cran-uri "fBasics" version)) + (sha256 + (base32 + "1lmmdwzvqhggy6rr7yc9y5f8hxxgyzsgwm3ry0sz5ljbgfijl7g6")))) + (properties `((upstream-name . "fBasics"))) + (build-system r-build-system) + (propagated-inputs + (list r-gss + r-mass + r-spatial + r-stabledist + r-timedate + r-timeseries)) + (home-page + "https://r-forge.r-project.org/scm/viewvc.php/pkg/fBasics/?root=rmetrics") + (synopsis "Metrics for markets and basic statistics") + (description + "This package provides a collection of functions to explore and to +investigate basic properties of financial returns and related quantities. The +covered fields include techniques of explorative data analysis and the +investigation of distributional properties, including parameter estimation and +hypothesis testing. Even more, there are several utility functions for data +handling and management.") + (license license:gpl2+))) + (define-public r-fractal (package (name "r-fractal") @@ -7930,6 +8828,28 @@ multivariate distributions.") chaotic time series analysis.") (license license:gpl2))) +(define-public r-fresh + (package + (name "r-fresh") + (version "0.2.0") + (source (origin + (method url-fetch) + (uri (cran-uri "fresh" version)) + (sha256 + (base32 + "1787mm6w2s5x9scxy7r9cb77rgpmy4ngwkn4z8g3gs48mrab4bd9")))) + (properties `((upstream-name . "fresh"))) + (build-system r-build-system) + (propagated-inputs (list r-htmltools r-rstudioapi r-sass r-shiny)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/dreamRs/fresh") + (synopsis "Create custom Bootstrap themes to use in Shiny") + (description + "Customize Bootstrap and Bootswatch themes, like colors, fonts, +grid layout, to use in Shiny applications, rmarkdown documents and +flexdashboard.") + (license license:gpl3))) + (define-public r-urca (package (name "r-urca") @@ -8012,14 +8932,14 @@ sample Robust Rank-Order Distributional Test.") (define-public r-expm (package (name "r-expm") - (version "0.999-6") + (version "0.999-7") (source (origin (method url-fetch) (uri (cran-uri "expm" version)) (sha256 (base32 - "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c")))) + "1wd03dcqxyi7kyznfq7107ix1bsp7rwzqqv6w7p37pdq2jwlkwi8")))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (native-inputs (list gfortran)) @@ -8099,14 +9019,14 @@ creation and manipulation of WAVE audio files.") (define-public r-np (package (name "r-np") - (version "0.60-14") + (version "0.60-16") (source (origin (method url-fetch) (uri (cran-uri "np" version)) (sha256 (base32 - "0v6mhcwdnqj5kjxwrzcqlff021ih2jdarwmikdm5bvjfwi8pyarl")))) + "1c01drwvh2jj0s40q19ghdf429s6px07akg6d0yfanah3706gydy")))) (build-system r-build-system) (propagated-inputs (list r-boot r-cubature r-quadprog r-quantreg)) @@ -8191,14 +9111,14 @@ powerful and convenient features.") (define-public r-heatmaply (package (name "r-heatmaply") - (version "1.3.0") + (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "heatmaply" version)) (sha256 (base32 - "1w8yyzb68laxd4zxycvgmpqj5wnyidjgv1vbzbxndp9p92f2cp8a")))) + "0zgaqmbc1nha38c8kx5xdjdjbwmykrf2acq8ydki8dqixv6b34la")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -8372,6 +9292,27 @@ facilitate data exploration.") experimental designs and random samples for common sampling designs.") (license license:expat))) +(define-public r-roptim + (package + (name "r-roptim") + (version "0.1.6") + (source (origin + (method url-fetch) + (uri (cran-uri "roptim" version)) + (sha256 + (base32 + "11h6qdi0rsv0bpps6nxkzzapan284q0gldzkmgx3ww5kvnic5w3y")))) + (properties `((upstream-name . "roptim"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp r-rcpparmadillo)) + (home-page "https://github.com/ypan1988/roptim/") + (synopsis "General purpose optimization in R using C++") + (description + "This package performs optimization in R using C++. A unified wrapper +interface is provided to call C functions of the five optimization algorithms +(Nelder-Mead, BFGS, CG, L-BFGS-B and SANN) underlying @code{optim()}.") + (license license:gpl2+))) + (define-public r-base64url (package (name "r-base64url") @@ -8399,6 +9340,34 @@ with a simple base32 encoder/decoder suited for case insensitive file systems.") (license license:gpl3))) +(define-public r-baseline + (package + (name "r-baseline") + (version "1.3-4") + (source (origin + (method url-fetch) + (uri (cran-uri "baseline" version)) + (sha256 + (base32 + "1kl68zvyi2zd73jy3axrvrymwn4y6l4pd62nz0fciwbgkjhz3yyx")))) + (properties `((upstream-name . "baseline"))) + (build-system r-build-system) + (propagated-inputs + (list r-gwidgets2tcltk ;for GUI + r-limsolve + r-sparsem)) + (home-page "https://github.com/khliland/baseline/") + (synopsis "Baseline correction of spectra") + (description + "This package is a collection of baseline correction algorithms. Beside +those it provides a framework and a Tcl/Tk enabled GUI for optimizing baseline +algorithm parameters. Typical use is the removal of the background effects from +spectra, which are originating from various types of spectroscopy and spectrometry. +Also, there is a possibility of optimizing this with regard to regression or +classification results. Correction methods include polynomial fitting, weighted +local smoothers and many more.") + (license license:gpl2))) + (define-public r-radiant-data (package (name "r-radiant-data") @@ -8770,13 +9739,13 @@ contain lags, diffs and missing values.") (define-public r-dynutils (package (name "r-dynutils") - (version "1.0.9") + (version "1.0.11") (source (origin (method url-fetch) (uri (cran-uri "dynutils" version)) (sha256 - (base32 "1pcj4igaw1g898xb42kcpzfmqy80xai5ki5bpnkf8hg738wm00qz")))) + (base32 "06an2bm1d131v28m240vii2wisbz3zs32wbamm2w7r8rl3yrxkh9")))) (properties `((upstream-name . "dynutils"))) (build-system r-build-system) (propagated-inputs @@ -8825,17 +9794,40 @@ variable) to other variables (explanatory variables) are derived and evaluated by the @dfn{Akaike Information Criterion} (AIC).") (license license:gpl2+))) +(define-public r-catdata + (package + (name "r-catdata") + (version "1.2.2") + (source (origin + (method url-fetch) + (uri (cran-uri "catdata" version)) + (sha256 + (base32 + "14kx7yi0cv6dyh9wjasb8gn6cp1bhglgwql7dc2a7lqvdcp0d5vj")))) + (properties `((upstream-name . "catdata"))) + (build-system r-build-system) + (propagated-inputs (list r-mass)) + (home-page "https://cran.r-project.org/package=catdata") + (synopsis + "Datasets and examples used in the book @emph{Regression for Categorical Data}") + (description + "This R package contains examples from the book @emph{Regression +for Categorical Data}, Tutz 2012, Cambridge University Press. The +names of the examples refer to the chapter and the data set that is +used.") + (license license:gpl2))) + (define-public r-arules (package (name "r-arules") - (version "1.7-4") + (version "1.7-5") (source (origin (method url-fetch) (uri (cran-uri "arules" version)) (sha256 (base32 - "0pmikfq1phs73lmvhb4j9rlxj3z7kbp9wb619q2gqxpi9948raij")))) + "0d04w28hl9gcrvkj0v0q77x4a89jhvzf1imw58xfgncap8mc6555")))) (build-system r-build-system) (propagated-inputs (list r-generics r-matrix)) @@ -8851,14 +9843,14 @@ and Eclat.") (define-public r-parsedate (package (name "r-parsedate") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "parsedate" version)) (sha256 (base32 - "1c2cpsvma3fkx6zp191bpfvf5rmpsr13g8rzqk6ycyb0n7b9k4qy")))) + "1cfinqlbchmkhkgmdwiy3mnxb17lp02jfk2gpw56hq9vh6wimhqz")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/parsedate") (synopsis @@ -8919,14 +9911,14 @@ misclassification probabilities of different models.") (define-public r-zip (package (name "r-zip") - (version "2.2.1") + (version "2.2.2") (source (origin (method url-fetch) (uri (cran-uri "zip" version)) (sha256 (base32 - "08hl0sqiwh9my9ivkvkig044w7ppk8h8n38j3i0kjcc1fh43v1ql")))) + "194f19649jqw8wa2bd1kj3873hqnqxsrbqdwnvlzngi8pcixwv71")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/zip") (synopsis "Cross-platform Zip compression") @@ -8939,14 +9931,14 @@ additional external tools on any platform.") (define-public r-openxlsx (package (name "r-openxlsx") - (version "4.2.5") + (version "4.2.5.1") (source (origin (method url-fetch) (uri (cran-uri "openxlsx" version)) (sha256 (base32 - "0695b265g7jwiqk5c3vmmfkvagx82bkpwhvqzhqaqmmn34l6vl35")))) + "1j2516plvlrp7l0mw7xqjhjjcidfdnfsybdhi2bx3n0910w29lk4")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-stringi r-zip)) @@ -9001,14 +9993,14 @@ simple method for converting between file types.") (define-public r-maptools (package (name "r-maptools") - (version "1.1-4") + (version "1.1-6") (source (origin (method url-fetch) (uri (cran-uri "maptools" version)) (sha256 (base32 - "1jgx8iiirj8qhrmh19mkisa35jcql7352dmc7lvwi5vxg3wjbvpk")))) + "024kyq81gwpl7shil63nng1z6pgqcwy6j6wj44gj7ch3vd9dz9fn")))) (build-system r-build-system) (propagated-inputs (list r-foreign r-lattice r-sp)) @@ -9387,6 +10379,28 @@ Tooltips and color gradients can be mapped to nodes using a numeric column in the source data frame.") (license license:gpl3+))) +(define-public r-rapiclient + (package + (name "r-rapiclient") + (version "0.1.3") + (source (origin + (method url-fetch) + (uri (cran-uri "rapiclient" version)) + (sha256 + (base32 + "1pm4kdga2nz1cpmchdb0ad8gr3bqfm84b1kl32cyc0x3x5rr2syz")))) + (properties `((upstream-name . "rapiclient"))) + (build-system r-build-system) + (propagated-inputs + (list r-httr r-jsonlite r-yaml)) + (home-page "https://github.com/bergant/rapiclient") + (synopsis "Dynamic OpenAPI/Swagger client") + (description + "This package lets you access services specified in OpenAPI (formerly +Swagger) format. It is not a code generator. The client is generated +dynamically as a list of R functions.") + (license license:expat))) + (define-public r-rappdirs (package (name "r-rappdirs") @@ -9410,14 +10424,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (define-public r-rastervis (package (name "r-rastervis") - (version "0.51.2") + (version "0.51.5") (source (origin (method url-fetch) (uri (cran-uri "rasterVis" version)) (sha256 (base32 - "0kgg6cm7xjqya2d46w0i1i1wjpkb8f99lyqy7rgwa7l9xmwzj5n1")))) + "18bsrw629p4pkyhrpjmiyhq73w882bhgpwmkih0gjnw3ywwgx7rs")))) (properties `((upstream-name . "rasterVis"))) (build-system r-build-system) (propagated-inputs @@ -9467,14 +10481,14 @@ those searches and pull data into their R sessions.") (define-public r-renv (package (name "r-renv") - (version "0.15.5") + (version "0.16.0") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 - "0bjq3ms5dg155clya62m462m93g90sxfxm7b4cqhqbx8vakskwdl")))) + "05m0idzjmg3wjlip9dy60nydk8dq7hdf3n9vnw6ldgp9f5mkx8gk")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (native-inputs @@ -9492,26 +10506,32 @@ reproducible.") (define-public r-learnr (package (name "r-learnr") - (version "0.10.1") + (version "0.11.2") (source (origin (method url-fetch) (uri (cran-uri "learnr" version)) (sha256 (base32 - "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31")))) + "1w8lcghnqvmggfp90hdpcjflvnxyp5shfk48vq5s4kci8414dm6j")))) (build-system r-build-system) + (native-inputs (list r-knitr)) (propagated-inputs (list r-checkmate + r-curl + r-digest r-ellipsis r-evaluate r-htmltools r-htmlwidgets r-jsonlite r-knitr + r-lifecycle r-markdown + r-promises r-rappdirs r-renv + r-rlang r-rmarkdown r-rprojroot r-shiny @@ -9584,14 +10604,14 @@ always locate the files relative to your project root.") (define-public r-reticulate (package (name "r-reticulate") - (version "1.26") + (version "1.27") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "1ibliic3qp597nskak2bfa6iyl721ssgcavwvfaf1c71plilimrz")))) + "19k96g43ll9zp72g9kmf9gg7k9cwwpyxzf2nd6fvx5jal5bq8mlx")))) (build-system r-build-system) (arguments (list @@ -9625,16 +10645,16 @@ Python to R they are converted back to R types.") (define-public r-bibtex (package (name "r-bibtex") - (version "0.4.2.3") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "bibtex" version)) (sha256 (base32 - "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv")))) + "0rwinwj0kw2872q2whhk03ianl9lcgs6dlhqzm513wj3bgpb90gc")))) (build-system r-build-system) - (propagated-inputs (list r-stringr)) + (propagated-inputs (list r-backports)) (home-page "https://github.com/romainfrancois/bibtex") (synopsis "Bibtex parser") (description "This package provides a utility for R to parse a bibtex @@ -9644,13 +10664,13 @@ file.") (define-public r-billboarder (package (name "r-billboarder") - (version "0.3.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "billboarder" version)) (sha256 - (base32 "189ngvg84rcwhrivxskmjv3srhadvzr4p1v8pf11axyv2qn01b0x")) + (base32 "1llac7fyyfax6q8n9b8lccyl9c8vxqvkfp341sz59mrw8yhwb2hr")) (snippet '(delete-file "inst/htmlwidgets/lib/billboard/billboard.pkgd.min.js")))) (properties `((upstream-name . "billboarder"))) @@ -9686,10 +10706,10 @@ file.") ("js-billboard" ,(origin (method url-fetch) - (uri "https://unpkg.com/billboard.js@3.2.0/dist/billboard.js") + (uri "https://unpkg.com/billboard.js@3.6.3/dist/billboard.js") (sha256 (base32 - "1kx5rqmn87pgal2cwmcij2rrnwa0fgcsw6y99m4i0l2sdm0qffv2")))))) + "1lyj4yl95qgh06iygb2y2mdg1zxijzxi5h85z7kp8ngm825z6rpi")))))) (home-page "https://github.com/dreamRs/billboarder") (synopsis "Create interactive charts with the JavaScript Billboard library") (description @@ -9750,14 +10770,14 @@ movies, and TV shows.") (define-public r-ggsignif (package (name "r-ggsignif") - (version "0.6.3") + (version "0.6.4") (source (origin (method url-fetch) (uri (cran-uri "ggsignif" version)) (sha256 (base32 - "1ad774c7s7y4i00xd89lfigr9aybl94q98ch598k3rchanr4b1fa")))) + "02mjailzyqkdnzky60dgampw2sq6mnn7s66fk0lhy32s8apm280i")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -9777,14 +10797,14 @@ and adds the annotation to the plot.") (define-public r-rstatix (package (name "r-rstatix") - (version "0.7.0") + (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "rstatix" version)) (sha256 (base32 - "0330y8iziffqg8j9j5h9zv4qcdyf8ybhmzxrr9fzq9nc6bf1gbm5")))) + "0c001w1mj8jw7gzmix90wzzb9kj45q173mzl7pmvykm77zpn61ak")))) (properties `((upstream-name . "rstatix"))) (build-system r-build-system) (propagated-inputs @@ -9814,14 +10834,14 @@ matrix.") (define-public r-ggpubr (package (name "r-ggpubr") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "ggpubr" version)) (sha256 (base32 - "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb")))) + "0fbm3rcpsabb7j7sdr69scqiq1bnx2623ji9ap9v4rmqqy8s08gv")))) (build-system r-build-system) (propagated-inputs (list r-cowplot @@ -9897,14 +10917,14 @@ clustering.") (define-public r-factominer (package (name "r-factominer") - (version "2.6") + (version "2.7") (source (origin (method url-fetch) (uri (cran-uri "FactoMineR" version)) (sha256 (base32 - "0xcg4vjs5v9k28hhxhkfkks7nvpxpp2cvim00kh67f4pq041c9l1")))) + "03952kcnwrm61kn5im55ky1j91nm5x4i4f5gs115li6gck63xf17")))) (properties `((upstream-name . "FactoMineR"))) (build-system r-build-system) (propagated-inputs @@ -10015,14 +11035,14 @@ results to the user.") (define-public r-hdf5r (package (name "r-hdf5r") - (version "1.3.6") + (version "1.3.7") (source (origin (method url-fetch) (uri (cran-uri "hdf5r" version)) (sha256 (base32 - "16iin6krx2c50wm4d1id71v3kci6djvlari3ahic25vw1dg1k81l")))) + "0nr9iywl2z7hrydvq5z61jvx6ls8wg72lzpr875p1jfi7s2052kf")))) (build-system r-build-system) (inputs (list hdf5 zlib)) @@ -10194,14 +11214,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rbibutils (package (name "r-rbibutils") - (version "2.2.9") + (version "2.2.11") (source (origin (method url-fetch) (uri (cran-uri "rbibutils" version)) (sha256 (base32 - "11pzbqykmn7m9gp5jspfcj6vij865wqf9ry6m3jkihvfj7zhfb5j")))) + "10g3fv8ninihjldhvh00yrp260dczhz3q519000jm3wp5w47b945")))) (properties `((upstream-name . "rbibutils"))) (build-system r-build-system) (home-page "https://geobosh.github.io/rbibutils/") @@ -10242,17 +11262,17 @@ references and Rd files.") (define-public r-officer (package (name "r-officer") - (version "0.4.4") + (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 - "1h6fcqw4bg644lwr5jggphyxp2d0ycya9q869z8099a50gc6h03f")))) + "1r885h8ma2py3idxkki2bnsbcimrw36qd6km2bhyhlav79n7bh4w")))) (build-system r-build-system) (propagated-inputs - (list r-r6 r-uuid r-xml2 r-zip)) + (list r-openssl r-r6 r-uuid r-xml2 r-zip)) (home-page "https://davidgohel.github.io/officer") (synopsis "Manipulation of Word and PowerPoint documents") (description @@ -10368,14 +11388,14 @@ or missing responses.") (define-public r-acdm (package (name "r-acdm") - (version "1.0.4.1") + (version "1.0.4.2") (source (origin (method url-fetch) (uri (cran-uri "ACDm" version)) (sha256 (base32 - "129ykw0j8z30mr4c01qzx6qy6h4bl87zxvmps0vkh8cqb7akninq")))) + "00i33b76gqllyc6ywwwrgyjvxfspqb3jf52b9sjaazlfwgn5xyjf")))) (properties `((upstream-name . "ACDm"))) (build-system r-build-system) (propagated-inputs @@ -10478,14 +11498,14 @@ Decomposition in R (Beaton et al 2014) <doi:10.1016/j.csda.2013.11.006>.") (define-public r-insight (package (name "r-insight") - (version "0.18.3") + (version "0.18.8") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "1bj6dliin3draqb447zyy1w4z277n8rj5sdl3lnx468bq1yqc8h9")))) + "01bm7w8f80i550gwv41kakaxp0d5a2pqa2s3ihz36snkczmdlapm")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -10614,14 +11634,14 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.8.0") + (version "0.8.3") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "03l9wgsikg1n2i3hxkb850kprs49nlrawyrm46k1d95b83d2qq8s")))) + "0fqc0zq1w7fdnql2m96g0rpichfpwrhyinnld29ddaw0d742gfj5")))) (build-system r-build-system) (propagated-inputs (list r-base64enc @@ -10649,14 +11669,14 @@ documents.") (define-public r-writexl (package (name "r-writexl") - (version "1.4.0") + (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "writexl" version)) (sha256 (base32 - "0mfzyn8n5x5x5gf382bqgq61zpw9dymrp5kzdm2sbszplmxf6xry")))) + "09whcadnwqcshicbhv1vnvdai087yimmnz9lvc3rld5nn8z66xcg")))) (build-system r-build-system) (inputs (list zlib)) (home-page "https://github.com/ropensci/writexl") @@ -10669,14 +11689,14 @@ libxlsxwriter.") (define-public r-biasedurn (package (name "r-biasedurn") - (version "1.07") + (version "2.0.8") (source (origin (method url-fetch) (uri (cran-uri "BiasedUrn" version)) (sha256 (base32 - "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3")))) + "0mmq8zf52p6y76nqm0fcvvg8bdlrfl12mlfr9fznz9zvm26pypi0")))) (properties `((upstream-name . "BiasedUrn"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/BiasedUrn/") @@ -10689,6 +11709,43 @@ noncentral hypergeometric distribution (also called extended hypergeometric distribution).") (license license:gpl3))) +(define-public r-golem + (package + (name "r-golem") + (version "0.3.5") + (source (origin + (method url-fetch) + (uri (cran-uri "golem" version)) + (sha256 + (base32 + "0rjkl1r83h0hcn30zssx64qm07sdx3g4v5rdxn56gbzfghw7ddcl")))) + (properties `((upstream-name . "golem"))) + (build-system r-build-system) + (propagated-inputs + (list r-attempt + r-cli + r-config + r-crayon + r-desc + r-fs + r-here + r-htmltools + r-pkgload + r-roxygen2 + r-rstudioapi + r-shiny + r-usethis + r-yaml)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/ThinkR-open/golem") + (synopsis "Framework for robust Shiny applications") + (description + "This package implements an opinionated framework for building a +production- ready Shiny application. Golem contains a series of tools like +dependency management, version management, easy installation and deployment or +documentation management.") + (license license:expat))) + (define-public r-goplot (package (name "r-goplot") @@ -10763,14 +11820,14 @@ matches version and feature constraints.") (define-public r-argparse (package (name "r-argparse") - (version "2.1.6") + (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "argparse" version)) (sha256 (base32 - "14p57nm0w3siqd473snzhpmnvsgl72x92pdcd64vhy2qg6nzmmra")))) + "193pjjy4vkmzmsc1w69szafgrisvn08gddilbxcg671sdk0dxd7k")))) (build-system r-build-system) (inputs (list python)) (propagated-inputs @@ -10857,14 +11914,14 @@ the work.") (define-public r-doby (package (name "r-doby") - (version "4.6.13") + (version "4.6.15") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 - "0qnfcw4rg5kd1mll3rq6vchz3lgdqfif9469p8x6ixsgrxxpivbz")))) + "14asz3bpyvxakvpap2aajk6f5j2d3d6vrvrgnlixg5q6gdbh465m")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs @@ -11168,14 +12225,14 @@ from the @code{stats} package (plus some extra parameters).") (define-public r-cmplot (package (name "r-cmplot") - (version "4.1.0") + (version "4.2.0") (source (origin (method url-fetch) (uri (cran-uri "CMplot" version)) (sha256 (base32 - "1h09prpiw7l32mr7jarp8ddrddg1431nfn4kw3bznfnv0sr78zfg")))) + "1icb7r8wj7x9vgcysr9qi28nvgxb9j3dhqw090smpp6d7b39zrjd")))) (properties `((upstream-name . "CMplot"))) (build-system r-build-system) (home-page "https://github.com/YinLiLin/CMplot") @@ -11193,14 +12250,14 @@ visualization and candidate genes around SNPs.") (define-public r-precrec (package (name "r-precrec") - (version "0.12.9") + (version "0.14.1") (source (origin (method url-fetch) (uri (cran-uri "precrec" version)) (sha256 (base32 - "1dfz2rqx2ww2l5r40ahg0qdj3rjrwiwh427mw7j5ynhpcj21j2qm")))) + "04pyqwc4p3bzwfcf7a74nkh7b2001053jagzvz9ghpyj380f66x8")))) (properties `((upstream-name . "precrec"))) (build-system r-build-system) (propagated-inputs @@ -11209,6 +12266,7 @@ visualization and candidate genes around SNPs.") r-ggplot2 r-gridextra r-rcpp + r-rlang r-withr)) (native-inputs (list r-knitr)) (home-page "https://evalclass.github.io/precrec/") @@ -11221,14 +12279,14 @@ of precision-recall and ROC (Receiver Operator Characteristics) curves.") (define-public r-netrep (package (name "r-netrep") - (version "1.2.4") + (version "1.2.6") (source (origin (method url-fetch) (uri (cran-uri "NetRep" version)) (sha256 (base32 - "1swlb2k9bc7whvslxbklz864j9ynvna73hvq5rhv61cv5vy05ksd")))) + "0hyj91fr4y9csj2dy4z9cpr92hh8gk3xnjr6zpk9n0wk37sx44h6")))) (properties `((upstream-name . "NetRep"))) (build-system r-build-system) (propagated-inputs @@ -11377,13 +12435,13 @@ ABC algorithms.") (define-public r-abctools (package (name "r-abctools") - (version "1.1.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "abctools" version)) (sha256 - (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97")))) + (base32 "02c473fqj7yd27flma2x7flqzqbrnba2xfcjy466nww0sm1vvhjg")))) (build-system r-build-system) (propagated-inputs (list r-abc r-abind r-hmisc r-plyr)) @@ -11399,16 +12457,16 @@ and coverage methods to tune the choice of threshold.") (define-public r-ggstance (package (name "r-ggstance") - (version "0.3.5") + (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "ggstance" version)) (sha256 - (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d")))) + (base32 "0wk3gbi5365sndi02gwd4c33vcrj5p8cfwakwjg010y5hgxx96nd")))) (build-system r-build-system) (propagated-inputs - (list r-ggplot2 r-plyr r-rlang r-withr)) + (list r-cli r-ggplot2 r-plyr r-rlang r-withr)) (home-page "https://cran.r-project.org/web/packages/ggstance/") (synopsis "Horizontal and vertical versions of @code{r-ggplot2}") (description @@ -11471,14 +12529,14 @@ repeated measures data, respectively.") (define-public r-gam (package (name "r-gam") - (version "1.20.2") + (version "1.22") (source (origin (method url-fetch) (uri (cran-uri "gam" version)) (sha256 (base32 - "1ndgnaq5fk1w6l6z93w5gd22887yxkykrchbdbx366qmz8v8wcyg")))) + "0gyrg73f63ccars1639n0gv6cnh8ixp7p7lgdxb2yjl240lk0c9i")))) (properties `((upstream-name . "gam"))) (build-system r-build-system) (propagated-inputs @@ -11521,14 +12579,14 @@ a library of prediction algorithms to be used in the super learner.") (define-public r-drtmle (package (name "r-drtmle") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "drtmle" version)) (sha256 (base32 - "12vplpz9bg5444jy29mbdr70hqby073vb3iw76v2csrwy3ws3f21")))) + "0qvdxzvpi7a66gx61v6fj31zy4y5cid18g4qgv5lir7qc74rbbx0")))) (properties `((upstream-name . "drtmle"))) (build-system r-build-system) (propagated-inputs @@ -11637,13 +12695,13 @@ subsequence} (LCS) using a dynamic programming algorithm.") (define-public r-mosaiccore (package (name "r-mosaiccore") - (version "0.9.2") + (version "0.9.2.1") (source (origin (method url-fetch) (uri (cran-uri "mosaicCore" version)) (sha256 - (base32 "0mnizi1y7jn2z8v066b6kv08az7vss6avips740pjhgvi8frhsag")))) + (base32 "1yns15yxr6215xf9qsxfvl24a9zvh1chw49n31dql7fy1zr1dkmp")))) (properties `((upstream-name . "mosaicCore"))) (build-system r-build-system) (propagated-inputs @@ -11741,14 +12799,14 @@ used to teach mathematics, statistics, computation and modeling.") (define-public r-raster (package (name "r-raster") - (version "3.6-3") + (version "3.6-13") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 - "1in3n0hqzcdhibjl3y82nwn6m6wcv4k3l6s2jw57jn32qgvy01lz")))) + "035hb1063lrlcs3l5aiccminax228ji0363hijmnxkvl7fsydxp1")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-sp r-terra)) @@ -11763,13 +12821,13 @@ Processing of very large files is supported.") (define-public r-mosaic (package (name "r-mosaic") - (version "1.8.4") + (version "1.8.4.2") (source (origin (method url-fetch) (uri (cran-uri "mosaic" version)) (sha256 - (base32 "0ix9c4rpa1h7cya9mqzqph9ain1ng61px5v4wwvlaf76zdr51c0i")))) + (base32 "12kpkb7vm54na9hjjkvzw6gm5plx0m6i0l9kihz2r30zanfx5jca")))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -12184,13 +13242,13 @@ singular or ill-conditioned Jacobian.") (define-public r-phyclust (package (name "r-phyclust") - (version "0.1-30") + (version "0.1-32") (source (origin (method url-fetch) (uri (cran-uri "phyclust" version)) (sha256 (base32 - "0fy9q95vmlm9idpax7alhpfwn30gflnc9md72g91jypyxkx5nr7p")))) + "1ga2pzksp97psqbl484fikfnr4bl3bgyys86wb3ya904xxwghy6c")))) (properties `((upstream-name . "phyclust"))) (build-system r-build-system) (propagated-inputs (list r-ape)) @@ -12319,13 +13377,13 @@ multiple-imputation datasets.") (define-public r-mixsqp (package (name "r-mixsqp") - (version "0.3-43") + (version "0.3-48") (source (origin (method url-fetch) (uri (cran-uri "mixsqp" version)) (sha256 (base32 - "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q")))) + "02cjg33m5iqziyy0xi11wvbm5qnlgfy51r1dbpjzyhqsrv1dfx48")))) (properties `((upstream-name . "mixsqp"))) (build-system r-build-system) (propagated-inputs @@ -12412,14 +13470,14 @@ analysis.") (define-public r-gee (package (name "r-gee") - (version "4.13-23") + (version "4.13-25") (source (origin (method url-fetch) (uri (cran-uri "gee" version)) (sha256 (base32 - "0v0fam678pqqkxmj95f1pwsi08y1rbz1wxnp1ig81jvpn0xpq8gq")))) + "128f810h88jxz1wdcmqjj3drb69b0rwx38l682i97rzb5wg8hh71")))) (properties `((upstream-name . "gee"))) (build-system r-build-system) (native-inputs @@ -12813,17 +13871,17 @@ the differences were not significantly different.") (define-public r-emmeans (package (name "r-emmeans") - (version "1.8.1-1") + (version "1.8.3") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "0xv55v50v3fdg289mfqirfm4p644gn4ckqnvs0wb09sl4m25xz3r")))) + "004fd6kzky44xixd87q2nl1sn37krmqfas5gsylbc1cbrwnjzxlz")))) (build-system r-build-system) (propagated-inputs - (list r-estimability r-mvtnorm r-numderiv r-xtable)) + (list r-estimability r-mvtnorm r-numderiv)) (native-inputs (list r-knitr)) (home-page "https://github.com/rvlenth/emmeans") @@ -12906,14 +13964,14 @@ correlation, censored, ordered and multivariate problems.") (define-public r-bayesplot (package (name "r-bayesplot") - (version "1.9.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (cran-uri "bayesplot" version)) (sha256 (base32 - "0hqy597ang53phxnl084hak35ffqz9lw9hygax7370gpkjws908a")))) + "1zqka7lg7a6ccli1yzhk1n13vbrlp8m0kjxmykjqmkz438mvjk5v")))) (build-system r-build-system) (inputs (list pandoc)) @@ -12969,17 +14027,18 @@ detection, parallelism through BLAS and parallel user templates.") (define-public r-sjstats (package (name "r-sjstats") - (version "0.18.1") + (version "0.18.2") (source (origin (method url-fetch) (uri (cran-uri "sjstats" version)) (sha256 - (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka")))) + (base32 "0a1y6bqyvgs0avzasr8g6vwcxcnj4d9g0rfz2qiznwadpjzqw66h")))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-broom + r-datawizard r-dplyr r-effectsize r-emmeans @@ -13012,14 +14071,14 @@ models.") (define-public r-glmmtmb (package (name "r-glmmtmb") - (version "1.1.4") + (version "1.1.5") (source (origin (method url-fetch) (uri (cran-uri "glmmTMB" version)) (sha256 (base32 - "1ldly6qn8iwqr41ndqlwsdz4v2n36giavsmx33vybn9g7r2fq4m7")))) + "1yh8q0l3l8hm408k8khjj1hff3nkqx0wq6a41fddwfmrq1alfjrk")))) (properties `((upstream-name . "glmmTMB"))) (build-system r-build-system) (propagated-inputs @@ -13072,14 +14131,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.9.2") + (version "0.10.1") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "0fdszf1dngqlbwcp7ynfdkzjgg0lang4d3b53ygjwsq7ph20xsw6")))) + "1m2zzznfbla8qdm0kxbj5vp431kpygpi4d70042hkg1ly3fyg7pz")))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-datawizard r-insight)) @@ -13098,17 +14157,17 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "1.1.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "1h60s10b1b5ciqg125mfnhq7nf2paq9svs2lfgwpwdvs4f8l4aq7")))) + "1j3l5v00f3xx2pwwfg1z9y31h8qja88nx7lycwj1y55ry5i6drr1")))) (build-system r-build-system) (propagated-inputs - (list r-insight r-mass r-sjlabelled)) + (list r-insight)) (native-inputs (list r-knitr)) (home-page "https://github.com/strengejacke/ggeffects") @@ -13126,14 +14185,14 @@ results using @code{ggplot2}.") (define-public r-effectsize (package (name "r-effectsize") - (version "0.7.0.5") + (version "0.8.2") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 - "0y8ng4wsms25qx2wmyrm97rbv5dgm5xyhh5ys99f0clr9lrcxr91")))) + "1ibkvvpkd4md73d53823wnwzk3iqi1k4vr99jkyiiybcn6mv5qkc")))) (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs @@ -13152,13 +14211,13 @@ conversion of indices such as Cohen's d, r, odds, etc.") (define-public r-sjplot (package (name "r-sjplot") - (version "2.8.11") + (version "2.8.12") (source (origin (method url-fetch) (uri (cran-uri "sjPlot" version)) (sha256 - (base32 "05iimcf1if1cx9bmsjb6f5gcq58hjiw10vx7kqd4nqnyhzcvy8yr")))) + (base32 "0g6r4p1r70jjzw74177kxcx2br2n206jwlqazw0vxcsbffb8a411")))) (properties `((upstream-name . "sjPlot"))) (build-system r-build-system) (propagated-inputs @@ -13219,13 +14278,13 @@ back to file after modifications.") (define-public r-gillespiessa2 (package (name "r-gillespiessa2") - (version "0.2.8") + (version "0.2.10") (source (origin (method url-fetch) (uri (cran-uri "GillespieSSA2" version)) (sha256 - (base32 "03ym8qx5yc1a6j9l973lc0rjzs8hiax8fq13j7m1fcb1pvnbvar5")))) + (base32 "0mvsjkjkm27j1y6mfipmxjmki4hpxw0cnmcmls7i5pacnrxc1gcb")))) (properties `((upstream-name . "GillespieSSA2"))) (build-system r-build-system) (propagated-inputs @@ -13381,14 +14440,14 @@ user credentials.") (define-public r-gert (package (name "r-gert") - (version "1.9.0") + (version "1.9.2") (source (origin (method url-fetch) (uri (cran-uri "gert" version)) (sha256 (base32 - "1lb9rf4c8ip8cll9mycx88x8q774bcmd01j4bwjx9h0kx1hgahkb")))) + "0pk6mf300kh6wwzvaqymwzlikkbf8zj0xpslgyydn7zvr95ipjj2")))) (properties `((upstream-name . "gert"))) (build-system r-build-system) (inputs @@ -13681,6 +14740,30 @@ problems into least squares ones first.") exact and interval-censored observations.") (license license:gpl2+))) +(define-public r-clustercrit + (package + (name "r-clustercrit") + (version "1.2.8") + (source (origin + (method url-fetch) + (uri (cran-uri "clusterCrit" version)) + (sha256 + (base32 + "10pz1bikdbkm2ky3xnagp0qv60whalavp6j39b4p7d75jj5xcxgk")))) + (properties `((upstream-name . "clusterCrit"))) + (build-system r-build-system) + (native-inputs (list gfortran)) + (home-page "https://www.r-project.org/") + (synopsis "Computing clustering validation indices") + (description + "The @code{clusterCrit} package provides an implementation of the +following indices: Czekanowski-Dice, Folkes-Mallows, Hubert Γ, Jaccard, +McNemar, Kulczynski, Phi, Rand, Rogers-Tanimoto, Russel-Rao or Sokal-Sneath. +ClusterCrit defines several functions which compute internal quality indices +or external comparison indices. The partitions are specified as an integer +vector giving the index of the cluster each observation belongs to.") + (license license:gpl2+))) + (define-public r-clusteval (package (name "r-clusteval") @@ -13702,6 +14785,31 @@ exact and interval-censored observations.") algorithms, clusterings, and individual clusters.") (license license:expat))) +(define-public r-clustergeneration + (package + (name "r-clustergeneration") + (version "1.3.7") + (source (origin + (method url-fetch) + (uri (cran-uri "clusterGeneration" version)) + (sha256 + (base32 + "0p1dwl08bf20h7pnspnsycrp3v48nm2miwcnlklyc4gdyzc2jksk")))) + (properties `((upstream-name . "clusterGeneration"))) + (build-system r-build-system) + (propagated-inputs (list r-mass)) + (home-page "https://cran.r-project.org/package=clusterGeneration") + (synopsis "Random cluster generation (with specified degree of separation)") + (description + "The clusterGeneration package provides functions for generating random +clusters, generating random covariance/correlation matrices, calculating a +separation index (data and population version) for pairs of clusters or +cluster distributions, and 1-D and 2-D projection plots to visualize clusters. +The package also contains a function to generate random clusters based on +factorial designs with factors such as degree of separation, number of +clusters, number of variables, number of noisy variables.") + (license license:gpl2+))) + (define-public r-tweedie (package (name "r-tweedie") @@ -13727,13 +14835,13 @@ and related methods.") (define-public r-rcppgsl (package (name "r-rcppgsl") - (version "0.3.11") + (version "0.3.12") (source (origin (method url-fetch) (uri (cran-uri "RcppGSL" version)) (sha256 - (base32 "1a5dms0axlzgpv1z2bhfrb77497h0ch1yslq0gidj14vr4kfm57h")))) + (base32 "1qmrwd0zc0kwbhpwxg5s5fxp0pmfh0hwcli8vqh1q41997yyy14m")))) (properties `((upstream-name . "RcppGSL"))) (build-system r-build-system) (propagated-inputs @@ -13774,14 +14882,14 @@ analysing multivariate abundance data in community ecology.") (define-public r-afex (package (name "r-afex") - (version "1.1-1") + (version "1.2-1") (source (origin (method url-fetch) (uri (cran-uri "afex" version)) (sha256 (base32 - "09q426s2zmzxx5ilxy0x5mflpb38pl075ss1s8xvpswkn6cia0b6")))) + "1jxahp2nq2clmi7wqi0n0b23xyvsjckvz9bmj81j35fv8v6wxa73")))) (build-system r-build-system) ;; This is needed for the vignette builder (arguments @@ -14001,14 +15109,14 @@ mathematics.") (define-public r-rcppannoy (package (name "r-rcppannoy") - (version "0.0.19") + (version "0.0.20") (source (origin (method url-fetch) (uri (cran-uri "RcppAnnoy" version)) (sha256 (base32 - "12k8ny981dmky5js8yl6bih5r5mq3w43f2f9admhkwqn0n80kcl9")))) + "11fgxbx3w36937h22v9pqx0nk5vpxp3hybj7k1b0lk8mj7hcginw")))) (properties `((upstream-name . "RcppAnnoy"))) (build-system r-build-system) (propagated-inputs @@ -14082,14 +15190,14 @@ other values.") (define-public r-ncdf4 (package (name "r-ncdf4") - (version "1.19") + (version "1.21") (source (origin (method url-fetch) (uri (cran-uri "ncdf4" version)) (sha256 (base32 - "0qzvin2fjzcb7h2knlnw14s6043pwi1nm7yf6p27ax7w269173fb")))) + "03dk47xz6qlpky9kkpkkxc472czq542yml3fdg39bic2yggffnig")))) (build-system r-build-system) (inputs (list netcdf zlib)) @@ -14108,13 +15216,13 @@ netCDF files.") (define-public r-biocmanager (package (name "r-biocmanager") - (version "1.30.18") + (version "1.30.19") (source (origin (method url-fetch) (uri (cran-uri "BiocManager" version)) (sha256 - (base32 "0dawbd546rznllpw5wq282r0viga4cck398d4s1inkk18mmi4qzp")))) + (base32 "1qhq1k1sr23bi2kmnd99mjs3ns0c2p20pmr2iq8a6bxbb0fap5v8")))) (properties `((upstream-name . "BiocManager"))) (build-system r-build-system) (native-inputs @@ -14129,14 +15237,14 @@ Bioconductor packages.") (define-public r-rgl (package (name "r-rgl") - (version "0.109.6") + (version "0.111.6") (source (origin (method url-fetch) (uri (cran-uri "rgl" version)) (sha256 (base32 - "1jl89v2gwk1d4q3vn7kx8x7abjbgiisfiyrs4d40qixr6iil8hrz")))) + "1h6nbcnbl0knmc91923wfhghs58yjc84mhnmk2byd474lrgzxynd")))) (build-system r-build-system) (native-inputs (list pkg-config @@ -14191,6 +15299,38 @@ or hash tables and to generate integer partitions. Cool-lex order is similar to colexicographical order.") (license license:gpl2))) +(define-public r-multidplyr + (package + (name "r-multidplyr") + (version "0.1.2") + (source (origin + (method url-fetch) + (uri (cran-uri "multidplyr" version)) + (sha256 + (base32 + "081x9n46dl6vpp5q6pilw3w5wpdi3r9kwi9n6h4k2p2iqg1s96lb")))) + (properties `((upstream-name . "multidplyr"))) + (build-system r-build-system) + (propagated-inputs + (list r-callr + r-cli + r-crayon + r-dplyr + r-magrittr + r-qs + r-r6 + r-rlang + r-tibble + r-tidyselect + r-vctrs)) + (native-inputs (list r-knitr)) + (home-page "https://multidplyr.tidyverse.org") + (synopsis "Multi-process dplyr backend") + (description + "Partition a data frame across multiple worker processes to provide +simple multicore parallelism.") + (license license:expat))) + (define-public r-misc3d (package (name "r-misc3d") @@ -14211,16 +15351,46 @@ isosurfaces.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) +(define-public r-missforest + (package + (name "r-missforest") + (version "1.5") + (source (origin + (method url-fetch) + (uri (cran-uri "missForest" version)) + (sha256 + (base32 + "13c38hpl60ca1kwyv61cxsla6ccmsj4qzp0vrxcq7b827fh5aw21")))) + (properties `((upstream-name . "missForest"))) + (build-system r-build-system) + (propagated-inputs + (list r-dorng + r-foreach + r-iterators + r-itertools + r-randomforest)) + (home-page "https://github.com/stekhoven/missForest") + (synopsis "Nonparametric missing value imputation using Random Forest") + (description + "The function @code{missForest} in this package is used to impute missing +values, particularly in the case of mixed-type data. It uses a random forest +trained on the observed values of a data matrix to predict the missing values. +It can be used to impute continuous and/or categorical data, including complex +interactions and non-linear relations. It yields an @acronym{OOB, out-of-bag} +imputation error estimate without the need of a test set or elaborate cross- +validation. It can be run in parallel to save computation time.") + (license license:gpl2+))) + (define-public r-ks (package (name "r-ks") - (version "1.13.5") + (version "1.14.0") (source (origin (method url-fetch) (uri (cran-uri "ks" version)) (sha256 - (base32 "05bqrjkbx2kn5aax0hy3xd6pf7nxka9bm1sp8ll1cc2gf1nx1i6i")))) + (base32 "14a3pcxxcsfkqz5j6n2wlxkp0gsdp5mzdq7ipcjb65q2gdmwbf9d")))) (build-system r-build-system) (propagated-inputs (list r-fnn @@ -14391,14 +15561,14 @@ al. (2010) <DOI:10.1016/j.neuroimage.2010.04.241>, Tabelow and Polzehl (2011) (define-public r-fmsb (package (name "r-fmsb") - (version "0.7.3") + (version "0.7.5") (source (origin (method url-fetch) (uri (cran-uri "fmsb" version)) (sha256 (base32 - "1gi94xr0b1yk9xzwfprfafxi25yic1lcivd66p73n6iqfzdaimbk")))) + "082qj08kzyzwvjacwq0sl3xxdx6iz5hgx6q24jv1mnvx7z5xn5ry")))) (build-system r-build-system) (home-page "http://minato.sip21c.org/msb/") (synopsis "Functions for medical statistics book with demographic data") @@ -14691,14 +15861,14 @@ Processing.") (define-public r-tm (package (name "r-tm") - (version "0.7-8") + (version "0.7-10") (source (origin (method url-fetch) (uri (cran-uri "tm" version)) (sha256 (base32 - "0mk2lsplynms15nw92vbdgsafg4bw1m0ik31gch1mnsnv61idsxi")))) + "15lxaqlgkl9chiz0aw05l55bvlh48jwdgplfl8f2d8xsaq4gmbvc")))) (properties `((upstream-name . "tm"))) (build-system r-build-system) (propagated-inputs @@ -14709,6 +15879,35 @@ Processing.") "This package provides a framework for text mining applications within R.") (license license:gpl3))) +(define-public r-waffle + (package + (name "r-waffle") + (version "0.7.0") + (source (origin + (method url-fetch) + (uri (cran-uri "waffle" version)) + (sha256 + (base32 + "1qjmai33p96cyavi9lgi6k30h6fj7db5sr569v9jf4kwx92c61df")))) + (properties `((upstream-name . "waffle"))) + (build-system r-build-system) + (propagated-inputs + (list r-extrafont + r-ggplot2 + r-gridextra + r-gtable + r-rcolorbrewer)) + (home-page "https://github.com/hrbrmstr/waffle/tree/cran") + (synopsis "Creating waffle chart visualizations in R") + (description + "This package creates square pie charts also known as waffle charts. +These can be used to communicate parts of a whole for categorical quantities. +To emulate the percentage view of a pie chart, a 10x10 grid should be used. +In this way each square is representing 1% of the total. Waffle provides +tools to create charts as well as stitch them together. Isotype pictograms +can be made by using glyphs.") + (license license:gpl2+))) + (define-public r-waveslim (package (name "r-waveslim") @@ -14782,16 +15981,17 @@ maps.") (define-public r-tidytree (package (name "r-tidytree") - (version "0.4.0") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 - (base32 "0dm71zdrb1qwaja23jlzjpraa609b6yxl8bhksz8slgpfm1jgs00")))) + (base32 "0phmvbpsxx85fvw4000d160qh8njrgmzpr3ja0gy59dgv1k1m0yb")))) (build-system r-build-system) (propagated-inputs (list r-ape + r-cli r-dplyr r-lazyeval r-magrittr @@ -15167,14 +16367,14 @@ handle.") (define-public r-tfmpvalue (package (name "r-tfmpvalue") - (version "0.0.8") + (version "0.0.9") (source (origin (method url-fetch) (uri (cran-uri "TFMPvalue" version)) (sha256 (base32 - "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd")))) + "1rsxqvq1nkyhwmhm7mf7rd02rvh7xinnhqbqic6q9vicbvkmdnxr")))) (properties `((upstream-name . "TFMPvalue"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -15193,13 +16393,13 @@ Touzet and Varre (2007).") (define-public r-rncl (package (name "r-rncl") - (version "0.8.6") + (version "0.8.7") (source (origin (method url-fetch) (uri (cran-uri "rncl" version)) (sha256 (base32 - "1ywgwqn82z8h6zpcxxq4hgngdpfa6dj0lr7bfq4cwfml9z075jgw")))) + "0flrqz7pansy11ds23qv06bcmh6vxqljq0517v6292ibbx7nx1qx")))) (build-system r-build-system) (propagated-inputs (list r-progress r-rcpp)) @@ -15258,19 +16458,18 @@ useful for building large phylogenies using multiple markers.") (define-public r-rnexml (package (name "r-rnexml") - (version "2.4.7") + (version "2.4.9") (source (origin (method url-fetch) (uri (cran-uri "RNeXML" version)) (sha256 (base32 - "1zp6pijsc73jx8cmxb1hng36nvaf5wnhldnzlqhmba9kv9niscfb")))) + "180w7c8n4xcn3x7haymi1fl3fpnklqfgmaki6jkxpm3hdiffmbsd")))) (build-system r-build-system) (propagated-inputs (list r-ape r-dplyr r-httr - r-lazyeval r-plyr r-reshape2 r-rlang @@ -15293,14 +16492,14 @@ and compatibility with @code{ape} objects.") (define-public r-rnifti (package (name "r-rnifti") - (version "1.4.1") + (version "1.4.3") (source (origin (method url-fetch) (uri (cran-uri "RNifti" version)) (sha256 (base32 - "058jzhw91wd4hb9l06mn0ihf1yp2fapz1fyb32w9bjwxq7qxvii2")))) + "1w627brzag9laxsfrr1kxh07glycl8l1n5xf5frn8m0jzvrn3d50")))) (properties `((upstream-name . "RNifti"))) (build-system r-build-system) (inputs (list zlib)) @@ -15336,13 +16535,13 @@ creating color scales and calculating color distances.") (define-public r-ore (package (name "r-ore") - (version "1.7.1.1") + (version "1.7.2.1") (source (origin (method url-fetch) (uri (cran-uri "ore" version)) (sha256 - (base32 "0rs5r5h11x4l4nsbl4xqzbl4ahajd5374fq05abcmfjnjr9j64w5")))) + (base32 "104506x9x14bs8lfhydwpgdh4qws2vqkvyy6xrlrviqlll6qbjgg")))) (build-system r-build-system) (home-page "https://github.com/jonclayden/ore") (synopsis "R interface to the Onigmo regular expression library") @@ -15401,6 +16600,30 @@ visualization; flexible image manipulation; metadata and sparse image handling.") (license license:gpl2))) +(define-public r-gridsvg + (package + (name "r-gridsvg") + (version "1.7-4") + (source (origin + (method url-fetch) + (uri (cran-uri "gridSVG" version)) + (sha256 + (base32 + "1jspjn56yrkx98hhs98npzm0k0kwpv8x1hg40kphx5ikhvincxmr")))) + (properties `((upstream-name . "gridSVG"))) + (build-system r-build-system) + (propagated-inputs + (list r-jsonlite r-xml)) + (home-page "https://cran.r-project.org/package=gridSVG") + (synopsis "Export grid gaphics as SVG") + (description + "This package provides functions to export graphics drawn with package +grid to SVG format. Extra functions provide access to SVG features that are +not available in standard R graphics, such as hyperlinks, animation, filters, +masks, clipping paths, and gradient and pattern fills.") + ;; Any version of the GPL. + (license (list license:gpl2 license:gpl3)))) + (define-public r-grimport (package (name "r-grimport") @@ -15697,18 +16920,19 @@ preparing, executing, and processing HTTP requests.") (define-public r-bigrquery (package (name "r-bigrquery") - (version "1.4.0") + (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "bigrquery" version)) (sha256 (base32 - "02msq61l7vamzpvbhvalh3qil1aa7pr68pwpsivbb6pvz6p4zyns")))) + "1rcz1zq0azrrchhxz4b0g4m9c3ymp4pasi7ji1nvx25w5x41sdmv")))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-bit64 + r-brio r-curl r-dbi r-gargle @@ -15731,14 +16955,14 @@ preparing, executing, and processing HTTP requests.") (define-public r-gmp (package (name "r-gmp") - (version "0.6-6") + (version "0.6-9") (source (origin (method url-fetch) (uri (cran-uri "gmp" version)) (sha256 (base32 - "14r7xlxjrwww6l726sispq6jhxy2yfwbcqrqgc9x4ma812l9byl7")))) + "00zh0phr8axva2y2c10nla7n9mgh3wvwvsyyd3y43jpb3xim6lv6")))) (build-system r-build-system) (arguments '(#:phases @@ -15783,6 +17007,29 @@ functions. To this end, the package interfaces with the @dfn{Multiple Precision Floating-Point Reliable} (MPFR) library.") (license license:gpl2+))) +(define-public r-rmutil + (package + (name "r-rmutil") + (version "1.1.10") + (source (origin + (method url-fetch) + (uri (cran-uri "rmutil" version)) + (sha256 + (base32 + "1yd5gkg4jg3rvqrfl8c5r07lcr37n1p9h1a7b6s45iswd77dg7w1")))) + (properties `((upstream-name . "rmutil"))) + (build-system r-build-system) + (native-inputs (list gfortran)) + (home-page "https://www.commanster.eu/rcode.html") + (synopsis + "Utilities for nonlinear regression and repeated measurements models") + (description + "This package provides a toolkit of functions for nonlinear regression +and repeated measurements. It was designated to be imported by other packages +such as @code{gnlm}, @code{stable}, @code{growth}, @code{repeated}, and +@code{event}.") + (license license:gpl2+))) + (define-public r-assertive-base (package (name "r-assertive-base") @@ -16191,14 +17438,14 @@ to throw errors if they aren't in the right form.") (define-public r-dotcall64 (package (name "r-dotcall64") - (version "1.0-1") + (version "1.0-2") (source (origin (method url-fetch) (uri (cran-uri "dotCall64" version)) (sha256 (base32 - "1im5k8jbviwj2i42mq1kmjskh80isa7jr9w8i0fknidrzzy2h2zi")))) + "1b546z9r26q4xpr17gy2wzfych52q17sxvzydpqfp9dyxf575iz0")))) (properties `((upstream-name . "dotCall64"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -16366,14 +17613,14 @@ package \"boot\".") (define-public r-survivalroc (package (name "r-survivalroc") - (version "1.0.3") + (version "1.0.3.1") (source (origin (method url-fetch) (uri (cran-uri "survivalROC" version)) (sha256 (base32 - "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l")))) + "0p6irjs8a9xxgxwax0y9fzapcib237if3iy8g6lzv793mzmsyx41")))) (properties `((upstream-name . "survivalROC"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/survivalROC") @@ -16401,6 +17648,26 @@ Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)") discovery rates.") (license license:gpl2))) +(define-public r-logging + (package + (name "r-logging") + (version "0.10-108") + (source (origin + (method url-fetch) + (uri (cran-uri "logging" version)) + (sha256 + (base32 + "13gd40ygx586vs6xcp6clg69a92aj8zxlk1rn3xzkx8klfjimjc5")))) + (properties `((upstream-name . "logging"))) + (build-system r-build-system) + (home-page "https://github.com/WLOGSolutions/r-logging") + (synopsis "R logging implementation of log4j") + (description + "This package implements the R version of the @code{log4j} package. It offers +hierarchic loggers, multiple handlers per logger, level based filtering, space +handling in messages and custom formatting.") + (license license:gpl3))) + (define-public r-longitudinal (package (name "r-longitudinal") @@ -16535,6 +17802,33 @@ library.") profiling R code.") (license license:gpl3))) +(define-public r-prospectr + (package + (name "r-prospectr") + (version "0.2.6") + (source (origin + (method url-fetch) + (uri (cran-uri "prospectr" version)) + (sha256 + (base32 + "1p53hcgcs2p09zhc2n7byjzrgvcgz6w7q00mlsn4kmnz7l4p7rrm")))) + (properties `((upstream-name . "prospectr"))) + (build-system r-build-system) + (propagated-inputs + (list r-foreach + r-iterators + r-lifecycle + r-mathjaxr + r-rcpp + r-rcpparmadillo)) + (home-page "https://github.com/l-ramirez-lopez/prospectr") + (synopsis "Functions for processing and sample selection of spectroscopic data") + (description + "@code{prospectr} provides miscellaneous functions to preprocess +spectroscopic data and conduct representative sample selection, or calibration +sampling.") + (license license:expat))) + (define-public r-protviz (package (name "r-protviz") @@ -16739,14 +18033,14 @@ by change of variable.") (define-public r-listenv (package (name "r-listenv") - (version "0.8.0") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "listenv" version)) (sha256 (base32 - "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx")))) + "11s8cy259al6x98xcz93jw6p87si01gcgzccnxhx69879zh42a1m")))) (build-system r-build-system) (arguments `(#:phases @@ -16767,14 +18061,14 @@ subsetting.") (define-public r-globals (package (name "r-globals") - (version "0.16.1") + (version "0.16.2") (source (origin (method url-fetch) (uri (cran-uri "globals" version)) (sha256 (base32 - "158y39qv99f1kc2i7w8d4lm2ls96plb43fzamz31im9xb9bkmxpp")))) + "02kpdlrx1bannaixz03c0f7bii9g36iy2nw779mfgi56byljcb38")))) (build-system r-build-system) (propagated-inputs (list r-codetools)) @@ -16791,14 +18085,14 @@ them in distributed compute environments.") (define-public r-parallelly (package (name "r-parallelly") - (version "1.32.1") + (version "1.33.0") (source (origin (method url-fetch) (uri (cran-uri "parallelly" version)) (sha256 (base32 - "146a9i999vrflr4g1fph1pgkl4bq0dw102bjw8pp1zy7kbsqbiii")))) + "0ymrpcxp2fnk1fpfig0kd1q3whzh7sykgcl91k53c2w20v2wwfpw")))) (properties `((upstream-name . "parallelly"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/parallelly") @@ -16819,14 +18113,14 @@ port-forwarding to your local computer.") (define-public r-future (package (name "r-future") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 - "1xhv0nf97yxxxsmxczyqqbnb4yn5sfn5vzvhm9dmw9csrmmadpbg")))) + "1njmgnq0qz7b9yvcp6351yz7ydz9hj8bnnaf1ys3md66v9mg1xf7")))) (build-system r-build-system) (arguments `(#:phases @@ -16854,14 +18148,14 @@ the local machine to, say, distributed processing on a remote compute cluster.") (define-public r-future-apply (package (name "r-future-apply") - (version "1.9.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (cran-uri "future.apply" version)) (sha256 (base32 - "0cr141mamjxby79sww02493yal9lahslvp3a3ic7f856rbawq8jg")))) + "1all7ri4nsjxfakw8pssif22j33ch1nhw3sc0raqrzhj93c2vsfy")))) (properties `((upstream-name . "future.apply"))) (build-system r-build-system) (arguments @@ -16961,14 +18255,14 @@ heuristics.") (define-public r-dorng (package (name "r-dorng") - (version "1.8.2") + (version "1.8.3") (source (origin (method url-fetch) (uri (cran-uri "doRNG" version)) (sha256 (base32 - "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k")))) + "1aqzy646c6aggscmwninr1hz0z4nkxibmrg1mm77p2jnf1lh914c")))) (properties `((upstream-name . "doRNG"))) (build-system r-build-system) (propagated-inputs @@ -16987,14 +18281,14 @@ chosen parallel environment and associated foreach backend.") (define-public r-blockmodeling (package (name "r-blockmodeling") - (version "1.1.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "blockmodeling" version)) (sha256 (base32 - "19mxmxsnl6rrh85p0sak91vcaw4dz2cnm70hdzfwnvdrr695yw2z")))) + "1f6jx8pwp3pnhs4wwxdrd1ska3h4w2423dpd11illxfajvnigkk9")))) (build-system r-build-system) (propagated-inputs (list r-matrix)) @@ -17032,6 +18326,29 @@ intersecting sets using a novel matrix design, along with visualizations of several common set, element and attribute related tasks.") (license license:expat))) +(define-public r-shinycustomloader + (package + (name "r-shinycustomloader") + (version "0.9.0") + (source (origin + (method url-fetch) + (uri (cran-uri "shinycustomloader" version)) + (sha256 + (base32 + "1klx71vr26g0gjf6hbiia1qidqii5d467i1sdjvlrg1hxdcggqff")))) + (properties `((upstream-name . "shinycustomloader"))) + (build-system r-build-system) + (propagated-inputs + (list r-glue + r-shiny)) + (home-page "https://cran.r-project.org/package=shinycustomloader") + (synopsis "Custom loader for Shiny outputs") + (description + "This package provides a custom @code{CSS/HTML} or @code{GIF/image} file +for the loading screen in R @code{Shiny}. It also can use the marquee to have +a custom text loading screen.") + (license license:gpl3))) + ;; This package includes a JavaScript file, which is not minified. When ;; upgrading please check that there are no new minified JavaScript files. (define-public r-shinybs @@ -17118,13 +18435,13 @@ effects from the jQuery UI library.") (define-public r-shinymanager (package (name "r-shinymanager") - (version "1.0.400") + (version "1.0.410") (source (origin (method url-fetch) (uri (cran-uri "shinymanager" version)) (sha256 - (base32 "1np2yp5pn8g9i4jhysfgprmdn13cpw4vaaagrd72rnk2r4hpmyx4")))) + (base32 "0nl672dgwj34wm4i3pxk28lv6qw9xsgg3hm0h78q3zdgk8a33kdn")))) (properties `((upstream-name . "shinymanager"))) (build-system r-build-system) (propagated-inputs @@ -17142,7 +18459,7 @@ effects from the jQuery UI library.") (home-page "https://github.com/datastorm-open/shinymanager") (synopsis "Authentication management for Shiny applications") (description - "This package provides simple and secure authentification mechanism for + "This package provides simple and secure authentication mechanism for single Shiny applications. Credentials are stored in an encrypted SQLite database.") (license license:gpl3))) @@ -17169,16 +18486,17 @@ identifying outliers.") (define-public r-bayesm (package (name "r-bayesm") - (version "3.1-4") + (version "3.1-5") (source (origin (method url-fetch) (uri (cran-uri "bayesm" version)) (sha256 - (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6")))) + (base32 "18j7h32nq4hx1qnxfgfgz3q39q35lmvsq3im90xjkphyli60f8zj")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo)) + (native-inputs (list r-knitr)) (home-page "http://www.perossi.org/home/bsm-1") (synopsis "Bayesian inference for marketing/micro-econometrics") (description @@ -17375,14 +18693,14 @@ to easily call your own custom JavaScript functions from R.") (define-public r-colourpicker (package (name "r-colourpicker") - (version "1.1.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "colourpicker" version)) (sha256 (base32 - "1q1wi3g403fbzp4ys3gsjbwdc86x770cx323qgi47ca8n219kl50")))) + "12k3m2s49pc1p2hzd4zqqzzdf94q7hhqz7zgp8w908a6w3p80b5w")))) (build-system r-build-system) (arguments `(#:phases @@ -17418,10 +18736,10 @@ to easily call your own custom JavaScript functions from R.") ("js-jquery" ,(origin (method url-fetch) - (uri "https://code.jquery.com/jquery-1.11.3.js") + (uri "https://code.jquery.com/jquery-3.6.1.js") (sha256 (base32 - "1v956yf5spw0156rni5z77hzqwmby7ajwdcd6mkhb6zvl36awr90")))) + "1lm4zcpvqdi7qi2s7bgci2z74wazq0z0bdvjmlrqbhmfrpk42ffz")))) ("js-salvattore" ,(origin (method url-fetch) @@ -17562,14 +18880,14 @@ probabilities from a standard bivariate normal CDF.") (define-public r-lavaan (package (name "r-lavaan") - (version "0.6-12") + (version "0.6-13") (source (origin (method url-fetch) (uri (cran-uri "lavaan" version)) (sha256 (base32 - "17h79pnww1mihvlp6ap0r6d8wnly9bwszj13l5dkby0284z2fj40")))) + "0glcam1g8zx3xvvp8nsbsj5vi8hba0sm20akyf4rivbr6s745y1a")))) (build-system r-build-system) (propagated-inputs (list r-mass r-mnormt r-numderiv r-pbivnorm)) @@ -17705,14 +19023,14 @@ graphs.") (define-public r-pbdzmq (package (name "r-pbdzmq") - (version "0.3-7") + (version "0.3-8") (source (origin (method url-fetch) (uri (cran-uri "pbdZMQ" version)) (sha256 (base32 - "020qy6fq8w8wq0j3bii14ahrlg8wzl0lrnndfr6scmrg9ghjnbfz")))) + "0rala2aqyva4cjpih8xbqq1nxhwfgbkcdwb1c3h5jjp5dv7lrvgd")))) (properties `((upstream-name . "pbdZMQ"))) (build-system r-build-system) (inputs @@ -17776,14 +19094,14 @@ running IRkernel session.") (define-public r-irkernel (package (name "r-irkernel") - (version "1.3") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "IRkernel" version)) (sha256 (base32 - "00qrmsywpzw2hfp88020zjaijma7q4hqm9h2cz53rywdjzywnzss")))) + "03343ds7sprql1c6h41dibk40rc3225mzxca452ns967fyhy71ii")))) (properties `((upstream-name . "IRkernel"))) (build-system r-build-system) (arguments @@ -17870,6 +19188,36 @@ 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-remacor + (package + (name "r-remacor") + (version "0.0.11") + (source (origin + (method url-fetch) + (uri (cran-uri "remaCor" version)) + (sha256 + (base32 + "0hhk1zrjz6sxg219h9ca7jya0vc8dmrvwaddajkcdns6bv3rj1km")))) + (properties `((upstream-name . "remaCor"))) + (build-system r-build-system) + (propagated-inputs + (list r-clustergeneration + r-ggplot2 + r-mvtnorm + r-rdpack + r-reshape2 + r-runit)) + (native-inputs (list r-knitr)) + (home-page "https://diseaseneurogenomics.github.io/remaCor/") + (synopsis "Random effects meta-analysis for correlated test statistics") + (description + "Meta-analysis is widely used to summarize estimated effects sizes across +multiple statistical tests. Standard fixed and random effect meta-analysis +methods assume that the estimated of the effect sizes are statistically +independent. Here we relax this assumption and enable meta-analysis when the +correlation matrix between effect size estimates is known.") + (license license:artistic2.0))) + (define-public r-rematch2 (package (name "r-rematch2") @@ -17944,14 +19292,14 @@ can be used with function approximation, eligibility traces (Singh & Sutton, (define-public r-lemon (package (name "r-lemon") - (version "0.4.5") + (version "0.4.6") (source (origin (method url-fetch) (uri (cran-uri "lemon" version)) (sha256 (base32 - "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4")))) + "0v1kbyk64yzsk92h6yq03kp9alc9632qprznsws61r8firiskim5")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 @@ -17960,7 +19308,6 @@ can be used with function approximation, eligibility traces (Singh & Sutton, r-knitr r-lattice r-plyr - r-rlang r-scales)) (native-inputs (list r-knitr)) @@ -18072,16 +19419,17 @@ partition functions are also given.") (define-public r-brobdingnag (package (name "r-brobdingnag") - (version "1.2-7") + (version "1.2-9") (source (origin (method url-fetch) (uri (cran-uri "Brobdingnag" version)) (sha256 (base32 - "0hnp5nrpnscykvgrrbgp7987660hcbv92zc2q8lmpnin4ws399vk")))) + "07p9416rdzfyiigbglxjpbcg7pfly9nw19yn2mwg98621cjjs0gr")))) (properties `((upstream-name . "Brobdingnag"))) (build-system r-build-system) + (propagated-inputs (list r-matrix)) (home-page "https://github.com/RobinHankin/Brobdingnag.git") (synopsis "Very large numbers in R") (description @@ -18092,6 +19440,26 @@ methods.") ;; Any version of the GPL (license license:gpl2+))) +(define-public r-unglue + (package + (name "r-unglue") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "unglue" version)) + (sha256 + (base32 "0w8ld4xllx0lj1jz8i2sj92f8136hlwri1d8ldpg1ymxj7aw93vg")))) + (properties `((upstream-name . "unglue"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=unglue") + (synopsis "Extract matched substrings using a pattern") + (description + "This package lets you use syntax inspired by the package @code{glue} to +extract matched substrings in a more intuitive and compact way than by using +standard regular expressions.") + (license license:gpl3))) + (define-public r-untb (package (name "r-untb") @@ -18183,14 +19551,14 @@ barplots or heatmaps.") (define-public r-seqinr (package (name "r-seqinr") - (version "4.2-16") + (version "4.2-23") (source (origin (method url-fetch) (uri (cran-uri "seqinr" version)) (sha256 (base32 - "0cj07b7km5mla63qhbkxg1mnqq6vh79lsyyfpnbm29gw68w2bwy4")))) + "14zv47cdrx9rpyxzccyikp0zxvcqrviw7bid0qhiixvji4bp88dg")))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-segmented)) @@ -18207,14 +19575,14 @@ utilities for sequence data management under the ACNUC system.") (define-public r-units (package (name "r-units") - (version "0.8-0") + (version "0.8-1") (source (origin (method url-fetch) (uri (cran-uri "units" version)) (sha256 (base32 - "06mjprqi06xprj6185k5cmrrdl025x0pd1r6a4x3s74ciq9zwilw")))) + "16ndhl4hkcll9r5vh8flp2bc3mavddfz8g6sqddj15scdcjbmqfk")))) (build-system r-build-system) (inputs (list udunits)) @@ -18256,14 +19624,14 @@ classes.") (define-public r-classint (package (name "r-classint") - (version "0.4-7") + (version "0.4-8") (source (origin (method url-fetch) (uri (cran-uri "classInt" version)) (sha256 (base32 - "0vk06k10mxcm6wn4b74njzc1kc1ividsn03ii523j4yfhy4kl3m3")))) + "1csrrb93lzy1pajs91qd0vyvl218jyskcksa43xfrfvibdzn3sba")))) (properties `((upstream-name . "classInt"))) (build-system r-build-system) (propagated-inputs @@ -18280,14 +19648,14 @@ univariate class intervals for mapping or other graphics purposes.") (define-public r-spdata (package (name "r-spdata") - (version "2.2.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "spData" version)) (sha256 (base32 - "07whxr039cxvk2nn65jada3i8vqqw34lgca9j17ah8chy9r0m73f")))) + "1ddkk8c4dblv5p2rqvqx8b89k8pazvvq48rlw661vf2iwwvm8d2m")))) (properties `((upstream-name . "spData"))) (build-system r-build-system) (propagated-inputs @@ -18356,14 +19724,14 @@ tessellation.") (define-public r-wk (package (name "r-wk") - (version "0.6.0") + (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "wk" version)) (sha256 (base32 - "1xga4rrqsr190g55by39az4nimnn06bf5b6mcjgwqvba0lvjhb5g")))) + "116kvg2a9gga14agqvmvj2rbgfpdyasbkjnfjcsw9a9dk0n7g9g5")))) (properties `((upstream-name . "wk"))) (build-system r-build-system) (home-page "https://paleolimbot.github.io/wk/") @@ -18380,14 +19748,14 @@ high-performance functions are provided here.") (define-public r-s2 (package (name "r-s2") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "s2" version)) (sha256 (base32 - "05n459rp5b1wk826sq3c5d2z1xwgkpfp8m1jnfshvs4gadlfkap3")))) + "07c9f8ghfjqdjcw50by3y4j8nbsmmcwd4a3vpcwsxr4mvybckq0w")))) (properties `((upstream-name . "s2"))) (build-system r-build-system) (arguments @@ -18421,14 +19789,14 @@ information about geometries.") (define-public r-sf (package (name "r-sf") - (version "1.0-8") + (version "1.0-9") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 - "0cl7m47ar3iw95rpwpmjl23frdbscxa15q39mlzmwswxwy871p1x")))) + "0fq1v2ksnllyd5yx7ch8f298aqiys4v6xacswy0h4xb418dcgh45")))) (build-system r-build-system) (inputs (list gdal geos proj sqlite zlib)) @@ -18451,16 +19819,40 @@ datum transformations.") ;; Either of these licenses (license (list license:gpl2 license:expat)))) +(define-public r-sftime + (package + (name "r-sftime") + (version "0.2-0") + (source (origin + (method url-fetch) + (uri (cran-uri "sftime" version)) + (sha256 + (base32 + "1ymi60ag8kqb3293bdcvb83zwsgrz000ylifjvlpzzmh1xsisanq")))) + (properties `((upstream-name . "sftime"))) + (build-system r-build-system) + (propagated-inputs (list r-sf)) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=sftime") + (synopsis "Simple feature objects that have a time column") + (description + "This package provides classes and methods for spatial objects +that have a registered time column, in particular for irregular +spatiotemporal data. The @code{time} column can be of any type, but +needs to be ordinal. Regularly laid out spatiotemporal data (vector +or raster data cubes) are handled by package stars'.") + (license license:asl2.0))) + (define-public r-spdep (package (name "r-spdep") - (version "1.2-5") + (version "1.2-7") (source (origin (method url-fetch) (uri (cran-uri "spdep" version)) (sha256 (base32 - "1ib5jgahjgjpj2ajp5g71r4fw0q1zkddixgmywi1n73nqr39qwp2")) + "1slykkgvn7blj59lbzj0g0r0dqlcbp0gwnw43sihlbdz4m45kb4x")) (snippet '(for-each delete-file '("inst/doc/CO69.html" "inst/doc/CO69.R" @@ -18496,14 +19888,14 @@ spanning tree.") (define-public r-adegenet (package (name "r-adegenet") - (version "2.1.7") + (version "2.1.8") (source (origin (method url-fetch) (uri (cran-uri "adegenet" version)) (sha256 (base32 - "0zkbxw9w0fcb4s3zv2a8nxcsihzkfz49psaipxw99nwgm7l9jrh9")))) + "09ahgz1ddsdn30fmi5kimdcrcnw18ryqpjcixhyp4xz0xwz2rmw0")))) (build-system r-build-system) (propagated-inputs (list r-ade4 @@ -18633,13 +20025,13 @@ either PDF/EPS files.") (define-public r-polspline (package (name "r-polspline") - (version "1.1.20") + (version "1.1.22") (source (origin (method url-fetch) (uri (cran-uri "polspline" version)) (sha256 - (base32 "1dd1jwiaglkkhajzvqfkd1x5r3wzjlk5ww0yxzmns0s1kr74i4k9")))) + (base32 "0ys5sxr5q55ip49dsc3kbgcr3bn9dj5bblmshwm4jz8d0a7ikwmj")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/polspline/") @@ -18738,14 +20130,14 @@ include (define-public r-haplo-stats (package (name "r-haplo-stats") - (version "1.8.9") + (version "1.9.2") (source (origin (method url-fetch) (uri (cran-uri "haplo.stats" version)) (sha256 (base32 - "0np9kw4f30xbvwr4f79g909ilis5n273ridmlwyzjxiskiry6mx0")))) + "1397rxcqqz29yaf3f2gphg1jhmfw3wvvjvqk7cz01jdh3pihdh56")))) (properties `((upstream-name . "haplo.stats"))) (build-system r-build-system) (propagated-inputs @@ -18766,14 +20158,14 @@ examples in the vignette.") (define-public r-bqtl (package (name "r-bqtl") - (version "1.0-33") + (version "1.0-34") (source (origin (method url-fetch) (uri (cran-uri "bqtl" version)) (sha256 (base32 - "1sbzpi9z94f010lw2y1gmifjrvpmiqs4m26za7vr1xz72azrqvs9")))) + "1xlkgyhlgrwqfzph4sbhh49pjzfnw5zdr3y4786rsnr3faksnxns")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/") @@ -18786,14 +20178,14 @@ lines. It includes maximum likelihood and Bayesian tools.") (define-public r-ibdreg (package (name "r-ibdreg") - (version "0.3.6") + (version "0.3.8") (source (origin (method url-fetch) (uri (cran-uri "ibdreg" version)) (sha256 (base32 - "1x8z0vr2cmdks12hxfm0wwxskb0cr669w5j5rpa2ln8q704yy41g")))) + "0c4svyfd7xjx9k6pl40l7y9rc67zschs0nz1l386xi1m7arsp44n")))) (build-system r-build-system) (home-page "https://www.mayo.edu/research/labs/\ statistical-genetics-genetic-epidemiology/software") @@ -18857,14 +20249,14 @@ exact test for Hardy-Weinberg equilibrium.") (define-public r-tdthap (package (name "r-tdthap") - (version "1.1-11") + (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "tdthap" version)) (sha256 (base32 - "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k")))) + "0x67k50vly92b9n5hpqp4hy87kh8r6nzadsj8xzz4lvcmb4vb6mq")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/tdthap/") (synopsis "TDT tests for extended haplotypes") @@ -18899,13 +20291,13 @@ SELECT or UPDATE queries to an end-point.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.29") + (version "0.31") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "08zpky94bdbjsbhi90pymxpczpfkjxwbx7p1v7ip8raw9b23skjv")))) + "0rkapx3zz0vwggnrpk0ns8bpqsblkp08xpr0srz93c3kzlsjdiac")))) (build-system r-build-system) (propagated-inputs (list r-htmltools @@ -18951,6 +20343,28 @@ authoring books and technical documents with R Markdown.") that accept short and long options.") (license license:gpl2+))) +(define-public r-osqp + (package + (name "r-osqp") + (version "0.6.0.7") + (source (origin + (method url-fetch) + (uri (cran-uri "osqp" version)) + (sha256 + (base32 + "00w2hr0pagnvpsk84z99c7alhv7xvs9wpcmkzbcg3qs14g888rgf")))) + (properties `((upstream-name . "osqp"))) + (build-system r-build-system) + (propagated-inputs (list r-matrix r-r6 r-rcpp)) + (home-page "https://osqp.org") + (synopsis "Quadratic Programming Solver using the OSQP Library") + (description + "This package provides bindings to the OSQP solver. The OSQP +solver is a numerical optimization package or solving convex quadratic +programs written in C and based on the alternating direction method of +multipliers. See <arXiv:1711.08013> for details.") + (license (list license:asl2.0)))) + (define-public r-kernlab (package (name "r-kernlab") @@ -19164,14 +20578,14 @@ interaction search in high-dimensional data.") (define-public r-rttf2pt1 (package (name "r-rttf2pt1") - (version "1.3.10") + (version "1.3.11") (source (origin (method url-fetch) (uri (cran-uri "Rttf2pt1" version)) (sha256 (base32 - "1fp1y0kxa5xg8w0dplm12wfm8h78az4k6ql1758wwhb3d17np241")))) + "1fbls9hy4s0hdszg449bpapx2mhknwiasvr15djf9f1hm0b2908p")))) (properties `((upstream-name . "Rttf2pt1"))) (build-system r-build-system) (home-page "https://github.com/wch/Rttf2pt1") @@ -19259,14 +20673,14 @@ the XKCD web comic.") (define-public r-babelgene (package (name "r-babelgene") - (version "22.3") + (version "22.9") (source (origin (method url-fetch) (uri (cran-uri "babelgene" version)) (sha256 (base32 - "1735h4s2vahv55pmq65zkgxq8d5x71i1is03rf17dric8yynjjhg")))) + "1ql5r1chl5ajzy9ppcnk755ia3m2a8n08m837dnm2ll3nzf02rnf")))) (properties `((upstream-name . "babelgene"))) (build-system r-build-system) (propagated-inputs @@ -19371,14 +20785,14 @@ package.") (define-public r-yulab-utils (package (name "r-yulab-utils") - (version "0.0.5") + (version "0.0.6") (source (origin (method url-fetch) (uri (cran-uri "yulab.utils" version)) (sha256 (base32 - "0sq5wc0mp84h6fs4wa2smvf7dcn0p0xarzb2ljvqc3p4vb2lvkbf")))) + "09bvj97xz9gishyhi1dzpjfl70v7xag8952fqfp60h18s6w52flp")))) (properties `((upstream-name . "yulab.utils"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=yulab.utils") @@ -19473,14 +20887,14 @@ color.") (define-public r-polyclip (package (name "r-polyclip") - (version "1.10-0") + (version "1.10-4") (source (origin (method url-fetch) (uri (cran-uri "polyclip" version)) (sha256 (base32 - "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl")))) + "0mkg5v045an49c3j279vvabm7p4d9jsnzlfp96dpblvihxvwkll4")))) (build-system r-build-system) (native-inputs (list pkg-config)) (home-page "http://www.angusj.com/delphi/clipper.php") @@ -19544,17 +20958,18 @@ sets of URLs.") (define-public r-ggforce (package (name "r-ggforce") - (version "0.3.4") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "ggforce" version)) (sha256 (base32 - "0lshvdb5kx0k5w36pc7fy653cs98w17spbw8f0jw36xb80sipiv2")))) + "0wqq8l7lq96k4w0vq12jcg7clvgia8s35jjbqq1s0py4cgxijhml")))) (build-system r-build-system) (propagated-inputs - (list r-ggplot2 + (list r-cli + r-ggplot2 r-gtable r-lifecycle r-mass @@ -19563,8 +20978,10 @@ sets of URLs.") r-rcppeigen r-rlang r-scales + r-systemfonts r-tidyselect r-tweenr + r-vctrs r-withr)) (home-page "https://ggforce.data-imaginist.com") (synopsis "Accelerating ggplot2") @@ -19575,6 +20992,35 @@ This package aims to be a collection of mainly new statistics and geometries that fills this gap.") (license license:expat))) +(define-public r-eulerr + (package + (name "r-eulerr") + (version "7.0.0") + (source (origin + (method url-fetch) + (uri (cran-uri "eulerr" version)) + (sha256 + (base32 + "16a84a2xgv1iqsir0hzn6qclljni4f3prpycb7qpp06vrd0yn8lw")))) + (properties `((upstream-name . "eulerr"))) + (build-system r-build-system) + (propagated-inputs + (list r-gensa + r-polyclip + r-polylabelr + r-rcpp + r-rcpparmadillo)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/jolars/eulerr") + (synopsis "Area-proportional Euler and Venn diagrams with ellipses") + (description + "This package generates area-proportional Euler diagrams using +numerical optimization. An Euler diagram is a generalization of a +Venn diagram, relaxing the criterion that all interactions need to be +represented. Diagrams may be fit with ellipses and circles via a wide +range of inputs and can be visualized in numerous ways.") + (license license:gpl3))) + (define-public r-europepmc (package (name "r-europepmc") @@ -19618,17 +21064,18 @@ databases, including ENA, PDB or ChEMBL are also accessible.") (define-public r-ggraph (package (name "r-ggraph") - (version "2.0.6") + (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "ggraph" version)) (sha256 (base32 - "02nl92vgyp5pc61r14mmmbfhg5nhb6fibjjb3djfag2ahc6wj2kv")))) + "07sw4h94dzbs44dcvvj80g8v8252k4iw8pkmzdrk4qagvhidnvv8")))) (build-system r-build-system) (propagated-inputs - (list r-digest + (list r-cli + r-digest r-dplyr r-ggforce r-ggplot2 @@ -19636,11 +21083,13 @@ databases, including ENA, PDB or ChEMBL are also accessible.") r-graphlayouts r-gtable r-igraph + r-lifecycle r-mass r-rcpp r-rlang r-scales r-tidygraph + r-vctrs r-viridis r-withr)) (native-inputs @@ -19658,14 +21107,14 @@ layer by layer.") (define-public r-gkmsvm (package (name "r-gkmsvm") - (version "0.81.0") + (version "0.82.0") (source (origin (method url-fetch) (uri (cran-uri "gkmSVM" version)) (sha256 (base32 - "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj")))) + "1m2cq4b0srghaj04p5ffbc21zv1rg7avi8pn765bybjhvrn567bm")))) (properties `((upstream-name . "gkmSVM"))) (build-system r-build-system) (propagated-inputs @@ -19913,13 +21362,13 @@ analysis.") (define-public r-png (package (name "r-png") - (version "0.1-7") + (version "0.1-8") (source (origin (method url-fetch) (uri (cran-uri "png" version)) (sha256 (base32 - "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2")))) + "077nca3x0l6mq2g6izknzcn994bqs3nfqk7wscrjbfk2dnxzldjs")))) (build-system r-build-system) (inputs (list libpng zlib)) @@ -19935,14 +21384,14 @@ in-memory raw vectors.") (define-public r-ggcorrplot (package (name "r-ggcorrplot") - (version "0.1.3") + (version "0.1.4") (source (origin (method url-fetch) (uri (cran-uri "ggcorrplot" version)) (sha256 (base32 - "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b")))) + "186a0mpdpipp24fjbd52l1gdgpqm6vl83ff8069d8nngyqbrx0jr")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-reshape2)) @@ -19958,14 +21407,14 @@ function for computing a matrix of correlation p-values.") (define-public r-ggfun (package (name "r-ggfun") - (version "0.0.7") + (version "0.0.9") (source (origin (method url-fetch) (uri (cran-uri "ggfun" version)) (sha256 (base32 - "0x71p3mm0sw72hv92368wy2yiy7zv826p3kddpwndqv1bywmyfx8")))) + "04kn367mzgrfwnwz97vw5jqp2kig94hmxmhyyic7ddvk3sfhwx2w")))) (properties `((upstream-name . "ggfun"))) (build-system r-build-system) (propagated-inputs @@ -20010,6 +21459,26 @@ inline CSS directives, and it can be rendered both with and without word wrap.") (license license:expat))) +(define-public r-ggghost + (package + (name "r-ggghost") + (version "0.2.1") + (source (origin + (method url-fetch) + (uri (cran-uri "ggghost" version)) + (sha256 + (base32 + "0kvsjadxxdf6yvzk4a6yqkg02q1ysslvf3m0a369bdim396z4hnv")))) + (properties `((upstream-name . "ggghost"))) + (build-system r-build-system) + (propagated-inputs (list r-animation r-ggplot2)) + (home-page "https://github.com/jonocarroll/ggghost") + (synopsis "Capture the spirit of your ggplot2 calls") + (description + "This package lets you create a reproducible @code{ggplot2} object by +storing the data and calls.") + (license license:gpl3+))) + (define-public r-ggtext (package (name "r-ggtext") @@ -20034,6 +21503,31 @@ complex formatted plot labels (titles, subtitles, facet labels, axis labels, etc.). Text boxes with automatic word wrap are also supported.") (license license:gpl2))) +(define-public r-ggthemeassist + (package + (name "r-ggthemeassist") + (version "0.1.5") + (source (origin + (method url-fetch) + (uri (cran-uri "ggThemeAssist" version)) + (sha256 + (base32 + "1biw91a8p13h62v4w3yim6ghr98khmyhb3qd0h04asf91vvmpxbv")))) + (properties `((upstream-name . "ggThemeAssist"))) + (build-system r-build-system) + (propagated-inputs + (list r-formatr + r-ggplot2 + r-miniui + r-rstudioapi + r-shiny)) + (home-page "https://github.com/calligross/ggthemeassist") + (synopsis "Add-in to customize ggplot2 themes") + (description + "This package provides an Rstudio add-in that delivers a graphical +interface for editing @code{ggplot2} theme elements.") + (license license:gpl3))) + ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-flexdashboard @@ -20253,14 +21747,14 @@ external dependencies. This package has is implemented purely in R.") (define-public r-aplot (package (name "r-aplot") - (version "0.1.7") + (version "0.1.9") (source (origin (method url-fetch) (uri (cran-uri "aplot" version)) (sha256 (base32 - "05l6pvhrl715xgdy7qmw6lyxigv9qn90ms3vf7awip8sdmghy9gn")))) + "04mv2jhkk47sqmm69dbcmy84han2k19sv6vnmk572xbm19i661xg")))) (properties `((upstream-name . "aplot"))) (build-system r-build-system) (propagated-inputs @@ -20282,14 +21776,14 @@ matched.") (define-public r-ggnewscale (package (name "r-ggnewscale") - (version "0.4.7") + (version "0.4.8") (source (origin (method url-fetch) (uri (cran-uri "ggnewscale" version)) (sha256 (base32 - "108a7y6sqqvzyfk247lbmnacfpwdl405rf1b3fa62cgx8ycsq4kb")))) + "004p5ai6rc5y8f6966k894jzw9v3m4zy36z50yapig7c85lzmzn7")))) (properties `((upstream-name . "ggnewscale"))) (build-system r-build-system) (propagated-inputs @@ -20328,14 +21822,14 @@ colored by the number of neighboring points. This is useful to visualize the (define-public r-arrow (package (name "r-arrow") - (version "9.0.0.1") + (version "10.0.1") (source (origin (method url-fetch) (uri (cran-uri "arrow" version)) (sha256 (base32 - "1vbjny6v1d4fdf01rphg4wg8ljs0bzrjyxlsjwjq58pd6g2qcdgc")))) + "0dwdi9sq7wv34ia6kg446pqf5za75hl6zrb2ly51p2zdr4g69p0y")))) (properties `((upstream-name . "arrow"))) (build-system r-build-system) (inputs @@ -20344,6 +21838,7 @@ colored by the number of neighboring points. This is useful to visualize the (list r-assertthat r-bit64 r-cpp11 + r-glue r-purrr r-r6 r-rlang @@ -20475,14 +21970,14 @@ Row} (CSR) format.") (define-public r-text2vec (package (name "r-text2vec") - (version "0.6.2") + (version "0.6.3") (source (origin (method url-fetch) (uri (cran-uri "text2vec" version)) (sha256 (base32 - "1as58w1hb6h0hpncwcr2nx9a8bj5fy6bfllx2a8ck8hal764iach")))) + "1hi7ydb7xkgbff4lwnnz1biyl8m90w16hn3x5rrzvscvm53sj4y7")))) (properties `((upstream-name . "text2vec"))) (build-system r-build-system) (propagated-inputs @@ -20584,14 +22079,14 @@ provides tools to compute this metric.") (define-public r-lintr (package (name "r-lintr") - (version "3.0.1") + (version "3.0.2") (source (origin (method url-fetch) (uri (cran-uri "lintr" version)) (sha256 (base32 - "18prww284sil98ck3gmkmfs6b4disn9nyfb00kfwwiwg7ay1df6g")))) + "1j9l5lsa88hl5b3lw1789868pm0m2sbahyqayj9213d7zspp0slz")))) (properties `((upstream-name . "lintr"))) (build-system r-build-system) (propagated-inputs @@ -20614,17 +22109,41 @@ errors and possible semantic issues. It supports on the fly checking of R code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.") (license license:expat))) +(define-public r-scs + (package + (name "r-scs") + (version "3.0-1") + (source (origin + (method url-fetch) + (uri (cran-uri "scs" version)) + (sha256 + (base32 + "04srf33zw4dxv22b1h5qwjch5yg7hrvk4iq8yvxqnbr8qzp1x26n")))) + (properties `((upstream-name . "scs"))) + (build-system r-build-system) + (home-page "https://github.com/FlorianSchwendinger/scs") + (synopsis "Splitting conic solver") + (description + "This package solves convex cone programs via operator splitting. +It can solve: linear programs, second-order cone programs, +semidefinite programs, exponential cone programs, and power cone +programs, or problems with any combination of those cones. SCS uses +AMD (a set of routines for permuting sparse matrices prior to +factorization) and LDL (a sparse LDL factorization and solve package) +from SuiteSparse.") + (license license:gpl3))) + (define-public r-sctransform (package (name "r-sctransform") - (version "0.3.4") + (version "0.3.5") (source (origin (method url-fetch) (uri (cran-uri "sctransform" version)) (sha256 (base32 - "1nhmsbkrww74a55avln5zhd77g92f15p885j5q0khajw35iqnv0g")))) + "02vfgv6v3knmn5nxadjyjkzqmni1sgaf3f9ywm7d0knn0pgmd3n0")))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -20653,14 +22172,14 @@ batch correction, and data correction.") (define-public r-styler (package (name "r-styler") - (version "1.7.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (cran-uri "styler" version)) (sha256 (base32 - "1ki260ga0jrmayhdlx2sl788yp5kkmi4wyl32nmvvyb55sng6j9y")))) + "1sc1xr9pfrbd2yyzyyxpj8dd81djmsr00gxgr0mr18habyl5yl0m")))) (build-system r-build-system) ;; This is needed by R.cache. (arguments @@ -20673,10 +22192,9 @@ batch correction, and data correction.") r-magrittr r-purrr r-r-cache - r-rematch2 r-rlang r-rprojroot - r-tibble + r-vctrs r-withr)) (native-inputs (list r-knitr)) @@ -20790,14 +22308,14 @@ experiments in a well-organized and reproducible way.") (define-public r-clue (package (name "r-clue") - (version "0.3-61") + (version "0.3-63") (source (origin (method url-fetch) (uri (cran-uri "clue" version)) (sha256 (base32 - "0cfw2k1kh4a8imdv7b5qw977xd6indampsabhfldj3rqrqb1ncbi")))) + "0c402fb3r1cxd0j6ikjhssq2k22lbnsq4k7vjpgvyx4a4ly2h4yr")))) (build-system r-build-system) (propagated-inputs (list r-cluster)) (home-page "https://cran.r-project.org/web/packages/clue/") @@ -21042,17 +22560,68 @@ perspective plots, slice plots, surface plots, scatter plots, etc. It includes data sets from oceanography.") (license license:gpl3+))) +(define-public r-plotroc + (package + (name "r-plotroc") + (version "2.3.0") + (source (origin + (method url-fetch) + (uri (cran-uri "plotROC" version)) + (sha256 + (base32 + "0kaz9hrimi9gi7cf7flag9kc9yrg5fdyylqa5hn53x4dy8vhj37g")) + (snippet + '(delete-file "inst/d3.v3.min.js")))) + (properties `((upstream-name . "plotROC"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (let ((source (assoc-ref inputs "d3.v3.js")) + (target "inst/d3.v3.min.js")) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target)))))))) + (propagated-inputs + (list r-ggplot2 + r-gridsvg + r-plyr + r-rlang + r-shiny)) + (native-inputs + `(("r-knitr" ,r-knitr) + ("esbuild" ,esbuild) + ("d3.v3.js" + ,(origin + (method url-fetch) + (uri "https://d3js.org/d3.v3.js") + (sha256 + (base32 + "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41")))))) + (home-page "https://sachsmc.github.io/plotROC/") + (synopsis "Generating useful receiver operating characteristic curve charts") + (description + "This package generates @acronym{ROC, receiver operating characteristic} +plots. Most ROC curve plots obscure the cutoff values and inhibit +interpretation and comparison of multiple curves. This attempts to address +those shortcomings by providing plotting and interactive tools. Functions are +provided to generate an interactive ROC curve plot for web use, and print +versions. A Shiny application implementing the functions is also included.") + (license license:expat))) + (define-public r-ggfortify (package (name "r-ggfortify") - (version "0.4.14") + (version "0.4.15") (source (origin (method url-fetch) (uri (cran-uri "ggfortify" version)) (sha256 (base32 - "038m74azpy43869ax1yi6wxbl1kr59iaxl8raiikjg749vcx6njw")))) + "1cfwv8jjy1yk0l5wnp48ql1javvrzq1wnh1lv49xp6rynz00lxm8")))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -21076,18 +22645,19 @@ results and plots in a unified style using the @code{ggplot2} package.") (define-public r-refmanager (package (name "r-refmanager") - (version "1.3.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "RefManageR" version)) (sha256 (base32 - "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps")))) + "1kjd66gp2z9fzrnyr1bqfd9p58q0bin3a187z9b56hiqmdjhyc78")))) (properties `((upstream-name . "RefManageR"))) (build-system r-build-system) (propagated-inputs - (list r-httr + (list r-bibtex + r-httr r-jsonlite r-lubridate r-plyr @@ -21283,6 +22853,33 @@ using a lasso (L1) penalty. Facilities are provided for estimates along a path of values for the regularization parameter.") (license license:gpl2))) +(define-public r-gldex + (package + (name "r-gldex") + (version "2.0.0.9.2") + (source (origin + (method url-fetch) + (uri (cran-uri "GLDEX" version)) + (sha256 + (base32 + "0pikq5aywky77sbbkga7s0ww3ywlarx336rgpyiigr72fmjvb289")))) + (properties `((upstream-name . "GLDEX"))) + (build-system r-build-system) + (propagated-inputs (list r-cluster r-spacefillr)) + (home-page "https://cran.r-project.org/package=GLDEX") + (synopsis "Fitting single and mixture of generalised lambda distributions") + (description + "@code{GLDEX} offers fitting algorithms corresponding to two major +objectives. One is to provide a smoothing device to fit distributions to data +using the weighted and unweighted discretised approach based on the bin width +of the histogram. The other is to provide a definitive fit to the data set +using the maximum likelihood and quantile matching estimation. Other methods +such as moment matching, starship method, and L moment matching are also +provided. Diagnostics on goodness of fit can be done via qqplots, KS-resample +tests and comparing mean, variance, skewness and kurtosis of the data with the +fitted distribution.") + (license license:gpl3+))) + (define-public r-rhpcblasctl (package (name "r-rhpcblasctl") @@ -21585,14 +23182,14 @@ be used further by e.g. graphic devices.") (define-public r-graphlayouts (package (name "r-graphlayouts") - (version "0.8.1") + (version "0.8.4") (source (origin (method url-fetch) (uri (cran-uri "graphlayouts" version)) (sha256 (base32 - "0yhg42p3jlz78kd712jd5525zm1h3n5gmjplfscjkgn342r3w92v")))) + "1zch8v0fc9lrm1pklcvi7g4g7zmqq3gxprm7pbdx018b35z8z3bp")))) (properties `((upstream-name . "graphlayouts"))) (build-system r-build-system) (propagated-inputs @@ -21610,14 +23207,14 @@ emphasize hidden group structures in networks or focus on specific nodes.") (define-public r-terra (package (name "r-terra") - (version "1.6-17") + (version "1.6-47") (source (origin (method url-fetch) (uri (cran-uri "terra" version)) (sha256 (base32 - "00mwigymvsqf7r3swbkdw8fwqzr05ddk84fhyhr16lfa4118z26v")))) + "13n6rxrrkn4wgcgq2kyyhn5nxw099hy9fbzxg78waxa6cxapwpmh")))) (properties `((upstream-name . "terra"))) (build-system r-build-system) (inputs @@ -21706,14 +23303,14 @@ cell RNA-seq experiments.") (define-public r-assertr (package (name "r-assertr") - (version "2.8") + (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "assertr" version)) (sha256 (base32 - "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650")))) + "1wi3mz968clvwqg6mbm32zhj4vyfskklk72b4028cjsfdry6bpfp")))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-mass r-rlang)) @@ -21731,14 +23328,14 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.18.2") + (version "0.20.0") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "04swg19zb34y3nmclf94v19yskqlb2diqg93jflhgagrv9550az9")))) + "16y92q4h385sqc7xgdcrdmdvw0l8plxxbhcdsnx4gqqgm8di9l9p")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs @@ -21759,13 +23356,13 @@ effect size.") (define-public r-rgdal (package (name "r-rgdal") - (version "1.5-32") + (version "1.6-3") (source (origin (method url-fetch) (uri (cran-uri "rgdal" version)) (sha256 - (base32 "1vbkyhw8nd7dw1r53qisphav31x6zvpbzilvnlvbjbj9hzhs90s5")))) + (base32 "0snz5m158as39h6zdcdrydwm5n2r2vayv3xy8n3g5mmkbxyyx7i2")))) (properties `((upstream-name . "rgdal"))) (build-system r-build-system) (inputs @@ -21812,18 +23409,21 @@ atmospheric physics.") (define-public r-lifecycle (package (name "r-lifecycle") - (version "1.0.2") + (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "lifecycle" version)) (sha256 (base32 - "0qssl9lmfn94kmvcg1xpd4md17jx31i3sdbb77dwas60z673qgvv")))) + "1hk9mblhap429fk77qpgc4hv0j91q5wpahi0y76w118m471zsnb4")))) (properties `((upstream-name . "lifecycle"))) (build-system r-build-system) (propagated-inputs - (list r-glue r-rlang)) + (list r-cli r-glue r-rlang)) + ;; We can't add this here because via r-stringr this package ends up being + ;; an input to r-knitr. + #; (native-inputs (list r-knitr)) ; for vignettes (home-page "https://github.com/r-lib/lifecycle") @@ -21890,13 +23490,13 @@ programming problems.") (define-public r-desolve (package (name "r-desolve") - (version "1.33") + (version "1.34") (source (origin (method url-fetch) (uri (cran-uri "deSolve" version)) (sha256 - (base32 "115nr3j1zp2016qpk9ab6r8n15zygvlihlmc10ilfznf0ng9gpki")))) + (base32 "08czbjvq07ax6q3k303w37q8lq50547cdx7yhp32mqnx8igk0m12")))) (properties `((upstream-name . "deSolve"))) (build-system r-build-system) (native-inputs @@ -21948,12 +23548,12 @@ to ODEs by numerical differencing.") (define-public r-pracma (package (name "r-pracma") - (version "2.3.8") + (version "2.4.2") (source (origin (method url-fetch) (uri (cran-uri "pracma" version)) (sha256 - (base32 "0r17siivm37k4gp253v9mlg5m7cwqp85h9kk2hbp2wkf81ad80i3")))) + (base32 "05lwx2yx7f45cr5amzbjv3b2p6ibspjxl0aglq2dga6rvxzk6l0x")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pracma/") (synopsis "Practical numerical math functions") @@ -22009,14 +23609,14 @@ as a boxplot function.") (define-public r-bio3d (package (name "r-bio3d") - (version "2.4-3") + (version "2.4-4") (source (origin (method url-fetch) (uri (cran-uri "bio3d" version)) (sha256 (base32 - "0x3apqxbk4lvvcnvvdsyjd9f6qh9f9qgml3ih69hl9ikj06iy0y6")))) + "1scxzmh22ca0nmpkvapsdcmq3n06j2wy74ljz1g27r1k1p0ylm2n")))) (properties `((upstream-name . "bio3d"))) (build-system r-build-system) (inputs (list zlib)) @@ -22870,14 +24470,14 @@ facilitates insertion into pipelines, and content inspection.") (define-public r-rngwell (package (name "r-rngwell") - (version "0.10-7") + (version "0.10-8") (source (origin (method url-fetch) (uri (cran-uri "rngWELL" version)) (sha256 (base32 - "0f1dxxaimfb0fww8ym9ciqf6q760ai46wxldl37m5mfpd57ca00c")))) + "0ad1mz11l27h6apil2hd7gwz5zhi9jkjrk2jnhbkd8d0wz9g0sis")))) (properties `((upstream-name . "rngWELL"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rngWELL/") @@ -22915,14 +24515,14 @@ and prints vectorized images.") (define-public r-randtoolbox (package (name "r-randtoolbox") - (version "2.0.2") + (version "2.0.3") (source (origin (method url-fetch) (uri (cran-uri "randtoolbox" version)) (sha256 (base32 - "0mvafd2gm1jpg19gdn6bw8668pqghi0xmcb56rl4fwamg8jg09xn")))) + "0i23wj9nmsfy3x2yzlfadzrvil2yhcrxs6qxrykrqs15r9jwx3hm")))) (properties `((upstream-name . "randtoolbox"))) (build-system r-build-system) (propagated-inputs @@ -22950,14 +24550,14 @@ See e.g. Gentle (2003) @url{doi:10.1007/b97336}.") (define-public r-lhs (package (name "r-lhs") - (version "1.1.5") + (version "1.1.6") (source (origin (method url-fetch) (uri (cran-uri "lhs" version)) (sha256 (base32 - "0fb3bc3s5pbwg92qkjbg7v8ah36wm6qs05vf098hwjakr7f6yg3s")))) + "0gyjdic714pqvq2jv1v0vh7hl9s83sg2zxx2gdkp38z6xx2cwzz3")))) (properties `((upstream-name . "lhs"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -23000,18 +24600,19 @@ to maximise an approximation to the expectation of the utility function.") (define-public r-acet (package (name "r-acet") - (version "1.8.1") + (version "1.8.2") (source (origin (method url-fetch) (uri (cran-uri "ACEt" version)) (sha256 (base32 - "0b5lfpnppyk0237phr2aybhx29nhm8ngwk2qa1y4lshrvsw97wg4")))) + "0583c9dg2yf01zf5p0bf24zipkm8yp7rwhn1dxyw2d0v881bbli6")))) (properties `((upstream-name . "ACEt"))) (build-system r-build-system) (propagated-inputs (list r-bh r-mass r-rcpp r-rcpparmadillo)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ACEt/") (synopsis "Estimating dynamic heritability and twin model comparison") (description @@ -23073,14 +24674,14 @@ models.") (define-public r-gamlss (package (name "r-gamlss") - (version "5.4-3") + (version "5.4-10") (source (origin (method url-fetch) (uri (cran-uri "gamlss" version)) (sha256 (base32 - "0xih19zqgpjl5qv5j38ana6x29y84shn2jfl2lk4kaw3q7yx86b6")))) + "1cm0rvihniad309j26ll8kabndqzs3wdh5dak70b60z4kljrfx4c")))) (properties `((upstream-name . "gamlss"))) (build-system r-build-system) (propagated-inputs @@ -23382,14 +24983,14 @@ provided as well.") (define-public r-tuner (package (name "r-tuner") - (version "1.4.0") + (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "tuneR" version)) (sha256 (base32 - "1sd0drxzbdy71bh35fccg9ajhpdhdpy0m9nja2lw82p1pzhyl7jn")))) + "1mfkhxprqkj5v2z23g0bj8mwdp6q5fj1krk5ggr79359bd1nl7pf")))) (properties `((upstream-name . "tuneR"))) (build-system r-build-system) (propagated-inputs (list r-signal)) @@ -23630,6 +25231,34 @@ dissimilarity useful for clustering mixed data, and, optionally, perform the clustering.") (license license:gpl2+))) +(define-public r-treemap + (package + (name "r-treemap") + (version "2.4-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "treemap" version)) + (sha256 + (base32 "1fg8gygw38x7msn32barx2irvcv8flm6wqvipnbj1qkh9w89y3q4")))) + (properties `((upstream-name . "treemap"))) + (build-system r-build-system) + (propagated-inputs + (list r-colorspace + r-data-table + r-ggplot2 + r-gridbase + r-igraph + r-rcolorbrewer + r-shiny)) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=treemap") + (synopsis "Treemap visualization") + (description + "A treemap is a space-filling visualization of hierarchical structures. +This package offers great flexibility to draw treemaps.") + (license license:gpl3+))) + (define-public r-acrosstic (package (name "r-acrosstic") @@ -23973,14 +25602,14 @@ conditional on one covariate, and multimodal regression.") (define-public r-rainbow (package (name "r-rainbow") - (version "3.6") + (version "3.7") (source (origin (method url-fetch) (uri (cran-uri "rainbow" version)) (sha256 (base32 - "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3")))) + "1cldipi3cb55d434wv03ymwygbisfwgq2b84gwwkgqpfal2xk78m")))) (properties `((upstream-name . "rainbow"))) (build-system r-build-system) (propagated-inputs @@ -24233,14 +25862,14 @@ communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.") (define-public r-expint (package (name "r-expint") - (version "0.1-7") + (version "0.1-8") (source (origin (method url-fetch) (uri (cran-uri "expint" version)) (sha256 (base32 - "01d0a7pc4qx7044a0cymnv5ld88r90vdvlqjbnzg9qlfbizdgyvw")))) + "1cn6c84pqf8bgk109qm4znn186h6s6cpll3d11cw144h0vh4yr8j")))) (properties `((upstream-name . "expint"))) (build-system r-build-system) (home-page "https://gitlab.com/vigou3/expint") @@ -24256,14 +25885,14 @@ API; see the package vignette for details.") (define-public r-actuar (package (name "r-actuar") - (version "3.3-0") + (version "3.3-1") (source (origin (method url-fetch) (uri (cran-uri "actuar" version)) (sha256 (base32 - "1qi9y2x93pxxbynwl06rbiasm86vb0jh7sckw1dw3s21rsx1f5c5")))) + "16nyhn0aw2mb8915ycr46rjvg9pbcps7zxs2sgvdws9kzm027mpj")))) (properties `((upstream-name . "actuar"))) (build-system r-build-system) (propagated-inputs (list r-expint)) @@ -24329,14 +25958,14 @@ number embedded in the file rather than the file extension.") (define-public r-imager (package (name "r-imager") - (version "0.42.13") + (version "0.42.16") (source (origin (method url-fetch) (uri (cran-uri "imager" version)) (sha256 (base32 - "0zygnmxwbbmj5i2l2affzdz90xvsa7b5pbkzkhjbm40is69rh2nr")))) + "00q2v000xanp03bzscmj3q9qnlhc97b1lgr4l19s9jmbf0hf9c5c")))) (properties `((upstream-name . "imager"))) (build-system r-build-system) (inputs @@ -24447,14 +26076,14 @@ done.") (define-public r-adagio (package (name "r-adagio") - (version "0.8.4") + (version "0.8.5") (source (origin (method url-fetch) (uri (cran-uri "adagio" version)) (sha256 (base32 - "0ihv05402iq003m0338f85pnqnlnrmx0pf1mg8cz9sgi5h98mbnl")))) + "0icwr3cark67jyg9zzqwyv9q4fs0j0xgb5i7nkwv9s7y5dlldl0b")))) (properties `((upstream-name . "adagio"))) (build-system r-build-system) (propagated-inputs @@ -24527,13 +26156,13 @@ Visualizations are also available for most of these settings.") (define-public r-torch (package (name "r-torch") - (version "0.8.1") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "torch" version)) (sha256 - (base32 "1dncf5njdzw1hf98knlv94rxcxnc5gl3cmk2cvlbn1z8mri86rlc")))) + (base32 "1iylnz0hsi00q7hngi2h24kg3nvjjg10z6iarqhp3wylsasgjs1f")))) (properties `((upstream-name . "torch"))) (build-system r-build-system) (arguments @@ -24662,14 +26291,14 @@ validation of bicluster solutions.") (define-public r-icge (package (name "r-icge") - (version "0.4.1") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "ICGE" version)) (sha256 (base32 - "0w6hbi3h98q6gsxqbb43p95v6xykgrasxcjivwm8hw9fly4avxyi")))) + "13p9v0g5qda8bpj3sj9p277l7idv4jscrsszg2kn080dapp3cppp")))) (properties `((upstream-name . "ICGE"))) (build-system r-build-system) (propagated-inputs @@ -24758,6 +26387,61 @@ Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd Edition), John Wiley and Sons.") (license license:gpl2))) +(define-public r-animation + (package + (name "r-animation") + (version "2.7") + (source (origin + (method url-fetch) + (uri (cran-uri "animation" version)) + (sha256 + (base32 + "0sg4sz5lkn85yzpcg22xkr7921cbnh7g74nlp9imjy7c0hdqyhc8")) + (snippet + '(for-each delete-file + '("inst/misc/scianimator/js/jquery.scianimator.min.js" + "inst/misc/scianimator/js/jquery-1.4.4.min.js"))))) + (properties `((upstream-name . "animation"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/misc/" + (symlink (search-input-file + inputs + "share/javascript/jquery.scianimator.min.js") + "scianimator/js/jquery.scianimator.min.js") + (invoke "esbuild" (assoc-ref inputs "js-jquery") + "--minify" + (string-append "--outfile=" + "scianimator/js/jquery-1.4.4.min.js")))))))) + (propagated-inputs (list r-magick)) + (inputs (list js-scianimator)) + (native-inputs + `(("esbuild" ,esbuild) + ("js-jquery" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-1.4.4.js") + (sha256 + (base32 + "10nl4smq63vrfb0c3n0fknm1zw7ss8gicy6wc6jb6l3rmyad075k")))))) + (home-page "https://yihui.org/animation/") + (synopsis "Gallery of animations and utilities to create animations") + (description + "This package provides functions for animations in statistics, covering +topics in probability theory, mathematical statistics, multivariate +statistics, non-parametric statistics, sampling survey, linear models, time +series, computational statistics, data mining and machine learning. These +functions may be helpful in teaching statistics and data analysis. Also +provided in this package are a series of functions to save animations to +various formats, e.g. GIF, HTML pages, PDF, and videos. PDF animations can be +inserted into Sweave / @code{knitr} easily.") + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-anthropometry (package (name "r-anthropometry") @@ -24793,16 +26477,40 @@ They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis.") (license license:gpl2+))) +(define-public r-anytime + (package + (name "r-anytime") + (version "0.3.9") + (source (origin + (method url-fetch) + (uri (cran-uri "anytime" version)) + (sha256 + (base32 + "0jjpqynai5nd7mfy1smb44356f3d5bmpxhs1i9x9jw5c959c35hh")))) + (properties `((upstream-name . "anytime"))) + (build-system r-build-system) + (propagated-inputs + (list r-bh + r-rcpp)) + (home-page "http://dirk.eddelbuettel.com/code/anytime.html") + (synopsis "Converter of input to POSIXct or Date") + (description + "The package converts the input in any one of character, integer, numeric, +factor, or an ordered type into @code{POSIXct} (or @code{Date}) objects, using +one of a number of predefined formats, and relying on Boost facilities for date +and time parsing.") + (license license:gpl2+))) + (define-public r-anndata (package (name "r-anndata") - (version "0.7.5.4") + (version "0.7.5.5") (source (origin (method url-fetch) (uri (cran-uri "anndata" version)) (sha256 - (base32 "0vn64b0rpnwbznn0h03b810mp8hcqxjzw69nzyjmndwa8r9ial2y")))) + (base32 "1ync82qp0v6zszibz8bwhlyknf99v3iki8cwq4n4vwmg9z7hrb54")))) (properties `((upstream-name . "anndata"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-matrix r-r6 r-reticulate)) @@ -24878,13 +26586,13 @@ finding peaks in spectra, converting humidity measures.") (define-public r-qqconf (package (name "r-qqconf") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "qqconf" version)) (sha256 (base32 - "11sh0q5bwmqdygqd1gspx7xc5mysj18whz11afnz6s1m820snhhw")))) + "1vvw79l8nqpqvmfpff5khgdjbs1s2q5ylg72lvkihd2qfk0d8cf5")))) (properties `((upstream-name . "qqconf"))) (build-system r-build-system) (inputs (list fftw)) @@ -24928,13 +26636,13 @@ from PLINK results.") (define-public r-gghighlight (package (name "r-gghighlight") - (version "0.3.3") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "gghighlight" version)) (sha256 - (base32 "0isfp5n0ijqpy3z5d7l75mlq15nbkjppv6812lcya6097ar2d381")))) + (base32 "0vfcn3gg6j7g20n2z1iwr94jnpqn0zl5j9jfc8bnbsrmz49dzqpd")))) (properties `((upstream-name . "gghighlight"))) (build-system r-build-system) (propagated-inputs @@ -25098,14 +26806,14 @@ automatically show a loader when the output is (re)calculating.") (define-public r-rsvg (package (name "r-rsvg") - (version "2.3.1") + (version "2.4.0") (source (origin (method url-fetch) (uri (cran-uri "rsvg" version)) (sha256 (base32 - "096w4d1gvfc65d4jg7ykp23k9f7cf7f8zvzfhvhd7qkfsbjpxqkj")))) + "1schf5gfqzvwmaigdsic5va9bbk9ycvcisiyll8xjjw116y9cxyb")))) (properties `((upstream-name . "rsvg"))) (build-system r-build-system) (inputs @@ -25389,14 +27097,14 @@ first.") (define-public r-fracdiff (package (name "r-fracdiff") - (version "1.5-1") + (version "1.5-2") (source (origin (method url-fetch) (uri (cran-uri "fracdiff" version)) (sha256 (base32 - "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q")))) + "0dzl011c92skf7hmx1zvdwsrashmfkxy9p2wig35nzr8609qhpxc")))) (properties `((upstream-name . "fracdiff"))) (build-system r-build-system) (home-page "https://github.com/mmaechler/fracdiff") @@ -25411,14 +27119,14 @@ Raftery, Appl.Statistics, 1989); it includes inference and basic methods.") (define-public r-forecast (package (name "r-forecast") - (version "8.17.0") + (version "8.20") (source (origin (method url-fetch) (uri (cran-uri "forecast" version)) (sha256 (base32 - "01633q2fg4cl8zg61dvsnrk8nk1iknk9jqk7p7xnkypxjckm7zl9")))) + "03ll4v4r2l4kk4lbwnrvmd24003qm6j81lzr06qlns311zf4dv9v")))) (properties `((upstream-name . "forecast"))) (build-system r-build-system) (propagated-inputs @@ -25445,6 +27153,33 @@ univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.") (license license:gpl3))) +(define-public r-forestplot + (package + (name "r-forestplot") + (version "3.1.1") + (source (origin + (method url-fetch) + (uri (cran-uri "forestplot" version)) + (sha256 + (base32 + "0jf7sl7z963r92l5r2irvnakmbmx554vbprg51smj6qns5a6dfcj")))) + (properties `((upstream-name . "forestplot"))) + (build-system r-build-system) + (propagated-inputs + (list r-abind r-checkmate)) + (native-inputs (list r-knitr)) + (home-page "https://gforge.se/packages/") + (synopsis "Advanced forest plot using @code{grid} graphics") + (description + "This package provides a forest plot that allows for multiple +confidence intervals per row, custom fonts for each text element, +custom confidence intervals, text mixed with expressions, and more. +The aim is to extend the use of forest plots beyond meta-analyses. +This is a more general version of the original @code{rmeta} package's +@code{forestplot()} function and relies heavily on the @code{grid} +package.") + (license license:gpl2))) + (define-public r-formattable (package (name "r-formattable") @@ -25496,16 +27231,17 @@ programming} (OOP) using R Reference Class.") (define-public r-proxyc (package (name "r-proxyc") - (version "0.3.2") + (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "proxyC" version)) (sha256 (base32 - "1nfl6nrzw2h7argn6mh3cyl1s9ynf6516fx4vgqrjvychnd98mkb")))) + "00p3604ny6qax5rr1865c27hfp90v2vga0xcrp3bb81xcfadl99y")))) (properties `((upstream-name . "proxyC"))) (build-system r-build-system) + (native-inputs (list r-knitr)) (propagated-inputs (list r-matrix r-rcpp r-rcpparmadillo r-rcppparallel)) (home-page "https://cran.r-project.org/package=proxyC") @@ -25521,14 +27257,14 @@ and Euclidean distance is particularly fast.") (define-public r-isocodes (package (name "r-isocodes") - (version "2022.01.10") + (version "2022.09.29") (source (origin (method url-fetch) (uri (cran-uri "ISOcodes" version)) (sha256 (base32 - "0gy7n5bgxnl4rawry0pg078bkks9lzsbsrwjq8q5cvxl4k3dwpdj")))) + "1rag5mb3bbyxp8n32rhfyy752cy9hh5j80lp9xljj70scvglzbjb")))) (properties `((upstream-name . "ISOcodes"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=ISOcodes") @@ -25610,14 +27346,14 @@ Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.") (define-public r-quanteda (package (name "r-quanteda") - (version "3.2.3") + (version "3.2.4") (source (origin (method url-fetch) (uri (cran-uri "quanteda" version)) (sha256 (base32 - "1blk9nhydvqyyz0kzhph7nh7ahcjzflmgyr4sv8fx5bpmn4hwjzk")))) + "1yg3lgckh6fncmw037p4gaa2bab59yh6izqix1cgyysjg4jpcw62")))) (properties `((upstream-name . "quanteda"))) (build-system r-build-system) (propagated-inputs @@ -25649,14 +27385,14 @@ machine learning, visually representing text and text analyses, and more.") (define-public r-topicmodels (package (name "r-topicmodels") - (version "0.2-12") + (version "0.2-13") (source (origin (method url-fetch) (uri (cran-uri "topicmodels" version)) (sha256 (base32 - "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g")))) + "16mw0l7wm5idc831csxlk176c42a5xw8qm8xhbnmmdl2hjk0cqbx")))) (properties `((upstream-name . "topicmodels"))) (build-system r-build-system) (inputs @@ -25732,14 +27468,14 @@ errors; tetrachoric and biserial correlations are special cases.") (define-public r-msm (package (name "r-msm") - (version "1.6.9") + (version "1.7") (source (origin (method url-fetch) (uri (cran-uri "msm" version)) (sha256 (base32 - "08vhazswyxr3y1zb9y60mbg3bappzlizxml8s08p65mh82xxkz5f")))) + "1c0dvmrjxx551n207fq4yjr56rdchaf1zzldxx4rx4b6g7jgi2bz")))) (properties `((upstream-name . "msm"))) (build-system r-build-system) (propagated-inputs @@ -26014,14 +27750,14 @@ Complete access to optimized C functions is made available with (define-public r-openmx (package (name "r-openmx") - (version "2.20.6") + (version "2.20.7") (source (origin (method url-fetch) (uri (cran-uri "OpenMx" version)) (sha256 (base32 - "1v969100hllh0lwlxd2gv0k7krrsp9gc07iinx0nn04wkzh0rib5")))) + "0ki3n2i9b9880mpfxazmd6zrblzl1jngi10qnbxxvxik1x2mq3vy")))) (properties `((upstream-name . "OpenMx"))) (build-system r-build-system) (propagated-inputs @@ -26121,18 +27857,18 @@ output in R.") (define-public r-bdgraph (package (name "r-bdgraph") - (version "2.68") + (version "2.72") (source (origin (method url-fetch) (uri (cran-uri "BDgraph" version)) (sha256 (base32 - "1mixzkk8shcbyrxydhchq483j2jh2icgmdshmrl79a8vsnz9mmrm")))) + "1kc3icd7glivbjlhl9fbmxqza5w2x000w0w8ii8np9gjrhdwrybw")))) (properties `((upstream-name . "BDgraph"))) (build-system r-build-system) (propagated-inputs - (list r-igraph)) + (list r-ggplot2 r-igraph r-proc)) (native-inputs (list r-knitr)) (home-page "https://www.uva.nl/profile/a.mohammadi") @@ -26144,6 +27880,25 @@ uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based on a continuous-time birth-death process.") (license license:gpl2+))) +(define-public r-bundesligr + (package + (name "r-bundesligr") + (version "0.1.0") + (source (origin + (method url-fetch) + (uri (cran-uri "bundesligR" version)) + (sha256 + (base32 + "0dnhbh9jh7dfbk7mfh8msq4ys5kakalr0kwkycycrb2q8rd049vp")))) + (properties `((upstream-name . "bundesligR"))) + (build-system r-build-system) + (home-page "https://github.com/ottlngr/bundesligR") + (synopsis "All final tables of the Bundesliga") + (description + "This package provides all final tables of Germany's highest football +league, the Bundesliga. It contains data from 1964 to 2016.") + (license license:gpl3))) + (define-public r-d3network (package (name "r-d3network") @@ -26169,14 +27924,14 @@ network, tree, dendrogram, and Sankey graphs from R using data frames.") (define-public r-qgraph (package (name "r-qgraph") - (version "1.9.2") + (version "1.9.3") (source (origin (method url-fetch) (uri (cran-uri "qgraph" version)) (sha256 (base32 - "0r225b7rnsv6wz41ij0msmqr1xy0iqxh9dbsvjixbi1hvgv91wds")))) + "14azjxlvb02wlbskbsv5x3a6gpfb8hfyijfpbay6fimnsaqnmbj6")))) (properties `((upstream-name . "qgraph"))) (build-system r-build-system) (propagated-inputs @@ -26427,14 +28182,14 @@ and reproducible way.") (define-public r-rsconnect (package (name "r-rsconnect") - (version "0.8.27") + (version "0.8.28") (source (origin (method url-fetch) (uri (cran-uri "rsconnect" version)) (sha256 (base32 - "170niwxcmyvad7qw8k115i5a48x3wiidcd82x9anikf7bxhdai0a")))) + "1q0njv25xiri4ql9mfrzlwdf3l3xg9xjjj2wva9rbniafx3skf95")))) (properties `((upstream-name . "rsconnect"))) (build-system r-build-system) (propagated-inputs @@ -26748,14 +28503,14 @@ trend test.") (define-public r-keyring (package (name "r-keyring") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "keyring" version)) (sha256 (base32 - "1j8l6nmh4dr70kwybiais8yh687fdwrj134xynq68igw1b1rm8ga")))) + "113rjhihqfhxdihnf6nwqbsknlnm8pqyhvnyxx624gyajl9mn3a7")))) (properties `((upstream-name . "keyring"))) (build-system r-build-system) (propagated-inputs @@ -26802,6 +28557,28 @@ Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in climate data.") (license license:lgpl2.1))) +(define-public r-rlecuyer + (package + (name "r-rlecuyer") + (version "0.3-5") + (source (origin + (method url-fetch) + (uri (cran-uri "rlecuyer" version)) + (sha256 + (base32 + "09mniai7v8gapr6hd3zm8sm3vi1zcyhgym389904ykb2yx7l68s7")))) + (properties `((upstream-name . "rlecuyer"))) + (build-system r-build-system) + (home-page + "https://www.iro.umontreal.ca/~lecuyer/myftp/papers/streams00.pdf") + (synopsis "R interface to RNG with multiple streams") + (description + "This package provides an interface to the C implementation of the random +number generator with multiple independent streams developed by L'Ecuyer et +al (2002). The main purpose of this package is to enable the use of this +random number generator in parallel R applications.") + (license license:gpl2+))) + (define-public r-rlinsolve (package (name "r-rlinsolve") @@ -26834,14 +28611,14 @@ linear systems can be manageable using the @code{Matrix} package along with (define-public r-zvcv (package (name "r-zvcv") - (version "2.1.1") + (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "ZVCV" version)) (sha256 (base32 - "0gc76j9i8fkm2v638nyzzb1qxl4zmapbspkkaffb8gi5qyjja448")))) + "0ws0v7i6r7skb8lv6j718k29v5qsy1b007jxidv81iv0jcz9zfpy")))) (properties `((upstream-name . "ZVCV"))) (build-system r-build-system) (propagated-inputs @@ -26924,14 +28701,14 @@ Encyclopedia of Integer Sequences} (OEIS) in the function help page.") (define-public r-isoband (package (name "r-isoband") - (version "0.2.5") + (version "0.2.7") (source (origin (method url-fetch) (uri (cran-uri "isoband" version)) (sha256 (base32 - "19bbi0n0kz33xdgmdprcmc6raphd1hcm1w1brc16z5phcsh3zxa6")))) + "0qfzkkvh4a97qlifhdqjgdnzmnph93qqyqsv5gg8cnxl8crj54vn")))) (properties `((upstream-name . "isoband"))) (build-system r-build-system) (native-inputs @@ -27064,13 +28841,13 @@ appropriate dog and cat images for many status codes.") (define-public r-latex2exp (package (name "r-latex2exp") - (version "0.9.5") + (version "0.9.6") (source (origin (method url-fetch) (uri (cran-uri "latex2exp" version)) (sha256 (base32 - "153br3xflvnnxqhkhm1wgwb2664bw08alhslgdcgjdk73clafhla")))) + "1jp0l0hi5kv4yh28qg2yj2z5fj33gnfvdz2g2v4ibn516fj2d636")))) (build-system r-build-system) (propagated-inputs (list r-stringr r-magrittr)) @@ -27086,13 +28863,13 @@ rendered as text, axis labels, etc. throughout R's plotting system.") (define-public r-oai (package (name "r-oai") - (version "0.3.2") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "oai" version)) (sha256 (base32 - "1zcbcxhw692s0y6izvwazyzhgx0iwsxsbcan2nk0mb7n11p7bypb")))) + "0czf8f2qcjl9lh48svicpis09d3iwz9cndfm7hq8wlz5dl3dwh7m")))) (build-system r-build-system) (propagated-inputs (list r-xml2 r-httr r-plyr r-stringr r-tibble)) @@ -27592,14 +29369,14 @@ here.") (define-public r-projpred (package (name "r-projpred") - (version "2.2.0") + (version "2.2.2") (source (origin (method url-fetch) (uri (cran-uri "projpred" version)) (sha256 (base32 - "1a5hsqwcmn1w9lwjhsqw06av7cmqhwyxsil9zfrnv1396zfkpxhy")))) + "0fycjmaqbcr3vp5708003flvi9ny4z04acgbcfly1ird0kcw9s3v")))) (properties `((upstream-name . "projpred"))) (build-system r-build-system) (propagated-inputs @@ -27609,6 +29386,7 @@ here.") r-lme4 r-loo r-magrittr + r-mass r-mgcv r-mvtnorm r-rcpp @@ -27712,14 +29490,14 @@ inference diagnostics. (define-public r-brms (package (name "r-brms") - (version "2.17.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (cran-uri "brms" version)) (sha256 (base32 - "0wff5rld4kgkk2nbllvm1h4c596igzgd0q7nx1cabgl11fja7r94")))) + "04g10yx66izpghrqip5h9i0w0bds4xw2vlhp6crydi6i7kh4p4b3")))) (properties `((upstream-name . "brms"))) (build-system r-build-system) (propagated-inputs @@ -27846,14 +29624,14 @@ amounts of memory.") (define-public r-boruta (package (name "r-boruta") - (version "7.0.0") + (version "8.0.0") (source (origin (method url-fetch) (uri (cran-uri "Boruta" version)) (sha256 (base32 - "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg")))) + "1irx7qg1sw69ggsk4jgxfd3pp741kd944fipnda1qbcbphg5prrq")))) (properties `((upstream-name . "Boruta"))) (build-system r-build-system) (propagated-inputs (list r-ranger)) @@ -27992,14 +29770,14 @@ input.") (define-public r-lightgbm (package (name "r-lightgbm") - (version "3.3.2") + (version "3.3.4") (source (origin (method url-fetch) (uri (cran-uri "lightgbm" version)) (sha256 (base32 - "12hbvm1va6sb5yny564jvhhzrkcq4j33rcdhqhwxaac2m08cpi8s")))) + "12hcq2idjgggs8l9a5aaxbw1wsfz6byzaxqn9k6afvkf3v5srp65")))) (properties `((upstream-name . "lightgbm"))) (build-system r-build-system) (propagated-inputs @@ -28258,13 +30036,13 @@ doi.org/10.1007/s10115-013-0679-x} for details.") (define-public r-memuse (package (name "r-memuse") - (version "4.2-1") + (version "4.2-2") (source (origin (method url-fetch) (uri (cran-uri "memuse" version)) (sha256 (base32 - "1wvwnjaaiv2647561z2b55dss35033ildx4kk8hzxfzgsjmdpsgm")))) + "1rdp8wi9sd03qdak7mifvdc1szgk0fdzmhbikdfsza8xshm2pp33")))) (properties `((upstream-name . "memuse"))) (build-system r-build-system) (home-page "https://github.com/shinra-dev/memuse") @@ -28385,17 +30163,101 @@ arrays collapsed in specific extents by summing along the appropriate diagonals. This package allows you to compute the tensor product of arrays.") (license license:gpl2+))) +(define-public r-spatstat-explore + (package + (name "r-spatstat-explore") + (version "3.0-5") + (source (origin + (method url-fetch) + (uri (cran-uri "spatstat.explore" version)) + (sha256 + (base32 + "0qn8dmymbnh9vdw0hysijkk2nwz5q69i62smpp8f3wy3z898lhwz")))) + (properties `((upstream-name . "spatstat.explore"))) + (build-system r-build-system) + (propagated-inputs + (list r-abind + r-goftest + r-matrix + r-nlme + r-spatstat-data + r-spatstat-geom + r-spatstat-random + r-spatstat-sparse + r-spatstat-utils)) + (home-page "https://spatstat.org/") + (synopsis "Exploratory data analysis for the spatstat family") + (description + "This package implements functionality for exploratory data +analysis and nonparametric analysis of spatial data, mainly spatial +point patterns, in the @code{spatstat} family of packages. Methods +include quadrat counts, K-functions and their simulation envelopes, +nearest neighbour distance and empty space statistics, Fry plots, pair +correlation function, kernel smoothed intensity, relative risk +estimation with cross-validated bandwidth selection, mark correlation +functions, segregation indices, mark dependence diagnostics, and +kernel estimates of covariate effects. Formal hypothesis tests of +random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, +Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and +tests for covariate effects (Cox-Berman-Waller-Lawson, +Kolmogorov-Smirnov, ANOVA) are also supported.") + (license license:gpl2+))) + +(define-public r-spatstat-model + (package + (name "r-spatstat-model") + (version "3.0-2") + (source (origin + (method url-fetch) + (uri (cran-uri "spatstat.model" version)) + (sha256 + (base32 + "0a6lf5y0k13h60s0lnwwfrmxswl7avcg4fhqmha1nmycidhga8z9")))) + (properties `((upstream-name . "spatstat.model"))) + (build-system r-build-system) + (propagated-inputs + (list r-abind + r-goftest + r-matrix + r-mgcv + r-nlme + r-rpart + r-spatstat-data + r-spatstat-explore + r-spatstat-geom + r-spatstat-random + r-spatstat-sparse + r-spatstat-utils + r-tensor)) + (home-page "https://spatstat.org/") + (synopsis "Parametric statistical modelling for the spatstat family") + (description + "This package implements functionality for exploratory data +analysis and nonparametric analysis of spatial data, mainly spatial +point patterns, in the spatstat family of packages. Methods include +quadrat counts, K-functions and their simulation envelopes, nearest +neighbour distance and empty space statistics, Fry plots, pair +correlation function, kernel smoothed intensity, relative risk +estimation with cross-validated bandwidth selection, mark correlation +functions, segregation indices, mark dependence diagnostics, and +kernel estimates of covariate effects. Formal hypothesis tests of +random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, +Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and +tests for covariate effects (Cox-Berman-Waller-Lawson, +Kolmogorov-Smirnov, ANOVA) are also supported.") + (license license:gpl2+))) + (define-public r-spatstat-utils (package (name "r-spatstat-utils") - (version "2.3-1") + (version "3.0-1") (source (origin (method url-fetch) (uri (cran-uri "spatstat.utils" version)) (sha256 (base32 - "08pybliv4r3v4rcazmlfr4a07sjfhrkmksdmhhq9k185vw4474av")))) + "06mrw3nc2pqz4897i7wqy04mdfnn6drggv8mr92r3zb4cn0cg8fb")))) (properties `((upstream-name . "spatstat.utils"))) (build-system r-build-system) @@ -28409,14 +30271,14 @@ which may also be useful for other purposes.") (define-public r-spatstat-sparse (package (name "r-spatstat-sparse") - (version "2.1-1") + (version "3.0-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat.sparse" version)) (sha256 (base32 - "00vkvv5pnm82gn7vqnzrrp68y46gbkhdq0hbwqx7nxjvf5lssdcs")))) + "1lhsa1gjahz6sp1yrlch0d01rnayyw8hip382vghyxljfly0mglr")))) (properties `((upstream-name . "spatstat.sparse"))) (build-system r-build-system) @@ -28433,14 +30295,14 @@ matrix calculations that are common in statistics, such as quadratic forms.") (define-public r-spatstat-data (package (name "r-spatstat-data") - (version "2.2-0") + (version "3.0-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat.data" version)) (sha256 (base32 - "1rf36zy29h9qabpv19hx84gjdiay7i9y9777d2zn17ahyss3p56k")))) + "0mvh33sk2sfhfk276j088adzldrg8p6pd5avl2j21428i250byfg")))) (properties `((upstream-name . "spatstat.data"))) (build-system r-build-system) (propagated-inputs @@ -28455,14 +30317,14 @@ package.") (define-public r-spatstat-geom (package (name "r-spatstat-geom") - (version "2.4-0") + (version "3.0-3") (source (origin (method url-fetch) (uri (cran-uri "spatstat.geom" version)) (sha256 (base32 - "0rwysq9a0ylbsr53q5kfh7wjk5mcdji211sc3s8gwzz8ki09mf1j")))) + "111wj507i2mxi0ak8sj468w26pr2f7hgv3ssmbf0qjkp1v35cnvf")))) (properties `((upstream-name . "spatstat.geom"))) (build-system r-build-system) (propagated-inputs @@ -28511,22 +30373,23 @@ user-level code from spatstat, except for the code for linear networks.") (define-public r-spatstat-linnet (package (name "r-spatstat-linnet") - (version "2.3-2") + (version "3.0-3") (source (origin (method url-fetch) (uri (cran-uri "spatstat.linnet" version)) (sha256 (base32 - "0y1py6x0xbw4ad3pjwcspi4ysgfh61f5fd79787zzgyyh2va8y4w")))) + "1y9crkj9sa1hnfsfkyyq8zv6fgafv07b8w0y01qps1rd6virnns0")))) (properties `((upstream-name . "spatstat.linnet"))) (build-system r-build-system) (propagated-inputs (list r-matrix - r-spatstat-core r-spatstat-data + r-spatstat-explore r-spatstat-geom + r-spatstat-model r-spatstat-random r-spatstat-sparse r-spatstat-utils)) @@ -28540,13 +30403,13 @@ for spatial data on a linear network.") (define-public r-spatstat-random (package (name "r-spatstat-random") - (version "2.2-0") + (version "3.0-1") (source (origin (method url-fetch) (uri (cran-uri "spatstat.random" version)) (sha256 - (base32 "0kb01s8k67ydcfqcnz3i55vpiksihh4xsg0w2p2bclxxkpdvpw25")))) + (base32 "1dp58dxw7ln9bsls9ssbb917qakvgr9nf2jci6zq31rv0rf8934k")))) (properties `((upstream-name . "spatstat.random"))) (build-system r-build-system) (propagated-inputs (list r-spatstat-data r-spatstat-geom r-spatstat-utils)) @@ -28568,19 +30431,20 @@ sampler).") (define-public r-spatstat (package (name "r-spatstat") - (version "2.3-4") + (version "3.0-2") (source (origin (method url-fetch) (uri (cran-uri "spatstat" version)) (sha256 (base32 - "1nlrp7660y68axlm4pczc5rxbdhbbac1ylh69azr4swj1gbzi82f")))) + "1k8qs5hsy0n4rh7ccp6bdnqgbw3fvjdp55bc0zhjqwbbhq8c0ax0")))) (properties `((upstream-name . "spatstat"))) (build-system r-build-system) (propagated-inputs - (list r-spatstat-core r-spatstat-data r-spatstat-geom - r-spatstat-linnet r-spatstat-random r-spatstat-utils)) + (list r-spatstat-data r-spatstat-explore r-spatstat-geom + r-spatstat-linnet r-spatstat-model r-spatstat-random + r-spatstat-utils)) (home-page "http://www.spatstat.org") (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests") (description @@ -28598,14 +30462,14 @@ formal inference.") (define-public r-gaston (package (name "r-gaston") - (version "1.5.7") + (version "1.5.9") (source (origin (method url-fetch) (uri (cran-uri "gaston" version)) (sha256 (base32 - "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i")))) + "1f4pr5s4p4rw1smvsh2gwjxp7hh43j1fpadl286ma9i62kirpyq7")))) (properties `((upstream-name . "gaston"))) (build-system r-build-system) (inputs (list zlib)) @@ -28624,14 +30488,14 @@ for linear mixed models (AIREML).") (define-public r-cpp11 (package (name "r-cpp11") - (version "0.4.2") + (version "0.4.3") (source (origin (method url-fetch) (uri (cran-uri "cpp11" version)) (sha256 (base32 - "16cvjfkbc7c0ymdmbcqg9px6pjsqx6qhyfq5frqj739mhazy0g20")))) + "1wcq4lq7xa62xn6zsg6r8nf6vdlvnlwxgfqndb7vnvd8f54hx9pi")))) (properties `((upstream-name . "cpp11"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -28744,18 +30608,23 @@ model.") (define-public r-clusterr (package (name "r-clusterr") - (version "1.2.6") + (version "1.2.9") (source (origin (method url-fetch) (uri (cran-uri "ClusterR" version)) (sha256 (base32 - "00mha8madcba83ix4fc04rb7sagfm0lxlh1wvs7dvjdrngps41jr")))) + "04aswnmxzpffc1fj2hf85pc5b10fh418k29a1x5cs1f1y7b3zav3")))) (properties `((upstream-name . "ClusterR"))) (build-system r-build-system) (propagated-inputs - (list r-ggplot2 r-gmp r-gtools r-rcpp r-rcpparmadillo)) + (list r-ggplot2 + r-gmp + r-gtools + r-lifecycle + r-rcpp + r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://github.com/mlampros/ClusterR") (synopsis "Clustering") @@ -28839,6 +30708,27 @@ addition, objects which include the k-d tree search structure can be returned to speed up repeated queries of the same set of target points.") (license license:bsd-3))) +(define-public r-nada + (package + (name "r-nada") + (version "1.6-1.1") + (source (origin + (method url-fetch) + (uri (cran-uri "NADA" version)) + (sha256 + (base32 + "0jp4mqr77cx7q5lff84s6wb0dwjy9mi0jyhbjc5fsx50bdczc3v7")))) + (properties `((upstream-name . "NADA"))) + (build-system r-build-system) + (propagated-inputs (list r-survival)) + (home-page "https://cran.r-project.org/package=NADA") + (synopsis "Nondetects and data analysis for environmental data") + (description + "This package contains methods described by Dennis Helsel in his +book @emph{Nondetects and Data Analysis: Statistics for Censored +Environmental Data}.") + (license license:gpl2+))) + (define-public r-naturalsort (package (name "r-naturalsort") @@ -28915,14 +30805,14 @@ censored data.") (define-public r-flexsurv (package (name "r-flexsurv") - (version "2.2") + (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "flexsurv" version)) (sha256 (base32 - "0244amsyf2izih6008n2535r3ddksgdnys8pyslrcb1c09spmjrw")))) + "1xqsihvrb8b5mzkr3mhg0ydm8kkcw1k0kgp6ndyavw8yahl059as")))) (properties `((upstream-name . "flexsurv"))) (build-system r-build-system) (propagated-inputs @@ -29199,13 +31089,13 @@ value.") (define-public r-confintr (package (name "r-confintr") - (version "0.1.2") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "confintr" version)) (sha256 (base32 - "06c42jhqp7gp9062jf8f9py1lh34vx38q0g7b6l5kyf7a310ixr6")))) + "1zpprv5ysmnqn83xdsixsm6jhsi1gck32z6x60gp0y8xs25mwcbg")))) (properties `((upstream-name . "confintr"))) (build-system r-build-system) (propagated-inputs (list r-boot)) @@ -29305,14 +31195,14 @@ model.") (define-public r-igraph (package (name "r-igraph") - (version "1.3.4") + (version "1.3.5") (source (origin (method url-fetch) (uri (cran-uri "igraph" version)) (sha256 (base32 - "1kyic5xmwgw5lm30rsvsf1x3m0yxysdlrnw63xn4fh8j4vcc66ms")))) + "1m4vbc1v2wvjn9df7w9ax0zpr3ys566bqazcakx7vddmnrkmsqcy")))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -29332,14 +31222,14 @@ more.") (define-public r-workflows (package (name "r-workflows") - (version "1.0.0") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "workflows" version)) (sha256 (base32 - "0bsizgqin5cya0xibs1nqzadrrxcph8n4bh5vlcfbqqzzkv7cx1b")))) + "1wlgx7gl4h9szw9lr6ck9mnkrflah0wfbs56fialbl7wd5jv6hcg")))) (properties `((upstream-name . "workflows"))) (build-system r-build-system) (propagated-inputs @@ -29348,6 +31238,7 @@ more.") r-glue r-hardhat r-lifecycle + r-modelenv r-parsnip r-rlang r-tidyselect @@ -29506,18 +31397,18 @@ different palettes and includes both diverging and sequential types.") (define-public r-slider (package (name "r-slider") - (version "0.2.2") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "slider" version)) (sha256 (base32 - "1vxk2bc33svwcki2j8zr5jcxswh27i0fqgzjw2a5a1pp9dh3fmd3")))) + "18gw0bxpbb00qcafmyv2avyj83s710hrj10x998ch9qbbyx1fsmw")))) (properties `((upstream-name . "slider"))) (build-system r-build-system) (propagated-inputs - (list r-ellipsis r-glue r-rlang r-vctrs r-warp)) + (list r-cli r-rlang r-vctrs r-warp)) (native-inputs (list r-knitr)) (home-page "https://github.com/DavisVaughan/slider") (synopsis "Sliding window functions") @@ -29542,7 +31433,7 @@ sliding windows are to be created.") (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") + (synopsis "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, @@ -29553,19 +31444,18 @@ pipeline friendly so that data processing with lists can be chained.") (define-public r-rsample (package (name "r-rsample") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "rsample" version)) (sha256 (base32 - "1iy61riwjch9z4m6k7whsrkl80sk9sww5lf1np4iq4vdfq6w01jb")))) + "1fmqfk1yihmh7lkszsf7pvn6zf67lpgff46hv2lpnfbssa3axllh")))) (properties `((upstream-name . "rsample"))) (build-system r-build-system) (propagated-inputs (list r-dplyr - r-ellipsis r-furrr r-generics r-glue @@ -29609,18 +31499,19 @@ Design} (SFD) and to test their quality.") (define-public r-dials (package (name "r-dials") - (version "1.0.0") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "dials" version)) (sha256 (base32 - "0flpd7bxknsscv0gk6c7zz1aid9y3z6sibkvjp9zcyc5wnqldrvj")))) + "1ly675h6shfclikwg82x8vwvrb63qmklamrbsqxsa0npbafqgvpb")))) (properties `((upstream-name . "dials"))) (build-system r-build-system) (propagated-inputs - (list r-dicedesign + (list r-cli + r-dicedesign r-dplyr r-glue r-hardhat @@ -29644,14 +31535,14 @@ for creating, simulating, or validating values for such parameters.") (define-public r-tune (package (name "r-tune") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "tune" version)) (sha256 (base32 - "0jh29dy4gwa1fyi01fp1305hkxw1mpkx704j6kydplh8h09rv80p")))) + "044bz8g3p8vj97w9ycpiw39iakzghxbqzmb4lxqpplpxymc8ybkm")))) (properties `((upstream-name . "tune"))) (build-system r-build-system) (propagated-inputs @@ -29869,14 +31760,14 @@ thinking for the fun stuff.") (define-public r-tokenizers (package (name "r-tokenizers") - (version "0.2.1") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "tokenizers" version)) (sha256 (base32 - "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98")))) + "0a8wm4cff3hrll991h2rimw79kpf2jsn78y7yksdk8m18931wmr4")))) (properties `((upstream-name . "tokenizers"))) (build-system r-build-system) (propagated-inputs @@ -29933,20 +31824,20 @@ vignettes in all common formats.") (define-public r-tidytext (package (name "r-tidytext") - (version "0.3.4") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "tidytext" version)) (sha256 (base32 - "0mk75wdiy4mixj1xlksw9ns4ajlj8ak90sgchjcg1zb90qp7gg56")))) + "05f8209qx1rvddnkl0h05yig09xahs8lqgq9w5dvdiwarji50rsj")))) (properties `((upstream-name . "tidytext"))) (build-system r-build-system) (propagated-inputs - (list r-dplyr + (list r-cli + r-dplyr r-generics - r-hunspell r-janeaustenr r-lifecycle r-matrix @@ -29968,14 +31859,14 @@ analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.") (define-public r-parsnip (package (name "r-parsnip") - (version "1.0.1") + (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "parsnip" version)) (sha256 (base32 - "0pzr39jhlzjhm2nx1zcgd0mdxd4dxbdzhzc1qrvfsz05jwfb6xxy")))) + "1s1d5zjwag5a13y67l7sz4zj1w0dv0k7vpb6inz4x87d5rgchfi1")))) (properties `((upstream-name . "parsnip"))) (build-system r-build-system) (propagated-inputs @@ -30009,14 +31900,14 @@ functions or computational engines (e.g. R, Spark, Stan, etc).") (define-public r-infer (package (name "r-infer") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "infer" version)) (sha256 (base32 - "1m5srhcmkh8wq12pvy57g3g703wilkl8r3gmm5s7lbj103iz7v8b")))) + "1s4q0nslykl0pb2w1i6ni6hkpp7awvp0wks79br3gk5wa1qkvs19")))) (properties `((upstream-name . "infer"))) (build-system r-build-system) (propagated-inputs @@ -30066,6 +31957,31 @@ expressive statistical grammar that coheres with the Tidy design framework.") model-related packages.") (license license:expat))) +(define-public r-modeest + (package + (name "r-modeest") + (version "2.4.0") + (source (origin + (method url-fetch) + (uri (cran-uri "modeest" version)) + (sha256 + (base32 + "087dw0013y4m7fcl06mxylh9lnp6acysl80d80r9srv4pw4r950s")))) + (properties `((upstream-name . "modeest"))) + (build-system r-build-system) + (propagated-inputs + (list r-fbasics + r-stable + r-stabledist + r-statip)) + (home-page "https://github.com/paulponcet/modeest") + (synopsis "Mode estimations for univariate data or distributions") + (description + "The package provides estimators of the mode of univariate unimodal (and +sometimes multimodal) data and values of the modes of usual probability +distributions.") + (license license:gpl3))) + (define-public r-conflicted (package (name "r-conflicted") @@ -30166,14 +32082,14 @@ this variability problem can be overcome.") (define-public r-mlecens (package (name "r-mlecens") - (version "0.1-5") + (version "0.1-7") (source (origin (method url-fetch) (uri (cran-uri "MLEcens" version)) (sha256 (base32 - "0cdl0y44clds4sg8hikhk354a5xrfbyfg8lxrbh1bfg410rkj186")))) + "1kdnm5ilfn5fclry3f1d518761hykrqgjhv69kc881r2fpcfa1lv")))) (properties `((upstream-name . "MLEcens"))) (build-system r-build-system) (home-page "http://stat.ethz.ch/~maathuis/") @@ -30287,14 +32203,14 @@ covariate (usually group indicator) and the scores.") (define-public r-qtl (package (name "r-qtl") - (version "1.52") + (version "1.58") (source (origin (method url-fetch) (uri (cran-uri "qtl" version)) (sha256 (base32 - "0q49g3ar1451whsl6ig7kz4mg8s9zxlcvgkj4ivyw4995wbwc2ij")))) + "15wxn3sdvmgjgmfxl0qsxhkr7b7kn1hz2962cd6k0qmffz0mmjkf")))) (build-system r-build-system) (home-page "https://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") @@ -30310,12 +32226,12 @@ genome scans.") (define-public r-qtl2 (package (name "r-qtl2") - (version "0.28") + (version "0.30") (source (origin (method url-fetch) (uri (cran-uri "qtl2" version)) (sha256 - (base32 "0ppc6dzlq77mppxc6bczai9gi40jrbxd1466y2cn2s8a4ah1jg9y")))) + (base32 "0c9v5hwfmlchrdzdysvmi6dsxyclc15sqbp65l4x6zwpd0828h6c")))) (build-system r-build-system) (propagated-inputs (list r-data-table @@ -30336,14 +32252,14 @@ designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.") (define-public r-seqminer (package (name "r-seqminer") - (version "8.4") + (version "8.5") (source (origin (method url-fetch) (uri (cran-uri "seqminer" version)) (sha256 (base32 - "1mbx1hw9dhgry7hhan43g6aiz2lyd5api7wxq3fwajyzjrc6p1g8")))) + "1ki8b4bgb3ky9y3x2g56h7i94lk345awgwkg10lys022jxhm30d7")))) (build-system r-build-system) (inputs (list zlib)) @@ -30358,14 +32274,14 @@ data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") (define-public r-maldiquant (package (name "r-maldiquant") - (version "1.21") + (version "1.22") (source (origin (method url-fetch) (uri (cran-uri "MALDIquant" version)) (sha256 (base32 - "1y1g3819ss06dry70kfhg2syddw71682qmzkcyppfsma6hhghw87")))) + "05fhr7945m0qxh7f5c4ax9v2k32s4n4v4xc1dm1crk1vbzha40bv")))) (properties `((upstream-name . "MALDIquant"))) (build-system r-build-system) (native-inputs @@ -30408,14 +32324,14 @@ data to rasters. It speeds up plotting of data with millions of points.") (define-public r-seuratobject (package (name "r-seuratobject") - (version "4.1.1") + (version "4.1.3") (source (origin (method url-fetch) (uri (cran-uri "SeuratObject" version)) (sha256 (base32 - "1h8b90vg9ysczk3p625n07bfrhmph3cxv9ymh896hqr7rn2qbwd6")))) + "1lw6v5mwq0sngjr33j99r5h42kaxlbq271a51xzkcnhnyra2fpaq")))) (properties `((upstream-name . "SeuratObject"))) (build-system r-build-system) (propagated-inputs @@ -30425,7 +32341,6 @@ data to rasters. It speeds up plotting of data with millions of points.") r-progressr r-rcpp r-rcppeigen - r-rgeos r-rlang r-sp)) (home-page "https://satijalab.org/seurat") @@ -30441,13 +32356,13 @@ other R users.") (define-public r-seurat (package (name "r-seurat") - (version "4.1.1") + (version "4.3.0") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "1klamxk6dj0jgpfwll5frcnj9h8lh8c5fxdn9ky7h8xk35lsj6i0")))) + "0z7rzxi1gli56k50s6w1363ndw18wykgk5xmc3g7jhpphqxwpfky")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs @@ -30475,6 +32390,7 @@ other R users.") r-pbapply r-plotly r-png + r-progressr r-rann r-rcolorbrewer r-rcpp @@ -30490,7 +32406,7 @@ other R users.") r-sctransform r-seuratobject r-shiny - r-spatstat-core + r-spatstat-explore r-spatstat-geom r-tibble r-uwot)) @@ -30646,14 +32562,14 @@ rate speciation and extinction.") (define-public r-calculus (package (name "r-calculus") - (version "0.3.4") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "calculus" version)) (sha256 (base32 - "0hpibnbxl3ngfgzxq8cp9hxsn1yv03dnxyycm3gkr5iv5gkbbpw9")))) + "18w64jp6ah2q09242bsnszjl2adqmcs4b0w44ixrc74rjjxwp1cd")))) (properties `((upstream-name . "calculus"))) (build-system r-build-system) (propagated-inputs @@ -30746,14 +32662,14 @@ and Yu (2020), arXiv:2009.06182.") (define-public r-locpol (package (name "r-locpol") - (version "0.7-0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "locpol" version)) (sha256 (base32 - "1p915n0l09kbwkly627074jslxl01yssp1rf0c7sygvsw6sgy5lm")))) + "1bip9x45kdnwc14rvk3ckzfbs32yc2wiid1ypmbbin4mk7364zxk")))) (properties `((upstream-name . "locpol"))) (build-system r-build-system) (home-page @@ -30910,13 +32826,13 @@ are.") (define-public r-mlr3misc (package (name "r-mlr3misc") - (version "0.10.0") + (version "0.11.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3misc" version)) (sha256 (base32 - "1wnzyij1x67smkb3gjb9gpp7iy5andfl0s1c78xx4wylhycc6m11")))) + "0haxj0zlflalw10nhdwmk45qsl164bgyjgnm101l2wybw795ixfi")))) (build-system r-build-system) (propagated-inputs (list r-backports r-checkmate r-data-table r-digest r-r6)) @@ -30932,13 +32848,13 @@ package also supersedes the package @code{BBmisc}.") (define-public r-mlr3pipelines (package (name "r-mlr3pipelines") - (version "0.4.1") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "mlr3pipelines" version)) (sha256 (base32 - "1zz55i8c08znxpcs6gp5inaw96c6la9wnsla0972ankvj1hsrcr2")))) + "09pk3dwjcg5rbpwa1k21srdpvf2dlxq4b5p71cvkha85jx2gdgh6")))) (build-system r-build-system) (propagated-inputs (list r-backports @@ -30995,13 +32911,13 @@ performing ordinal regression.") (define-public r-paradox (package (name "r-paradox") - (version "0.10.0") + (version "0.11.0") (source (origin (method url-fetch) (uri (cran-uri "paradox" version)) (sha256 (base32 - "08h92wk8splf0w3rach9zbk3xz13phgcd1yybmgbs0sj4vx93whd")))) + "03v26qb0l8yhys7z5v2p9pwnc5wh26fvq4p0a0rh67qap6157dyx")))) (build-system r-build-system) (propagated-inputs (list r-backports r-checkmate r-data-table r-mlr3misc r-r6)) @@ -31016,13 +32932,13 @@ implemented as @code{R6} classes.") (define-public r-mlr3 (package (name "r-mlr3") - (version "0.14.0") + (version "0.14.1") (source (origin (method url-fetch) (uri (cran-uri "mlr3" version)) (sha256 (base32 - "0cnyby4947g1w0h45nd3ld5zr4k19xrwp565mq1hnqkjwmyjsgdj")))) + "192hvc0may73m396j2igwm46ym6f345w6q0q69kqhia58fp6h3nd")))) (build-system r-build-system) (propagated-inputs (list r-r6 @@ -31053,13 +32969,13 @@ computational operations, add-on packages provide additional functionality.") (define-public r-mlr3learners (package (name "r-mlr3learners") - (version "0.5.4") + (version "0.5.6") (source (origin (method url-fetch) (uri (cran-uri "mlr3learners" version)) (sha256 (base32 - "0sa2qjvhvjzsfssln9ah08zknzdcps1z28xzgkdfgi6dj25a0y3k")))) + "1m0psjqcl2pfy73wmc29vyz122v0kqmws6d0dgl7wsy1csfjsjm2")))) (build-system r-build-system) (propagated-inputs (list r-checkmate @@ -31080,14 +32996,14 @@ vector machines, and gradient boosting.") (define-public r-bbotk (package (name "r-bbotk") - (version "0.5.4") + (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "bbotk" version)) (sha256 (base32 - "02dp0b62dv02rvxsgj63mkmmcdzrlf06vxjr5gqy9rhq5s2mg4fa")))) + "1gw0rkbiv93ifl9110r9sr0p9g4vg7qc11mznmmjq0a5vzmqgpm9")))) (properties `((upstream-name . "bbotk"))) (build-system r-build-system) (propagated-inputs @@ -31110,13 +33026,13 @@ annealing.") (define-public r-mlr3tuning (package (name "r-mlr3tuning") - (version "0.14.0") + (version "0.17.2") (source (origin (method url-fetch) (uri (cran-uri "mlr3tuning" version)) (sha256 (base32 - "10q4m37sg79y1v0gwk7bjrnc5b0a6sb80ramnza93mx9gx3vl99m")))) + "1w08bwk843nfs3d810lnfh3wmd7gkq9141m7lcn9ail2x4ib91bb")))) (build-system r-build-system) (propagated-inputs (list r-bbotk @@ -31402,14 +33318,14 @@ the font tool-set provided by the @code{systemfonts} package.") (define-public r-ragg (package (name "r-ragg") - (version "1.2.2") + (version "1.2.4") (source (origin (method url-fetch) (uri (cran-uri "ragg" version)) (sha256 (base32 - "1q43pwmljsqgrikkh2g1n7bpz9c8py5dnj44cfg3y2br7b4m2q9v")))) + "1k8dd08a2f3dg4zrq37cfvljqg413snhzmd0440amvrfd9iyaiy5")))) (properties `((upstream-name . "ragg"))) (build-system r-build-system) (inputs @@ -31464,14 +33380,14 @@ in output to the equivalent HTML.") (define-public r-pkgdown (package (name "r-pkgdown") - (version "2.0.6") + (version "2.0.7") (source (origin (method url-fetch) (uri (cran-uri "pkgdown" version)) (sha256 (base32 - "0sbz3kzd0hbdnszylsb281arldn2z1c9yxifhj4zv2dilp46b6nj")))) + "0sim3fwayf4mpxqi8y9v7clnkzs56amhxsc75lc1k0zskn374f7k")))) (properties `((upstream-name . "pkgdown"))) (build-system r-build-system) (inputs (list pandoc)) @@ -31802,14 +33718,14 @@ text but not always easily handled by analysis algorithms. The (define-public r-ndjson (package (name "r-ndjson") - (version "0.8.0") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "ndjson" version)) (sha256 (base32 - "0lvzbgfi1sg4kya1mvv67z14qk3vz9q57x22qh57xq8ampdkg812")) + "18j5bibranvbv84hvbsg6glmvhfancdsf2w6j99n3nw53bcgb12d")) (modules '((guix build utils))) (snippet '(begin @@ -31895,14 +33811,14 @@ Also support writing data frame into ODS file.") (define-public r-qpdf (package (name "r-qpdf") - (version "1.2.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "qpdf" version)) (sha256 (base32 - "1a1d7zad2l94z068mic6dg9wr9bq8mlmqszrj8vxps1441mb6gfh")) + "0x2n9b4avnm0p1cz6i90a3p6qjpwr68g4v0xa8d1rr3gbgqfraf8")) (modules '((guix build utils))) (snippet '(begin @@ -31932,17 +33848,45 @@ split, combine, and compress. This package interfaces directly to the data you need the @code{pdftools} package.") (license license:asl2.0))) +(define-public r-pbdmpi + (package + (name "r-pbdmpi") + (version "0.4-6") + (source (origin + (method url-fetch) + (uri (cran-uri "pbdMPI" version)) + (sha256 + (base32 + "0r6kbrvc0z4mb2dhrz1iqdyx0c03f682b5xfi1igp7z3rszd1va1")))) + (properties `((upstream-name . "pbdMPI"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'install 'mpi-setup + ,%openmpi-setup)))) + (inputs (list openmpi)) + (propagated-inputs (list r-float r-rlecuyer)) + (native-inputs (list pkg-config)) + (home-page "https://pbdr.org/") + (synopsis "Programming with Big Data -- Interface to MPI") + (description + "This package provides an efficient interface to MPI by utilizing S4 +classes and methods with a focus on @dfn{Single Program/Multiple Data} (SPMD) +parallel programming style, which is intended for batch parallel execution.") + (license license:mpl2.0))) + (define-public r-pdftools (package (name "r-pdftools") - (version "3.3.0") + (version "3.3.2") (source (origin (method url-fetch) (uri (cran-uri "pdftools" version)) (sha256 (base32 - "151f7vaznxigwka4qhp17v4gnahm245rfgcvb8j132vix7md44q9")))) + "012s98ghj3mk0adghbx2nyrwnja0707ym13nhjpjwj4xd7bll7s5")))) (properties `((upstream-name . "pdftools"))) (build-system r-build-system) (inputs (list zlib poppler)) @@ -32040,14 +33984,14 @@ and formatted text files with additional meta-data, such including @code{.csv}, (define-public r-packcircles (package (name "r-packcircles") - (version "0.3.4") + (version "0.3.5") (source (origin (method url-fetch) (uri (cran-uri "packcircles" version)) (sha256 (base32 - "05pv5c4k4njkr0xw6i6ksiy34hcyx2lbiqpv5gxw81yrkm0rxfyk")))) + "0m8ivgc5y1f9ramqw6sxb02ri6aqxz3av0l5csl32mdldrb126nc")))) (properties `((upstream-name . "packcircles"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -32064,14 +34008,14 @@ and formatted text files with additional meta-data, such including @code{.csv}, (define-public r-lwgeom (package (name "r-lwgeom") - (version "0.2-8") + (version "0.2-10") (source (origin (method url-fetch) (uri (cran-uri "lwgeom" version)) (sha256 (base32 - "0d4b1djwrzla91mmyya2m1250mb44fzmq3d36w5mk81d4bg952pl")))) + "1gdvp2q4mzlg1kpjqxkiqxw1r5c4n5pxwvhdbzp89a3gyyjgh7zf")))) (properties `((upstream-name . "lwgeom"))) (build-system r-build-system) (inputs @@ -32090,14 +34034,14 @@ light-weight geometry library used by @url{http://postgis.net/,PostGIS}.") (define-public r-stars (package (name "r-stars") - (version "0.5-6") + (version "0.6-0") (source (origin (method url-fetch) (uri (cran-uri "stars" version)) (sha256 (base32 - "0qcli9bangpym4yp96yfibd5f4li5qw1622jnbvzfd9n8aakqhg0")))) + "0zwbsqp8bihcq5sjdw05pvbh4l9s68p0qw3ffkk0jphsipvy9za9")))) (properties `((upstream-name . "stars"))) (build-system r-build-system) (propagated-inputs @@ -32174,20 +34118,21 @@ supply the workflow to create thematic maps. This package also facilitates (define-public r-rtweet (package (name "r-rtweet") - (version "1.0.2") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "rtweet" version)) (sha256 (base32 - "1dhdq2c2zl88h29caqpm7zh2i5970q7rfg98zf2xb7x4zak7bq9x")))) + "0dq6ckf2mp6wm6y8xzjby21s356760fmck1m8nsnv5gz8lhy6dhg")))) (properties `((upstream-name . "rtweet"))) (build-system r-build-system) (propagated-inputs (list r-bit64 r-curl r-httr + r-httr2 r-jsonlite r-lifecycle r-progress @@ -32425,14 +34370,14 @@ indicator, a quantitative variable or a survival time.") (define-public r-gsalib (package (name "r-gsalib") - (version "2.1") + (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "gsalib" version)) (sha256 (base32 - "1k3zjdydzb0dfh1ihih08d4cw6rdamgb97cdqna9mf0qdjc3pcp1")))) + "145zyc2sqa0acn9crilpw5njms7w7ca3jgl499lhsahlb6ws98rx")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/gsalib") (synopsis "Utility functions for GATK") @@ -32615,14 +34560,14 @@ time zone manipulations.") (define-public r-vroom (package (name "r-vroom") - (version "1.5.7") + (version "1.6.0") (source (origin (method url-fetch) (uri (cran-uri "vroom" version)) (sha256 (base32 - "1plz20x6s01gkkcac51lhx4r2s024pgh778ri7y25hkiiwacp1yh")))) + "19kcsa4i1pc4vvwp2y21izj5rv4a9mvl8a9rylx6jhk4j7gwq657")))) (properties `((upstream-name . "vroom"))) (build-system r-build-system) (propagated-inputs @@ -32723,13 +34668,13 @@ using either @code{httpuv} or @code{Rhttpd}.") (define-public r-protolite (package (name "r-protolite") - (version "2.1.1") + (version "2.1.3") (source (origin (method url-fetch) (uri (cran-uri "protolite" version)) (sha256 - (base32 "0g1r3lzmvx1w44qzqzdvxfn21zmz11srlp6cr76kd7pd5wzjv82p")))) + (base32 "1sr56hrd5n79igy3168993cxzqkzizhal4s1g22pd0rgdixm27ch")))) (properties `((upstream-name . "protolite"))) (build-system r-build-system) (inputs @@ -32797,14 +34742,14 @@ Apache2.") (define-public r-exactextractr (package (name "r-exactextractr") - (version "0.9.0") + (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "exactextractr" version)) (sha256 (base32 - "13di9s0lv9kdv2p3hp9ksrr0rh98z6m998pj5a1xq9zl6iakankh")))) + "18glacc1v0kj65g6fbqnhvgg83sr334chdfll7nhjnx44my3dkzh")))) (properties `((upstream-name . "exactextractr"))) (build-system r-build-system) (inputs (list geos)) @@ -32881,7 +34826,16 @@ package.") "0cx5k0mzn6bm8ff58yrqz3hjidxcawxgqbpijnynvin1m4395i4j")))) (properties `((upstream-name . "qs"))) (build-system r-build-system) - (inputs (list zlib)) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; Our zstd is at 1.5.0, but this package bundles 1.5.2. + (add-after 'unpack 'use-older-zstd + (lambda _ + (substitute* "configure" + (("100502") "100500"))))))) + (inputs (list lz4 zlib (list zstd "lib"))) (propagated-inputs (list r-rapiserialize r-rcpp r-stringfish)) (native-inputs @@ -32896,14 +34850,14 @@ object to and from disk.") (define-public r-rgeos (package (name "r-rgeos") - (version "0.5-9") + (version "0.6-1") (source (origin (method url-fetch) (uri (cran-uri "rgeos" version)) (sha256 (base32 - "1m73y0nwrdwsjrl48c4fg1kdqnh79835brnmxv9ak01ndbzcp45b")))) + "1wppxr9iibb0gi1hr6qzda9dc8spf6297lkfddl41j78q14bs3a2")))) (properties `((upstream-name . "rgeos"))) (build-system r-build-system) (inputs @@ -32977,14 +34931,14 @@ Tensorflow graphs.") (define-public r-tensorflow (package (name "r-tensorflow") - (version "2.9.0") + (version "2.11.0") (source (origin (method url-fetch) (uri (cran-uri "tensorflow" version)) (sha256 (base32 - "12c6ndxx4g6fqjakpzp9pgl29ghswhqyr6q9jahpk0cawizh2znj")))) + "1nqb3vgsw1xrpi1skw6yqwgdri3i8d9np0jylzfj7plizx63z64b")))) (properties `((upstream-name . "tensorflow"))) (build-system r-build-system) (inputs (list tensorflow)) @@ -33008,19 +34962,18 @@ between them.") (define-public r-keras (package (name "r-keras") - (version "2.9.0") + (version "2.11.0") (source (origin (method url-fetch) (uri (cran-uri "keras" version)) (sha256 (base32 - "06513d1fp7cxk4v03xm9lhgj6xmp9dqqvw3lnzwbzjwdkfj948yc")))) + "19r11mlxpdl09f7sfwzflnjhx2a6jgm57hjzg81pk8kprk4w7lvp")))) (properties `((upstream-name . "keras"))) (build-system r-build-system) (propagated-inputs - (list r-ellipsis - r-generics + (list r-generics r-glue r-magrittr r-r6 @@ -33223,14 +35176,14 @@ to archive and assign DOIs to data, software, figures, and more.") (define-public r-dismo (package (name "r-dismo") - (version "1.3-8") + (version "1.3-9") (source (origin (method url-fetch) (uri (cran-uri "dismo" version)) (sha256 (base32 - "17dwk4fv9l903fp38ab9arc4dfyrj1sbllfxlybkdwm9lpsn1qv6")))) + "1vmyjch2nv7x80kj453bjbzfsdyhcmf9hw68lh2b05kpnqfm491r")))) (properties `((upstream-name . "dismo"))) (build-system r-build-system) (propagated-inputs @@ -33281,14 +35234,14 @@ fully reproducible.") (define-public r-paws-common (package (name "r-paws-common") - (version "0.5.0") + (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "paws.common" version)) (sha256 (base32 - "12dz3giv1xajdqq79s5gin9kw4x74w2iaw62ha6ssf8whrc3wmh5")))) + "090csb0wjnsfhkphws5anrnml18y1k54yi48lxav8wp5kqj4wlb6")))) (properties `((upstream-name . "paws.common"))) (build-system r-build-system) (propagated-inputs @@ -33404,14 +35357,14 @@ and more.") (define-public r-paws-application-integration (package (name "r-paws-application-integration") - (version "0.1.12") + (version "0.1.13") (source (origin (method url-fetch) (uri (cran-uri "paws.application.integration" version)) (sha256 (base32 - "0llyd9hc679pad1ih0rcc38q5xxpzinhwrl8cvrkgsjgbc3agq42")))) + "0qxrjmqywp4ychjwfbripfin4vlv0k041ycmr3pjr6p3dg910i3w")))) (properties `((upstream-name . "paws.application.integration"))) (build-system r-build-system) @@ -34342,13 +36295,13 @@ formatting and delivering log messages with low overhead.") (define-public r-fasterize (package (name "r-fasterize") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "fasterize" version)) (sha256 - (base32 "10bzl77c1b9jhcn1xp467qzp2n8c7s3wpxn53qjh1nwvbri5kd32")))) + (base32 "1ckxi2iyxdahhgbliblcrkzziblfagzr54srjk27yp1lcgivvvs4")))) (properties `((upstream-name . "fasterize"))) (build-system r-build-system) (propagated-inputs @@ -34367,13 +36320,13 @@ options for aggregating multi-layer rasters.") (define-public r-bien (package (name "r-bien") - (version "1.2.5") + (version "1.2.6") (source (origin (method url-fetch) (uri (cran-uri "BIEN" version)) (sha256 - (base32 "0s98n6zbf48vssd3h63k6kashcxv1kawcb026n0ngsfpc5dv6i48")))) + (base32 "17zrj5ckxaz4mdbgywxi8kf51ssbf2md1d2azf30dh96kzc2ayps")))) (properties `((upstream-name . "BIEN"))) (build-system r-build-system) (native-inputs @@ -34385,11 +36338,9 @@ options for aggregating multi-layer rasters.") r-fasterize r-foreach r-raster - r-rgdal - r-rgeos r-rpostgresql r-sf - r-sp)) + r-terra)) (home-page "https://cran.r-project.org/package=BIEN") (synopsis "Tools for accessing the BIEN database") (description @@ -34424,14 +36375,14 @@ be efficient and easy to use.") (define-public r-ggh4x (package (name "r-ggh4x") - (version "0.2.2") + (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "ggh4x" version)) (sha256 (base32 - "11mskrby3gyjhkvnkcwl2ar1bdh4h45y48dfnm4kzgc7nwvdl3ia")))) + "0da5r8zfx1ixhk266byspfm2aifhm0jrvbk264xya712pxayiw4a")))) (properties `((upstream-name . "ggh4x"))) (build-system r-build-system) (propagated-inputs @@ -34457,14 +36408,14 @@ smaller collection of stats, geoms and axis guides.") (define-public r-gghalves (package (name "r-gghalves") - (version "0.1.3") + (version "0.1.4") (source (origin (method url-fetch) (uri (cran-uri "gghalves" version)) (sha256 (base32 - "1lj4c38fzxwg8gy57ymf00lqjdplb7v2a0lnd262c1d5cavqiws4")))) + "1qsxq2zbz4zcpqc7949apznn9f2c959jwwx010bl4gf2p6vchfx7")))) (properties `((upstream-name . "gghalves"))) (build-system r-build-system) (propagated-inputs @@ -34564,6 +36515,30 @@ analyses.") for rendering equations in the HTML help files.") (license (list license:asl2.0 license:gpl3)))) +(define-public r-spacefillr + (package + (name "r-spacefillr") + (version "0.3.2") + (source (origin + (method url-fetch) + (uri (cran-uri "spacefillr" version)) + (sha256 + (base32 + "0raaw9ib8b2dzkh4w28wpxcgxs7ky328yaayb64lc39syf7g19dv")))) + (properties `((upstream-name . "spacefillr"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp)) + (home-page "https://github.com/tylermorganwall/spacefillr") + (synopsis "Space-Filling Random and Quasi-Random Sequences") + (description + "@code{spacefillr} enables generation of random and quasi-random +space-filling sequences. It supports the following sequences: Halton, Sobol, +Owen-scrambled Sobol, Owen-scrambled Sobol with errors distributed as blue +noise, progressive jittered, progressive multi-jittered (PMJ), PMJ with blue +noise, PMJ02, and PMJ02 with blue noise. The package also includes a C++ +API.") + (license license:expat))) + (define-public r-spacetime (package (name "r-spacetime") @@ -34591,24 +36566,33 @@ matching or aggregation, retrieving coordinates, print, summary, etc.") (define-public r-gstat (package (name "r-gstat") - (version "2.0-9") + (version "2.1-0") (source (origin (method url-fetch) (uri (cran-uri "gstat" version)) (sha256 (base32 - "19m4zcj1qvg6gs8yjr5ijvd6rrv4av5yp5rmhnb88f0m5qn06b0j")))) + "0vrdiyjav92wbbms8ljmv1i0l8cdjblfnmhyrsd1a7v0z93fp9jp")))) (properties `((upstream-name . "gstat"))) (build-system r-build-system) - (propagated-inputs (list r-lattice r-sp r-zoo r-spacetime r-fnn)) + (propagated-inputs + (list r-fnn + r-lattice + r-sp + r-sf + r-sftime + r-spacetime + r-stars + r-zoo)) (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}.") + "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 @@ -34678,13 +36662,13 @@ calculate a dimension's unknown value from other dimensions' measurements.") (define-public r-sungeo (package (name "r-sungeo") - (version "0.2.288") + (version "0.2.292") (source (origin (method url-fetch) (uri (cran-uri "SUNGEO" version)) (sha256 (base32 - "0c8y0ngx1020rw2v00rxmq8syd72f41ckik5sg7gigg7d80gi31w")) + "1xav5by7sl21cwfg9m1ij1lz1kvdlqkkp2ah67rnj9vp4vk7nkfg")) (modules '((guix build utils))) (snippet '(begin ;; Fortunately, the package does not actually use @@ -34695,28 +36679,28 @@ calculate a dimension's unknown value from other dimensions' measurements.") (("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)) + (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 |