diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 286 |
1 files changed, 232 insertions, 54 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ce36a6a8da..b0160347c9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1,7 +1,8 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com> -;;; Copyright © 2017, 2018 Roel Janssen <roel@gnu.org> +;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org> ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com> ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com> @@ -13,6 +14,7 @@ ;;; 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 Eric Brown <brown@fastmail.com> ;;; Copyright © 2018, 2019 Brett Gilio <brettg@posteo.net> ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com> ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz> @@ -95,6 +97,56 @@ the system clipboards.") (license license:gpl3))) +(define-public r-scales + (package + (name "r-scales") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "scales" version)) + (sha256 + (base32 "00rdbfj5mwc3kr8pskidn3n2zkp4ms6cx36xazz54pxw3pysdr0y")))) + (build-system r-build-system) + (propagated-inputs + `(("r-farver" ,r-farver) + ("r-labeling" ,r-labeling) + ("r-lifecycle" ,r-lifecycle) + ("r-munsell" ,r-munsell) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-r6" ,r-r6) + ("r-viridislite" ,r-viridislite))) + (home-page "https://github.com/hadley/scales") + (synopsis "Scale functions for visualization") + (description + "This package provides graphical scales that map data to aesthetics, and +provides methods for automatically determining breaks and labels for axes and +legends.") + (license license:expat))) + +(define-public r-pheatmap + (package + (name "r-pheatmap") + (version "1.0.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "pheatmap" version)) + (sha256 + (base32 + "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap")))) + (build-system r-build-system) + (propagated-inputs + `(("r-gtable" ,r-gtable) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-scales" ,r-scales))) + (home-page "https://cran.r-project.org/web/packages/pheatmap") + (synopsis "Pretty heatmaps") + (description + "This package provides an implementation of heatmaps that offers more +control over dimensions and appearance.") + (license license:gpl2+))) + (define-public r-ellipsis (package (name "r-ellipsis") @@ -243,14 +295,14 @@ data types as well.") (define-public r-tidyverse (package (name "r-tidyverse") - (version "1.2.1") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "tidyverse" version)) (sha256 (base32 - "0yy3fkjksgcn6wkbgsb0pbnmsyqs4m01mziqafhig578nixs4rxd")))) + "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -267,6 +319,7 @@ data types as well.") ("r-lubridate" ,r-lubridate) ("r-magrittr" ,r-magrittr) ("r-modelr" ,r-modelr) + ("r-pillar" ,r-pillar) ("r-purrr" ,r-purrr) ("r-readr" ,r-readr) ("r-readxl" ,r-readxl) @@ -314,14 +367,13 @@ scraping tasks, inspired by libraries like @code{BeautifulSoup}.") (define-public r-selectr (package (name "r-selectr") - (version "0.4-1") + (version "0.4-2") (source (origin (method url-fetch) (uri (cran-uri "selectr" version)) (sha256 - (base32 - "1jp27rxks4w29l47k42869hp8hnkzq2rnvsqbr44wd19fqb2zm4b")))) + (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m")))) (build-system r-build-system) (propagated-inputs `(("r-stringr" ,r-stringr) @@ -906,14 +958,13 @@ application framework for R, making it easy to create attractive dashboards.") (define-public r-shinyfiles (package (name "r-shinyfiles") - (version "0.7.3") + (version "0.7.5") (source (origin (method url-fetch) (uri (cran-uri "shinyFiles" version)) (sha256 - (base32 - "01as3l9ffj5dwac0vviais2x5l3027zxlj67kcvkdwxaj5hql33i")))) + (base32 "1143m941hma9hc77c3xcw26c0ygfhn9ii2sbp9wrydxv4gc7mr8a")))) (properties `((upstream-name . "shinyFiles"))) (build-system r-build-system) (propagated-inputs @@ -2339,14 +2390,14 @@ transportation problems.") (define-public r-limsolve (package (name "r-limsolve") - (version "1.5.5.3") + (version "1.5.6") (source (origin (method url-fetch) (uri (cran-uri "limSolve" version)) (sha256 (base32 - "1ll6ir42h3g2fzf0wqai213bm82gpwjj2hfma2np3mz024sc09rg")))) + "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr")))) (properties `((upstream-name . "limSolve"))) (build-system r-build-system) (propagated-inputs @@ -2584,14 +2635,14 @@ regression using Kernel Ridge Regression.") (define-public r-prodlim (package (name "r-prodlim") - (version "2019.10.13") + (version "2019.11.13") (source (origin (method url-fetch) (uri (cran-uri "prodlim" version)) (sha256 (base32 - "0rsyfpz667y5cijmq33l318mrdw8r340khp72gcg8n490b1g0176")))) + "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8")))) (build-system r-build-system) (propagated-inputs `(("r-kernsmooth" ,r-kernsmooth) @@ -3396,14 +3447,14 @@ structure.") (define-public r-vioplot (package (name "r-vioplot") - (version "0.3.2") + (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "vioplot" version)) (sha256 (base32 - "13kfjp747bnzksai8j39y2hyl3ljc6n53c2cfhaw78q3d63x0lbv")))) + "1jjrsds7p1jnnr4970h43526b9cdv3azizjbalbfzjjylc53lrca")))) (build-system r-build-system) (propagated-inputs `(("r-sm" ,r-sm) @@ -3827,14 +3878,14 @@ of merit, ordering functions, and enhanced versions of @code{pairs} and (define-public r-webshot (package (name "r-webshot") - (version "0.5.1") + (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "webshot" version)) (sha256 (base32 - "08sb1xi376pfy1vwilk2d68zljsg9yiv04n2dkqz383gdhh0sxdr")))) + "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) @@ -4843,14 +4894,13 @@ the application.") (define-public r-algdesign (package (name "r-algdesign") - (version "1.1-7.3") + (version "1.1-7.3.1") (source (origin (method url-fetch) (uri (cran-uri "AlgDesign" version)) (sha256 - (base32 - "0bl7mx4dnmkgs2x1fj7cqnrp7jx18mqwxyga0rzlniq12h8mc3fz")))) + (base32 "1s69yx0wxi9kqj9kyib0yvd363d7g4zrz0cvz1hn97ladr8656bz")))) (properties `((upstream-name . "AlgDesign"))) (build-system r-build-system) (home-page "https://github.com/jvbraun/AlgDesign") @@ -6053,14 +6103,14 @@ to help insert or delete content at a specific location in the document.") (define-public r-abn (package (name "r-abn") - (version "2.1") + (version "2.2") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "08jlvb6i5f7ry2dwm0jgrnn2w95vr0l67dpx13n9878lz9ld131b")))) + "19w6bdjyp4zwqs6p0flry4qxqynf9rh8ykdrfrp61wrdf7kysw0d")))) (build-system r-build-system) (inputs `(("gsl" ,gsl))) @@ -6204,14 +6254,14 @@ other add-on packages.") (define-public r-insight (package (name "r-insight") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "1izqh4j0gzyk25cga67gs0i6rl0j471h5y2c3y1maz79r32fs7fd")))) + "1alxc483r3d1ydp983m2872mxd4nj3j25qv47zzgj10nbi4y32sq")))) (build-system r-build-system) (home-page "https://easystats.github.io/insight/") (synopsis "Easy access to model information for various model objects") @@ -8176,14 +8226,13 @@ detection, parallelism through BLAS and parallel user templates.") (define-public r-sjstats (package (name "r-sjstats") - (version "0.17.6") + (version "0.17.7") (source (origin (method url-fetch) (uri (cran-uri "sjstats" version)) (sha256 - (base32 - "11z1wfi0d74d1rld0320l3vmv6rl41wa0v9bjc44rk06yc90wld2")))) + (base32 "029rl05p88bp01favz300m980r1khcx2a2kn88yqbnbgkjjgqqc6")))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) @@ -8333,22 +8382,47 @@ are also supported. The two main functions are @code{ggpredict()} and results using @code{ggplot2}.") (license license:gpl3))) +(define-public r-effectsize + (package + (name "r-effectsize") + (version "0.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "effectsize" version)) + (sha256 + (base32 + "07vgmxdl75798hgdh90zysafjh97rmmj2wjjyr6xff4fbhi8rlkb")))) + (properties `((upstream-name . "effectsize"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bayestestr" ,r-bayestestr) + ("r-insight" ,r-insight) + ("r-parameters" ,r-parameters))) + (home-page "https://github.com/easystats/effectsize") + (synopsis "Indices of effect size and standardized parameters") + (description + "This package provides utilities to work with indices of effect size and +standardized parameters for a wide variety of models, allowing computation and +conversion of indices such as Cohen's d, r, odds, etc.") + (license license:gpl3))) + (define-public r-sjplot (package (name "r-sjplot") - (version "2.7.2") + (version "2.8.0") (source (origin (method url-fetch) (uri (cran-uri "sjPlot" version)) (sha256 - (base32 "1kx1qqgp4fhwwwpqn9mv8m1pnpjxfs7ww36ns7j1ja4a7ydwn2hp")))) + (base32 "0ahz6v6bhvq1537inwakmrafs44hs2m9w0ra8q17fz626nn9rb9b")))) (properties `((upstream-name . "sjPlot"))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) - ("r-broom" ,r-broom) ("r-dplyr" ,r-dplyr) + ("r-effectsize" ,r-effectsize) ("r-forcats" ,r-forcats) ("r-ggeffects" ,r-ggeffects) ("r-ggplot2" ,r-ggplot2) @@ -8360,7 +8434,7 @@ results using @code{ggplot2}.") ("r-magrittr" ,r-magrittr) ("r-mass" ,r-mass) ("r-modelr" ,r-modelr) - ("r-nlme" ,r-nlme) + ("r-parameters" ,r-parameters) ("r-performance" ,r-performance) ("r-psych" ,r-psych) ("r-purrr" ,r-purrr) @@ -9048,14 +9122,13 @@ netCDF files.") (define-public r-biocmanager (package (name "r-biocmanager") - (version "1.30.9") + (version "1.30.10") (source (origin (method url-fetch) (uri (cran-uri "BiocManager" version)) (sha256 - (base32 - "1l9b2mr99nhpvk1wkd93397i0d6z4vvbq3zm8dk86gb1pfci26sx")))) + (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk")))) (properties `((upstream-name . "BiocManager"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/BiocManager/") @@ -9582,13 +9655,13 @@ maps.") (define-public r-tidytree (package (name "r-tidytree") - (version "0.2.9") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 - (base32 "1l9rk71dzlwg8736l0g4rdlq3pghxkfzmlxyln8y4bxx7ym51i6g")))) + (base32 "1sbfwcxf9v1lhpa0392b49b6qfjrq7nlqz2djqzk5aknj9j64zvy")))) (build-system r-build-system) (propagated-inputs `(("r-ape" ,r-ape) @@ -9971,14 +10044,14 @@ Touzet and Varre (2007).") (define-public r-rnifti (package (name "r-rnifti") - (version "0.11.1") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "RNifti" version)) (sha256 (base32 - "0jcgdg5k2swmi57aqj347kfi1fc4nvag7pxdfz61kc0vqqamm0wg")))) + "0l61hjnzv043ibpkgrhc0yngaqmc58lkvii8j1dzh022z5wbqrj8")))) (properties `((upstream-name . "RNifti"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) @@ -11147,19 +11220,16 @@ library.") (define-public r-protviz (package (name "r-protviz") - (version "0.4.0") + (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "protViz" version)) (sha256 (base32 - "150i2q4nakz28f39kmhrchz4qsr8ax6y02512md94k8hq4hamxg1")))) + "0cznzm1ijlq33yd5wsa61prav77y2vi698w0n2fx1xcv504c4bjv")))) (properties `((upstream-name . "protViz"))) (build-system r-build-system) - (inputs - `(("perl" ,perl) - ("python-2" ,python-2))) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (home-page "https://github.com/protViz/protViz/") (synopsis "Visualizing and analyzing mass spectrometry data in proteomics") @@ -11226,14 +11296,14 @@ model with finite state space using the Aalen-Johansen estimator.") (define-public r-epi (package (name "r-epi") - (version "2.38") + (version "2.40") (source (origin (method url-fetch) (uri (cran-uri "Epi" version)) (sha256 (base32 - "0ald9fjynrlyah8nzwfs49a08j4myd3c5bm56zn61gg5pyyhi8hd")))) + "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5")))) (properties `((upstream-name . "Epi"))) (build-system r-build-system) (propagated-inputs @@ -11408,14 +11478,14 @@ them in distributed compute environments.") (define-public r-future (package (name "r-future") - (version "1.15.0") + (version "1.15.1") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 - "1cbp7agb9lipjxsh7xm1yphh8a4hrjy7wrbkvhsxn1swh0c4s3b7")))) + "101hi8warqa0py9l6c5p98f7i9xjhx01w655z6a35jx1dhspykzd")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -13125,14 +13195,13 @@ lspec, polyclass, and polymars.") (define-public r-rms (package (name "r-rms") - (version "5.1-3.1") + (version "5.1-4") (source (origin (method url-fetch) (uri (cran-uri "rms" version)) (sha256 - (base32 - "0drbr3g0x5pbxyzy50wnf92rbal8izizrcqslqhg0gsfg9adjih9")))) + (base32 "19knh1sw0icw6jh9wfb2hq5jf49i2qfvp9myvqm5paa495689x9q")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -13361,13 +13430,13 @@ SELECT or UPDATE queries to an end-point.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.15") + (version "0.16") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "0pgkabaqsckaz8z1nlza84jp172jyzv17kx5dily43jfx5psy2ap")))) + "1gwgvx1yg6q3wccnhidr3gshdvlgr42i4pvlg4h29kpsa7smjiv1")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) @@ -15540,14 +15609,14 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.2.0") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "1mgggb3l67wgjiccq4y84wbs2dw9qk01akd553yiwbwky9rpawgh")))) + "0ifb9g1h8sn661q7jf9d8glk58gxdcym5ywbmx7phwn0y3is5wdv")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs @@ -15674,3 +15743,112 @@ unique identifiers, and whether it is a certain length. In addition, files and to efficiently import multiple tabular data files into one data.table.") (license license:gpl3))) + +(define-public r-quadprog + (package + (name "r-quadprog") + (version "1.5-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "quadprog" version)) + (sha256 + (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/quadprog") + (synopsis "Functions to solve quadratic programming problems") + (description + "This package contains routines and documentation for solving quadratic +programming problems.") + (license license:gpl3+))) + +(define-public r-desolve + (package + (name "r-desolve") + (version "1.25") + (source + (origin + (method url-fetch) + (uri (cran-uri "deSolve" version)) + (sha256 + (base32 "0735y3p5glhqx69rzrc8qgmvs7p7w0p98qxmvylb6bgqp6kp0cbp")))) + (properties `((upstream-name . "deSolve"))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://desolve.r-forge.r-project.org/") + (synopsis "Solvers for initial value problems of differential equations") + (description "This package provides functions that solve initial +value problems of a system of first-order ordinary differential equations (ODE), +of partial differential equations (PDE), of differential algebraic equations +(DAE), and of delay differential equations. The functions provide an interface +to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection, +to the FORTRAN functions dvode and daspk and a C-implementation of solvers of +the Runge-Kutta family with fixed or variable time steps. The package contains +routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial +differential equations (PDE) that have been converted to ODEs by numerical +differencing.") + (license license:gpl2+))) + +(define-public r-pracma + (package + (name "r-pracma") + (version "2.2.5") + (source (origin + (method url-fetch) + (uri (cran-uri "pracma" version)) + (sha256 + (base32 "0isd3s0i4mzmva8lkh0j76hwjy1w50q7d1n9lhxsnnkgalx3xs1g")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/pracma/") + (synopsis "Practical numerical math functions") + (description "This package provides functions for numerical analysis and +linear algebra, numerical optimization, differential equations, plus some +special functions. It uses Matlab function names where appropriate to simplify +porting.") + (license license:gpl3+))) + +(define-public r-subplex + (package + (name "r-subplex") + (version "1.5-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "subplex" version)) + (sha256 + (base32 + "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/subplex") + (synopsis "Unconstrained optimization using the subplex algorithm") + (description + "This package implements the Subplex optimization algorithm. +It solves unconstrained optimization problems using a simplex method on +subspaces. The method is well suited for optimizing objective functions that +are noisy or are discontinuous at the solution.") + (license license:gpl3+))) + +(define-public r-txtplot + (package + (name "r-txtplot") + (version "1.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "txtplot" version)) + (sha256 + (base32 + "1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/txtplot/") + (synopsis "Text-based plotting") + (description "This package provides functions to produce rudimentary ASCII +graphics directly in the terminal window. This package provides a basic +plotting function (and equivalents of curve, density, acf and barplot) as well +as a boxplot function.") + (license license:lgpl3+))) |