diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 453 |
1 files changed, 442 insertions, 11 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 749eed8b57..6ce0ed1424 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1,10 +1,13 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net> -;;; Copyright © 2017 Roel Janssen <roel@gnu.org> -;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2017, 2018 Roel Janssen <roel@gnu.org> +;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com> ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com> ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net> +;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com> +;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net> +;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -35,6 +38,252 @@ #:use-module (gnu packages statistics) #:use-module (gnu packages web)) +(define-public r-tidyverse + (package + (name "r-tidyverse") + (version "1.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "tidyverse" version)) + (sha256 + (base32 + "0yy3fkjksgcn6wkbgsb0pbnmsyqs4m01mziqafhig578nixs4rxd")))) + (build-system r-build-system) + (propagated-inputs + `(("r-broom" ,r-broom) + ("r-cli" ,r-cli) + ("r-crayon" ,r-crayon) + ("r-dbplyr" ,r-dbplyr) + ("r-dplyr" ,r-dplyr) + ("r-forcats" ,r-forcats) + ("r-ggplot2" ,r-ggplot2) + ("r-haven" ,r-haven) + ("r-hms" ,r-hms) + ("r-httr" ,r-httr) + ("r-jsonlite" ,r-jsonlite) + ("r-lubridate" ,r-lubridate) + ("r-magrittr" ,r-magrittr) + ("r-modelr" ,r-modelr) + ("r-purrr" ,r-purrr) + ("r-readr" ,r-readr) + ("r-readxl" ,r-readxl) + ("r-reprex" ,r-reprex) + ("r-rlang" ,r-rlang) + ("r-rstudioapi" ,r-rstudioapi) + ("r-rvest" ,r-rvest) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-xml2" ,r-xml2))) + (home-page "https://tidyverse.tidyverse.org") + (synopsis "Install and load packages from the \"Tidyverse\"") + (description + "The @code{tidyverse} is a set of packages that work in harmony because +they share common data representations and API design. This package is +designed to make it easy to install and load multiple tidyverse packages in a +single step.") + (license license:gpl3))) + +(define-public r-rvest + (package + (name "r-rvest") + (version "0.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "rvest" version)) + (sha256 + (base32 + "04mv99z8dixywx96kfy4215g6ib23s7qvd77hcf9pxqxzcvqhvhd")))) + (build-system r-build-system) + (propagated-inputs + `(("r-httr" ,r-httr) + ("r-magrittr" ,r-magrittr) + ("r-selectr" ,r-selectr) + ("r-xml2" ,r-xml2))) + (home-page "https://github.com/hadley/rvest") + (synopsis "Simple web scraping for R") + (description + "@code{r-rvest} helps you scrape information from web pages. It is +designed to work with @code{magrittr} to make it easy to express common web +scraping tasks, inspired by libraries like @code{BeautifulSoup}.") + (license license:gpl3))) + +(define-public r-selectr + (package + (name "r-selectr") + (version "0.3-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "selectr" version)) + (sha256 + (base32 + "0kdrj64rqg4z6hg92y9r2h602a2i73r5rnlpg23ys33d5d32n8jy")))) + (build-system r-build-system) + (propagated-inputs `(("r-stringr" ,r-stringr))) + (home-page "https://sjp.co.nz/projects/selectr/") + (synopsis "Translate CSS selectors to XPath expressions") + (description + "@code{r-selectr} translates a CSS3 selector into an equivalent XPath +expression. This allows you to use CSS selectors when working with the XML +package as it can only evaluate XPath expressions. Also provided are +convenience functions useful for using CSS selectors on XML nodes. This +package is a port of the Python package @code{cssselect}.") + (license license:bsd-3))) + +(define-public r-reprex + (package + (name "r-reprex") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "reprex" version)) + (sha256 + (base32 + "105d9vsmqfilgpw8psfb2wyiz1hvcycvh4cqhb3ab37lm3rcavvs")))) + (build-system r-build-system) + (propagated-inputs + `(("r-callr" ,r-callr) + ("r-knitr" ,r-knitr) + ("r-rmarkdown" ,r-rmarkdown) + ("r-whisker" ,r-whisker))) + (home-page "https://github.com/tidyverse/reprex") + (synopsis "Prepare reproducible R code examples for sharing") + (description + "This package provides a convenience wrapper that uses the +@code{rmarkdown} package to render small snippets of code to target formats +that include both code and output. The goal is to encourage the sharing of +small, reproducible, and runnable examples on code-oriented websites or email. +@code{reprex} also extracts clean, runnable R code from various common formats, +such as copy/paste from an R session.") + (license license:expat))) + +(define-public r-callr + (package + (name "r-callr") + (version "2.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "callr" version)) + (sha256 + (base32 + "0m51p39vfwldxv6h8x4y9w3laf8q9bldhfqhlcrlx3xhy3irb1bp")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-crayon" ,r-crayon) + ("r-debugme" ,r-debugme) + ("r-r6" ,r-r6) + ("r-testthat" ,r-testthat))) + (home-page "https://github.com/r-lib/callr#readme") + (synopsis "Call R from R") + (description + "It is sometimes useful to perform a computation in a separate R process, +without affecting the current R process at all. This packages does exactly +that.") + (license license:expat))) + +(define-public r-readxl + (package + (name "r-readxl") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "readxl" version)) + (sha256 + (base32 + "1bf7gxw9r11m4llyymplxiaa4gzgyj4bwmwad5in756pzq3jzmpv")))) + (build-system r-build-system) + (propagated-inputs + `(("r-cellranger" ,r-cellranger) + ("r-rcpp" ,r-rcpp) + ("r-tibble" ,r-tibble))) + (home-page "https://readxl.tidyverse.org") + (synopsis "Read Excel files") + (description + "This package lets you import Excel files into R. It supports +@file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via +the embedded @code{RapidXML} C++ library.") + ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and + ;; 'rapidxml' which is Boost. + (license (list license:gpl3 license:bsd-2 license:boost1.0)))) + +(define-public r-modelr + (package + (name "r-modelr") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "modelr" version)) + (sha256 + (base32 + "1rqw0b583vp107zqp4h3wj51dvv4hb3wszfr1f5f48xassc53f95")))) + (build-system r-build-system) + (propagated-inputs + `(("r-broom" ,r-broom) + ("r-dplyr" ,r-dplyr) + ("r-lazyeval" ,r-lazyeval) + ("r-magrittr" ,r-magrittr) + ("r-purrr" ,r-purrr) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/tidyverse/modelr") + (synopsis "Helper functions for modelling in pipelines") + (description + "Functions for modelling that help you seamlessly integrate modelling +into a pipeline of data manipulation and visualisation.") + (license license:gpl3))) + +(define-public r-haven + (package + (name "r-haven") + (version "1.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "haven" version)) + (sha256 + (base32 + "1fkcvsrnw8waqwggv0aydbvbi99x5kp9g78xfxj4w6s3xvdzcysz")))) + (build-system r-build-system) + (propagated-inputs + `(("r-forcats" ,r-forcats) + ("r-hms" ,r-hms) + ("r-rcpp" ,r-rcpp) + ("r-readr" ,r-readr) + ("r-tibble" ,r-tibble))) + (home-page "https://haven.tidyverse.org") + (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files") + (description + "This package lets you mport foreign statistical formats into R via the +embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.") + (license license:expat))) + +(define-public r-amap + (package + (name "r-amap") + (version "0.8-14") + (source (origin + (method url-fetch) + (uri (cran-uri "amap" version)) + (sha256 + (base32 + "1dz37z9v4zvyvqrs4xvpfv468jwvpxav60qn2w0049bw8llj6xdl")))) + (build-system r-build-system) + (inputs + `(("gfortran" ,gfortran))) + (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/") + (synopsis "Another multidimensional analysis package") + (description "This package provides tools for clustering and principal +component analysis (with robust methods, and parallelized functions).") + (license license:gpl2+))) + (define-public r-ape (package (name "r-ape") @@ -131,6 +380,27 @@ 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-pastecs + (package + (name "r-pastecs") + (version "1.3.21") + (source (origin + (method url-fetch) + (uri (cran-uri "pastecs" version)) + (sha256 + (base32 + "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc")))) + (build-system r-build-system) + (propagated-inputs + `(("r-boot" ,r-boot))) + (home-page "http://www.sciviews.org/pastecs") + (synopsis "Analysis of space-time ecological series") + (description + "This package provides functions for regulation, decomposition and analysis +of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER +initiative to bring PASSTEC 2000 functionalities to R.") + (license license:gpl2+))) + (define-public r-plogr (package (name "r-plogr") @@ -757,14 +1027,14 @@ or excesses over a high threshold.") (define-public r-lmtest (package (name "r-lmtest") - (version "0.9-35") + (version "0.9-36") (source (origin (method url-fetch) (uri (cran-uri "lmtest" version)) (sha256 (base32 - "107br1l7p52wxvazs031f4h5ryply97qywg9dzrkw4ydnvqq4j9g")))) + "0sym9sm1vl6bbgq01jhz1plxqmgh8hrgrn7rw0mwvsalcn6id7xy")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,r-zoo))) @@ -779,6 +1049,26 @@ tools for inference in parametric models are provided.") ;; Either version is okay (license (list license:gpl2 license:gpl3)))) +(define-public r-idr + (package + (name "r-idr") + (version "1.2") + (source (origin + (method url-fetch) + (uri (cran-uri "idr" version)) + (sha256 + (base32 + "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/idr/") + (synopsis "Irreproducible discovery rate") + (description + "This is a package for estimating the copula mixture model and plotting +correspondence curves in \"Measuring reproducibility of high-throughput +experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779, +by Li, Brown, Huang, and Bickel") + (license license:gpl2+))) + (define-public r-inline (package (name "r-inline") @@ -1329,14 +1619,14 @@ created using basic graphics.") (define-public r-broom (package (name "r-broom") - (version "0.4.3") + (version "0.4.4") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "119pc2jnxvm13cvd77c7d14p3bn68f4jm310vj3yfck40101n9if")))) + "081x87sy6dmfvkgwfjrl5ax51k77ciyzg9x3xql25vdi92rmwj3m")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -1625,6 +1915,29 @@ University Press. It provides smoothing methods for nonparametric regression and density estimation") (license license:gpl2+))) +(define-public r-venndiagram + (package + (name "r-venndiagram") + (version "1.6.20") + (source (origin + (method url-fetch) + (uri (cran-uri "VennDiagram" version)) + (sha256 + (base32 + "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775")))) + (properties `((upstream-name . "VennDiagram"))) + (build-system r-build-system) + (propagated-inputs + `(("r-futile-logger" ,r-futile-logger))) + (home-page "https://cran.r-project.org/web/packages/VennDiagram/") + (synopsis "Generate High-Resolution Venn and Euler Plots") + (description + "This package provides a set of functions to generate high-resolution +Venn and Euler plots. It includes handling for several special cases, +including two-case scaling, and extensive customization of plot shape and +structure.") + (license license:gpl2+))) + (define-public r-vioplot (package (name "r-vioplot") @@ -2288,16 +2601,16 @@ published results; and a routine for graphical display.") (define-public r-network (package (name "r-network") - (version "1.13.0") + (version "1.13.0.1") (source (origin (method url-fetch) (uri (cran-uri "network" version)) (sha256 (base32 - "11sg330xb7gcnl3f6lwhhjdabz6mk43828i2np635pqw4s4yl13s")))) + "1bbkbqkqf1d7irfwh08c13c2pfypir1ssvlqrln83irqns1ikdv0")))) (build-system r-build-system) - (home-page "http://statnet.org/") + (home-page "https://statnet.org/") (synopsis "Classes for relational data") (description "This package provides tools to create and modify network objects. The @@ -2319,7 +2632,7 @@ supports arbitrary vertex/edge/graph attributes.") (properties `((upstream-name . "statnet.common"))) (build-system r-build-system) - (home-page "http://www.statnet.org") + (home-page "https://statnet.org") (synopsis "R scripts and utilities used by the Statnet software") (description "This package provides non-statistical utilities used by the software developed by the Statnet Project.") @@ -2340,7 +2653,7 @@ software developed by the Statnet Project.") (propagated-inputs `(("r-network" ,r-network) ("r-statnet-common" ,r-statnet-common))) - (home-page "http://www.statnet.org") + (home-page "https://statnet.org") (synopsis "Tools for social network analysis") (description "This package provides a range of tools for social network analysis, @@ -3273,3 +3586,121 @@ those functions to be used with time series including specifications that may contain lags, diffs and missing values.") ;; Any GPL version. (license license:gpl2+))) + +(define-public r-catdap + (package + (name "r-catdap") + (version "1.3.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "catdap" version)) + (sha256 + (base32 + "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/catdap/") + (synopsis "Tools for categorical data analysis") + (description + "This package provides functions for analyzing multivariate data. +Dependencies of the distribution of the specified variable (response +variable) to other variables (explanatory variables) are derived and +evaluated by the @dfn{Akaike Information Criterion} (AIC).") + (license license:gpl2+))) + +(define-public r-arules + (package + (name "r-arules") + (version "1.6-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "arules" version)) + (sha256 + (base32 + "14gbq5k2zkx4wc7kkfazz313ngij89qp1xmyxfg3nq3v1s84c3sl")))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix))) + (home-page "https://github.com/mhahsler/arules") + (synopsis "Mining association rules and frequent itemsets") + (description + "This package provides an infrastructure for representing, manipulating +and analyzing transaction data and patterns (frequent itemsets and association rules). +It also provides C implementations of the association mining algorithms Apriori +and Eclat.") + (license license:gpl3))) + +(define-public r-parsedate + (package + (name "r-parsedate") + (version "1.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "parsedate" version)) + (sha256 + (base32 + "0mg7hbm3903iwvmpn51gjpaaq03rsp72hjb1g8h5g84r81iha002")))) + (build-system r-build-system) + (home-page "https://github.com/gaborcsardi/parsedate") + (synopsis + "Recognize and parse dates in various formats") + (description + "This package provides three functions for dealing with dates: +@code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and +time formats, @code{parse_date} parses dates in unspecified formats, +and @code{format_iso_8601} formats a date in ISO 8601 format.") + (license license:gpl2))) + +(define-public r-abc-data + (package + (name "r-abc-data") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "abc.data" version)) + (sha256 + (base32 + "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj")))) + (properties `((upstream-name . "abc.data"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/abc.data/") + (synopsis "Data for Approximate Bayesian Computation (ABC) package") + (description + "This package contains data which are used by functions of the abc +package which implements several @dfn{Approximate Bayesian Computation} (ABC) +algorithms for performing parameter estimation, model selection, and +goodness-of-fit.") + (license license:gpl3+))) + +(define-public r-abc + (package + (name "r-abc") + (version "2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "abc" version)) + (sha256 + (base32 + "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-abc-data" ,r-abc-data) + ("r-locfit" ,r-locfit) + ("r-mass" ,r-mass) + ("r-nnet" ,r-nnet) + ("r-quantreg" ,r-quantreg))) + (home-page "https://cran.r-project.org/web/packages/abc/") + (synopsis "Tools for Approximate Bayesian Computation (ABC)") + (description + "This package implements several @dfn{Approximate Bayesian +Computation} (ABC) algorithms for performing parameter estimation, model +selection, and goodness-of-fit. Cross-validation tools are also available for +measuring the accuracy of ABC estimates, and to calculate the +misclassification probabilities of different models.") + (license license:gpl3+))) |