diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 365 |
1 files changed, 347 insertions, 18 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 106b8c7fe6..eb6bf9c38b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8,6 +8,7 @@ ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com> ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net> ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net> +;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; ;;; This file is part of GNU Guix. ;;; @@ -461,16 +462,34 @@ print, summary, plot, update, etc. @end itemize\n") (license license:gpl2))) +(define-public r-ps + (package + (name "r-ps") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ps" version)) + (sha256 + (base32 "1zm9qkyvy1fvcjvmgw51iqw8x1xzkpy7rx7xnchwfj0xpzal0ljx")))) + (build-system r-build-system) + (home-page "http://ps.r-lib.org") + (synopsis "List, query, and manipulate system processes") + (description + "The ps package implements an API to list, query, and manipulate system +processes. Most of its code is based on the @code{psutil} Python package.") + (license license:bsd-3))) + (define-public r-rcpp (package (name "r-rcpp") - (version "0.12.17") + (version "0.12.18") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "08xg8h3w25sdb3xr18g9pa0x8cirkdgljqapxmw56ss1j9fc89s2")))) + (base32 "006kpg2ph109rh1l13lqk26pp4as4fvl5661vrcczjygacgd1v7w")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ integration") @@ -1276,14 +1295,14 @@ data). Weighted versions of MLE, MME and QME are available.") (define-public r-energy (package (name "r-energy") - (version "1.7-4") + (version "1.7-5") (source (origin (method url-fetch) (uri (cran-uri "energy" version)) (sha256 (base32 - "12skvlridfq4jd5mh0yxl79ps0zi2xnlh4hsdgxad0gm7qky8awd")))) + "15k9dg0a82cs9ypm0wpcsff3il1hzhnnv86dv5ngby1r144czhi4")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) @@ -1411,14 +1430,14 @@ available in a vignette.") (define-public r-lava (package (name "r-lava") - (version "1.6.2") + (version "1.6.3") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 - "1r47pps39cgvxhg1s0bqknf4jl91pbb0c76q5icxivhwb172fqcm")))) + "0cayjspry3r2lcbvl77v5v52b2zarri3b8xsf87pw5a3jn9anxcf")))) (build-system r-build-system) (propagated-inputs `(("r-numderiv" ,r-numderiv) @@ -1887,14 +1906,14 @@ or between integer vectors representing generic sequences.") (define-public r-jomo (package (name "r-jomo") - (version "2.6-2") + (version "2.6-3") (source (origin (method url-fetch) (uri (cran-uri "jomo" version)) (sha256 (base32 - "0zyqwa2y08asj9xqwnngh6da1b9cqcx8pzc9cxwrmgnxd5nnsjb7")))) + "14s8q0j5zgl1g1pfxg3a4y1jzvs0wl61ir4992wsj7safskj7zvi")))) (build-system r-build-system) (propagated-inputs `(("r-lme4" ,r-lme4) @@ -1933,14 +1952,14 @@ clustered data.") (define-public r-mitml (package (name "r-mitml") - (version "0.3-5") + (version "0.3-6") (source (origin (method url-fetch) (uri (cran-uri "mitml" version)) (sha256 (base32 - "1s888r9y2ri39b48h1iypps6lddqkqv3g31l2sjmi2pvyccfpkwb")))) + "1pkqv4qazih3byws5z6629pp232n8ra56lip7502727b0b4bsndw")))) (build-system r-build-system) (propagated-inputs `(("r-haven" ,r-haven) @@ -2459,18 +2478,19 @@ constants, and control debugging of packages via environment variables.") (define-public r-processx (package (name "r-processx") - (version "3.1.0") + (version "3.2.0") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 (base32 - "0wjr3cqwvnjxbvln25szffmkns5w0xysivdjr6chxap4nh515b0i")))) + "1pzx4ap4xa07gf9zkd6hacdsnb9sp3kb60a7v7ljl0ywrcpn1fn4")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-crayon" ,r-crayon) + ("r-ps" ,r-ps) ("r-r6" ,r-r6) ("r-testthat" ,r-testthat))) (home-page "https://github.com/r-lib/processx3") @@ -2610,14 +2630,14 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.2") + (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 (base32 - "0zl22fcw90kdvzkjyf6vbmdmn9rz3bl51522fasvmykypffyng4a")))) + "1r11dd49ngmjgbjdv28a9c1jp8cg1l50x0acbsamzz576p8i2wl9")))) (build-system r-build-system) (home-page "https://github.com/yihui/xfun") (synopsis "Miscellaneous functions") @@ -2693,15 +2713,17 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.5") + (version "0.6") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "1pg4jfyvandjwz3lmr38pbqi9d045iwkk3xklhsfhhxq6aviq9p7")))) + "16y9dldaff2kx1fkm92p7zlph0dcrdmlmavpdgf5y9jbhmc8g83f")))) (build-system r-build-system) + (propagated-inputs + `(("r-xfun" ,r-xfun))) (home-page "https://github.com/yihui/tinytex") (synopsis "Helper functions for TeX Live and compiling LaTeX documents") (description @@ -3109,14 +3131,14 @@ interface.") (define-public r-trend (package (name "r-trend") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "trend" version)) (sha256 (base32 - "06yifqbsvxbmk5gld4z2nnyhf59v8ks5xjwacmb25mv9r6bn388b")))) + "1bd567n15k2vpmgbx02584k5kglrc58mlb5kgd07wdss3knpa48q")))) (build-system r-build-system) (propagated-inputs `(("r-extradistr" ,r-extradistr))) @@ -4615,3 +4637,310 @@ matches version and feature constraints.") write shebang scripts that gracefully accept positional and optional arguments and automatically generate usage notices.") (license license:gpl2+))) + +(define-public r-hash + (package + (name "r-hash") + (version "2.2.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "hash" version)) + (sha256 + (base32 + "0mkx59bmni3b283znvbndnkbar85fzavzdfgmwrhskidsqcz34yz")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/hash/") + (synopsis "Implementation of hash/associated arrays/dictionaries") + (description + "This package implements a data structure similar to hashes in Perl and +dictionaries in Python but with a purposefully R flavor. For objects of +appreciable size, access using hashes outperforms native named lists and +vectors.") + (license license:gpl2+))) + +(define-public r-orddom + (package + (name "r-orddom") + (version "3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "orddom" version)) + (sha256 + (base32 + "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh")))) + (build-system r-build-system) + (propagated-inputs `(("r-psych" ,r-psych))) + (home-page "https://cran.r-project.org/web/packages/orddom/") + (synopsis "Ordinal dominance statistics") + (description + "This package provides tools to compute ordinal, statistics and effect +sizes as an alternative to mean comparison: Cliff's delta or success rate +difference (SRD), Vargha and Delaney's A or the Area Under a Receiver +Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's +Common Language Effect Size (CLES) or Grissom & Kim's Probability of +Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover, +comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of +Group (Non-)Overlap considerations.") + (license license:gpl2))) + +(define-public r-doby + (package + (name "r-doby") + (version "4.6-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "doBy" version)) + (sha256 + (base32 + "1y02awzid23bxz8hx6j8pxd6i7jaq8pdw3k60rag8y6m69incrw5")))) + (properties `((upstream-name . "doBy"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-magrittr" ,r-magrittr) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-plyr" ,r-plyr))) + (home-page "http://people.math.aau.dk/~sorenh/software/doBy/") + (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities") + (description + "This package contains: + +@itemize +@item facilities for working with grouped data: @code{do} + something to data stratified @code{by} some variables. +@item implementations of least-squares means, general linear contrasts, and +@item miscellaneous other utilities. +@end itemize\n") + (license license:gpl2+))) + +(define-public r-refgenome + (package + (name "r-refgenome") + (version "1.7.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "refGenome" version)) + (sha256 + (base32 + "15p0ra2p1pwhy5ixbhsz1g79c5sc2aap4i4c8kil0m2syg9y45sn")))) + (properties `((upstream-name . "refGenome"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dbi" ,r-dbi) + ("r-doby" ,r-doby) + ("r-rsqlite" ,r-rsqlite))) + (home-page "https://cran.r-project.org/web/packages/refGenome/") + (synopsis + "Gene and splice site annotation using annotation data from Ensembl and UCSC") + (description + "This package contains functionality for importing and managing of +downloaded genome annotation data from the Ensembl genome browser (European +Bioinformatics Institute) and from the UCSC genome browser (University of +California, Santa Cruz) and annotation routines for genomic positions and +splice site positions.") + (license license:gpl2))) + +(define-public r-basix + (package + (name "r-basix") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "BASIX" version)) + (sha256 + (base32 + "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id")))) + (properties `((upstream-name . "BASIX"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/BASIX/") + (synopsis "Efficient C/C++ toolset for R") + (description + "BASIX provides some efficient C/C++ implementations of native R +procedures to speed up calculations in R.") + (license license:gpl2))) + +(define-public r-blockfest + (package + (name "r-blockfest") + (version "1.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "BlockFeST" version)) + (sha256 + (base32 + "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5")))) + (properties `((upstream-name . "BlockFeST"))) + (build-system r-build-system) + (propagated-inputs `(("r-basix" ,r-basix))) + (home-page "https://cran.r-project.org/web/packages/BlockFeST/") + (synopsis "Bayesian calculation of region-specific fixation index") + (description + "This package provides an R implementation of an extension of the +BayeScan software for codominant markers, adding the option to group +individual SNPs into pre-defined blocks. A typical application of this new +approach is the identification of genomic regions, genes, or gene sets +containing one or more SNPs that evolved under directional selection.") + (license license:gpl2))) + +(define-public r-proc + (package + (name "r-proc") + (version "1.12.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "pROC" version)) + (sha256 + (base32 + "05ad69a6fxy9k903cw3h4q59ch2jv6qfg9yjdbw3cgiiazcafrlj")))) + (properties `((upstream-name . "pROC"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-plyr" ,r-plyr) + ("r-rcpp" ,r-rcpp))) + (home-page "http://expasy.org/tools/pROC/") + (synopsis "Display and analyze ROC curves") + (description + "This package provides tools for visualizing, smoothing and comparing +receiver operating characteristic (ROC curves). The area under the +curve (AUC) can be compared with statistical tests based on U-statistics or +bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.") + (license license:gpl3+))) + +(define-public r-rootsolve + (package + (name "r-rootsolve") + (version "1.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "rootSolve" version)) + (sha256 + (base32 + "08ic6ggcc5dw4nv9xsqkm3vnvswmxyhnqnv1rdjv1h2gy1ivpcq8")))) + (properties `((upstream-name . "rootSolve"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/rootSolve/") + (synopsis "Tools for the analysis of ordinary differential equations") + (description + "This package provides routines to find the root of nonlinear functions, +and to perform steady-state and equilibrium analysis of @dfn{ordinary +differential equations} (ODE). It includes routines that: + +@enumerate +@item generate gradient and jacobian matrices (full and banded), +@item find roots of non-linear equations by the Newton-Raphson method, +@item estimate steady-state conditions of a system of (differential) equations + in full, banded or sparse form, using the Newton-Raphson method, or by + dynamically running, +@item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D, + and 3-D partial differential equations, that have been converted to ordinary + differential equations by numerical differencing (using the method-of-lines + approach). +@end enumerate\n") + (license license:gpl2+))) + +(define-public r-abcanalysis + (package + (name "r-abcanalysis") + (version "1.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ABCanalysis" version)) + (sha256 + (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi")))) + (properties `((upstream-name . "ABCanalysis"))) + (build-system r-build-system) + (propagated-inputs `(("r-plotrix" ,r-plotrix))) + (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/") + (synopsis "Computed ABC Analysis") + (description + "Multivariate data sets often differ in several factors or derived statistical +parameters, which have to be selected for a valid interpretation. Basing this +selection on traditional statistical limits leads occasionally to the perception +of losing information from a data set. This package provides tools to calculate +these limits on the basis of the mathematical properties of the distribution of +the analyzed items.") + (license license:gpl3))) + +(define-public r-slam + (package + (name "r-slam") + (version "0.1-43") + (source + (origin + (method url-fetch) + (uri (cran-uri "slam" version)) + (sha256 + (base32 "0hy4qzngcgafxxr6ld7n9a9wy979ji998gpcc32vidwyab66dj5h")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/slam/") + (synopsis "Sparse lightweight arrays and matrices") + (description + "This package contains data structures and algorithms for sparse arrays and matrices, +based on index arrays and simple triplet representations, respectively.") + (license license:gpl2))) + +(define-public r-manipulatewidget + (package + (name "r-manipulatewidget") + (version "0.10.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "manipulateWidget" version)) + (sha256 + (base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x")))) + (properties + `((upstream-name . "manipulateWidget"))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-codetools" ,r-codetools) + ("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-knitr" ,r-knitr) + ("r-miniui" ,r-miniui) + ("r-shiny" ,r-shiny) + ("r-webshot" ,r-webshot))) + (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/") + (synopsis "Add even more interactivity to interactive charts") + (description + "This package lets you create in just a few lines of R code a nice user interface to +modify the data or the graphical parameters of one or multiple interactive +charts. It is useful to quickly explore visually some data or for package +developers to generate user interfaces easy to maintain.") + (license license:gpl2+))) + +(define-public r-a3 + (package + (name "r-a3") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "A3" version)) + (sha256 + (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw")))) + (properties `((upstream-name . "A3"))) + (build-system r-build-system) + (propagated-inputs + `(("r-pbapply" ,r-pbapply) + ("r-xtable" ,r-xtable))) + (home-page "https://cran.r-project.org/web/packages/A3/") + (synopsis "Error metrics for predictive models") + (description + "This package supplies tools for tabulating and analyzing the results of predictive +models. The methods employed are applicable to virtually any predictive model +and make comparisons between different methodologies straightforward.") + (license license:gpl2+))) |