diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 255 |
1 files changed, 254 insertions, 1 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index dbc2b4614d..8277026c32 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 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org> @@ -62,6 +62,7 @@ #:use-module (gnu packages imagemagick) #:use-module (gnu packages java) #:use-module (gnu packages javascript) + #:use-module (gnu packages lisp-xyz) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) @@ -12574,6 +12575,12 @@ running IRkernel session.") "--name" "ir" "--prefix" out (string-append out "/site-library/IRkernel/kernelspec")) + ;; Record the absolute file name of the 'R' executable in + ;; 'kernel.json'. + (substitute* (string-append out "/share/jupyter" + "/kernels/ir/kernel.json") + (("\\[\"R\",") + (string-append "[\"" (which "R") "\","))) #t)))))) (inputs `(("jupyter" ,jupyter))) @@ -12583,6 +12590,8 @@ running IRkernel session.") ("r-evaluate" ,r-evaluate) ("r-irdisplay" ,r-irdisplay) ("r-jsonlite" ,r-jsonlite) + ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel) + ("r-minimal" ,r-minimal) ("r-pbdzmq" ,r-pbdzmq) ("r-repr" ,r-repr) ("r-uuid" ,r-uuid))) @@ -18988,3 +18997,247 @@ algorithm to identify key players, and Valente's bridging metric. The betweenness, Key Players, and bridging implementations are parallelized with OpenMP.") (license license:gpl2))) + +(define-public r-emplik + (package + (name "r-emplik") + (version "1.0-4.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "emplik" version)) + (sha256 + (base32 + "1g4hz85bvw29c77zs0ig487z92jjl682vv457x81l077h0psvk7c")))) + (properties `((upstream-name . "emplik"))) + (build-system r-build-system) + (propagated-inputs + `(("r-quantreg" ,r-quantreg))) + (home-page "http://www.ms.uky.edu/~mai/EmpLik.html") + (synopsis "Empirical likelihood ratio for censored/truncated data") + (description + "This package provides empirical likelihood ratio tests for +means/quantiles/hazards from possibly censored and/or truncated data. It also +does regression.") + (license license:gpl2+))) + +(define-public r-imputeyn + (package + (name "r-imputeyn") + (version "1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "imputeYn" version)) + (sha256 + (base32 + "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs")))) + (properties `((upstream-name . "imputeYn"))) + (build-system r-build-system) + (propagated-inputs + `(("r-boot" ,r-boot) + ("r-emplik" ,r-emplik) + ("r-mvtnorm" ,r-mvtnorm) + ("r-quadprog" ,r-quadprog) + ("r-survival" ,r-survival))) + (home-page "https://cran.r-project.org/web/packages/imputeYn/") + (synopsis "Impute last largest censored observation under weighted least squares") + (description + "This package allows for the imputation of the last largest censored +observantions. This method brings less bias and more efficient estimates for +AFT models.") + (license license:gpl2))) + +(define-public r-adapenetclass + (package + (name "r-adapenetclass") + (version "1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "AdapEnetClass" version)) + (sha256 + (base32 + "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc")))) + (properties `((upstream-name . "AdapEnetClass"))) + (build-system r-build-system) + (propagated-inputs + `(("r-glmnet" ,r-glmnet) + ("r-imputeyn" ,r-imputeyn) + ("r-lars" ,r-lars) + ("r-quadprog" ,r-quadprog))) + (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/") + (synopsis "Class of adaptive elastic net methods for censored data") + (description + "This package provides methods for variable selection for AFT models.") + (license license:gpl2))) + +(define-public r-flock + (package + (name "r-flock") + (version "0.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "flock" version)) + (sha256 + (base32 + "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7")))) + (properties `((upstream-name . "flock"))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/flock/") + (synopsis "Process synchronization using file locks") + (description + "This package implements synchronization between R processes (spawned by +using the @code{parallel} package for instance) using file locks. It supports +both exclusive and shared locking.") + (license license:asl2.0))) + +(define-public r-archivist + (package + (name "r-archivist") + (version "2.3.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "archivist" version)) + (sha256 + (base32 + "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7")))) + (properties `((upstream-name . "archivist"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dbi" ,r-dbi) + ("r-digest" ,r-digest) + ("r-flock" ,r-flock) + ("r-httr" ,r-httr) + ("r-lubridate" ,r-lubridate) + ("r-magrittr" ,r-magrittr) + ("r-rcurl" ,r-rcurl) + ("r-rsqlite" ,r-rsqlite))) + (home-page "https://pbiecek.github.io/archivist/") + (synopsis "Tools for storing, restoring and searching for R objects") + (description + "Data exploration and modelling is a process in which a lot of data +artifacts are produced. Artifacts like: subsets, data aggregates, plots, +statistical models, different versions of data sets and different versions of +results. Archivist helps to store and manage artifacts created in R. It +allows you to store selected artifacts as binary files together with their +metadata and relations. Archivist allows sharing artifacts with others. It +can look for already created artifacts by using its class, name, date of the +creation or other properties. It also makes it easy to restore such +artifacts.") + (license license:gpl2))) + +(define-public r-versions + (package + (name "r-versions") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "versions" version)) + (sha256 + (base32 + "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd")))) + (properties `((upstream-name . "versions"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/versions/") + (synopsis "Query and install specific versions of CRAN packages") + (description + "This package allows you to install specified versions of R packages +hosted on CRAN and provides functions to list available versions and the +versions of currently installed packages.") + (license license:bsd-3))) + +(define-public r-adapr + (package + (name "r-adapr") + (version "2.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "adapr" version)) + (sha256 + (base32 + "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw")))) + (properties `((upstream-name . "adapr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-archivist" ,r-archivist) + ("r-devtools" ,r-devtools) + ("r-digest" ,r-digest) + ("r-doparallel" ,r-doparallel) + ("r-gdata" ,r-gdata) + ("r-ggplot2" ,r-ggplot2) + ("r-git2r" ,r-git2r) + ("r-igraph" ,r-igraph) + ("r-knitr" ,r-knitr) + ("r-plotly" ,r-plotly) + ("r-plyr" ,r-plyr) + ("r-rmarkdown" ,r-rmarkdown) + ("r-shiny" ,r-shiny) + ("r-shinydashboard" ,r-shinydashboard) + ("r-versions" ,r-versions))) + (home-page "https://cran.r-project.org/web/packages/adapr/") + (synopsis "Implementation of an accountable data analysis process") + (description + "This package tracks reading and writing within R scripts that are +organized into a directed acyclic graph. It contains an interactive Shiny +application @code{adaprApp()}. It uses Git and file hashes to track version +histories of inputs and outputs.") + (license license:lgpl2.0))) + +(define-public r-adapsamp + (package + (name "r-adapsamp") + (version "1.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "AdapSamp" version)) + (sha256 + (base32 + "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis")))) + (properties `((upstream-name . "AdapSamp"))) + (build-system r-build-system) + (propagated-inputs `(("r-pracma" ,r-pracma))) + (home-page "https://cran.r-project.org/web/packages/AdapSamp/") + (synopsis "Adaptive sampling algorithms") + (description + "For distributions whose probability density functions are log-concave, +the adaptive rejection sampling algorithm can be used to build envelope +functions for sampling. For others, the modified adaptive rejection sampling +algorithm, the concave-convex adaptive rejection sampling algorithm, and the +adaptive slice sampling algorithm can be used. This R package mainly includes +these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and +@code{rASS()}. These functions can realize sampling based on the algorithms +above.") + (license license:gpl2))) + +(define-public r-adaptalint + (package + (name "r-adaptalint") + (version "0.2.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "adaptalint" version)) + (sha256 + (base32 + "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf")))) + (properties `((upstream-name . "adaptalint"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-lintr" ,r-lintr) + ("r-purrr" ,r-purrr))) + (home-page "https://cran.r-project.org/web/packages/adaptalint/") + (synopsis "Check R code style") + (description + "This package provides tools to infer the code style (which style rules +are followed and which ones are not) from one package and use it to check +another. This makes it easier to find and correct the most important problems +first.") + (license license:gpl3))) |