diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 238 |
1 files changed, 237 insertions, 1 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4ad1bfa760..7aa3ebde97 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -104,6 +104,7 @@ #:use-module (gnu packages python-xyz) #:use-module (gnu packages sqlite) #:use-module (gnu packages statistics) + #:use-module (gnu packages tbb) #:use-module (gnu packages tcl) #:use-module (gnu packages tex) #:use-module (gnu packages textutils) @@ -115,6 +116,35 @@ #:use-module (gnu packages xml) #:use-module (gnu packages xorg)) +(define-public r-aer + (package + (name "r-aer") + (version "1.2-10") + (source (origin + (method url-fetch) + (uri (cran-uri "AER" version)) + (sha256 + (base32 + "1p6vxr0220lim5i4gwsvphqrfd65zbs8h3qydz4gipca9asmy2k5")))) + (properties `((upstream-name . "AER"))) + (build-system r-build-system) + (propagated-inputs + (list r-car + r-formula + r-lmtest + r-sandwich + r-survival + r-zoo)) + (home-page "https://cran.r-project.org/package=AER") + (synopsis "Applied econometrics with R") + (description + "This package provides functions, data sets, examples, demos, and +vignettes for the book Christian Kleiber and Achim Zeileis (2008), Applied +Econometrics with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2. (See +the vignette \"AER\" for a package overview.)") + ;; Either version of the GPL + (license (list license:gpl2 license:gpl3)))) + (define-public r-afpt (package (name "r-afpt") @@ -392,6 +422,28 @@ Gaussian quadrature for a numerical solution.") Distance (EMD).") (license license:expat))) +(define-public r-glmpca + (package + (name "r-glmpca") + (version "0.2.0") + (source (origin + (method url-fetch) + (uri (cran-uri "glmpca" version)) + (sha256 + (base32 + "02xjf0gg52925hw9nw2j0znfmzfzfwbv0fxjl9d2fy9j63drr2h4")))) + (properties `((upstream-name . "glmpca"))) + (build-system r-build-system) + (propagated-inputs (list r-mass)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/willtownes/glmpca") + (synopsis "Dimension Reduction of Non-Normally Distributed Data") + (description + "This package implements a generalized version of principal components +analysis (GLM-PCA) for dimension reduction of non-normally distributed data +such as counts or binary matrices.") + (license license:lgpl3+))) + (define-public r-googledrive (package (name "r-googledrive") @@ -748,6 +800,42 @@ similar rank-based tests for equal probability distributions due to Neuhauser WebAssembly engine.") (license license:expat))) +(define-public r-rvenn + (package + (name "r-rvenn") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "RVenn" version)) + (sha256 + (base32 + "016m00xv59lkwm2is32v5nr4lw5a1ymdnz34r3ffflcv9bfrc6n4")))) + (properties `((upstream-name . "RVenn"))) + (build-system r-build-system) + (propagated-inputs + (list r-ggforce + r-ggplot2 + r-magrittr + r-pheatmap + r-purrr + r-rlang + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=RVenn") + (synopsis "Set operations for many sets") + (description + "The base functions for set operations in @code{R} can be used for only two +sets. This package @code{RVenn} provides functions for dealing with multiple sets. +It uses @code{purr} to find the union, intersection and difference of three or +more sets. This package also provides functions for pairwise set operations among +several sets. Further, based on @code{ggplot2} and @code{ggforce}, a Venn diagram +can be drawn for two or three sets. For bigger data sets, a clustered heatmap +showing the presence or absence of the elements of the sets can be drawn based on +the @code{pheatmap} package. Finally, enrichment test can be applied to two sets +whether an overlap is statistically significant or not.") + (license license:gpl3))) + (define-public r-dot (package (name "r-dot") @@ -1060,6 +1148,65 @@ the reasonable size limit without losing vector properties of the scale-sensitive information.") (license license:expat))) +(define-public r-ggvenn + (package + (name "r-ggvenn") + (version "0.1.9") + (source (origin + (method url-fetch) + (uri (cran-uri "ggvenn" version)) + (sha256 + (base32 + "0bm52j3idchignp6nrw7c76jlbfkjf5zng258957vq019vx9qxrq")))) + (properties `((upstream-name . "ggvenn"))) + (build-system r-build-system) + (propagated-inputs (list r-dplyr r-ggplot2)) + (home-page "https://cran.r-project.org/package=ggvenn") + (synopsis "Draw Venn diagram with ggplot2") + (description + "This package offers an easy to use way to draw a Venn diagram with +@code{ggplot2}.") + (license license:expat))) + +(define-public r-ggvenndiagram + (package + (name "r-ggvenndiagram") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggVennDiagram" version)) + (sha256 + (base32 + "1mjs488npnxd53nsw936iw2vzv7z38h8d02pm4lwrz4i83jg3www")))) + (properties `((upstream-name . "ggVennDiagram"))) + (build-system r-build-system) + (propagated-inputs + (list r-dplyr + r-ggplot2 + r-magrittr + r-plotly + r-purrr + r-rvenn + r-sf + r-stringr + r-tibble)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/gaospecial/ggVennDiagram") + (synopsis "Implementention of the Venn diagram using ggplot2") + (description + "This package implements easy-to-use functions to generate 2-7 sets Venn +plot in publication quality. @code{ggVennDiagram} plot Venn using +well-defined geometry dataset and @code{ggplot2}. The shapes of 2-4 sets Venn +use circles and ellipses, while the shapes of 4-7 sets Venn use irregular +polygons (4 has both forms), which are developed and imported from another +package @code{venn}. We provide internal functions to integrate shape data +with user provided sets data, and calculated the geometry of every +regions/intersections of them, then separately plot Venn in three components: +set edges, set labels, and regions. From version 1.0, it is possible to +customize these components as you demand in ordinary @code{ggplot2} grammar.") + (license license:gpl3))) + (define-public r-lmds (package (name "r-lmds") @@ -1482,6 +1629,28 @@ qualitative palettes with many (20-30 or more) colors. See Coombes and colleagues (2019) @url{https://doi:10.18637/jss.v090.c01}.") (license license:asl2.0))) +(define-public r-polylabelr + (package + (name "r-polylabelr") + (version "0.2.0") + (source (origin + (method url-fetch) + (uri (cran-uri "polylabelr" version)) + (sha256 + (base32 + "01b2v0l5g8nxwbd6nwqv8ahypgh6gfhd4qabg75brlj7z1iyfzf2")))) + (properties `((upstream-name . "polylabelr"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp)) + (home-page "https://github.com/jolars/polylabelr") + (synopsis "Finding pole of inaccessibility (visual center) of a polygon") + (description + "This package provides a wrapper around the @code{C++} library @code{ +polylabel} from @code{Mapbox}, providing an efficient routine for finding the +approximate pole of inaccessibility of a polygon, which usually serves as an +excellent candidate for labeling of a polygon.") + (license license:expat))) + (define-public r-poorman (package (name "r-poorman") @@ -3512,6 +3681,24 @@ coordinates.") @end enumerate\n") (license license:gpl2+))) +(define-public r-gensa + (package + (name "r-gensa") + (version "1.1.7") + (source (origin + (method url-fetch) + (uri (cran-uri "GenSA" version)) + (sha256 + (base32 + "03xqwxm7v7rnihx730a4p65dfwhjh4345r3d78y0qxxplk8d76cx")))) + (properties `((upstream-name . "GenSA"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=GenSA") + (synopsis "Generalized simulated annealing") + (description "This package performs search for the global minimum of a very +complex non-linear objective function with a very large number of optima.") + (license license:gpl2))) + (define-public r-geosphere (package (name "r-geosphere") @@ -6393,6 +6580,27 @@ Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization of Eigenmatrices} (JADE).") (license license:gpl2+))) +(define-public r-ips + (package + (name "r-ips") + (version "0.0.11") + (source (origin + (method url-fetch) + (uri (cran-uri "ips" version)) + (sha256 + (base32 + "02jxanfhsjrabj33nwjv71vdc87hiyzikyqrfdj9ix6dky6lm199")))) + (properties `((upstream-name . "ips"))) + (build-system r-build-system) + (propagated-inputs (list r-ape r-phangorn r-plyr r-seqinr r-xml)) + (home-page "https://cran.r-project.org/package=ips") + (synopsis "Interfaces to phylogenetic software in R") + (description + "This package provides functions that wrap popular phylogenetic software +for sequence alignment, masking of sequence alignments, and estimation of +phylogenies and ancestral character states.") + (license license:gpl3))) + (define-public r-dtw (package (name "r-dtw") @@ -9216,6 +9424,14 @@ always locate the files relative to your project root.") (base32 "0b1szzsqyc8wcfpkn5517bb1ds064vs2hky71my3p74kfngay991")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'build-reproducibly + (lambda _ + (setenv "PYTHONHASHSEED" "0") + (setenv "PYTHONDONTWRITEBYTECODE" "1")))))) (inputs (list python)) (propagated-inputs (list r-here @@ -13657,9 +13873,20 @@ package provides a minimal R interface by relying on the Rcpp package.") (uri (cran-uri "RcppParallel" version)) (sha256 (base32 - "1sn211ajlb1p12sglxqns175rg078yvww268m8cp0vvd7cmk55k3")))) + "1sn211ajlb1p12sglxqns175rg078yvww268m8cp0vvd7cmk55k3")) + (modules '((guix build utils))) + (snippet + '(delete-file-recursively "src/tbb/")))) (properties `((upstream-name . "RcppParallel"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'use-system-tbb + (lambda* (#:key inputs #:allow-other-keys) + (setenv "TBB_ROOT" (assoc-ref inputs "tbb"))))))) + (inputs (list tbb-2020)) (home-page "https://rcppcore.github.io/RcppParallel/") (synopsis "Parallel programming tools for Rcpp") (description @@ -19040,6 +19267,15 @@ packages with Rcpp.") (base32 "17znizh4yabh2zs9mzyr0sl6p0pw49961i61br7cl1b7v9sza18q")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'build-reproducibly + (lambda _ + (substitute* "R/aaa.R" + (("BASEDATETIME <- Sys.time.*") + "BASEDATETIME <- structure(0, class = c(\"POSIXct\", \"POSIXt\"))\n"))))))) (propagated-inputs (list r-farver r-magrittr r-rcpp r-rlang)) (home-page "https://github.com/thomasp85/tweenr") |