diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 327 |
1 files changed, 299 insertions, 28 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5d4af23227..aa5bdc958d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -30,6 +30,7 @@ #:use-module (guix download) #:use-module (guix utils) #:use-module (guix build-system r) + #:use-module (gnu packages compression) #:use-module (gnu packages gcc) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) @@ -556,14 +557,14 @@ ellipses, circles, cylinders, arrows, ...") (define-public r-globaloptions (package (name "r-globaloptions") - (version "0.0.13") + (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "GlobalOptions" version)) (sha256 (base32 - "04jvha0mafslqz5nr99xjylg9n2x31gj9v4mgyg7qcmfwpqyw3ch")))) + "1wlyqz1yhmhjwslrd7q69jbd9vsbjkjfc01g60kl3cdpyr8hlyjn")))) (properties `((upstream-name . "GlobalOptions"))) (build-system r-build-system) (home-page "https://github.com/jokergoo/GlobalOptions") @@ -576,14 +577,14 @@ validation and filtering on the values, making options invisible or private.") (define-public r-circlize (package (name "r-circlize") - (version "0.4.3") + (version "0.4.4") (source (origin (method url-fetch) (uri (cran-uri "circlize" version)) (sha256 (base32 - "0pg947gkryygikfbv6admx8gsg02b6g219j6a1sdnqij2908yxna")))) + "1l28maiqi549z191srncxgabx5fnvf0lld7smzwfd3vr5cx8nqww")))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace) @@ -681,14 +682,14 @@ compare different dendrograms to one another.") (define-public r-getoptlong (package (name "r-getoptlong") - (version "0.1.6") + (version "0.1.7") (source (origin (method url-fetch) (uri (cran-uri "GetoptLong" version)) (sha256 (base32 - "1d98gcvlvp9nz5lbnzr0kkpc2hbkx74hlhrnybqhg1gdwc3g09pm")))) + "1fl3w2n602ldybc5qj7qw4xmzzb804bsjkqwf6dswzj0vf0qiadr")))) (properties `((upstream-name . "GetoptLong"))) (build-system r-build-system) (inputs @@ -896,14 +897,14 @@ most popular ones.") (define-public r-sp (package (name "r-sp") - (version "1.2-7") + (version "1.3-1") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 (base32 - "0q04yfgyjannsrzl0ppwcv0simrxrrbx2iz5mzaafc5x38zf0q3d")))) + "17xm1ig80p9wc860hm3bgishz6lj9fxgwqidj7rkbk4ap99qp62p")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -1009,14 +1010,14 @@ SpatialVx.") (define-public r-extremes (package (name "r-extremes") - (version "2.0-8") + (version "2.0-9") (source (origin (method url-fetch) (uri (cran-uri "extRemes" version)) (sha256 (base32 - "0pnpib3g2r9x8hfqhvq23j8m3jh62lp28ipnqir5yadnzv850gfm")))) + "0cpvcajk9xyy7662nqkyx333vrxpwsc5nmv0bfnhsbgijz5y0hvm")))) (properties `((upstream-name . "extRemes"))) (build-system r-build-system) (propagated-inputs @@ -1595,14 +1596,14 @@ Core algorithms are executed in parallel on systems supporting OpenMP.") (define-public r-rcpproll (package (name "r-rcpproll") - (version "0.2.2") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "RcppRoll" version)) (sha256 (base32 - "19xzvxym8zbighndygkq4imfwc0abh4hqyq3qrr8aakyd096iisi")))) + "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb")))) (properties `((upstream-name . "RcppRoll"))) (build-system r-build-system) (propagated-inputs @@ -1822,14 +1823,14 @@ color labels, layout, etc.") (define-public r-stringdist (package (name "r-stringdist") - (version "0.9.4.7") + (version "0.9.5.1") (source (origin (method url-fetch) (uri (cran-uri "stringdist" version)) (sha256 (base32 - "1qg80wmcrpkba9njvgjdg15bgw7ddks40kkfh5x61as9lhchy4i4")))) + "0gap1g9xwhp0zxqsznkc2carpvi80z03prr4q8m528684lznx2xa")))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/stringdist") (synopsis "Approximate string matching and string distance functions") @@ -2718,17 +2719,19 @@ supports arbitrary vertex/edge/graph attributes.") (define-public r-statnet-common (package (name "r-statnet-common") - (version "4.0.0") + (version "4.1.2") (source (origin (method url-fetch) (uri (cran-uri "statnet.common" version)) (sha256 (base32 - "0yw6l5b4qv0jqlg4zyczas7m12a5pyqghs6ydxy2f6v6vxkijvi0")))) + "0h3g687214rlycca0fjrpy1lqbqsrginxqhmhl2mb2jinqqxcfgd")))) (properties `((upstream-name . "statnet.common"))) (build-system r-build-system) + (propagated-inputs + `(("r-coda" ,r-coda))) (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 @@ -2971,14 +2974,14 @@ Cryer and Kung-Sik Chan.") (define-public r-extradistr (package (name "r-extradistr") - (version "1.8.8") + (version "1.8.9") (source (origin (method url-fetch) (uri (cran-uri "extraDistr" version)) (sha256 (base32 - "0ywn4qwnamv36l1hw27l9y5kh3v6ha5781wsv2bz6szqjgg7kdb3")))) + "1fg8vjpal33y51iqzglk1yvy46d7js0l0wfbdy698lq8a06hq19p")))) (properties `((upstream-name . "extraDistr"))) (build-system r-build-system) (propagated-inputs @@ -3041,14 +3044,14 @@ applied econometric analysis.") (define-public r-cubature (package (name "r-cubature") - (version "1.3-11") + (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "cubature" version)) (sha256 (base32 - "06f6gsvbb732p80r6hxvzh4ik546icxfvx21dyh65ypmw3kgm64k")))) + "1hd23b8v2kpqp5gr0va8p2q7j8w9rik6ks7zrr4b8mb2mwrakk74")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) @@ -3324,14 +3327,14 @@ environment within Shiny.") (define-public r-radiant-data (package (name "r-radiant-data") - (version "0.8.1") + (version "0.9.5") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 - "1ylina1jlrmvjkj8pwg0ip5jv1038vnzyckmf542xl7g11x8rvw1")) + "0mbxfqn79nphii4hb6kxl2wc0w0ra16y378rp2yw9a9926zdb7mb")) (modules '((guix build utils))) (snippet '(begin @@ -3347,6 +3350,7 @@ environment within Shiny.") ("r-curl" ,r-curl) ("r-dplyr" ,r-dplyr) ("r-dt" ,r-dt) + ("r-glue" ,r-glue) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-import" ,r-import) @@ -3355,16 +3359,19 @@ environment within Shiny.") ("r-lubridate" ,r-lubridate) ("r-magrittr" ,r-magrittr) ("r-markdown" ,r-markdown) - ("r-pryr" ,r-pryr) + ("r-plotly" ,r-plotly) ("r-psych" ,r-psych) ("r-readr" ,r-readr) + ("r-readxl" ,r-readxl) + ("r-rlang" ,r-rlang) ("r-rmarkdown" ,r-rmarkdown) ("r-rstudioapi" ,r-rstudioapi) ("r-scales" ,r-scales) ("r-shiny" ,r-shiny) ("r-shinyace" ,r-shinyace) ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + ("r-tidyr" ,r-tidyr) + ("r-writexl" ,r-writexl))) (home-page "https://github.com/radiant-rstats/radiant.data") (synopsis "Data menu for Radiant: business analytics using R and Shiny") (description @@ -3915,14 +3922,14 @@ exchanging spatial objects with other R packages.") (define-public r-later (package (name "r-later") - (version "0.7.2") + (version "0.7.3") (source (origin (method url-fetch) (uri (cran-uri "later" version)) (sha256 (base32 - "0l5ln7sjyi2rj7bx8iamxykqlfarv05zb9882ikizppb1cr1hgyw")))) + "04j2phymxgkk4hv9pfa5w3s98w5d7fvm11blrdhxmray4n618msw")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) @@ -4125,14 +4132,14 @@ obtain a better initial configuration in non-metric MDS.") (define-public r-reticulate (package (name "r-reticulate") - (version "1.7") + (version "1.8") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "1ghhc4hbmwpp79ilbdbshynhs61i8sv8z6p1al04jy7ij0lcglxy")))) + "0zwb4ikf021nw7axdn7qlr6bq4xkph3anfy314idkspy1iil4nmr")))) (build-system r-build-system) (inputs `(("python" ,python))) (propagated-inputs @@ -4190,3 +4197,267 @@ generating multiple logo plots, and aiding the visualisation with annotations. Sequence logos can easily be combined with other ggplot2 plots.") ;; Unspecified version of the LGPL. (license license:lgpl3+))) + +(define-public r-ggsci + (package + (name "r-ggsci") + (version "2.9") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggsci" version)) + (sha256 + (base32 + "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-scales" ,r-scales))) + (home-page "https://nanx.me/ggsci/") + (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2") + (description + "This package provides a collection of ggplot2 color palettes inspired by +plots in scientific journals, data visualization libraries, science fiction +movies, and TV shows.") + (license license:gpl3))) + +(define-public r-ggsignif + (package + (name "r-ggsignif") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggsignif" version)) + (sha256 + (base32 + "1rn58d7pb3axk6chiihryykrzw76adaa2yiafq4d0j6qbhax78f7")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2))) + (home-page "https://github.com/const-ae/ggsignif") + (synopsis "Significance brackets for ggplot2") + (description + "Enrich your ggplots with group-wise comparisons. This package provides +an easy way to indicate if two groups are significantly different. Commonly +this is shown by a bracket on top connecting the groups of interest which +itself is annotated with the level of significance. The package provides a +single layer that takes the groups for comparison and the test as arguments +and adds the annotation to the plot.") + (license license:gpl3))) + +(define-public r-ggpubr + (package + (name "r-ggpubr") + (version "0.1.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggpubr" version)) + (sha256 + (base32 + "0mvw215bj887958p34f0dzlrb8mgyfcz9b5zvsschvbhamqinqna")))) + (build-system r-build-system) + (propagated-inputs + `(("r-cowplot" ,r-cowplot) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-ggsci" ,r-ggsci) + ("r-ggsignif" ,r-ggsignif) + ("r-gridextra" ,r-gridextra) + ("r-magrittr" ,r-magrittr) + ("r-purrr" ,r-purrr) + ("r-scales" ,r-scales) + ("r-tidyr" ,r-tidyr))) + (home-page "http://www.sthda.com/english/rpkgs/ggpubr") + (synopsis "ggplot2-based publication-ready plots") + (description + "The ggplot2 package is an excellent and flexible package for elegant +data visualization in R. However the default generated plots require some +formatting before we can send them for publication. The ggpubr package +provides some easy-to-use functions for creating and customizing ggplot2-based +publication-ready plots.") + (license license:gpl2))) + +(define-public r-ellipse + (package + (name "r-ellipse") + (version "0.4.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ellipse" version)) + (sha256 + (base32 + "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/ellipse/") + (synopsis "Functions for drawing ellipses and ellipse-like confidence regions") + (description + "This package contains various routines for drawing ellipses and +ellipse-like confidence regions, implementing the plots described in Murdoch +and Chow (1996), A graphical display of large correlation matrices, The +American Statistician 50, 178-180. There are also routines implementing the +profile plots described in Bates and Watts (1988), Nonlinear Regression +Analysis and its Applications.") + (license license:gpl2+))) + +(define-public r-flashclust + (package + (name "r-flashclust") + (version "1.01-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "flashClust" version)) + (sha256 + (base32 + "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8")))) + (properties `((upstream-name . "flashClust"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/flashClust/") + (synopsis "Implementation of optimal hierarchical clustering") + (description + "This package provides a fast implementation of hierarchical +clustering.") + (license license:gpl2+))) + +(define-public r-factominer + (package + (name "r-factominer") + (version "1.41") + (source + (origin + (method url-fetch) + (uri (cran-uri "FactoMineR" version)) + (sha256 + (base32 + "1h20hydav6l2b7bngqw1av4l5rrh0wk58nhailga1f4qw9lrv259")))) + (properties `((upstream-name . "FactoMineR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-car" ,r-car) + ("r-cluster" ,r-cluster) + ("r-ellipse" ,r-ellipse) + ("r-flashclust" ,r-flashclust) + ("r-lattice" ,r-lattice) + ("r-leaps" ,r-leaps) + ("r-mass" ,r-mass) + ("r-scatterplot3d" ,r-scatterplot3d))) + (home-page "http://factominer.free.fr") + (synopsis "Multivariate exploratory data analysis and data mining") + (description + "This package provides exploratory data analysis methods to summarize, +visualize and describe datasets. The main principal component methods are +available, those with the largest potential in terms of applications: +principal component analysis (PCA) when variables are quantitative, +correspondence analysis (CA) and multiple correspondence analysis (MCA) when +variables are categorical, Multiple Factor Analysis when variables are +structured in groups, etc. and hierarchical cluster analysis.") + (license license:gpl2+))) + +(define-public r-factoextra + (package + (name "r-factoextra") + (version "1.0.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "factoextra" version)) + (sha256 + (base32 + "1l6m8k7qhdw8ndar8nhmym0lfyd1i2iszl1cicjax0vq23ss6xw1")))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-cluster" ,r-cluster) + ("r-dendextend" ,r-dendextend) + ("r-factominer" ,r-factominer) + ("r-ggplot2" ,r-ggplot2) + ("r-ggpubr" ,r-ggpubr) + ("r-ggrepel" ,r-ggrepel) + ("r-reshape2" ,r-reshape2) + ("r-tidyr" ,r-tidyr))) + (home-page "http://www.sthda.com/english/rpkgs/factoextra") + (synopsis "Extract and visualize the results of multivariate data analyses") + (description + "This package provides some easy-to-use functions to extract and +visualize the output of multivariate data analyses, including +@code{PCA} (Principal Component Analysis), @code{CA} (Correspondence +Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor +Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and +@code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R +packages. It contains also functions for simplifying some clustering analysis +steps and provides ggplot2-based elegant data visualization.") + (license license:gpl2))) + +(define-public r-nbclust + (package + (name "r-nbclust") + (version "3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "NbClust" version)) + (sha256 + (base32 + "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c")))) + (properties `((upstream-name . "NbClust"))) + (build-system r-build-system) + (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package") + (synopsis "Determine the best number of clusters in a data set") + (description + "NbClust provides 30 indexes for determining the optimal number of +clusters in a data set and offers the best clustering scheme from different +results to the user.") + (license license:gpl2))) + +(define-public r-hdf5r + (package + (name "r-hdf5r") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "hdf5r" version)) + (sha256 + (base32 + "1s6p4cj909kc635fh5xpl87bqlcdj3dn3r1wk5g40abimk2b0pva")))) + (build-system r-build-system) + (inputs + `(("hdf5" ,hdf5) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-bit64" ,r-bit64) + ("r-r6" ,r-r6))) + (home-page "https://hhoeflin.github.io/hdf5r") + (synopsis "Interface to the HDF5 binary data format") + (description + "HDF5 is a data model, library and file format for storing and managing +large amounts of data. This package provides a nearly feature complete, +object oriented wrapper for the HDF5 API using R6 classes. Additionally, +functionality is added so that HDF5 objects behave very similar to their +corresponding R counterparts.") + (license license:asl2.0))) + +(define-public r-writexl + (package + (name "r-writexl") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "writexl" version)) + (sha256 + (base32 + "0r2v12dc4zqmr1agp6vbw0fc48i278018684x84psjjqfmnv14cf")))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (home-page "https://github.com/ropensci/writexl") + (synopsis "Export data frames to xlsx format") + (description + "This package provides a data frame to xlsx exporter based on +libxlsxwriter.") + (license license:bsd-2))) |