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-rw-r--r--gnu/packages/cran.scm255
1 files changed, 200 insertions, 55 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 96044e114a..fa71035796 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -36,7 +36,9 @@
#:use-module (gnu packages mpi)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
+ #:use-module (gnu packages python)
#:use-module (gnu packages statistics)
+ #:use-module (gnu packages tls)
#:use-module (gnu packages web))
(define-public r-tidyverse
@@ -167,21 +169,18 @@ such as copy/paste from an R session.")
(define-public r-callr
(package
(name "r-callr")
- (version "2.0.3")
+ (version "2.0.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "callr" version))
(sha256
(base32
- "1k3mflgn10hcvy74y4pbigpv74zb66fz1phfd3c8isqmn88xbxzi"))))
+ "1053qqq632z94pqq2v5dynjpgyv1b1c8zvidmcllw7zn8zha8gqf"))))
(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)))
+ `(("r-r6" ,r-r6)
+ ("r-processx" ,r-processx)))
(home-page "https://github.com/r-lib/callr#readme")
(synopsis "Call R from R")
(description
@@ -316,14 +315,14 @@ and several other tools.")
(define-public r-abbyyr
(package
(name "r-abbyyr")
- (version "0.5.1")
+ (version "0.5.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "abbyyR" version))
(sha256
(base32
- "1s8zf18sh0s89vk3dl09fzrq50csmmfvmsanf5vfkv9n5lx6pklg"))))
+ "1jh1c1ad6mgw7brdh2isnza1qpjlfxnqr7jl76yd93axyfl76xjx"))))
(properties `((upstream-name . "abbyyR")))
(build-system r-build-system)
(propagated-inputs
@@ -427,13 +426,13 @@ error stream.")
(define-public r-rcpp
(package
(name "r-rcpp")
- (version "0.12.16")
+ (version "0.12.17")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rcpp" version))
(sha256
- (base32 "1rm8hcy72p1jvxikvmkwg20pjqmvmfvqb45lfghmddp2adp67qfl"))))
+ (base32 "08xg8h3w25sdb3xr18g9pa0x8cirkdgljqapxmw56ss1j9fc89s2"))))
(build-system r-build-system)
(home-page "http://www.rcpp.org")
(synopsis "Seamless R and C++ integration")
@@ -729,14 +728,14 @@ any subsequent lookup as it keeps the hash table in memory.")
(define-public r-ff
(package
(name "r-ff")
- (version "2.2-13")
+ (version "2.2-14")
(source
(origin
(method url-fetch)
(uri (cran-uri "ff" version))
(sha256
(base32
- "1nvd6kx46xzyc99a44mgynd94pvd2h495m5a7b1g67k5w2phiywb"))))
+ "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
(build-system r-build-system)
(propagated-inputs `(("r-bit" ,r-bit)))
(home-page "http://ff.r-forge.r-project.org/")
@@ -843,23 +842,26 @@ package also provides a C++ API, that works with or without Rcpp.")
(define-public r-ggally
(package
(name "r-ggally")
- (version "1.3.2")
+ (version "1.4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "GGally" version))
(sha256
(base32
- "02px7j28wzbhcgcwm2m0pxb6g7s5zvphl64ix55pkvag4m2ky57l"))))
+ "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws"))))
(properties `((upstream-name . "GGally")))
(build-system r-build-system)
+ (inputs
+ `(("libressl" ,libressl)))
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
("r-gtable" ,r-gtable)
("r-plyr" ,r-plyr)
("r-progress" ,r-progress)
("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-reshape" ,r-reshape)))
+ ("r-reshape" ,r-reshape)
+ ("r-rlang" ,r-rlang)))
(home-page "https://ggobi.github.io/ggally")
(synopsis "Extension to ggplot2")
(description
@@ -1077,13 +1079,13 @@ by Li, Brown, Huang, and Bickel")
(define-public r-inline
(package
(name "r-inline")
- (version "0.3.14")
+ (version "0.3.15")
(source (origin
(method url-fetch)
(uri (cran-uri "inline" version))
(sha256
(base32
- "0cf9vya9h4znwgp6s1nayqqmh6mwyw7jl0isk1nx4j2ijszxcd7x"))))
+ "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/inline")
(synopsis "Functions to inline C, C++, Fortran function calls from R")
@@ -1122,14 +1124,14 @@ classes in the @code{stats4} package.")
(define-public r-emdbook
(package
(name "r-emdbook")
- (version "1.3.9")
+ (version "1.3.10")
(source
(origin
(method url-fetch)
(uri (cran-uri "emdbook" version))
(sha256
(base32
- "09xbdyw8a4pvrsg3ryr8drby0njy4avc5wsjj4ffibdaicpchy69"))))
+ "0880cx6rqm9vgd2zxnd2k0igfl80gy7ak15w36clwlzavab59hmv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bbmle" ,r-bbmle)
@@ -1234,14 +1236,14 @@ data). Weighted versions of MLE, MME and QME are available.")
(define-public r-energy
(package
(name "r-energy")
- (version "1.7-2")
+ (version "1.7-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "energy" version))
(sha256
(base32
- "19c7bgjnm4ggf7w5mk64c5shkma3sa9wc8x117iqv7pk1bvvyy3p"))))
+ "12skvlridfq4jd5mh0yxl79ps0zi2xnlh4hsdgxad0gm7qky8awd"))))
(build-system r-build-system)
(propagated-inputs
`(("r-boot" ,r-boot)
@@ -1315,14 +1317,14 @@ samples.")
(define-public r-cvst
(package
(name "r-cvst")
- (version "0.2-1")
+ (version "0.2-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "CVST" version))
(sha256
(base32
- "17xacyi8cf37rr2xswx96qy7pwkaqq394awdlswykz3qlyzx4zx2"))))
+ "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
(properties `((upstream-name . "CVST")))
(build-system r-build-system)
(propagated-inputs
@@ -1774,14 +1776,14 @@ for certain use cases.")
(define-public r-ggrepel
(package
(name "r-ggrepel")
- (version "0.7.0")
+ (version "0.8.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggrepel" version))
(sha256
(base32
- "0g0qfm6g71rv27423c1x846ipilnj213knyzrcr09vrpxc87l618"))))
+ "1m3p84d6nh9mzzvxb82vgig3ngcvkz86rjwzl9a66ckdf5p611k3"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
@@ -1841,23 +1843,98 @@ can be computed between character vectors while taking proper care of encoding
or between integer vectors representing generic sequences.")
(license license:gpl3+)))
+(define-public r-jomo
+ (package
+ (name "r-jomo")
+ (version "2.6-2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "jomo" version))
+ (sha256
+ (base32
+ "0zyqwa2y08asj9xqwnngh6da1b9cqcx8pzc9cxwrmgnxd5nnsjb7"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-lme4" ,r-lme4)
+ ("r-survival" ,r-survival)))
+ (home-page "https://cran.r-project.org/web/packages/jomo/")
+ (synopsis "Multilevel Joint Modelling Multiple Imputation")
+ (description
+ "Similarly to Schafer's package pan, jomo is a package for multilevel
+joint modelling multiple imputation @url{Carpenter and Kenward (2013),
+http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
+possibility of handling binary and categorical data through latent normal
+variables, the option to use cluster-specific covariance matrices and to
+impute compatibly with the substantive model.")
+ (license license:gpl2)))
+
+(define-public r-pan
+ (package
+ (name "r-pan")
+ (version "1.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "pan" version))
+ (sha256
+ (base32
+ "1p3nigmhrnlch86g89hn7l0wvkifx3k9n59g0psi95yck43kza76"))))
+ (build-system r-build-system)
+ (native-inputs `(("gfortran" ,gfortran)))
+ (home-page "https://cran.r-project.org/web/packages/pan/")
+ (synopsis "Multiple imputation for multivariate panel or clustered data")
+ (description
+ "This package implements multiple imputation for multivariate panel or
+clustered data.")
+ (license license:gpl3)))
+
+(define-public r-mitml
+ (package
+ (name "r-mitml")
+ (version "0.3-5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "mitml" version))
+ (sha256
+ (base32
+ "1s888r9y2ri39b48h1iypps6lddqkqv3g31l2sjmi2pvyccfpkwb"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-haven" ,r-haven)
+ ("r-jomo" ,r-jomo)
+ ("r-pan" ,r-pan)))
+ (home-page "https://cran.r-project.org/web/packages/mitml/")
+ (synopsis "Tools for multiple imputation in multilevel modeling")
+ (description
+ "This package provides tools for multiple imputation of missing data in
+multilevel modeling. It includes a user-friendly interface to the packages
+pan and jomo, and several functions for visualization, data management and the
+analysis of multiply imputed data sets.")
+ (license license:gpl2+)))
+
(define-public r-mice
(package
(name "r-mice")
- (version "2.46.0")
+ (version "3.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "mice" version))
(sha256
(base32
- "1gjvlk67zvgipfczsca8zqk97vg3sivv82hblsdwp14s7smhjcax"))))
+ "1p8a5ham90iaak4w17114pdnw535r2l9sxr402yrkc4gbwfbpdlq"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-lattice" ,r-lattice)
+ `(("r-broom" ,r-broom)
+ ("r-dplyr" ,r-dplyr)
+ ("r-lattice" ,r-lattice)
("r-mass" ,r-mass)
+ ("r-mitml" ,r-mitml)
("r-nnet" ,r-nnet)
("r-rcpp" ,r-rcpp)
+ ("r-rlang" ,r-rlang)
("r-rpart" ,r-rpart)
("r-survival" ,r-survival)))
(home-page "https://cran.r-project.org/web/packages/mice/")
@@ -1923,14 +2000,14 @@ programming} (SQP) based solver).")
(define-public r-hardyweinberg
(package
(name "r-hardyweinberg")
- (version "1.5.9")
+ (version "1.6.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "HardyWeinberg" version))
(sha256
(base32
- "0qk3lly5qczn61rj0q9xzscppspvk238yjgr4p71pkzkjhiv40jz"))))
+ "16n8qanxx0p5ny5zqxafn8hwb1xv94y1wig1iql8as5a5qh8lwcz"))))
(properties `((upstream-name . "HardyWeinberg")))
(build-system r-build-system)
(propagated-inputs
@@ -1955,14 +2032,14 @@ acceptance regions, log-ratio plots and Q-Q plots.")
(define-public r-sm
(package
(name "r-sm")
- (version "2.2-5.4")
+ (version "2.2-5.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "sm" version))
(sha256
(base32
- "0hnq5s2fv94gaj0nyqc1vjdjd64vsp9z23nqa8hxvjcaf996rwj9"))))
+ "1rw2mxygxsmk8mn4wag1ppjgzk0rlvh6zd8q02qrhjrn9jhi5qj3"))))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
(home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
@@ -2146,14 +2223,14 @@ Analysis with R\" by Michael Friendly and David Meyer (2015).")
(define-public r-ica
(package
(name "r-ica")
- (version "1.0-1")
+ (version "1.0-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "ica" version))
(sha256
(base32
- "1bkl4a72l0k6gm82l3jxnib898z20cw17zg81jj39l9dn65rlmcq"))))
+ "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/ica/")
(synopsis "Independent component analysis")
@@ -2166,14 +2243,14 @@ of Eigenmatrices} (JADE).")
(define-public r-dtw
(package
(name "r-dtw")
- (version "1.18-1")
+ (version "1.20-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "dtw" version))
(sha256
(base32
- "1b91vahba09cqlb8b1ry4dlv4rbldb4s2p6w52gmyw31vxdv5nnr"))))
+ "1w301xwizncy5r8v9rwwdxfshydgp3l1pnjla1fjn6n8lx3imjj3"))))
(build-system r-build-system)
(propagated-inputs `(("r-proxy" ,r-proxy)))
(home-page "http://dtw.r-forge.r-project.org/")
@@ -2256,14 +2333,14 @@ plots in @code{ggplot2}.")
(define-public r-ggjoy
(package
(name "r-ggjoy")
- (version "0.4.0")
+ (version "0.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggjoy" version))
(sha256
(base32
- "1s24zn7gmk52bvjjhanxby7rxbnc2yfl0nx5nv7x7z0zja8gg7nb"))))
+ "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
@@ -2341,20 +2418,20 @@ constants, and control debugging of packages via environment variables.")
(define-public r-processx
(package
(name "r-processx")
- (version "2.0.0.1")
+ (version "3.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "processx" version))
(sha256
(base32
- "0yw23lp9xjvbpswzghkmjiayw7p19hbvmgv58k3i6b8g5nav4qcg"))))
+ "0wjr3cqwvnjxbvln25szffmkns5w0xysivdjr6chxap4nh515b0i"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
("r-crayon" ,r-crayon)
- ("r-debugme" ,r-debugme)
- ("r-r6" ,r-r6)))
+ ("r-r6" ,r-r6)
+ ("r-testthat" ,r-testthat)))
(home-page "https://github.com/r-lib/processx3")
(synopsis "Execute and control system processes")
(description
@@ -2551,14 +2628,14 @@ packages maintained by Yihui Xie.")
(define-public r-utf8
(package
(name "r-utf8")
- (version "1.1.3")
+ (version "1.1.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "utf8" version))
(sha256
(base32
- "03s4j6059q0nly68vpk6wy3p3f5ypakw93fj35kzd82b4z1r9cs3"))))
+ "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
(build-system r-build-system)
(home-page "https://github.com/patperry/r-utf8")
(synopsis "Unicode text processing")
@@ -2571,14 +2648,14 @@ display.")
(define-public r-pillar
(package
(name "r-pillar")
- (version "1.2.2")
+ (version "1.2.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "pillar" version))
(sha256
(base32
- "1kmqvny3rw4p5kgxz6mhqfpp7j3nnpp22dfai4kjrr2cfmj6wvb7"))))
+ "1rzhssprqgam1nq3s0f5rzxhxsq02azcghvxf6k8kmsmddf1n7f8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cli" ,r-cli)
@@ -3263,18 +3340,19 @@ files.")
(define-public r-shinyace
(package
(name "r-shinyace")
- (version "0.2.1")
+ (version "0.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "shinyAce" version))
(sha256
(base32
- "0ycka8rsw0178q9klfid97vdn5cbyx3r778nis5s3dqipdyazdm9"))))
+ "1hqgszbiv99dibhwr21v21ll4s2hjn3ccqdicsm0z3gk77bh8iyb"))))
(properties `((upstream-name . "shinyAce")))
(build-system r-build-system)
(propagated-inputs
- `(("r-shiny" ,r-shiny)))
+ `(("r-shiny" ,r-shiny)
+ ("r-jsonlite" ,r-jsonlite)))
(home-page "http://cran.r-project.org/web/packages/shinyAce")
(synopsis "Ace editor bindings for Shiny")
(description
@@ -3384,14 +3462,14 @@ It also includes interpolation functions.")
(define-public r-psych
(package
(name "r-psych")
- (version "1.8.3.3")
+ (version "1.8.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "psych" version))
(sha256
(base32
- "1zhp8j81nkzd65168zdw9ylypb9n07ajan21x0wqcn8jdbg970sg"))))
+ "1kzv9nc7rwn1sj1zxd8xrbs6c7qlka7j2c8lsr4f20znkd3qx8gf"))))
(build-system r-build-system)
(propagated-inputs
`(("r-foreign" ,r-foreign)
@@ -3766,19 +3844,41 @@ measuring the accuracy of ABC estimates, and to calculate the
misclassification probabilities of different models.")
(license license:gpl3+)))
+(define-public r-zip
+ (package
+ (name "r-zip")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "zip" version))
+ (sha256
+ (base32
+ "0rgr9pcdhdq3k8n29h2ircp3ri1ibhrx81gja1y7331v15xyrabg"))))
+ (build-system r-build-system)
+ (home-page "https://github.com/gaborcsardi/zip")
+ (synopsis "Cross-platform Zip compression")
+ (description
+ "This package provides a cross-platform Zip compression library for R.
+It is a replacement for the @code{zip} function, that does not require any
+additional external tools on any platform.")
+ (license license:cc0)))
+
(define-public r-openxlsx
(package
(name "r-openxlsx")
- (version "4.0.17")
+ (version "4.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "openxlsx" version))
(sha256
(base32
- "1mq4lasp12kc30sxcsmz9gskd114l8s7z7wd6svv2nm8qllrhsqi"))))
+ "1n7z22pm78xa77fvn77kdn68az6xzxk36y11sqf0w6h6adri4yxb"))))
(build-system r-build-system)
- (propagated-inputs `(("r-rcpp" ,r-rcpp)))
+ (propagated-inputs
+ `(("r-rcpp" ,r-rcpp)
+ ("r-zip" ,r-zip)))
(home-page "https://github.com/awalker89/openxlsx")
(synopsis "Read, write and edit XLSX files")
(description
@@ -4060,3 +4160,48 @@ bootstrap using a truncated geometric distribution, a comprehensive test for
weak stationarity, column means by group, weighted biplots, and a heuristic to
obtain a better initial configuration in non-metric MDS.")
(license license:gpl2)))
+
+(define-public r-reticulate
+ (package
+ (name "r-reticulate")
+ (version "1.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "reticulate" version))
+ (sha256
+ (base32
+ "1ghhc4hbmwpp79ilbdbshynhs61i8sv8z6p1al04jy7ij0lcglxy"))))
+ (build-system r-build-system)
+ (inputs `(("python" ,python)))
+ (propagated-inputs
+ `(("r-jsonlite" ,r-jsonlite)
+ ("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://github.com/rstudio/reticulate")
+ (synopsis "R interface to Python")
+ (description
+ "This package provides an interface from R to Python modules, classes,
+and functions. When calling into Python, R data types are automatically
+converted to their equivalent Python types. When values are returned from
+Python to R they are converted back to R types.")
+ (license license:asl2.0)))
+
+(define-public r-bibtex
+ (package
+ (name "r-bibtex")
+ (version "0.4.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "bibtex" version))
+ (sha256
+ (base32
+ "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz"))))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-stringr" ,r-stringr)))
+ (home-page "https://github.com/romainfrancois/bibtex")
+ (synopsis "Bibtex parser")
+ (description "This package provides a utility for R to parse a bibtex
+file.")
+ (license license:gpl2+)))