;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de>
+;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
#:use-module (gnu packages tcl)
#:use-module (gnu packages tls)
#:use-module (gnu packages web)
+ #:use-module (gnu packages xml)
#:use-module (gnu packages xorg))
(define-public r-rticles
(define-public r-ggpmisc
(package
(name "r-ggpmisc")
- (version "0.3.5")
+ (version "0.3.6")
(source (origin
(method url-fetch)
(uri (cran-uri "ggpmisc" version))
(sha256
(base32
- "0ma2d3a3v8n85sghxr9anl6vgbs8gi82i1dllw99n81gsm59wgin"))))
+ "05i81q9rg8zf35vgcxhn3yhkc9dlvcpwpxncq1q3zs0rxhfkf208"))))
(build-system r-build-system)
(propagated-inputs
`(("r-broom" ,r-broom)
("r-dplyr" ,r-dplyr)
+ ("r-glue" ,r-glue)
("r-ggplot2" ,r-ggplot2)
("r-gridextra" ,r-gridextra)
("r-lubridate" ,r-lubridate)
(define-public r-callr
(package
(name "r-callr")
- (version "3.4.3")
+ (version "3.4.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "callr" version))
(sha256
(base32
- "1dc20gdawy9mhnc452qlshv2p4krs6c2gymvpv365mn141zjgdq1"))))
+ "1hgc4mfwv83104fh93v8g2srpwzjayq7krgzi9r0apq784r61642"))))
(build-system r-build-system)
(propagated-inputs
`(("r-r6" ,r-r6)
(define-public r-jsonlite
(package
(name "r-jsonlite")
- (version "1.7.0")
+ (version "1.7.1")
(source (origin
(method url-fetch)
(uri (cran-uri "jsonlite" version))
(sha256
(base32
- "1izfrk5yahsz6s69wanfspn72qdffjglbr5305akj72ig9fnladq"))))
+ "1wygpnycmyf339x92hwapqk7nc1gs9cadx890b809a9spjhah41a"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr)))
(define-public r-shape
(package
(name "r-shape")
- (version "1.4.4")
+ (version "1.4.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "shape" version))
(sha256
(base32
- "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
+ "17qqhjyfhxv9la07ykaslb50c8g4d0cgfypx4y91h9i2yjw7jjh9"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/shape")
(synopsis "Functions for plotting graphical shapes")
(define-public r-lmtest
(package
(name "r-lmtest")
- (version "0.9-37")
+ (version "0.9-38")
(source
(origin
(method url-fetch)
(uri (cran-uri "lmtest" version))
(sha256
(base32
- "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
+ "0sr19bmw2cpagfvwg772m79wvl1i2hww1xfr69bzr3rr8pm2r8ij"))))
(build-system r-build-system)
(propagated-inputs
`(("r-zoo" ,r-zoo)))
(define-public r-inline
(package
(name "r-inline")
- (version "0.3.15")
+ (version "0.3.16")
(source (origin
(method url-fetch)
(uri (cran-uri "inline" version))
(sha256
(base32
- "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
+ "0x9m2hwin6anfhkf61cnsbqn4qp1pr2gy1pbwbdgbdz2cmns85nj"))))
(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")
(define-public r-psych
(package
(name "r-psych")
- (version "2.0.7")
+ (version "2.0.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "psych" version))
(sha256
(base32
- "13z26yk9nrgviyakkij3jc7mja8wy7al9ripab07mvy21kli79bc"))))
+ "0ymds7ql2dv994m73h68dnhbsws8bl09p2rqvl6xsq6c6xr0yryg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)
(define-public r-xts
(package
(name "r-xts")
- (version "0.12-0")
+ (version "0.12.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "xts" version))
(sha256
(base32
- "0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz"))))
+ "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n"))))
(build-system r-build-system)
(propagated-inputs `(("r-zoo" ,r-zoo)))
(home-page "https://github.com/joshuaulrich/xts")
(define-public r-processx
(package
(name "r-processx")
- (version "3.4.3")
+ (version "3.4.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "processx" version))
(sha256
- (base32 "07dhzijqnj2zkm3qrk4ppsv8wscn8ysdsjbidlg9zrbj1wcg4izj"))))
+ (base32 "0as8lzfpbz5rcpcpczvrrgd67whngkmw12q33r2yn3k7lq80z95a"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ps" ,r-ps)
(define-public r-xfun
(package
(name "r-xfun")
- (version "0.16")
+ (version "0.17")
(source
(origin
(method url-fetch)
(uri (cran-uri "xfun" version))
(sha256
- (base32 "1x7b71xhbl44fyccz69l24nbgyxawm2km90s4h1l3zr5z2vly0sg"))))
+ (base32 "1zd5qi1rrz3b1lpisapa2yscanz39ghaamf28g7aq3z9ai2a2ymj"))))
(build-system r-build-system)
;; knitr itself depends on xfun
#;
(define-public r-tsa
(package
(name "r-tsa")
- (version "1.2")
+ (version "1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "TSA" version))
(sha256
(base32
- "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
+ "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb"))))
(properties `((upstream-name . "TSA")))
(build-system r-build-system)
(propagated-inputs
`(("r-leaps" ,r-leaps)
("r-locfit" ,r-locfit)
- ("r-mgcv" ,r-mgcv)))
+ ("r-mgcv" ,r-mgcv)
+ ("r-tseries" ,r-tseries)))
(home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
(synopsis "Time series analysis")
(description
(define-public r-extradistr
(package
(name "r-extradistr")
- (version "1.8.11")
+ (version "1.9.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "extraDistr" version))
(sha256
(base32
- "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
+ "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
(properties `((upstream-name . "extraDistr")))
(build-system r-build-system)
(propagated-inputs
(define-public r-officer
(package
(name "r-officer")
- (version "0.3.13")
+ (version "0.3.14")
(source
(origin
(method url-fetch)
(uri (cran-uri "officer" version))
(sha256
(base32
- "15v5dishdsrw95nj6f7x23llzla3sgbvw35ibdk8ld3miwzxb2kr"))))
+ "1nyv4710bcd2afh1l1qiy5zrspjcdvc7mrzz5189dwy9xvgxi31h"))))
(build-system r-build-system)
(propagated-inputs
`(("r-magrittr" ,r-magrittr)
(define-public r-insight
(package
(name "r-insight")
- (version "0.9.1")
+ (version "0.9.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "insight" version))
(sha256
(base32
- "0d6yzg5s0mz07bzxwfc77rpv4l20jpzrnhviqgkp02qw6a4nrwa6"))))
+ "0853kq4j8kic8z2gh5mxfqkwxjs4bdphlajzyvxka7af4r04bfmi"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr)))
(define-public r-flextable
(package
(name "r-flextable")
- (version "0.5.10")
+ (version "0.5.11")
(source
(origin
(method url-fetch)
(uri (cran-uri "flextable" version))
(sha256
(base32
- "1j7yvjiavar21ywck6nyz0p6bd66fnj99bq8lljdz4rrl3314yb8"))))
+ "1yb872izzr9yja7q2vfqm0imcbcgs0fvi4b19arhdlwwa42figj4"))))
(build-system r-build-system)
(propagated-inputs
`(("r-base64enc" ,r-base64enc)
(define-public r-mosaiccore
(package
(name "r-mosaiccore")
- (version "0.6.0")
+ (version "0.8.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "mosaicCore" version))
(sha256
- (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
+ (base32 "00va6x1i8d3wkm1bgsms9dsjfn5a1l43prpl9pqirgq3zm85hrqj"))))
(properties `((upstream-name . "mosaicCore")))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
- ("r-lazyeval" ,r-lazyeval)
("r-mass" ,r-mass)
("r-rlang" ,r-rlang)
("r-tidyr" ,r-tidyr)))
(define-public r-mosaicdata
(package
(name "r-mosaicdata")
- (version "0.18.0")
+ (version "0.20.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "mosaicData" version))
(sha256
- (base32 "0cx5dg26ha7nzkdyghkbbd6ikncj60qv1538az77lfgn2jylvkbz"))))
+ (base32 "05mrwvs7awhpv2gvk0jjva74gndfgh2cl17slxcjhwlpga8nmxji"))))
(properties `((upstream-name . "mosaicData")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/mosaicData/")
(define-public r-performance
(package
(name "r-performance")
- (version "0.4.8")
+ (version "0.5.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "performance" version))
(sha256
(base32
- "1gl3m1pw0wrj9m9cgd0vzbj9swfwjg4aa40gpliplb9y7dcmgi4l"))))
+ "01csmn52d6rhlmcj7gi6ckc6v6a8pymnrpx9l729h13igxsnaf28"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bayestestr" ,r-bayestestr)
(define-public r-ggeffects
(package
(name "r-ggeffects")
- (version "0.15.1")
+ (version "0.16.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggeffects" version))
(sha256
(base32
- "12z58casz0yl1w7nfs64bz4miz0mmc300ap3rz4d2cc4z0rg0r47"))))
+ "0v8n8jmp6x1iagbyc5jgf1d29yz5hd3ibnyl9n9f73vqq5bzj0p5"))))
(build-system r-build-system)
(propagated-inputs
`(("r-insight" ,r-insight)
(define-public r-rcpphnsw
(package
(name "r-rcpphnsw")
- (version "0.2.0")
+ (version "0.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "RcppHNSW" version))
(sha256
(base32
- "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
+ "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0"))))
(properties `((upstream-name . "RcppHNSW")))
(build-system r-build-system)
(propagated-inputs `(("r-rcpp" ,r-rcpp)))
(define-public r-misc3d
(package
(name "r-misc3d")
- (version "0.8-4")
+ (version "0.9-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "misc3d" version))
(sha256
(base32
- "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
+ "10jf5r1x588vi54bzaqgi9mgcqlkiga2c3jvmqmk3lavc8fjksd1"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/misc3d/")
(synopsis "Miscellaneous 3D Plots")
(define-public r-rnifti
(package
(name "r-rnifti")
- (version "1.2.1")
+ (version "1.2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "RNifti" version))
(sha256
(base32
- "1a5s75iwwngzmi7y69j7xkcrrfvjyjrfalv9ldpgwii4cwkbyf10"))))
+ "0h837jdspy071ckij8szqd8149bm113jpqwbclg87is4brsm5jzg"))))
(properties `((upstream-name . "RNifti")))
(build-system r-build-system)
(propagated-inputs `(("r-rcpp" ,r-rcpp)))
(define-public r-fields
(package
(name "r-fields")
- (version "10.3")
+ (version "11.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "fields" version))
(sha256
- (base32 "12k97vfjlz5h8vynirnvik1nyj1iw25n8xl7awmx9mpd6wvgy2s9"))))
+ (base32 "0x8hbl0rn7gnhn7w45wd757g9in27884qr6vy30xrk150qaq941y"))))
(build-system r-build-system)
(propagated-inputs
`(("r-maps" ,r-maps)
(define-public r-etm
(package
(name "r-etm")
- (version "1.1")
+ (version "1.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "etm" version))
(sha256
(base32
- "02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd"))))
+ "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
(build-system r-build-system)
(propagated-inputs
`(("r-data-table" ,r-data-table)
(define-public r-shinyjs
(package
(name "r-shinyjs")
- (version "1.1")
+ (version "2.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "shinyjs" version))
(sha256
(base32
- "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9"))))
+ "1zzq356dvd8ciajy6r5n4ybgx9xk7ydwv25j86xlcsqznkxdkkf2"))))
(build-system r-build-system)
(propagated-inputs
`(("r-digest" ,r-digest)
("r-htmltools" ,r-htmltools)
("r-jsonlite" ,r-jsonlite)
("r-shiny" ,r-shiny)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://deanattali.com/shinyjs")
(synopsis "Improve the user experience of your Shiny apps")
(description
(define-public r-deldir
(package
(name "r-deldir")
- (version "0.1-28")
+ (version "0.1-29")
(source
(origin
(method url-fetch)
(uri (cran-uri "deldir" version))
(sha256
(base32
- "12ys8jdcrgzhf9m2yirlqfars397qb0q0pbypahmfa66lgr6wdx5"))))
+ "1vwh8c8zxspyls05q9kgzz5p85i8k8aax5ir45np2bmg0pjvh6kv"))))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
(home-page "https://cran.r-project.org/web/packages/deldir")
(define-public r-sf
(package
(name "r-sf")
- (version "0.9-5")
+ (version "0.9-6")
(source
(origin
(method url-fetch)
(uri (cran-uri "sf" version))
(sha256
(base32
- "0c58asqrvz1pkdkb0lkzwz8cwb43pmxd39z0jp217hk7p7q3ngwf"))))
+ "01yqlnx9v7lzb6g4ywjlncz67cnkizszarnf2dmd4fi8abhw4zs9"))))
(build-system r-build-system)
(inputs
`(("gdal" ,gdal)
(define-public r-dalex
(package
(name "r-dalex")
- (version "1.3.1.1")
+ (version "2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "DALEX" version))
(sha256
(base32
- "0akw1yzhb3shpg6yb89vralqd2z80z5yk9azqaa55dx56as52kjs"))))
+ "1yn61cbqvyycn617pzhd7kgd34xsnmqvj3s10inn2ywycybk7byi"))))
(properties `((upstream-name . "DALEX")))
(build-system r-build-system)
(propagated-inputs
(define-public r-systemfonts
(package
(name "r-systemfonts")
- (version "0.3.0")
+ (version "0.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "systemfonts" version))
(sha256
(base32
- "16n25bin46r0vq59wjdskkb8631gzf7grwnp2wnk0zb9c2qr48ax"))))
+ "0ldxgcayyisp2gcbv4xw9zpb48bp4czi8016kq5nqdqhv1qb3sz0"))))
(properties `((upstream-name . "systemfonts")))
(build-system r-build-system)
(propagated-inputs
(define-public r-parameters
(package
(name "r-parameters")
- (version "0.8.2")
+ (version "0.8.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "parameters" version))
(sha256
(base32
- "0kamszscywvdh4gikl5mmma7s5p7spmhirq3wrgf7x7f4gppbbmh"))))
+ "1vax5p1znq2ddbks2i614hbrnn2x6x71942xx49p813qk8dh284l"))))
(properties `((upstream-name . "parameters")))
(build-system r-build-system)
(propagated-inputs
(define-public r-gamlss
(package
(name "r-gamlss")
- (version "5.1-7")
+ (version "5.2-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "gamlss" version))
(sha256
(base32
- "0ywqwsp4k6jgnicp1gdsglji61l5cnackl52700v8kmkk83bq4c8"))))
+ "1q82md0439si0n7vqbbbdk45sjr0ad7i8mgrn3kwnr4h213pb4nk"))))
(properties `((upstream-name . "gamlss")))
(build-system r-build-system)
(propagated-inputs
(define-public r-forecast
(package
(name "r-forecast")
- (version "8.12")
+ (version "8.13")
(source
(origin
(method url-fetch)
(uri (cran-uri "forecast" version))
(sha256
(base32
- "1ycj5z4wd5a16nlcjy07dqm8jkih240xa02cn4wvysnnhkapyq7b"))))
+ "0vrql5d4v28890np2m6ws1nr1fcl6frs1bz74vfkihkixcmkl3j9"))))
(properties `((upstream-name . "forecast")))
(build-system r-build-system)
(propagated-inputs
(define-public r-scatterpie
(package
(name "r-scatterpie")
- (version "0.1.4")
+ (version "0.1.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "scatterpie" version))
(sha256
(base32
- "0g5sn0iv6c1q7y51j4gbbbnil5089dgk1w4q94c7h5y3x7wfrzqb"))))
+ "0h48l0699lpfagv09f53yismir84945m56qwzk52lc7wxyvkfcp1"))))
(properties `((upstream-name . "scatterpie")))
(build-system r-build-system)
(propagated-inputs
(define-public r-rfast
(package
(name "r-rfast")
- (version "2.0.0")
+ (version "2.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rfast" version))
(sha256
(base32
- "010dm5h2vayvfbh0zny7i2c7fmn83r2b54849r0b4id3wjpmg3xy"))))
+ "1cq3mcg49hsvqhwn6f4dgsx7f8ma4qnwr5n6s7m22qy57rg31958"))))
(properties `((upstream-name . "Rfast")))
(build-system r-build-system)
(propagated-inputs
value.")
(license license:gpl3)))
+(define-public r-adaptivesparsity
+ (package
+ (name "r-adaptivesparsity")
+ (version "1.6")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "AdaptiveSparsity" version))
+ (sha256
+ (base32
+ "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
+ (properties
+ `((upstream-name . "AdaptiveSparsity")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'link-against-armadillo
+ (lambda _
+ (substitute* "src/Makevars"
+ (("PKG_LIBS=" prefix)
+ (string-append prefix "-larmadillo")))
+ #t)))))
+ (propagated-inputs
+ `(("r-mass" ,r-mass)
+ ("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)))
+ (inputs
+ `(("armadillo" ,armadillo)))
+ (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
+ (synopsis "Adaptive sparsity models")
+ (description
+ "This package implements the Figueiredo machine learning algorithm for
+adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
+geometric models.")
+ (license license:lgpl3+)))
+
+(define-public r-diffusionmap
+ (package
+ (name "r-diffusionmap")
+ (version "1.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "diffusionMap" version))
+ (sha256
+ (base32
+ "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
+ (properties `((upstream-name . "diffusionMap")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-igraph" ,r-igraph)
+ ("r-matrix" ,r-matrix)
+ ("r-scatterplot3d" ,r-scatterplot3d)))
+ (home-page "https://www.r-project.org")
+ (synopsis "Diffusion map")
+ (description "This package implements the diffusion map method of data
+parametrization, including creation and visualization of diffusion maps,
+clustering with diffusion K-means and regression using the adaptive regression
+model.")
+ (license license:gpl2)))
+
+(define-public r-igraph
+ (package
+ (name "r-igraph")
+ (version "1.2.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "igraph" version))
+ (sha256
+ (base32
+ "126z1ygbmi3g7hk97snf22rnx680dyi30idssm5zacba5rdngp8c"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (inputs
+ `(("gmp" ,gmp)
+ ("glpk" ,glpk)
+ ("libxml2" ,libxml2)
+ ("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-magrittr" ,r-magrittr)
+ ("r-matrix" ,r-matrix)
+ ("r-pkgconfig" ,r-pkgconfig)))
+ (home-page "https://igraph.org")
+ (synopsis "Network analysis and visualization")
+ (description
+ "This package provides routines for simple graphs and network analysis.
+It can handle large graphs very well and provides functions for generating
+random and regular graphs, graph visualization, centrality methods and much
+more.")
+ (license license:gpl2+)))
+
(define-public r-workflows
(package
(name "r-workflows")
(define-public r-tune
(package
(name "r-tune")
- (version "0.1.0")
+ (version "0.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "tune" version))
(sha256
(base32
- "0xiidzkl0hbd0f7jh1v2kkg26wdgy33w74c9bmpjgy317ckhsz8h"))))
+ "0293xkmv1nyvm72wxznnlm3qpf6475xzl2sf52mnrjxxr7i447p1"))))
(properties `((upstream-name . "tune")))
(build-system r-build-system)
(propagated-inputs
("r-rsample" ,r-rsample)
("r-tibble" ,r-tibble)
("r-tidyr" ,r-tidyr)
+ ("r-vctrs" ,r-vctrs)
("r-workflows" ,r-workflows)
("r-yardstick" ,r-yardstick)))
(home-page "https://github.com/tidymodels/tune")
(define-public r-tidypredict
(package
(name "r-tidypredict")
- (version "0.4.5")
+ (version "0.4.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidypredict" version))
(sha256
(base32
- "1i6zl6wjz6wbpkmkc9z9ikp8zgck3qh38lar0r6q2jzl8fxpimg4"))))
+ "1fx1nr8fry3nwy2391g26zkqakdf8f3j7zyrihbc0qhscvbdskiy"))))
(properties `((upstream-name . "tidypredict")))
(build-system r-build-system)
(propagated-inputs
(define-public r-tidytext
(package
(name "r-tidytext")
- (version "0.2.4")
+ (version "0.2.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidytext" version))
(sha256
(base32
- "0gck3f039qkpkwn92jlyfan76w0xydg17bh6nsg9qlba7c35kzs6"))))
+ "0kwbpffdnqrb6hgrrmrfnx890imbzvp5bs6sj1k72if28qijarm5"))))
(properties `((upstream-name . "tidytext")))
(build-system r-build-system)
(propagated-inputs
("r-matrix" ,r-matrix)
("r-purrr" ,r-purrr)
("r-rlang" ,r-rlang)
- ("r-stopwords" ,r-stopwords)
("r-stringr" ,r-stringr)
+ ("r-tibble" ,r-tibble)
("r-tokenizers" ,r-tokenizers)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(define-public r-parsnip
(package
(name "r-parsnip")
- (version "0.1.1")
+ (version "0.1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "parsnip" version))
(sha256
(base32
- "1p33absjd2lnq5aikr42him4b724qzxr1pzvdnazg789f763i47l"))))
+ "12121qj1800i7g3km5kqzlb7hms55crmp6il575c2i475h5qx8d3"))))
(properties `((upstream-name . "parsnip")))
(build-system r-build-system)
(propagated-inputs
(define-public r-infer
(package
(name "r-infer")
- (version "0.5.2")
+ (version "0.5.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "infer" version))
(sha256
(base32
- "0m00xhzrvmskwj4jwncakwxhzivn9pyiylq4r8s6ny4yiwqg303m"))))
+ "1q0lnxnv8krv4n9z80sh4b442s89rvnbph5bddy34z83bkncwv2g"))))
(properties `((upstream-name . "infer")))
(build-system r-build-system)
(propagated-inputs
expressive statistical grammar that coheres with the Tidy design framework.")
(license license:cc0)))
+(define-public r-modeldata
+ (package
+ (name "r-modeldata")
+ (version "0.0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "modeldata" version))
+ (sha256
+ (base32
+ "13q6hhbwqbwnjvg8bz6iwwfx96p1saqq3r34cjrbnpgzmr1nn11l"))))
+ (properties `((upstream-name . "modeldata")))
+ (build-system r-build-system)
+ (home-page "https://modeldata.tidymodels.org")
+ (synopsis "Data sets useful for modeling packages")
+ (description
+ "This package provides data sets used for demonstrating or testing
+model-related packages.")
+ (license license:expat)))
+
(define-public r-tidymodels
(package
(name "r-tidymodels")
- (version "0.1.0")
+ (version "0.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidymodels" version))
(sha256
(base32
- "1bi5vh80f6f2ibhyaapgnl7q1mkkx8425vj6ci0ml5rb7l8jhjm8"))))
+ "0w2xnr642klmqlflkw6rkvqcrgs01i8f34nk9wdax3fsl1yx2wi4"))))
(properties `((upstream-name . "tidymodels")))
(build-system r-build-system)
(propagated-inputs
("r-ggplot2" ,r-ggplot2)
("r-infer" ,r-infer)
("r-magrittr" ,r-magrittr)
+ ("r-modeldata" ,r-modeldata)
("r-parsnip" ,r-parsnip)
- ("r-pillar" ,r-pillar)
("r-purrr" ,r-purrr)
("r-recipes" ,r-recipes)
("r-rlang" ,r-rlang)
("r-rsample" ,r-rsample)
("r-rstudioapi" ,r-rstudioapi)
("r-tibble" ,r-tibble)
- ("r-tidyposterior" ,r-tidyposterior)
- ("r-tidypredict" ,r-tidypredict)
- ("r-tidytext" ,r-tidytext)
+ ("r-tidyr" ,r-tidyr)
("r-tune" ,r-tune)
("r-workflows" ,r-workflows)
("r-yardstick" ,r-yardstick)))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ `(("r-knitr" ,r-knitr)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("pandoc" ,pandoc)
+ ("pandoc-citeproc" ,pandoc-citeproc))) ; for vignettes
(home-page "https://github.com/tidymodels/tidymodels")
(synopsis "Tidy collection for modeling and statistical analysis")
(description
statistical analysis that share the underlying design philosophy, grammar, and
data structures of the tidyverse.")
(license license:gpl3)))
+
+(define-public r-mlecens
+ (package
+ (name "r-mlecens")
+ (version "0.1-4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "MLEcens" version))
+ (sha256
+ (base32
+ "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945"))))
+ (properties `((upstream-name . "MLEcens")))
+ (build-system r-build-system)
+ (home-page "http://stat.ethz.ch/~maathuis/")
+ (synopsis "Computation of the MLE for bivariate (interval) censored data")
+ (description
+ "This package contains functions to compute the nonparametric
+@dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
+@code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
+To be more precise, we consider the situation where we observe a set of
+rectangles that are known to contain the unobservable realizations of (X,Y).
+We compute the MLE based on such a set of rectangles. The methods can also be
+used for univariate censored data (see data set @code{cosmesis}), and for
+censored data with competing risks (see data set @code{menopause}). The
+package also provides functions to visualize the observed data and the MLE.")
+ (license license:gpl2+)))
+
+(define-public r-perm
+ (package
+ (name "r-perm")
+ (version "1.0-0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "perm" version))
+ (sha256
+ (base32
+ "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk"))))
+ (properties `((upstream-name . "perm")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/perm/")
+ (synopsis "Exact or asymptotic permutation tests")
+ (description
+ "This package provides several methods for performing permutation tests.
+It has three main functions, to perform linear permutation tests. These tests
+are tests where the test statistic is the sum of the product of a
+covariate (usually group indicator) and the scores.")
+ ;; Any version of the GPL
+ (license license:gpl2+)))
+
+(define-public r-qtl
+ (package
+ (name "r-qtl")
+ (version "1.46-2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "qtl" version))
+ (sha256
+ (base32
+ "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a"))))
+ (build-system r-build-system)
+ (home-page "https://rqtl.org/")
+ (synopsis "R package for analyzing QTL experiments in genetics")
+ (description "R/qtl is an extension library for the R statistics system.
+It is used to analyze experimental crosses for identifying genes contributing
+to variation in quantitative traits (so-called quantitative trait loci, QTLs).
+
+Using a hidden Markov model, R/qtl estimates genetic maps, to identify
+genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
+genome scans.")
+ (license license:gpl3)))
+
+(define-public r-qtl2
+ (package
+ (name "r-qtl2")
+ (version "0.22-11")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "qtl2" version))
+ (sha256
+ (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-data-table" ,r-data-table)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppeigen" ,r-rcppeigen)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-yaml" ,r-yaml)))
+ (home-page "https://kbroman.org/qtl2/")
+ (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
+ (description
+ "This package provides a set of tools to perform @dfn{Quantitative Trait
+Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
+@code{R/qtl} package to better handle high-dimensional data and complex cross
+designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
+ (license license:gpl3)))
+
+(define-public r-seqminer
+ (package
+ (name "r-seqminer")
+ (version "8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "seqminer" version))
+ (sha256
+ (base32
+ "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
+ (build-system r-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "http://seqminer.genomic.codes")
+ (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
+ (description
+ "This package provides tools to integrate nucleotide sequencing
+data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
+ ;; Any version of the GPL is acceptable
+ (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-maldiquant
+ (package
+ (name "r-maldiquant")
+ (version "1.19.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "MALDIquant" version))
+ (sha256
+ (base32
+ "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
+ (properties `((upstream-name . "MALDIquant")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/MALDIquant")
+ (synopsis "Quantitative analysis of mass spectrometry data")
+ (description
+ "This package provides a complete analysis pipeline for matrix-assisted
+laser desorption/ionization-time-of-flight (MALDI-TOF) and other
+two-dimensional mass spectrometry data. In addition to commonly used plotting
+and processing methods it includes distinctive features, namely baseline
+subtraction methods such as morphological filters (TopHat) or the
+statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
+alignment using warping functions, handling of replicated measurements as well
+as allowing spectra with different resolutions.")
+ (license license:gpl3+)))
+
+(define-public r-seurat
+ (package
+ (name "r-seurat")
+ (version "3.2.1")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "Seurat" version))
+ (sha256
+ (base32
+ "0jipc4xpmx56jzc31w6nsl77ah8x8wq7jclg2mxhjql4ixkwmz54"))))
+ (properties `((upstream-name . "Seurat")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-cluster" ,r-cluster)
+ ("r-cowplot" ,r-cowplot)
+ ("r-fitdistrplus" ,r-fitdistrplus)
+ ("r-future" ,r-future)
+ ("r-future-apply" ,r-future-apply)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggrepel" ,r-ggrepel)
+ ("r-ggridges" ,r-ggridges)
+ ("r-httr" ,r-httr)
+ ("r-ica" ,r-ica)
+ ("r-igraph" ,r-igraph)
+ ("r-irlba" ,r-irlba)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-kernsmooth" ,r-kernsmooth)
+ ("r-leiden" ,r-leiden)
+ ("r-lmtest" ,r-lmtest)
+ ("r-mass" ,r-mass)
+ ("r-matrix" ,r-matrix)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-miniui" ,r-miniui)
+ ("r-patchwork" ,r-patchwork)
+ ("r-pbapply" ,r-pbapply)
+ ("r-plotly" ,r-plotly)
+ ("r-png" ,r-png)
+ ("r-rann" ,r-rann)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppannoy" ,r-rcppannoy)
+ ("r-rcppeigen" ,r-rcppeigen)
+ ("r-rcppprogress" ,r-rcppprogress)
+ ("r-reticulate" ,r-reticulate)
+ ("r-rlang" ,r-rlang)
+ ("r-rocr" ,r-rocr)
+ ("r-rsvd" ,r-rsvd)
+ ("r-rtsne" ,r-rtsne)
+ ("r-scales" ,r-scales)
+ ("r-sctransform" ,r-sctransform)
+ ("r-shiny" ,r-shiny)
+ ("r-spatstat" ,r-spatstat)
+ ("r-tibble" ,r-tibble)
+ ("r-uwot" ,r-uwot)))
+ (home-page "http://www.satijalab.org/seurat")
+ (synopsis "Seurat is an R toolkit for single cell genomics")
+ (description
+ "This package is an R package designed for QC, analysis, and
+exploration of single cell RNA-seq data. It easily enables widely-used
+analytical techniques, including the identification of highly variable genes,
+dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
+algorithms; density clustering, hierarchical clustering, k-means, and the
+discovery of differentially expressed genes and markers.")
+ (license license:gpl3)))
+
+(define-public r-phangorn
+ (package
+ (name "r-phangorn")
+ (version "2.5.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "phangorn" version))
+ (sha256
+ (base32
+ "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-fastmatch" ,r-fastmatch)
+ ("r-igraph" ,r-igraph)
+ ("r-magrittr" ,r-magrittr)
+ ("r-matrix" ,r-matrix)
+ ("r-quadprog" ,r-quadprog)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://github.com/KlausVigo/phangorn")
+ (synopsis "Phylogenetic analysis in R")
+ (description
+ "Phangorn is a package for phylogenetic analysis in R. It supports
+estimation of phylogenetic trees and networks using Maximum Likelihood,
+Maximum Parsimony, distance methods and Hadamard conjugation.")
+ (license license:gpl2+)))
+
+(define-public r-diversitree
+ (package
+ (name "r-diversitree")
+ (version "0.9-14")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "diversitree" version))
+ (sha256
+ (base32
+ "0xkxw4n1rsagip51smh9k0h0lmnnvsajqcxma7yh95ifdkyrcyy4"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-desolve" ,r-desolve)
+ ("r-rcpp" ,r-rcpp)
+ ("r-subplex" ,r-subplex)))
+ (home-page "https://www.zoology.ubc.ca/prog/diversitree")
+ (synopsis "Comparative 'phylogenetic' analyses of diversification")
+ (description "This package contains a number of comparative \"phylogenetic\"
+methods, mostly focusing on analysing diversification and character evolution.
+Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
+and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
+Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
+include Markov models of discrete and continuous trait evolution and constant
+rate speciation and extinction.")
+ (license license:gpl2+)))
+
+(define-public r-absfiltergsea
+ (package
+ (name "r-absfiltergsea")
+ (version "1.5.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "AbsFilterGSEA" version))
+ (sha256
+ (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
+ (properties `((upstream-name . "AbsFilterGSEA")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-deseq" ,r-deseq)
+ ("r-limma" ,r-limma)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)))
+ (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
+ (synopsis "Improved false positive control of gene-permuting with absolute filtering")
+ (description
+ "This package provides a function that performs gene-permuting of a gene-set
+enrichment analysis (GSEA) calculation with or without the absolute filtering.
+ Without filtering, users can perform (original) two-tailed or one-tailed
+absolute GSEA.")
+ (license license:gpl2)))
HCoop / jackhill / guix / guix.git / blobdiff