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-rw-r--r--gnu/packages/statistics.scm420
1 files changed, 331 insertions, 89 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 3c966e049f..ff0b9c2833 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -34,6 +34,7 @@
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages statistics)
+ #:use-module (guix gexp)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
@@ -109,6 +110,14 @@
(base32
"0lqrash677b09zxdlxp89z6k02y4i23mbqg83956dwl69wc53dan"))))
(build-system gnu-build-system)
+ (arguments
+ (list #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'check 'prepare-tests
+ ;; Prevent irrelevant errors that cause test output mismatches:
+ ;; ‘Fontconfig error: No writable cache directories’
+ (lambda _
+ (setenv "XDG_CACHE_HOME" (getcwd)))))))
(inputs
(list cairo
gettext-minimal
@@ -676,13 +685,13 @@ nonlinear mixed-effects models.")
(define-public r-mgcv
(package
(name "r-mgcv")
- (version "1.8-38")
+ (version "1.8-39")
(source
(origin
(method url-fetch)
(uri (cran-uri "mgcv" version))
(sha256
- (base32 "1fyx8b0xjyx75mp90v314gayzydkca5y90p76jnwxzfnhxbys4nd"))))
+ (base32 "15h1k9qyn8s8xy4x2361mj42vdq8ml5xskzqpkc45zj1a3gss6w4"))))
(build-system r-build-system)
(propagated-inputs
(list r-matrix r-nlme))
@@ -717,14 +726,14 @@ single hidden layer, and for multinomial log-linear models.")
(define-public r-rpart
(package
(name "r-rpart")
- (version "4.1-15")
+ (version "4.1.16")
(source
(origin
(method url-fetch)
(uri (cran-uri "rpart" version))
(sha256
(base32
- "0p5frya963ppn476p5dxs2mnarsalksr6gw9zzmjsn8ikq7bx3ib"))))
+ "0p22657j6ps6z1dn0ja2fhq4k5xd1rv3cpwzk6nmjd2si8jpbv17"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/rpart")
(synopsis "Recursive partitioning and regression trees")
@@ -756,14 +765,14 @@ analysis.")
(define-public r-survival
(package
(name "r-survival")
- (version "3.2-13")
+ (version "3.3-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "survival" version))
(sha256
(base32
- "0zrikancm9shixvgng89f1610sphlwljczi0fnjbdqn4l85rrarz"))))
+ "1isdrcvrzi118xiyigckj9sq1xl4m92180brmpzdqzhcrl2qg1ql"))))
(build-system r-build-system)
(propagated-inputs
(list r-matrix))
@@ -986,13 +995,13 @@ algorithms.")
(define-public r-magrittr
(package
(name "r-magrittr")
- (version "2.0.1")
+ (version "2.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "magrittr" version))
(sha256
- (base32 "0pxd99fvg406whqsk9wh756rayrwh84xn3h44zmlpcy23kanbhkm"))))
+ (base32 "19k3q76qlri459iyyfgn9gl0w9lnv9v604yhpbc94nx71l6zvrkv"))))
(build-system r-build-system)
;; knitr needs magrittr
#;
@@ -1031,15 +1040,16 @@ Munsell colour system.")
(define-public r-permute
(package
(name "r-permute")
- (version "0.9-5")
+ (version "0.9-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "permute" version))
(sha256
(base32
- "0ra8p5mf2590azrkas8z2ry7mif77xqxd29n4zgyi5vll225726j"))))
+ "1h4dyhcsv8p3h3qxsy98pib9v79dddvrnq7qx6abkblsazxqzy7g"))))
(build-system r-build-system)
+ (native-inputs (list r-knitr))
;; Tests do not run correctly, but running them properly would entail a
;; circular dependency with vegan.
(home-page "https://github.com/gavinsimpson/permute")
@@ -1241,13 +1251,13 @@ aesthetic attributes.")
(define-public r-ggdendro
(package
(name "r-ggdendro")
- (version "0.1.22")
+ (version "0.1.23")
(source (origin
(method url-fetch)
(uri (cran-uri "ggdendro" version))
(sha256
(base32
- "0skbj487b6f6pj2iz4yq2b9gbgb39cv5dyzhdl3w7ay1k0s5z9ph"))))
+ "1f4fz9llmbpb8gh90aid7dvriadx16xdhsl7832yw4pyqj4fjcrs"))))
(build-system r-build-system)
(propagated-inputs
(list r-ggplot2 r-mass))
@@ -1267,19 +1277,19 @@ agnes cluster diagrams.")
(define-public r-gdtools
(package
(name "r-gdtools")
- (version "0.2.3")
+ (version "0.2.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "gdtools" version))
(sha256
(base32
- "1p3ip0qwpg8f63jfx0b8vbac6l20ddid8xvxzkfi6i858pybnawp"))))
+ "0a1hqg5b484ji4g9dy0zi06wn9w7pk6hiy5ljzc1zgj9mbhlr21j"))))
(build-system r-build-system)
(native-inputs
(list pkg-config))
(inputs
- (list cairo freetype zlib))
+ (list cairo fontconfig freetype zlib))
(propagated-inputs
(list r-rcpp r-systemfonts))
(home-page "https://cran.r-project.org/web/packages/gdtools")
@@ -1292,14 +1302,14 @@ and to generate base64 encoded string from raster matrix.")
(define-public r-svglite
(package
(name "r-svglite")
- (version "2.0.0")
+ (version "2.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "svglite" version))
(sha256
(base32
- "19ggknw5322yw7r1bzhw0bqggcrpn0qxddk7kblpqnra2zz2brkn"))))
+ "16wwhfmp9agdz9azslgd8qs77fllhdp6p0m304qfh2p8qy8gah5d"))))
(build-system r-build-system)
(inputs
(list libpng zlib))
@@ -1397,13 +1407,13 @@ for template use among CRAN packages.")
(define-public r-evaluate
(package
(name "r-evaluate")
- (version "0.14")
+ (version "0.15")
(source (origin
(method url-fetch)
(uri (cran-uri "evaluate" version))
(sha256
(base32
- "0a2y7j534gbgixkwj9r1z76l2vssw4g1hznzbpclc076wkdqpj58"))))
+ "0pbwj02y2j7r0msa7747ih1p32xm9bcyr8fa7bysfslb199ywnl8"))))
(build-system r-build-system)
(home-page "https://github.com/hadley/evaluate")
(synopsis "Parsing and evaluation tools for R")
@@ -1509,13 +1519,13 @@ syntax that can be converted to XHTML or other formats.")
(define-public r-yaml
(package
(name "r-yaml")
- (version "2.2.1")
+ (version "2.3.5")
(source (origin
(method url-fetch)
(uri (cran-uri "yaml" version))
(sha256
(base32
- "10r7g26x73am45niigm3k466030nymnr3v3fjljafzrr5aybf58i"))))
+ "0h2ixd95ww12ir13fdzbvjq4lsz6l8hmgv4bbsi89qd0ah2nrpry"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/yaml/")
(synopsis "Methods to convert R data to YAML and back")
@@ -1630,13 +1640,13 @@ you call it again with the same arguments it returns the pre-computed value.")
(define-public r-crayon
(package
(name "r-crayon")
- (version "1.4.2")
+ (version "1.5.0")
(source (origin
(method url-fetch)
(uri (cran-uri "crayon" version))
(sha256
(base32
- "0mxq87qsvz5znfncrb6yjchzv6iwpn9lr386i02y6xiycizkjd7f"))))
+ "0m3rckps0c8v14h9vqnr81acv0az1jqwlsradcbkb2ndvnpjq4j4"))))
(build-system r-build-system)
(home-page "https://github.com/gaborcsardi/crayon")
(synopsis "Colored terminal output for R")
@@ -1732,13 +1742,13 @@ defined in different packages.")
(define-public r-rlang
(package
(name "r-rlang")
- (version "0.4.12")
+ (version "1.0.2")
(source (origin
(method url-fetch)
(uri (cran-uri "rlang" version))
(sha256
(base32
- "05cr08smr8dlk10m810rw4qi1yhgnny83rwkxib0l4my71br29ia"))))
+ "1k6pzl2x80pycpllvd8n1k62h5cfdwc0hsdwvbicrcxhdwz7rs4d"))))
(build-system r-build-system)
(home-page "http://rlang.tidyverse.org")
(synopsis "Functions for base types, core R and Tidyverse features")
@@ -1780,17 +1790,16 @@ and printing capabilities than traditional data frames.")
(define-public r-dplyr
(package
(name "r-dplyr")
- (version "1.0.7")
+ (version "1.0.8")
(source (origin
(method url-fetch)
(uri (cran-uri "dplyr" version))
(sha256
(base32
- "0g8jsxclj9cgm7a2lyazy78sj62rbzw812lsw3fdsbz0pknkmznj"))))
+ "0xb04ckp29pva1h2rfahqhmk9gcwp2dbbx3av8ip40v7dnha6siv"))))
(build-system r-build-system)
(propagated-inputs
- (list r-ellipsis
- r-generics
+ (list r-generics
r-glue
r-lifecycle
r-magrittr
@@ -1899,14 +1908,14 @@ side.")
(define-public r-locfit
(package
(name "r-locfit")
- (version "1.5-9.4")
+ (version "1.5-9.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "locfit" version))
(sha256
(base32
- "1vcw16qww4v4547w0gfvhqg60l051bsdlxa6zfcgcj9xbxf6dlyr"))))
+ "08yywswywmvyys8380576n43h3xyiviq1p2392zcivlbknnjp7zx"))))
(build-system r-build-system)
(propagated-inputs
(list r-lattice))
@@ -2258,18 +2267,18 @@ worries about execution time overhead.")
(define-public r-bbmisc
(package
(name "r-bbmisc")
- (version "1.11")
+ (version "1.12")
(source
(origin
(method url-fetch)
(uri (cran-uri "BBmisc" version))
(sha256
(base32
- "1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y"))))
+ "0gh5f342rwra79i7imv50x8vrhd2zkifm7khb0yv3ndpd4zn62lh"))))
(properties `((upstream-name . "BBmisc")))
(build-system r-build-system)
(propagated-inputs
- (list r-checkmate))
+ (list r-checkmate r-data-table))
(home-page "https://github.com/berndbischl/BBmisc")
(synopsis "Miscellaneous functions for R package development")
(description
@@ -2333,13 +2342,13 @@ SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
(define-public r-brew
(package
(name "r-brew")
- (version "1.0-6")
+ (version "1.0-7")
(source (origin
(method url-fetch)
(uri (cran-uri "brew" version))
(sha256
(base32
- "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
+ "0vp7d628j6zzxhh6xfw5jlkv7wh6z2l3snbwjgv7jd56vk0mkf1q"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/brew")
(synopsis "Templating framework for report generation")
@@ -2352,17 +2361,17 @@ module, Java Server Pages, and Python's psp module.")
(define-public r-desc
(package
(name "r-desc")
- (version "1.4.0")
+ (version "1.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "desc" version))
(sha256
(base32
- "0jfnwn1kpiill8v4hmzdk90yz4gk2ha0prr2p0hq36s40v3y8842"))))
+ "0m3g5m0g08k674zh4lq0ihmqiwz8jpsfqrdwfqp5p4ngxi8vp7lg"))))
(build-system r-build-system)
(propagated-inputs
- (list r-crayon r-r6 r-rprojroot))
+ (list r-cli r-r6 r-rprojroot))
(home-page "https://github.com/r-pkgs/desc")
(synopsis "Manipulate DESCRIPTION Files")
(description
@@ -2374,14 +2383,14 @@ other packages.")
(define-public r-commonmark
(package
(name "r-commonmark")
- (version "1.7")
+ (version "1.8.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "commonmark" version))
(sha256
(base32
- "024iz1qp2kv6iz6y69ir0jk3qhjps86rhkzlcmhqsxx97rx7cjni"))))
+ "0s765c650id19ygx57bsjsw93fwxywmp50zid671bkxi6wlyf1vx"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/commonmark")
(synopsis "CommonMark and Github Markdown Rendering in R")
@@ -2431,14 +2440,14 @@ collation, and NAMESPACE files.")
(define-public r-openssl
(package
(name "r-openssl")
- (version "1.4.6")
+ (version "2.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "openssl" version))
(sha256
(base32
- "0na3yficxg0hjql9pvz96f66yh4g5k2hfwcricb705z7f2pk5f23"))))
+ "0jsnzxa72bfxsdai25xyklmmrraaf9yv2nmqmf0bgzrkbzkgsa7b"))))
(build-system r-build-system)
(arguments
(list
@@ -2580,13 +2589,13 @@ tools to simplify the devolpment of R packages.")
(define-public r-withr
(package
(name "r-withr")
- (version "2.4.3")
+ (version "2.5.0")
(source (origin
(method url-fetch)
(uri (cran-uri "withr" version))
(sha256
(base32
- "0k4x2bd9wb24n3dyg7rdjicdjs5ay2kk5lfgkrcjsv6cki2wgnlv"))))
+ "1h4bzj0am9lawbh1cam1jmgk1xjmn9da14r90w3q984hswz7nc9p"))))
(build-system r-build-system)
(native-inputs
(list r-knitr))
@@ -2622,13 +2631,13 @@ time-of-day values, based on the @code{difftime} class.")
(define-public r-readr
(package
(name "r-readr")
- (version "2.1.1")
+ (version "2.1.2")
(source (origin
(method url-fetch)
(uri (cran-uri "readr" version))
(sha256
(base32
- "115w3hgp1w6hr0h2nz840i6mm1pnqzwfbxcmf9ca3qs7llc7k4q3"))))
+ "06qcw57yz0fhh3ni41d5w68cbmwmb6zkp47chllwzax43wxd1bwl"))))
(build-system r-build-system)
(propagated-inputs
(list r-cli
@@ -2712,13 +2721,13 @@ well as additional utilities such as panel and axis annotation functions.")
(define-public r-rcpparmadillo
(package
(name "r-rcpparmadillo")
- (version "0.10.7.5.0")
+ (version "0.10.8.1.0")
(source (origin
(method url-fetch)
(uri (cran-uri "RcppArmadillo" version))
(sha256
(base32
- "0516j6n657kxm8sdbxf3jd9z40px9mv7zza4fz8nih63f5iiw1kw"))))
+ "1x7mk85rc4pmn17nm63k6rbkarsmghjapznias268545nfpib97g"))))
(properties `((upstream-name . "RcppArmadillo")))
(build-system r-build-system)
(propagated-inputs
@@ -2804,17 +2813,18 @@ certain criterion, e.g., it contains a certain regular file.")
(define-public r-rmarkdown
(package
(name "r-rmarkdown")
- (version "2.11")
+ (version "2.13")
(source
(origin
(method url-fetch)
(uri (cran-uri "rmarkdown" version))
(sha256
- (base32 "0xcpg9d009a71p5i6jczw02qcp907p5d52lp6vclrsp7019jawck"))))
+ (base32 "0i07p3dxxv2s2a4xmyhc3qxmwg86vakniq5jjjclmcq2sahvw5vj"))))
(properties `((upstream-name . "rmarkdown")))
(build-system r-build-system)
(propagated-inputs
- (list r-evaluate
+ (list r-bslib
+ r-evaluate
r-htmltools
r-jquerylib
r-jsonlite
@@ -2918,13 +2928,13 @@ a column in data frame.")
(define-public r-rsqlite
(package
(name "r-rsqlite")
- (version "2.2.9")
+ (version "2.2.10")
(source (origin
(method url-fetch)
(uri (cran-uri "RSQLite" version))
(sha256
(base32
- "075vsnbkcwpwnn87b06mhbg2fflqhjvbylhbkg0d3v3rl7zg28s4"))))
+ "1a00i24g4d4gvp7qmivpyfm24yfz4w4wsy2kplgfz0i0j0rzzbh6"))))
(properties `((upstream-name . "RSQLite")))
(build-system r-build-system)
(propagated-inputs
@@ -2991,13 +3001,13 @@ ldap, and also supports cookies, redirects, authentication, etc.")
(define-public r-xml
(package
(name "r-xml")
- (version "3.99-0.8")
+ (version "3.99-0.9")
(source (origin
(method url-fetch)
(uri (cran-uri "XML" version))
(sha256
(base32
- "0l3bsgqw4bicv3sl2bfag7p4rh1y2pcyg0ajr73kkbg85qf6j7q8"))))
+ "02ba407ddgil4jbjzrbw756hlxzy3mihc5dk1ngcbvsp67gxw5cw"))))
(properties
`((upstream-name . "XML")))
(build-system r-build-system)
@@ -3112,15 +3122,16 @@ statements.")
(define-public r-segmented
(package
(name "r-segmented")
- (version "1.3-4")
+ (version "1.4-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "segmented" version))
(sha256
(base32
- "0bchqcy308kbywavgyg9kb4543rbkfn753q9c6d7l7aw7sxvyxl2"))))
+ "0xn28gyqzmyz0kv352rkkznbj806arxj2am5a9gqsn1qzv9l0s9h"))))
(build-system r-build-system)
+ (propagated-inputs (list r-mass))
(home-page "https://cran.r-project.org/web/packages/segmented")
(synopsis "Regression models with breakpoints estimation")
(description
@@ -3176,14 +3187,14 @@ standard R subsetting and Kronecker products.")
(define-public r-iterators
(package
(name "r-iterators")
- (version "1.0.13")
+ (version "1.0.14")
(source
(origin
(method url-fetch)
(uri (cran-uri "iterators" version))
(sha256
(base32
- "190i1y2493v5c9z8978rb3idlwsjymy67k1assa9znljqbj313kp"))))
+ "0yv7rh6ghlfx727xy2aq64a7skyxp9msakaffs641q9h15d0gwyf"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/iterators")
(synopsis "Iterator construct for R")
@@ -3196,14 +3207,14 @@ data.")
(define-public r-foreach
(package
(name "r-foreach")
- (version "1.5.1")
+ (version "1.5.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "foreach" version))
(sha256
(base32
- "1qb83b1jvpmk8d6kfibkm5q2hiki0x5gipy758mwa62n56gdcnpv"))))
+ "1r5gdf9fp3rprvrhf0gzl9qmmqhgdn5gscpm5hk8zxpraf3qscsn"))))
(build-system r-build-system)
(propagated-inputs
(list r-codetools r-iterators))
@@ -3225,14 +3236,14 @@ parallel.")
(define-public r-doparallel
(package
(name "r-doparallel")
- (version "1.0.16")
+ (version "1.0.17")
(source
(origin
(method url-fetch)
(uri (cran-uri "doParallel" version))
(sha256
(base32
- "1cjf0mxrxgls5pl7aj22fv9j488craib1wkc9np4f3gkckwjdfzi"))))
+ "1mxbg2qqda1775vb4s26gz27p5n91lljgjmlqxq4sras22njasmr"))))
(properties `((upstream-name . "doParallel")))
(build-system r-build-system)
(propagated-inputs
@@ -3247,14 +3258,14 @@ using the parallel package.")
(define-public r-domc
(package
(name "r-domc")
- (version "1.3.7")
+ (version "1.3.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "doMC" version))
(sha256
(base32
- "0kdmfhp5m1wisjbfyl9d040jrmjmhcgjb0vdi536g2i9vixb5yny"))))
+ "18qrcvqwm4cclvk8spvyi281y8prwzivj52xmzk1l9a82j2ny65j"))))
(properties `((upstream-name . "doMC")))
(build-system r-build-system)
(propagated-inputs
@@ -3554,13 +3565,13 @@ using the multicore functionality of the parallel package.")
"datatables-extensions/Select"))))
(package
(name "r-dt")
- (version "0.20")
+ (version "0.21")
(source (origin
(method url-fetch)
(uri (cran-uri "DT" version))
(sha256
(base32
- "17xs18i439p15agyk7z2xyyrwgrpn5pw09kd3jwxn7qhxi4pyvf6"))
+ "1yhlph9h8z78wqjddv598l2xrqpp605d70cxfb69m53hanw4hmzn"))
(modules '((guix build utils)))
(snippet
'(for-each delete-file
@@ -4146,14 +4157,14 @@ more complete @code{viridis} package.")
(define-public r-tidyselect
(package
(name "r-tidyselect")
- (version "1.1.1")
+ (version "1.1.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidyselect" version))
(sha256
(base32
- "0ss8mq05mwif64cj8zmrfx0ljgy3n0fvyv7f37782shr8rknmsqq"))))
+ "0w423pmg9wjx6q2rnp2ap66323rxvpmzd4nnsqq4m58pajqs7283"))))
(build-system r-build-system)
(propagated-inputs
(list r-ellipsis r-glue r-purrr r-rlang r-vctrs))
@@ -4171,14 +4182,14 @@ selection.")
(define-public r-tidyr
(package
(name "r-tidyr")
- (version "1.1.4")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidyr" version))
(sha256
(base32
- "0h8jfsmn4r7zgfyjmg2qkjd54n0sncq07xjh4mdf2cx4k2z9h30b"))))
+ "1a0k296a0jb2xi5zgfrqfmmw8197bwibjl7a04fm49vqx6livl4c"))))
(build-system r-build-system)
(propagated-inputs
(list r-cpp11
@@ -5033,14 +5044,14 @@ perform @dfn{independent component analysis} (ICA) and projection pursuit.")
(define-public r-randomforest
(package
(name "r-randomforest")
- (version "4.6-14")
+ (version "4.7-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "randomForest" version))
(sha256
(base32
- "0kbmm0l42fc2d1rdq0l7k09d34kd87q4lx651ffsic4y84h8kf7l"))))
+ "04q6gb917md4yw837cf9vlx1q8ljl06jw7yhykzb6nl47w55jnkq"))))
(properties `((upstream-name . "randomForest")))
(build-system r-build-system)
(home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
@@ -5233,14 +5244,14 @@ analysis} (PCA) by projection pursuit.")
(define-public r-rrcov
(package
(name "r-rrcov")
- (version "1.6-0")
+ (version "1.6-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "rrcov" version))
(sha256
(base32
- "0i69gv55c86gkclwhch0jzdfyb20l20mx1nx1xp9qz71nd4klpvr"))))
+ "18x8y2b9n2plpn4086nkjk9c27p7gb78kbrv5pj9r8fb0idl5rn5"))))
(build-system r-build-system)
(propagated-inputs
(list r-lattice r-mvtnorm r-pcapp r-robustbase))
@@ -5284,14 +5295,14 @@ generally.")
(define-public r-robust
(package
(name "r-robust")
- (version "0.6-1")
+ (version "0.7-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "robust" version))
(sha256
(base32
- "0z8i0qqlsa6vpl457qir3dlsynhjfn2g22436d776vxwyqjx4vs9"))))
+ "1fc4h19b7gn9ya2j2ia8vfgsycwlyc23frj54k11dr45w4qaq6jy"))))
(build-system r-build-system)
(propagated-inputs
(list r-fit-models r-lattice r-mass r-robustbase r-rrcov))
@@ -5361,13 +5372,13 @@ groupings.")
(define-public r-vgam
(package
(name "r-vgam")
- (version "1.1-5")
+ (version "1.1-6")
(source
(origin
(method url-fetch)
(uri (cran-uri "VGAM" version))
(sha256
- (base32 "1fx123h4x5awzshv0m4jqbbllrdjfpslb2i8gl9phm1y1wahn69h"))))
+ (base32 "05yl1lbpambwg3i3rqn6aanaym7c3s8g7hi0bph98iyxqnx62sj4"))))
(properties `((upstream-name . "VGAM")))
(build-system r-build-system)
(native-inputs
@@ -5496,18 +5507,18 @@ using modular prediction and response module classes.")
(define-public r-quantreg
(package
(name "r-quantreg")
- (version "5.86")
+ (version "5.88")
(source
(origin
(method url-fetch)
(uri (cran-uri "quantreg" version))
(sha256
- (base32 "01fnp6ndh7npxj76xlynndacsgmcfr9kgh2waw0clx3mmwlwilbi"))))
+ (base32 "0grsha18zkiil0qnxc1d7kc3w26i6aaa4av9n9ahdm8yf59yah0r"))))
(build-system r-build-system)
(native-inputs
(list gfortran))
(propagated-inputs
- (list r-conquer r-matrix r-matrixmodels r-sparsem))
+ (list r-matrix r-matrixmodels r-sparsem))
(home-page "https://www.r-project.org")
(synopsis "Quantile regression")
(description
@@ -5521,20 +5532,21 @@ expected shortfall risk are also included.")
(define-public r-nloptr
(package
(name "r-nloptr")
- (version "1.2.2.3")
+ (version "2.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "nloptr" version))
(sha256
(base32
- "1zznk9f2w2g02zqzay21k8xqzfvc6icxfzp6bx2wpd77sm7vf25g"))))
+ "16k124ll14p3ygny6i1zd7yza83bv2sk87x922n1bfn9rx4k3jk5"))))
(build-system r-build-system)
(native-inputs
(list r-knitr ; for building vignettes
pkg-config gfortran))
(inputs
(list nlopt))
+ (propagated-inputs (list r-testthat))
(home-page "https://cran.r-project.org/web/packages/nloptr")
(synopsis "R interface to NLopt")
(description
@@ -5548,14 +5560,14 @@ algorithms.")
(define-public r-lme4
(package
(name "r-lme4")
- (version "1.1-27.1")
+ (version "1.1-28")
(source
(origin
(method url-fetch)
(uri (cran-uri "lme4" version))
(sha256
(base32
- "1i9f8kl2qj48j75dbn1vmwxz1xlbikdr7v2yq542w6dq74z8gyi5"))))
+ "03nw76bfyas6cdm9chyxqm5ks6r0qklf2fdy7h4pqrqss325x1fi"))))
(build-system r-build-system)
(propagated-inputs
(list r-boot
@@ -5756,14 +5768,14 @@ first and second order derivatives.")
(define-public r-sn
(package
(name "r-sn")
- (version "2.0.1")
+ (version "2.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "sn" version))
(sha256
(base32
- "1z58kwvq8igjm3biyyjdlhs2qq8hfjq5d9x0lzy80yk5hw08kcw6"))))
+ "140p1pl5sq0laxhcm16kbqm986hlhqj90gj3jccga491gh14jywm"))))
(build-system r-build-system)
(propagated-inputs
(list r-mnormt r-numderiv r-quantreg))
@@ -6072,6 +6084,130 @@ table made by the command @code{show256Colors()}. You can also set the colors
to any arbitrary string. In this case, it is up to you to set valid values.")
(license license:gpl3+)))
+(define-public r-nnlm
+ (let ((commit "4574bca9456fe2285b668b4c22a908cffbad10a0")
+ (revision "1"))
+ (package
+ (name "r-nnlm")
+ (version (git-version "0.4.4" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/linxihui/NNLM")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1qzvav4ch0j1k7jcqzk9cvl8dx79fapmvdzmzzyl8smscybhfgba"))))
+ (properties `((upstream-name . "NNLM")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-rcpp r-rcpparmadillo r-rcppprogress))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/linxihui/NNLM")
+ (synopsis "Fast and versatile non-negative matrix factorization")
+ (description
+ "This is a package for @dfn{Non-Negative Linear Models} (NNLM). It
+implements fast sequential coordinate descent algorithms for non-negative
+linear regression and @dfn{non-negative matrix factorization} (NMF). It
+supports mean square error and Kullback-Leibler divergence loss. Many other
+features are also implemented, including missing value imputation, domain
+knowledge integration, designable W and H matrices and multiple forms of
+regularizations.")
+ (license license:bsd-2))))
+
+(define-public r-swne
+ (let ((commit "05fc3ee4e09b2c34d99c69d3b97cece4c1c34143")
+ (revision "1"))
+ (package
+ (name "r-swne")
+ (version (git-version "0.6.20" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/yanwu2014/swne")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0crlpg9kclbv4v8250p3086a3lk6f2hcq79psqkdylc1qnrx3kfx"))))
+ (properties `((upstream-name . "swne")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-fnn
+ r-ggplot2
+ r-ggrepel
+ r-hash
+ r-ica
+ r-igraph
+ r-irlba
+ r-jsonlite
+ r-liger
+ r-mass
+ r-matrix
+ r-mgcv
+ r-nnlm ;not listed but required at install time
+ r-plyr
+ r-proxy
+ r-rcolorbrewer
+ r-rcpp
+ r-rcpparmadillo
+ r-rcppeigen
+ r-reshape
+ r-reshape2
+ r-snow
+ r-umap
+ r-usedist))
+ (home-page "https://github.com/yanwu2014/swne")
+ (synopsis "Visualize high dimensional datasets")
+ (description
+ "@dfn{Similarity Weighted Nonnegative Embedding} (SWNE) is a method for
+visualizing high dimensional datasets. SWNE uses Nonnegative Matrix
+Factorization to decompose datasets into latent factors, projects those
+factors onto 2 dimensions, and embeds samples and key features in 2 dimensions
+relative to the factors. SWNE can capture both the local and global dataset
+structure, and allows relevant features to be embedded directly onto the
+visualization, facilitating interpretation of the data.")
+ (license license:gpl2))))
+
+(define-public r-languageserver
+ (let ((commit "004da9388f9b19990f031c8dc9b527fb406378ba")
+ (revision "1"))
+ (package
+ (name "r-languageserver")
+ (version (git-version "0.3.12" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/REditorSupport/languageserver")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "05f22bjpc87fngzq4jsk2q2yb2i3ha03b377r0wx15d0b8xaa1ix"))))
+ (properties `((upstream-name . "languageserver")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-callr
+ r-collections
+ r-fs
+ r-jsonlite
+ r-lintr
+ r-r6
+ r-roxygen2
+ r-stringi
+ r-styler
+ r-xml2
+ r-xmlparsedata))
+ (home-page "https://github.com/REditorSupport/languageserver")
+ (synopsis "Language Server for R")
+ (description
+ "This package provides an implementation of the Language Server
+Protocol for R. The
+@url{https://microsoft.github.io/language-server-protocol/,Language Server
+protocol} is used by an editor client to integrate features like auto
+completion.")
+ (license license:expat))))
+
(define-public python-rpy2
(package
(name "python-rpy2")
@@ -6851,3 +6987,109 @@ is used to allow menus, dialogs, and the response to mouse actions to be
customized.")
(home-page "http://homepage.divms.uiowa.edu/~luke/xls/xlsinfo/")
(license license:expat))))
+
+(define-public r-rlrsim
+ (package
+ (name "r-rlrsim")
+ (version "3.1-6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "RLRsim" version))
+ (sha256
+ (base32 "1wkkibr250frsbfq70m9jdrylxb492zibf5w03z6zis98pjffssp"))))
+ (properties `((upstream-name . "RLRsim")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-lme4 r-mgcv r-nlme r-rcpp))
+ (home-page "https://github.com/fabian-s/RLRsim")
+ (synopsis
+ "Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive Models")
+ (description
+ "Rapid, simulation-based exact (restricted) likelihood ratio tests for testing
+the presence of variance components/nonparametric terms for models fit with
+@code{nlme::lme()}, @code{lme4::lmer()}, @code{lmeTest::lmer()},
+@code{gamm4::gamm4()}, @code{mgcv::gamm()} and @code{SemiPar::spm()}.")
+ (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-binom
+ (package
+ (name "r-binom")
+ (version "1.1-1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "binom" version))
+ (sha256
+ (base32 "0mjj92dqf5q69jxzqya4izb1mly3mkydbnmlm4wb3zqqg82a324c"))))
+ (properties `((upstream-name . "binom")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/package=binom")
+ (synopsis "Binomial Confidence Intervals For Several Parameterizations")
+ (description
+ "Constructs confidence intervals on the probability of success in a binomial
+experiment via several parameterizations")
+ (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-simr
+ (package
+ (name "r-simr")
+ (version "1.0.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "simr" version))
+ (sha256
+ (base32 "1q8ip54c5pc7pjf8127jpk56nr3f8rmwqdcrr84faj4lfbr27wqb"))))
+ (properties `((upstream-name . "simr")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-binom
+ r-car
+ r-iterators
+ r-lme4
+ r-lmertest
+ r-pbkrtest
+ r-plotrix
+ r-plyr
+ r-rlrsim
+ r-stringr))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/pitakakariki/simr")
+ (synopsis
+ "Power analysis for generalized linear mixed models by simulation")
+ (description
+ "This package lets you calculate power for generalized linear mixed
+models, using simulation. It was designed to work with models fit using the
+@code{lme4} package. The package is described in
+@url{doi:10.1111/2041-210X.12504, Green and MacLeod (2016)}.")
+ (license license:gpl2+)))
+
+(define-public r-mixedpower
+ (package
+ (name "r-mixedpower")
+ (version "2.0")
+ (source
+ (origin
+ ;; Not available on CRAN.
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/DejanDraschkow/mixedpower")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1dy1i8lijbq59xl7482j17a0r4rsdy61smzddk8jsr8nygp2gqy8"))))
+ (properties `((upstream-name . "mixedpower")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-doparallel r-foreach r-ggplot2 r-lme4 r-reshape2))
+ (home-page "https://github.com/DejanDraschkow/mixedpower")
+ (synopsis
+ "Pilotdata based simulations for estimating power in linear mixed models")
+ (description
+ "Implementation of a simulation based aproach to power analysis. Mixedpower uses
+lotdata and a linear mixed model fitted with lme4 to simulate new data sets.
+wer is computed seperate for every effect in the model output as the relation
+significant simulations to all simulations. More conservative simulations as
+protection against a bias in the pilotdata are available aswell as methods for
+otting the results.")
+ (license license:gpl3)))
generated by cgit v1.2.3 (git 2.45.2) at 2024-07-11 13:45:44 +0000