diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 507 |
1 files changed, 440 insertions, 67 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 838428fde9..1bc5aa78ff 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -41,6 +41,7 @@ #:use-module (gnu packages icu4c) #:use-module (gnu packages image) #:use-module (gnu packages java) + #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages multiprecision) #:use-module (gnu packages pcre) @@ -237,13 +238,13 @@ effects of different types of color-blindness.") (define-public r-digest (package (name "r-digest") - (version "0.6.9") + (version "0.6.10") (source (origin (method url-fetch) (uri (cran-uri "digest" version)) (sha256 - (base32 "0ixy1mb7kfl20lkckqiilpw03g1ip4ibihs03gicz7w625hc7zcm")))) + (base32 "07825781nl85gx3pqskc04ywgs0f874qj9z2nyrwz7h0aqks0l8c")))) (build-system r-build-system) ;; Vignettes require r-knitr, which requires r-digest, so we have to ;; disable them and the tests. @@ -300,6 +301,30 @@ non-estimable cases correctly.") \"tables\" of grobs.") (license license:gpl2+))) +(define-public r-pheatmap + (package + (name "r-pheatmap") + (version "1.0.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "pheatmap" version)) + (sha256 + (base32 + "1ik0k69kb4n7xl3bkx4p09kw08ri93855zcsxq1c668171jqfiji")))) + (build-system r-build-system) + (propagated-inputs + `(("r-gtable" ,r-gtable) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-scales" ,r-scales))) + (home-page + "http://cran.r-project.org/web/packages/pheatmap") + (synopsis "Pretty heatmaps") + (description + "This package provides an implementation of heatmaps that offers more +control over dimensions and appearance.") + (license license:gpl2+))) + (define-public r-labeling (package (name "r-labeling") @@ -361,13 +386,13 @@ Munsell colour system.") (define-public r-rcpp (package (name "r-rcpp") - (version "0.12.5") + (version "0.12.7") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "1vw0zbd6zhqixqg7h8ahn1dr1hb492365x419nrp2lhvr60r8i0k")))) + (base32 "1ipid4yfqp1k5c70f7bz7izzq63srmrcxhiqrnyilk2wgrvd7ypb")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ Integration") @@ -382,17 +407,39 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see 'citation(\"Rcpp\")' for details on these last two.") (license license:gpl2+))) +(define-public r-matrix + (package + (name "r-matrix") + (version "1.2-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "Matrix" version)) + (sha256 + (base32 + "18x3mdq5cdhbk1lw5cj7vbr41lk8w9p4i5kzh8wslgq6p3d9ac3c")))) + (properties `((upstream-name . "Matrix"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice))) + (home-page "http://Matrix.R-forge.R-project.org/") + (synopsis "Sparse and dense matrix classes and methods") + (description + "This package provides classes and methods for dense and sparse matrices +and operations on them using LAPACK and SuiteSparse.") + (license license:gpl2+))) + (define-public r-mgcv (package (name "r-mgcv") - (version "1.8-12") + (version "1.8-14") (source (origin (method url-fetch) (uri (cran-uri "mgcv" version)) (sha256 (base32 - "1khzy36nn6xbnzqfc2953ng0sv8w91mns1ymhibaqn1150x1qid0")))) + "0ly9x23q6kd7aqrsb8qjsj8jc597h3068iaqjmkkdv56r5dln29f")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/mgcv") (synopsis "Mixed generalised additive model computation") @@ -406,14 +453,14 @@ distributions beyond the exponential family.") (define-public r-permute (package (name "r-permute") - (version "0.9-0") + (version "0.9-4") (source (origin (method url-fetch) (uri (cran-uri "permute" version)) (sha256 (base32 - "0w68cqw6s4pixix8bh1qzsy1pm64jqh1cjznw74h82ygp8sj7p73")))) + "1w8wzk1fg9q7wvisnfp2js70dg0m9wi12gkdhpyngpbdcgssahd5")))) (build-system r-build-system) ;; Tests do not run correctly, but running them properly would entail a ;; circular dependency with vegan. @@ -429,13 +476,13 @@ in which the whole-plots or split-plots or both can be freely exchangeable.") (define-public r-plyr (package (name "r-plyr") - (version "1.8.3") + (version "1.8.4") (source (origin (method url-fetch) (uri (cran-uri "plyr" version)) (sha256 - (base32 "06v4zxawpjz37rp2q2ii5q43g664z9s29j4ydn0cz3crn7lzl6pk")))) + (base32 "1igar5pcjqh0jyxv0z3jah8rz617vfa86vw0r5c7c031b7bj5db0")))) (build-system r-build-system) (native-inputs `(("r-rcpp" ,r-rcpp))) (home-page "http://had.co.nz/plyr") @@ -485,17 +532,40 @@ designed by Cynthia Brewer as described at http://colorbrewer2.org") ;; Includes code licensed under bsd-4 (license license:asl2.0))) +(define-public r-sendmailr + (package + (name "r-sendmailr") + (version "1.2-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "sendmailR" version)) + (sha256 + (base32 + "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4")))) + (properties `((upstream-name . "sendmailR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc))) + (home-page + "http://cran.r-project.org/web/packages/sendmailR") + (synopsis "Send email using R") + (description + "This package contains a simple SMTP client which provides a portable +solution for sending email, including attachments, from within R.") + (license license:gpl2+))) + (define-public r-stringi (package (name "r-stringi") - (version "1.0-1") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "stringi" version)) (sha256 (base32 - "1ld38536sswyywp6pyys3v8vkngbk5cksrhdxp8jyr6bz7qf8j77")))) + "0rg14hga1g2havd3imhk04iyh1dnisnmxf7yhiiwhs7y72hphc94")))) (build-system r-build-system) (inputs `(("icu4c" ,icu4c))) (native-inputs `(("pkg-config" ,pkg-config))) @@ -514,13 +584,13 @@ transliteration, concatenation, date-time formatting and parsing, etc.") (define-public r-stringr (package (name "r-stringr") - (version "1.0.0") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "stringr" version)) (sha256 - (base32 "0jnz6r9yqyf7dschr2fnn1slg4wn6b4ik5q00j4zrh43bfw7s9pq")))) + (base32 "0css5j4psl80br75chg6s1s3ipzf89f71bnbys34flp9yghg1cfc")))) (build-system r-build-system) (propagated-inputs `(("r-magrittr" ,r-magrittr) @@ -685,13 +755,13 @@ wrong.") (define-public r-lazyeval (package (name "r-lazyeval") - (version "0.1.10") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "lazyeval" version)) (sha256 (base32 - "02qfpn2fmy78vx4jxr7g7rhqzcm1kcivfwai7lbh0vvpawia0qwh")))) + "1jwdz40nznlc44hpjli7h98gnpa4d98ifggmj7z88h84n9aqywqk")))) (build-system r-build-system) (home-page "https://github.com/hadley/lazyeval") (synopsis "Lazy (non-standard) evaluation in R") @@ -703,13 +773,13 @@ evaluation (NSE) in R.") (define-public r-dbi (package (name "r-dbi") - (version "0.4-1") + (version "0.5-1") (source (origin (method url-fetch) (uri (cran-uri "DBI" version)) (sha256 (base32 - "13n6ibmrma42qmq17qgkyjsc0ciwqf17sd7lw7w26pwpyjd4mwgg")))) + "1idwm9lkmz6ns6h0vvgml18mg0k7vjqiv9p5svrdcmx7r1rirpdi")))) (build-system r-build-system) (home-page "https://github.com/rstats-db/DBI") (synopsis "R database interface") @@ -802,13 +872,13 @@ supported via Andre Simon's highlight package.") (define-public r-mime (package (name "r-mime") - (version "0.4") + (version "0.5") (source (origin (method url-fetch) (uri (cran-uri "mime" version)) (sha256 (base32 - "145cdcg252w2zsq67dmvmsqka60msfp7agymlxs3gl3ihgiwg46p")))) + "0i91m3ivaja1k33jwcvz16pfjypkci27awm8glil7sxhmwaj3izw")))) (build-system r-build-system) (home-page "https://github.com/yihui/mime") (synopsis "R package to map filenames to MIME types") @@ -864,13 +934,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.13") + (version "1.14") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "0v69846myi4fbjp8wiik4295fhba67s3i6ccysghm6x031i2f26q")))) + "1v0s0knb294p7a2xkwy35bhg0w8p3qcgyphd748sj86hh8a30vds")))) (build-system r-build-system) (propagated-inputs `(("r-evaluate" ,r-evaluate) @@ -995,13 +1065,13 @@ you call it again with the same arguments it returns the pre-computed value.") (define-public r-crayon (package (name "r-crayon") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "crayon" version)) (sha256 (base32 - "0d38fm06h272a8iqlc0d45m2rh36giwqw7mwq4z8hkp4vs975fmm")))) + "0s2yam18slph7xsw4pyc9f92gdyf609r5w92yax69zh57kb7asws")))) (build-system r-build-system) (propagated-inputs `(("r-memoise" ,r-memoise))) @@ -1061,13 +1131,13 @@ flexible and easy to set up.") (define-public r-r6 (package (name "r-r6") - (version "2.1.2") + (version "2.1.3") (source (origin (method url-fetch) (uri (cran-uri "R6" version)) (sha256 (base32 - "0yad91i9p4r8bbz6nq8zny39y767n9an7ak5p275ynx8km6v3yqv")))) + "19qrkgxvssyi51fm80h93sabzz0n2vgqgv1w8xjqbsap0nx379vy")))) (build-system r-build-system) (home-page "https://github.com/wch/R6/") (synopsis "Classes with reference semantics in R") @@ -1080,23 +1150,47 @@ private members, and they support inheritance, even when the classes are defined in different packages.") (license license:expat))) +(define-public r-tibble + (package + (name "r-tibble") + (version "1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "tibble" version)) + (sha256 + (base32 + "011i352ylq9b4xfcj7h10h7qsqd9qkc1rzc0pr1gf8qjb788p2pd")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-lazyeval" ,r-lazyeval) + ("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/hadley/tibble") + (synopsis "Simple data frames") + (description + "This package provides a @code{tbl_df} class that offers better checking +and printing capabilities than traditional data frames.") + (license license:expat))) + (define-public r-dplyr (package (name "r-dplyr") - (version "0.4.3") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "dplyr" version)) (sha256 (base32 - "1p8rbn4p4yrx2840dapwiahf9iqa8gnvd35nyc200wfhmrxlqdlc")))) + "0ks5cklb03laqf5ygcw986g1lv7wk1ipvypjlha8xly2y4lvilwk")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-r6" ,r-r6) ("r-magrittr" ,r-magrittr) ("r-lazyeval" ,r-lazyeval) - ("r-dbi" ,r-dbi))) + ("r-dbi" ,r-dbi) + ("r-tibble" ,r-tibble))) (native-inputs `(("r-rcpp" ,r-rcpp) ("r-bh" ,r-bh))) @@ -1431,14 +1525,14 @@ and environmental data in the framework of Euclidean exploratory methods.") (define-public r-xml2 (package (name "r-xml2") - (version "0.1.2") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "xml2" version)) (sha256 (base32 - "0jjilz36h7vbdbkpvjnja1vgjf6d1imql3z4glqn2m2b74w5qm4c")))) + "0f2alsrk3yykznbhnz4pcsg9mb72cv607vbapqx5kqfv39772kgr")))) (build-system r-build-system) (inputs `(("libxml2" ,libxml2))) @@ -1455,14 +1549,14 @@ files in R. It is built on top of the libxml2 C library.") (define-public r-multitaper (package (name "r-multitaper") - (version "1.0-11") + (version "1.0-12") (source (origin (method url-fetch) (uri (cran-uri "multitaper" version)) (sha256 (base32 - "1s0lmjzpyd7zmc2p1ywv5fm7qkq357p70b76gw9wjlms6d81j1n4")))) + "011qpkwpjclfc24y2qqigmdnikqwdnanflfhihigh5b5k7qwgm5j")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -1481,13 +1575,13 @@ jackknifed confidence intervals are available for most estimates.") (define-public r-rversions (package (name "r-rversions") - (version "1.0.2") + (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "rversions" version)) (sha256 (base32 - "0xmi461g1rf5ngb7r1sri798jn6icld1xq25wj9jii2ca8j8xv68")))) + "0i2gi05nrvknr7g89rbppkswyfcwwd4r9gp75fdfhpah8sgq1l11")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) @@ -1518,6 +1612,126 @@ previous R versions and their release dates.") limited to R.") (license license:gpl3+))) +(define-public r-backports + (package + (name "r-backports") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "backports" version)) + (sha256 + (base32 + "0s04mbb7imqc00jl37i081y4yf7qdimk687dyrkvb20nixvjvjyh")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/backports") + (synopsis "Reimplementations of functions introduced since R 3.0.0") + (description + "Provides implementations of functions which have been introduced in R +since version 3.0.0. The backports are conditionally exported which results +in R resolving the function names to the version shipped with R (if available) +and uses the implemented backports as fallback. This way package developers +can make use of the new functions without worrying about the minimum required +R version.") + (license license:gpl2+))) + +(define-public r-checkmate + (package + (name "r-checkmate") + (version "1.8.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "checkmate" version)) + (sha256 + (base32 + "1nqyi58jl33af82y8kw8iy9xbna2080y1khhy90kf6lim6q74024")))) + (build-system r-build-system) + (propagated-inputs + `(("r-backports" ,r-backports))) + (home-page "https://github.com/mllg/checkmate") + (synopsis "Fast and versatile argument checks") + (description + "This package provides tests and assertions to perform frequent argument +checks. A substantial part of the package was written in C to minimize any +worries about execution time overhead.") + (license license:bsd-3))) + +(define-public r-bbmisc + (package + (name "r-bbmisc") + (version "1.10") + (source + (origin + (method url-fetch) + (uri (cran-uri "BBmisc" version)) + (sha256 + (base32 + "0cw2mhw7qhdrx91zzd5iwyh7ch9fy4wxga8j63731q6sxr1airjl")))) + (properties `((upstream-name . "BBmisc"))) + (build-system r-build-system) + (propagated-inputs + `(("r-checkmate" ,r-checkmate))) + (home-page "https://github.com/berndbischl/BBmisc") + (synopsis "Miscellaneous functions for R package development") + (description + "This package provides miscellaneous helper functions for the development +of R packages.") + (license license:bsd-3))) + +(define-public r-fail + (package + (name "r-fail") + (version "1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "fail" version)) + (sha256 + (base32 + "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d")))) + (build-system r-build-system) + (propagated-inputs + `(("r-bbmisc" ,r-bbmisc) + ("r-checkmate" ,r-checkmate))) + (home-page "https://github.com/mllg/fail") + (synopsis "File abstraction interface layer (FAIL)") + (description + "This package provides a more comfortable interface to work with R data +or source files in a key-value fashion.") + (license license:bsd-3))) + +(define-public r-batchjobs + (package + (name "r-batchjobs") + (version "1.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "BatchJobs" version)) + (sha256 + (base32 + "1kb99024jih5bycc226bl4jyvbbl1sg72q3m2wnlshl7s8p6vva0")))) + (properties `((upstream-name . "BatchJobs"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bbmisc" ,r-bbmisc) + ("r-brew" ,r-brew) + ("r-checkmate" ,r-checkmate) + ("r-dbi" ,r-dbi) + ("r-digest" ,r-digest) + ("r-fail" ,r-fail) + ("r-rsqlite" ,r-rsqlite) + ("r-sendmailr" ,r-sendmailr) + ("r-stringr" ,r-stringr))) + (home-page "https://github.com/tudo-r/BatchJobs") + (synopsis "Batch computing with R") + (description + "This package provides @code{Map}, @code{Reduce} and @code{Filter} +variants to generate jobs on batch computing systems like PBS/Torque, LSF, +SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.") + (license license:bsd-2))) + (define-public r-brew (package (name "r-brew") @@ -1564,14 +1778,14 @@ collation, and NAMESPACE files.") (define-public r-openssl (package (name "r-openssl") - (version "0.9.3") + (version "0.9.4") (source (origin (method url-fetch) (uri (cran-uri "openssl" version)) (sha256 (base32 - "0ldqam7d9fyxwhr651ld6lsh05lg4v2y8ajxwzq9ywzjmfb3vlpz")))) + "0rpb3xdzab453yjddr8ryad53ll27zss8abnj30aqa2lzbg4jwyb")))) (build-system r-build-system) (inputs `(("openssl" ,openssl))) @@ -1593,13 +1807,13 @@ integers.") (define-public r-httr (package (name "r-httr") - (version "1.1.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "httr" version)) (sha256 (base32 - "08sq34pknsfcy8lm06nydi12mbaxpqpgb025ahr33v9d3g0wvh6p")))) + "03kkjlhyvvi5znwaxfm6cmdsg3q7ivwsvkzgabhjdj2jxs80pfg7")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) @@ -1647,13 +1861,13 @@ pure C implementation of the Git core methods.") (define-public r-rstudioapi (package (name "r-rstudioapi") - (version "0.5") + (version "0.6") (source (origin (method url-fetch) (uri (cran-uri "rstudioapi" version)) (sha256 (base32 - "0sgnqfx0m3hzh57k10s7ndrbw7yqjjjcgfikafya98jcc7wmpwym")))) + "1zkvz72z6nw0xc8bhb21y5x1nk6avijs0w8n4vsbvw9sn76wc96s")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/rstudioapi") (synopsis "Safely access the RStudio API") @@ -1665,13 +1879,13 @@ informative error messages when it's not available.") (define-public r-devtools (package (name "r-devtools") - (version "1.11.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (cran-uri "devtools" version)) (sha256 (base32 - "0ik3l3q62sspdph613f9ik5yz36s8q5nrc50dqgn3pxzvpwpdj2i")))) + "16l18szmj482vf3dvl2fqwwa4zaqylmic1pk7dwh428cp0d86mzi")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) @@ -1695,13 +1909,13 @@ tools to simplify the devolpment of R packages.") (define-public r-withr (package (name "r-withr") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "withr" version)) (sha256 (base32 - "0zbj3rd7dc0ycknmay7y7rm1qvnh9n05jw93gjggz46j2zfmy93y")))) + "042z8nmqqilgrvhmbqrjc05qys3gzwq1rqy2wxp2bi5d41859493")))) (build-system r-build-system) (home-page "https://github.com/jimhester/withr") (synopsis "Run code with temporarily modified global state") @@ -1711,20 +1925,42 @@ in which global state has been temporarily modified. Many of these functions were originally a part of the r-devtools package.") (license license:gpl2+))) +(define-public r-hms + (package + (name "r-hms") + (version "0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "hms" version)) + (sha256 + (base32 + "0ln1dc26mkl5pc26vvyf01d35x75q6cjaj39cccxp67chbwbdlds")))) + (build-system r-build-system) + (home-page "https://github.com/rstats-db/hms") + (synopsis "Pretty time of day") + (description + "This package implements an S3 class for storing and formatting +time-of-day values, based on the @code{difftime} class.") + (license license:gpl3+))) + (define-public r-readr (package (name "r-readr") - (version "0.2.2") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "readr" version)) (sha256 (base32 - "156422xwvskynna5kjc8h1qqnn50kxgjrihl2h2b7vm9sxxdyr2m")))) + "0xji0dbal6xcxnsmjj678fw29n7wrj45wrd5ng99yhqqijcm9f6g")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) ("r-rcpp" ,r-rcpp) + ("r-hms" ,r-hms) + ("r-tibble" ,r-tibble) + ("r-r6" ,r-r6) ("r-bh" ,r-bh))) (home-page "https://github.com/hadley/readr") (synopsis "Read tabular data") @@ -1736,13 +1972,13 @@ disk (or a connection).") (define-public r-plotrix (package (name "r-plotrix") - (version "3.6-2") + (version "3.6-3") (source (origin (method url-fetch) (uri (cran-uri "plotrix" version)) (sha256 (base32 - "1jn1k3skmlgyvpijj6vlcn5m2zgrsdh00g1fq8n5dqs1pkl1sqrw")))) + "0h97jra8zqssi9j4i0psa6c7ya49ya8jd2qc18lc61a4s2yn8w91")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/plotrix") (synopsis "Various plotting functions") @@ -1771,13 +2007,13 @@ scaling functions for R.") (define-public r-lattice (package (name "r-lattice") - (version "0.20-33") + (version "0.20-34") (source (origin (method url-fetch) (uri (cran-uri "lattice" version)) (sha256 (base32 - "0car12x5vl9k180i9pc86lq3cvwqakdpqn3lgdf98k9n2h52cilg")))) + "0615h69czr73k47whhzimf1qxv5qk0cabcrkljwhyrn6m6piq6ja")))) (build-system r-build-system) (home-page "http://lattice.r-forge.r-project.org/") (synopsis "High-level data visualization system") @@ -1815,13 +2051,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.6.700.6.0") + (version "0.7.400.2.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "0x736cjg1pbvn8c6h91c88qmmz4pddvvqg88k9c9kwhn24fjrra0")) + "0g2658iy43higy1cay00ljibgnwh0zv5gcwvbhckjs48y8z1a2pb")) (modules '((guix build utils))) ;; Remove bundled armadillo sources (snippet @@ -1899,19 +2135,35 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "0.9.6") + (version "1.0") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 (base32 - "09ajq5miqzz46q0i9svvbh93dbi7xbjn4702d6z3scdz272gx7l2")))) + "0c7gs9c8xdjfxviw0syh13pf3vys2b2ssixmnyqbji64xdscn7pz")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; See https://github.com/rstudio/rmarkdown/pull/800 + ;; The resource files are in the store and have mode 444. After + ;; copying the files R fails to remove them again because it doesn't + ;; have write access to them. + (add-after 'unpack 'copy-files-without-mode + (lambda _ + (substitute* "R/render.R" + (("file.copy\\(from = from," prefix) + (string-append prefix + " copy.mode = FALSE, "))) + #t))))) (propagated-inputs `(("r-catools" ,r-catools) ("r-htmltools" ,r-htmltools) + ("r-jsonlite" ,r-jsonlite) + ("r-base64enc" ,r-base64enc) ("r-knitr" ,r-knitr) ("r-yaml" ,r-yaml) ("ghc-pandoc" ,ghc-pandoc))) @@ -2074,13 +2326,13 @@ plotted and compared with the asymptotic curve.") (define-public r-lambda-r (package (name "r-lambda-r") - (version "1.1.7") + (version "1.1.9") (source (origin (method url-fetch) (uri (cran-uri "lambda.r" version)) (sha256 (base32 - "1lxzrwyminc3dfb07pbn1rmj45kplxgsb17b06pzflj728knbqwa")))) + "1j6287iqvs3ill6r5g6ksf5809qp0l0nf20ib8266m1r09lc9j14")))) (properties `((upstream-name . "lambda.r"))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/lambda.r") @@ -2117,13 +2369,13 @@ options defined in other packages.") (define-public r-futile-logger (package (name "r-futile-logger") - (version "1.4.1") + (version "1.4.3") (source (origin (method url-fetch) (uri (cran-uri "futile.logger" version)) (sha256 (base32 - "1plld1icxrcay7llplbd4i8inpg97crpnczk58mbk26j8glqbr51")))) + "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy")))) (properties `((upstream-name . "futile.logger"))) (build-system r-build-system) (propagated-inputs @@ -2138,6 +2390,26 @@ convenient and easy to use replacement for @code{cat} and @code{print} statements.") (license license:lgpl3+))) +(define-public r-segmented + (package + (name "r-segmented") + (version "0.5-1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "segmented" version)) + (sha256 + (base32 + "1740cvx2q4v23g4q0zkvg50s5bv8jcrlzzhm7fac4xn0riwmzp5i")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/segmented") + (synopsis "Regression models with breakpoints estimation") + (description + "Given a regression model, segmented updates the model by adding one or +more segmented (i.e., piecewise-linear) relationships. Several variables with +multiple breakpoints are allowed.") + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-snow (package (name "r-snow") @@ -2162,13 +2434,13 @@ worker processes and collect and return the results on the master.") (define-public r-sparsem (package (name "r-sparsem") - (version "1.7") + (version "1.72") (source (origin (method url-fetch) (uri (cran-uri "SparseM" version)) (sha256 (base32 - "0s9kab5khk7daqf6nfp1wm1qnhkssnnwnymisfwyk3kz4q5maqfz")))) + "0zpb1swn9xjkb22sky10ixff7vqfiz9m36nkbc1qqbm9frcldnka")))) (properties `((upstream-name . "SparseM"))) (inputs @@ -2297,13 +2569,13 @@ using the multicore functionality of the parallel package.") (define-public r-dt (package (name "r-dt") - (version "0.1") + (version "0.2") (source (origin (method url-fetch) (uri (cran-uri "DT" version)) (sha256 (base32 - "0mj7iiy1gglw7kixybmb7kr1bcl5r006zcb3klkw7p6vvvzdm6qj")))) + "1g86p0jcjqi2ph5rhm45jkzibsa6yfcj8n5cg3giy90sqgjzkdx1")))) (properties `((upstream-name . "DT"))) (build-system r-build-system) @@ -2349,14 +2621,14 @@ flexible than the orphaned \"base64\" package.") (define-public r-irlba (package (name "r-irlba") - (version "2.0.0") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "irlba" version)) (sha256 (base32 - "1gms3rxrm24ri4vjvnpl4v47m7bx0zk63z8y85rbhsvx230xdy0m")))) + "0yb8b8g6f3cb0f56r702fn2px8nf5rx8cyy2scq36xai9w7f25jj")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/irlba") (synopsis "Methods for eigendecomposition of large matrices") @@ -2463,6 +2735,50 @@ for reproducibility. Notably, convenient default methods greatly facilitate the way current RNG settings can be changed.") (license license:gpl3+))) +(define-public r-rtsne + (package + (name "r-rtsne") + (version "0.11") + (source + (origin + (method url-fetch) + (uri (cran-uri "Rtsne" version)) + (sha256 + (base32 + "0zi4nxgpiv1gpdmcnqdhz5kymzp8m5xj02zpf290p1yyydl76bhy")))) + (properties `((upstream-name . "Rtsne"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/jkrijthe/Rtsne") + (synopsis "T-distributed stochastic neighbor embedding") + (description + "This package provides an R wrapper around the fast T-distributed +Stochastic Neighbor Embedding using a Barnes-Hut implementation.") + ;; The declared license for this package is BSD-3, but it also includes + ;; code licensed under BSD-4. + (license (list license:bsd-3 license:bsd-4)))) + +(define-public r-e1071 + (package + (name "r-e1071") + (version "1.6-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "e1071" version)) + (sha256 + (base32 + "1069qwj9gsjq6par2cgfah8nn5x2w38830761x1f7mqpmk0gnj3h")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/e1071") + (synopsis "Miscellaneous functions for probability theory") + (description + "This package provides functions for latent class analysis, short time +Fourier transform, fuzzy clustering, support vector machines, shortest path +computation, bagged clustering, naive Bayes classifier, and more.") + (license license:gpl2+))) + (define-public r-nmf (package (name "r-nmf") @@ -2729,14 +3045,14 @@ most common form of color blindness.") (define-public r-tidyr (package (name "r-tidyr") - (version "0.4.1") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "tidyr" version)) (sha256 (base32 - "0xp6lyr2l4ix2mrilx4qmca7wm5qmbhvi24m4nf7qsgwp54gnv2h")))) + "1bpwbphgl43ym433b0nrshwhr7pprmj1wkpkamdzix1zvf9dcbc2")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -2834,6 +3150,63 @@ noncentral hypergeometric distribution (also called extended hypergeometric distribution).") (license license:gpl3+))) +(define-public r-rpart + (package + (name "r-rpart") + (version "4.1-10") + (source + (origin + (method url-fetch) + (uri (cran-uri "rpart" version)) + (sha256 + (base32 + "119dvh2cpab4vq9blvbkil5hgq6w018amiwlda3ii0fki39axpf5")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/rpart") + (synopsis "Recursive partitioning and regression trees") + (description + "This package provides recursive partitioning functions for +classification, regression and survival trees.") + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-hmisc + (package + (name "r-hmisc") + (version "3.17-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "Hmisc" version)) + (sha256 + (base32 + "1hr2kycpm0h3li9gnlbx9pl6h13das7g2wqfk6cip1kx6lv00ypw")))) + (properties `((upstream-name . "Hmisc"))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (propagated-inputs + `(("r-acepack" ,r-acepack) + ("r-cluster" ,r-cluster) + ("r-data-table" ,r-data-table) + ("r-foreign" ,r-foreign) + ("r-formula" ,r-formula) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-gtable" ,r-gtable) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-nnet" ,r-nnet) + ("r-rpart" ,r-rpart))) + (home-page "http://biostat.mc.vanderbilt.edu/Hmisc") + (synopsis "Miscellaneous data analysis and graphics functions") + (description + "This package contains many functions useful for data analysis, +high-level graphics, utility operations, functions for computing sample size +and power, importing and annotating datasets, imputing missing values, +advanced table making, variable clustering, character string manipulation, +conversion of R objects to LaTeX code, and recoding variables.") + (license license:gpl2+))) + (define-public r-runit (package (name "r-runit") |