diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 1743 |
1 files changed, 1638 insertions, 105 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 847e3ccacb..09cb2a1d02 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -42,8 +42,10 @@ #:use-module (gnu packages databases) #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) + #:use-module (gnu packages ghostscript) #:use-module (gnu packages gl) #:use-module (gnu packages gnome) + #:use-module (gnu packages graph) #:use-module (gnu packages gtk) #:use-module (gnu packages haskell) #:use-module (gnu packages image) @@ -52,6 +54,7 @@ #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) + #:use-module (gnu packages multiprecision) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) @@ -63,14 +66,14 @@ (define-public r-clipr (package (name "r-clipr") - (version "0.4.1") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "clipr" version)) (sha256 (base32 - "061x84ildc7g1p91yw5iyj8lpqdf4hqv36as85lw8c6qv9ywbsqv")))) + "1grx0lyww1cxmdvsr44wmbhz9i6zmiwxbchb97gxrfi9gy5kyc7x")))) (build-system r-build-system) (home-page "https://github.com/mdlincoln/clipr") (synopsis "Read and write from the system clipboard") @@ -210,18 +213,17 @@ such as copy/paste from an R session.") (define-public r-callr (package (name "r-callr") - (version "3.0.0") + (version "3.1.1") (source (origin (method url-fetch) (uri (cran-uri "callr" version)) (sha256 (base32 - "1rxbxy6kn7dj90z9hpppr9cnpvnxzknba2dwrdp0lrk5dh462qz3")))) + "15l1qfa3aigba2ghgr2gwcjjy7anagrwg8khsd36fymwkmqj5g69")))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-r6" ,r-r6) + `(("r-r6" ,r-r6) ("r-processx" ,r-processx))) (home-page "https://github.com/r-lib/callr#readme") (synopsis "Call R from R") @@ -234,17 +236,18 @@ that.") (define-public r-readxl (package (name "r-readxl") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "readxl" version)) (sha256 (base32 - "05ii8knrg4jji6h7bv6bfpn279b6x52yrskdx5rv7b0hcpy22gdn")))) + "1mwm389skl4ahcwsmhvx31pjkrn6y9igpnhsczwg6yza886q7j19")))) (build-system r-build-system) (propagated-inputs `(("r-cellranger" ,r-cellranger) + ("r-progress" ,r-progress) ("r-rcpp" ,r-rcpp) ("r-tibble" ,r-tibble))) (home-page "https://readxl.tidyverse.org") @@ -287,13 +290,13 @@ into a pipeline of data manipulation and visualisation.") (define-public r-httpuv (package (name "r-httpuv") - (version "1.4.5") + (version "1.4.5.1") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 - "1ddpcarzf694h0gy5pdz7l5glqfv4hr9dmxb4vw7yqd0bga174gi")))) + "0mqd40jckdpkjw1jjd860cdwkb03l6dkh931maijfdaqr1w9hwvn")))) (build-system r-build-system) (native-inputs `(("r-rcpp" ,r-rcpp) @@ -317,13 +320,13 @@ particularly easy to create complete web applications using httpuv alone.") (define-public r-jsonlite (package (name "r-jsonlite") - (version "1.5") + (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "jsonlite" version)) (sha256 (base32 - "00lfg464jhf7k01bal9pcjvbdf5cxk6xi2h46hccp1x3h883g434")))) + "0lyvhnr6n57h3a89bvipii7x17nvfaycm9j5j50bfrlr48jv9ic8")))) (build-system r-build-system) (home-page "http://arxiv.org/abs/1403.2805") (synopsis "Robust, high performance JSON parser and generator for R") @@ -422,14 +425,14 @@ applications.") (define-public r-htmltable (package (name "r-htmltable") - (version "1.12") + (version "1.13.1") (source (origin (method url-fetch) (uri (cran-uri "htmlTable" version)) (sha256 (base32 - "1n5136vb7mi4rxl5jgwdmdhn4mwv2pcqyw2mrj406ih4hy6hpxa2")))) + "1l44b33xgj2698k6nz17r8fl0ink14ryzng803apm9d6bnv357v8")))) (properties `((upstream-name . "htmlTable"))) (build-system r-build-system) (propagated-inputs @@ -455,13 +458,13 @@ LaTeX.") (define-public r-curl (package (name "r-curl") - (version "3.2") + (version "3.3") (source (origin (method url-fetch) (uri (cran-uri "curl" version)) (sha256 (base32 - "15hmy71310hnf9yqvz0icx4cq939gv6iqaifzlfdh2ia8akawdhn")))) + "1gd5i25anzi28lg1f8p7g63z9d46xi0qaw4lxpml5p0f52lvkc0c")))) (build-system r-build-system) (arguments `(#:phases @@ -478,7 +481,10 @@ LaTeX.") (("#ifdef _WIN32") "#if 1")) #t))))) (inputs - `(("libcurl" ,curl))) + `(("libcurl" ,curl) + ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) (home-page "https://github.com/jeroenooms/curl") (synopsis "HTTP client for R") (description @@ -782,14 +788,14 @@ work well on small screens.") (define-public r-feather (package (name "r-feather") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "feather" version)) (sha256 (base32 - "1q6dbkfnkpnabq8lb6bm9ma44cfcghx2lm23pyk3vg7943wrn1pi")))) + "138vnlwhkwayyim4rbx6rnf91kzhfij6v2f91ppx2174ky5611h6")))) (build-system r-build-system) (propagated-inputs `(("r-hms" ,r-hms) @@ -923,14 +929,14 @@ including functions for geolocation and routing.") (define-public r-haven (package (name "r-haven") - (version "1.1.2") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "haven" version)) (sha256 (base32 - "0pp8xjf5lzqg1wr8cwxj4njx99vxwlflwjrd7jvyzwlfpwh7n1qa")))) + "12qh8nba1dxlsmcihrx126wmjyj8n511k17vqj10lfgvpwq2sydy")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -1141,13 +1147,13 @@ print, summary, plot, update, etc. (define-public r-ps (package (name "r-ps") - (version "1.2.1") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 - (base32 "1zxylcb0nr4qb5v6j199mc2pfgf2bpf00jrw47jajmv59qb0fwmx")))) + (base32 "1lcq7r0q4jb8x6k023zr2ydj2dg925bqqbkhx1phpnyjrk897498")))) (build-system r-build-system) (home-page "http://ps.r-lib.org") (synopsis "List, query, and manipulate system processes") @@ -1367,14 +1373,14 @@ validation and filtering on the values, making options invisible or private.") (define-public r-circlize (package (name "r-circlize") - (version "0.4.4") + (version "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "circlize" version)) (sha256 (base32 - "1l28maiqi549z191srncxgabx5fnvf0lld7smzwfd3vr5cx8nqww")))) + "0qhn9jzw7gd0jp9rmqrlbmy5ql6hjsa68pkp0acfz1h215dl8ah9")))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace) @@ -1397,14 +1403,14 @@ multi-dimensional data.") (define-public r-powerlaw (package (name "r-powerlaw") - (version "0.70.1") + (version "0.70.2") (source (origin (method url-fetch) (uri (cran-uri "poweRlaw" version)) (sha256 (base32 - "04sr0nhdd1v915m0zf5gasznzgi08ykcy20kkwdw0l5mvvdbic8m")))) + "1asr6ikr7hmj78jyg8r1gwvcjg14addkxdiz92nh06lv71a183r4")))) (properties `((upstream-name . "poweRlaw"))) (build-system r-build-system) (propagated-inputs @@ -1734,13 +1740,13 @@ matrices.") (define-public r-rmpi (package (name "r-rmpi") - (version "0.6-7") + (version "0.6-9") (source (origin (method url-fetch) (uri (cran-uri "Rmpi" version)) (sha256 (base32 - "1b62gs7w1xqadqd7ir41jnxlcf14gcqfxd0915kn9ckdlsdrh0sw")))) + "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj")))) (properties `((upstream-name . "Rmpi"))) (build-system r-build-system) (arguments @@ -2165,14 +2171,14 @@ available in a vignette.") (define-public r-lava (package (name "r-lava") - (version "1.6.3") + (version "1.6.4") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 - "0cayjspry3r2lcbvl77v5v52b2zarri3b8xsf87pw5a3jn9anxcf")))) + "0627cjlg55kzbzcy82w6wykmw2i57qhgfcabn2zy3ydfdswyxij1")))) (build-system r-build-system) (propagated-inputs `(("r-numderiv" ,r-numderiv) @@ -2247,7 +2253,9 @@ the Kaplan-Meier and Aalen-Johansen methods.") "0ssy2qriiy6zdawriqcbl67qiq68ipml3frq7aqlq70r2fqyyw48")))) (properties `((upstream-name . "dimRed"))) (build-system r-build-system) - (propagated-inputs `(("r-drr" ,r-drr))) + (propagated-inputs + `(("r-drr" ,r-drr) + ("r-magrittr" ,r-magrittr))) (home-page "https://github.com/gdkrmr/dimRed") (synopsis "Framework for dimensionality reduction") (description @@ -2303,14 +2311,14 @@ dimensioned arrays.") (define-public r-rmysql (package (name "r-rmysql") - (version "0.10.15") + (version "0.10.16") (source (origin (method url-fetch) (uri (cran-uri "RMySQL" version)) (sha256 (base32 - "0bmc7w5fnkjaf333sgc0hskiy332m9gmfaxg0yzkjxscpizdw43n")))) + "1gh4b730g2v78jg5iln8fkz808ri2vhnhnw43wzkkjpy53jh48sp")))) (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (native-inputs @@ -2329,6 +2337,32 @@ is being phased out. A modern MySQL client based on Rcpp is available from the RMariaDB package.") (license license:gpl2))) +(define-public r-rpostgresql + (package + (name "r-rpostgresql") + (version "0.6-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "RPostgreSQL" version)) + (sha256 + (base32 + "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088")))) + (properties `((upstream-name . "RPostgreSQL"))) + (build-system r-build-system) + (inputs + `(("postgresql" ,postgresql))) + (propagated-inputs + `(("r-dbi" ,r-dbi))) + (home-page "https://github.com/tomoakin/RPostgreSQL") + (synopsis "R interface to the PostgreSQL database system") + (description + "This package provides a Database Interface (DBI) compliant driver for R +to access PostgreSQL database systems.") + ;; The whole package is released under GPL version 2. It includes code + ;; under the PostgreSQL license. + (license license:gpl2))) + (define-public r-geometry (package (name "r-geometry") @@ -2362,14 +2396,14 @@ Delaunay triangulation and convex hull computation.") (define-public r-ddalpha (package (name "r-ddalpha") - (version "1.3.4") + (version "1.3.8") (source (origin (method url-fetch) (uri (cran-uri "ddalpha" version)) (sha256 (base32 - "16cn0bhbaz9l9k4y79sv2d4f7pvs7dyka273y89igs5jvr99kfj1")))) + "0gi0hl14ghgf65zxsvgzh9z6xx1nyi49cpx192lmwrwqn3dy7ba0")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) @@ -2500,21 +2534,42 @@ displays of path diagrams, factor analysis and structural equation models are created using basic graphics.") (license license:gpl2+))) +(define-public r-generics + (package + (name "r-generics") + (version "0.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "generics" version)) + (sha256 + (base32 + "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi")))) + (build-system r-build-system) + (home-page "https://github.com/r-lib/generics") + (synopsis "Common S3 generics not provided by base R methods") + (description + "In order to reduce potential package dependencies and conflicts, +generics provides a number of commonly used S3 generics that are not provided +by base R methods related to model fitting.") + (license license:gpl2))) + (define-public r-broom (package (name "r-broom") - (version "0.5.0") + (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "1r3831vq0fd5sh5841xr844sghg88z7ws91hg4jgnzbbkxfjp4ag")))) + "0bmf38yvwalqf5j5yrr48nsk5k3n75s0gwcw621hp5lgrgvnp7ns")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) ("r-dplyr" ,r-dplyr) + ("r-generics" ,r-generics) ("r-nlme" ,r-nlme) ("r-purrr" ,r-purrr) ("r-reshape2" ,r-reshape2) @@ -2562,7 +2617,8 @@ provides a one-row summary of model-level statistics.") ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble) ("r-tidyselect" ,r-tidyselect) - ("r-timedate" ,r-timedate))) + ("r-timedate" ,r-timedate) + ("r-withr" ,r-withr))) (home-page "https://github.com/topepo/recipes") (synopsis "Preprocessing tools to create design matrices") (description @@ -2770,14 +2826,14 @@ clustered data.") (define-public r-mitml (package (name "r-mitml") - (version "0.3-6") + (version "0.3-7") (source (origin (method url-fetch) (uri (cran-uri "mitml" version)) (sha256 (base32 - "1pkqv4qazih3byws5z6629pp232n8ra56lip7502727b0b4bsndw")))) + "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6")))) (build-system r-build-system) (propagated-inputs `(("r-haven" ,r-haven) @@ -3052,14 +3108,14 @@ where possible.") (define-public r-laeken (package (name "r-laeken") - (version "0.4.6") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "laeken" version)) (sha256 (base32 - "1rhkv1kk508pwln1d325iq4fink2ncssps0ypxi52j9d7wk78la6")))) + "1g9r3y7b0gl91hijk9awa8rjk97mqpkxinzq2cgmx0m38ng9ylpa")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) @@ -3295,21 +3351,18 @@ constants, and control debugging of packages via environment variables.") (define-public r-processx (package (name "r-processx") - (version "3.2.0") + (version "3.2.1") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 (base32 - "1pzx4ap4xa07gf9zkd6hacdsnb9sp3kb60a7v7ljl0ywrcpn1fn4")))) + "1skjyi767avc3safajlj3ikk9lf11zzyjybdcmx8m9y59rf319ql")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-crayon" ,r-crayon) - ("r-ps" ,r-ps) - ("r-r6" ,r-r6) - ("r-testthat" ,r-testthat))) + `(("r-ps" ,r-ps) + ("r-r6" ,r-r6))) (home-page "https://github.com/r-lib/processx3") (synopsis "Execute and control system processes") (description @@ -3366,14 +3419,14 @@ available.") (define-public r-gclus (package (name "r-gclus") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "gclus" version)) (sha256 (base32 - "02ba6zj9bjwrzykamjp40ajynx9xjx9h2i85n0ym0r5lcki4x6fn")))) + "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster))) (home-page "https://cran.r-project.org/web/packages/gclus/") @@ -3485,14 +3538,14 @@ display.") (define-public r-pillar (package (name "r-pillar") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "1q6arybmfqxhp5zqj1fri5pb8v7ywcv7bmgf81rrmgl892p4bn5f")))) + "1xnbb9sr5wn9dmp6m7cr4z7i6pmjvyabnfcx6x7i7mvdjmgvaf5k")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -3530,14 +3583,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.9") + (version "0.10") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "08w5hyq3ysh631d5whgcfv1bb007cdc0bjhb83vwmhazs6rgvyjy")))) + "02bz8zaka5j51zin976n5nmk19a0390d0gwgj4zrbh48hl313rqm")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) @@ -3599,14 +3652,14 @@ supports arbitrary vertex/edge/graph attributes.") (define-public r-statnet-common (package (name "r-statnet-common") - (version "4.1.4") + (version "4.2.0") (source (origin (method url-fetch) (uri (cran-uri "statnet.common" version)) (sha256 (base32 - "14dydm4c4dzc4v6ldxpn04q551nczzfablwibrd8lzgja8x9ksic")))) + "0q942g6kqmqxfss1cxb3yg8y5r1k1h5cyy99s1cfisrn6hqc6xhi")))) (properties `((upstream-name . "statnet.common"))) (build-system r-build-system) @@ -3799,14 +3852,14 @@ financial trading strategies.") (define-public r-tseries (package (name "r-tseries") - (version "0.10-45") + (version "0.10-46") (source (origin (method url-fetch) (uri (cran-uri "tseries" version)) (sha256 (base32 - "14s1glh5zzdvdl05a2z7ymhgf962svxf8xircghg5sc649lb33n0")))) + "08kjw0bfj5gfcrxpblwqxwna8a5g9gnr7ya61qb02r263pyhm50j")))) (build-system r-build-system) (propagated-inputs `(("r-quadprog" ,r-quadprog) @@ -3943,14 +3996,14 @@ applied econometric analysis.") (define-public r-cubature (package (name "r-cubature") - (version "1.4-1") + (version "2.0.3") (source (origin (method url-fetch) (uri (cran-uri "cubature" version)) (sha256 (base32 - "10jl5l3xnigiq95829ssq69xbim97k851187dghc30awszcx4clh")))) + "0wvs80i4axj7pdcy9gjl08qzjbcjkldha94xy4gdxc34vgmh7gvr")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) @@ -4233,14 +4286,14 @@ files.") (define-public r-shinyace (package (name "r-shinyace") - (version "0.3.2") + (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "shinyAce" version)) (sha256 (base32 - "1fbk5i6w6cpam8s3acf4bgdp8hajn4digjjix3i6i4q3p2rvn6zx")))) + "02q6wqw349nlyf3mbf18cxif1xv9cal5qzccrdlnv73szqn9jk7j")))) (properties `((upstream-name . "shinyAce"))) (build-system r-build-system) (propagated-inputs @@ -4502,14 +4555,14 @@ multivariate plot methods.") (define-public r-fnn (package (name "r-fnn") - (version "1.1.2.1") + (version "1.1.2.2") (source (origin (method url-fetch) (uri (cran-uri "FNN" version)) (sha256 (base32 - "1n61jrcmakqif8f827x4qnlhm2jqpj5fgjj65c4p0kdd8lzw8pqp")))) + "09k3k0h9ikbwq6225l7gd0nhimbji722680cr66c8n7zpvxn06mm")))) (properties `((upstream-name . "FNN"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/FNN") @@ -4620,14 +4673,14 @@ evaluated by the @dfn{Akaike Information Criterion} (AIC).") (define-public r-arules (package (name "r-arules") - (version "1.6-1") + (version "1.6-2") (source (origin (method url-fetch) (uri (cran-uri "arules" version)) (sha256 (base32 - "0glfqgxr87900kigmkby2ff7qrjvd6aq595q85y056i5ckjcp615")))) + "0vnss6akk3564kbci3h5rq8ylpckz77cgmflly3gn6fki66f7g96")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -4760,14 +4813,14 @@ dependency on Java.") (define-public r-rio (package (name "r-rio") - (version "0.5.10") + (version "0.5.16") (source (origin (method url-fetch) (uri (cran-uri "rio" version)) (sha256 (base32 - "158xg3vj0glk3fslwi6fywwmfym2b6kn3fdmjligdfy5lf68khix")))) + "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) @@ -5492,14 +5545,14 @@ to help insert or delete content at a specific location in the document.") (define-public r-abn (package (name "r-abn") - (version "1.2") + (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "00k0razgdb5y5f62622fm7rxkcxrxg470nyyb02dvpfp60254kvs")))) + "1q9hzpxwg835711kxwygd0l2awal6f015f8s6fprwz7graz1wbbm")))) (build-system r-build-system) (inputs `(("gsl" ,gsl))) @@ -5620,14 +5673,14 @@ parse and convert strings into cases like snake or camel among others.") (define-public r-prediction (package (name "r-prediction") - (version "0.3.6") + (version "0.3.6.1") (source (origin (method url-fetch) (uri (cran-uri "prediction" version)) (sha256 (base32 - "19d7312f5lkqfglfvlgssnvyw7gl161s0xradcry44r1i6qp05j1")))) + "1znxpacd79fjkf84w3493p1vmafanqfxsspwpwpkmda323bsxj0n")))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table))) @@ -5644,14 +5697,14 @@ other add-on packages.") (define-public r-sjlabelled (package (name "r-sjlabelled") - (version "1.0.14") + (version "1.0.16") (source (origin (method url-fetch) (uri (cran-uri "sjlabelled" version)) (sha256 (base32 - "0ayfzhm9bwjfaarq5z0gvn9kapjwj3532azgin97nr5fnjdhvgaw")))) + "1zi1ncna16zl9hcy7mzara4kjxqkgwcw9ncp388ss353wwc9y2nc")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -5661,9 +5714,7 @@ other add-on packages.") ("r-prediction" ,r-prediction) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) - ("r-snakecase" ,r-snakecase) - ("r-tibble" ,r-tibble) - ("r-tidyselect" ,r-tidyselect))) + ("r-snakecase" ,r-snakecase))) (home-page "https://github.com/strengejacke/sjlabelled") (synopsis "Labelled data utility functions") (description @@ -5677,14 +5728,14 @@ vice versa), or to deal with multiple declared missing values.") (define-public r-sjmisc (package (name "r-sjmisc") - (version "2.7.6") + (version "2.7.7") (source (origin (method url-fetch) (uri (cran-uri "sjmisc" version)) (sha256 (base32 - "1jhrigikjpkdar3jxvi7qhqsg6lgjkjqhqll9vaay98b88rfc2im")))) + "0xm9pmq17maivmjsygwx3bdjd71hf829qbx735hyxa69z9dhp24q")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -5790,14 +5841,14 @@ documents.") (define-public r-writexl (package (name "r-writexl") - (version "1.0") + (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "writexl" version)) (sha256 (base32 - "0r2v12dc4zqmr1agp6vbw0fc48i278018684x84psjjqfmnv14cf")))) + "0w4wnpl3yhaqp63p32bk60xrbmd7xd11kxifjbzrghi7d4483a46")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (home-page "https://github.com/ropensci/writexl") @@ -5887,14 +5938,14 @@ support for default values, positional argument support, etc.") (define-public r-findpython (package (name "r-findpython") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "findpython" version)) (sha256 (base32 - "1y08jk2ffmkf9zpwiz2xymjhfwqvls9vzsnq62v278ghw9d571jl")))) + "1zfcdcp4d48d2pzf5n59kqrfk2z9nnyzkx5j00gfmgfkadnv93x5")))) (build-system r-build-system) (home-page "https://github.com/trevorld/findpython") (synopsis "Functions to find an acceptable Python binary") @@ -5907,21 +5958,21 @@ matches version and feature constraints.") (define-public r-argparse (package (name "r-argparse") - (version "1.1.1") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "argparse" version)) (sha256 (base32 - "0fzrbj87b274vf96azdnsjxk2nf45d5wy58vzmlah4b4h7q4j524")))) + "1qrp7hc8sm6ryw0zws76al865ansig1xbx8ljxz4wabh60msrz3i")))) (build-system r-build-system) (inputs `(("python" ,python))) (propagated-inputs `(("r-findpython" ,r-findpython) ("r-getopt" ,r-getopt) ("r-jsonlite" ,r-jsonlite) - ("r-proto" ,r-proto))) + ("r-r6" ,r-r6))) (home-page "https://github.com/trevorld/argparse") (synopsis "Command line optional and positional argument parser") (description @@ -6012,14 +6063,14 @@ Group (Non-)Overlap considerations.") (define-public r-refgenome (package (name "r-refgenome") - (version "1.7.3") + (version "1.7.3.1") (source (origin (method url-fetch) (uri (cran-uri "refGenome" version)) (sha256 (base32 - "15p0ra2p1pwhy5ixbhsz1g79c5sc2aap4i4c8kil0m2syg9y45sn")))) + "1s4lxv5pqk6d0f0a9iclgv88yl346fwvzgraxh0gwpbym1yhh787")))) (properties `((upstream-name . "refGenome"))) (build-system r-build-system) (propagated-inputs @@ -6168,13 +6219,13 @@ the analyzed items.") (define-public r-slam (package (name "r-slam") - (version "0.1-43") + (version "0.1-44") (source (origin (method url-fetch) (uri (cran-uri "slam" version)) (sha256 - (base32 "0hy4qzngcgafxxr6ld7n9a9wy979ji998gpcc32vidwyab66dj5h")))) + (base32 "11n956kid70931z0qyiql3v7nac1cfkamq44kzf9wl670pf8b033")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/slam/") (synopsis "Sparse lightweight arrays and matrices") @@ -7266,14 +7317,14 @@ Hothorn, Westfall, 2010, CRC Press).") (define-public r-emmeans (package (name "r-emmeans") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "0kdyy4qp332c4yyvp1cnh48h6ks6ffir5rjcv0py0vm3m8c3hh61")))) + "1sf7gmdb7aqhdpx489vg693ivc5677n4yjx27ixv8v7pjh8mlwwx")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) @@ -7398,14 +7449,14 @@ detection, parallelism through BLAS and parallel user templates.") (define-public r-sjstats (package (name "r-sjstats") - (version "0.17.2") + (version "0.17.3") (source (origin (method url-fetch) (uri (cran-uri "sjstats" version)) (sha256 (base32 - "0c7g35vn7r9rylhp0gj1yfslg7jybwrhpqpp7vdcd90xfccih24r")))) + "02na2pzxp88yp52h7vs959fgydiddmns39m9x4i0vz8fp016bdf8")))) (build-system r-build-system) (propagated-inputs `(("r-bayesplot" ,r-bayesplot) @@ -7444,14 +7495,14 @@ models.") (define-public r-glmmtmb (package (name "r-glmmtmb") - (version "0.2.2.0") + (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "glmmTMB" version)) (sha256 (base32 - "1clpkjlmsjmn3m1z5jqv8cgw6bvpqsy4nx6k947r0jya017ny5y5")))) + "035hkywa37bz555fv6znxd4hfcs5w884365wfnwk4jx5vann4vvb")))) (properties `((upstream-name . "glmmTMB"))) (build-system r-build-system) (propagated-inputs @@ -7461,7 +7512,7 @@ models.") ("r-rcppeigen" ,r-rcppeigen) ("r-tmb" ,r-tmb))) (native-inputs - `(("r-knitr" ,r-knitr))) + `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "https://github.com/glmmTMB") (synopsis "Generalized linear mixed models") (description @@ -7476,14 +7527,14 @@ differentiation.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "070c3fxmzajq2fy816s5pfqdyjlnzkabj97z7fcsva4h5rnqi9d6")))) + "152xyadj5m171z7dlzzy40y1fp2l9v46525dlw2al3qr0b7zpm61")))) (build-system r-build-system) (propagated-inputs `(("r-crayon" ,r-crayon) @@ -7515,14 +7566,14 @@ results using @code{ggplot2}.") (define-public r-sjplot (package (name "r-sjplot") - (version "2.6.1") + (version "2.6.2") (source (origin (method url-fetch) (uri (cran-uri "sjPlot" version)) (sha256 (base32 - "13qvw2s3r96qfi8kfsn76m050ccnmckl31a9qv94xws8da99v2fk")))) + "0x9pbchmz4qf4c9bi52dhhgv1phfj03q1hnxic8vndl6xwib63cy")))) (properties `((upstream-name . "sjPlot"))) (build-system r-build-system) (propagated-inputs @@ -7978,14 +8029,14 @@ the interfaces between R and C++.") (define-public r-mvabund (package (name "r-mvabund") - (version "3.13.1") + (version "4.0.1") (source (origin (method url-fetch) (uri (cran-uri "mvabund" version)) (sha256 (base32 - "1z8bj9zbc8h7w1xki9sc2p2rq6lv8gbcmiy9819z54d7lx1i9cnj")))) + "0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -8874,3 +8925,1485 @@ Furthermore, functions are available for fast singular value decomposition, for computing the pseudoinverse, and for checking the rank and positive definiteness of a matrix.") (license license:gpl3+))) + +(define-public r-rspectra + (package + (name "r-rspectra") + (version "0.13-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "RSpectra" version)) + (sha256 + (base32 + "1sw80chwyyjzf5px278l6xmp94yhwrlj5xh8d3wlw3dnvdkycca7")))) + (properties `((upstream-name . "RSpectra"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen))) + (home-page "https://github.com/yixuan/RSpectra") + (synopsis "Solvers for large-scale Eigenvalue and SVD problems") + (description + "This package provides an R interface to the Spectra library for +large-scale eigenvalue and SVD problems. It is typically used to compute a +few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues, +which is usually more efficient than @code{eigen()} if k << n.") + ;; MPL 2 or later. + (license license:mpl2.0))) + +(define-public r-vbsr + (package + (name "r-vbsr") + (version "0.0.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "vbsr" version)) + (sha256 + (base32 + "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/vbsr") + (synopsis "Variational Bayes spike regression regularized linear models") + (description + "This package provides an efficient algorithm for solving ultra-sparse +regularized regression models using a variational Bayes algorithm with a spike +prior. The algorithm is solved on a path, with coordinate updates, and is +capable of generating very sparse models. Very general model +diagnostics for controlling type-1 errors are also provided.") + (license license:gpl2))) + +(define-public r-flare + (package + (name "r-flare") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "flare" version)) + (sha256 + (base32 + "0ygif9a7a99qwv0b488wymmmncp6f5ww9yz13s4qs6p8yf37x1r1")))) + (build-system r-build-system) + (propagated-inputs + `(("r-igraph" ,r-igraph) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix))) + (home-page "https://cran.r-project.org/web/packages/flare") + (synopsis "Family of Lasso regression implementations") + (description + "This packages provides implementations of a family of Lasso variants +including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating +high dimensional sparse linear models.") + (license license:gpl2))) + +(define-public r-lassopv + (package + (name "r-lassopv") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "lassopv" version)) + (sha256 + (base32 + "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z")))) + (build-system r-build-system) + (propagated-inputs `(("r-lars" ,r-lars))) + (home-page "https://github.com/lingfeiwang/lassopv") + (synopsis "Non-parametric p-value estimation for predictors in Lasso") + (description + "This package enables you to estimate the p-values for predictors x +against target variable y in Lasso regression, using the regularization +strength when each predictor enters the active set of regularization path for +the first time as the statistic.") + (license license:gpl3))) + +(define-public r-splitstackshape + (package + (name "r-splitstackshape") + (version "1.4.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "splitstackshape" version)) + (sha256 + (base32 + "03w6h64ga4zqilffdway4l38l5cbman4yrspkzhbigds12aqz25r")))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table))) + (home-page "https://github.com/mrdwab/splitstackshape") + (synopsis "Stack and reshape datasets after splitting concatenated values") + (description + "Online data collection tools like Google Forms often export +multiple-response questions with data concatenated in cells. The +@code{concat.split} (cSplit) family of functions provided by this package +splits such data into separate cells. This package also includes functions to +stack groups of columns and to reshape wide data, even when the data are +\"unbalanced\"---something which @code{reshape} (from base R) does not handle, +and which @code{melt} and @code{dcast} from @code{reshape2} do not easily +handle.") + (license license:gpl3))) + +(define-public r-tfmpvalue + (package + (name "r-tfmpvalue") + (version "0.0.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "TFMPvalue" version)) + (sha256 + (base32 + "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd")))) + (properties `((upstream-name . "TFMPvalue"))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/ge11232002/TFMPvalue") + (synopsis "P-value computation for position weight matrices") + (description + "In putative @dfn{Transcription Factor Binding Sites} (TFBSs) +identification from sequence/alignments, we are interested in the significance +of certain match scores. TFMPvalue provides the accurate calculation of a +p-value with a score threshold for position weight matrices, or the score with +a given p-value. It is an interface to code originally made available by +Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. +Touzet and Varre (2007).") + (license license:gpl2))) + +(define-public r-rnifti + (package + (name "r-rnifti") + (version "0.10.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "RNifti" version)) + (sha256 + (base32 + "07sfzps4yg5zdhbxh6i4rbjvbjvvf2d8i9jcf64ywbmi557sw1zv")))) + (properties `((upstream-name . "RNifti"))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/jonclayden/RNifti") + (synopsis "Fast R and C++ access to NIfTI images") + (description + "This package provides very fast read and write access to images stored +in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between +compiled C and interpreted R code. It also provides a C/C++ API that can be +used by other packages.") + (license license:gpl2))) + +(define-public r-shades + (package + (name "r-shades") + (version "1.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "shades" version)) + (sha256 + (base32 + "0v0xp9l1zyq4iysmkrbdwk4r1rksjj8p5c1726yrcgyg55mj59nv")))) + (build-system r-build-system) + (home-page "https://github.com/jonclayden/shades") + (synopsis "Simple color manipulation") + (description + "This package provides functions for easily manipulating colors, +creating color scales and calculating color distances.") + (license license:bsd-3))) + +(define-public r-ore + (package + (name "r-ore") + (version "1.6.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "ore" version)) + (sha256 + (base32 + "1l1ziljgm5gwjhvjq42wi5vcwbxlaj5dl9w8bhz0wh8vx4ajj07m")))) + (build-system r-build-system) + (home-page "https://github.com/jonclayden/ore") + (synopsis "R interface to the Onigmo regular expression library") + (description + "This package provides an alternative to R's built-in functionality for +handling regular expressions, based on the Onigmo library. It offers +first-class compiled regex objects, partial matching and function-based +substitutions, amongst other features.") + (license license:bsd-3))) + +(define-public r-reportr + (package + (name "r-reportr") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "reportr" version)) + (sha256 + (base32 + "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw")))) + (build-system r-build-system) + (propagated-inputs `(("r-ore" ,r-ore))) + (home-page "https://github.com/jonclayden/reportr") + (synopsis "General message and error reporting system") + (description + "This package provides a system for reporting messages, which offers +certain useful features over the standard R system, such as the incorporation +of output consolidation, message filtering, assertions, expression +substitution, automatic generation of stack traces for debugging, and +conditional reporting based on the current \"output level\".") + (license license:gpl2))) + +(define-public r-tractor-base + (package + (name "r-tractor-base") + (version "3.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "tractor.base" version)) + (sha256 + (base32 + "0i62dwra0yh565ryz75byfgqv22bqwz7138zs48w46yj2h8q9hyj")))) + (properties `((upstream-name . "tractor.base"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ore" ,r-ore) + ("r-reportr" ,r-reportr) + ("r-rnifti" ,r-rnifti) + ("r-shades" ,r-shades))) + (home-page "http://www.tractor-mri.org.uk") + (synopsis "Read, manipulate and visualize magnetic resonance images") + (description + "This package provides functions for working with magnetic resonance +images. It supports reading and writing of popular file formats (DICOM, +Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive +visualization; flexible image manipulation; metadata and sparse image +handling.") + (license license:gpl2))) + +(define-public r-grimport + (package + (name "r-grimport") + (version "0.9-1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "grImport" version)) + (sha256 + (base32 + "19d05ygpiv47lfzhfih35pdfll0axbrgd6p86l59mmg2d0j0s8bd")))) + (properties `((upstream-name . "grImport"))) + (build-system r-build-system) + (inputs + `(("ghostscript" ,ghostscript))) + (propagated-inputs + `(("r-xml" ,r-xml))) + (home-page "https://cran.r-project.org/web/packages/grImport") + (synopsis "Convert, import, and draw PostScript pictures") + (description + "This package provides functions for converting, importing, and drawing +PostScript pictures in R plots.") + (license license:gpl2+))) + +(define-public r-kohonen + (package + (name "r-kohonen") + (version "3.0.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "kohonen" version)) + (sha256 + (base32 + "1zbfqa1qdlry8w6xhypkiknc5gn98v1ijhlsfka8zjg8ajhqgn1q")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/kohonen") + (synopsis "Supervised and unsupervised self-organising maps") + (description + "This package provides functions to train @dfn{self-organising +maps} (SOMs). Also interrogation of the maps and prediction using trained +maps are supported. The name of the package refers to Teuvo Kohonen, the +inventor of the SOM.") + (license license:gpl2+))) + +(define-public r-nnls + (package + (name "r-nnls") + (version "1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "nnls" version)) + (sha256 + (base32 + "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/nnls") + (synopsis "Lawson-Hanson algorithm for non-negative least squares") + (description + "This package provides an R interface to the Lawson-Hanson implementation +of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows +the combination of non-negative and non-positive constraints.") + (license license:gpl2+))) + +(define-public r-iso + (package + (name "r-iso") + (version "0.0-17") + (source + (origin + (method url-fetch) + (uri (cran-uri "Iso" version)) + (sha256 + (base32 + "0lljc99sdzdqj6d56qbsggibr6pkdwkh821bj70ianikyvmdc1y0")))) + (properties `((upstream-name . "Iso"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "http://www.stat.auckland.ac.nz/~rolf/") + (synopsis "Functions to perform isotonic regression") + (description + "This package provides support for linear order and unimodal +order (univariate) isotonic regression and bivariate isotonic regression with +linear order on both variables.") + (license license:gpl2+))) + +(define-public r-chemometricswithr + (package + (name "r-chemometricswithr") + (version "0.1.13") + (source + (origin + (method url-fetch) + (uri (cran-uri "ChemometricsWithR" version)) + (sha256 + (base32 + "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq")))) + (properties + `((upstream-name . "ChemometricsWithR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-devtools" ,r-devtools) + ("r-kohonen" ,r-kohonen) + ("r-mass" ,r-mass) + ("r-pls" ,r-pls))) + (home-page "https://github.com/rwehrens/CWR") + (synopsis "Chemometrics with R") + (description + "This package provides functions and scripts used in the book +\"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and +Life Sciences\" by Ron Wehrens, Springer (2011).") + (license license:gpl2+))) + +(define-public r-als + (package + (name "r-als") + (version "0.0.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "ALS" version)) + (sha256 + (base32 + "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a")))) + (properties `((upstream-name . "ALS"))) + (build-system r-build-system) + (propagated-inputs + `(("r-iso" ,r-iso) + ("r-nnls" ,r-nnls))) + (home-page "https://cran.r-project.org/web/packages/ALS") + (synopsis "Multivariate curve resolution alternating least squares") + (description + "Alternating least squares is often used to resolve components +contributing to data with a bilinear structure; the basic technique may be +extended to alternating constrained least squares. This package provides an +implementation of @dfn{multivariate curve resolution alternating least +squares} (MCR-ALS). + +Commonly applied constraints include unimodality, non-negativity, and +normalization of components. Several data matrices may be decomposed +simultaneously by assuming that one of the two matrices in the bilinear +decomposition is shared between datasets.") + (license license:gpl2+))) + +(define-public r-strucchange + (package + (name "r-strucchange") + (version "1.5-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "strucchange" version)) + (sha256 + (base32 + "0cdgvl6kphm2i59bmnppn1y3kv65ml111bk7yzpcx7vv8wh2w3kl")))) + (build-system r-build-system) + (propagated-inputs + `(("r-sandwich" ,r-sandwich) + ("r-zoo" ,r-zoo))) + (home-page "https://cran.r-project.org/web/packages/strucchange") + (synopsis "Testing, monitoring, and dating structural changes") + (description + "This package provides tools for testing, monitoring and dating +structural changes in (linear) regression models. It features tests/methods +from the generalized fluctuation test framework as well as from the F +test (Chow test) framework. This includes methods to fit, plot and test +fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F +statistics, respectively. It is possible to monitor incoming data online +using fluctuation processes. Finally, the breakpoints in regression models +with structural changes can be estimated together with confidence intervals. +Emphasis is always given to methods for visualizing the data.") + ;; Either of these two GPL versions + (license (list license:gpl2 license:gpl3)))) + +(define-public r-pixmap + (package + (name "r-pixmap") + (version "0.4-11") + (source + (origin + (method url-fetch) + (uri (cran-uri "pixmap" version)) + (sha256 + (base32 + "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/pixmap") + (synopsis "Tools for bitmap images") + (description + "This package provides functions for importing, exporting, plotting and +other manipulations of bitmapped images.") + (license license:gpl2))) + +(define-public r-rapidjsonr + (package + (name "r-rapidjsonr") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "rapidjsonr" version)) + (sha256 + (base32 + "0h4phjjhykbb45rg5b1xn48vqxdcvcngbm0416ds8in7j469wbwd")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/rapidjsonr") + (synopsis "JSON parser") + (description + "This package provides JSON parsing capability through the Rapidjson +library.") + (license license:expat))) + +(define-public r-ontologyindex + (package + (name "r-ontologyindex") + (version "2.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "ontologyIndex" version)) + (sha256 + (base32 + "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry")))) + (properties `((upstream-name . "ontologyIndex"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/ontologyIndex") + (synopsis "Functions for processing ontologies in R") + (description + "This package provides functions for reading ontologies into R as lists +and manipulating sets of ontological terms.") + (license license:gpl2+))) + +(define-public r-bigrquery + (package + (name "r-bigrquery") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "bigrquery" version)) + (sha256 + (base32 + "0z7wsqxla1pg2454l35kkfaz2s9hppwvpz1pds286ddldbbmyzis")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-curl" ,r-curl) + ("r-dbi" ,r-dbi) + ("r-glue" ,r-glue) + ("r-httr" ,r-httr) + ("r-jsonlite" ,r-jsonlite) + ("r-prettyunits" ,r-prettyunits) + ("r-progress" ,r-progress) + ("r-rapidjsonr" ,r-rapidjsonr) + ("r-rcpp" ,r-rcpp) + ("r-tibble" ,r-tibble))) + (home-page "https://github.com/rstats-db/bigrquery") + (synopsis "R interface to Google's BigQuery API") + (description + "This package provides an R interface to Google's BigQuery database.") + (license license:gpl3))) + +(define-public r-gmp + (package + (name "r-gmp") + (version "0.5-13.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "gmp" version)) + (sha256 + (base32 + "1xd6jjra4niqv1kps91y348lwgvy73p2faxaia4gfzdnrpw7wsxf")))) + (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-CC + (lambda _ (setenv "CC" "gcc") #t))))) + (inputs `(("gmp" ,gmp))) + (home-page "https://cran.r-project.org/web/packages/gmp") + (synopsis "Multiple precision arithmetic") + (description + "This package supports multiple precision arithmetic (big integers and +rationals, prime number tests, matrix computation), \"arithmetic without +limitations\" using the GNU Multiple Precision library.") + ;; Any version of the GPL. + (license license:gpl3+))) + +(define-public r-rmpfr + (package + (name "r-rmpfr") + (version "0.7-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "Rmpfr" version)) + (sha256 + (base32 + "0172px5ryi7i0gyyin9z2bzif8vnj292gk0s1w5p3c12g9hj2c4v")))) + (properties `((upstream-name . "Rmpfr"))) + (build-system r-build-system) + (inputs + `(("mpfr" ,mpfr))) + (propagated-inputs + `(("r-gmp" ,r-gmp))) + (home-page "http://rmpfr.r-forge.r-project.org/") + (synopsis "R bindings to the MPFR library") + (description + "This package supports arithmetic (via S4 classes and methods) for +arbitrary precision floating point numbers, including transcendental +functions. To this end, the package interfaces with the @dfn{Multiple +Precision Floating-Point Reliable} (MPFR) library.") + (license license:gpl2+))) + +(define-public r-assertive-base + (package + (name "r-assertive-base") + (version "0.0-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.base" version)) + (sha256 + (base32 + "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh")))) + (properties + `((upstream-name . "assertive.base"))) + (build-system r-build-system) + (home-page "https://bitbucket.org/richierocks/assertive.base") + (synopsis "Core of the assertive package") + (description + "This package provides a minimal set of predicates and assertions used by +the assertive package. This is mainly for use by other package developers who +want to include run-time testing features in their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-properties + (package + (name "r-assertive-properties") + (version "0.0-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.properties" version)) + (sha256 + (base32 + "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw")))) + (properties + `((upstream-name . "assertive.properties"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base))) + (home-page "https://bitbucket.org/richierocks/assertive.properties") + (synopsis "Assertions to check properties of variables") + (description + "This package provides a set of predicates and assertions for checking +the properties of variables, such as length, names and attributes. This is +mainly for use by other package developers who want to include run-time +testing features in their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-numbers + (package + (name "r-assertive-numbers") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.numbers" version)) + (sha256 + (base32 + "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds")))) + (properties + `((upstream-name . "assertive.numbers"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base))) + (home-page "https://bitbucket.org/richierocks/assertive.numbers") + (synopsis "Assertions to check properties of numbers") + (description + "This package provides a set of predicates and assertions for checking +the properties of numbers. This is mainly for use by other package developers +who want to include run-time testing features in their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-sets + (package + (name "r-assertive-sets") + (version "0.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.sets" version)) + (sha256 + (base32 + "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7")))) + (properties + `((upstream-name . "assertive.sets"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base))) + (home-page "https://bitbucket.org/richierocks/assertive.sets") + (synopsis "Assertions to check properties of sets") + (description + "This package provides a set of predicates and assertions for checking +the properties of sets. This is mainly for use by other package developers +who want to include run-time testing features in their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-matrices + (package + (name "r-assertive-matrices") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.matrices" version)) + (sha256 + (base32 + "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil")))) + (properties + `((upstream-name . "assertive.matrices"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base))) + (home-page "https://bitbucket.org/richierocks/assertive.matrices") + (synopsis "Assertions to check properties of matrices") + (description + "This package provides a set of predicates and assertions for checking +the properties of matrices. This is mainly for use by other package +developers who want to include run-time testing features in their own +packages.") + (license license:gpl3+))) + +(define-public r-assertive-models + (package + (name "r-assertive-models") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.models" version)) + (sha256 + (base32 + "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr")))) + (properties + `((upstream-name . "assertive.models"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base))) + (home-page "https://bitbucket.org/richierocks/assertive.models") + (synopsis "Assertions to check properties of models") + (description + "This package provides a set of predicates and assertions for checking +the properties of models. This is mainly for use by other package developers +who want to include run-time testing features in their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-reflection + (package + (name "r-assertive-reflection") + (version "0.0-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.reflection" version)) + (sha256 + (base32 + "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj")))) + (properties + `((upstream-name . "assertive.reflection"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base))) + (home-page "https://bitbucket.org/richierocks/assertive.reflection") + (synopsis "Assertions for checking the state of R") + (description + "This package provides a set of predicates and assertions for checking +the state and capabilities of R, the operating system it is running on, and +the IDE being used. This is mainly for use by other package developers who +want to include run-time testing features in their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-types + (package + (name "r-assertive-types") + (version "0.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.types" version)) + (sha256 + (base32 + "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb")))) + (properties + `((upstream-name . "assertive.types"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-properties" ,r-assertive-properties) + ("r-codetools" ,r-codetools))) + (home-page "https://bitbucket.org/richierocks/assertive.types") + (synopsis "Assertions to check types of variables") + (description + "This package provides a set of predicates and assertions for checking +the types of variables. This is mainly for use by other package developers +who want to include run-time testing features in their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-files + (package + (name "r-assertive-files") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.files" version)) + (sha256 + (base32 + "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy")))) + (properties + `((upstream-name . "assertive.files"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-numbers" ,r-assertive-numbers))) + (home-page "https://bitbucket.org/richierocks/assertive.files") + (synopsis "Assertions to check properties of files") + (description + "This package provides a set of predicates and assertions for checking +the properties of files and connections. This is mainly for use by other +package developers who want to include run-time testing features in their own +packages.") + (license license:gpl3+))) + +(define-public r-assertive-code + (package + (name "r-assertive-code") + (version "0.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.code" version)) + (sha256 + (base32 + "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g")))) + (properties + `((upstream-name . "assertive.code"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-properties" ,r-assertive-properties) + ("r-assertive-types" ,r-assertive-types))) + (home-page "https://bitbucket.org/richierocks/assertive.code") + (synopsis "Assertions to check properties of code") + (description + "This package provides a set of predicates and assertions for checking +the properties of code. This is mainly for use by other package developers +who want to include run-time testing features in their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-datetimes + (package + (name "r-assertive-datetimes") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.datetimes" version)) + (sha256 + (base32 + "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78")))) + (properties + `((upstream-name . "assertive.datetimes"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-types" ,r-assertive-types))) + (home-page "https://bitbucket.org/richierocks/assertive.datetimes") + (synopsis "Assertions to check properties of dates and times") + (description + "This package provides a set of predicates and assertions for checking +the properties of dates and times. This is mainly for use by other package +developers who want to include run-time testing features in their own +packages.") + (license license:gpl3+))) + +(define-public r-assertive-strings + (package + (name "r-assertive-strings") + (version "0.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.strings" version)) + (sha256 + (base32 + "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm")))) + (properties + `((upstream-name . "assertive.strings"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-types" ,r-assertive-types) + ("r-stringi" ,r-stringi))) + (home-page "https://bitbucket.org/richierocks/assertive.strings") + (synopsis "Assertions to check properties of strings") + (description + "This package provides a set of predicates and assertions for checking +the properties of strings. This is mainly for use by other package developers +who want to include run-time testing features in their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-data-us + (package + (name "r-assertive-data-us") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.data.us" version)) + (sha256 + (base32 + "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq")))) + (properties + `((upstream-name . "assertive.data.us"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-strings" ,r-assertive-strings))) + (home-page "https://bitbucket.org/richierocks/assertive.data.us") + (synopsis "Assertions to check properties of strings") + (description + "This package provides a set of predicates and assertions for checking +the properties of US-specific complex data types. This is mainly for use by +other package developers who want to include run-time testing features in +their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-data-uk + (package + (name "r-assertive-data-uk") + (version "0.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.data.uk" version)) + (sha256 + (base32 + "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b")))) + (properties + `((upstream-name . "assertive.data.uk"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-strings" ,r-assertive-strings))) + (home-page "https://bitbucket.org/richierocks/assertive.data.uk") + (synopsis "Assertions to check properties of strings") + (description + "This package provides a set of predicates and assertions for checking +the properties of UK-specific complex data types. This is mainly for use by +other package developers who want to include run-time testing features in +their own packages.") + (license license:gpl3+))) + +(define-public r-assertive-data + (package + (name "r-assertive-data") + (version "0.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive.data" version)) + (sha256 + (base32 + "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s")))) + (properties + `((upstream-name . "assertive.data"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-strings" ,r-assertive-strings))) + (home-page "https://bitbucket.org/richierocks/assertive.data") + (synopsis "Assertions to check properties of data") + (description + "This package provides a set of predicates and assertions for checking +the properties of (country independent) complex data types. This is mainly +for use by other package developers who want to include run-time testing +features in their own packages.") + (license license:gpl3+))) + +(define-public r-assertive + (package + (name "r-assertive") + (version "0.3-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "assertive" version)) + (sha256 + (base32 + "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertive-base" ,r-assertive-base) + ("r-assertive-code" ,r-assertive-code) + ("r-assertive-data" ,r-assertive-data) + ("r-assertive-data-uk" ,r-assertive-data-uk) + ("r-assertive-data-us" ,r-assertive-data-us) + ("r-assertive-datetimes" ,r-assertive-datetimes) + ("r-assertive-files" ,r-assertive-files) + ("r-assertive-matrices" ,r-assertive-matrices) + ("r-assertive-models" ,r-assertive-models) + ("r-assertive-numbers" ,r-assertive-numbers) + ("r-assertive-properties" ,r-assertive-properties) + ("r-assertive-reflection" ,r-assertive-reflection) + ("r-assertive-sets" ,r-assertive-sets) + ("r-assertive-strings" ,r-assertive-strings) + ("r-assertive-types" ,r-assertive-types) + ("r-knitr" ,r-knitr))) + (home-page "https://bitbucket.org/richierocks/assertive") + (synopsis "Readable check functions to ensure code integrity") + (description + "This package provides lots of predicates (@code{is_*} functions) to +check the state of your variables, and assertions (@code{assert_*} functions) +to throw errors if they aren't in the right form.") + (license license:gpl3+))) + +(define-public r-dotcall64 + (package + (name "r-dotcall64") + (version "1.0-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "dotCall64" version)) + (sha256 + (base32 + "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9")))) + (properties `((upstream-name . "dotCall64"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64") + (synopsis "Enhanced foreign function interface supporting long vectors") + (description + "This package provides @code{.C64()}, an enhanced version of @code{.C()} +and @code{.Fortran()} from the R foreign function interface. @code{.C64()} +supports long vectors, arguments of type 64-bit integer, and provides a +mechanism to avoid unnecessary copies of read-only and write-only arguments. +This makes it a convenient and fast interface to C/C++ and Fortran code.") + (license license:gpl2+))) + +(define-public r-spam + (package + (name "r-spam") + (version "2.2-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "spam" version)) + (sha256 + (base32 + "04bfwwna013hrbl4k6w1cdiz5bkc83jlasivriyn5l9gkj2qskr2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-dotcall64" ,r-dotcall64))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://www.math.uzh.ch/pages/spam/") + (synopsis "Sparse matrix algebra") + (description + "This package provides a set of functions for sparse matrix algebra. +Differences with other sparse matrix packages are: + +@enumerate +@item it only supports (essentially) one sparse matrix format; +@item it is based on transparent and simple structure(s); +@item it is tailored for MCMC calculations within G(M)RF; +@item and it is fast and scalable (with the extension package @code{spam64}). +@end enumerate\n") + ;; Either of these licenses + (license (list license:bsd-3 license:lgpl2.0)))) + +(define-public r-fields + (package + (name "r-fields") + (version "9.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "fields" version)) + (sha256 + (base32 + "1v7z48a8jmdcil28rj8c3455k6rssr5v9qi6dyhhpbb193bj8121")))) + (build-system r-build-system) + (propagated-inputs + `(("r-maps" ,r-maps) + ("r-spam" ,r-spam))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "http://www.image.ucar.edu/fields") + (synopsis "Tools for spatial data") + (description + "This is a package for curve, surface and function fitting with an +emphasis on splines, spatial data and spatial statistics. The major methods +include cubic, and thin plate splines, Kriging, and compactly supported +covariance functions for large data sets.") + (license license:gpl2+))) + +(define-public r-spatialextremes + (package + (name "r-spatialextremes") + (version "2.0-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "SpatialExtremes" version)) + (sha256 + (base32 + "1y0h1pcfqp9ynxsr3yrfbihlwm25ypyb88jmm5k2g7xvm8h9g050")))) + (properties + `((upstream-name . "SpatialExtremes"))) + (build-system r-build-system) + (propagated-inputs + `(("r-fields" ,r-fields) + ("r-maps" ,r-maps))) + (home-page "http://spatialextremes.r-forge.r-project.org/") + (synopsis "Modelling spatial extremes") + (description + "This package provides tools for the statistical modelling of spatial +extremes using max-stable processes, copula or Bayesian hierarchical models. +More precisely, this package allows (conditional) simulations from various +parametric max-stable models, analysis of the extremal spatial dependence, the +fitting of such processes using composite likelihoods or least square (simple +max-stable processes only), model checking and selection and prediction.") + (license license:gpl2+))) + +(define-public r-drc + (package + (name "r-drc") + (version "3.0-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "drc" version)) + (sha256 + (base32 + "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y")))) + (build-system r-build-system) + (propagated-inputs + `(("r-car" ,r-car) + ("r-gtools" ,r-gtools) + ("r-mass" ,r-mass) + ("r-multcomp" ,r-multcomp) + ("r-plotrix" ,r-plotrix) + ("r-scales" ,r-scales))) + (home-page "https://cran.r-project.org/web/packages/drc") + (synopsis "Analysis of dose-response curves") + (description + "This package provides a suite of flexible and versatile model fitting +and after-fitting functions for the analysis of dose-response data.") + (license license:gpl2+))) + +(define-public r-rmeta + (package + (name "r-rmeta") + (version "3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rmeta" version)) + (sha256 + (base32 + "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/rmeta") + (synopsis "Tools for meta-analysis") + (description + "This package provides functions for simple fixed and random effects +meta-analysis for two-sample comparisons and cumulative meta-analyses. It +draws standard summary plots, funnel plots, and computes summaries and tests +for association and heterogeneity.") + (license license:gpl2))) + +(define-public r-bootstrap + (package + (name "r-bootstrap") + (version "2017.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "bootstrap" version)) + (sha256 + (base32 + "08lmsy7k8wsgv89yc904c6fidcymr1ma2ry4fl0p69p21v4iiwa4")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/bootstrap") + (synopsis "Functions for the book \"An Introduction to the Bootstrap\"") + (description + "This package provides software and data for the book \"An Introduction +to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall. +This package is primarily provided for projects already based on it, and for +support of the book. New projects should preferentially use the recommended +package \"boot\".") + (license license:bsd-3))) + +(define-public r-survivalroc + (package + (name "r-survivalroc") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "survivalROC" version)) + (sha256 + (base32 + "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l")))) + (properties `((upstream-name . "survivalROC"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/survivalROC") + (synopsis "Time-dependent ROC curve estimation from censored survival data") + (description + "Compute time-dependent ROC curve from censored survival data using +Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty, +Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)") + (license license:gpl2+))) + +(define-public r-longitudinal + (package + (name "r-longitudinal") + (version "1.1.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "longitudinal" version)) + (sha256 + (base32 + "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l")))) + (build-system r-build-system) + (propagated-inputs `(("r-corpcor" ,r-corpcor))) + (home-page "http://strimmerlab.org/software/longitudinal/") + (synopsis "Analysis of multiple time course data") + (description + "This package contains general data structures and functions for +longitudinal data with multiple variables, repeated measurements, and +irregularly spaced time points. It also implements a shrinkage estimator of +dynamical correlation and dynamical covariance.") + (license license:gpl3+))) + +(define-public r-genenet + (package + (name "r-genenet") + (version "1.2.13") + (source + (origin + (method url-fetch) + (uri (cran-uri "GeneNet" version)) + (sha256 + (base32 + "0w52apk0nnr8nsskf26ff7ana8xiksr8wqmkjxzwhzgg7fncm61p")))) + (properties `((upstream-name . "GeneNet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-corpcor" ,r-corpcor) + ("r-fdrtool" ,r-fdrtool) + ("r-longitudinal" ,r-longitudinal))) + (home-page "http://strimmerlab.org/software/genenet/") + (synopsis "Modeling and inferring gene networks") + (description + "This package analyzes gene expression (time series) data with focus on +the inference of gene networks. In particular, GeneNet implements the methods +of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007) +for learning large-scale gene association networks (including assignment of +putative directions).") + (license license:gpl3+))) + +(define-public r-rbamtools + (package + (name "r-rbamtools") + (version "2.16.11.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "rbamtools" version)) + (sha256 + (base32 + "0gzkb1xyrkriv45wq8gv7qfwjslnvwkfkk5jjc4wg5kmm0ydpdzj")))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (propagated-inputs + `(("r-refgenome" ,r-refgenome))) + (home-page "https://cran.r-project.org/web/packages/rbamtools") + (synopsis "Read and write BAM (binary alignment) files") + (description + "This package provides an R interface to functions of the SAMtools +library.") + (license license:artistic2.0))) + +(define-public r-protviz + (package + (name "r-protviz") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "protViz" version)) + (sha256 + (base32 + "150i2q4nakz28f39kmhrchz4qsr8ax6y02512md94k8hq4hamxg1")))) + (properties `((upstream-name . "protViz"))) + (build-system r-build-system) + (inputs + `(("perl" ,perl) + ("python-2" ,python-2))) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/protViz/protViz/") + (synopsis "Visualizing and analyzing mass spectrometry data in proteomics") + (description + "This package helps with quality checks, visualizations and analysis of +mass spectrometry data, coming from proteomics experiments. The package is +developed, tested and used at the Functional Genomics Center Zurich, where it +is used mainly for prototyping, teaching, and having fun with proteomics data. +But it can also be used to do data analysis for small scale data sets.") + (license license:gpl3))) + +(define-public r-cmprsk + (package + (name "r-cmprsk") + (version "2.2-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "cmprsk" version)) + (sha256 + (base32 + "1imr3wpnj4g57n2x4ryahl4lk8lvq9y2r7319zv3k82mznha8bcm")))) + (build-system r-build-system) + (propagated-inputs + `(("r-survival" ,r-survival))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/cmprsk") + (synopsis "Subdistribution analysis of competing risks") + (description + "This package provides tool for estimation, testing and regression +modeling of subdistribution functions in competing risks, as described in +Gray (1988), A class of K-sample tests for comparing the cumulative incidence +of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999), +A proportional hazards model for the subdistribution of a competing risk, +JASA, 94:496-509.") + (license license:gpl2+))) + +(define-public r-etm + (package + (name "r-etm") + (version "1.0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "etm" version)) + (sha256 + (base32 + "0ws103b3pmli0z4xbyfxkly2wnnnxnnwc0r66qjjqjrlvm7pffl1")))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-lattice" ,r-lattice) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-survival" ,r-survival))) + (home-page "https://cran.r-project.org/web/packages/etm") + (synopsis "Empirical transition matrix") + (description + "The @dfn{empirical transition matrix} (etm) package permits to estimate +the matrix of transition probabilities for any time-inhomogeneous multistate +model with finite state space using the Aalen-Johansen estimator.") + (license license:expat))) + +(define-public r-epi + (package + (name "r-epi") + (version "2.32") + (source + (origin + (method url-fetch) + (uri (cran-uri "Epi" version)) + (sha256 + (base32 + "14n24xlm7pwdc54w2hlpjhfal1zpzm87rv3rjfckiz47d3w7dwqm")))) + (properties `((upstream-name . "Epi"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cmprsk" ,r-cmprsk) + ("r-data-table" ,r-data-table) + ("r-etm" ,r-etm) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-mgcv" ,r-mgcv) + ("r-numderiv" ,r-numderiv) + ("r-plyr" ,r-plyr) + ("r-survival" ,r-survival) + ("r-zoo" ,r-zoo))) + (home-page "http://BendixCarstensen.com/Epi/") + (synopsis "Statistical analysis in epidemiology") + (description + "This package provides functions for demographic and epidemiological +analysis in the Lexis diagram, i.e. register and cohort follow-up data, in +particular representation, manipulation and simulation of multistate data - +the Lexis suite of functions, which includes interfaces to the @code{mstate}, +@code{etm} and @code{cmprsk} packages. It also contains functions for +Age-Period-Cohort and Lee-Carter modeling and a function for interval censored +data and some useful functions for tabulation and plotting, as well as a +number of epidemiological data sets.") + (license license:gpl2))) + +(define-public r-ppls + (package + (name "r-ppls") + (version "1.6-1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ppls" version)) + (sha256 + (base32 + "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx")))) + (build-system r-build-system) + (propagated-inputs `(("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/ppls") + (synopsis "Penalized partial least squares") + (description + "This package contains linear and nonlinear regression methods based on +partial least squares and penalization techniques. Model parameters are +selected via cross-validation, and confidence intervals ans tests for the +regression coefficients can be conducted via jackknifing.") + (license license:gpl2+))) + +(define-public r-huge + (package + (name "r-huge") + (version "1.2.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "huge" version)) + (sha256 + (base32 + "134d951x42vy9dcmf155fbvik2934nh6qm2w5jlx3x2c6cf7faq4")))) + (build-system r-build-system) + (propagated-inputs + `(("r-igraph" ,r-igraph) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix))) + (home-page "https://cran.r-project.org/web/packages/huge") + (synopsis "High-dimensional undirected graph estimation") + (description + "This package provides a general framework for high-dimensional +undirected graph estimation. It integrates data preprocessing, neighborhood +screening, graph estimation, and model selection techniques into a pipeline.") + (license license:gpl2))) + +(define-public r-parcor + (package + (name "r-parcor") + (version "0.2-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "parcor" version)) + (sha256 + (base32 + "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0")))) + (build-system r-build-system) + (propagated-inputs + `(("r-epi" ,r-epi) + ("r-genenet" ,r-genenet) + ("r-glmnet" ,r-glmnet) + ("r-mass" ,r-mass) + ("r-ppls" ,r-ppls))) + (home-page "https://cran.r-project.org/web/packages/parcor") + (synopsis "Regularized estimation of partial correlation matrices") + (description + "This package estimates the matrix of partial correlations based on +different regularized regression methods: lasso, adaptive lasso, PLS, and +Ridge Regression. In addition, the package provides model selection for +lasso, adaptive lasso and Ridge regression based on cross-validation.") + (license license:gpl2+))) + +(define-public r-mcmc + (package + (name "r-mcmc") + (version "0.9-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "mcmc" version)) + (sha256 + (base32 + "1i3rahph8pbhi5dsyjnkazqklg4lhh3azlyvx4kvabx50q0awxn6")))) + (build-system r-build-system) + (home-page "http://www.stat.umn.edu/geyer/mcmc/") + (synopsis "Markov chain Monte Carlo") + (description + "This package simulates continuous distributions of random vectors using +@dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R +function that evaluates the log unnormalized density. Algorithms are random +walk Metropolis algorithm (function @code{metrop}), simulated +tempering (function @code{temper}), and morphometric random walk +Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity +by change of variable.") + (license license:expat))) |