diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 3176 |
1 files changed, 3076 insertions, 100 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ad8c6ebe67..dbc2b4614d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15,7 +15,7 @@ ;;; Copyright © 2018 Leo Famulari <leo@famulari.name> ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2018 Eric Brown <brown@fastmail.com> -;;; Copyright © 2018, 2019 Brett Gilio <brettg@posteo.net> +;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org> ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com> ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz> ;;; @@ -73,6 +73,7 @@ #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) #:use-module (gnu packages statistics) + #:use-module (gnu packages tcl) #:use-module (gnu packages tls) #:use-module (gnu packages web) #:use-module (gnu packages xorg)) @@ -729,10 +730,34 @@ objects in HTML format.") and vice-versa.") (license license:gpl2+))) +(define-public r-fastmap + (package + (name "r-fastmap") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "fastmap" version)) + (sha256 + (base32 + "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27")))) + (properties `((upstream-name . "fastmap"))) + (build-system r-build-system) + (home-page "https://r-lib.github.io/fastmap/") + (synopsis "Fast implementation of a key-value store") + (description + "This package provides a fast implementation of a key-value store. +Environments are commonly used as key-value stores, but every time a new key +is used, it is added to R's global symbol table, causing a small amount of +memory leakage. This can be problematic in cases where many different keys +are used. Fastmap avoids this memory leak issue by implementing the map using +data structures in C++.") + (license license:expat))) + (define-public r-shiny (package (name "r-shiny") - (version "1.2.0") + (version "1.4.0") (source (origin (method git-fetch) @@ -742,7 +767,7 @@ and vice-versa.") (file-name (git-file-name name version)) (sha256 (base32 - "1kl3dh68h4cnrm3rqn9pddk5n6bsmr5x0626bkfv0qqi0q92zin4")))) + "17ac48g414h9dhi0k4wrah4gyik0q5r0xw3kc01c02qfjwimqsx7")))) (build-system r-build-system) (arguments `(#:modules ((guix build r-build-system) @@ -771,7 +796,7 @@ and vice-versa.") "/share/javascript/html5shiv.min.js")) (replace-file "json2-min.js" (string-append (assoc-ref inputs "js-json2") - "/share/javascript/json2.min.js")) + "/share/javascript/json2-min.js")) (replace-file "strftime/strftime-min.js" (string-append (assoc-ref inputs "js-strftime") "/share/javascript/strftime.min.js")) @@ -802,10 +827,15 @@ and vice-versa.") ("shiny.js" . "shiny.min.js") ("jquery.js" . - "jquery.min.js"))))) + "jquery.min.js") + ("legacy/jquery.js" . + "legacy/jquery.min.js") + ("showdown/src/showdown.js" . + "showdown/compressed/showdown.js"))))) #t))))) (propagated-inputs `(("r-crayon" ,r-crayon) + ("r-fastmap" ,r-fastmap) ("r-httpuv" ,r-httpuv) ("r-mime" ,r-mime) ("r-jsonlite" ,r-jsonlite) @@ -1262,14 +1292,14 @@ coordinates.") (define-public r-rgooglemaps (package (name "r-rgooglemaps") - (version "1.4.4") + (version "1.4.5") (source (origin (method url-fetch) (uri (cran-uri "RgoogleMaps" version)) (sha256 (base32 - "0sbklacc4jl5524ixhc11mh6smrzdz4l9pji6cn402i6zdn9z05x")))) + "1acf0qc9597apcidjzrpvwhg9ihypr38jigc10jvqn33qbn1i9s7")))) (properties `((upstream-name . "RgoogleMaps"))) (build-system r-build-system) (propagated-inputs `(("r-png" ,r-png))) @@ -1394,13 +1424,13 @@ embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.") (define-public r-amap (package (name "r-amap") - (version "0.8-17") + (version "0.8-18") (source (origin (method url-fetch) (uri (cran-uri "amap" version)) (sha256 (base32 - "1il94bkhl8192vawq4gr2gwyhqhid27jr2312rhvr72ssg8p713b")))) + "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -2331,21 +2361,44 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and ;; Any version of the LGPL. (license license:lgpl3+))) +(define-public r-bdsmatrix + (package + (name "r-bdsmatrix") + (version "1.3-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "bdsmatrix" version)) + (sha256 + (base32 + "17ddvz4gnih7rx0lr1gzk280xyh6x796cf2x794dvplpiiq83skh")))) + (properties `((upstream-name . "bdsmatrix"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/bdsmatrix/") + (synopsis "Routines for block diagonal symmetric matrices") + (description + "This package provides procedures to work with block diagonal symmetric +matrices, a special case of sparse matrices.") + (license license:lgpl2.0))) + (define-public r-bbmle (package (name "r-bbmle") - (version "1.0.20") + (version "1.0.22") (source (origin (method url-fetch) (uri (cran-uri "bbmle" version)) (sha256 (base32 - "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc")))) + "1idn55w5f3iw4r0ydyww8xyinninw07sxlwfqb565vmdrs87dwl4")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) + `(("r-bdsmatrix" ,r-bdsmatrix) + ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-mvtnorm" ,r-mvtnorm) ("r-numderiv" ,r-numderiv))) (home-page "https://cran.r-project.org/web/packages/bbmle") (synopsis "Tools for General Maximum Likelihood Estimation") @@ -2747,14 +2800,14 @@ dimensioned arrays.") (define-public r-rmysql (package (name "r-rmysql") - (version "0.10.17") + (version "0.10.18") (source (origin (method url-fetch) (uri (cran-uri "RMySQL" version)) (sha256 (base32 - "1xamf99ih44dvaxg5x4ivj0hkqssmabgqd7gh8b8q1srw7yg8kbm")))) + "0r4626sk78fhlgivr0c7mwg9mj29ayr0iz5x90rdl4d5nc2r6kq4")))) (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (inputs @@ -2961,14 +3014,14 @@ problems as well as resampling based estimators of prediction error.") (define-public r-psych (package (name "r-psych") - (version "1.8.12") + (version "1.9.12") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 - "0hvp0dkkkn0szaf5rkirr3kb8qmr4bxwl775m5wmpvn1kc25w5vf")))) + "13r7fyjsl93m121awnwfhya8a0lw0l2byn60yqdbf9gp3lmb9ny0")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) @@ -3015,14 +3068,14 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "0.5.2") + (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "0qmclih5dm5sqzy4hplcfy677kr12pm9pnpv3r319g14dd27pbqn")))) + "177m249dxbf9pf249610qrl58v025ws41ipfihy66751pwsv2n8d")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -3050,14 +3103,14 @@ provides a one-row summary of model-level statistics.") (define-public r-recipes (package (name "r-recipes") - (version "0.1.7") + (version "0.1.8") (source (origin (method url-fetch) (uri (cran-uri "recipes" version)) (sha256 (base32 - "1gw8x7vqj7k18mfpiqinyfwzv9i5r0pb51k7xcfxsjap6m9nks98")))) + "1n32qc2a3n9cykm8dv9qcr77kdhqfsjiqf6kgfk9s0lnpx2zaldm")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -3206,14 +3259,14 @@ with the package @code{optim}.") (define-public r-ordinal (package (name "r-ordinal") - (version "2019.4-25") + (version "2019.12-10") (source (origin (method url-fetch) (uri (cran-uri "ordinal" version)) (sha256 (base32 - "1pvrkly4x12w32n7w1qljdwzqnlkv7rfa7rx0nz5vbiw29xas4i8")))) + "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -3306,14 +3359,14 @@ analysis of multiply imputed data sets.") (define-public r-mice (package (name "r-mice") - (version "3.6.0") + (version "3.7.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 - "0pgcxdmp77604h6f4x8hhs6j4xdjgf5b9zvnixyzdj8vcgdjpivv")))) + "1wx1s1gc07iz63w4m8z0i1n5mc273f89grp5d3hfla7ypicjkasf")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -3769,14 +3822,14 @@ rules, boxes, trees, and Unicode symbols with ASCII alternatives.") (define-public r-argparser (package (name "r-argparser") - (version "0.4") + (version "0.6") (source (origin (method url-fetch) (uri (cran-uri "argparser" version)) (sha256 (base32 - "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9")))) + "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x")))) (build-system r-build-system) (home-page "https://bitbucket.org/djhshih/argparser") (synopsis "Command-line argument parser") @@ -4017,14 +4070,14 @@ to variables on the left-hand side of the assignment.") (define-public r-vctrs (package (name "r-vctrs") - (version "0.2.0") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 - "05h0y8qzwc899qj84gkhg4jwzscd065as00d4d8smv42h4i8zkjv")))) + "0rlwjfvvhv3s5mj4lqhwlqwddpizyp46i1qbcvw0mzb5q8b0nkz0")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -4056,14 +4109,14 @@ to variables on the left-hand side of the assignment.") (define-public r-pillar (package (name "r-pillar") - (version "1.4.2") + (version "1.4.3") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "0988047mf0xdhdkqqmavzx4ifjhndjnxniyrrhrdq1nvnrvbpfms")))) + "02sn7zw80wq33jgxk2i6m5jb83sk7y72dfhgyy0apfinv05w92ss")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -4102,14 +4155,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.17") + (version "0.18") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "0mgxrbj4gam2gvxfk26nq820vsfjggj81m2l7j9m8vp361k15r0w")))) + "04mpbhadixbxmnazj0q6cj973cajchscvyh1k6a5b3qk26dp5krr")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) @@ -4195,14 +4248,14 @@ detect possible inconsistencies.") (define-public r-sna (package (name "r-sna") - (version "2.4") + (version "2.5") (source (origin (method url-fetch) (uri (cran-uri "sna" version)) (sha256 (base32 - "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2")))) + "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k")))) (build-system r-build-system) (propagated-inputs `(("r-network" ,r-network) @@ -4248,14 +4301,14 @@ of these tests are also included.") (define-public r-ttr (package (name "r-ttr") - (version "0.23-5") + (version "0.23-6") (source (origin (method url-fetch) (uri (cran-uri "TTR" version)) (sha256 (base32 - "0fxipnyxaz55n4camrk9cs71x9w4dsmjrihysv8i1s6khf825rg6")))) + "0rg22ma3x07s9djlxscfw5jcq1gbir05cwhgvwfi53x1sf4hmhdg")))) (properties `((upstream-name . "TTR"))) (build-system r-build-system) (propagated-inputs @@ -5598,14 +5651,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (define-public r-renv (package (name "r-renv") - (version "0.9.1") + (version "0.9.2") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 - "0mwqpcay6v1hnvhggsrn1chvdlhi9hwvsswas8ysygfy5wxxz1sm")))) + "1jwnabryn77s29ybwdfzlnd7c8m05xmi69kp5qbvdxy2gjwjzcdr")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (home-page "https://rstudio.github.io/renv") @@ -5691,18 +5744,19 @@ obtain a better initial configuration in non-metric MDS.") (define-public r-reticulate (package (name "r-reticulate") - (version "1.13") + (version "1.14") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "1qwxh7zq9igl7dxl5g5qjbvv0mlac3w80djnkm0w8rxnaval3gmd")))) + "0icb9zl9zlx75njv7y1dr450k0yw2n3q2jkr4nicnphdyfn69gkn")))) (build-system r-build-system) (inputs `(("python" ,python))) (propagated-inputs - `(("r-jsonlite" ,r-jsonlite) + `(("r-rappdirs" ,r-rappdirs) + ("r-jsonlite" ,r-jsonlite) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp))) (home-page "https://github.com/rstudio/reticulate") @@ -5717,14 +5771,14 @@ Python to R they are converted back to R types.") (define-public r-bibtex (package (name "r-bibtex") - (version "0.4.2") + (version "0.4.2.1") (source (origin (method url-fetch) (uri (cran-uri "bibtex" version)) (sha256 (base32 - "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz")))) + "1ks1w59ldwmfd1sj8ap7smyhf8dhykv7xnwrl8z9xzkcfpv1rbc0")))) (build-system r-build-system) (propagated-inputs `(("r-stringr" ,r-stringr))) (home-page "https://github.com/romainfrancois/bibtex") @@ -6118,14 +6172,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rdpack (package (name "r-rdpack") - (version "0.11-0") + (version "0.11-1") (source (origin (method url-fetch) (uri (cran-uri "Rdpack" version)) (sha256 (base32 - "11cd27s6zp5cxnwxcvz6rjf00y0r7aq8ywhzwpf1r4xy1z44kd4g")))) + "080y15p2hl4jsq91ak2f1y2kx1iqq5c5wzyx3zyhjwp01cahy0jq")))) (properties `((upstream-name . "Rdpack"))) (build-system r-build-system) (propagated-inputs @@ -6686,14 +6740,14 @@ Group (Non-)Overlap considerations.") (define-public r-deriv (package (name "r-deriv") - (version "3.9.0") + (version "4.0") (source (origin (method url-fetch) (uri (cran-uri "Deriv" version)) (sha256 (base32 - "0hlqm216bg3l79gq6m0am0xz6vd3l2hgjnjm6lym3mkmgkka4kxw")))) + "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n")))) (properties `((upstream-name . "Deriv"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/Deriv") @@ -6841,14 +6895,14 @@ bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.") (define-public r-rootsolve (package (name "r-rootsolve") - (version "1.8.1") + (version "1.8.2") (source (origin (method url-fetch) (uri (cran-uri "rootSolve" version)) (sha256 (base32 - "0skrspq7sd7gaq73w91km14v8znc8chncgy64hvjgcng2xw15phx")))) + "0rj7c4zcrzgz7sb0vgvh7swpfafnw4040cxp7ypas3s8fnihn54l")))) (properties `((upstream-name . "rootSolve"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -6899,13 +6953,13 @@ the analyzed items.") (define-public r-slam (package (name "r-slam") - (version "0.1-46") + (version "0.1-47") (source (origin (method url-fetch) (uri (cran-uri "slam" version)) (sha256 - (base32 "1ihhbx76miwys35gsbhijriadvrw4f51lc3v45pnn6cvcfd9hr0b")))) + (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/slam/") (synopsis "Sparse lightweight arrays and matrices") @@ -7821,16 +7875,68 @@ analysis.") ;; Either version of the GPL. (license (list license:gpl2 license:gpl3)))) +(define-public r-gee + (package + (name "r-gee") + (version "4.13-20") + (source + (origin + (method url-fetch) + (uri (cran-uri "gee" version)) + (sha256 + (base32 + "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak")))) + (properties `((upstream-name . "gee"))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/gee/") + (synopsis "Generalized estimation equation solver") + (description + "This package provides a solver for generalized estimation equations.") + (license license:gpl2))) + +(define-public r-tab + (package + (name "r-tab") + (version "4.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "tab" version)) + (sha256 + (base32 + "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm")))) + (properties `((upstream-name . "tab"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-gee" ,r-gee) + ("r-knitr" ,r-knitr) + ("r-mass" ,r-mass) + ("r-survey" ,r-survey) + ("r-survival" ,r-survival) + ("r-xtable" ,r-xtable))) + (home-page "https://cran.r-project.org/web/packages/tab/") + (synopsis "Create summary tables for statistical reports") + (description + "This package contains functions for creating various types of summary +tables, e.g. comparing characteristics across levels of a categorical variable +and summarizing fitted generalized linear models, generalized estimating +equations, and Cox proportional hazards models. Functions are available to +handle data from simple random samples as well as complex surveys.") + (license license:gpl3+))) + (define-public r-dvmisc (package (name "r-dvmisc") - (version "1.1.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "dvmisc" version)) (sha256 - (base32 "0x391pxg5mqgp5xxc8qwhwxky8ds7d9gr9iwmsb12c92kxfk00bv")))) + (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi")))) (build-system r-build-system) (propagated-inputs `(("r-cubature" ,r-cubature) @@ -7840,10 +7946,10 @@ analysis.") ("r-mass" ,r-mass) ("r-mvtnorm" ,r-mvtnorm) ("r-pracma" ,r-pracma) - ("r-purrr" ,r-purrr) ("r-rbenchmark" ,r-rbenchmark) ("r-rcpp" ,r-rcpp) - ("r-survey" ,r-survey))) + ("r-survey" ,r-survey) + ("r-tab" ,r-tab))) (home-page "https://cran.r-project.org/web/packages/dvmisc/") (synopsis "Faster computation of common statistics and miscellaneous functions") (description @@ -8118,14 +8224,14 @@ packages maintained by Torsten Hothorn.") (define-public r-multcomp (package (name "r-multcomp") - (version "1.4-10") + (version "1.4-11") (source (origin (method url-fetch) (uri (cran-uri "multcomp" version)) (sha256 (base32 - "1kzmdn9jmz5bmhf3wsfr12ljbasmwsgcsfdia52k0bi6q0swdg19")))) + "0jw9661hs4396wz9vflk3rak0ryzj1cg2pnndsn1gb4fjyf2vlhb")))) (build-system r-build-system) (propagated-inputs `(("r-codetools" ,r-codetools) @@ -8403,14 +8509,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.4.0") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "0lxpmp9smn5r3xvfik36nr608wcpmmximjh0v2sckyvjf7hnb4s0")))) + "1pcjmqqm178dvdcpzkv5p4sj7glsppcny7znljb2nqkxh539a59p")))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) @@ -8430,22 +8536,20 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "0.13.0") + (version "0.14.0") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "0ryfbaav0k874kbwmhbiv7fan93dmkpaimm1iw5kryjhhs3917lb")))) + "1djz82xww86h8f33m2vm40lliicppgyhm6hyn3h6rzrqjrlrsmdw")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-insight" ,r-insight) + `(("r-insight" ,r-insight) ("r-magrittr" ,r-magrittr) ("r-mass" ,r-mass) ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) ("r-sjlabelled" ,r-sjlabelled) ("r-sjmisc" ,r-sjmisc))) (home-page "https://github.com/strengejacke/ggeffects") @@ -9011,14 +9115,14 @@ experiments using ANOVA or mixed models.") (define-public r-lmertest (package (name "r-lmertest") - (version "3.1-0") + (version "3.1-1") (source (origin (method url-fetch) (uri (cran-uri "lmerTest" version)) (sha256 (base32 - "1nkz8cmxa5yb8q4i65bmhnn5pd4bhwcyjplyscynb24z3f64xp9b")))) + "0r2vvs3nl6p8xla3gd943khb4ixp0alvspqpnz2y6n3wk8zgh3jj")))) (properties `((upstream-name . "lmerTest"))) (build-system r-build-system) (propagated-inputs @@ -9456,14 +9560,14 @@ for evolution along a phylogenetic tree.") (define-public r-fmsb (package (name "r-fmsb") - (version "0.6.3") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "fmsb" version)) (sha256 (base32 - "1n29bnyp20pvpk2lsa9fblsj5w7amp14snc74pk5w3yr5y6rj0s5")))) + "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45")))) (build-system r-build-system) (home-page "http://minato.sip21c.org/msb/") (synopsis "Functions for medical statistics book with demographic data") @@ -9637,14 +9741,14 @@ Processing.") (define-public r-tm (package (name "r-tm") - (version "0.7-6") + (version "0.7-7") (source (origin (method url-fetch) (uri (cran-uri "tm" version)) (sha256 (base32 - "0spv43kjbpxq3rdxx8ysgrncjyc35ydiwk7gp8n4sig45iqyz59r")))) + "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh")))) (properties `((upstream-name . "tm"))) (build-system r-build-system) (propagated-inputs @@ -9733,13 +9837,13 @@ maps.") (define-public r-tidytree (package (name "r-tidytree") - (version "0.3.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 - (base32 "1sbfwcxf9v1lhpa0392b49b6qfjrq7nlqz2djqzk5aknj9j64zvy")))) + (base32 "1bnzs62z2l8ck2h9gabmxvayizv4nfn8dmyzry83fv0cspjbyiv7")))) (build-system r-build-system) (propagated-inputs `(("r-ape" ,r-ape) @@ -11053,13 +11157,13 @@ This makes it a convenient and fast interface to C/C++ and Fortran code.") (define-public r-spam (package (name "r-spam") - (version "2.5-0") + (version "2.5-1") (source (origin (method url-fetch) (uri (cran-uri "spam" version)) (sha256 - (base32 "1wfv45jq8zy8kyjr308zicc1461y1777qll1cy6lw4071f9rvba2")))) + (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi")))) (build-system r-build-system) (propagated-inputs `(("r-dotcall64" ,r-dotcall64))) @@ -12402,14 +12506,14 @@ compatible with @code{rzmq} are also provided.") (define-public r-repr (package (name "r-repr") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "repr" version)) (sha256 (base32 - "0jy43g34r38fqprcdys0p9pliahrj5l64a9bbkzy206qgz0j5ppc")))) + "0wn9fdddqjgn0bdfl75x89rcxahbgqs324bhg0pfq6va5q2mlbbw")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -14805,18 +14909,17 @@ code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.") (define-public r-sctransform (package (name "r-sctransform") - (version "0.2.0") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "sctransform" version)) (sha256 (base32 - "1r5kiqqs318q59h2i8m7c6nhghp9w6q26ss2y5a390lkhsawgx6p")))) + "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn")))) (build-system r-build-system) (propagated-inputs - `(("r-future" ,r-future) - ("r-future-apply" ,r-future-apply) + `(("r-future-apply" ,r-future-apply) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-mass" ,r-mass) @@ -15092,14 +15195,14 @@ annotated biological functions.") (define-public r-plot3d (package (name "r-plot3d") - (version "1.1.1") + (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "plot3D" version)) (sha256 (base32 - "0chn70fqwyca8lbnjnpbcj08ni0dfbax2gjmzhk2c4w72c04mzpn")))) + "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r")))) (properties `((upstream-name . "plot3D"))) (build-system r-build-system) (propagated-inputs `(("r-misc3d" ,r-misc3d))) @@ -15824,19 +15927,18 @@ PROJ.4 library.") (define-public r-insol (package (name "r-insol") - (version "1.2") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "insol" version)) (sha256 (base32 - "14ikz05375pjn9hby7kwkhcnykjilbnkdy5i8lsl7c5qdbhmqcm5")))) + "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1")))) (properties `((upstream-name . "insol"))) (build-system r-build-system) (propagated-inputs - `(("r-raster" ,r-raster) - ("r-rgdal" ,r-rgdal))) + `(("r-raster" ,r-raster))) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://meteoexploration.com/R/insol/index.html") @@ -15927,40 +16029,41 @@ programming problems.") (define-public r-desolve (package (name "r-desolve") - (version "1.25") + (version "1.27") (source (origin (method url-fetch) (uri (cran-uri "deSolve" version)) (sha256 - (base32 "0735y3p5glhqx69rzrc8qgmvs7p7w0p98qxmvylb6bgqp6kp0cbp")))) + (base32 "1qhjq4vxlxd9qmhf6i26x1k7bzhldlxzbby1zgcplicdvlqk951d")))) (properties `((upstream-name . "deSolve"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://desolve.r-forge.r-project.org/") (synopsis "Solvers for initial value problems of differential equations") - (description "This package provides functions that solve initial -value problems of a system of first-order ordinary differential equations (ODE), -of partial differential equations (PDE), of differential algebraic equations -(DAE), and of delay differential equations. The functions provide an interface -to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection, -to the FORTRAN functions dvode and daspk and a C-implementation of solvers of -the Runge-Kutta family with fixed or variable time steps. The package contains -routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial -differential equations (PDE) that have been converted to ODEs by numerical -differencing.") + (description "This package provides functions that solve initial value +problems of a system of first-order @dfn{ordinary differential +equations} (ODE), of @dfn{partial differential equations} (PDE), of +@dfn{differential algebraic equations} (DAE), and of delay differential +equations. The functions provide an interface to the FORTRAN functions +@code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK +collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a +C-implementation of solvers of the Runge-Kutta family with fixed or variable +time steps. The package contains routines designed for solving ODEs resulting +from 1-D, 2-D and 3-D partial differential equations that have been converted +to ODEs by numerical differencing.") (license license:gpl2+))) (define-public r-pracma (package (name "r-pracma") - (version "2.2.5") + (version "2.2.9") (source (origin (method url-fetch) (uri (cran-uri "pracma" version)) (sha256 - (base32 "0isd3s0i4mzmva8lkh0j76hwjy1w50q7d1n9lhxsnnkgalx3xs1g")))) + (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pracma/") (synopsis "Practical numerical math functions") @@ -16012,3 +16115,2876 @@ graphics directly in the terminal window. This package provides a basic plotting function (and equivalents of curve, density, acf and barplot) as well as a boxplot function.") (license license:lgpl3+))) + +(define-public r-bio3d + (package + (name "r-bio3d") + (version "2.4-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "bio3d" version)) + (sha256 + (base32 + "0ikpk1ppdp50m9kd289z616i382j9i7ji1zchyd4xqfyk8lnxf4s")))) + (properties `((upstream-name . "bio3d"))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "http://thegrantlab.org/bio3d/") + (synopsis "Biological structure analysis") + (description + "This package provides utilities to process, organize and explore protein +structure, sequence and dynamics data. Features include the ability to read +and write structure, sequence and dynamic trajectory data, perform sequence +and structure database searches, data summaries, atom selection, alignment, +superposition, rigid core identification, clustering, torsion analysis, +distance matrix analysis, structure and sequence conservation analysis, normal +mode analysis, principal component analysis of heterogeneous structure data, +and correlation network analysis from normal mode and molecular dynamics data. +In addition, various utility functions are provided to enable the statistical +and graphical power of the R environment to work with biological sequence and +structural data.") + (license license:gpl2+))) + +(define-public r-bios2cor + (package + (name "r-bios2cor") + (version "2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "Bios2cor" version)) + (sha256 + (base32 + "1rrz0vs6wbkwys3l5jv1rdnlhyb4r1q9pv7jlnmsx6c1b4f4vz5n")))) + (properties `((upstream-name . "Bios2cor"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bigmemory" ,r-bigmemory) + ("r-bio3d" ,r-bio3d) + ("r-circular" ,r-circular) + ("r-igraph" ,r-igraph))) + (home-page "https://cran.r-project.org/web/packages/Bios2cor/") + (synopsis "From biological sequences and simulations to correlation analysis") + (description + "This package provides utilities for computation and analysis of +correlation/covariation in multiple sequence alignments and in side chain +motions during molecular dynamics simulations. Features include the +computation of correlation/covariation scores using a variety of scoring +functions between either sequence positions in alignments or side chain +dihedral angles in molecular dynamics simulations and utilities to analyze the +correlation/covariation matrix through a variety of tools including network +representation and principal components analysis. In addition, several +utility functions are based on the R graphical environment to provide friendly +tools for help in data interpretation.") + (license license:gpl2+))) + +;; This package includes minified JavaScript files. When upgrading please +;; check that there are no new minified JavaScript files. +(define-public r-networkd3 + (package + (name "r-networkd3") + (version "0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "networkD3" version)) + (sha256 + (base32 + "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k")) + (snippet + '(begin + (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js") + #t)))) + (properties `((upstream-name . "networkD3"))) + (build-system r-build-system) + (arguments + `(#:modules ((guix build utils) + (guix build r-build-system) + (srfi srfi-1) + (ice-9 popen)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/htmlwidgets/lib/" + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "d3.v4.js") + "d3-4.5.0/d3.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #t "Processing ~a --> ~a~%" + source target) + (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) + (call-with-output-file target + (lambda (port) + (dump-port minified port))))) + sources targets)))) + #t))))) + (native-inputs + `(("uglify-js" ,uglify-js) + ;; NOTE: Make sure that this version of d3 is still valid when + ;; upgrading the package. + ("d3.v4.js" + ,(origin + (method url-fetch) + (uri "https://d3js.org/d3.v4.js") + (sha256 + (base32 + "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))))) + (propagated-inputs + `(("r-htmlwidgets" ,r-htmlwidgets) + ("r-igraph" ,r-igraph) + ("r-magrittr" ,r-magrittr))) + (home-page "https://cran.r-project.org/package=networkD3") + (synopsis "D3 JavaScript network graphs from R") + (description + "This package creates D3 JavaScript network, tree, dendrogram, and Sankey +graphs from R.") + (license license:gpl3+))) + +(define-public r-aasea + (package + (name "r-aasea") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "aaSEA" version)) + (sha256 + (base32 + "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h")))) + (properties `((upstream-name . "aaSEA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bios2cor" ,r-bios2cor) + ("r-dt" ,r-dt) + ("r-hmisc" ,r-hmisc) + ("r-magrittr" ,r-magrittr) + ("r-networkd3" ,r-networkd3) + ("r-plotly" ,r-plotly) + ("r-seqinr" ,r-seqinr) + ("r-shiny" ,r-shiny) + ("r-shinydashboard" ,r-shinydashboard))) + (home-page "https://cran.r-project.org/web/packages/aaSEA/") + (synopsis "Amino acid substitution effect analyzer") + (description + "Given a protein multiple sequence alignment, it is a daunting task to +assess the effects of substitutions along sequence length. The aaSEA package +is intended to help researchers to rapidly analyze property changes caused by +single, multiple and correlated amino acid substitutions in proteins.") + (license license:gpl3))) + +(define-public r-abacus + (package + (name "r-abacus") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ABACUS" version)) + (sha256 + (base32 + "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i")))) + (properties `((upstream-name . "ABACUS"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-shiny" ,r-shiny))) + (home-page "https://shiny.abdn.ac.uk/Stats/apps/") + (synopsis "Apps-based activities for communicating and understanding statistics") + (description + "This package provides a set of Shiny apps for effective communication +and understanding in statistics. The current version includes properties of +normal distribution, properties of sampling distribution, one-sample z and t +tests, two samples independent (unpaired) t test and analysis of variance.") + (license license:gpl3))) + +(define-public r-abc-rap + (package + (name "r-abc-rap") + (version "0.9.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ABC.RAP" version)) + (sha256 + (base32 + "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk")))) + (properties `((upstream-name . "ABC.RAP"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/ABC.RAP/") + (synopsis "Array-based CpG region analysis pipeline") + (description + "This package aims to identify candidate genes that are differentially +methylated between cases and controls. It applies Student's t-test and delta +beta analysis to identify candidate genes containing multiple CpG sites.") + (license license:gpl3))) + +(define-public r-abcadm + (package + (name "r-abcadm") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "abcADM" version)) + (sha256 + (base32 + "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10")))) + (properties `((upstream-name . "abcADM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/abcADM/") + (synopsis "Fit accumulated damage models and estimate reliability using ABC") + (description + "This package provides tools to estimate parameters of accumulated +damage (load duration) models based on failure time data under a Bayesian +framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess +long-term reliability under stochastic load profiles.") + (license license:gpl3))) + +(define-public r-rglpk + (package + (name "r-rglpk") + (version "0.6-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "Rglpk" version)) + (sha256 + (base32 + "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2")))) + (properties `((upstream-name . "Rglpk"))) + (build-system r-build-system) + (propagated-inputs + `(("r-slam" ,r-slam))) + (inputs + `(("glpk" ,glpk))) + (home-page "http://R-Forge.R-project.org/projects/rglp/") + (synopsis "R interface to the GNU Linear Programming Kit") + (description + "This package provides an R interface to the GNU Linear Programming Kit, +software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed +integer linear programming} (MILP) and other related problems.") + ;; Either license + (license (list license:gpl2 license:gpl3)))) + +(define-public r-abcdefba + (package + (name "r-abcdefba") + (version "0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "abcdeFBA" version)) + (sha256 + (base32 + "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4")))) + (properties `((upstream-name . "abcdeFBA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-corrplot" ,r-corrplot) + ("r-lattice" ,r-lattice) + ("r-rgl" ,r-rgl) + ("r-rglpk" ,r-rglpk))) + (home-page "https://cran.r-project.org/web/packages/abcdeFBA/") + (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package") + (description + "This package provides functions for Constraint Based Simulation using +Flux Balance Analysis and informative analysis of the data generated during +simulation.") + (license license:gpl2))) + +(define-public r-abcrlda + (package + (name "r-abcrlda") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "abcrlda" version)) + (sha256 + (base32 + "0j29ifsvmxfx2g6v4bpbb4s6miwfpf4vlkpbgj6f2q078s4clc85")))) + (properties `((upstream-name . "abcrlda"))) + (build-system r-build-system) + (home-page "https://ieeexplore.ieee.org/document/8720003/") + (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis") + (description + "This package offers methods to perform @dfn{asymptotically +bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for +cost-sensitive binary classification. The bias-correction is an estimate of +the bias term added to regularized discriminant analysis that minimizes the +overall risk.") + (license license:gpl3))) + +(define-public r-abemus + (package + (name "r-abemus") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "abemus" version)) + (sha256 + (base32 + "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb")))) + (properties `((upstream-name . "abemus"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table))) + (home-page "https://cran.r-project.org/web/packages/abemus/") + (synopsis "Adaptive base error model in ultra-deep sequencing data") + (description + "This package provides an implementation of @dfn{Adaptive Base Error +Model in Ultra-deep Sequencing data} (ABEMUS), which combines +platform-specific genetic knowledge and empirical signal to readily detect and +quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating +cell free DNA} (cfDNA).") + (license license:gpl3))) + +;; This package includes minified JavaScript files. When upgrading please +;; check that there are no new minified JavaScript files. +(define-public r-rintrojs + (package + (name "r-rintrojs") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "rintrojs" version)) + (sha256 + (base32 + "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427")))) + (properties `((upstream-name . "rintrojs"))) + (build-system r-build-system) + (arguments + `(#:modules ((guix build utils) + (guix build r-build-system) + (srfi srfi-1) + (ice-9 popen)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/javascript/introjs/" + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "intro.js") + "intro.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #t "Processing ~a --> ~a~%" + source target) + (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) + (call-with-output-file target + (lambda (port) + (dump-port minified port))))) + sources targets)))) + #t))))) + (native-inputs + `(("uglify-js" ,uglify-js) + ("intro.js" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js") + (sha256 + (base32 + "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8")))))) + (propagated-inputs + `(("r-jsonlite" ,r-jsonlite) + ("r-shiny" ,r-shiny))) + (home-page "https://github.com/carlganz/rintrojs") + (synopsis "Wrapper for the Intro.js library") + (description + "This package provides a wrapper for the @url{http://www.introjs.com, +Intro.js} library. This package makes it easy to include step-by-step +introductions, and clickable hints in a Shiny application. It supports both +static introductions in the UI, and programmatic introductions from the +server-side.") + (license license:agpl3+))) + +(define-public r-sysfonts + (package + (name "r-sysfonts") + (version "0.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "sysfonts" version)) + (sha256 + (base32 + "0wng902plryf2d8fc7k7m3jx11acz51kb2d91cqbyhq7xpk06z43")))) + (properties `((upstream-name . "sysfonts"))) + (build-system r-build-system) + (inputs + `(("freetype" ,freetype) + ("libpng" ,libpng) + ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://github.com/yixuan/sysfonts") + (synopsis "Loading fonts into R") + (description + "This is a package to simplify loading of system fonts and Google Fonts +into R, in order to support other packages.") + (license license:gpl2))) + +(define-public r-showtextdb + (package + (name "r-showtextdb") + (version "2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "showtextdb" version)) + (sha256 + (base32 + "1qwwj9x2jvadvwn60h75k99c9xi7yhqjsgaakahz5paxgj583bsh")))) + (properties `((upstream-name . "showtextdb"))) + (build-system r-build-system) + (propagated-inputs + `(("r-sysfonts" ,r-sysfonts))) + (home-page "https://cran.r-project.org/web/packages/showtextdb/") + (synopsis "Font files for the 'showtext' package") + (description + "This package provides font files that can be used by the @code{showtext} +package.") + (license license:asl2.0))) + +(define-public r-showtext + (package + (name "r-showtext") + (version "0.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "showtext" version)) + (sha256 + (base32 + "1ihgqzfia36b0n9aa41p1w98wxxvs1lxh1zz0570hbfqmph1sk73")))) + (properties `((upstream-name . "showtext"))) + (build-system r-build-system) + (inputs + `(("freetype" ,freetype) + ("libpng" ,libpng) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-showtextdb" ,r-showtextdb) + ("r-sysfonts" ,r-sysfonts))) + (native-inputs `(("pkg-config" ,pkg-config))) + (home-page "https://github.com/yixuan/showtext") + (synopsis "Using fonts more easily in R graphs") + (description + "This package aims to make it easy to use various types of +fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports +most output formats of R graphics including PNG, PDF and SVG. Text glyphs +will be converted into polygons or raster images, hence after the plot has +been created, it no longer relies on the font files. No external software +such as Ghostscript is needed to use this package.") + (license license:asl2.0))) + +(define-public r-emojifont + (package + (name "r-emojifont") + (version "0.5.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "emojifont" version)) + (sha256 + (base32 + "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k")))) + (properties `((upstream-name . "emojifont"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-proto" ,r-proto) + ("r-showtext" ,r-showtext) + ("r-sysfonts" ,r-sysfonts))) + (home-page "https://guangchuangyu.github.io/emojifont") + (synopsis "Emoji and Font Awesome in R graphics") + (description + "This package enables the use of emoji and the Font Awesome glyphs in +both base and ggplot2 graphics.") + (license license:artistic2.0))) + +(define-public r-abstractr + (package + (name "r-abstractr") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "abstractr" version)) + (sha256 + (base32 + "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig")))) + (properties `((upstream-name . "abstractr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-colourpicker" ,r-colourpicker) + ("r-emojifont" ,r-emojifont) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-rintrojs" ,r-rintrojs) + ("r-shiny" ,r-shiny) + ("r-shinythemes" ,r-shinythemes))) + (home-page "https://matt-kumar.shinyapps.io/portfolio") + (synopsis "R-Shiny application for creating visual abstracts") + (description + "This package provides an R Shiny application to create visual abstracts +for original research. A variety of user defined options and formatting are +included.") + (license license:gpl3))) + +(define-public r-abtest + (package + (name "r-abtest") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "abtest" version)) + (sha256 + (base32 + "1ky3cf827kj24bhcpk00v5zl5jdkii1gca0x81ay1cjkzfispgws")))) + (properties `((upstream-name . "abtest"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-mvtnorm" ,r-mvtnorm) + ("r-plotrix" ,r-plotrix) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-sn" ,r-sn) + ("r-truncnorm" ,r-truncnorm) + ("r-vgam" ,r-vgam))) + (home-page "https://cran.r-project.org/web/packages/abtest/") + (synopsis "Bayesian A/B testing") + (description + "This package provides functions for Bayesian A/B testing including prior +elicitation options based on Kass and Vaidyanathan (1992) +@url{doi:10.1111/j.2517-6161.1992.tb01868.x}.") + (license license:gpl2+))) + +(define-public r-accept + (package + (name "r-accept") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "accept" version)) + (sha256 + (base32 + "1r4mhy9g4wjcjgdd0gwdarmr09292il3vdkmx0hz7vh9mffyr9kx")))) + (properties `((upstream-name . "accept"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-extrafont" ,r-extrafont) + ("r-mass" ,r-mass) + ("r-plotly" ,r-plotly) + ("r-stringr" ,r-stringr) + ("r-viridis" ,r-viridis))) + (home-page "https://cran.r-project.org/web/packages/accept/") + (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)") + (description + "This package allows clinicians to predict the rate and severity of +future acute exacerbation in @dfn{Chronic Obstructive Pulmonary +Disease} (COPD) patients, based on the clinical prediction model published in +Adibi et al. (2019) @url{doi:10.1101/651901}.") + (license license:gpl3))) + +(define-public r-smpracticals + (package + (name "r-smpracticals") + (version "1.4-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "SMPracticals" version)) + (sha256 + (base32 + "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf")))) + (properties `((upstream-name . "SMPracticals"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ellipse" ,r-ellipse) + ("r-mass" ,r-mass) + ("r-nlme" ,r-nlme) + ("r-survival" ,r-survival))) + (home-page "http://statwww.epfl.ch/davison/SM/") + (synopsis "Practicals for use with Davison (2003) Statistical Models") + (description + "This package contains the datasets and a few functions for use with the +practicals outlined in Appendix A of the book Statistical Models (Davison, +2003, Cambridge University Press). The practicals themselves can be found at +@url{http://statwww.epfl.ch/davison/SM/}.") + (license license:gpl2+))) + +(define-public r-fgui + (package + (name "r-fgui") + (version "1.0-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "fgui" version)) + (sha256 + (base32 + "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv")))) + (properties `((upstream-name . "fgui"))) + (build-system r-build-system) + (home-page + "https://sites.google.com/site/thomashoffmannproject/software/fgui") + (synopsis "Create GUI for R functions") + (description + "Rapidly create a GUI for a function you created by automatically +creating widgets for arguments of the function. This package automatically +parses help routines for context-sensitive help to these arguments. The +interface is essentially a wrapper to some Tcl/Tk routines to both simplify +and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be +incorporated into the interface for greater customization for the more +experienced.") + ;; Any version of the GPL. + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-tcltk2 + (package + (name "r-tcltk2") + (version "1.2-11") + (source + (origin + (method url-fetch) + (uri (cran-uri "tcltk2" version)) + (sha256 + (base32 + "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d")))) + (properties `((upstream-name . "tcltk2"))) + (build-system r-build-system) + (inputs + `(("tcl" ,tcl) + ("tk" ,tk))) + (home-page "http://www.sciviews.org/SciViews-R") + (synopsis "Tcl/Tk additions") + (description + "This package provides a series of additional Tcl commands and Tk widgets +with style and various functions to supplement the tcltk package") + (license license:lgpl3))) + +(define-public r-accrual + (package + (name "r-accrual") + (version "1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "accrual" version)) + (sha256 + (base32 + "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z")))) + (properties `((upstream-name . "accrual"))) + (build-system r-build-system) + (propagated-inputs + `(("r-fgui" ,r-fgui) + ("r-smpracticals" ,r-smpracticals) + ("r-tcltk2" ,r-tcltk2))) + (home-page "https://cran.r-project.org/web/packages/accrual/") + (synopsis "Bayesian accrual prediction") + (description + "Subject recruitment for medical research is challenging. Slow patient +accrual leads to delay in research. Accrual monitoring during the process of +recruitment is critical. Researchers need reliable tools to manage the +accrual rate. This package provides an implementation of a Bayesian method +that integrates researcher's experience on previous trials and data from the +current study, providing reliable prediction on accrual rate for clinical +studies. It provides functions for Bayesian accrual prediction which can be +easily used by statisticians and clinical researchers.") + (license license:gpl2))) + +(define-public r-accrued + (package + (name "r-accrued") + (version "1.4.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "accrued" version)) + (sha256 + (base32 + "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5")))) + (properties `((upstream-name . "accrued"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/accrued/") + (synopsis "Data quality visualization tools for partially accruing data") + (description + "This is a package for visualizing data quality of partially accruing +data.") + (license license:gpl3))) + +(define-public r-mda + (package + (name "r-mda") + (version "0.4-10") + (source + (origin + (method url-fetch) + (uri (cran-uri "mda" version)) + (sha256 + (base32 + "19g6kn6g0shidrjfffklbmzc5w7mcimrxhagx4nmpslg59ibqdkh")))) + (properties `((upstream-name . "mda"))) + (build-system r-build-system) + (propagated-inputs `(("r-class" ,r-class))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/mda/") + (synopsis "Mixture and flexible discriminant analysis") + (description + "This is a package for mixture and flexible discriminant analysis, +@dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.") + (license license:gpl2))) + +(define-public r-elasticnet + (package + (name "r-elasticnet") + (version "1.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "elasticnet" version)) + (sha256 + (base32 + "0p9dplnsp28z4s2fl6afbwrgd0aj339fak8mmndicmrh7bb7rpmb")))) + (properties `((upstream-name . "elasticnet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lars" ,r-lars))) + (home-page "http://www.stat.umn.edu/~hzou") + (synopsis "Elastic-Net for sparse estimation and sparse PCA") + (description + "This package provides functions for fitting the entire solution path of +the Elastic-Net and also provides functions for estimating sparse Principal +Components. The Lasso solution paths can be computed by the same function.") + (license license:gpl2+))) + +(define-public r-sparselda + (package + (name "r-sparselda") + (version "0.1-9") + (source + (origin + (method url-fetch) + (uri (cran-uri "sparseLDA" version)) + (sha256 + (base32 + "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb")))) + (properties `((upstream-name . "sparseLDA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-elasticnet" ,r-elasticnet) + ("r-mass" ,r-mass) + ("r-mda" ,r-mda))) + (home-page "http://www.imm.dtu.dk/~lhc") + (synopsis "Sparse discriminant analysis") + (description + "This package performs sparse linear discriminant analysis for Gaussians +and mixture of Gaussian models.") + (license license:gpl2+))) + +(define-public r-accsda + (package + (name "r-accsda") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "accSDA" version)) + (sha256 + (base32 + "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61")))) + (properties `((upstream-name . "accSDA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-ggthemes" ,r-ggthemes) + ("r-gridextra" ,r-gridextra) + ("r-mass" ,r-mass) + ("r-rarpack" ,r-rarpack) + ("r-sparselda" ,r-sparselda))) + (home-page "https://github.com/gumeo/accSDA/wiki") + (synopsis "Accelerated sparse discriminant analysis") + (description + "This package provides an implementation of sparse linear discriminant +analysis, which is a supervised classification method for multiple classes. +Various novel optimization approaches to this problem are implemented +including @dfn{alternating direction method of multipliers} (ADMM), +@dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG). +Functions for performing cross validation are also supplied along with basic +prediction and plotting functions. @dfn{Sparse zero variance +discriminant} (SZVD) analysis is also included in the package.") + (license license:gpl2+))) + +(define-public r-ace2fastq + (package + (name "r-ace2fastq") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ace2fastq" version)) + (sha256 + (base32 + "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic")))) + (properties `((upstream-name . "ace2fastq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-stringr" ,r-stringr))) + (home-page "https://github.com/c5sire/ace2fastq") + (synopsis "ACE file to FASTQ converter") + (description + "The ACE file format is used in genomics to store contigs from sequencing +machines. This tools converts it into FASTQ format. Both formats contain the +sequence characters and their corresponding quality information. Unlike the +FASTQ file, the ACE file stores the quality values numerically. The +conversion algorithm uses the standard Sanger formula. The package +facilitates insertion into pipelines, and content inspection.") + (license license:gpl3))) + +(define-public r-rngwell + (package + (name "r-rngwell") + (version "0.10-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "rngWELL" version)) + (sha256 + (base32 + "0b4ys525gksgqwqx9id4bdgyi9mwj6n3r87xdzf4fc9hp3cc16jb")))) + (properties `((upstream-name . "rngWELL"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/rngWELL/") + (synopsis "Toolbox for WELL random number generators") + (description + "This is a dedicated package to WELL pseudo random generators, which were +introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based +on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.") + (license license:bsd-3))) + +(define-public r-randtoolbox + (package + (name "r-randtoolbox") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "randtoolbox" version)) + (sha256 + (base32 + "141p13ajgzmb2s89rlac7zrra92mi1izvpfrngb4kqzlf3igdsqd")))) + (properties `((upstream-name . "randtoolbox"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rngwell" ,r-rngwell))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/randtoolbox/") + (synopsis "Toolbox for pseudo and quasi random number generation") + (description + "This package provides + +@enumerate +@item pseudo random generators, such as general linear +congruential generators, multiple recursive generators and generalized +feedback shift register (SF-Mersenne Twister algorithm and WELL +generators) + +@item quasi random generators, such as the Torus algorithm, the Sobol +sequence, the Halton sequence (including the Van der Corput sequence), and + +@item some generator tests: the gap test, the serial test, the poker test. +@end enumerate + +See e.g. Gentle (2003) @url{doi:10.1007/b97336}.") + (license license:bsd-3))) + +(define-public r-lhs + (package + (name "r-lhs") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "lhs" version)) + (sha256 + (base32 + "0lzaqr7xi3ckln5nglv5xf5njm359slpz1jc6s02hpsqdw6armd4")))) + (properties `((upstream-name . "lhs"))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/bertcarnell/lhs") + (synopsis "Latin Hypercube Samples") + (description + "This package provides a number of methods for creating and augmenting +Latin Hypercube Samples.") + (license license:gpl3))) + +(define-public r-acebayes + (package + (name "r-acebayes") + (version "1.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "acebayes" version)) + (sha256 + (base32 + "1xm6bw0qm2vlcrk274x0bawzb2lnacb1wsmzba5mg3i75a55pqln")))) + (properties `((upstream-name . "acebayes"))) + (build-system r-build-system) + (propagated-inputs + `(("r-compare" ,r-compare) + ("r-lhs" ,r-lhs) + ("r-randtoolbox" ,r-randtoolbox) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (home-page "https://cran.r-project.org/web/packages/acebayes/") + (synopsis "Optimal Bayesian experimental design using the ACE algorithm") + (description + "Finding an optimal Bayesian experimental design involves maximizing an +objective function given by the expectation of some appropriately chosen +utility function with respect to the joint distribution of unknown +quantities (including responses). This objective function is usually not +available in closed form and the design space can be continuous and of high +dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE) +to maximise an approximation to the expectation of the utility function.") + (license license:gpl2))) + +(define-public r-acet + (package + (name "r-acet") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACEt" version)) + (sha256 + (base32 + "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq")))) + (properties `((upstream-name . "ACEt"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-mass" ,r-mass) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (home-page "https://cran.r-project.org/web/packages/ACEt/") + (synopsis "Estimating dynamic heritability and twin model comparison") + (description + "This package supports twin models that are able to estimate the dynamic +behaviour of the variance components in the classical twin models with respect +to age using B-splines and P-splines.") + (license license:gpl2+))) + +(define-public r-acfmperiod + (package + (name "r-acfmperiod") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "acfMPeriod" version)) + (sha256 + (base32 + "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5")))) + (properties `((upstream-name . "acfMPeriod"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/acfMPeriod/") + (synopsis "Estimation of the ACF from the M-periodogram") + (description + "This package support non-robust and robust computations of the sample +autocovariance (ACOVF) and sample autocorrelation functions (ACF) of +univariate and multivariate processes. The methodology consists in reversing +the diagonalization procedure involving the periodogram or the +cross-periodogram and the Fourier transform vectors, and, thus, obtaining the +ACOVF or the ACF as discussed in Fuller (1995) +@url{doi:10.1002/9780470316917}. The robust version is obtained by fitting +robust M-regressors to obtain the M-periodogram or M-cross-periodogram as +discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.") + (license license:gpl2+))) + +(define-public r-gamlss-data + (package + (name "r-gamlss-data") + (version "5.1-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "gamlss.data" version)) + (sha256 + (base32 + "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd")))) + (properties `((upstream-name . "gamlss.data"))) + (build-system r-build-system) + (home-page "http://www.gamlss.org/") + (synopsis "GAMLSS data") + (description + "This package provides data used as examples to demonstrate GAMLSS +models.") + ;; Either version of the license + (license (list license:gpl2 license:gpl3)))) + +(define-public r-gamlss + (package + (name "r-gamlss") + (version "5.1-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "gamlss" version)) + (sha256 + (base32 + "0gcngfck0dk2rhjg0z1fnc61dqs0s049jy2rkywaf57531s2k8bc")))) + (properties `((upstream-name . "gamlss"))) + (build-system r-build-system) + (propagated-inputs + `(("r-gamlss-data" ,r-gamlss-data) + ("r-gamlss-dist" ,r-gamlss-dist) + ("r-mass" ,r-mass) + ("r-nlme" ,r-nlme) + ("r-survival" ,r-survival))) + (home-page "http://www.gamlss.org/") + (synopsis "Generalized additive models for location scale and shape") + (description + "This package provides functions for fitting the generalized additive +models for location scale and shape introduced by Rigby and +Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models +use a distributional regression approach where all the parameters of the +conditional distribution of the response variable are modelled using +explanatory variables.") + ;; Either version of the license + (license (list license:gpl2 license:gpl3)))) + +(define-public r-acid + (package + (name "r-acid") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "acid" version)) + (sha256 + (base32 + "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd")))) + (properties `((upstream-name . "acid"))) + (build-system r-build-system) + (propagated-inputs + `(("r-gamlss" ,r-gamlss) + ("r-gamlss-dist" ,r-gamlss-dist) + ("r-hmisc" ,r-hmisc))) + (home-page "https://cran.r-project.org/web/packages/acid/") + (synopsis "Analysing conditional income distributions") + (description + "This package provides functions for the analysis of income distributions +for subgroups of the population as defined by a set of variables like age, +gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture +distribution as well as functions for moments, inequality measures, entropy +measures and polarisation measures of income distributions. This package thus +aides the analysis of income inequality by offering tools for the exploratory +analysis of income distributions at the disaggregated level.") + (license license:gpl3))) + +(define-public r-acm4r + (package + (name "r-acm4r") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "acm4r" version)) + (sha256 + (base32 + "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa")))) + (properties `((upstream-name . "acm4r"))) + (build-system r-build-system) + (propagated-inputs `(("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/acm4r/") + (synopsis "Align-and-count method comparisons of RFLP data") + (description + "This is a package to compare sequence fragment lengths or molecular +weights from pairs of lanes. The number of matching bands in the +@dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using +the align-and-count method.") + ;; Any version of the GPL + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-filematrix + (package + (name "r-filematrix") + (version "1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "filematrix" version)) + (sha256 + (base32 + "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b")))) + (properties `((upstream-name . "filematrix"))) + (build-system r-build-system) + ;; These inputs are needed for vignettes + (native-inputs + `(("r-knitr" ,r-knitr) + ("r-rmarkdown" ,r-rmarkdown) + ("pandoc-citeproc" ,ghc-pandoc-citeproc))) + (home-page "https://github.com/andreyshabalin/filematrix") + (synopsis "File-backed matrix class with convenient read and write access") + (description + "This package provides an interface for working with large matrices +stored in files, not in computer memory. It supports multiple non-character +data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4 +byte real values). Access to parts of the matrix is done by indexing, exactly +as with usual R matrices. It supports very large matrices; the package has +been tested on multi-terabyte matrices. It allows for more than 2^32 rows or +columns, ad allows for quick addition of extra columns to a filematrix.") + (license license:lgpl3))) + +(define-public r-acmeeqtl + (package + (name "r-acmeeqtl") + (version "1.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACMEeqtl" version)) + (sha256 + (base32 + "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz")))) + (properties `((upstream-name . "ACMEeqtl"))) + (build-system r-build-system) + (propagated-inputs + `(("r-filematrix" ,r-filematrix))) + (home-page "https://github.com/andreyshabalin/ACMEeqtl") + (synopsis "Estimation of interpretable eQTL effect sizes") + (description + "This package provides a non-linear model, termed ACME, that reflects a +parsimonious biological model for allelic contributions of cis-acting eQTLs. +With non-linear least-squares algorithm the maximum likelihood parameters can +be estimated. The ACME model provides interpretable effect size estimates and +p-values with well controlled Type-I error.") + (license license:lgpl3))) + +(define-public r-acmer + (package + (name "r-acmer") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "acmeR" version)) + (sha256 + (base32 + "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7")))) + (properties `((upstream-name . "acmeR"))) + (build-system r-build-system) + (propagated-inputs `(("r-foreign" ,r-foreign))) + (home-page "https://cran.r-project.org/web/packages/acmeR/") + (synopsis "ACME estimator of bird and bat mortality by wind turbines") + (description + "This package provides an implementation of the ACME estimator, described +in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran +Mortality at Wind Turbines. Unlike most other models, this estimator supports +decreasing-hazard Weibull model for persistence; decreasing search proficiency +as carcasses age; variable bleed-through at successive searches; and interval +mortality estimates. The package provides, based on search data, functions +for estimating the mortality inflation factor in Frequentist and Bayesian +settings.") + (license license:expat))) + +(define-public r-r-huge + (package + (name "r-r-huge") + (version "0.9.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "R.huge" version)) + (sha256 + (base32 + "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi")))) + (properties `((upstream-name . "R.huge"))) + (build-system r-build-system) + (propagated-inputs + `(("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo) + ("r-r-utils" ,r-r-utils))) + (home-page "https://github.com/HenrikBengtsson/R.huge") + (synopsis "Methods for accessing huge amounts of data") + (description + "This is a deprecated package for accessing huge amounts of data. + Cross-platform alternatives are the following packages: bigmemory (CRAN), +ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside +the @code{aroma.affymetrix} package.") + (license license:lgpl2.1+))) + +(define-public r-r-filesets + (package + (name "r-r-filesets") + (version "2.13.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "R.filesets" version)) + (sha256 + (base32 + "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg")))) + (properties `((upstream-name . "R.filesets"))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-r-cache" ,r-r-cache) + ("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo) + ("r-r-utils" ,r-r-utils))) + (home-page "https://github.com/HenrikBengtsson/R.filesets") + (synopsis "Easy handling of and access to files") + (description + "This package provides classes and methods to locate, setup, subset, +navigate and iterate file sets, i.e. sets of files located in one or more +directories on the file system. The API is designed such that these classes +can be extended via inheritance to provide a richer API for special file +formats. Moreover, a specific name format is defined such that filenames and +directories can be considered to have full names which consists of a name +followed by comma-separated tags. This adds additional flexibility to +identify file sets and individual files.") + (license license:lgpl2.1+))) + +(define-public r-r-devices + (package + (name "r-r-devices") + (version "2.16.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "R.devices" version)) + (sha256 + (base32 + "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd")))) + (properties `((upstream-name . "R.devices"))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo) + ("r-r-utils" ,r-r-utils))) + (home-page "https://github.com/HenrikBengtsson/R.devices") + (synopsis "Unified handling of graphics devices") + (description + "This package provides functions for creating plots and image files in a +unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). +Default device options as well as scales and aspect ratios are controlled in a +uniform way across all device types. Switching output format requires minimal +changes in code. This package is ideal for large-scale batch processing, +because it will never leave open graphics devices or incomplete image files +behind, even on errors or user interrupts.") + (license license:lgpl2.1+))) + +(define-public r-acnr + (package + (name "r-acnr") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "acnr" version)) + (sha256 + (base32 + "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym")))) + (properties `((upstream-name . "acnr"))) + (build-system r-build-system) + (home-page "https://github.com/mpierrejean/acnr") + (synopsis "Annotated copy-number regions") + (description + "This package provides SNP array data from different types of copy-number +regions. These regions were identified manually by the authors of the package +and may be used to generate realistic data sets with known truth.") + (license license:lgpl2.1+))) + +(define-public r-acopula + (package + (name "r-acopula") + (version "0.9.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "acopula" version)) + (sha256 + (base32 + "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln")))) + (properties `((upstream-name . "acopula"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/acopula/") + (synopsis "Modelling dependence with multivariate Archimax copulas") + (description + "Archimax copulas are a mixture of Archimedean and EV copulas. This +package provides definitions of several parametric families of generator and +dependence function, computes CDF and PDF, estimates parameters, tests for +goodness of fit, generates random sample and checks copula properties for +custom constructs. In the 2-dimensional case explicit formulas for density +are used, contrary to higher dimensions when all derivatives are linearly +approximated. Several non-archimax families (normal, FGM, Plackett) are +provided as well.") + (license license:gpl2))) + +(define-public r-tuner + (package + (name "r-tuner") + (version "1.3.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "tuneR" version)) + (sha256 + (base32 + "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx")))) + (properties `((upstream-name . "tuneR"))) + (build-system r-build-system) + (propagated-inputs `(("r-signal" ,r-signal))) + (home-page "https://cran.r-project.org/web/packages/tuneR/") + (synopsis "Analysis of music and speech") + (description + "This is a package for the analysis of music and speech. Analyze music +and speech, extract features like MFCCs, handle wave files and their +representation in various ways, read MP3, read MIDI, perform steps of a +transcription, ...") + ;; Either of these versions. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-seewave + (package + (name "r-seewave") + (version "2.1.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "seewave" version)) + (sha256 + (base32 + "1qg8f5gik9pw6f9mcxqmrc9x3003s8vdm6g01pjjpyc9qaqiz2vi")))) + (properties `((upstream-name . "seewave"))) + (build-system r-build-system) + (propagated-inputs + `(("r-tuner" ,r-tuner))) + (home-page "http://rug.mnhn.fr/seewave") + (synopsis "Sound analysis and synthesis") + (description + "This package provides functions for analysing, manipulating, displaying, +editing and synthesizing time waves (particularly sound). This package +processes time analysis (oscillograms and envelopes), spectral content, +resonance quality factor, entropy, cross correlation and autocorrelation, +zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D +and 3D spectrograms and many other analyses.") + (license license:gpl2+))) + +(define-public r-acousticndlcoder + (package + (name "r-acousticndlcoder") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "AcousticNDLCodeR" version)) + (sha256 + (base32 + "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb")))) + (properties + `((upstream-name . "AcousticNDLCodeR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-seewave" ,r-seewave) + ("r-tuner" ,r-tuner) + ("r-zoo" ,r-zoo))) + (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/") + (synopsis "Coding sound files for use with NDL") + (description + "Make acoustic cues to use with the R package @code{ndl}. +The package implements functions used in the PLoS ONE paper \"Words from +spontaneous conversational speech can be recognized with human-like accuracy +by an error-driven learning algorithm that discriminates between meanings +straight from smart acoustic features, bypassing the phoneme as recognition +unit.\" @url{doi:10.1371/journal.pone.0174623}") + (license license:gpl2+))) + +(define-public r-acp + (package + (name "r-acp") + (version "2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "acp" version)) + (sha256 + (base32 + "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn")))) + (properties `((upstream-name . "acp"))) + (build-system r-build-system) + (propagated-inputs + `(("r-quantmod" ,r-quantmod) + ("r-tseries" ,r-tseries))) + (home-page "https://cran.r-project.org/web/packages/acp/") + (synopsis "Autoregressive conditional Poisson") + (description + "This package supports the analysis of count data exhibiting +autoregressive properties, using the @dfn{Autoregressive Conditional Poisson} +model (ACP(p,q)) proposed by Heinen (2003).") + (license license:gpl2))) + +(define-public r-ada + (package + (name "r-ada") + (version "2.0-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "ada" version)) + (sha256 + (base32 + "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r")))) + (properties `((upstream-name . "ada"))) + (build-system r-build-system) + (propagated-inputs `(("r-rpart" ,r-rpart))) + (home-page "https://cran.r-project.org/web/packages/ada/") + (synopsis "Stochastic boosting") + (description + "This package provides a straightforward, well-documented, and broad +boosting routine for classification, ideally suited for small to +moderate-sized data sets. It performs discrete, real, and gentle boost under +both exponential and logistic loss on a given data set.") + ;; Any version of the GPL. + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-genalg + (package + (name "r-genalg") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "genalg" version)) + (sha256 + (base32 + "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s")))) + (properties `((upstream-name . "genalg"))) + (build-system r-build-system) + (home-page "https://github.com/egonw/genalg") + (synopsis "R based genetic algorithm") + (description + "This package provides an R based genetic algorithm for binary and +floating point chromosomes.") + (license license:gpl2))) + +(define-public r-kernelfactory + (package + (name "r-kernelfactory") + (version "0.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "kernelFactory" version)) + (sha256 + (base32 + "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j")))) + (properties `((upstream-name . "kernelFactory"))) + (build-system r-build-system) + (propagated-inputs + `(("r-auc" ,r-auc) + ("r-genalg" ,r-genalg) + ("r-kernlab" ,r-kernlab) + ("r-randomforest" ,r-randomforest))) + (home-page "https://cran.r-project.org/web/packages/kernelFactory/") + (synopsis "Ensemble of kernel machines") + (description + "Kernel factory is an ensemble method where each base classifier (random +forest) is fit on the kernel matrix of a subset of the training data.") + (license license:gpl2+))) + +(define-public r-dummies + (package + (name "r-dummies") + (version "1.5.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "dummies" version)) + (sha256 + (base32 + "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm")))) + (properties `((upstream-name . "dummies"))) + (build-system r-build-system) + (home-page "http://www.decisionpatterns.com") + (synopsis "Create dummy/indicator variables flexibly and efficiently") + (description + "This package lets you expand factors, characters and other eligible +classes into dummy/indicator variables.") + (license license:gpl2+))) + +(define-public r-acrm + (package + (name "r-acrm") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "aCRM" version)) + (sha256 + (base32 + "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v")))) + (properties `((upstream-name . "aCRM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ada" ,r-ada) + ("r-dummies" ,r-dummies) + ("r-kernelfactory" ,r-kernelfactory) + ("r-randomforest" ,r-randomforest))) + (home-page "https://cran.r-project.org/web/packages/aCRM/") + (synopsis "Convenience functions for analytical customer relationship management") + (description + "This package provides convenience functions for data preparation and +modeling often used in @dfn{analytical customer relationship +management} (aCRM).") + (license license:gpl2+))) + +(define-public r-treeclust + (package + (name "r-treeclust") + (version "1.1-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "treeClust" version)) + (sha256 + (base32 + "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z")))) + (properties `((upstream-name . "treeClust"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-rpart" ,r-rpart))) + (home-page "https://cran.r-project.org/web/packages/treeClust/") + (synopsis "Cluster distances through trees") + (description + "This package provides tools to create a measure of inter-point +dissimilarity useful for clustering mixed data, and, optionally, perform the +clustering.") + (license license:gpl2+))) + +(define-public r-acrosstic + (package + (name "r-acrosstic") + (version "1.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "AcrossTic" version)) + (sha256 + (base32 + "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0")))) + (properties `((upstream-name . "AcrossTic"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lpsolve" ,r-lpsolve) + ("r-treeclust" ,r-treeclust))) + (home-page "https://cran.r-project.org/web/packages/AcrossTic/") + (synopsis "Cost-minimal regular spanning subgraph with TreeClust") + (description + "This is a package for constructing minimum-cost regular spanning +subgraph as part of a non-parametric two-sample test for equality of +distribution.") + (license license:gpl2+))) + +(define-public r-acrt + (package + (name "r-acrt") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "acrt" version)) + (sha256 + (base32 + "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s")))) + (properties `((upstream-name . "acrt"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-sandwich" ,r-sandwich))) + (home-page "https://cran.r-project.org/web/packages/acrt/") + (synopsis "Autocorrelation robust testing") + (description + "This package provides functions for testing affine hypotheses on the +regression coefficient vector in regression models with autocorrelated +errors.") + (license license:gpl2))) + +(define-public r-acs + (package + (name "r-acs") + (version "2.1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "acs" version)) + (sha256 + (base32 + "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5")))) + (properties `((upstream-name . "acs"))) + (build-system r-build-system) + (propagated-inputs + `(("r-httr" ,r-httr) + ("r-plyr" ,r-plyr) + ("r-rcpp" ,r-rcpp) + ("r-stringr" ,r-stringr) + ("r-xml" ,r-xml))) + (home-page "http://dusp.mit.edu/faculty/ezra-glenn") + (synopsis "Work with data from the US Census") + (description + "This package provides a general toolkit for downloading, managing, +analyzing, and presenting data from the +@url{https://www.census.gov/data/developers/data-sets.html, U.S. Census}, +including SF1 (Decennial short-form), SF3 (Decennial long-form), and the +American Community Survey (ACS). Confidence intervals provided with ACS data +are converted to standard errors to be bundled with estimates in complex +@code{acs} objects. The package provides new methods to conduct standard +operations on @code{acs} objects and present/plot data in statistically +appropriate ways.") + (license license:gpl3))) + +(define-public r-acss-data + (package + (name "r-acss-data") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "acss.data" version)) + (sha256 + (base32 + "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv")))) + (properties `((upstream-name . "acss.data"))) + (build-system r-build-system) + (home-page "http://complexitycalculator.com/methodology.html") + (synopsis "Data for algorithmic complexity of short strings") + (description + "This is a data only package providing the algorithmic complexity of +short strings, computed using the coding theorem method. For a given set of +symbols in a string, all possible or a large number of random samples of +Turing machines with a given number of states (e.g., 5) and number of symbols +corresponding to the number of symbols in the strings were simulated until +they reached a halting state or failed to end. This package contains data on +4.5 million strings from length 1 to 12 simulated on Turing machines with 2, +4, 5, 6, and 9 symbols. The complexity of the string corresponds to the +distribution of the halting states.") + (license license:gpl2+))) + +(define-public r-acss + (package + (name "r-acss") + (version "0.2-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "acss" version)) + (sha256 + (base32 + "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk")))) + (properties `((upstream-name . "acss"))) + (build-system r-build-system) + (propagated-inputs + `(("r-acss-data" ,r-acss-data) + ("r-zoo" ,r-zoo))) + (home-page "http://complexitycalculator.com/methodology.html") + (synopsis "Algorithmic complexity for short strings") + (description + "The main purpose of this package is to provide the algorithmic +complexity for short strings, an approximation of the Kolmogorov Complexity of +a short string using the coding theorem method. While the database containing +the complexity is provided in the data only package @code{acss.data}, this +package provides functions accessing the data such as @code{prob_random} +returning the posterior probability that a given string was produced by a +random process. In addition, two traditional (but problematic) measures of +complexity are also provided: entropy and change complexity.") + (license license:gpl2+))) + +(define-public r-acswr + (package + (name "r-acswr") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACSWR" version)) + (sha256 + (base32 + "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n")))) + (properties `((upstream-name . "ACSWR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/ACSWR/") + (synopsis "Companion package for the book \"A Course in Statistics with R\"") + (description + "This is a companion package for the book \"A Course in Statistics with +R\" (ISBN 978-1-119-15272-9.)") + (license license:gpl2))) + +(define-public r-alabama + (package + (name "r-alabama") + (version "2015.3-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "alabama" version)) + (sha256 + (base32 + "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036")))) + (properties `((upstream-name . "alabama"))) + (build-system r-build-system) + (propagated-inputs `(("r-numderiv" ,r-numderiv))) + (home-page "https://cran.r-project.org/web/packages/alabama/") + (synopsis "Constrained nonlinear optimization") + (description + "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization +Algorithm; it is used for optimizing smooth nonlinear objective functions with +constraints. Linear or nonlinear equality and inequality constraints are +allowed.") + (license license:gpl2+))) + +(define-public r-gdina + (package + (name "r-gdina") + (version "2.7.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "GDINA" version)) + (sha256 + (base32 + "0875xfbm36gqzr0116xzlbm8rlff85rybr4s4hjzfflfvjdhgvfx")))) + (properties `((upstream-name . "GDINA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-alabama" ,r-alabama) + ("r-ggplot2" ,r-ggplot2) + ("r-mass" ,r-mass) + ("r-nloptr" ,r-nloptr) + ("r-numderiv" ,r-numderiv) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rsolnp" ,r-rsolnp) + ("r-shiny" ,r-shiny) + ("r-shinydashboard" ,r-shinydashboard))) + (home-page "https://github.com/Wenchao-Ma/GDINA") + (synopsis "Generalized DINA model framework") + (description + "This package provides a set of psychometric tools for cognitive +diagnosis modeling based on the generalized deterministic inputs, noisy and +gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7} +and its extensions, including the sequential G-DINA model by Ma and de la +Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the +polytomous G-DINA model by Chen and de la Torre +@url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute +distribution can be independent, saturated, higher-order, loglinear smoothed +or structured. Q-matrix validation, item and model fit statistics, model +comparison at test and item level and differential item functioning can also +be conducted. A graphical user interface is also provided.") + (license license:gpl3))) + +(define-public r-actcd + (package + (name "r-actcd") + (version "1.2-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACTCD" version)) + (sha256 + (base32 + "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p")))) + (properties `((upstream-name . "ACTCD"))) + (build-system r-build-system) + (propagated-inputs + `(("r-gdina" ,r-gdina) + ("r-r-methodss3" ,r-r-methodss3))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/ACTCD/") + (synopsis "Asymptotic classification theory for cognitive diagnosis") + (description + "This is a package supporting cluster analysis for cognitive diagnosis +based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009; +@url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of +sum-scores, cluster analysis techniques can be used to classify examinees into +latent classes based on their attribute patterns. In addition to the +algorithms used to classify data, three labeling approaches are proposed to +label clusters so that examinees' attribute profiles can be obtained.") + (license license:gpl2+))) + +(define-public r-ineq + (package + (name "r-ineq") + (version "0.2-13") + (source + (origin + (method url-fetch) + (uri (cran-uri "ineq" version)) + (sha256 + (base32 + "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0")))) + (properties `((upstream-name . "ineq"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/ineq/") + (synopsis "Measuring inequality, concentration, and poverty") + (description + "This package provides tools for measuring inequality, concentration, and +poverty measures. It provides both empirical and theoretical Lorenz curves.") + ;; Either of these two versions. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-actfrag + (package + (name "r-actfrag") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ActFrag" version)) + (sha256 + (base32 + "06l5a679j6289008ls57v420mnzpq9a4ln7svi5bh0vpvws7sr9d")))) + (properties `((upstream-name . "ActFrag"))) + (build-system r-build-system) + (propagated-inputs + `(("r-accelerometry" ,r-accelerometry) + ("r-dplyr" ,r-dplyr) + ("r-ineq" ,r-ineq) + ("r-survival" ,r-survival) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/junruidi/ActFrag") + (synopsis "Activity fragmentation metrics extraction") + (description + "This package provides functions to extract commonly used fragmentation +metrics to quantify time accumulation strategies based on minute level +actigraphy-measured activity counts data.") + (license license:gpl3))) + +(define-public r-fda + (package + (name "r-fda") + (version "2.4.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "fda" version)) + (sha256 + (base32 + "0n39rzbhg1hipzn51rzmbchn2358qgapg08iv7lmiqj5y7i9qns2")))) + (properties `((upstream-name . "fda"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix))) + (home-page "http://www.functionaldata.org") + (synopsis "Functional data analysis") + (description + "These functions were developed to support functional data analysis as +described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data +Analysis. The package includes data sets and script files working many +examples.") + (license license:gpl2+))) + +(define-public r-actigraphy + (package + (name "r-actigraphy") + (version "1.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "Actigraphy" version)) + (sha256 + (base32 + "0y0ccmxhdfhdmi4k6pbfvnqknkqbgvfsf2qf7z7rc4xpfgym6574")))) + (properties `((upstream-name . "Actigraphy"))) + (build-system r-build-system) + (propagated-inputs + `(("r-fda" ,r-fda) + ("r-sdmtools" ,r-sdmtools))) + (home-page "https://cran.r-project.org/web/packages/Actigraphy/") + (synopsis "Actigraphy data analysis") + (description + "This package provides tools for functional linear modeling and analysis +of actigraphy data.") + (license license:asl2.0))) + +(define-public r-activedriver + (package + (name "r-activedriver") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ActiveDriver" version)) + (sha256 + (base32 + "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa")))) + (properties `((upstream-name . "ActiveDriver"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/ActiveDriver/") + (synopsis "Tools for finding cancer driver proteins") + (description + "This package provides a mutation analysis tool that discovers cancer +driver genes with frequent mutations in protein signalling sites such as +post-translational modifications (phosphorylation, ubiquitination, etc). The +Poisson generalized linear regression model identifies genes where cancer +mutations in signalling sites are more frequent than expected from the +sequence of the entire gene. Integration of mutations with signalling +information helps find new driver genes and propose candidate mechanisms to +known drivers.") + (license license:gpl2+))) + +(define-public r-activitycounts + (package + (name "r-activitycounts") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "activityCounts" version)) + (sha256 + (base32 + "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz")))) + (properties + `((upstream-name . "activityCounts"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lubridate" ,r-lubridate) + ("r-magrittr" ,r-magrittr) + ("r-seewave" ,r-seewave) + ("r-signal" ,r-signal) + ("r-tibble" ,r-tibble))) + (home-page "https://github.com/walkabillylab/activityCounts") + (synopsis "Generate ActiLife counts") + (description + "ActiLife generates activity counts from data collected by Actigraph +accelerometers. Actigraph is one of the most common research-grade +accelerometers. There is considerable research validating and developing +algorithms for human activity using ActiLife counts. Unfortunately, ActiLife +counts are proprietary and difficult to implement if researchers use different +accelerometer brands. The code creates ActiLife counts from raw acceleration +data for different accelerometer brands.") + (license license:gpl3))) + +(define-public r-activityindex + (package + (name "r-activityindex") + (version "0.3.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "ActivityIndex" version)) + (sha256 + (base32 + "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk")))) + (properties `((upstream-name . "ActivityIndex"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-matrixstats" ,r-matrixstats) + ("r-r-utils" ,r-r-utils))) + (home-page "https://cran.r-project.org/web/packages/ActivityIndex/") + (synopsis "Activity Index calculation using raw accelerometry data") + (description + "This is a package to read raw accelerometry from GT3X+ accelerometry +data and plain table data to calculate the Activity Index from Bai et +al. (2016) @url{doi:10.1371/journal.pone.0160644}.") + (license license:gpl3))) + +(define-public r-activpal + (package + (name "r-activpal") + (version "0.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "activPAL" version)) + (sha256 + (base32 + "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na")))) + (properties `((upstream-name . "activPAL"))) + (build-system r-build-system) + (propagated-inputs + `(("r-devtools" ,r-devtools) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-lubridate" ,r-lubridate) + ("r-magrittr" ,r-magrittr) + ("r-tidyr" ,r-tidyr))) + (home-page "https://cran.r-project.org/web/packages/activPAL") + (synopsis "Processing and chart generation from activPAL events files") + (description + "This package contains functions to generate pre-defined summary +statistics from activPAL events files. The package also contains functions to +produce informative graphics that visualize physical activity behaviour and +trends. This includes generating graphs that align physical activity +behaviour with additional time based observations described by other data +sets, such as sleep diaries and continuous glucose monitoring data.") + (license license:gpl3))) + +(define-public r-activpalprocessing + (package + (name "r-activpalprocessing") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "activpalProcessing" version)) + (sha256 + (base32 + "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1")))) + (properties + `((upstream-name . "activpalProcessing"))) + (build-system r-build-system) + (propagated-inputs + `(("r-chron" ,r-chron))) + (home-page "https://cran.r-project.org/web/packages/activpalProcessing/") + (synopsis "Process activPAL events files") + (description + "This package performs estimation of physical activity and sedentary +behavior variables from activPAL events files.") + ;; Either version of the GPL. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-actogrammr + (package + (name "r-actogrammr") + (version "0.2.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "actogrammr" version)) + (sha256 + (base32 + "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa")))) + (properties `((upstream-name . "actogrammr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-lubridate" ,r-lubridate) + ("r-readr" ,r-readr) + ("r-tidyr" ,r-tidyr))) + (home-page "https://cran.r-project.org/web/packages/actogrammr/") + (synopsis "Read in activity data and plot actograms") + (description + "Read in activity measurements from standard file formats used by +circadian rhythm researchers, currently only ClockLab format, and process and +plot the data. The central type of plot is the actogram, as first described +in \"Activity and distribution of certain wild mice in relation to biotic +communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.") + (license license:gpl3))) + +(define-public r-expint + (package + (name "r-expint") + (version "0.1-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "expint" version)) + (sha256 + (base32 + "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7")))) + (properties `((upstream-name . "expint"))) + (build-system r-build-system) + (home-page "https://gitlab.com/vigou3/expint") + (synopsis "Exponential integral and incomplete Gamma function") + (description + "This package provides the exponential integrals @code{E_1(x)}, +@code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma +function @code{G(a, x)} defined for negative values of its first argument. +The package also gives easy access to the underlying C routines through an +API; see the package vignette for details.") + (license license:gpl2+))) + +(define-public r-actuar + (package + (name "r-actuar") + (version "2.3-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "actuar" version)) + (sha256 + (base32 + "0aw3hlan5y22mdqk1wvnw9ksqhwp4yy5hi0dpv21p7s0hyxhphih")))) + (properties `((upstream-name . "actuar"))) + (build-system r-build-system) + (propagated-inputs `(("r-expint" ,r-expint))) + (home-page "https://gitlab.com/vigou3/actuar") + (synopsis "Actuarial functions and heavy tailed distributions") + (description + "This package provides functions and data sets for actuarial science: +modeling of loss distributions; risk theory and ruin theory; simulation of +compound models, discrete mixtures and compound hierarchical models; +credibility theory. It boasts support for many additional probability +distributions to model insurance loss amounts and loss frequency: 19 +continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete +distribution; zero-truncated and zero-modified extensions of the standard +discrete distributions. It also supports phase-type distributions commonly +used to compute ruin probabilities.") + (license license:gpl2+))) + +(define-public r-bmp + (package + (name "r-bmp") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "bmp" version)) + (sha256 + (base32 + "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx")))) + (properties `((upstream-name . "bmp"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/bmp/") + (synopsis "Read Bitmap (BMP) images") + (description + "This package provides pure R tools to read BMP format images. It is +currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.") + (license license:gpl2+))) + +(define-public r-readbitmap + (package + (name "r-readbitmap") + (version "0.1.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "readbitmap" version)) + (sha256 + (base32 + "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk")))) + (properties `((upstream-name . "readbitmap"))) + (build-system r-build-system) + (inputs + `(("libjpeg" ,libjpeg) + ("libpng" ,libpng))) + (propagated-inputs + `(("r-bmp" ,r-bmp) + ("r-jpeg" ,r-jpeg) + ("r-png" ,r-png) + ("r-tiff" ,r-tiff))) + (home-page "https://github.com/jefferis/readbitmap") + (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)") + (description + "This package provides tools to identify and read BMP, JPEG, PNG, and +TIFF format bitmap images. Identification defaults to the use of the magic +number embedded in the file rather than the file extension.") + (license license:gpl2+))) + +(define-public r-imager + (package + (name "r-imager") + (version "0.41.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "imager" version)) + (sha256 + (base32 + "19fqgjhg04garbipx20g72h9dd6k0jj4ac48nby6km4h665vrs4v")))) + (properties `((upstream-name . "imager"))) + (build-system r-build-system) + (inputs + `(("fftw" ,fftw) + ("libtiff" ,libtiff) + ("libx11" ,libx11) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-cairo" ,r-cairo) + ("r-downloader" ,r-downloader) + ("r-igraph" ,r-igraph) + ("r-jpeg" ,r-jpeg) + ("r-magrittr" ,r-magrittr) + ("r-plyr" ,r-plyr) + ("r-png" ,r-png) + ("r-purrr" ,r-purrr) + ("r-rcpp" ,r-rcpp) + ("r-readbitmap" ,r-readbitmap) + ("r-stringr" ,r-stringr))) + (native-inputs `(("pkg-config" ,pkg-config))) + (home-page "http://dahtah.github.io/imager") + (synopsis "Image processing library") + (description + "This is a package for fast image processing for images in up to 4 +dimensions (two spatial dimensions, one time/depth dimension, one color +dimension). It provides most traditional image processing tools (filtering, +morphology, transformations, etc.) as well as various functions for easily +analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a +simple, modern C++ library for image processing.") + (license license:lgpl3))) + +(define-public r-acuityview + (package + (name "r-acuityview") + (version "0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "AcuityView" version)) + (sha256 + (base32 + "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l")))) + (properties `((upstream-name . "AcuityView"))) + (build-system r-build-system) + (propagated-inputs + `(("r-fftwtools" ,r-fftwtools) + ("r-imager" ,r-imager) + ("r-plotrix" ,r-plotrix))) + (home-page "https://cran.r-project.org/web/packages/AcuityView/") + (synopsis "Display scenes as seen by an animal with less acute vision") + (description + "This package provides a simple method for representing a visual scene as +it may be seen by an animal with less acute vision.") + (license license:gpl2+))) + +(define-public r-adabag + (package + (name "r-adabag") + (version "4.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "adabag" version)) + (sha256 + (base32 + "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7")))) + (properties `((upstream-name . "adabag"))) + (build-system r-build-system) + (propagated-inputs + `(("r-caret" ,r-caret) + ("r-doparallel" ,r-doparallel) + ("r-foreach" ,r-foreach) + ("r-rpart" ,r-rpart))) + (home-page "https://cran.r-project.org/web/packages/adabag/") + (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging") + (description + "This package implements Freund and Schapire's Adaboost.M1 algorithm and +Breiman's Bagging algorithm using classification trees as individual +classifiers. Once these classifiers have been trained, they can be used to +predict on new data. Also, cross validation estimation of the error can be +done.") + (license license:gpl2+))) + +(define-public r-adagio + (package + (name "r-adagio") + (version "0.7.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "adagio" version)) + (sha256 + (base32 + "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k")))) + (properties `((upstream-name . "adagio"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/adagio/") + (synopsis "Discrete and global optimization routines") + (description + "This package provides methods and algorithms for discrete optimization, +e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and +Hooke-Jeeves minimization, and some (evolutionary) global optimization +functions.") + (license license:gpl3+))) + +(define-public r-univoutl + (package + (name "r-univoutl") + (version "0.1-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "univOutl" version)) + (sha256 + (base32 + "193wrpkvgmlrx43nag8w3ivrlqm37nm6g86wcvd3bgw3hchs70gi")))) + (properties `((upstream-name . "univOutl"))) + (build-system r-build-system) + (propagated-inputs + `(("r-hmisc" ,r-hmisc) + ("r-robustbase" ,r-robustbase))) + (home-page "https://github.com/marcellodo/univOutl") + (synopsis "Detection of univariate outliers") + (description + "This package provides well-known outlier detection techniques in the +univariate case. Methods to deal with skewed distribution are included too. +The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of +historical data is implemented as well. When available, survey weights can be +used in outliers detection.") + (license license:gpl2+))) + +(define-public r-tolerance + (package + (name "r-tolerance") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "tolerance" version)) + (sha256 + (base32 + "17qh4ad1f3fbcpwlxxqh8qr9bnwjcl4yxk0l3fkbr6b2l4rc5p86")))) + (properties `((upstream-name . "tolerance"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rgl" ,r-rgl))) + (home-page "https://cran.r-project.org/web/packages/tolerance/") + (synopsis "Statistical tolerance intervals and regions") + (description + "This package provides functions for estimating tolerance +limits (intervals) for various univariate distributions (binomial, Cauchy, +discrete Pareto, exponential, two-parameter exponential, extreme value, +hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric, +normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot), +Bayesian normal tolerance limits, multivariate normal tolerance regions, +nonparametric tolerance intervals, tolerance bands for regression +settings (linear regression, nonlinear regression, nonparametric regression, +and multivariate regression), and analysis of variance tolerance intervals. +Visualizations are also available for most of these settings.") + (license license:gpl2+))) + +(define-public r-additivitytests + (package + (name "r-additivitytests") + (version "1.1-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "additivityTests" version)) + (sha256 + (base32 + "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw")))) + (properties + `((upstream-name . "additivityTests"))) + (build-system r-build-system) + (home-page "https://github.com/simecek/additivityTests") + (synopsis "Additivity tests in the two way Anova with single sub-class numbers") + (description + "This package provides an implementation of the Tukey, Mandel, +Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.") + (license license:gpl3))) + +(define-public r-flexclust + (package + (name "r-flexclust") + (version "1.4-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "flexclust" version)) + (sha256 + (base32 + "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2")))) + (properties `((upstream-name . "flexclust"))) + (build-system r-build-system) + (propagated-inputs + `(("r-class" ,r-class) + ("r-lattice" ,r-lattice) + ("r-modeltools" ,r-modeltools))) + (home-page "https://cran.r-project.org/web/packages/flexclust/") + (synopsis "Flexible cluster algorithms") + (description + "The main function @code{kcca} implements a general framework for +k-centroids cluster analysis supporting arbitrary distance measures and +centroid computation. Further cluster methods include hard competitive +learning, neural gas, and QT clustering. There are numerous visualization +methods for cluster results (neighborhood graphs, convex cluster hulls, +barcharts of centroids, ...), and bootstrap methods for the analysis of +cluster stability.") + (license license:gpl2))) + +(define-public r-biclust + (package + (name "r-biclust") + (version "2.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "biclust" version)) + (sha256 + (base32 + "1y5n6wfa1lx88ck3x09rcg0dh3pw89225h85hmq2la1s1fpa48i0")))) + (properties `((upstream-name . "biclust"))) + (build-system r-build-system) + (propagated-inputs + `(("r-additivitytests" ,r-additivitytests) + ("r-colorspace" ,r-colorspace) + ("r-flexclust" ,r-flexclust) + ("r-ggplot2" ,r-ggplot2) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-tidyr" ,r-tidyr))) + (home-page "https://cran.r-project.org/web/packages/biclust/") + (synopsis "BiCluster algorithms") + (description + "The main function @code{biclust()} provides several algorithms to find +biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax. +In addition, the package provides methods for data +preprocessing (normalization and discretization), visualization, and +validation of bicluster solutions.") + (license license:gpl3))) + +(define-public r-icge + (package + (name "r-icge") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "ICGE" version)) + (sha256 + (base32 + "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa")))) + (properties `((upstream-name . "ICGE"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/ICGE/") + (synopsis "Cluster estimation and identification of atypical units") + (description + "ICGE is a package that helps to estimate the number of real clusters in +data as well as to identify atypical units. The underlying methods are based +on distances rather than on unit x variables.") + (license license:gpl2+))) + +(define-public r-depth + (package + (name "r-depth") + (version "2.1-1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "depth" version)) + (sha256 + (base32 + "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m")))) + (properties `((upstream-name . "depth"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-circular" ,r-circular) + ("r-rgl" ,r-rgl))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/depth/") + (synopsis "Nonparametric depth functions for multivariate analysis") + (description + "This package provides tools for depth functions methodology applied to +multivariate analysis. Besides allowing calculation of depth values and +depth-based location estimators, the package includes functions or drawing +contour plots and perspective plots of depth functions. Euclidian and +spherical depths are supported.") + (license license:gpl2))) + +(define-public r-archetypes + (package + (name "r-archetypes") + (version "2.2-0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "archetypes" version)) + (sha256 + (base32 + "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0")))) + (properties `((upstream-name . "archetypes"))) + (build-system r-build-system) + (propagated-inputs + `(("r-modeltools" ,r-modeltools) + ("r-nnls" ,r-nnls))) + (home-page "https://cran.r-project.org/web/packages/archetypes") + (synopsis "Archetypal analysis") + (description + "The main function @code{archetypes} implements a framework for +archetypal analysis supporting arbitrary problem solving mechanisms for the +different conceptual parts of the algorithm.") + (license license:gpl2+))) + +(define-public r-shapes + (package + (name "r-shapes") + (version "1.2.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "shapes" version)) + (sha256 + (base32 + "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s")))) + (properties `((upstream-name . "shapes"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-minpack-lm" ,r-minpack-lm) + ("r-rgl" ,r-rgl) + ("r-scatterplot3d" ,r-scatterplot3d))) + (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes") + (synopsis "Statistical shape analysis") + (description + "This package provides routines for the statistical analysis of landmark +shapes, including Procrustes analysis, graphical displays, principal +components analysis, permutation and bootstrap tests, thin-plate spline +transformation grids and comparing covariance matrices. See Dryden, I.L. and +Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd +Edition), John Wiley and Sons.") + (license license:gpl2))) + +(define-public r-anthropometry + (package + (name "r-anthropometry") + (version "1.13") + (source + (origin + (method url-fetch) + (uri (cran-uri "Anthropometry" version)) + (sha256 + (base32 + "1f568ri1s6psaby8y737vrkarbjg64v89d4jyw23hy17apdmszr8")))) + (properties `((upstream-name . "Anthropometry"))) + (build-system r-build-system) + (propagated-inputs + `(("r-archetypes" ,r-archetypes) + ("r-biclust" ,r-biclust) + ("r-cluster" ,r-cluster) + ("r-depth" ,r-depth) + ("r-fnn" ,r-fnn) + ("r-icge" ,r-icge) + ("r-nnls" ,r-nnls) + ("r-rgl" ,r-rgl) + ("r-shapes" ,r-shapes))) + (home-page "https://cran.r-project.org/web/packages/Anthropometry/") + (synopsis "Statistical methods for anthropometric data") + (description + "This package provides statistical methods especially developed to +analyze anthropometric data. These methods are aimed at providing effective +solutions to some commons problems related to Ergonomics and Anthropometry. +They are based on clustering, the statistical concept of data depth, +statistical shape analysis and archetypal analysis.") + (license license:gpl2+))) + +(define-public r-adamethods + (package + (name "r-adamethods") + (version "1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "adamethods" version)) + (sha256 + (base32 + "0mp73zh5x6h18gv29v981kb9n632kb58lvlcxwr6vcvrx393nrxh")))) + (properties `((upstream-name . "adamethods"))) + (build-system r-build-system) + (propagated-inputs + `(("r-anthropometry" ,r-anthropometry) + ("r-archetypes" ,r-archetypes) + ("r-fnn" ,r-fnn) + ("r-foreach" ,r-foreach) + ("r-nnls" ,r-nnls) + ("r-tolerance" ,r-tolerance) + ("r-univoutl" ,r-univoutl))) + (home-page "https://cran.r-project.org/web/packages/adamethods/") + (synopsis "Archetypoid algorithms and anomaly detection") + (description + "This package is a collection of several algorithms to obtain +archetypoids with small and large databases and with both classical +multivariate data and functional data (univariate and multivariate). Some of +these algorithms also allow to detect anomalies (outliers).") + (license license:gpl2+))) + +(define-public r-idpmisc + (package + (name "r-idpmisc") + (version "1.1.19") + (source + (origin + (method url-fetch) + (uri (cran-uri "IDPmisc" version)) + (sha256 + (base32 + "13qcvfm703frs367paddz1wq9k3p17f9p5347m56bhky5hjkaphd")))) + (properties `((upstream-name . "IDPmisc"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice))) + (home-page "https://cran.r-project.org/web/packages/IDPmisc/") + (synopsis "Functions for data analyses and visualization") + (description + "This package provides different high-level graphics functions for +displaying large datasets, displaying circular data in a very flexible way, +finding local maxima, brewing color ramps, drawing nice arrows, zooming +2D-plots, creating figures with differently colored margin and plot region. +In addition, the package contains auxiliary functions for data manipulation +like omitting observations with irregular values or selecting data by logical +vectors, which include NAs. Other functions are especially useful in +spectroscopy and analyses of environmental data: robust baseline fitting, +finding peaks in spectra, converting humidity measures.") + (license license:gpl3+))) + +(define-public r-qqman + (package + (name "r-qqman") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "qqman" version)) + (sha256 + (base32 + "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s")))) + (properties `((upstream-name . "qqman"))) + (build-system r-build-system) + (propagated-inputs + `(("r-calibrate" ,r-calibrate))) + (home-page "https://cran.r-project.org/web/packages/qqman/") + (synopsis "Q-Q and Manhattan plots for GWAS data") + (description + "This package allows you to create Q-Q and Manhattan plots for GWAS data +from PLINK results.") + (license license:gpl3))) + +(define-public r-ggplot-multistats + (package + (name "r-ggplot-multistats") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggplot.multistats" version)) + (sha256 + (base32 + "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il")))) + (properties + `((upstream-name . "ggplot.multistats"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-hexbin" ,r-hexbin) + ("r-rlang" ,r-rlang) + ("r-scales" ,r-scales))) + (home-page "https://github.com/flying-sheep/ggplot.multistats") + (synopsis "Multiple summary statistics for binned stats/geometries") + (description + "This package provides the ggplot binning layer @code{stat_summaries_hex()}, +which functions similar to its singular form, but allows the use of multiple +statistics per bin. Those statistics can be mapped to multiple bin +aesthetics.") + (license license:gpl3))) + +(define-public r-knn-covertree + (package + (name "r-knn-covertree") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "knn.covertree" version)) + (sha256 + (base32 + "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz")))) + (properties `((upstream-name . "knn.covertree"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen))) + (home-page "https://github.com/flying-sheep/knn.covertree") + (synopsis "Accurate kNN Implementation with multiple distance measures") + (description + "Similarly to the FNN package, this package allows calculation of the k +nearest neighbors (kNN) of a data matrix. The implementation is based on +cover trees introduced by Alina Beygelzimer, Sham Kakade, and John +Langford (2006) @url{doi:10.1145/1143844.1143857}.") + (license license:agpl3+))) + +(define-public r-poibin + (package + (name "r-poibin") + (version "1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "poibin" version)) + (sha256 + (base32 + "1rllgmk7yanb5amysl33kmi11lx86q5kqblyb8qqb3ckj2w4jhm2")))) + (properties `((upstream-name . "poibin"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/poibin/") + (synopsis "Poisson binomial distribution") + (description + "This package provides an implementation of both the exact and +approximation methods for computing the @dfn{cumulative distribution +function} (CDF) of the Poisson binomial distribution. It also provides the +@dfn{probability mass function} (PMF), quantile function, and random number +generation for the Poisson binomial distribution.") + (license license:gpl2))) + +(define-public r-diagram + (package + (name "r-diagram") + (version "1.6.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "diagram" version)) + (sha256 + (base32 + "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw")))) + (properties `((upstream-name . "diagram"))) + (build-system r-build-system) + (propagated-inputs + `(("r-shape" ,r-shape))) + (home-page "https://cran.r-project.org/web/packages/diagram/") + (synopsis "Visualize simple graphs (networks) and plot flow diagrams") + (description + "This package provides tools to visualize simple graphs (networks) based +on a transition matrix, utilities to plot flow diagrams, visualizing webs, +electrical networks, etc. It also includes supporting material for the book +\"A practical guide to ecological modelling - using R as a simulation +platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book +\"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and +Francesca Mazzia (2012).") + (license license:gpl2+))) + +(define-public r-lim + (package + (name "r-lim") + (version "1.4.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "LIM" version)) + (sha256 + (base32 + "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8")))) + (properties `((upstream-name . "LIM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-diagram" ,r-diagram) + ("r-limsolve" ,r-limsolve))) + (home-page "https://cran.r-project.org/web/packages/LIM/") + (synopsis "Linear inverse model examples and solution methods") + (description + "This package provides functions that read and solve linear inverse +problems (food web problems, linear programming problems).") + (license license:gpl2+))) + +(define-public r-shinycssloaders + (package + (name "r-shinycssloaders") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "shinycssloaders" version)) + (sha256 + (base32 + "1bpzsm7m7c366sjl1qndp4m5dg2vlm68rjgdy9n1ija9xbp0r2g4")))) + (properties + `((upstream-name . "shinycssloaders"))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-glue" ,r-glue) + ("r-shiny" ,r-shiny))) + (home-page "https://github.com/andrewsali/shinycssloaders") + (synopsis "Add CSS loading animations to Shiny outputs") + (description + "This package provides tools to create a lightweight Shiny wrapper for +the css-loaders created by Luke Hass +@url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will +automatically show a loader when the output is (re)calculating.") + (license license:gpl3))) + +(define-public r-rsvg + (package + (name "r-rsvg") + (version "1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "rsvg" version)) + (sha256 + (base32 + "11mccgf6hfskg45wqc114sx3qy2r494y6axdf73z6xwhs1wpm97g")))) + (properties `((upstream-name . "rsvg"))) + (build-system r-build-system) + (inputs + `(("librsvg" ,librsvg) + ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://github.com/jeroen/rsvg#readme") + (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays") + (description + "This package allows you to render vector-based SVG images into +high-quality custom-size bitmap arrays using the librsvg2 library. The +resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In +addition, the package can convert images directly to various formats such as +PDF or PostScript.") + (license license:expat))) + +(define-public r-influencer + (package + (name "r-influencer") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "influenceR" version)) + (sha256 + (base32 + "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag")))) + (properties `((upstream-name . "influenceR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-igraph" ,r-igraph) + ("r-matrix" ,r-matrix))) + (home-page "https://github.com/rcc-uchicago/influenceR") + (synopsis "Tools to quantify structural importance of nodes in a network") + (description + "This package provides functionality to compute various node centrality +measures on networks. Included are functions to compute betweenness +centrality (by utilizing Madduri and Bader's SNAP library), implementations of +Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's +algorithm to identify key players, and Valente's bridging metric. The +betweenness, Key Players, and bridging implementations are parallelized with +OpenMP.") + (license license:gpl2))) |