diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 2409 |
1 files changed, 2307 insertions, 102 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5a3762fd7a..3942c2fb0c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -40,19 +40,24 @@ #:use-module (guix build-system r) #:use-module (gnu packages algebra) #:use-module (gnu packages base) + #:use-module (gnu packages bioinformatics) + #:use-module (gnu packages c) #:use-module (gnu packages compression) #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) + #:use-module (gnu packages geo) #:use-module (gnu packages ghostscript) #:use-module (gnu packages gl) #:use-module (gnu packages gnome) #:use-module (gnu packages graph) #:use-module (gnu packages gtk) #:use-module (gnu packages haskell) + #:use-module (gnu packages icu4c) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) + #:use-module (gnu packages java) #:use-module (gnu packages javascript) #:use-module (gnu packages lisp) #:use-module (gnu packages machine-learning) @@ -60,6 +65,7 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) #:use-module (gnu packages networking) + #:use-module (gnu packages pcre) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) @@ -72,14 +78,14 @@ (define-public r-clipr (package (name "r-clipr") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "clipr" version)) (sha256 (base32 - "1grx0lyww1cxmdvsr44wmbhz9i6zmiwxbchb97gxrfi9gy5kyc7x")))) + "0k9kimkmmj9k7290sxiqn4kd1vvm4w7q9a44wp0w30b7yjpavx2m")))) (build-system r-build-system) (home-page "https://github.com/mdlincoln/clipr") (synopsis "Read and write from the system clipboard") @@ -113,14 +119,14 @@ are not used.") (define-public r-sys (package (name "r-sys") - (version "3.1") + (version "3.2") (source (origin (method url-fetch) (uri (cran-uri "sys" version)) (sha256 (base32 - "0aj3wcyah3r7c9s3rbs0c8nifd4vqmkzg9fqkrb7f838ww0qw24q")))) + "1k5vk5q9wa5sin0n226i05nymg469s24f6lx64yyhb7yc624j698")))) (build-system r-build-system) (home-page "https://github.com/jeroen/sys") (synopsis "Powerful and reliable tools for running system commands in R") @@ -236,14 +242,14 @@ single step.") (define-public r-rvest (package (name "r-rvest") - (version "0.3.2") + (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "rvest" version)) (sha256 (base32 - "04mv99z8dixywx96kfy4215g6ib23s7qvd77hcf9pxqxzcvqhvhd")))) + "0vsm38w83zf0djcrc5ymb1ysg88hmgq2w937ql7pqgvk5px8f2mi")))) (build-system r-build-system) (propagated-inputs `(("r-httr" ,r-httr) @@ -394,13 +400,13 @@ into a pipeline of data manipulation and visualisation.") (define-public r-httpuv (package (name "r-httpuv") - (version "1.5.0") + (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 - "19m9514yj5sg0rz1zvi8w1z98srnrql4iirgr794fkaap6bs7i2f")))) + "042piypg4c8sqrlcdl3dwajkafkbglsky3x7d0jpjv8s5wxnpfxm")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) @@ -786,14 +792,14 @@ application framework for R, making it easy to create attractive dashboards.") (define-public r-shinyfiles (package (name "r-shinyfiles") - (version "0.7.2") + (version "0.7.3") (source (origin (method url-fetch) (uri (cran-uri "shinyFiles" version)) (sha256 (base32 - "0dlcjrw96x72grg6j915070x8x98l7629pn86gf148iknflm7gd5")))) + "01as3l9ffj5dwac0vviais2x5l3027zxlj67kcvkdwxaj5hql33i")))) (properties `((upstream-name . "shinyFiles"))) (build-system r-build-system) (propagated-inputs @@ -889,14 +895,14 @@ work well on small screens.") (define-public r-feather (package (name "r-feather") - (version "0.3.2") + (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "feather" version)) (sha256 (base32 - "138vnlwhkwayyim4rbx6rnf91kzhfij6v2f91ppx2174ky5611h6")))) + "0ls8lmygyjq60467s88h66d7fczjp1d3a2106rfq4dx9lyfvdfsa")))) (build-system r-build-system) (propagated-inputs `(("r-hms" ,r-hms) @@ -923,8 +929,8 @@ data store designed for maximum speed.") (home-page "https://cran.r-project.org/web/packages/maps") (synopsis "Draw geographical maps") (description "This package provides an R module for display of maps. -Projection code and larger maps are in separate packages ('mapproj' and -'mapdata').") +Projection code and larger maps are in separate packages (@code{mapproj} and +@code{mapdata}).") (license license:gpl2))) (define-public r-mapproj @@ -1218,14 +1224,14 @@ error stream.") (define-public r-pls (package (name "r-pls") - (version "2.7-0") + (version "2.7-1") (source (origin (method url-fetch) (uri (cran-uri "pls" version)) (sha256 (base32 - "0xaqqgmdvfh7g7v1m4bcwjqzph68b9cq3bn4kjisfsadl54i5p2x")))) + "0jw3zl5z06023zxr74phnvwax8m3i4a4i6lsqiq6j15aq9zq3zgq")))) (build-system r-build-system) (home-page "http://mevik.net/work/software/pls.html") (synopsis "Partial Least Squares and Principal Component Regression") @@ -1345,9 +1351,9 @@ a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about Rcpp is provided by several vignettes included in this package, via the -'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel +@code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see -'citation(\"Rcpp\")' for details on these last two.") +@code{citation(\"Rcpp\")} for details on these last two.") (license license:gpl2+))) (define-public r-bindr @@ -1479,14 +1485,14 @@ validation and filtering on the values, making options invisible or private.") (define-public r-circlize (package (name "r-circlize") - (version "0.4.5") + (version "0.4.6") (source (origin (method url-fetch) (uri (cran-uri "circlize" version)) (sha256 (base32 - "0qhn9jzw7gd0jp9rmqrlbmy5ql6hjsa68pkp0acfz1h215dl8ah9")))) + "1yjnb88pnzk5c1p0vjxykc7cr3394ln5axviqcf12ajibvy8rj6f")))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace) @@ -1899,14 +1905,14 @@ quantile mixture from L-moments and trimmed L-moments.") (define-public r-distillery (package (name "r-distillery") - (version "1.0-4") + (version "1.0-6") (source (origin (method url-fetch) (uri (cran-uri "distillery" version)) (sha256 (base32 - "1m0pgmlvk7bsb6q3kxagnq422babk61sf73naavac68v8x2q8fix")))) + "1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429")))) (build-system r-build-system) (home-page "http://www.ral.ucar.edu/staff/ericg") (synopsis "Functions for confidence intervals and object information") @@ -1920,19 +1926,18 @@ SpatialVx.") (define-public r-extremes (package (name "r-extremes") - (version "2.0-9") + (version "2.0-10") (source (origin (method url-fetch) (uri (cran-uri "extRemes" version)) (sha256 (base32 - "0cpvcajk9xyy7662nqkyx333vrxpwsc5nmv0bfnhsbgijz5y0hvm")))) + "08fj72gpq2d6695hbm3cgwgal64z009ykrirby7g6r0akfcsx5ic")))) (properties `((upstream-name . "extRemes"))) (build-system r-build-system) (propagated-inputs - `(("r-car" ,r-car) - ("r-distillery" ,r-distillery) + `(("r-distillery" ,r-distillery) ("r-lmoments" ,r-lmoments))) (home-page "http://www.assessment.ucar.edu/toolkit/") (synopsis "Extreme value analysis") @@ -1945,14 +1950,14 @@ or excesses over a high threshold.") (define-public r-lmtest (package (name "r-lmtest") - (version "0.9-36") + (version "0.9-37") (source (origin (method url-fetch) (uri (cran-uri "lmtest" version)) (sha256 (base32 - "0sym9sm1vl6bbgq01jhz1plxqmgh8hrgrn7rw0mwvsalcn6id7xy")))) + "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,r-zoo))) @@ -2476,20 +2481,20 @@ to access PostgreSQL database systems.") (define-public r-geometry (package (name "r-geometry") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "geometry" version)) (sha256 (base32 - "0lpih1a93jz021krdv78zf6fq95g8i0xw4r9aj5gq36a0vzc3i0y")))) + "0v3ivaw8vbjyxg08dd573qk3kqfyknj5hli9503dza6p6xz0dzmm")))) (build-system r-build-system) (propagated-inputs `(("r-magic" ,r-magic) ("r-lpsolve" ,r-lpsolve) ("r-rcpp" ,r-rcpp) - ("r-cppprogress" ,r-rcppprogress))) + ("r-rcppprogress" ,r-rcppprogress))) (home-page "http://geometry.r-forge.r-project.org/") (synopsis "Mesh generation and surface tesselation") (description @@ -2510,14 +2515,14 @@ Delaunay triangulation and convex hull computation.") (define-public r-ddalpha (package (name "r-ddalpha") - (version "1.3.8") + (version "1.3.9") (source (origin (method url-fetch) (uri (cran-uri "ddalpha" version)) (sha256 (base32 - "0gi0hl14ghgf65zxsvgzh9z6xx1nyi49cpx192lmwrwqn3dy7ba0")))) + "1vzs0cvl6xw3h9i00rg3hs02xwgxcnh8326y10kxmhs3qq4m7nb2")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) @@ -2588,14 +2593,14 @@ provided.") (define-public r-ipred (package (name "r-ipred") - (version "0.9-8") + (version "0.9-9") (source (origin (method url-fetch) (uri (cran-uri "ipred" version)) (sha256 (base32 - "01xcg3c121ndfpz9dirqxszknh4yb1p222p7f1wbwwhdrg1i27cw")))) + "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d")))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class) @@ -2669,14 +2674,14 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "0.5.1") + (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "0bmf38yvwalqf5j5yrr48nsk5k3n75s0gwcw621hp5lgrgvnp7ns")))) + "0qmclih5dm5sqzy4hplcfy677kr12pm9pnpv3r319g14dd27pbqn")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -2862,14 +2867,14 @@ with the package @code{optim}.") (define-public r-ordinal (package (name "r-ordinal") - (version "2019.3-9") + (version "2019.4-25") (source (origin (method url-fetch) (uri (cran-uri "ordinal" version)) (sha256 (base32 - "0xsr2715ghh1q5hjnx7d8lyavzfvpi370blm1xdljn3p4kar8ldi")))) + "1pvrkly4x12w32n7w1qljdwzqnlkv7rfa7rx0nz5vbiw29xas4i8")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -3045,14 +3050,14 @@ programming} (SQP) based solver).") (define-public r-hardyweinberg (package (name "r-hardyweinberg") - (version "1.6.1") + (version "1.6.2") (source (origin (method url-fetch) (uri (cran-uri "HardyWeinberg" version)) (sha256 (base32 - "16n8qanxx0p5ny5zqxafn8hwb1xv94y1wig1iql8as5a5qh8lwcz")))) + "15i7b444hikkfgqmx2ki827998xwra38k9v7a7kavwz6zmq5mmv9")))) (properties `((upstream-name . "HardyWeinberg"))) (build-system r-build-system) (propagated-inputs @@ -3312,14 +3317,14 @@ normalizations, minimum variance matching, and so on.") (define-public r-sdmtools (package (name "r-sdmtools") - (version "1.1-221") + (version "1.1-221.1") (source (origin (method url-fetch) (uri (cran-uri "SDMTools" version)) (sha256 (base32 - "1kacrpamshv7wz83yn45sfbw4m9c44xrrngzcklnwx8gcxx2knm6")))) + "1fsgnlc7glawimzijp11j53g5bnfp1mdq9wb0754idmxcdi8a99q")))) (properties `((upstream-name . "SDMTools"))) (build-system r-build-system) (propagated-inputs `(("r-r-utils" ,r-r-utils))) @@ -3612,14 +3617,14 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.5") + (version "0.6") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 (base32 - "1wkrapc490r9l9z6mz623zn9ijq64mckc17xg2s7n3s9yaxj98lb")))) + "123wmnykmlq9prqx1g9ij9vyqx25pib2jnqjrwy39rfmzbsypbx3")))) (build-system r-build-system) (home-page "https://github.com/yihui/xfun") (synopsis "Miscellaneous functions") @@ -3696,14 +3701,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.11") + (version "0.12") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "017g0niwmx8qafsn9b01gp60j5fgwxch0dnkmjgpxxr1k4h1r64x")))) + "03ggxbd4y1ipcmjw5ixa6g6wg4ydargnln7g08bdrdi96zyyq1fh")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) @@ -3745,14 +3750,14 @@ published results; and a routine for graphical display.") (define-public r-network (package (name "r-network") - (version "1.14-377") + (version "1.15") (source (origin (method url-fetch) (uri (cran-uri "network" version)) (sha256 (base32 - "0iiy5n17kysrdfs20zr7qald4lwkvws0axi1qkr8f7vzv7w04g01")))) + "1cscw5978fyixhkicf06c4b2g1yf6gyi8vx86cz3dy75d41mrgjw")))) (build-system r-build-system) (propagated-inputs `(("r-magrittr" ,r-magrittr) @@ -3944,14 +3949,14 @@ Fisher's method), and Sidak correction.") (define-public r-quantmod (package (name "r-quantmod") - (version "0.4-13") + (version "0.4-14") (source (origin (method url-fetch) (uri (cran-uri "quantmod" version)) (sha256 (base32 - "16aldg96z7amp5mr90nb8127yy04gxsihfr26km5p3cx3j117yv0")))) + "1csljagnpkr1mmc18h70b64zbyj07kx972nip9dng39jfg7ilnyr")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) @@ -5176,14 +5181,14 @@ obtain a better initial configuration in non-metric MDS.") (define-public r-reticulate (package (name "r-reticulate") - (version "1.11.1") + (version "1.12") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "1cyb92dvv9iibsk28i0gm5hm2xqbsn0y6d67id74c8rhai9y8i9v")))) + "0pqr1rcs8yg9nlh729mvlws93cqhpmv49j9bcgarh7vxzkwyv0kb")))) (build-system r-build-system) (inputs `(("python" ,python))) (propagated-inputs @@ -5484,14 +5489,14 @@ results to the user.") (define-public r-hdf5r (package (name "r-hdf5r") - (version "1.0.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "hdf5r" version)) (sha256 (base32 - "0h222q80li8rs3cv4c5lvv3g91ygd51w43ay6fwyk9q9d315vwrj")))) + "10gynjwaaxks8y9c2fl8k040j0nbwn372nil70009yfk9wrkx0aq")))) (build-system r-build-system) (inputs `(("hdf5" ,hdf5) @@ -5534,14 +5539,14 @@ patterned after functions in the snow package.") (define-public r-polynom (package (name "r-polynom") - (version "1.3-9") + (version "1.4-0") (source (origin (method url-fetch) (uri (cran-uri "polynom" version)) (sha256 (base32 - "1s4xxv5rvpigawknvq27v9vzvs83phfsj5h8mim2lmf5bj950nnk")))) + "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/polynom/") (synopsis "Functions for univariate polynomial manipulations") @@ -5600,14 +5605,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rdpack (package (name "r-rdpack") - (version "0.10-1") + (version "0.11-0") (source (origin (method url-fetch) (uri (cran-uri "Rdpack" version)) (sha256 (base32 - "0bbjnw88h54v40hzim00i8yd3p4rk9i84zfdmgcbnylscwvsf0av")))) + "11cd27s6zp5cxnwxcvz6rjf00y0r7aq8ywhzwpf1r4xy1z44kd4g")))) (properties `((upstream-name . "Rdpack"))) (build-system r-build-system) (propagated-inputs @@ -5627,14 +5632,14 @@ references and Rd files.") (define-public r-officer (package (name "r-officer") - (version "0.3.3") + (version "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 - "1ggdp8pbspn24sjshx1h48klivrx401vwk2df49j4wpwxh6dx26y")))) + "1m4b3mcn5j5q3nq0jp1nranh4rdb8vxcpabn6ryqk9m6709fvhjz")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -5815,14 +5820,14 @@ other add-on packages.") (define-public r-insight (package (name "r-insight") - (version "0.1.2") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "0cy00j4m9r690hrjdmv8wzwn8mbnkjd3g527nvsmid64h9jgks5f")))) + "0fn9cd5qxqlpjv3d05mk66k5z5ll60x5la51mby5h7k4l6bqmsiz")))) (build-system r-build-system) (home-page "https://easystats.github.io/insight/") (synopsis "Easy access to model information for various model objects") @@ -5947,21 +5952,21 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.5.1") + (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "0arxgal67ahsq8v0zbvc767qadn7lg3f7mmqa9gjjz6sri0y6gsx")))) + "0sabdvkdlx5i1nr7nz68cappwsibzsjxpmiz3yp948ckbfmkdb27")))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) + `(("r-base64enc" ,r-base64enc) + ("r-data-table" ,r-data-table) ("r-gdtools" ,r-gdtools) ("r-htmltools" ,r-htmltools) ("r-knitr" ,r-knitr) - ("r-magick" ,r-magick) ("r-officer" ,r-officer) ("r-rlang" ,r-rlang) ("r-rmarkdown" ,r-rmarkdown) @@ -6054,14 +6059,14 @@ Venn diagram, heatmap).") (define-public r-getopt (package (name "r-getopt") - (version "1.20.2") + (version "1.20.3") (source (origin (method url-fetch) (uri (cran-uri "getopt" version)) (sha256 (base32 - "13p35lbpy7i578752fa71sbfvcsqw5qfa9p6kf8b5m3c5p9i4v1x")))) + "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk")))) (build-system r-build-system) (home-page "https://github.com/trevorld/getopt") (synopsis "Command-line option processor for R") @@ -7188,6 +7193,26 @@ replicating the evaluation as many times as specified, and returning the results conveniently wrapped into a data frame.") (license license:gpl2+))) +(define-public r-mitools + (package + (name "r-mitools") + (version "2.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "mitools" version)) + (sha256 + (base32 + "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j")))) + (build-system r-build-system) + (propagated-inputs `(("r-dbi" ,r-dbi))) + (home-page "https://cran.r-project.org/web/packages/mitools/") + (synopsis "Tools for multiple imputation of missing data") + (description + "This package provides tools to perform analyses and combine results from +multiple-imputation datasets.") + (license license:gpl2))) + (define-public r-magick (package (name "r-magick") @@ -7224,19 +7249,20 @@ console, resulting in an interactive editing environment.") (define-public r-survey (package (name "r-survey") - (version "3.35-1") + (version "3.36") (source (origin (method url-fetch) (uri (cran-uri "survey" version)) (sha256 (base32 - "1nv4sdfmidvyjgvp3zvn5iw35bb8w0v7095is2pdy8cckkgdvr8i")))) + "0xclsy4ram4k48vzh5m5bpmknnpwxnss85v73s4czsjj5ffjxwwh")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) ("r-matrix" ,r-matrix) ("r-minqa" ,r-minqa) + ("r-mitools" ,r-mitools) ("r-numderiv" ,r-numderiv) ("r-survival" ,r-survival))) (home-page "http://r-survey.r-forge.r-project.org/survey/") @@ -7506,14 +7532,14 @@ observation.") (define-public r-sandwich (package (name "r-sandwich") - (version "2.5-0") + (version "2.5-1") (source (origin (method url-fetch) (uri (cran-uri "sandwich" version)) (sha256 (base32 - "168kq5kk34xbhfsxsanard9zriyp6cw0s09ralzb57kk42pl9hbc")))) + "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,r-zoo))) @@ -7579,14 +7605,14 @@ Hothorn, Westfall, 2010, CRC Press).") (define-public r-emmeans (package (name "r-emmeans") - (version "1.3.3") + (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "1hpal1vq6gryzvgfvv9f328idg0mgjvlfnhaj069dhb7zqfwhzlk")))) + "09gxphan34c615y4lhjdqkg5cz4ih9b1r3bb4chs3mwmiav1rxqn")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) @@ -7804,6 +7830,58 @@ Laplace approximation. Gradients are calculated using automatic differentiation.") (license license:agpl3+))) +(define-public r-bayestestr + (package + (name "r-bayestestr") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "bayestestR" version)) + (sha256 + (base32 + "1m6gj55z3shm3m3mgqj8nk73wij67y617sl04rbj400wz9qrhfva")))) + (properties `((upstream-name . "bayestestR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-insight" ,r-insight))) + (home-page "https://github.com/easystats/bayestestR") + (synopsis "Describe Bayesian models and posterior distributions") + (description + "This package provides utilities to understand and describe posterior +distributions and Bayesian models. It includes point-estimates such as +@dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest +Density Interval} (HDI), and indices used for null-hypothesis testing (such as +ROPE percentage and pd).") + (license license:gpl3))) + +(define-public r-performance + (package + (name "r-performance") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "performance" version)) + (sha256 + (base32 + "19lfx25hkavzbycrh6hq4v24a0dz4s60ryq6jyihjlxgrb9g7cnw")))) + (build-system r-build-system) + (propagated-inputs + `(("r-bayestestr" ,r-bayestestr) + ("r-insight" ,r-insight))) + (home-page "https://easystats.github.io/performance/") + (synopsis "Assessment of regression models performance") + (description + "This package provides utilities for computing measures to assess model +quality, which are not directly provided by R's @code{base} or @code{stats} +packages. These include e.g. measures like r-squared, intraclass correlation +coefficient, root mean squared error or functions to check models for +overdispersion, singularity or zero-inflation and more. Functions apply to a +large variety of regression models, including generalized linear models, mixed +effects models and Bayesian models.") + (license license:gpl3))) + (define-public r-ggeffects (package (name "r-ggeffects") @@ -7841,29 +7919,32 @@ results using @code{ggplot2}.") (define-public r-sjplot (package (name "r-sjplot") - (version "2.6.2") + (version "2.6.3") (source (origin (method url-fetch) (uri (cran-uri "sjPlot" version)) (sha256 (base32 - "0x9pbchmz4qf4c9bi52dhhgv1phfj03q1hnxic8vndl6xwib63cy")))) + "0h1mkmp5mrkbf7y3zh6m4cnm737cpg1m5si0lrmal7j2ixqicwjy")))) (properties `((upstream-name . "sjPlot"))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) + `(("r-bayestestr" ,r-bayestestr) + ("r-broom" ,r-broom) ("r-dplyr" ,r-dplyr) ("r-forcats" ,r-forcats) ("r-ggeffects" ,r-ggeffects) ("r-ggplot2" ,r-ggplot2) ("r-glmmtmb" ,r-glmmtmb) + ("r-insight" ,r-insight) ("r-knitr" ,r-knitr) ("r-lme4" ,r-lme4) ("r-magrittr" ,r-magrittr) ("r-mass" ,r-mass) ("r-modelr" ,r-modelr) ("r-nlme" ,r-nlme) + ("r-performance" ,r-performance) ("r-psych" ,r-psych) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) @@ -7974,14 +8055,14 @@ terminals that do not support Unicode.") (define-public r-usethis (package (name "r-usethis") - (version "1.4.0") + (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "usethis" version)) (sha256 (base32 - "1gadckx3sxz9gxvpkprj9x7zcgg2nz5m4q0vi76ya9li1v03rwwn")))) + "0pn6ka3726psaqlx573g6nxi90apf0rn5m4k2lz1jr66xdc19sag")))) (build-system r-build-system) (propagated-inputs `(("r-clipr" ,r-clipr) @@ -7993,10 +8074,13 @@ terminals that do not support Unicode.") ("r-gh" ,r-gh) ("r-git2r" ,r-git2r) ("r-glue" ,r-glue) + ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-rprojroot" ,r-rprojroot) ("r-rstudioapi" ,r-rstudioapi) - ("r-whisker" ,r-whisker))) + ("r-whisker" ,r-whisker) + ("r-withr" ,r-withr) + ("r-yaml" ,r-yaml))) (home-page "https://github.com/r-lib/usethis") (synopsis "Automate R package and project setup") (description @@ -8032,14 +8116,14 @@ more information about packages, and where they were installed from.") (define-public r-remotes (package (name "r-remotes") - (version "2.0.2") + (version "2.0.4") (source (origin (method url-fetch) (uri (cran-uri "remotes" version)) (sha256 (base32 - "0rsjxmhwpr51ilsdjfqn06mj8yr2d7nckcn3arv1ljn23qfkpcxa")))) + "1jbn4kjimcr82zv5lnqxqa2487a96vn6jxf7wc6gnpxr6k06d61p")))) (build-system r-build-system) (home-page "https://github.com/r-lib/remotes#readme") (synopsis "R package installation from remote repositories") @@ -8156,14 +8240,14 @@ ways.") (define-public r-summarytools (package (name "r-summarytools") - (version "0.9.2") + (version "0.9.3") (source (origin (method url-fetch) (uri (cran-uri "summarytools" version)) (sha256 (base32 - "1q83kii6prqf9z5v8cxj1q2944kx9x7dcxyqix3m883a94dmgivy")))) + "1wfbkgvicaic37zgpr6zcm4a58yx43p59h0sqggdj44ncqs7147f")))) (build-system r-build-system) (propagated-inputs `(("r-checkmate" ,r-checkmate) @@ -8176,6 +8260,7 @@ ways.") ("r-pryr" ,r-pryr) ("r-rapportools" ,r-rapportools) ("r-rcurl" ,r-rcurl) + ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr))) (home-page "https://github.com/dcomtois/summarytools") (synopsis "Tools to quickly and neatly summarize data") @@ -8800,14 +8885,14 @@ parametrizations of Nolan.") (define-public r-gsl (package (name "r-gsl") - (version "2.1-5") + (version "2.1-6") (source (origin (method url-fetch) (uri (cran-uri "gsl" version)) (sha256 (base32 - "18kzgwmyfqg570gn2b33fm6mj87fiaa4a3bx954yrj8iq28im71v")))) + "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m")))) (build-system r-build-system) (inputs `(("gsl" ,gsl))) @@ -9206,14 +9291,14 @@ definiteness of a matrix.") (define-public r-rspectra (package (name "r-rspectra") - (version "0.13-1") + (version "0.14-0") (source (origin (method url-fetch) (uri (cran-uri "RSpectra" version)) (sha256 (base32 - "1sw80chwyyjzf5px278l6xmp94yhwrlj5xh8d3wlw3dnvdkycca7")))) + "12w5vnz39gyciza0fl7fw4f9i9kjw763h3mvk1sxd97c5dsn26jg")))) (properties `((upstream-name . "RSpectra"))) (build-system r-build-system) (propagated-inputs @@ -9302,14 +9387,14 @@ the first time as the statistic.") (define-public r-splitstackshape (package (name "r-splitstackshape") - (version "1.4.6") + (version "1.4.8") (source (origin (method url-fetch) (uri (cran-uri "splitstackshape" version)) (sha256 (base32 - "03w6h64ga4zqilffdway4l38l5cbman4yrspkzhbigds12aqz25r")))) + "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35")))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table))) @@ -10258,14 +10343,14 @@ Differences with other sparse matrix packages are: (define-public r-fields (package (name "r-fields") - (version "9.6") + (version "9.7") (source (origin (method url-fetch) (uri (cran-uri "fields" version)) (sha256 (base32 - "1v7z48a8jmdcil28rj8c3455k6rssr5v9qi6dyhhpbb193bj8121")))) + "0hsr6r0zyv8zqkfyd9fmjk6v901m2r8pmswvsmps6w5zvpi0p5kw")))) (build-system r-build-system) (propagated-inputs `(("r-maps" ,r-maps) @@ -10613,14 +10698,14 @@ regression coefficients can be conducted via jackknifing.") (define-public r-huge (package (name "r-huge") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "huge" version)) (sha256 (base32 - "06s22i2cdn6g2r8kq5csyspinayh8dxxg9gkwcf4sa1lmrgb0bf9")))) + "1j93gvi1jyq3ld9jhdqhrpm2is54rk3ilmf3yw7fx6gva0y6hjqd")))) (build-system r-build-system) (propagated-inputs `(("r-igraph" ,r-igraph) @@ -11586,19 +11671,20 @@ compatible with @code{rzmq} are also provided.") (define-public r-repr (package (name "r-repr") - (version "0.19.2") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "repr" version)) (sha256 (base32 - "1mhhzakkagb8z568yx3p2ixs8fcifm7f8l2yq285zrz8jmnpckfx")))) + "0j8z4sl67fgnbywkhgg0bns68mbgf9iqnw4qiym2rjy1b08fpclq")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-htmltools" ,r-htmltools) - ("r-jsonlite" ,r-jsonlite))) + ("r-jsonlite" ,r-jsonlite) + ("r-pillar" ,r-pillar))) (home-page "https://cran.r-project.org/web/packages/repr/") (synopsis "Serializable representations") (description @@ -11632,14 +11718,14 @@ running IRkernel session.") (define-public r-irkernel (package (name "r-irkernel") - (version "0.8.15") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "IRkernel" version)) (sha256 (base32 - "1n0nc3paij8fgbp7l2b4405zk9k4y3gdi2bz6z8x6j0h5mi6k6a6")))) + "0i5gpis2g30zi96h9r9awbw4724xd6p4sv8y7shyfzgc4qccpizp")))) (properties `((upstream-name . "IRkernel"))) (build-system r-build-system) (arguments @@ -11801,14 +11887,14 @@ al. (2010).") (define-public r-reinforcelearn (package (name "r-reinforcelearn") - (version "0.2.0") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "reinforcelearn" version)) (sha256 (base32 - "0naakmyb14d2cf7cy5ir52qh3bp51gvs6hyhfi3f72yl2jfnnpzg")))) + "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b")))) (build-system r-build-system) (propagated-inputs `(("r-checkmate" ,r-checkmate) @@ -11823,3 +11909,2122 @@ algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm can be used with function approximation, eligibility traces (Singh & Sutton, 1996) and experience replay (Mnih et al., 2013).") (license license:expat))) + +(define-public r-lemon + (package + (name "r-lemon") + (version "0.4.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "lemon" version)) + (sha256 + (base32 + "0wsn5bfg10wq4dnrgpyraz2bzx9p19c7hf1pwj3h4zmpqfgsdbpw")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-gtable" ,r-gtable) + ("r-knitr" ,r-knitr) + ("r-lattice" ,r-lattice) + ("r-plyr" ,r-plyr) + ("r-scales" ,r-scales))) + (home-page "https://github.com/stefanedwards/lemon") + (synopsis "Freshen up your ggplot2 plots") + (description + "This package provides functions for working with legends and axis lines +of ggplot2, facets that repeat axis lines on all panels, and some knitr +extensions.") + (license license:gpl3))) + +(define-public r-wgaim + (package + (name "r-wgaim") + (version "1.4-11") + (source + (origin + (method url-fetch) + (uri (cran-uri "wgaim" version)) + (sha256 + (base32 + "1jjyp100dcjjczp61xlvhmy48ynniqcys535vzbgswhr7fvijymg")))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice) + ("r-qtl" ,r-qtl))) + (home-page "https://cran.r-project.org/web/packages/wgaim") + (synopsis "Whole genome average interval mapping for QTL detection") + (description + "This package integrates sophisticated mixed modelling methods with a +whole genome approach to detecting significant QTL in linkage maps.") + (license license:gpl2+))) + +(define-public r-bedr + (package + (name "r-bedr") + (version "1.0.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "bedr" version)) + (sha256 + (base32 + "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j")))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-r-utils" ,r-r-utils) + ("r-testthat" ,r-testthat) + ("r-venndiagram" ,r-venndiagram) + ("r-yaml" ,r-yaml) + ("bedops" ,bedops) + ("bedtools" ,bedtools) + ("htslib" ,htslib))) ; for tabix + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://cran.r-project.org/web/packages/bedr") + (synopsis "Genomic region processing") + (description + "This package is for genomic regions processing using command line tools +such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient +utilities to perform genome arithmetic e.g indexing, formatting and merging. +The bedr package's API enhances access to these tools as well as offers +additional utilities for genomic regions processing.") + (license license:gpl2))) + +(define-public r-partitions + (package + (name "r-partitions") + (version "1.9-19") + (source + (origin + (method url-fetch) + (uri (cran-uri "partitions" version)) + (sha256 + (base32 + "1pklfnjdc094c8nzkqcdvqzdh8v3p5n8jbg4pf9678iw648saiyx")))) + (build-system r-build-system) + (propagated-inputs + `(("r-gmp" ,r-gmp) + ("r-polynom" ,r-polynom))) + (home-page "https://cran.r-project.org/web/packages/partitions") + (synopsis "Additive partitions of integers") + (description + "This package provides tools to enumerates the partitions, unequal +partitions, and restricted partitions of an integer; the three corresponding +partition functions are also given.") + ;; Any version of the GPL + (license license:gpl2+))) + +(define-public r-brobdingnag + (package + (name "r-brobdingnag") + (version "1.2-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "Brobdingnag" version)) + (sha256 + (base32 + "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r")))) + (properties `((upstream-name . "Brobdingnag"))) + (build-system r-build-system) + (home-page "https://github.com/RobinHankin/Brobdingnag.git") + (synopsis "Very large numbers in R") + (description + "This package handles very large numbers in R. Real numbers are held +using their natural logarithms, plus a logical flag indicating sign. The +package includes a vignette that gives a step-by-step introduction to using S4 +methods.") + ;; Any version of the GPL + (license license:gpl2+))) + +(define-public r-untb + (package + (name "r-untb") + (version "1.7-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "untb" version)) + (sha256 + (base32 + "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6")))) + (build-system r-build-system) + (propagated-inputs + `(("r-brobdingnag" ,r-brobdingnag) + ("r-partitions" ,r-partitions) + ("r-polynom" ,r-polynom))) + (home-page "https://github.com/RobinHankin/untb.git") + (synopsis "Ecological drift under the UNTB") + (description + "This package provides numerical simulations, and visualizations, of +Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).") + (license license:gpl2+))) + +(define-public r-stepwise + (package + (name "r-stepwise") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "stepwise" version)) + (sha256 + (base32 + "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2")))) + (build-system r-build-system) + (home-page "http://stat.sfu.ca/statgen/research/stepwise.html") + (synopsis "Stepwise detection of recombination breakpoints") + (description + "This package provides a stepwise approach to identifying recombination +breakpoints in a genomic sequence alignment.") + (license license:gpl2+))) + +(define-public r-snpmaxsel + (package + (name "r-snpmaxsel") + (version "1.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "SNPmaxsel" version)) + (sha256 + (base32 + "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z")))) + (properties `((upstream-name . "SNPmaxsel"))) + (build-system r-build-system) + (propagated-inputs + `(("r-combinat" ,r-combinat) + ("r-mvtnorm" ,r-mvtnorm))) + (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html") + (synopsis "Maximally selected statistics for SNP data") + (description + "This package implements asymptotic methods related to maximally selected +statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP) +data.") + (license license:gpl2+))) + +(define-public r-acsnminer + (package + (name "r-acsnminer") + (version "0.16.8.25") + (source (origin + (method url-fetch) + (uri (cran-uri "ACSNMineR" version)) + (sha256 + (base32 + "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l")))) + (properties `((upstream-name . "ACSNMineR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra))) + (home-page "https://cran.r-project.org/web/packages/ACSNMineR") + (synopsis "Gene enrichment analysis") + (description + "This package provides tools to compute and represent gene set enrichment +or depletion from your data based on pre-saved maps from the @dfn{Atlas of +Cancer Signalling Networks} (ACSN) or user imported maps. The gene set +enrichment can be run with hypergeometric test or Fisher exact test, and can +use multiple corrections. Visualization of data can be done either by +barplots or heatmaps.") + (license license:gpl2+))) + +(define-public r-seqinr + (package + (name "r-seqinr") + (version "3.4-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "seqinr" version)) + (sha256 + (base32 + "17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ade4" ,r-ade4) + ("r-segmented" ,r-segmented))) + (inputs + `(("zlib" ,zlib))) + (home-page "http://seqinr.r-forge.r-project.org/") + (synopsis "Biological sequences retrieval and analysis") + (description + "This package provides tools for exploratory data analysis and data +visualization of biological sequence (DNA and protein) data. It also includes +utilities for sequence data management under the ACNUC system.") + (license license:gpl2+))) + +(define-public r-units + (package + (name "r-units") + (version "0.6-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "units" version)) + (sha256 + (base32 + "0w7iwp8c66d5gj4rsb8c87vb0ja39hym6fmfnqaqwb3is1snfa2y")))) + (build-system r-build-system) + (inputs + `(("udunits" ,udunits))) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/r-quantities/units/") + (synopsis "Measurement Units for R Vectors") + (description + "This package provides support for measurement units in R vectors, +matrices and arrays: automatic propagation, conversion, derivation and +simplification of units; raising errors in case of unit incompatibility. It +is compatible with the @code{POSIXct}, @code{Date} and @code{difftime} +classes.") + (license license:gpl2))) + +(define-public r-classint + (package + (name "r-classint") + (version "0.3-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "classInt" version)) + (sha256 + (base32 + "0c2z6shlxa928xa20yl956r06lx20mji3mwipdvmj3f4z5g6hgm9")))) + (properties `((upstream-name . "classInt"))) + (build-system r-build-system) + (propagated-inputs + `(("r-class" ,r-class) + ("r-e1071" ,r-e1071) + ("r-kernsmooth" ,r-kernsmooth))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://github.com/r-spatial/classInt/") + (synopsis "Choose univariate class intervals") + (description + "This package provides selected commonly used methods for choosing +univariate class intervals for mapping or other graphics purposes.") + (license license:gpl2+))) + +(define-public r-spdata + (package + (name "r-spdata") + (version "0.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "spData" version)) + (sha256 + (base32 + "162cqb331ki43jx4r8lpkjpn2l712figd896rnawg9j1jmjyl96y")))) + (properties `((upstream-name . "spData"))) + (build-system r-build-system) + (home-page "https://github.com/Nowosad/spData") + (synopsis "Datasets for spatial analysis") + (description + "This a package containing diverse spatial datasets for demonstrating, +benchmarking and teaching spatial data analysis. It includes R data of class +@code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a +range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some +of the datasets are designed to illustrate specific analysis techniques. +@code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to +illustrate point pattern analysis techniques.") + (license license:cc0))) + +(define-public r-learnbayes + (package + (name "r-learnbayes") + (version "2.15.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "LearnBayes" version)) + (sha256 + (base32 + "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv")))) + (properties `((upstream-name . "LearnBayes"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/LearnBayes") + (synopsis "Functions for learning Bayesian inference") + (description + "This package provides a collection of functions helpful in learning the +basic tenets of Bayesian statistical inference. It contains functions for +summarizing basic one and two parameter posterior distributions and predictive +distributions. It contains MCMC algorithms for summarizing posterior +distributions defined by the user. It also contains functions for regression +models, hierarchical models, Bayesian tests, and illustrations of Gibbs +sampling.") + (license license:gpl2+))) + +(define-public r-deldir + (package + (name "r-deldir") + (version "0.1-16") + (source + (origin + (method url-fetch) + (uri (cran-uri "deldir" version)) + (sha256 + (base32 + "0549kj0hlkdyvm5axsm3np30wg53fm2pxybijzw0avlgsd2y2n2q")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/deldir") + (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation") + (description + "This package provides tools for calculating the Delaunay triangulation +and the Dirichlet or Voronoi tessellation (with respect to the entire plane) +of a planar point set. It plots triangulations and tessellations in various +ways, clips tessellations to sub-windows, calculates perimeters of +tessellations, and summarizes information about the tiles of the +tessellation.") + (license license:gpl2+))) + +(define-public r-sf + (package + (name "r-sf") + (version "0.7-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "sf" version)) + (sha256 + (base32 + "0vnyr7xyfcl928kbrb1k8l4fkd0cjrfq486g6gxpvy5j0cc2h4i1")))) + (build-system r-build-system) + (inputs + `(("gdal" ,gdal) + ("geos" ,geos) + ("proj" ,proj.4) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-classint" ,r-classint) + ("r-dbi" ,r-dbi) + ("r-magrittr" ,r-magrittr) + ("r-rcpp" ,r-rcpp) + ("r-units" ,r-units))) + (native-inputs `(("pkg-config" ,pkg-config))) + (home-page "https://github.com/r-spatial/sf/") + (synopsis "Simple features for R") + (description + "This package provides support for simple features, a standardized way to +encode spatial vector data. It binds to GDAL for reading and writing data, to +GEOS for geometrical operations, and to PROJ for projection conversions and +datum transformations.") + ;; Either of these licenses + (license (list license:gpl2 license:expat)))) + +(define-public r-spdep + (package + (name "r-spdep") + (version "1.1-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "spdep" version)) + (sha256 + (base32 + "06mk81kc1ml2wjc8wwwgr0wasjcr4mwrxpfa8vfc373bmnha635s")))) + (build-system r-build-system) + (propagated-inputs + `(("r-boot" ,r-boot) + ("r-coda" ,r-coda) + ("r-deldir" ,r-deldir) + ("r-expm" ,r-expm) + ("r-gmodels" ,r-gmodels) + ("r-learnbayes" ,r-learnbayes) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-nlme" ,r-nlme) + ("r-sf" ,r-sf) + ("r-sp" ,r-sp) + ("r-spdata" ,r-spdata))) + (home-page "https://github.com/r-spatial/spdep/") + (synopsis "Spatial dependence: weighting schemes, statistics and models") + (description + "This package provides a collection of functions to create spatial +weights matrix objects from polygon contiguities, from point patterns by +distance and tessellations, for summarizing these objects, and for permitting +their use in spatial data analysis, including regional aggregation by minimum +spanning tree.") + (license license:gpl2+))) + +(define-public r-adegenet + (package + (name "r-adegenet") + (version "2.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "adegenet" version)) + (sha256 + (base32 + "0ynfblp0hbd3dp3k86fn1wyhqr28lk6hs2bg4q7gyf0sfdfzwhrh")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ade4" ,r-ade4) + ("r-ape" ,r-ape) + ("r-boot" ,r-boot) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-igraph" ,r-igraph) + ("r-mass" ,r-mass) + ("r-reshape2" ,r-reshape2) + ("r-seqinr" ,r-seqinr) + ("r-shiny" ,r-shiny) + ("r-spdep" ,r-spdep) + ("r-vegan" ,r-vegan))) + (home-page "https://github.com/thibautjombart/adegenet") + (synopsis "Exploratory analysis of genetic and genomic data") + (description + "This package provides a toolset for the exploration of genetic and +genomic data. Adegenet provides formal (S4) classes for storing and handling +various genetic data, including genetic markers with varying ploidy and +hierarchical population structure (@code{genind} class), alleles counts by +populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It +also implements original multivariate methods (DAPC, sPCA), graphics, +statistical tests, simulation tools, distance and similarity measures, and +several spatial methods. A range of both empirical and simulated datasets is +also provided to illustrate various methods.") + (license license:gpl2+))) + +(define-public r-pegas + (package + (name "r-pegas") + (version "0.11") + (source + (origin + (method url-fetch) + (uri (cran-uri "pegas" version)) + (sha256 + (base32 + "0l21bapzbjcvblbvks3jh9rpy9hng1ccd7f0glhqw695lc737bpx")))) + (build-system r-build-system) + (propagated-inputs + `(("r-adegenet" ,r-adegenet) + ("r-ape" ,r-ape))) + (home-page "http://ape-package.ird.fr/pegas.html") + (synopsis "Population and evolutionary genetics analysis system") + (description + "This package provides functions for reading, writing, plotting, +analysing, and manipulating allelic and haplotypic data, including from VCF +files, and for the analysis of population nucleotide sequences and +micro-satellites including coalescent analyses, linkage disequilibrium, +population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, +minimum spanning tree and network, and median-joining networks.") + (license license:gpl2+))) + +(define-public r-rmetasim + (package + (name "r-rmetasim") + (version "3.1.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "rmetasim" version)) + (sha256 + (base32 + "0sz4mdprdi6sgkfwfdvh2hr9nxiwq17sw0vggq3cvs7lzb0i6m9r")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ade4" ,r-ade4) + ("r-adegenet" ,r-adegenet) + ("r-gtools" ,r-gtools) + ("r-pegas" ,r-pegas))) + (home-page "https://cran.r-project.org/web/packages/rmetasim") + (synopsis "Individual-based population genetic simulation environment") + (description + "This package provides an interface between R and the metasim simulation +engine. The simulation environment is documented in: Strand, A.(2002), +Metasim 1.0: an individual-based environment for simulating population +genetics of complex population dynamics.") + ;; Any GPL version + (license license:gpl2+))) + +(define-public r-genetics + (package + (name "r-genetics") + (version "1.3.8.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "genetics" version)) + (sha256 + (base32 + "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh")))) + (build-system r-build-system) + (propagated-inputs + `(("r-combinat" ,r-combinat) + ("r-gdata" ,r-gdata) + ("r-gtools" ,r-gtools) + ("r-mass" ,r-mass) + ("r-mvtnorm" ,r-mvtnorm))) + (home-page "https://cran.r-project.org/web/packages/genetics/") + (synopsis "Population genetics") + (description + "This package provides classes and methods for handling genetic data. +It includes classes to represent genotypes and haplotypes at single markers up +to multiple markers on multiple chromosomes. Function include allele +frequencies, flagging homo/heterozygotes, flagging carriers of certain +alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating +and testing for linkage disequilibrium, ...") + ;; Any GPL version. + (license license:gpl2+))) + +(define-public r-snp-plotter + (package + (name "r-snp-plotter") + (version "0.5.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "snp.plotter" version)) + (sha256 + (base32 + "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv")))) + (properties `((upstream-name . "snp.plotter"))) + (build-system r-build-system) + (propagated-inputs `(("r-genetics" ,r-genetics))) + (home-page "https://cran.r-project.org/web/packages/snp.plotter/") + (synopsis "Plot p-values using single SNP and/or haplotype data") + (description + "This package helps you create plots of p-values using single SNP and/or +haplotype data. Main features of the package include options to display a +@dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple +datasets simultaneously. Plots can be created using global and/or individual +haplotype p-values along with single SNP p-values. Images are created as +either PDF/EPS files.") + (license license:gpl2+))) + +(define-public r-polspline + (package + (name "r-polspline") + (version "1.1.14") + (source + (origin + (method url-fetch) + (uri (cran-uri "polspline" version)) + (sha256 + (base32 + "0g4s5nwi13yfs6b169yw8vrs48nvjyc014k2v7ybcxarl8z81va0")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/polspline/") + (synopsis "Polynomial spline routines") + (description + "This package provides routines for the polynomial spline fitting +routines hazard regression, hazard estimation with flexible tails, logspline, +lspec, polyclass, and polymars.") + (license license:gpl2+))) + +(define-public r-rms + (package + (name "r-rms") + (version "5.1-3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "rms" version)) + (sha256 + (base32 + "0drbr3g0x5pbxyzy50wnf92rbal8izizrcqslqhg0gsfg9adjih9")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-hmisc" ,r-hmisc) + ("r-htmltable" ,r-htmltable) + ("r-htmltools" ,r-htmltools) + ("r-lattice" ,r-lattice) + ("r-multcomp" ,r-multcomp) + ("r-nlme" ,r-nlme) + ("r-polspline" ,r-polspline) + ("r-quantreg" ,r-quantreg) + ("r-rpart" ,r-rpart) + ("r-sparsem" ,r-sparsem) + ("r-survival" ,r-survival))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "http://biostat.mc.vanderbilt.edu/rms") + (synopsis "Regression modeling strategies") + (description + "This is a package for regression modeling, testing, estimation, +validation, graphics, prediction, and typesetting by storing enhanced model +design attributes in the fit. The rms package is a collection of functions +that assist with and streamline modeling. It also contains functions for +binary and ordinal logistic regression models, ordinal models for continuous Y +with a variety of distribution families, and the Buckley-James multiple +regression model for right-censored responses, and implements penalized +maximum likelihood estimation for logistic and ordinary linear models. The +package works with almost any regression model, but it was especially written +to work with binary or ordinal regression models, Cox regression, accelerated +failure time models, ordinary linear models, the Buckley-James model, +generalized least squares for serially or spatially correlated observations, +generalized linear models, and quantile regression.") + (license license:gpl2+))) + +(define-public r-haplo-stats + (package + (name "r-haplo-stats") + (version "1.7.9") + (source + (origin + (method url-fetch) + (uri (cran-uri "haplo.stats" version)) + (sha256 + (base32 + "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx")))) + (properties `((upstream-name . "haplo.stats"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rms" ,r-rms))) + (native-inputs + `(("r-r-rsp" ,r-r-rsp))) ; for vignettes + (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software") + (synopsis "Analysis of haplotypes when linkage phase is ambiguous") + (description + "This package provides routines for the analysis of indirectly measured +haplotypes. The statistical methods assume that all subjects are unrelated +and that haplotypes are ambiguous (due to unknown linkage phase of the genetic +markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()}, +@code{haplo.score()}, and @code{haplo.power()}; all of which have detailed +examples in the vignette.") + (license license:gpl2+))) + +(define-public r-bqtl + (package + (name "r-bqtl") + (version "1.0-32") + (source + (origin + (method url-fetch) + (uri (cran-uri "bqtl" version)) + (sha256 + (base32 + "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/") + (synopsis "Bayesian QTL mapping toolkit") + (description + "This is a QTL mapping toolkit for inbred crosses and recombinant inbred +lines. It includes maximum likelihood and Bayesian tools.") + (license license:gpl2+))) + +(define-public r-ibdreg + (package + (name "r-ibdreg") + (version "0.2.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "ibdreg" version)) + (sha256 + (base32 + "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g")))) + (build-system r-build-system) + (home-page "https://www.mayo.edu/research/labs/\ +statistical-genetics-genetic-epidemiology/software") + (synopsis "Regression methods for IBD linkage with covariates") + (description + "This package provides a method to test genetic linkage with covariates +by regression methods with response IBD sharing for relative pairs. Account +for correlations of IBD statistics and covariates for relative pairs within +the same pedigree.") + (license license:gpl2+))) + +(define-public r-dlmap + (package + (name "r-dlmap") + (version "1.13") + (source + (origin + (method url-fetch) + (uri (cran-uri "dlmap" version)) + (sha256 + (base32 + "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ibdreg" ,r-ibdreg) + ("r-mgcv" ,r-mgcv) + ("r-nlme" ,r-nlme) + ("r-qtl" ,r-qtl) + ("r-wgaim" ,r-wgaim))) + (home-page "https://cran.r-project.org/web/packages/dlmap/") + (synopsis "Detection localization mapping for QTL") + (description + "This is package for QTL mapping in a mixed model framework with separate +detection and localization stages. The first stage detects the number of QTL +on each chromosome based on the genetic variation due to grouped markers on +the chromosome; the second stage uses this information to determine the most +likely QTL positions. The mixed model can accommodate general fixed and +random effects, including spatial effects in field trials and pedigree +effects. It is applicable to backcrosses, doubled haploids, recombinant +inbred lines, F2 intercrosses, and association mapping populations.") + (license license:gpl2))) + +(define-public r-ldheatmap + (package + (name "r-ldheatmap") + (version "0.99-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "LDheatmap" version)) + (sha256 + (base32 + "0il3g3n3bzv74lz7dlhyiwc2x2417v6yhx2g47pahxdzqa09kf4s")))) + (properties `((upstream-name . "LDheatmap"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genetics" ,r-genetics) + ("r-snpstats" ,r-snpstats))) + (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html") + (synopsis "Graphical display of pairwise linkage disequilibria between SNPs") + (description + "This package provides tools to produce a graphical display, as a heat +map, of measures of pairwise linkage disequilibria between SNPs. Users may +optionally include the physical locations or genetic map distances of each SNP +on the plot.") + (license license:gpl3))) + +(define-public r-hwde + (package + (name "r-hwde") + (version "0.67") + (source + (origin + (method url-fetch) + (uri (cran-uri "hwde" version)) + (sha256 + (base32 + "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/hwde/") + (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium") + (description + "This package fits models for genotypic disequilibria, as described in +Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast +terms are available that account for first order interactions between loci. +It also implements, for a single locus in a single population, a conditional +exact test for Hardy-Weinberg equilibrium.") + (license license:gpl2+))) + +(define-public r-tdthap + (package + (name "r-tdthap") + (version "1.1-9") + (source + (origin + (method url-fetch) + (uri (cran-uri "tdthap" version)) + (sha256 + (base32 + "0y01x0hcf0rw06cpn4pk17b0shf4v2c9was7vfs0zhsbq8qcwx7r")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/tdthap/") + (synopsis "TDT tests for extended haplotypes") + (description + "Functions and examples are provided for transmission/disequilibrium +tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999) +\"Transmission/disequilibrium tests for extended marker haplotypes\".") + (license license:artistic2.0))) + +(define-public r-sparql + (package + (name "r-sparql") + (version "1.16") + (source (origin + (method url-fetch) + (uri (cran-uri "SPARQL" version)) + (sha256 + (base32 + "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc")))) + (properties `((upstream-name . "SPARQL"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcurl" ,r-rcurl) + ("r-xml" ,r-xml))) + (home-page "https://cran.r-project.org/web/packages/SPARQL") + (synopsis "SPARQL client for R") + (description "This package provides an interface to use SPARQL to pose +SELECT or UPDATE queries to an end-point.") + ;; The only license indication is found in the DESCRIPTION file, + ;; which states GPL-3. So we cannot assume GPLv3+. + (license license:gpl3))) + +(define-public r-bookdown + (package + (name "r-bookdown") + (version "0.9") + (source (origin + (method url-fetch) + (uri (cran-uri "bookdown" version)) + (sha256 + (base32 + "0vg1s1w0l9pm95asqb21yf39mfk1nc9rdhmlys9xwr7p7i7rsz32")))) + (build-system r-build-system) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-knitr" ,r-knitr) + ("r-rmarkdown" ,r-rmarkdown) + ("r-tinytex" ,r-tinytex) + ("r-yaml" ,r-yaml) + ("r-xfun" ,r-xfun))) + (home-page "https://github.com/rstudio/bookdown") + (synopsis "Authoring books and technical documents with R markdown") + (description "This package provides output formats and utilities for +authoring books and technical documents with R Markdown.") + (license license:gpl3))) + +(define-public r-optparse + (package + (name "r-optparse") + (version "1.6.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "optparse" version)) + (sha256 + (base32 + "0zrp6jakjhawrwfri270ym83vj5a7nvjk0w6b41z41ahw2da99dm")))) + (build-system r-build-system) + (propagated-inputs + `(("r-getopt" ,r-getopt))) + (home-page "https://github.com/trevorld/optparse") + (synopsis "Command line option parser") + (description + "This package provides a command line parser inspired by Python's +@code{optparse} library to be used with Rscript to write shebang scripts +that accept short and long options.") + (license license:gpl2+))) + +(define-public r-wgcna + (package + (name "r-wgcna") + (version "1.67") + (source + (origin + (method url-fetch) + (uri (cran-uri "WGCNA" version)) + (sha256 + (base32 + "09387w85lxvwr8ax2i2h602b4dgfv4wbvsl9aj1q0b1vfs4rkk69")))) + (properties `((upstream-name . "WGCNA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-doparallel" ,r-doparallel) + ("r-dynamictreecut" ,r-dynamictreecut) + ("r-fastcluster" ,r-fastcluster) + ("r-foreach" ,r-foreach) + ("r-go-db" ,r-go-db) + ("r-hmisc" ,r-hmisc) + ("r-impute" ,r-impute) + ("r-rcpp" ,r-rcpp) + ("r-robust" ,r-robust) + ("r-survival" ,r-survival) + ("r-matrixstats" ,r-matrixstats) + ("r-preprocesscore" ,r-preprocesscore))) + (home-page + "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") + (synopsis "Weighted correlation network analysis") + (description + "This package provides functions necessary to perform Weighted +Correlation Network Analysis on high-dimensional data. It includes functions +for rudimentary data cleaning, construction and summarization of correlation +networks, module identification and functions for relating both variables and +modules to sample traits. It also includes a number of utility functions for +data manipulation and visualization.") + (license license:gpl2+))) + +(define-public r-kernlab + (package + (name "r-kernlab") + (version "0.9-27") + (source + (origin + (method url-fetch) + (uri (cran-uri "kernlab" version)) + (sha256 + (base32 + "1m0xqf6gyvwayz7w3c83y32ayvnlz0jicj8ijk808zq9sh7dbbgn")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/kernlab") + (synopsis "Kernel-based machine learning tools") + (description + "This package provides kernel-based machine learning methods for +classification, regression, clustering, novelty detection, quantile regression +and dimensionality reduction. Among other methods @code{kernlab} includes +Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes +and a QP solver.") + (license license:gpl2))) + +(define-public r-hierfstat + (package + (name "r-hierfstat") + (version "0.04-22") + (source + (origin + (method url-fetch) + (uri (cran-uri "hierfstat" version)) + (sha256 + (base32 + "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ade4" ,r-ade4) + ("r-adegenet" ,r-adegenet) + ("r-gtools" ,r-gtools))) + (home-page "https://cran.r-project.org/web/packages/hierfstat/") + (synopsis "Estimation and tests of hierarchical F-statistics") + (description + "This package allows the estimation of hierarchical F-statistics from +haploid or diploid genetic data with any numbers of levels in the hierarchy, +following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions +are also given to test via randomisations the significance of each F and +variance components, using the likelihood-ratio statistics G.") + (license license:gpl2+))) + +(define-public r-hapassoc + (package + (name "r-hapassoc") + (version "1.2-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "hapassoc" version)) + (sha256 + (base32 + "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s")))) + (build-system r-build-system) + (home-page "http://stat.sfu.ca/statgen/research/hapassoc.html") + (synopsis "Inference of trait associations with SNP haplotypes") + (description + "Hapassoc performs likelihood inference of trait associations with +haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The +functions are developed primarily for data collected in cohort or +cross-sectional studies. They can accommodate uncertain haplotype phase and +handle missing genotypes at some SNPs.") + (license license:gpl2))) + +(define-public r-sampling + (package + (name "r-sampling") + (version "2.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "sampling" version)) + (sha256 + (base32 + "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m")))) + (build-system r-build-system) + (propagated-inputs + `(("r-lpsolve" ,r-lpsolve) + ("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/sampling/") + (synopsis "Survey sampling") + (description + "This package provides functions for drawing and calibrating samples.") + (license license:gpl2+))) + +(define-public r-r2html + (package + (name "r-r2html") + (version "2.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "R2HTML" version)) + (sha256 + (base32 + "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9")))) + (properties `((upstream-name . "R2HTML"))) + (build-system r-build-system) + (home-page "https://github.com/nalimilan/R2HTML") + (synopsis "HTML export for R objects") + (description + "This package includes HTML functions and methods to write in an HTML +file. Thus, making HTML reports is easy. It includes a function that allows +redirection on the fly, which appears to be very useful for teaching purposes, +as the student can keep a copy of the produced output to keep all that they +did during the course. The package comes with a vignette describing how to +write HTML reports for statistical analysis. Finally, a driver for Sweave +allows to parse HTML flat files containing R code and to automatically write +the corresponding outputs (tables and graphs).") + (license license:gpl2+))) + +(define-public r-rjava + (package + (name "r-rjava") + (version "0.9-11") + (source + (origin + (method url-fetch) + (uri (cran-uri "rJava" version)) + (sha256 + (base32 + "0s9cjy1wh7snmbqwznh8f1r4ipylr7mgda4a979z963a8lqy32n2")))) + (properties `((upstream-name . "rJava"))) + (build-system r-build-system) + (arguments + `(#:modules ((guix build utils) + (guix build r-build-system) + (ice-9 match)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-JAVA_HOME + (lambda* (#:key inputs #:allow-other-keys) + (let ((jdk (assoc-ref inputs "jdk"))) + (setenv "JAVA_HOME" jdk) + (setenv "JAVA" (which "java")) + (setenv "JAR" (which "jar")) + (setenv "JAVAC" (which "javac")) + (setenv "JAVAH" (which "javah")) + (setenv "JAVA_CPPFLAGS" + (string-append "-I" jdk "/include " + "-I" jdk "/include/linux")) + (match (find-files (string-append jdk "/jre/lib/") "libjvm.so") + ((lib) (setenv "JAVA_LIBS" lib)) + (_ (error "Could not find libjvm.so")))) + #t))))) + (inputs + `(("icu4c" ,icu4c) + ("jdk" ,icedtea-8 "jdk") + ("pcre" ,pcre) + ("zlib" ,zlib))) + (home-page "http://www.rforge.net/rJava/") + (synopsis "Low-Level R to Java interface") + (description + "This package provides a low-level interface to the Java VM very much +like .C/.Call and friends. It allows the creation of objects, calling methods +and accessing fields.") + (license license:gpl2))) + +(define-public r-svmisc + (package + (name "r-svmisc") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "svMisc" version)) + (sha256 + (base32 + "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2")))) + (properties `((upstream-name . "svMisc"))) + (build-system r-build-system) + (home-page "https://github.com/SciViews/svMisc") + (synopsis "Miscellaneous functions for SciViews") + (description + "This package provides miscellaneous functions for SciViews or general +use, including tools to manage a temporary environment attached to the search +path for temporary variables you do not want to @code{save()} or +@code{load()}; test the current platform; showing progress bars, etc.") + (license license:gpl2))) + +(define-public r-xyz + (package + (name "r-xyz") + (version "0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "xyz" version)) + (sha256 + (base32 + "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/xyz/") + (synopsis "Algorithm for fast interaction search in high-dimensional data") + (description + "High dimensional interaction search by brute force requires a quadratic +computational cost in the number of variables. The xyz algorithm provably +finds strong interactions in almost linear time. For details of the algorithm +see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast +interaction search in high-dimensional data.") + ;; Any version of the GPL. + (license license:gpl2+))) + +(define-public r-rttf2pt1 + (package + (name "r-rttf2pt1") + (version "1.3.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "Rttf2pt1" version)) + (sha256 + (base32 + "12hf9r3mhjr9sawdvf7qhjf1zph2q64f77i81jwvy7awidbm0kja")))) + (properties `((upstream-name . "Rttf2pt1"))) + (build-system r-build-system) + (home-page "https://github.com/wch/Rttf2pt1") + (synopsis "Font conversion utility") + (description + "This package contains the program @code{ttf2pt1}, for use with the +@code{extrafont} package.") + ;; Most of the files are covered under the Expat license. Some files are + ;; covered under BSD-3. Deviations for individual files are recorded in + ;; the LICENSE file. + (license (list license:bsd-3 license:expat + (license:non-copyleft "file://LICENSE"))))) + +(define-public r-extrafontdb + (package + (name "r-extrafontdb") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "extrafontdb" version)) + (sha256 + (base32 + "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs")))) + (build-system r-build-system) + (home-page "https://github.com/wch/extrafontdb") + (synopsis "Database for the extrafont package") + (description + "This package holds the database for the @code{extrafont} package.") + (license license:gpl2))) + +(define-public r-extrafont + (package + (name "r-extrafont") + (version "0.17") + (source + (origin + (method url-fetch) + (uri (cran-uri "extrafont" version)) + (sha256 + (base32 + "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g")))) + (build-system r-build-system) + (propagated-inputs + `(("r-extrafontdb" ,r-extrafontdb) + ("r-rttf2pt1" ,r-rttf2pt1))) + (home-page "https://github.com/wch/extrafont") + (synopsis "Tools for using fonts in R") + (description + "The extrafont package makes it easier to use fonts other than the basic +PostScript fonts that R uses. Fonts that are imported into extrafont can be +used with PDF or PostScript output files. There are two hurdles for using +fonts in PDF (or Postscript) output files: + +@enumerate +@item Making R aware of the font and the dimensions of the characters. +@item Embedding the fonts in the PDF file so that the PDF can be displayed + properly on a device that doesn't have the font. This is usually needed if + you want to print the PDF file or share it with others. +@end enumerate + +The extrafont package makes both of these things easier.") + (license license:gpl2))) + +(define-public r-xkcd + (package + (name "r-xkcd") + (version "0.0.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "xkcd" version)) + (sha256 + (base32 + "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f")))) + (build-system r-build-system) + (propagated-inputs + `(("r-extrafont" ,r-extrafont) + ("r-ggplot2" ,r-ggplot2) + ("r-hmisc" ,r-hmisc))) + (home-page "https://cran.r-project.org/web/packages/xkcd/") + (synopsis "Plot ggplot2 graphics in the XKCD style") + (description + "This package provides the means to plot ggplot2 graphs in the style of +the XKCD web comic.") + (license license:gpl3))) + +(define-public r-msigdbr + (package + (name "r-msigdbr") + (version "6.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "msigdbr" version)) + (sha256 + (base32 + "1264j1hs74kq7hyh68vfynadfi6mdpq46qm1hnwzkzzhmbzpb9cg")))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-magrittr" ,r-magrittr) + ("r-rlang" ,r-rlang) + ("r-tibble" ,r-tibble))) + (home-page "https://github.com/igordot/msigdbr") + (synopsis "MSigDB gene sets for multiple organisms") + (description + "This package provides the @dfn{Molecular Signatures Database} (MSigDB) +gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA) +software in a standard R data frame with key-value pairs. Included are the +original human gene symbols and Entrez IDs as well as the equivalents for +various frequently studied model organisms such as mouse, rat, pig, fly, and +yeast.") + ;; The package is covered under the Expat license, but the upstream MSigDB + ;; files are made available under the Creative Commons Attribution 4.0 + ;; International license. + (license (list license:expat license:cc-by4.0)))) + +(define-public r-gridgraphics + (package + (name "r-gridgraphics") + (version "0.3-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "gridGraphics" version)) + (sha256 + (base32 + "1p94flvq5h3x817pl1m0aj3sim87x6zdbpv9xrgdnqw3rxfzwgqs")))) + (properties `((upstream-name . "gridGraphics"))) + (build-system r-build-system) + (home-page "https://github.com/pmur002/gridgraphics") + (synopsis "Redraw base graphics using @code{grid} graphics") + (description + "This package provides functions to convert a page of plots drawn with +the @code{graphics} package into identical output drawn with the @code{grid} +package. The result looks like the original @code{graphics}-based plot, but +consists of @code{grid} grobs and viewports that can then be manipulated with +@code{grid} functions (e.g., edit grobs and revisit viewports).") + (license license:gpl2+))) + +(define-public r-farver + (package + (name "r-farver") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "farver" version)) + (sha256 + (base32 + "1dllgx121al374gyp9pjv1m8ip4imm8zhbgyh1970dsz2c4z71i0")))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/thomasp85/farver") + (synopsis "Vectorized color conversion and comparison") + (description + "The encoding of color can be handled in many different ways, using +different color spaces. As different color spaces have different uses, +efficient conversion between these representations are important. This +package provides a set of functions that gives access to very fast color space +conversion and comparisons implemented in C++, and offers 100-fold speed +improvements over the @code{convertColor} function in the @code{grDevices} +package.") + (license license:expat))) + +(define-public r-ggplotify + (package + (name "r-ggplotify") + (version "0.0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggplotify" version)) + (sha256 + (base32 + "14hqlpvnaq5psz1ljcpw9isa06827rg3fm5c1dx159rsjfi56yby")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gridgraphics" ,r-gridgraphics) + ("r-rvcheck" ,r-rvcheck))) + (home-page "https://github.com/GuangchuangYu/ggplotify") + (synopsis "Convert plots to @code{grob} or @code{ggplot} object") + (description + "This package provides tools to convert plot function calls (using +expression or formula) to @code{grob} or @code{ggplot} objects that are +compatible with the @code{grid} and @code{ggplot2} environment. With this +package, we are able to e.g. use @code{cowplot} to align plots produced by +@code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by +converting them to @code{ggplot} objects.") + (license license:artistic2.0))) + +(define-public r-triebeard + (package + (name "r-triebeard") + (version "0.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "triebeard" version)) + (sha256 + (base32 + "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz")))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/Ironholds/triebeard/") + (synopsis "Radix trees in Rcpp") + (description + "Radix trees, or tries, are key-value data structures optimized for +efficient lookups, similar in purpose to hash tables. This package provides +an implementation of radix trees for use in R programming and in developing +packages with Rcpp.") + (license license:expat))) + +(define-public r-tweenr + (package + (name "r-tweenr") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "tweenr" version)) + (sha256 + (base32 + "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg")))) + (build-system r-build-system) + (propagated-inputs + `(("r-farver" ,r-farver) + ("r-magrittr" ,r-magrittr) + ("r-rcpp" ,r-rcpp) + ("r-rlang" ,r-rlang))) + (home-page "https://github.com/thomasp85/tweenr") + (synopsis "Interpolate data for smooth animations") + (description + "In order to create smooth animation between states of data, tweening is +necessary. This package provides a range of functions for creating tweened +data that can be used as basis for animation. Furthermore it adds a number of +vectorized interpolaters for common R data types such as numeric, date and +color.") + (license license:expat))) + +(define-public r-polyclip + (package + (name "r-polyclip") + (version "1.10-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "polyclip" version)) + (sha256 + (base32 + "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl")))) + (build-system r-build-system) + (native-inputs `(("pkg-config" ,pkg-config))) + (home-page "http://www.angusj.com/delphi/clipper.php") + (synopsis "Polygon clipping") + (description + "This package provides an R port of the library Clipper. It performs +polygon clipping operations (intersection, union, set minus, set difference) +for polygonal regions of arbitrary complexity, including holes. It computes +offset polygons (spatial buffer zones, morphological dilations, Minkowski +dilations) for polygonal regions and polygonal lines. It computes the +Minkowski Sum of general polygons. There is a function for removing +self-intersections from polygon data.") + (license license:boost1.0))) + +(define-public r-urltools + (package + (name "r-urltools") + (version "1.7.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "urltools" version)) + (sha256 + (base32 + "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-triebeard" ,r-triebeard))) + (home-page "https://github.com/Ironholds/urltools/") + (synopsis "Vectorized tools for URL handling and parsing") + (description + "This package provides a toolkit for all URL-handling needs, including +encoding and decoding, parsing, parameter extraction and modification. All +functions are designed to be both fast and entirely vectorized. It is +intended to be useful for people dealing with web-related datasets, such as +server-side logs, although may be useful for other situations involving large +sets of URLs.") + (license license:expat))) + +(define-public r-ggforce + (package + (name "r-ggforce") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggforce" version)) + (sha256 + (base32 + "0snxx9zhcccxa7pz9pf3bjqmcmv9mz4m47v81hklnhm25jj40xg2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gtable" ,r-gtable) + ("r-mass" ,r-mass) + ("r-polyclip" ,r-polyclip) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-rlang" ,r-rlang) + ("r-scales" ,r-scales) + ("r-tweenr" ,r-tweenr))) + (home-page "https://ggforce.data-imaginist.com") + (synopsis "Accelerating ggplot2") + (description + "The aim of the ggplot2 package is to aid in visual data investigations. +This focus has led to a lack of facilities for composing specialized plots. +Thi package aims to be a collection of mainly new statistics and geometries +that fills this gap.") + (license license:expat))) + +(define-public r-europepmc + (package + (name "r-europepmc") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "europepmc" version)) + (sha256 + (base32 + "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h")))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-httr" ,r-httr) + ("r-jsonlite" ,r-jsonlite) + ("r-plyr" ,r-plyr) + ("r-progress" ,r-progress) + ("r-purrr" ,r-purrr) + ("r-urltools" ,r-urltools) + ("r-xml2" ,r-xml2))) + (home-page "https://github.com/ropensci/europepmc/") + (synopsis "R Interface to the Europe PubMed Central RESTful Web Service") + (description + "This package provides an R Client for the +@url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web +Service}. It gives access to both metadata on life science literature and +open access full texts. Europe PMC indexes all PubMed content and other +literature sources including Agricola, a bibliographic database of citations +to the agricultural literature, or Biological Patents. In addition to +bibliographic metadata, the client allows users to fetch citations and +reference lists. Links between life-science literature and other EBI +databases, including ENA, PDB or ChEMBL are also accessible.") + (license license:gpl3))) + +(define-public r-ggraph + (package + (name "r-ggraph") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggraph" version)) + (sha256 + (base32 + "0fpmp326mryd1k1qvacjadksrnhbla8h960i18lmrimzrag7692c")))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-dplyr" ,r-dplyr) + ("r-ggforce" ,r-ggforce) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-gtable" ,r-gtable) + ("r-igraph" ,r-igraph) + ("r-mass" ,r-mass) + ("r-plyr" ,r-plyr) + ("r-rcpp" ,r-rcpp) + ("r-scales" ,r-scales) + ("r-viridis" ,r-viridis))) + (home-page "https://cran.r-project.org/web/packages/ggraph/") + (synopsis "Implementation of grammar of graphics for graphs and networks") + (description + "The grammar of graphics as implemented in ggplot2 is a poor fit for +graph and network visualizations due to its reliance on tabular data input. +The ggraph package is an extension of the ggplot2 API tailored to graph +visualizations and provides the same flexible approach to building up plots +layer by layer.") + (license license:gpl3))) + +(define-public r-varselrf + (package + (name "r-varselrf") + (version "0.7-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "varSelRF" version)) + (sha256 + (base32 + "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i")))) + (properties `((upstream-name . "varSelRF"))) + (build-system r-build-system) + (propagated-inputs + `(("r-randomforest" ,r-randomforest))) + (home-page "http://ligarto.org/rdiaz/Software/Software.html") + (synopsis "Variable selection using random forests") + (description + "This package provides tools for the variable selection from random +forests using both backwards variable elimination (for the selection of small +sets of non-redundant variables) and selection based on the importance +spectrum (somewhat similar to scree plots; for the selection of large, +potentially highly-correlated variables). The main applications are in +high-dimensional data (e.g., microarray data, and other genomics and +proteomics applications).") + (license license:gpl2+))) + +(define-public r-pamr + (package + (name "r-pamr") + (version "1.56.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "pamr" version)) + (sha256 + (base32 + "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh")))) + (build-system r-build-system) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-survival" ,r-survival))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/pamr/") + (synopsis "Prediction Analysis for Microarrays") + (description + "This package provides some functions for sample classification in +microarrays.") + (license license:gpl2))) + +(define-public r-rda + (package + (name "r-rda") + (version "1.0.2-2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "rda" version)) + (sha256 + (base32 + "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/rda/") + (synopsis "Shrunken centroids regularized discriminant analysis") + (description + "This package provides tools for shrunken centroids regularized +discriminant analysis for the purpose of classifying high dimensional data.") + (license license:gpl2+))) + +(define-public r-ggvis + (package + (name "r-ggvis") + (version "0.4.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggvis" version)) + (sha256 + (base32 + "1bxggjr2313kfy895j0fvrv4bg7yh2z87907lk48i1kn5c9flchk")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-dplyr" ,r-dplyr) + ("r-htmltools" ,r-htmltools) + ("r-jsonlite" ,r-jsonlite) + ("r-lazyeval" ,r-lazyeval) + ("r-magrittr" ,r-magrittr) + ("r-shiny" ,r-shiny))) + (home-page "https://ggvis.rstudio.com/") + (synopsis "Interactive grammar of graphics") + (description + "This package is a data visualization package for R providing an +implementation of an interactive grammar of graphics, taking the best parts of +ggplot2, combining them with the reactive framework of Shiny and drawing web +graphics using Vega.") + (license license:gpl2))) + +(define-public r-gbm + (package + (name "r-gbm") + (version "2.1.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "gbm" version)) + (sha256 + (base32 + "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6")))) + (build-system r-build-system) + (propagated-inputs + `(("r-gridextra" ,r-gridextra) + ("r-lattice" ,r-lattice) + ("r-survival" ,r-survival))) + (home-page "https://github.com/gbm-developers/gbm") + (synopsis "Generalized boosted regression models") + (description + "This package is an implementation of extensions to Freund and Schapire's +AdaBoost algorithm and Friedman's gradient boosting machine. It includes +regression methods for least squares, absolute loss, t-distribution loss, +quantile regression, logistic, multinomial logistic, Poisson, Cox proportional +hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss, +and Learning to Rank measures (LambdaMart).") + (license license:gpl2+))) + +(define-public r-threejs + (package + (name "r-threejs") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "threejs" version)) + (sha256 + (base32 + "1s3rdlzy7man6177ycayg6xsh6k8y1r9rdj9yzn3b93j2rs0nxbi")))) + (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" + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "js-jquery") + "htmlwidgets/lib/jquery/jquery.min.js") + (,(assoc-ref inputs "js-threejs-85") + "htmlwidgets/lib/threejs-85/three.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #t "Processing ~a --> ~a~%" + source target) + (delete-file target) + (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) + (call-with-output-file target + (lambda (port) + (dump-port minified port))))) + sources targets)))) + #t))))) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-crosstalk" ,r-crosstalk) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-igraph" ,r-igraph))) + (native-inputs + `(("uglify-js" ,uglify-js) + ("js-jquery" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-3.3.1.js") + (sha256 + (base32 + "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))) + ("js-threejs-85" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/mrdoob/three.js/r85/build/three.js") + (sha256 + (base32 + "17khh3dmijdjw4qb9qih1rqhxgrmm3pc6w8lzdx6rf6a3mrc9xnl")))))) + (home-page "https://bwlewis.github.io/rthreejs") + (synopsis "Interactive 3D scatter plots, networks and globes") + (description + "Create interactive 3D scatter plots, network plots, and globes in R +using the three.js visualization library.") + (license license:expat))) + +(define-public r-mlbench + (package + (name "r-mlbench") + (version "2.1-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "mlbench" version)) + (sha256 + (base32 + "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/mlbench/") + (synopsis "Machine learning benchmark problems") + (description + "This package provides a collection of artificial and real-world machine +learning benchmark problems, including, e.g., several data sets from the UCI +repository.") + (license license:gpl2))) + +(define-public r-mpm + (package + (name "r-mpm") + (version "1.0-22") + (source + (origin + (method url-fetch) + (uri (cran-uri "mpm" version)) + (sha256 + (base32 + "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk")))) + (build-system r-build-system) + (propagated-inputs + `(("r-kernsmooth" ,r-kernsmooth) + ("r-mass" ,r-mass))) + (home-page "http://mpm.r-forge.r-project.org") + (synopsis "Multivariate projection methods") + (description + "This is a package for exploratory graphical analysis of multivariate +data, specifically gene expression data with different projection methods: +principal component analysis, correspondence analysis, spectral map +analysis.") + (license license:gpl2+))) + +(define-public r-png + (package + (name "r-png") + (version "0.1-7") + (source (origin + (method url-fetch) + (uri (cran-uri "png" version)) + (sha256 + (base32 + "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2")))) + (build-system r-build-system) + (inputs + `(("libpng" ,libpng) + ("zlib" ,zlib))) + (home-page "http://www.rforge.net/png/") + (synopsis "Read and write PNG images") + (description + "This package provides an easy and simple way to read, write and display +bitmap images stored in the PNG format. It can read and write both files and +in-memory raw vectors.") + ;; Any of these GPL versions. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-ggcorrplot + (package + (name "r-ggcorrplot") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggcorrplot" version)) + (sha256 + (base32 + "12sxvd9kjgszpbk35m7fj1wv7x40bp79c0g0by1xax70r3495h93")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-reshape2" ,r-reshape2))) + (home-page "http://www.sthda.com/english/wiki/ggcorrplot") + (synopsis "Visualization of a correlation matrix using ggplot2") + (description + "The ggcorrplot package can be used to visualize easily a correlation +matrix using ggplot2. It provides a solution for reordering the correlation +matrix and displays the significance level on the plot. It also includes a +function for computing a matrix of correlation p-values.") + (license license:gpl2))) + +(define-public r-flexdashboard + (package + (name "r-flexdashboard") + (version "0.5.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "flexdashboard" version)) + (sha256 + (base32 + "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x")))) + (build-system r-build-system) + (arguments + `(#:modules ((guix build utils) + (guix build r-build-system) + (srfi srfi-1) + (srfi srfi-26) + (ice-9 popen) + (ice-9 textual-ports)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst" + ;; Concatenate all components of prism.js + (let ((contents (string-join + (map (lambda (name) + (call-with-input-file + (assoc-ref inputs name) + get-string-all)) + (list "js-prism" + "js-prism-r" + "js-prism-line-numbers")) + "\n"))) + (call-with-output-file "prism-src.js" + (cut display contents <>))) + (call-with-values + (lambda () + (unzip2 + `(("www/stickytableheaders/jquery.stickytableheaders.js" + "www/stickytableheaders/jquery.stickytableheaders.min.js") + ("www/sly/sly.js" + "www/sly/sly.min.js") + ("prism-src.js" + "www/prism/prism.js") + (,(assoc-ref inputs "js-raphael") + "htmlwidgets/lib/raphael/raphael-2.1.4.min.js") + (,(assoc-ref inputs "js-featherlight") + "www/featherlight/featherlight.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #t "Processing ~a --> ~a~%" + source target) + (delete-file target) + (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) + (call-with-output-file target + (lambda (port) + (dump-port minified port))))) + sources targets)))) + #t))))) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-jsonlite" ,r-jsonlite) + ("r-knitr" ,r-knitr) + ("r-rmarkdown" ,r-rmarkdown) + ("r-shiny" ,r-shiny))) + (native-inputs + `(("uglify-js" ,uglify-js) + ("js-raphael" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js") + (sha256 + (base32 + "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x")))) + ("js-prism" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js") + (sha256 + (base32 + "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c")))) + ("js-prism-r" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js") + (sha256 + (base32 + "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki")))) + ("js-prism-line-numbers" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js") + (sha256 + (base32 + "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991")))) + ("js-featherlight" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js") + (sha256 + (base32 + "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb")))))) + (home-page "https://rmarkdown.rstudio.com/flexdashboard") + (synopsis "R Markdown format for flexible dashboards") + (description + "This package provides an R Markdown format for converting an R Markdown +document to a grid-oriented dashboard. The dashboard flexibly adapts the size +of its components to the containing web page.") + (license license:expat))) + +(define-public r-preseqr + (package + (name "r-preseqr") + (version "4.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "preseqR" version)) + (sha256 + (base32 + "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1")))) + (properties `((upstream-name . "preseqR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-polynom" ,r-polynom))) + (home-page "https://cran.r-project.org/web/packages/preseqR/") + (synopsis "Predicting species accumulation curves") + (description + "This package can be used to predict the r-species accumulation +curve (r-SAC), which is the number of species represented at least r times as +a function of the sampling effort. When r = 1, the curve is known as the +species accumulation curve, or the library complexity curve in high-throughput +genomic sequencing. The package includes both parametric and nonparametric +methods, as described by Deng C, et al. (2018).") + (license license:gpl3))) + +(define-public r-mapplots + (package + (name "r-mapplots") + (version "1.5.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "mapplots" version)) + (sha256 + (base32 + "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/mapplots/") + (synopsis "Data visualization on maps") + (description + "This package helps you create simple maps; add sub-plots like pie plots +to a map or any other plot; format, plot and export gridded data. The package +was developed for displaying fisheries data but most functions can be used for +more generic data visualisation.") + (license license:gpl2+))) + +(define-public r-pmcmr + (package + (name "r-pmcmr") + (version "4.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "PMCMR" version)) + (sha256 + (base32 + "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij")))) + (properties `((upstream-name . "PMCMR"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/PMCMR/") + (synopsis "Calculate pairwise multiple comparisons of mean rank sums") + (description + "This is a deprecated package for calculating pairwise multiple +comparisons of mean rank sums. This package is superseded by the novel +PMCMRplus package. The PMCMR package is no longer maintained, but kept for +compatibility of reverse depending packages for some time.") + (license license:gpl3+))) + +(define-public r-downloader + (package + (name "r-downloader") + (version "0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "downloader" version)) + (sha256 + (base32 + "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q")))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest))) + (home-page "https://github.com/wch/downloader") + (synopsis "Download files over HTTP and HTTPS") + (description + "This package provides a wrapper for the @code{download.file} function, +making it possible to download files over HTTPS across platforms. The +@code{RCurl} package provides this functionality (and much more) but has +external dependencies. This package has is implemented purely in R.") + (license license:gpl2))) + +(define-public r-rex + (package + (name "r-rex") + (version "1.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "rex" version)) + (sha256 + (base32 + "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x")))) + (build-system r-build-system) + (propagated-inputs + `(("r-lazyeval" ,r-lazyeval) + ("r-magrittr" ,r-magrittr))) + (home-page "https://github.com/kevinushey/rex") + (synopsis "Friendly regular expressions") + (description + "This package provides a friendly interface for the construction of +regular expressions. Regular expressions are a very powerful feature, however +they are often difficult to interpret. Rex allows you to build complex +regular expressions from human readable expressions") + (license license:expat))) + +(define-public r-sctransform + (package + (name "r-sctransform") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "sctransform" version)) + (sha256 + (base32 + "1r5kiqqs318q59h2i8m7c6nhghp9w6q26ss2y5a390lkhsawgx6p")))) + (build-system r-build-system) + (propagated-inputs + `(("r-future" ,r-future) + ("r-future-apply" ,r-future-apply) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-reshape2" ,r-reshape2))) + (home-page "https://github.com/ChristophH/sctransform") + (synopsis "Variance stabilizing transformations for Single Cell UMI Data") + (description + "This package provides a normalization method for single-cell UMI count +data using a variance stabilizing transformation. The transformation is based +on a negative binomial regression model with regularized parameters. As part +of the same regression framework, this package also provides functions for +batch correction, and data correction.") + (license license:gpl3))) + +(define-public r-styler + (package + (name "r-styler") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "styler" version)) + (sha256 + (base32 + "1z24mi88snbz1avjw9phq0lzmigddvycc56s83nxzr9w9z85mh05")))) + (build-system r-build-system) + (propagated-inputs + `(("r-backports" ,r-backports) + ("r-cli" ,r-cli) + ("r-magrittr" ,r-magrittr) + ("r-purrr" ,r-purrr) + ("r-rematch2" ,r-rematch2) + ("r-rlang" ,r-rlang) + ("r-rprojroot" ,r-rprojroot) + ("r-tibble" ,r-tibble) + ("r-withr" ,r-withr) + ("r-xfun" ,r-xfun))) + (home-page "https://github.com/r-lib/styler") + (synopsis "Non-invasive pretty printing of R code") + (description + "This is a package for pretty-printing R code without changing the user's +formatting intent.") + (license license:gpl3))) |