diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 451 |
1 files changed, 440 insertions, 11 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ec950ce0ac..6ce9bdd16f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -32,11 +32,15 @@ #:use-module (guix download) #:use-module (guix utils) #:use-module (guix build-system r) + #:use-module (gnu packages base) #:use-module (gnu packages compression) + #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) + #:use-module (gnu packages gl) #:use-module (gnu packages gnome) #:use-module (gnu packages gtk) #:use-module (gnu packages haskell) + #:use-module (gnu packages image) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) @@ -45,7 +49,8 @@ #:use-module (gnu packages python) #:use-module (gnu packages statistics) #:use-module (gnu packages tls) - #:use-module (gnu packages web)) + #:use-module (gnu packages web) + #:use-module (gnu packages xorg)) (define-public r-clipr (package @@ -566,14 +571,16 @@ you to rapidly iterate while developing a package.") (define-public r-rcpp (package (name "r-rcpp") - (version "0.12.19") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "10mmiaawv9iwglc6z4y51mdpsfb1sivqmwr6xnfqkllcnpabdbk3")))) + (base32 "1hlbw4k79q9ich4w27b01gsvwrsnrflii8zjlcmgfzm1vpq8ndxp")))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ integration") (description @@ -2042,17 +2049,18 @@ Laplace approximation and adaptive Gauss-Hermite quadrature.") (define-public r-jomo (package (name "r-jomo") - (version "2.6-4") + (version "2.6-5") (source (origin (method url-fetch) (uri (cran-uri "jomo" version)) (sha256 (base32 - "05g2rj9g7rgyb22b0gybw042nydyqsqsb31v05hifzavri8ij01x")))) + "109q5m69clrvvialxdxznd0wdb54ajhx84nj8slx8bf909a427mj")))) (build-system r-build-system) (propagated-inputs `(("r-lme4" ,r-lme4) + ("r-mass" ,r-mass) ("r-ordinal" ,r-ordinal) ("r-survival" ,r-survival))) (home-page "https://cran.r-project.org/web/packages/jomo/") @@ -3071,6 +3079,26 @@ Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden, Cambridge University Press, 1993.") (license license:gpl2))) +(define-public r-aggregation + (package + (name "r-aggregation") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "aggregation" version)) + (sha256 + (base32 + "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/aggregation/") + (synopsis "Methods for p-value aggregation") + (description + "This package contains functionality for performing the following methods +of p-value aggregation: Fisher's method, the Lancaster method (weighted +Fisher's method), and Sidak correction.") + (license license:gpl3))) + (define-public r-quantmod (package (name "r-quantmod") @@ -3452,6 +3480,36 @@ dendrograms.") ;; Either version of the license. (license (list license:gpl2 license:gpl3)))) +(define-public r-h5 + (package + (name "r-h5") + (version "0.9.9") + (source + (origin + (method url-fetch) + (uri (cran-uri "h5" version)) + (sha256 + (base32 + "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx")))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib) + ("hdf5" ,hdf5))) + (native-inputs + `(("which" ,which))) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/mannau/h5") + (synopsis "Interface to the HDF5 Library") + (description + "This package provides an S4 interface to the HDF5 library supporting +fast storage and retrieval of R-objects like vectors, matrices and arrays to +binary files in a language independent format. The HDF5 format can therefore +be used as an alternative to R's save/load mechanism. Since h5 is able to +access only subsets of stored data it can also handle data sets which do not +fit into memory.") + (license license:bsd-2))) + (define-public r-cgdsr (package (name "r-cgdsr") @@ -4392,14 +4450,14 @@ and adds the annotation to the plot.") (define-public r-ggpubr (package (name "r-ggpubr") - (version "0.1.8") + (version "0.1.9") (source (origin (method url-fetch) (uri (cran-uri "ggpubr" version)) (sha256 (base32 - "0psl2zndm4wk6nnj1nv305islpxfvfgd87gjh2ph8yqn4mxpnfi1")))) + "0rvfgii2gxarra7d33n6c63ky0mivxxyx35acsrn94xkbd8mbcsj")))) (build-system r-build-system) (propagated-inputs `(("r-cowplot" ,r-cowplot) @@ -4670,6 +4728,32 @@ Extract argument descriptions and other parts of the help pages of functions.") (license license:gpl2+))) +(define-public r-rjags + (package + (name "r-rjags") + (version "4-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "rjags" version)) + (sha256 + (base32 + "17xmjksj69f9wk4x71jxk4cgiqhaf2fj6bjm0mgzp4qln5x84a8m")))) + (build-system r-build-system) + (propagated-inputs + `(("r-coda" ,r-coda))) + (inputs + `(("jags" ,jags))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "http://mcmc-jags.sourceforge.net") + (synopsis "Bayesian graphical models using MCMC") + (description + "This package provides an R interface to the JAGS MCMC library. JAGS is +Just Another Gibbs Sampler. It is a program for analysis of Bayesian +hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") + (license license:gpl2))) + (define-public r-rdpack (package (name "r-rdpack") @@ -4732,6 +4816,112 @@ be added or removed. When working with Word documents, a cursor can be used to help insert or delete content at a specific location in the document.") (license license:gpl3))) +(define-public r-abn + (package + (name "r-abn") + (version "1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "abn" version)) + (sha256 + (base32 + "00k0razgdb5y5f62622fm7rxkcxrxg470nyyb02dvpfp60254kvs")))) + (build-system r-build-system) + (inputs + `(("gsl" ,gsl))) + (propagated-inputs + `(("r-cairo" ,r-cairo) + ("r-lme4" ,r-lme4) + ("r-mass" ,r-mass) + ("r-nnet" ,r-nnet) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rjags" ,r-rjags))) + (home-page "http://www.r-bayesian-networks.org") + (synopsis "Modelling multivariate data with additive bayesian networks") + (description + "Bayesian network analysis is a form of probabilistic graphical models +which derives from empirical data a directed acyclic graph, DAG, describing +the dependency structure between random variables. An additive Bayesian +network model consists of a form of a DAG where each node comprises a +@dfn{generalized linear model} (GLM). Additive Bayesian network models are +equivalent to Bayesian multivariate regression using graphical modelling, they +generalises the usual multivariable regression, GLM, to multiple dependent +variables. This package provides routines to help determine optimal Bayesian +network models for a given data set, where these models are used to identify +statistical dependencies in messy, complex data.") + (license license:gpl2+))) + +(define-public r-acd + (package + (name "r-acd") + (version "1.5.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACD" version)) + (sha256 + (base32 + "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6")))) + (properties `((upstream-name . "ACD"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/ACD/") + (synopsis "Categorical data analysis with complete or missing responses") + (description + "This package provides tools for categorical data analysis with complete +or missing responses.") + (license license:gpl2+))) + +(define-public r-acdm + (package + (name "r-acdm") + (version "1.0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "ACDm" version)) + (sha256 + (base32 + "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil")))) + (properties `((upstream-name . "ACDm"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-plyr" ,r-plyr) + ("r-rsolnp" ,r-rsolnp) + ("r-zoo" ,r-zoo))) + (home-page "https://cran.r-project.org/web/packages/ACDm/") + (synopsis "Tools for Autoregressive Conditional Duration Models") + (description + "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle +and Russell, 1998) models. It creates trade, price or volume durations from +transactions (tic) data, performs diurnal adjustments, fits various ACD models +and tests them.") + (license license:gpl2+))) + +(define-public r-overlap + (package + (name "r-overlap") + (version "0.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "overlap" version)) + (sha256 + (base32 + "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/overlap/") + (synopsis "Estimates of coefficient of overlapping for animal activity patterns") + (description + "This package provides functions to fit kernel density functions to data +on temporal activity patterns of animals; estimate coefficients of overlapping +of densities for two species; and calculate bootstrap estimates of confidence +intervals.") + (license license:gpl3+))) + (define-public r-snakecase (package (name "r-snakecase") @@ -6507,14 +6697,14 @@ Bayesian modeling.") (define-public r-tmb (package (name "r-tmb") - (version "1.7.14") + (version "1.7.15") (source (origin (method url-fetch) (uri (cran-uri "TMB" version)) (sha256 (base32 - "0bpc504nz8xfwr8ack52dj4hpjcykn6zyf8n228z32dw9d5n96dl")))) + "1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs")))) (properties `((upstream-name . "TMB"))) (build-system r-build-system) (propagated-inputs @@ -6885,14 +7075,14 @@ directories or URLs with their associated programs.") (define-public r-rcmdcheck (package (name "r-rcmdcheck") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "rcmdcheck" version)) (sha256 (base32 - "1ga19jqix0zs7xyz2j155zyagwbv22r6dgv55g6wdjigc67qfsix")))) + "0ys1nd7690mhwzslyzg8fq1wxr28nz8g6av5iykkrshb8lkxg7ly")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) @@ -7325,3 +7515,242 @@ netCDF files.") "This package provides a convenient tool to install and update Bioconductor packages.") (license license:artistic2.0))) + +(define-public r-rgl + (package + (name "r-rgl") + (version "0.99.16") + (source + (origin + (method url-fetch) + (uri (cran-uri "rgl" version)) + (sha256 + (base32 + "0q8sg8fr0140ilssqhscaxkjc29w1rpp6f4k50amw3zzs9g58ak9")))) + (build-system r-build-system) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("freetype" ,freetype) + ("libpng" ,libpng) + ("glu" ,glu) + ("libx11" ,libx11) + ("ghc-pandoc" ,ghc-pandoc) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-crosstalk" ,r-crosstalk) + ("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-jsonlite" ,r-jsonlite) + ("r-knitr" ,r-knitr) + ("r-magrittr" ,r-magrittr) + ("r-manipulatewidget" ,r-manipulatewidget) + ("r-shiny" ,r-shiny))) + (home-page "https://r-forge.r-project.org/projects/rgl/") + (synopsis "3D visualization using OpenGL") + (description + "This package provides medium to high level functions for 3D interactive graphics, +including functions modelled on base graphics (@code{plot3d()}, etc.) as well +as functions for constructing representations of geometric +objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to +various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D +image formats, including PNG, Postscript, SVG, PGF.") + ;; Any version of the GPL. + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-multicool + (package + (name "r-multicool") + (version "0.1-10") + (source + (origin + (method url-fetch) + (uri (cran-uri "multicool" version)) + (sha256 + (base32 + "1ybg9piya9psqg42w9i3zsnavbxhkfklfwl7cb420i5nkq6wpc2v")))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/multicool/") + (synopsis "Permutations of multisets in cool-lex order") + (description + "This package provides a set of tools to permute multisets without loops +or hash tables and to generate integer partitions. Cool-lex order is similar +to colexicographical order.") + (license license:gpl2))) + +(define-public r-misc3d + (package + (name "r-misc3d") + (version "0.8-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "misc3d" version)) + (sha256 + (base32 + "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/misc3d/") + (synopsis "Miscellaneous 3D Plots") + (description + "This package provides a collection of miscellaneous 3d plots, including +isosurfaces.") + ;; Any version of the GPL. + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-ks + (package + (name "r-ks") + (version "1.11.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "ks" version)) + (sha256 + (base32 + "0z749c3xzpf6n0g7xcfplrhap1di8k7kcfr7vigh95ywnigyhs8d")))) + (build-system r-build-system) + (propagated-inputs + `(("r-fnn" ,r-fnn) + ("r-kernlab" ,r-kernlab) + ("r-kernsmooth" ,r-kernsmooth) + ("r-matrix" ,r-matrix) + ("r-mclust" ,r-mclust) + ("r-mgcv" ,r-mgcv) + ("r-misc3d" ,r-misc3d) + ("r-multicool" ,r-multicool) + ("r-mvtnorm" ,r-mvtnorm))) + (home-page "http://www.mvstat.net/tduong/") + (synopsis "Kernel smoothing") + (description + "This package provides kernel smoothers for univariate and multivariate +data, including density functions, density derivatives, cumulative +distributions, modal clustering, discriminant analysis, and two-sample +hypothesis testing.") + ;; Either version of the GPL. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-feature + (package + (name "r-feature") + (version "1.2.13") + (source + (origin + (method url-fetch) + (uri (cran-uri "feature" version)) + (sha256 + (base32 + "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ks" ,r-ks) + ("r-misc3d" ,r-misc3d) + ("r-rgl" ,r-rgl))) + (home-page "http://www.mvstat.net/tduong/") + (synopsis "Inferential feature significance for kernel density estimation") + (description + "The feature package contains functions to display and compute kernel +density estimates, significant gradient and significant curvature regions. +Significant gradient and/or curvature regions often correspond to significant +features (e.g. local modes).") + ;; Either version of the GPL. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-arm + (package + (name "r-arm") + (version "1.10-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "arm" version)) + (sha256 + (base32 + "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg")))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-coda" ,r-coda) + ("r-lme4" ,r-lme4) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-nlme" ,r-nlme))) + (home-page "https://cran.r-project.org/web/packages/arm/") + (synopsis "Data analysis using regression and multilevel/hierarchical models") + (description + "This package provides functions to accompany A. Gelman and J. Hill, +Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge +University Press, 2007.") + (license license:gpl3+))) + +(define-public r-circular + (package + (name "r-circular") + (version "0.4-93") + (source + (origin + (method url-fetch) + (uri (cran-uri "circular" version)) + (sha256 + (base32 + "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn")))) + (build-system r-build-system) + (propagated-inputs + `(("r-boot" ,r-boot) + ("r-mvtnorm" ,r-mvtnorm))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/circular/") + (synopsis "Circular statistics") + (description + "This package provides tools for circular statistics, from \"Topics in +circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World +Scientific.") + (license license:gpl2+))) + +(define-public r-activity + (package + (name "r-activity") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "activity" version)) + (sha256 + (base32 + "1lqajgxfps2h6amz1791vp3f52rs9ghmanq1nqfxqd2jmk3idkrx")))) + (build-system r-build-system) + (propagated-inputs + `(("r-circular" ,r-circular) + ("r-overlap" ,r-overlap) + ("r-pbapply" ,r-pbapply))) + (home-page "https://cran.r-project.org/web/packages/activity/") + (synopsis "Animal activity statistics") + (description + "This package provides functions to fit kernel density functions to +animal activity time data; plot activity distributions; quantify overall +levels of activity; statistically compare activity metrics through +bootstrapping; and evaluate variation in linear variables with time (or other +circular variables).") + (license license:gpl3))) + +(define-public r-ouch + (package + (name "r-ouch") + (version "2.11-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ouch" version)) + (sha256 + (base32 + "0xkwwi62vdahlcg3k32zb1nfwsx87zdssk79mvcxgfsw9bw4gahx")))) + (build-system r-build-system) + (propagated-inputs `(("r-subplex" ,r-subplex))) + (home-page "http://kingaa.github.io/ouch/") + (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses") + (description + "This package provides tools to fit and compare Ornstein-Uhlenbeck models +for evolution along a phylogenetic tree.") + (license license:gpl2+))) |