diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 900 |
1 files changed, 900 insertions, 0 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5bd5c60d49..eac6293fc9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14,6 +14,7 @@ ;;; Copyright © 2018 Leo Famulari <leo@famulari.name> ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2018, 2019 Brett Gilio <brettg@posteo.net> +;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -58,9 +59,11 @@ #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) + #:use-module (gnu packages networking) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) + #:use-module (gnu packages python-xyz) #:use-module (gnu packages statistics) #:use-module (gnu packages tls) #:use-module (gnu packages web) @@ -10839,3 +10842,900 @@ using @code{S3}.") for model selection. The calibration methods available are based on the slope heuristics.") (license license:gpl2+))) + +(define-public r-dorng + (package + (name "r-dorng") + (version "1.7.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "doRNG" version)) + (sha256 + (base32 + "1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7")))) + (properties `((upstream-name . "doRNG"))) + (build-system r-build-system) + (propagated-inputs + `(("r-foreach" ,r-foreach) + ("r-iterators" ,r-iterators) + ("r-pkgmaker" ,r-pkgmaker) + ("r-rngtools" ,r-rngtools))) + (home-page "https://renozao.github.io/doRNG/") + (synopsis "Generic reproducible parallel backend for foreach loops") + (description + "This package provides functions to perform reproducible parallel +@code{foreach} loops, using independent random streams as generated by +L'Ecuyer's combined multiple-recursive generator. It enables to easily +convert standard @code{%dopar%} loops into fully reproducible loops, +independently of the number of workers, the task scheduling strategy, or the +chosen parallel environment and associated foreach backend.") + (license license:gpl2+))) + +(define-public r-blockmodeling + (package + (name "r-blockmodeling") + (version "0.3.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "blockmodeling" version)) + (sha256 + (base32 + "11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-doparallel" ,r-doparallel) + ("r-dorng" ,r-dorng) + ("r-foreach" ,r-foreach) + ("r-matrix" ,r-matrix))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/blockmodeling") + (synopsis "Generalized and classical blockmodeling of valued networks") + (description + "This package is primarily meant as an implementation of generalized +blockmodeling for valued networks. In addition, measures of similarity or +dissimilarity based on structural equivalence and regular equivalence (REGE +algorithms) can be computed and partitioned matrices can be plotted.") + (license license:gpl2+))) + +(define-public r-upsetr + (package + (name "r-upsetr") + (version "1.3.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "UpSetR" version)) + (sha256 + (base32 + "08vj7l92b8fpqyqwxshll2mhk3yhgyr74axvr2lf29z78bapymhz")))) + (properties `((upstream-name . "UpSetR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-plyr" ,r-plyr) + ("r-scales" ,r-scales))) + (home-page "https://github.com/hms-dbmi/UpSetR") + (synopsis "Visualize intersecting sets") + (description + "This package provides a more scalable alternative to Venn and Euler +diagrams for visualizing intersecting sets. Create visualizations of +intersecting sets using a novel matrix design, along with visualizations of +several common set, element and attribute related tasks.") + (license license:expat))) + +;; This package includes a JavaScript file, which is not minified. When +;; upgrading please check that there are no new minified JavaScript files. +(define-public r-shinybs + (package + (name "r-shinybs") + (version "0.61") + (source + (origin + (method url-fetch) + (uri (cran-uri "shinyBS" version)) + (sha256 + (base32 + "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji")))) + (properties `((upstream-name . "shinyBS"))) + (build-system r-build-system) + ;; The tests spawn Shiny browser apps. They cannot be run + ;; non-interactively. + (arguments '(#:tests? #f)) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-shiny" ,r-shiny))) + (home-page "https://ebailey78.github.io/shinyBS/") + (synopsis "Twitter Bootstrap components for Shiny") + (description + "This package adds additional Twitter Bootstrap components to Shiny.") + (license license:gpl3))) + +(define-public r-outliers + (package + (name "r-outliers") + (version "0.14") + (source + (origin + (method url-fetch) + (uri (cran-uri "outliers" version)) + (sha256 + (base32 + "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/outliers/index.html") + (synopsis "Tests for outliers") + (description + "This package provides a collection of some tests commonly used for +identifying outliers.") + (license license:gpl2+))) + +(define-public r-bayesm + (package + (name "r-bayesm") + (version "3.1-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "bayesm" version)) + (sha256 + (base32 + "0y30cza92s6kgvmxjpr6f5g0qbcck7hslqp89ncprarhxiym2m28")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (home-page "http://www.perossi.org/home/bsm-1") + (synopsis "Bayesian inference for marketing/micro-econometrics") + (description + "This package covers many important models used in marketing and +micro-econometrics applications, including Bayes Regression (univariate or +multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and +Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP), +Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate +Mixtures of Normals (including clustering), Dirichlet Process Prior Density +Estimation with normal base, Hierarchical Linear Models with normal prior and +covariates, Hierarchical Linear Models with a mixture of normals prior and +covariates, Hierarchical Multinomial Logits with a mixture of normals prior +and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior +and covariates, Hierarchical Negative Binomial Regression Models, Bayesian +analysis of choice-based conjoint data, Bayesian treatment of linear +instrumental variables models, Analysis of Multivariate Ordinal survey data +with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random +Coefficient Logit Models.") + (license license:gpl2+))) + +(define-public r-tensora + (package + (name "r-tensora") + (version "0.36.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "tensorA" version)) + (sha256 + (base32 + "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7")))) + (properties `((upstream-name . "tensorA"))) + (build-system r-build-system) + (home-page "http://www.stat.boogaart.de/tensorA") + (synopsis "Advanced tensor arithmetic with named indices") + (description + "This package provides convenience functions for advanced linear algebra +with tensors and computation with datasets of tensors on a higher level +abstraction. It includes Einstein and Riemann summing conventions, dragging, +co- and contravariate indices, and parallel computations on sequences of +tensors.") + (license license:gpl2+))) + +(define-public r-rarpack + (package + (name "r-rarpack") + (version "0.11-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rARPACK" version)) + (sha256 + (base32 + "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63")))) + (properties `((upstream-name . "rARPACK"))) + (build-system r-build-system) + (propagated-inputs `(("r-rspectra" ,r-rspectra))) + (home-page "https://github.com/yixuan/rARPACK") + (synopsis "Solvers for large scale eigenvalue and SVD problems") + (description + "This package was previously an R wrapper of the ARPACK library, and now +a shell of the R package RSpectra, an R interface to the Spectra library for +solving large scale eigenvalue/vector problems. The current version of +rARPACK simply imports and exports the functions provided by RSpectra. New +users of rARPACK are advised to switch to the RSpectra package.") + (license license:bsd-3))) + +(define-public r-compositions + (package + (name "r-compositions") + (version "1.40-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "compositions" version)) + (sha256 + (base32 + "12mp05yi7jkdqg9iwh6bc9sx6sdxagcnrirznxy9hq8502p7238i")))) + (build-system r-build-system) + (propagated-inputs + `(("r-bayesm" ,r-bayesm) + ("r-energy" ,r-energy) + ("r-robustbase" ,r-robustbase) + ("r-tensora" ,r-tensora))) + (home-page "http://www.stat.boogaart.de/compositions") + (synopsis "Compositional data analysis") + (description + "This package provides functions for the consistent analysis of +compositional data (e.g. portions of substances) and positive +numbers (e.g. concentrations).") + (license license:gpl2+))) + +(define-public r-cobs + (package + (name "r-cobs") + (version "1.3-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "cobs" version)) + (sha256 + (base32 + "1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-quantreg" ,r-quantreg) + ("r-sparsem" ,r-sparsem))) + (home-page "https://cran.r-project.org/web/packages/cobs") + (synopsis "Constrained B-Splines (sparse matrix based)") + (description + "This package provides qualitatively constrained (regression) smoothing +splines via linear programming and sparse matrices.") + (license license:gpl2+))) + +(define-public r-drimpute + (package + (name "r-drimpute") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "DrImpute" version)) + (sha256 + (base32 + "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b")))) + (properties `((upstream-name . "DrImpute"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (home-page "https://github.com/ikwak2/DrImpute") + (synopsis "Imputing dropout events in single-cell RNA-Seq data") + (description + "This is an R package for imputing dropout events. Many statistical +methods in cell type identification, visualization and lineage reconstruction +do not account for dropout events. DrImpute can improve the performance of +such software by imputing dropout events.") + (license license:gpl3))) + +(define-public r-gamlss-dist + (package + (name "r-gamlss-dist") + (version "5.1-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "gamlss.dist" version)) + (sha256 + (base32 + "1cd0vl9klcb849i8xwyjm8ihb1da92631j1rxdbnflgffkzrkya4")))) + (properties `((upstream-name . "gamlss.dist"))) + (build-system r-build-system) + (propagated-inputs `(("r-mass" ,r-mass))) + (home-page "http://www.gamlss.org/") + (synopsis "Distributions for Generalized Additive Models for location scale and shape") + (description + "This package provides a set of distributions which can be used for +modelling the response variables in Generalized Additive Models for Location +Scale and Shape. The distributions can be continuous, discrete or mixed +distributions. Extra distributions can be created, by transforming, any +continuous distribution defined on the real line, to a distribution defined on +ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit} +transformation, respectively.") + ;; Either version of the GPL. + (license (list license:gpl2 license:gpl3)))) + +;; This package includes JavaScript files, which are not minified. When +;; upgrading please check that there are no new minified JavaScript files. +(define-public r-shinyjs + (package + (name "r-shinyjs") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "shinyjs" version)) + (sha256 + (base32 + "113zpijri0l80rlgrvqn6bxk0sdqgl79h7yhja2p76f9dc9i2sr8")))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-htmltools" ,r-htmltools) + ("r-jsonlite" ,r-jsonlite) + ("r-shiny" ,r-shiny))) + (home-page "https://deanattali.com/shinyjs") + (synopsis "Improve the user experience of your Shiny apps") + (description + "Perform common useful JavaScript operations in Shiny apps that will +greatly improve your apps without having to know any JavaScript. Examples +include: hiding an element, disabling an input, resetting an input back to its +original value, delaying code execution by a few seconds, and many more useful +functions for both the end user and the developer. Shinyjs can also be used +to easily call your own custom JavaScript functions from R.") + (license license:agpl3+))) + +;; This package includes minified JavaScript files. When upgrading please +;; check that there are no new minified JavaScript files. +(define-public r-colourpicker + (package + (name "r-colourpicker") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "colourpicker" version)) + (sha256 + (base32 + "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi")))) + (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-salvattore") + "examples/colourInput/www/salvattore.min.js") + (,(assoc-ref inputs "js-jquery") + "htmlwidgets/lib/jquery/jquery.min.js") + ("www/shared/colourpicker/js/colourpicker.js" + "www/shared/colourpicker/js/colourpicker.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-ggplot2" ,r-ggplot2) + ("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-jsonlite" ,r-jsonlite) + ("r-miniui" ,r-miniui) + ("r-shiny" ,r-shiny) + ("r-shinyjs" ,r-shinyjs))) + (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-salvattore" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js") + (sha256 + (base32 + "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5")))))) + (home-page "https://github.com/daattali/colourpicker") + (synopsis "Color picker tool for Shiny and for selecting colors in plots") + (description + "This package provides a color picker that can be used as an input in +Shiny apps or Rmarkdown documents. The color picker supports alpha opacity, +custom color palettes, and many more options. A plot color helper tool is +available as an RStudio Addin, which helps you pick colors to use in your +plots. A more generic color picker RStudio Addin is also provided to let you +select colors to use in your R code.") + (license license:expat))) + +(define-public r-ggextra + (package + (name "r-ggextra") + (version "0.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggExtra" version)) + (sha256 + (base32 + "1m5zpn3l3p1y3d2692gyz50m63d58m2a3b7zb595kvcffdx2qr5b")))) + (properties `((upstream-name . "ggExtra"))) + (build-system r-build-system) + (propagated-inputs + `(("r-colourpicker" ,r-colourpicker) + ("r-ggplot2" ,r-ggplot2) + ("r-gtable" ,r-gtable) + ("r-miniui" ,r-miniui) + ("r-scales" ,r-scales) + ("r-shiny" ,r-shiny) + ("r-shinyjs" ,r-shinyjs))) + (home-page "https://github.com/daattali/ggExtra") + (synopsis "Marginal histograms for ggplot2 and other enhancements") + (description + "This package is a collection of functions and layers to enhance ggplot2. +The flagship function is @code{ggMarginal()}, which can be used to add +marginal histograms/boxplots/density plots to ggplot2 scatterplots.") + (license license:expat))) + +(define-public r-minpack-lm + (package + (name "r-minpack-lm") + (version "1.2-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "minpack.lm" version)) + (sha256 + (base32 + "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql")))) + (properties `((upstream-name . "minpack.lm"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/minpack.lm") + (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm") + (description + "The @code{nls.lm} function provides an R interface to @code{lmder} and +@code{lmdif} from the MINPACK library, for solving nonlinear least-squares +problems by a modification of the Levenberg-Marquardt algorithm, with support +for lower and upper parameter bounds. The implementation can be used via +@code{nls}-like calls using the @code{nlsLM} function.") + (license license:gpl3))) + +(define-public r-moments + (package + (name "r-moments") + (version "0.14") + (source + (origin + (method url-fetch) + (uri (cran-uri "moments" version)) + (sha256 + (base32 + "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/moments") + (synopsis "Moments, cumulants, skewness, kurtosis and related tests") + (description + "This package provides functions to calculate: moments, Pearson's +kurtosis, Geary's kurtosis and skewness; it also includes tests related to +them (Anscombe-Glynn, D'Agostino, Bonett-Seier).") + (license license:gpl2+))) + +(define-public r-msir + (package + (name "r-msir") + (version "1.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "msir" version)) + (sha256 + (base32 + "1ipzgdffsqly3dp91pw7yp3h5cwn08l9qsj7cdmrykd42jc98950")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mclust" ,r-mclust) + ("r-rgl" ,r-rgl))) + (home-page "https://cran.r-project.org/web/packages/msir") + (synopsis "Model-based sliced inverse regression") + (description + "This is an R package for dimension reduction based on finite Gaussian +mixture modeling of inverse regression.") + (license license:gpl2+))) + +(define-public r-pbivnorm + (package + (name "r-pbivnorm") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "pbivnorm" version)) + (sha256 + (base32 + "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://github.com/brentonk/pbivnorm") + (synopsis "Vectorized bivariate normal CDF") + (description + "This package provides a vectorized R function for calculating +probabilities from a standard bivariate normal CDF.") + (license license:gpl2+))) + +(define-public r-lavaan + (package + (name "r-lavaan") + (version "0.6-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "lavaan" version)) + (sha256 + (base32 + "0hw856kv11zqn6nd4216rh19i6xbnc1rh044r7jvvxkhzgbqkyxz")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-mnormt" ,r-mnormt) + ("r-numderiv" ,r-numderiv) + ("r-pbivnorm" ,r-pbivnorm))) + (home-page "http://lavaan.ugent.be") + (synopsis "Latent variable analysis") + (description + "This package provides tools to fit a variety of latent variable models, +including confirmatory factor analysis, structural equation modeling and +latent growth curve models.") + (license license:gpl2+))) + +(define-public r-nonnest2 + (package + (name "r-nonnest2") + (version "0.5-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "nonnest2" version)) + (sha256 + (base32 + "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6")))) + (build-system r-build-system) + (propagated-inputs + `(("r-compquadform" ,r-compquadform) + ("r-lavaan" ,r-lavaan) + ("r-mvtnorm" ,r-mvtnorm) + ("r-sandwich" ,r-sandwich))) + (home-page "https://cran.r-project.org/web/packages/nonnest2/") + (synopsis "Tests of non-nested models") + (description + "This package allows for testing of non-nested models. It includes tests +of model distinguishability and of model fit that can be applied to both +nested and non-nested models. The package also includes functionality to +obtain confidence intervals associated with AIC and BIC.") + ;; Either version of the GPL. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-penalized + (package + (name "r-penalized") + (version "0.9-51") + (source + (origin + (method url-fetch) + (uri (cran-uri "penalized" version)) + (sha256 + (base32 + "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-survival" ,r-survival))) + (home-page "https://cran.r-project.org/web/packages/penalized/") + (synopsis "Penalized estimation in GLMs and in the Cox model") + (description + "This package provides tools for fitting possibly high dimensional +penalized regression models. The penalty structure can be any combination of +an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity +constraint on the regression coefficients. The supported regression models +are linear, logistic and Poisson regression and the Cox Proportional Hazards +model. Cross-validation routines allow optimization of the tuning +parameters.") + (license license:gpl2+))) + +(define-public r-zim + (package + (name "r-zim") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ZIM" version)) + (sha256 + (base32 + "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig")))) + (properties `((upstream-name . "ZIM"))) + (build-system r-build-system) + (propagated-inputs `(("r-mass" ,r-mass))) + (home-page "https://github.com/biostatstudio/ZIM") + (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros") + (description + "Analyze count time series with excess zeros. Two types of statistical +models are supported: Markov regression and state-space models. They are also +known as observation-driven and parameter-driven models respectively in the +time series literature. The functions used for Markov regression or +observation-driven models can also be used to fit ordinary regression models +with independent data under the zero-inflated Poisson (ZIP) or zero-inflated +negative binomial (ZINB) assumption. The package also contains miscellaneous +functions to compute density, distribution, quantile, and generate random +numbers from ZIP and ZINB distributions.") + (license license:gpl3))) + +(define-public r-nor1mix + (package + (name "r-nor1mix") + (version "1.2-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "nor1mix" version)) + (sha256 + (base32 + "1bvk888qml9qr7q703s7qzgm0sqfchcjdjqwqllm5vrjx0cnapj3")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/nor1mix/") + (synopsis "Normal (1-d) mixture models") + (description + "This package provides S3 classes and methods for one-dimensional normal +mixture models, for, e.g., density estimation or clustering algorithms +research and teaching; it provides the widely used Marron-Wand densities. It +also provides tools for efficient random number generation and graphics.") + (license license:gpl2+))) + +(define-public r-beanplot + (package + (name "r-beanplot") + (version "1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "beanplot" version)) + (sha256 + (base32 + "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/beanplot/") + (synopsis "Visualization via beanplots") + (description + "This package provides beanplots, an alternative to +boxplot/stripchart/violin plots. It can be used to plot univariate comparison +graphs.") + (license license:gpl2))) + +(define-public r-pbdzmq + (package + (name "r-pbdzmq") + (version "0.3-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "pbdZMQ" version)) + (sha256 + (base32 + "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf")))) + (properties `((upstream-name . "pbdZMQ"))) + (build-system r-build-system) + (inputs + `(("zeromq" ,zeromq) + ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://pbdr.org/") + (synopsis "R interface to ZeroMQ") + (description + "ZeroMQ is a well-known library for high-performance asynchronous +messaging in scalable, distributed applications. This package provides high +level R wrapper functions to easily utilize ZeroMQ. The main focus is on +interactive client/server programming frameworks. A few wrapper functions +compatible with @code{rzmq} are also provided.") + (license license:gpl3))) + +(define-public r-repr + (package + (name "r-repr") + (version "0.19.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "repr" version)) + (sha256 + (base32 + "1mhhzakkagb8z568yx3p2ixs8fcifm7f8l2yq285zrz8jmnpckfx")))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-htmltools" ,r-htmltools) + ("r-jsonlite" ,r-jsonlite))) + (home-page "https://cran.r-project.org/web/packages/repr/") + (synopsis "Serializable representations") + (description + "This package provides string and binary representations of objects for +several formats and MIME types.") + (license license:gpl3))) + +(define-public r-irdisplay + (package + (name "r-irdisplay") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "IRdisplay" version)) + (sha256 + (base32 + "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli")))) + (properties `((upstream-name . "IRdisplay"))) + (build-system r-build-system) + (propagated-inputs + `(("r-repr" ,r-repr))) + (home-page "https://cran.r-project.org/web/packages/IRdisplay/") + (synopsis "Jupyter display machinery") + (description + "This package provides an interface to the rich display capabilities of +Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a +running IRkernel session.") + (license license:expat))) + +(define-public r-irkernel + (package + (name "r-irkernel") + (version "0.8.15") + (source + (origin + (method url-fetch) + (uri (cran-uri "IRkernel" version)) + (sha256 + (base32 + "1n0nc3paij8fgbp7l2b4405zk9k4y3gdi2bz6z8x6j0h5mi6k6a6")))) + (properties `((upstream-name . "IRkernel"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'install 'install-kernelspec + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (setenv "HOME" "/tmp") + (invoke "jupyter" "kernelspec" "install" + "--name" "ir" + "--prefix" out + (string-append out "/site-library/IRkernel/kernelspec")) + #t)))))) + (inputs + `(("jupyter" ,jupyter))) + (propagated-inputs + `(("r-crayon" ,r-crayon) + ("r-digest" ,r-digest) + ("r-evaluate" ,r-evaluate) + ("r-irdisplay" ,r-irdisplay) + ("r-jsonlite" ,r-jsonlite) + ("r-pbdzmq" ,r-pbdzmq) + ("r-repr" ,r-repr) + ("r-uuid" ,r-uuid))) + (home-page "https://cran.r-project.org/web/packages/IRkernel/") + (synopsis "Native R kernel for Jupyter") + (description + "The R kernel for the Jupyter environment executes R code which the +front-end (Jupyter Notebook or other front-ends) submits to the kernel via the +network.") + (license license:expat))) + +(define-public r-gmodels + (package + (name "r-gmodels") + (version "2.18.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "gmodels" version)) + (sha256 + (base32 + "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-gdata" ,r-gdata) + ("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/gmodels/") + (synopsis "Various R programming tools for model fitting") + (description + "This package provides various R programming tools for model fitting.") + (license license:gpl2))) + +(define-public r-apcluster + (package + (name "r-apcluster") + (version "1.4.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "apcluster" version)) + (sha256 + (base32 + "188hdfmwjjx3aic599nwmkzjqm9j9jighi5bly6qd43c1vj6ih2s")))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/apcluster/") + (synopsis "Affinity propagation clustering") + (description + "This package implements affinity propagation clustering introduced by +Frey and Dueck (2007). The package further provides leveraged affinity +propagation and an algorithm for exemplar-based agglomerative clustering that +can also be used to join clusters obtained from affinity propagation. Various +plotting functions are available for analyzing clustering results.") + (license license:gpl2+))) + +(define-public r-valr + (package + (name "r-valr") + (version "0.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "valr" version)) + (sha256 + (base32 + "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika")))) + (build-system r-build-system) + (propagated-inputs + `(("r-broom" ,r-broom) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-rcpp" ,r-rcpp) + ("r-readr" ,r-readr) + ("r-rlang" ,r-rlang) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble))) + (home-page "http://github.com/rnabioco/valr") + (synopsis "Genome interval arithmetic in R") + (description + "This package enables you to read and manipulate genome intervals and +signals. It provides functionality similar to command-line tool suites within +R, enabling interactive analysis and visualization of genome-scale data.") + (license license:expat))) + +(define-public r-rematch2 + (package + (name "r-rematch2") + (version "2.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "rematch2" version)) + (sha256 + (base32 + "16k0i5p7fa3qfxv59ijyn638wpz8n4jrkrnilqmh5g9l8f8bn4h6")))) + (build-system r-build-system) + (propagated-inputs + `(("r-tibble" ,r-tibble))) + (home-page "https://github.com/r-lib/rematch2") + (synopsis "Tidy output from regular expression matching") + (description + "This package provides wrappers on @code{regexpr} and @code{gregexpr} to +return the match results in tidy data frames.") + (license license:expat))) |