diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 325 |
1 files changed, 315 insertions, 10 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9a27c82d21..9eb54c0358 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -52,14 +52,14 @@ colors are provided.") (define-public r-glue (package (name "r-glue") - (version "1.1.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "glue" version)) (sha256 (base32 - "01awmqby7rwzhzr51m7d87wqibx7ggl6xair8fi3z3q1hkyyv7ih")))) + "0vi9y8ix95g6hjqdz9c9y4119apbdjcypdv0ag8cl6vaxqs5n9qr")))) (build-system r-build-system) (home-page "https://github.com/tidyverse/glue") (synopsis "Interpreted string literals") @@ -539,14 +539,14 @@ plot networks.") (define-public r-proxy (package (name "r-proxy") - (version "0.4-17") + (version "0.4-19") (source (origin (method url-fetch) (uri (cran-uri "proxy" version)) (sha256 (base32 - "0bg1fn96qrj8whmnl7c3gv244ksm2ykxxsd0zrmw4lb6465pizl2")))) + "0ladwgi70jw2a3adgg2xadw8hz3mm6llsw428c1fcrl305sy49vb")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/proxy") (synopsis "Distance and similarity measures") @@ -717,14 +717,14 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and (define-public r-bbmle (package (name "r-bbmle") - (version "1.0.19") + (version "1.0.20") (source (origin (method url-fetch) (uri (cran-uri "bbmle" version)) (sha256 (base32 - "014h6mw16gv4acs2p78dy7lla7s428n633aybsb1mbi6250dg0p8")))) + "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) @@ -733,11 +733,11 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and (home-page "http://cran.r-project.org/web/packages/bbmle") (synopsis "Tools for General Maximum Likelihood Estimation") (description - "Methods and functions for fitting maximum likelihood models in R. This -package modifies and extends the @code{mle} classes in the @code{stats4} -package.") + "This package provides methods and functions for fitting maximum +likelihood models in R. This package modifies and extends the @code{mle} +classes in the @code{stats4} package.") ;; Any version of the GPL - (license (list license:gpl2 license:gpl3)))) + (license license:gpl2+))) (define-public r-emdbook (package @@ -1243,3 +1243,308 @@ X, and likewise for Y. Pdist strictly computes distances across the two matrices, not within the same matrix, making computations significantly faster for certain use cases.") (license license:gpl3+))) + +(define-public r-ggrepel + (package + (name "r-ggrepel") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggrepel" version)) + (sha256 + (base32 + "0g0qfm6g71rv27423c1x846ipilnj213knyzrcr09vrpxc87l618")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-rcpp" ,r-rcpp) + ("r-scales" ,r-scales))) + (home-page "http://github.com/slowkow/ggrepel") + (synopsis "Repulsive text and label geometries for ggplot2") + (description + "This package provides text and label geometries for ggplot2 that help to +avoid overlapping text labels. Labels repel away from each other and away +from the data points.") + (license license:gpl3))) + +(define-public r-corrplot + (package + (name "r-corrplot") + (version "0.84") + (source + (origin + (method url-fetch) + (uri (cran-uri "corrplot" version)) + (sha256 + (base32 + "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd")))) + (build-system r-build-system) + (home-page "https://github.com/taiyun/corrplot") + (synopsis "Visualization of a correlation matrix") + (description + "This package provides a graphical display of a correlation matrix or +general matrix. It also contains some algorithms to do matrix reordering. In +addition, corrplot is good at details, including choosing color, text labels, +color labels, layout, etc.") + ;; Any version of the GPL + (license license:gpl2+))) + +(define-public r-stringdist + (package + (name "r-stringdist") + (version "0.9.4.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "stringdist" version)) + (sha256 + (base32 + "0j5b7hr53nr9xq44famkpwzi4khix93ffani5pwldqkf8bpdvhci")))) + (build-system r-build-system) + (home-page "https://github.com/markvanderloo/stringdist") + (synopsis "Approximate string matching and string distance functions") + (description + "This package implements an approximate string matching version of R's +native @code{match} function. It can calculate various string distances based +on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), +qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro, +Jaro-Winkler). An implementation of soundex is provided as well. Distances +can be computed between character vectors while taking proper care of encoding +or between integer vectors representing generic sequences.") + (license license:gpl3+))) + +(define-public r-mice + (package + (name "r-mice") + (version "2.46.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "mice" version)) + (sha256 + (base32 + "1gjvlk67zvgipfczsca8zqk97vg3sivv82hblsdwp14s7smhjcax")))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-nnet" ,r-nnet) + ("r-rcpp" ,r-rcpp) + ("r-rpart" ,r-rpart) + ("r-survival" ,r-survival))) + (home-page "https://cran.r-project.org/web/packages/mice/") + (synopsis "Multivariate imputation by chained equations") + (description + "Multiple imputation using @dfn{Fully Conditional Specification} (FCS) +implemented by the MICE algorithm as described in @url{Van Buuren and +Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each +variable has its own imputation model. Built-in imputation models are +provided for continuous data (predictive mean matching, normal), binary +data (logistic regression), unordered categorical data (polytomous logistic +regression) and ordered categorical data (proportional odds). MICE can also +impute continuous two-level data (normal model, pan, second-level variables). +Passive imputation can be used to maintain consistency between variables. +Various diagnostic plots are available to inspect the quality of the +imputations.") + ;; Any of these two versions. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-hardyweinberg + (package + (name "r-hardyweinberg") + (version "1.5.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "HardyWeinberg" version)) + (sha256 + (base32 + "0xbcchmzii0jv0ygr91n72r39j1axraxd2i607b56v4yd5d8sy4k")))) + (properties `((upstream-name . "HardyWeinberg"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mice" ,r-mice) + ("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/package=HardyWeinberg") + (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium") + (description + "This package contains tools for exploring Hardy-Weinberg equilibrium for +diallelic genetic marker data. All classical tests (chi-square, exact, +likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are +included in the package, as well as functions for power computation and for +the simulation of marker data under equilibrium and disequilibrium. Routines +for dealing with markers on the X-chromosome are included. Functions for +testing equilibrium in the presence of missing data by using multiple +imputation are also provided. Implements several graphics for exploring the +equilibrium status of a large set of diallelic markers: ternary plots with +acceptance regions, log-ratio plots and Q-Q plots.") + (license license:gpl2+))) + +(define-public r-sm + (package + (name "r-sm") + (version "2.2-5.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "sm" version)) + (sha256 + (base32 + "0hnq5s2fv94gaj0nyqc1vjdjd64vsp9z23nqa8hxvjcaf996rwj9")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "http://www.stats.gla.ac.uk/~adrian/sm/") + (synopsis "Smoothing methods for nonparametric regression and density estimation") + (description + "This is software accompanying the book 'Applied Smoothing Techniques for +Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford +University Press. It provides smoothing methods for nonparametric regression +and density estimation") + (license license:gpl2+))) + +(define-public r-vioplot + (package + (name "r-vioplot") + (version "0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "vioplot" version)) + (sha256 + (base32 + "16wkb26kv6qr34hv5zgqmgq6zzgysg9i78pvy2c097lr60v087v0")))) + (build-system r-build-system) + (propagated-inputs `(("r-sm" ,r-sm))) + (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler") + (synopsis "Violin plot") + (description + "This package provides a violin plot, which is a combination of a box +plot and a kernel density plot.") + (license license:bsd-3))) + +(define-public r-rsofia + (package + (name "r-rsofia") + (version "1.1") + (source (origin + (method url-fetch) + ;; This package has been removed from CRAN, so we can + ;; only fetch it from the archives. + (uri (string-append "https://cran.r-project.org/src/" + "contrib/Archive/RSofia/RSofia_" + version ".tar.gz")) + (sha256 + (base32 + "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn")))) + (properties `((upstream-name . "RSofia"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia") + (synopsis "Port of sofia-ml to R") + (description "This package is a port of sofia-ml to R. Sofia-ml is a +suite of fast incremental algorithms for machine learning that can be used for +training models for classification or ranking.") + (license license:asl2.0))) + +(define-public r-xts + (package + (name "r-xts") + (version "0.10-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "xts" version)) + (sha256 + (base32 + "1w7lxy3hbf005fvpzbwiznj8jbxi07s4189vbgxisd35l9a4v6q4")))) + (build-system r-build-system) + (propagated-inputs `(("r-zoo" ,r-zoo))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://github.com/joshuaulrich/xts") + (synopsis "Extensible time series") + (description + "This package provides for uniform handling of R's different time-based +data classes by extending @code{zoo}, maximizing native format information +preservation and allowing for user-level customization and extension, while +simplifying cross-class interoperability.") + (license license:gpl2+))) + +(define-public r-performanceanalytics + (package + (name "r-performanceanalytics") + (version "1.4.3541") + (source + (origin + (method url-fetch) + (uri (cran-uri "PerformanceAnalytics" version)) + (sha256 + (base32 + "1czchsccsbdfjw743j6rm101q2q01pggyl8zmlva213pwm86zb3v")))) + (properties + `((upstream-name . "PerformanceAnalytics"))) + (build-system r-build-system) + (propagated-inputs + `(("r-xts" ,r-xts) + ("r-zoo" ,r-zoo))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "http://r-forge.r-project.org/projects/returnanalytics/") + (synopsis "Econometric tools for performance and risk analysis") + (description "This is a collection of econometric functions for +performance and risk analysis. This package aims to aid practitioners and +researchers in utilizing the latest research in analysis of non-normal return +streams. In general, it is most tested on return (rather than price) data on +a regular scale, but most functions will work with irregular return data as +well, and increasing numbers of functions will work with P&L or price data +where possible.") + ;; Either version may be picked. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-laeken + (package + (name "r-laeken") + (version "0.4.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "laeken" version)) + (sha256 + (base32 + "1rhkv1kk508pwln1d325iq4fink2ncssps0ypxi52j9d7wk78la6")))) + (build-system r-build-system) + (propagated-inputs + `(("r-boot" ,r-boot) + ("r-mass" ,r-mass))) + (home-page "http://cran.r-project.org/web/packages/laeken/") + (synopsis "Estimation of indicators on social exclusion and poverty") + (description "This package provides tools for the estimation of indicators +on social exclusion and poverty, as well as an implementation of Pareto tail +modeling for empirical income distributions.") + (license license:gpl2+))) + +(define-public r-vcd + (package + (name "r-vcd") + (version "1.4-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "vcd" version)) + (sha256 + (base32 + "05azric2w8mrsdk7y0484cjygcgcmbp96q2v500wvn91fj98kkhp")))) + (build-system r-build-system) + (propagated-inputs + `(("r-colorspace" ,r-colorspace) + ("r-lmtest" ,r-lmtest) + ("r-mass" ,r-mass))) + (home-page "http://cran.r-project.org/web/packages/vcd/") + (synopsis "Visualizing categorical data") + (description "This package provides visualization techniques, data sets, +summary and inference procedures aimed particularly at categorical data. +Special emphasis is given to highly extensible grid graphics. The package was +originally inspired by the book \"Visualizing Categorical Data\" by Michael +Friendly and is now the main support package for a new book, \"Discrete Data +Analysis with R\" by Michael Friendly and David Meyer (2015).") + (license license:gpl2))) |