diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 329 |
1 files changed, 309 insertions, 20 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index bb7576352f..e00a8a4ba2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -23,6 +23,7 @@ #:use-module (guix utils) #:use-module (guix build-system r) #:use-module (gnu packages gcc) + #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages perl) #:use-module (gnu packages statistics) @@ -91,13 +92,13 @@ error stream.") (define-public r-rcpp (package (name "r-rcpp") - (version "0.12.12") + (version "0.12.13") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "1byyqvlgb2p46p1gv243k73rk69fa8pa4l5m5asmckag2pkb2glz")))) + (base32 "1bm84yc48475plgsnnbvzi6nzkixpnfw8ry86ax63f9g524asw55")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ integration") @@ -202,14 +203,14 @@ on (non-orthogonal) variable vectors in scatterplots and biplots.") (define-public r-shape (package (name "r-shape") - (version "1.4.2") + (version "1.4.3") (source (origin (method url-fetch) (uri (cran-uri "shape" version)) (sha256 (base32 - "0yk3cmsa57svcvbnm21pyr0s0qbhnllka8nmsg4yb41frjlqph66")))) + "1v9xp60p813rnx41vchkh32qmcb4z2zp9l7r1a8a6f8aqylnq3vj")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/shape") (synopsis "Functions for plotting graphical shapes") @@ -241,14 +242,14 @@ validation and filtering on the values, making options invisible or private.") (define-public r-circlize (package (name "r-circlize") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "circlize" version)) (sha256 (base32 - "0p1zx1aawkblz48kzzfn5w1k3lbwv9wrk1k5gcfjrr2b4sz1pp5b")))) + "1w7i3jgxgq510axglzmw54ma9kq7k4c86i9ccndz10mrwc51fji0")))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace) @@ -271,14 +272,14 @@ patterns behind multiple dimensional data.") (define-public r-powerlaw (package (name "r-powerlaw") - (version "0.70.0") + (version "0.70.1") (source (origin (method url-fetch) (uri (cran-uri "poweRlaw" version)) (sha256 (base32 - "1p2la3hslxq2xa8jkwvci6zcpn47cvyr9xqd5agp1riwwp2xw5gh")))) + "04sr0nhdd1v915m0zf5gasznzgi08ykcy20kkwdw0l5mvvdbic8m")))) (properties `((upstream-name . "poweRlaw"))) (build-system r-build-system) (propagated-inputs @@ -459,14 +460,14 @@ quantities.") (define-public r-reshape (package (name "r-reshape") - (version "0.8.6") + (version "0.8.7") (source (origin (method url-fetch) (uri (cran-uri "reshape" version)) (sha256 (base32 - "1f1ngalc22knhdm9djv1m6abnjqpv1frdzxfkpakhph2l67bk7fq")))) + "14ir3w4bb3bsz8jsak27nj7kpn227pdgr9653gjq5wc93rywi9ig")))) (build-system r-build-system) (propagated-inputs `(("r-plyr" ,r-plyr) @@ -505,14 +506,14 @@ package also provides a C++ API, that works with or without Rcpp.") (define-public r-ggally (package (name "r-ggally") - (version "1.3.0") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "GGally" version)) (sha256 (base32 - "12ddab0nd0f9c7bb6cx3c22mliyvc8xsxv26aqz3cvfbla8crp3b")))) + "02px7j28wzbhcgcwm2m0pxb6g7s5zvphl64ix55pkvag4m2ky57l")))) (properties `((upstream-name . "GGally"))) (build-system r-build-system) (propagated-inputs @@ -556,14 +557,14 @@ most popular ones.") (define-public r-sp (package (name "r-sp") - (version "1.2-4") + (version "1.2-5") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 (base32 - "0crba3j00mb2xv2yk60rpa57gn97xq4ql3a6p9cjzqjxzv2cknk2")))) + "09yydnacp33yx0kn537k96fjlbf75fjafqfknpa5gvci4l888bqd")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -623,14 +624,14 @@ quantile mixture from L-moments and trimmed L-moments.") (define-public r-distillery (package (name "r-distillery") - (version "1.0-2") + (version "1.0-4") (source (origin (method url-fetch) (uri (cran-uri "distillery" version)) (sha256 (base32 - "12m4cacvc18fd3aayc8iih5q6bwsmvf29b55fwp7vs8wp1h8nd8c")))) + "1m0pgmlvk7bsb6q3kxagnq422babk61sf73naavac68v8x2q8fix")))) (build-system r-build-system) (home-page "http://www.ral.ucar.edu/staff/ericg") (synopsis "Functions for confidence intervals and object information") @@ -851,14 +852,14 @@ data). Weighted versions of MLE, MME and QME are available.") (define-public r-energy (package (name "r-energy") - (version "1.7-0") + (version "1.7-2") (source (origin (method url-fetch) (uri (cran-uri "energy" version)) (sha256 (base32 - "1g4hqi6mgsnd1w4q7dd2m40ljh2jdmvad91ksbq9fscnrqpvji1x")))) + "19c7bgjnm4ggf7w5mk64c5shkma3sa9wc8x117iqv7pk1bvvyy3p")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) @@ -904,14 +905,14 @@ George Marsaglia are included.") (define-public r-ksamples (package (name "r-ksamples") - (version "1.2-6") + (version "1.2-7") (source (origin (method url-fetch) (uri (cran-uri "kSamples" version)) (sha256 (base32 - "1pbam0zqq44slpxdgl2s2fsfdgl7i0pgm8bzlvnm0fy0na24bgdj")))) + "0f19rjngk0lg6s8c6h5l55qpxp8sl4vxj3kpi05cizzncny9b9bj")))) (properties `((upstream-name . "kSamples"))) (build-system r-build-system) (propagated-inputs @@ -928,3 +929,291 @@ sampling from populations, given the observed tie pattern. Except for Steel's test and the JT test it also combines these tests across several blocks of samples.") (license license:gpl2+))) + +(define-public r-cvst + (package + (name "r-cvst") + (version "0.2-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "CVST" version)) + (sha256 + (base32 + "17xacyi8cf37rr2xswx96qy7pwkaqq394awdlswykz3qlyzx4zx2")))) + (properties `((upstream-name . "CVST"))) + (build-system r-build-system) + (propagated-inputs + `(("r-kernlab" ,r-kernlab) + ("r-matrix" ,r-matrix))) + (home-page "http://cran.r-project.org/web/packages/CVST") + (synopsis "Fast cross-validation via sequential testing") + (description + "This package implements the fast cross-validation via sequential +testing (CVST) procedure. CVST is an improved cross-validation procedure +which uses non-parametric testing coupled with sequential analysis to +determine the best parameter set on linearly increasing subsets of the data. +Additionally to the CVST the package contains an implementation of the +ordinary k-fold cross-validation with a flexible and powerful set of helper +objects and methods to handle the overall model selection process. The +implementations of the Cochran's Q test with permutations and the sequential +testing framework of Wald are generic and can therefore also be used in other +contexts.") + (license license:gpl2+))) + +(define-public r-lava + (package + (name "r-lava") + (version "1.5.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "lava" version)) + (sha256 + (base32 + "1vcm04h9i39gmf2prl5d4j4il4gs6skzr6y2fvl1vn4hklna87f4")))) + (build-system r-build-system) + (propagated-inputs + `(("r-numderiv" ,r-numderiv) + ("r-survival" ,r-survival))) + (home-page "https://github.com/kkholst/lava") + (synopsis "Latent variable models") + (description + "This package provides tools for the estimation and simulation of latent +variable models.") + (license license:gpl3))) + +(define-public r-drr + (package + (name "r-drr") + (version "0.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "DRR" version)) + (sha256 + (base32 + "1scfwp6ry6apxzqjclsmn2frxp9qfw6zxsxn5w0j0q3sz42hz1h2")))) + (properties `((upstream-name . "DRR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cvst" ,r-cvst) + ("r-kernlab" ,r-kernlab) + ("r-matrix" ,r-matrix))) + (home-page "http://cran.r-project.org/web/packages/DRR") + (synopsis "Dimensionality reduction via regression") + (description + "This package provides an implementation of dimensionality reduction via +regression using Kernel Ridge Regression.") + (license license:gpl3))) + +(define-public r-prodlim + (package + (name "r-prodlim") + (version "1.6.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "prodlim" version)) + (sha256 + (base32 + "0m51rkivx1zr6whdqwj66jpnkmp4385m06kkha3dp8qqf4jna9iz")))) + (build-system r-build-system) + (propagated-inputs + `(("r-kernsmooth" ,r-kernsmooth) + ("r-lava" ,r-lava) + ("r-rcpp" ,r-rcpp) + ("r-survival" ,r-survival))) + (home-page "http://cran.r-project.org/web/packages/prodlim") + (synopsis "Product-limit estimation for censored event history analysis") + (description + "This package provides a fast and user-friendly implementation of +nonparametric estimators for censored event history (survival) analysis with +the Kaplan-Meier and Aalen-Johansen methods.") + (license license:gpl2+))) + +(define-public r-dimred + (package + (name "r-dimred") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "dimRed" version)) + (sha256 + (base32 + "0fasca5fsbrxdwv30hch7vb9snb844l7l8p5fjf239dq45xfy37v")))) + (properties `((upstream-name . "dimRed"))) + (build-system r-build-system) + (propagated-inputs `(("r-drr" ,r-drr))) + (home-page "https://github.com/gdkrmr/dimRed") + (synopsis "Framework for dimensionality reduction") + (description + "This package provides a collection of dimensionality reduction +techniques from R packages and provides a common interface for calling the +methods.") + (license license:gpl3))) + +(define-public r-timedate + (package + (name "r-timedate") + (version "3012.100") + (source + (origin + (method url-fetch) + (uri (cran-uri "timeDate" version)) + (sha256 + (base32 + "0cn4h23y2y2bbg62qgm79xx4cvfla5xbpmi9hbdvkvpmm5yfyqk2")))) + (properties `((upstream-name . "timeDate"))) + (build-system r-build-system) + (home-page "https://www.rmetrics.org") + (synopsis "Chronological and calendar objects") + (description + "This package provides an environment for teaching \"Financial +Engineering and Computational Finance\" and for managing chronological and +calendar objects.") + (license license:gpl2+))) + +(define-public r-ddalpha + (package + (name "r-ddalpha") + (version "1.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ddalpha" version)) + (sha256 + (base32 + "0pczw9543y7f92m7gyk7rxcjn8vsjaldc5vl0r56ywip9i374zbh")))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-class" ,r-class) + ("r-mass" ,r-mass) + ("r-rcpp" ,r-rcpp) + ("r-robustbase" ,r-robustbase) + ("r-sfsmisc" ,r-sfsmisc))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "http://cran.r-project.org/web/packages/ddalpha") + (synopsis "Depth-Based classification and calculation of data depth") + (description + "This package contains procedures for depth-based supervised learning, +which are entirely non-parametric, in particular the DDalpha-procedure (Lange, +Mosler and Mozharovskyi, 2014). The training data sample is transformed by a +statistical depth function to a compact low-dimensional space, where the final +classification is done. It also offers an extension to functional data and +routines for calculating certain notions of statistical depth functions. 50 +multivariate and 5 functional classification problems are included.") + (license license:gpl2))) + +(define-public r-gower + (package + (name "r-gower") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "gower" version)) + (sha256 + (base32 + "1mbrj1lam3jfbby2j32shmmj5cn09zx3rkxbamq7q8sdg39b54gb")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/markvanderloo/gower") + (synopsis "Gower's distance") + (description + "This package provides tools to compute Gower's distance (or similarity) +coefficient between records, and to compute the top-n matches between records. +Core algorithms are executed in parallel on systems supporting OpenMP.") + (license license:gpl3))) + +(define-public r-rcpproll + (package + (name "r-rcpproll") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "RcppRoll" version)) + (sha256 + (base32 + "19xzvxym8zbighndygkq4imfwc0abh4hqyq3qrr8aakyd096iisi")))) + (properties `((upstream-name . "RcppRoll"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "http://cran.r-project.org/web/packages/RcppRoll") + (synopsis "Efficient rolling and windowed operations") + (description + "This package provides fast and efficient routines for common rolling / +windowed operations. Routines for the efficient computation of windowed mean, +median, sum, product, minimum, maximum, standard deviation and variance are +provided.") + (license license:gpl2+))) + +(define-public r-ipred + (package + (name "r-ipred") + (version "0.9-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "ipred" version)) + (sha256 + (base32 + "1vrw1pqcpnc04x1r2h9grdfm6bivs358sww5gg90jwlvxcw69lxq")))) + (build-system r-build-system) + (propagated-inputs + `(("r-class" ,r-class) + ("r-mass" ,r-mass) + ("r-nnet" ,r-nnet) + ("r-prodlim" ,r-prodlim) + ("r-rpart" ,r-rpart) + ("r-survival" ,r-survival))) + (home-page "http://cran.r-project.org/web/packages/ipred") + (synopsis "Improved predictors") + (description + "This package provides improved predictive models by indirect +classification and bagging for classification, regression and survival +problems as well as resampling based estimators of prediction error.") + (license license:gpl2+))) + +(define-public r-recipes + (package + (name "r-recipes") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "recipes" version)) + (sha256 + (base32 + "0rydk403qihxmcv3zz323r3ywk4g1v7ibvj452rxhm0z22sqk9kb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ddalpha" ,r-ddalpha) + ("r-dimred" ,r-dimred) + ("r-dplyr" ,r-dplyr) + ("r-gower" ,r-gower) + ("r-ipred" ,r-ipred) + ("r-lubridate" ,r-lubridate) + ("r-magrittr" ,r-magrittr) + ("r-purrr" ,r-purrr) + ("r-rcpproll" ,r-rcpproll) + ("r-rlang" ,r-rlang) + ("r-tibble" ,r-tibble) + ("r-tidyselect" ,r-tidyselect) + ("r-timedate" ,r-timedate))) + (home-page "https://github.com/topepo/recipes") + (synopsis "Preprocessing tools to create design matrices") + (description + "Recipes is an extensible framework to create and preprocess design +matrices. Recipes consist of one or more data manipulation and analysis +\"steps\". Statistical parameters for the steps can be estimated from an +initial data set and then applied to other data sets. The resulting design +matrices can then be used as inputs into statistical or machine learning +models.") + (license license:gpl2))) |