diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 198 |
1 files changed, 84 insertions, 114 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 8ebb16a03c..f2a6971826 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -35,6 +35,7 @@ #:use-module (guix build-system python) #:use-module (guix build-system trivial) #:use-module (gnu packages) + #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages cran) #:use-module (gnu packages curl) @@ -56,6 +57,7 @@ #:use-module (gnu packages readline) #:use-module (gnu packages ssh) #:use-module (gnu packages texinfo) + #:use-module (gnu packages time) #:use-module (gnu packages tls) #:use-module (gnu packages base) #:use-module (gnu packages web) @@ -366,6 +368,8 @@ k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.") (base32 "1bkvqmv8h2c423q9ag2afb6s9j2vcdlxsf559zzbimraphrr2c2b")))) (build-system r-build-system) + (inputs + `(("gfortran" ,gfortran))) (home-page "http://cran.r-project.org/web/packages/cluster") (synopsis "Methods for cluster analysis") (description @@ -388,7 +392,8 @@ Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".") (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/codetools") (synopsis "Code analysis tools for R") - (description "This package provides code analysis tools for R.") + (description "This package provides code analysis tools for R to check R +code for possible problems.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) @@ -425,13 +430,15 @@ for reading and writing some dBase files.") "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb")))) (properties `((upstream-name . "KernSmooth"))) (build-system r-build-system) + (inputs + `(("gfortran" ,gfortran))) (home-page "http://cran.r-project.org/web/packages/KernSmooth") (synopsis "Functions for kernel smoothing") (description "This package provides functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) \"Kernel Smoothing\".") - ;; Unlimited distribution + ;; Unlimited use and distribution (license (license:non-copyleft "file://LICENCE.note")))) (define-public r-lattice @@ -1159,13 +1166,13 @@ wrong.") (define-public r-lazyeval (package (name "r-lazyeval") - (version "0.2.0") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "lazyeval" version)) (sha256 (base32 - "1jwdz40nznlc44hpjli7h98gnpa4d98ifggmj7z88h84n9aqywqk")))) + "0q9zx78ncy2ffzrf9sh053069kd3w1xn1ss3gsbyf3y4jhza9cw3")))) (build-system r-build-system) (home-page "https://github.com/hadley/lazyeval") (synopsis "Lazy (non-standard) evaluation in R") @@ -1409,13 +1416,13 @@ the execution time of R expressions.") (define-public r-pryr (package (name "r-pryr") - (version "0.1.2") + (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "pryr" version)) (sha256 (base32 - "1in350a8hxwf580afavasvn3jc7x2p1b7nlwmj1scakfz74vghk5")))) + "1b1rcywq9sqzgjsnh3ynnx16gp41n94kkzfalm3y4kyy3ls8ikba")))) (build-system r-build-system) (propagated-inputs `(("r-stringr" ,r-stringr) @@ -1540,13 +1547,13 @@ defined in different packages.") (define-public r-rlang (package (name "r-rlang") - (version "0.1.2") + (version "0.1.4") (source (origin (method url-fetch) (uri (cran-uri "rlang" version)) (sha256 (base32 - "1yc5qyq6h0nrya7m2fqnfv19zh5xwsl28jx6zi2g1zz6ra4cvkwh")))) + "1x5rwwsx7xrlyspy41yl5nhyvfgzl73195nsdb4rc6z85ab6r6wd")))) (build-system r-build-system) (home-page "http://rlang.tidyverse.org") (synopsis "Functions for base types, core R and Tidyverse features") @@ -1664,28 +1671,6 @@ features require SQL translation to be provided by the package author.") transformations.") (license license:expat))) -(define-public r-cluster - (package - (name "r-cluster") - (version "2.0.6") - (source - (origin - (method url-fetch) - (uri (cran-uri "cluster" version)) - (sha256 - (base32 - "1z4gbz7chxxi4ly6c0yjlikwgf8aa8dlg05cn5cd6pjr21zvh97l")))) - (build-system r-build-system) - (inputs - `(("gfortran" ,gfortran))) - (home-page "http://cran.r-project.org/web/packages/cluster") - (synopsis "Methods for data cluster analysis") - (description - "This package provides tools that are useful in finding groups in data. -It is based on the methods described in Kaufman and Rousseeuw (1990) \"Finding -Groups in Data\".") - (license license:gpl2+))) - (define-public r-formula (package (name "r-formula") @@ -1750,13 +1735,13 @@ times.") (define-public r-data-table (package (name "r-data-table") - (version "1.10.4-2") + (version "1.10.4-3") (source (origin (method url-fetch) (uri (cran-uri "data.table" version)) (sha256 (base32 - "159dgcjlrpq17iy7y3a6v2wnlrszjlz031cj4aqcl9bbfkh07mr7")))) + "12caklgr19vy9wprdks6zh825vr1iw1cajgwcnbpyvmijqdlz2xs")))) (build-system r-build-system) (home-page "https://github.com/Rdatatable/data.table/wiki") (synopsis "Enhanced version of data.frame R object") @@ -1955,14 +1940,14 @@ files in R. It is built on top of the libxml2 C library.") (define-public r-multitaper (package (name "r-multitaper") - (version "1.0-13") + (version "1.0-14") (source (origin (method url-fetch) (uri (cran-uri "multitaper" version)) (sha256 (base32 - "1ckf9bhvd5k7ypaw2viqh3cyj9jij0ygcp4q9pxwqs508s6yx3a5")))) + "04wd9bbhyx7697pfy0fpj02v1csr48hkpqj62h9p8a6w84ji4k68")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -2044,14 +2029,14 @@ R version.") (define-public r-checkmate (package (name "r-checkmate") - (version "1.8.4") + (version "1.8.5") (source (origin (method url-fetch) (uri (cran-uri "checkmate" version)) (sha256 (base32 - "1xpq73myr39i33mwihvy494sam77hb3z15yr172a31d8wn1qi53g")))) + "1q6igk50lq4fp5d3imgcn1j063h3gsp214ra4nlf534hf4wjlkg9")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports))) @@ -2236,14 +2221,14 @@ collation, and NAMESPACE files.") (define-public r-openssl (package (name "r-openssl") - (version "0.9.7") + (version "0.9.8") (source (origin (method url-fetch) (uri (cran-uri "openssl" version)) (sha256 (base32 - "178fcp9f245i0k9s2w45kbw0ml0r9pfc73ak8hvicw4jz639wzb9")))) + "0wm7pkm5yfsxmpyr8n0pvj1398wqg5gzp5clqrg5nb2mflxv2nlc")))) (build-system r-build-system) (inputs `(("libressl" ,libressl))) @@ -2361,14 +2346,16 @@ tools to simplify the devolpment of R packages.") (define-public r-withr (package (name "r-withr") - (version "2.0.0") + (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "withr" version)) (sha256 (base32 - "0ncq9ygx33rx7aazn53p0a0vbr5xv0r6wbkzcwbhbwyd8k55bgin")))) + "12v263fj6l3ds9nrsj6q7h6zhbivp3w2jk7w9dpk1610d3nx9gf8")))) (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice))) (home-page "https://github.com/jimhester/withr") (synopsis "Run code with temporarily modified global state") (description @@ -2947,24 +2934,6 @@ traverse through all the elements of a vector, list, or other collection of data.") (license license:asl2.0))) -(define-public r-codetools - (package - (name "r-codetools") - (version "0.2-15") - (source - (origin - (method url-fetch) - (uri (cran-uri "codetools" version)) - (sha256 - (base32 - "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf")))) - (build-system r-build-system) - (home-page "https://cran.r-project.org/web/packages/codetools") - (synopsis "Code analysis tools for R") - (description "This package provides code analysis tools for R to check R -code for possible problems.") - (license (list license:gpl2+ license:gpl3+)))) - (define-public r-foreach (package (name "r-foreach") @@ -3094,14 +3063,14 @@ flexible than the orphaned \"base64\" package.") (define-public r-irlba (package (name "r-irlba") - (version "2.2.1") + (version "2.3.1") (source (origin (method url-fetch) (uri (cran-uri "irlba" version)) (sha256 (base32 - "0zfb7x1701n6gask0f8y2yq0vmb82xkxf6limp43ivx551hx600s")))) + "1dclzzkm75sbbqda5scj2hlqnw2sksgxbiqagxs4359fwfszi0k0")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -3416,13 +3385,13 @@ maintenance for package developers.") (define-public r-r-utils (package (name "r-r-utils") - (version "2.5.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (cran-uri "R.utils" version)) (sha256 (base32 - "17q3w5dlly5xl2srrzsmf9s7vs5d576vqbcs6sr2p5x4qvqa1q8s")))) + "03j7hrs03kyj9qrjxyp5kqv4lpqqpk6xwbkzx6j15d8928yrjr2x")))) (properties `((upstream-name . "R.utils"))) (build-system r-build-system) (propagated-inputs @@ -3590,14 +3559,14 @@ the 'lite' version of the more complete @code{viridis} package.") (define-public r-tidyselect (package (name "r-tidyselect") - (version "0.2.2") + (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "tidyselect" version)) (sha256 (base32 - "1lndr0ajd3fhycmrw2fdaiyf32in5pgl5ig901q221g24n87vmnd")))) + "0b0w30yq30c7bwpaghp3hp0nncqwcmvrra9j58fhx9jihay3l68c")))) (build-system r-build-system) (propagated-inputs `(("r-glue" ,r-glue) @@ -3675,14 +3644,14 @@ It uses and relies on grid graphics and formal (S4) classes and methods.") (define-public r-purrr (package (name "r-purrr") - (version "0.2.3") + (version "0.2.4") (source (origin (method url-fetch) (uri (cran-uri "purrr" version)) (sha256 (base32 - "0j1y0nbvljcis9hgic4wbbzslcsidhpw0wzs7d2hx7a2ygi6mkma")))) + "0wgbnbrqncjpggg8f9bdpcd1gy351s5f0az5k8lc55cvs9lhz3gd")))) (build-system r-build-system) (propagated-inputs `(("r-tibble" ,r-tibble) @@ -3981,14 +3950,14 @@ hierarchical clustering dendrograms.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.38.1") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "1ggvmak13rhxc4ghf16ncjfvgszc8yvza93s2l9kn8yiwr96vp2h")))) + "0mrdgbkb9dcfr9gsqyxfpshnxx60mq97pl98b8yl00l2gfwz48ph")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) @@ -4175,30 +4144,6 @@ plot can be quickly adjusted using a flexible parameter dispatching mechanism.") (license license:gpl2+))) -(define-public r-kernsmooth - (package - (name "r-kernsmooth") - (version "2.23-15") - (source - (origin - (method url-fetch) - (uri (cran-uri "KernSmooth" version)) - (sha256 - (base32 - "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb")))) - (properties `((upstream-name . "KernSmooth"))) - (build-system r-build-system) - (inputs - `(("gfortran" ,gfortran))) - (home-page "http://cran.r-project.org/web/packages/KernSmooth") - (synopsis "Functions for kernel smoothing") - (description - "This package provides functions for kernel smoothing (and density -estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) -\"Kernel Smoothing\".") - ;; Unlimited use and distribution - (license (license:non-copyleft "file://LICENSE.note")))) - (define-public r-zoo (package (name "r-zoo") @@ -4664,10 +4609,10 @@ and resampling-based inference.") (home-page "https://cran.r-project.org/web/packages/prabclus") (synopsis "Parametric bootstrap tests for spatial neighborhood clustering") (description - "This package provides a distance-based parametric bootstrap tests -for clustering with spatial neighborhood information. Some distance measures, -clustering of presence-absence, abundance and multilocus genetical data for -species delimitation, nearest neighbor based noise detection.") + "This package provides distance-based parametric bootstrap tests for +clustering with spatial neighborhood information. It implements some distance +measures, clustering of presence-absence, abundance and multilocus genetical +data for species delimitation, nearest neighbor based noise detection.") (license license:gpl2+))) (define-public r-deoptimr @@ -4696,14 +4641,14 @@ can be efficiently implemented directly in the R language.") (define-public r-robustbase (package (name "r-robustbase") - (version "0.92-7") + (version "0.92-8") (source (origin (method url-fetch) (uri (cran-uri "robustbase" version)) (sha256 (base32 - "13xz4am7y0s0kl5bmbcw3dlhl7ji8h9sjx56wsgmj6r9n35nrggw")))) + "080ynchq8pvhnmbivj4fp74n0x9lyr9923sg0s9gq5irgm68kgxw")))) (build-system r-build-system) (inputs `(("gfortran" ,gfortran))) @@ -5037,14 +4982,14 @@ using modular prediction and response module classes.") (define-public r-quantreg (package (name "r-quantreg") - (version "5.33") + (version "5.34") (source (origin (method url-fetch) (uri (cran-uri "quantreg" version)) (sha256 (base32 - "1dirmxa4cd05nb0yv0ga6ivw5hkr2zr2cb2lixl1nb6amqn024is")))) + "0bmgfgnmzqwmwwaraliry682yb8kcr396q3rlzrd2qzaa9sgxxh4")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -5394,17 +5339,18 @@ is supported.") (define-public r-lubridate (package (name "r-lubridate") - (version "1.6.0") + (version "1.7.1") (source (origin (method url-fetch) (uri (cran-uri "lubridate" version)) (sha256 (base32 - "0ci6rwij9i1inn840m0mlh1nqgh6vm2lada9kdnjpcjp5kyfv1qs")))) + "0pzvazzybzvln3y676yims7whsc74g8i7kgf2nsfbxdq5943z349")))) (build-system r-build-system) (propagated-inputs - `(("r-stringr" ,r-stringr))) + `(("r-rcpp" ,r-rcpp) + ("r-stringr" ,r-stringr))) (home-page "http://cran.r-project.org/web/packages/lubridate") (synopsis "Make dealing with dates a little easier") @@ -5432,17 +5378,17 @@ easy and fun.") (home-page "http://strimmerlab.org/software/fdrtool/") (synopsis "Estimation of false discovery rates and higher criticism") (description - "This package provides tools to estimate both tail area-based false -discovery rates (Fdr) as well as local false discovery rates (fdr) for a -variety of null models (p-values, z-scores, correlation coefficients, -t-scores). The proportion of null values and the parameters of the null -distribution are adaptively estimated from the data. In addition, the package -contains functions for non-parametric density estimation (Grenander -estimator), for monotone regression (isotonic regression and antitonic -regression with weights), for computing the greatest convex minorant (GCM) and -the least concave majorant (LCM), for the half-normal and correlation -distributions, and for computing empirical higher criticism (HC) scores and -the corresponding decision threshold.") + "This package provides tools to estimate tail area-based false discovery +rates as well as local false discovery rates for a variety of null +models (p-values, z-scores, correlation coefficients, t-scores). The +proportion of null values and the parameters of the null distribution are +adaptively estimated from the data. In addition, the package contains +functions for non-parametric density estimation (Grenander estimator), for +monotone regression (isotonic regression and antitonic regression with +weights), for computing the @dfn{greatest convex minorant} (GCM) and the +@dfn{least concave majorant} (LCM), for the half-normal and correlation +distributions, and for computing empirical @dfn{higher criticism} (HC) scores +and the corresponding decision threshold.") (license license:gpl3+))) (define-public r-forcats @@ -5527,3 +5473,27 @@ tools.") "The goal of tgconfig is to provide infrastructure for managing package parameters.") (license license:gpl3)))) + +(define-public r-directlabels + (package + (name "r-directlabels") + (version "2017.03.31") + (source + (origin + (method url-fetch) + (uri (cran-uri "directlabels" version)) + (sha256 + (base32 + "01ahw0c56mnzwl611s8hnghicww4c4dgf5v2wv6bl1s1pramw9pr")))) + (build-system r-build-system) + (propagated-inputs + `(("r-quadprog" ,r-quadprog))) + (home-page "http://directlabels.r-forge.r-project.org/") + (synopsis "Direct labels for multicolor plots") + (description + "This package provides an extensible framework for automatically placing +direct labels onto multicolor plots. Label positions are described using +positioning methods that can be re-used across several different plots. There +are heuristics for examining @code{trellis} and @code{ggplot} objects and +inferring an appropriate positioning method.") + (license license:gpl3))) |