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authorNicolas Goaziou <mail@nicolasgoaziou.fr>2021-06-23 09:36:35 +0200
committerNicolas Goaziou <mail@nicolasgoaziou.fr>2021-06-23 09:36:35 +0200
commitcde7068e8cb28b7245cfa07b8aa788039012f972 (patch)
treee5f2bba3243d21e6ce77a5705aa77fc60372f8d0 /gnu/installer
parent6b83da96162fe212a4e306b259c2c52f17878ec5 (diff)
downloadguix-cde7068e8cb28b7245cfa07b8aa788039012f972.tar.gz
guix-cde7068e8cb28b7245cfa07b8aa788039012f972.zip
gnu: texmacs: Update to 2.1.
* gnu/packages/text-editors.scm (texmacs): Update to 2.1. [arguments]: Remove #t at the end of phases.
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:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages python-build) #:use-module (gnu packages python-science) #:use-module (gnu packages python-xyz) #:use-module (gnu packages readline) #:use-module (gnu packages ruby) #:use-module (gnu packages shells) #:use-module (gnu packages sphinx) #:use-module (gnu packages ssh) #:use-module (gnu packages swig) #:use-module (gnu packages tbb) #:use-module (gnu packages tcl) #:use-module (gnu packages tex) #:use-module (gnu packages texinfo) #:use-module (gnu packages time) #:use-module (gnu packages tls) #:use-module (gnu packages base) #:use-module (gnu packages uglifyjs) #:use-module (gnu packages version-control) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (gnu packages xorg) #:use-module (srfi srfi-1) #:use-module (ice-9 match)) (define-public pspp (package (name "pspp") (version "2.0.1") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/pspp/pspp-" version ".tar.gz")) (sha256 (base32 "002c08rxym056mn7a73jwjmcazqd4gh5j1cyml603y4ckvqb1nwf")))) (build-system gnu-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (add-after 'unpack 'patch-test-suite (lambda _ (substitute* "tests/output/tex.at" (("AT_CHECK\\(\\[LC_ALL=C.UTF-8 pspp") "AT_CHECK([LC_ALL=en_US.UTF-8 pspp")))) (add-before 'check 'prepare-tests ;; Prevent irrelevant errors that cause test output mismatches: ;; ‘Fontconfig error: No writable cache directories’ (lambda _ (setenv "XDG_CACHE_HOME" (getcwd))))))) (inputs (list cairo gettext-minimal gsl libxml2 pango readline gtk+ gtksourceview-3 spread-sheet-widget zlib)) (native-inputs (list autoconf ;for tests `(,glib "bin") ;for glib-genmarshal perl pkg-config python-3 ;for tests texinfo)) (home-page "https://www.gnu.org/software/pspp/") (synopsis "Statistical analysis") (description "GNU PSPP is a statistical analysis program. It can perform descriptive statistics, T-tests, linear regression and non-parametric tests. It features both a graphical interface as well as command-line input. PSPP is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data can be imported from spreadsheets, text files and database sources and it can be output in text, PostScript, PDF or HTML.") (license license:gpl3+))) (define-public jags (package (name "jags") (version "4.3.1") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/" (version-major version) ".x/Source/" "JAGS-" version ".tar.gz")) (sha256 (base32 "0aa2w4g5057vn1qjp954s2kwxfmy1h7p5yn56fyi7sz9nmaq69gr")))) (build-system gnu-build-system) (arguments (list #:configure-flags #~(list "--with-lapack=-lopenblas" "--with-blas=-lopenblas"))) (home-page "https://mcmc-jags.sourceforge.net/") (native-inputs (list gfortran openblas)) (synopsis "Gibbs sampler") (description "JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. JAGS was written with three aims in mind: @enumerate @item To have a cross-platform engine for the BUGS language; @item To be extensible, allowing users to write their own functions, distributions and samplers; @item To be a platform for experimentation with ideas in Bayesian modelling. @end enumerate\n") (license license:gpl2))) (define-public libxls (package (name "libxls") (version "1.6.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/libxls/libxls/releases/download/" "v" version "/libxls-" version ".tar.gz")) (sha256 (base32 "0wg3ymr43aa1j3scyl9x83b2xgg7wilzpil0dj91a8dzji6w7b2x")))) (build-system gnu-build-system) (home-page "https://github.com/libxls/libxls") (synopsis "Read binary (.xls) Excel spreadsheet files") (description "libxls is a C library to read .xls spreadsheet files in the binary OLE BIFF8 format as created by Excel 97 and later versions. It cannot write them. This package also provides @command{xls2csv} to export Excel files to CSV.") (license license:bsd-2))) ;; Update this package together with the set of recommended packages: r-boot, ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice, ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival. (define r-with-tests (package (name "r-with-tests") (version "4.4.1") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" (version-major version) "/R-" version ".tar.gz")) (sha256 (base32 "0kfrn8v8l555n5xrpf753jar5wa3vs622p967ffjkdxfx9fngjxl")))) (build-system gnu-build-system) (arguments (list #:disallowed-references `(,tzdata-for-tests) #:make-flags #~(list (string-append "LDFLAGS=-Wl,-rpath=" #$output "/lib/R/lib") ;; This affects the embedded timestamp of only the core packages. "PKG_BUILT_STAMP=1970-01-01") #:phases #~(modify-phases %standard-phases (add-before 'configure 'do-not-compress-serialized-files (lambda _ ;; This ensures that Guix can detect embedded store references; ;; see bug #28157 for details. (substitute* "src/library/base/makebasedb.R" (("compress = TRUE") "compress = FALSE")) (substitute* '("src/library/tools/Makefile.in" "share/make/basepkg.mk" "share/make/lazycomp.mk") (("makeLazyLoading\\(") "makeLazyLoading(compress=FALSE,")))) (add-before 'configure 'patch-coreutils-paths (lambda* (#:key inputs #:allow-other-keys) (let ((uname-bin (search-input-file inputs "/bin/uname")) (rm-bin (search-input-file inputs "/bin/rm"))) (substitute* "src/scripts/R.sh.in" (("uname") uname-bin)) (substitute* "src/unix/sys-std.c" (("rm -Rf ") (string-append rm-bin " -Rf "))) (substitute* "src/library/parallel/R/detectCores.R" (("'grep") (string-append "'" (search-input-file inputs "/bin/grep"))) (("\\| wc -l") (string-append "| " (search-input-file inputs "/bin/wc") " -l")))))) (add-after 'unpack 'patch-tests (lambda _ ;; This is needed because R is run during the check phase and ;; /bin/sh doesn't exist in the build container. (substitute* "src/unix/sys-unix.c" (("\"/bin/sh\"") (string-append "\"" (which "sh") "\""))) ;; This test fails because line numbers are off by two. (substitute* "tests/reg-packages.R" (("8 <= print" m) (string-append "## " m))))) (add-after 'unpack 'build-reproducibly (lambda _ ;; The documentation contains time stamps to demonstrate ;; documentation generation in different phases. (substitute* "src/library/tools/man/Rd2HTML.Rd" (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S") "(removed for reproducibility)")) ;; Remove timestamp from tracing environment. This fixes ;; reproducibility of "methods.rd{b,x}". (substitute* "src/library/methods/R/trace.R" (("dateCreated = Sys.time\\(\\)") "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")")) ;; Ensure that gzipped files are reproducible. (substitute* '("src/library/grDevices/Makefile.in" "doc/manual/Makefile.in") (("R_GZIPCMD\\)" line) (string-append line " -n"))) ;; The "srcfile" procedure in "src/library/base/R/srcfile.R" ;; queries the mtime of a given file and records it in an object. ;; This is acceptable at runtime to detect stale source files, ;; but it destroys reproducibility at build time. ;; Similarly, the "srcfilecopy" procedure records the current ;; time. We change both of them to respect SOURCE_DATE_EPOCH. (substitute* "src/library/base/R/srcfile.R" (("timestamp <- (timestamp.*|file.mtime.*)" _ time) (string-append "timestamp <- \ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\ } else { " time "}, origin=\"1970-01-01\")\n"))) ;; This library is installed using "install_package_description", ;; so we need to pass the "builtStamp" argument. (substitute* "src/library/tools/Makefile.in" (("(install_package_description\\(.*\"')\\)\"" line prefix) (string-append prefix ", builtStamp='1970-01-01')\""))) (substitute* "src/library/Recommended/Makefile.in" (("INSTALL_OPTS =" m) (string-append m " --built-timestamp=1970-01-01" m))) ;; R bundles an older version of help2man, which does not respect ;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man, ;; because that breaks a test. (with-fluids ((%default-port-encoding "ISO-8859-1")) (substitute* "tools/help2man.pl" (("my \\$date = strftime \"%B %Y\", localtime" line) (string-append line " 1")))) ;; The "References" section of this file when converted to ;; package.rds is sometimes stored with a newline, sometimes with ;; a space. We avoid this problem by removing the line break ;; that is suspected to be the culprit. (substitute* "src/library/methods/DESCRIPTION.in" (("\\(2008\\)\n") "(2008) ") ((" ``Software") "``Software") (("Data Analysis:.") "Data Analysis:\n") (("Programming with R") " Programming with R")) (substitute* "src/library/tools/DESCRIPTION.in" (("codetools, methods, xml2, curl, commonmark, knitr, xfun, mathjaxr") "codetools, methods, xml2, curl, commonmark, knitr, xfun, mathjaxr")))) (add-before 'build 'set-locales (lambda _ (setlocale LC_ALL "C") (setenv "LC_ALL" "C"))) (add-before 'configure 'set-default-pager ;; Set default pager to "cat", because otherwise it is "false", ;; making "help()" print nothing at all. (lambda _ (setenv "PAGER" "cat"))) (add-before 'configure 'set-timezone ;; Some tests require the timezone to be set. However, the ;; timezone may not just be "UTC", or else a brittle regression ;; test in reg-tests-1d will fail. ;; We also need TZ during the configure step. (lambda* (#:key inputs #:allow-other-keys) (setenv "TZ" "UTC+1") (setenv "TZDIR" (search-input-directory inputs "share/zoneinfo")))) (add-before 'check 'set-home ;; Some tests require that HOME be set. (lambda _ (setenv "HOME" "/tmp"))) (add-after 'build 'make-info (lambda _ (invoke "make" "info"))) (add-after 'build 'install-info (lambda _ (invoke "make" "install-info")))) #:configure-flags #~(list ;; We build the recommended packages here, because they are needed in ;; order to run the test suite. We disable them in the r-minimal ;; package. "--with-cairo" "--with-blas=-lopenblas" "--with-libpng" "--with-jpeglib" "--with-libtiff" "--with-ICU" "--with-tcltk" (string-append "--with-tcl-config=" #$(this-package-input "tcl") "/lib/tclConfig.sh") (string-append "--with-tk-config=" #$(this-package-input "tk") "/lib/tkConfig.sh") "--enable-R-shlib" "--enable-BLAS-shlib" "--with-system-tre"))) ;; R has some support for Java. When the JDK is available at configure ;; time environment variables pointing to the JDK will be recorded under ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R ;; CMD javareconf". "R CMD javareconf" appears to only be used to update ;; the recorded environment variables in $R_HOME/etc. Refer to ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support ;; for additional information. ;; As the JDK is a rather large input with only very limited effects on R, ;; we decided to drop it. (native-inputs (list bzip2 perl pkg-config texinfo ; for building HTML manuals (texlive-updmap.cfg (list texlive-etoolbox texlive-fancyvrb texlive-inconsolata texlive-upquote texlive-xkeyval)) tzdata-for-tests xz)) (inputs (list coreutils curl openblas gfortran grep icu4c libjpeg-turbo libpng libtiff libxt ;; We need not only cairo here, but pango to ensure that tests for the ;; "cairo" bitmapType plotting backend succeed. pango pcre2 readline tcl tk which zlib ;; This avoids a reference to the ungraftable static bash. R uses the ;; detected shell for the "system" procedure. bash-minimal)) (native-search-paths (list (search-path-specification (variable "R_LIBS_SITE") (files (list "site-library/"))))) (home-page "https://www.r-project.org/") (synopsis "Environment for statistical computing and graphics") (description "R is a language and environment for statistical computing and graphics. It provides a variety of statistical techniques, such as linear and nonlinear modeling, classical statistical tests, time-series analysis, classification and clustering. It also provides robust support for producing publication-quality data plots. A large amount of 3rd-party packages are available, greatly increasing its breadth and scope.") (license license:gpl3+))) (define-public r-minimal (package (inherit r-with-tests) (name "r-minimal") (arguments (substitute-keyword-arguments (package-arguments r-with-tests) ((#:tests? #f #f) #f) ((#:disallowed-references refs '()) (cons perl refs)) ((#:configure-flags flags) ;; Do not build the recommended packages. The build system creates ;; random temporary directories and embeds their names in some ;; package files. We build these packages with the r-build-system ;; instead. #~(cons "--without-recommended-packages" #$flags)) ((#:phases phases '%standard-phases) #~(modify-phases #$phases (add-after 'install 'remove-extraneous-references (lambda* (#:key inputs outputs #:allow-other-keys) (substitute* (string-append #$output "/lib/R/etc/Makeconf") (("^# configure.*") "# Removed to avoid extraneous references\n")) (substitute* (string-append #$output "/lib/R/bin/libtool") (((string-append "(-L)?(" (format #false "~a/[^-]+-(~{~a~^|~})-[^/]+" (%store-directory) '("bzip2" "file" "glibc-utf8-locales" "graphite2" "libselinux" "libsepol" "perl" "texinfo" "texlive-bin" "util-macros" "xz")) "|" (format #false "~a/[^-]+-glibc-[^-]+-static" (%store-directory)) ")/lib")) "")))))))))) (define-public rmath-standalone (package (inherit r-minimal) (name "rmath-standalone") (arguments '(#:phases (modify-phases %standard-phases (add-before 'configure 'set-timezone ;; We need TZ during the configure step. (lambda* (#:key inputs #:allow-other-keys) (setenv "TZ" "UTC+1") (setenv "TZDIR" (search-input-directory inputs "share/zoneinfo")))) (add-after 'configure 'chdir (lambda _ (chdir "src/nmath/standalone/")))))) (synopsis "Standalone R math library") (description "This package provides the R math library as an independent package."))) (define-public r-boot (package (name "r-boot") (version "1.3-30") (source (origin (method url-fetch) (uri (cran-uri "boot" version)) (sha256 (base32 "15zysf5manfsap7x0zvjzgdvs9whv137iasjydp1php6sqmxc2am")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/boot") (synopsis "Bootstrap functions for R") (description "This package provides functions and datasets for bootstrapping from the book \"Bootstrap Methods and Their Application\" by A.C. Davison and D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.") ;; Unlimited distribution (license (license:non-copyleft "file://R/bootfuns.q")))) (define-public r-mass (package (name "r-mass") (version "7.3-61") (source (origin (method url-fetch) (uri (cran-uri "MASS" version)) (sha256 (base32 "140ah1719zad8gd0glvy9qlkxxakgz12i5r5gk2bgmwxayzwhi1i")))) (properties `((upstream-name . "MASS"))) (build-system r-build-system) (home-page "https://www.stats.ox.ac.uk/pub/MASS4/") (synopsis "Support functions and datasets for Venables and Ripley's MASS") (description "This package provides functions and datasets for the book \"Modern Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.") ;; Either version may be picked. (license (list license:gpl2 license:gpl3)))) (define-public r-class (package (name "r-class") (version "7.3-22") (source (origin (method url-fetch) (uri (cran-uri "class" version)) (sha256 (base32 "0p6i10jk8mb85bkx4lvixw85lsmgnk4cizcdw33zqhrqx5j436dn")))) (build-system r-build-system) (propagated-inputs (list r-mass)) (home-page "https://www.stats.ox.ac.uk/pub/MASS4/") (synopsis "R functions for classification") (description "This package provides various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.") ;; Either of the two versions can be picked. (license (list license:gpl2 license:gpl3)))) (define-public r-cluster (package (name "r-cluster") (version "2.1.6") (source (origin (method url-fetch) (uri (cran-uri "cluster" version)) (sha256 (base32 "0r1i243mjbsx00ccg3f46c5iwnfmjxmhhdjvrj3m799mzpx0xifi")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/cluster") (synopsis "Methods for cluster analysis") (description "This package provides methods for cluster analysis. It is a much extended version of the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".") (license license:gpl2+))) (define-public r-codetools (package (name "r-codetools") (version "0.2-20") (source (origin (method url-fetch) (uri (cran-uri "codetools" version)) (sha256 (base32 "0qx8zrlickl45wzzbydsbx5f1vmzhn71x7amzpfj71qpxisz7riv")))) (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.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) (define-public r-foreign (package (name "r-foreign") (version "0.8-87") (source (origin (method url-fetch) (uri (cran-uri "foreign" version)) (sha256 (base32 "0mi8vf3bsvrn2nh9kxjlgsmvxrc8icw51scr0mscqyp8r3saq90s")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/foreign") (synopsis "Read data stored by other statistics software") (description "This package provides functions for reading and writing data stored by some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and for reading and writing some dBase files.") (license license:gpl2+))) (define-public r-kernsmooth (package (name "r-kernsmooth") (version "2.23-24") (source (origin (method url-fetch) (uri (cran-uri "KernSmooth" version)) (sha256 (base32 "0pxc53sw9f4hhxnl3zkalkkk0fvzcfxw7c4ibrb95zbzahwyrcyh")))) (properties `((upstream-name . "KernSmooth"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://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://LICENCE.note")))) (define-public r-lattice (package (name "r-lattice") (version "0.22-6") (source (origin (method url-fetch) (uri (cran-uri "lattice" version)) (sha256 (base32 "1xq09lfjlca6c7mn412hjjav0q66p7wmjrwx5f3ygv3jwh8p4dsb")))) (build-system r-build-system) (home-page "https://lattice.r-forge.r-project.org/") (synopsis "High-level data visualization system") (description "The lattice package provides a powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to handle most nonstandard requirements.") (license license:gpl2+))) (define-public r-matrix (package (name "r-matrix") (version "1.7-0") (source (origin (method url-fetch) (uri (cran-uri "Matrix" version)) (sha256 (base32 "0dxd13y6x6pz54ccbcalw2sm646h9pls4bby9zmj40ipvyhbp5zv")))) (properties `((upstream-name . "Matrix"))) (build-system r-build-system) (propagated-inputs (list r-lattice)) (home-page "https://Matrix.R-forge.R-project.org/") (synopsis "Sparse and dense matrix classes and methods") (description "This package provides classes and methods for dense and sparse matrices and operations on them using LAPACK and SuiteSparse.") (license license:gpl2+))) (define-public r-nlme (package (name "r-nlme") (version "3.1-166") (source (origin (method url-fetch) (uri (cran-uri "nlme" version)) (sha256 (base32 "0qlpj3hjnlvd7x3ayjhvvpxlc2z4bfwk9qpglw8mnxbqipp18yi3")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/nlme") (synopsis "Linear and nonlinear mixed effects models") (description "This package provides tools to fit and compare Gaussian linear and nonlinear mixed-effects models.") (license license:gpl2+))) (define-public r-mgcv (package (name "r-mgcv") (version "1.9-1") (source (origin (method url-fetch) (uri (cran-uri "mgcv" version)) (sha256 (base32 "0cnvbdda243as2bxfsgnnk7xjmp1msgr9i4vbd84jfnxpqvvq3vh")))) (build-system r-build-system) (propagated-inputs (list r-matrix r-nlme)) (home-page "https://cran.r-project.org/web/packages/mgcv") (synopsis "Mixed generalised additive model computation") (description "GAMs, GAMMs and other generalized ridge regression with multiple smoothing parameter estimation by GCV, REML or UBRE/AIC. The library includes a @code{gam()} function, a wide variety of smoothers, JAGS support and distributions beyond the exponential family.") (license license:gpl2+))) (define-public r-nnet (package (name "r-nnet") (version "7.3-19") (source (origin (method url-fetch) (uri (cran-uri "nnet" version)) (sha256 (base32 "1rrc70shnrnn7gyq5fhnmw841a06d8y0vp5pp8xv1lvhj931y959")))) (build-system r-build-system) (home-page "https://www.stats.ox.ac.uk/pub/MASS4/") (synopsis "Feed-forward neural networks and multinomial log-linear models") (description "This package provides functions for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.") (license (list license:gpl2+ license:gpl3+)))) (define-public r-rpart (package (name "r-rpart") (version "4.1.23") (source (origin (method url-fetch) (uri (cran-uri "rpart" version)) (sha256 (base32 "1bxbvbv3jwz1j6yhgswbr6qy574n9rbp3cnwl9badkm6dbnrmf7r")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rpart") (synopsis "Recursive partitioning and regression trees") (description "This package provides recursive partitioning functions for classification, regression and survival trees.") (license (list license:gpl2+ license:gpl3+)))) (define-public r-spatial (package (name "r-spatial") (version "7.3-17") (source (origin (method url-fetch) (uri (cran-uri "spatial" version)) (sha256 (base32 "1msxbxz50qmzjxgix2vcq0f50b4cdvj8nz3qlilp397jrzc3w07i")))) (build-system r-build-system) (home-page "https://www.stats.ox.ac.uk/pub/MASS4/") (synopsis "Functions for kriging and point pattern analysis") (description "This package provides functions for kriging and point pattern analysis.") ;; Either version may be picked. (license (list license:gpl2 license:gpl3)))) (define-public r-survival (package (name "r-survival") (version "3.7-0") (source (origin (method url-fetch) (uri (cran-uri "survival" version)) (sha256 (base32 "1vzy8kg159yqnvg733air11la2qrirwcqhn9d67h5c18r67b15nd")))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (home-page "https://github.com/therneau/survival") (synopsis "Survival analysis") (description "This package contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.") (license license:lgpl2.0+))) (define-public r (package (inherit r-minimal) (name "r") (source #f) (build-system trivial-build-system) (arguments '(#:builder (begin (mkdir %output) #t))) (propagated-inputs (list r-minimal r-boot r-class r-cluster r-codetools r-foreign r-kernsmooth r-lattice r-mass r-matrix r-mgcv r-nlme r-nnet r-rpart r-spatial r-survival)))) (define-public r-bit (package (name "r-bit") (version "4.0.5") (source (origin (method url-fetch) (uri (cran-uri "bit" version)) (sha256 (base32 "1g5zakrzkhrqh3d7p1zka6zzzw11rdlbrvxsh05s7dkli1m57wph")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://ff.r-forge.r-project.org") (synopsis "Class for vectors of 1-bit booleans") (description "This package provides bitmapped vectors of booleans (no @code{NA}s), coercion from and to logicals, integers and integer subscripts, fast boolean operators and fast summary statistics. With @code{bit} class vectors of true binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.") (license license:gpl2))) (define-public r-bit64 (package (name "r-bit64") (version "4.0.5") (source (origin (method url-fetch) (uri (cran-uri "bit64" version)) (sha256 (base32 "0y0m7q1rwam1g88cjx7zyi07mj5dipxd9jkl90f294syx8k6ipr5")))) (build-system r-build-system) (propagated-inputs (list r-bit)) (home-page "https://ff.r-forge.r-project.org/") (synopsis "S3 class for vectors of 64 bit integers") (description "The bit64 package provides serializable S3 atomic 64 bit (signed) integers that can be used in vectors, matrices, arrays and @code{data.frames}. Methods are available for coercion from and to logicals, integers, doubles, characters and factors as well as many elementwise and summary functions. Many fast algorithmic operations such as @code{match} and @code{order} support interactive data exploration and manipulation and optionally leverage caching.") (license license:gpl2))) (define-public r-chorddiag (package (name "r-chorddiag") (version "0.1.3") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/mattflor/chorddiag") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1bpy9q861l1hyyiqbx2f7qzp7j7im8bkcfdwgxzk5fm0250p359a")) ;; Delete minified JavaScript file (snippet '(delete-file "inst/htmlwidgets/lib/d3/d3.min.js")))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/d3" (let ((source (assoc-ref inputs "d3.v4.js")) (target "d3.min.js")) (format #true "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))))))))) (propagated-inputs (list r-htmlwidgets r-rcolorbrewer)) (native-inputs `(("esbuild" ,esbuild) ("r-knitr" ,r-knitr) ("d3.v4.js" ,(origin (method url-fetch) (uri "https://d3js.org/d3.v4.js") (sha256 (base32 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))))) (home-page "https://github.com/mattflor/chorddiag") (synopsis "Create D3 chord diagram") (description "This package provides tools to create interactive chords diagrams via the D3 Javascript library. Chord diagrams show directed relationships among a group of entities. This package is based on @url{http://bl.ocks.org/mbostock/4062006} with some modifications (fading) and additions (tooltips, bipartite diagram type).") (license license:gpl3+))) (define-public r-dichromat (package (name "r-dichromat") (version "2.0-0.1") (source (origin (method url-fetch) (uri (cran-uri "dichromat" version)) (sha256 (base32 "10b0avdar3d1y8x2ya3x5kqxqg0z0mq872hdzvc1nn4amplph1d1")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/dichromat") (synopsis "Color schemes for dichromats") (description "Dichromat collapses red-green or green-blue distinctions to simulate the effects of different types of color-blindness.") (license license:gpl2+))) (define-public r-digest (package (name "r-digest") (version "0.6.37") (source (origin (method url-fetch) (uri (cran-uri "digest" version)) (sha256 (base32 "0883iyjbd50f0gwz6hgdmcsrk0i0fkjaix9hz6d4m2jbk54x3i42")))) (build-system r-build-system) ;; Vignettes require r-knitr, which requires r-digest, so we have to ;; disable them and the tests. (arguments `(#:tests? #f #:configure-flags (list "--no-build-vignettes"))) (native-inputs (list r-simplermarkdown)) (home-page "https://dirk.eddelbuettel.com/code/digest.html") (synopsis "Create cryptographic hash digests of R objects") (description "This package contains an implementation of a function @code{digest()} for the creation of hash digests of arbitrary R objects (using the md5, sha-1, sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison of R language objects, as well as a function @code{hmac()} to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as OpenSSL should be used.") (license license:gpl2+))) (define-public r-estimability (package (name "r-estimability") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "estimability" version)) (sha256 (base32 "1sa42rczhzfj0dkn8v1pq6b752rh6h7x553gcgl7g27x75mbk9iw")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/estimability") (synopsis "Tools for assessing estimability of linear predictions") (description "This package provides tools for determining estimability of linear functions of regression coefficients, and @code{epredict} methods that handle non-estimable cases correctly.") (license license:gpl2+))) (define-public r-labeling (package (name "r-labeling") (version "0.4.3") (source (origin (method url-fetch) (uri (cran-uri "labeling" version)) (sha256 (base32 "1wk4wa1s8f17b5lf8vs5hxsmyadp2ccmyg4hamq7sdvlrk14yby6")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/labeling") (synopsis "Axis labeling algorithms") (description "The labeling package provides a range of axis labeling algorithms.") (license license:expat))) (define-public r-magrittr (package (name "r-magrittr") (version "2.0.3") (source (origin (method url-fetch) (uri (cran-uri "magrittr" version)) (sha256 (base32 "1ljmrrm36y31db5z4cl863ap8k3jcaxk0qzy3f0cn6iag4zzigx2")))) (build-system r-build-system) ;; knitr needs magrittr #; (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/magrittr/index.html") (synopsis "Forward-pipe operator for R") (description "Magrittr provides a mechanism for chaining commands with a new forward-pipe operator, %>%. This operator will forward a value, or the result of an expression, into the next function call/expression. There is flexible support for the type of right-hand side expressions. For more information, see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"") (license license:expat))) (define-public r-munsell (package (name "r-munsell") (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "munsell" version)) (sha256 (base32 "19i9jjawlqciw4n4h99a4sm0lbc77la3pqyzjvnwsrh7qjdgv8h3")))) (build-system r-build-system) (propagated-inputs (list r-colorspace)) (home-page "https://cran.r-project.org/web/packages/munsell") (synopsis "Munsell colour system") (description "The Munsell package contains Functions for exploring and using the Munsell colour system.") (license license:expat))) (define-public r-permute (package (name "r-permute") (version "0.9-7") (source (origin (method url-fetch) (uri (cran-uri "permute" version)) (sha256 (base32 "1h4dyhcsv8p3h3qxsy98pib9v79dddvrnq7qx6abkblsazxqzy7g")))) (build-system r-build-system) (native-inputs (list r-knitr)) ;; Tests do not run correctly, but running them properly would entail a ;; circular dependency with vegan. (home-page "https://github.com/gavinsimpson/permute") (synopsis "Functions for Generating Restricted Permutations of Data") (description "This package provides a set of restricted permutation designs for freely exchangeable, line transects (time series), spatial grid designs and permutation of blocks (groups of samples). @code{permute} also allows split-plot designs, in which the whole-plots or split-plots or both can be freely exchangeable.") (license license:gpl2+))) (define-public r-plyr (package (name "r-plyr") (version "1.8.9") (source (origin (method url-fetch) (uri (cran-uri "plyr" version)) (sha256 (base32 "00z1mvqisnzbbwcwax1gm9ilahpgp21kk4l7hqdz8fym27vygd8m")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "http://had.co.nz/plyr") (synopsis "Tools for Splitting, Applying and Combining Data") (description "Plyr is a set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put all the pieces back together. For example, you might want to fit a model to each spatial location or time point in your study, summarise data by panels or collapse high-dimensional arrays to simpler summary statistics.") (license license:expat))) (define-public r-proto (package (name "r-proto") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "proto" version)) (sha256 (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j")))) (build-system r-build-system) (home-page "https://github.com/hadley/proto") (synopsis "Prototype object-based programming") (description "Proto is an object oriented system using object-based, also called prototype-based, rather than class-based object oriented ideas.") (license license:gpl2+))) (define-public r-rcolorbrewer (package (name "r-rcolorbrewer") (version "1.1-3") (source (origin (method url-fetch) (uri (cran-uri "RColorBrewer" version)) (sha256 (base32 "1h0s0f4vvlk40cagp3qwhd0layzkjcnqkiwjyhwqns257i1gahjg")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/RColorBrewer") (synopsis "ColorBrewer palettes") (description "This package provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org") ;; Includes code licensed under bsd-4 (license license:asl2.0))) (define-public r-sendmailr (package (name "r-sendmailr") (version "1.4-0") (source (origin (method url-fetch) (uri (cran-uri "sendmailR" version)) (sha256 (base32 "1balci88r2ci51xdh5zaqm3ss3vnry8pbkx2qngppc7n2gy932sv")))) (properties `((upstream-name . "sendmailR"))) (build-system r-build-system) (propagated-inputs (list r-base64enc)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/sendmailR") (synopsis "Send email using R") (description "This package contains a simple SMTP client which provides a portable solution for sending email, including attachments, from within R.") (license license:gpl2+))) (define-public r-stringi (package (name "r-stringi") (version "1.8.4") (source (origin (method url-fetch) (uri (cran-uri "stringi" version)) (sha256 (base32 "1wv9qqxl84l44kpvkx0lmyciinrh9pa5512jm56gsaqs9pvgh6f2")))) (build-system r-build-system) (inputs (list icu4c)) (native-inputs (list pkg-config)) (home-page "http://stringi.rexamine.com/") (synopsis "Character string processing facilities") (description "This package allows for fast, correct, consistent, portable, as well as convenient character string/text processing in every locale and any native encoding. Owing to the use of the ICU library, the package provides R users with platform-independent functions known to Java, Perl, Python, PHP, and Ruby programmers. Among available features there are: pattern searching (e.g. via regular expressions), random string generation, string collation, transliteration, concatenation, date-time formatting and parsing, etc.") (license license:bsd-3))) (define-public r-stringr (package (name "r-stringr") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "stringr" version)) (sha256 (base32 "1pj5xwg8kq2jllmszgkw96qj37wlb0x0vx4f3m5j211zpd8yrbd4")))) (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-lifecycle r-magrittr r-rlang r-stringi r-vctrs)) ;; We can't add r-knitr here, because this package ends up being an input ;; to r-knitr. #; (native-inputs (list r-knitr)) (home-page "https://github.com/hadley/stringr") (synopsis "Simple, consistent wrappers for common string operations") (description "Stringr is a consistent, simple and easy to use set of wrappers around the fantastic @code{stringi} package. All function and argument names (and positions) are consistent, all functions deal with \"NA\"'s and zero length vectors in the same way, and the output from one function is easy to feed into the input of another.") (license license:gpl2+))) (define-public r-reshape2 (package (name "r-reshape2") (version "1.4.4") (source (origin (method url-fetch) (uri (cran-uri "reshape2" version)) (sha256 (base32 "1n0jrajpvc8hjkh9z4g8bwq63qy5vy5cgl2pzjardyih4ngcz3fq")))) (build-system r-build-system) (propagated-inputs (list r-plyr r-rcpp r-stringr)) (home-page "https://github.com/hadley/reshape") (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package") (description "Reshape2 is an R library to flexibly restructure and aggregate data using just two functions: melt and dcast (or acast).") (license license:expat))) (define-public r-ggplot2 (package (name "r-ggplot2") (version "3.5.1") (source (origin (method url-fetch) (uri (cran-uri "ggplot2" version)) (sha256 (base32 "08a72kizg42mdm35170fnpn8l6r4n3j1yvbgiq1k8dlvz4jb8n3w")))) (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-gtable r-isoband r-lifecycle r-mass r-mgcv r-rlang r-scales r-svglite ; Needed for 'ggsave' r-tibble r-vctrs r-withr)) (native-inputs (list r-knitr)) (home-page "https://ggplot2.tidyverse.org") (synopsis "Implementation of the grammar of graphics") (description "Ggplot2 is an implementation of the grammar of graphics in R. It combines the advantages of both base and lattice graphics: conditioning and shared axes are handled automatically, and you can still build up a plot step by step from multiple data sources. It also implements a sophisticated multidimensional conditioning system and a consistent interface to map data to aesthetic attributes.") (license license:gpl2+))) (define-public r-ggdendro (package (name "r-ggdendro") (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "ggdendro" version)) (sha256 (base32 "0sdayyzvhkbli0ha68mc0f7cgp36njv9ign37d63l21hvd6w6h0r")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-mass)) (native-inputs (list r-knitr)) (home-page "https://github.com/andrie/ggdendro") (synopsis "Create Dendrograms and Tree Diagrams Using ggplot2") (description "This is a set of tools for dendrograms and tree plots using ggplot2. The ggplot2 philosophy is to clearly separate data from the presentation. Unfortunately the plot method for dendrograms plots directly to a plot device with out exposing the data. The ggdendro package resolves this by making available functions that extract the dendrogram plot data. The package provides implementations for tree, rpart, as well as diana and agnes cluster diagrams.") (license license:gpl2+))) (define-public r-gdtools (package (name "r-gdtools") (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "gdtools" version)) (sha256 (base32 "155ky9fdi023b5fjk1gh3607xlgm3hymq232fq03ip2aaywc74nj")))) (build-system r-build-system) (native-inputs (list pkg-config)) (inputs (list cairo fontconfig freetype zlib)) (propagated-inputs (list r-curl r-fontquiver r-gfonts r-htmltools r-rcpp r-systemfonts)) (home-page "https://cran.r-project.org/web/packages/gdtools") (synopsis "Utilities for graphical rendering") (description "The @code{gdtools} package provides functionalities to get font metrics and to generate base64 encoded string from raster matrix.") (license license:gpl3))) (define-public r-svglite (package (name "r-svglite") (version "2.1.3") (source (origin (method url-fetch) (uri (cran-uri "svglite" version)) (sha256 (base32 "0m0axxrkiih4wmrp9qh803p4l92fdgrsbxaww38z89widx75da7h")))) (properties `((upstream-name . "svglite"))) (build-system r-build-system) (inputs (list libpng zlib)) (propagated-inputs (list r-cpp11 r-systemfonts)) (native-inputs (list r-knitr)) (home-page "https://svglite.r-lib.org") (synopsis "SVG graphics device") (description "@code{svglite} is a graphics device that produces clean @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or hand editing. Compared to the built-in @code{svg()}, @code{svglite} is considerably faster, produces smaller files, and leaves text as is.") (license license:gpl2+))) (define-public r-assertthat (package (name "r-assertthat") (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "assertthat" version)) (sha256 (base32 "17wy5bdfzg73sg2clisg1k3zyn1adkj59x56m5nwia2k8z67zkw5")))) (build-system r-build-system) (home-page "https://github.com/hadley/assertthat") (synopsis "Easy pre and post assertions") (description "Assertthat is an extension to stopifnot() that makes it easy to declare the pre and post conditions that your code should satisfy, while also producing friendly error messages so that your users know what they've done wrong.") (license license:gpl3+))) (define-public r-lazyeval (package (name "r-lazyeval") (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "lazyeval" version)) (sha256 (base32 "1m10i059csrcqkcn59a8wspn784alxsq3symzhn24mhhl894346n")))) (build-system r-build-system) (home-page "https://github.com/hadley/lazyeval") (synopsis "Lazy (non-standard) evaluation in R") (description "This package provides the tools necessary to do non-standard evaluation (NSE) in R.") (license license:gpl3+))) (define-public r-dbi (package (name "r-dbi") (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "DBI" version)) (sha256 (base32 "1gid1mfzq1j3n5fsnpzdb50p2m73z92s6njp0sgr503aaskhhryg")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/rstats-db/DBI") (synopsis "R database interface") (description "The DBI package provides a database interface (DBI) definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.") (license license:lgpl2.0+))) (define-public r-bh (package (name "r-bh") (version "1.84.0-0") (source (origin (method url-fetch) (uri (cran-uri "BH" version)) (sha256 (base32 "1b7igvvy9f13l969a26j2bdzib2laq3m4w1x0xsxjb2pbxsn1dkg")))) (build-system r-build-system) (home-page "https://github.com/eddelbuettel/bh") (synopsis "R package providing subset of Boost headers") (description "This package aims to provide the most useful subset of Boost libraries for template use among CRAN packages.") (license license:boost1.0))) (define-public r-evaluate (package (name "r-evaluate") (version "0.24.0") (source (origin (method url-fetch) (uri (cran-uri "evaluate" version)) (sha256 (base32 "1mkzb2f8rv0qd33h3gqq7idkpxnnx7zcr93xsmbm4lp7b157cgg2")))) (build-system r-build-system) (home-page "https://github.com/hadley/evaluate") (synopsis "Parsing and evaluation tools for R") (description "This package provides tools that allow you to recreate the parsing, evaluation and display of R code, with enough information that you can accurately recreate what happens at the command line. The tools can easily be adapted for other output formats, such as HTML or LaTeX.") (license license:gpl3+))) (define-public r-formatr (package (name "r-formatr") (version "1.14") (source (origin (method url-fetch) (uri (cran-uri "formatR" version)) (sha256 (base32 "0k271w4bhlj7r9igkiyfw7d7bg30s2mn4sr4alb8f9w57wnapfjf")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://yihui.org/formatr/") (synopsis "Format R code automatically") (description "This package provides a function to format R source code. Spaces and indent will be added to the code automatically, and comments will be preserved under certain conditions, so that R code will be more human-readable and tidy. There is also a Shiny app as a user interface in this package.") (license license:gpl3+))) (define-public r-highr (package (name "r-highr") (version "0.11") (source (origin (method url-fetch) (uri (cran-uri "highr" version)) (sha256 (base32 "19z0gwdy46z6gb46b3fs2ljxa2cn0bpvx7aam0jk75h180l183g9")))) (build-system r-build-system) (propagated-inputs (list r-xfun)) ;; We cannot add knitr to the inputs, because highr depends on xfun, which ;; is an input to knitr. #; (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/yihui/highr") (synopsis "Syntax highlighting for R source code") (description "This package provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package.") (license license:gpl3+))) (define-public r-httpgd (let ((commit "3f5f55822c4dce930155b91cedcfd4d483e3294e") (revision "1")) (package (name "r-httpgd") (version (git-version "2.0.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/nx10/httpgd") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "14i7mhbv1vcz2886w9lii9zhgr4zhhc844349syb989nhhzg552n")))) (properties `((upstream-name . "httpgd"))) (build-system r-build-system) (propagated-inputs (list r-asioheaders r-cpp11 r-unigd)) (native-inputs (list r-knitr)) (home-page "https://github.com/nx10/httpgd") (synopsis "'HTTP' Server Graphics Device") (description "This package provides a graphics device for R that is accessible via network protocols. This package was created to make it easier to embed live R graphics in integrated development environments and other applications. The included HTML/@code{JavaScript} client (plot viewer) aims to provide a better overall user experience when dealing with R graphics. The device asynchronously serves graphics via HTTP and @code{WebSockets}'.") (license license:gpl2+)))) (define-public r-mime (package (name "r-mime") (version "0.12") (source (origin (method url-fetch) (uri (cran-uri "mime" version)) (sha256 (base32 "0j9qbq9jfsp61h2d0xmb87pa2wi8nhb1h2wih7l5drf1sr8i0059")))) (build-system r-build-system) (home-page "https://github.com/yihui/mime") (synopsis "R package to map filenames to MIME types") (description "This package guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems.") (license license:gpl2))) (define-public r-markdown (package (name "r-markdown") (version "1.13") (source (origin (method url-fetch) (uri (cran-uri "markdown" version)) (sha256 (base32 "1nfgngskgb4r34r3cnkm0gn7p1axpcb7rpyi0jxg4nygfk322m1q")))) (build-system r-build-system) ;; Skip check phase because the tests require the r-knitr package to be ;; installed. This prevents installation failures. Knitr normally ;; shouldn't be available since r-markdown is a dependency of the r-knitr ;; package. (arguments `(#:tests? #f)) (propagated-inputs (list r-commonmark r-xfun)) (home-page "https://github.com/rstudio/markdown") (synopsis "Markdown rendering for R") (description "This package provides R bindings to the Sundown Markdown rendering library (https://github.com/vmg/sundown). Markdown is a plain-text formatting syntax that can be converted to XHTML or other formats.") (license license:gpl2))) (define-public r-yaml (package (name "r-yaml") (version "2.3.10") (source (origin (method url-fetch) (uri (cran-uri "yaml" version)) (sha256 (base32 "0v9al1fh82vpjhml91j73sim7gfyc0154kxaam41sdkf6qnx8dp2")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/yaml/") (synopsis "Methods to convert R data to YAML and back") (description "This package implements the libyaml YAML 1.1 parser and emitter (http://pyyaml.org/wiki/LibYAML) for R.") (license license:bsd-3))) (define-public r-knitr (package (name "r-knitr") (version "1.48") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 "15zipywk2ayrmy0p7q4d18512c2cgr9kk1lmc7gyi8bxv8k5j6sh")))) (build-system r-build-system) (propagated-inputs (list r-evaluate r-highr r-xfun r-yaml)) (home-page "https://yihui.org/knitr/") (synopsis "General-purpose package for dynamic report generation in R") (description "This package provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.") ;; The code is released under any version of the GPL. As it is used by ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+ ;; here. (license license:gpl2+))) (define-public r-knitrbootstrap (package (name "r-knitrbootstrap") (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "knitrBootstrap" version)) (sha256 (base32 "157mn2gm7djfiw1b55vdr2ylrmgxlpfg95bmm82ghv5g6vr26smd")))) (properties `((upstream-name . "knitrBootstrap"))) (build-system r-build-system) (propagated-inputs (list r-knitr r-markdown r-rmarkdown)) (native-inputs (list r-knitr)) (home-page "https://github.com/jimhester/knitrBootstrap") (synopsis "Knitr bootstrap framework") (description "This package provides a framework to create Bootstrap 3 HTML reports from knitr Rmarkdown.") (license license:expat))) (define-public r-microbenchmark (package (name "r-microbenchmark") (version "1.4.10") (source (origin (method url-fetch) (uri (cran-uri "microbenchmark" version)) (sha256 (base32 "10dlp4295jb5l7lhz80f4mkz3jccv02v277z666wx3bhfaz43k04")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/microbenchmark/") (synopsis "Accurate timing functions for R") (description "This package provides infrastructure to accurately measure and compare the execution time of R expressions.") (license license:bsd-2))) (define-public r-pryr (package (name "r-pryr") (version "0.1.6") (source (origin (method url-fetch) (uri (cran-uri "pryr" version)) (sha256 (base32 "013p2xxd51kr9ddx051cvn45mzgj44fm47nkchdb13l0885a7hb8")))) (build-system r-build-system) (propagated-inputs (list r-codetools r-lobstr r-rcpp r-stringr)) (home-page "https://github.com/hadley/pryr") (synopsis "Tools for computing on the R language") (description "This package provides useful tools to pry back the covers of R and understand the language at a deeper level.") (license license:gpl2))) (define-public r-memoise (package (name "r-memoise") (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "memoise" version)) (sha256 (base32 "1srdzv2bp0splislrabmf1sfbqfi3hn189nq7kxhgjn8k3p38l7q")))) (build-system r-build-system) (propagated-inputs (list r-cachem r-rlang)) (home-page "https://github.com/hadley/memoise") (synopsis "Memoise functions for R") (description "This R package caches the results of a function so that when you call it again with the same arguments it returns the pre-computed value.") (license license:expat))) (define-public r-crayon (package (name "r-crayon") (version "1.5.3") (source (origin (method url-fetch) (uri (cran-uri "crayon" version)) (sha256 (base32 "0sfsx4k77fsx1dx9c186dg273psrr3awz4ivfvmbbvs1amla0x1y")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/crayon") (synopsis "Colored terminal output for R") (description "Colored terminal output on terminals that support ANSI color and highlight codes. It also works in Emacs ESS. ANSI color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the \"chalk\" JavaScript project.") (license license:expat))) (define-public r-praise (package (name "r-praise") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "praise" version)) (sha256 (base32 "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/praise") (synopsis "Functions to praise users") (description "This package provides template functions to assist in building friendly R packages that praise their users.") (license license:expat))) (define-public r-testthat (package (name "r-testthat") (version "3.2.1.1") (source (origin (method url-fetch) (uri (cran-uri "testthat" version)) (sha256 (base32 "1xz94i0r62lslyqya8gz6i2r100wi26y5c2822v2i7lkflwwx1fp")))) (build-system r-build-system) (propagated-inputs (list r-brio r-callr r-cli r-desc r-digest r-evaluate r-jsonlite r-lifecycle r-magrittr r-pkgload r-praise r-processx r-ps r-r6 r-rlang r-waldo r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/hadley/testthat") (synopsis "Unit testing for R") (description "This package provides a unit testing system for R designed to be fun, flexible and easy to set up.") (license license:expat))) (define-public r-r6 (package (name "r-r6") (version "2.5.1") (source (origin (method url-fetch) (uri (cran-uri "R6" version)) (sha256 (base32 "0j5z0b0myzjyyykk310xsa9n2mcm9bz8yqbq4xgz2yzdq8lvv4ld")))) (build-system r-build-system) (home-page "https://github.com/wch/R6/") (synopsis "Classes with reference semantics in R") (description "The R6 package allows the creation of classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.") (license license:expat))) (define-public r-rlang (package (name "r-rlang") (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "rlang" version)) (sha256 (base32 "1qd6chyciwhj6f6w56d3pcy4q8qdvqkyn2s709qjiwwba0klbmzj")))) (build-system r-build-system) (home-page "http://rlang.tidyverse.org") (synopsis "Functions for base types, core R and Tidyverse features") (description "This package provides a toolbox for working with base types, core R features like the condition system, and core @code{Tidyverse} features like tidy evaluation.") (license license:gpl3))) (define-public r-tibble (package (name "r-tibble") (version "3.2.1") (source (origin (method url-fetch) (uri (cran-uri "tibble" version)) (sha256 (base32 "0c916wl19wbhncv05hjzs2vmvvbcxlswjl6i232ygmkzal62v9v5")))) (build-system r-build-system) (propagated-inputs (list r-fansi r-lifecycle r-magrittr r-pkgconfig r-pillar r-rlang r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/hadley/tibble") (synopsis "Simple data frames") (description "This package provides a @code{tbl_df} class that offers better checking and printing capabilities than traditional data frames.") (license license:expat))) (define-public r-dplyr (package (name "r-dplyr") (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "dplyr" version)) (sha256 (base32 "1jsq8pj12bngy66xms486j8a65wxvyqs944q9rxkiaylsla08wyg")))) (build-system r-build-system) (propagated-inputs (list r-cli r-generics r-glue r-lifecycle r-magrittr r-pillar r-r6 r-rlang r-tibble r-tidyselect r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/hadley/dplyr") (synopsis "Tools for working with data frames in R") (description "dplyr is the next iteration of plyr. It is focused on tools for working with data frames. It has three main goals: 1) identify the most important data manipulation tools needed for data analysis and make them easy to use in R; 2) provide fast performance for in-memory data by writing key pieces of code in C++; 3) use the same code interface to work with data no matter where it is stored, whether in a data frame, a data table or database.") (license license:expat))) (define-public r-dbplyr (package (name "r-dbplyr") (version "2.5.0") (source (origin (method url-fetch) (uri (cran-uri "dbplyr" version)) (sha256 (base32 "1zxw4ignzm2fzixsf6n80f44b9q7434vamy2xj4v31wlx3dmnixv")))) (build-system r-build-system) (propagated-inputs (list r-blob r-cli r-dbi r-dplyr r-glue r-lifecycle r-magrittr r-pillar r-purrr r-r6 r-rlang r-tibble r-tidyr r-tidyselect r-vctrs r-withr)) (native-inputs (list r-knitr)) (home-page "https://github.com/tidyverse/dbplyr") (synopsis "Dplyr back end for databases") (description "This package provides a dplyr back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a @code{DBI} back end; more advanced features require SQL translation to be provided by the package author.") (license license:expat))) (define-public r-acepack (package (name "r-acepack") (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "acepack" version)) (sha256 (base32 "14dccqpww3bv59236r0vr6bibhsafhbm7qshdjxp5ww3nw9cvzsv")))) (properties `((upstream-name . "acepack") (updater-extra-inputs . ("gfortran")))) (build-system r-build-system) (inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/acepack") (synopsis "Functions for regression transformations") (description "This package provides ACE and AVAS methods for choosing regression transformations.") (license license:expat))) (define-public r-formula (package (name "r-formula") (version "1.2-5") (source (origin (method url-fetch) (uri (cran-uri "Formula" version)) (sha256 (base32 "0p1m9pqcn8ns0sn67js53677q8gwxgbl4bymcn5y2r0dc1s4c9c6")))) (properties `((upstream-name . "Formula"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/Formula") (synopsis "Extended model formulas") (description "This package provides a new class @code{Formula}, which extends the base class @code{formula}. It supports extended formulas with multiple parts of regressors on the right-hand side and/or multiple responses on the left-hand side.") (license (list license:gpl2+ license:gpl3+)))) (define-public r-locfit (package (name "r-locfit") (version "1.5-9.10") (source (origin (method url-fetch) (uri (cran-uri "locfit" version)) (sha256 (base32 "01mcfsqqqwdf9iggabyckid7rf5c9f0v0hjz8g58fflr2hc6c82c")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) (home-page "https://cran.r-project.org/web/packages/locfit") (synopsis "Local regression, likelihood and density estimation") (description "This package provides functions used for local regression, likelihood and density estimation.") (license (list license:gpl2+ license:gpl3+)))) (define-public r-chron (package (name "r-chron") (version "2.3-61") (source (origin (method url-fetch) (uri (cran-uri "chron" version)) (sha256 (base32 "16rvqkb7c969795d1z1ypb2cfly70zp24qs8ndsq0hx04mv9b5m0")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/chron") (synopsis "Chronological R objects which can handle dates and times") (description "This package provides chronological R objects which can handle dates and times.") (license license:gpl2))) (define-public r-data-table (package (name "r-data-table") (version "1.16.0") (source (origin (method url-fetch) (uri (cran-uri "data.table" version)) (sha256 (base32 "1kgrdv2iijn7qd39prwvcrglcp992xf2jl5a9zc81plr032sxy2q")))) (properties `((upstream-name . "data.table"))) (build-system r-build-system) (inputs (list zlib)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/Rdatatable/data.table/wiki") (synopsis "Enhanced version of data.frame R object") (description "The R package @code{data.table} is an extension of @code{data.frame} providing functions for fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group, column listing and fast file reading.") (license license:gpl3+))) (define-public r-xtable (package (name "r-xtable") (version "1.8-4") (source (origin (method url-fetch) (uri (cran-uri "xtable" version)) (sha256 (base32 "077xfm0gphvhsay75amd9v90zk57kjgrrlgih04fyrbqqblc1gjs")))) (build-system r-build-system) (native-inputs (list r-knitr)) ; for vignettes (home-page "https://xtable.r-forge.r-project.org/") (synopsis "Export R tables to LaTeX or HTML") (description "This package provides tools to export R data as LaTeX and HTML tables.") (license license:gpl2+))) (define-public python-vega-datasets (package (name "python-vega-datasets") (version "0.9.0") (source (origin (method url-fetch) (uri (pypi-uri "vega_datasets" version)) (sha256 (base32 "1h1zv607mars2j73v8fdwihjh479blqxyw29nhmc73lf40s9iglx")) (modules '((guix build utils))) (patches (search-patches "python-vega-datasets-remove-la-riots-code.patch")))) (build-system pyproject-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (add-after 'unpack 'remove-la-riots-dataset ;; Remove dataset with unclear license. (lambda _ (delete-file "vega_datasets/_data/la-riots.csv")))))) (native-inputs (list python-pytest)) (propagated-inputs (list python-pandas)) (home-page "https://github.com/altair-viz/vega_datasets") (synopsis "Example datasets used by Vega-related projects") (description "This package provides a collection of datasets used in Vega and Vega-Lite examples.") (license license:expat))) (define-public python-altair (package (name "python-altair") (version "5.0.1") (source (origin (method git-fetch) ; no tests in PyPI (uri (git-reference (url "https://github.com/altair-viz/altair") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1r74v5n51br9pjhxdzrr62cdgnwkapci93aifnl8dqmfpizfpd7d")))) (build-system pyproject-build-system) (arguments ;; First two open an external connection. ;; Last introduces a circular dependency on altair-viewer. (list #:test-flags #~(list "-k" (string-append "not test_from_and_to_json_roundtrip" " and not test_render_examples_to_chart" " and not test_save_html")))) (propagated-inputs (list python-jinja2 python-jsonschema python-numpy python-pandas python-toolz python-typing-extensions)) (native-inputs (list python-black python-hatchling python-ipython python-m2r python-pytest python-vega-datasets)) (home-page "https://altair-viz.github.io/") (synopsis "Declarative statistical visualization library for Python") (description "Vega-Altair is a declarative statistical visualization library for Python.") (license license:expat))) (define-public python-hdmedians (package (name "python-hdmedians") (version "0.14.2") (source (origin (method url-fetch) (uri (pypi-uri "hdmedians" version)) (sha256 (base32 "1mn2k8srnmfy451l7zvb2l4hn9701bc5awjm6q3vmqbicyqyqyml")))) (build-system pyproject-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-before 'check 'build-extensions (lambda _ ;; Cython extensions have to be built before running the tests. (invoke "python" "setup.py" "build_ext" "--inplace")))))) (propagated-inputs (list python-cython python-numpy)) (native-inputs (list python-nose)) (home-page "http://github.com/daleroberts/hdmedians") (synopsis "High-dimensional medians") (description "Various definitions for a high-dimensional median exist and this Python package provides a number of fast implementations of these definitions. Medians are extremely useful due to their high breakdown point (up to 50% contamination) and have a number of nice applications in machine learning, computer vision, and high-dimensional statistics.") (license license:asl2.0))) (define-public python-arviz (package (name "python-arviz") (version "0.19.0") (source (origin (method git-fetch) ; PyPI misses some test files (uri (git-reference (url "https://github.com/arviz-devs/arviz") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0wj1yxr6as368vkr4mk9fz4584nyy12gq2v20l7542lnaabw403z")))) (build-system pyproject-build-system) (arguments ;; FIXME: matplotlib tests fail because of the "--save" test flag. (list #:test-flags #~'("--ignore" "arviz/tests/base_tests/test_plots_matplotlib.py") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'remove-radon (lambda _ (delete-file ;; This dataset is loaded remotely, it's not supposed to ;; be copied locally. "arviz/data/example_data/code/radon/radon.json"))) (add-before 'check 'write-permission (lambda _ ;; 3 tests require write permission. (setenv "HOME" "/tmp")))))) (native-inputs (list python-cloudpickle python-pytest)) (propagated-inputs (list python-dm-tree python-h5netcdf python-matplotlib python-numpy python-packaging python-pandas python-scipy python-typing-extensions python-xarray python-xarray-einstats)) (home-page "https://github.com/arviz-devs/arviz") (synopsis "Exploratory analysis of Bayesian models") (description "ArviZ is a Python package for exploratory analysis of Bayesian models. It includes functions for posterior analysis, data storage, model checking, comparison and diagnostics.") (license license:asl2.0))) (define-public python-pymc (package (name "python-pymc") (version "5.11.0") (source (origin (method git-fetch) ; no tests in PyPI (uri (git-reference (url "https://github.com/pymc-devs/pymc") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0x94qzq3z02fxlliz1xfdpb2pbn7nhp4skzcxz6qdavbj9xqcxys")))) (build-system pyproject-build-system) (arguments (list #:tests? #f ; tests are too computationally intensive #:phases #~(modify-phases %standard-phases (add-after 'unpack 'versioneer (lambda _ (with-output-to-file "setup.cfg" (lambda () (display "\ [versioneer] VCS = git style = pep440 versionfile_source = pymc/_version.py versionfile_build = pymc/_version.py tag_prefix = parentdir_prefix = pymc- "))) (invoke "versioneer" "install") (substitute* "setup.py" (("versioneer.get_version\\(\\)") (string-append "\"" #$version "\""))))) ;; To create the compiledir for tests. (add-before 'check 'write-permissions (lambda* (#:key tests? #:allow-other-keys) (when tests? (setenv "HOME" "/tmp"))))))) (native-inputs (list python-pytest-cov python-versioneer)) (propagated-inputs (list python-arviz python-cachetools python-cloudpickle python-fastprogress python-numpy python-pandas python-pytensor python-scipy python-typing-extensions)) (home-page "https://github.com/pymc-devs/pymc") (synopsis "Library for probabilistic programming in Python") (description "PyMC (formerly PyMC3) is a Python package for Bayesian statistical modeling focusing on advanced Markov chain Monte Carlo (MCMC) and variational inference (VI) algorithms.") (license license:asl2.0))) (define-public python-chaospy (package (name "python-chaospy") (version "4.3.13") (source (origin ;; PyPI misses Pytest fixtures. (method git-fetch) (uri (git-reference (url "https://github.com/jonathf/chaospy") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1bn4jmwygs5h0dskbniivj20qblgm75pyi9hcjf47r25kawd730m")))) (build-system pyproject-build-system) (arguments (list #:phases #~(modify-phases %standard-phases ;; The deprecation warnings break the tests. (add-after 'unpack 'dont-treat-deprecation-warnings-as-error (lambda _ (substitute* "pyproject.toml" (("\"error::DeprecationWarning\",") ""))))))) (propagated-inputs (list python-importlib-metadata python-numpoly python-numpy python-scipy)) (native-inputs (list python-pytest python-scikit-learn)) (home-page "https://chaospy.readthedocs.io/en/master/") (synopsis "Numerical tool for performing uncertainty quantification") (description "Chaospy is a numerical toolbox for performing uncertainty quantification using polynomial chaos expansions, advanced Monte Carlo methods implemented in Python. It also include a full suite of tools for doing low-discrepancy sampling, quadrature creation, polynomial manipulations, and a lot more.") (license license:expat))) (define-public python-patsy (package (name "python-patsy") (version "0.5.2") (source (origin (method url-fetch) (uri (pypi-uri "patsy" version)) (sha256 (base32 "17dn72519gvwifw3i8mzwlslxmxkl8ihzfrxg1iblsk70iwdwlsh")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? (invoke "pytest" "-vv"))))))) (propagated-inputs (list python-numpy python-scipy python-six)) (native-inputs (list python-pytest)) (home-page "https://github.com/pydata/patsy") (synopsis "Describe statistical models and build design matrices") (description "Patsy is a Python package for describing statistical models and for building design matrices.") ;; The majority of the code is distributed under BSD-2. The module ;; patsy.compat contains code derived from the Python standard library, ;; and is covered by the PSFL. (license (list license:bsd-2 license:psfl)))) (define-public python-lifelines (package (name "python-lifelines") (version "0.28.0") (source (origin (method url-fetch) (uri (pypi-uri "lifelines" version)) (sha256 (base32 "0pmjb3z1rw1ia64gw87r6y9x1g4kwpw239gqzsa9qh7xadj75kzf")))) (build-system pyproject-build-system) (arguments (list #:test-flags ;; This accuracy test fails because 0.012 is not < 0.01. '(list "-k" "not test_weibull_with_delayed_entries"))) (propagated-inputs (list python-autograd python-autograd-gamma python-formulaic python-matplotlib python-numpy python-pandas python-scipy)) (native-inputs (list python-dill python-flaky python-joblib python-pytest)) (home-page "https://github.com/CamDavidsonPilon/lifelines") (synopsis "Survival analysis including Kaplan Meier, Nelson Aalen and regression") (description "This package enables survival analysis in Python, including Kaplan Meier, Nelson Aalen and regression.") (license license:expat))) (define-public python-mapie (package (name "python-mapie") (version "0.8.6") (source (origin (method url-fetch) (uri (pypi-uri "MAPIE" version)) (sha256 (base32 "013ljcjjl3k9yb3166fnvr6nsb9ph4rhidpdjjks78qw0w1j7faa")))) (build-system pyproject-build-system) ;; See https://github.com/scikit-learn-contrib/MAPIE/issues/432 (arguments (list #:test-flags '(list "-k" (string-append "not test_correct_results" " and not test_correct_results_binary")))) (native-inputs (list python-pandas python-pytest)) (propagated-inputs (list python-numpy python-scikit-learn)) (home-page "https://github.com/scikit-learn-contrib/MAPIE") (synopsis "Module for estimating prediction intervals") (description "MAPIE allows you to easily estimate prediction intervals (or prediction sets) using your favourite scikit-learn-compatible model for single-output regression or multi-class classification settings. Prediction intervals output by MAPIE encompass both aleatoric and epistemic uncertainties and are backed by strong theoretical guarantees thanks to conformal prediction methods intervals.") (license license:bsd-3))) (define-public python-emcee (package (name "python-emcee") (version "3.1.6") (source (origin (method url-fetch) (uri (pypi-uri "emcee" version)) (sha256 (base32 "0zb3ihja3hyj6zjbhkpxhyyppnv58q2jjg0yd1lwmydqdaplvbqi")))) (build-system pyproject-build-system) (propagated-inputs (list python-numpy)) (native-inputs (list python-coverage python-pytest python-pytest-cov python-setuptools-scm)) (home-page "https://emcee.readthedocs.io/en/stable/") (synopsis "Ensemble sampling toolkit for MCMC") (description "@code{emcee} is a Python implementation of the affine-invariant ensemble sampler for Markov chain Monte Carlo (MCMC).") (license license:expat))) (define-public python-statsmodels (package (name "python-statsmodels") (version "0.14.0") (source (origin (method url-fetch) (uri (pypi-uri "statsmodels" version)) (sha256 (base32 "1927ysv7m46m1x3wz05i0s3r5x0nasmidf2yy54djrp9i7bcfxb8")) (modules '((guix build utils))) (snippet '(for-each delete-file (find-files "." "\\.c$"))))) (build-system pyproject-build-system) (arguments (list ;; The test suite is very large and rather brittle. Tests often fail ;; because of minor changes in dependencies that upstream hasn't fixed ;; in a new release. #:tests? #f #:phases #~(modify-phases %standard-phases (add-after 'unpack 'set-matplotlib-backend-to-agg (lambda _ ;; Set the matplotlib backend to Agg to avoid problems using the ;; GTK backend without a display. (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py") '("statsmodels/tsa/vector_ar/tests/test_var.py" "statsmodels/duration/tests/test_survfunc.py")) (("import matplotlib\\.pyplot as plt" line) (string-append "import matplotlib;matplotlib.use('Agg');" line)))))))) (propagated-inputs (list python-numpy python-packaging python-pandas python-patsy python-scipy)) (native-inputs (list python-colorama python-cython python-flake8 python-isort python-joblib python-matplotlib python-pytest python-pytest-randomly python-pytest-xdist python-setuptools-scm)) (home-page (string-append "https://www.statsmodels.org/v" version "/")) (synopsis "Statistical modeling and econometrics in Python") (description "Statsmodels is a Python package that provides a complement to scipy for statistical computations including descriptive statistics and estimation and inference for statistical models.") (license license:bsd-3))) (define-public python-openturns (package (name "python-openturns") (version "1.21.3") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/openturns/openturns") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0nf77p6zv2br23n3c0yidnclb0234ni07y67h1h1f2bng4kdn8jp")))) (build-system cmake-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (delete 'check) ;; This is a Python package which is fully managed by CMake. In ;; cmake-build-system the check phase runs before install, but the ;; Python modules required for testing are only installed in the ;; install phase. Move check to after the install phase. (add-after 'install 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? (invoke "ctest" "--exclude-regex" ;; XXX: Cpp tests fail in 'No such file or directory', ;; skip for now and only run the Python tests. ;; TODO: To pass the Python tests below, Ipopt must be ;; built with MUMPS support, but simply adding mumps ;; to the inputs doesn't work for it to be found, ;; possibly because MUMPS doesn't generate a .pc file. (string-join (list "^cpp" "pyinstallcheck_Bonmin_std" "pyinstallcheck_Bonmin_4dsoo" "pyinstallcheck_Bonmin_MIT15" "pyinstallcheck_Bonmin_swiler2014" "pyinstallcheck_Ipopt_std" "pyinstallcheck_example_plot_optimization_bonmin" "pyinstallcheck_coupling_tools") "|")))))))) (native-inputs (list bison dvisvgm flex python-numpydoc python-sphinx ;; python-sphinx-gallery ;; Currently broken swig)) (inputs (list openblas ; the only required dependency ;; The dependecies below are all optional. bonmin boost cbc ;; Maybe this should be propagated by Bonmin? ceres cminpack dlib hdf5 hmat ipopt libxml2 mpc mpfr nlopt pagmo primesieve python-wrapper spectra tbb)) (propagated-inputs (list python-chaospy python-dill python-matplotlib python-numpy python-pandas python-scipy)) (home-page "https://openturns.github.io/www/") (synopsis "Uncertainty treatment library") (description "OpenTURNS is a scientific C++ and Python library including an internal data model and algorithms dedicated to the treatment of uncertainties. The main goal of this library is giving to specific applications all the functionalities needed to treat uncertainties in studies.") (license license:lgpl3+))) (define-public r-coda (package (name "r-coda") (version "0.19-4.1") (source (origin (method url-fetch) (uri (cran-uri "coda" version)) (sha256 (base32 "1mlaf3ffql3phc12vlfss0vqqdj415mxsg84vsdgymmvdzc53d7l")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) (home-page "https://cran.r-project.org/web/packages/coda") (synopsis "This is a package for Output Analysis and Diagnostics for MCMC") (description "This package provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain.") (license license:gpl2+))) (define-public r-ade4 (package (name "r-ade4") (version "1.7-22") (source (origin (method url-fetch) (uri (cran-uri "ade4" version)) (sha256 (base32 "1d4knc1c1hha4gwcakbllzmff4g0mh56y058dn6wp9m2hd7gaz80")))) (build-system r-build-system) (propagated-inputs (list r-mass r-pixmap r-rcpp r-rcpparmadillo r-sp)) (home-page "https://pbil.univ-lyon1.fr/ADE-4") (synopsis "Multivariate data analysis and graphical display") (description "The ade4 package contains data analysis functions to analyze ecological and environmental data in the framework of Euclidean exploratory methods.") (license license:gpl2+))) (define-public r-xml2 (package (name "r-xml2") (version "1.3.6") (source (origin (method url-fetch) (uri (cran-uri "xml2" version)) (sha256 (base32 "13rhvmrjdqwc5psn501vz9jfmqwlf4rc30w6vrnn3wxzk7zr26g8")))) (build-system r-build-system) (inputs (list libxml2 zlib)) (propagated-inputs (list r-cli r-rlang)) (native-inputs (list pkg-config r-knitr)) (home-page "https://github.com/hadley/xml2") (synopsis "Parse XML with R") (description "This package provides a simple, consistent interface to working with XML files in R. It is built on top of the libxml2 C library.") (license license:gpl2+))) (define-public r-multitaper (package (name "r-multitaper") (version "1.0-17") (source (origin (method url-fetch) (uri (cran-uri "multitaper" version)) (sha256 (base32 "1wqa2whcjxwjqg9z46i48dvrga17fdj63r05kg993r1fpriclc1l")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://github.com/wesleyburr/multitaper/") (synopsis "Multitaper spectral analysis tools") (description "This package implements multitaper spectral estimation techniques using prolate spheroidal sequences (Slepians) and sine tapers for time series analysis. It includes an adaptive weighted multitaper spectral estimate, a coherence estimate, Thomson's Harmonic F-test, and complex demodulation. The Slepians sequences are generated efficiently using a tridiagonal matrix solution, and jackknifed confidence intervals are available for most estimates.") (license license:gpl2+))) (define-public r-rversions (package (name "r-rversions") (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "rversions" version)) (sha256 (base32 "0q5ip3rkhcxz7472fbqddrw3a2wm31b18w7ax0pi6wc27qiihn6y")))) (build-system r-build-system) (propagated-inputs (list r-curl r-xml2)) (home-page "https://github.com/metacran/rversions") (synopsis "Query R versions, including 'r-release' and 'r-oldrel'") (description "This package provides functions to query the main R repository to find the versions that @code{r-release} and @code{r-oldrel} refer to, and also all previous R versions and their release dates.") (license license:expat))) (define-public r-whisker (package (name "r-whisker") (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "whisker" version)) (sha256 (base32 "1g7jy6dnc5igs7yqy1n7cmy0ia8dm2yi3qj1mil2y0q88m4m2ldz")))) (build-system r-build-system) (home-page "https://github.com/edwindj/whisker") (synopsis "Logicless mustache templating for R") (description "This package provides logicless templating, with a syntax that is not limited to R.") (license license:gpl3+))) (define-public r-backports (package (name "r-backports") (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "backports" version)) (sha256 (base32 "18kwi50bvha6p5jfl833grmhqzi55adnd3glcy4yh18mizdxjghd")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/backports") (synopsis "Reimplementations of functions introduced since R 3.0.0") (description "Provides implementations of functions which have been introduced in R since version 3.0.0. The backports are conditionally exported which results in R resolving the function names to the version shipped with R (if available) and uses the implemented backports as fallback. This way package developers can make use of the new functions without worrying about the minimum required R version.") (license license:gpl2+))) (define-public r-checkmate (package (name "r-checkmate") (version "2.3.2") (source (origin (method url-fetch) (uri (cran-uri "checkmate" version)) (sha256 (base32 "1qw81bs3lhwr1m6wlbs0l0j669051n60x4ca2821599ddhnp6mbj")))) (build-system r-build-system) (propagated-inputs (list r-backports)) (native-inputs (list r-knitr)) (home-page "https://github.com/mllg/checkmate") (synopsis "Fast and versatile argument checks") (description "This package provides tests and assertions to perform frequent argument checks. A substantial part of the package was written in C to minimize any worries about execution time overhead.") (license license:bsd-3))) (define-public r-bbmisc (package (name "r-bbmisc") (version "1.13") (source (origin (method url-fetch) (uri (cran-uri "BBmisc" version)) (sha256 (base32 "01a43raxj374cg6khs14r0bxvfm8v1sp0p2ambp7npnizvwxqi8i")))) (properties `((upstream-name . "BBmisc"))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-data-table)) (home-page "https://github.com/berndbischl/BBmisc") (synopsis "Miscellaneous functions for R package development") (description "This package provides miscellaneous helper functions for the development of R packages.") (license license:bsd-3))) (define-public r-fail (package (name "r-fail") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "fail" version)) (sha256 (base32 "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d")))) (build-system r-build-system) (propagated-inputs (list r-bbmisc r-checkmate)) (home-page "https://github.com/mllg/fail") (synopsis "File abstraction interface layer (FAIL)") (description "This package provides a more comfortable interface to work with R data or source files in a key-value fashion.") (license license:bsd-3))) (define-public r-batchjobs (package (name "r-batchjobs") (version "1.9") (source (origin (method url-fetch) (uri (cran-uri "BatchJobs" version)) (sha256 (base32 "0xsw25j2ks9bqgz189qdcyj8hzz93snknlik83nj04s6vy0w7aax")))) (properties `((upstream-name . "BatchJobs"))) (build-system r-build-system) (propagated-inputs (list r-backports r-bbmisc r-brew r-checkmate r-data-table r-dbi r-digest r-rsqlite r-sendmailr r-stringi)) (home-page "https://github.com/tudo-r/BatchJobs") (synopsis "Batch computing with R") (description "This package provides @code{Map}, @code{Reduce} and @code{Filter} variants to generate jobs on batch computing systems like PBS/Torque, LSF, SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.") (license license:bsd-2))) (define-public r-brew (package (name "r-brew") (version "1.0-10") (source (origin (method url-fetch) (uri (cran-uri "brew" version)) (sha256 (base32 "13x3vnrhfcvr479r4dya61a5vcky2gb4kv2xbivy0ah39qrzg0a1")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/brew") (synopsis "Templating framework for report generation") (description "The brew package implements a templating framework for mixing text and R code for report generation. The template syntax is similar to PHP, Ruby's erb module, Java Server Pages, and Python's psp module.") (license license:gpl2+))) (define-public r-desc (package (name "r-desc") (version "1.4.3") (source (origin (method url-fetch) (uri (cran-uri "desc" version)) (sha256 (base32 "09ig14bm68cps6d1mrmj6hhjr01i6gz1ri35qpkwk3yp7nkqsijl")))) (build-system r-build-system) (propagated-inputs (list r-cli r-r6)) (home-page "https://github.com/r-pkgs/desc") (synopsis "Manipulate DESCRIPTION Files") (description "This package provides tools to read, write, create, and manipulate DESCRIPTION files. It is intended for packages that create or manipulate other packages.") (license license:expat))) (define-public r-commonmark (package (name "r-commonmark") (version "1.9.1") (source (origin (method url-fetch) (uri (cran-uri "commonmark" version)) (sha256 (base32 "0fxm1nn4al0yn79iqix9cp5j5chr8jq56d29ayqrpag49hzs25wm")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/commonmark") (synopsis "CommonMark and Github Markdown Rendering in R") (description "The CommonMark specification defines a rationalized version of markdown syntax. This package uses the @code{cmark} reference implementation for converting markdown text into various formats including HTML, LaTeX and groff man. In addition, it exposes the markdown parse tree in XML format. The latest version of this package also adds support for Github extensions including tables, autolinks and strikethrough text.") (license license:bsd-2))) (define-public r-roxygen2 (package (name "r-roxygen2") (version "7.3.2") (source (origin (method url-fetch) (uri (cran-uri "roxygen2" version)) (sha256 (base32 "0701v8dglv0mdsjs1mijpylpciiijb2schplavkf5drjj6gqg25p")))) (build-system r-build-system) (propagated-inputs (list r-brew r-cli r-commonmark r-cpp11 r-desc r-knitr r-pkgload r-purrr r-r6 r-rlang r-stringi r-stringr r-withr r-xml2)) (native-inputs (list r-knitr)) (home-page "https://github.com/klutometis/roxygen") (synopsis "In-source documentation system for R") (description "Roxygen2 is a Doxygen-like in-source documentation system for Rd, collation, and NAMESPACE files.") (license license:gpl2+))) (define-public r-openssl (package (name "r-openssl") (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "openssl" version)) (sha256 (base32 "13gp6q8s0pdjvnd7mnmdqhmmsb0mf4m3snq99j6js8c4sll27895")))) (properties `((upstream-name . "openssl") (updater-extra-inputs . ("openssl")))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'do-not-use-versioned-linking (lambda _ (substitute* "configure" (("PKG_LIBS=\"\\$\\{PKG_LIBS_VERSIONED\\}\"") "PKG_LIBS=\"${PKG_LIBS}\""))))))) (inputs (list openssl zlib)) (native-inputs (list pkg-config r-knitr)) (propagated-inputs (list r-askpass)) (home-page "https://github.com/jeroenooms/openssl") (synopsis "Toolkit for encryption, signatures and certificates") (description "This package provides R bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384 and P-521. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES block cipher is used in CBC mode for symmetric encryption; RSA for asymmetric (public key) encryption. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and @code{bignum} math methods for manually performing crypto calculations on large multibyte integers.") (license license:expat))) (define-public r-httr (package (name "r-httr") (version "1.4.7") (source (origin (method url-fetch) (uri (cran-uri "httr" version)) (sha256 (base32 "0fisvq3zydmqagn7lj6x98zxkcl7l95gfydl27zkigb7zg1fcm8m")))) (build-system r-build-system) (propagated-inputs (list r-curl r-jsonlite r-mime r-openssl r-r6)) (native-inputs (list r-knitr)) (home-page "https://github.com/hadley/httr") (synopsis "Tools for working with URLs and HTTP") (description "The aim of httr is to provide a wrapper for RCurl customised to the demands of modern web APIs. It provides useful tools for working with HTTP organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration functions make it easy to control additional request components.") (license license:expat))) (define-public r-git2r (package (name "r-git2r") (version "0.33.0") (source (origin (method url-fetch) (uri (cran-uri "git2r" version)) (sha256 (base32 "158q1rzh9j0xb6l09j6banzvx8l26bhvip2z4lf6ymi21s6vcm8q")))) (build-system r-build-system) (inputs (list libgit2 zlib)) (native-inputs (list pkg-config)) (home-page "https://github.com/ropensci/git2r") (synopsis "Access Git repositories with R") (description "This package provides an R interface to the libgit2 library, which is a pure C implementation of the Git core methods.") ;; GPLv2 only with linking exception. (license license:gpl2))) (define-public r-rstudioapi (package (name "r-rstudioapi") (version "0.16.0") (source (origin (method url-fetch) (uri (cran-uri "rstudioapi" version)) (sha256 (base32 "1rjgxn7p15a69vfkhwrxywag6w9k4ccnklpvhr1sb1wy35ksizvl")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/rstudioapi") (synopsis "Safely access the RStudio API") (description "This package provides functions to access the RStudio API and provide informative error messages when it's not available.") 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This package includes the header files from the templated Armadillo library.") ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or ;; later, as is the rest of 'Rcpp'. (license license:gpl2+))) (define-public r-bitops (package (name "r-bitops") (version "1.0-8") (source (origin (method url-fetch) (uri (cran-uri "bitops" version)) (sha256 (base32 "0f1744pi3qb1av41man6xp2xalwcjslz3qbk35gccpb4d6glp8bq")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/bitops") (synopsis "Bitwise operations") (description "This package provides functions for bitwise operations on integer vectors.") (license license:gpl2+))) (define-public r-catools (package (name "r-catools") (version "1.18.2") (source (origin (method url-fetch) (uri (cran-uri "caTools" version)) (sha256 (base32 "14q2ry8gaszjl0m97qg62dxv5bpj6k02qwyi7q2lnxgcmwai3mkm")))) (properties `((upstream-name . 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(license license:lgpl2.1+))) (define-public r-mvtnorm (package (name "r-mvtnorm") (version "1.2-6") (source (origin (method url-fetch) (uri (cran-uri "mvtnorm" version)) (sha256 (base32 "0cfdd8l58yn48vc4zf4n5vfs3g02wdnvmkdf5zyybn3f54ydrpn4")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://mvtnorm.R-forge.R-project.org") (synopsis "Package for multivariate normal and t-distributions") (description "This package can compute multivariate normal and t-probabilities, quantiles, random deviates and densities.") (license license:gpl2))) (define-public r-matrixstats (package (name "r-matrixstats") (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "matrixStats" version)) (sha256 (base32 "0ni4jgw3jfbwakzrcz6jcjr1zsnaq924jz2a9d8kq92vv43ycgj1")))) (properties `((upstream-name . 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(license license:artistic2.0))) (define-public r-viridis (package (name "r-viridis") (version "0.6.5") (source (origin (method url-fetch) (uri (cran-uri "viridis" version)) (sha256 (base32 "0p00s24d8bsifw3r0afwrx98bqixnf5krpbw42hfwp8ipsv5qaw6")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridextra r-viridislite)) (native-inputs (list r-knitr)) ; for vignettes (home-page "https://github.com/sjmgarnier/viridis") (synopsis "Matplotlib default color map") (description "This package is a port of the new @url{matplotlib, http://matplotlib.org/} color maps (@code{viridis}--the default--, @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are designed in such a way that they will analytically be perfectly perceptually-uniform, both in regular form and also when converted to black-and-white. They are also designed to be perceived by readers with the most common form of color blindness.") (license license:x11))) (define-public r-viridislite (package (name "r-viridislite") (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "viridisLite" version)) (sha256 (base32 "18g1rk24kr47jl01r70vvni2146fl9xxpjcvjp6d5k6y64fi2gw9")))) (properties `((upstream-name . "viridisLite"))) (build-system r-build-system) (home-page "https://github.com/sjmgarnier/viridisLite") (synopsis "Default color maps from matplotlib") (description "This package is a port of the new @code{matplotlib} color maps (@code{viridis}, @code{magma}, @code{plasma} and @code{inferno}) to R. matplotlib is a popular plotting library for Python. These color maps are designed in such a way that they will analytically be perfectly perceptually-uniform, both in regular form and also when converted to black-and-white. They are also designed to be perceived by readers with the most common form of color blindness. This is the @code{lite} version of the more complete @code{viridis} package.") (license license:expat))) (define-public r-tidyselect (package (name "r-tidyselect") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "tidyselect" version)) (sha256 (base32 "0g4h8mfm5ima0izy4h0c65q478473xsj4hskh15dzg5z1fx9g7hn")))) (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-lifecycle r-rlang r-vctrs r-withr)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/tidyselect") (synopsis "Select from a set of strings") (description "This package provides a backend for the selecting functions of the tidyverse. It makes it easy to implement select-like functions in your own packages in a way that is consistent with other tidyverse interfaces for selection.") (license license:gpl3))) (define-public r-tidyr (package (name "r-tidyr") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "tidyr" version)) (sha256 (base32 "0pc3ad9k36lk3c5qbgx4blhs8aihqyysfxljyirgahsmrdhw4878")))) (build-system r-build-system) (propagated-inputs (list r-cli r-cpp11 r-dplyr r-glue r-lifecycle r-magrittr r-purrr r-rlang r-stringr r-tibble r-tidyselect r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/hadley/tidyr") (synopsis "Tidy data with `spread()` and `gather()` functions") (description "tidyr is a reframing of the reshape2 package designed to accompany the tidy data framework, and to work hand-in-hand with magrittr and dplyr to build a solid pipeline for data analysis. It is designed specifically for tidying data, not the general reshaping that reshape2 does, or the general aggregation that reshape did. In particular, built-in methods only work for data frames, and tidyr provides no margins or aggregation.") (license license:expat))) (define-public r-hexbin (package (name "r-hexbin") (version "1.28.3") (source (origin (method url-fetch) (uri (cran-uri "hexbin" version)) (sha256 (base32 "0pyy97bh9xf9hijg3iw1z4ri01571r1fx7xqm3fjkzx4q48kbcqf")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) (native-inputs (list gfortran r-knitr)) ; for vignettes (home-page "https://github.com/edzer/hexbin") (synopsis "Hexagonal binning routines") (description "This package provides binning and plotting functions for hexagonal bins. It uses and relies on grid graphics and formal (S4) classes and methods.") (license license:gpl2+))) (define-public r-purrr (package (name "r-purrr") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "purrr" version)) (sha256 (base32 "0qxvifs5gakjbivs8dgz6nrp6df2ypr3c4dlj84gyga3i2xwc6rc")))) (build-system r-build-system) (propagated-inputs (list r-cli r-lifecycle r-magrittr r-rlang r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/hadley/purrr") (synopsis "Functional programming tools") (description "This package completes R's functional programming tools with missing features present in other programming languages.") (license license:gpl3+))) (define-public r-plotly (package (name "r-plotly") (version "4.10.4") (source (origin (method url-fetch) (uri (cran-uri "plotly" version)) (sha256 (base32 "0ryqcs9y7zan36zs6n1hxxy91pajldpax8q7cwcimlsmxnvrbafg")) (modules '((guix build utils))) (snippet '(with-directory-excursion "inst/htmlwidgets/lib/" (for-each delete-file '("plotlyjs/plotly-latest.min.js" "colourpicker/colourpicker.min.js" "typedarray/typedarray.min.js" "selectize/selectize.min.js")))))) (build-system r-build-system) (arguments (list #:modules '((guix build utils) (guix build r-build-system) (srfi srfi-1)) #:phases '(modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/" (symlink (string-append (assoc-ref inputs "js-selectize") "/share/javascript/selectize.min.js") "selectize/selectize.min.js") (call-with-values (lambda () (unzip2 `((,(assoc-ref inputs "js-plotly") "plotlyjs/plotly-latest.min.js") (,(string-append (assoc-ref inputs "js-colourpicker") "/js/colourpicker.js") "colourpicker/colourpicker.min.js") (,(string-append (assoc-ref inputs "js-typedarray") "/typedarray.js") "typedarray/typedarray.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs (list r-base64enc r-crosstalk r-data-table r-digest r-dplyr r-ggplot2 r-htmltools r-htmlwidgets r-httr r-jsonlite r-lazyeval r-magrittr r-promises r-purrr r-rcolorbrewer r-rlang r-scales r-tibble r-tidyr r-vctrs r-viridislite)) (native-inputs `(("esbuild" ,esbuild) ("js-colourpicker" ,(let ((commit "27c2a266d51e18a9fe6d7542264152b27c7d34e0") (version "1.1") (revision "0")) (origin (method git-fetch) (uri (git-reference (url "https://github.com/daattali/jquery-colourpicker") (commit commit))) (file-name (git-file-name "jquery-colourpicker" (git-version version revision commit))) (sha256 (base32 "0lg8amh8xh6p246j38rqghrljd7v5z34i169ra6403z8ga33wiqb"))))) ("js-plotly" ,(let ((version "2.11.1")) (origin (method url-fetch) (uri (string-append "https://raw.githubusercontent.com/plotly/plotly.js/v" version "/dist/plotly.js")) (sha256 (base32 "1mxd8s4v3i885w5i02cyzqsrvqfr9w0svdclvqxbd05dly4bdkbj"))))) ("js-selectize" ,js-selectize) ;; This is not quite the same as the bundled minified script from 2016, ;; but it seems to be the original with fixes from late 2017. ("js-typedarray" ,(let ((commit "9f7d4168657e2c164d647a6959f402f2c33eb5b4") (version "0") (revision "0")) (origin (method git-fetch) (uri (git-reference (url "https://github.com/inexorabletash/polyfill/") (commit commit))) (file-name (git-file-name "typedarray-polyfill" (git-version version revision commit))) (sha256 (base32 "0f9np4mmyhny03n3xpwzs07rld30lnfqsnh97x1v7xm0qy0zjanf"))))))) (home-page "https://plot.ly/r") (synopsis "Create interactive web graphics") (description "This package enables the translation of ggplot2 graphs to an interactive web-based version and/or the creation of custom web-based visualizations directly from R. Once uploaded to a plotly account, plotly graphs (and the data behind them) can be viewed and modified in a web browser.") (license license:x11))) (define-public r-biased-urn (package (name "r-biased-urn") (version "2.0.12") (source (origin (method url-fetch) (uri (cran-uri "BiasedUrn" version)) (sha256 (base32 "14jpijms81pgl4zyqrhwwdfj0jmlmml21blspvin8lqw8fbbbcr9")))) (properties `((upstream-name . "BiasedUrn"))) (build-system r-build-system) (home-page "https://www.agner.org/random/") (synopsis "Biased urn model distributions") (description "This package provides statistical models of biased sampling in the form of univariate and multivariate noncentral hypergeometric distributions, including Wallenius' noncentral hypergeometric distribution and Fisher's noncentral hypergeometric distribution (also called extended hypergeometric distribution).") (license license:gpl3+))) (define-public r-rematch (package (name "r-rematch") (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "rematch" version)) (sha256 (base32 "09jwg3glp32q4ml4khhzi8j7bzg9zhqqdg1m6r8gibh756zzgnhm")))) (build-system r-build-system) (home-page "https://github.com/MangoTheCat/rematch") (synopsis "Match regular expressions with a nicer API") (description "This package provides a small wrapper on @code{regexpr} to extract the matches and captured groups from the match of a regular expression to a character vector.") (license license:expat))) (define-public r-cellranger (package (name "r-cellranger") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "cellranger" version)) (sha256 (base32 "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x")))) (build-system r-build-system) (propagated-inputs (list r-rematch r-tibble)) (home-page "https://github.com/rsheets/cellranger") (synopsis "Translate spreadsheet cell ranges to rows and columns") (description "This package provides helper functions to work with spreadsheets and the @code{A1:D10} style of cell range specification.") (license license:expat))) (define-public r-googlesheets (package (name "r-googlesheets") (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "googlesheets" version)) (sha256 (base32 "11q07nxys72wkxx9mawmjyf20gvwvrb7h3gpa73h6lgh2vgrwnv8")))) (build-system r-build-system) (propagated-inputs (list r-cellranger r-dplyr r-httr r-jsonlite r-purrr r-readr r-stringr r-tibble r-tidyr r-xml2)) (home-page "https://github.com/jennybc/googlesheets") (synopsis "Manage Google spreadsheets from R") (description "This package provides tools to interact with Google Sheets from within R.") (license license:expat))) (define-public r-spams (package (name "r-spams") (version "2.6.1") (source (origin (method git-fetch) (uri (git-reference (url "https://gitlab.inria.fr/thoth/spams-devel") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0qvj87fw4sm54c7dvhxjgmgvnyyrrz9fk6dqp3ak0gwgb42gqh60")))) (build-system r-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (add-after 'patch-generated-file-shebangs 'patch-paths (lambda _ (substitute* (cons* "swig/setRelease" "swig/R/docmatlab2R" "swig/R/mkdist" (find-files "." "(^mk|\\.sh$)")) (("/bin/pwd") "pwd") (("/bin/rm") "rm")))) (add-after 'patch-paths 'mkdist (lambda _ (chdir "swig/R") (setenv "TEXINPUTS" (string-append (getcwd) "/../../doc:")) (substitute* "mkdist" (("^SWIG=.*") (string-append "SWIG=" (which "swig"))) (("^../mkdoc") "")) ;requires texlive-aeguill (invoke "./mkdist") (chdir "dist/spams-R/spams"))) ;; Don't tune for the building machine. (add-after 'mkdist 'no-mtune (lambda _ (substitute* "src/Makevars" (("-mtune=native") "")))) (add-after 'no-mtune 'use-c++11 (lambda _ (substitute* "src/Makevars" (("-DUSE_BLAS_LIB" m) (string-append m " -std=c++11")))))))) (native-inputs (list hevea perl swig (texlive-updmap.cfg (list texlive-aeguill texlive-jknapltx)))) (propagated-inputs (list r-lattice r-matrix)) (home-page "https://gitlab.inria.fr/thoth/spams-devel/") (synopsis "Toolbox for solving sparse estimation problems") (description "SPAMS (SPArse Modeling Software) is an optimization toolbox for solving various sparse estimation problems. It includes tools for the following problems: @enumerate @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle component analysis} (PCA), ...) @item Solving sparse decomposition problems with LARS, coordinate descent, OMP, SOMP, proximal methods @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse group lasso, tree-structured regularization, structured sparsity with overlapping groups,...). @end enumerate\n") (license license:gpl3+))) (define-public r-base64 (package (name "r-base64") (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "base64" version)) (sha256 (base32 "1w9m4n29xmj7px8fbmha04vq146bxfqi7ipj1ag09hlm05y6h8jd")))) (build-system r-build-system) (propagated-inputs (list r-openssl)) (home-page "https://cran.r-project.org/web/packages/base64") (synopsis "Base64 encoder and decoder") (description "This package is a compatibility wrapper to replace the orphaned package by Romain Francois. New applications should use the openssl or base64enc package instead.") (license license:expat))) (define-public r-hmisc (package (name "r-hmisc") (version "5.1-3") (source (origin (method url-fetch) (uri (cran-uri "Hmisc" version)) (sha256 (base32 "1sq5qvlr9swhdvf3l420y9fxq5s1qw8aiyl9a62sb357ywppfq9w")))) (properties `((upstream-name . "Hmisc"))) (build-system r-build-system) (native-inputs (list gfortran)) (propagated-inputs (list r-base64enc r-cluster r-colorspace r-data-table r-foreign r-formula r-ggplot2 r-gridextra r-gtable r-htmltable r-htmltools r-knitr r-nnet r-rmarkdown r-rpart r-viridis)) (home-page "http://biostat.mc.vanderbilt.edu/Hmisc") (synopsis "Miscellaneous data analysis and graphics functions") (description "This package contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX code, and recoding variables.") (license license:gpl2+))) (define-public r-runit (package (name "r-runit") (version "0.4.33") (source (origin (method url-fetch) (uri (cran-uri "RUnit" version)) (sha256 (base32 "0pybwvd57vf71vvlxdrynw5n6s5gnbqnwvq0qpd395ggqypwb95j")))) (properties `((upstream-name . "RUnit"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/RUnit") (synopsis "R unit test framework") (description "This package provides R functions implementing a standard unit testing framework, with additional code inspection and report generation tools.") (license license:gpl2+))) (define-public r-dynamictreecut (package (name "r-dynamictreecut") (version "1.63-1") (source (origin (method url-fetch) (uri (cran-uri "dynamicTreeCut" version)) (sha256 (base32 "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3")))) (properties `((upstream-name . "dynamicTreeCut"))) (build-system r-build-system) (home-page "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/") (synopsis "Detect clusters in hierarchical clustering dendrograms") (description "This package contains methods for the detection of clusters in hierarchical clustering dendrograms.") (license license:gpl2+))) (define-public r-fastcluster (package (name "r-fastcluster") (version "1.2.6") (source (origin (method url-fetch) (uri (cran-uri "fastcluster" version)) (sha256 (base32 "06cd3w62ijf0yx2yq0xgx6qw5lcrnn1033ygx6bl9dmhix2haal5")))) (build-system r-build-system) (home-page "http://danifold.net/fastcluster.html") (synopsis "Fast hierarchical clustering routines") (description "This package implements fast hierarchical, agglomerative clustering routines. Part of the functionality is designed as drop-in replacement for existing routines: @code{linkage()} in the SciPy package @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package, and the @code{flashClust} package. It provides the same functionality with the benefit of a much faster implementation. Moreover, there are memory-saving routines for clustering of vector data, which go beyond what the existing packages provide.") (license license:bsd-2))) (define-public r-sfsmisc (package (name "r-sfsmisc") (version "1.1-19") (source (origin (method url-fetch) (uri (cran-uri "sfsmisc" version)) (sha256 (base32 "0fzjbicaa3x16skxgil84b4h6ylbcfi6vf30z7r8rqfj6pfk36c6")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/sfsmisc") (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich") (description "This package provides useful utilities from Seminar fuer Statistik ETH Zurich, including many that are related to graphics.") (license license:gpl2+))) (define-public r-gtools (package (name "r-gtools") (version "3.9.5") (source (origin (method url-fetch) (uri (cran-uri "gtools" version)) (sha256 (base32 "0jqpvygxgr4m1rgaj5rzd048fwxvpcr4n1vx8bfabc9d2p0vdsfy")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/gtools") (synopsis "Various R programming tools") (description "This package contains a collection of various functions to assist in R programming, such as tools to assist in developing, updating, and maintaining R and R packages, calculating the logit and inverse logit transformations, tests for whether a value is missing, empty or contains only @code{NA} and @code{NULL} values, and many more.") (license license:gpl2))) (define-public r-gdata (package (name "r-gdata") (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "gdata" version)) (sha256 (base32 "0zxi0634dkgczw7gicj8r6mhb83cpkxhsy2iivz0b9v52y9bjmm4")))) (build-system r-build-system) (propagated-inputs (list r-gtools)) (home-page "https://cran.r-project.org/web/packages/gdata") (synopsis "Various R programming tools for data manipulation") (description "This package provides various R programming tools for data manipulation, including: @itemize @item medical unit conversions @item combining objects @item character vector operations @item factor manipulation @item obtaining information about R objects @item generating fixed-width format files @item extricating components of date and time objects @item operations on columns of data frames @item matrix operations @item operations on vectors and data frames @item value of last evaluated expression @item wrapper for @code{sample} that ensures consistent behavior for both scalar and vector arguments @end itemize\n") (license license:gpl2+))) (define-public r-gplots (package (name "r-gplots") (version "3.1.3.1") (source (origin (method url-fetch) (uri (cran-uri "gplots" version)) (sha256 (base32 "1whs45axg1vp2p3jjya4aq68bl6vp11g059saj2av0vmyaadxq8s")))) (build-system r-build-system) (propagated-inputs (list r-catools r-gtools r-kernsmooth)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/gplots") (synopsis "Various R programming tools for plotting data") (description "This package provides various R programming tools for plotting data, including: @itemize @item calculating and plotting locally smoothed summary function @item enhanced versions of standard plots @item manipulating colors @item calculating and plotting two-dimensional data summaries @item enhanced regression diagnostic plots @item formula-enabled interface to @code{stats::lowess} function @item displaying textual data in plots @item balloon plots @item plotting \"Venn\" diagrams @item displaying Open-Office style plots @item plotting multiple data on same region, with separate axes @item plotting means and confidence intervals @item spacing points in an x-y plot so they don't overlap @end itemize\n") (license license:gpl2+))) (define-public r-rocr (package (name "r-rocr") (version "1.0-11") (source (origin (method url-fetch) (uri (cran-uri "ROCR" version)) (sha256 (base32 "0amvvrkiflmr3qygrsgrsja4gaf2v6r6h6i2bgpsm8r069vmlf2p")))) (properties `((upstream-name . "ROCR"))) (build-system r-build-system) (propagated-inputs (list r-gplots)) (native-inputs (list r-knitr)) (home-page "https://rocr.bioinf.mpi-sb.mpg.de/") (synopsis "Visualizing the performance of scoring classifiers") (description "ROCR is a flexible tool for creating cutoff-parameterized 2D performance curves by freely combining two from over 25 performance measures (new performance measures can be added using a standard interface). Curves from different cross-validation or bootstrapping runs can be averaged by different methods, and standard deviations, standard errors or box plots can be used to visualize the variability across the runs. The parameterization can be visualized by printing cutoff values at the corresponding curve positions, or by coloring the curve according to cutoff. All components of a performance plot can be quickly adjusted using a flexible parameter dispatching mechanism.") (license license:gpl2+))) (define-public r-ztable (package (name "r-ztable") (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "ztable" version)) (sha256 (base32 "1ps7ix0hc84s0p0ra6bkjxky3cffs1rvdcagqzj78lbdq22dk5j8")))) (build-system r-build-system) (propagated-inputs (list r-flextable r-magrittr r-officer r-rcolorbrewer r-rstudioapi r-scales r-stringr)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ztable") (synopsis "Zebra-striped tables in LaTeX and HTML formats for R") (description "This package provides functions to make zebra-striped tables (tables with alternating row colors) in LaTeX and HTML formats easily from @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova}, @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and @code{cbind.mytable} objects.") (license license:gpl2+))) (define-public r-vipor (package (name "r-vipor") (version "0.4.7") (source (origin (method url-fetch) (uri (cran-uri "vipor" version)) (sha256 (base32 "17hb6y1i9bva0fr4k9m6wncmnzdjad1b7fhsvfhva4xavpll3bds")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/vipor") (synopsis "Plot categorical data using noise and density estimates") (description "This package provides tools to generate a violin point plot, a combination of a violin/histogram plot and a scatter plot by offsetting points within a category based on their density using quasirandom noise.") (license license:gpl2+))) (define-public r-beeswarm (package (name "r-beeswarm") (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "beeswarm" version)) (sha256 (base32 "016mqcbdksialkmap56rprzna9b6cd6896ml9gl2n2h8yjdk7x2i")))) (build-system r-build-system) (home-page "https://www.cbs.dtu.dk/~eklund/beeswarm/") (synopsis "Implementation of bee swarm plots") (description "This package provides an implementation of bee swarm plots. The bee swarm plot is a one-dimensional scatter plot like stripchart, but with closely-packed, non-overlapping points.") (license license:artistic2.0))) (define-public r-sourcetools (package (name "r-sourcetools") (version "0.1.7-1") (source (origin (method url-fetch) (uri (cran-uri "sourcetools" version)) (sha256 (base32 "1l9i9ram12pjks8h2gzmj119wf4ixwyhljsfv289dn8dgbdjp0cn")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/sourcetools") (synopsis "Tools for reading, tokenizing and parsing R code") (description "The sourcetools package provides both an R and C++ interface for the tokenization of R code, and helpers for interacting with the tokenized representation of R code.") (license license:expat))) (define-public r-ggbeeswarm (package (name "r-ggbeeswarm") (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "ggbeeswarm" version)) (sha256 (base32 "1rcw54isai05np4fj19vcxx2vcxq7y2nm3az9m8xwbc9pdjs4z7x")))) (build-system r-build-system) (propagated-inputs (list r-beeswarm r-cli r-ggplot2 r-lifecycle r-vipor)) (home-page "https://github.com/eclarke/ggbeeswarm") (synopsis "Categorical scatter (violin point) plots") (description "This package provides two methods of plotting categorical scatter plots such that the arrangement of points within a category reflects the density of data at that region, and avoids over-plotting.") (license license:gpl2+))) (define-public r-ggthemes (package (name "r-ggthemes") (version "5.1.0") (source (origin (method url-fetch) (uri (cran-uri "ggthemes" version)) (sha256 (base32 "03mxigi34nd05wjigm8lpcbyhp4c8jxz7zm04qs27clbzsn1jj07")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-lifecycle r-purrr r-scales r-stringr r-tibble)) (home-page "https://cran.rstudio.com/web/packages/ggthemes") (synopsis "Extra themes, scales and geoms for @code{ggplot2}") (description "This package provides extra themes and scales for @code{ggplot2} that replicate the look of plots by Edward Tufte and Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The Wall Street Journal, among others. This package also provides @code{geoms} for Tufte's box plot and range frame.") (license license:gpl2))) (define-public r-statmod (package (name "r-statmod") (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "statmod" version)) (sha256 (base32 "1jbf07h0mnncn2qp4wcw5bnbvsw3lizpd3cg0cpb8mcxn3wkw76n")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/statmod") (native-inputs (list gfortran)) (synopsis "Statistical modeling") (description "This package provides a collection of algorithms and functions to aid statistical modeling. It includes growth curve comparisons, limiting dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. It also includes advanced generalized linear model functions that implement secure convergence, dispersion modeling and Tweedie power-law families.") ;; Statmod is distributed under either license (license (list license:gpl2 license:gpl3)))) (define-public r-rann (package (name "r-rann") (version "2.6.2") (source (origin (method url-fetch) (uri (cran-uri "RANN" version)) (sha256 (base32 "0wlpkf6vilw871ac2bxy5nr790cfs6sax5k8m0fhasxbansxbxvf")))) (properties `((upstream-name . "RANN"))) (build-system r-build-system) (home-page "https://github.com/jefferis/RANN") (synopsis "Fast nearest neighbour search") (description "This package finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library. Provides approximate, exact searches, fixed radius searches, bd and kb trees.") (license license:gpl3+))) (define-public r-fivethirtyeight (package (name "r-fivethirtyeight") (version "0.1.0") (source (origin (method url-fetch) (uri (string-append "https://mran.microsoft.com/src/contrib/" "fivethirtyeight_" version ".tar.gz")) (sha256 (base32 "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl")))) (build-system r-build-system) (propagated-inputs (list r-knitr r-rmarkdown r-dplyr r-readr r-ggplot2 r-magrittr r-stringr)) (home-page "https://mran.microsoft.com/package/fivethirtyeight/") (synopsis "Data and code behind the stories at FiveThirtyEight") (description "This R package provides access to the code and data sets published by the statistics blog FiveThirtyEight.") (license license:expat))) (define-public r-compquadform (package (name "r-compquadform") (version "1.4.3") (source (origin (method url-fetch) (uri (cran-uri "CompQuadForm" version)) (sha256 (base32 "1i30hrqdk64q17vsn918c3q79brchgx2wzh1gbsgbn0dh1ncabq4")))) (properties `((upstream-name . "CompQuadForm"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/CompQuadForm") (synopsis "Distribution function of quadratic forms in normal variables") (description "This package provides functions to compute the distribution function of quadratic forms in normal variables using Imhof's method, Davies's algorithm, Farebrother's algorithm or Liu et al.'s algorithm.") (license license:gpl2+))) (define-public r-cowplot (package (name "r-cowplot") (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "cowplot" version)) (sha256 (base32 "0wxjynpbamyimpms7psbac7xgwswzlidczpc037q20y5yld9fml7")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gtable r-rlang r-scales)) (native-inputs (list r-knitr)) (home-page "https://github.com/wilkelab/cowplot") (synopsis "Streamlined plot theme and plot annotations for ggplot2") (description "This package provides some helpful extensions and modifications to the ggplot2 package to combine multiple ggplot2 plots into one and label them with letters, as is often required for scientific publications.") (license license:gpl2))) (define-public r-mixtools (package (name "r-mixtools") (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "mixtools" version)) (sha256 (base32 "03by64xi7yka0hzc1qyz1jdqzah6isvr3cdsc7g5v6hb4f178kl5")))) (build-system r-build-system) (propagated-inputs (list r-mass r-kernlab r-plotly r-scales r-segmented r-survival)) (home-page "https://cran.r-project.org/web/packages/mixtools") (synopsis "Tools for analyzing finite mixture models") (description "This package provides a collection of R functions for analyzing finite mixture models.") (license license:gpl2+))) (define-public r-lars (package (name "r-lars") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "lars" version)) (sha256 (base32 "17al1g0pvfz9frs2kxicqr8dyp7ciz3x87yx2l4lqd53ls6nm7n6")))) (build-system r-build-system) (inputs (list gfortran)) (home-page "https://web.stanford.edu/~hastie/Papers/LARS/") (synopsis "Least angle regression software") (description "Least Angle Regression (\"LAR\") is a model selection algorithm; a useful and less greedy version of traditional forward selection methods. A simple modification of the LAR algorithm implements Tibshirani's Lasso; the Lasso modification of LARS calculates the entire Lasso path of coefficients for a given problem at the cost of a single least squares fit. Another LARS modification efficiently implements epsilon Forward Stagewise linear regression.") (license license:gpl2))) (define-public r-fastica (package (name "r-fastica") (version "1.2-5.1") (source (origin (method url-fetch) (uri (cran-uri "fastICA" version)) (sha256 (base32 "11frycqqv4hsky2yaf2rb850wwqizgjnvna31kasb625lklnx4b5")))) (properties `((upstream-name . "fastICA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/fastICA") (synopsis "FastICA algorithms to perform ICA and projection pursuit") (description "This package provides an implementation of the FastICA algorithm to perform @dfn{independent component analysis} (ICA) and projection pursuit.") ;; Any GPL version. (license license:gpl3+))) (define-public r-randomforest (package (name "r-randomforest") (version "4.7-1.1") (source (origin (method url-fetch) (uri (cran-uri "randomForest" version)) (sha256 (base32 "1micz9794j7xmj755ln2692rzip8azndflxgdg6xn3j86issi7pm")))) (properties `((upstream-name . "randomForest"))) (build-system r-build-system) (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/") (native-inputs (list gfortran)) (synopsis "Breiman and Cutler's random forests for classification and regression") (description "This package provides the Breiman and Cutler's random forests algorithm, based on a forest of trees using random inputs, for classification and regression.") (license license:gpl2+))) (define-public r-diptest (package (name "r-diptest") (version "0.77-1") (source (origin (method url-fetch) (uri (cran-uri "diptest" version)) (sha256 (base32 "04r8c6xy5vympxaxmgnjib4pqh97f9k6b43i66qhzkl3yh0awki2")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/diptest") (synopsis "Hartigan's dip test statistic for unimodality") (description "This package computes Hartigan's dip test statistic for unimodality, multimodality and provides a test with simulation based p-values, where the original public code has been corrected.") (license license:gpl2+))) (define-public r-modeltools (package (name "r-modeltools") (version "0.2-23") (source (origin (method url-fetch) (uri (cran-uri "modeltools" version)) (sha256 (base32 "1vqh69256h344sbj5affm0kmc77dakrxp6442xfdnfd0y5d8sgkb")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/modeltools") (synopsis "Tools and classes for statistical models") (description "This package provides a collection of tools to deal with statistical models. The functionality is experimental and the user interface is likely to change in the future.") (license license:gpl2))) (define-public r-flexmix (package (name "r-flexmix") (version "2.3-19") (source (origin (method url-fetch) (uri (cran-uri "flexmix" version)) (sha256 (base32 "1s8jpii6ws6hra8w11fn3x84wrdrrlycnrhn5ijy6ibdpc6a9xdd")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-modeltools r-nnet)) (home-page "https://cran.r-project.org/web/packages/flexmix") (synopsis "Flexible mixture modeling") (description "This package implements a general framework for finite mixtures of regression models using the EM algorithm. FlexMix provides the E-step and all data handling, while the M-step can be supplied by the user to easily define new models. Existing drivers implement mixtures of standard linear models, generalized linear models and model-based clustering.") (license license:gpl2+))) (define-public r-mclust (package (name "r-mclust") (version "6.1.1") (source (origin (method url-fetch) (uri (cran-uri "mclust" version)) (sha256 (base32 "0xb726ssy224mzfg37nq5hffkdwi2hwjp1y9gwngk9vfbs703myx")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) (home-page "https://www.stat.washington.edu/mclust/") (synopsis "Gaussian mixture modelling for model-based clustering etc.") (description "This package provides Gaussian finite mixture models fitted via EM algorithm for model-based clustering, classification, and density estimation, including Bayesian regularization, dimension reduction for visualisation, and resampling-based inference.") (license license:gpl2+))) (define-public r-prabclus (package (name "r-prabclus") (version "2.3-3") (source (origin (method url-fetch) (uri (cran-uri "prabclus" version)) (sha256 (base32 "1haq8dvvi21fdnzl7ykm28sif5nv9pybir96vrqfcmy3k8500p80")))) (build-system r-build-system) (propagated-inputs (list r-mass r-mclust)) (home-page "https://cran.r-project.org/web/packages/prabclus") (synopsis "Parametric bootstrap tests for spatial neighborhood clustering") (description "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 (package (name "r-deoptimr") (version "1.1-3") (source (origin (method url-fetch) (uri (cran-uri "DEoptimR" version)) (sha256 (base32 "1526g3fzii8kcy29gy6gjvaw4k9cxxidq8bh7m4j485h0wdsdn4d")))) (properties `((upstream-name . "DEoptimR"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/DEoptimR") (synopsis "Differential evolution optimization in pure R") (description "This package provides a differential evolution (DE) stochastic algorithms for global optimization of problems with and without constraints. The aim is to curate a collection of its state-of-the-art variants that (1) do not sacrifice simplicity of design, (2) are essentially tuning-free, and (3) can be efficiently implemented directly in the R language.") (license license:gpl2+))) (define-public r-robustbase (package (name "r-robustbase") (version "0.99-4") (source (origin (method url-fetch) (uri (cran-uri "robustbase" version)) (sha256 (base32 "1g0cykxx5glq0sljjwl6f3cs872apfd5xw59px77mvjbrm7x0y59")))) (build-system r-build-system) (native-inputs (list gfortran)) (propagated-inputs (list r-deoptimr)) (home-page "https://robustbase.r-forge.r-project.org/") (synopsis "Basic robust statistics") (description "This package analyzes data with robust methods such as regression methodology including model selections and multivariate statistics.") (license license:gpl2+))) (define-public r-pcapp (package (name "r-pcapp") (version "2.0-5") (source (origin (method url-fetch) (uri (cran-uri "pcaPP" version)) (sha256 (base32 "043w3g3f57j2d0irnrxm58mzzisg7xmnsl17v7wijsh1czcswkv7")))) (properties `((upstream-name . "pcaPP"))) (build-system r-build-system) (propagated-inputs (list r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/pcaPP") (synopsis "Robust PCA by projection pursuit") (description "This package provides functions for robust @dfn{principal component analysis} (PCA) by projection pursuit.") (license license:gpl3+))) (define-public r-rrcov (package (name "r-rrcov") (version "1.7-6") (source (origin (method url-fetch) (uri (cran-uri "rrcov" version)) (sha256 (base32 "1pj8w4w4yd730qy7bl8h3z7d5xj05avnq0fbj2gnxrz489yc18mq")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-mvtnorm r-pcapp r-robustbase)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/rrcov") (synopsis "Scalable robust estimators with high breakdown Point") (description "This package provides an implementation of robust location and scatter estimation and robust multivariate analysis with high breakdown point.") (license license:gpl2+))) (define-public r-fit-models (package (name "r-fit-models") (version "0.64") (source (origin (method url-fetch) (uri (cran-uri "fit.models" version)) (sha256 (base32 "1nk4x2q8cv79zcls61saf627ac0fci6jcrd6lmzk61asm2zhc27p")))) (properties `((upstream-name . "fit.models"))) (build-system r-build-system) (propagated-inputs (list r-lattice)) (home-page "https://cran.r-project.org/web/packages/fit.models") (synopsis "Compare fitted models") (description "The @code{fit.models} function and its associated methods (coefficients, print, summary, plot, etc.) were originally provided in the @code{robust} package to compare robustly and classically fitted model objects. The aim of the @code{fit.models} package is to separate this fitted model object comparison functionality from the robust package and to extend it to support fitting methods (e.g., classical, robust, Bayesian, regularized, etc.) more generally.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) (define-public r-robust (package (name "r-robust") (version "0.7-5") (source (origin (method url-fetch) (uri (cran-uri "robust" version)) (sha256 (base32 "1k0s5i9r0lyz3qsw76dd514qclggqj9k2axmgj86df81j6f2mh53")))) (build-system r-build-system) (propagated-inputs (list r-fit-models r-lattice r-mass r-robustbase r-rrcov)) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/robust") (synopsis "Port of the S+ \"Robust Library\"") (description "This package is a port of the S+ \"Robust Library\". It provides methods for robust statistics, notably for robust regression and robust multivariate analysis.") (license license:gpl2))) (define-public r-trimcluster (package (name "r-trimcluster") (version "0.1-5") (source (origin (method url-fetch) (uri (cran-uri "trimcluster" version)) (sha256 (base32 "12siv8yx8dcavsz8jk96lwscbj257ar8jpaxksl2zb06987g4fcj")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/trimcluster") (synopsis "Cluster analysis with trimming") (description "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and Matran (1997). This optimizes the k-means criterion under trimming a portion of the points.") ;; Any GPL version (license (list license:gpl2+ license:gpl3+)))) (define-public r-fpc (package (name "r-fpc") (version "2.2-12") (source (origin (method url-fetch) (uri (cran-uri "fpc" version)) (sha256 (base32 "11s7211mnb9c72061mrcdfdwfph6nmbwcnpjgl32i2p7qys9cnam")))) (build-system r-build-system) (propagated-inputs (list r-class r-cluster r-diptest r-flexmix r-kernlab r-mass r-mclust r-prabclus r-robustbase)) (home-page "https://cran.r-project.org/web/packages/fpc") (synopsis "Flexible procedures for clustering") (description "This package provides various methods for clustering and cluster validation. For example, it provides fixed point clustering, linear regression clustering, clustering by merging Gaussian mixture components, as well as symmetric and asymmetric discriminant projections for visualisation of the separation of groupings.") (license license:gpl2+))) (define-public r-vgam (package (name "r-vgam") (version "1.1-11") (source (origin (method url-fetch) (uri (cran-uri "VGAM" version)) (sha256 (base32 "199kicvlxciff9x243h357n4bjl00yg9k5jgs9awzz5wsadr17fy")))) (properties `((upstream-name . "VGAM"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM") (synopsis "Vector generalized linear and additive models") (description "This package is an implementation of about 6 major classes of statistical regression models. Currently only fixed-effects models are implemented, i.e., no random-effects models. Many (150+) models and distributions are estimated by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring. VGLMs can be loosely thought of as multivariate generalised linear models.") (license license:gpl2+))) (define-public r-pbapply (package (name "r-pbapply") (version "1.7-2") (source (origin (method url-fetch) (uri (cran-uri "pbapply" version)) (sha256 (base32 "04xf1p7c0066cwnxfmzaikbc322bxnw022ziv8kkhzlc6268rvdf")))) (build-system r-build-system) (home-page "https://github.com/psolymos/pbapply") (synopsis "Adding progress bar to apply functions") (description "This lightweight package that adds progress bar to vectorized R functions apply. The implementation can easily be added to functions where showing the progress is useful e.g. bootstrap.") (license license:gpl2))) (define-public r-minqa (package (name "r-minqa") (version "1.2.8") (source (origin (method url-fetch) (uri (cran-uri "minqa" version)) (sha256 (base32 "0rslvg4imaijzb5z6vzsx4zqhrna1jk6qkp2kxnzqy0rn2wy8har")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list gfortran)) (home-page "https://optimizer.r-forge.r-project.org") (synopsis "Derivative-free optimization algorithms by quadratic approximation") (description "This package provides a derivative-free optimization by quadratic approximation based on an interface to Fortran implementations by M. J. D. Powell.") (license license:gpl2))) (define-public r-rcppeigen (package (name "r-rcppeigen") (version "0.3.4.0.2") (source (origin (method url-fetch) (uri (cran-uri "RcppEigen" version)) (sha256 (base32 "1fs2wmsq2s6nzhkrx59li4x1zvcjhk9mhmc2pdz8pm4z2ai7pbgc")))) (properties `((upstream-name . 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"ModelMetrics"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-data-table)) (home-page "https://cran.r-project.org/web/packages/ModelMetrics") (synopsis "Rapid calculation of model metrics") (description "Written in C++ using @code{Rcpp}, this package provides a collection of metrics for evaluating models.") (license license:gpl2+))) (define-public r-matrixmodels (package (name "r-matrixmodels") (version "0.5-3") (source (origin (method url-fetch) (uri (cran-uri "MatrixModels" version)) (sha256 (base32 "03zjfxjk4l2dl1117slz163w0ky675d23sjfni4d7fdhqq359ny2")))) (properties `((upstream-name . "MatrixModels"))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (home-page "https://cran.r-project.org/web/packages/MatrixModels") (synopsis "Modelling with sparse and dense matrices") (description "This package models with sparse and dense matrix matrices, using modular prediction and response module classes.") (license license:gpl2+))) (define-public r-quantreg (package (name "r-quantreg") (version "5.98") (source (origin (method url-fetch) (uri (cran-uri "quantreg" version)) (sha256 (base32 "0qbad2wzw7qvsrm821k2vr0dsx75jj3qbs2sl9k3ymngv1cv5359")))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases ;; This is needed for building vignettes (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (native-inputs (list gfortran r-r-rsp)) ;for vignettes (propagated-inputs (list r-mass r-matrix r-matrixmodels r-sparsem r-survival)) (home-page "https://www.r-project.org") (synopsis "Quantile regression") (description "This package provides an estimation and inference methods for models of conditional quantiles: linear and nonlinear parametric and non-parametric models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also included.") (license license:gpl2+))) (define-public r-nloptr (package (name "r-nloptr") (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "nloptr" version)) (sha256 (base32 "1snqvav2pxjhssn1nld49mjj89cn2zv7gjn2y8ch22gbzmfzbnjc")))) (build-system r-build-system) (native-inputs (list gfortran pkg-config r-knitr)) (inputs (list nlopt)) (home-page "https://cran.r-project.org/web/packages/nloptr") (synopsis "R interface to NLopt") (description "This package is interface to NLopt, a library for nonlinear optimization. NLopt is a library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms.") (license license:lgpl3))) (define-public r-lme4 (package (name "r-lme4") (version "1.1-35.5") (source (origin (method url-fetch) (uri (cran-uri "lme4" version)) (sha256 (base32 "0w2i2d3q19kbx3scd7p7dyfpfpcqb3d5h47y5rb2jr59gvdn8rkx")))) (build-system r-build-system) (propagated-inputs (list r-boot r-lattice r-mass r-matrix r-minqa r-nlme r-nloptr r-rcpp r-rcppeigen)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/lme4") (synopsis "Linear mixed-effects models using eigen and S4") (description "This package provides fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the Eigen C++ library for numerical linear algebra and RcppEigen glue.") (license license:gpl2+))) (define-public r-pbkrtest (package (name "r-pbkrtest") (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "pbkrtest" version)) (sha256 (base32 "0qxswrk54r40qmi9ky7jzv53mrlr2w2mrlf1czma597nzrb52gmh")))) (build-system r-build-system) (propagated-inputs (list r-broom r-doby r-dplyr r-lme4 r-mass r-matrix r-numderiv)) (native-inputs (list r-knitr)) (home-page "https://people.math.aau.dk/~sorenh/software/pbkrtest/") (synopsis "Methods for linear mixed model comparison") (description "This package implements a parametric bootstrap test and a Kenward Roger modification of F-tests for linear mixed effects models and a parametric bootstrap test for generalized linear mixed models.") (license license:gpl2+))) (define-public r-cardata (package (name "r-cardata") (version "3.0-5") (source (origin (method url-fetch) (uri (cran-uri "carData" version)) (sha256 (base32 "06j52rpbqi6fj7chfjwjbwbr6slrbb7i3aygv66gnfiyndcp3rq2")))) (properties `((upstream-name . "carData"))) (build-system r-build-system) (home-page "https://r-forge.r-project.org/projects/car/") (synopsis "Data Sets for the book Companion to Applied Regression") (description "This package provides datasets to accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Third Edition, Sage.") (license license:gpl2+))) (define-public r-car (package (name "r-car") (version "3.1-2") (source (origin (method url-fetch) (uri (cran-uri "car" version)) (sha256 (base32 "1j3l8r3j05769gdfrqz0n38xviq6pww1cjrgdd0fkj3sjy8k89l9")))) (build-system r-build-system) (propagated-inputs (list r-abind r-cardata r-lme4 r-mass r-mgcv r-nlme r-nnet r-pbkrtest r-quantreg r-scales)) (native-inputs (list r-knitr)) (home-page "https://r-forge.r-project.org/projects/car/") (synopsis "Companion to applied regression") (description "This package provides functions and datasets from book Companion to Applied regression, Second Edition, Sage, 2011.") (license license:gpl2+))) (define-public r-rcppprogress (package (name "r-rcppprogress") (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "RcppProgress" version)) (sha256 (base32 "0j2b37gwjpgmrnr00srdzm751hzlpsjb54ph63xxmcdfnwhlnqmi")))) (properties `((upstream-name . "RcppProgress"))) (build-system r-build-system) (home-page "https://github.com/kforner/rcpp_progress") (synopsis "Interruptible progress bar for C++ in R packages") (description "This package displays a progress bar in the R console for long running computations taking place in C++ code, and support for interrupting those computations even in multithreaded code, typically using OpenMP.") (license license:gpl3+))) (define-public r-tmvnsim (package (name "r-tmvnsim") (version "1.0-2") (source (origin (method url-fetch) (uri (cran-uri "tmvnsim" version)) (sha256 (base32 "03xsvsg9bqvgl98ywid3h91mmlhax5s6wvmypp3hq91vmc5kvxlp")))) (properties `((upstream-name . "tmvnsim"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://www.r-project.org") (synopsis "Truncated multivariate normal simulation") (description "This package implements importance sampling from the truncated multivariate normal using the @dfn{Geweke-Hajivassiliou-Keane} (GHK) simulator. Unlike Gibbs sampling which can get stuck in one truncation sub-region depending on initial values, this package allows truncation based on disjoint regions that are created by truncation of absolute values. The GHK algorithm uses simple Cholesky transformation followed by recursive simulation of univariate truncated normals hence there are also no convergence issues. Importance sample is returned along with sampling weights, based on which, one can calculate integrals over truncated regions for multivariate normals.") (license license:gpl2))) (define-public r-mnormt (package (name "r-mnormt") (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "mnormt" version)) (sha256 (base32 "020ka48jsxm9l109ksvy2l17xcpm51avm0l971dgs2mgg01sgz4m")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt") (synopsis "Multivariate normal and \"t\" distributions") (description "This package provides functions for computing the density and the distribution function of multivariate normal and \"t\" random variables, and for generating random vectors sampled from these distributions. Probabilities are computed via non-Monte Carlo methods.") (license license:gpl2+))) (define-public r-numderiv (package (name "r-numderiv") (version "2016.8-1.1") (source (origin (method url-fetch) (uri (cran-uri "numDeriv" version)) (sha256 (base32 "0idk02pqkziik932bd8k72d1q775g1is3m4bc861pcxfz6gx3i6q")))) (properties `((upstream-name . "numDeriv"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/numDeriv") (synopsis "Accurate numerical derivatives") (description "This package provides methods for calculating accurate numerical first and second order derivatives.") (license license:gpl2))) (define-public r-sn (package (name "r-sn") (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "sn" version)) (sha256 (base32 "1g92vwbg0kqnqpsgianid2r91334p5shi39hr26v2z6wj5nvbxpr")))) (build-system r-build-system) (propagated-inputs (list r-mnormt r-numderiv r-quantreg)) (native-inputs (list r-r-rsp)) (home-page "http://azzalini.stat.unipd.it/SN") (synopsis "The skew-normal and skew-t distributions") (description "This package provides functionalities to build and manipulate probability distributions of the skew-normal family and some related ones, notably the skew-t family, and provides related statistical methods for data fitting and diagnostics, in the univariate and the multivariate case.") (license license:gpl2+))) (define-public r-tclust (package (name "r-tclust") (version "2.0-4") (source (origin (method url-fetch) (uri (cran-uri "tclust" version)) (sha256 (base32 "0y05aqpmal7ky33hs8n1phai94d7f48ich43jvy4m5wbfxkp2rm6")))) (build-system r-build-system) ;; These are all suggested packages, not build dependencies. (propagated-inputs (list r-doparallel r-foreach r-mass r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/web/packages/tclust") (synopsis "Robust trimmed clustering") (description "This package implements different robust clustering algorithms (@code{tclust}) based on trimming and including some graphical diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).") (license license:gpl3))) (define-public r-ranger (package (name "r-ranger") (version "0.16.0") (source (origin (method url-fetch) (uri (cran-uri "ranger" version)) (sha256 (base32 "12c52gqqwaaid5b062gad18ir1vala1z3a0z5j4af1xqzlxgk583")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-matrix r-rcppeigen)) (home-page "https://github.com/imbs-hl/ranger") (synopsis "Fast implementation of random forests") (description "This package provides a fast implementation of Random Forests, particularly suited for high dimensional data. Ensembles of classification, regression, survival and probability prediction trees are supported. Data from genome-wide association studies can be analyzed efficiently.") (license license:gpl3))) (define-public r-tsne (package (name "r-tsne") (version "0.1-3.1") (source (origin (method url-fetch) (uri (cran-uri "tsne" version)) (sha256 (base32 "126q6ha25wx9mdsfngzkyp8j2fj81ri1knjdq1iyvwx3q1dwdaql")))) (build-system r-build-system) (home-page "https://github.com/jdonaldson/rtsne/") (synopsis "t-Distributed Stochastic Neighbor Embedding for R") (description "This package provides a pure R implementation of the t-SNE algorithm.") (license license:gpl2+))) (define-public r-cairo (package (name "r-cairo") (version "1.6-2") (source (origin (method url-fetch) (uri (cran-uri "Cairo" version)) (sha256 (base32 "0qjdsj6mpbwvnp8cimc4yrqfq3z68pfcd78ahsai52hpjdplqvvb")))) (properties `((upstream-name . "Cairo"))) (build-system r-build-system) (inputs (list cairo harfbuzz icu4c libjpeg-turbo libtiff zlib)) (native-inputs (list pkg-config)) (home-page "https://www.rforge.net/Cairo/") (synopsis "R graphics device using Cairo graphics library") (description "This package provides a Cairo graphics device that can be use to create high-quality vector (PDF, PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). Since it uses the same back-end for all output, copying across formats is WYSIWYG. Files are created without the dependence on X11 or other external programs. This device supports alpha channel (semi-transparent drawing) and resulting images can contain transparent and semi-transparent regions. It is ideal for use in server environments (file output) and as a replacement for other devices that don't have Cairo's capabilities such as alpha support or anti-aliasing. Backends are modular such that any subset of backends is supported.") (license license:gpl2))) (define-public r-lubridate (package (name "r-lubridate") (version "1.9.3") (source (origin (method url-fetch) (uri (cran-uri "lubridate" version)) (sha256 (base32 "1zvzycng2hsks9d7552nb93abzjrs43c975rc16s3c1is8318vib")))) (build-system r-build-system) (propagated-inputs (list r-generics r-timechange)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/lubridate/") (synopsis "Make dealing with dates a little easier") (description "This package provides functions to work with date-times and time-spans: fast and user friendly parsing of date-time data, extraction and updating of components of a date-time (years, months, days, hours, minutes, and seconds), algebraic manipulation on date-time and time-span objects. The @code{lubridate} package has a consistent and memorable syntax that makes working with dates easy and fun.") (license license:gpl2))) (define-public r-fdrtool (package (name "r-fdrtool") (version "1.2.18") (source (origin (method url-fetch) (uri (cran-uri "fdrtool" version)) (sha256 (base32 "1vxswr56c63vvl2q6m0j0a5psdw724vspf6zxlr1k9zsdfcnd6b4")))) (build-system r-build-system) (home-page "https://strimmerlab.org/software/fdrtool/") (synopsis "Estimation of false discovery rates and higher criticism") (description "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 (package (name "r-forcats") (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "forcats" version)) (sha256 (base32 "0ki5c84n7xm4iw4aj629l51hm84f6p5wa3bw88d1wbnr15wibfy5")))) (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-lifecycle r-magrittr r-tibble r-rlang)) (native-inputs (list r-knitr)) (home-page "https://forcats.tidyverse.org") (synopsis "Tools for working with factors") (description "This package provides helpers for reordering factor levels (including moving specified levels to front, ordering by first appearance, reversing, and randomly shuffling), and tools for modifying factor levels (including collapsing rare levels into other, \"anonymizing\", and manually \"recoding\").") (license license:gpl3))) (define-public r-tgconfig (let ((commit "15cf199436ae0b2ac0006b2ca7f0aeeb5c9d4445") (revision "1")) (package (name "r-tgconfig") (version (git-version "0.1.2" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/tanaylab/tgconfig") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "159m8hhbk9ip2fdy6zsa96v0173q1awcrzdz2rr2796awfaxjgx1")))) (properties `((upstream-name . "tgconfig"))) (build-system r-build-system) (propagated-inputs (list r-yaml)) (home-page "https://github.com/tanaylab/tgconfig") (synopsis "Infrastructure for managing package parameters") (description "This is a package to provide infrastructure for managing package parameters. Parameters are easy to get in relevant functions within a package, and rrror is thrown if a parameter is missing. Developers are able to register parameters and set their default value in a config file that is part of the package in YAML format, and users are able to override parameters using their own YAML. Users get an exception when trying to override a parameter that was not registered, and can load multiple parameters to the current environment.") (license license:gpl3+)))) (define-public r-tgutil (let ((commit "db4ff8b98082f8e4dbdeacb452641d215fd3c7ff") (revision "1")) (package (name "r-tgutil") (version (git-version "0.1.15" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/tanaylab/tgutil") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "00rsqs7f896piywh84jr8fkphbbx4jb7radf6znhhj6fip63yn91")))) (properties `((upstream-name . "tgutil"))) (build-system r-build-system) (propagated-inputs (list r-broom r-cowplot r-data-table r-dplyr r-ggplot2 r-glue r-magrittr r-matrix r-matrixstats r-qlcmatrix r-readr r-rlang r-scales r-tibble r-tidyr)) (home-page "https://github.com/tanaylab/tgutil") (synopsis "Simple utility functions for Tanay lab code") (description "This package provides simple utility functions that are shared across several packages maintained by the Tanay lab.") (license license:gpl3)))) (define-public r-catterplots (let ((commit "ae17cd5e49ddda4ecfe0eba8a4c21df8c88e72c4") (revision "3")) (package (name "r-catterplots") (version (git-version "0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/Gibbsdavidl/CatterPlots") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0qa8liylffpxgdg8xcgjar5dsvczqhn3akd4w35113hnyg1m4xyg")))) (build-system r-build-system) (propagated-inputs (list r-png)) (home-page "https://github.com/Gibbsdavidl/CatterPlots") (synopsis "Scatter plots with cat shaped points") (description "Did you ever wish you could make scatter plots with cat shaped points? Now you can!") (license license:asl2.0)))) (define-public r-colorout (package (name "r-colorout") (version "1.2-2") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/jalvesaq/colorout") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1rsx69wjpa73c6x2hacvvvbzdzxn7wg06gizf97kasjdlb7azmp3")))) (build-system r-build-system) (home-page "https://github.com/jalvesaq/colorout") (synopsis "Colorize output in the R REPL") (description "@code{colorout} is an R package that colorizes R output when running in terminal emulator. R STDOUT is parsed and numbers, negative numbers, dates in the standard format, strings, and R constants are identified and wrapped by special ANSI scape codes that are interpreted by terminal emulators as commands to colorize the output. R STDERR is also parsed to identify the expressions warning and error and their translations to many languages. If these expressions are found, the output is colorized accordingly; otherwise, it is colorized as STDERROR (blue, by default). You can customize the colors according to your taste, guided by the color table made by the command @code{show256Colors()}. You can also set the colors to any arbitrary string. In this case, it is up to you to set valid values.") (license license:gpl3+))) (define-public r-nnlm (let ((commit "4574bca9456fe2285b668b4c22a908cffbad10a0") (revision "1")) (package (name "r-nnlm") (version (git-version "0.4.4" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/linxihui/NNLM") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1qzvav4ch0j1k7jcqzk9cvl8dx79fapmvdzmzzyl8smscybhfgba")))) (properties `((upstream-name . "NNLM"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo r-rcppprogress)) (native-inputs (list r-knitr)) (home-page "https://github.com/linxihui/NNLM") (synopsis "Fast and versatile non-negative matrix factorization") (description "This is a package for @dfn{Non-Negative Linear Models} (NNLM). It implements fast sequential coordinate descent algorithms for non-negative linear regression and @dfn{non-negative matrix factorization} (NMF). It supports mean square error and Kullback-Leibler divergence loss. Many other features are also implemented, including missing value imputation, domain knowledge integration, designable W and H matrices and multiple forms of regularizations.") (license license:bsd-2)))) (define-public r-swne (let ((commit "05fc3ee4e09b2c34d99c69d3b97cece4c1c34143") (revision "1")) (package (name "r-swne") (version (git-version "0.6.20" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/yanwu2014/swne") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0crlpg9kclbv4v8250p3086a3lk6f2hcq79psqkdylc1qnrx3kfx")))) (properties `((upstream-name . "swne"))) (build-system r-build-system) (propagated-inputs (list r-fnn r-ggplot2 r-ggrepel r-hash r-ica r-igraph r-irlba r-jsonlite r-liger r-mass r-matrix r-mgcv r-nnlm ;not listed but required at install time r-plyr r-proxy r-rcolorbrewer r-rcpp r-rcpparmadillo r-rcppeigen r-reshape r-reshape2 r-snow r-umap r-usedist)) (home-page "https://github.com/yanwu2014/swne") (synopsis "Visualize high dimensional datasets") (description "@dfn{Similarity Weighted Nonnegative Embedding} (SWNE) is a method for visualizing high dimensional datasets. SWNE uses Nonnegative Matrix Factorization to decompose datasets into latent factors, projects those factors onto 2 dimensions, and embeds samples and key features in 2 dimensions relative to the factors. SWNE can capture both the local and global dataset structure, and allows relevant features to be embedded directly onto the visualization, facilitating interpretation of the data.") (license license:gpl2)))) (define-public r-languageserver (let ((commit "004da9388f9b19990f031c8dc9b527fb406378ba") (revision "1")) (package (name "r-languageserver") (version (git-version "0.3.12" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/REditorSupport/languageserver") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "05f22bjpc87fngzq4jsk2q2yb2i3ha03b377r0wx15d0b8xaa1ix")))) (properties `((upstream-name . "languageserver"))) (build-system r-build-system) (propagated-inputs (list r-callr r-collections r-fs r-jsonlite r-lintr r-r6 r-roxygen2 r-stringi r-styler r-xml2 r-xmlparsedata)) (home-page "https://github.com/REditorSupport/languageserver") (synopsis "Language Server for R") (description "This package provides an implementation of the Language Server Protocol for R. The @url{https://microsoft.github.io/language-server-protocol/,Language Server protocol} is used by an editor client to integrate features like auto completion.") (license license:expat)))) (define-public python-rpy2 (package (name "python-rpy2") (version "3.5.15") (source (origin (method url-fetch) (uri (pypi-uri "rpy2" version)) (sha256 (base32 "0asvybb7kmr48pfkibp1qi3h3vlq2fl0mazaf0xj6zywhi5awks4")))) (build-system python-build-system) (arguments '(#:phases (modify-phases %standard-phases (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? (setenv "TZ" "UTC") (invoke "pytest" "-v" "rpy2/tests/"))))))) (propagated-inputs (list python-cffi python-six python-jinja2 python-numpy python-pandas python-pytz python-ipython python-tzlocal)) (inputs (list readline icu4c pcre r-minimal r-survival r-ggplot2 r-rsqlite r-dplyr r-dbplyr python-numpy zlib)) (native-inputs (list python-coverage python-ipython python-numpy python-pandas python-pytest python-pytest-cov)) (home-page "https://rpy2.github.io") (synopsis "Python interface to the R language") (description "rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions.") ;; Any of these licenses can be picked for the R interface. The whole ;; project is released under GPLv2+ according to the license declaration ;; in "setup.py". (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+)))) (define-public java-jdistlib (package (name "java-jdistlib") (version "0.4.5") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-" version "-src.jar")) (sha256 (base32 "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11")))) (build-system ant-build-system) (arguments `(#:jar-name "jdistlib.jar" #:jdk ,icedtea-8 #:tests? #f ; no dedicated test directory #:phases (modify-phases %standard-phases (add-after 'unpack 'fix-broken-encoding (lambda _ (with-fluids ((%default-port-encoding "ISO-8859-1")) (substitute* "src/jdistlib/Beta.java" (("Scheff.+-Tukey") "Scheffe-Tukey"))) #t))))) (propagated-inputs (list java-jtransforms)) (native-inputs (list java-junit)) (home-page "https://jdistlib.sourceforge.net/") (synopsis "Java library of statistical distributions") (description "JDistlib is the Java Statistical Distribution Library, a Java package that provides routines for various statistical distributions.") ;; The files that were translated from R code are under GPLv2+; some files ;; are under the GPLv3, which is a mistake. The author confirmed in an ;; email that this whole project should be under GPLv2+. (license license:gpl2+))) (define-public emacs-ess (let ((commit "ab2faeca1ba6c456333312c58f58ef9e5ef4aa8b") (version "24.01.1") (revision "1")) (package (name "emacs-ess") (version (git-version version revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/emacs-ess/ESS") (commit commit))) (sha256 (base32 "0jfdfqpa3x1zm65cllkzhqir057xd3hxi4z2ddii1i26zy56iikf")) (file-name (git-file-name name version)) (modules '((guix build utils))) (snippet #~(begin ;; Stop ESS from trying to bundle an external julia-mode.el. (substitute* "lisp/Makefile" ((" \\$\\(JULIAS)") "") (("\ttest.*julia-mode.*\\.el") "")) ;; Only build docs in info format. (substitute* "doc/Makefile" (("all : info text") "all : info") (("install: install-info install-other-docs") "install: install-info")) ;; Stop install-info from trying to update the info directory. (substitute* "doc/Makefile" ((".*/dir.*") "")) ;; Avoid generating ess-autoloads.el twice. (substitute* "Makefile" (("all: lisp doc etc autoloads") "all: lisp doc etc")) ;; Install to correct directories. (substitute* "Makefile" (("mkdir -p \\$\\(ESSDESTDIR)") "$(MAKE) -C lisp install; $(MAKE) -C doc install") (("\\$\\(INSTALL) -R \\./\\* \\$\\(ESSDESTDIR)/") "$(MAKE) -C etc install")))))) (build-system gnu-build-system) (arguments (let ((base-directory "/share/emacs/site-lisp")) (list #:modules '((guix build gnu-build-system) (guix build utils) (guix build emacs-utils)) #:imported-modules `(,@%default-gnu-imported-modules (guix build emacs-build-system) (guix build emacs-utils)) #:make-flags #~(list (string-append "PREFIX=" #$output) (string-append "ETCDIR=" #$output #$base-directory "/etc") (string-append "LISPDIR=" #$output #$base-directory) (string-append "INFODIR=" #$output "/share/info")) #:phases #~(modify-phases %standard-phases (delete 'configure) (add-before 'check 'skip-failing-tests (lambda _ (let-syntax ((disable-tests (syntax-rules () ((_ ()) (syntax-error "test names list must not be empty")) ((_ (test-name ...)) (substitute* (find-files "test" "\\.el$") (((string-append "^\\(ert-deftest " test-name ".*") all) (string-append all "(skip-unless nil)\n")) ...)))) (disable-etests ;different test syntax (syntax-rules () ((_ ()) (syntax-error "test names list must not be empty")) ((_ (test-name ...)) (for-each (lambda (file) (emacs-batch-edit-file file '(progn (dolist (test (list test-name ...)) (goto-char (point-min)) (let ((s (format "etest-deftest %s " test))) (when (search-forward s nil t) (beginning-of-line) (kill-sexp)))) (basic-save-buffer)))) (find-files "test" "\\.el$")))))) (disable-tests ("ess--derive-connection-path" "ess-eval-line-test" "ess-eval-region-test" "ess-mock-remote-process" "ess-r-load-ESSR-github-fetch-no" "ess-r-load-ESSR-github-fetch-yes" "ess-set-working-directory-test" "ess-test-r-startup-directory")) (disable-etests ("ess-r-eval-ns-env-roxy-tracebug-test" "ess-r-eval-sink-freeze-test" ;; Looks like an off-by-one error. "ess--command-browser-unscoped-essr"))))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? (invoke "make" "test")))))))) (native-inputs (list perl r-roxygen2 texinfo)) (inputs (list emacs-minimal r-minimal)) (propagated-inputs (list emacs-julia-mode)) (home-page "https://ess.r-project.org/") (synopsis "Emacs mode for statistical analysis programs") (description "Emacs Speaks Statistics (ESS) is an add-on package for GNU Emacs. It is designed to support editing of scripts and interaction with various statistical analysis programs such as R, Julia, and JAGS.") (license license:gpl3+)))) (define-public emacs-poly-r (package (name "emacs-poly-r") (version "0.2.2") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/polymode/poly-R") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0a4wx73jkngw5nbq1fa4jfhba6bsmyn6vnsf887x3xhb5v3ykhsg")))) (build-system emacs-build-system) (propagated-inputs (list emacs-ess emacs-poly-noweb emacs-polymode-markdown emacs-polymode)) (properties '((upstream-name . "poly-R"))) (home-page "https://github.com/polymode/poly-markdown") (synopsis "Polymodes for the R language") (description "This package provides a number of polymodes for working with mixed R files, including Rmarkdown files.") (license license:gpl3+))) (define-public readstat (package (name "readstat") (version "1.1.9") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/WizardMac/ReadStat") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0aqalr86d7h9sp9zjkydw3ap4s54qgq2ml6p8gd0gnn1jf0ljm72")))) (build-system gnu-build-system) (native-inputs (list autoconf automake gnu-gettext libtool)) (inputs (list zlib)) (home-page "https://github.com/WizardMac/ReadStat") (synopsis "Convert SAS, Stata, and SPSS files") (description "Command-line tool and C library for reading files from popular stats packages like SAS, Stata and SPSS.") (license license:expat))) (define-public python-pyreadstat (package (name "python-pyreadstat") (version "1.2.4") ;; No tests in the PyPI tarball. (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/Roche/pyreadstat") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0zysrzixvqw2lwwykxqg5yj8a0zyv5s2bmk22x30f4rj2hgvq1pv")) (patches (search-patches "python-pyreadstat-link-libiconv.patch")))) (arguments '(#:phases (modify-phases %standard-phases (add-before 'check 'change-home-dir (lambda _ ;; test_sav_expand and test_sav_write_basic_expanduser need a ;; home directory with write permissions. (setenv "HOME" "/tmp"))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? ;; The source also contains tests/test_version.py ;; which checks the version in __init__.py against the ;; one in setup.py. Since this requires texlive ;; dependencies to run and is also not mentioned in ;; how_to_test.md, this test is skipped. (invoke "python" "tests/test_basic.py"))))))) (build-system python-build-system) (propagated-inputs (list python-pandas)) (inputs (list libiconv zlib)) (native-inputs (list python-cython-3)) (home-page "https://github.com/Roche/pyreadstat") (synopsis "Read and write SAS, SPSS and Stata files into/from Pandas DataFrames") (description "This Python package can be used to read and write SAS, SPSS and Stata files into/from Pandas DataFrames. It is a wrapper around the C library @code{readstat}.") (license license:asl2.0))) (define-public r-quantpsyc (package (name "r-quantpsyc") (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "QuantPsyc" version)) (sha256 (base32 "1dbj830p5837fiwa800nzsaf19lf95vc3n7jmds2q9v06mrz6syq")))) (properties `((upstream-name . "QuantPsyc"))) (build-system r-build-system) (propagated-inputs (list r-boot r-dplyr r-mass r-purrr)) (home-page "https://cran.r-project.org/web/packages/QuantPsyc/") (synopsis "Quantitative Psychology Tools") (description "Contains functions useful for data screening, testing moderation, mediation and estimating power.") (license license:gpl2+))) (define-public r-clubsandwich (package (name "r-clubsandwich") (version "0.5.11") (source (origin (method url-fetch) (uri (cran-uri "clubSandwich" version)) (sha256 (base32 "1y9iy86w2440y22279is7vgi9m9v876p5954nhq5lg9ghpzbwzdq")))) (properties `((upstream-name . "clubSandwich"))) (build-system r-build-system) (propagated-inputs (list r-lifecycle r-sandwich)) (native-inputs (list r-knitr)) (home-page "https://github.com/jepusto/clubSandwich") (synopsis "Cluster-Robust (Sandwich) Variance Estimators with Small-Sample Corrections") (description "Provides several cluster-robust variance estimators (i.e., sandwich estimators) for ordinary and weighted least squares linear regression models, including the bias-reduced linearization estimator introduced by Bell and McCaffrey (2002) @url{http://www.statcan.gc.ca/pub/12-001-x/2002002/article/9058-eng.pdf} and developed further by Pustejovsky and Tipton (2017) @url{doi:10.1080/07350015.2016.1247004}. The package includes functions for estimating the variance- covariance matrix and for testing single- and multiple- contrast hypotheses based on Wald test statistics. Tests of single regression coefficients use Satterthwaite or saddle-point corrections. Tests of multiple- contrast hypotheses use an approximation to Hotelling's T-squared distribution. Methods are provided for a variety of fitted models, including @code{lm()} and @code{mlm} objects, @code{glm()}, ivreg (from package @code{AER}), @code{plm()} (from package @code{plm}), @code{gls()} and @code{lme()} (from @code{nlme}), @code{robu()} (from @code{robumeta}), and @code{rma.uni()} and @code{rma.mv()} (from @code{metafor}).") (license license:gpl3))) (define-public r-puniform (package (name "r-puniform") (version "0.2.7") (source (origin (method url-fetch) (uri (cran-uri "puniform" version)) (sha256 (base32 "15q5wlcps7387rjz7p1f5kifg1fl5yxxy7gjx6fvspvqwjkjbs4z")))) (properties `((upstream-name . "puniform"))) (build-system r-build-system) (propagated-inputs (list r-adgoftest r-metafor r-numderiv r-rcpp r-rcpparmadillo)) (home-page "https://github.com/RobbievanAert/puniform") (synopsis "Meta-Analysis Methods Correcting for Publication Bias") (description "This package provides meta-analysis methods that correct for publication bias and outcome reporting bias. Four methods and a visual tool are currently included in the package. @enumerate @item The p-uniform method as described in van Assen, van Aert, and Wicherts (2015) @url{doi:10.1037/met0000025} can be used for estimating the average effect size, testing the null hypothesis of no effect, and testing for publication bias using only the statistically significant effect sizes of primary studies. @item The p-uniform* method as described in van Aert and van Assen (2019) @url{doi:10.31222/osf.io/zqjr9}. This method is an extension of the p-uniform method that allows for estimation of the average effect size and the between-study variance in a meta-analysis, and uses both the statistically significant and nonsignificant effect sizes. @item The hybrid method as described in van Aert and van Assen (2017) @url{doi:10.3758/s13428-017-0967-6}. The hybrid method is a meta-analysis method for combining an original study and replication and while taking into account statistical significance of the original study. The p-uniform and hybrid method are based on the statistical theory that the distribution of p-values is uniform conditional on the population effect size. @item The fourth method in the package is the Snapshot Bayesian Hybrid Meta-Analysis Method as described in van Aert and van Assen (2018) @url{doi:10.1371/journal.pone.0175302}. This method computes posterior probabilities for four true effect sizes (no, small, medium, and large) based on an original study and replication while taking into account publication bias in the original study. The method can also be used for computing the required sample size of the replication akin to power analysis in null hypothesis significance testing. @end enumerate The meta-plot is a visual tool for meta-analysis that provides information on the primary studies in the meta-analysis, the results of the meta-analysis, and characteristics of the research on the effect under study (van Assen and others, 2020). Helper functions to apply the Correcting for Outcome Reporting Bias (CORB) method to correct for outcome reporting bias in a meta-analysis (van Aert & Wicherts, 2020).") (license license:gpl2+))) (define-public r-esc (package (name "r-esc") (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "esc" version)) (sha256 (base32 "0gns7gz55p6pha05413r3hlvd7f2v1amxkg13d197mab1ypqic7q")))) (properties `((upstream-name . "esc"))) (build-system r-build-system) (home-page "https://strengejacke.github.io/esc/") (synopsis "Effect Size Computation for Meta Analysis") (description "Implementation of the web-based @url{http://www.campbellcollaboration.org/escalc/html/EffectSizeCalculator-Home.php,'Practical Meta-Analysis Effect Size Calculator'} from David B. Wilson in R. Based on the input, the effect size can be returned as standardized mean difference, Cohen's f, Hedges' g, Pearson's r or Fisher's transformation z, odds ratio or log odds, or eta squared effect size.") (license license:gpl3))) (define-public r-kknn (package (name "r-kknn") (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "kknn" version)) (sha256 (base32 "1nzkg3dxaiqp87p56wm895qx5xn86hv5hjr73qvl1yiaxiq0x112")))) (properties `((upstream-name . "kknn"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-matrix)) (home-page "https://github.com/KlausVigo/kknn") (synopsis "Weighted k-Nearest Neighbors") (description "Weighted k-Nearest Neighbors for Classification, Regression and Clustering.") (license license:gpl2+))) (define-public r-logspline (package (name "r-logspline") (version "2.1.22") (source (origin (method url-fetch) (uri (cran-uri "logspline" version)) (sha256 (base32 "00pdcfj1hmafxzs7gqw3n072p6pxp9hvsdm062n0xkiby6igffkp")))) (properties `((upstream-name . "logspline"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/logspline/") (synopsis "Routines for Logspline Density Estimation") (description "Contains routines for logspline density estimation. The function @code{oldlogspline()} uses the same algorithm as the logspline package version 1.0.x; i.e., the Kooperberg and Stone (1992) algorithm (with an improved interface). The recommended routine @code{logspline()} uses an algorithm from @url{doi:10.1214/aos/1031594728,Stone et al (1997)}.") (license license:asl2.0))) (define-public r-effects (package (name "r-effects") (version "4.2-2") (source (origin (method url-fetch) (uri (cran-uri "effects" version)) (sha256 (base32 "0nlj79am9a1yg737dhfa8dj1kj2hly9pfknmphsbcvlgxqn35vig")))) (properties `((upstream-name . "effects"))) (build-system r-build-system) (propagated-inputs (list r-cardata r-colorspace r-estimability r-insight r-lattice r-lme4 r-nnet r-survey)) (native-inputs (list r-knitr)) (home-page "https://www.r-project.org") (synopsis "Effect Displays for Linear, Generalized Linear, and Other Models") (description "Graphical and tabular effect displays, e.g., of interactions, for various statistical models with linear predictors.") (license license:gpl2+))) (define-public r-bayesfactor (package (name "r-bayesfactor") (version "0.9.12-4.7") (source (origin (method url-fetch) (uri (cran-uri "BayesFactor" version)) (sha256 (base32 "0z9p9vdcmcdwqmixaiqnhli2b06whbap6y4pqx4a5gcdgxlj09zr")))) (properties `((upstream-name . "BayesFactor"))) (build-system r-build-system) (propagated-inputs (list r-coda r-hypergeo r-matrix r-matrixmodels r-mvtnorm r-pbapply r-rcpp r-rcppeigen r-stringr)) (native-inputs (list r-knitr)) (home-page "https://richarddmorey.github.io/BayesFactor/") (synopsis "Computation of Bayes Factors for Common Designs") (description "This package provides a suite of functions for computing various Bayes factors for simple designs, including contingency tables, one- and two-sample designs, one-way designs, general ANOVA designs, and linear regression.") (license license:gpl2))) (define-public r-norm (package (name "r-norm") (version "1.0-11.1") (source (origin (method url-fetch) (uri (cran-uri "norm" version)) (sha256 (base32 "1g33g721c0f2b275b334ir6n0h81fh567vs9vrxk60y21z1ydzy2")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/norm/") (synopsis "Analysis of multivariate normal datasets with missing values") (description "Multiple imputation of multivariate continuous data under a normal model.") ;; Custom license, see https://cran.r-project.org/web/packages/norm/LICENSE. (license (license:non-copyleft "file://LICENSE")))) (define-public r-naniar (package (name "r-naniar") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "naniar" version)) (sha256 (base32 "0i3gijr1l7hbcp75cyj26pxmm493lnvasl8aba9vv4w8lz1lck59")))) (build-system r-build-system) (propagated-inputs (list r-cli r-dplyr r-forcats r-ggplot2 r-glue r-lifecycle r-magrittr r-norm r-purrr r-rlang r-tibble r-tidyr r-upsetr r-vctrs r-viridis r-visdat)) (native-inputs (list r-knitr)) (home-page "https://github.com/njtierney/naniar") (synopsis "Data structures, summaries, and visualisations for missing data") (description "Missing values are ubiquitous in data and need to be explored and handled in the initial stages of analysis. The package provides data structures and functions that facilitate the plotting of missing values and examination of imputations. This allows missing data dependencies to be explored with minimal deviation from the common work patterns of @code{ggplot2} and tidy data.") (license license:expat))) (define-public r-glinternet (package (name "r-glinternet") (version "1.0.12") (source (origin (method url-fetch) (uri (cran-uri "glinternet" version)) (sha256 (base32 "0aphdscj0s6kqxlkgqkw2d6snrylz6hiis6307pl8ldh7q5cvm33")))) (build-system r-build-system) (home-page "http://web.stanford.edu/~hastie/Papers/glinternet_jcgs.pdf") (synopsis "Learning interactions via hierarchical group-lasso regularization") (description "Group-Lasso INTERaction-NET. Fits linear pairwise-interaction models that satisfy strong hierarchy: if an interaction coefficient is estimated to be nonzero, then its two associated main effects also have nonzero estimated coefficients. Accommodates categorical variables (factors) with arbitrary numbers of levels, continuous variables, and combinations thereof. Implements the machinery described in the paper \"Learning interactions via hierarchical group-lasso regularization\" (JCGS 2015, Volume 24, Issue 3). Michael Lim & Trevor Hastie (2015)") (license license:gpl2))) (define-public r-datasaurus (package (name "r-datasaurus") (version "0.1.8") (source (origin (method url-fetch) (uri (cran-uri "datasauRus" version)) (sha256 (base32 "08yx87k4kl3i9g3m1j9532whvs4l0l3v5gwj8sk7qlb3m3wajakr")))) (properties `((upstream-name . "datasauRus"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://github.com/lockedata/datasauRus") (synopsis "Datasets from the Datasaurus Dozen") (description "The Datasaurus Dozen is a set of datasets with the same summary statistics. They retain the same summary statistics despite having radically different distributions. The datasets represent a larger and quirkier object lesson that is typically taught via Anscombe's Quartet (available in the 'datasets' package). Anscombe's Quartet contains four very different distributions with the same summary statistics and as such highlights the value of visualisation in understanding data, over and above summary statistics. As well as being an engaging variant on the Quartet, the data is generated in a novel way. The simulated annealing process used to derive datasets from the original Datasaurus is detailed in \"Same Stats, Different Graphs: Generating Datasets with Varied Appearance and Identical Statistics through Simulated Annealing\" @url{doi:10.1145/3025453.3025912}.") (license license:expat))) (define-public r-lmom (package (name "r-lmom") (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "lmom" version)) (sha256 (base32 "1482kbb4cm65m2d1xlxml93yjd3d43iiap6nvzg5vd33i9iyh2jb")))) (properties `((upstream-name . "lmom"))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/package=lmom") (synopsis "L-Moments for R") (description "This package provides functions related to L-moments: computation of L-moments and trimmed L-moments of distributions and data samples; parameter estimation; L-moment ratio diagram; plot vs. quantiles of an extreme-value distribution.") (license license:cpl1.0))) (define-public r-gld (package (name "r-gld") (version "2.6.6") (source (origin (method url-fetch) (uri (cran-uri "gld" version)) (sha256 (base32 "1i7xpyxd7r1fkjy9zkzd3rfsnb35v5c5fkafs1zd9d8729wfj8za")))) (properties `((upstream-name . "gld"))) (build-system r-build-system) (propagated-inputs (list r-e1071 r-lmom)) (home-page "https://cran.r-project.org/package=gld") (synopsis "Estimation and Use of the Generalised (Tukey) Lambda Distribution") (description "The generalised lambda distribution, or Tukey lambda distribution, provides a wide variety of shapes with one functional form. This package provides random numbers, quantiles, probabilities, densities and density quantiles for four different types of the distribution, the FKML (Freimer et al 1988), RS (Ramberg and Schmeiser 1974), GPD (van Staden and Loots 2009) and FM5 - see documentation for details. It provides the density function, distribution function, and Quantile-Quantile plots. It implements a variety of estimation methods for the distribution, including diagnostic plots. Estimation methods include the starship (all 4 types), method of L-Moments for the GPD and FKML types, and a number of methods for only the FKML type. These include maximum likelihood, maximum product of spacings, Titterington's method, Moments, Trimmed L-Moments and Distributional Least Absolutes.") (license license:gpl2+))) (define-public r-exact (package (name "r-exact") (version "3.3") (source (origin (method url-fetch) (uri (cran-uri "Exact" version)) (sha256 (base32 "0hikz8f19blywxs66xj6zf4krwyivsy3w165qvrnb0m2l6dx1l7v")))) (properties `((upstream-name . "Exact"))) (build-system r-build-system) (propagated-inputs (list r-rootsolve)) (home-page "https://cran.r-project.org/package=Exact") (synopsis "Unconditional Exact Test") (description "Performs unconditional exact tests and power calculations for 2x2 contingency tables. For comparing two independent proportions, performs @url{doi:10.1038/156177a0, Barnard's test (1945)} using the original CSM test (@url{doi:10.1093/biomet/34.1-2.123, Barnard (1947)}), using Fisher's p-value referred to as @url{doi:10.1111/j.1467-9574.1970.tb00104.x, Boschloo's test (1970)}, or using a Z-statistic (@url{doi:10.2307/2981892, Suissa and Shuster (1985)}). For comparing two binary proportions, performs unconditional exact test using McNemar's Z-statistic (@url{doi:10.1191/0962280203sm312ra, Berger and Sidik (2003)}), using McNemar's Z-statistic with continuity correction, or using CSM test. Calculates confidence intervals for the difference in proportion.") (license license:gpl2))) (define-public r-desctools (package (name "r-desctools") (version "0.99.56") (source (origin (method url-fetch) (uri (cran-uri "DescTools" version)) (sha256 (base32 "1lvh19q3f4yidcxilba6bw2l2lllm6zc0aiqjgh8bvz01rq19f09")))) (properties `((upstream-name . "DescTools"))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-before 'check 'pre-check (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-boot r-cli r-data-table r-exact r-expm r-gld r-httr r-mass r-mvtnorm r-rcpp r-readxl r-rstudioapi r-withr)) (native-inputs (list gfortran r-r-rsp)) (home-page "https://andrisignorell.github.io/DescTools/") (synopsis "Tools for Descriptive Statistics") (description "This package provides a collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The BigCamelCase style was consequently applied to functions borrowed from contributed R packages as well.") (license license:gpl2+))) (define-public xlispstat (let ((commit "f1bea6053df658ee48612bf1f63c35de99e2c649") (revision "0")) (package (name "xlispstat") (version (git-version "3.52.23" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/jhbadger/xlispstat.git") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1p0cmgy19kbkxia139cb5w9dnkp2cdqp5n3baag6cq3prn3n71mf")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; Parallel builds are not supported #:configure-flags (list "--with-gcc") #:phases (modify-phases %standard-phases (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? (with-output-to-file "exit.lsp" (lambda () (display "(exit)"))) (invoke "./xlisp" "tests/test" "exit"))))))) (inputs (list tcsh libx11 libxmu libxext libxpm libxaw ncurses gnuplot)) (native-inputs (list pkg-config)) (synopsis "Statistical analysis environment with interactive graphics") (description "XLISP-STAT is a statistical environment based on a Lisp dialect called XLISP. To facilitate statistical computations, standard functions for addition, logarithms, etc., have been modified to operate on lists and arrays of numbers, and a number of basic statistical functions have been added. Many of these functions have been written in Lisp, and additional functions can be added easily by a user. Several basic forms of plots, including histograms, scatterplots, rotatable plots and scatterplot matrices are provided. These plots support various forms of interactive highlighting operations and can be linked so points highlighted in one plot will be highlighted in all linked plots. Interactions with the plots are controlled by the mouse, menus and dialog boxes. An object-oriented programming system is used to allow menus, dialogs, and the response to mouse actions to be customized.") (home-page "https://homepage.divms.uiowa.edu/~luke/xls/xlsinfo/") (license license:expat)))) (define-public r-rlrsim (package (name "r-rlrsim") (version "3.1-8") (source (origin (method url-fetch) (uri (cran-uri "RLRsim" version)) (sha256 (base32 "06i4slc7fj8xifq20i1vqfadfw2p81b0kfzga60139hnryz1zpva")))) (properties `((upstream-name . "RLRsim"))) (build-system r-build-system) (propagated-inputs (list r-lme4 r-mgcv r-nlme r-rcpp)) (home-page "https://github.com/fabian-s/RLRsim") (synopsis "Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive Models") (description "Rapid, simulation-based exact (restricted) likelihood ratio tests for testing the presence of variance components/nonparametric terms for models fit with @code{nlme::lme()}, @code{lme4::lmer()}, @code{lmeTest::lmer()}, @code{gamm4::gamm4()}, @code{mgcv::gamm()} and @code{SemiPar::spm()}.") (license (list license:gpl2+ license:gpl3+)))) (define-public r-binom (package (name "r-binom") (version "1.1-1.1") (source (origin (method url-fetch) (uri (cran-uri "binom" version)) (sha256 (base32 "1yxyhsd0savwirlmgnq6973slfakqyfvjm0zz60cmc9v490my8gf")))) (properties `((upstream-name . "binom"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=binom") (synopsis "Binomial Confidence Intervals For Several Parameterizations") (description "Constructs confidence intervals on the probability of success in a binomial experiment via several parameterizations") (license (list license:gpl2+ license:gpl3+)))) (define-public r-simr (package (name "r-simr") (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "simr" version)) (sha256 (base32 "1rfnhyqvdazvar7r1ml71lskh1hdk3yfzv5jlcz18wzffscgkgmb")))) (properties `((upstream-name . "simr"))) (build-system r-build-system) (propagated-inputs (list r-binom r-car r-iterators r-lme4 r-lmertest r-pbkrtest r-plotrix r-plyr r-rlrsim r-stringr)) (native-inputs (list r-knitr)) (home-page "https://github.com/pitakakariki/simr") (synopsis "Power analysis for generalized linear mixed models by simulation") (description "This package lets you calculate power for generalized linear mixed models, using simulation. It was designed to work with models fit using the @code{lme4} package. The package is described in @url{doi:10.1111/2041-210X.12504, Green and MacLeod (2016)}.") (license license:gpl2+))) (define-public r-mixedpower ;; This commit contains fixes for R>=4.2 and contains new features. A ;; newer release does not exist. (let ((commit "b2b87068546327d8f592d141e5482e0478c1b2ee") (revision "2")) (package (name "r-mixedpower") (version (git-version "2.0" revision commit)) (source (origin ;; Not available on CRAN. (method git-fetch) (uri (git-reference (url "https://github.com/DejanDraschkow/mixedpower") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0pys66a6c1k2fp5qk9grhzg1q1d3q51rggcilmdssimkmcsm234z")))) (properties `((upstream-name . "mixedpower"))) (build-system r-build-system) (propagated-inputs (list r-doparallel r-foreach r-ggplot2 r-lme4 r-reshape2)) (home-page "https://github.com/DejanDraschkow/mixedpower") (synopsis "Pilotdata based simulations for estimating power in linear mixed models") (description "Mixedpower uses pilotdata and a linear mixed model fitted with lme4 to simulate new data sets. Power is computed seperate for every effect in the model output as the relation of significant simulations to all simulations. More conservative simulations as a protection against a bias in the pilotdata are available as well as methods for plotting the results.") (license license:gpl3)))) (define-public r-colorway (let ((commit "8ba8f0026aba37752c6770de45bf53b1b0f48afc") (revision "1")) (package (name "r-colorway") (version (git-version "0.2.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/hypercompetent/colorway") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0r6yhnzx3ll1z12pp6y8fqbrx7v18rcff2j2179bqy9ca2d2d94l")))) (properties `((upstream-name . "colorway"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-rlang)) (home-page "https://github.com/hypercompetent/colorway") (synopsis "Functions for colors in R") (description "This package provides a collection of (mostly simple) functions for generating and manipulating colors in R.") (license license:gpl3)))) (define-public r-reghelper (package (name "r-reghelper") (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "reghelper" version)) (sha256 (base32 "1vd8kd719kyjp65zym6zx3vax1q2kbhpl6la71d5aa59s54ylri3")))) (properties `((upstream-name . "reghelper"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-lme4 r-mass r-nlme r-rlang)) (home-page "https://github.com/jeff-hughes/reghelper") (synopsis "Helper Functions for Regression Analysis") (description "This package provides a set of functions used to automate commonly used methods in regression analysis. This includes plotting interactions, and calculating simple slopes, standardized coefficients, regions of significance (Johnson & Neyman, 1936; cf. Spiller et al., 2012), etc.") (license license:gpl3))) (define-public r-mumin (package (name "r-mumin") (version "1.48.4") (source (origin (method url-fetch) (uri (cran-uri "MuMIn" version)) (sha256 (base32 "04zn63snv218c44nllfh8bqh5xg0gamd9fcpwxisvi9gwb3f20i0")))) (properties `((upstream-name . "MuMIn"))) (build-system r-build-system) (propagated-inputs (list r-insight r-matrix r-nlme)) (home-page "https://cran.r-project.org/package=MuMIn") (synopsis "Multi-Model Inference") (description "Tools for performing model selection and model averaging. Automated model selection through subsetting the maximum model, with optional constraints for model inclusion. Model parameter and prediction averaging based on model weights derived from information criteria (AICc and alike) or custom model weighting schemes.") (license license:gpl2))) (define-public ruby-enumerable-statistics (package (name "ruby-enumerable-statistics") (version "2.0.7") ;; Source at RubyGems.org doesn't have tests. (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/mrkn/enumerable-statistics.git") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1a8k2dvm1v0g6hcrbnzy0f7d63hdmpmldfdkl8wr32nbl05xnifa")) (modules '((guix build utils))) (snippet `(begin (substitute* "enumerable-statistics.gemspec" ;; benchmark-driver gem is used for ;; performance benchmarking, and isn't ;; needed for tests. (("spec.add_development_dependency \"benchmark-driver\"\n") "")))))) (build-system ruby-build-system) (native-inputs (list bundler ruby-rake ruby-rake-compiler ruby-rspec ruby-test-unit ruby-fuubar ruby-yard)) (synopsis "Library which provides statistics features for Enumerable") (description "@code{Enumerable::Statistics} provides some methods to calculate statistical summary in arrays and enumerables.") (home-page "https://github.com/mrkn/enumerable-statistics") (license license:expat))) (define-public python-pgmpy (package (name "python-pgmpy") (version "0.1.24") (source (origin (method git-fetch) ;pypi package does not include test data (uri (git-reference (url "https://github.com/pgmpy/pgmpy") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0fvzh6v0yhgdryczamvzhfy2ymywkh0ssx4rl47xnfvi43hnij90")))) (build-system pyproject-build-system) (propagated-inputs (list python-daft python-joblib python-networkx python-numpy python-opt-einsum python-pandas python-pyparsing python-pytorch python-scikit-learn python-scipy python-statsmodels python-tqdm)) (native-inputs (list python-mock python-pytest)) (home-page "https://github.com/pgmpy/pgmpy") (synopsis "Probabilistic Graphical Models library") (description "This package provides a library for Probabilistic Graphical Models. It can be used for learning (Structure and Parameter), inference (Probabilistic and Causal), and simulations in Bayesian Networks.") (license license:expat)))
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