diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 279 |
1 files changed, 216 insertions, 63 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 8964c85c9c..915eaeac18 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -417,14 +417,14 @@ available, greatly increasing its breadth and scope.") (define-public r-boot (package (name "r-boot") - (version "1.3-26") + (version "1.3-27") (source (origin (method url-fetch) (uri (cran-uri "boot" version)) (sha256 (base32 - "161l3q3kdmi7s3xwl3xxg3x3zx8787hsvsr2mmawwxq2cad131fl")))) + "1v9anpxj4p83kd40gyfy8a454b2jmn11incrzym7wdvh8mdxpcil")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/boot") (synopsis "Bootstrap functions for R") @@ -438,14 +438,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.") (define-public r-mass (package (name "r-mass") - (version "7.3-53") + (version "7.3-53.1") (source (origin (method url-fetch) (uri (cran-uri "MASS" version)) (sha256 (base32 - "0f2bwsbqr3nzsqxva051lg8wd068naqif3vc48hac0m3mmq4x0j1")))) + "0ra46441y4iwcpd8px7j7vcjfj09fawl5khilaivjbg3gswiwnz4")))) (properties `((upstream-name . "MASS"))) (build-system r-build-system) (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") @@ -481,14 +481,14 @@ k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.") (define-public r-cluster (package (name "r-cluster") - (version "2.1.0") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "cluster" version)) (sha256 (base32 - "055af3yz2biqbsbwm4arwr1yqnj4gicpzv2i6dbfl5pnz2z5byga")))) + "0qw06n1f7771mszc9y1f1c9zngd82zlf2s2z30p9514vxh4wgf5x")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -630,13 +630,13 @@ nonlinear mixed-effects models.") (define-public r-mgcv (package (name "r-mgcv") - (version "1.8-33") + (version "1.8-34") (source (origin (method url-fetch) (uri (cran-uri "mgcv" version)) (sha256 - (base32 "1x1bdzz2b2f05626xygwqp30b4rhblgg76hs15j9ab4fjan7pjwq")))) + (base32 "1pkky9xb3wsinqd75gkfbgw270vx8zh52id6bf1xj9njnzrkmc8m")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix) @@ -711,14 +711,14 @@ analysis.") (define-public r-survival (package (name "r-survival") - (version "3.2-7") + (version "3.2-9") (source (origin (method url-fetch) (uri (cran-uri "survival" version)) (sha256 (base32 - "0ila864g5b9yhjhk3jirgdpi06sksc0axa78890dmkvyv9rwsmjk")))) + "1dkpdci2lvx141193wd69445y65w8k2pa89lc3l83i5jaj56svdn")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -1203,19 +1203,21 @@ and to generate base64 encoded string from raster matrix.") (define-public r-svglite (package (name "r-svglite") - (version "1.2.3.2") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "svglite" version)) (sha256 (base32 - "00n8bg4iligl0h24v42cka417w26zmcxrr4r6k8wdal1riwhgmi5")))) + "19ggknw5322yw7r1bzhw0bqggcrpn0qxddk7kblpqnra2zz2brkn")))) (build-system r-build-system) + (inputs + `(("libpng" ,libpng) + ("zlib" ,zlib))) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-gdtools" ,r-gdtools) - ("r-rcpp" ,r-rcpp))) + `(("r-cpp11" ,r-cpp11) + ("r-systemfonts" ,r-systemfonts))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/hadley/svglite") @@ -1328,14 +1330,16 @@ adapted for other output formats, such as HTML or LaTeX.") (define-public r-formatr (package (name "r-formatr") - (version "1.7") + (version "1.8") (source (origin (method url-fetch) (uri (cran-uri "formatR" version)) (sha256 (base32 - "1nsxbrx31k3y6yql30qkrvdfyznlia2qfvwv95mfiy7m7wdn4rm3")))) + "04q6y53ji7ll131khbwiz584wl8sinhh3z82p6r8dqa9f618ay6z")))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://yihui.org/formatr/") (synopsis "Format R code automatically") (description @@ -1367,13 +1371,13 @@ supported via Andre Simon's highlight package.") (define-public r-mime (package (name "r-mime") - (version "0.9") + (version "0.10") (source (origin (method url-fetch) (uri (cran-uri "mime" version)) (sha256 (base32 - "107sqarmyhxlch5nrg796i5z03p9mshskisiq2fm628ajk99gkrc")))) + "1xz37fizlx4w3g8kbim7vr5slqd6cmaq5sa0s4q7ayl1bahk6ckq")))) (build-system r-build-system) (home-page "https://github.com/yihui/mime") (synopsis "R package to map filenames to MIME types") @@ -1584,13 +1588,13 @@ R packages that praise their users.") (define-public r-testthat (package (name "r-testthat") - (version "3.0.1") + (version "3.0.2") (source (origin (method url-fetch) (uri (cran-uri "testthat" version)) (sha256 (base32 - "1l1s4jgmgbsf711ma5i58ssgkz98an7hijcxvwfz314nf5fc8zr9")))) + "03sbk36vrjhzfap6a9czxw93r7h06rh3mb01inbrhrh5r2pd00qq")))) (build-system r-build-system) (propagated-inputs `(("r-brio" ,r-brio) @@ -1664,19 +1668,17 @@ like tidy evaluation.") (define-public r-tibble (package (name "r-tibble") - (version "3.0.6") + (version "3.1.0") (source (origin (method url-fetch) (uri (cran-uri "tibble" version)) (sha256 (base32 - "0f41gnq0wwmy1z96lg3gicvm54jh685f7i3ag8yfk39r3ql2vzpv")))) + "0khmypf49la8n5gx72n7gr6dl6r6ja404i578g6sg0ail3g2i7lm")))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-crayon" ,r-crayon) - ("r-ellipsis" ,r-ellipsis) + `(("r-ellipsis" ,r-ellipsis) ("r-fansi" ,r-fansi) ("r-lifecycle" ,r-lifecycle) ("r-magrittr" ,r-magrittr) @@ -1696,13 +1698,13 @@ and printing capabilities than traditional data frames.") (define-public r-dplyr (package (name "r-dplyr") - (version "1.0.4") + (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "dplyr" version)) (sha256 (base32 - "0fh9ivw4jgdhcdz2mcs0b869jb479cjzr2c0s2x3552is5qqzxlv")))) + "0w3fr6sn0mw5mjs27669czpc8vpjj6ayrjavw8v0gd7ccsfa0hbm")))) (build-system r-build-system) (propagated-inputs `(("r-ellipsis" ,r-ellipsis) @@ -1853,13 +1855,13 @@ times.") (define-public r-data-table (package (name "r-data-table") - (version "1.13.6") + (version "1.14.0") (source (origin (method url-fetch) (uri (cran-uri "data.table" version)) (sha256 (base32 - "16ryrpzl86krww5nx7a97i09y5xqld4lw4d9pa1vzjl99x6ds36m")))) + "0kgbvap5v2spnkz3dwfm4jh4qcpvbzdn9s8bzfnhzabz9qjdxw8k")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -1980,7 +1982,7 @@ inference for statistical models.") (define-public python2-statsmodels (let ((stats (package-with-python2 python-statsmodels))) - (package (inherit stats) + (package/inherit stats (propagated-inputs `(("python2-pytz" ,python2-pytz) ("python2-numpy" ,python2-numpy) @@ -2268,18 +2270,17 @@ module, Java Server Pages, and Python's psp module.") (define-public r-desc (package (name "r-desc") - (version "1.2.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "desc" version)) (sha256 (base32 - "1s6s13fk6sxwcj8wzkwxl9vr33153xx11p5wi9avqx3rzkabavz6")))) + "1sw4vya3l971gpccq4gnjywgbl73bgx8la18l0wy617qv94f905y")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-crayon" ,r-crayon) + `(("r-crayon" ,r-crayon) ("r-r6" ,r-r6) ("r-rprojroot" ,r-rprojroot))) (home-page "https://github.com/r-pkgs/desc") @@ -2635,13 +2636,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.10.2.1.0") + (version "0.10.2.2.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "03i9npq2mcv08ppp1ab2vzr412d4q9vldcc87nz2djbh9ai3xnv5")))) + "193smj6vp3cn3qjhrx2llgi5c7hs069crhvi85xj2vzx80fx6r9q")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs @@ -2727,13 +2728,13 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "2.6") + (version "2.7") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 - (base32 "1c7nrpnv2v43msv7nia90rjh6s5x9m5wlb3mpiwy04fyfb29krz6")))) + (base32 "0shj637qhpcf30il3lhl3k5bxi5l3x3gf612hbqlakp1qrgrf8lm")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs @@ -2842,13 +2843,13 @@ a column in data frame.") (define-public r-rsqlite (package (name "r-rsqlite") - (version "2.2.3") + (version "2.2.4") (source (origin (method url-fetch) (uri (cran-uri "RSQLite" version)) (sha256 (base32 - "1sps1qn1x5r5l216rx0yfda7zk365b2xyzii3zv6f78nzdsgadbj")))) + "050s7gv42v43d15yqj2sdrh82iikfpm32idfnw4nbjjjnlcg7wxf")))) (properties `((upstream-name . "RSQLite"))) (build-system r-build-system) (propagated-inputs @@ -2900,7 +2901,7 @@ if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) } `(("libcurl" ,curl))) (propagated-inputs `(("r-bitops" ,r-bitops))) - (home-page "http://www.omegahat.org/RCurl") + (home-page "http://www.omegahat.net/RCurl") (synopsis "General network client interface for R") (description "The package allows one to compose general HTTP requests and provides @@ -2931,7 +2932,7 @@ ldap, and also supports cookies, redirects, authentication, etc.") ("zlib" ,zlib))) (native-inputs `(("pkg-config" ,pkg-config))) - (home-page "http://www.omegahat.org/RSXML") + (home-page "http://www.omegahat.net/RSXML") (synopsis "Tools for parsing and generating XML within R") (description "Many approaches for both reading and creating XML (and HTML) @@ -3039,14 +3040,14 @@ statements.") (define-public r-segmented (package (name "r-segmented") - (version "1.3-2") + (version "1.3-3") (source (origin (method url-fetch) (uri (cran-uri "segmented" version)) (sha256 (base32 - "00fc5lcq5qqmw2c2cimrxw8jmd0jysx2p238c2ycykkb13jdwm5n")))) + "16036lp0dq7qqzy8wc4qsgv58zksz6hmgw51v88gl6xclryc670y")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/segmented") (synopsis "Regression models with breakpoints estimation") @@ -3080,13 +3081,13 @@ worker processes and collect and return the results on the master.") (define-public r-sparsem (package (name "r-sparsem") - (version "1.78") + (version "1.81") (source (origin (method url-fetch) (uri (cran-uri "SparseM" version)) (sha256 (base32 - "0cmlm0lps3daalvp5jzjnjfys388hgkyc8yw0g5r2351h749xdyn")))) + "0csbqd9wm6r4162mday1iaigzf9wv2rp1zq8hnihys6f38w8z0xx")))) (properties `((upstream-name . "SparseM"))) (native-inputs @@ -3278,13 +3279,13 @@ analysis of large sparse or dense matrices.") (define-public r-glmnet (package (name "r-glmnet") - (version "4.1") + (version "4.1-1") (source (origin (method url-fetch) (uri (cran-uri "glmnet" version)) (sha256 - (base32 "1js01qnznm20h4pslaw1ragxhrzk0w4nw7r6ryg7i27l344za2lg")))) + (base32 "0zpfq0m1y5zks5p9r28553ykywwrhrb3ds8m6b7sm6hj4n1c4csd")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran) @@ -3747,14 +3748,14 @@ selection.") (define-public r-tidyr (package (name "r-tidyr") - (version "1.1.2") + (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "tidyr" version)) (sha256 (base32 - "0v7x1pgmwmjypzdr4j2ig2klgrrgryi3qvw8hwqv65a5h9kwpz08")))) + "0cpbrvr759z8p7r9lpkjhj2dcdymsbnaib0rma9b4jb7i3qzmh2a")))) (build-system r-build-system) (propagated-inputs `(("r-cpp11" ,r-cpp11) @@ -4035,13 +4036,13 @@ package instead.") (define-public r-hmisc (package (name "r-hmisc") - (version "4.4-2") + (version "4.5-0") (source (origin (method url-fetch) (uri (cran-uri "Hmisc" version)) (sha256 - (base32 "1j7vkckmahdh90ndcl646sjpxq82y4x55ngxqvkni22mv16wc2j9")))) + (base32 "11qj73zj16p113jpwn2vv06l99kqlcxcmrldbpyi5s7pwing9jnx")))) (properties `((upstream-name . "Hmisc"))) (build-system r-build-system) (native-inputs @@ -4354,13 +4355,13 @@ within a category based on their density using quasirandom noise.") (define-public r-beeswarm (package (name "r-beeswarm") - (version "0.2.3") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "beeswarm" version)) (sha256 (base32 - "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581")))) + "1jsggypyww77hkcic03kdb3fp8h938qs142xi0lapzh62bkn2pjj")))) (build-system r-build-system) (home-page "https://www.cbs.dtu.dk/~eklund/beeswarm/") (synopsis "Implementation of bee swarm plots") @@ -5089,14 +5090,14 @@ metrics for evaluating models.") (define-public r-matrixmodels (package (name "r-matrixmodels") - (version "0.4-1") + (version "0.5-0") (source (origin (method url-fetch) (uri (cran-uri "MatrixModels" version)) (sha256 (base32 - "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy")))) + "1va6i6bpkq71rzl9i4xgyc5x7qcksa3nfzihlaggf6aj30dayzx8")))) (properties `((upstream-name . "MatrixModels"))) (build-system r-build-system) (propagated-inputs @@ -5111,13 +5112,13 @@ using modular prediction and response module classes.") (define-public r-quantreg (package (name "r-quantreg") - (version "5.83") + (version "5.85") (source (origin (method url-fetch) (uri (cran-uri "quantreg" version)) (sha256 - (base32 "05vbnz88qxk141dfxwl6ql2zshw15h0hddf8ajnsk2dxfdb6vdkp")))) + (base32 "1y8sgl16yby1k7g23y6bdnfllwnxj3iik3fqp96iwm5jd8blb7q4")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -5201,14 +5202,14 @@ C++ library for numerical linear algebra and RcppEigen glue.") (define-public r-pbkrtest (package (name "r-pbkrtest") - (version "0.5-0.1") + (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "pbkrtest" version)) (sha256 (base32 - "0sgl8r74cknmp8lnq5jvc1w181274ylgk6w4pxf4mzkfii42argm")))) + "1if7msv9i7jhg1as1f7m81a95dnwhwj3yfs24bqr0f6r0ch4b8xj")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -5508,14 +5509,14 @@ is supported.") (define-public r-lubridate (package (name "r-lubridate") - (version "1.7.9.2") + (version "1.7.10") (source (origin (method url-fetch) (uri (cran-uri "lubridate" version)) (sha256 (base32 - "0yfvlgksasmia7rsp83lsipjpgvlly5qkldcfxj68lfaz9l2sspf")))) + "1s653d6rnpf9bkynxmbq4fdjdcz7r9ma19aph8f5y9ck70his4hm")))) (build-system r-build-system) (propagated-inputs `(("r-generics" ,r-generics) @@ -5923,3 +5924,155 @@ popular stats packages like SAS, Stata and SPSS.") (home-page "https://github.com/WizardMac/ReadStat") (license license:expat))) +(define-public r-quantpsyc + (package + (name "r-quantpsyc") + (version "1.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "QuantPsyc" version)) + (sha256 + (base32 + "1i9bh88r8zxndzjqsj14qw64gnvm5a9kvhjhzk3qsrvl3qzjgh93")))) + (properties `((upstream-name . "QuantPsyc"))) + (build-system r-build-system) + (propagated-inputs + `(("r-boot" ,r-boot) ("r-mass" ,r-mass))) + (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 "0.5.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "clubSandwich" version)) + (sha256 + (base32 + "0jazgka18bb5n58d5sn94q7rc9sac82qrpl2i5b4rkx9q2pb39cn")))) + (properties `((upstream-name . "clubSandwich"))) + (build-system r-build-system) + (propagated-inputs + `(("r-sandwich" ,r-sandwich))) + (native-inputs `(("r-knitr" ,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 "0.2.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "puniform" version)) + (sha256 + (base32 + "0v2977y9cwjx74xk0ig745g09wn7nrcsrg4f6v315sglsm18iaa8")))) + (properties `((upstream-name . "puniform"))) + (build-system r-build-system) + (propagated-inputs + `(("r-adgoftest" ,r-adgoftest) + ("r-metafor" ,r-metafor) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,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))) |