diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 833 |
1 files changed, 695 insertions, 138 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5c5258d6e0..fccf0002a7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -307,14 +307,14 @@ etc.") (define-public r-datawizard (package (name "r-datawizard") - (version "0.6.4") + (version "0.6.5") (source (origin (method url-fetch) (uri (cran-uri "datawizard" version)) (sha256 (base32 - "0iv3h08bzmijrxyv2jz70jf53i2bk14kh0vq9a93fms5z08jv19p")))) + "0il98vmy8l4wrisqz9xli7iki2ajdlsxyhh4k4grrd28gzkj8lgb")))) (properties `((upstream-name . "datawizard"))) (build-system r-build-system) (propagated-inputs @@ -399,6 +399,25 @@ visualization of their differences.") (description "This package implements Dirichlet regression models.") (license license:gpl2+))) +(define-public r-dirmult + (package + (name "r-dirmult") + (version "0.1.3-5") + (source (origin + (method url-fetch) + (uri (cran-uri "dirmult" version)) + (sha256 + (base32 + "05whzhl81nyag7321hw98xa63r440s9bgj1764346yvm9bvzjqi4")))) + (properties `((upstream-name . "dirmult"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=dirmult") + (synopsis "Estimation in Dirichlet-Multinomial distribution") + (description + "This package estimates the parameters in Dirichlet-Multinomial and +computes log-likelihoods.") + (license license:gpl2+))) + (define-public r-dixontest (package (name "r-dixontest") @@ -615,7 +634,7 @@ the output locally.") (home-page "https://cran.r-project.org/package=gson") (synopsis "Base Class and Methods for 'gson' Format") (description - "This packages proposes a new file format named @code{gson} for storing + "This package proposes a new file format named @code{gson} for storing gene set and related information, and provides read, write and other utilities to process this file format.") (license license:artistic2.0))) @@ -648,6 +667,56 @@ from CRAN, but also from Bioconductor or even arbitrary git or mercurial repositories, replacing the need for installation via @code{devtools}.") (license license:gpl3+))) +(define-public r-gunifrac + (package + (name "r-gunifrac") + (version "1.7") + (source (origin + (method url-fetch) + (uri (cran-uri "GUniFrac" version)) + (sha256 + (base32 + "13qb5fw9km6p5x8li9x3liqbh833wf2v73npj8jl3msplzfk82vp")))) + (properties `((upstream-name . "GUniFrac"))) + (build-system r-build-system) + (propagated-inputs + (list r-ape + r-dirmult + r-foreach + r-ggplot2 + r-ggrepel + r-mass + r-matrix + r-matrixstats + r-modeest + r-rcpp + r-rmutil + r-statmod + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=GUniFrac") + (synopsis + "Generalized UniFrac distances and methods for microbiome data analysis") + (description + "This package provides a suite of methods for powerful and robust +microbiome data analysis, including data normalization, data simulation, +community-level association testing and differential abundance analysis. It +implements generalized UniFrac distances, @dfn{Geometric Mean of Pairwise +Ratios} (GMPR) normalization, semiparametric data simulator, distance-based +statistical methods, and feature- based statistical methods. The +distance-based statistical methods include three extensions of PERMANOVA: + +@itemize +@item PERMANOVA using the Freedman-Lane permutation scheme, +@item PERMANOVA omnibus test using multiple matrices, and +@item analytical approach to approximating PERMANOVA p-value. +@end itemize + +Feature-based statistical methods include linear model-based methods for +differential abundance analysis of zero-inflated high-dimensional +compositional data.") + (license license:gpl3))) + (define-public r-ids (package (name "r-ids") @@ -1300,14 +1369,14 @@ variables.") (define-public r-ggpp (package (name "r-ggpp") - (version "0.4.5") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "ggpp" version)) (sha256 (base32 - "02inwvfz2zxsj7bq0nz11c5spnyaf8zhjnlfllpwfjfy46qrx2p9")))) + "0zmxnzsdmwv9v77fifgiknalwif59261kslq8848x1xch8f82l77")))) (properties `((upstream-name . "ggpp"))) (build-system r-build-system) (propagated-inputs @@ -1505,13 +1574,13 @@ axis} (SMA), and @dfn{ranged major axis} (RMA).") (define-public r-ggpmisc (package (name "r-ggpmisc") - (version "0.5.1") + (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 - "18085n6id5v3g3w1z1010im85i4yii4wib2cmcxwqk7qvk9rsrqi")))) + "1zvq580vi1h2afdgxaqabjhfsphvmdchwiaahqvvhljxmpmh82q6")))) (build-system r-build-system) (propagated-inputs (list r-confintr @@ -1540,13 +1609,13 @@ respecting the grammar of its graphics paradigm.") (define-public r-ggside (package (name "r-ggside") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "ggside" version)) (sha256 (base32 - "1vl7kzgmi5xxxsqvyg4cm4xwd3lfjgysay1lw6hri5vj22mnga5h")))) + "1z50z4xpxfpqdz26hja6xw3q403p00cr5qawjxl0qg4jixl7j65p")))) (properties `((upstream-name . "ggside"))) (build-system r-build-system) (propagated-inputs @@ -1555,7 +1624,8 @@ respecting the grammar of its graphics paradigm.") r-gtable r-rlang r-scales - r-tibble)) + r-tibble + r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=ggside") (synopsis "Side grammar graphics that extends @code{ggplot2}") @@ -2633,13 +2703,13 @@ Zucchini.") (define-public r-httpuv (package (name "r-httpuv") - (version "1.6.6") + (version "1.6.7") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 - "14qjf7bpl7pay89b7vi2vccl342q8xs6101a9x6qijy54k9myfa1")) + "0jjb2w59x8a4k24j9rc4rjm37h1ccrfq1nzd40inbnd6kcqf3lkm")) ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv ;; only contains fixes for building on Solaris. (patches (search-patches "r-httpuv-1.6.6-unvendor-libuv.patch")) @@ -2680,13 +2750,13 @@ particularly easy to create complete web applications using httpuv alone.") (define-public r-jsonlite (package (name "r-jsonlite") - (version "1.8.3") + (version "1.8.4") (source (origin (method url-fetch) (uri (cran-uri "jsonlite" version)) (sha256 (base32 - "1w685bwhvqxh8y3b4rmzmbbxsj0sqrdad4rni7dxbiqzd2piszy5")))) + "0y0jzf74c3q1sghgarvwmrkvxs7yahywd342m8c0jsr28bhapskr")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -2750,16 +2820,16 @@ a list of p-values.") (define-public r-htmltools (package (name "r-htmltools") - (version "0.5.3") + (version "0.5.4") (source (origin (method url-fetch) (uri (cran-uri "htmltools" version)) (sha256 (base32 - "0krjyz99q7zvdfg60b128c0zwr36h54gb05jw9c874d8kqv1ni9c")))) + "0zij9zrgsi82q5c65sf4pbidnzrkfr763g0n4ypdhf8dd6l2i0h0")))) (build-system r-build-system) (propagated-inputs - (list r-base64enc r-digest r-fastmap r-rlang)) + (list r-base64enc r-digest r-ellipsis r-fastmap r-rlang)) (home-page "https://cran.r-project.org/web/packages/htmltools") (synopsis "R tools for HTML") (description @@ -2769,16 +2839,18 @@ a list of p-values.") (define-public r-htmlwidgets (package (name "r-htmlwidgets") - (version "1.5.4") + (version "1.6.0") (source (origin (method url-fetch) (uri (cran-uri "htmlwidgets" version)) (sha256 (base32 - "1hgz8sx8xrvfcdwa4q15k942w4qsqg8lyxbbf7qyfzbi807wcgqs")))) + "06prjx6ic2bddaw50ksz6l7hsidkzwb69m85vzc0apxvwaygz0gh")))) (build-system r-build-system) (propagated-inputs - (list r-htmltools r-jsonlite r-yaml)) + (list r-htmltools r-jsonlite + r-knitr r-rmarkdown + r-yaml)) (native-inputs (list r-knitr)) (home-page "https://github.com/ramnathv/htmlwidgets") @@ -3108,18 +3180,17 @@ expression estimates for all genes.") (define-public r-bslib (package (name "r-bslib") - (version "0.4.1") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "bslib" version)) (sha256 (base32 - "0bz6w34shk2pijq5hvjv2bg8xhhg4yazn4wcix7436yi9k41zgaf")) + "069ghbzp0bsmbw2nzw28cmbym65i3a90v50y7qksy2g4pfhvfh4s")) (snippet '(for-each delete-file '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js" - "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js" "inst/lib/bs3/assets/javascripts/bootstrap.min.js" "inst/lib/bs4/dist/js/bootstrap.bundle.min.js" "inst/lib/bs5/dist/js/bootstrap.bundle.min.js"))))) @@ -3155,11 +3226,13 @@ expression estimates for all genes.") (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs - (list r-cachem + (list r-base64enc + r-cachem r-htmltools r-jquerylib r-jsonlite r-memoise + r-mime r-rlang r-sass)) (native-inputs @@ -3174,10 +3247,10 @@ expression estimates for all genes.") ("js-bootstrap5-bundle" ,(origin (method url-fetch) - (uri "https://raw.githubusercontent.com/twbs/bootstrap/v5.1.3/dist/js/bootstrap.bundle.js") + (uri "https://raw.githubusercontent.com/twbs/bootstrap/v5.2.2/dist/js/bootstrap.bundle.js") (sha256 (base32 - "116979i2vr1y9i6g7n5iir19p85xwr642scbl9jcqdr0w9801nw6")))))) + "1ibfb1lwwm50did0b4fvxaqc7xyljmp20f3qb1ybdlvcy22mk8bg")))))) (home-page "https://rstudio.github.io/bslib/") (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown") (description @@ -3724,13 +3797,13 @@ annotation data to keep updated.") (define-public r-ggtern (package (name "r-ggtern") - (version "3.4.0") + (version "3.4.1") (source (origin (method url-fetch) (uri (cran-uri "ggtern" version)) (sha256 - (base32 "01j1rvff3vz72vwqsy3bh81aav7gfymg4sbvc267vg0r3a16ywcg")))) + (base32 "0w0kg6755kfpczqpaly251fgqv31js9gdzr17x734l2adycji3yr")))) (properties `((upstream-name . "ggtern"))) (build-system r-build-system) (propagated-inputs @@ -4569,6 +4642,27 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see @code{citation(\"Rcpp\")} for details on these last two.") (license license:gpl2+))) +(define-public r-rcppde + (package + (name "r-rcppde") + (version "0.1.6") + (source (origin + (method url-fetch) + (uri (cran-uri "RcppDE" version)) + (sha256 + (base32 + "1i9jj595nqpb16y22z2b8fcf0gq1fg0pbiisbd837p1cyw4nff69")))) + (properties `((upstream-name . "RcppDE"))) + (build-system r-build-system) + (propagated-inputs + (list r-rcpp r-rcpparmadillo)) + (home-page "https://cran.r-project.org/package=RcppDE") + (synopsis "Global optimization by differential evolution in C++") + (description + "This package provides an iteration of the @code{DEoptim} function. It +performs global optimization by differential evolution.") + (license license:gpl2+))) + (define-public r-rcppml (package (name "r-rcppml") @@ -4832,6 +4926,33 @@ approach is used to estimate the lower cut-off for the scaling region.") ;; Any of these GPL versions. (license (list license:gpl2 license:gpl3)))) +(define-public r-ptw + (package + (name "r-ptw") + (version "1.9-16") + (source (origin + (method url-fetch) + (uri (cran-uri "ptw" version)) + (sha256 + (base32 + "0rma3h9ksc5qigdvk5vappb4ipd4rpk64wckzcxvxspakr5w71vy")))) + (properties `((upstream-name . "ptw"))) + (build-system r-build-system) + (propagated-inputs (list r-rcppde)) + (home-page "https://github.com/rwehrens/ptw") + (synopsis "Parametric time warping") + (description + "Parametric time warping aligns patterns. It aims to put corresponding +features at the same locations. The algorithm searches for an optimal +polynomial describing the warping. It is possible to align one sample to a +reference, several samples to the same reference, or several samples to +several references. One can choose between calculating individual warpings, +or one global warping for a set of samples and one reference. Two +optimization criteria are implemented: @acronym{RMS, Root Mean Square} error +and @acronym{WCC, Weighted Cross Correlation}. Both warping of peak profiles +and of peak lists are supported.") + (license license:gpl2+))) + (define-public r-compare (package (name "r-compare") @@ -5825,13 +5946,13 @@ available in a vignette.") (define-public r-progressr (package (name "r-progressr") - (version "0.11.0") + (version "0.12.0") (source (origin (method url-fetch) (uri (cran-uri "progressr" version)) (sha256 - (base32 "1nbc6vvsyqa1gvh1a1m4prnvng88wsa0r35i9fiwq84a6j18qrnq")))) + (base32 "0nahvfcnx45n0q24r4j9cjqmmgh302ra3207izs6fzfda7sqn25q")))) (properties `((upstream-name . "progressr"))) (build-system r-build-system) (propagated-inputs @@ -5967,14 +6088,14 @@ included in this package.") (define-public r-timedate (package (name "r-timedate") - (version "4021.106") + (version "4021.107") (source (origin (method url-fetch) (uri (cran-uri "timeDate" version)) (sha256 (base32 - "1qhh1d85s8r4wkcf4fljfm67lnkj8flnx9iz4hdg305xdkng3b8l")))) + "1i54a425r5hi08yl9rb2qh1nynh29ppv9b4h46cxyzn1ybqlr9sg")))) (properties `((upstream-name . "timeDate"))) (build-system r-build-system) (home-page "https://www.rmetrics.org") @@ -6011,14 +6132,14 @@ dimensioned arrays.") (define-public r-rmysql (package (name "r-rmysql") - (version "0.10.24") + (version "0.10.25") (source (origin (method url-fetch) (uri (cran-uri "RMySQL" version)) (sha256 (base32 - "0hbjcf0gzkkg8h50msj4a6ymax9s3j4aw44jl1mqcxkdmfn9l6ya")))) + "1527ba5vqg4ss6rqxrkxa1a66r1m9h4zmdnv9xdzva8fv2dhy4zd")))) (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (inputs @@ -6272,21 +6393,20 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "14i8729m38nxf5q344isgq4006p3b50wi3q8jgckxqphhnj5lpjb")))) + "13hj4y3ajrn7x8hvirp2vfh1c8j2pdrz3dnxc5f0dr7jyfhp4dcy")))) (build-system r-build-system) (propagated-inputs (list r-backports r-dplyr r-ellipsis r-generics - r-ggplot2 r-glue r-purrr r-rlang @@ -6452,6 +6572,59 @@ color labels, layout, etc.") ;; Any version of the GPL (license license:gpl2+))) +(define-public r-stable + (package + (name "r-stable") + (version "1.1.6") + (source (origin + (method url-fetch) + (uri (cran-uri "stable" version)) + (sha256 + (base32 + "194xsa291v5f0jya1c3aigbclg8cci427ffpb8brxamm6n57hf12")))) + (properties `((upstream-name . "stable"))) + (build-system r-build-system) + (propagated-inputs (list r-rmutil)) + (home-page "https://www.commanster.eu/rcode.html") + (synopsis + "Probability functions and regression models for stable distributions") + (description + "This package provides density, distribution, quantile and hazard +functions of a stable variate, as well as generalized regression models for +the parameters of a stable distribution.") + (license license:gpl2+))) + +(define-public r-statip + (package + (name "r-statip") + (version "0.2.3") + (source (origin + (method url-fetch) + (uri (cran-uri "statip" version)) + (sha256 + (base32 + "0kymc3ds1nx0h11ffmm3vmqr1w34gd0k788vf72x2v45h8c1ma2n")))) + (properties `((upstream-name . "statip"))) + (build-system r-build-system) + (propagated-inputs + (list r-clue r-rpart)) + (home-page "https://github.com/paulponcet/statip") + (synopsis "Statistical functions for probability distributions and regression") + (description + "This package provides a collection of miscellaneous statistical +functions for: +@itemize +@item probability distributions, +@item probability density estimation, +@item most frequent value estimation, +@item other statistical measures of location, +@item construction of histograms, +@item calculation of the Hellinger distance, +@item use of classical kernels, and +@item univariate piecewise-constant regression. +@end itemize") + (license license:gpl3))) + (define-public r-stringdist (package (name "r-stringdist") @@ -6842,14 +7015,14 @@ structure.") (define-public r-vioplot (package (name "r-vioplot") - (version "0.3.7") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "vioplot" version)) (sha256 (base32 - "1dmdasp3jldc41233z6r08w3j76vyyp9m3jrj7n4ahk48yd5siq6")))) + "1db7g0378jbcd6ssb7afff4y4r0v472qnb625hfwixx4wf1v8aap")))) (build-system r-build-system) (propagated-inputs (list r-sm r-zoo)) @@ -7171,6 +7344,26 @@ distributions over time or space. This package enables the creation of such plots in @code{ggplot2}.") (license license:gpl2))) +(define-public r-gss + (package + (name "r-gss") + (version "2.2-3") + (source (origin + (method url-fetch) + (uri (cran-uri "gss" version)) + (sha256 + (base32 + "0jr45lkpcndg5nynjsfnxn1wwkh4gkhsgv4hlvw6jn2frw0n8c14")))) + (properties `((upstream-name . "gss"))) + (build-system r-build-system) + (native-inputs (list gfortran)) + (home-page "https://cran.r-project.org/package=gss") + (synopsis "General smoothing splines") + (description + "This package provides a comprehensive collection for structural +multivariate function estimation using smoothing splines.") + (license license:gpl2+))) + (define-public r-cli (package (name "r-cli") @@ -7214,13 +7407,13 @@ script.") (define-public r-aricode (package (name "r-aricode") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "aricode" version)) (sha256 (base32 - "0772l9gyrih48l1kymih0mb7szjqqnwcm4lzj0yzp4cs8l2mdf4f")))) + "1w5jnql49f0wd5h4b89l69s7qldp7qm90p4jm0j4kz9w0vvm2kjz")))) (properties `((upstream-name . "aricode"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp)) @@ -7235,6 +7428,31 @@ information} (NMI), @dfn{adjusted mutual information} (AMI), @dfn{normalized variation information} (NVI) and entropy.") (license license:gpl3+))) +(define-public r-attempt + (package + (name "r-attempt") + (version "0.3.1") + (source (origin + (method url-fetch) + (uri (cran-uri "attempt" version)) + (sha256 + (base32 + "1ylgg7jcp8wqmxgf1mydnvh26k0mr8jyjla4hw06730r40yrs58m")))) + (properties `((upstream-name . "attempt"))) + (build-system r-build-system) + (propagated-inputs (list r-rlang)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/ColinFay/attempt") + (synopsis "Tools for defensive programming") + (description + "This package provides tools for defensive programming. It is inspired +by @code{purrr} mappers and based on @code{rlang}. Attempt extends and +facilitates defensive programming by providing a consistent grammar, and a set +of functions for common tests and conditions. Attempt only depends on +@code{rlang}, and focuses on speed, so it can be integrated with other +functions and used in the data analysis.") + (license license:expat))) + (define-public r-debugme (package (name "r-debugme") @@ -7280,6 +7498,28 @@ standard output and error of the processes, using non-blocking connections. timeout. It can also poll several processes at once.") (license license:expat))) +(define-public r-timeseries + (package + (name "r-timeseries") + (version "4021.105") + (source (origin + (method url-fetch) + (uri (cran-uri "timeSeries" version)) + (sha256 + (base32 + "1k6vihbs20m7zjrxh13y9mmsvnia3844c7j13p0b7m5i9fb6rqxz")))) + (properties `((upstream-name . "timeSeries"))) + (build-system r-build-system) + (propagated-inputs (list r-timedate)) + (home-page + "https://r-forge.r-project.org/scm/viewvc.php/pkg/timeSeries/?root=rmetrics") + (synopsis "Metrics for financial time series objects") + (description + "This package implements S4 classes and various tools for financial time +series. Basic functions such as scaling and sorting, subsetting, mathematical +operations and statistical functions are provided.") + (license license:gpl2+))) + (define-public r-tsp (package (name "r-tsp") @@ -7499,6 +7739,9 @@ estimated from a given sample.") (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-lifecycle r-rlang)) + ;; We can't have r-knitr among the inputs here, because r-vctrs ends up + ;; being an eventual input to r-knitr. + #; (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/vctrs") @@ -7592,14 +7835,14 @@ packages that work with genomic data.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.42") + (version "0.43") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "1c925r62h84mhwd7v5j35ckdldf6cwb3wzczdn5s72hig0cplpr0")))) + "01183i6z6jyyqmmxri3xmscn7k6hswi2q7r0b5ix0s7pd1cz57jq")))) (build-system r-build-system) (propagated-inputs (list r-xfun)) @@ -8265,6 +8508,37 @@ functions and random generation functions for a large number of univariate and multivariate distributions.") (license license:gpl2))) +(define-public r-fbasics + (package + (name "r-fbasics") + (version "4021.93") + (source (origin + (method url-fetch) + (uri (cran-uri "fBasics" version)) + (sha256 + (base32 + "1lmmdwzvqhggy6rr7yc9y5f8hxxgyzsgwm3ry0sz5ljbgfijl7g6")))) + (properties `((upstream-name . "fBasics"))) + (build-system r-build-system) + (propagated-inputs + (list r-gss + r-mass + r-spatial + r-stabledist + r-timedate + r-timeseries)) + (home-page + "https://r-forge.r-project.org/scm/viewvc.php/pkg/fBasics/?root=rmetrics") + (synopsis "Metrics for markets and basic statistics") + (description + "This package provides a collection of functions to explore and to +investigate basic properties of financial returns and related quantities. The +covered fields include techniques of explorative data analysis and the +investigation of distributional properties, including parameter estimation and +hypothesis testing. Even more, there are several utility functions for data +handling and management.") + (license license:gpl2+))) + (define-public r-fractal (package (name "r-fractal") @@ -9407,14 +9681,14 @@ simple method for converting between file types.") (define-public r-maptools (package (name "r-maptools") - (version "1.1-5") + (version "1.1-6") (source (origin (method url-fetch) (uri (cran-uri "maptools" version)) (sha256 (base32 - "1p155w26hpmqc589kxha0xgw5b4x6610a3im7ap4mjx1sfavvn9w")))) + "024kyq81gwpl7shil63nng1z6pgqcwy6j6wj44gj7ch3vd9dz9fn")))) (build-system r-build-system) (propagated-inputs (list r-foreign r-lattice r-sp)) @@ -10309,14 +10583,14 @@ clustering.") (define-public r-factominer (package (name "r-factominer") - (version "2.6") + (version "2.7") (source (origin (method url-fetch) (uri (cran-uri "FactoMineR" version)) (sha256 (base32 - "0xcg4vjs5v9k28hhxhkfkks7nvpxpp2cvim00kh67f4pq041c9l1")))) + "03952kcnwrm61kn5im55ky1j91nm5x4i4f5gs115li6gck63xf17")))) (properties `((upstream-name . "FactoMineR"))) (build-system r-build-system) (propagated-inputs @@ -10606,14 +10880,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rbibutils (package (name "r-rbibutils") - (version "2.2.10") + (version "2.2.11") (source (origin (method url-fetch) (uri (cran-uri "rbibutils" version)) (sha256 (base32 - "1xqpij07d19nvg18kyikpm37r3fharkdmxzm0cjddmqwv757lim6")))) + "10g3fv8ninihjldhvh00yrp260dczhz3q519000jm3wp5w47b945")))) (properties `((upstream-name . "rbibutils"))) (build-system r-build-system) (home-page "https://geobosh.github.io/rbibutils/") @@ -11101,6 +11375,43 @@ noncentral hypergeometric distribution (also called extended hypergeometric distribution).") (license license:gpl3))) +(define-public r-golem + (package + (name "r-golem") + (version "0.3.5") + (source (origin + (method url-fetch) + (uri (cran-uri "golem" version)) + (sha256 + (base32 + "0rjkl1r83h0hcn30zssx64qm07sdx3g4v5rdxn56gbzfghw7ddcl")))) + (properties `((upstream-name . "golem"))) + (build-system r-build-system) + (propagated-inputs + (list r-attempt + r-cli + r-config + r-crayon + r-desc + r-fs + r-here + r-htmltools + r-pkgload + r-roxygen2 + r-rstudioapi + r-shiny + r-usethis + r-yaml)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/ThinkR-open/golem") + (synopsis "Framework for robust Shiny applications") + (description + "This package implements an opinionated framework for building a +production- ready Shiny application. Golem contains a series of tools like +dependency management, version management, easy installation and deployment or +documentation management.") + (license license:expat))) + (define-public r-goplot (package (name "r-goplot") @@ -11175,14 +11486,14 @@ matches version and feature constraints.") (define-public r-argparse (package (name "r-argparse") - (version "2.1.6") + (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "argparse" version)) (sha256 (base32 - "14p57nm0w3siqd473snzhpmnvsgl72x92pdcd64vhy2qg6nzmmra")))) + "193pjjy4vkmzmsc1w69szafgrisvn08gddilbxcg671sdk0dxd7k")))) (build-system r-build-system) (inputs (list python)) (propagated-inputs @@ -11269,14 +11580,14 @@ the work.") (define-public r-doby (package (name "r-doby") - (version "4.6.14") + (version "4.6.15") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 - "1ps6r7yxs0a6rpfi2yzrb9j41862za3gdl1aq9vw3j5cmgrk8w1n")))) + "14asz3bpyvxakvpap2aajk6f5j2d3d6vrvrgnlixg5q6gdbh465m")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs @@ -13225,17 +13536,17 @@ the differences were not significantly different.") (define-public r-emmeans (package (name "r-emmeans") - (version "1.8.2") + (version "1.8.3") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "02fj957f67m1ik9n31h1p726hjnlhwlvd1wz93glfrcagm2p6nbq")))) + "004fd6kzky44xixd87q2nl1sn37krmqfas5gsylbc1cbrwnjzxlz")))) (build-system r-build-system) (propagated-inputs - (list r-estimability r-mvtnorm r-numderiv r-xtable)) + (list r-estimability r-mvtnorm r-numderiv)) (native-inputs (list r-knitr)) (home-page "https://github.com/rvlenth/emmeans") @@ -13794,14 +14105,14 @@ user credentials.") (define-public r-gert (package (name "r-gert") - (version "1.9.1") + (version "1.9.2") (source (origin (method url-fetch) (uri (cran-uri "gert" version)) (sha256 (base32 - "1p8z5qap06qf680r25y78wgnprzl9ib3xp3kvsw01bh819v1h7bm")))) + "0pk6mf300kh6wwzvaqymwzlikkbf8zj0xpslgyydn7zvr95ipjj2")))) (properties `((upstream-name . "gert"))) (build-system r-build-system) (inputs @@ -14094,6 +14405,30 @@ problems into least squares ones first.") exact and interval-censored observations.") (license license:gpl2+))) +(define-public r-clustercrit + (package + (name "r-clustercrit") + (version "1.2.8") + (source (origin + (method url-fetch) + (uri (cran-uri "clusterCrit" version)) + (sha256 + (base32 + "10pz1bikdbkm2ky3xnagp0qv60whalavp6j39b4p7d75jj5xcxgk")))) + (properties `((upstream-name . "clusterCrit"))) + (build-system r-build-system) + (native-inputs (list gfortran)) + (home-page "https://www.r-project.org/") + (synopsis "Computing clustering validation indices") + (description + "The @code{clusterCrit} package provides an implementation of the +following indices: Czekanowski-Dice, Folkes-Mallows, Hubert Γ, Jaccard, +McNemar, Kulczynski, Phi, Rand, Rogers-Tanimoto, Russel-Rao or Sokal-Sneath. +ClusterCrit defines several functions which compute internal quality indices +or external comparison indices. The partitions are specified as an integer +vector giving the index of the cluster each observation belongs to.") + (license license:gpl2+))) + (define-public r-clusteval (package (name "r-clusteval") @@ -14495,14 +14830,14 @@ other values.") (define-public r-ncdf4 (package (name "r-ncdf4") - (version "1.19") + (version "1.20") (source (origin (method url-fetch) (uri (cran-uri "ncdf4" version)) (sha256 (base32 - "0qzvin2fjzcb7h2knlnw14s6043pwi1nm7yf6p27ax7w269173fb")))) + "1kpi5xygx1nj8ybxrn9z0jxi3lbcibdvc7mjgyvm6f9plwjlxjvq")))) (build-system r-build-system) (inputs (list netcdf zlib)) @@ -15104,14 +15439,14 @@ Processing.") (define-public r-tm (package (name "r-tm") - (version "0.7-9") + (version "0.7-10") (source (origin (method url-fetch) (uri (cran-uri "tm" version)) (sha256 (base32 - "0a3ylj9735i21fh6iz63fkh1pnf2hs8ipp8wjdj25dahl18yhlyv")))) + "15lxaqlgkl9chiz0aw05l55bvlh48jwdgplfl8f2d8xsaq4gmbvc")))) (properties `((upstream-name . "tm"))) (build-system r-build-system) (propagated-inputs @@ -15122,6 +15457,35 @@ Processing.") "This package provides a framework for text mining applications within R.") (license license:gpl3))) +(define-public r-waffle + (package + (name "r-waffle") + (version "0.7.0") + (source (origin + (method url-fetch) + (uri (cran-uri "waffle" version)) + (sha256 + (base32 + "1qjmai33p96cyavi9lgi6k30h6fj7db5sr569v9jf4kwx92c61df")))) + (properties `((upstream-name . "waffle"))) + (build-system r-build-system) + (propagated-inputs + (list r-extrafont + r-ggplot2 + r-gridextra + r-gtable + r-rcolorbrewer)) + (home-page "https://github.com/hrbrmstr/waffle/tree/cran") + (synopsis "Creating waffle chart visualizations in R") + (description + "This package creates square pie charts also known as waffle charts. +These can be used to communicate parts of a whole for categorical quantities. +To emulate the percentage view of a pie chart, a 10x10 grid should be used. +In this way each square is representing 1% of the total. Waffle provides +tools to create charts as well as stitch them together. Isotype pictograms +can be made by using glyphs.") + (license license:gpl2+))) + (define-public r-waveslim (package (name "r-waveslim") @@ -15195,16 +15559,17 @@ maps.") (define-public r-tidytree (package (name "r-tidytree") - (version "0.4.1") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 - (base32 "1sq982x0pqvrn4d77m6v5xbbr9c8dkrwvw3as1pc5cg12x6kdi7v")))) + (base32 "0phmvbpsxx85fvw4000d160qh8njrgmzpr3ja0gy59dgv1k1m0yb")))) (build-system r-build-system) (propagated-inputs (list r-ape + r-cli r-dplyr r-lazyeval r-magrittr @@ -15671,13 +16036,13 @@ useful for building large phylogenies using multiple markers.") (define-public r-rnexml (package (name "r-rnexml") - (version "2.4.8") + (version "2.4.9") (source (origin (method url-fetch) (uri (cran-uri "RNeXML" version)) (sha256 (base32 - "0l5qpg6f107k927vnnki7g9yfs20xkpd7c5pkvbj8bpybbwjkm16")))) + "180w7c8n4xcn3x7haymi1fl3fpnklqfgmaki6jkxpm3hdiffmbsd")))) (build-system r-build-system) (propagated-inputs (list r-ape @@ -15813,6 +16178,30 @@ visualization; flexible image manipulation; metadata and sparse image handling.") (license license:gpl2))) +(define-public r-gridsvg + (package + (name "r-gridsvg") + (version "1.7-4") + (source (origin + (method url-fetch) + (uri (cran-uri "gridSVG" version)) + (sha256 + (base32 + "1jspjn56yrkx98hhs98npzm0k0kwpv8x1hg40kphx5ikhvincxmr")))) + (properties `((upstream-name . "gridSVG"))) + (build-system r-build-system) + (propagated-inputs + (list r-jsonlite r-xml)) + (home-page "https://cran.r-project.org/package=gridSVG") + (synopsis "Export grid gaphics as SVG") + (description + "This package provides functions to export graphics drawn with package +grid to SVG format. Extra functions provide access to SVG features that are +not available in standard R graphics, such as hyperlinks, animation, filters, +masks, clipping paths, and gradient and pattern fills.") + ;; Any version of the GPL. + (license (list license:gpl2 license:gpl3)))) + (define-public r-grimport (package (name "r-grimport") @@ -16144,14 +16533,14 @@ preparing, executing, and processing HTTP requests.") (define-public r-gmp (package (name "r-gmp") - (version "0.6-8") + (version "0.6-9") (source (origin (method url-fetch) (uri (cran-uri "gmp" version)) (sha256 (base32 - "0fba80f28fcb2w2spiy6wg7dr5cz7w6gf9z3yrkc6p60zbxdaccf")))) + "00zh0phr8axva2y2c10nla7n9mgh3wvwvsyyd3y43jpb3xim6lv6")))) (build-system r-build-system) (arguments '(#:phases @@ -16196,6 +16585,29 @@ functions. To this end, the package interfaces with the @dfn{Multiple Precision Floating-Point Reliable} (MPFR) library.") (license license:gpl2+))) +(define-public r-rmutil + (package + (name "r-rmutil") + (version "1.1.10") + (source (origin + (method url-fetch) + (uri (cran-uri "rmutil" version)) + (sha256 + (base32 + "1yd5gkg4jg3rvqrfl8c5r07lcr37n1p9h1a7b6s45iswd77dg7w1")))) + (properties `((upstream-name . "rmutil"))) + (build-system r-build-system) + (native-inputs (list gfortran)) + (home-page "https://www.commanster.eu/rcode.html") + (synopsis + "Utilities for nonlinear regression and repeated measurements models") + (description + "This package provides a toolkit of functions for nonlinear regression +and repeated measurements. It was designated to be imported by other packages +such as @code{gnlm}, @code{stable}, @code{growth}, @code{repeated}, and +@code{event}.") + (license license:gpl2+))) + (define-public r-assertive-base (package (name "r-assertive-base") @@ -16779,14 +17191,14 @@ package \"boot\".") (define-public r-survivalroc (package (name "r-survivalroc") - (version "1.0.3") + (version "1.0.3.1") (source (origin (method url-fetch) (uri (cran-uri "survivalROC" version)) (sha256 (base32 - "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l")))) + "0p6irjs8a9xxgxwax0y9fzapcib237if3iy8g6lzv793mzmsyx41")))) (properties `((upstream-name . "survivalROC"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/survivalROC") @@ -16814,6 +17226,26 @@ Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)") discovery rates.") (license license:gpl2))) +(define-public r-logging + (package + (name "r-logging") + (version "0.10-108") + (source (origin + (method url-fetch) + (uri (cran-uri "logging" version)) + (sha256 + (base32 + "13gd40ygx586vs6xcp6clg69a92aj8zxlk1rn3xzkx8klfjimjc5")))) + (properties `((upstream-name . "logging"))) + (build-system r-build-system) + (home-page "https://github.com/WLOGSolutions/r-logging") + (synopsis "R logging implementation of log4j") + (description + "This package implements the R version of the @code{log4j} package. It offers +hierarchic loggers, multiple handlers per logger, level based filtering, space +handling in messages and custom formatting.") + (license license:gpl3))) + (define-public r-longitudinal (package (name "r-longitudinal") @@ -17152,14 +17584,14 @@ by change of variable.") (define-public r-listenv (package (name "r-listenv") - (version "0.8.0") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "listenv" version)) (sha256 (base32 - "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx")))) + "11s8cy259al6x98xcz93jw6p87si01gcgzccnxhx69879zh42a1m")))) (build-system r-build-system) (arguments `(#:phases @@ -17204,14 +17636,14 @@ them in distributed compute environments.") (define-public r-parallelly (package (name "r-parallelly") - (version "1.32.1") + (version "1.33.0") (source (origin (method url-fetch) (uri (cran-uri "parallelly" version)) (sha256 (base32 - "146a9i999vrflr4g1fph1pgkl4bq0dw102bjw8pp1zy7kbsqbiii")))) + "0ymrpcxp2fnk1fpfig0kd1q3whzh7sykgcl91k53c2w20v2wwfpw")))) (properties `((upstream-name . "parallelly"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/parallelly") @@ -17232,14 +17664,14 @@ port-forwarding to your local computer.") (define-public r-future (package (name "r-future") - (version "1.29.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 - "0ws3jp82qjpnvgn5xrxdq7hg7r97rkylj329f9jqr69g3paiyvc5")))) + "1njmgnq0qz7b9yvcp6351yz7ydz9hj8bnnaf1ys3md66v9mg1xf7")))) (build-system r-build-system) (arguments `(#:phases @@ -17374,14 +17806,14 @@ heuristics.") (define-public r-dorng (package (name "r-dorng") - (version "1.8.2") + (version "1.8.3") (source (origin (method url-fetch) (uri (cran-uri "doRNG" version)) (sha256 (base32 - "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k")))) + "1aqzy646c6aggscmwninr1hz0z4nkxibmrg1mm77p2jnf1lh914c")))) (properties `((upstream-name . "doRNG"))) (build-system r-build-system) (propagated-inputs @@ -17445,6 +17877,29 @@ intersecting sets using a novel matrix design, along with visualizations of several common set, element and attribute related tasks.") (license license:expat))) +(define-public r-shinycustomloader + (package + (name "r-shinycustomloader") + (version "0.9.0") + (source (origin + (method url-fetch) + (uri (cran-uri "shinycustomloader" version)) + (sha256 + (base32 + "1klx71vr26g0gjf6hbiia1qidqii5d467i1sdjvlrg1hxdcggqff")))) + (properties `((upstream-name . "shinycustomloader"))) + (build-system r-build-system) + (propagated-inputs + (list r-glue + r-shiny)) + (home-page "https://cran.r-project.org/package=shinycustomloader") + (synopsis "Custom loader for Shiny outputs") + (description + "This package provides a custom @code{CSS/HTML} or @code{GIF/image} file +for the loading screen in R @code{Shiny}. It also can use the marquee to have +a custom text loading screen.") + (license license:gpl3))) + ;; This package includes a JavaScript file, which is not minified. When ;; upgrading please check that there are no new minified JavaScript files. (define-public r-shinybs @@ -17582,16 +18037,17 @@ identifying outliers.") (define-public r-bayesm (package (name "r-bayesm") - (version "3.1-4") + (version "3.1-5") (source (origin (method url-fetch) (uri (cran-uri "bayesm" version)) (sha256 - (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6")))) + (base32 "18j7h32nq4hx1qnxfgfgz3q39q35lmvsq3im90xjkphyli60f8zj")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo)) + (native-inputs (list r-knitr)) (home-page "http://www.perossi.org/home/bsm-1") (synopsis "Bayesian inference for marketing/micro-econometrics") (description @@ -18357,14 +18813,14 @@ can be used with function approximation, eligibility traces (Singh & Sutton, (define-public r-lemon (package (name "r-lemon") - (version "0.4.5") + (version "0.4.6") (source (origin (method url-fetch) (uri (cran-uri "lemon" version)) (sha256 (base32 - "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4")))) + "0v1kbyk64yzsk92h6yq03kp9alc9632qprznsws61r8firiskim5")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 @@ -18373,7 +18829,6 @@ can be used with function approximation, eligibility traces (Singh & Sutton, r-knitr r-lattice r-plyr - r-rlang r-scales)) (native-inputs (list r-knitr)) @@ -18621,14 +19076,14 @@ utilities for sequence data management under the ACNUC system.") (define-public r-units (package (name "r-units") - (version "0.8-0") + (version "0.8-1") (source (origin (method url-fetch) (uri (cran-uri "units" version)) (sha256 (base32 - "06mjprqi06xprj6185k5cmrrdl025x0pd1r6a4x3s74ciq9zwilw")))) + "16ndhl4hkcll9r5vh8flp2bc3mavddfz8g6sqddj15scdcjbmqfk")))) (build-system r-build-system) (inputs (list udunits)) @@ -18770,14 +19225,14 @@ tessellation.") (define-public r-wk (package (name "r-wk") - (version "0.7.0") + (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "wk" version)) (sha256 (base32 - "1pm2293xqcgjckghbf6q9sk7jh74njiynq3wqq1dbwigiz9jfhz2")))) + "116kvg2a9gga14agqvmvj2rbgfpdyasbkjnfjcsw9a9dk0n7g9g5")))) (properties `((upstream-name . "wk"))) (build-system r-build-system) (home-page "https://paleolimbot.github.io/wk/") @@ -19337,13 +19792,13 @@ SELECT or UPDATE queries to an end-point.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.30") + (version "0.31") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "1i54sbrdv2c9l6pcm3229wlwdnhn0x6f2918adszm5k8qdp0h74i")))) + "0rkapx3zz0vwggnrpk0ns8bpqsblkp08xpr0srz93c3kzlsjdiac")))) (build-system r-build-system) (propagated-inputs (list r-htmltools @@ -20041,13 +20496,13 @@ that fills this gap.") (define-public r-eulerr (package (name "r-eulerr") - (version "6.1.1") + (version "7.0.0") (source (origin (method url-fetch) (uri (cran-uri "eulerr" version)) (sha256 (base32 - "0lldp2319qd08y87f862gx8a77rvikcnkmdl9xgx4glynfs3hk19")))) + "16a84a2xgv1iqsir0hzn6qclljni4f3prpycb7qpp06vrd0yn8lw")))) (properties `((upstream-name . "eulerr"))) (build-system r-build-system) (propagated-inputs @@ -20868,14 +21323,14 @@ colored by the number of neighboring points. This is useful to visualize the (define-public r-arrow (package (name "r-arrow") - (version "10.0.0") + (version "10.0.1") (source (origin (method url-fetch) (uri (cran-uri "arrow" version)) (sha256 (base32 - "04qsj68zsqcwkv1ryp4l0is474siyi1b64dy41fr74ryj7mbamg8")))) + "0dwdi9sq7wv34ia6kg446pqf5za75hl6zrb2ly51p2zdr4g69p0y")))) (properties `((upstream-name . "arrow"))) (build-system r-build-system) (inputs @@ -21606,6 +22061,57 @@ perspective plots, slice plots, surface plots, scatter plots, etc. It includes data sets from oceanography.") (license license:gpl3+))) +(define-public r-plotroc + (package + (name "r-plotroc") + (version "2.3.0") + (source (origin + (method url-fetch) + (uri (cran-uri "plotROC" version)) + (sha256 + (base32 + "0kaz9hrimi9gi7cf7flag9kc9yrg5fdyylqa5hn53x4dy8vhj37g")) + (snippet + '(delete-file "inst/d3.v3.min.js")))) + (properties `((upstream-name . "plotROC"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (let ((source (assoc-ref inputs "d3.v3.js")) + (target "inst/d3.v3.min.js")) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target)))))))) + (propagated-inputs + (list r-ggplot2 + r-gridsvg + r-plyr + r-rlang + r-shiny)) + (native-inputs + `(("r-knitr" ,r-knitr) + ("esbuild" ,esbuild) + ("d3.v3.js" + ,(origin + (method url-fetch) + (uri "https://d3js.org/d3.v3.js") + (sha256 + (base32 + "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41")))))) + (home-page "https://sachsmc.github.io/plotROC/") + (synopsis "Generating useful receiver operating characteristic curve charts") + (description + "This package generates @acronym{ROC, receiver operating characteristic} +plots. Most ROC curve plots obscure the cutoff values and inhibit +interpretation and comparison of multiple curves. This attempts to address +those shortcomings by providing plotting and interactive tools. Functions are +provided to generate an interactive ROC curve plot for web use, and print +versions. A Shiny application implementing the functions is also included.") + (license license:expat))) + (define-public r-ggfortify (package (name "r-ggfortify") @@ -22202,14 +22708,14 @@ emphasize hidden group structures in networks or focus on specific nodes.") (define-public r-terra (package (name "r-terra") - (version "1.6-41") + (version "1.6-47") (source (origin (method url-fetch) (uri (cran-uri "terra" version)) (sha256 (base32 - "0n0si3b6l88w0svvpc999slqack1djdd96jc0m8fdkwp0nwi3hkc")))) + "13n6rxrrkn4wgcgq2kyyhn5nxw099hy9fbzxg78waxa6cxapwpmh")))) (properties `((upstream-name . "terra"))) (build-system r-build-system) (inputs @@ -22351,13 +22857,13 @@ effect size.") (define-public r-rgdal (package (name "r-rgdal") - (version "1.6-2") + (version "1.6-3") (source (origin (method url-fetch) (uri (cran-uri "rgdal" version)) (sha256 - (base32 "0g83r9lzq79hs7mk31kqym1sjqnmk53j3nikrn2vk257v854pavy")))) + (base32 "0snz5m158as39h6zdcdrydwm5n2r2vayv3xy8n3g5mmkbxyyx7i2")))) (properties `((upstream-name . "rgdal"))) (build-system r-build-system) (inputs @@ -22416,6 +22922,9 @@ atmospheric physics.") (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-rlang)) + ;; We can't add this here because via r-stringr this package ends up being + ;; an input to r-knitr. + #; (native-inputs (list r-knitr)) ; for vignettes (home-page "https://github.com/r-lib/lifecycle") @@ -23542,14 +24051,14 @@ See e.g. Gentle (2003) @url{doi:10.1007/b97336}.") (define-public r-lhs (package (name "r-lhs") - (version "1.1.5") + (version "1.1.6") (source (origin (method url-fetch) (uri (cran-uri "lhs" version)) (sha256 (base32 - "0fb3bc3s5pbwg92qkjbg7v8ah36wm6qs05vf098hwjakr7f6yg3s")))) + "0gyjdic714pqvq2jv1v0vh7hl9s83sg2zxx2gdkp38z6xx2cwzz3")))) (properties `((upstream-name . "lhs"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -24922,14 +25431,14 @@ number embedded in the file rather than the file extension.") (define-public r-imager (package (name "r-imager") - (version "0.42.13") + (version "0.42.16") (source (origin (method url-fetch) (uri (cran-uri "imager" version)) (sha256 (base32 - "0zygnmxwbbmj5i2l2affzdz90xvsa7b5pbkzkhjbm40is69rh2nr")))) + "00q2v000xanp03bzscmj3q9qnlhc97b1lgr4l19s9jmbf0hf9c5c")))) (properties `((upstream-name . "imager"))) (build-system r-build-system) (inputs @@ -25441,6 +25950,30 @@ They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis.") (license license:gpl2+))) +(define-public r-anytime + (package + (name "r-anytime") + (version "0.3.9") + (source (origin + (method url-fetch) + (uri (cran-uri "anytime" version)) + (sha256 + (base32 + "0jjpqynai5nd7mfy1smb44356f3d5bmpxhs1i9x9jw5c959c35hh")))) + (properties `((upstream-name . "anytime"))) + (build-system r-build-system) + (propagated-inputs + (list r-bh + r-rcpp)) + (home-page "http://dirk.eddelbuettel.com/code/anytime.html") + (synopsis "Converter of input to POSIXct or Date") + (description + "The package converts the input in any one of character, integer, numeric, +factor, or an ordered type into @code{POSIXct} (or @code{Date}) objects, using +one of a number of predefined formats, and relying on Boost facilities for date +and time parsing.") + (license license:gpl2+))) + (define-public r-anndata (package (name "r-anndata") @@ -26096,13 +26629,13 @@ space models and automatic ARIMA modelling.") (define-public r-forestplot (package (name "r-forestplot") - (version "3.1.0") + (version "3.1.1") (source (origin (method url-fetch) (uri (cran-uri "forestplot" version)) (sha256 (base32 - "0xk30mpb87sab2afnk2j474qjjf4j6x1ifh9j5n7w690f481iqqb")))) + "0jf7sl7z963r92l5r2irvnakmbmx554vbprg51smj6qns5a6dfcj")))) (properties `((upstream-name . "forestplot"))) (build-system r-build-system) (propagated-inputs @@ -26286,14 +26819,14 @@ Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.") (define-public r-quanteda (package (name "r-quanteda") - (version "3.2.3") + (version "3.2.4") (source (origin (method url-fetch) (uri (cran-uri "quanteda" version)) (sha256 (base32 - "1blk9nhydvqyyz0kzhph7nh7ahcjzflmgyr4sv8fx5bpmn4hwjzk")))) + "1yg3lgckh6fncmw037p4gaa2bab59yh6izqix1cgyysjg4jpcw62")))) (properties `((upstream-name . "quanteda"))) (build-system r-build-system) (propagated-inputs @@ -26325,14 +26858,14 @@ machine learning, visually representing text and text analyses, and more.") (define-public r-topicmodels (package (name "r-topicmodels") - (version "0.2-12") + (version "0.2-13") (source (origin (method url-fetch) (uri (cran-uri "topicmodels" version)) (sha256 (base32 - "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g")))) + "16mw0l7wm5idc831csxlk176c42a5xw8qm8xhbnmmdl2hjk0cqbx")))) (properties `((upstream-name . "topicmodels"))) (build-system r-build-system) (inputs @@ -26797,14 +27330,14 @@ output in R.") (define-public r-bdgraph (package (name "r-bdgraph") - (version "2.70") + (version "2.71") (source (origin (method url-fetch) (uri (cran-uri "BDgraph" version)) (sha256 (base32 - "1s148fvvg1c0n4swsvcinlwckj86jys5nvwp4wlyzh3aw9siyqz7")))) + "1lihsbliq7f91ywdq5cabzd5fbyhb10h62ss3n2l7i2fdglb77d1")))) (properties `((upstream-name . "BDgraph"))) (build-system r-build-system) (propagated-inputs @@ -26864,14 +27397,14 @@ network, tree, dendrogram, and Sankey graphs from R using data frames.") (define-public r-qgraph (package (name "r-qgraph") - (version "1.9.2") + (version "1.9.3") (source (origin (method url-fetch) (uri (cran-uri "qgraph" version)) (sha256 (base32 - "0r225b7rnsv6wz41ij0msmqr1xy0iqxh9dbsvjixbi1hvgv91wds")))) + "14azjxlvb02wlbskbsv5x3a6gpfb8hfyijfpbay6fimnsaqnmbj6")))) (properties `((upstream-name . "qgraph"))) (build-system r-build-system) (propagated-inputs @@ -28710,14 +29243,14 @@ input.") (define-public r-lightgbm (package (name "r-lightgbm") - (version "3.3.3") + (version "3.3.4") (source (origin (method url-fetch) (uri (cran-uri "lightgbm" version)) (sha256 (base32 - "1a4nacdpsqd5mr7jnw1g9nyn8w7p0hskfm07cy8yrj3h8a5hmcz8")))) + "12hcq2idjgggs8l9a5aaxbw1wsfz6byzaxqn9k6afvkf3v5srp65")))) (properties `((upstream-name . "lightgbm"))) (build-system r-build-system) (propagated-inputs @@ -29402,14 +29935,14 @@ formal inference.") (define-public r-gaston (package (name "r-gaston") - (version "1.5.7") + (version "1.5.8") (source (origin (method url-fetch) (uri (cran-uri "gaston" version)) (sha256 (base32 - "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i")))) + "1pv37csq3gvkld7hfxgbq72n35gx1wg3bvrcvzzzf0qsfb6g42cc")))) (properties `((upstream-name . "gaston"))) (build-system r-build-system) (inputs (list zlib)) @@ -29548,14 +30081,14 @@ model.") (define-public r-clusterr (package (name "r-clusterr") - (version "1.2.7") + (version "1.2.9") (source (origin (method url-fetch) (uri (cran-uri "ClusterR" version)) (sha256 (base32 - "1sl218scrf5s02v54bmmk2sz1vrnlq16c14c0lcg1n7x8d76sgk6")))) + "04aswnmxzpffc1fj2hf85pc5b10fh418k29a1x5cs1f1y7b3zav3")))) (properties `((upstream-name . "ClusterR"))) (build-system r-build-system) (propagated-inputs @@ -30384,19 +30917,18 @@ pipeline friendly so that data processing with lists can be chained.") (define-public r-rsample (package (name "r-rsample") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "rsample" version)) (sha256 (base32 - "1iy61riwjch9z4m6k7whsrkl80sk9sww5lf1np4iq4vdfq6w01jb")))) + "1fmqfk1yihmh7lkszsf7pvn6zf67lpgff46hv2lpnfbssa3axllh")))) (properties `((upstream-name . "rsample"))) (build-system r-build-system) (propagated-inputs (list r-dplyr - r-ellipsis r-furrr r-generics r-glue @@ -30841,14 +31373,14 @@ functions or computational engines (e.g. R, Spark, Stan, etc).") (define-public r-infer (package (name "r-infer") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "infer" version)) (sha256 (base32 - "1m5srhcmkh8wq12pvy57g3g703wilkl8r3gmm5s7lbj103iz7v8b")))) + "1s4q0nslykl0pb2w1i6ni6hkpp7awvp0wks79br3gk5wa1qkvs19")))) (properties `((upstream-name . "infer"))) (build-system r-build-system) (propagated-inputs @@ -30898,6 +31430,31 @@ expressive statistical grammar that coheres with the Tidy design framework.") model-related packages.") (license license:expat))) +(define-public r-modeest + (package + (name "r-modeest") + (version "2.4.0") + (source (origin + (method url-fetch) + (uri (cran-uri "modeest" version)) + (sha256 + (base32 + "087dw0013y4m7fcl06mxylh9lnp6acysl80d80r9srv4pw4r950s")))) + (properties `((upstream-name . "modeest"))) + (build-system r-build-system) + (propagated-inputs + (list r-fbasics + r-stable + r-stabledist + r-statip)) + (home-page "https://github.com/paulponcet/modeest") + (synopsis "Mode estimations for univariate data or distributions") + (description + "The package provides estimators of the mode of univariate unimodal (and +sometimes multimodal) data and values of the modes of usual probability +distributions.") + (license license:gpl3))) + (define-public r-conflicted (package (name "r-conflicted") @@ -31119,14 +31676,14 @@ covariate (usually group indicator) and the scores.") (define-public r-qtl (package (name "r-qtl") - (version "1.52") + (version "1.54") (source (origin (method url-fetch) (uri (cran-uri "qtl" version)) (sha256 (base32 - "0q49g3ar1451whsl6ig7kz4mg8s9zxlcvgkj4ivyw4995wbwc2ij")))) + "1rzkxkmcgd6drxbgqp6w6jab5bs7vla2x2ndv3l4nlbcwzi41jw0")))) (build-system r-build-system) (home-page "https://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") @@ -31142,12 +31699,12 @@ genome scans.") (define-public r-qtl2 (package (name "r-qtl2") - (version "0.28") + (version "0.30") (source (origin (method url-fetch) (uri (cran-uri "qtl2" version)) (sha256 - (base32 "0ppc6dzlq77mppxc6bczai9gi40jrbxd1466y2cn2s8a4ah1jg9y")))) + (base32 "0c9v5hwfmlchrdzdysvmi6dsxyclc15sqbp65l4x6zwpd0828h6c")))) (build-system r-build-system) (propagated-inputs (list r-data-table @@ -31912,14 +32469,14 @@ vector machines, and gradient boosting.") (define-public r-bbotk (package (name "r-bbotk") - (version "0.7.0") + (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "bbotk" version)) (sha256 (base32 - "0g3x3r1dkp9w57arpqc6iccvsawjdf7vlv8c27cb1r36b0z45fi6")))) + "1gw0rkbiv93ifl9110r9sr0p9g4vg7qc11mznmmjq0a5vzmqgpm9")))) (properties `((upstream-name . "bbotk"))) (build-system r-build-system) (propagated-inputs @@ -31942,13 +32499,13 @@ annealing.") (define-public r-mlr3tuning (package (name "r-mlr3tuning") - (version "0.17.0") + (version "0.17.1") (source (origin (method url-fetch) (uri (cran-uri "mlr3tuning" version)) (sha256 (base32 - "1dg02qyyymflgws47sly3b7wd8nj4i9vv7ybx42hgvd55al3smdp")))) + "03habi7dm5xgwfb4zjn9nhvyym46qcljy31jz32fxalsap1mk9jb")))) (build-system r-build-system) (propagated-inputs (list r-bbotk @@ -32296,14 +32853,14 @@ in output to the equivalent HTML.") (define-public r-pkgdown (package (name "r-pkgdown") - (version "2.0.6") + (version "2.0.7") (source (origin (method url-fetch) (uri (cran-uri "pkgdown" version)) (sha256 (base32 - "0sbz3kzd0hbdnszylsb281arldn2z1c9yxifhj4zv2dilp46b6nj")))) + "0sim3fwayf4mpxqi8y9v7clnkzs56amhxsc75lc1k0zskn374f7k")))) (properties `((upstream-name . "pkgdown"))) (build-system r-build-system) (inputs (list pandoc)) @@ -33756,14 +34313,14 @@ object to and from disk.") (define-public r-rgeos (package (name "r-rgeos") - (version "0.5-9") + (version "0.6-1") (source (origin (method url-fetch) (uri (cran-uri "rgeos" version)) (sha256 (base32 - "1m73y0nwrdwsjrl48c4fg1kdqnh79835brnmxv9ak01ndbzcp45b")))) + "1wppxr9iibb0gi1hr6qzda9dc8spf6297lkfddl41j78q14bs3a2")))) (properties `((upstream-name . "rgeos"))) (build-system r-build-system) (inputs @@ -34141,14 +34698,14 @@ fully reproducible.") (define-public r-paws-common (package (name "r-paws-common") - (version "0.5.1") + (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "paws.common" version)) (sha256 (base32 - "17cfvx2ma0zcrj3grpsadx8p5r97s2z6c23qqmzry7ys9mn6k9f1")))) + "090csb0wjnsfhkphws5anrnml18y1k54yi48lxav8wp5kqj4wlb6")))) (properties `((upstream-name . "paws.common"))) (build-system r-build-system) (propagated-inputs @@ -35202,13 +35759,13 @@ formatting and delivering log messages with low overhead.") (define-public r-fasterize (package (name "r-fasterize") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "fasterize" version)) (sha256 - (base32 "10bzl77c1b9jhcn1xp467qzp2n8c7s3wpxn53qjh1nwvbri5kd32")))) + (base32 "1ckxi2iyxdahhgbliblcrkzziblfagzr54srjk27yp1lcgivvvs4")))) (properties `((upstream-name . "fasterize"))) (build-system r-build-system) (propagated-inputs |