diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 5432 |
1 files changed, 4569 insertions, 863 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6f931f06c2..ebfe9fd506 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17,7 +17,7 @@ ;;; Copyright © 2018 Marius Bakke <[email protected]> ;;; Copyright © 2018, 2019 Brett Gilio <[email protected]> ;;; Copyright © 2019 Nicolò Balzarotti <[email protected]> -;;; Copyright © 2019, 2020 Wiktor Żelazny <[email protected]> +;;; Copyright © 2019, 2020, 2021 Wiktor Żelazny <[email protected]> ;;; Copyright © 2019 Arne Babenhauserheide <[email protected]> ;;; Copyright © 2019, 2020 Efraim Flashner <[email protected]> ;;; Copyright © 2020 Todor Kondić <[email protected]> @@ -33,7 +33,7 @@ ;;; Copyright © 2020 Magali Lemes <[email protected]> ;;; Copyright © 2020 Simon Tournier <[email protected]> ;;; Copyright © 2020 Aniket Patil <[email protected]> -;;; Copyright © 2021 Tim Howes <[email protected]> +;;; Copyright © 2021 Marcel Schilling <[email protected]> ;;; ;;; This file is part of GNU Guix. ;;; @@ -84,7 +84,6 @@ #:use-module (gnu packages java) #:use-module (gnu packages javascript) #:use-module (gnu packages libevent) - #:use-module (gnu packages lisp-xyz) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) @@ -96,6 +95,7 @@ #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pulseaudio) ;libsndfile + #:use-module (gnu packages protobuf) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) #:use-module (gnu packages sqlite) @@ -103,7 +103,9 @@ #:use-module (gnu packages tcl) #:use-module (gnu packages textutils) #:use-module (gnu packages tls) + #:use-module (gnu packages uglifyjs) #:use-module (gnu packages version-control) + #:use-module (gnu packages video) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (gnu packages xorg)) @@ -111,14 +113,14 @@ (define-public r-brio (package (name "r-brio") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "brio" version)) (sha256 (base32 - "0ai2pqw5zk11r0rl2xshsq095ix1sdp2vjlixz2qxvy27x145ykh")))) + "1vviykwx1z71yhk1xl87riaygj8sq0sj7ixyig1irqsi66aydpa2")))) (properties `((upstream-name . "brio"))) (build-system r-build-system) (home-page "https://github.com/r-lib/brio") @@ -132,14 +134,14 @@ files and provide more explicit control over line endings.") (define-public r-cachem (package (name "r-cachem") - (version "1.0.4") + (version "1.0.6") (source (origin (method url-fetch) (uri (cran-uri "cachem" version)) (sha256 (base32 - "1b1gk837rk9kbfq385ybrrk12ckxwvhjvf0z9635l3vw49wal4mh")))) + "0r0q5w8lsxak46crnkbi739qzys90hlw7cqqqhv99xzkpkvm554s")))) (properties `((upstream-name . "cachem"))) (build-system r-build-system) (propagated-inputs @@ -153,6 +155,60 @@ can limit either their total size or the age of the oldest object (or both), automatically pruning objects to maintain the constraints.") (license license:expat))) +(define-public r-curry + (package + (name "r-curry") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "curry" version)) + (sha256 + (base32 + "1ps9hvbnb02m0b8hlw4admwbziyjvswj08ldi2dk3ymnrpawcc29")))) + (properties `((upstream-name . "curry"))) + (build-system r-build-system) + (home-page "https://github.com/thomasp85/curry") + (synopsis "Partial function application") + (description + "Partial application is the process of reducing the arity of a function +by fixing one or more arguments, thus creating a new function lacking the +fixed arguments. The @code{curry} package provides three different ways of +performing partial function application by fixing arguments from either end of +the argument list (currying and tail currying) or by fixing multiple named +arguments (partial application). This package provides this functionality +through the @code{%<%}, @code{%-<%}, and @code{%><%} operators which allows +for a programming style comparable to modern functional languages. Compared +to other implementations such a @code{purrr::partial()} the operators in +@code{curry} composes functions with named arguments, aiding in autocomplete +etc.") + (license license:gpl2+))) + +(define-public r-datawizard + (package + (name "r-datawizard") + (version "0.2.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "datawizard" version)) + (sha256 + (base32 + "15q491qix4a9b10wkb5bm9jnnr62smjw4qdrw4bd51i1kgvd6kl5")))) + (properties `((upstream-name . "datawizard"))) + (build-system r-build-system) + (propagated-inputs + `(("r-insight" ,r-insight))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://easystats.github.io/datawizard/") + (synopsis "Easy data wrangling") + (description + "This package provides a lightweight package to easily manipulate, +clean, transform, and prepare your data for analysis. It also forms the data +wrangling backend for the packages in the @code{easystats} ecosystem.") + (license license:gpl3))) + (define-public r-diffobj (package (name "r-diffobj") @@ -175,17 +231,132 @@ automatically pruning objects to maintain the constraints.") visualization of their differences.") (license license:gpl2+))) +(define-public r-emdist + (package + (name "r-emdist") + (version "0.3-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "emdist" version)) + (sha256 + (base32 + "1z14pb9z9nkd0f2c8pln4hzkfqa9dk9n3vg8czc8jiv0ndnqi7rq")))) + (properties `((upstream-name . "emdist"))) + (build-system r-build-system) + (home-page "http://www.rforge.net/emd") + (synopsis "Earth mover's distance") + (description + "This package provides tools to calculate the Earth Mover's +Distance (EMD).") + (license license:expat))) + +(define-public r-googledrive + (package + (name "r-googledrive") + (version "2.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "googledrive" version)) + (sha256 + (base32 + "09jsiknzyfgxd0nzdr3wrrjw24allch2x74h96qg8vh8dad4cp30")))) + (properties `((upstream-name . "googledrive"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cli" ,r-cli) + ("r-gargle" ,r-gargle) + ("r-glue" ,r-glue) + ("r-httr" ,r-httr) + ("r-jsonlite" ,r-jsonlite) + ("r-lifecycle" ,r-lifecycle) + ("r-magrittr" ,r-magrittr) + ("r-pillar" ,r-pillar) + ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) + ("r-tibble" ,r-tibble) + ("r-uuid" ,r-uuid) + ("r-vctrs" ,r-vctrs) + ("r-withr" ,r-withr))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://googledrive.tidyverse.org") + (synopsis "Interface to Google Drive") + (description "This package lets you manage Google Drive files from R.") + (license license:expat))) + +(define-public r-ids + (package + (name "r-ids") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ids" version)) + (sha256 + (base32 + "1s6ga94gds5ydr9f8qbjfgfpg2dvbnkcrlybqlb33hk3c0c2l8dn")))) + (properties `((upstream-name . "ids"))) + (build-system r-build-system) + (propagated-inputs + `(("r-openssl" ,r-openssl) + ("r-uuid" ,r-uuid))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/richfitz/ids") + (synopsis "Generate random identifiers") + (description + "This package lets you generate random or human readable and +pronounceable identifiers.") + (license license:expat))) + +(define-public r-googlesheets4 + (package + (name "r-googlesheets4") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "googlesheets4" version)) + (sha256 + (base32 + "0yncqwv9l5knyrv88ys5gwcv44hl1j0mbklpins6v7f9m9v7s40a")))) + (properties `((upstream-name . "googlesheets4"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cellranger" ,r-cellranger) + ("r-cli" ,r-cli) + ("r-curl" ,r-curl) + ("r-gargle" ,r-gargle) + ("r-glue" ,r-glue) + ("r-googledrive" ,r-googledrive) + ("r-httr" ,r-httr) + ("r-ids" ,r-ids) + ("r-magrittr" ,r-magrittr) + ("r-purrr" ,r-purrr) + ("r-rematch2" ,r-rematch2) + ("r-rlang" ,r-rlang) + ("r-tibble" ,r-tibble) + ("r-vctrs" ,r-vctrs))) + (home-page "https://github.com/tidyverse/googlesheets4") + (synopsis "Access Google Sheets using the Sheets API V4") + (description + "This package lets you interact with Google Sheets through the +@url{https://developers.google.com/sheets/api,Sheets API v4}. This package +can read and write both the metadata and the cell data in a Sheet.") + (license license:expat))) + (define-public r-waldo (package (name "r-waldo") - (version "0.2.5") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "waldo" version)) (sha256 (base32 - "09jhwpgd6hg4qyip4r7wzpjz0jr139fyspd5ncriqimp522snqbr")))) + "16q1xjbl9g04l1r1x3nid9hmz1sa35q6j33bigdzh4y4zcd8qb7c")))) (properties `((upstream-name . "waldo"))) (build-system r-build-system) (propagated-inputs @@ -208,14 +379,14 @@ easier.") (define-public r-rticles (package (name "r-rticles") - (version "0.19") + (version "0.21") (source (origin (method url-fetch) (uri (cran-uri "rticles" version)) (sha256 (base32 - "1zcj5y54z1max1df9j2iclm6zlcic4wj684y18wcnmmdwfs51818")))) + "0xk0xz97k8r8srmniihn3y4dkxddxf97yjbsljcxlgcq8f0zcc2s")))) (properties `((upstream-name . "rticles"))) (build-system r-build-system) (propagated-inputs @@ -231,6 +402,54 @@ easier.") for authoring journal articles and conference submissions.") (license license:gpl3))) +(define-public r-benchmarkmedata + (package + (name "r-benchmarkmedata") + (version "1.0.4") + (source (origin + (method url-fetch) + (uri (cran-uri "benchmarkmeData" version)) + (sha256 + (base32 + "1n4vjkagqlm6kw2hilf4gjfcdjad0bcg652j9nl2ygbq3kdnh1vf")))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-tibble" ,r-tibble))) + (home-page "https://github.com/csgillespie/benchmarkme-data") + (synopsis "Data set for the @code{benchmarkme} package") + (description "This package contains the data set for the crowd-sourced +benchmarks from running the @code{benchmarkme} package.") + (license license:gpl2+))) + +(define-public r-benchmarkme + (package + (name "r-benchmarkme") + (version "1.0.7") + (source (origin + (method url-fetch) + (uri (cran-uri "benchmarkme" version)) + (sha256 + (base32 + "0ymgsxzrvnpyvs0cff09d3lrkl12qyqx5bwammsc4vgl5ng9p69p")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (propagated-inputs + `(("r-benchmarkmedata" ,r-benchmarkmedata) + ("r-doparallel" ,r-doparallel) + ("r-dplyr" ,r-dplyr) + ("r-foreach" ,r-foreach) + ("r-httr" ,r-httr) + ("r-matrix" ,r-matrix) + ("r-tibble" ,r-tibble))) + (home-page "https://csgillespie.github.io/benchmarkme/") + (synopsis "Crowd-sourced system benchmarks") + (description "This package provides functionality to benchmark your CPU +and compare against other CPUs. Also provides functions for obtaining system +specifications, such as RAM, CPU type, and R version.") + (license license:gpl2+))) + (define-public r-bezier (package (name "r-bezier") @@ -253,14 +472,14 @@ degree elevation and curve fitting.") (define-public r-v8 (package (name "r-v8") - (version "3.4.0") + (version "3.4.2") (source (origin (method url-fetch) (uri (cran-uri "V8" version)) (sha256 (base32 - "1g9z22pc8ydx1yhv57ww2d2jg5hvrl7ilwa79x89zgn17jha5j7m")))) + "1vfj89shfzx7b6papi2y671l8gksng775kilmqzl5gx87i3l61i1")))) (properties `((upstream-name . "V8"))) (build-system r-build-system) (arguments @@ -282,7 +501,8 @@ degree elevation and curve fitting.") (assoc-ref inputs "node") "/lib")) #t))))) (inputs - `(("node" ,libnode))) + `(("node" ,libnode) + ("zlib" ,zlib))) (propagated-inputs `(("r-curl" ,r-curl) ("r-jsonlite" ,r-jsonlite) @@ -361,6 +581,32 @@ ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors.") (license license:gpl2+))) +(define-public r-fingerprint + (package + (name "r-fingerprint") + (version "3.5.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "fingerprint" version)) + (sha256 + (base32 "04jcwkydjrs31pia6kq8z2n9s54im950q08hs2ay15xjxxkmb8ic")))) + (properties `((upstream-name . "fingerprint"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=fingerprint") + (synopsis "Functions to Operate on Binary Fingerprint Data") + (description + "This package provides functions to manipulate binary fingerprints of +arbitrary length. A fingerprint is represented by an object of S4 class +@code{fingerprint}. The bitwise logical functions in R are overridden so that +they can be used directly with @code{fingerprint} objects. A number of +distance metrics are also available. Fingerprints can be converted to +Euclidean vectors (i.e., points on the unit hypersphere) and can also be +folded. Arbitrary fingerprint formats can be handled via line handlers. +Currently handlers are provided for CDK, MOE and BCI fingerprint data.") + ;; Any version of the GPL + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-ggalluvial (package (name "r-ggalluvial") @@ -390,35 +636,99 @@ multi-dimensional or repeated-measures data with categorical or ordinal variables.") (license license:gpl3))) +(define-public r-ggpp + (package + (name "r-ggpp") + (version "0.4.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggpp" version)) + (sha256 + (base32 + "0m2wq9kqlxqxlzyx9fd0c4iw6qb7kpjrq7fqqa2kvwyj79vx6ahj")))) + (properties `((upstream-name . "ggpp"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-glue" ,r-glue) + ("r-gridextra" ,r-gridextra) + ("r-lubridate" ,r-lubridate) + ("r-magrittr" ,r-magrittr) + ("r-mass" ,r-mass) + ("r-polynom" ,r-polynom) + ("r-rlang" ,r-rlang) + ("r-scales" ,r-scales) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-xts" ,r-xts) + ("r-zoo" ,r-zoo))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://docs.r4photobiology.info/ggpp/") + (synopsis "Grammar extensions to ggplot2") + (description + "This package contains extensions to ggplot2. + +@enumerate +@item Geomas: @code{geom_table}, @code{geom_plot} and @code{geom_grob} add + insets to plots using native data coordinates, while @code{geom_table_npc}, + @code{geom_plot_npc} and @code{geom_grob_npc} do the same using @code{npc} + coordinates through new aesthetics @code{npcx} and @code{npcy}. +@item Statistics: select observations based on 2D density. +@item Positions: radial nudging away from a center point and nudging away from + a line or curve. +@end enumerate +") + (license license:gpl2+))) + +(define-public r-lmodel2 + (package + (name "r-lmodel2") + (version "1.7-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "lmodel2" version)) + (sha256 + (base32 "1fiin2nkffbihz1s8ixmw9lgf8mn3j9krr8iiflizk10mdv54hnb")))) + (properties `((upstream-name . "lmodel2"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=lmodel2") + (synopsis "Model II regression") + (description + "This package computes model II simple linear regression using +@dfn{ordinary least squares} (OLS), @dfn{major axis} (MA), @dfn{standard major +axis} (SMA), and @dfn{ranged major axis} (RMA).") + (license license:gpl2))) + (define-public r-ggpmisc (package (name "r-ggpmisc") - (version "0.3.9") + (version "0.4.3") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 - "0nb0lpwqph9334s9sq77mk3nd22icy9d9hywz4awhf6nvp5rcc2v")))) + "0ff84ybj4648c1v05ng3l62g9n52igjwvm320qkfbdzdxzncpzik")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-generics" ,r-generics) - ("r-glue" ,r-glue) ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) + ("r-ggpp" ,r-ggpp) + ("r-lmodel2" ,r-lmodel2) ("r-lubridate" ,r-lubridate) - ("r-magrittr" ,r-magrittr) ("r-mass" ,r-mass) ("r-plyr" ,r-plyr) ("r-polynom" ,r-polynom) + ("r-quantreg" ,r-quantreg) ("r-rlang" ,r-rlang) ("r-scales" ,r-scales) ("r-splus2r" ,r-splus2r) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-xts" ,r-xts) - ("r-zoo" ,r-zoo))) + ("r-tibble" ,r-tibble))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://www.r4photobiology.info/") @@ -454,14 +764,14 @@ organisms via the @code{g:Profiler} toolkit.") (define-public r-gprofiler2 (package (name "r-gprofiler2") - (version "0.2.0") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "gprofiler2" version)) (sha256 (base32 - "0q8hl3gdxy34c0181ql405fdklz82nfvmwdcafd5mzf935rjpyjg")))) + "0r0h34b35xzgd9rh55yndn0anxy0z45zdlqa6qfmpn91b6v1bb1g")))) (properties `((upstream-name . "gprofiler2"))) (build-system r-build-system) (propagated-inputs @@ -550,6 +860,28 @@ provides methods for automatically determining breaks and labels for axes and legends.") (license license:expat))) +(define-public r-pacman + (package + (name "r-pacman") + (version "0.5.1") + (source (origin + (method url-fetch) + (uri (cran-uri "pacman" version)) + (sha256 + (base32 + "0z7gngd6h83cpjhq1vg75wvzhdjbgjh7gj5d4zvvi9gd2lmagjcy")))) + (build-system r-build-system) + (propagated-inputs + `(("r-remotes" ,r-remotes))) + (home-page "https://github.com/trinker/pacman") + (synopsis "Package Management Tool") + (description "This package provides tools to more conveniently perform +tasks associated with add-on packages. @code{pacman} conveniently wraps +library and package related functions and names them in an intuitive and +consistent fashion. It seeks to combine functionality from lower level +functions which can speed up workflow.") + (license license:gpl2))) + (define-public r-pheatmap (package (name "r-pheatmap") @@ -600,14 +932,14 @@ information.") (define-public r-ellipsis (package (name "r-ellipsis") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "ellipsis" version)) (sha256 (base32 - "1nvmkcca57d9067rcggw1gby80ibx5hplk2myz0cs9zwilaib2jg")))) + "0n0mm9jngklv7j9wa64jdji035z0smmnsp2dfwcz9isrxgjnc0m9")))) (build-system r-build-system) (propagated-inputs `(("r-rlang" ,r-rlang))) @@ -669,13 +1001,13 @@ objects.") (define-public r-mboost (package (name "r-mboost") - (version "2.9-4") + (version "2.9-5") (source (origin (method url-fetch) (uri (cran-uri "mboost" version)) (sha256 (base32 - "1dgyc38axfk2a430wsdnnk76xikizkyxf5r0l1kbp6cacrx6idz0")))) + "0yg07fdd1sbjfhhxn1dqgph2vzqyq7l52cdk5iq2a2zy1vh176yg")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) @@ -698,13 +1030,13 @@ high-dimensional data.") (define-public r-shadowtext (package (name "r-shadowtext") - (version "0.0.7") + (version "0.0.9") (source (origin (method url-fetch) (uri (cran-uri "shadowtext" version)) (sha256 (base32 - "1s1ip8zfr684a3ld7hvf524bhn2j31k6d1wbhh1ni0flsggv2ckf")))) + "1g6mgnfnzf2c17yzqk3zybfc5y62p5ndrbikxb3xcm2hiljiiqna")))) (properties `((upstream-name . "shadowtext"))) (build-system r-build-system) (propagated-inputs @@ -826,14 +1158,14 @@ data types as well.") (define-public r-tidyverse (package (name "r-tidyverse") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "tidyverse" version)) (sha256 (base32 - "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd")))) + "0ck6xmsw5p168jmw2fqv79fzfnw5jckfra7mfii261j6kl89bkw3")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -841,8 +1173,11 @@ data types as well.") ("r-crayon" ,r-crayon) ("r-dbplyr" ,r-dbplyr) ("r-dplyr" ,r-dplyr) + ("r-dtplyr" ,r-dtplyr) ("r-forcats" ,r-forcats) ("r-ggplot2" ,r-ggplot2) + ("r-googledrive" ,r-googledrive) + ("r-googlesheets4" ,r-googlesheets4) ("r-haven" ,r-haven) ("r-hms" ,r-hms) ("r-httr" ,r-httr) @@ -862,6 +1197,8 @@ data types as well.") ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-xml2" ,r-xml2))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://tidyverse.tidyverse.org") (synopsis "Install and load packages from the \"Tidyverse\"") (description @@ -874,13 +1211,13 @@ single step.") (define-public r-rvest (package (name "r-rvest") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "rvest" version)) (sha256 - (base32 "04spcv6nxlmx5bxncq0vybfqrs8jgjamzyrn6wmkdcwii8jvyn53")))) + (base32 "1v99bpp2077s4y5phvkzpgjyr8cs9axifm1c3npw6jmh8x9j91h8")))) (build-system r-build-system) (propagated-inputs `(("r-httr" ,r-httr) @@ -927,14 +1264,14 @@ package is a port of the Python package @code{cssselect}.") (define-public r-reprex (package (name "r-reprex") - (version "2.0.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "reprex" version)) (sha256 (base32 - "1lcnxczy28n4g3rvph09va7svcznfyqa7zdggklqb924qvy7flwh")))) + "09k4rasp7mz6n796dsklcbc5l7prljiznrm7fra16qybr9kqcv8f")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) @@ -984,14 +1321,14 @@ same time tries to group instances from the same class together.") (define-public r-callr (package (name "r-callr") - (version "3.6.0") + (version "3.7.0") (source (origin (method url-fetch) (uri (cran-uri "callr" version)) (sha256 (base32 - "050s7l1ipi6snbj6xnk052l6acycnxjyzv84026adw5x8kki0yz6")))) + "02inaf3c7b0hikii7p2zwaphrq5myv4in92d9jxd1ilmhla5awnn")))) (build-system r-build-system) (propagated-inputs `(("r-r6" ,r-r6) @@ -1004,6 +1341,29 @@ without affecting the current R process at all. This package does exactly that.") (license license:expat))) +(define-public r-depmixs4 + (package + (name "r-depmixs4") + (version "1.5-0") + (source (origin + (method url-fetch) + (uri (cran-uri "depmixS4" version)) + (sha256 + (base32 + "1pacvhw5m4fsk3ysbal50fdqbvlaz8ywyqp6bn1wh42wipqbb2i8")))) + (propagated-inputs + `(("r-nnet" ,r-nnet) + ("r-nlme" ,r-nlme) + ("r-mass" ,r-mass) + ("r-rsolnp" ,r-rsolnp))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/depmixS4/") + (synopsis "Dependent Mixture Models") + (description "This package fits latent (hidden) Markov models on mixed +categorical and continuous (time series) data, otherwise known as dependent +mixture models.") + (license license:gpl2+))) + (define-public r-readxl (package (name "r-readxl") @@ -1031,6 +1391,36 @@ the embedded @code{RapidXML} C++ library.") ;; 'rapidxml' which is Boost. (license (list license:gpl3 license:bsd-2 license:boost1.0)))) +(define-public r-model4you + (package + (name "r-model4you") + (version "0.9-7") + (source (origin + (method url-fetch) + (uri (cran-uri "model4you" version)) + (sha256 + (base32 + "0pni9v3nradvy8sp2m07903vc7z610xrh426lf19dxss12kgrfi8")))) + (build-system r-build-system) + (propagated-inputs + `(("r-formula" ,r-formula) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-partykit" ,r-partykit) + ("r-sandwich" ,r-sandwich) + ("r-survival" ,r-survival))) + (home-page "https://cran.r-project.org/web/packages/model4you/") + (synopsis "Stratified and personalised models based on trees and forests") + (description + "This package provides procedures for model-based trees for subgroup +analyses in clinical trials and model-based forests for the estimation and +prediction of personalised treatment effects. Currently partitioning of linear +models, @code{lm()}, generalised linear models, @code{glm()}, and +Weibull models, @code{survreg()}, are supported. Advanced plotting functionality is +supported for the trees and a test for parameter heterogeneity is provided for +the personalised models.") + (license license:gpl2+))) + (define-public r-modelr (package (name "r-modelr") @@ -1078,26 +1468,46 @@ and make inference with discrete time and discrete space hidden Markov models.") (license license:gpl2+))) +(define-public r-hiddenmarkov + (package + (name "r-hiddenmarkov") + (version "1.8-13") + (source (origin + (method url-fetch) + (uri (cran-uri "HiddenMarkov" version)) + (sha256 + (base32 + "05dm3nl0ffsz2ziw3bz5bivyxk7r5bxs8xhky3hz660qaqzd51ki")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/HiddenMarkov/") + (synopsis "Hidden markov models for R") + (description "This package contains functions for the analysis of Discrete +Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated +Poisson Process. It includes functions for simulation, parameter estimation, +and the Viterbi algorithm. The algorithms are based of those of Walter +Zucchini.") + (license license:gpl2+))) + (define-public r-httpuv (package (name "r-httpuv") - (version "1.5.5") + (version "1.6.3") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 - "05rir03xwamwfq5691vx0x957sgmr4i8iv5vpx5rv1f74y4wkrhb")) + "0xh8y05k4jxdwp9xh4x478y3scnv80q05l9gxk2ni6f0dk43iqxz")) ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv ;; only contains fixes for building on Solaris. (patches (search-patches "r-httpuv-1.5.5-unvendor-libuv.patch")) (modules '((guix build utils))) + ;; Cannot unbundle http-parser, because it contains local + ;; modifications. (snippet - `(begin - (delete-file-recursively "src/libuv") - ;; Cannot unbundle http-parser, because it contains local - ;; modifications. - #t)))) + '(delete-file-recursively "src/libuv")))) (build-system r-build-system) (arguments `(#:phases @@ -1110,13 +1520,12 @@ models.") ;; Fix https://github.com/rstudio/httpuv/issues/282 (substitute* "src/http.cpp" (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);") - "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);")) - #t))))) + "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);"))))))) (inputs - `(("libuv" ,libuv))) + `(("libuv" ,libuv) + ("zlib" ,zlib))) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-later" ,r-later) + `(("r-later" ,r-later) ("r-promises" ,r-promises) ("r-r6" ,r-r6) ("r-rcpp" ,r-rcpp))) @@ -1161,13 +1570,13 @@ in systems and applications.") (define-public r-servr (package (name "r-servr") - (version "0.21") + (version "0.23") (source (origin (method url-fetch) (uri (cran-uri "servr" version)) (sha256 (base32 - "12fk585hmz735v4hra8da9wld1fmd67byqnf95m7jjyh7l3dmh1z")))) + "1f1fgfgjgjsbn2krkbyw2qwkm0k4lq9p9jakg9zwyqlgpkdd34j4")))) (build-system r-build-system) (propagated-inputs `(("r-httpuv" ,r-httpuv) @@ -1182,20 +1591,44 @@ documents that can be converted to HTML files (e.g., R Markdown) under a given directory.") (license license:expat))) +(define-public r-howmany + (package + (name "r-howmany") + (version "0.3-1") + (source (origin + (method url-fetch) + (uri (cran-uri "howmany" version)) + (sha256 + (base32 + "045ck8qahfg2swbgyf7dpl32ryq1m4sbalhr7m5qdgpm62vz8h7f")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/howmany/") + (synopsis "Lower bound for the number of correct rejections") + (description "When testing multiple hypotheses simultaneously, this package +provides functionality to calculate a lower bound for the number of correct +rejections (as a function of the number of rejected hypotheses), which holds +simultaneously -with high probability- for all possible number of rejections. +As a special case, a lower bound for the total number of false null hypotheses +can be inferred. Dependent test statistics can be handled for multiple tests +of associations. For independent test statistics, it is sufficient to provide +a list of p-values.") + (license license:gpl2+))) + (define-public r-htmltools (package (name "r-htmltools") - (version "0.5.1.1") + (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "htmltools" version)) (sha256 (base32 - "1fm4cymz4hz6lds80m9j5q00xy5flkrmfn5dkrn3s3rkzqpyggzh")))) + "1yv74ydyqm28gfhimmr7825sj1iaawpwsnzq05c2ma756q2dbivx")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-digest" ,r-digest) + ("r-fastmap" ,r-fastmap) ("r-rlang" ,r-rlang))) (home-page "https://cran.r-project.org/web/packages/htmltools") (synopsis "R tools for HTML") @@ -1206,13 +1639,13 @@ directory.") (define-public r-htmlwidgets (package (name "r-htmlwidgets") - (version "1.5.3") + (version "1.5.4") (source (origin (method url-fetch) (uri (cran-uri "htmlwidgets" version)) (sha256 (base32 - "0a8g7wqd3qxnhwkm9c9bkzg29db7gvjiaa5y038ln8nch8qq7981")))) + "1hgz8sx8xrvfcdwa4q15k942w4qsqg8lyxbbf7qyfzbi807wcgqs")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) @@ -1231,13 +1664,13 @@ applications.") (define-public r-htmltable (package (name "r-htmltable") - (version "2.1.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "htmlTable" version)) (sha256 - (base32 "1gzh0bdxi55p1ckxv4k0a41b1j0grwv2w3lkqz4c3gkw66dk6ja0")))) + (base32 "05zy9acx4s80dr880q69i4rcjqgmbz18gn7pyazda9gsnm981j96")))) (properties `((upstream-name . "htmlTable"))) (build-system r-build-system) (propagated-inputs @@ -1265,13 +1698,13 @@ LaTeX.") (define-public r-curl (package (name "r-curl") - (version "4.3") + (version "4.3.2") (source (origin (method url-fetch) (uri (cran-uri "curl" version)) (sha256 (base32 - "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl")))) + "0s55022hy8shjm1pzax1dqzrg20bv4nvlwnjnddk3dp89g5zmcch")))) (build-system r-build-system) (arguments `(#:phases @@ -1289,13 +1722,13 @@ LaTeX.") (string-append "\ const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\"); if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); } -" m))) - #t))))) +" m)))))))) (inputs `(("libcurl" ,curl) ("zlib" ,zlib))) (native-inputs - `(("pkg-config" ,pkg-config))) + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) (home-page "https://github.com/jeroenooms/curl") (synopsis "HTTP client for R") (description @@ -1430,19 +1863,19 @@ multi-state models.") (define-public r-jquerylib (package (name "r-jquerylib") - (version "0.1.3") + (version "0.1.4") (source (origin (method url-fetch) (uri (cran-uri "jquerylib" version)) (sha256 (base32 - "1s0d6mws13hwkx07jqmry7vp30a05b2p9w7ir68bmkhasidwkzdq")) + "04a40v4znpj98j7y6009d74a6g9dchj5rr3p08cgz9p3rlfw3g7h")) (snippet '(for-each delete-file - '("inst/lib/jquery-1.12.4.min.js" - "inst/lib/jquery-2.2.4.min.js" - "inst/lib/jquery-3.5.1.min.js"))))) + '("inst/lib/1.12.4/jquery-1.12.4.min.js" + "inst/lib/2.2.4/jquery-2.2.4.min.js" + "inst/lib/3.6.0/jquery-3.6.0.min.js"))))) (properties `((upstream-name . "jquerylib"))) (build-system r-build-system) (arguments @@ -1457,12 +1890,12 @@ multi-state models.") (call-with-values (lambda () (unzip2 - `(("jquery-1.12.4.js" - "jquery-1.12.4.min.js") - ("jquery-2.2.4.js" - "jquery-2.2.4.min.js") - ("jquery-3.5.1.js" - "jquery-3.5.1.min.js")))) + `(("1.12.4/jquery-1.12.4.js" + "1.12.4/jquery-1.12.4.min.js") + ("2.2.4/jquery-2.2.4.js" + "2.2.4/jquery-2.2.4.min.js") + ("3.6.0/jquery-3.6.0.js" + "3.6.0/jquery-3.6.0.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" @@ -1487,19 +1920,18 @@ jQuery.") (define-public r-sass (package (name "r-sass") - (version "0.3.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "sass" version)) (sha256 (base32 - "1cxqwsdyz71mgflqqa65mfr161jlv8q9mshs1y19pxp6pz5wnv0s")))) + "0axw358bbk3vxsqg3wq0bz3xigasa6af8fxvi2ga8hli4cawl1kx")))) (properties `((upstream-name . "sass"))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-fs" ,r-fs) + `(("r-fs" ,r-fs) ("r-htmltools" ,r-htmltools) ("r-r6" ,r-r6) ("r-rappdirs" ,r-rappdirs) @@ -1519,20 +1951,21 @@ language, which is stable, powerful, and CSS compatible.") (define-public r-bslib (package (name "r-bslib") - (version "0.2.4") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "bslib" version)) (sha256 (base32 - "0qlpv2lqr3hjykszmnll7vi4zhmrz4rgcfl0sifxc6cha6jy2nac")) + "0zfjavz5jw4lfbrmc3rgsivcrxq2ia9jwmfbcrdxnxlmyri8qinr")) (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/bs-sass/assets/javascripts/bootstrap.min.js" - "inst/lib/bs/dist/js/bootstrap.bundle.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"))))) (properties `((upstream-name . "bslib"))) (build-system r-build-system) (arguments @@ -1551,10 +1984,12 @@ language, which is stable, powerful, and CSS compatible.") "bs-a11y-p/plugins/js/bootstrap-accessibility.min.js") ("bs-colorpicker/js/bootstrap-colorpicker.js" "bs-colorpicker/js/bootstrap-colorpicker.min.js") - ("bs-sass/assets/javascripts/bootstrap.js" - "bs-sass/assets/javascripts/bootstrap.min.js") - (,(assoc-ref inputs "js-bootstrap-bundle") - "bs/dist/js/bootstrap.bundle.min.js")))) + ("bs3/assets/javascripts/bootstrap.js" + "bs3/assets/javascripts/bootstrap.min.js") + (,(assoc-ref inputs "js-bootstrap4-bundle") + "bs4/dist/js/bootstrap.bundle.min.js") + (,(assoc-ref inputs "js-bootstrap5-bundle") + "bs5/dist/js/bootstrap.bundle.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" @@ -1563,22 +1998,27 @@ language, which is stable, powerful, and CSS compatible.") (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-htmltools" ,r-htmltools) + `(("r-htmltools" ,r-htmltools) ("r-jquerylib" ,r-jquerylib) ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) ("r-rlang" ,r-rlang) ("r-sass" ,r-sass))) (native-inputs `(("esbuild" ,esbuild) - ("js-bootstrap-bundle" + ("js-bootstrap4-bundle" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.6.0/dist/js/bootstrap.bundle.js") + (sha256 + (base32 + "04abvgp923w36qfqkkl2syim3bl119nwxbgials90z1jyb8jgss1")))) + ("js-bootstrap5-bundle" ,(origin (method url-fetch) - (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.5.3/dist/js/bootstrap.bundle.js") + (uri "https://raw.githubusercontent.com/twbs/bootstrap/v5.0.2/dist/js/bootstrap.bundle.js") (sha256 (base32 - "1lcsxj7gcm56va3gck47ggpwzjxrzq27sgjzdw6c54qkp0487sak")))))) + "06vin94nqw1vzs4zrqcms8z9js9fckbj8gwyx07awm8jkjhnqfhl")))))) (home-page "https://rstudio.github.io/bslib/") (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown") (description @@ -1701,7 +2141,7 @@ previewing themes in real time.") ("js-strftime" ,js-strftime) ("js-highlight" ,js-highlight))) (native-inputs - `(("uglify-js" ,uglify-js) + `(("uglifyjs" ,node-uglify-js) ("gfortran" ,gfortran) ("js-bootstrap-accessibility" ,(origin @@ -1768,7 +2208,7 @@ responsive, and powerful applications with minimal effort.") (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) - (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) + (let ((minified (open-pipe* OPEN_READ "uglifyjs" source))) (call-with-output-file target (lambda (port) (dump-port minified port))))) @@ -1783,7 +2223,7 @@ responsive, and powerful applications with minimal effort.") (inputs `(("js-requirejs" ,js-requirejs))) (native-inputs - `(("uglify-js" ,uglify-js) + `(("uglifyjs" ,node-uglify-js) ("js-jquery" ,(origin (method url-fetch) @@ -1821,7 +2261,7 @@ supports interactive trees, to enable rich, editable trees in Shiny.") (lambda _ (with-directory-excursion "inst/AdminLTE" (delete-file "app.min.js") - (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js"))) + (let ((minified (open-pipe* OPEN_READ "uglifyjs" "app.js"))) (call-with-output-file "app.min.js" (lambda (port) (dump-port minified port)))))))))) @@ -1830,7 +2270,7 @@ supports interactive trees, to enable rich, editable trees in Shiny.") ("r-promises" ,r-promises) ("r-shiny" ,r-shiny))) (native-inputs - `(("uglify-js" ,uglify-js))) + `(("uglifyjs" ,node-uglify-js))) (home-page "https://rstudio.github.io/shinydashboard/") (synopsis "Create dashboards with shiny") (description "This package provides an extension to the Shiny web @@ -1898,14 +2338,14 @@ Bootstrap themes, which are packaged for use with Shiny applications.") (define-public r-d3r (package (name "r-d3r") - (version "0.9.1") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "d3r" version)) (sha256 (base32 - "0kc82vvyfxhxvqfalngn36prn3sxdiinsx04rn99ha6zdc27zp5k")))) + "1qijkllfaaw0lb29j8mappm8jz9kg8gkihxq5wqhb4gabsazdwva")))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) @@ -1926,7 +2366,9 @@ Bootstrap themes, which are packaged for use with Shiny applications.") (,(assoc-ref inputs "d3.v5.js") "v5/dist/d3.min.js") (,(assoc-ref inputs "d3.v6.js") - "v6/dist/d3.min.js")))) + "v6/dist/d3.min.js") + (,(assoc-ref inputs "d3.v7.js") + "v7/dist/d3.min.js")))) (lambda (sources targets) (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" @@ -1934,8 +2376,7 @@ Bootstrap themes, which are packaged for use with Shiny applications.") (delete-file target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) - sources targets)))) - #t))))) + sources targets))))))))) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-htmltools" ,r-htmltools) @@ -1970,7 +2411,14 @@ Bootstrap themes, which are packaged for use with Shiny applications.") (uri "https://d3js.org/d3.v6.js") (sha256 (base32 - "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9")))))) + "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9")))) + ("d3.v7.js" + ,(origin + (method url-fetch) + (uri "https://d3js.org/d3.v7.js") + (sha256 + (base32 + "0sd6vavxs8mx5xyb8xahlqghdiczqd284a7d5wravhqnrj0bw097")))))) (home-page "https://github.com/timelyportfolio/d3r") (synopsis "d3.js utilities for R") (description @@ -2260,14 +2708,14 @@ data store designed for maximum speed.") (define-public r-maps (package (name "r-maps") - (version "3.3.0") + (version "3.4.0") (source (origin (method url-fetch) (uri (cran-uri "maps" version)) (sha256 (base32 - "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr")))) + "0ispkx1szgwxhr0zzhdzgqqwcgc6psg7vry4sj4rb89w76rcq63r")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/maps") (synopsis "Draw geographical maps") @@ -2348,14 +2796,14 @@ applications. That is, compute distances and related measures for angular (define-public r-jpeg (package (name "r-jpeg") - (version "0.1-8.1") + (version "0.1-9") (source (origin (method url-fetch) (uri (cran-uri "jpeg" version)) (sha256 (base32 - "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x")))) + "0wihj538wdnr71wdldym83qadb4kh68a6rkallwbh2f25r27b881")))) (build-system r-build-system) (inputs `(("libjpeg" ,libjpeg-turbo))) (home-page "https://www.rforge.net/jpeg/") @@ -2406,20 +2854,18 @@ including functions for geolocation and routing.") (define-public r-haven (package (name "r-haven") - (version "2.3.1") + (version "2.4.3") (source (origin (method url-fetch) (uri (cran-uri "haven" version)) (sha256 (base32 - "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf")) + "0pr9jcdk1r9pi9iz0xm1g5yy5qyjk5r7hh9467abx4kpwx3hzdwm")) (modules '((guix build utils))) (snippet - '(begin - ;; unvendor readstat - (delete-file-recursively "src/readstat") - #t)))) + ;; unvendor readstat + '(delete-file-recursively "src/readstat")))) (build-system r-build-system) (arguments '(#:phases @@ -2428,26 +2874,25 @@ including functions for geolocation and routing.") (lambda _ ;; Not required, since we’re not building readstat. (substitute* "src/Makevars" - (("-lz") "-lreadstat")) - #t))))) + (("-lz") "-lreadstat"))))))) (inputs `(("readstat" ,readstat))) (native-inputs `(("r-knitr" ,r-knitr))) (propagated-inputs - `(("r-forcats" ,r-forcats) + `(("r-cpp11" ,r-cpp11) + ("r-forcats" ,r-forcats) ("r-hms" ,r-hms) - ("r-rcpp" ,r-rcpp) ("r-rlang" ,r-rlang) ("r-readr" ,r-readr) ("r-tibble" ,r-tibble) ("r-tidyselect" ,r-tidyselect) ("r-vctrs" ,r-vctrs))) (home-page "https://haven.tidyverse.org") - (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files") + (synopsis "Import and export SPSS, Stata and SAS files") (description - "This package lets you mport foreign statistical formats into R via the -embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.") + "This package lets you import foreign statistical formats into R via the +@url{https://github.com/WizardMac/ReadStat,ReadStat} C library.") (license license:expat))) (define-public r-amap @@ -2472,14 +2917,14 @@ component analysis (with robust methods, and parallelized functions).") (define-public r-ape (package (name "r-ape") - (version "5.4-1") + (version "5.5") (source (origin (method url-fetch) (uri (cran-uri "ape" version)) (sha256 (base32 - "1r7fwyz30ippcl1ibqiv1xryf44x5crcks5kx19h146ffj76qcgh")))) + "16i9sny7j90zi0k3znfff5lpnj5naxcy1142v73zxslr9g3h3am3")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) @@ -2528,13 +2973,13 @@ XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.") (define-public r-colorspace (package (name "r-colorspace") - (version "2.0-0") + (version "2.0-2") (source (origin (method url-fetch) (uri (cran-uri "colorspace" version)) (sha256 - (base32 "13h1hara0s6xn16bgkrbd0flszah1yiylwfwxwn2inqqk6pm6sjf")))) + (base32 "0fhq2aykdkxh3r90i8aqjyb37p5api3mjd19ch8mzv99q4pcv4dq")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -2620,13 +3065,13 @@ initiative to bring PASSTEC 2000 functionalities to R.") (define-public r-partykit (package (name "r-partykit") - (version "1.2-13") + (version "1.2-15") (source (origin (method url-fetch) (uri (cran-uri "partykit" version)) (sha256 (base32 - "15bfhqvx2y4vclnc3sw4v7ggs70pk57b3qk9aqjfvdrx444d2gd4")))) + "1b73s5l19yicwginqsg5xr7fzb005x372n0wb34kk6jb5x5lbsdj")))) (build-system r-build-system) (propagated-inputs `(("r-formula" ,r-formula) @@ -2666,13 +3111,13 @@ error stream.") (define-public r-pls (package (name "r-pls") - (version "2.7-3") + (version "2.8-0") (source (origin (method url-fetch) (uri (cran-uri "pls" version)) (sha256 - (base32 "0b3ls12w19wc4xkhnsgmb333y9lyzwq3syjc3k8zs1agnw59c7cg")))) + (base32 "1gqq8rcq6p0hs2gfzwfj690rz3pwywmnv8qzcv0wsd6aaqkskwzg")))) (build-system r-build-system) (home-page "https://mevik.net/work/software/pls.html") (synopsis "Partial Least Squares and Principal Component Regression") @@ -2746,20 +3191,19 @@ is configured appropriately so R can use them.") (define-public r-pkgload (package (name "r-pkgload") - (version "1.2.0") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "pkgload" version)) (sha256 (base32 - "185xr79z2vncq62bni7x4qv3p7dxvnfsbdnnglma0a196hz6pj7v")))) + "0yxvik8kij0mqlki46hf6xnbfvmxwk0r2a3zwjpg0fwcd2s835a8")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) ("r-crayon" ,r-crayon) ("r-desc" ,r-desc) - ("r-pkgbuild" ,r-pkgbuild) ("r-rlang" ,r-rlang) ("r-rprojroot" ,r-rprojroot) ("r-rstudioapi" ,r-rstudioapi) @@ -2772,16 +3216,36 @@ attaching it. This is a key part of the @code{devtools} package as it allows you to rapidly iterate while developing a package.") (license license:gpl3))) +(define-public r-pvclust + (package + (name "r-pvclust") + (version "2.2-0") + (source (origin + (method url-fetch) + (uri (cran-uri "pvclust" version)) + (sha256 + (base32 + "0082icm54k2yq60k06qpr92a626k39j2jr0046lva4ylmhxqb4kq")))) + (build-system r-build-system) + (home-page "https://github.com/shimo-lab/pvclust") + (synopsis + "Hierarchical clustering with P-values via multiscale bootstrap resampling") + (description "This package provides an implementation of multiscale bootstrap +resampling for assessing the uncertainty in hierarchical cluster analysis. It +provides an AU (approximately unbiased) P-value as well as a BP (bootstrap probability) +value for each cluster in a dendrogram.") + (license license:gpl2+))) + (define-public r-rcpp (package (name "r-rcpp") - (version "1.0.6") + (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "04ph6lm36cmvz01ng53pvvf3jxvzsn9smyflkfc7l3q0pib4gwn9")))) + (base32 "07fwlgmx0ib4nziqbrylla2dlakw04vzny9w4qbfvnhn49rs9r8m")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ integration") @@ -2817,6 +3281,27 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see safely be interrupted from R.") (license license:expat))) +(define-public r-rcppnumerical + (package + (name "r-rcppnumerical") + (version "0.4-0") + (source (origin + (method url-fetch) + (uri (cran-uri "RcppNumerical" version)) + (sha256 + (base32 + "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen))) + (home-page "https://github.com/yixuan/RcppNumerical") + (synopsis"Numerical computing libraries integration with @code{Rcpp}") + (description "This package provides a collection of libraries for numerical +computing (numerical integration, optimization, etc.) and their integration +with @code{Rcpp}.") + (license license:gpl2+))) + (define-public r-bindr (package (name "r-bindr") @@ -2906,14 +3391,14 @@ on (non-orthogonal) variable vectors in scatterplots and biplots.") (define-public r-shape (package (name "r-shape") - (version "1.4.5") + (version "1.4.6") (source (origin (method url-fetch) (uri (cran-uri "shape" version)) (sha256 (base32 - "17qqhjyfhxv9la07ykaslb50c8g4d0cgfypx4y91h9i2yjw7jjh9")))) + "0yqbrrx2ywmfl99s6d1n6jblc63k1mxbiqyv8y0kq8jws1g3w45r")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/shape") (synopsis "Functions for plotting graphical shapes") @@ -2946,14 +3431,14 @@ validation and filtering on the values, making options invisible or private.") (define-public r-circlize (package (name "r-circlize") - (version "0.4.12") + (version "0.4.13") (source (origin (method url-fetch) (uri (cran-uri "circlize" version)) (sha256 (base32 - "1x2j6a80bb4fly3dm91ias964s1gb1cmzj3lyh69ikwjaam0rdmk")))) + "16rnqlkgzhnm69y70k9fiz8vvwlm5dyng04hlxqvvaxix3wdpfkc")))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace) @@ -3025,14 +3510,14 @@ rows, dropping names) to see if the modified versions are identical.") (define-public r-dendextend (package (name "r-dendextend") - (version "1.14.0") + (version "1.15.1") (source (origin (method url-fetch) (uri (cran-uri "dendextend" version)) (sha256 (base32 - "0n3qg76apgbqbvxv2yp5qwpy6nx03xmmc9mdfyq4dqblqhdld29p")))) + "0zf4w4rc2jj30i3x0m0gnkwidfmn3cvz1wirp20amq4v3n9420md")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -3083,14 +3568,14 @@ use in R. It also provides a simple way for variable interpolation in R.") (define-public r-fastmatch (package (name "r-fastmatch") - (version "1.1-0") + (version "1.1-3") (source (origin (method url-fetch) (uri (cran-uri "fastmatch" version)) (sha256 (base32 - "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90")))) + "0qcq1gwl9pijgp34giyq5y9rk0ly3d7xza2b7r68xx63ifqa1vqx")))) (build-system r-build-system) (home-page "https://www.rforge.net/fastmatch") (synopsis "Fast match function") @@ -3166,6 +3651,25 @@ statistical functions and other utilities to ease their usage.") quantities.") (license license:expat))) +(define-public r-princurve + (package + (name "r-princurve") + (version "2.1.6") + (source (origin + (method url-fetch) + (uri (cran-uri "princurve" version)) + (sha256 + (base32 + "0wzk329bxljkzz57y220lsfckpsn45w348m6dcxh29zbj0ik65h2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/rcannood/princurve") + (synopsis "Fit a principal curve in arbitrary dimension") + (description "This package provides procedures for fitting a principal +curve to a data matrix in arbitrary dimensions.") + (license license:gpl2))) + (define-public r-reshape (package (name "r-reshape") @@ -3247,14 +3751,14 @@ package also provides a C++ API, that works with or without Rcpp.") (define-public r-ggally (package (name "r-ggally") - (version "2.1.1") + (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "GGally" version)) (sha256 (base32 - "0lly659kd43cnz1bmmzqj6dbf4v0nm8dhj8xq2wlv9qbnfhq5r9p")))) + "1r98zgh2grn8330cf26r1c20gl131zm778szvn5wj6q6pwv2yd9h")))) (properties `((upstream-name . "GGally"))) (build-system r-build-system) (inputs @@ -3286,14 +3790,14 @@ plot networks.") (define-public r-proxy (package (name "r-proxy") - (version "0.4-25") + (version "0.4-26") (source (origin (method url-fetch) (uri (cran-uri "proxy" version)) (sha256 (base32 - "1m893djrv6ckadmlx9n5bxfp0ycdh2w63sy6yxfyj1migvc7072f")))) + "0k8sr24mjfvxp12sf1j9228ah3ngy15nqmm0jw14x5s32f1assv7")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/proxy") (synopsis "Distance and similarity measures") @@ -3329,13 +3833,13 @@ print, summary, etc.") (define-public r-laplacesdemon (package (name "r-laplacesdemon") - (version "16.1.4") + (version "16.1.6") (source (origin (method url-fetch) (uri (cran-uri "LaplacesDemon" version)) (sha256 - (base32 "1nv1kx86cg8f2s8q15pzskc0lg94bb250p0fhybrx5sjqv1s2lj1")))) + (base32 "1dsfp65cg06f25zjzd5ib4qyn1alfhbhpgyvpcw5n6bszn13idap")))) (properties `((upstream-name . "LaplacesDemon"))) (build-system r-build-system) (home-page "https://github.com/LaplacesDemonR/LaplacesDemon") @@ -3422,14 +3926,14 @@ quantile mixture from L-moments and trimmed L-moments.") (define-public r-distillery (package (name "r-distillery") - (version "1.2") + (version "1.2-1") (source (origin (method url-fetch) (uri (cran-uri "distillery" version)) (sha256 (base32 - "10nhh9p0hp294pp4aav0y0zsmir2qbn05sf3k52rmzmm36q2kc8y")))) + "1ymmxyamkq0zbz2m4gllln1ihks2hcib6gs0mls92as79srz122b")))) (build-system r-build-system) (home-page "https://ral.ucar.edu/staff/ericg/") (synopsis "Functions for confidence intervals and object information") @@ -3462,14 +3966,14 @@ which should be seen for details.") (define-public r-extremes (package (name "r-extremes") - (version "2.1") + (version "2.1-1") (source (origin (method url-fetch) (uri (cran-uri "extRemes" version)) (sha256 (base32 - "1b69r3mzl6hp3g3rqxyc77m8r40jyq7c2d87q85af7xqkn6hnxid")))) + "00ps7yggp89sx1j0w6c8dk0la3k95rwjv1iz7rdfqy7i46xjf6as")))) (properties `((upstream-name . "extRemes"))) (build-system r-build-system) (propagated-inputs @@ -3531,13 +4035,13 @@ by Li, Brown, Huang, and Bickel") (define-public r-inline (package (name "r-inline") - (version "0.3.17") + (version "0.3.19") (source (origin (method url-fetch) (uri (cran-uri "inline" version)) (sha256 (base32 - "1wslsn60q959yrr27cwanba43qlpfaxzdli46i9dc26lxfr5fa3r")))) + "1mcr9hgq6kkq03n7pkcccxa7vg8jma0q7lfxc5vvkc6snydk1s8f")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/inline") (synopsis "Functions to inline C, C++, Fortran function calls from R") @@ -3551,13 +4055,13 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and (define-public r-inum (package (name "r-inum") - (version "1.0-3") + (version "1.0-4") (source (origin (method url-fetch) (uri (cran-uri "inum" version)) (sha256 (base32 - "1sz11b4vlpskhmq9vvc1jix63a5g7lij6368w8qbnkjmjd97k7i4")))) + "1khkzja8lwn9075864vbyajqina9m588ahf1fsrrajrsqilyzssz")))) (build-system r-build-system) (propagated-inputs `(("r-libcoin" ,r-libcoin))) @@ -3610,14 +4114,14 @@ matrices, a special case of sparse matrices.") (define-public r-bbmle (package (name "r-bbmle") - (version "1.0.23.1") + (version "1.0.24") (source (origin (method url-fetch) (uri (cran-uri "bbmle" version)) (sha256 (base32 - "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0")))) + "1bck8rmink4wsk8pcbnj4d60svxymp29pxbzwj8p9gzsg42c1v81")))) (build-system r-build-system) (propagated-inputs `(("r-bdsmatrix" ,r-bdsmatrix) @@ -3626,6 +4130,8 @@ matrices, a special case of sparse matrices.") ("r-matrix" ,r-matrix) ("r-mvtnorm" ,r-mvtnorm) ("r-numderiv" ,r-numderiv))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/bbmle") (synopsis "Tools for General Maximum Likelihood Estimation") (description @@ -3721,14 +4227,14 @@ functions from LINPACK.") (define-public r-fitdistrplus (package (name "r-fitdistrplus") - (version "1.1-3") + (version "1.1-5") (source (origin (method url-fetch) (uri (cran-uri "fitdistrplus" version)) (sha256 (base32 - "1pjnqx0j26dai2fa4ip56wspmfsrcm9dpmxkg15y9623w5b58vbp")))) + "1p9rvvh05zqb9vzhcyzdh7i8lbmb53nj8nyn0gqcmp7wafg9cd1f")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -3884,20 +4390,47 @@ acceleration scheme. A tutorial style introduction to this package is available in a vignette.") (license license:gpl2+))) +(define-public r-progressr + (package + (name "r-progressr") + (version "0.9.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "progressr" version)) + (sha256 + (base32 "03sk5cv8cywahlszjkd8pfqmhbj6cv0j54d3lassa7h44f20zryg")))) + (properties `((upstream-name . "progressr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest))) + (home-page "https://progressr.futureverse.org") + (synopsis "Inclusive, unifying API for progress updates") + (description + "This package provides a minimal, unifying API for scripts and packages +to report progress updates from anywhere including when using parallel +processing. The package is designed such that the developer can to focus on +what progress should be reported on without having to worry about how to +present it. The end user has full control of how, where, and when to render +these progress updates.") + (license license:gpl3+))) + (define-public r-lava (package (name "r-lava") - (version "1.6.9") + (version "1.6.10") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 - "07difbrz8zmvdyns63958v0zw4hyv48956mcww8zh7064a564k83")))) + "0bi3c1aqwlq7jbz4raz6vga4r264w7lldi0i62xjlbl7hnlgi23s")))) (build-system r-build-system) (propagated-inputs - `(("r-numderiv" ,r-numderiv) + `(("r-future-apply" ,r-future-apply) + ("r-numderiv" ,r-numderiv) + ("r-progressr" ,r-progressr) ("r-squarem" ,r-squarem) ("r-survival" ,r-survival))) (native-inputs @@ -4029,14 +4562,14 @@ dimensioned arrays.") (define-public r-rmysql (package (name "r-rmysql") - (version "0.10.21") + (version "0.10.22") (source (origin (method url-fetch) (uri (cran-uri "RMySQL" version)) (sha256 (base32 - "0cbb5ln9iigl816nzvsls9zil5qlfr8yv2aginapqv6n69nz0srs")))) + "05hiwqakhz11kra24yyxrss8b8n32wg7k39j7hwdnvhh1n96scnl")))) (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (inputs @@ -4056,14 +4589,14 @@ the RMariaDB package.") (define-public r-rpostgresql (package (name "r-rpostgresql") - (version "0.6-2") + (version "0.7") (source (origin (method url-fetch) (uri (cran-uri "RPostgreSQL" version)) (sha256 (base32 - "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088")))) + "1bqfdbs09f65ssc6bx4z3kkmia8ja6qbnijxizw63p0fbcakq2q4")))) (properties `((upstream-name . "RPostgreSQL"))) (build-system r-build-system) (inputs @@ -4215,14 +4748,14 @@ provided.") (define-public r-ipred (package (name "r-ipred") - (version "0.9-11") + (version "0.9-12") (source (origin (method url-fetch) (uri (cran-uri "ipred" version)) (sha256 (base32 - "04hfg27c72v0fz4091w3rgbc2vd7g6yl78y9plvsvh0vjlx8ymmp")))) + "0hsq00382pfd9hzpcgphjxazbxm4zx0k2r6pk6kib56k0ibm7qfn")))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class) @@ -4242,14 +4775,14 @@ problems as well as resampling based estimators of prediction error.") (define-public r-psych (package (name "r-psych") - (version "2.1.3") + (version "2.1.9") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 - "1ibh1ivr280wpmk3qjgm715dk79wx0ikjl9jjjcqs03q6vz4wmdx")))) + "032h33i2qlwsw2iq82nri5y8hs7d593w40aghcvnibpi2wxf0x8l")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) @@ -4297,14 +4830,14 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "0.7.6") + (version "0.7.9") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "1ljcl8mh0yqxw3qxzar482qwbxbcaim1x6y1wm82ws12pfdw0j8n")))) + "1z65qyhkhkyalxhrvpsa7n8pickj9fjs8r4gzdvjp2rpggwramhx")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -4335,17 +4868,18 @@ provides a one-row summary of model-level statistics.") (define-public r-recipes (package (name "r-recipes") - (version "0.1.15") + (version "0.1.16") (source (origin (method url-fetch) (uri (cran-uri "recipes" version)) (sha256 (base32 - "0xif0ak3w90xmfzlxvb5pnzc3scpfl1pyhrjffi3mq4asvsd52l0")))) + "1mayfdbn6q775d4gbdjrrhdbmpsxga57kwh0h7bwv8rk0vmvik23")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) + ("r-ellipsis" ,r-ellipsis) ("r-generics" ,r-generics) ("r-glue" ,r-glue) ("r-gower" ,r-gower) @@ -4428,15 +4962,17 @@ from the data points.") (define-public r-corrplot (package (name "r-corrplot") - (version "0.84") + (version "0.90") (source (origin (method url-fetch) (uri (cran-uri "corrplot" version)) (sha256 (base32 - "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd")))) + "1pfmjqgakf7706l9257lqqnb6kin79gc94xfg7w47x2ijchiz1yr")))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/taiyun/corrplot") (synopsis "Visualization of a correlation matrix") (description @@ -4450,13 +4986,13 @@ color labels, layout, etc.") (define-public r-stringdist (package (name "r-stringdist") - (version "0.9.6.3") + (version "0.9.8") (source (origin (method url-fetch) (uri (cran-uri "stringdist" version)) (sha256 - (base32 "06rzbgw43vzg496xca82pydf3g2rz6iw6h50ai0prbp9hbwrhvfd")))) + (base32 "1fv1hbdlm8qwx57b2aj50mw0say5k48awzavx65mfk67qp6ddk7g")))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/stringdist") (synopsis "Approximate string matching and string distance functions") @@ -4602,14 +5138,14 @@ clustered data.") (define-public r-mitml (package (name "r-mitml") - (version "0.4-1") + (version "0.4-2") (source (origin (method url-fetch) (uri (cran-uri "mitml" version)) (sha256 (base32 - "1bw92fl6xp3yvawh3nbjzs4hp4alpwj6vnv6lsysd74aqndw447c")))) + "0zrmchsk012linw3m5rda6hj8xpxpwzbf4alq0nc1pzvl99aa558")))) (build-system r-build-system) (propagated-inputs `(("r-haven" ,r-haven) @@ -4710,14 +5246,14 @@ programming} (SQP) based solver).") (define-public r-hardyweinberg (package (name "r-hardyweinberg") - (version "1.7.1") + (version "1.7.2") (source (origin (method url-fetch) (uri (cran-uri "HardyWeinberg" version)) (sha256 (base32 - "0afjz818yvaq3akvgpy4irnlpspd2dj71qkrwj81lm9y36ypwlw6")))) + "0g10jh71yp0pcag44z409xqb6d941l7y887a632962bk5rgn6q5p")))) (properties `((upstream-name . "HardyWeinberg"))) (build-system r-build-system) (propagated-inputs @@ -4742,14 +5278,14 @@ acceptance regions, log-ratio plots and Q-Q plots.") (define-public r-sm (package (name "r-sm") - (version "2.2-5.6") + (version "2.2-5.7") (source (origin (method url-fetch) (uri (cran-uri "sm" version)) (sha256 (base32 - "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q")))) + "03z8igsjqr32x407asxvkrbayvm6yhv9xyfs0n8fkmv8zk5a41r6")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "http://www.stats.gla.ac.uk/~adrian/sm/") @@ -4787,14 +5323,14 @@ structure.") (define-public r-vioplot (package (name "r-vioplot") - (version "0.3.6") + (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "vioplot" version)) (sha256 (base32 - "15vmrm9gwdhfg8mnq8rsg7m59kzc9h53cv96am4ds1dkm56w4n6p")))) + "1dmdasp3jldc41233z6r08w3j76vyyp9m3jrj7n4ahk48yd5siq6")))) (build-system r-build-system) (propagated-inputs `(("r-sm" ,r-sm) @@ -4933,6 +5469,44 @@ Friendly and is now the main support package for a new book, \"Discrete Data Analysis with R\" by Michael Friendly and David Meyer (2015).") (license license:gpl2))) +(define-public r-vcfr + (package + (name "r-vcfr") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (cran-uri "vcfR" version)) + (sha256 + (base32 + "0lhxb3ac4fafwik9q3cds46svzf0hyca8k54chw3dpk50c0zz1yx")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-dplyr" ,r-dplyr) + ("r-magrittr" ,r-magrittr) + ("r-memuse" ,r-memuse) + ("r-pinfsc50" ,r-pinfsc50) + ("r-rcpp" ,r-rcpp) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-vegan" ,r-vegan) + ("r-viridislite" ,r-viridislite))) + (home-page "https://github.com/knausb/vcfR") + (synopsis "Manipulate and visualize VCF data") + (description "This package facilitates easy manipulation of variant call +format (VCF) data. Functions are provided to rapidly read from and write to +VCF files. Once VCF data is read into R, a parser function extracts matrices +of data. This information can then be used for quality control or other +purposes. Additional functions provide visualization of genomic data. Once +processing is complete data may be written to a VCF file. It also may be +converted into other popular R objects. This package provides a link between +VCF data and familiar R software.") + (license license:gpl3))) + (define-public r-ica (package (name "r-ica") @@ -5070,14 +5644,14 @@ plots in @code{ggplot2}.") (define-public r-cli (package (name "r-cli") - (version "2.4.0") + (version "3.0.1") (source (origin (method url-fetch) (uri (cran-uri "cli" version)) (sha256 (base32 - "0l1s9yv23bc7mm0hfdlamgz4wjfrisv8aylr65ihjs98jsynrkg3")))) + "1zdld2cr83k4v7yrwa2csvcafwslwr610vk70mv1a3knrnv2b6nq")))) (build-system r-build-system) (propagated-inputs `(("r-glue" ,r-glue))) @@ -5132,13 +5706,13 @@ constants, and control debugging of packages via environment variables.") (define-public r-processx (package (name "r-processx") - (version "3.5.1") + (version "3.5.2") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 - (base32 "1z7zag7g041xlhzhkdfl33y2phc877h1pwj9k69p69b967qi6p6k")))) + (base32 "0azw8sx6nv6pp8m8jrwq01b9na2swrnznn7dwrhn07268w82svzd")))) (build-system r-build-system) (propagated-inputs `(("r-ps" ,r-ps) @@ -5245,21 +5819,19 @@ Markdown documents.") (define-public r-seriation (package (name "r-seriation") - (version "1.2-9") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "seriation" version)) (sha256 (base32 - "1glxn098ar1v96xlwp85kjxzfd1nyfzp2f82x5z3fm87yv57k4lb")))) + "1vl0zfdvxdccvda8lwkjhg5rivj2q5gjm4qvkqwny6asm06x80ny")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) ("r-colorspace" ,r-colorspace) - ("r-dendextend" ,r-dendextend) ("r-gclus" ,r-gclus) - ("r-gplots" ,r-gplots) ("r-mass" ,r-mass) ("r-qap" ,r-qap) ("r-registry" ,r-registry) @@ -5279,13 +5851,13 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.22") + (version "0.26") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 - (base32 "0ix3p0iw2c60whn5mvsflh0vhm4yixhw4s9d9v4023qhp077nw9y")))) + (base32 "1997s00dzkyj15xk9w1r2h6i49srpgqzvhhyvd5pk1kwkd4809ly")))) (build-system r-build-system) ;; knitr itself depends on xfun #; @@ -5301,17 +5873,18 @@ packages maintained by Yihui Xie.") (define-public r-utf8 (package (name "r-utf8") - (version "1.2.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "utf8" version)) (sha256 (base32 - "1yw7vjn3gpkqddc91rbfh4kk0zmn2kp0jycrd3066sissh01jhdk")))) + "1x6qg19z4qih9lk3mvnmx0vailm1khp5lylw4hlwz6rssj3yw6m7")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + `(("r-knitr" ,r-knitr) + ("r-rmarkdown" ,r-rmarkdown))) ; for vignettes (home-page "https://github.com/patperry/r-utf8") (synopsis "Unicode text processing") (description @@ -5344,14 +5917,14 @@ to variables on the left-hand side of the assignment.") (define-public r-vctrs (package (name "r-vctrs") - (version "0.3.7") + (version "0.3.8") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 - "03hyxk3x635xfdn2x707gygdb2xk0cayl1nl44zib9bwqyyb7nas")))) + "1c8v5lmap6iq4jpi7p3w05hsv2dq7rjg057pvnfyc5d1xmsqnkkz")))) (build-system r-build-system) (propagated-inputs `(("r-ellipsis" ,r-ellipsis) @@ -5382,14 +5955,14 @@ to variables on the left-hand side of the assignment.") (define-public r-pillar (package (name "r-pillar") - (version "1.5.1") + (version "1.6.3") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "0wp68cg95895aybi7yjqy0sidvc68lmfqndinpd63dysci9x3r8c")))) + "1ica4zjr3kmcpqh2668nmsv5dbvm4yri5952vcxja4djsgfnry3j")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -5410,6 +5983,25 @@ columns of data using the full range of colours provided by modern terminals.") (license license:gpl3))) +(define-public r-pinfsc50 + (package + (name "r-pinfsc50") + (version "1.2.0") + (source (origin + (method url-fetch) + (uri (cran-uri "pinfsc50" version)) + (sha256 + (base32 + "1547xyxmfb7zi8h9bsm6k67dcw4hpp129xzvmgwfw7r6p4af47zd")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/pinfsc50/") + (synopsis "Genomic data for the plant pathogen Phytophthora infestans") + (description "This package contains genomic data for the plant pathogen +Phytophthora infestans. It includes a variant file, a sequence file and an +annotation file. This package is intended to be used as example data for +packages that work with genomic data.") + (license license:gpl2+))) + (define-public r-uuid (package (name "r-uuid") @@ -5432,14 +6024,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.31") + (version "0.33") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "04a3ncaxix30n9m73slpsn1idxv7j1f7fy3nhxpvkk514x9rgg0p")))) + "10lqn704dqv5k5v6y964l8c77rwy4ilrc1hcb99j4vxpx3p4nd43")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) @@ -5456,14 +6048,14 @@ automatically.") (define-public r-tinytest (package (name "r-tinytest") - (version "1.2.4") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "tinytest" version)) (sha256 (base32 - "1asryjrah3fj39gg0c6yxgpr142j5bg2n990v7q8r0a5pb8gcr45")))) + "1mq31f7bzcz5bkgzl9khm1i80axfzra7gcjqxd2yqb4wrw1m3x4s")))) (properties `((upstream-name . "tinytest"))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/tinytest") @@ -5491,17 +6083,18 @@ features: (define-public r-network (package (name "r-network") - (version "1.16.1") + (version "1.17.1") (source (origin (method url-fetch) (uri (cran-uri "network" version)) (sha256 (base32 - "1cgy7vlbinyndl0zkzvnpcmi240wry6iwfb42sz1mj5c9iwkar7b")))) + "19q563v5xfkbmr0ws9nhqx4wrxkf9jsck51rqc8mm2gq2h03lg7w")))) (build-system r-build-system) (propagated-inputs `(("r-magrittr" ,r-magrittr) + ("r-statnet-common" ,r-statnet-common) ("r-tibble" ,r-tibble))) (home-page "https://statnet.org/") (synopsis "Classes for relational data") @@ -5561,20 +6154,19 @@ vectors.") (define-public r-statnet-common (package (name "r-statnet-common") - (version "4.4.1") + (version "4.5.0") (source (origin (method url-fetch) (uri (cran-uri "statnet.common" version)) (sha256 (base32 - "1z89an46xcl1d7dacj4irhk6pkajdz7v85b2347vczwdf622pksf")))) + "0bw8dwnv568i60xrj6d7gv0hnna1x7rvqaayy5i0827khvdj7nrw")))) (properties `((upstream-name . "statnet.common"))) (build-system r-build-system) (propagated-inputs - `(("r-coda" ,r-coda) - ("r-rle" ,r-rle))) + `(("r-coda" ,r-coda))) (home-page "https://statnet.org") (synopsis "R scripts and utilities used by the Statnet software") (description "This package provides non-statistical utilities used by the @@ -5958,14 +6550,14 @@ applied econometric analysis.") (define-public r-cubature (package (name "r-cubature") - (version "2.0.4.1") + (version "2.0.4.2") (source (origin (method url-fetch) (uri (cran-uri "cubature" version)) (sha256 (base32 - "006la36gxdikvmdnq4ny7ik7r30id4z3b3fqsl57dpqwkpsbsgrq")))) + "0kk9lw3s66h0sayza3in8rdj7bmgqn4v5lfckhslarpvj2fxsnv0")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) @@ -6081,14 +6673,14 @@ creation and manipulation of WAVE audio files.") (define-public r-np (package (name "r-np") - (version "0.60-10") + (version "0.60-11") (source (origin (method url-fetch) (uri (cran-uri "np" version)) (sha256 (base32 - "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2")))) + "1a9kzn37cddwfdki5zjmzanxp75pccdjnsvqfrh84hhcsy51pcx3")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) @@ -6155,6 +6747,30 @@ fixed values. Other functions include a custom @code{geom}, and helper functions to enforce symmetric scales or add tags to facetted plots.") (license license:gpl3))) +(define-public r-heatmap3 + (package + (name "r-heatmap3") + (version "1.1.9") + (source + (origin + (method url-fetch) + (uri (cran-uri "heatmap3" version)) + (sha256 + (base32 + "0sfvizmmwfk1bjhn6zfx5a4qqfgj1ldg8x90b65crqibgfa36k2r")))) + (build-system r-build-system) + (propagated-inputs + `(("r-fastcluster" ,r-fastcluster))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/web/packages/heatmap3/") + (synopsis "Improved heatmap package") + (description + "This package provides an improved heatmap package. It is completely +compatible with the original R function @code{heatmap}, and provides more +powerful and convenient features.") + (license license:gpl2+))) + (define-public r-heatmaply (package (name "r-heatmaply") @@ -6436,14 +7052,14 @@ and within plot factors interact.") (define-public r-signal (package (name "r-signal") - (version "0.7-6") + (version "0.7-7") (source (origin (method url-fetch) (uri (cran-uri "signal" version)) (sha256 (base32 - "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b")))) + "0qaf39vfmhn3d0bdjqd805ayfkaj48dkmf5dqd47bpk7dp21b837")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass))) (native-inputs `(("gfortran" ,gfortran))) @@ -6562,14 +7178,14 @@ specific S3-method.") (define-public r-vim (package (name "r-vim") - (version "6.1.0") + (version "6.1.1") (source (origin (method url-fetch) (uri (cran-uri "VIM" version)) (sha256 (base32 - "1a8aw0ysaf0al95m2la2zx1p3g5mnwqx0x30br1s1dqqkfnv57hz")))) + "0fbpm6y3hhiw8srnbc38k19b859jcqzsh78ib8yvj86gck5av0bm")))) (properties `((upstream-name . "VIM"))) (build-system r-build-system) (propagated-inputs @@ -6726,14 +7342,14 @@ evaluated by the @dfn{Akaike Information Criterion} (AIC).") (define-public r-arules (package (name "r-arules") - (version "1.6-7") + (version "1.6-8") (source (origin (method url-fetch) (uri (cran-uri "arules" version)) (sha256 (base32 - "0m80kndfbannw8h53nqdd5wl8h33q2z259aa1cp1nwadaxf9fc1q")))) + "1gy6wrys1qqik65dyr325hdbfmd3fx9a2lzdnrr29g751hprjx2l")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -6749,14 +7365,14 @@ and Eclat.") (define-public r-parsedate (package (name "r-parsedate") - (version "1.2.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "parsedate" version)) (sha256 (base32 - "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr")))) + "05l6f1n3dsm383w7jfg3j38klvmzzfvc7qi9zr5ij13rljj8s1vb")))) (build-system r-build-system) (propagated-inputs `(("r-rematch2" ,r-rematch2))) @@ -6823,14 +7439,14 @@ misclassification probabilities of different models.") (define-public r-zip (package (name "r-zip") - (version "2.1.1") + (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "zip" version)) (sha256 (base32 - "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i")))) + "1n5ryjdj3i16b4mdp29wapgaklz3yzas5k8ffx7q6fa0jry9i5cz")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/zip") (synopsis "Cross-platform Zip compression") @@ -6843,14 +7459,14 @@ additional external tools on any platform.") (define-public r-openxlsx (package (name "r-openxlsx") - (version "4.2.3") + (version "4.2.4") (source (origin (method url-fetch) (uri (cran-uri "openxlsx" version)) (sha256 (base32 - "0vz4nlrwgsiifrgza8kfd9i1c0ya6plymrgk59vyy2z54vc8kvyd")))) + "0vn8ifxb7ccip6b1ijf5lpa6c0n5y5ll8fbabybsb8nfc0y1nmxg")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) @@ -6871,14 +7487,14 @@ dependency on Java.") (define-public r-rio (package (name "r-rio") - (version "0.5.26") + (version "0.5.27") (source (origin (method url-fetch) (uri (cran-uri "rio" version)) (sha256 (base32 - "1k6zxjb2bb0z6rv7zmkbaz85cbvs84mj602ikkwk60alh8kpdw2d")))) + "02nxwg1d2m1h09a6ismhcp71gmq1c8rhbbl98if2v7xsvdn63sz0")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) @@ -6907,14 +7523,14 @@ simple method for converting between file types.") (define-public r-maptools (package (name "r-maptools") - (version "1.1-1") + (version "1.1-2") (source (origin (method url-fetch) (uri (cran-uri "maptools" version)) (sha256 (base32 - "0pn4gwh2rl6pfh2vbc7ln86kzlg22cfpd02z95j7zpjidz2mva8l")))) + "0fa4a43zax8gn3jdp4ngqav61x4g6l33bg9wzqbngkbjhipck59r")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) @@ -6935,18 +7551,17 @@ exchanging spatial objects with other R packages.") (define-public r-later (package (name "r-later") - (version "1.1.0.1") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "later" version)) (sha256 (base32 - "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki")))) + "0acqg29hcm2iq1418b54np7zb5pnr3xzrwc3ijv2pz9wra10ix88")))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-rcpp" ,r-rcpp) + `(("r-rcpp" ,r-rcpp) ("r-rlang" ,r-rlang))) (native-inputs `(("r-knitr" ,r-knitr))) @@ -7061,22 +7676,20 @@ it.") (define-public r-rgexf (package (name "r-rgexf") - (version "0.16.0") + (version "0.16.2") (source (origin (method url-fetch) (uri (cran-uri "rgexf" version)) (sha256 (base32 - "1vj5ha1qx0xzflchxf25ycys6clfn9y32m1717afzkvhmkwisrra")) + "00c2zka1n3k7p1l0mlchr063s6x58p9r3fb64d4wgl4rvsq55q3f")) + ;; Delete minified JavaScript files (snippet - '(begin - ;; Delete minified JavaScript files - (for-each delete-file - '("inst/gexf-js/js/jquery-2.0.2.min.js" - "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js" - "inst/gexf-js/js/jquery.mousewheel.min.js")) - #true)))) + '(for-each delete-file + '("inst/gexf-js/js/jquery-2.0.2.min.js" + "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js" + "inst/gexf-js/js/jquery.mousewheel.min.js"))))) (properties `((upstream-name . "rgexf"))) (build-system r-build-system) (arguments @@ -7105,8 +7718,7 @@ it.") source target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) - sources targets)))) - #t))))) + sources targets))))))))) (propagated-inputs `(("r-igraph" ,r-igraph) ("r-servr" ,r-servr) @@ -7176,6 +7788,41 @@ data.frame and more. This is useful for decision trees, machine learning, finance, conversion from and to JSON, and many other applications.") (license license:gpl2+))) +(define-public r-dtplyr + (package + (name "r-dtplyr") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "dtplyr" version)) + (sha256 + (base32 + "0cn7vxn92dcxrnabccla6ppf5x7pxfz6pjlmamp0imfphmr1ns4r")))) + (properties `((upstream-name . "dtplyr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-crayon" ,r-crayon) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-ellipsis" ,r-ellipsis) + ("r-glue" ,r-glue) + ("r-lifecycle" ,r-lifecycle) + ("r-rlang" ,r-rlang) + ("r-tibble" ,r-tibble) + ("r-tidyselect" ,r-tidyselect) + ("r-vctrs" ,r-vctrs))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/tidyverse/dtplyr") + (synopsis "Data Table back-end for dplyr") + (description + "This package provides a @code{data.table} backend for @code{dplyr}. The +goal of @code{dtplyr} is to allow you to write @code{dplyr} code that is +automatically translated to the equivalent, but usually much faster, +@code{data.table} code.") + (license license:expat))) + (define-public r-collapsibletree (package (name "r-collapsibletree") @@ -7251,14 +7898,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (define-public r-rastervis (package (name "r-rastervis") - (version "0.50.1") + (version "0.50.3") (source (origin (method url-fetch) (uri (cran-uri "rasterVis" version)) (sha256 (base32 - "1fkmyllydnmk3j2cmgf86r91wyxf2kh573x8bkck7wgkfniw4h7w")))) + "10njks2kwyh5rp2b6sf2hffxzzwwhskb8m98l73p8yrvsdri1gyj")))) (properties `((upstream-name . "rasterVis"))) (build-system r-build-system) (propagated-inputs @@ -7310,14 +7957,14 @@ those searches and pull data into their R sessions.") (define-public r-renv (package (name "r-renv") - (version "0.13.2") + (version "0.14.0") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 - "0jlsf6vfvqhr4i35xy3xf1ixkfillivzy3wbpl6ca9vyjpnhiwj1")))) + "194hcxikdnna526bvyz9y60ccmmm9fib5g0w9dqivrg0fld23lyh")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (native-inputs @@ -7402,24 +8049,49 @@ weak stationarity, column means by group, weighted biplots, and a heuristic to obtain a better initial configuration in non-metric MDS.") (license license:gpl2))) +(define-public r-here + (package + (name "r-here") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "here" version)) + (sha256 + (base32 "0srlr8h8qmr0wrmp7gs4g2ry5dni2hx8n947bik3s3a26f091v88")))) + (properties `((upstream-name . "here"))) + (build-system r-build-system) + (propagated-inputs `(("r-rprojroot" ,r-rprojroot))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://here.r-lib.org/") + (synopsis "Simpler way to find files") + (description + "This package lets you construct paths to your project's files. Use the +@code{here} function as a drop-in replacement for @code{file.path}, it will +always locate the files relative to your project root.") + (license license:expat))) + (define-public r-reticulate (package (name "r-reticulate") - (version "1.18") + (version "1.22") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "04w5c9jfxakb4rr2qjynxgagb42khsja3y4dwgxywiplb1d8agxk")))) + "0v7m2pv94lfqiw8rhz3c9g66vvz4qvih4vd29rhfk2phmcwpnvmh")))) (build-system r-build-system) (inputs `(("python" ,python))) (propagated-inputs - `(("r-rappdirs" ,r-rappdirs) + `(("r-here" ,r-here) ("r-jsonlite" ,r-jsonlite) ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp))) + ("r-png" ,r-png) + ("r-rappdirs" ,r-rappdirs) + ("r-rcpp" ,r-rcpp) + ("r-withr" ,r-withr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/rstudio/reticulate") @@ -7500,14 +8172,14 @@ movies, and TV shows.") (define-public r-ggsignif (package (name "r-ggsignif") - (version "0.6.1") + (version "0.6.3") (source (origin (method url-fetch) (uri (cran-uri "ggsignif" version)) (sha256 (base32 - "0rjy9wqsq67jjm1jz3j7hm599x0rshrrhw2w01iaqb9kf506hvjh")))) + "1ad774c7s7y4i00xd89lfigr9aybl94q98ch598k3rchanr4b1fa")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -7721,14 +8393,14 @@ steps and provides ggplot2-based elegant data visualization.") (define-public r-fansi (package (name "r-fansi") - (version "0.4.2") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "fansi" version)) (sha256 (base32 - "0i7wmaflkjzdbggqv31wnsj3m9imvc6db429vyjk64xrz1ng1vd2")))) + "0kx5kjhr8dvqz1mq1zkijkgp29jv8b0irm1xplx1d74n2v1zh6wx")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes @@ -7763,14 +8435,14 @@ results to the user.") (define-public r-hdf5r (package (name "r-hdf5r") - (version "1.3.3") + (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "hdf5r" version)) (sha256 (base32 - "0i8m4yjxggrs05slq2afvz2ckl1yc9wq7gd1s7dq2gjn46zkry50")))) + "0lxbdw1xf5yp82fkdj4wzp5mslay3qxd65459vh09dj131h5gl34")))) (build-system r-build-system) (inputs `(("hdf5" ,hdf5) @@ -7855,14 +8527,14 @@ functions.") (define-public r-rjags (package (name "r-rjags") - (version "4-10") + (version "4-11") (source (origin (method url-fetch) (uri (cran-uri "rjags" version)) (sha256 (base32 - "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx")))) + "0vs86jji4h26y8aczy8r08jiq7ax0idlrm87mmvaa5sxlqmqa705")))) (build-system r-build-system) (propagated-inputs `(("r-coda" ,r-coda))) @@ -7881,14 +8553,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rbibutils (package (name "r-rbibutils") - (version "2.1") + (version "2.2.3") (source (origin (method url-fetch) (uri (cran-uri "rbibutils" version)) (sha256 (base32 - "13phw0dk3p3s1z45ff7dbqnn27zws1209mp3d4763zh7xnsdsl44")))) + "1rzc2icik26qlnrbq58c24lc9m0grl83p0hyr70whallqfipa174")))) (properties `((upstream-name . "rbibutils"))) (build-system r-build-system) (home-page "https://geobosh.github.io/rbibutils/") @@ -7903,14 +8575,14 @@ implemented in bibutils.") (define-public r-rdpack (package (name "r-rdpack") - (version "2.1.1") + (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "Rdpack" version)) (sha256 (base32 - "11psw5yiamq0g7jc6fqn2wis565i60qgda4a5d09qi8fyzd6mnfb")))) + "0s51c5fw1ka75b8cxk5bh27h6wcy5169yl93sjlxji2k27n9fj3i")))) (properties `((upstream-name . "Rdpack"))) (build-system r-build-system) (propagated-inputs @@ -7929,14 +8601,14 @@ references and Rd files.") (define-public r-officer (package (name "r-officer") - (version "0.3.18") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 - "1j3bv4j8x5ijj0j447vpdsk4p8pl3ncwdwnns6n3plfrqgsf3vsg")))) + "1za3vb1wmsianh9ygm6h5lyf796rni6w2adplz4z6z93r3mz4cmv")))) (build-system r-build-system) (propagated-inputs `(("r-r6" ,r-r6) @@ -7984,14 +8656,14 @@ on the methods that are implemented can be found in Kosmidis (2008) (define-public r-brglm (package (name "r-brglm") - (version "0.7.1") + (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "brglm" version)) (sha256 (base32 - "1v68ma1agwhxar76mfvdfkcnd5h4gmxiz8j491rhdsckg271j7sa")))) + "08shcz0j1npdn7xkhsvlzs3z4rdwq3g4rk6a4xx8wirqw8n8s2an")))) (properties `((upstream-name . "brglm"))) (build-system r-build-system) (propagated-inputs @@ -8015,14 +8687,14 @@ reduced-bias estimates.") (define-public r-entropy (package (name "r-entropy") - (version "1.2.1") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "entropy" version)) (sha256 (base32 - "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd")))) + "0fhhsy8ci9c73xwr2b167dfix0b7kqsk6kf46qqv1lmvbv11vxqa")))) (properties `((upstream-name . "entropy"))) (build-system r-build-system) (home-page "https://www.strimmerlab.org/software/entropy/") @@ -8037,41 +8709,6 @@ mutual information, and chi-squared statistic of independence. In addition there are functions for discretizing continuous random variables.") (license license:gpl3+))) -(define-public r-abn - (package - (name "r-abn") - (version "2.3-0") - (source - (origin - (method url-fetch) - (uri (cran-uri "abn" version)) - (sha256 - (base32 - "17vdrqm6qp5aijg00ah2imj3pqr6cl5r43hgg8dijbrbhznarci6")))) - (build-system r-build-system) - (inputs - `(("gsl" ,gsl))) - (propagated-inputs - `(("r-lme4" ,r-lme4) - ("r-nnet" ,r-nnet) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rjags" ,r-rjags))) - (home-page "https://r-bayesian-networks.org/") - (synopsis "Modelling multivariate data with additive bayesian networks") - (description - "Bayesian network analysis is a form of probabilistic graphical models -which derives from empirical data a directed acyclic graph, DAG, describing -the dependency structure between random variables. An additive Bayesian -network model consists of a form of a DAG where each node comprises a -@dfn{generalized linear model} (GLM). Additive Bayesian network models are -equivalent to Bayesian multivariate regression using graphical modelling, they -generalises the usual multivariable regression, GLM, to multiple dependent -variables. This package provides routines to help determine optimal Bayesian -network models for a given data set, where these models are used to identify -statistical dependencies in messy, complex data.") - (license license:gpl2+))) - (define-public r-acd (package (name "r-acd") @@ -8123,14 +8760,14 @@ and tests them.") (define-public r-overlap (package (name "r-overlap") - (version "0.3.3") + (version "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "overlap" version)) (sha256 (base32 - "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd")))) + "1arxprhz035ab78ks88n6scwnlwmnb97mlac5gsx90ipb6gkgcyk")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/overlap/") (synopsis "Estimates of coefficient of overlapping for animal activity patterns") @@ -8190,14 +8827,14 @@ other add-on packages.") (define-public r-insight (package (name "r-insight") - (version "0.13.2") + (version "0.14.4") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "03b7kd17h25mi1si40ibcp3jpasyqpj51mr8js0ywywyfw7909j1")))) + "0h63nr337zbczbj9izyb7g5dlzwail5w70hbbn45paq6vybkqks3")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -8218,14 +8855,14 @@ information are missing.") (define-public r-sjlabelled (package (name "r-sjlabelled") - (version "1.1.7") + (version "1.1.8") (source (origin (method url-fetch) (uri (cran-uri "sjlabelled" version)) (sha256 (base32 - "0d3fsjd2gxchv8mlx9l5pf8xvkmx4pgvizam83f3qss07bmvpzwg")))) + "17gskxr43rgbg7syla3b78g2qgksq2kj07iad4139xycqxblxya0")))) (build-system r-build-system) (propagated-inputs `(("r-insight" ,r-insight))) @@ -8244,14 +8881,14 @@ vice versa), or to deal with multiple declared missing values.") (define-public r-sjmisc (package (name "r-sjmisc") - (version "2.8.6") + (version "2.8.7") (source (origin (method url-fetch) (uri (cran-uri "sjmisc" version)) (sha256 (base32 - "1nfrkv5jfnwb85blpv7yk7xac1myzi2c30bqcf7xicniknkjwycr")))) + "17hcjb2j690qi2zrkwc14sr1wsid6dy6v7bfsf0bc94ql812k8g2")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -8326,14 +8963,14 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.6.4") + (version "0.6.8") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "1ykjfnqhn8nd9f3l4jj8hf1bbjjckkna3p7fdsg0a73c05a17yma")))) + "1b4hyrarxbk4d1ma5gy162b13nm5r5ysi049bxgcfim50rh40igs")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -8361,14 +8998,14 @@ documents.") (define-public r-writexl (package (name "r-writexl") - (version "1.3.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "writexl" version)) (sha256 (base32 - "1njdhvh8605wd2j8glrbxfyc36p2n88prpq080jn44s9lgfmbgsb")))) + "0mfzyn8n5x5x5gf382bqgq61zpw9dymrp5kzdm2sbszplmxf6xry")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (home-page "https://github.com/ropensci/writexl") @@ -8478,14 +9115,14 @@ matches version and feature constraints.") (define-public r-argparse (package (name "r-argparse") - (version "2.0.3") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "argparse" version)) (sha256 (base32 - "1c2r417m1dxk1jhcggv3g4zax5a59k9rqs9jcs6xy2pa2333jqfj")))) + "1k6v35g3bppcr896h4v39zh1sxxia1bxxh29xv0mhad1nvmv25j9")))) (build-system r-build-system) (inputs `(("python" ,python))) (propagated-inputs @@ -8574,24 +9211,26 @@ the work.") (define-public r-doby (package (name "r-doby") - (version "4.6.9") + (version "4.6.11") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 - "02f545md5yhbpp3wb3q2c8zabqwgf02555r5c6g7znab5zjbyr00")))) + "1xhjh2d7zfgw8wbcj5yfscvmwbjar1w544ika13da69dydm44j81")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) + ("r-curry" ,r-curry) ("r-deriv" ,r-deriv) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-magrittr" ,r-magrittr) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) + ("r-microbenchmark" ,r-microbenchmark) ("r-pbkrtest" ,r-pbkrtest) ("r-tibble" ,r-tibble))) (native-inputs @@ -8684,14 +9323,14 @@ containing one or more SNPs that evolved under directional selection.") (define-public r-proc (package (name "r-proc") - (version "1.17.0.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (cran-uri "pROC" version)) (sha256 (base32 - "1gd6a47d6bcfd237s3g7r9rws8x2sg7zrvq5k6clpc41zdpp4712")))) + "1abvbzdss12n64pp9vlgnn0q3abh0nj4n0a8cinwwvhphjrm9vym")))) (properties `((upstream-name . "pROC"))) (build-system r-build-system) (propagated-inputs @@ -8709,14 +9348,14 @@ bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.") (define-public r-rootsolve (package (name "r-rootsolve") - (version "1.8.2.1") + (version "1.8.2.2") (source (origin (method url-fetch) (uri (cran-uri "rootSolve" version)) (sha256 (base32 - "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128")))) + "1p7nh09g2815vqpvi6c5vvjshkwjn00nx5d3gdyjs304q5312q0a")))) (properties `((upstream-name . "rootSolve"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -8785,13 +9424,13 @@ based on index arrays and simple triplet representations, respectively.") (define-public r-manipulatewidget (package (name "r-manipulatewidget") - (version "0.10.1") + (version "0.11.0") (source (origin (method url-fetch) (uri (cran-uri "manipulateWidget" version)) (sha256 - (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx")))) + (base32 "0iysgl6ab8fvg1xxdx6hr3swqwbkfqzjkk4x5sbvmawbl2a395gj")))) (properties `((upstream-name . "manipulateWidget"))) (build-system r-build-system) @@ -8803,7 +9442,10 @@ based on index arrays and simple triplet representations, respectively.") ("r-knitr" ,r-knitr) ("r-miniui" ,r-miniui) ("r-shiny" ,r-shiny) + ("r-shinyjs" ,r-shinyjs) ("r-webshot" ,r-webshot))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/") (synopsis "Add even more interactivity to interactive charts") (description @@ -8855,6 +9497,144 @@ and make comparisons between different methodologies straightforward.") several entropy estimators.") (license license:gpl3+))) +(define-public r-nsprcomp + (package + (name "r-nsprcomp") + (version "0.5.1-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "nsprcomp" version)) + (sha256 + (base32 + "1zlc1ximx96f235c0l8qfs6vbp1kpnbf943wxsfahnnlnxvwi59f")))) + (properties `((upstream-name . "nsprcomp"))) + (build-system r-build-system) + (home-page "https://sigg-iten.ch/research/") + (synopsis "Non-negative and sparse PCA") + (description + "This package implements two methods for performing a constrained +principal component analysis (PCA), where non-negativity and/or sparsity +constraints are enforced on the principal axes (PAs). The function +@code{nsprcomp} computes one principal component (PC) after the other. Each +PA is optimized such that the corresponding PC has maximum additional variance +not explained by the previous components. In contrast, the function +@code{nscumcomp} jointly computes all PCs such that the cumulative variance is +maximal. Both functions have the same interface as the @code{prcomp} function +from the @code{stats} package (plus some extra parameters).") + (license license:gpl2+))) + +(define-public r-cmplot + (package + (name "r-cmplot") + (version "3.6.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "CMplot" version)) + (sha256 + (base32 + "13y05j5gsdc712fn7yvcz5nx2pbcdvl201hfb6jzpvl86qx2l0j1")))) + (properties `((upstream-name . "CMplot"))) + (build-system r-build-system) + (home-page "https://github.com/YinLiLin/CMplot") + (synopsis "Circle Manhattan plot") + (description + "Circle Manhattan Plot is an R package that can lay out genome-wide +association study P-value results in both traditional rectangular patterns, +QQ-plot and novel circular ones. United in only one bull's eye style plot, +association results from multiple traits can be compared interactively, +thereby to reveal both similarities and differences between signals. +Additional functions include: highlight signals, a group of SNPs, chromosome +visualization and candidate genes around SNPs.") + (license license:gpl2+))) + +(define-public r-precrec + (package + (name "r-precrec") + (version "0.12.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "precrec" version)) + (sha256 + (base32 + "0vwzaqnh9ymrm52dd79bihwqprnygz0d71ay8fv51hdw0zg6saya")))) + (properties `((upstream-name . "precrec"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-data-table" ,r-data-table) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-rcpp" ,r-rcpp) + ("r-withr" ,r-withr))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://evalclass.github.io/precrec/") + (synopsis "Calculate accurate precision-recall and ROC curves") + (description + "This package provides tools for accurate calculations and visualization +of precision-recall and ROC (Receiver Operator Characteristics) curves.") + (license license:gpl3))) + +(define-public r-netrep + (package + (name "r-netrep") + (version "1.2.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "NetRep" version)) + (sha256 + (base32 + "1swlb2k9bc7whvslxbklz864j9ynvna73hvq5rhv61cv5vy05ksd")))) + (properties `((upstream-name . "NetRep"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-bh" ,r-bh) + ("r-foreach" ,r-foreach) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rhpcblasctl" ,r-rhpcblasctl) + ("r-statmod" ,r-statmod))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/package=NetRep") + (synopsis "Permutation testing network module preservation across datasets") + (description + "This package provides functions for assessing the +replication/preservation of a network module's topology across datasets +through permutation testing.") + (license license:gpl2))) + +(define-public r-intergraph + (package + (name "r-intergraph") + (version "2.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "intergraph" version)) + (sha256 + (base32 + "18a7xgb2rp0w9jl2rkh8nzyjprrs5w7h2iidvc8c38bzx3qpggkc")))) + (properties `((upstream-name . "intergraph"))) + (build-system r-build-system) + (propagated-inputs + `(("r-igraph" ,r-igraph) + ("r-network" ,r-network))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "http://mbojan.github.io/intergraph") + (synopsis "Coercion routines for network data objects") + (description + "Functions implemented in this package allow to coerce (i.e. convert) +network data between classes provided by other R packages. Currently +supported classes are those defined in packages @code{network} and +@code{igraph}.") + (license license:gpl3))) + (define-public r-abcoptim (package (name "r-abcoptim") @@ -8982,6 +9762,233 @@ and coverage methods to tune the choice of threshold.") @end enumerate") (license license:gpl3))) +(define-public r-ggnetwork + (package + (name "r-ggnetwork") + (version "0.5.10") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggnetwork" version)) + (sha256 + (base32 + "0gqdgy5yh700dg0f7xb80hczlnqfisn8l55j7amd1n7fp2x5sr8v")))) + (properties `((upstream-name . "ggnetwork"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-igraph" ,r-igraph) + ("r-network" ,r-network) + ("r-sna" ,r-sna))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/briatte/ggnetwork") + (synopsis "Geometries to plot networks with ggplot2") + (description + "This package provides geometries to plot network objects with the +ggplot2 package.") + (license license:gpl3))) + +(define-public r-cvauc + (package + (name "r-cvauc") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "cvAUC" version)) + (sha256 + (base32 + "13bk97l5nn97h85iz93zxazhr63n21nwyrpnl856as9qp59yvn64")))) + (properties `((upstream-name . "cvAUC"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-rocr" ,r-rocr))) + (home-page "https://github.com/ledell/cvAUC") + (synopsis "Cross-validated area under the ROC curve confidence intervals") + (description + "This package contains various tools for working with and evaluating +cross-validated area under the ROC curve (AUC) estimators. The primary +functions of the package are @code{ci.cvAUC} and @code{ci.pooled.cvAUC}, which +report cross-validated AUC and compute confidence intervals for +cross-validated AUC estimates based on influence curves for i.i.d. and pooled +repeated measures data, respectively.") + (license license:asl2.0))) + +(define-public r-gam + (package + (name "r-gam") + (version "1.20") + (source + (origin + (method url-fetch) + (uri (cran-uri "gam" version)) + (sha256 + (base32 + "1zhy2fp7pxac8xp3z3hndhprj4s5gx3305b627vc78bal1ml3swi")))) + (properties `((upstream-name . "gam"))) + (build-system r-build-system) + (propagated-inputs + `(("r-foreach" ,r-foreach))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/package=gam") + (synopsis "Generalized additive models") + (description + "This package provides functions for fitting and working with generalized +additive models, as described in chapter 7 of \"Statistical Models in +S\" (Chambers and Hastie (eds), 1991), and \"Generalized Additive +Models\" (Hastie and Tibshirani, 1990).") + (license license:gpl2))) + +(define-public r-superlearner + (package + (name "r-superlearner") + (version "2.0-28") + (source + (origin + (method url-fetch) + (uri (cran-uri "SuperLearner" version)) + (sha256 + (base32 + "00any24msgflyagy87nznpfjz5g9v15frqda6c679wa8plx26hjz")))) + (properties `((upstream-name . "SuperLearner"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cvauc" ,r-cvauc) + ("r-gam" ,r-gam) + ("r-nnls" ,r-nnls))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/ecpolley/SuperLearner") + (synopsis "Super learner prediction") + (description + "This package implements the super learner prediction method and contains +a library of prediction algorithms to be used in the super learner.") + (license license:gpl3))) + +(define-public r-drtmle + (package + (name "r-drtmle") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "drtmle" version)) + (sha256 + (base32 + "08a6k0nrg6mqdslwjc71583x52vnax87nbfalk98zczwvrrdwvxa")))) + (properties `((upstream-name . "drtmle"))) + (build-system r-build-system) + (propagated-inputs + `(("r-future-apply" ,r-future-apply) + ("r-np" ,r-np) + ("r-superlearner" ,r-superlearner))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/benkeser/drtmle") + (synopsis "Doubly-robust nonparametric estimation and inference") + (description + "This package implements targeted minimum loss-based estimators of +counterfactual means and causal effects that are doubly-robust with respect +both to consistency and asymptotic normality.") + (license license:expat))) + +(define-public r-dofuture + (package + (name "r-dofuture") + (version "0.12.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "doFuture" version)) + (sha256 + (base32 + "1hqzdlgcrc5l6xjwdylsc9iiysi2wx8k1j1vmw3wryj26057c9y4")))) + (properties `((upstream-name . "doFuture"))) + (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) + (propagated-inputs + `(("r-foreach" ,r-foreach) + ("r-future" ,r-future) + ("r-globals" ,r-globals) + ("r-iterators" ,r-iterators))) + (native-inputs + `(("r-r-rsp" ,r-r-rsp))) ; vignette builder + (home-page "https://github.com/HenrikBengtsson/doFuture") + (synopsis "Foreach parallel adapter using the future API") + (description + "This package provides a @code{%dopar%} adapter such that any type of +futures can be used as backends for the @code{foreach} framework.") + (license license:lgpl2.1+))) + +(define-public r-superheat + (package + (name "r-superheat") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "superheat" version)) + (sha256 + (base32 + "01v8s6px1k5fajlm6py3ksr1i853kwwlky1yryzhy3p1cxhwgg83")))) + (properties `((upstream-name . "superheat"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-ggdendro" ,r-ggdendro) + ("r-ggplot2" ,r-ggplot2) + ("r-gtable" ,r-gtable) + ("r-magrittr" ,r-magrittr) + ("r-plyr" ,r-plyr) + ("r-scales" ,r-scales))) + (home-page "https://cran.r-project.org/package=superheat") + (synopsis "Graphical tool for exploring complex datasets using heatmaps") + (description + "This package provides a system for generating extendable and +customizable heatmaps for exploring complex datasets, including big data and +data with multiple data types.") + (license license:cc0))) + +(define-public r-qualv + (package + (name "r-qualv") + (version "0.3-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "qualV" version)) + (sha256 + (base32 + "1yyqk223ydcc0125gsn33a4mcdp8bd76fpn8kj9bfz9g78b8dqmx")))) + (properties `((upstream-name . "qualV"))) + (build-system r-build-system) + (propagated-inputs + `(("r-kernsmooth" ,r-kernsmooth))) + (home-page "http://qualV.R-Forge.R-Project.org/") + (synopsis "Qualitative Validation Methods") + (description + "This package provides qualitative methods for the validation of dynamic +models. It contains + +@enumerate +@item an orthogonal set of deviance measures for absolute, relative and + ordinal scale and +@item approaches accounting for time shifts. +@end enumerate + +The first approach transforms time to take time delays and speed differences +into account. The second divides the time series into interval units +according to their main features and finds the @dfn{longest common +subsequence} (LCS) using a dynamic programming algorithm.") + (license license:gpl2+))) + (define-public r-mosaiccore (package (name "r-mosaiccore") @@ -9092,14 +10099,14 @@ used to teach mathematics, statistics, computation and modeling.") (define-public r-raster (package (name "r-raster") - (version "3.4-5") + (version "3.4-13") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 - "19g4chd0nyhnz6hc2j0v9ahjcgz64vvja4y3mrj1pfis1dwhsqn6")))) + "120k4bkgwddrx8ijgdhsgjz8g8dxcwp9bx3kfzrhw00q1b289hir")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) @@ -9179,15 +10186,17 @@ biological data by Michael Whitlock and Dolph Schluter.") (define-public r-svgui (package (name "r-svgui") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "svGUI" version)) (sha256 - (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc")))) + (base32 "0ch5gdfk834xj9w3vxpm3x4770fz3nnlyn8b0jsw9f3n2as7g979")))) (properties `((upstream-name . "svGUI"))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/SciViews/svGUI/") (synopsis "Functions for managing GUI clients in R") (description @@ -9200,13 +10209,13 @@ calls to the particular toolkits in use in function of the context.") (define-public r-svdialogs (package (name "r-svdialogs") - (version "1.0.0") + (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "svDialogs" version)) (sha256 - (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97")))) + (base32 "0j00xjvkwv992ir48czhvyj29rb9vpd243vbyyj2binn0q0qa431")))) (properties `((upstream-name . "svDialogs"))) (build-system r-build-system) (inputs @@ -9215,6 +10224,8 @@ calls to the particular toolkits in use in function of the context.") (propagated-inputs `(("r-rstudioapi" ,r-rstudioapi) ("r-svgui" ,r-svgui))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/SciViews/svDialogs/") (synopsis "Portable dialog boxes") (description @@ -9294,14 +10305,14 @@ genotypes as \"graphical genotypes\".") (define-public r-furrr (package (name "r-furrr") - (version "0.2.2") + (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "furrr" version)) (sha256 (base32 - "0kfd4hw1yn2mfxzjgiz4r6yi2vsp1j0wy5hdhzd6wha7vi9h7hg5")))) + "001p2yhznrpnrjvdcmf2h3wpgdnw01wnqgid7wbq8bhavhi3888a")))) (build-system r-build-system) (propagated-inputs `(("r-ellipsis" ,r-ellipsis) @@ -9687,14 +10698,14 @@ samples is large and the number of mixture components is not too large.") (define-public r-magick (package (name "r-magick") - (version "2.7.1") + (version "2.7.3") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 - "16svy84dq25g69axqgympsrh8dzssa1w3zz08zc8m6nprr3jqwqf")))) + "0h942bn7wfnzbbgq9hrs75c7igmg5r1c5sad2v0znhza4cp7p1w3")))) (build-system r-build-system) (inputs `(("imagemagick" ,imagemagick) @@ -9721,14 +10732,14 @@ console, resulting in an interactive editing environment.") (define-public r-survey (package (name "r-survey") - (version "4.0") + (version "4.1-1") (source (origin (method url-fetch) (uri (cran-uri "survey" version)) (sha256 (base32 - "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh")))) + "0ljsszybzri531q6xab04r6zq11vchfs7y0snjzk57m3g0b9ms05")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) @@ -9776,24 +10787,24 @@ analysis.") (define-public r-tab (package (name "r-tab") - (version "4.1.1") + (version "5.1.1") (source (origin (method url-fetch) (uri (cran-uri "tab" version)) (sha256 (base32 - "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm")))) + "1kg8c1safi9klkx2mdkmsf5dn9piy4jljwd4ma7g4jz2rwl4jzhv")))) (properties `((upstream-name . "tab"))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) - ("r-gee" ,r-gee) + ("r-kableextra" ,r-kableextra) ("r-knitr" ,r-knitr) ("r-mass" ,r-mass) - ("r-survey" ,r-survey) - ("r-survival" ,r-survival) - ("r-xtable" ,r-xtable))) + ("r-survey" ,r-survey))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/tab/") (synopsis "Create summary tables for statistical reports") (description @@ -10056,14 +11067,14 @@ observation.") (define-public r-sandwich (package (name "r-sandwich") - (version "3.0-0") + (version "3.0-1") (source (origin (method url-fetch) (uri (cran-uri "sandwich" version)) (sha256 (base32 - "0afm6snak7r11dxyl3qirqdjah6d9pdv4afmxwam1nq9bqxyb3w2")))) + "12aa5083k3sfrfq1jy3l94wffss9h0rga8j71jy3n8pkhiq4nn7n")))) (build-system r-build-system) (propagated-inputs `(("r-zoo" ,r-zoo))) @@ -10101,14 +11112,14 @@ packages maintained by Torsten Hothorn.") (define-public r-multcomp (package (name "r-multcomp") - (version "1.4-16") + (version "1.4-17") (source (origin (method url-fetch) (uri (cran-uri "multcomp" version)) (sha256 (base32 - "1s8qmljawalisggniy7va5l5cicsgvs0lp20c33vxlvyiy0dbb1s")))) + "02zv739mbmx672yrqqx8am229h7ps476wphig7jrrbfgay29sl21")))) (build-system r-build-system) (propagated-inputs `(("r-codetools" ,r-codetools) @@ -10129,14 +11140,14 @@ Hothorn, Westfall, 2010, CRC Press).") (define-public r-emmeans (package (name "r-emmeans") - (version "1.5.5-1") + (version "1.6.3") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "0l5dd71ihhs7zy6ygniy07iisgy7a1ai1w41hqf84swb0j3cl6iz")))) + "1mwcq3hvpx04qnn5k0bv1mikjgm9mk6m83i8hj350s1c1a0mi40n")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) @@ -10226,14 +11237,14 @@ correlation, censored, ordered and multivariate problems.") (define-public r-bayesplot (package (name "r-bayesplot") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (cran-uri "bayesplot" version)) (sha256 (base32 - "0j69a78l5z0wyxcz607amaa4jc8kwwvcia9wxyir65b8ks9gj1d6")))) + "0aman4273i8hy3z0qay1nrsr7v27m4icm1j6f4w59ylix80l5myq")))) (build-system r-build-system) (inputs `(("pandoc" ,pandoc) @@ -10262,14 +11273,14 @@ Bayesian modeling.") (define-public r-tmb (package (name "r-tmb") - (version "1.7.19") + (version "1.7.21") (source (origin (method url-fetch) (uri (cran-uri "TMB" version)) (sha256 (base32 - "0vnjh8d5gnjswil8ld3gbbspy4m5l2pzar1mpj62qxn2mwx0cc4s")))) + "1lf9vf28l48xhw2irxfxl4vsqzj7skzblydw32p18zddzpapl0z9")))) (properties `((upstream-name . "TMB"))) (build-system r-build-system) (propagated-inputs @@ -10333,20 +11344,21 @@ models.") (define-public r-glmmtmb (package (name "r-glmmtmb") - (version "1.0.2.1") + (version "1.1.2.3") (source (origin (method url-fetch) (uri (cran-uri "glmmTMB" version)) (sha256 (base32 - "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab")))) + "1yfwwz2dhd34vgagg8hi7irkqw8padavbc7337jdiwgk3w01wqsm")))) (properties `((upstream-name . "glmmTMB"))) (build-system r-build-system) (propagated-inputs `(("r-lme4" ,r-lme4) ("r-matrix" ,r-matrix) ("r-nlme" ,r-nlme) + ("r-numderiv" ,r-numderiv) ("r-rcppeigen" ,r-rcppeigen) ("r-tmb" ,r-tmb))) (native-inputs @@ -10365,18 +11377,19 @@ differentiation.") (define-public r-bayestestr (package (name "r-bayestestr") - (version "0.8.2") + (version "0.11.0") (source (origin (method url-fetch) (uri (cran-uri "bayestestR" version)) (sha256 (base32 - "06y7vccgln1882yv04may9p6s915py8nnhg82d5ppbpxzcifi7l4")))) + "0bwfw1lh4yp8y77sfmxzqqqy5aw59q1lqhfcssa46ph6d4hyxwic")))) (properties `((upstream-name . "bayestestR"))) (build-system r-build-system) (propagated-inputs - `(("r-insight" ,r-insight))) + `(("r-datawizard" ,r-datawizard) + ("r-insight" ,r-insight))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/easystats/bayestestR") @@ -10392,17 +11405,18 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.7.0") + (version "0.7.3") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "1z45vy8gg77c2imcspwqf94anzi6c40wwbq0h7hg6zy76jsgvbyj")))) + "03qdsdl4x3hwqlbs7hlqb73xypd13p5zj519y0zcydqkf25391sp")))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) + ("r-datawizard" ,r-datawizard) ("r-insight" ,r-insight))) (home-page "https://easystats.github.io/performance/") (synopsis "Assessment of regression models performance") @@ -10419,14 +11433,14 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "1.0.2") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "0qh8x8yi8gkb5x7zfxmb1c689k7bhc1f5947yymny34j7xdsb9s8")))) + "0xrb105kblkj3l9zlj9yy52rjlmx5x2aai1wwb5zvjr1f6nlc84l")))) (build-system r-build-system) (propagated-inputs `(("r-insight" ,r-insight) @@ -10449,14 +11463,14 @@ results using @code{ggplot2}.") (define-public r-effectsize (package (name "r-effectsize") - (version "0.4.4-1") + (version "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 - "02rwf3lxnzgc8yh0wridsc6lqr9s6v0cqzbk4biwnr494rvs46zb")))) + "0rp0r75p8q467lmrsr1gl9wjpib9jz7ksx5rm6c7q2lfg9b9zrjf")))) (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs @@ -10476,17 +11490,18 @@ conversion of indices such as Cohen's d, r, odds, etc.") (define-public r-sjplot (package (name "r-sjplot") - (version "2.8.7") + (version "2.8.9") (source (origin (method url-fetch) (uri (cran-uri "sjPlot" version)) (sha256 - (base32 "1g4qabg654kwdm09ihp4h3mg64a1d7a7gsn6w56rwsidqqaxilq0")))) + (base32 "07b9p5wbb6xmyapg9j6i4cdcj7j9wj9gi30gljj6j2lj1flgdd7q")))) (properties `((upstream-name . "sjPlot"))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) + ("r-datawizard" ,r-datawizard) ("r-dplyr" ,r-dplyr) ("r-effectsize" ,r-effectsize) ("r-ggeffects" ,r-ggeffects) @@ -10566,14 +11581,14 @@ repositories.") (define-public r-gh (package (name "r-gh") - (version "1.2.1") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "gh" version)) (sha256 (base32 - "16xa1qb1r28f8yc6ybjrxiq2zigxj886dp9k29jpsn5091xbzkq0")))) + "077drbxz3rx7idv6w24ipj1p6jnzv86a3iyryab699cc9q2kjh54")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -10633,14 +11648,14 @@ terminals that do not support Unicode.") (define-public r-credentials (package (name "r-credentials") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "credentials" version)) (sha256 (base32 - "1w9zj34xdwz9bszsvhv2cbgq96y5sgxbh7ndn31pgfcpzlkfq6f1")))) + "0q3s1bibwvw1p541k8a5cjx4dj1iabl4crg61fgjxkniclxag5c7")))) (properties `((upstream-name . "credentials"))) (build-system r-build-system) (arguments @@ -10677,14 +11692,14 @@ user credentials.") (define-public r-gert (package (name "r-gert") - (version "1.3.0") + (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "gert" version)) (sha256 (base32 - "1fh72p92wj83yv1ch77jms6k1gjqfji8cmgw23vpxd0p8l9jj4h7")))) + "1y3318whcifdng87wyngfjq18601zrlj4d8sx40v2c2m5kqmhfv2")))) (properties `((upstream-name . "gert"))) (build-system r-build-system) (inputs @@ -10777,14 +11792,14 @@ more information about packages, and where they were installed from.") (define-public r-remotes (package (name "r-remotes") - (version "2.3.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (cran-uri "remotes" version)) (sha256 (base32 - "0f35648bdxhvplcfj80r4hfj5w21f1s01kcz6b29d098c1mnfzb7")))) + "048lihmwksl72fg4fdmhihblj9ipxl22x9wfpgwsbsv79zjc7rfd")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -10877,18 +11892,20 @@ quick reporting.") (define-public r-pander (package (name "r-pander") - (version "0.6.3") + (version "0.6.4") (source (origin (method url-fetch) (uri (cran-uri "pander" version)) (sha256 (base32 - "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi")))) + "1knjcr50xxns3w3kh15myjpsizn4d7fdqx071a4yj90imif07qjh")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://rapporter.github.io/pander") (synopsis "Render R objects into Pandoc's markdown") (description @@ -10903,14 +11920,14 @@ ways.") (define-public r-summarytools (package (name "r-summarytools") - (version "0.9.9") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "summarytools" version)) (sha256 (base32 - "0ig7vgjvldbndwhky1bsi38zifr9ji8xvvfqbfffplac08llvrbr")))) + "04qcysfywljnqkcz2b7kzpy0xv3ykkvvb14vnda63z1wvmadyhkn")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -11028,13 +12045,13 @@ and related methods.") (define-public r-rcppgsl (package (name "r-rcppgsl") - (version "0.3.8") + (version "0.3.9") (source (origin (method url-fetch) (uri (cran-uri "RcppGSL" version)) (sha256 - (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz")))) + (base32 "0zhfkn3w5q2k2ggizrikz9an8hm90g6mr60paq0z8xgp5hpkrlk6")))) (properties `((upstream-name . "RcppGSL"))) (build-system r-build-system) (propagated-inputs @@ -11055,14 +12072,14 @@ the interfaces between R and C++.") (define-public r-mvabund (package (name "r-mvabund") - (version "4.1.9") + (version "4.1.12") (source (origin (method url-fetch) (uri (cran-uri "mvabund" version)) (sha256 (base32 - "19kyg0agjk7gxipa5kmklz4cqh97xrdbibmmy1g99r1gp3s9ml30")))) + "107pwv2bwird1a98chcnbld2wqj9prkf4pkncyrrp304zpdkkby1")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -11080,14 +12097,14 @@ analysing multivariate abundance data in community ecology.") (define-public r-afex (package (name "r-afex") - (version "0.28-1") + (version "1.0-1") (source (origin (method url-fetch) (uri (cran-uri "afex" version)) (sha256 (base32 - "0blwqr5ni3psav1dcdmhfi4jy3b4scm5njimqfpr1d81zadvgc6g")))) + "1k04n6gwk2n8kg0l3yk5j3wrqgkv5f6w04yjpif9y451hx5w7svg")))) (build-system r-build-system) (propagated-inputs `(("r-car" ,r-car) @@ -11166,24 +12183,106 @@ using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et al. (2016)).") (license license:gpl2))) +(define-public r-cmdfun + (package + (name "r-cmdfun") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "cmdfun" version)) + (sha256 + (base32 + "1pbcq7hi2lcmqnghmy3q2fsk0c9fy5m0637acyzmc096fxbx723j")))) + (properties `((upstream-name . "cmdfun"))) + (build-system r-build-system) + (propagated-inputs + `(("r-magrittr" ,r-magrittr) + ("r-purrr" ,r-purrr) + ("r-r-utils" ,r-r-utils) + ("r-rlang" ,r-rlang) + ("r-testthat" ,r-testthat) + ("r-usethis" ,r-usethis))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://snystrom.github.io/cmdfun/") + (synopsis "Framework for building interfaces to shell commands") + (description + "Writing interfaces to command line software is cumbersome. The cmdfun +package provides a framework for building function calls to seamlessly +interface with shell commands by allowing lazy evaluation of command line +arguments. It also provides methods for handling user-specific paths to tool +installs or secrets like API keys. Its focus is to equally serve package +builders who wish to wrap command line software, and to help analysts stay +inside R when they might usually leave to execute non-R software.") + (license license:expat))) + +(define-public r-rslurm + (package + (name "r-rslurm") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rslurm" version)) + (sha256 + (base32 + "0fn2na8prsaxa03x5wi3105gpsxc35qvgmik7wy3nylvx4wdfv9g")))) + (properties `((upstream-name . "rslurm"))) + (build-system r-build-system) + (propagated-inputs `(("r-whisker" ,r-whisker))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "http://cyberhelp.sesync.org/rslurm/") + (synopsis "Submit R calculations to a Slurm cluster") + (description + "This package provides functions that simplify submitting R scripts to a +Slurm workload manager, in part by automating the division of embarrassingly +parallel calculations across cluster nodes.") + (license license:gpl3))) + +(define-public r-chk + (package + (name "r-chk") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "chk" version)) + (sha256 + (base32 + "1fxsxgvd08lkb6amjgs4x48dhqr046mmjngjfgy2ya9cl2shd7ls")))) + (properties `((upstream-name . "chk"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lifecycle" ,r-lifecycle) + ("r-rlang" ,r-rlang))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/poissonconsulting/chk") + (synopsis "Check user-supplied function arguments") + (description + "This is a package for developers to check user-supplied function +arguments. It is designed to be simple, fast and customizable. Error +messages follow the tidyverse style guide.") + (license license:expat))) + (define-public r-weights (package (name "r-weights") - (version "1.0.1") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "weights" version)) (sha256 (base32 - "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5")))) + "1fnchf7f0hyl514bk8sc3l884kg25kb5xm4mc2l28n6hm7l6bgpg")))) (build-system r-build-system) (propagated-inputs `(("r-gdata" ,r-gdata) ("r-hmisc" ,r-hmisc) + ("r-lme4" ,r-lme4) ("r-mice" ,r-mice))) - (home-page - "https://cran.r-project.org/web/packages/weights/") + (home-page "https://cran.r-project.org/web/packages/weights/") (synopsis "Weighting and weighted statistics") (description "This package Provides a variety of functions for producing simple weighted statistics, such as weighted Pearson's correlations, partial @@ -11197,14 +12296,14 @@ address a bug.") (define-public r-rcppannoy (package (name "r-rcppannoy") - (version "0.0.18") + (version "0.0.19") (source (origin (method url-fetch) (uri (cran-uri "RcppAnnoy" version)) (sha256 (base32 - "0n68cf77gz34iq6w6ad87pbqwqam45nxp1gjzns4g6qhf7qdvrz4")))) + "12k8ny981dmky5js8yl6bih5r5mq3w43f2f9admhkwqn0n80kcl9")))) (properties `((upstream-name . "RcppAnnoy"))) (build-system r-build-system) (propagated-inputs @@ -11244,14 +12343,14 @@ package provides a minimal R interface by relying on the Rcpp package.") (define-public r-rcppparallel (package (name "r-rcppparallel") - (version "5.0.3") + (version "5.1.4") (source (origin (method url-fetch) (uri (cran-uri "RcppParallel" version)) (sha256 (base32 - "0ihcirny4al2ydymxhdfacwmybmrgrz5nm0lbf49gk2zy8w124ki")))) + "10pa9vaz7p4m6hjca2cpy6vj7rvgly4zv0q1g2xfsmcchyk4bdbn")))) (properties `((upstream-name . "RcppParallel"))) (build-system r-build-system) (home-page "https://rcppcore.github.io/RcppParallel/") @@ -11294,13 +12393,13 @@ netCDF files.") (define-public r-biocmanager (package (name "r-biocmanager") - (version "1.30.12") + (version "1.30.16") (source (origin (method url-fetch) (uri (cran-uri "BiocManager" version)) (sha256 - (base32 "0c2anza01pc36manj3cvycbq8p57qpq18dsimk3y3gpks70hhqf3")))) + (base32 "0m9qxwqajg8lp0z06blbpgk3zw0z73aly1cvmjk6mvwja6jm99vm")))) (properties `((upstream-name . "BiocManager"))) (build-system r-build-system) (native-inputs @@ -11315,14 +12414,14 @@ Bioconductor packages.") (define-public r-rgl (package (name "r-rgl") - (version "0.105.22") + (version "0.107.14") (source (origin (method url-fetch) (uri (cran-uri "rgl" version)) (sha256 (base32 - "1y69phym8pkdh1k808y3rp1030xmhjpc8vig9035v9n1r7v7a1kz")))) + "1z5h4wbjj18prcykc96rqcn699pnqw6vybwj2mpbbbdw2lr3q8b7")))) (build-system r-build-system) (native-inputs `(("pkg-config" ,pkg-config) @@ -11340,9 +12439,7 @@ Bioconductor packages.") ("r-htmlwidgets" ,r-htmlwidgets) ("r-jsonlite" ,r-jsonlite) ("r-knitr" ,r-knitr) - ("r-magrittr" ,r-magrittr) - ("r-manipulatewidget" ,r-manipulatewidget) - ("r-shiny" ,r-shiny))) + ("r-magrittr" ,r-magrittr))) (home-page "https://r-forge.r-project.org/projects/rgl/") (synopsis "3D visualization using OpenGL") (description @@ -11358,14 +12455,14 @@ image formats, including PNG, Postscript, SVG, PGF.") (define-public r-multicool (package (name "r-multicool") - (version "0.1-11") + (version "0.1-12") (source (origin (method url-fetch) (uri (cran-uri "multicool" version)) (sha256 (base32 - "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w")))) + "0djacq0irfqz4nlnx238kja73yvr1n5qybbfyl6bw1n6qgcjhza8")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) (home-page "https://cran.r-project.org/web/packages/multicool/") @@ -11399,13 +12496,13 @@ isosurfaces.") (define-public r-ks (package (name "r-ks") - (version "1.12.0") + (version "1.13.2") (source (origin (method url-fetch) (uri (cran-uri "ks" version)) (sha256 - (base32 "1sff6rlpq64lqyvwgral9zbcan30wpgmfb26hw9y6wzypd9gxbz6")))) + (base32 "02gnpyjqdlj6dl2x9i7mmks4f5nrh85j3h0kfa0v1v6wi8blx7kw")))) (build-system r-build-system) (propagated-inputs `(("r-fnn" ,r-fnn) @@ -11416,7 +12513,8 @@ isosurfaces.") ("r-mgcv" ,r-mgcv) ("r-multicool" ,r-multicool) ("r-mvtnorm" ,r-mvtnorm) - ("r-plot3d" ,r-plot3d))) + ("r-plot3d" ,r-plot3d) + ("r-pracma" ,r-pracma))) (home-page "https://www.mvstat.net/tduong/") (synopsis "Kernel smoothing") (description @@ -11536,14 +12634,14 @@ circular variables).") (define-public r-ouch (package (name "r-ouch") - (version "2.15-1") + (version "2.17") (source (origin (method url-fetch) (uri (cran-uri "ouch" version)) (sha256 (base32 - "0myddn3b28pswyk42kvwhyvkj30q41f677vpxclxacdfkhgvrj6q")))) + "1a7r24j59xz3lxa5wc694j6b80j8m5l86zd1sw9pvs66l8gd98kf")))) (build-system r-build-system) (propagated-inputs `(("r-subplex" ,r-subplex))) (home-page "https://kingaa.github.io/ouch/") @@ -11556,14 +12654,14 @@ for evolution along a phylogenetic tree.") (define-public r-fmsb (package (name "r-fmsb") - (version "0.7.0") + (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "fmsb" version)) (sha256 (base32 - "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45")))) + "09pq7p7i6vkq9av7l7x9hicl9sqh7xn96f9pac117hy6z852jvi2")))) (build-system r-build-system) (home-page "http://minato.sip21c.org/msb/") (synopsis "Functions for medical statistics book with demographic data") @@ -11597,14 +12695,14 @@ parametrizations of Nolan.") (define-public r-gsl (package (name "r-gsl") - (version "2.1-6") + (version "2.1-7") (source (origin (method url-fetch) (uri (cran-uri "gsl" version)) (sha256 (base32 - "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m")))) + "05rvky8sh3jrlz0xbd6nss8h8ykfg1v10dymhlmcykl6v5csz1hs")))) (build-system r-build-system) (inputs `(("gsl" ,gsl))) @@ -11667,20 +12765,21 @@ after it was discovered that the NSA had backdoored Dual EC DRBG.") (define-public r-softimpute (package (name "r-softimpute") - (version "1.4") + (version "1.4-1") (source (origin (method url-fetch) (uri (cran-uri "softImpute" version)) (sha256 (base32 - "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq")))) + "1v2a4d688ij5zcvkzpra9yx40xckdfnllnfnyq2450zf3n1kjk7a")))) (properties `((upstream-name . "softImpute"))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) (native-inputs - `(("gfortran" ,gfortran))) + `(("gfortran" ,gfortran) + ("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/softImpute") (synopsis "Matrix completion via iterative soft-thresholded SVD") (description @@ -11864,13 +12963,13 @@ maps.") (define-public r-tidytree (package (name "r-tidytree") - (version "0.3.3") + (version "0.3.5") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 - (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6")))) + (base32 "0zk46n3nh577k2jy34isdw845hk0blkvqk7rg5nmix5b65qsp762")))) (build-system r-build-system) (propagated-inputs `(("r-ape" ,r-ape) @@ -11878,7 +12977,9 @@ maps.") ("r-lazyeval" ,r-lazyeval) ("r-magrittr" ,r-magrittr) ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble))) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-tidyselect" ,r-tidyselect))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/GuangchuangYu/tidytree") @@ -11893,17 +12994,17 @@ manipulate tree data.") (define-public r-rvcheck (package (name "r-rvcheck") - (version "0.1.8") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "rvcheck" version)) (sha256 - (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac")))) + (base32 "09gx29q882vh4q1qbb8z8lc3pgmpn7bk8skzcm85mrf3x3vgvkpa")))) (build-system r-build-system) (propagated-inputs `(("r-biocmanager" ,r-biocmanager) - ("r-rlang" ,r-rlang))) + ("r-yulab-utils" ,r-yulab-utils))) (home-page "https://cran.r-project.org/web/packages/rvcheck") (synopsis "R package version check") (description @@ -12084,14 +13185,14 @@ structure of any data type.") (define-public r-corpcor (package (name "r-corpcor") - (version "1.6.9") + (version "1.6.10") (source (origin (method url-fetch) (uri (cran-uri "corpcor" version)) (sha256 (base32 - "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf")))) + "028fw61n61i79fhnaqx7gmdifdpbvp3yiaq9vvfrbv4k7i84r83i")))) (build-system r-build-system) (home-page "http://strimmerlab.org/software/corpcor/") (synopsis "Efficient estimation of covariance and (partial) correlation") @@ -12252,17 +13353,100 @@ Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. Touzet and Varre (2007).") (license license:gpl2))) +(define-public r-rncl + (package + (name "r-rncl") + (version "0.8.4") + (source (origin + (method url-fetch) + (uri (cran-uri "rncl" version)) + (sha256 + (base32 + "0ss9jqrvv7bhvl5j74cjrp8r866d9dlavrbbfscwz3mhkgfx06bb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-progress" ,r-progress) + ("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/fmichonneau/rncl") + (synopsis "Interface to the Nexus class library") + (description "This package provides an interface to the Nexus class +library which allows parsing of NEXUS, Newick and other phylogenetic tree + file formats. It provides elements of the file that can be used to build + phylogenetic objects such as @code{ape}'s @code{phylo} or @code{phylobase}'s +@code{phylo4(d)}. This functionality is demonstrated with +@code{read_newick_phylo()} and @code{read_nexus_phylo()}.") + (license license:bsd-2))) + +(define-public r-phylobase + (package + (name "r-phylobase") + (version "0.8.10") + (source (origin + (method url-fetch) + (uri (cran-uri "phylobase" version)) + (sha256 + (base32 + "0jzr1gdvmi4l640hwwzh9bxqmpja69bn3ygnaqx37awvyh7khi2s")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ade4" ,r-ade4) + ("r-ape" ,r-ape) + ("r-rcpp" ,r-rcpp) + ("r-rncl" ,r-rncl) + ("r-rnexml" ,r-rnexml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/fmichonneau/phylobase") + (synopsis "Base package for phylogenetic structures and comparative data") + (description "This package provides a base @code{S4} class for comparative +methods, incorporating one or more trees and trait data.") + (license license:gpl2+))) + +(define-public r-rnexml + (package + (name "r-rnexml") + (version "2.4.5") + (source (origin + (method url-fetch) + (uri (cran-uri "RNeXML" version)) + (sha256 + (base32 + "1wsl4xq9w5bp3wk69dw57bg0qcw1vs6ajwya4p0w1r00ck5pwrib")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-dplyr" ,r-dplyr) + ("r-httr" ,r-httr) + ("r-lazyeval" ,r-lazyeval) + ("r-plyr" ,r-plyr) + ("r-reshape2" ,r-reshape2) + ("r-stringi" ,r-stringi) + ("r-stringr" ,r-stringr) + ("r-tidyr" ,r-tidyr) + ("r-uuid" ,r-uuid) + ("r-xml" ,r-xml) + ("r-xml2" ,r-xml2))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://docs.ropensci.org/RNeXML/") + (synopsis "Semantically rich I/O for the NeXML Format") + (description "This package provides access to phyloinformatic data in +NeXML format. The package should add new functionality to R such as the +possibility to manipulate NeXML objects in more various and refined way +and compatibility with @code{ape} objects.") + (license license:bsd-3))) + (define-public r-rnifti (package (name "r-rnifti") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "RNifti" version)) (sha256 (base32 - "1zr0q79id62csmc30c7gs4hbmavk8n6p50a981sfz51dczhjj5ny")))) + "0bz10ar6hrgkvlzh9j2im24kwi3s2nnax668z40a2wj6s5xghqlr")))) (properties `((upstream-name . "RNifti"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) @@ -12637,14 +13821,14 @@ and manipulating sets of ontological terms.") (define-public r-gargle (package (name "r-gargle") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "gargle" version)) (sha256 (base32 - "03y29dzz54bw9px5k8a72vmc000lcyrkc5l0izkqcciyi9ijkr3w")))) + "0fypj70c1fjmvs57birik76wfx8a2fs4gzicbb52k57i6clwlijd")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -12669,14 +13853,14 @@ preparing, executing, and processing HTTP requests.") (define-public r-bigrquery (package (name "r-bigrquery") - (version "1.3.2") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "bigrquery" version)) (sha256 (base32 - "16whccv7f94vf57dvbbrhdskz3nnbmpa11a14kp7aynckldlfy0v")))) + "02msq61l7vamzpvbhvalh3qil1aa7pr68pwpsivbb6pvz6p4zyns")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -12687,6 +13871,7 @@ preparing, executing, and processing HTTP requests.") ("r-glue" ,r-glue) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) + ("r-lifecycle" ,r-lifecycle) ("r-prettyunits" ,r-prettyunits) ("r-progress" ,r-progress) ("r-rapidjsonr" ,r-rapidjsonr) @@ -12729,14 +13914,14 @@ limitations\" using the GNU Multiple Precision library.") (define-public r-rmpfr (package (name "r-rmpfr") - (version "0.8-3") + (version "0.8-4") (source (origin (method url-fetch) (uri (cran-uri "Rmpfr" version)) (sha256 (base32 - "1m9wwwch9wg886147brr2zfih65yfdfs3vmfvim1w6jykycasc9a")))) + "0xaqbgkpnjg53zcp56c59cz5dh3jvvwqnzvyxqzy77c6yvkwy3hx")))) (properties `((upstream-name . "Rmpfr"))) (build-system r-build-system) (inputs @@ -13198,13 +14383,13 @@ This makes it a convenient and fast interface to C/C++ and Fortran code.") (define-public r-spam (package (name "r-spam") - (version "2.6-0") + (version "2.7-0") (source (origin (method url-fetch) (uri (cran-uri "spam" version)) (sha256 - (base32 "0p5ycvpry955ldrgbbq3syy91wx9425mddpn8r5m9xwlirjxv3v3")))) + (base32 "03c50wfyrzcmrcv9mkgj8dmdg2cwkh4p4ys8gaclr8w7ym45qav3")))) (build-system r-build-system) (propagated-inputs `(("r-dotcall64" ,r-dotcall64))) @@ -13229,17 +14414,18 @@ Differences with other sparse matrix packages are: (define-public r-fields (package (name "r-fields") - (version "11.6") + (version "12.5") (source (origin (method url-fetch) (uri (cran-uri "fields" version)) (sha256 - (base32 "1nsrgkw9w3mwd3sajyzc06h49gg1s0bkq6xh5b66h1n4jbcx2046")))) + (base32 "08jfqlz42vq23h2yq279cs2rva9fadi4q6cmk4dvixrmyprx5xyk")))) (build-system r-build-system) (propagated-inputs `(("r-maps" ,r-maps) - ("r-spam" ,r-spam))) + ("r-spam" ,r-spam) + ("r-viridis" ,r-viridis))) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://www.image.ucar.edu/fields") @@ -13370,6 +14556,23 @@ Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty, Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)") (license license:gpl2+))) +(define-public r-locfdr + (package + (name "r-locfdr") + (version "1.1-8") + (source (origin + (method url-fetch) + (uri (cran-uri "locfdr" version)) + (sha256 + (base32 + "1falkbp2xz07am8jlhwlvyqvxnli4nwl188kd0g58vdfjcjy3mj2")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/locfdr/") + (synopsis "Computes local false discovery rates") + (description "This package can be used to compute local false +discovery rates.") + (license license:gpl2))) + (define-public r-longitudinal (package (name "r-longitudinal") @@ -13444,14 +14647,14 @@ library.") (define-public r-protviz (package (name "r-protviz") - (version "0.6.8") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "protViz" version)) (sha256 (base32 - "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a")))) + "0l1pmfr9kmc90rl5s9b0141451rxrjmiiasp3lsvl2x3ps0smqaj")))) (properties `((upstream-name . "protViz"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) @@ -13581,13 +14784,13 @@ regression coefficients can be conducted via jackknifing.") (define-public r-huge (package (name "r-huge") - (version "1.3.4.1") + (version "1.3.5") (source (origin (method url-fetch) (uri (cran-uri "huge" version)) (sha256 - (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq")))) + (base32 "1sl457a1lndrx98y2j9a2smanawx2iqlhl82iand0g3p5xp8ch4j")))) (build-system r-build-system) (propagated-inputs `(("r-igraph" ,r-igraph) @@ -13666,6 +14869,11 @@ by change of variable.") (base32 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx")))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (native-inputs `(("r-r-rsp" ,r-r-rsp))) ; vignette builder (home-page "https://github.com/HenrikBengtsson/listenv") @@ -13704,14 +14912,14 @@ them in distributed compute environments.") (define-public r-parallelly (package (name "r-parallelly") - (version "1.24.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (cran-uri "parallelly" version)) (sha256 (base32 - "1x04pxcyyzmg1rl9mcd7mmxglzmxgy40fmbwpy7vf5y7z15rzrp6")))) + "0qy6gj1xybiziks5gvw5px81n3klgr16kvb1qn1xp6j030xqibpl")))) (properties `((upstream-name . "parallelly"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/parallelly") @@ -13732,15 +14940,20 @@ port-forwarding to your local computer.") (define-public r-future (package (name "r-future") - (version "1.21.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 - "0bfiy17n5rghxw0702k0vgpjkk13268lniifdlx59flf0q16d7lh")))) + "1kgdpfipnwi15wz2xvlfg3bmq424hhjzja5bks01v3phra2lmcl7")))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs `(("r-digest" ,r-digest) ("r-globals" ,r-globals) @@ -13765,16 +14978,21 @@ the local machine to, say, distributed processing on a remote compute cluster.") (define-public r-future-apply (package (name "r-future-apply") - (version "1.7.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (cran-uri "future.apply" version)) (sha256 (base32 - "1ns5cf80vyabvyz9qp6kpvkg4jycinn7x6v7x6692fgjapdnmyig")))) + "1ix61bfbk43pwnjb0wk8lkfgdsy5zi8svk74gar5nrl90b5w6nqd")))) (properties `((upstream-name . "future.apply"))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs `(("r-future" ,r-future) ("r-globals" ,r-globals))) @@ -13793,14 +15011,14 @@ machine or distributed on a compute cluster.") (define-public r-rsvd (package (name "r-rsvd") - (version "1.0.3") + (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "rsvd" version)) (sha256 (base32 - "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk")))) + "07p2hjmpcwcsang8z9sjkpy94rydcin7m3hyvcgzgm5cd6w8c1p4")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -13900,14 +15118,14 @@ chosen parallel environment and associated foreach backend.") (define-public r-blockmodeling (package (name "r-blockmodeling") - (version "1.0.0") + (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "blockmodeling" version)) (sha256 (base32 - "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i")))) + "1vc8gy4slsywcwxq532373i0dq73fhs5cac9mr6zz2pjaaxjghhq")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -14121,14 +15339,14 @@ users of rARPACK are advised to switch to the RSpectra package.") (define-public r-compositions (package (name "r-compositions") - (version "2.0-1") + (version "2.0-2") (source (origin (method url-fetch) (uri (cran-uri "compositions" version)) (sha256 (base32 - "03qslsfx11gshls901zlhw47prd55mf16w4mkmd8x1dgiwq938l4")))) + "05pji62pzgfk9dyiybmr16q0h6mdzsmvyzxdni3hn0dvl4a7mr5m")))) (build-system r-build-system) (propagated-inputs `(("r-bayesm" ,r-bayesm) @@ -14288,7 +15506,7 @@ to easily call your own custom JavaScript functions from R.") (format #t "Processing ~a --> ~a~%" source target) (delete-file target) - (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) + (let ((minified (open-pipe* OPEN_READ "uglifyjs" source))) (call-with-output-file target (lambda (port) (dump-port minified port))))) @@ -14304,7 +15522,7 @@ to easily call your own custom JavaScript functions from R.") ("r-shinyjs" ,r-shinyjs))) (native-inputs `(("r-knitr" ,r-knitr) - ("uglify-js" ,uglify-js) + ("uglifyjs" ,node-uglify-js) ("js-jquery" ,(origin (method url-fetch) @@ -14452,14 +15670,14 @@ probabilities from a standard bivariate normal CDF.") (define-public r-lavaan (package (name "r-lavaan") - (version "0.6-8") + (version "0.6-9") (source (origin (method url-fetch) (uri (cran-uri "lavaan" version)) (sha256 (base32 - "18l49f1v7nrngwra4v983ic8w1d4w23ws8xf36337dq0j6809qj0")))) + "12hhbwxaiprs9bmclwhhdpv42h4mrl4gj92zq3wk8rb883mw816l")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -14678,14 +15896,14 @@ running IRkernel session.") (define-public r-irkernel (package (name "r-irkernel") - (version "1.1.1") + (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "IRkernel" version)) (sha256 (base32 - "1y06v3difaiihxfm2abm88nnjzvkla4p346cm1nxmga4iwb2k8gm")))) + "14gz3790iv6gg6yi9wslk1yn0jq57yvhxgm840qh818xfkdxpd2z")))) (properties `((upstream-name . "IRkernel"))) (build-system r-build-system) (arguments @@ -14776,14 +15994,14 @@ plotting functions are available for analyzing clustering results.") (define-public r-valr (package (name "r-valr") - (version "0.6.2") + (version "0.6.3") (source (origin (method url-fetch) (uri (cran-uri "valr" version)) (sha256 (base32 - "1vbp89zfylgih5acvw7lcx3a0dbbd7dhq7yhywr7kq02737qykdx")))) + "1lzdlw0mw06rymyjzwf4i8rx1z6zxpwxxqfsc9ggqlnhq6bfhy93")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -15129,14 +16347,14 @@ barplots or heatmaps.") (define-public r-seqinr (package (name "r-seqinr") - (version "4.2-5") + (version "4.2-8") (source (origin (method url-fetch) (uri (cran-uri "seqinr" version)) (sha256 (base32 - "1z1jipgrn9nrnxlx7bcf8c2chwpa3kfva0zgyb12xbr3kisn166y")))) + "1xz9spln6s9mcwpgcv1m4jymn4gnl1bb6vh90bphqcn0vvlk8jsq")))) (build-system r-build-system) (propagated-inputs `(("r-ade4" ,r-ade4) @@ -15154,14 +16372,14 @@ utilities for sequence data management under the ACNUC system.") (define-public r-units (package (name "r-units") - (version "0.7-1") + (version "0.7-2") (source (origin (method url-fetch) (uri (cran-uri "units" version)) (sha256 (base32 - "0wwndzjjgqj795xvx1jwa86nwd8adfiwj0pn15yyzzk9baky2axw")))) + "1ss0f15h4yqzk488ilsa5d2ibrj3wzwplx4160mn600i8ciy02xr")))) (build-system r-build-system) (inputs `(("udunits" ,udunits))) @@ -15230,14 +16448,14 @@ univariate class intervals for mapping or other graphics purposes.") (define-public r-spdata (package (name "r-spdata") - (version "0.3.8") + (version "0.3.10") (source (origin (method url-fetch) (uri (cran-uri "spData" version)) (sha256 (base32 - "1mlsqy9cbilfc80cbdlbgsngvzdkrd9yjdkxnw2b1gzxnj6jcqbs")))) + "0c3kg2daz65znnmcaf5l108c88anzlfrsjlnmv2kxqr1lx8z9zl5")))) (properties `((upstream-name . "spData"))) (build-system r-build-system) (propagated-inputs @@ -15304,17 +16522,74 @@ tessellations, and summarizes information about the tiles of the tessellation.") (license license:gpl2+))) +(define-public r-wk + (package + (name "r-wk") + (version "0.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "wk" version)) + (sha256 + (base32 + "0fj2wzswv3dfninsyw9irf52fc2d0lag5b822x841vdfpvh01mbi")))) + (properties `((upstream-name . "wk"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cpp11" ,r-cpp11))) + (home-page "https://paleolimbot.github.io/wk/") + (synopsis "Lightweight well-known geometry parsing") + (description + "This package provides a minimal R and C++ API for parsing well-known +binary and well-known text representation of geometries to and from R-native +formats. Well-known binary is compact and fast to parse; well-known text is +human-readable and is useful for writing tests. These formats are only useful +in R if the information they contain can be accessed in R, for which +high-performance functions are provided here.") + (license license:expat))) + +(define-public r-s2 + (package + (name "r-s2") + (version "1.0.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "s2" version)) + (sha256 + (base32 + "1xd42bpbm090dqlldavbn6c1h1mfwhlws9536avan00w3szlxk56")))) + (properties `((upstream-name . "s2"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-wk" ,r-wk))) + (inputs + `(("openssl" ,openssl))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://r-spatial.github.io/s2/") + (synopsis "Spherical geometry operators using the S2 geometry library") + (description + "This package provides R bindings for Google's s2 library for geometric +calculations on the sphere. High-performance constructors and exporters +provide high compatibility with existing spatial packages, transformers +construct new geometries from existing geometries, predicates provide a means +to select geometries based on spatial relationships, and accessors extract +information about geometries.") + (license license:asl2.0))) + (define-public r-sf (package (name "r-sf") - (version "0.9-8") + (version "1.0-2") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 - "096gg2hbynn6mv3w8n69x987fklg5rrgd0d4nbqaw7vhg1jhlmqi")))) + "0hh54krf4gjwrzxj2r3p5q7amdf8kblv8nm7hmbwmfv1rs30i1gc")))) (build-system r-build-system) (inputs `(("gdal" ,gdal) @@ -15327,6 +16602,7 @@ tessellation.") ("r-dbi" ,r-dbi) ("r-magrittr" ,r-magrittr) ("r-rcpp" ,r-rcpp) + ("r-s2" ,r-s2) ("r-units" ,r-units))) (native-inputs `(("pkg-config" ,pkg-config) @@ -15344,28 +16620,43 @@ datum transformations.") (define-public r-spdep (package (name "r-spdep") - (version "1.1-7") - (source - (origin - (method url-fetch) - (uri (cran-uri "spdep" version)) - (sha256 - (base32 - "0sg417d95paww625663lgmk6jwhs88djqzc96gbs1hxazlf77qb1")))) + (version "1.1-11") + (source (origin + (method url-fetch) + (uri (cran-uri "spdep" version)) + (sha256 + (base32 + "1ym523dzpiji6c8ypa3gvw8va36gl1gnzcsvdg9drly3mlq42rpr")) + (snippet + '(for-each delete-file '("inst/doc/nb_igraph.html" + "inst/doc/nb_igraph.R" + "inst/doc/nb_igraph.Rmd" + "inst/doc/sids.html" + "inst/doc/sids.R" + "inst/doc/nb.html" + "inst/doc/nb.R" + "inst/doc/CO69.html" + "inst/doc/CO69.R" + "inst/doc/nb_sf.html" + "inst/doc/nb_sf.R" + "inst/doc/nb_sf.Rmd"))))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) ("r-coda" ,r-coda) ("r-deldir" ,r-deldir) + ("r-e1071" ,r-e1071) ("r-expm" ,r-expm) ("r-gmodels" ,r-gmodels) ("r-learnbayes" ,r-learnbayes) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-nlme" ,r-nlme) + ("r-s2" ,r-s2) ("r-sf" ,r-sf) ("r-sp" ,r-sp) - ("r-spdata" ,r-spdata))) + ("r-spdata" ,r-spdata) + ("r-units" ,r-units))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/r-spatial/spdep/") @@ -15381,14 +16672,14 @@ spanning tree.") (define-public r-adegenet (package (name "r-adegenet") - (version "2.1.3") + (version "2.1.4") (source (origin (method url-fetch) (uri (cran-uri "adegenet" version)) (sha256 (base32 - "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407")))) + "0sxbw5l92xmkazndxbqaa2cxmgk8bqzzbk77q9li850s2i1fdssp")))) (build-system r-build-system) (propagated-inputs `(("r-ade4" ,r-ade4) @@ -15420,13 +16711,13 @@ also provided to illustrate various methods.") (define-public r-pegas (package (name "r-pegas") - (version "0.14") + (version "1.0-1") (source (origin (method url-fetch) (uri (cran-uri "pegas" version)) (sha256 - (base32 "0lr06gajzdanj8ax91kgpxsj863m367v2s1z5gnxps3999n0xybx")))) + (base32 "0ykx84p7c8cad5d1mj8cm1d5cz2paacdjx4ll4qzmq827lcyycz1")))) (build-system r-build-system) (propagated-inputs `(("r-adegenet" ,r-adegenet) @@ -15593,14 +16884,14 @@ generalized linear models, and quantile regression.") (define-public r-arsenal (package (name "r-arsenal") - (version "3.6.2") + (version "3.6.3") (source (origin (method url-fetch) (uri (cran-uri "arsenal" version)) (sha256 (base32 - "0spm0s23xs5bm88slkz6a65mbs663qhnravwxp7rkdkr378vb5fn")))) + "0qvs3ld28djnjnggdhqjwq8sbv8zz322qahlvf7dnx35yqf6xkms")))) (properties `((upstream-name . "arsenal"))) (build-system r-build-system) (propagated-inputs `(("r-knitr" ,r-knitr))) @@ -15632,14 +16923,14 @@ include (define-public r-haplo-stats (package (name "r-haplo-stats") - (version "1.8.6") + (version "1.8.7") (source (origin (method url-fetch) (uri (cran-uri "haplo.stats" version)) (sha256 (base32 - "1imz4gs0n57vixwwbirrihpgvn2pyj5da4rgjcjk14n2xkk0nay7")))) + "1q2zn72j92bwhcdswk4qqfgzch56p9pcy2xhkd3safvqp3l9rzpw")))) (properties `((upstream-name . "haplo.stats"))) (build-system r-build-system) (propagated-inputs @@ -15661,14 +16952,14 @@ examples in the vignette.") (define-public r-bqtl (package (name "r-bqtl") - (version "1.0-32") + (version "1.0-33") (source (origin (method url-fetch) (uri (cran-uri "bqtl" version)) (sha256 (base32 - "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci")))) + "1sbzpi9z94f010lw2y1gmifjrvpmiqs4m26za7vr1xz72azrqvs9")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/") @@ -15681,14 +16972,14 @@ lines. It includes maximum likelihood and Bayesian tools.") (define-public r-ibdreg (package (name "r-ibdreg") - (version "0.3.1") + (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "ibdreg" version)) (sha256 (base32 - "0kgx9iavgm6d6njhki7bm82d6lw2c7kcch2pryd339js2hm0l5gq")))) + "1x8z0vr2cmdks12hxfm0wwxskb0cr669w5j5rpa2ln8q704yy41g")))) (build-system r-build-system) (home-page "https://www.mayo.edu/research/labs/\ statistical-genetics-genetic-epidemiology/software") @@ -15799,22 +17090,28 @@ SELECT or UPDATE queries to an end-point.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.21") + (version "0.24") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "0xms1srx9l2mn8xaxnpic0s21y8k56bhwpj45wy7b0yscmxgmh27")))) + "1qqvvfbpbd6sin8vpvr3zzlhlyx1i6b98yp77xj5zl220nid5slb")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) + ("r-jquerylib" ,r-jquerylib) ("r-knitr" ,r-knitr) ("r-rmarkdown" ,r-rmarkdown) ("r-tinytex" ,r-tinytex) ("r-xfun" ,r-xfun) ("r-yaml" ,r-yaml) ("pandoc" ,pandoc))) + ;; We cannot add knitr because this package depends on xfun, which is an + ;; input to knitr. + #; + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/rstudio/bookdown") (synopsis "Authoring books and technical documents with R markdown") (description "This package provides output formats and utilities for @@ -15967,14 +17264,14 @@ the corresponding outputs (tables and graphs).") (define-public r-rjava (package (name "r-rjava") - (version "0.9-13") + (version "1.0-5") (source (origin (method url-fetch) (uri (cran-uri "rJava" version)) (sha256 (base32 - "1x3mihyqzr61j52rwaqciw43mkjzmhib4s6qf57v6xj40ksqh5jv")))) + "1pkgndppk498by44sai440l3i7vzndknbngn1q748cv39xvsbnrg")))) (properties `((upstream-name . "rJava"))) (build-system r-build-system) (arguments @@ -16001,7 +17298,6 @@ the corresponding outputs (tables and graphs).") (inputs `(("icu4c" ,icu4c) ("jdk" ,icedtea-8 "jdk") - ("pcre" ,pcre) ("zlib" ,zlib))) (home-page "https://www.rforge.net/rJava/") (synopsis "Low-Level R to Java interface") @@ -16014,16 +17310,18 @@ and accessing fields.") (define-public r-svmisc (package (name "r-svmisc") - (version "1.1.0") + (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "svMisc" version)) (sha256 (base32 - "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2")))) + "0y8mhiblyzwads4gf4whmxi7c6wdmqs3ahbj132l79bbdk40p83a")))) (properties `((upstream-name . "svMisc"))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/SciViews/svMisc") (synopsis "Miscellaneous functions for SciViews") (description @@ -16061,14 +17359,14 @@ interaction search in high-dimensional data.") (define-public r-rttf2pt1 (package (name "r-rttf2pt1") - (version "1.3.8") + (version "1.3.9") (source (origin (method url-fetch) (uri (cran-uri "Rttf2pt1" version)) (sha256 (base32 - "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn")))) + "0w9ybqvr4bvpa2dyfkrscg4in0x2dkzmxdn1n6003j1rss7f8rw6")))) (properties `((upstream-name . "Rttf2pt1"))) (build-system r-build-system) (home-page "https://github.com/wch/Rttf2pt1") @@ -16156,20 +17454,52 @@ The extrafont package makes both of these things easier.") the XKCD web comic.") (license license:gpl3))) +(define-public r-babelgene + (package + (name "r-babelgene") + (version "21.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "babelgene" version)) + (sha256 + (base32 + "1gk5pm3b3shr1id66a11ywc1b823gbj8yckg24szzfhj8g4ixyf0")))) + (properties `((upstream-name . "babelgene"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-rlang" ,r-rlang))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page + "https://igordot.github.io/babelgene/") + (synopsis "Gene orthologs for model organisms in a Tidy data format") + (description + "Genomic analysis of model organisms often requires the use of databases +based on human data or making comparisons to patient-derived resources. This +requires converting genes between human and non-human analogues. The +babelgene R package provides predicted gene orthologs/homologs for frequently +studied model organisms in an R-friendly tidy/long format. The package +integrates orthology assertion predictions sourced from multiple databases as +compiled by the HGNC Comparison of Orthology Predictions (HCOP).") + (license license:expat))) + (define-public r-msigdbr (package (name "r-msigdbr") - (version "7.2.1") + (version "7.4.1") (source (origin (method url-fetch) (uri (cran-uri "msigdbr" version)) (sha256 (base32 - "1rc2p9vw57pn4prmfgay4w18qd53ggq7wxfsi9kp7w25ciip1dq1")))) + "103m52av68pkjfh8f81qh6j3cs1mj1lg831ciwybr34cax767jr1")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) + `(("r-babelgene" ,r-babelgene) + ("r-dplyr" ,r-dplyr) ("r-magrittr" ,r-magrittr) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble) @@ -16237,22 +17567,42 @@ improvements over the @code{convertColor} function in the @code{grDevices} package.") (license license:expat))) +(define-public r-yulab-utils + (package + (name "r-yulab-utils") + (version "0.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "yulab.utils" version)) + (sha256 + (base32 + "1haq6k0r64gs76p2vvrm42m64r8s32kzyz573pw9789y32zn0s5q")))) + (properties `((upstream-name . "yulab.utils"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=yulab.utils") + (synopsis "Supporting functions for packages maintained by YuLab-SMU") + (description + "Miscellaneous functions commonly used by YuLab-SMU, such as +@code{install_zip_gh} to install R packages from Github ZIP files.") + (license license:artistic2.0))) + (define-public r-ggplotify (package (name "r-ggplotify") - (version "0.0.5") + (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "ggplotify" version)) (sha256 (base32 - "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3")))) + "12mk3fa8fdjxj7xxz21jkr7h91w5wdgwjqhszcz1qffwsgb773qp")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-gridgraphics" ,r-gridgraphics) - ("r-rvcheck" ,r-rvcheck))) + ("r-yulab-utils" ,r-yulab-utils))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/GuangchuangYu/ggplotify") @@ -16402,14 +17752,14 @@ that fills this gap.") (define-public r-europepmc (package (name "r-europepmc") - (version "0.4") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "europepmc" version)) (sha256 (base32 - "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym")))) + "16japbndid34shqg8n0bmjrxn84xmhrylvz832zclcllm6i93fn1")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -16665,7 +18015,7 @@ and Learning to Rank measures (LambdaMart).") (format #t "Processing ~a --> ~a~%" source target) (delete-file target) - (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) + (let ((minified (open-pipe* OPEN_READ "uglifyjs" source))) (call-with-output-file target (lambda (port) (dump-port minified port))))) @@ -16677,7 +18027,7 @@ and Learning to Rank measures (LambdaMart).") ("r-htmlwidgets" ,r-htmlwidgets) ("r-igraph" ,r-igraph))) (native-inputs - `(("uglify-js" ,uglify-js) + `(("uglifyjs" ,node-uglify-js) ("js-jquery" ,(origin (method url-fetch) @@ -16790,6 +18140,31 @@ matrix and displays the significance level on the plot. It also includes a function for computing a matrix of correlation p-values.") (license license:gpl2))) +(define-public r-ggfun + (package + (name "r-ggfun") + (version "0.0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggfun" version)) + (sha256 + (base32 + "07njcjcj212zxanq8x3nkh7mgvqmym08rx5s41rz9flhk9gkc9jr")))) + (properties `((upstream-name . "ggfun"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-rlang" ,r-rlang))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/package=ggfun") + (synopsis "Miscellaneous functions for ggplot2") + (description + "This package provides useful functions to edit ggplot object (e.g., +setting fonts for theme and layers, adding rounded rectangle as background for +each of the legends).") + (license license:artistic2.0))) + (define-public r-gridtext (package (name "r-gridtext") @@ -16912,7 +18287,7 @@ etc.). Text boxes with automatic word wrap are also supported.") (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) - (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) + (let ((minified (open-pipe* OPEN_READ "uglifyjs" source))) (call-with-output-file target (lambda (port) (dump-port minified port))))) @@ -16926,7 +18301,7 @@ etc.). Text boxes with automatic word wrap are also supported.") ("r-rmarkdown" ,r-rmarkdown) ("r-shiny" ,r-shiny))) (native-inputs - `(("uglify-js" ,uglify-js) + `(("uglifyjs" ,node-uglify-js) ("js-raphael" ,(origin (method url-fetch) @@ -17062,6 +18437,119 @@ making it possible to download files over HTTPS across platforms. The external dependencies. This package has is implemented purely in R.") (license license:gpl2))) +(define-public r-aplot + (package + (name "r-aplot") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "aplot" version)) + (sha256 + (base32 + "067yzy35spvs6jbccqpmvnjilglxzda6qqlqhjv311kfvnppzsyf")))) + (properties `((upstream-name . "aplot"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggfun" ,r-ggfun) + ("r-ggplot2" ,r-ggplot2) + ("r-ggplotify" ,r-ggplotify) + ("r-magrittr" ,r-magrittr) + ("r-patchwork" ,r-patchwork) + ("r-yulab-utils" ,r-yulab-utils))) + (home-page "https://github.com/YuLab-SMU/aplot") + (synopsis "Decorate a ggplot with associated information") + (description + "Users may want to align plots with associated information that requires +axes to be exactly matched in subplots, e.g. hierarchical clustering with a +heatmap. This package provides utilities to align associated subplots to a +main plot at different sides (left, right, top and bottom) with axes exactly +matched.") + (license license:artistic2.0))) + +(define-public r-ggnewscale + (package + (name "r-ggnewscale") + (version "0.4.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggnewscale" version)) + (sha256 + (base32 + "1hjysfagd2lqy8yivqq9q7l6hbvyq8kasw3zqh5fk9xn18ikc702")))) + (properties `((upstream-name . "ggnewscale"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2))) + (home-page "https://cran.r-project.org/package=ggnewscale") + (synopsis "Multiple fill and color scales in ggplot2") + (description + "This package lets you use multiple fill and color scales in ggplot2.") + (license license:gpl3))) + +(define-public r-ggpointdensity + (package + (name "r-ggpointdensity") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggpointdensity" version)) + (sha256 + (base32 + "0c9a14j3b0hvamqylhzldw2hjdxmfbllwahjkf3gg2rw337ld9iy")))) + (properties + `((upstream-name . "ggpointdensity"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2))) + (home-page "https://github.com/LKremer/ggpointdensity") + (synopsis "Cross between a 2D density plot and a scatter plot") + (description + "This package provides a cross between a 2D density plot and a scatter +plot, implemented as a ggplot2 @code{geom}. Points in the scatter plot are +colored by the number of neighboring points. This is useful to visualize the +2D-distribution of points in case of overplotting.") + (license license:gpl3))) + +(define-public r-arrow + (package + (name "r-arrow") + (version "5.0.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "arrow" version)) + (sha256 + (base32 + "1ajkcmasj22j5k15ms7iyd1rg9qpdj5jya6nmhzh8z4iiv7gy13j")))) + (properties `((upstream-name . "arrow"))) + (build-system r-build-system) + (inputs + `(("apache-arrow" ,apache-arrow "lib") + ("zlib" ,zlib))) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-bit64" ,r-bit64) + ("r-purrr" ,r-purrr) + ("r-r6" ,r-r6) + ("r-rlang" ,r-rlang) + ("r-tidyselect" ,r-tidyselect) + ("r-vctrs" ,r-vctrs))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) + (home-page "https://github.com/apache/arrow/") + (synopsis "R integration to Apache Arrow") + (description + "Apache Arrow is a cross-language development platform for in-memory +data. It specifies a standardized language-independent columnar memory format +for flat and hierarchical data, organized for efficient analytic operations on +modern hardware. This package provides an R interface to the Arrow C++ +library.") + (license license:asl2.0))) + (define-public r-rex (package (name "r-rex") @@ -17087,6 +18575,160 @@ they are often difficult to interpret. Rex allows you to build complex regular expressions from human readable expressions") (license license:expat))) +(define-public r-mlapi + (package + (name "r-mlapi") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "mlapi" version)) + (sha256 + (base32 + "023vk5bp8cjcq88sapkl87kdxr92bay1dyxl6xirnyj699pyj51k")))) + (properties `((upstream-name . "mlapi"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-r6" ,r-r6))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/package=mlapi") + (synopsis "Abstract classes for building scikit-learn like API") + (description + "This package provides R6 abstract classes for building machine learning +models with a scikit-learn like API. Scikit-learn is a popular module for the +Python programming language whose design became a de facto standard in +industry for machine learning tasks.") + (license license:expat))) + +(define-public r-float + (package + (name "r-float") + (version "0.2-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "float" version)) + (sha256 + (base32 + "1bx5yxkb123001v31jjk7h7f0qissmjydvbil5cj3jvmqkayq1a1")))) + (properties `((upstream-name . "float"))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://github.com/wrathematics/float") + (synopsis "32-bit floats") + (description + "R comes with a suite of utilities for linear algebra with +\"numeric\" (double precision) vectors/matrices. However, sometimes single +precision (or less!) is more than enough for a particular task. This package +extends R's linear algebra facilities to include 32-bit float (single +precision) data. Float vectors/matrices have half the precision of their +\"numeric\"-type counterparts but are generally faster to numerically operate +on, for a performance vs accuracy trade-off.") + (license license:bsd-2))) + +(define-public r-rsparse + (package + (name "r-rsparse") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rsparse" version)) + (sha256 + (base32 + "1blg59gsidh0sn6yy761pisz2phml0hzgqc24s5s8q9q903rddr9")))) + (properties `((upstream-name . "rsparse"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-float" ,r-float) + ("r-lgr" ,r-lgr) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rhpcblasctl" ,r-rhpcblasctl))) + (home-page "https://github.com/rexyai/rsparse") + (synopsis "Statistical learning on sparse matrices") + (description + "This package implements many algorithms for statistical learning on +sparse matrices: matrix factorizations, matrix completion, elastic net +regressions, factorization machines. The rsparse package also enhances the +Matrix package by providing methods for multithreaded <sparse, dense> matrix +products and native slicing of the sparse matrices in @dfn{Compressed Sparse +Row} (CSR) format.") + (license license:gpl2+))) + +(define-public r-text2vec + (package + (name "r-text2vec") + (version "0.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "text2vec" version)) + (sha256 + (base32 + "0r75cv77x2zm1z66s95hic71dpbqmybz39n48q6mz7gfd3m7312y")))) + (properties `((upstream-name . "text2vec"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-digest" ,r-digest) + ("r-lgr" ,r-lgr) + ("r-matrix" ,r-matrix) + ("r-mlapi" ,r-mlapi) + ("r-r6" ,r-r6) + ("r-rcpp" ,r-rcpp) + ("r-rsparse" ,r-rsparse) + ("r-stringi" ,r-stringi))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "http://text2vec.org") + (synopsis "Text mining framework for R") + (description + "This package provides fast and memory-friendly tools for text +vectorization, topic modeling (LDA, LSA), word embeddings (GloVe), +similarities. It provides a source-agnostic streaming API, which allows +researchers to perform analysis of collections of documents which are larger +than available RAM. All core functions are parallelized to benefit from +multicore machines.") + (license license:gpl2+))) + +(define-public r-mcmcpack + (package + (name "r-mcmcpack") + (version "1.5-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "MCMCpack" version)) + (sha256 + (base32 + "1khavqsimiwbfq7gyw5jyj67jxfd579pnc7mngnd655zc8yzspvr")))) + (properties `((upstream-name . "MCMCpack"))) + (build-system r-build-system) + (propagated-inputs + `(("r-coda" ,r-coda) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-mcmc" ,r-mcmc) + ("r-quantreg" ,r-quantreg))) + (home-page "https://cran.r-project.org/package=MCMCpack") + (synopsis "Markov Chain Monte Carlo (MCMC) package") + (description + "This package contains functions to perform Bayesian inference using +posterior simulation for a number of statistical models. Most simulation is +done in compiled C++ written in the Scythe Statistical Library. All models +return @code{coda} @code{mcmc} objects that can then be summarized using the +@code{coda} package. Some useful utility functions such as density functions, +pseudo-random number generators for statistical distributions, a general +purpose Metropolis sampling algorithm, and tools for visualization are +provided.") + (license license:gpl3))) + (define-public r-xmlparsedata (package (name "r-xmlparsedata") @@ -17205,18 +18847,24 @@ batch correction, and data correction.") (define-public r-styler (package (name "r-styler") - (version "1.4.1") + (version "1.6.2") (source (origin (method url-fetch) (uri (cran-uri "styler" version)) (sha256 (base32 - "10fj4cnazicb2z9djbv5pszcmrf7wbzagbjvksffqpdc5vbbbw5x")))) + "0p7p2mh4f469drfn5z4wc4xrg06mpnm9wkw76fghclf8m9vcqbx6")))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs `(("r-backports" ,r-backports) ("r-cli" ,r-cli) + ("r-glue" ,r-glue) ("r-magrittr" ,r-magrittr) ("r-purrr" ,r-purrr) ("r-r-cache" ,r-r-cache) @@ -17338,14 +18986,14 @@ experiments in a well-organized and reproducible way.") (define-public r-clue (package (name "r-clue") - (version "0.3-58") + (version "0.3-59") (source (origin (method url-fetch) (uri (cran-uri "clue" version)) (sha256 (base32 - "1rwwxlnpl1k0n4k96vxc9zajw9kb4syqwzj76fvaf0qim8p6ddia")))) + "0ychvjbqkcgqdp5gy4hsi4297phywd7fj89y3yi5ckmnmjb39kjm")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster))) (home-page "https://cran.r-project.org/web/packages/clue/") @@ -17383,19 +19031,21 @@ dimensional low-discrepancy sequence.") (define-public r-dqrng (package (name "r-dqrng") - (version "0.2.1") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "dqrng" version)) (sha256 (base32 - "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1")))) + "1fwsldqcri2lccna4icbmmlqic3w4xyjm7rn0xmikrsw4kzapvjb")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-rcpp" ,r-rcpp) ("r-sitmo" ,r-sitmo))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://www.daqana.org/dqrng") (synopsis "Fast pseudo random number generators") (description @@ -17415,14 +19065,14 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.") (define-public r-ingredients (package (name "r-ingredients") - (version "2.0.1") + (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "ingredients" version)) (sha256 (base32 - "0w46h1f28y5ypqm3ypsvk7yk9v7k8p21f1pzjl3ima8r1ivmhv12")))) + "11bv4l4fn9kr7y2nfzrwnaya8fi9w3nwcm9vzlqb7dva83rkqbsc")))) (properties `((upstream-name . "ingredients"))) (build-system r-build-system) (propagated-inputs @@ -17455,14 +19105,14 @@ feature effects. Key functions are: (define-public r-ibreakdown (package (name "r-ibreakdown") - (version "1.3.1") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "iBreakDown" version)) (sha256 (base32 - "1bfl5bh0x6z5a0cmdmx68sap9zdxa3kwdnyk57csxapc362yz108")))) + "00jzrndb3ahsv6ihp2pvs732n9cc944m83vdinrl9v1pxd82prkh")))) (properties `((upstream-name . "iBreakDown"))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) @@ -17481,14 +19131,14 @@ classification and regression models.") (define-public r-dae (package (name "r-dae") - (version "3.1-37") + (version "3.2-11") (source (origin (method url-fetch) (uri (cran-uri "dae" version)) (sha256 (base32 - "102fgbdpn7yvm1zj180cv4sr1096sz35d4gndsv7w9kriqyi1c1l")))) + "0jrdfaw6aqv7k323yscsfpdkb3c4vi5ibncl6m96b9820pvycsz8")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -17520,14 +19170,14 @@ been used in the call to @code{aov}.") (define-public r-dalex (package (name "r-dalex") - (version "2.2.0") + (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 - "1qnjbhilv4jfmwqxfi9xc5ysrh8gr84a2a5imjfci7d1n3zcnryn")))) + "0x8rcl3p1h1dpzgsfnalfjhvv345gg5v0z8dxqwrk6i32xk5wmzb")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs @@ -17576,14 +19226,14 @@ annotated biological functions.") (define-public r-plot3d (package (name "r-plot3d") - (version "1.3") + (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "plot3D" version)) (sha256 (base32 - "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r")))) + "1h59zlsyzbjylaziwavppl9bjmnba4iiq34772y3dys6fqclajnh")))) (properties `((upstream-name . "plot3D"))) (build-system r-build-system) (propagated-inputs `(("r-misc3d" ,r-misc3d))) @@ -17598,14 +19248,14 @@ includes data sets from oceanography.") (define-public r-ggfortify (package (name "r-ggfortify") - (version "0.4.11") + (version "0.4.12") (source (origin (method url-fetch) (uri (cran-uri "ggfortify" version)) (sha256 (base32 - "1wfm7l9bz6msh7rflgfv9dgbxh1ikz2ay0v7sgk9nkc24y6lhbpk")))) + "13f3ggn94czw7xw5qxwrdncr2h7z7bvwgw8zxni8wkc8x3kbz5rd")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -17695,17 +19345,18 @@ the current document.") (define-public r-xgboost (package (name "r-xgboost") - (version "1.3.2.1") + (version "1.4.1.1") (source (origin (method url-fetch) (uri (cran-uri "xgboost" version)) (sha256 (base32 - "117q8xqm82589517fi8xicd8724v9c0wnq3qpl84h6nm3aw65x1g")))) + "1i706h6yhayzbqlqa1z6fgjc56kxm3isz0jw6d26fpyfjlw6z64z")))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) + ("r-jsonlite" ,r-jsonlite) ("r-magrittr" ,r-magrittr) ("r-matrix" ,r-matrix))) (native-inputs @@ -17845,14 +19496,14 @@ path of values for the regularization parameter.") (define-public r-rhpcblasctl (package (name "r-rhpcblasctl") - (version "0.20-137") + (version "0.21-247") (source (origin (method url-fetch) (uri (cran-uri "RhpcBLASctl" version)) (sha256 (base32 - "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv")))) + "09276fpkj6xa0zpzzdckclj923b0xr0rhfjiiwfli3kyqi2m37v2")))) (properties `((upstream-name . "RhpcBLASctl"))) (build-system r-build-system) (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/") @@ -17913,14 +19564,14 @@ computed using the L1 (Manhattan, taxicab) metric.") (define-public r-leiden (package (name "r-leiden") - (version "0.3.7") + (version "0.3.9") (source (origin (method url-fetch) (uri (cran-uri "leiden" version)) (sha256 (base32 - "14iqn5iqcya6bqbjvjivpd7q9gwc323sj29y7ssrbhb3sz9982bp")))) + "03gaxpcab3a1av5lk8r5ll1s858gvyx5ndknci1sia96w1v44xc1")))) (properties `((upstream-name . "leiden"))) (build-system r-build-system) (propagated-inputs @@ -18118,14 +19769,14 @@ both R code and compiled C/C++/FORTRAN code.") (define-public r-systemfonts (package (name "r-systemfonts") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "systemfonts" version)) (sha256 (base32 - "15x7qx8iigkybgz6b6s66i3mh75vgynzpd50nw05wflfwzcv87a0")))) + "1a9nzd4nqawr6ni3mw7xc2yq77fb2f91aarnc906mq26510rdb11")))) (properties `((upstream-name . "systemfonts"))) (build-system r-build-system) (propagated-inputs @@ -18176,14 +19827,14 @@ emphasize hidden group structures in networks or focus on specific nodes.") (define-public r-terra (package (name "r-terra") - (version "1.1-4") + (version "1.3-22") (source (origin (method url-fetch) (uri (cran-uri "terra" version)) (sha256 (base32 - "1vsh55sq56shc8s2vmkl27yvrdbrbn3l6jrigqf2hmvppkb2jsbg")))) + "1z5zql68q4n81ccpl02hndhbavhhqs65bli1hjxlqdwdq192whkh")))) (properties `((upstream-name . "terra"))) (build-system r-build-system) (inputs @@ -18301,14 +19952,14 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.12.0") + (version "0.14.0") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "0dfqn4l4qmlpwmdva2ahyhlngkzdm0sgiirbdrf3mbbw52bhlmpm")))) + "03x2h8izbpz9cq25i0a6dh99m26a9isgpv4kxsfkx97qzlh9cd67")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs @@ -18330,13 +19981,13 @@ effect size.") (define-public r-rgdal (package (name "r-rgdal") - (version "1.5-23") + (version "1.5-27") (source (origin (method url-fetch) (uri (cran-uri "rgdal" version)) (sha256 - (base32 "0vnb7kw762y349pda4aq1hx0smafylmn3635l963qykfji5p99cw")))) + (base32 "0mjpxs2dvbngbchlb0kfs0jcac7v88slwxmka81ds92lggnmb9b2")))) (properties `((upstream-name . "rgdal"))) (build-system r-build-system) (inputs @@ -18386,14 +20037,14 @@ atmospheric physics.") (define-public r-lifecycle (package (name "r-lifecycle") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "lifecycle" version)) (sha256 (base32 - "13hgxk93q9387s8dnqpm8dfx610y0pr76khqksj4kbgj2fr4lcq3")))) + "183v1z1h037pvsgrj6vakpwhnhsr29hsw8p16k59dgpi00f6x9qx")))) (properties `((upstream-name . "lifecycle"))) (build-system r-build-system) (propagated-inputs @@ -18465,13 +20116,13 @@ programming problems.") (define-public r-desolve (package (name "r-desolve") - (version "1.28") + (version "1.29") (source (origin (method url-fetch) (uri (cran-uri "deSolve" version)) (sha256 - (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac")))) + (base32 "02hrd31ky9id7q2bwkj436j4fj4xbs3j9sfmyi1nl7hml5dy2vr6")))) (properties `((upstream-name . "deSolve"))) (build-system r-build-system) (native-inputs @@ -18555,18 +20206,20 @@ as a boxplot function.") (define-public r-bio3d (package (name "r-bio3d") - (version "2.4-1") + (version "2.4-2") (source (origin (method url-fetch) (uri (cran-uri "bio3d" version)) (sha256 (base32 - "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7")))) + "1jvcmpzi9knhxq5jsbhg8slm8hnlx2y8smmwwrbnbyd0rmk5fhci")))) (properties `((upstream-name . "bio3d"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "http://thegrantlab.org/bio3d/") (synopsis "Biological structure analysis") (description @@ -18654,14 +20307,14 @@ tools for help in data interpretation.") (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) - (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) + (let ((minified (open-pipe* OPEN_READ "uglifyjs" source))) (call-with-output-file target (lambda (port) (dump-port minified port))))) sources targets)))) #t))))) (native-inputs - `(("uglify-js" ,uglify-js) + `(("uglifyjs" ,node-uglify-js) ;; NOTE: Make sure that this version of d3 is still valid when ;; upgrading the package. ("d3.v4.js" @@ -18890,50 +20543,39 @@ cell free DNA} (cfDNA).") (define-public r-rintrojs (package (name "r-rintrojs") - (version "0.2.2") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "rintrojs" version)) (sha256 (base32 - "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427")))) + "00l5mk80gj3xkbf3m1kip566ic98bhd88lh0bg69ybkpk4gifpyw")) + (snippet + '(delete-file "inst/javascript/introjs/intro.min.js")))) (properties `((upstream-name . "rintrojs"))) (build-system r-build-system) (arguments - `(#:modules ((guix build utils) - (guix build r-build-system) - (srfi srfi-1) - (ice-9 popen)) - #:phases + `(#:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/javascript/introjs/" - (call-with-values - (lambda () - (unzip2 - `((,(assoc-ref inputs "intro.js") - "intro.min.js")))) - (lambda (sources targets) - (for-each (lambda (source target) - (format #t "Processing ~a --> ~a~%" - source target) - (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) - (call-with-output-file target - (lambda (port) - (dump-port minified port))))) - sources targets)))) - #t))))) + (let ((source (assoc-ref inputs "intro.js")) + (target "intro.min.js")) + (format #true "Processing ~a --> ~a~%" + source target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))))))))) (native-inputs - `(("uglify-js" ,uglify-js) + `(("esbuild" ,esbuild) ("intro.js" ,(origin (method url-fetch) - (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js") + (uri "https://cdn.jsdelivr.net/npm/[email protected]/intro.js") (sha256 (base32 - "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8")))))) + "0vh5n7hqqyx2pdvlqq6xadfqibcn78h5961rwhpf817kpxfzv8v7")))))) (propagated-inputs `(("r-jsonlite" ,r-jsonlite) ("r-shiny" ,r-shiny))) @@ -18945,19 +20587,20 @@ Intro.js} library. This package makes it easy to include step-by-step introductions, and clickable hints in a Shiny application. It supports both static introductions in the UI, and programmatic introductions from the server-side.") - (license license:agpl3+))) + ;; The intro.js library is licensed under Expat. + (license (list license:agpl3+ license:expat)))) (define-public r-sysfonts (package (name "r-sysfonts") - (version "0.8.3") + (version "0.8.5") (source (origin (method url-fetch) (uri (cran-uri "sysfonts" version)) (sha256 (base32 - "00kbazxw6zd1kakfshffdj928krca53bw9k78k0zar40mbqxiwd5")))) + "1fhf0x5sqx3mv72j9d0clkq1qzqiqxbxn1h808f7ccf0mb04v43y")))) (properties `((upstream-name . "sysfonts"))) (build-system r-build-system) (inputs @@ -18998,14 +20641,14 @@ package.") (define-public r-showtext (package (name "r-showtext") - (version "0.9-2") + (version "0.9-4") (source (origin (method url-fetch) (uri (cran-uri "showtext" version)) (sha256 (base32 - "0y5mw6ffk92r7b22irrfhdmj4hxfl0d1wjxj14hznbapc4qm6f0z")))) + "1gvj32wrs5q31bmg5dy6n85d0igm3jhkldhdv8kscw0pfrk89y36")))) (properties `((upstream-name . "showtext"))) (build-system r-build-system) (inputs @@ -19032,14 +20675,14 @@ such as Ghostscript is needed to use this package.") (define-public r-emojifont (package (name "r-emojifont") - (version "0.5.3") + (version "0.5.5") (source (origin (method url-fetch) (uri (cran-uri "emojifont" version)) (sha256 (base32 - "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k")))) + "1hhrwilv36hd9gs1kcl2zsi6519md0h9aixjrm6lfclxvz8r6k1i")))) (properties `((upstream-name . "emojifont"))) (build-system r-build-system) (propagated-inputs @@ -19047,6 +20690,8 @@ such as Ghostscript is needed to use this package.") ("r-proto" ,r-proto) ("r-showtext" ,r-showtext) ("r-sysfonts" ,r-sysfonts))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://guangchuangyu.github.io/emojifont") (synopsis "Emoji and Font Awesome in R graphics") (description @@ -19086,14 +20731,14 @@ included.") (define-public r-qgam (package (name "r-qgam") - (version "1.3.2") + (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "qgam" version)) (sha256 (base32 - "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7")))) + "0vx2wf3rqc3j8i0870xrwxndkbgza0nnh7f0yxi8h67lfi7gws4s")))) (properties `((upstream-name . "qgam"))) (build-system r-build-system) (propagated-inputs @@ -19146,26 +20791,50 @@ elicitation options based on Kass and Vaidyanathan (1992) @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.") (license license:gpl2+))) +(define-public r-reldist + (package + (name "r-reldist") + (version "1.6-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "reldist" version)) + (sha256 + (base32 + "09vips7spcz0fahrpy0bl15hk43zgnq74h189hmygyi41l95aywa")))) + (properties `((upstream-name . "reldist"))) + (build-system r-build-system) + (propagated-inputs + `(("r-hmisc" ,r-hmisc) + ("r-mgcv" ,r-mgcv))) + (home-page "http://www.stat.ucla.edu/~handcock/RelDist") + (synopsis "Relative distribution methods") + (description + "This package provides tools for the comparison of distributions. This +includes nonparametric estimation of the relative distribution PDF and CDF and +numerical summaries as described in \"Relative Distribution Methods in the +Social Sciences\" by Mark S. Handcock and Martina Morris, Springer-Verlag, +1999, Springer-Verlag, ISBN 0387987789.") + ;; See also https://cran.r-project.org/web/packages/reldist/LICENSE for + ;; attribution requirements. + (license license:gpl3))) + (define-public r-accept (package (name "r-accept") - (version "0.7.1") + (version "0.8.3") (source (origin (method url-fetch) (uri (cran-uri "accept" version)) (sha256 (base32 - "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y")))) + "0qn4lm6bk0z2iijwsfbymx1c9y39988fw124ncgmlrgw5kv80b7x")))) (properties `((upstream-name . "accept"))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) - ("r-extrafont" ,r-extrafont) - ("r-mass" ,r-mass) - ("r-plotly" ,r-plotly) - ("r-stringr" ,r-stringr) - ("r-viridis" ,r-viridis))) + ("r-reldist" ,r-reldist))) (home-page "https://cran.r-project.org/web/packages/accept/") (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)") (description @@ -19451,6 +21120,31 @@ introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.") (license license:bsd-3))) +(define-public r-rnmf + (package + (name "r-rnmf") + (version "0.5.0") + (source (origin + (method url-fetch) + (uri (cran-uri "rNMF" version)) + (sha256 + (base32 + "1nz6h0j5ywdh48m0swmhp34hbkycd7n13rclrxaw85qi9wc42597")))) + (build-system r-build-system) + (propagated-inputs + `(("r-knitr" ,r-knitr) + ("r-nnls" ,r-nnls))) + (home-page "https://cran.r-project.org/web/packages/rNMF/") + (synopsis "Robust nonnegative matrix factorization") + (description + "This package provides an implementation of robust nonnegative matrix +factorization (rNMF). The rNMF algorithm decomposes a nonnegative high +dimension data matrix into the product of two low rank nonnegative matrices, +while detecting and trimming outliers. The main function is @code{rnmf()}. +The package also includes a visualization tool, @code{see()}, that arranges +and prints vectorized images.") + (license license:gpl2+))) + (define-public r-randtoolbox (package (name "r-randtoolbox") @@ -19491,14 +21185,14 @@ See e.g. Gentle (2003) @url{doi:10.1007/b97336}.") (define-public r-lhs (package (name "r-lhs") - (version "1.1.1") + (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "lhs" version)) (sha256 (base32 - "1p4h03qlijs2a59wfd4rlvdlb9i87pw2zm8xsjd6yzz8vlm9yglh")))) + "1l861h76q5w0nbnbybhgg7hiw7fks677jakyd49n1whwvd48sfz4")))) (properties `((upstream-name . "lhs"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) @@ -19843,6 +21537,11 @@ the @code{aroma.affymetrix} package.") "08xv8b3c81nf54viyr3w912al18483k5gfnjpg7bxbdfk70dfzbh")))) (properties `((upstream-name . "R.filesets"))) (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs `(("r-digest" ,r-digest) ("r-r-cache" ,r-r-cache) @@ -19942,14 +21641,14 @@ provided as well.") (define-public r-tuner (package (name "r-tuner") - (version "1.3.3") + (version "1.3.3.1") (source (origin (method url-fetch) (uri (cran-uri "tuneR" version)) (sha256 (base32 - "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx")))) + "12nixpqrc5gp7p2clr7ia6jwb0jq2i3brlxiwlp00ixmnm5g1jyd")))) (properties `((upstream-name . "tuneR"))) (build-system r-build-system) (propagated-inputs `(("r-signal" ,r-signal))) @@ -19966,14 +21665,14 @@ transcription, ...") (define-public r-seewave (package (name "r-seewave") - (version "2.1.6") + (version "2.1.8") (source (origin (method url-fetch) (uri (cran-uri "seewave" version)) (sha256 (base32 - "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844")))) + "1szcvryvl4kb3av2pcvl14bz6whl7xrq4wb1ck6w7lfc4mrlirhh")))) (properties `((upstream-name . "seewave"))) (build-system r-build-system) (inputs @@ -20159,6 +21858,23 @@ modeling often used in @dfn{analytical customer relationship management} (aCRM).") (license license:gpl2+))) +(define-public r-tree + (package + (name "r-tree") + (version "1.0-41") + (source (origin + (method url-fetch) + (uri (cran-uri "tree" version)) + (sha256 + (base32 + "13jwdxx3na16mly176n01zdkaqn4a8x9fc43rq5xx5vx31drkkr1")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/tree/") + (synopsis "Classification and regression trees") + (description "This package provides procedures to work with classification +and regression trees.") + (license license:gpl2+))) + (define-public r-treeclust (package (name "r-treeclust") @@ -20369,14 +22085,14 @@ allowed.") (define-public r-gdina (package (name "r-gdina") - (version "2.8.0") + (version "2.8.7") (source (origin (method url-fetch) (uri (cran-uri "GDINA" version)) (sha256 (base32 - "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7")))) + "08cdjp4mqn81j3wa770v7n8zkslys9jqqb3d3c09dkfmgdk6hga4")))) (properties `((upstream-name . "GDINA"))) (build-system r-build-system) (propagated-inputs @@ -20832,14 +22548,14 @@ API; see the package vignette for details.") (define-public r-actuar (package (name "r-actuar") - (version "3.1-2") + (version "3.1-4") (source (origin (method url-fetch) (uri (cran-uri "actuar" version)) (sha256 (base32 - "0gaqm8bkjly2b1jkr1nqnxlp5vqvfpj0a4jd70jv4f9ndlif676y")))) + "0m9b4787a866cddf1skjz6634237dvg1i5qyqss4sgvcrbmx3hw0")))) (properties `((upstream-name . "actuar"))) (build-system r-build-system) (propagated-inputs `(("r-expint" ,r-expint))) @@ -20909,14 +22625,14 @@ number embedded in the file rather than the file extension.") (define-public r-imager (package (name "r-imager") - (version "0.42.8") + (version "0.42.10") (source (origin (method url-fetch) (uri (cran-uri "imager" version)) (sha256 (base32 - "1kzl93l6k9i4528bbycbqxdn28mj7hnx0fbxisva859xl1wys5c5")))) + "1vmfmmawbk8sgyba87igaxpwb926nb1ji8a08ad3dqfj7aq9x4q1")))) (properties `((upstream-name . "imager"))) (build-system r-build-system) (inputs @@ -20975,14 +22691,14 @@ it may be seen by an animal with less acute vision.") (define-public r-caret (package (name "r-caret") - (version "6.0-86") + (version "6.0-88") (source (origin (method url-fetch) (uri (cran-uri "caret" version)) (sha256 (base32 - "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns")))) + "174cyyhsw8s6jp80spmi40qq9sw5ys0r58v4ikp53kiw1dhd247s")))) (build-system r-build-system) (propagated-inputs `(("r-foreach" ,r-foreach) @@ -21035,17 +22751,18 @@ done.") (define-public r-adagio (package (name "r-adagio") - (version "0.7.1") + (version "0.8.4") (source (origin (method url-fetch) (uri (cran-uri "adagio" version)) (sha256 (base32 - "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k")))) + "0ihv05402iq003m0338f85pnqnlnrmx0pf1mg8cz9sgi5h98mbnl")))) (properties `((upstream-name . "adagio"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (propagated-inputs + `(("r-lpsolve" ,r-lpsolve))) (home-page "https://cran.r-project.org/web/packages/adagio/") (synopsis "Discrete and global optimization routines") (description @@ -21165,14 +22882,14 @@ cluster stability.") (define-public r-biclust (package (name "r-biclust") - (version "2.0.2") + (version "2.0.3") (source (origin (method url-fetch) (uri (cran-uri "biclust" version)) (sha256 (base32 - "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b")))) + "0lgyc2f04dhr65cwga78pradxsdzgjrpp8vphchqn60ab1z95dlp")))) (properties `((upstream-name . "biclust"))) (build-system r-build-system) (propagated-inputs @@ -21196,18 +22913,19 @@ validation of bicluster solutions.") (define-public r-icge (package (name "r-icge") - (version "0.3") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "ICGE" version)) (sha256 (base32 - "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa")))) + "0w6hbi3h98q6gsxqbb43p95v6xykgrasxcjivwm8hw9fly4avxyi")))) (properties `((upstream-name . "ICGE"))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) + ("r-fastcluster" ,r-fastcluster) ("r-mass" ,r-mass))) (home-page "https://cran.r-project.org/web/packages/ICGE/") (synopsis "Cluster estimation and identification of atypical units") @@ -21302,14 +23020,14 @@ Edition), John Wiley and Sons.") (define-public r-anthropometry (package (name "r-anthropometry") - (version "1.14") + (version "1.15") (source (origin (method url-fetch) (uri (cran-uri "Anthropometry" version)) (sha256 (base32 - "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y")))) + "03xw0ggb2qqlldrv0qpjwmncnari742habb46im7y65bhgnr2awx")))) (properties `((upstream-name . "Anthropometry"))) (build-system r-build-system) (propagated-inputs @@ -21396,18 +23114,20 @@ finding peaks in spectra, converting humidity measures.") (define-public r-qqman (package (name "r-qqman") - (version "0.1.4") + (version "0.1.8") (source (origin (method url-fetch) (uri (cran-uri "qqman" version)) (sha256 (base32 - "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s")))) + "1a6qp5wv9bvwjchfw8x4jh48hkynlnfr21a8vqgnswldvwbq7njq")))) (properties `((upstream-name . "qqman"))) (build-system r-build-system) (propagated-inputs `(("r-calibrate" ,r-calibrate))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/qqman/") (synopsis "Q-Q and Manhattan plots for GWAS data") (description @@ -21572,14 +23292,14 @@ automatically show a loader when the output is (re)calculating.") (define-public r-rsvg (package (name "r-rsvg") - (version "2.1") + (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "rsvg" version)) (sha256 (base32 - "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn")))) + "10p6aps2rsvhf4xgngl9x20cf2wqbzhlpjds8biyihvj58c1q8nn")))) (properties `((upstream-name . "rsvg"))) (build-system r-build-system) (inputs @@ -21601,14 +23321,14 @@ PDF or PostScript.") (define-public r-influencer (package (name "r-influencer") - (version "0.1.0") + (version "0.1.0.1") (source (origin (method url-fetch) (uri (cran-uri "influenceR" version)) (sha256 (base32 - "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag")))) + "0rj7rm236vn3v8302nwl12s0kvpv6xpdbm3q3gxk7vgwfl8nzi33")))) (properties `((upstream-name . "influenceR"))) (build-system r-build-system) (propagated-inputs @@ -21725,14 +23445,14 @@ both exclusive and shared locking.") (define-public r-archivist (package (name "r-archivist") - (version "2.3.5") + (version "2.3.6") (source (origin (method url-fetch) (uri (cran-uri "archivist" version)) (sha256 (base32 - "0sk16bcafgswrvwh39ysbgm6jvsg20yil4pdsg3wsp81nnsrb43k")))) + "0q1qysack30xzxdbvvi56rk7r85hsj4ghls9r70ki7bl3rqwr4c9")))) (properties `((upstream-name . "archivist"))) (build-system r-build-system) (propagated-inputs @@ -21897,14 +23617,14 @@ Raftery, Appl.Statistics, 1989); it includes inference and basic methods.") (define-public r-forecast (package (name "r-forecast") - (version "8.14") + (version "8.15") (source (origin (method url-fetch) (uri (cran-uri "forecast" version)) (sha256 (base32 - "12bfw029xb1dndcjyn2r7a51i7hnkkbdilp69k97sz2v8b7v1y3s")))) + "0x4ij55sb45qnwba3bybs50vsvv82q3j8p47xmbv959h13nsnfn7")))) (properties `((upstream-name . "forecast"))) (build-system r-build-system) (propagated-inputs @@ -21955,14 +23675,14 @@ programming} (OOP) using R Reference Class.") (define-public r-proxyc (package (name "r-proxyc") - (version "0.1.5") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "proxyC" version)) (sha256 (base32 - "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6")))) + "1j8zsxdnpi8bywd7hhm47icgl1jhfyd8myj78bqgk7warai6m3iq")))) (properties `((upstream-name . "proxyC"))) (build-system r-build-system) (propagated-inputs @@ -22073,14 +23793,14 @@ Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.") (define-public r-quanteda (package (name "r-quanteda") - (version "3.0.0") + (version "3.1.0") (source (origin (method url-fetch) (uri (cran-uri "quanteda" version)) (sha256 (base32 - "0b1jfkdhpsg5jhjz4p0nf4cmi9p8w40wv3i2f17jf2x1n1y2hjj8")))) + "0gafbb73gcxx2gq9q7bg88alyhymkr471lp394m5ydij6mdm4hb9")))) (properties `((upstream-name . "quanteda"))) (build-system r-build-system) (propagated-inputs @@ -22279,14 +23999,14 @@ imputed data sets with the appropriate degree of sampling uncertainty.") (define-public r-matrixcalc (package (name "r-matrixcalc") - (version "1.0-3") + (version "1.0-5") (source (origin (method url-fetch) (uri (cran-uri "matrixcalc" version)) (sha256 (base32 - "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp")))) + "1jkgl1v1q7cqpl1rf49qahdr9y0f33f0ldsbgby8xhfv0vpy21jr")))) (properties `((upstream-name . "matrixcalc"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/matrixcalc/") @@ -22328,18 +24048,19 @@ least squares.") (define-public r-semtools (package (name "r-semtools") - (version "0.5-4") + (version "0.5-5") (source (origin (method url-fetch) (uri (cran-uri "semTools" version)) (sha256 (base32 - "15kban4ds2mssxqslm126b89p8biya14c9m68sqk61vzvx5dm2vq")))) + "1dpsn43ifvfy5v8w2fqdy54yclmy0d3qlzix67lflr2r7isq7y6x")))) (properties `((upstream-name . "semTools"))) (build-system r-build-system) (propagated-inputs - `(("r-lavaan" ,r-lavaan))) + `(("r-lavaan" ,r-lavaan) + ("r-pbivnorm" ,r-pbivnorm))) (home-page "https://github.com/simsem/semTools/wiki") (synopsis "Useful tools for structural equation modeling") (description @@ -22349,14 +24070,14 @@ least squares.") (define-public r-regsem (package (name "r-regsem") - (version "1.6.2") + (version "1.8.0") (source (origin (method url-fetch) (uri (cran-uri "regsem" version)) (sha256 (base32 - "14nrzyrkrijdrr4jwkri5zra2wh36w68wy6xs600l2z1633h2lmn")))) + "1v33wkrsawcvaa06cijp8ybwi82a0x34y59hdknwdbywplnirzr8")))) (properties `((upstream-name . "regsem"))) (build-system r-build-system) (propagated-inputs @@ -22420,14 +24141,14 @@ and analyze Stan models.") (define-public r-rpf (package (name "r-rpf") - (version "1.0.5") + (version "1.0.8") (source (origin (method url-fetch) (uri (cran-uri "rpf" version)) (sha256 (base32 - "0kz7i7g3l16irz6bxgnkxdmmd931m1fk6rl72dvs21ir5brr010l")))) + "039r6yz2ax7i9sv8vi98yg7llwb966ay6mrifpmp6q3xh1f634kl")))) (properties `((upstream-name . "rpf"))) (build-system r-build-system) (propagated-inputs @@ -22450,14 +24171,14 @@ Complete access to optimized C functions is made available with (define-public r-openmx (package (name "r-openmx") - (version "2.19.1") + (version "2.19.8") (source (origin (method url-fetch) (uri (cran-uri "OpenMx" version)) (sha256 (base32 - "0fbndmwb3krypsavgm3blqkhh8blmi3p186yxmvgv3a9m6r154rj")))) + "0q37mwxqhgdi05rwdfwfapgazfp541xsvw3yskf21lv11y2yjjyb")))) (properties `((upstream-name . "OpenMx"))) (build-system r-build-system) (propagated-inputs @@ -22468,6 +24189,7 @@ Complete access to optimized C functions is made available with ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) + ("r-rcppparallel" ,r-rcppparallel) ("r-rpf" ,r-rpf) ("r-stanheaders" ,r-stanheaders))) (native-inputs `(("gfortran" ,gfortran))) @@ -22563,14 +24285,14 @@ output in R.") (define-public r-bdgraph (package (name "r-bdgraph") - (version "2.63") + (version "2.64") (source (origin (method url-fetch) (uri (cran-uri "BDgraph" version)) (sha256 (base32 - "05q6dbvdnxmh7myvw60zqcqx16f80i8d6qa4y7xnfkx02l9lwiyc")))) + "0pnzbw09c7amsvj8l4p1jnmss4rkbr1dsmagiygh8lj5fbrklgr4")))) (properties `((upstream-name . "BDgraph"))) (build-system r-build-system) (propagated-inputs @@ -22727,14 +24449,14 @@ well as Ravand and Robitzsch (2015).") (define-public r-tam (package (name "r-tam") - (version "3.5-19") + (version "3.7-16") (source (origin (method url-fetch) (uri (cran-uri "TAM" version)) (sha256 (base32 - "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7")))) + "1969xm1f7s183h0xnd4g1bxhjp80rl7kad29zwcig0fmw6bs2mpd")))) (properties `((upstream-name . "TAM"))) (build-system r-build-system) (propagated-inputs @@ -22858,14 +24580,14 @@ interesting features. iheatmapr uses the plotly library for interactivity.") (define-public r-packrat (package (name "r-packrat") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "packrat" version)) (sha256 (base32 - "01cn2vf95nc8bh0hh8imkn030yra3hx64q1fb8jwsr52p9s397fr")))) + "1hnwhdgqljqs3m7c4rjlyndyc0k85jpa4rbfymxkm3zjg3yy3g78")))) (properties `((upstream-name . "packrat"))) (build-system r-build-system) (home-page "https://github.com/rstudio/packrat/") @@ -22879,14 +24601,14 @@ and reproducible way.") (define-public r-rsconnect (package (name "r-rsconnect") - (version "0.8.16") + (version "0.8.24") (source (origin (method url-fetch) (uri (cran-uri "rsconnect" version)) (sha256 (base32 - "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz")))) + "19p4w9dmhsl1vdvwv3hfmd5qzf4296g0x878idfajvrx0wgfysyg")))) (properties `((upstream-name . "rsconnect"))) (build-system r-build-system) (propagated-inputs @@ -22943,14 +24665,14 @@ documents, Shiny applications, Plumber APIs, plots, and static web content.") (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) - (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) + (let ((minified (open-pipe* OPEN_READ "uglifyjs" source))) (call-with-output-file target (lambda (port) (dump-port minified port))))) sources targets)))) #t))))) (native-inputs - `(("uglify-js" ,uglify-js) + `(("uglifyjs" ,node-uglify-js) ;; They actually use version 1.11.1, but this more recent version ;; should be just fine. ("js-jquery" @@ -23215,20 +24937,20 @@ trend test.") (define-public r-keyring (package (name "r-keyring") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "keyring" version)) (sha256 (base32 - "1hpfd4hbx43i39l995rg86kfxi7wlyla1gv8mwcdr4xx7z122zzq")))) + "1rqz29ycsmfqixhnzhhfd89j9ivnmp7x2z3vxdla622zmakbcy4c")))) (properties `((upstream-name . "keyring"))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) + `(("r-askpass" ,r-askpass) + ("r-assertthat" ,r-assertthat) ("r-filelock" ,r-filelock) - ("r-getpass" ,r-getpass) ("r-openssl" ,r-openssl) ("r-r6" ,r-r6) ("r-rappdirs" ,r-rappdirs) @@ -23272,14 +24994,14 @@ climate data.") (define-public r-rlinsolve (package (name "r-rlinsolve") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "Rlinsolve" version)) (sha256 (base32 - "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc")))) + "1xv500n1480qyakw0isanw1s5ywykhc207hqja4804s5s2m8zfjw")))) (properties `((upstream-name . "Rlinsolve"))) (build-system r-build-system) (propagated-inputs @@ -23304,14 +25026,14 @@ linear systems can be manageable using the @code{Matrix} package along with (define-public r-zvcv (package (name "r-zvcv") - (version "2.1.0") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "ZVCV" version)) (sha256 (base32 - "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r")))) + "0gc76j9i8fkm2v638nyzzb1qxl4zmapbspkkaffb8gi5qyjja448")))) (properties `((upstream-name . "ZVCV"))) (build-system r-build-system) (propagated-inputs @@ -23394,14 +25116,14 @@ Encyclopedia of Integer Sequences} (OEIS) in the function help page.") (define-public r-isoband (package (name "r-isoband") - (version "0.2.4") + (version "0.2.5") (source (origin (method url-fetch) (uri (cran-uri "isoband" version)) (sha256 (base32 - "0z1qpxcl8b6fi691fbdr3vrb19mn4pas1iff62zl1bafzbdvpmcn")))) + "19bbi0n0kz33xdgmdprcmc6raphd1hcm1w1brc16z5phcsh3zxa6")))) (properties `((upstream-name . "isoband"))) (build-system r-build-system) (native-inputs @@ -23557,13 +25279,13 @@ rendered as text, axis labels, etc. throughout R's plotting system.") (define-public r-oai (package (name "r-oai") - (version "0.3.0") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "oai" version)) (sha256 (base32 - "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g")))) + "1zcbcxhw692s0y6izvwazyzhgx0iwsxsbcan2nk0mb7n11p7bypb")))) (build-system r-build-system) (propagated-inputs `(("r-xml2" ,r-xml2) @@ -23571,6 +25293,8 @@ rendered as text, axis labels, etc. throughout R's plotting system.") ("r-plyr" ,r-plyr) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/ropensci/oai/") (synopsis "General purpose OAI-PMH services client") (description "@code{oai} provides a general purpose client to work with @@ -23701,14 +25425,14 @@ evaluated interactively.") (define-public r-bridgesampling (package (name "r-bridgesampling") - (version "1.0-0") + (version "1.1-2") (source (origin (method url-fetch) (uri (cran-uri "bridgesampling" version)) (sha256 (base32 - "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y")))) + "0sry1xwiv4y52k44hq6z8y2kysp5kxgl4dix3m94svg3ladd7v2l")))) (properties `((upstream-name . "bridgesampling"))) (build-system r-build-system) @@ -23947,20 +25671,19 @@ infinite-precision rational arithmetic.") (define-public r-rxnat (package (name "r-rxnat") - (version "1.0.14") + (version "1.0.15") (source (origin (method url-fetch) (uri (cran-uri "Rxnat" version)) (sha256 (base32 - "00fl68pa0c2vy4xlny67pn41lzgm7b97wgg3dwm6z35izca62l11")))) + "0siylypjd8cgcmr2c443w8krg8sgr5gz4zapbinanp8vsfzivdv2")))) (properties `((upstream-name . "Rxnat"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) + `(("r-httr" ,r-httr) ("r-rcurl" ,r-rcurl) ("r-tibble" ,r-tibble))) (native-inputs @@ -24049,14 +25772,14 @@ estimation.") (define-public r-optimx (package (name "r-optimx") - (version "2020-4.2") + (version "2021-6.12") (source (origin (method url-fetch) (uri (cran-uri "optimx" version)) (sha256 (base32 - "00bi2sr2hr7x6cfwlsn7hz2r56lcyv9naa8vmfcgr1r269fc50b3")))) + "059md564p2pk5nis9kbcn1kw2fw130vg53fxlr5xzpv1c9gfhq3k")))) (properties `((upstream-name . "optimx"))) (build-system r-build-system) (propagated-inputs `(("r-numderiv" ,r-numderiv))) @@ -24113,17 +25836,101 @@ packages, but other reference models can also be used. See the package vignette for more information and examples.") (license license:gpl3))) +(define-public r-distributional + (package + (name "r-distributional") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "distributional" version)) + (sha256 + (base32 + "0ps30ijlf0xwranxkq1z29d76d3zgy8drwxpnxp6ffmyma8mm3h2")))) + (properties + `((upstream-name . "distributional"))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-ellipsis" ,r-ellipsis) + ("r-farver" ,r-farver) + ("r-generics" ,r-generics) + ("r-ggplot2" ,r-ggplot2) + ("r-lifecycle" ,r-lifecycle) + ("r-numderiv" ,r-numderiv) + ("r-rlang" ,r-rlang) + ("r-scales" ,r-scales) + ("r-vctrs" ,r-vctrs))) + (home-page "https://pkg.mitchelloharawild.com/distributional/") + (synopsis "Vectorized probability distributions") + (description + "This package provides vectorized distribution objects with tools for +manipulating, visualizing, and using probability distributions. It was +designed to allow model prediction outputs to return distributions rather than +their parameters, allowing users to directly interact with predictive +distributions in a data-oriented workflow. In addition to providing generic +replacements for p/d/q/r functions, other useful statistics can be computed +including means, variances, intervals, and highest density regions.") + (license license:gpl3))) + +(define-public r-posterior + (package + (name "r-posterior") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "posterior" version)) + (sha256 + (base32 + "1lpldkkkxv94dr30q5wb5qr61qrgp9shqnskgwriigy1phnjdxpg")))) + (properties `((upstream-name . "posterior"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-checkmate" ,r-checkmate) + ("r-distributional" ,r-distributional) + ("r-matrixstats" ,r-matrixstats) + ("r-pillar" ,r-pillar) + ("r-rlang" ,r-rlang) + ("r-tensora" ,r-tensora) + ("r-tibble" ,r-tibble) + ("r-vctrs" ,r-vctrs))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://mc-stan.org/posterior/") + (synopsis "Tools for working with posterior distributions") + (description + "This package provides useful tools for both users and developers of +packages for fitting Bayesian models or working with output from Bayesian +models. The primary goals of the package are to: + +@enumerate +@item Efficiently convert between many different useful formats of +draws (samples) from posterior or prior distributions. + +@item Provide consistent methods for operations commonly performed on draws, +for example, subsetting, binding, or mutating draws. + +@item Provide various summaries of draws in convenient formats. + +@item Provide lightweight implementations of state of the art posterior +inference diagnostics. +@end enumerate +") + (license license:bsd-3))) + (define-public r-brms (package (name "r-brms") - (version "2.15.0") + (version "2.16.1") (source (origin (method url-fetch) (uri (cran-uri "brms" version)) (sha256 (base32 - "0byc3fyvf9qbvvgwf55ih5d4br1nnxlbaidq9fvr11bmv38h25y1")))) + "1i0vkkfziac29vncw4igja5m7a6rhw9rqwifrw3y47q6zgczp7kl")))) (properties `((upstream-name . "brms"))) (build-system r-build-system) (propagated-inputs @@ -24141,6 +25948,7 @@ vignette for more information and examples.") ("r-mgcv" ,r-mgcv) ("r-nleqslv" ,r-nleqslv) ("r-nlme" ,r-nlme) + ("r-posterior" ,r-posterior) ("r-projpred" ,r-projpred) ("r-rcpp" ,r-rcpp) ("r-rstan" ,r-rstan) @@ -24202,21 +26010,21 @@ multi-state models.") (define-public r-scatterpie (package (name "r-scatterpie") - (version "0.1.5") + (version "0.1.7") (source (origin (method url-fetch) (uri (cran-uri "scatterpie" version)) (sha256 (base32 - "0h48l0699lpfagv09f53yismir84945m56qwzk52lc7wxyvkfcp1")))) + "1pmspv8a7k20zyd5xvmav2k9mnjrkfhdij3rr9k504zyki8hfy1z")))) (properties `((upstream-name . "scatterpie"))) (build-system r-build-system) (propagated-inputs `(("r-ggforce" ,r-ggforce) + ("r-ggfun" ,r-ggfun) ("r-ggplot2" ,r-ggplot2) ("r-rlang" ,r-rlang) - ("r-rvcheck" ,r-rvcheck) ("r-tidyr" ,r-tidyr))) (native-inputs `(("r-knitr" ,r-knitr))) @@ -24373,14 +26181,14 @@ counting and recursive k-means partitioning.") (define-public r-hardhat (package (name "r-hardhat") - (version "0.1.5") + (version "0.1.6") (source (origin (method url-fetch) (uri (cran-uri "hardhat" version)) (sha256 (base32 - "1b7f9i9fy39j9n03g40vd6nzgq9fgq914xg3svf84najlknvjzly")))) + "07mx8c24gy0xfmip9hb5w29gp10sfnpnilzc1pi0hjadnrqz8mks")))) (properties `((upstream-name . "hardhat"))) (build-system r-build-system) (propagated-inputs @@ -24406,14 +26214,14 @@ input.") (define-public r-lightgbm (package (name "r-lightgbm") - (version "3.2.0") + (version "3.2.1") (source (origin (method url-fetch) (uri (cran-uri "lightgbm" version)) (sha256 (base32 - "0aw1zcrg7nhddfaif9544hn8g8qcylv6vzpkf8d3kl07nzvgxkvj")))) + "1136di7k3gs9kk7vd9bc3mdm0qrx3a546ngar8inmgyhi0zk6pkd")))) (properties `((upstream-name . "lightgbm"))) (build-system r-build-system) (propagated-inputs @@ -24477,16 +26285,19 @@ values.") (define-public r-rismed (package (name "r-rismed") - (version "2.2") + (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "RISmed" version)) (sha256 (base32 - "0nwixhngi4r2f73362salivsmsf7l52bm13jqvhdq8mfiigm80vd")))) + "0vpi88gzi9r85v6nhjz9jbw671zkrmyazwna2z881346wfyr3l8b")))) (properties `((upstream-name . "RISmed"))) (build-system r-build-system) + (propagated-inputs + `(("r-httr" ,r-httr) + ("r-xml2" ,r-xml2))) (home-page "https://cran.r-project.org/web/packages/RISmed") (synopsis "Download content from NCBI databases") (description @@ -24681,6 +26492,26 @@ theory; see @url{Strumbel and Kononenko (2014), doi.org/10.1007/s10115-013-0679-x} for details.") (license license:gpl2+))) +(define-public r-memuse + (package + (name "r-memuse") + (version "4.1-0") + (source (origin + (method url-fetch) + (uri (cran-uri "memuse" version)) + (sha256 + (base32 + "1bbjp8y0ji71956fbaxiil7ynq2nkmmgz7i9xps83m3bbp5d3mjq")))) + (properties `((upstream-name . "memuse"))) + (build-system r-build-system) + (home-page "https://github.com/shinra-dev/memuse") + (synopsis "Memory Estimation Utilities") + (description + "This package provides procedures to answer the following questions: +How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is +your current R session using? How much ram do you even have?") + (license license:bsd-2))) + (define-public r-metrics (package (name "r-metrics") @@ -24707,14 +26538,14 @@ simple interface for all functions.") (define-public r-iml (package (name "r-iml") - (version "0.10.0") + (version "0.10.1") (source (origin (method url-fetch) (uri (cran-uri "iml" version)) (sha256 (base32 - "0xm3q42qahq798ilgg050df0mahhbdfd3fx3i7cpx606h38si0x7")))) + "1wz6xqhvqkzj723nw7qrlwb1171wvvpxhv3pa8cq7vcbkiflq37r")))) (properties `((upstream-name . "iml"))) (build-system r-build-system) (propagated-inputs @@ -24724,7 +26555,7 @@ simple interface for all functions.") ("r-future" ,r-future) ("r-future-apply" ,r-future-apply) ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) + ("r-keras" ,r-keras) ("r-metrics" ,r-metrics) ("r-prediction" ,r-prediction) ("r-r6" ,r-r6))) @@ -24795,14 +26626,14 @@ diagonals. This package allows you to compute the tensor product of arrays.") (define-public r-spatstat-utils (package (name "r-spatstat-utils") - (version "2.1-0") + (version "2.2-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat.utils" version)) (sha256 (base32 - "18gqsc1a85pk69aifi10wprv1c0lci3zxp4wqjb27dlmlbz6jdgd")))) + "1aypccpv0zavxwmqzvlka8981n9km7ml3jbmxz21sql58997xn2s")))) (properties `((upstream-name . "spatstat.utils"))) (build-system r-build-system) @@ -24866,14 +26697,14 @@ package.") (define-public r-spatstat-geom (package (name "r-spatstat-geom") - (version "2.0-1") + (version "2.2-2") (source (origin (method url-fetch) (uri (cran-uri "spatstat.geom" version)) (sha256 (base32 - "1r7nlgh62apchidg28fxq1a22iv1b29y5xmsg1kjwfvkbq8zxsvh")))) + "0rx28g064641yrk2h23qpyc0bgs20lpsnqmyl1d06530ga6r1qc3")))) (properties `((upstream-name . "spatstat.geom"))) (build-system r-build-system) (propagated-inputs @@ -24892,14 +26723,14 @@ for the geometry of linear networks.") (define-public r-spatstat-core (package (name "r-spatstat-core") - (version "2.0-0") + (version "2.3-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat.core" version)) (sha256 (base32 - "19wv27nfx48xkqa1amys4jf93k0d8xns20p84n5kqyibscdsksgx")))) + "1j962lzllqzxkd57j6immyj94pc53ff9mlvw1iscw7cnn9nyr5ap")))) (properties `((upstream-name . "spatstat.core"))) (build-system r-build-system) (propagated-inputs @@ -24924,14 +26755,14 @@ user-level code from spatstat, except for the code for linear networks.") (define-public r-spatstat-linnet (package (name "r-spatstat-linnet") - (version "2.1-1") + (version "2.3-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat.linnet" version)) (sha256 (base32 - "1ia0qgggddiwhhyd3q516f3p6by0p4xnq26wqz7410n2ja60bbb4")))) + "1yd2z629f7908xw9kyqiahk3qn9ajpl6qffbkv887zmq3p28kh7h")))) (properties `((upstream-name . "spatstat.linnet"))) (build-system r-build-system) @@ -24940,6 +26771,7 @@ user-level code from spatstat, except for the code for linear networks.") ("r-spatstat-core" ,r-spatstat-core) ("r-spatstat-data" ,r-spatstat-data) ("r-spatstat-geom" ,r-spatstat-geom) + ("r-spatstat-sparse" ,r-spatstat-sparse) ("r-spatstat-utils" ,r-spatstat-utils))) (home-page "http://spatstat.org/") (synopsis "Linear networks functionality of the spatstat package") @@ -24951,14 +26783,14 @@ for spatial data on a linear network.") (define-public r-spatstat (package (name "r-spatstat") - (version "2.1-0") + (version "2.2-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat" version)) (sha256 (base32 - "0vr5md53247v6crvjvg9m82vc6h914zzvkzfkga8x79hv35ii4as")))) + "0lz3sidn05xjswxaxhagal6jj5hra6aya0azxybjw7mgspl903wg")))) (properties `((upstream-name . "spatstat"))) (build-system r-build-system) (propagated-inputs @@ -25012,14 +26844,14 @@ for linear mixed models (AIREML).") (define-public r-cpp11 (package (name "r-cpp11") - (version "0.2.7") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "cpp11" version)) (sha256 (base32 - "1m31yq3kn5wqvm0ahj08kb4bszbbhfybx3l2x975cjzgv3058h8x")))) + "11qyliiw2qrac56mq5h9v7gy3dvwjj1i26pvygwbpprhvh3zss0p")))) (properties `((upstream-name . "cpp11"))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -25064,14 +26896,14 @@ aggregation for comparing different implementations in order to provide a (define-public r-rfast (package (name "r-rfast") - (version "2.0.1") + (version "2.0.3") (source (origin (method url-fetch) (uri (cran-uri "Rfast" version)) (sha256 (base32 - "1cq3mcg49hsvqhwn6f4dgsx7f8ma4qnwr5n6s7m22qy57rg31958")))) + "1bmhmli6q4kg8321595k0yy91w9cblk14s6qbc9wf8f05108rg15")))) (properties `((upstream-name . "Rfast"))) (build-system r-build-system) (propagated-inputs @@ -25087,17 +26919,41 @@ maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions.") (license license:gpl2+))) +(define-public r-rffc + (package + (name "r-rffc") + (version "1.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://download.r-forge.r-project.org/src/contrib/" + "rfFC_" version ".tar.gz")) + (sha256 + (base32 + "05x9wgzsmx4vb12lmcspymgmpb2xw8bwryb8ysg7vzg2nkh0ma3g")))) + (build-system r-build-system) + (propagated-inputs + `(("r-randomforest",r-randomforest))) + (home-page "https://r-forge.r-project.org/projects/rffc/") + (synopsis "Random Forest Feature Contributions") + (description "This package provides functions for extracting feature +contributions from a random forest model from package @code{randomForest}. +Feature contributions provide detailed information about the relationship +between data variables and the predicted value returned by random forest +model.") + (license license:gpl2))) + (define-public r-clusterr (package (name "r-clusterr") - (version "1.2.2") + (version "1.2.5") (source (origin (method url-fetch) (uri (cran-uri "ClusterR" version)) (sha256 (base32 - "1ky172bk15a78hky77vl60j7c81nq2495sxjrv53is25nkac7sjm")))) + "1fsb9pzs1paw1cbyr5a56lfh8h2d50232p6isk0xg5sl110ql7kx")))) (properties `((upstream-name . "ClusterR"))) (build-system r-build-system) (propagated-inputs @@ -25194,17 +27050,65 @@ addition, objects which include the k-d tree search structure can be returned to speed up repeated queries of the same set of target points.") (license license:bsd-3))) +(define-public r-naturalsort + (package + (name "r-naturalsort") + (version "0.1.3") + (source (origin + (method url-fetch) + (uri (cran-uri "naturalsort" version)) + (sha256 + (base32 + "0mz801y9mzld9ypp3xmsjw2d8l9q97sdnv09wrci9xi3yg2sjf6d")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/naturalsort/") + (synopsis "Natural ordering") + (description "This package provides functions related to human natural +ordering. It handles adjacent digits in a character sequence as a number +so that natural sort function arranges a character vector by their numbers, +not digit characters.") + (license license:bsd-3))) + +(define-public r-visdat + (package + (name "r-visdat") + (version "0.5.3") + (source (origin + (method url-fetch) + (uri (cran-uri "visdat" version)) + (sha256 + (base32 + "1ikqp29nncbw1xlwyb9dqqgcdk9q0bs3wxhnhnjpb11vcjv7cz2j")))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-glue" ,r-glue) + ("r-magrittr" ,r-magrittr) + ("r-purrr" ,r-purrr) + ("r-readr" ,r-readr) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://visdat.njtierney.com/") + (synopsis "Preliminary Visualisation of Data") + (description "This package provides procedures to create preliminary exploratory +data visualisations of an entire dataset to identify problems or unexpected features +using @code{ggplot2}.") + (license license:expat))) + (define-public r-muhaz (package (name "r-muhaz") - (version "1.2.6.3") + (version "1.2.6.4") (source (origin (method url-fetch) (uri (cran-uri "muhaz" version)) (sha256 (base32 - "1lzc8arbpcxgfap3dfsgq8crpp1cxd9qlbrhvyvl79zgpxjqx4q2")))) + "1ddy8ayr4rdhzcipdvxdwd7z5g9hfp0ppacl7xf6f2612cn1185g")))) (properties `((upstream-name . "muhaz"))) (build-system r-build-system) (propagated-inputs @@ -25222,14 +27126,14 @@ censored data.") (define-public r-flexsurv (package (name "r-flexsurv") - (version "2.0") + (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "flexsurv" version)) (sha256 (base32 - "0vshsijqlzsz0xh426vsswpai1v5c990ggyniqqzsjbg3mn8dbl9")))) + "0kwij9nkdvnsn1kn12fj3hjkd2qpgw7bdda4qad7basq5p6divlp")))) (properties `((upstream-name . "flexsurv"))) (build-system r-build-system) (propagated-inputs @@ -25268,14 +27172,14 @@ models.") (define-public r-transphylo (package (name "r-transphylo") - (version "1.4.4") + (version "1.4.5") (source (origin (method url-fetch) (uri (cran-uri "TransPhylo" version)) (sha256 (base32 - "1506c97y8dnhd0c38rgvmg70q0l3xmmn07mjglhnw7hi5n5y9mv9")))) + "0g92kwi1nlmpc8m4pc9kv9xhczryr2kn9icfr3js7da7vy8g50xy")))) (properties `((upstream-name . "TransPhylo"))) (build-system r-build-system) (propagated-inputs @@ -25373,14 +27277,14 @@ the @code{survival} package.") (define-public r-exactranktests (package (name "r-exactranktests") - (version "0.8-31") + (version "0.8-32") (source (origin (method url-fetch) (uri (cran-uri "exactRankTests" version)) (sha256 (base32 - "1154dkcid3njhamdp87qs9bnx7l8bdqkcjsds9q9f2xmizs9x8gw")))) + "0p7h7w470p5qpsbrhw12zlsshyai56za5dsdva8cf9sikn0955qr")))) (properties `((upstream-name . "exactRankTests"))) (build-system r-build-system) @@ -25601,14 +27505,14 @@ more.") (define-public r-workflows (package (name "r-workflows") - (version "0.2.2") + (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "workflows" version)) (sha256 (base32 - "19ipcxx4qfz28cjkgr1vny03yhmbd3m2v64v30gk5pf73nazvmaz")))) + "0bca4s49qabam4ny8vckxcghj3z0xfhwfhs5h1136kihrr5pm6mw")))) (properties `((upstream-name . "workflows"))) (build-system r-build-system) (propagated-inputs @@ -25617,6 +27521,7 @@ more.") ("r-generics" ,r-generics) ("r-glue" ,r-glue) ("r-hardhat" ,r-hardhat) + ("r-lifecycle" ,r-lifecycle) ("r-parsnip" ,r-parsnip) ("r-rlang" ,r-rlang) ("r-tidyselect" ,r-tidyselect) @@ -25643,6 +27548,33 @@ workflow. The advantages are: ") (license license:expat))) +(define-public r-lobstr + (package + (name "r-lobstr") + (version "1.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "lobstr" version)) + (sha256 + (base32 + "0vkif17825x33cz8r89j0qph4wj5l8fzfgl8nh2g7m2v140cxjdq")))) + (properties `((upstream-name . "lobstr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-crayon" ,r-crayon) + ("r-rcpp" ,r-rcpp) + ("r-rlang" ,r-rlang))) + (home-page "https://github.com/r-lib/lobstr") + (synopsis "Visualize R data structures with trees") + (description + "This package provides a set of tools for inspecting and understanding R +data structures inspired by @code{str}. It includes @code{ast} for +visualizing abstract syntax trees, @code{ref} for showing shared references, +@code{cst} for showing call stack trees, and @code{obj_size} for computing +object sizes.") + (license license:gpl3))) + (define-public r-gpfit (package (name "r-gpfit") @@ -25724,14 +27656,14 @@ observations.") (define-public r-slider (package (name "r-slider") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "slider" version)) (sha256 (base32 - "1jijh8f3qcn8fa677sqvgl2fb4r5vca1cw4l2vbcqscxb2hr4bqw")))) + "1vxk2bc33svwcki2j8zr5jcxswh27i0fqgzjw2a5a1pp9dh3fmd3")))) (properties `((upstream-name . "slider"))) (build-system r-build-system) (propagated-inputs @@ -25753,14 +27685,14 @@ sliding windows are to be created.") (define-public r-rsample (package (name "r-rsample") - (version "0.0.9") + (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "rsample" version)) (sha256 (base32 - "03qwsvylgmj2a2h764mzy0x57pgzmvjvl0ypmbn4lcf912bvrd2c")))) + "00w8r0p499fm8cyw297gznr83mbgy9a3znzpbgj0zq9dry1a266b")))) (properties `((upstream-name . "rsample"))) (build-system r-build-system) (propagated-inputs @@ -25768,6 +27700,7 @@ sliding windows are to be created.") ("r-ellipsis" ,r-ellipsis) ("r-furrr" ,r-furrr) ("r-generics" ,r-generics) + ("r-lifecycle" ,r-lifecycle) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-slider" ,r-slider) @@ -25807,14 +27740,14 @@ Design} (SFD) and to test their quality.") (define-public r-dials (package (name "r-dials") - (version "0.0.9") + (version "0.0.10") (source (origin (method url-fetch) (uri (cran-uri "dials" version)) (sha256 (base32 - "0g9wj2py4wz703rh4p7hk8qxqnkm7zyrypv4qz4vaqziazjsmxks")))) + "1vhqcfwgic01pkw0i3000fvqq9yxfzsv26c0psfjhxkkdcz8h2px")))) (properties `((upstream-name . "dials"))) (build-system r-build-system) (propagated-inputs @@ -25839,14 +27772,14 @@ for creating, simulating, or validating values for such parameters.") (define-public r-tune (package (name "r-tune") - (version "0.1.3") + (version "0.1.6") (source (origin (method url-fetch) (uri (cran-uri "tune" version)) (sha256 (base32 - "05r5jzg96g2z10a2w4w8wq1ysfaxr91acwrvn75pmcy4rmixf293")))) + "1356w98ljiay8fwa7narr7j5hfbvi69gy03gr7kqiwnfglyksrza")))) (properties `((upstream-name . "tune"))) (build-system r-build-system) (propagated-inputs @@ -25858,6 +27791,8 @@ for creating, simulating, or validating values for such parameters.") ("r-ggplot2" ,r-ggplot2) ("r-glue" ,r-glue) ("r-gpfit" ,r-gpfit) + ("r-hardhat" ,r-hardhat) + ("r-lifecycle" ,r-lifecycle) ("r-parsnip" ,r-parsnip) ("r-purrr" ,r-purrr) ("r-recipes" ,r-recipes) @@ -25866,6 +27801,7 @@ for creating, simulating, or validating values for such parameters.") ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-vctrs" ,r-vctrs) + ("r-withr" ,r-withr) ("r-workflows" ,r-workflows) ("r-yardstick" ,r-yardstick))) (home-page "https://github.com/tidymodels/tune") @@ -25880,20 +27816,23 @@ methods, and post-processing steps.") (define-public r-workflowsets (package (name "r-workflowsets") - (version "0.0.1") + (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "workflowsets" version)) (sha256 (base32 - "1q41isvj7hhbkx3y8k6kazpiygig92xannsz8dpklh0k3j9l3c2p")))) + "0596hb17mshpag3vjy2wl6fi2mdw54i9gc5za10vzy8vpkigb9jy")))) (properties `((upstream-name . "workflowsets"))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) ("r-dplyr" ,r-dplyr) + ("r-hardhat" ,r-hardhat) + ("r-generics" ,r-generics) ("r-ggplot2" ,r-ggplot2) + ("r-lifecycle" ,r-lifecycle) ("r-prettyunits" ,r-prettyunits) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) @@ -26081,14 +28020,14 @@ vignettes in all common formats.") (define-public r-tidytext (package (name "r-tidytext") - (version "0.3.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "tidytext" version)) (sha256 (base32 - "1icbfw4zkbs9sp6vk814mw2zzm0bc0d7af92vhriqxaga0gbwdkx")))) + "182gad5pzz6zvhbla3d496sxwiszc1qz8kzzkksaacwpsrc61f9h")))) (properties `((upstream-name . "tidytext"))) (build-system r-build-system) (propagated-inputs @@ -26116,14 +28055,14 @@ analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.") (define-public r-parsnip (package (name "r-parsnip") - (version "0.1.5") + (version "0.1.7") (source (origin (method url-fetch) (uri (cran-uri "parsnip" version)) (sha256 (base32 - "0c12lyfxqsdprqlcmgy421py38z28h88d68pxb1c4fw14v1c2d06")))) + "12chngdzplwkk1c9k8y7cwaqlyy72yamlknp7ksg7g9p3b58f1fb")))) (properties `((upstream-name . "parsnip"))) (build-system r-build-system) (propagated-inputs @@ -26131,6 +28070,8 @@ analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.") ("r-generics" ,r-generics) ("r-globals" ,r-globals) ("r-glue" ,r-glue) + ("r-hardhat" ,r-hardhat) + ("r-lifecycle" ,r-lifecycle) ("r-magrittr" ,r-magrittr) ("r-prettyunits" ,r-prettyunits) ("r-purrr" ,r-purrr) @@ -26151,24 +28092,28 @@ functions or computational engines (e.g. R, Spark, Stan, etc).") (define-public r-infer (package (name "r-infer") - (version "0.5.4") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "infer" version)) (sha256 (base32 - "0wvvgqjhyv7ql98cjzqad61wbmk7xrqd1ybk894jr5cmza13c8w2")))) + "1qbpcn7jqbvgwnpiyylj021j8m33p58a204yd1pfkpzd3x2lbsm6")))) (properties `((upstream-name . "infer"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) + `(("r-broom" ,r-broom) + ("r-dplyr" ,r-dplyr) + ("r-generics" ,r-generics) ("r-ggplot2" ,r-ggplot2) ("r-glue" ,r-glue) ("r-magrittr" ,r-magrittr) + ("r-patchwork" ,r-patchwork) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble))) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/tidymodels/infer") @@ -26181,14 +28126,14 @@ expressive statistical grammar that coheres with the Tidy design framework.") (define-public r-modeldata (package (name "r-modeldata") - (version "0.1.0") + (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "modeldata" version)) (sha256 (base32 - "0lbvmicvhw560jn9qk5dywrl6mgj1rf7zh7p86lf97c6bmz0zp2r")))) + "0jgrwf9k8p9j3ywg3yv2wzwsx3snlwm3dd9vfqwhlr7j63jg3cm4")))) (properties `((upstream-name . "modeldata"))) (build-system r-build-system) (home-page "https://modeldata.tidymodels.org") @@ -26198,27 +28143,54 @@ expressive statistical grammar that coheres with the Tidy design framework.") model-related packages.") (license license:expat))) +(define-public r-conflicted + (package + (name "r-conflicted") + (version "1.0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "conflicted" version)) + (sha256 + (base32 + "0xp04cdvmp3b1phazhmjqn0vmax1b2218xsb5854ffv43m7qvrra")))) + (properties `((upstream-name . "conflicted"))) + (build-system r-build-system) + (propagated-inputs + `(("r-memoise" ,r-memoise) + ("r-rlang" ,r-rlang))) + (home-page "https://github.com/r-lib/conflicted") + (synopsis "Alternative conflict resolution strategy") + (description + "R's default conflict management system gives the most recently loaded +package precedence. This can make it hard to detect conflicts, particularly +when they arise because a package update creates ambiguity that did not +previously exist. The @code{conflicted} package takes a different approach, +making every conflict an error and forcing you to choose which function to +use.") + (license license:gpl3))) + (define-public r-tidymodels (package (name "r-tidymodels") - (version "0.1.2") + (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "tidymodels" version)) (sha256 (base32 - "09njrl655sh82xrzckgg56a6ndfrjla5fy8675wj4jsj14jpv0fw")))) + "18vz0xsgxrfzcfxpvilhj1w0f4v4lx5ws37nwmy40lhv3v05nxn8")))) (properties `((upstream-name . "tidymodels"))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) ("r-cli" ,r-cli) + ("r-conflicted" ,r-conflicted) ("r-dials" ,r-dials) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-infer" ,r-infer) - ("r-magrittr" ,r-magrittr) ("r-modeldata" ,r-modeldata) ("r-parsnip" ,r-parsnip) ("r-purrr" ,r-purrr) @@ -26230,6 +28202,7 @@ model-related packages.") ("r-tidyr" ,r-tidyr) ("r-tune" ,r-tune) ("r-workflows" ,r-workflows) + ("r-workflowsets" ,r-workflowsets) ("r-yardstick" ,r-yardstick))) (native-inputs `(("r-knitr" ,r-knitr) @@ -26470,16 +28443,18 @@ data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") (define-public r-maldiquant (package (name "r-maldiquant") - (version "1.19.3") + (version "1.20") (source (origin (method url-fetch) (uri (cran-uri "MALDIquant" version)) (sha256 (base32 - "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57")))) + "1h9i158czlzwbn5zakkqd2ggc9g90r73vdspmp6kgfcmy9frvwzz")))) (properties `((upstream-name . "MALDIquant"))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/MALDIquant") (synopsis "Quantitative analysis of mass spectrometry data") (description @@ -26519,22 +28494,21 @@ data to rasters. It speeds up plotting of data with millions of points.") (define-public r-seuratobject (package (name "r-seuratobject") - (version "4.0.0") + (version "4.0.2") (source (origin (method url-fetch) (uri (cran-uri "SeuratObject" version)) (sha256 (base32 - "03k27z7g76wy7mfja2cpxq183xk0906k9gxb2j6p1zw341gv4gii")))) + "076bd6xmpnspnz7raw03mfgknnygx79sj3c9q6yhpanc46i9gvk4")))) (properties `((upstream-name . "SeuratObject"))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) - ("r-rlang" ,r-rlang) - ("r-sctransform" ,r-sctransform))) + ("r-rlang" ,r-rlang))) (home-page "https://satijalab.org/seurat") (synopsis "Data structures for single cell data") (description @@ -26548,13 +28522,13 @@ other R users.") (define-public r-seurat (package (name "r-seurat") - (version "4.0.1") + (version "4.0.4") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "17cmp9mimvykb8ny796dn1zwmvg0pwwjw1zcixyamc5q1lwnxi3p")))) + "1pa2v29mx39swblzwzqc7rpql2rizhi2nj426r1i63wyla6lcxc0")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs @@ -26615,14 +28589,14 @@ discovery of differentially expressed genes and markers.") (define-public r-phangorn (package (name "r-phangorn") - (version "2.6.3") + (version "2.7.1") (source (origin (method url-fetch) (uri (cran-uri "phangorn" version)) (sha256 (base32 - "08yqz8qlw960x4b52wzrm22f242xnpc8695pjkhy7bi1nzm303ga")))) + "160kks4bg4iwy8g234g6aiiqbvz7ki5k9csyax3kjv7ia5wddafq")))) (build-system r-build-system) (propagated-inputs `(("r-ape" ,r-ape) @@ -26645,14 +28619,14 @@ Maximum Parsimony, distance methods and Hadamard conjugation.") (define-public r-diversitree (package (name "r-diversitree") - (version "0.9-15") + (version "0.9-16") (source (origin (method url-fetch) (uri (cran-uri "diversitree" version)) (sha256 (base32 - "1sk3sgn5hi04978s5s7gy6pzp28g3v9rglmiamlgs96c9wyyyff7")))) + "0rzrk7xsn4gy271pbcw3azndhx0c06bmsgrg6libjmlfnmq6j8sc")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -26676,14 +28650,14 @@ rate speciation and extinction.") (define-public r-calculus (package (name "r-calculus") - (version "0.3.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "calculus" version)) (sha256 (base32 - "1wa5ap89cfcp0ancj9ivx5s2y0wqr2vmp9y115g7f6g772jwhscj")))) + "0m9cjc3bqv88vrrj51kd7c7xnczka5w9q0ln4l4nk514gvlr79bn")))) (properties `((upstream-name . "calculus"))) (build-system r-build-system) (propagated-inputs @@ -26765,14 +28739,14 @@ kernel estimators.") (define-public r-lpme (package (name "r-lpme") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "lpme" version)) (sha256 (base32 - "0si90nkgl8bqk8yvd2igdsrngiwqh8891072pfpzipifnd0f5448")))) + "1b0w5ji8hjayni1sh5id193cmanf6n11p16fijkxln4sv4lks4aw")))) (properties `((upstream-name . "lpme"))) (build-system r-build-system) (propagated-inputs @@ -26846,13 +28820,13 @@ Services (AWS) Simple Storage Service (S3) REST API.") (define-public r-lgr (package (name "r-lgr") - (version "0.4.2") + (version "0.4.3") (source (origin (method url-fetch) (uri (cran-uri "lgr" version)) (sha256 (base32 - "0k4kacjk7swm3gmdpha1rg44xb29vzvhvx48jhpb78glj5c9phyr")))) + "18s92qyakhvp336kk2777ydypwfrfwfz6a1gqkq812zy3kcb4mcc")))) (build-system r-build-system) (propagated-inputs `(("r-r6" ,r-r6))) @@ -26870,13 +28844,13 @@ well as email and push notifications.") (define-public r-mlr3measures (package (name "r-mlr3measures") - (version "0.3.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3measures" version)) (sha256 (base32 - "18jk4kdj9771r16smz7xhmmiilcdg1qlavln5hrpvkx780zh3hj6")))) + "1qlqfan5akz42zwkcz3ncln6rd9c302dy4cyp7nx0jcafr5i459f")))) (build-system r-build-system) (propagated-inputs `(("r-checkmate" ,r-checkmate) @@ -26893,18 +28867,19 @@ are.") (define-public r-mlr3misc (package (name "r-mlr3misc") - (version "0.8.0") + (version "0.9.4") (source (origin (method url-fetch) (uri (cran-uri "mlr3misc" version)) (sha256 (base32 - "0mzicqs8rhzppyd7v3ljqs35k8pp7p2jg5cs7hx21mxr831bwsys")))) + "14lcpvxrrl68l3khmy5r266b7yjjlg97pz4xvha0ypx8hlpbqik2")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) ("r-checkmate" ,r-checkmate) ("r-data-table" ,r-data-table) + ("r-digest" ,r-digest) ("r-r6" ,r-r6))) (home-page "https://mlr3misc.mlr-org.com/") (synopsis "Helper functions for mlr3") @@ -26943,20 +28918,20 @@ implemented as @code{R6} classes.") (define-public r-mlr3 (package (name "r-mlr3") - (version "0.11.0") + (version "0.12.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3" version)) (sha256 (base32 - "0qh9vdac1als2123wf51bwa7spdqk33iydlawi5n5dpci892iahl")))) + "0nimwczsgrj29r9qrlz32qc3fkj02369zql7jhkrn3lk3mfy5zmz")))) (build-system r-build-system) (propagated-inputs `(("r-r6" ,r-r6) ("r-backports" ,r-backports) ("r-checkmate" ,r-checkmate) ("r-data-table" ,r-data-table) - ("r-digest" ,r-digest) + ("r-future" ,r-future) ("r-future-apply" ,r-future-apply) ("r-lgr" ,r-lgr) ("r-mlbench" ,r-mlbench) @@ -26979,16 +28954,17 @@ computational operations, add-on packages provide additional functionality.") (define-public r-mlr3learners (package (name "r-mlr3learners") - (version "0.4.5") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3learners" version)) (sha256 (base32 - "02v4y32yn1m0akkqzhfg65ib21rgy9iz8db4kdcrvi949clkxnfk")))) + "1gkbbn5ah2iv4pv5q2jf4lrqkga744d4y9jlyhyjqf0x75y9wkg2")))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) + `(("r-checkmate" ,r-checkmate) + ("r-data-table" ,r-data-table) ("r-mlr3" ,r-mlr3) ("r-mlr3misc" ,r-mlr3misc) ("r-paradox" ,r-paradox) @@ -27005,14 +28981,14 @@ vector machines, and gradient boosting.") (define-public r-bbotk (package (name "r-bbotk") - (version "0.3.2") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "bbotk" version)) (sha256 (base32 - "0bd9nxfgsj4ixpgky1mj6knb8l8nivvxpqpyw8vgpkj0za7gp4gr")))) + "09cw6z397laszsg5wsgpjh7jda74amqrcl2p25bgjg33ina2nvg7")))) (properties `((upstream-name . "bbotk"))) (build-system r-build-system) (propagated-inputs @@ -27035,18 +29011,19 @@ annealing.") (define-public r-mlr3tuning (package (name "r-mlr3tuning") - (version "0.8.0") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3tuning" version)) (sha256 (base32 - "16rvsf0jf06yvalydbs7zzn2994hvvyfw975ydiyv3wy1qzgr8bv")))) + "0i428kdbak81j1wlwmdf9y40hqi63azhyny802ms2z04wl8lwnvs")))) (build-system r-build-system) (propagated-inputs `(("r-bbotk" ,r-bbotk) ("r-checkmate" ,r-checkmate) ("r-data-table" ,r-data-table) + ("r-digest" ,r-digest) ("r-lgr" ,r-lgr) ("r-mlr3" ,r-mlr3) ("r-mlr3misc" ,r-mlr3misc) @@ -27211,61 +29188,28 @@ unit tests of graphics).") (define-public r-vdiffr (package (name "r-vdiffr") - (version "0.3.3") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "vdiffr" version)) (sha256 (base32 - "0i0xdr8dakbkkgrhp0zvlnv3rxhc8h5naqq416mr5zv9q8i4p8jc")) - (snippet - '(begin - (delete-file "inst/htmlwidgets/lib/jquery.min.js"))))) + "1zjwjw8lqqnx7cxj2aik5rn1g67zsyf0bq08yfwwmsi7v2x6ly3x")))) (properties `((upstream-name . "vdiffr"))) (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/" - (let ((source (assoc-ref inputs "js-jquery")) - (target "jquery.min.js")) - (format #true "Processing ~a --> ~a~%" - source target) - (invoke "esbuild" source "--minify" - (string-append "--outfile=" target))))))))) (inputs - `(("freetype" ,freetype) - ("harfbuzz" ,harfbuzz))) + `(("libpng" ,libpng) + ("zlib" ,zlib))) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-devtools" ,r-devtools) + `(("r-cpp11" ,r-cpp11) ("r-diffobj" ,r-diffobj) - ("r-fontquiver" ,r-fontquiver) - ("r-freetypeharfbuzz" ,r-freetypeharfbuzz) - ("r-gdtools" ,r-gdtools) ("r-glue" ,r-glue) ("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-purrr" ,r-purrr) - ("r-r6" ,r-r6) - ("r-rcpp" ,r-rcpp) + ("r-lifecycle" ,r-lifecycle) ("r-rlang" ,r-rlang) - ("r-shiny" ,r-shiny) ("r-testthat" ,r-testthat) - ("r-usethis" ,r-usethis) ("r-xml2" ,r-xml2))) - (native-inputs - `(("esbuild" ,esbuild) - ("js-jquery" - ,(origin - (method url-fetch) - (uri "https://code.jquery.com/jquery-1.12.4.js") - (sha256 - (base32 - "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3")))))) (home-page "https://github.com/r-lib/vdiffr") (synopsis "Visual regression testing and graphical diffing") (description @@ -27334,14 +29278,14 @@ clusterings as resolution increases.") (define-public r-textshaping (package (name "r-textshaping") - (version "0.3.3") + (version "0.3.5") (source (origin (method url-fetch) (uri (cran-uri "textshaping" version)) (sha256 (base32 - "0yl3cv6r8k27h4lzbrsikjydhz94skdjmxx4zqzihvb7h3jfnlpn")))) + "06bdc5wxvgv38fnzpyjj9p62ifpfshaangkn96gw05yxn11s46h0")))) (properties `((upstream-name . "textshaping"))) (build-system r-build-system) (inputs @@ -27367,14 +29311,14 @@ the font tool-set provided by the @code{systemfonts} package.") (define-public r-ragg (package (name "r-ragg") - (version "1.1.2") + (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "ragg" version)) (sha256 (base32 - "0q28bwjdxpxm1wlkd8sxdf1m1q8wp4mmzp83d3m09nyy90ydkd8w")))) + "0ppypfq1vipwjngmiwdx1sj6x7m41v3dlnbsixdlnrf2nx82kxb2")))) (properties `((upstream-name . "ragg"))) (build-system r-build-system) (inputs @@ -27566,14 +29510,14 @@ percentages, citations, person tags, phone numbers, times, and zip codes.") (define-public r-mgsub (package (name "r-mgsub") - (version "1.7.2") + (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "mgsub" version)) (sha256 (base32 - "02l1b96zv36ia0c97wgcwfhi037mbn3wy9c64hcw0n0w67yj77rr")))) + "1mci6x65h94qiz9cwikx2inbrwkykv43zbs8abfbx416zrh2bbn9")))) (properties `((upstream-name . "mgsub"))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -27590,14 +29534,14 @@ in same length matches).") (define-public r-textshape (package (name "r-textshape") - (version "1.7.1") + (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "textshape" version)) (sha256 (base32 - "02111kj3kka84mpx7s19bjna9cas8diw5fxz51v5ggz0ldswa5pa")))) + "0k9injxykgj2qprc7dygd7gafvcbh3r9x84qzaa1al21pk0dz7ds")))) (properties `((upstream-name . "textshape"))) (build-system r-build-system) (propagated-inputs @@ -27674,14 +29618,14 @@ and word lists.") (define-public r-english (package (name "r-english") - (version "1.2-5") + (version "1.2-6") (source (origin (method url-fetch) (uri (cran-uri "english" version)) (sha256 (base32 - "0d6rin40wy2y6k75x8d5qvf03rfy139f309wrl8xwbdb1h8fjkd1")))) + "1g3nmy5p8wj3ix1vp1qmkmy3dyqisrw0md8cjrx4klqkp0wqlms9")))) (properties `((upstream-name . "english"))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -27732,14 +29676,14 @@ text but not always easily handled by analysis algorithms. The (define-public r-striprtf (package (name "r-striprtf") - (version "0.5.2") + (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "striprtf" version)) (sha256 (base32 - "1ra6aalalig6drsj26z9s24lmb10zssagqrvgqqi4358zbm8gwcd")))) + "0dqcsh3fb8j0mmmxvxjl77rryhmrjm7a3scqvk2xkgxk4xq6q316")))) (properties `((upstream-name . "striprtf"))) (build-system r-build-system) (propagated-inputs @@ -27901,14 +29845,14 @@ data you need the @code{pdftools} package.") (define-public r-pdftools (package (name "r-pdftools") - (version "2.3.1") + (version "3.0.1") (source (origin (method url-fetch) (uri (cran-uri "pdftools" version)) (sha256 (base32 - "01i5g2mjkshis0zlm7lrvi7kkzl4dn3if1hzwkgzf9n2mi33ndsx")))) + "1dcbs5n5y8zi7bbyx491m9ik8kkmjr301x8ms85fmwdfb5a97m8k")))) (properties `((upstream-name . "pdftools"))) (build-system r-build-system) (inputs @@ -27972,14 +29916,14 @@ latter.") (define-public r-readtext (package (name "r-readtext") - (version "0.80") + (version "0.81") (source (origin (method url-fetch) (uri (cran-uri "readtext" version)) (sha256 (base32 - "0q8ajnp99fwvh14ppkm2z3gqwdwmjrvxvsfb4q7ad0dhkqric05y")))) + "0k782h5hns5v5h8a6qyfqck2hc15nq0awg8bsp196q4zviv5jw3c")))) (properties `((upstream-name . "readtext"))) (build-system r-build-system) (propagated-inputs @@ -28035,14 +29979,14 @@ and formatted text files with additional meta-data, such including @code{.csv}, (define-public r-lwgeom (package (name "r-lwgeom") - (version "0.2-6") + (version "0.2-7") (source (origin (method url-fetch) (uri (cran-uri "lwgeom" version)) (sha256 (base32 - "1733iwinn426bcmgjxp4j0scvbz35rvqkanmw7g7f47l6j7w14vn")))) + "1qgszbw03haqfjdc07ivkg8r0yd50ldkiqq27ppkaibw7mgiak5k")))) (properties `((upstream-name . "lwgeom"))) (build-system r-build-system) (inputs @@ -28066,14 +30010,14 @@ light-weight geometry library used by @url{http://postgis.net/,PostGIS}.") (define-public r-stars (package (name "r-stars") - (version "0.5-2") + (version "0.5-3") (source (origin (method url-fetch) (uri (cran-uri "stars" version)) (sha256 (base32 - "0w2svw02ywvclq0nsnjns1n0rfr54q7x30y64y14n7zfr969ly1n")))) + "00cljaz98iy3wymabp7b47qgxdybg9jgjkw7q6da1ginmy14m524")))) (properties `((upstream-name . "stars"))) (build-system r-build-system) (propagated-inputs @@ -28203,14 +30147,14 @@ Application Program Interfaces (API)}.") (define-public r-eyelinker (package (name "r-eyelinker") - (version "0.2.0") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "eyelinker" version)) (sha256 (base32 - "14rfcdxad9iazwd46q6bm8gg1ryh6s8kf7arj00hhb7xz3gvk9c2")))) + "0wijd45p6j2qal6wnj7zywks8p9v3m9cmyp7axmk44mrjdjx2i71")))) (properties `((upstream-name . "eyelinker"))) (build-system r-build-system) (propagated-inputs @@ -28232,14 +30176,14 @@ Application Program Interfaces (API)}.") (define-public r-btm (package (name "r-btm") - (version "0.3.5") + (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "BTM" version)) (sha256 (base32 - "1x6bncb7r97z8bdyxnn2frdi9kyawfy6c2041mv9f42zdrfzm6jb")))) + "0ab0wr8nbwn1w1j9hpwfz52lm1sw0qk93713y9k0hpm3pw9dq4jr")))) (properties `((upstream-name . "BTM"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) @@ -28260,17 +30204,119 @@ Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013) BTM-WWW13.pdf}.") (license license:asl2.0))) +(define-public r-delaporte + (package + (name "r-delaporte") + (version "8.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "Delaporte" version)) + (sha256 + (base32 + "0ijhmwclpg5czs2sl2vykcw8qj2pxy26xf6knh62rqq6p6sm43f4")))) + (properties `((upstream-name . "Delaporte"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://github.com/aadler/Delaporte") + (synopsis "Statistical functions for the Delaporte distribution") + (description + "This package provides probability mass, distribution, quantile, +random-variate generation, and method-of-moments parameter-estimation +functions for the Delaporte distribution with parameterization based on +Vose (2008). The Delaporte is a discrete probability distribution which can +be considered the convolution of a negative binomial distribution with a +Poisson distribution. Alternatively, it can be considered a counting +distribution with both Poisson and negative binomial components. It has been +studied in actuarial science as a frequency distribution which has more +variability than the Poisson, but less than the negative binomial.") + (license license:bsd-2))) + +(define-public r-rjsonio + (package + (name "r-rjsonio") + (version "1.3-1.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "RJSONIO" version)) + (sha256 + (base32 + "17x0ayk7daprbc8w2hvb2jl9mfnw4dic9yc3sr5adcjqfzmcklc2")))) + (properties `((upstream-name . "RJSONIO"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=RJSONIO") + (synopsis "Serialize R objects to JSON") + (description + "This is a package that allows conversion to and from data in JavaScript +Object Notation (JSON) format. This allows R objects to be inserted into +Javascript/ECMAScript/ActionScript code and allows R programmers to read and +convert JSON content to R objects. This is an alternative to the @code{rjson} +package.") + (license license:bsd-3))) + +(define-public r-revgeo + (package + (name "r-revgeo") + (version "0.15") + (source + (origin + (method url-fetch) + (uri (cran-uri "revgeo" version)) + (sha256 + (base32 + "1ns7d1817475lriss6wwgvdm6lj760p40yxqaifla13c2xb73a55")))) + (properties `((upstream-name . "revgeo"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcurl" ,r-rcurl) + ("r-rjsonio" ,r-rjsonio))) + (home-page "https://cran.r-project.org/package=revgeo") + (synopsis "Reverse geocoding") + (description + "The @code{revgeo} procedure allows you to use the Photon geocoder for +OpenStreetMap, Google Maps, and Bing to reverse geocode coordinate pairs with +minimal hassle.") + (license license:gpl3+))) + +(define-public r-qpcr + (package + (name "r-qpcr") + (version "1.4-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "qpcR" version)) + (sha256 + (base32 + "1r01q7jv3w59yx1gc0qw91rq7rvdhqsi8y57sqqkmwyqfw2x2vsv")))) + (properties `((upstream-name . "qpcR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-minpack-lm" ,r-minpack-lm) + ("r-rgl" ,r-rgl) + ("r-robustbase" ,r-robustbase))) + (home-page "https://cran.r-project.org/package=qpcR") + (synopsis "Modelling and analysis of real-time PCR data") + (description + "This is a package for model fitting, optimal model selection and +calculation of various features that are essential in the analysis of +quantitative real-time polymerase chain reaction (qPCR).") + (license license:gpl2+))) + (define-public r-textplot (package (name "r-textplot") - (version "0.1.4") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "textplot" version)) (sha256 (base32 - "1sgkndy2cxk8c76h8hwajn6f78w5jj2n8vsmaxh9kj931crzn8cy")))) + "1fhnwbcgkliq71lry21762djhlbap1qg4mgil0np46aa6619l21m")))) (properties `((upstream-name . "textplot"))) (build-system r-build-system) (propagated-inputs @@ -28308,35 +30354,6 @@ indicator, a quantitative variable or a survival time.") ;; Any version of the LGPL (license license:lgpl3+))) -(define-public r-samr - (package - (name "r-samr") - (version "3.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "samr" version)) - (sha256 - (base32 - "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15")))) - (properties `((upstream-name . "samr"))) - (build-system r-build-system) - (propagated-inputs - `(("r-gsa" ,r-gsa) - ("r-impute" ,r-impute) - ("r-matrixstats" ,r-matrixstats) - ("r-openxlsx" ,r-openxlsx) - ("r-shiny" ,r-shiny) - ("r-shinyfiles" ,r-shinyfiles))) - (native-inputs `(("gfortran" ,gfortran))) - (home-page "https://statweb.stanford.edu/~tibs/SAM/") - (synopsis "Significance analysis of Microarrays") - (description - "This is a package for significance analysis of Microarrays for -differential expression analysis, RNAseq data and related problems.") - ;; Any version of the LGPL - (license license:lgpl3+))) - (define-public r-randomforestsrc (package (name "r-randomforestsrc") @@ -28362,3 +30379,1692 @@ quantile regression and solutions for class imbalanced data. It provides a fast interface using subsampling and confidence regions for variable importance.") (license license:gpl3+))) + +(define-public r-contfrac + (package + (name "r-contfrac") + (version "1.1-12") + (source + (origin + (method url-fetch) + (uri (cran-uri "contfrac" version)) + (sha256 + (base32 + "0sq5c7ny235yrkv2xc4insgxby6rvzc1qsj8h301cd2if3lwbgwm")))) + (properties `((upstream-name . "contfrac"))) + (build-system r-build-system) + (home-page + "https://github.com/RobinHankin/contfrac") + (synopsis "Continued Fractions") + (description + "Various utilities for evaluating continued fractions.") + (license license:gpl2))) + +(define-public r-elliptic + (package + (name "r-elliptic") + (version "1.4-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "elliptic" version)) + (sha256 + (base32 + "1dhba0yfxjd5rlqsxp5a7s2hclfkla9wigsr39dlma67l6qjjmxn")))) + (properties `((upstream-name . "elliptic"))) + (build-system r-build-system) + (inputs `(("pari-gp" ,pari-gp))) + (propagated-inputs `(("r-mass" ,r-mass))) + (home-page + "https://github.com/RobinHankin/elliptic") + (synopsis + "Weierstrass and Jacobi Elliptic Functions") + (description + "A suite of elliptic and related functions including Weierstrass and +Jacobi forms. Also includes various tools for manipulating and visualizing +complex functions.") + (license license:gpl2))) + +(define-public r-hypergeo + (package + (name "r-hypergeo") + (version "1.2-13") + (source + (origin + (method url-fetch) + (uri (cran-uri "hypergeo" version)) + (sha256 + (base32 + "13jdiy216znwhr91iqnh03mvkmyscw439syb3h4i67dd78sphnvd")))) + (properties `((upstream-name . "hypergeo"))) + (build-system r-build-system) + (propagated-inputs + `(("r-contfrac" ,r-contfrac) + ("r-desolve" ,r-desolve) + ("r-elliptic" ,r-elliptic))) + (home-page + "https://cran.r-project.org/web/packages/hypergeo/") + (synopsis "The Gauss Hypergeometric Function") + (description + "The Gaussian hypergeometric function for complex numbers.") + (license license:gpl2))) + +(define-public r-gganimate + (package + (name "r-gganimate") + (version "1.0.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "gganimate" version)) + (sha256 + (base32 + "046v6j92xxgaghsnh88dy5h8x040qsfa8csvhp4dmsfmrrf0dz0f")))) + (properties `((upstream-name . "gganimate"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'absolute-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "R/renderers.R" + (("'ffmpeg'") + (string-append "'" (assoc-ref inputs "ffmpeg") "/bin/ffmpeg'")))))))) + (inputs + ;; For video output. + `(("ffmpeg" ,ffmpeg))) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-glue" ,r-glue) + ("r-plyr" ,r-plyr) + ("r-progress" ,r-progress) + ("r-rlang" ,r-rlang) + ("r-scales" ,r-scales) + ("r-stringi" ,r-stringi) + ("r-tweenr" ,r-tweenr) + ;; For GIF/SVG output. gifski is faster, but depends on Rust. + ("r-magick" ,r-magick) + ;; For HTML output. + ("r-base64enc" ,r-base64enc) + ("r-htmltools" ,r-htmltools))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://gganimate.com") + (synopsis "Grammar of Animated Graphics") + (description + "This package extends the grammar of graphics as implemented by +@code{ggplot2} to include the description of animation. It does this by +providing a range of new grammar classes that can be added to the plot object +in order to customise how it should change with time.") + (license license:expat))) + +;; This library bundles ‘date’ from (gnu packages calendar). We cannot unbundle +;; it, because its C++ libtz.so is built with different compiler flags than +;; ours. +(define-public r-tzdb + (package + (name "r-tzdb") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "tzdb" version)) + (sha256 + (base32 + "1sl8nacx2i1h9vcvggiyzwd2zwvgrvfvsv3xa9072br62gkpay2c")))) + (properties `((upstream-name . "tzdb"))) + (build-system r-build-system) + (propagated-inputs `(("r-cpp11" ,r-cpp11))) + (home-page "https://github.com/r-lib/tzdb") + (synopsis "Time Zone Database Information") + (description + "This package provides an up-to-date copy of the Internet Assigned +Numbers Authority (IANA) Time Zone Database. It is updated periodically to +reflect changes made by political bodies to time zone boundaries, UTC offsets, +and daylight saving time rules. Additionally, this package provides a C++ +interface for working with the @code{date} library. @code{date} provides +comprehensive support for working with dates and date-times, which this package +exposes to make it easier for other R packages to utilize. Headers are +provided for calendar specific calculations, along with a limited interface for +time zone manipulations.") + (license license:expat))) + +(define-public r-vroom + (package + (name "r-vroom") + (version "1.5.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "vroom" version)) + (sha256 + (base32 + "1zk5nk9y64lspwhsasb7d2yg8i6ihyg2slys1qqa6qpi1266hi8x")))) + (properties `((upstream-name . "vroom"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bit64" ,r-bit64) + ("r-cli" ,r-cli) + ("r-cpp11" ,r-cpp11) + ("r-crayon" ,r-crayon) + ("r-glue" ,r-glue) + ("r-hms" ,r-hms) + ("r-lifecycle" ,r-lifecycle) + ("r-progress" ,r-progress) + ("r-rlang" ,r-rlang) + ("r-tibble" ,r-tibble) + ("r-tidyselect" ,r-tidyselect) + ("r-tzdb" ,r-tzdb) + ("r-vctrs" ,r-vctrs) + ("r-withr" ,r-withr))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://vroom.r-lib.org") + (synopsis + "Read and Write Rectangular Text Data") + (description + "This package reads and writes data files like @acronym{CSV}, +@acronym{TSV} and @acronym{FWF}. When reading it uses a quick initial indexing +step, then reads the values lazily, so only the data you actually use needs to +be read. The writer formats the data in parallel and writes to disk +asynchronously from formatting.") + (license license:expat))) + +(define-public r-rmisc + (package + (name "r-rmisc") + (version "1.5") + (source (origin + (method url-fetch) + (uri (cran-uri "Rmisc" version)) + (sha256 + (base32 + "1ijjhfy3v91fspid77rrkc5dkcb2lav37wc3f4k5lwrn24wzy5y8")))) + (build-system r-build-system) + (propagated-inputs + `(("r-plyr" ,r-plyr) + ("r-rcpp" ,r-rcpp) + ("r-lattice" ,r-lattice))) + (home-page "https://cran.r-project.org/web/packages/Rmisc/") + (synopsis "Ryan Miscellaneous") + (description "The Rmisc library contains functions for data analysis and +utility operations.") + (license license:gpl3))) + +(define-public r-webutils + (package + (name "r-webutils") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "webutils" version)) + (sha256 + (base32 "16a6ds0fnb6y8i1r9ba1hf1ydb53am57s070b3hi5jmrs84b9qik")))) + (properties `((upstream-name . "webutils"))) + (build-system r-build-system) + (propagated-inputs + `(("r-curl" ,r-curl) + ("r-jsonlite" ,r-jsonlite))) + (home-page "https://github.com/jeroen/webutils") + (synopsis "Utility functions for developing web applications") + (description + "This package parses HTTP request data in @code{application/json}, +@code{multipart/form-data}, or @code{application/x-www-form-urlencoded} +format. It includes an example of hosting and parsing HTML form data in R +using either @code{httpuv} or @code{Rhttpd}.") + (license license:expat))) + +(define-public r-protolite + (package + (name "r-protolite") + (version "2.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "protolite" version)) + (sha256 + (base32 "0g1r3lzmvx1w44qzqzdvxfn21zmz11srlp6cr76kd7pd5wzjv82p")))) + (properties `((upstream-name . "protolite"))) + (build-system r-build-system) + (inputs + `(("protobuf" ,protobuf))) + (propagated-inputs + `(("r-jsonlite" ,r-jsonlite) + ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("protobuf" ,protobuf) + ("pkg-config" ,pkg-config))) + (home-page "https://github.com/jeroen/protolite") + (synopsis "Highly optimized protocol buffer serializers") + (description + "This package provides pure C++ implementations for reading and writing +several common data formats based on Google protocol-buffers. It currently +supports @code{rexp.proto} for serialized R objects, @code{geobuf.proto} for +binary geojson, and @code{mvt.proto} for vector tiles. This package uses the +auto-generated C++ code by protobuf-compiler, hence the entire serialization +is optimized at compile time. The @code{RProtoBuf} package on the other hand +uses the protobuf runtime library to provide a general-purpose toolkit for +reading and writing arbitrary protocol-buffer data in R.") + (license license:expat))) + +(define-public r-opencpu + (package + (name "r-opencpu") + (version "2.2.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "opencpu" version)) + (sha256 + (base32 "1qlwx8iq30qfy2sh0v31pxg955bj4zs0r7v8yklbdwb3qw7kv30g")))) + (properties `((upstream-name . "opencpu"))) + (build-system r-build-system) + (inputs + `(("pandoc" ,pandoc))) + (propagated-inputs + `(("r-brew" ,r-brew) + ("r-curl" ,r-curl) + ("r-evaluate" ,r-evaluate) + ("r-httpuv" ,r-httpuv) + ("r-jsonlite" ,r-jsonlite) + ("r-knitr" ,r-knitr) + ("r-mime" ,r-mime) + ("r-openssl" ,r-openssl) + ("r-protolite" ,r-protolite) + ("r-rappdirs" ,r-rappdirs) + ("r-remotes" ,r-remotes) + ("r-sys" ,r-sys) + ("r-webutils" ,r-webutils) + ("r-zip" ,r-zip))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://www.opencpu.org") + (synopsis "API for embedded scientific computing") + (description + "This package provides a system for embedded scientific computing and +reproducible research with R. The OpenCPU server exposes a simple but +powerful HTTP API for RPC and data interchange with R. This provides a +reliable and scalable foundation for statistical services or building R web +applications. The OpenCPU server runs either as a single-user development +server within the interactive R session, or as a multi-user stack based on +Apache2.") + (license license:asl2.0))) + +(define-public r-exactextractr + (package + (name "r-exactextractr") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "exactextractr" version)) + (sha256 + (base32 + "1fwbl0rn0990cs2rvvwjbflp9mall6hjkindpjmdcy6qafiviid6")))) + (properties `((upstream-name . "exactextractr"))) + (build-system r-build-system) + (inputs `(("geos" ,geos))) + (propagated-inputs + `(("r-raster" ,r-raster) + ("r-rcpp" ,r-rcpp) + ("r-sf" ,r-sf))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://isciences.gitlab.io/exactextractr/") + (synopsis "Fast extraction from raster datasets using polygons") + (description + "This package provides a replacement for the @code{extract} function from +the @code{raster} package that is suitable for extracting raster values using +@code{sf} polygons.") + (license license:asl2.0))) + +(define-public r-stringfish + (package + (name "r-stringfish") + (version "0.15.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "stringfish" version)) + (sha256 + (base32 + "0m8485p1gb5z2n2g5nyr38zixw4iv8xxm7bxspxlxvx6alhn03pn")))) + (properties `((upstream-name . "stringfish"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcppparallel" ,r-rcppparallel))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) + (home-page "https://github.com/traversc/stringfish") + (synopsis "Alternative string implementation") + (description + "This package provides an extendable, performant and multithreaded +@code{alt-string} implementation backed by C++ vectors and strings.") + (license license:gpl3))) + +(define-public r-rapiserialize + (package + (name "r-rapiserialize") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "RApiSerialize" version)) + (sha256 + (base32 + "0gm2j8kh40imhncwwx1sx9kmraaxcxycvgwls53lcyy2ap344k9j")))) + (properties `((upstream-name . "RApiSerialize"))) + (build-system r-build-system) + (home-page + "https://cran.r-project.org/package=RApiSerialize") + (synopsis "R API serialization") + (description + "This package provides other packages with access to the internal R +serialization code. Access to this code is provided at the C function level +by using the registration of native function mechanism. Client packages +simply include a single header file RApiSerializeAPI.h provided by this +package.") + (license license:gpl2+))) + +(define-public r-qs + (package + (name "r-qs") + (version "0.25.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "qs" version)) + (sha256 + (base32 + "0qzrhc5jsygj813k956b00h4b6haynz44rk6a4v34fv4ywq9ba7w")))) + (properties `((upstream-name . "qs"))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (propagated-inputs + `(("r-rapiserialize" ,r-rapiserialize) + ("r-rcpp" ,r-rcpp) + ("r-stringfish" ,r-stringfish))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) + (home-page "https://github.com/traversc/qs") + (synopsis "Quick serialization of R objects") + (description + "This package provides functions for quickly writing and reading any R +object to and from disk.") + (license license:gpl3))) + +(define-public r-rgeos + (package + (name "r-rgeos") + (version "0.5-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "rgeos" version)) + (sha256 + (base32 + "05539shf38slvq38pf92h9q57vmzn2vfqbirl3pbbvvc2j957cqd")))) + (properties `((upstream-name . "rgeos"))) + (build-system r-build-system) + (inputs + `(("geos" ,geos))) + (propagated-inputs + `(("r-sp" ,r-sp))) + (home-page "https://cran.r-project.org/package=rgeos") + (synopsis "Interface to Geometry Engine (GEOS)") + (description + "This package provides an R interface to Geometry Engine (GEOS) using the +C API for topology operations on geometries.") + (license license:gpl2+))) + +(define-public r-tfruns + (package + (name "r-tfruns") + (version "1.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "tfruns" version)) + (sha256 + (base32 + "04lfckg1if3kfwcl4s4fcc9aw04crwk4m1qr55ag22j2x2jlb2l9")))) + (properties `((upstream-name . "tfruns"))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-config" ,r-config) + ("r-jsonlite" ,r-jsonlite) + ("r-magrittr" ,r-magrittr) + ("r-reticulate" ,r-reticulate) + ("r-rlang" ,r-rlang) + ("r-rstudioapi" ,r-rstudioapi) + ("r-tidyselect" ,r-tidyselect) + ("r-whisker" ,r-whisker) + ("r-yaml" ,r-yaml))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/rstudio/tfruns") + (synopsis "Training run tools for TensorFlow") + (description + "Create and manage unique directories for each TensorFlow training run. +This package provides a unique, time stamped directory for each run along with +functions to retrieve the directory of the latest run or latest several +runs.") + (license license:asl2.0))) + +(define-public r-tfautograph + (package + (name "r-tfautograph") + (version "0.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "tfautograph" version)) + (sha256 + (base32 + "0fmaq1ggjyxgf2ss7qb8jk74sfwc3s1vc123pd5glclxcy1ib0j2")))) + (properties `((upstream-name . "tfautograph"))) + (build-system r-build-system) + (inputs `(("tensorflow" ,tensorflow))) + (propagated-inputs + `(("r-backports" ,r-backports) + ("r-reticulate" ,r-reticulate))) + (home-page "https://t-kalinowski.github.io/tfautograph/") + (synopsis "Autograph R for Tensorflow") + (description + "This package lets you translate R control flow expressions into +Tensorflow graphs.") + (license license:gpl3))) + +(define-public r-tensorflow + (package + (name "r-tensorflow") + (version "2.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "tensorflow" version)) + (sha256 + (base32 + "1lkzxc3b5gkcg4hwqr57cysplcba6ff44qz8lbvk19kxnrhjaf9g")))) + (properties `((upstream-name . "tensorflow"))) + (build-system r-build-system) + (inputs `(("tensorflow" ,tensorflow))) + (propagated-inputs + `(("r-config" ,r-config) + ("r-processx" ,r-processx) + ("r-reticulate" ,r-reticulate) + ("r-rstudioapi" ,r-rstudioapi) + ("r-tfautograph" ,r-tfautograph) + ("r-tfruns" ,r-tfruns) + ("r-yaml" ,r-yaml))) + (home-page "https://github.com/rstudio/tensorflow") + (synopsis "R interface to TensorFlow") + (description + "R interface to TensorFlow a library for numerical computation using data +flow graphs. Nodes in the graph represent mathematical operations, while the +graph edges represent the multidimensional data arrays (tensors) communicated +between them.") + (license license:asl2.0))) + +(define-public r-keras + (package + (name "r-keras") + (version "2.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "keras" version)) + (sha256 + (base32 + "1pgdcypp9x9dw7aa5ka7qqgd24jdcp3ja94jpm7j6l6j4930k5vd")))) + (properties `((upstream-name . "keras"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ellipsis" ,r-ellipsis) + ("r-generics" ,r-generics) + ("r-glue" ,r-glue) + ("r-magrittr" ,r-magrittr) + ("r-r6" ,r-r6) + ("r-reticulate" ,r-reticulate) + ("r-rlang" ,r-rlang) + ("r-tensorflow" ,r-tensorflow) + ("r-tfruns" ,r-tfruns) + ("r-zeallot" ,r-zeallot))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://keras.rstudio.com") + (synopsis "R Interface to 'Keras'") + (description + "This package provides an interface to Keras, a high-level neural +networks API. Keras was developed with a focus on enabling fast +experimentation, supports both convolution based networks and recurrent +networks (as well as combinations of the two), and runs seamlessly on both CPU +and GPU devices.") + (license license:expat))) + +(define-public r-zzlite + (package + (name "r-zzlite") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "zzlite" version)) + (sha256 + (base32 + "0vi1slx2s4r5zf82lazqv0c3m12xq73wlgsbz6af4y00h0bkr3ps")))) + (properties `((upstream-name . "zzlite"))) + (build-system r-build-system) + (propagated-inputs + `(("r-httr" ,r-httr) + ("r-jsonlite" ,r-jsonlite))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/package=zzlite") + (synopsis "Wrapper for the Zamzar file conversion API") + (description + "This package provides a minor collection of HTTP wrappers for the Zamzar +file conversion API. The wrappers makes it easy to utilize the API and thus +convert between more than 100 different file formats (ranging from audio +files, images, movie formats, etc., etc.) through an R session.") + (license license:gpl3))) + +(define-public r-ztree + (package + (name "r-ztree") + (version "1.0.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "zTree" version)) + (sha256 + (base32 + "1mywxrx6bw7dzhrdwyxbjzc8ikgvw423zycyji0jjr69cfhpmywv")))) + (properties `((upstream-name . "zTree"))) + (build-system r-build-system) + (propagated-inputs + `(("r-plyr" ,r-plyr))) + (home-page "https://cran.r-project.org/package=zTree") + (synopsis "Functions to import data from z-Tree into R") + (description + "This package provides tools for reading @code{.xls} and @code{.sbj} +files which are written by the proprietary program z-Tree for developing and +carrying out economic experiments.") + (license license:gpl3))) + +(define-public r-distributionutils + (package + (name "r-distributionutils") + (version "0.6-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "DistributionUtils" version)) + (sha256 + (base32 + "08vq54pyqxlqsj6q6gsg5ikqa0z3x842j52ld5dxaq272p6xchvl")))) + (properties + `((upstream-name . "DistributionUtils"))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/package=DistributionUtils") + (synopsis "Distribution utilities") + (description + "This package provides utilities for dealing with distributions. +Functionality includes sample skewness and kurtosis, log-histogram, tail +plots, moments by integration, changing the point about which a moment is +calculated, functions for testing distributions using inversion tests and the +Massart inequality. Also included is an implementation of the incomplete +Bessel K function.") + (license license:gpl2+))) + +(define-public r-ztpln + (package + (name "r-ztpln") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ztpln" version)) + (sha256 + (base32 + "18rbfdp22jaxg4nkqzj2393nhjdl1gzv4xhmr6aci76ymdixsfnl")))) + (properties `((upstream-name . "ztpln"))) + (build-system r-build-system) + (propagated-inputs + `(("r-distributionutils" ,r-distributionutils) + ("r-mixtools" ,r-mixtools) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-rcppnumerical" ,r-rcppnumerical))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/mattocci27/ztpln") + (synopsis "Zero-truncated Poisson lognormal distribution") + (description + "This package provides functions for obtaining the density, random +variates and maximum likelihood estimates of the Zero-truncated Poisson +lognormal distribution and their mixture distribution.") + (license license:expat))) + +(define-public r-zscorer + (package + (name "r-zscorer") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "zscorer" version)) + (sha256 + (base32 + "0aijhs0fyird5gq68x4dxchb02mxa7ijk10k9zjhngghxbjj7iqn")))) + (properties `((upstream-name . "zscorer"))) + (build-system r-build-system) + (propagated-inputs + `(("r-shiny" ,r-shiny))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/nutriverse/zscorer") + (synopsis "Child Anthropometry z-Score Calculator") + (description + "This package provides a tool for calculating z-scores and centiles for +weight-for-age, length/height-for-age, weight-for-length/height, BMI-for-age, +head circumference-for-age, age circumference-for-age, subscapular +skinfold-for-age, triceps skinfold-for-age based on the WHO Child Growth +Standards.") + (license license:agpl3+))) + +(define-public r-zra + (package + (name "r-zra") + (version "0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "ZRA" version)) + (sha256 + (base32 + "1sx1q5yf68hhlb5j1hicpj594rmgajqr25llg7ax416j0m2rnagi")))) + (properties `((upstream-name . "ZRA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dygraphs" ,r-dygraphs) + ("r-forecast" ,r-forecast))) + (home-page "https://cran.r-project.org/package=ZRA") + (synopsis "Dynamic plots for time series forecasting") + (description + "This package combines a forecast of a time series, using the function @code{forecast}, +with the dynamic plots from @code{dygraphs}.") + (license license:gpl2+))) + +(define-public r-rfigshare + (package + (name "r-rfigshare") + (version "0.3.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "rfigshare" version)) + (sha256 + (base32 + "1qgzn0mpjy4czy0pnbi395fxxx84arkg8r7rk8aidmd34584gjiq")))) + (properties `((upstream-name . "rfigshare"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-httpuv" ,r-httpuv) + ("r-httr" ,r-httr) + ("r-plyr" ,r-plyr) + ("r-rjsonio" ,r-rjsonio) + ("r-xml" ,r-xml) + ("r-yaml" ,r-yaml))) + (home-page "https://github.com/ropensci/rfigshare") + (synopsis "R Interface to figshare") + (description + "This package provides an interface to figshare, a scientific repository +to archive and assign DOIs to data, software, figures, and more.") + (license license:cc0))) + +(define-public r-dismo + (package + (name "r-dismo") + (version "1.3-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "dismo" version)) + (sha256 + (base32 + "1jj9d78f251bxgrwbv1ycn677qnhvl40bfan12x8fhlaq4d36rgx")))) + (properties `((upstream-name . "dismo"))) + (build-system r-build-system) + (propagated-inputs + `(("r-raster" ,r-raster) + ("r-rcpp" ,r-rcpp) + ("r-sp" ,r-sp))) + (home-page "https://rspatial.org/raster/sdm/") + (synopsis "Species distribution modeling") + (description + "This package provides methods for species distribution modeling, i.e., +predicting the environmental similarity of any site to that of the locations +of known occurrences of a species.") + (license license:gpl3+))) + +(define-public r-zoon + (package + (name "r-zoon") + (version "0.6.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "zoon" version)) + (sha256 + (base32 + "02y29vr2yn8al69km8faiqrwjrc1r3hsvw3dg8lwjr65cxw1krip")))) + (properties `((upstream-name . "zoon"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dismo" ,r-dismo) + ("r-plyr" ,r-plyr) + ("r-randomforest" ,r-randomforest) + ("r-raster" ,r-raster) + ("r-rcurl" ,r-rcurl) + ("r-rfigshare" ,r-rfigshare) + ("r-rgdal" ,r-rgdal) + ("r-roxygen2" ,r-roxygen2) + ("r-rworldmap" ,r-rworldmap) + ("r-sp" ,r-sp) + ("r-testthat" ,r-testthat))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/zoonproject/zoon") + (synopsis "Reproducible, accessible and shareable species distribution modelling") + (description + "This package reads user submitted modules from an online repository, +runs full species distribution modelling workflows and returns output that is +fully reproducible.") + (license license:bsd-3))) + +(define-public r-paws-common + (package + (name "r-paws-common") + (version "0.3.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "paws.common" version)) + (sha256 + (base32 + "1khq1rv0yij4l0vi2x6hslnzpsd6m5n6nipfac7g3na9ah93h8i9")))) + (properties `((upstream-name . "paws.common"))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-digest" ,r-digest) + ("r-httr" ,r-httr) + ("r-jsonlite" ,r-jsonlite) + ("r-xml2" ,r-xml2))) + (home-page "https://cran.r-project.org/package=paws.common") + (synopsis "Paws low-level Amazon Web Services API") + (description + "This package provides functions for making low-level API requests to +Amazon Web Services. The functions handle building, signing, and sending +requests, and receiving responses. They are designed to help build +higher-level interfaces to individual services, such as Simple Storage +Service (S3).") + (license license:asl2.0))) + +(define-public r-paws-customer-engagement + (package + (name "r-paws-customer-engagement") + (version "0.1.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "paws.customer.engagement" version)) + (sha256 + (base32 + "0ac6hzn4ilfjhzdmc9x80999fl18cz16mky31qd3y09m93w2xkdj")))) + (properties + `((upstream-name . "paws.customer.engagement"))) + (build-system r-build-system) + (propagated-inputs + `(("r-paws-common" ,r-paws-common))) + (home-page "https://github.com/paws-r/paws") + (synopsis "Amazon Web Services customer engagement services") + (description + "This package provides an interface to Amazon Web Services customer +engagement services, including Simple Email Service, Connect contact center +service, and more.") + (license license:asl2.0))) + +(define-public r-paws-cost-management + (package + (name "r-paws-cost-management") + (version "0.1.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "paws.cost.management" version)) + (sha256 + (base32 + "0in4f8ygw5g2v6vl3lz2y0v51llglh8b1ymbd04d54xxlgn83knh")))) + (properties + `((upstream-name . "paws.cost.management"))) + (build-system r-build-system) + (propagated-inputs + `(("r-paws-common" ,r-paws-common))) + (home-page "https://github.com/paws-r/paws") + (synopsis "Amazon Web Services cost management services") + (description + "This package provides an interface to Amazon Web Services cost +management services, including cost and usage reports, budgets, pricing, and +more.") + (license license:asl2.0))) + +(define-public r-paws-developer-tools + (package + (name "r-paws-developer-tools") + (version "0.1.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "paws.developer.tools" version)) + (sha256 + (base32 "16gb8g8s67al7qdd95fbigxqkih9a9p7slkyf3cga42wb6miiby2")))) + (properties `((upstream-name . "paws.developer.tools"))) + (build-system r-build-system) + (propagated-inputs + `(("r-paws-common" ,r-paws-common))) + (home-page "https://github.com/paws-r/paws") + (synopsis "Amazon Web Services developer tools services") + (description + "This package provides an interface to Amazon Web Services developer +tools services, including version control, continuous integration and +deployment, and more.") + (license license:asl2.0))) + +(define-public r-paws-end-user-computing + (package + (name "r-paws-end-user-computing") + (version "0.1.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "paws.end.user.computing" version)) + (sha256 + (base32 "1xxsz86nx128sizym9np8vldzkbym0p3i6vcy94kq1y0cylaicv3")))) + (properties `((upstream-name . "paws.end.user.computing"))) + (build-system r-build-system) + (propagated-inputs + `(("r-paws-common" ,r-paws-common))) + (home-page "https://github.com/paws-r/paws") + (synopsis "Amazon Web Services end user computing services") + (description + "This package provides an interface to Amazon Web Services end user +computing services, including collaborative document editing, mobile intranet, +and more.") + (license license:asl2.0))) + +(define-public r-paws-application-integration + (package + (name "r-paws-application-integration") + (version "0.1.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "paws.application.integration" version)) + (sha256 + (base32 + "0llyd9hc679pad1ih0rcc38q5xxpzinhwrl8cvrkgsjgbc3agq42")))) + (properties + `((upstream-name . "paws.application.integration"))) + (build-system r-build-system) + (propagated-inputs + `(("r-paws-common" ,r-paws-common))) + (home-page "https://github.com/paws-r/paws") + (synopsis "Amazon Web Services application integration services") + (description + "This package provides an interface to Amazon Web Services application +integration services, including Simple Queue Service (SQS) message queue, +Simple Notification Service (SNS) publish/subscribe messaging, and more.") + (license license:asl2.0))) + +(define-public r-paws-security-identity + (package + (name "r-paws-security-identity") + (version "0.1.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "paws.security.identity" version)) + (sha256 + (base32 + "092lz2ipn5iqr593x7ra8c0bj64yf6315mdc3llgwrjyb4vfxif9")))) + (properties + `((upstream-name . "paws.security.identity"))) + (build-system r-build-system) + (propagated-inputs + `(("r-paws-common" ,r-paws-common))) + (home-page "https://github.com/paws-r/paws") + (synopsis "Amazon Web Services security, identity, and compliance services") + (description + "This package provides an interface to Amazon Web Services security, +identity, and compliance services, including the Identity and Access +Management (IAM) service for managing access to services and resources, and +more.") + (license license:asl2.0))) + +(define-public r-paws-analytics + (package + (name "r-paws-analytics") + (version "0.1.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "paws.analytics" version)) + (sha256 + (base32 + "04gnaxmj21l312xkrsd9bisi0bz9h6h5fyhwlqylcxi077z1yb2g")))) + (properties + `((upstream-name . "paws.analytics"))) + (build-system r-build-system) + (propagated-inputs + `(("r-paws-common" ,r-paws-common))) + (home-page "https://github.com/paws-r/paws") + (synopsis "Amazon Web Services analytics services") + (description + "This package provides an interface to Amazon Web Services analytics +services, including Elastic MapReduce Hadoop and Spark big data service, +Elasticsearch search engine, and more.") + (license license:asl2.0))) + +(define-public r-paws-machine-learning + (package + (name "r-paws-machine-learning") + (version "0.1.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "paws.machine.learning" version)) + (sha256 + (base32 + "01w2y5952pk50xjbzby2pc51xrkrzjpfxbmii1b10cl2xgzfkxsa")))) + (properties + `((upstream-name . "paws.machine.learning"))) + (build-system r-build-system) + (propagated-inputs + `(("r-paws-common" ,r-paws-common))) + (home-page "https://github.com/paws-r/paws") + (synopsis "Amazon Web Services machine learning services") + (description + "This package provides an interface to Amazon Web Services machine +learning services, including SageMaker managed machine learning service, +natural language processing, speech recognition, translation, and more.") + (license license:asl2.0))) + +(define-public r-paws-management + (package + (name "r-paws-management") + (version "0.1.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "paws.management" version)) + (sha256 + (base32 + "09k7wg0jlj40zs2yb3vldffpkdcjg7ap98n7c5lxr5plpca08swg")))) + (properties + `((upstream-name . "paws.management"))) + (build-system r-build-system) + (propagated-inputs + `(("r-paws-common" ,r-paws-common))) + (home-page "https://github.com/paws-r/paws") + (synopsis "Amazon Web Services management and governance services") + (description + "This package provides an interface to Amazon Web Services management and +governance services, including CloudWatch application and infrastructure +monitoring, Auto Scaling for automatically scaling resources, and more.") + (license license:asl2.0))) + +(define-public r-paws-networking + (package + (name "r-paws-networking") + (version "0.1.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "paws.networking" version)) + (sha256 + (base32 + "02hxaa5nlj70mdggh379ij3fn09xm8h5ldzsyf45c342prpl6zwj")))) + (properties + `((upstream-name . "paws.networking"))) + (build-system r-build-system) + (propagated-inputs + `(("r-paws-common" ,r-paws-common))) + (home-page "https://github.com/paws-r/paws") + (synopsis "Amazon Web Services networking and content delivery services") + (description + "This package provides an interface to Amazon Web Services networking and +content delivery services, including Route 53 Domain Name System service, +CloudFront content delivery, load balancing, and more.") + (license license:asl2.0))) + +(define-public r-paws-database + (package + (name "r-paws-database") + (version "0.1.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "paws.database" version)) + (sha256 + (base32 + "08jpwz95fw3f68j0wxh2lg57nn60khflldab0ryhkkbcw1iy0qyz")))) + (properties `((upstream-name . "paws.database"))) + (build-system r-build-system) + (propagated-inputs + `(("r-paws-common" ,r-paws-common))) + (home-page "https://github.com/paws-r/paws") + (synopsis + "Amazon Web Services Database Services") + (description + "This package provides an interface to Amazon Web Services database +services, including Relational Database Service (RDS), DynamoDB NoSQL +database, and more.") + (license license:asl2.0))) + +(define-public r-paws-storage + (package + (name "r-paws-storage") + (version "0.1.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "paws.storage" version)) + (sha256 + (base32 + "06m887vpqp5d6k3zxdlga599dsv8v3rladk7xqaxqnld1f17am04")))) + (properties `((upstream-name . "paws.storage"))) + (build-system r-build-system) + (propagated-inputs + `(("r-paws-common" ,r-paws-common))) + (home-page "https://github.com/paws-r/paws") + (synopsis "Amazon Web Services storage services") + (description + "This package provides an interface to Amazon Web Services storage +services, including Simple Storage Service (S3).") + (license license:asl2.0))) + +(define-public r-paws-compute + (package + (name "r-paws-compute") + (version "0.1.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "paws.compute" version)) + (sha256 + (base32 + "1km6fng6il5fcjlrbbndahsw2dr2ql83hwac9wlpd67zm3wy9lky")))) + (properties `((upstream-name . "paws.compute"))) + (build-system r-build-system) + (propagated-inputs + `(("r-paws-common" ,r-paws-common))) + (home-page "https://github.com/paws-r/paws") + (synopsis "Amazon Web Services compute services") + (description + "This package provides an interface to Amazon Web Services compute +services, including Elastic Compute Cloud (EC2), Lambda +functions-as-a-service, containers, batch processing, and more.") + (license license:asl2.0))) + +(define-public r-paws + (package + (name "r-paws") + (version "0.1.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "paws" version)) + (sha256 + (base32 + "0kn1z045r106fwqcaz52hb02bhrcblh479cajfjiq480s1iljcw6")))) + (properties `((upstream-name . "paws"))) + (build-system r-build-system) + (propagated-inputs + `(("r-paws-analytics" ,r-paws-analytics) + ("r-paws-application-integration" ,r-paws-application-integration) + ("r-paws-compute" ,r-paws-compute) + ("r-paws-cost-management" ,r-paws-cost-management) + ("r-paws-customer-engagement" ,r-paws-customer-engagement) + ("r-paws-database" ,r-paws-database) + ("r-paws-developer-tools" ,r-paws-developer-tools) + ("r-paws-end-user-computing" ,r-paws-end-user-computing) + ("r-paws-machine-learning" ,r-paws-machine-learning) + ("r-paws-management" ,r-paws-management) + ("r-paws-networking" ,r-paws-networking) + ("r-paws-security-identity" ,r-paws-security-identity) + ("r-paws-storage" ,r-paws-storage))) + (home-page "https://github.com/paws-r/paws") + (synopsis "Amazon Web Services software development kit") + (description + "This package provides an interface to Amazon Web Services, including +storage, database, and compute services, such as Simple Storage Service (S3), +DynamoDB NoSQL database, and Lambda functions-as-a-service.") + (license license:asl2.0))) + +(define-public r-zoomgroupstats + (package + (name "r-zoomgroupstats") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "zoomGroupStats" version)) + (sha256 + (base32 + "0gndiq92cy6gi7f833hdjvqii3cn83wz5rjvygcvjl3dw4pwv966")))) + (properties + `((upstream-name . "zoomGroupStats"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-lubridate" ,r-lubridate) + ("r-magick" ,r-magick) + ("r-openxlsx" ,r-openxlsx) + ("r-paws" ,r-paws) + ("r-pbapply" ,r-pbapply) + ("r-stringr" ,r-stringr) + ("r-syuzhet" ,r-syuzhet))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "http://zoomgroupstats.org") + (synopsis "Analyze text, audio, and video from Zoom meetings") + (description + "This package provides utilities for processing and analyzing the files +that are exported from a recorded Zoom meeting. This includes analyzing data +captured through video cameras and microphones, the text-based chat, and +meta-data. You can analyze aspects of the conversation among meeting +participants and their emotional expressions throughout the meeting.") + (license license:expat))) + +(define-public r-zoom + (package + (name "r-zoom") + (version "2.0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "zoom" version)) + (sha256 + (base32 + "03f5rxfr6ncf1j6vpn7pip21q7ylj4bx0a5xphqb6x6i33lxf1g5")))) + (properties `((upstream-name . "zoom"))) + (build-system r-build-system) + (home-page "https://github.com/cbarbu/R-package-zoom") + (synopsis "Spatial data visualization tool") + (description + "This package provides @code{zm}, a utility that allows you to +zoom/navigate any plot when called with any active plot.") + (license license:gpl3+))) + +(define-public r-zoolog + (package + (name "r-zoolog") + (version "0.4.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "zoolog" version)) + (sha256 + (base32 + "1wxxxscw4ji4p4599vdw6vcrkqm0g75x1gh13m4758lb51wav9ks")))) + (properties `((upstream-name . "zoolog"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rdpack" ,r-rdpack) + ("r-stringi" ,r-stringi))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://josempozo.github.io/zoolog/") + (synopsis "Zooarchaeological analysis with log-ratios") + (description + "This package includes functions and reference data to generate and +manipulate log-ratios (also known as @dfn{log size index} (LSI) values) from +measurements obtained on zooarchaeological material. Log ratios are used to +compare the relative (rather than the absolute) dimensions of animals from +archaeological contexts. The zoolog package is also able to seamlessly +integrate data and references with heterogeneous nomenclature, which is +internally managed by a zoolog thesaurus.") + (license license:gpl3))) + +(define-public r-filehash + (package + (name "r-filehash") + (version "2.4-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "filehash" version)) + (sha256 + (base32 + "14zv7h5195dmfksgk8qvjgc2qq8253vga6267aa1bqs5bpvmdl5n")))) + (properties `((upstream-name . "filehash"))) + (build-system r-build-system) + (home-page "http://github.com/rdpeng/filehash") + (synopsis "Simple key-value database") + (description + "This package implements a simple key-value style database where +character string keys are associated with data values that are stored on the +disk. A simple interface is provided for inserting, retrieving, and deleting +data from the database. Utilities are provided that allow filehash databases +to be treated much like environments and lists are already used in R. These +utilities are provided to encourage interactive and exploratory analysis on +large datasets.") + (license license:gpl2+))) + +(define-public r-mlearning + (package + (name "r-mlearning") + (version "1.0-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "mlearning" version)) + (sha256 + (base32 + "0r8xfaxw83s2r27b8x5qd0k4r5ayxpkafzn9b1a0jvsr87i6520r")))) + (properties `((upstream-name . "mlearning"))) + (build-system r-build-system) + (propagated-inputs + `(("r-class" ,r-class) + ("r-e1071" ,r-e1071) + ("r-ipred" ,r-ipred) + ("r-mass" ,r-mass) + ("r-nnet" ,r-nnet) + ("r-randomforest" ,r-randomforest))) + (home-page "http://www.sciviews.org/zooimage") + (synopsis "Machine learning algorithms with unified interface") + (description + "This package provides a unified interface to various machine learning +algorithms. Confusion matrices are provided too.") + (license license:gpl2+))) + +(define-public r-zooimage + (package + (name "r-zooimage") + (version "5.5.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "zooimage" version)) + (sha256 + (base32 + "0ck8w0zb9l1n9xvjwqshq9q9l8pigy3yslq2hnfbgcwk17kk9mp8")))) + (properties `((upstream-name . "zooimage"))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-dt" ,r-dt) + ("r-filehash" ,r-filehash) + ("r-jpeg" ,r-jpeg) + ("r-mass" ,r-mass) + ("r-mda" ,r-mda) + ("r-mlearning" ,r-mlearning) + ("r-png" ,r-png) + ("r-shiny" ,r-shiny) + ("r-svdialogs" ,r-svdialogs) + ("r-svmisc" ,r-svmisc) + ("r-tiff" ,r-tiff))) + (home-page "http://www.sciviews.org/zooimage") + (synopsis "Analysis of numerical plankton images") + (description + "This package provides a solution for analyzing digital images of +plankton. In combination with ImageJ, an image analysis system, it processes +digital images, measures individuals, trains for automatic classification of +taxa, and finally, measures plankton samples (abundances, total and partial +size spectra or biomasses, etc.).") + (license license:gpl2+))) + +(define-public r-zooarch + (package + (name "r-zooarch") + (version "1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "zooaRch" version)) + (sha256 + (base32 + "0grc378xppv0303sf4flfqz5002vq5a23nzbq4bsff41rww7dihc")))) + (properties `((upstream-name . "zooaRch"))) + (build-system r-build-system) + (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page + "https://cran.r-project.org/package=zooaRch") + (synopsis + "Analytical Tools for Zooarchaeological Data") + (description + "The analysis and inference of faunal remains recovered from +archaeological sites concerns the field of zooarchaeology. The zooaRch +package provides analytical tools to make inferences on zooarchaeological +data. Functions in this package allow users to read, manipulate, visualize, +and analyze zooarchaeological data.") + (license license:gpl2+))) + +(define-public r-zonebuilder + (package + (name "r-zonebuilder") + (version "0.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "zonebuilder" version)) + (sha256 + (base32 + "0mxf3dz0d6bi5wwjilqivdxhy5ypnq5svky8zygha0clv45l4dmn")))) + (properties `((upstream-name . "zonebuilder"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-sf" ,r-sf))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/zonebuilders/zonebuilder") + (synopsis "Create and explore geographic zoning systems") + (description + "This package provides functions, documentation and example data to help +divide geographic space into discrete polygons (zones). The functions are +motivated by research into the merits of different zoning systems. A flexible +@code{ClockBoard} zoning system is provided, which breaks-up space by +concentric rings and radial lines emanating from a central point.") + (license license:gpl3))) + +(define-public r-zonator + (package + (name "r-zonator") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "zonator" version)) + (sha256 + (base32 + "1plxchpd4ypp36phl13pi9yvlrqi3lk83lv5rldrhdqynhcgfw2k")))) + (properties `((upstream-name . "zonator"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-raster" ,r-raster) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-reshape2" ,r-reshape2) + ("r-rgdal" ,r-rgdal))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://cbig.github.io/zonator/") + (synopsis "Utilities for Zonation spatial conservation prioritization") + (description + "Create new analysis setups and deal with results of Zonation +conservation prioritization software.") + (license license:bsd-2))) + +(define-public r-mmwrweek + (package + (name "r-mmwrweek") + (version "0.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "MMWRweek" version)) + (sha256 + (base32 + "1l1ks44v52iggw9nhs56lfj6804yab5b17k8fzrc6h1kvj3vda0s")))) + (properties `((upstream-name . "MMWRweek"))) + (build-system r-build-system) + (home-page "http://wwwn.cdc.gov/nndss/document/MMWR_Week_overview.pdf") + (synopsis "Convert dates to MMWR day, week, and year") + (description + "The first day of any MMWR week is Sunday. MMWR week numbering is +sequential beginning with 1 and incrementing with each week to a maximum of 52 +or 53. MMWR week #1 of an MMWR year is the first week of the year that has at +least four days in the calendar year. This package provides functionality to +convert dates to MMWR day, week, and year and the reverse.") + (license license:gpl2+))) + +(define-public r-crul + (package + (name "r-crul") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "crul" version)) + (sha256 + (base32 + "1kjsc5gkx5k5cfwlfjp2cjm9cdzq2l1m68bnrjmahw3lkz8wzdph")))) + (properties `((upstream-name . "crul"))) + (build-system r-build-system) + (propagated-inputs + `(("r-curl" ,r-curl) + ("r-httpcode" ,r-httpcode) + ("r-jsonlite" ,r-jsonlite) + ("r-mime" ,r-mime) + ("r-r6" ,r-r6) + ("r-urltools" ,r-urltools))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/ropensci/crul") + (synopsis "HTTP client") + (description + "This package provides a simple HTTP client, with tools for making HTTP +requests, and mocking HTTP requests. The package is built on R6, and takes +inspiration from Ruby's @code{faraday} gem.") + (license license:expat))) + +(define-public r-fauxpas + (package + (name "r-fauxpas") + (version "0.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "fauxpas" version)) + (sha256 + (base32 + "129fzqb7wsskbn50s8x0marr4wm8jrns6hiycqcsk166k3dnyyy8")))) + (properties `((upstream-name . "fauxpas"))) + (build-system r-build-system) + (propagated-inputs + `(("r-httpcode" ,r-httpcode) + ("r-r6" ,r-r6) + ("r-whisker" ,r-whisker))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://docs.ropensci.org/fauxpas") + (synopsis "HTTP error helpers") + (description + "This package provides HTTP error helpers. Methods are included for +general purpose HTTP error handling, as well as individual methods for every +HTTP status code, both via status code numbers as well as their descriptive +names. It supports the ability to adjust behavior to stop, message or +warning. It includes the ability to use a custom whisker template to have any +configuration of status code, short description, and verbose message.") + (license license:expat))) + +(define-public r-webmockr + (package + (name "r-webmockr") + (version "0.8.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "webmockr" version)) + (sha256 + (base32 + "0j40srwi0yasmllb9wsww4m6zkiyzqd549cis4dxd7c7p24hak8j")))) + (properties `((upstream-name . "webmockr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64enc" ,r-base64enc) + ("r-crul" ,r-crul) + ("r-curl" ,r-curl) + ("r-fauxpas" ,r-fauxpas) + ("r-jsonlite" ,r-jsonlite) + ("r-magrittr" ,r-magrittr) + ("r-r6" ,r-r6) + ("r-urltools" ,r-urltools))) + (home-page "https://github.com/ropensci/webmockr") + (synopsis "Stubbing and setting expectations on HTTP Requests") + (description + "This is a package for stubbing and setting expectations on HTTP +requests. It includes tools for stubbing HTTP requests, including expected +request conditions and response conditions. You can match on HTTP method, +query parameters, request body, headers and more. It can be used for unit +tests or outside of a testing context.") + (license license:expat))) + +(define-public r-mockery + (package + (name "r-mockery") + (version "0.4.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "mockery" version)) + (sha256 + (base32 + "16zayzi2qdmiy513hvlci9f4p8jwry24006yfzrgmrvf6sf293lq")))) + (properties `((upstream-name . "mockery"))) + (build-system r-build-system) + (propagated-inputs + `(("r-testthat" ,r-testthat))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/jfiksel/mockery") + (synopsis "Mocking library for R") + (description + "The two main functionalities of this package are creating mock +objects (functions) and selectively intercepting calls to a given function +that originate in some other function. It can be used with any testing +framework available for R. Mock objects can be injected with either this +package's own @code{stub} function or a similar @code{with_mock} facility +present in the @code{testthat} package.") + (license license:expat))) + +(define-public r-zoltr + (package + (name "r-zoltr") + (version "0.5.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "zoltr" version)) + (sha256 + (base32 + "12zh7y3pwidclscgvd0b0iaqq9j5y8mc8xd6pz4vs0jy5qs3ahar")))) + (properties `((upstream-name . "zoltr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-base64url" ,r-base64url) + ("r-dplyr" ,r-dplyr) + ("r-httr" ,r-httr) + ("r-jsonlite" ,r-jsonlite) + ("r-magrittr" ,r-magrittr) + ("r-mmwrweek" ,r-mmwrweek) + ("r-mockery" ,r-mockery) + ("r-readr" ,r-readr) + ("r-rlang" ,r-rlang) + ("r-webmockr" ,r-webmockr))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/reichlab/zoltr") + (synopsis "Interface to the Zoltar forecast repository API") + (description + "Zoltar is a website that provides a repository of model forecast results +in a standardized format and a central location. It supports storing, +retrieving, comparing, and analyzing time series forecasts for prediction +challenges of interest to the modeling community. This package provides +functions for working with the Zoltar API, including connecting and +authenticating, getting information about projects, models, and forecasts, +deleting and uploading forecast data, and downloading scores.") + (license license:gpl3))) + +(define-public r-zoib + (package + (name "r-zoib") + (version "1.5.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "zoib" version)) + (sha256 + (base32 + "0inm7f2pc68ksqxvq12xp9jc99vj7ydylvs24ip12nksbj5k1n8f")))) + (properties `((upstream-name . "zoib"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-coda" ,r-coda) + ("r-formula" ,r-formula) + ("r-rjags" ,r-rjags))) + (home-page "https://www.r-project.org") + (synopsis "Bayesian inference for beta regression") + (description + "This package lets you fit beta regression and zero-or-one inflated beta +regression and obtain Bayesian inference of the model via the Markov Chain +Monte Carlo approach implemented in JAGS.") + (license license:gpl3+))) + +(define-public r-logger + (package + (name "r-logger") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "logger" version)) + (sha256 + (base32 "0p607da2rdrfj9sbrrq9hpqp26nyj3imd1590c13bxskqfhv0sz8")))) + (properties `((upstream-name . "logger"))) + (build-system r-build-system) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://daroczig.github.io/logger/") + (synopsis "Lightweight and flexible logging utility") + (description + "Inspired by the the @code{futile.logger} R package and @code{logging} +Python module, this utility provides a flexible and extensible way of +formatting and delivering log messages with low overhead.") + (license license:agpl3+))) + +(define-public r-ggh4x + (package + (name "r-ggh4x") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggh4x" version)) + (sha256 + (base32 + "0gv9ckkdqbcjknzsv8h3955wnikawdfypr279v74hvwyq86af29r")))) + (properties `((upstream-name . "ggh4x"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gtable" ,r-gtable) + ("r-rlang" ,r-rlang) + ("r-scales" ,r-scales) + ("r-vctrs" ,r-vctrs))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/teunbrand/ggh4x") + (synopsis "Extension for ggplot2") + (description "This package is a @code{ggplot2} extension. It provides some +utility functions that do not entirely fit within the grammar of graphics +concept. The package extends @code{ggpplots} facets through customisation, by +setting individual scales per panel, resizing panels and providing nested +facets. It also allows multiple colour, fill scales per plot and hosts a +smaller collection of stats, geoms and axis guides.") + (license license:expat))) |