diff --git a/guix-cran/packages/a.scm b/guix-cran/packages/a.scm index 80e8252..f822473 100644 --- a/guix-cran/packages/a.scm +++ b/guix-cran/packages/a.scm @@ -10889,13 +10889,13 @@ effects thanks to @code{jQuery} @code{AniView}'.") (define-public r-anisna (package (name "r-anisna") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "aniSNA" version)) (sha256 - (base32 "0vmpdmqr3cwpk588y116bv2nv1xcaya0mg53zcl3yc223df134zp")))) + (base32 "1rvrpcw1j5xwz8ns7njvf8blal8nh6c45avy5rpzb5kifiv8yxgy")))) (properties `((upstream-name . "aniSNA"))) (build-system r-build-system) (propagated-inputs (list r-stringr diff --git a/guix-cran/packages/b.scm b/guix-cran/packages/b.scm index 08e3738..d28a455 100644 --- a/guix-cran/packages/b.scm +++ b/guix-cran/packages/b.scm @@ -11530,6 +11530,30 @@ partitions the system in fast and slow reactions. @code{bioPN} algorithms are developed in C to achieve adequate performance.") (license license:gpl2+))) +(define-public r-biopixr + (package + (name "r-biopixr") + (version "0.2.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "biopixR" version)) + (sha256 + (base32 "1341yg226r4bzh3cw4ygjnychd5vnm9xfbb0agyd7razz49iahz7")))) + (properties `((upstream-name . "biopixR"))) + (build-system r-build-system) + (propagated-inputs (list r-magick r-imager r-foreach r-data-table)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/Brauckhoff/biopixR") + (synopsis "Extracting Insights from Biological Images") + (description + "Combines the magick and imager packages to streamline image analysis, focusing +on feature extraction and quantification from biological images, especially +microparticles. By providing high throughput pipelines and clustering +capabilities, @code{biopixR} facilitates efficient insight generation for +researchers (Schneider J. et al. (2019) ).") + (license license:lgpl3+))) + (define-public r-biopetsurv (package (name "r-biopetsurv") diff --git a/guix-cran/packages/c.scm b/guix-cran/packages/c.scm index c6a0832..82d600f 100644 --- a/guix-cran/packages/c.scm +++ b/guix-cran/packages/c.scm @@ -15,11 +15,11 @@ #:use-module (gnu packages check) #:use-module (gnu packages pkg-config) #:use-module (gnu packages geo) - #:use-module (gnu packages bioinformatics) #:use-module (gnu packages maths) #:use-module (gnu packages machine-learning) #:use-module (gnu packages compression) #:use-module (gnu packages haskell-xyz) + #:use-module (gnu packages bioinformatics) #:use-module (gnu packages photo) #:use-module (guix-cran packages z) #:use-module (guix-cran packages y) @@ -5515,13 +5515,13 @@ position of the first crossing (or none).") (define-public r-crossover (package (name "r-crossover") - (version "0.1-21") + (version "0.1-22") (source (origin (method url-fetch) (uri (cran-uri "Crossover" version)) (sha256 - (base32 "0mqpfasqdgv4s77ln3c45pjgl2l7wb7b68jl46fzln184n0838l7")))) + (base32 "05fsl22h2q6l0g9hscs4f0w4d3skd9anr570ddmnqicxzdfpap5r")))) (properties `((upstream-name . "Crossover"))) (build-system r-build-system) (inputs (list openjdk)) @@ -6620,13 +6620,13 @@ Surmann (2017). .") (define-public r-crew (package (name "r-crew") - (version "0.9.0") + (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "crew" version)) (sha256 - (base32 "17g1sdjlkj7ck5y5k7la2skxkvjd474rkqzq01fgqhiixkygignk")))) + (base32 "1qf7w2px7bw9rgar6fap1v4yyd7899izpq87yl2pqzgbxf93dz1j")))) (properties `((upstream-name . "crew"))) (build-system r-build-system) (propagated-inputs (list r-tidyselect @@ -6649,10 +6649,10 @@ Surmann (2017). .") "In computationally demanding analysis projects, statisticians and data scientists asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. The NNG'-powered mirai R -package by Gao (2023) is a sleek and -sophisticated scheduler that efficiently processes these intense workloads. The -crew package extends mirai with a unifying interface for third-party worker -launchers. Inspiration also comes from packages. future by Bengtsson (2021) +package by Gao (2023) is a sleek and sophisticated +scheduler that efficiently processes these intense workloads. The crew package +extends mirai with a unifying interface for third-party worker launchers. +Inspiration also comes from packages. future by Bengtsson (2021) , rrq by @code{FitzJohn} and Ashton (2023) , clustermq by Schubert (2019) ), and batchtools by Lang, Bischel, and @@ -8563,13 +8563,13 @@ confidence intervals.") (define-public r-coxmos (package (name "r-coxmos") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "Coxmos" version)) (sha256 - (base32 "0y7dcwzkj8yqwn44qd1cb1379a0xl5a1949sg7wn6gpgzyn9vgi4")))) + (base32 "052af5hx820wmvflvz4pv3jlmmwap9d0lzx9k7v1ps6cidarz0wm")))) (properties `((upstream-name . "Coxmos"))) (build-system r-build-system) (propagated-inputs (list r-tidyr @@ -17638,18 +17638,19 @@ the analysed objects.") (define-public r-compind (package (name "r-compind") - (version "3.0") + (version "3.1") (source (origin (method url-fetch) (uri (cran-uri "Compind" version)) (sha256 - (base32 "0g5m1dpnadgqszk079rxf6rm0d17qnvfzi7fwbs99sl2nimy3ni9")))) + (base32 "0k45gazca94dscqhy05p68k755al4gd1gilz5svq5h6cv5fijhxk")))) (properties `((upstream-name . "Compind"))) (build-system r-build-system) (propagated-inputs (list r-spdep r-sp r-smaa + r-rcompadre r-psych r-np r-nonparaeff @@ -31600,13 +31601,13 @@ your local computer.") (define-public r-cheapr (package (name "r-cheapr") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "cheapr" version)) (sha256 - (base32 "0qmnfhxgzn4gcn2wx7zwz30kj5zgvcs7dfkayrarf9qmm9ys8rnd")))) + (base32 "0qrdvzq01m0kc243jcddiz8am2l4c5a39bv3qb0m2rpvgg1z8a4c")))) (properties `((upstream-name . "cheapr"))) (build-system r-build-system) (propagated-inputs (list r-cpp11 r-collapse)) @@ -31858,6 +31859,28 @@ algorithms are implemented in C++.") (license (list license:gpl3 (license:fsdg-compatible "file://LICENSE"))))) +(define-public r-changes + (package + (name "r-changes") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "changeS" version)) + (sha256 + (base32 "1igd2qvs5y2g63byvwn0djbgc5lqi9zx7a0g2dkda1q6snl65yi7")))) + (properties `((upstream-name . "changeS"))) + (build-system r-build-system) + (propagated-inputs (list r-stringr r-nls-multstart r-ggplot2)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/matloff/changeS") + (synopsis "S-Curve Fit for Changepoint Analysis") + (description + "Estimation of changepoints using an \"S-curve\" approximation. Formation of +confidence intervals for changepoint locations and magnitudes. Both abrupt and +gradual changes can be modeled.") + (license license:gpl2+))) + (define-public r-changeranger (package (name "r-changeranger") diff --git a/guix-cran/packages/d.scm b/guix-cran/packages/d.scm index b452a56..6115e8d 100644 --- a/guix-cran/packages/d.scm +++ b/guix-cran/packages/d.scm @@ -2853,6 +2853,30 @@ information on dtangle see Hunt et al. (2019) .") (license license:gpl3))) +(define-public r-dtableone + (package + (name "r-dtableone") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "Dtableone" version)) + (sha256 + (base32 "0pv04l4wxf44zva5w96i02g4z8zx3zgjxxjacfg0vh2f7gx4pjnq")))) + (properties `((upstream-name . "Dtableone"))) + (build-system r-build-system) + (propagated-inputs (list r-proc r-irr r-epir r-dplyr)) + (home-page "https://cran.r-project.org/package=Dtableone") + (synopsis "Tabular Comparison of Paired Diagnostic Tests") + (description + "Offers statistical methods to compare diagnostic performance between two binary +diagnostic tests on the same subject in clinical studies. Includes functions +for generating formatted tables to display diagnostic outcomes, facilitating a +clear and comprehensive comparison directly through the R console. Inspired by +and extending the functionalities of the DT@code{ComPair}', tableone', and +gtsummary packages.") + (license license:gpl2))) + (define-public r-dswe (package (name "r-dswe") @@ -26384,13 +26408,13 @@ stochastic disability-adjusted life year (DALY) calculation.") (define-public r-daltoolbox (package (name "r-daltoolbox") - (version "1.0.727") + (version "1.0.747") (source (origin (method url-fetch) (uri (cran-uri "daltoolbox" version)) (sha256 - (base32 "0ycbbqcdkk9yhwrrln5xh4j5xfsga4hcn0jc7fgczpjdgv07g8w8")))) + (base32 "0mh8f5zm97mfzm55pjy157a079cs4azis4x0h0j9cflsd0k4nnyd")))) (properties `((upstream-name . "daltoolbox"))) (build-system r-build-system) (propagated-inputs (list r-tree diff --git a/guix-cran/packages/e.scm b/guix-cran/packages/e.scm index e66b9ce..d9e3633 100644 --- a/guix-cran/packages/e.scm +++ b/guix-cran/packages/e.scm @@ -1760,16 +1760,16 @@ offers enhanced visualizations with interactive elements.") (define-public r-expirest (package (name "r-expirest") - (version "0.1.5") + (version "0.1.6") (source (origin (method url-fetch) (uri (cran-uri "expirest" version)) (sha256 - (base32 "08gwy1fikj7kg7h6fc7w15621jc0prdqdhzx14ad6dvdi5rd33gv")))) + (base32 "1pav81y4n23q42kfvbsdinfyklxwhspsxvfdyvs891zsvy2m93yn")))) (properties `((upstream-name . "expirest"))) (build-system r-build-system) - (propagated-inputs (list r-rlang r-ggplot2)) + (propagated-inputs (list r-rlang r-lifecycle r-ggplot2)) (home-page "https://github.com/piusdahinden/expirest") (synopsis "Expiry Estimation Procedures") (description @@ -19021,13 +19021,13 @@ original package description is in Goslee and Urban (2007) (define-public r-ecodiet (package (name "r-ecodiet") - (version "2.0.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "EcoDiet" version)) (sha256 - (base32 "1lgjymm2anb7f11gvg0875wyjjfzbh0y1vwinbidpn2kmgm9b05h")))) + (base32 "0vw6q5yf5aq4gdim7yr188f9hbrd5giaivl27y4qrz987i152v8c")))) (properties `((upstream-name . "EcoDiet"))) (build-system r-build-system) (inputs (list jags)) diff --git a/guix-cran/packages/f.scm b/guix-cran/packages/f.scm index 255b316..3e81b04 100644 --- a/guix-cran/packages/f.scm +++ b/guix-cran/packages/f.scm @@ -8282,6 +8282,29 @@ descriptions of FNETS methodology and Owens, Cho and Barigozzi (2024+) <@code{arXiv:2301.11675>} accompanying the R package.") (license license:gpl3+))) +(define-public r-fmx + (package + (name "r-fmx") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "fmx" version)) + (sha256 + (base32 "1biz4vn8inhbmcqfcpdkgja5rz6pzz0h5h8cd5qqqbmyzl4x1acj")))) + (properties `((upstream-name . "fmx"))) + (build-system r-build-system) + (propagated-inputs (list r-vgam r-tukeygh77 r-sn r-goftest)) + (home-page "https://cran.r-project.org/package=fmx") + (synopsis "Finite Mixture Parametrization") + (description + "This package provides a parametrization framework for finite mixture +distribution using S4 objects. Density, cumulative density, quantile and +simulation functions are defined. Currently normal, Tukey g-&-h, skew-normal +and skew-t distributions are well tested. The gamma, negative binomial +distributions are being tested.") + (license license:gpl2))) + (define-public r-fmultivar (package (name "r-fmultivar") @@ -21387,17 +21410,16 @@ experiments with noncompliance.") (define-public r-fact (package (name "r-fact") - (version "0.1.0") + (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "FACT" version)) (sha256 - (base32 "0frj0qgdq8j8khy4dlv63zismjczijm0q7j5ha59m0dgxr93khfg")))) + (base32 "0klks2r2jf5v5z2n3gvqbssrpdd6nccbk7izvdl1cknisq8z5w4b")))) (properties `((upstream-name . "FACT"))) (build-system r-build-system) (propagated-inputs (list r-r6 - r-prediction r-iml r-gridextra r-ggplot2 diff --git a/guix-cran/packages/g.scm b/guix-cran/packages/g.scm index 9c9f5d2..adc11a0 100644 --- a/guix-cran/packages/g.scm +++ b/guix-cran/packages/g.scm @@ -10811,13 +10811,13 @@ testing for group sequential design, described in Maurer and Bretz (2013) (define-public r-gmcp (package (name "r-gmcp") - (version "0.8-16") + (version "0.8-17") (source (origin (method url-fetch) (uri (cran-uri "gMCP" version)) (sha256 - (base32 "0jkq538xif87asrllmdbcf9hz9z4p5j1xnvf3fp2kc9p48jqdx75")))) + (base32 "0w5qxjyn5z7mygsvrmqk5ab827abhp7v4d8ha8279gjjkfswq5fi")))) (properties `((upstream-name . "gMCP"))) (build-system r-build-system) (inputs (list openjdk)) @@ -15663,18 +15663,19 @@ and aesthetics. This method was described by Balachandran VP (2015) (define-public r-ggscatridges (package (name "r-ggscatridges") - (version "0.1.0") + (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "ggScatRidges" version)) (sha256 - (base32 "02p9pkfw3jscmc5c836qq73z9jpyxv4fp1ci5ma6mcwyzzzfnjpc")))) + (base32 "1blwzynrzywdgqllcgjjb0j0xc8fwplybnx3mfmiysppcvrk47p9")))) (properties `((upstream-name . "ggScatRidges"))) (build-system r-build-system) (propagated-inputs (list r-viridis r-hrbrthemes r-ggridges + r-ggrepel r-ggpubr r-ggplot2 r-cowplot)) @@ -22473,24 +22474,23 @@ Apparicio ).") (define-public r-geocausal (package (name "r-geocausal") - (version "0.2.0") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "geocausal" version)) (sha256 - (base32 "00i4prrgi02xv0h4r5xfmnl6h9b6arqnvd3vhzrgcmdqv4nl76xk")))) + (base32 "0kbjyk9al54y2k9w96rpchv2gwk5f96g6a536fp4sfbhqlmpc0f3")))) (properties `((upstream-name . "geocausal"))) (build-system r-build-system) - (propagated-inputs (list r-tidyselect + (propagated-inputs (list r-tidyterra + r-tidyselect r-tidyr r-terra r-spatstat-model r-spatstat-geom r-spatstat-explore - r-sp r-sf - r-raster r-purrr r-progressr r-mclust @@ -28581,6 +28581,37 @@ distribution. Standard methods and GAMLSS diagnostics can be used with the resulting fitted object.") (license (list license:gpl2 license:gpl3)))) +(define-public r-gamlss-ggplots + (package + (name "r-gamlss-ggplots") + (version "2.1-12") + (source + (origin + (method url-fetch) + (uri (cran-uri "gamlss.ggplots" version)) + (sha256 + (base32 "0lm0nlc2rb4yl6fliv0017qpgyaaky7hws6arv36dgqqih9dmcii")))) + (properties `((upstream-name . "gamlss.ggplots"))) + (build-system r-build-system) + (propagated-inputs (list r-yaimpute + r-mgcv + r-ggridges + r-ggplot2 + r-gamlss-inf + r-gamlss-foreach + r-gamlss-dist + r-gamlss + r-foreach + r-ellipse)) + (home-page "https://www.gamlss.com/") + (synopsis + "Plotting Functions for Generalized Additive Model for Location Scale and Shape") + (description + "This package provides functions for plotting Generalized Additive Models for +Location Scale and Shape from the gamlss package, Stasinopoulos and Rigby (2007) +, using the graphical methods from ggplot2'.") + (license (list license:gpl2 license:gpl3)))) + (define-public r-gamlss-foreach (package (name "r-gamlss-foreach") diff --git a/guix-cran/packages/h.scm b/guix-cran/packages/h.scm index 1718ee2..fed1c10 100644 --- a/guix-cran/packages/h.scm +++ b/guix-cran/packages/h.scm @@ -9403,31 +9403,31 @@ Alice (2023) \"Health Data Science in R\" (define-public r-hdshop (package (name "r-hdshop") - (version "0.1.3") + (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "HDShOP" version)) (sha256 - (base32 "18i17vv71wc0rqfl2i9bcfl1ry3bd61x9nd6g57x37ggjp7i6j5k")))) + (base32 "129j1dr3vjdg23dy45wws470v05j5azq8nq88b670kdgfw1586qm")))) (properties `((upstream-name . "HDShOP"))) (build-system r-build-system) - (propagated-inputs (list r-rdpack)) + (propagated-inputs (list r-rdpack r-lattice)) (home-page "https://github.com/Otryakhin-Dmitry/global-minimum-variance-portfolio") (synopsis "High-Dimensional Shrinkage Optimal Portfolios") (description "Constructs shrinkage estimators of high-dimensional mean-variance portfolios and performs high-dimensional tests on optimality of a given portfolio. The -techniques developed in Bodnar et al. (2018) , -Bodnar et al. (2019) , Bodnar et al. (2020) - are central to the package. They provide simple -and feasible estimators and tests for optimal portfolio weights, which are -applicable for large p and large n situations where p is the portfolio dimension -(number of stocks) and n is the sample size. The package also includes tools -for constructing portfolios based on shrinkage estimators of the mean vector and -covariance matrix as well as a new Bayesian estimator for the Markowitz -efficient frontier recently developed by Bauder et al. (2021) +techniques developed in Bodnar et al. (2018 , +2019 , 2020 , 2021 +) are central to the package. They provide +simple and feasible estimators and tests for optimal portfolio weights, which +are applicable for large p and large n situations where p is the portfolio +dimension (number of stocks) and n is the sample size. The package also +includes tools for constructing portfolios based on shrinkage estimators of the +mean vector and covariance matrix as well as a new Bayesian estimator for the +Markowitz efficient frontier recently developed by Bauder et al. (2021) .") (license license:gpl3))) diff --git a/guix-cran/packages/i.scm b/guix-cran/packages/i.scm index 410ea8a..1fcc22f 100644 --- a/guix-cran/packages/i.scm +++ b/guix-cran/packages/i.scm @@ -8309,16 +8309,21 @@ available vignettes and from the URL bellow.") (define-public r-inlajoint (package (name "r-inlajoint") - (version "24.2.4") + (version "24.3.25") (source (origin (method url-fetch) (uri (cran-uri "INLAjoint" version)) (sha256 - (base32 "0q7wpm058qzzah8bxsghx3v88vijzhpxp30rbbrlq2xznhhsjksk")))) + (base32 "03hd29x8arww3fkyzgj8wv1b0sm5nl994bmg6m2sb4xg00slhp05")))) (properties `((upstream-name . "INLAjoint"))) (build-system r-build-system) - (propagated-inputs (list r-numderiv r-matrix r-lme4 r-ggplot2)) + (propagated-inputs (list r-numderiv + r-nlme + r-mvtnorm + r-matrix + r-lme4 + r-ggplot2)) (native-inputs (list r-r-rsp)) (home-page "https://github.com/DenisRustand/INLAjoint") (synopsis @@ -9125,13 +9130,13 @@ network from single-cell sequencing data.") (define-public r-inext-beta3d (package (name "r-inext-beta3d") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "iNEXT.beta3D" version)) (sha256 - (base32 "1ia5midwraq1im0gh61fcpg2whq43mlby80b92y5fjdhh0ghbx8f")))) + (base32 "16g64jy68hmq2dr3snc5v35kl7g9ghglljm8qr8jmnny26kmpgan")))) (properties `((upstream-name . "iNEXT.beta3D"))) (build-system r-build-system) (propagated-inputs (list r-tidytree @@ -9165,13 +9170,13 @@ et al. (2023) for more details.") (define-public r-inext-3d (package (name "r-inext-3d") - (version "1.0.2") + (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "iNEXT.3D" version)) (sha256 - (base32 "09m4r8j5c56l7qxzz5kxx8pzbf7lri40vqz4s4arpj9b7b5imfl7")))) + (base32 "03jrdy7axxq8c1bsr0z9v7444c9kcvmv7cal03jxfl61lmw6hzzh")))) (properties `((upstream-name . "iNEXT.3D"))) (build-system r-build-system) (propagated-inputs (list r-tidytree @@ -13361,6 +13366,33 @@ AUTHORS for a list of copyright holders and authors.") software is described in Pritikin & Falk (2020) .") (license license:agpl3+))) +(define-public r-ieugwasr + (package + (name "r-ieugwasr") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ieugwasr" version)) + (sha256 + (base32 "0a38rnh34m6y0hdxk6y1s9lfg399cc9kfgpgapf2qmj7ca13d58z")))) + (properties `((upstream-name . "ieugwasr"))) + (build-system r-build-system) + (propagated-inputs (list r-rlang + r-magrittr + r-jsonlite + r-httr + r-googleauthr + r-dplyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/MRCIEU/ieugwasr") + (synopsis "Interface to the 'OpenGWAS' Database API") + (description + "Interface to the @code{OpenGWAS} database API . +Includes a wrapper to make generic calls to the API, plus convenience functions +for specific queries.") + (license license:expat))) + (define-public r-ietd (package (name "r-ietd") diff --git a/guix-cran/packages/m.scm b/guix-cran/packages/m.scm index 980afe6..a50dc22 100644 --- a/guix-cran/packages/m.scm +++ b/guix-cran/packages/m.scm @@ -1178,19 +1178,19 @@ covariance matrix based on permutations of the transformed data residuals.") (define-public r-mvnormtest (package (name "r-mvnormtest") - (version "0.1-9") + (version "0.1-9-3") (source (origin (method url-fetch) (uri (cran-uri "mvnormtest" version)) (sha256 - (base32 "1iaxjwp7bgxhaa4xqvgqb61316mq2fb0452d0pabhmbxkvmvdnj6")))) + (base32 "1hxxy08ldm2dczjfb34q1xk8yfs54pdishq4hnws8xy0cjh4xngg")))) (properties `((upstream-name . "mvnormtest"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=mvnormtest") - (synopsis "Normality test for multivariate variables") + (synopsis "Normality Test for Multivariate Variables") (description - "Generalization of shapiro-wilk test for multivariate variables.") + "Generalization of Shapiro-Wilk test for multivariate variables.") (license (list license:gpl2+ license:gpl3+)))) (define-public r-mvnormaltest @@ -27071,13 +27071,13 @@ by Li, Xiao, and Luo (2020) .") (define-public r-mf-beta4 (package (name "r-mf-beta4") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "MF.beta4" version)) (sha256 - (base32 "0l3qafpavjshfayvz603141ch9s9a4pl3ly1llfkrmm3rmspb261")))) + (base32 "0j2absng9k14yad0ajh13ybchdd9jby2m69vzxfk8qz6kv4hdvxq")))) (properties `((upstream-name . "MF.beta4"))) (build-system r-build-system) (propagated-inputs (list r-tidyverse @@ -28950,6 +28950,42 @@ on a diffusion graph kernel and trophic levels. Importantly, this package provides a layout method applicable for large trophic networks.") (license license:gpl3))) +(define-public r-metanet + (package + (name "r-metanet") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "MetaNet" version)) + (sha256 + (base32 "0r3id0ap91g948a10yka1lz82jib3ww91n24vlk4pbik7flxbqpk")))) + (properties `((upstream-name . "MetaNet"))) + (build-system r-build-system) + (propagated-inputs (list r-tibble + r-rlang + r-reshape2 + r-rcolorbrewer + r-pcutils + r-magrittr + r-igraph + r-ggrepel + r-ggplot2 + r-ggnewscale + r-dplyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/Asa12138/MetaNet") + (synopsis "Network Analysis for Omics Data") + (description + "Comprehensive network analysis package. Calculate correlation network fastly, +accelerate lots of analysis by parallel computing. Support for multi-omics +data, search sub-nets fluently. Handle bigger data, more than 10,000 nodes in +each omics. Offer various layout method for multi-omics network and some +interfaces to other software ('Gephi', Cytoscape', ggplot2'), easy to visualize. + Provide comprehensive topology indexes calculation, including ecological +network stability.") + (license license:gpl3))) + (define-public r-metan (package (name "r-metan") diff --git a/guix-cran/packages/n.scm b/guix-cran/packages/n.scm index 0ffc5d4..015eb5b 100644 --- a/guix-cran/packages/n.scm +++ b/guix-cran/packages/n.scm @@ -9097,13 +9097,13 @@ repositories of the nflverse project.") (define-public r-nflplotr (package (name "r-nflplotr") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "nflplotR" version)) (sha256 - (base32 "11rmfwgpa5r0n98r4prngbfgdvk55vxkzp7pl5qlddhbh5jjcl9y")))) + (base32 "1j6vhd1ysanc47ixa56gj0dgxqhiwdkbvkcmhdpkwc3zs5c78lzn")))) (properties `((upstream-name . "nflplotR"))) (build-system r-build-system) (propagated-inputs (list r-scales @@ -13432,16 +13432,21 @@ data: large document collections, logfiles, and other text data.") (define-public r-ncmeta (package (name "r-ncmeta") - (version "0.3.6") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "ncmeta" version)) (sha256 - (base32 "0pk5wn0hmf5n1bgx96xighpmr2kkka3fgl6was9z2rsr0k981mc2")))) + (base32 "1aamxs3yza1hsgvkp6740lv1dc21a87mzl06n6w3zxkjshri020w")))) (properties `((upstream-name . "ncmeta"))) (build-system r-build-system) - (propagated-inputs (list r-tidyr r-tibble r-rnetcdf r-rlang r-dplyr)) + (propagated-inputs (list r-tidyr + r-tibble + r-rnetcdf + r-rlang + r-dplyr + r-cftime)) (home-page "https://github.com/hypertidy/ncmeta") (synopsis "Straightforward 'NetCDF' Metadata") (description diff --git a/guix-cran/packages/p.scm b/guix-cran/packages/p.scm index 89420ec..2b499c1 100644 --- a/guix-cran/packages/p.scm +++ b/guix-cran/packages/p.scm @@ -6550,17 +6550,18 @@ also time series of carbon fluxes, energy balances and soil water are available. (define-public r-profoc (package (name "r-profoc") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "profoc" version)) (sha256 - (base32 "1clickjw8v43p6p35mkyw303adnnr0zrm5ppnvslz2gjlybfp94q")))) + (base32 "1vs5l6f18maga6v27wschxzsbr5i4wqwsd64mz4z666rf92d7l60")))) (properties `((upstream-name . "profoc"))) (build-system r-build-system) (propagated-inputs (list r-tibble r-splines2 + r-rcpptimer r-rcppprogress r-rcpparmadillo r-rcpp @@ -14969,6 +14970,30 @@ includes simple linear trends with statistically in-significant slope coefficient.") (license license:gpl2))) +(define-public r-polytree + (package + (name "r-polytree") + (version "0.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "PolyTree" version)) + (sha256 + (base32 "0np5v1255crfp1x7613rdzgkzkm64ikkjm67xrsncijr202yh1gq")))) + (properties `((upstream-name . "PolyTree"))) + (build-system r-build-system) + (propagated-inputs (list r-igraph r-foci)) + (home-page "https://cran.r-project.org/package=PolyTree") + (synopsis "Estimate Causal Polytree from Data") + (description + "Given a data matrix with rows representing data vectors and columns representing +variables, produces a directed polytree for the underlying causal structure. +Based on the algorithm developed in Chatterjee and Vidyasagar (2022) +. The method is fully nonparametric, making no use of +linearity assumptions, and especially useful when the number of variables is +large.") + (license license:expat))) + (define-public r-polysegratiomm (package (name "r-polysegratiomm") @@ -16527,13 +16552,13 @@ in the neighborhood.") (define-public r-pointblank (package (name "r-pointblank") - (version "0.12.0") + (version "0.12.1") (source (origin (method url-fetch) (uri (cran-uri "pointblank" version)) (sha256 - (base32 "0ysd78ad00a08knw5lmd09rq7sr41p8grfq5f7f2xr487q67mzgk")))) + (base32 "1wwb9ncji7450rbbmrh9mznl4pnpmxq8ibx785bz9dsswdglzfhq")))) (properties `((upstream-name . "pointblank"))) (build-system r-build-system) (arguments @@ -23200,28 +23225,6 @@ thresholds in the tree to account for old and recent divergence. Additionally, it has functions for IDW interpolation using genetic data and midpoints.") (license license:gpl2+))) -(define-public r-phyinsight - (package - (name "r-phyinsight") - (version "0.1.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "PhyInsight" version)) - (sha256 - (base32 "1r7y10g2vriy360f7j8agmjw5sgzm2vr2dypj8v78ssklb6apd08")))) - (properties `((upstream-name . "PhyInsight"))) - (build-system r-build-system) - (propagated-inputs (list r-decipher r-bold r-biostrings r-ape)) - (native-inputs (list r-knitr)) - (home-page "https://jamesc845.github.io/PhyInsight/") - (synopsis "DNA Sequence Analysis & Generation Tree Creation") - (description - "Provide insights using automated DNA sequence manipulation and tree creation. -Currently, the package exclusively retrieves data from the BOLD System database -().") - (license license:gpl3))) - (define-public r-phyext2 (package (name "r-phyext2") diff --git a/guix-cran/packages/q.scm b/guix-cran/packages/q.scm index b43a3cc..b579bd1 100644 --- a/guix-cran/packages/q.scm +++ b/guix-cran/packages/q.scm @@ -2304,6 +2304,43 @@ consist of a large number of generations, or estimate identity coefficients from genotypic data in certain circumstances.") (license license:gpl2+))) +(define-public r-qtlpoly + (package + (name "r-qtlpoly") + (version "0.2.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "qtlpoly" version)) + (sha256 + (base32 "1lcfb19akddxljwvgsryjvhks0lqkdg7f1br1l2szd6qyd4mmdvs")))) + (properties `((upstream-name . "qtlpoly"))) + (build-system r-build-system) + (propagated-inputs (list r-rlrsim + r-rcppprogress + r-rcpparmadillo + r-rcpp + r-quadprog + r-nlme + r-mvtnorm + r-matrix + r-mass + r-mappoly + r-gtools + r-ggplot2 + r-foreach + r-doparallel + r-compquadform + r-abind)) + (home-page "https://gabrielgesteira.github.io/QTLpoly/") + (synopsis "Random-Effect Multiple QTL Mapping in Autopolyploids") + (description + "This package performs random-effect multiple interval mapping (REMIM) in +full-sib families of autopolyploid species based on restricted maximum +likelihood (REML) estimation and score statistics, as described in Pereira et +al. (2020) .") + (license license:gpl3))) + (define-public r-qtlnet (package (name "r-qtlnet") diff --git a/guix-cran/packages/r.scm b/guix-cran/packages/r.scm index b6888f8..a8e33c8 100644 --- a/guix-cran/packages/r.scm +++ b/guix-cran/packages/r.scm @@ -25,7 +25,6 @@ #:use-module (gnu packages python) #:use-module (gnu packages prolog) #:use-module (gnu packages c) - #:use-module (gnu packages bioinformatics) #:use-module (gnu packages geo) #:use-module (gnu packages python-science) #:use-module (gnu packages databases) @@ -13649,16 +13648,21 @@ problems.") (define-public r-rocbc (package (name "r-rocbc") - (version "2.0.0") + (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "rocbc" version)) (sha256 - (base32 "18p7ydnaayia072dhpxlb184ib4rv0zmm8zymcry76znny2milm6")))) + (base32 "06ki3rn5pmkxigpq9ymg8mjw7kgslfjlzqzc3ifww83q97dvkfnb")))) (properties `((upstream-name . "rocbc"))) (build-system r-build-system) - (propagated-inputs (list r-splancs r-pracma r-mvtnorm r-formattable + (propagated-inputs (list r-splancs + r-proc + r-pracma + r-mvtnorm + r-mrmcaov + r-formattable r-clinfun)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=rocbc") @@ -48502,13 +48506,13 @@ mitigation goals.") (define-public r-r2dii-match (package (name "r-r2dii-match") - (version "0.1.4") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "r2dii.match" version)) (sha256 - (base32 "1nb0yik39wdcc22c0clszg9j3xk5sm5i9rzzcyj7zij55pcak7np")))) + (base32 "12h7bn4dha4fiplwm7az4fyaa8cdkn3b4j3ndmwr6c2r11gfwy0n")))) (properties `((upstream-name . "r2dii.match"))) (build-system r-build-system) (propagated-inputs (list r-tidyselect @@ -48541,13 +48545,13 @@ financial portfolio aligns with climate goals.") (define-public r-r2dii-data (package (name "r-r2dii-data") - (version "0.4.1") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "r2dii.data" version)) (sha256 - (base32 "1sf8jyzn9ly8hn1fdph440pl666hcgpjds51h8apprqivn3ky9cv")))) + (base32 "1f8gvian0l3wsw9bwyxzlwv0qpw4mz1qq4747hjm8d4jr37hi0r6")))) (properties `((upstream-name . "r2dii.data"))) (build-system r-build-system) (propagated-inputs (list r-lifecycle)) diff --git a/guix-cran/packages/s.scm b/guix-cran/packages/s.scm index 254de2a..7f75b5f 100644 --- a/guix-cran/packages/s.scm +++ b/guix-cran/packages/s.scm @@ -4147,31 +4147,6 @@ calculation, estimation of expected precision for the estimates of totals, and calculation of optimal sample size allocation.") (license license:gpl2+))) -(define-public r-surveygraph - (package - (name "r-surveygraph") - (version "0.1.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "surveygraph" version)) - (sha256 - (base32 "0bvdvylck3m2891v2aap73ygpqkndrxl4ah1bjpa0lyajgvwlbzh")))) - (properties `((upstream-name . "surveygraph"))) - (build-system r-build-system) - (native-inputs (list r-knitr)) - (home-page "https://surveygraph.ie/") - (synopsis "Network Representations of Attitudes") - (description - "This package provides a tool for computing network representations of attitudes, -extracted from tabular data such as sociological surveys. By treating a survey -as a bipartite network, we measure the similarity between respondents and survey -items to produce network edges. We do this in both a respondent network, as -well as a survey item network. Used in combination with graph visualisation -libraries, this techniques helps practitioners in the social sciences identify -network structure that may be present within a survey at a glance.") - (license license:expat))) - (define-public r-surveyexplorer (package (name "r-surveyexplorer") @@ -24711,13 +24686,13 @@ with nested data.") (define-public r-sparklyr (package (name "r-sparklyr") - (version "1.8.4") + (version "1.8.5") (source (origin (method url-fetch) (uri (cran-uri "sparklyr" version)) (sha256 - (base32 "0xc38xq8izpg0fh4kjb5f223jvhrczs66aydw32kyk6mx07c43ch")))) + (base32 "15rgyjq8avyw6n21z57zb10af41ga16vgcddqv6may3z94sjslz0")))) (properties `((upstream-name . "sparklyr"))) (build-system r-build-system) (inputs (list)) @@ -24727,10 +24702,8 @@ with nested data.") r-uuid r-tidyselect r-tidyr - r-tibble r-rstudioapi r-rlang - r-rappdirs r-purrr r-openssl r-jsonlite @@ -24742,7 +24715,7 @@ with nested data.") r-dbplyr r-dbi r-config)) - (home-page "https://spark.rstudio.com/") + (home-page "https://spark.posit.co/") (synopsis "R Interface to Apache Spark") (description "R interface to Apache Spark, a fast and general engine for big data processing, @@ -32168,13 +32141,13 @@ and @code{DeYoung} (1987) .") (define-public r-skpr (package (name "r-skpr") - (version "1.6.2") + (version "1.7.1") (source (origin (method url-fetch) (uri (cran-uri "skpr" version)) (sha256 - (base32 "0hc3lk9d1c92cfv7cvk85jb9pp8ilh8sgwjg3vgr11yxnzay7hmk")))) + (base32 "1g19pq73map54sypkarvyw191zgf4cbmr1hskr8amg75wvw8mg11")))) (properties `((upstream-name . "skpr"))) (build-system r-build-system) (propagated-inputs (list r-viridis @@ -32187,7 +32160,6 @@ and @code{DeYoung} (1987) .") r-magrittr r-lmertest r-lme4 - r-lazyeval r-iterators r-future r-foreach @@ -32682,17 +32654,17 @@ enables users to write @code{JavaScript} applications using the syntax of R.") (define-public r-skellam (package (name "r-skellam") - (version "0.2.0") + (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "skellam" version)) (sha256 - (base32 "0r5wbs5h7xc3k2vjxd4axwnxr9cmwm008fcyj1vyixkg8fa680gx")))) + (base32 "0hmms6709v7mzp6qgcxljjxq4nccqiwphn1nk3jh6mp2n0zvaqjd")))) (properties `((upstream-name . "skellam"))) (build-system r-build-system) (native-inputs (list r-knitr)) - (home-page "http://r-forge.r-project.org/projects/healthqueues/") + (home-page "https//r-forge.r-project.org/projects/healthqueues/") (synopsis "Densities and Sampling for the Skellam Distribution") (description "This package provides functions for the Skellam distribution, including: density diff --git a/guix-cran/packages/t.scm b/guix-cran/packages/t.scm index 90e7ed6..0acfae7 100644 --- a/guix-cran/packages/t.scm +++ b/guix-cran/packages/t.scm @@ -2732,24 +2732,19 @@ GPH estimator proposed by Reisen et al. (2017) . (define-public r-tspredit (package (name "r-tspredit") - (version "1.0.747") + (version "1.0.767") (source (origin (method url-fetch) (uri (cran-uri "tspredit" version)) (sha256 - (base32 "0hsh3r2r4g63fjlsasw9iwddxfr5xbghi17kc3arn85jkwr6k9yz")))) + (base32 "0gxsbhigq0qxiw6kx4p7wgqjx7c09qj03w7j6600p2jzaqz959zj")))) (properties `((upstream-name . "tspredit"))) (build-system r-build-system) - (propagated-inputs (list r-smotefamily - r-mfilter - r-leaps + (propagated-inputs (list r-mfilter r-kfas - r-glmnet - r-fselector r-forecast r-dplyr - r-doby r-desctools r-daltoolbox)) (home-page "https://github.com/cefet-rj-dal/daltoolbox") @@ -23232,6 +23227,29 @@ assets covering a wide variety of course and time spans. See API key for free-but-capped access to the data.") (license license:gpl2+))) +(define-public r-tcpmor + (package + (name "r-tcpmor") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "TCPMOR" version)) + (sha256 + (base32 "10zbslpkc9kd7piakrkch71y20pgzmfw6vfmi6slsicqq50grca6")))) + (properties `((upstream-name . "TCPMOR"))) + (build-system r-build-system) + (propagated-inputs (list r-semipar)) + (home-page "https://cran.r-project.org/package=TCPMOR") + (synopsis "Two Cut-Points with Maximum Odds Ratio") + (description + "Enables the computation of the two cut-points with maximum odds ratio (OR) value +method for data analysis, particularly suited for binary classification tasks. +Users can identify optimal cut-points in a continuous variable by maximizing the +odds ratio while maintaining an equal risk level, useful for tasks such as +medical diagnostics, risk assessment, or predictive modeling.") + (license license:expat))) + (define-public r-tcplfit2 (package (name "r-tcplfit2") diff --git a/guix-cran/packages/v.scm b/guix-cran/packages/v.scm index b8fbe4a..5ffa006 100644 --- a/guix-cran/packages/v.scm +++ b/guix-cran/packages/v.scm @@ -2934,16 +2934,16 @@ International Meteor Organization .") (define-public r-visitorcounts (package (name "r-visitorcounts") - (version "1.0.2") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "VisitorCounts" version)) (sha256 - (base32 "0qm5qccikwdkdc9pm0gck5id3rjicb07jbds4fbvn3db071bzrdy")))) + (base32 "1i43g2k3n3c1baxj8q86v33mvvmcg16vv2a46y4ji5nqnqay7183")))) (properties `((upstream-name . "VisitorCounts"))) (build-system r-build-system) - (propagated-inputs (list r-rssa)) + (propagated-inputs (list r-rssa r-ggplot2)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=VisitorCounts") (synopsis "Modeling and Forecasting Visitor Counts Using Social Media") @@ -2953,8 +2953,9 @@ social media data and (partial) on-site visitor counts. Specifically, the model is built based on an automatic decomposition of the trend and seasonal components of the social media-based park visitor counts, from which short-term forecasts of the visitor counts and percent changes in the visitor counts can be -made. A reference for generating social media-based visitor counts can be found -at Wood, Guerry, Silver, and Lacayo (2013) .") +made. A reference for the underlying model that @code{VisitorCounts} uses can +be found at Russell Goebel', Austin Schmaltz, Beth Ann Brackett', Spencer A. +Wood, Kimihiro Noguchi (2023) .") (license license:gpl3))) (define-public r-visit @@ -6758,13 +6759,13 @@ extra functions exist (@code{varImpACC} and @code{varImpAUC}).") (define-public r-variationaldcm (package (name "r-variationaldcm") - (version "2.0.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "variationalDCM" version)) (sha256 - (base32 "0kf9dw8nm728wf825bflvjma49qgdr0sm4zmnnfp1n3xwj2lswxn")))) + (base32 "1qdbl72a251q3l72d6zjd2ins2q924yvmj394qa7yvb7q2wkw5sw")))) (properties `((upstream-name . "variationalDCM"))) (build-system r-build-system) (propagated-inputs (list r-mvtnorm)) diff --git a/guix-cran/packages/w.scm b/guix-cran/packages/w.scm index aed844b..46c884f 100644 --- a/guix-cran/packages/w.scm +++ b/guix-cran/packages/w.scm @@ -5792,13 +5792,13 @@ or webmorph templates.") (define-public r-webmap (package (name "r-webmap") - (version "1.0.7") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "webmap" version)) (sha256 - (base32 "0md00ahy6v8rhr1ch6nikqgjs86arbal48d7k2hl3q75f15jx0v9")))) + (base32 "1j73d0hx9rrvc81id98lp2s2ya4whdkppw27cbz4rcwpa6lgzyg3")))) (properties `((upstream-name . "webmap"))) (build-system r-build-system) (arguments diff --git a/guix-cran/packages/z.scm b/guix-cran/packages/z.scm index d168cb3..0febd1d 100644 --- a/guix-cran/packages/z.scm +++ b/guix-cran/packages/z.scm @@ -951,13 +951,13 @@ environment, by Daniel Wallach (INRA), David Makowski (INRA), James W. Jones (define-public r-zdeskr (package (name "r-zdeskr") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "zdeskR" version)) (sha256 - (base32 "15kb85xmn133yby4p03afkib3wrv5baswsdalj8sigyv452id7k6")))) + (base32 "11nk8rvsqipqh9w13hi31yy3yv6hd2dk1si61p3frr9g5lsbi5l0")))) (properties `((upstream-name . "zdeskR"))) (build-system r-build-system) (propagated-inputs (list r-tidyselect