From 466d876bcc15a1a6c2053eb150548f7f471f75b7 Mon Sep 17 00:00:00 2001 From: User for Guix CRAN updates Date: Thu, 28 Mar 2024 05:07:32 +0100 Subject: [PATCH] Automated CRAN import 2024-03-28 Compatible with the following channels: (list (channel (name 'guix) (url "https://git.savannah.gnu.org/git/guix.git") (branch "master") (commit "0e8f7ee3a95011dd9ebdc99e0f3b754160524b5d") (introduction (make-channel-introduction "9edb3f66fd807b096b48283debdcddccfea34bad" (openpgp-fingerprint "BBB0 2DDF 2CEA F6A8 0D1D E643 A2A0 6DF2 A33A 54FA"))))) --- guix-cran/packages/a.scm | 137 +++++++----------------------- guix-cran/packages/b.scm | 92 +------------------- guix-cran/packages/c.scm | 68 +++++++++++---- guix-cran/packages/d.scm | 35 +++++++- guix-cran/packages/e.scm | 40 +-------- guix-cran/packages/f.scm | 68 ++++++++++++--- guix-cran/packages/g.scm | 158 ++++++++++++----------------------- guix-cran/packages/h.scm | 117 ++++++++++++++++++++++++-- guix-cran/packages/i.scm | 6 +- guix-cran/packages/j.scm | 11 +-- guix-cran/packages/k.scm | 26 ++++++ guix-cran/packages/l.scm | 59 ++++--------- guix-cran/packages/m.scm | 43 ++++++++-- guix-cran/packages/o.scm | 127 ++++++++++++++-------------- guix-cran/packages/p.scm | 83 +++++++++++++------ guix-cran/packages/r.scm | 149 ++++++++++++++++++--------------- guix-cran/packages/s.scm | 175 ++++++++++++++++++--------------------- guix-cran/packages/t.scm | 11 +-- guix-cran/packages/v.scm | 82 +++++++++++------- 19 files changed, 761 insertions(+), 726 deletions(-) diff --git a/guix-cran/packages/a.scm b/guix-cran/packages/a.scm index f822473..dfa4ce1 100644 --- a/guix-cran/packages/a.scm +++ b/guix-cran/packages/a.scm @@ -7424,79 +7424,6 @@ vignettes. The data sets were formerly distributed with @code{ArchaeoPhases}', however they exceed current CRAN policy for package size.") (license license:gpl3))) -(define-public r-archaeophases - (package - (name "r-archaeophases") - (version "1.8") - (source - (origin - (method url-fetch) - (uri (cran-uri "ArchaeoPhases" version)) - (sha256 - (base32 "00d8lpasz96l55v3982mqg85b237lxvsjl65p288yzj87860v2kj")))) - (properties `((upstream-name . "ArchaeoPhases"))) - (build-system r-build-system) - (propagated-inputs (list r-toordinal - r-shiny - r-reshape2 - r-readr - r-magrittr - r-hdrcde - r-gtools - r-gplots - r-ggraph - r-ggplot2 - r-ggalt - r-dplyr - r-digest - r-coda)) - (native-inputs (list r-knitr)) - (home-page "https://cran.r-project.org/package=ArchaeoPhases") - (synopsis - "Post-Processing of the Markov Chain Simulated by 'ChronoModel', 'Oxcal' or 'BCal'") - (description - "This package provides a list of functions for the statistical analysis of -archaeological dates and groups of dates. It is based on the post-processing of -the Markov Chains whose stationary distribution is the posterior distribution of -a series of dates. Such output can be simulated by different applications as -for instance @code{ChronoModel} (see ), Oxcal (see -) or BCal (see -). The only requirement is to have a csv file -containing a sample from the posterior distribution. Note that this package -interacts with data available through the @code{ArchaeoPhases.dataset} package -which is available in a separate repository. The size of the -@code{ArchaeoPhases.dataset} package is approximately 4 MB.") - (license license:gpl3))) - -(define-public r-archaeochron - (package - (name "r-archaeochron") - (version "0.1") - (source - (origin - (method url-fetch) - (uri (cran-uri "ArchaeoChron" version)) - (sha256 - (base32 "1qma2432mm73h72g9ah1k02wlcb6yrhc6mpai9nj7v58s126ffxn")))) - (properties `((upstream-name . "ArchaeoChron"))) - (build-system r-build-system) - (propagated-inputs (list r-rjags r-coda r-bchron r-archaeophases)) - (native-inputs (list r-knitr)) - (home-page "https://cran.r-project.org/package=ArchaeoChron") - (synopsis "Bayesian Modeling of Archaeological Chronologies") - (description - "This package provides a list of functions for the Bayesian modeling of -archaeological chronologies. The Bayesian models are implemented in JAGS ('JAGS -stands for Just Another Gibbs Sampler. It is a program for the analysis of -Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation. -See and \"JAGS Version 4.3.0 user manual\", -Martin Plummer (2017) -.). The inputs are -measurements with their associated standard deviations and the study period. -The output is the MCMC sample of the posterior distribution of the event date -with or without radiocarbon calibration.") - (license license:gpl3))) - (define-public r-arcgisutils (package (name "r-arcgisutils") @@ -9291,42 +9218,6 @@ all possible comparisons (APC) methodology developed by Miller (2005) .") (license license:gpl3))) -(define-public r-apcalign - (package - (name "r-apcalign") - (version "0.1.3") - (source - (origin - (method url-fetch) - (uri (cran-uri "APCalign" version)) - (sha256 - (base32 "1kbkwpf7lzg7lznl0ysnwwilmklqyqd02qc1vl0pfbd407pqlyyv")))) - (properties `((upstream-name . "APCalign"))) - (build-system r-build-system) - (propagated-inputs (list r-tibble - r-stringr - r-stringi - r-rlang - r-readr - r-purrr - r-jsonlite - r-httr - r-forcats - r-dplyr - r-curl - r-crayon - r-arrow)) - (native-inputs (list r-knitr)) - (home-page "https://traitecoevo.github.io/APCalign/") - (synopsis "Resolving Plant Taxon Names Using the Australian Plant Census") - (description - "The process of resolving taxon names is necessary when working with biodiversity -data. APCalign uses the Australian Plant Census (APC) and the Australian Plant -Name Index (APNI) to align and update plant taxon names to current, accepted -standards. APCalign also supplies information about the established status of -plant taxa across different states/territories.") - (license license:expat))) - (define-public r-apc (package (name "r-apc") @@ -21022,6 +20913,34 @@ frequently used inequality and poverty metrics (such as the Palma ratio, the concentration and Theil indices and the FGT family of measures).") (license license:expat))) +(define-public r-accelstab + (package + (name "r-accelstab") + (version "2.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "AccelStab" version)) + (sha256 + (base32 "072wm4421bir8ij1g5zj0rn26h28vz7np6glmvapv18q4kfz1x88")))) + (properties `((upstream-name . "AccelStab"))) + (build-system r-build-system) + (propagated-inputs (list r-scales r-mvtnorm r-minpack-lm r-ggplot2 r-dplyr)) + (home-page "https://github.com/AccelStab/AccelStab") + (synopsis "Accelerated Stability Kinetic Modelling") + (description + "Estimate the Š@code{esták–Berggren} kinetic model (degradation model) from +experimental data. A A closed-form (analytic) solution to the degradation model +is implemented as a non-linear fit, allowing for the extrapolation of the +degradation of a drug product - both in time and temperature. Parametric +bootstrap, with kinetic parameters drawn from the multivariate t-distribution, +and analytical formulae (the delta method) are available options to calculate +the confidence and prediction intervals. The results (modelling, extrapolations +and statistical intervals) can be visualised with multiple plots. The examples +illustrate the accelerated stability modelling in drugs and vaccines +development.") + (license license:agpl3+))) + (define-public r-acca (package (name "r-acca") diff --git a/guix-cran/packages/b.scm b/guix-cran/packages/b.scm index d28a455..05def48 100644 --- a/guix-cran/packages/b.scm +++ b/guix-cran/packages/b.scm @@ -5865,37 +5865,6 @@ unitary matrices, evaluation of matrix permanents (both real and complex) and evaluation of complex permanent minors.") (license license:gpl2))) -(define-public r-boso - (package - (name "r-boso") - (version "1.0.3") - (source - (origin - (method url-fetch) - (uri (cran-uri "BOSO" version)) - (sha256 - (base32 "0zax40x2d62vcn8zznmzmykk33mv4vbjfl88i3r1djbvalcdf5cf")))) - (properties `((upstream-name . "BOSO"))) - (build-system r-build-system) - (propagated-inputs (list r-matrix r-mass)) - (native-inputs (list r-knitr)) - (home-page "https://cran.r-project.org/package=BOSO") - (synopsis "Bilevel Optimization Selector Operator") - (description - "This package provides a novel feature selection algorithm for linear regression -called BOSO (Bilevel Optimization Selector Operator). The main contribution is -the use a bilevel optimization problem to select the variables in the training -problem that minimize the error in the validation set. Preprint available: -[Valcarcel, L. V., San Jose-Eneriz, E., Cendoya, X., Rubio, A., Agirre, X., -Prosper, F., & Planes, F. J. (2020). \"BOSO: a novel feature selection algorithm -for linear regression with high-dimensional data.\" @code{bioRxiv}. -]. In order to run the vignette, it is -recommended to install the bestsubset package, using the following command: -devtools::install_github(repo=\"ryantibs/best-subset\", subdir=\"bestsubset\"). If -you do not have gurobi, run -devtools::install_github(repo=\"lvalcarcel/best-subset\", subdir=\"bestsubset\").") - (license license:gpl3))) - (define-public r-borrowr (package (name "r-borrowr") @@ -12348,32 +12317,6 @@ available at . Documentation for Biobricks.ai is available at .") (license license:expat))) -(define-public r-bioassays - (package - (name "r-bioassays") - (version "1.0.1") - (source - (origin - (method url-fetch) - (uri (cran-uri "bioassays" version)) - (sha256 - (base32 "1y32wxkv14l7r0f35y4hxxxh3zpw2gd4hsjmkajhmzmnvg5jdw78")))) - (properties `((upstream-name . "bioassays"))) - (build-system r-build-system) - (propagated-inputs (list r-rlang - r-reshape2 - r-nplr - r-magrittr - r-ggplot2 - r-dplyr)) - (native-inputs (list r-knitr)) - (home-page "https://cran.r-project.org/package=bioassays") - (synopsis "Summarising Multi Well Plate Cellular Assay") - (description - "The goal is to help users to analyse data from multi wells with minimum effort. -Using these functions several plates can be analyzed automatically.") - (license license:gpl3))) - (define-public r-bioacoustics (package (name "r-bioacoustics") @@ -14518,13 +14461,13 @@ of functions of R API to communicate with UCI-protocol based chess engines.") (define-public r-bigbits (package (name "r-bigbits") - (version "1.1") + (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "bigBits" version)) (sha256 - (base32 "0vakcy5ymd4b5mhz5vjbkhp82bikdajh6wag4cgzbl3vdvx85xhf")))) + (base32 "0qrbm4d3rihy7dvc3lvailmarq1n2hs7qv6wqrgjd0pxnz62j7p7")))) (properties `((upstream-name . "bigBits"))) (build-system r-build-system) (propagated-inputs (list r-rmpfr r-gmp)) @@ -20218,37 +20161,6 @@ implementations of the methods of Oh and Raftery (2001) .") (license license:gpl2+))) -(define-public r-baylum - (package - (name "r-baylum") - (version "0.3.1") - (source - (origin - (method url-fetch) - (uri (cran-uri "BayLum" version)) - (sha256 - (base32 "1n40zz0156kw6fwqvlhx3svmvwa2049z4ly9lxcid84dwyxxyn0r")))) - (properties `((upstream-name . "BayLum"))) - (build-system r-build-system) - (propagated-inputs (list r-runjags - r-rjags - r-luminescence - r-kernsmooth - r-hexbin - r-coda - r-archaeophases)) - (native-inputs (list r-r-rsp)) - (home-page "https://CRAN.r-project.org/package=BayLum") - (synopsis - "Chronological Bayesian Models Integrating Optically Stimulated Luminescence and Radiocarbon Age Dating") - (description - "Bayesian analysis of luminescence data and C-14 age estimates. Bayesian models -are based on the following publications: Combes, B. & Philippe, A. (2017) - and Combes et al (2015) -. This includes, amongst others, data import, -export, application of age models and palaeodose model.") - (license license:gpl3))) - (define-public r-baygel (package (name "r-baygel") diff --git a/guix-cran/packages/c.scm b/guix-cran/packages/c.scm index 82d600f..45988a6 100644 --- a/guix-cran/packages/c.scm +++ b/guix-cran/packages/c.scm @@ -955,6 +955,37 @@ classification (binary and multiclass). Described in chp. 5 of Jeyaraman, B. P., Olsen, L. R., & Wambugu M. (2019, ISBN: 9781838550134).") (license license:expat))) +(define-public r-cvmortalitymult + (package + (name "r-cvmortalitymult") + (version "0.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "CvmortalityMult" version)) + (sha256 + (base32 "19j24g0x3f6k91r95z8sl4c2l0y2nbjm8068r21pr4fnfsz5gdj1")))) + (properties `((upstream-name . "CvmortalityMult"))) + (build-system r-build-system) + (propagated-inputs (list r-tmap r-stmomo r-sf r-gnm r-forecast)) + (home-page "https://github.com/davidAtance/CvmortalityMult") + (synopsis "Cross-Validation for Multi-Population Mortality Models") + (description + "Implementation of cross-validation method for testing the forecasting accuracy +of several multi-population mortality models. The family of multi-population +includes several multi-population mortality models proposed through the +actuarial and demography literature. The package includes functions for fitting +and forecast the mortality rates of several populations. Additionally, we +include functions for testing the forecasting accuracy of different +multi-population models. References. Atance, D., Debon, A., and Navarro, E. +(2020) . Bergmeir, C. & Benitez, J.M. (2012) +. Debon, A., Montes, F., & Martinez-Ruiz, F. +(2011) . Lee, R.D. & Carter, L.R. (1992) +. Russolillo, M., Giordano, G., & Haberman, +S. (2011) . Santolino, M. (2023) +.") + (license license:expat))) + (define-public r-cvmgof (package (name "r-cvmgof") @@ -29687,13 +29718,13 @@ headless Chrome web browser.") (define-public r-chromer (package (name "r-chromer") - (version "0.6") + (version "0.8") (source (origin (method url-fetch) (uri (cran-uri "chromer" version)) (sha256 - (base32 "1jn5dwl8i1di8hns3kjww6sqyba768j1302w3f43v9965vfr1xnp")))) + (base32 "0x9xhih0a19mqwiqs7bljcdgki874ii653v91frkwsr2y2yd9j7c")))) (properties `((upstream-name . "chromer"))) (build-system r-build-system) (propagated-inputs (list r-tibble r-httr r-dplyr)) @@ -29701,8 +29732,9 @@ headless Chrome web browser.") (synopsis "Interface to Chromosome Counts Database API") (description "This package provides a programmatic interface to the Chromosome Counts Database -(), Rice et al. (2014) . This -package is part of the R@code{OpenSci} suite ().") +(), Rice et al. (2014) +. This package is part of the R@code{OpenSci} suite +().") (license license:expat))) (define-public r-chromconverter @@ -34364,13 +34396,13 @@ command \"example(@code{fitVolDist})\".") (define-public r-celltrackr (package (name "r-celltrackr") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "celltrackR" version)) (sha256 - (base32 "08hbgpwcpf7v8l7qmszhjh0w4f4zjcizrdsxksihxpwdi9r4al3w")))) + (base32 "1y0bdn75malabyrnrqrw5vh2sr6j09hpy8gbk1vnmkbvg9dy2xh3")))) (properties `((upstream-name . "celltrackR"))) (build-system r-build-system) (propagated-inputs (list r-pracma r-ellipse)) @@ -34378,18 +34410,18 @@ command \"example(@code{fitVolDist})\".") (home-page "http://www.motilitylab.net") (synopsis "Motion Trajectory Analysis") (description - "This package provides methodology to analyze cells that move in a two- or -three-dimensional space. Available measures include displacement, confinement -ratio, autocorrelation, straightness, turning angle, and fractal dimension. -Measures can be applied to entire tracks, steps, or subtracks with varying -length. While the methodology has been developed for cell trajectory analysis, -it is applicable to anything that moves including animals, people, or vehicles. -Some of the methodology implemented in this packages was described by: -Beauchemin, Dixit, and Perelson (2007) , -Beltman, Maree, and de Boer (2009) , Gneiting and Schlather -(2004) , Mokhtari, Mech, Zitzmann, Hasenberg, -Gunzer, and Figge (2013) , Moreau, Lemaitre, -Terriac, Azar, Piel, Lennon-Dumenil, and Bousso (2012) + "This package provides methods for analyzing (cell) motion in two or three +dimensions. Available measures include displacement, confinement ratio, +autocorrelation, straightness, turning angle, and fractal dimension. Measures +can be applied to entire tracks, steps, or subtracks with varying length. While +the methodology has been developed for cell trajectory analysis, it is +applicable to anything that moves including animals, people, or vehicles. Some +of the methodology implemented in this packages was described by: Beauchemin, +Dixit, and Perelson (2007) , Beltman, Maree, +and de Boer (2009) , Gneiting and Schlather (2004) +, Mokhtari, Mech, Zitzmann, Hasenberg, Gunzer, +and Figge (2013) , Moreau, Lemaitre, Terriac, +Azar, Piel, Lennon-Dumenil, and Bousso (2012) , Textor, Peixoto, Henrickson, Sinn, von Andrian, and Westermann (2011) , Textor, Sinn, and de Boer (2013) , Textor, Henrickson, Mandl, von diff --git a/guix-cran/packages/d.scm b/guix-cran/packages/d.scm index 6115e8d..fa26296 100644 --- a/guix-cran/packages/d.scm +++ b/guix-cran/packages/d.scm @@ -25318,13 +25318,13 @@ extra layer of validation around input and output data.") (define-public r-databraryr (package (name "r-databraryr") - (version "0.6.2") + (version "0.6.3") (source (origin (method url-fetch) (uri (cran-uri "databraryr" version)) (sha256 - (base32 "0zlzsax460njv9370rw1y94vfhs22hmviz0c12bsab814i8vb3mm")))) + (base32 "0v76zaqq3kqvzwjmz6r4k816crxc2wrdymfxgjr0c02glcchhsiv")))) (properties `((upstream-name . "databraryr"))) (build-system r-build-system) (propagated-inputs (list r-xfun @@ -26405,6 +26405,37 @@ computational workflow for analysis of matabolomic data..") stochastic disability-adjusted life year (DALY) calculation.") (license license:gpl2+))) +(define-public r-daltoolboxdp + (package + (name "r-daltoolboxdp") + (version "1.0.767") + (source + (origin + (method url-fetch) + (uri (cran-uri "daltoolboxdp" version)) + (sha256 + (base32 "1l34wb2vl9wmf0vrhis29w4hz1m9jx9qdfi494rfnwals054j3ah")))) + (properties `((upstream-name . "daltoolboxdp"))) + (build-system r-build-system) + (propagated-inputs (list r-smotefamily + r-leaps + r-glmnet + r-fselector + r-doby + r-daltoolbox)) + (home-page "https://github.com/cefet-rj-dal/daltoolboxdp") + (synopsis "Data Pre-Processing Extensions") + (description + "An important aspect of data analytics is related to data management support for +artificial intelligence. It is related to preparing data correctly. This +package provides extensions to support data preparation in terms of both data +sampling and data engineering. Overall, the package provides researchers with a +comprehensive set of functionalities for data science based on experiment lines, +promoting ease of use, extensibility, and integration with various tools and +libraries. Information on Experiment Line is based on Ogasawara et al. (2009) +.") + (license license:expat))) + (define-public r-daltoolbox (package (name "r-daltoolbox") diff --git a/guix-cran/packages/e.scm b/guix-cran/packages/e.scm index d9e3633..55327ce 100644 --- a/guix-cran/packages/e.scm +++ b/guix-cran/packages/e.scm @@ -1783,38 +1783,6 @@ standard approach that is recommended by guidance Q1E \"Evaluation of stability data\" from the International Council for Harmonisation (ICH).") (license license:gpl2+))) -(define-public r-expimage - (package - (name "r-expimage") - (version "0.9.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "ExpImage" version)) - (sha256 - (base32 "1f6pddzfwmpv0gnzbpbkqzg6scafzjmpicblqz3m36nnj87l9pn7")))) - (properties `((upstream-name . "ExpImage"))) - (build-system r-build-system) - (propagated-inputs (list r-schemr - r-rstudioapi - r-raster - r-randomforest - r-progress - r-ggplot2 - r-foreach - r-doparallel - r-crayon)) - (native-inputs (list r-knitr)) - (home-page "https://www.youtube.com/channel/UCDGyvLCJnv9RtTY1YMBMVNQ") - (synopsis "Tool For Analysis of Images in Experiments") - (description - "This package provides tools created for image analysis in researches. There are -functions associated with image editing, segmentation, and obtaining biometric -measurements (Este pacote foi idealizado para para a analise de imagens em -pesquisas. Ha funcoes associadas a edicao de imagens, segmentacao, e obtencao -de medidas biometricas).") - (license license:gpl3))) - (define-public r-expgenetic (package (name "r-expgenetic") @@ -8075,13 +8043,13 @@ kindly provided by Dr. John Lieske of the Mayo Clinic.") (define-public r-equateirt (package (name "r-equateirt") - (version "2.3.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (cran-uri "equateIRT" version)) (sha256 - (base32 "18rs6n4kgbiikkljppnacd1zkv2wp8xc8ibk9xslrhshxwwr0576")))) + (base32 "0i3bvldalqrlz9qalpylybn896nkdpm5xk4m62sxhm1bfrd0nm98")))) (properties `((upstream-name . "equateIRT"))) (build-system r-build-system) (propagated-inputs (list r-statmod r-mirt)) @@ -12142,13 +12110,13 @@ efficiently.") (define-public r-emt (package (name "r-emt") - (version "1.3") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "EMT" version)) (sha256 - (base32 "0zmcakph88qg9f1p7icn4llw92nh1jfijxsx3rhl7g9d4rihprq5")))) + (base32 "0g4s99cbww9wi89acbpn8ggkfkf39nq0km0nhm5956r62sjw2wfr")))) (properties `((upstream-name . "EMT"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=EMT") diff --git a/guix-cran/packages/f.scm b/guix-cran/packages/f.scm index 3e81b04..73d29b4 100644 --- a/guix-cran/packages/f.scm +++ b/guix-cran/packages/f.scm @@ -10365,6 +10365,31 @@ display the result.") nls', @code{nlsList} and nlme frameworks.") (license license:gpl2))) +(define-public r-flexor + (package + (name "r-flexor") + (version "0.9.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "flexOR" version)) + (sha256 + (base32 "1am17ggfzak5jn7rxsj5wf2fhgsq7zqpc79xql3jxfw9dqynp9id")))) + (properties `((upstream-name . "flexOR"))) + (build-system r-build-system) + (propagated-inputs (list r-mgcv r-gam)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/martaaaa/flexOR") + (synopsis "Flexible Odds Ratio Curves") + (description + "This package provides flexible hazard ratio curves that enable modeling +non-linear relationships between continuous predictors and survival outcomes. +This package facilitates a deeper understanding of the impact of each continuous +predictor on the outcome by presenting results in terms of odds ratio (OR) +curves based on splines. These curves allow for comparison against a specified +reference value, aiding in the interpretation of the predictor's effect.") + (license license:gpl3))) + (define-public r-flexmsm (package (name "r-flexmsm") @@ -12050,13 +12075,13 @@ fossil calibrations, and diversification rate information for ray-finned fishes. (define-public r-fishrman (package (name "r-fishrman") - (version "1.2.2") + (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "fishRman" version)) (sha256 - (base32 "09kzjcngycf1xvcyszqfsrn6iypn4n86cz0h2cmwv0i6hc8k0jwb")))) + (base32 "1pyryc6pilyy68z7443gi6ixi8b0hy338l9zfw74isrxywbygy8n")))) (properties `((upstream-name . "fishRman"))) (build-system r-build-system) (propagated-inputs (list r-viridis @@ -12076,11 +12101,9 @@ fossil calibrations, and diversification rate information for ray-finned fishes. (home-page "https://github.com/Shyentist/fish-r-man") (synopsis "The Fisheries Scientist's Toolbox") (description - "This package provides a bundle of analytics tools for fisheries scientists. -Data on fishing effort by Global Fishing Watch can be retrieved via the -package's API , as well as data on Exclusive -Economic Zones by Marine Regions'. A shiny R App is included for a no-code -solution for retrieval, analysis, and visualization.") + "This package provides a bundle of analytics tools for fisheries scientists. A +shiny R App is included for a no-code solution for retrieval, analysis, and +visualization.") (license license:agpl3+))) (define-public r-fishresp @@ -14572,13 +14595,13 @@ accepts fundamental items and digital elevation models.") (define-public r-fgarch (package (name "r-fgarch") - (version "4032.91") + (version "4033.92") (source (origin (method url-fetch) (uri (cran-uri "fGarch" version)) (sha256 - (base32 "0jl76w657hlx1mf977dcm2yv1sv1fsy1nfiqnfnccqscyx9iz0z5")))) + (base32 "038lcx1sxkldqvmy9y14gmmbkqn4gqzlnff80s11fny004h6hdf8")))) (properties `((upstream-name . "fGarch"))) (build-system r-build-system) (propagated-inputs (list r-timeseries @@ -14588,7 +14611,7 @@ accepts fundamental items and digital elevation models.") r-fastica r-cvar)) (native-inputs (list gfortran)) - (home-page "https://www.rmetrics.org") + (home-page "https://geobosh.github.io/fGarchDoc/") (synopsis "Rmetrics - Autoregressive Conditional Heteroskedastic Modelling") (description @@ -21732,6 +21755,31 @@ the user, keep track of information in pipelines, help in the wrangling, munging, assessment and visualization of data frame-like material.") (license license:gpl3))) +(define-public r-fabprediction + (package + (name "r-fabprediction") + (version "1.0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "fabPrediction" version)) + (sha256 + (base32 "1vachv2fgjlh932q28266b6x59sdvrmwp8si9pa4b543sdzklpms")))) + (properties `((upstream-name . "fabPrediction"))) + (build-system r-build-system) + (propagated-inputs (list r-sae)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/betsybersson/fabPrediction") + (synopsis + "Compute FAB (Frequentist and Bayes) Conformal Prediction Intervals") + (description + "Computes and plots prediction intervals for numerical data or prediction sets +for categorical data using prior information. Empirical Bayes procedures to +estimate the prior information from multi-group data are included. See, +e.g.,Bersson and Hoff (2022) <@code{arXiv:2204.08122>} \"Optimal Conformal +Prediction for Small Areas\".") + (license license:gpl3))) + (define-public r-fabmix (package (name "r-fabmix") diff --git a/guix-cran/packages/g.scm b/guix-cran/packages/g.scm index adc11a0..2069bc3 100644 --- a/guix-cran/packages/g.scm +++ b/guix-cran/packages/g.scm @@ -5749,13 +5749,13 @@ without access to Hugin to use code written to use RHugin'.") (define-public r-grattaninflators (package (name "r-grattaninflators") - (version "0.5.0") + (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "grattanInflators" version)) (sha256 - (base32 "0lp000wgl1jkfhbb69kpxlpnarwwybzys6waxppacd5xlimynl12")))) + (base32 "1ggdkr8z4zh6myq5wx0kdszb4b6wa9qf9v8zd169chgiy6an5glx")))) (properties `((upstream-name . "grattanInflators"))) (build-system r-build-system) (propagated-inputs (list r-hutils r-fy r-data-table)) @@ -5770,13 +5770,13 @@ about date input quality, performance, or the ABS catalogue.") (define-public r-grattan (package (name "r-grattan") - (version "2024.0.0") + (version "2024.1.1") (source (origin (method url-fetch) (uri (cran-uri "grattan" version)) (sha256 - (base32 "0wq7k7h4kgq7q5r53n53bddssywx6lb3jqi74jfd3gdgixx2sp6q")))) + (base32 "0cxgj20c7gk55p22rmy1al44if4pk90yf9zify2jz9h7pviwgpjx")))) (properties `((upstream-name . "grattan"))) (build-system r-build-system) (propagated-inputs (list r-magrittr @@ -5827,16 +5827,17 @@ lines.") (define-public r-gratia (package (name "r-gratia") - (version "0.8.2") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "gratia" version)) (sha256 - (base32 "0gfilxh697laf1y20kmrzjrgd1xypf529cw9xxzy64z7rn0jraih")))) + (base32 "1hkfaw2vwm4dw73fn4glkwnhvbf2wc3iyz5979rsfabn5i6g91br")))) (properties `((upstream-name . "gratia"))) (build-system r-build-system) - (propagated-inputs (list r-vctrs + (propagated-inputs (list r-withr + r-vctrs r-tidyselect r-tidyr r-tibble @@ -5850,6 +5851,7 @@ lines.") r-mgcv r-lifecycle r-ggplot2 + r-ggokabeito r-dplyr r-cli)) (native-inputs (list r-knitr)) @@ -6810,17 +6812,18 @@ is provided in vignettes included in the package and in the paper by Højsgaar (define-public r-grafzahl (package (name "r-grafzahl") - (version "0.0.8") + (version "0.0.11") (source (origin (method url-fetch) (uri (cran-uri "grafzahl" version)) (sha256 - (base32 "1pccxzraz9sri69774svj3sb1fxq00lq8261z0fcm0j17mqmysyq")))) + (base32 "0zx6fqwklyi3sc1p59nb71mgrfnp7bqw5axmddj3706cawlrqrb8")))) (properties `((upstream-name . "grafzahl"))) (build-system r-build-system) (propagated-inputs (list r-reticulate r-quanteda r-lime r-jsonlite)) - (home-page "https://github.com/chainsawriot/grafzahl") + (native-inputs (list r-knitr)) + (home-page "https://gesistsa.github.io/grafzahl/") (synopsis "Supervised Machine Learning for Textual Data Using Transformers and 'Quanteda'") (description @@ -12188,6 +12191,36 @@ models by L1-penalized estimation is provided, see Groll and Tutz (2014) heterogeneity.") (license license:gpl2))) +(define-public r-glmmisrep + (package + (name "r-glmmisrep") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "glmMisrep" version)) + (sha256 + (base32 "0czcmr2lh7xnz8l1q74r7zlsfajl9r4x4nh5hmjfbdybf4rj81js")))) + (properties `((upstream-name . "glmMisrep"))) + (build-system r-build-system) + (propagated-inputs (list r-poisson-glm-mix r-mass)) + (home-page "https://cran.r-project.org/package=glmMisrep") + (synopsis "Generalized Linear Models Adjusting for Misrepresentation") + (description + "Fit Generalized Linear Models to continuous and count outcomes, as well as +estimate the prevalence of misrepresentation of an important binary predictor. +Misrepresentation typically arises when there is an incentive for the binary +factor to be misclassified in one direction (e.g., in insurance settings where +policy holders may purposely deny a risk status in order to lower the insurance +premium). This is accomplished by treating a subset of the response variable as +resulting from a mixture distribution. Model parameters are estimated via the +Expectation Maximization algorithm and standard errors of the estimates are +obtained from closed forms of the Observed Fisher Information. For an +introduction to the models and the misrepresentation framework, see Xia et. +al., (2023) +.") + (license license:gpl2+))) + (define-public r-glmmfields (package (name "r-glmmfields") @@ -13034,36 +13067,6 @@ transform residuals are included in the package. Several standard data sets are included in the package.") (license license:gpl2+))) -(define-public r-glancedata - (package - (name "r-glancedata") - (version "1.0.1") - (source - (origin - (method url-fetch) - (uri (cran-uri "glancedata" version)) - (sha256 - (base32 "01j7syjn33pc7hq032nmyak38wn35yv3n7is9g2ggs14kj3xqb0c")))) - (properties `((upstream-name . "glancedata"))) - (build-system r-build-system) - (propagated-inputs (list r-tidyr - r-tibble - r-purrr - r-openxlsx - r-gridextra - r-ggplot2 - r-ggally - r-forcats - r-dplyr)) - (native-inputs (list r-knitr)) - (home-page "https://cran.r-project.org/package=glancedata") - (synopsis "Generate tables and plots to get summaries of data") - (description - "Generate data frames for all the variables with some summaries and also some -plots for numerical variables. Several functions from the tidyverse and GGally -packages are used.") - (license license:gpl3))) - (define-public r-glamlasso (package (name "r-glamlasso") @@ -13753,13 +13756,13 @@ that the data are optimally primed for precise and thorough analysis.") (define-public r-giscor (package (name "r-giscor") - (version "0.4.1") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "giscoR" version)) (sha256 - (base32 "00hszk0pnf5i65sp12073gq1bfybpaazdigs6q5j0gyvaqcacbl9")))) + (base32 "1c614w22kk90mdn856kyv26dwmnmsx54xv35x29w74lyw15c1nbi")))) (properties `((upstream-name . "giscoR"))) (build-system r-build-system) (propagated-inputs (list r-sf r-rappdirs r-geojsonsf r-countrycode)) @@ -14774,13 +14777,13 @@ method can be found in Anton Rask Lundborg, Rajen D. Shah and Jonas Peters (define-public r-ghclass (package (name "r-ghclass") - (version "0.2.1") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "ghclass" version)) (sha256 - (base32 "0jpfc2mjwi6i3bcrfjjl6k4im4m110pq2n00mij2n9czz6v2chla")))) + (base32 "10sq9rissf3w7rp8449vzigl7bj7y3iqx0vci2m559ihjmsdkn6i")))) (properties `((upstream-name . "ghclass"))) (build-system r-build-system) (propagated-inputs (list r-withr @@ -14789,6 +14792,7 @@ method can be found in Anton Rask Lundborg, Rajen D. Shah and Jonas Peters r-rlang r-purrr r-lubridate + r-lifecycle r-httr r-glue r-gh @@ -16993,35 +16997,6 @@ and the response is present. Base on the results published in guide ISO/TS 28037 (2010) .") (license license:gpl2+))) -(define-public r-ggmosaic - (package - (name "r-ggmosaic") - (version "0.3.3") - (source - (origin - (method url-fetch) - (uri (cran-uri "ggmosaic" version)) - (sha256 - (base32 "1zm1zfbd0qk6icw65m9hz1hgyqj632ibq3qilidvx5jy7jh8nbpy")))) - (properties `((upstream-name . "ggmosaic"))) - (build-system r-build-system) - (propagated-inputs (list r-tidyr - r-scales - r-rlang - r-purrr - r-productplots - r-plotly - r-ggrepel - r-ggplot2 - r-dplyr)) - (native-inputs (list r-knitr)) - (home-page "https://github.com/haleyjeppson/ggmosaic") - (synopsis "Mosaic Plots in the 'ggplot2' Framework") - (description - "Mosaic plots in the ggplot2 framework. Mosaic plot functionality is provided in -a single ggplot2 layer by calling the geom mosaic'.") - (license license:gpl2+))) - (define-public r-ggmnonreg (package (name "r-ggmnonreg") @@ -17768,35 +17743,6 @@ guide, including convenience functions for for loading and using the Source Sans 3 font.") (license license:gpl3+))) -(define-public r-gghdr - (package - (name "r-gghdr") - (version "0.2.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "gghdr" version)) - (sha256 - (base32 "1id0ky2mf656xqsmg76f627zw8iff4q1wzgih32nryk0hfvm2gfi")))) - (properties `((upstream-name . "gghdr"))) - (build-system r-build-system) - (propagated-inputs (list r-tibble - r-scales - r-hdrcde - r-ggplot2 - r-farver - r-digest)) - (native-inputs (list r-knitr)) - (home-page "https://github.com/Sayani07/gghdr") - (synopsis "Visualisation of Highest Density Regions in 'ggplot2'") - (description - "This package provides ggplot2 framework for visualising Highest Density Regions -(HDR) . This work is based on the package -hdrcde' and displays highest density -regions in ggplot2 for one and two dimensions and univariate densities -conditional on one covariate.") - (license license:gpl3))) - (define-public r-gghalfnorm (package (name "r-gghalfnorm") @@ -20170,13 +20116,13 @@ keeping a tabular (long) structure for easier processing.") (define-public r-getdesigns (package (name "r-getdesigns") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "GETdesigns" version)) (sha256 - (base32 "1rc8vcpfv240qmg3xgqx1rlygw7l3hjkh1napj3pc9j6ffpyyk2a")))) + (base32 "1kd08vdra3akdkvk6n9i6w4m2qmlnkjqjnssdn8f317vwbhjcmf3")))) (properties `((upstream-name . "GETdesigns"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=GETdesigns") @@ -26124,13 +26070,13 @@ function arguments introduced in GDAL version 3.5.2 or earlier are supported.") (define-public r-gdalraster (package (name "r-gdalraster") - (version "1.9.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (cran-uri "gdalraster" version)) (sha256 - (base32 "1bii8gr1b5fjfi2bwspxvn0d6bl7k3l3x2426l16p9pw8r7sk3wn")))) + (base32 "1rwz0p83lmxgz3v0mrnjk4wh1yv5ijwxy5nmvmn6jzvk6l5wbjfp")))) (properties `((upstream-name . "gdalraster"))) (build-system r-build-system) (inputs (list zlib diff --git a/guix-cran/packages/h.scm b/guix-cran/packages/h.scm index fed1c10..278f5d2 100644 --- a/guix-cran/packages/h.scm +++ b/guix-cran/packages/h.scm @@ -1059,6 +1059,28 @@ R., Costa, A.M., Szemis, J.M., & Webb, J.A. (2017) R. J. (2013) .") (license license:gpl3))) +(define-public r-hydrodcindex + (package + (name "r-hydrodcindex") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "hydroDCindex" version)) + (sha256 + (base32 "0nci4jj2aca2kaq4cgrv9sq9pksjaagqik2y8j1c2a1w39qjzyan")))) + (properties `((upstream-name . "hydroDCindex"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=hydroDCindex") + (synopsis "Duration Curve Hydrological Model Indexes") + (description + "Compute duration curves of daily flow series, both real and modeled, to be +compared through indexes of flow duration curves. The package functions include +comparative plots and goodness of fit tests. Flow duration curve indexes are +based on: Yilmaz et al., (2008) .") + (license license:gpl3))) + (define-public r-hydrocode (package (name "r-hydrocode") @@ -2174,6 +2196,60 @@ framework to facilitate the measurement of HTTP request time and cache performance.") (license license:expat))) +(define-public r-httk + (package + (name "r-httk") + (version "2.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "httk" version)) + (sha256 + (base32 "1ws9bxrl0r59nni6avvr7qgs866p90l88x9xyfw2s90j5q2zzil5")))) + (properties `((upstream-name . "httk"))) + (build-system r-build-system) + (propagated-inputs (list r-truncnorm + r-survey + r-rdpack + r-purrr + r-mvtnorm + r-msm + r-magrittr + r-ggplot2 + r-desolve + r-data-table)) + (native-inputs (list r-r-rsp r-knitr)) + (home-page + "https://www.epa.gov/chemical-research/rapid-chemical-exposure-and-dose-research") + (synopsis "High-Throughput Toxicokinetics") + (description + "Pre-made models that can be rapidly tailored to various chemicals and species +using chemical-specific in vitro data and physiological information. These +tools allow incorporation of chemical toxicokinetics (\"TK\") and in vitro-in vivo +extrapolation (\"IVIVE\") into bioinformatics, as described by Pearce et al. +(2017) (). Chemical-specific in vitro data +characterizing toxicokinetics have been obtained from relatively high-throughput +experiments. The chemical-independent (\"generic\") physiologically-based +(\"PBTK\") and empirical (for example, one compartment) \"TK\" models included here +can be parameterized with in vitro data or in silico predictions which are +provided for thousands of chemicals, multiple exposure routes, and various +species. High throughput toxicokinetics (\"HTTK\") is the combination of in vitro +data and generic models. We establish the expected accuracy of HTTK for +chemicals without in vivo data through statistical evaluation of HTTK +predictions for chemicals where in vivo data do exist. The models are systems +of ordinary differential equations that are developed in MCSim and solved using +compiled (C-based) code for speed. A Monte Carlo sampler is included for +simulating human biological variability (Ring et al., 2017 +) and propagating parameter uncertainty +(Wambaugh et al., 2019 ). Empirically calibrated +methods are included for predicting tissue:plasma partition coefficients and +volume of distribution (Pearce et al., 2017 ). +These functions and data provide a set of tools for using IVIVE to convert +concentrations from high-throughput screening experiments (for example, Tox21, +@code{ToxCast}) to real-world exposures via reverse dosimetry (also known as +\"RTK\") (Wetmore et al., 2015 ).") + (license license:gpl3))) + (define-public r-htt (package (name "r-htt") @@ -2275,6 +2351,37 @@ probing (HR-SIP), multi-window high resolution stable isotope probing and meteorology time-series stored in a Sqlite data base.") (license license:gpl2))) +(define-public r-htseed + (package + (name "r-htseed") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "HTSeed" version)) + (sha256 + (base32 "01h9lm2ljp67qfcl7vlh804r7q15arqx103jb9pvk2wx1c27qy3x")))) + (properties `((upstream-name . "HTSeed"))) + (build-system r-build-system) + (propagated-inputs (list r-dplyr)) + (home-page "https://cran.r-project.org/package=HTSeed") + (synopsis "Fitting of Hydrotime Model for Seed Germination Time Course") + (description + "The seed germination process starts with water uptake by the seed and ends with +the protrusion of radicle and plumule under varying temperatures and soil water +potential. Hydrotime is a way to describe the relationship between water +potential and seed germination rates at germination percentages. One important +quantity before applying hydrotime modeling of germination percentages is to +consider the proportion of viable seeds that could germinate under saturated +conditions. This package can be used to apply correction factors at various +water potentials before estimating parameters like stress tolerance, and +uniformity of the hydrotime model. Three different distributions namely, +Gaussian, Logistic, and Extreme value distributions have been considered to fit +the model to the seed germination time course. Details can be found in Bradford +(2002) , and Bradford and Still(2004) +.") + (license license:gpl3))) + (define-public r-hts (package (name "r-hts") @@ -11500,21 +11607,19 @@ rate only in the weak sense, rather than the strong sense as intended.") (define-public r-harbinger (package (name "r-harbinger") - (version "1.0.737") + (version "1.0.747") (source (origin (method url-fetch) (uri (cran-uri "harbinger" version)) (sha256 - (base32 "0amqpx3pfvnx30dknxs4759b7c4qd4839zkrwf4ayg5klc06v7zd")))) + (base32 "0955n7mriy1yl5lw1cip6x3ynn5bz6z02j8hvn4mi9ysy9sky837")))) (properties `((upstream-name . "harbinger"))) (build-system r-build-system) - (propagated-inputs (list r-tspred - r-tsmp + (propagated-inputs (list r-tsmp r-strucchange r-stringr r-rugarch - r-reticulate r-ggplot2 r-forecast r-dtwclust @@ -11522,7 +11627,7 @@ rate only in the weak sense, rather than the strong sense as intended.") r-daltoolbox r-changepoint)) (home-page "https://github.com/cefet-rj-dal/harbinger") - (synopsis "An Unified Time Series Event Detection Framework") + (synopsis "Unified Time Series Event Detection Framework") (description "By analyzing time series, it is possible to observe significant changes in the behavior of observations that frequently characterize events. Events present diff --git a/guix-cran/packages/i.scm b/guix-cran/packages/i.scm index 1fcc22f..ab6d671 100644 --- a/guix-cran/packages/i.scm +++ b/guix-cran/packages/i.scm @@ -1521,16 +1521,16 @@ adapted from Bowen et al. (2018, ).") (define-public r-isotree (package (name "r-isotree") - (version "0.5.24-3") + (version "0.6.1-1") (source (origin (method url-fetch) (uri (cran-uri "isotree" version)) (sha256 - (base32 "02cnk9y8kc5zc9jzzhhxhgqi2z19yj2glvylbmydiagwli1aqvfl")))) + (base32 "0v0lr1aimlvgm6bpnaz1z4707fnrqvzfc3rziz0vcbzgycs0abvd")))) (properties `((upstream-name . "isotree"))) (build-system r-build-system) - (propagated-inputs (list r-rcpp)) + (propagated-inputs (list r-rcpp r-jsonlite)) (native-inputs (list r-knitr)) (home-page "https://github.com/david-cortes/isotree") (synopsis "Isolation-Based Outlier Detection") diff --git a/guix-cran/packages/j.scm b/guix-cran/packages/j.scm index 24da941..3704188 100644 --- a/guix-cran/packages/j.scm +++ b/guix-cran/packages/j.scm @@ -697,13 +697,13 @@ full-texts delivered by Data for Research by JSTOR.") (define-public r-jstable (package (name "r-jstable") - (version "1.1.7") + (version "1.1.9") (source (origin (method url-fetch) (uri (cran-uri "jstable" version)) (sha256 - (base32 "1rg913xfyzyxrfpvidxh80y4m4ls9ns14d24j2kv7qsaxhzq00si")))) + (base32 "0a7pyl04ngacnfml1qvnnwb9kwcdk2sp7mwxhyxah9iqpgpmrg66")))) (properties `((upstream-name . "jstable"))) (build-system r-build-system) (propagated-inputs (list r-tibble @@ -941,13 +941,13 @@ available at the following URL: (define-public r-jsmodule (package (name "r-jsmodule") - (version "1.5.1") + (version "1.5.2") (source (origin (method url-fetch) (uri (cran-uri "jsmodule" version)) (sha256 - (base32 "1n3fq2i53vsbh0z6p8142mi00cy9zxbsh34s048h97hg0ljzwkz6")))) + (base32 "0wllv07667izvsihhh0hhikxsyawxhpb560r6lli80phjpn88d28")))) (properties `((upstream-name . "jsmodule"))) (build-system r-build-system) (propagated-inputs (list r-timeroc @@ -958,6 +958,7 @@ available at the following URL: r-shinycustomloader r-shiny r-see + r-scales r-rvg r-rstudioapi r-readxl @@ -982,7 +983,7 @@ available at the following URL: r-dt r-data-table)) (native-inputs (list r-knitr)) - (home-page "https://github.com/jinseob2kim/jsmodule") + (home-page "https://jinseob2kim.github.io/jsmodule/") (synopsis "'RStudio' Addins and 'Shiny' Modules for Medical Research") (description "RStudio addins and Shiny modules for descriptive statistics, regression and diff --git a/guix-cran/packages/k.scm b/guix-cran/packages/k.scm index 4c390f8..ee0380f 100644 --- a/guix-cran/packages/k.scm +++ b/guix-cran/packages/k.scm @@ -4357,6 +4357,32 @@ CB, EG, SG, NEAT CE/PSE and NEC designs, supporting Gaussian, logistic and uniform kernels and unsmoothed and pre-smoothed input data.") (license (list license:gpl2 license:gpl3)))) +(define-public r-kepted + (package + (name "r-kepted") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "KEPTED" version)) + (sha256 + (base32 "1xlmmr2qy00gq6hsh1vazb9mb27hz2pjbw8chxb1p1a7d9ps0yrg")))) + (properties `((upstream-name . "KEPTED"))) + (build-system r-build-system) + (propagated-inputs (list r-expm r-cubature r-compquadform)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/tyy20/KEPTED") + (synopsis + "Kernel-Embedding-of-Probability Test for Elliptical Distribution") + (description + "This package provides an implementation of a kernel-embedding of probability +test for elliptical distribution. This is an asymptotic test for elliptical +distribution under general alternatives, and the location and shape parameters +are assumed to be unknown. Some side-products are posted, including the +transformation between rectangular and polar coordinates and two product-type +kernel functions. See Tang and Li (2024) <@code{arXiv:2306.10594>} for details.") + (license license:bsd-3))) + (define-public r-kensyn (package (name "r-kensyn") diff --git a/guix-cran/packages/l.scm b/guix-cran/packages/l.scm index a6e33b8..732caa3 100644 --- a/guix-cran/packages/l.scm +++ b/guix-cran/packages/l.scm @@ -998,13 +998,13 @@ palettes from users photos directly.") (define-public r-ltasr (package (name "r-ltasr") - (version "0.1.2") + (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "LTASR" version)) (sha256 - (base32 "1cq00w9pg4mmgsg7ydm9azr0f9hgxa7vskpfrmh90j6xixqmpn4c")))) + (base32 "1dab18np0jkb9s8lkrmsk52h0f714ry851kvbnqs2kdl3zrsrl2f")))) (properties `((upstream-name . "LTASR"))) (build-system r-build-system) (propagated-inputs (list r-zoo @@ -1018,7 +1018,7 @@ palettes from users photos directly.") r-lubridate r-knitr r-dplyr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-r-rsp r-knitr)) (home-page "https://cran.r-project.org/package=LTASR") (synopsis "Functions to Replicate the Center for Disease Control and Prevention's 'LTAS' Software in R") @@ -3972,21 +3972,26 @@ Hochreiter, S., & Schmidhuber, J. (1997) .") (define-public r-lomb (package (name "r-lomb") - (version "2.2.0") + (version "2.5.0") (source (origin (method url-fetch) (uri (cran-uri "lomb" version)) (sha256 - (base32 "0hb9ilybd9b4i0b5778b4lin899gnix2xwxlcqiy05lhb8qxzzij")))) + (base32 "1jlmdbxlxk2a1sbkzn3x18z82i0mwhjhy72j1l02qcnyxp3clbh4")))) (properties `((upstream-name . "lomb"))) (build-system r-build-system) - (propagated-inputs (list r-pracma r-plotly r-gridextra r-ggplot2)) + (propagated-inputs (list r-pracma r-plotly r-knitr r-gridextra r-ggplot2)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=lomb") (synopsis "Lomb-Scargle Periodogram") (description - "Computes the Lomb-Scargle Periodogram for unevenly sampled time series. -Includes a randomization procedure to obtain exact p-values.") + "Computes the Lomb-Scargle Periodogram and actogram for evenly or unevenly +sampled time series. Includes a randomization procedure to obtain exact +p-values. Partially based on C original by Press et al. (Numerical Recipes) and +the Python module Astropy. For more information see Ruf, T. (1999). The +Lomb-Scargle periodogram in biological rhythm research: analysis of incomplete +and unequally spaced time-series. Biological Rhythm Research, 30(2), 178-201.") (license license:gpl3+))) (define-public r-lomar @@ -6144,13 +6149,13 @@ model inference feature through simulation and games.") (define-public r-lmtp (package (name "r-lmtp") - (version "1.3.2") + (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "lmtp" version)) (sha256 - (base32 "124rahrbvrkr1mvazjwz7b42333az9sh26nml9snrcicl0ysjyzv")))) + (base32 "12vq5rail8xdw84ms6nv4ncmdygk485vffyzqc9kcc7wxlbr127i")))) (properties `((upstream-name . "lmtp"))) (build-system r-build-system) (propagated-inputs (list r-superlearner @@ -6395,36 +6400,6 @@ Rev-Gumbel [L+RC], Rice [L], Singh Maddala [L], Slash [TL], 3p Student t [L], Truncated Exponential [L], Wakeby [L], and Weibull [L].") (license (list license:gpl2+ license:gpl3+)))) -(define-public r-lmofit - (package - (name "r-lmofit") - (version "0.1.6") - (source - (origin - (method url-fetch) - (uri (cran-uri "LMoFit" version)) - (sha256 - (base32 "10xiaa5h8c0sq9z70yjs29z8jnjyqgybdv33d6s2100h3n46jd31")))) - (properties `((upstream-name . "LMoFit"))) - (build-system r-build-system) - (propagated-inputs (list r-sf r-pracma r-lmom r-ggplot2)) - (native-inputs (list r-knitr)) - (home-page "https://cran.r-project.org/package=LMoFit") - (synopsis "Advanced L-Moment Fitting of Distributions") - (description - "This package provides a complete framework for frequency analysis is provided by -L@code{MoFit}'. It has functions related to the determination of sample -L-moments as in Hosking, J.R.M. (1990) , -the fitting of various distributions as in Zaghloul et al. (2020) - and Hosking, J.R.M. (2019) -, besides plotting and manipulating -L-space diagrams as in Papalexiou, S.M. & Koutsoyiannis, D. (2016) - for two-shape parametric distributions on -the L-moment ratio diagram. Additionally, the quantile, probability density, -and cumulative probability functions of various distributions are provided in a -user-friendly manner.") - (license license:gpl3))) - (define-public r-lmn (package (name "r-lmn") @@ -11110,13 +11085,13 @@ package is heavily inspired by the (define-public r-lessr (package (name "r-lessr") - (version "4.3.0") + (version "4.3.1") (source (origin (method url-fetch) (uri (cran-uri "lessR" version)) (sha256 - (base32 "16nnnswv7d0dz4bw8fvys1i7zd6c56l419fyk9bv0k37vhdnrini")))) + (base32 "1znf4zja1gh2v6s2jja3hr9b97gl4dw2wq9yb72yrs18l7917lhv")))) (properties `((upstream-name . "lessR"))) (build-system r-build-system) (propagated-inputs (list r-shiny diff --git a/guix-cran/packages/m.scm b/guix-cran/packages/m.scm index a50dc22..908e6ad 100644 --- a/guix-cran/packages/m.scm +++ b/guix-cran/packages/m.scm @@ -10247,6 +10247,31 @@ for linear and generalised linear models.") Parameters. Modified likelihood estimates are provided.") (license license:gpl2))) +(define-public r-mpitbr + (package + (name "r-mpitbr") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "mpitbR" version)) + (sha256 + (base32 "01p82d0dzjlq3b0zyg25i7fh6l0amj55kcavcysqsjy2i0352fvb")))) + (properties `((upstream-name . "mpitbR"))) + (build-system r-build-system) + (propagated-inputs (list r-survey r-purrr)) + (home-page "https://github.com/girelaignacio/mpitbR") + (synopsis "Calculate Alkire-Foster Multidimensional Poverty Measures") + (description + "Estimate Multidimensional Poverty Indices disaggregated by population subgroups +based on the Alkire and Foster method (2011) +. This includes the calculation of standard +errors and confidence intervals. Other partial indices such as incidence, +intensity and indicator-specific measures as well as intertemporal changes +analysis can also be estimated. The standard errors and confidence intervals +are calculated considering the complex survey design.") + (license license:gpl3+))) + (define-public r-mpindex (package (name "r-mpindex") @@ -23886,13 +23911,13 @@ data.") (define-public r-migconnectivity (package (name "r-migconnectivity") - (version "0.4.6") + (version "0.4.7") (source (origin (method url-fetch) (uri (cran-uri "MigConnectivity" version)) (sha256 - (base32 "0lyqjhhnba83niv1rmgxz3f9kq022fnck3l2m27zc1lw92l6lhfv")))) + (base32 "08bzis7rkczymvr2bqiih59yn94l0fjhkn0p9lpv875pwbvhmw1j")))) (properties `((upstream-name . "MigConnectivity"))) (build-system r-build-system) (inputs (list jags)) @@ -25996,13 +26021,13 @@ Regression with spatial autocorrelation, Geniaux and Martinetti (2017) (define-public r-mgwnbr (package (name "r-mgwnbr") - (version "0.1.0") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "mgwnbr" version)) (sha256 - (base32 "0c9y3jfg1s5cvpw6yjjcq80shdx1khx799qpcvba534vgz3mkh49")))) + (base32 "0vmpvfnnq1ylsivizz888akaq74ybz890nspj40zx5wr7dv2rkz7")))) (properties `((upstream-name . "mgwnbr"))) (build-system r-build-system) (propagated-inputs (list r-sp)) @@ -26015,13 +26040,13 @@ covariate. Uses the negative binomial distribution as default, but also accepts the normal, Poisson, or logistic distributions. Can fit the global versions of each regression and also the geographically weighted alternatives with only one scale, since they are all particular cases of the multiscale approach. Hanchen -Yu (2024). Exploring Multiscale Geographically Weighted Negative Binomial -Regression, Annals of the American Association of Geographers +Yu (2024). \"Exploring Multiscale Geographically Weighted Negative Binomial +Regression\", Annals of the American Association of Geographers . Fotheringham AS, Yang W, Kang W (2017). -Multiscale Geographically Weighted Regression (MGWR), Annals of the American +\"Multiscale Geographically Weighted Regression (MGWR)\", Annals of the American Association of Geographers . Da Silva AR, -Rodrigues TCV (2014). Geographically Weighted Negative Binomial Regression - -incorporating overdispersion, Statistics and Computing +Rodrigues TCV (2014). \"Geographically Weighted Negative Binomial Regression - +incorporating overdispersion\", Statistics and Computing .") (license license:gpl3))) diff --git a/guix-cran/packages/o.scm b/guix-cran/packages/o.scm index 8ba76e9..8a857b5 100644 --- a/guix-cran/packages/o.scm +++ b/guix-cran/packages/o.scm @@ -5209,13 +5209,13 @@ Lugosi (2006) for an overview.") (define-public r-openxlsx2 (package (name "r-openxlsx2") - (version "1.4") + (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "openxlsx2" version)) (sha256 - (base32 "0hrikqbmylr0sbxq478alm290c5a8mlxwxmnhlzxvbmzfbv2ywhl")))) + (base32 "08na53jwpidxfzlqwxzc1dmf06q51ncdgz9sb1yfrw37jwp1frj7")))) (properties `((upstream-name . "openxlsx2"))) (build-system r-build-system) (propagated-inputs (list r-zip r-stringi r-rcpp r-r6 r-magrittr)) @@ -5732,39 +5732,6 @@ weather data in a tidy format. No API key is required. The API specification is located at .") (license license:gpl3+))) -(define-public r-openland - (package - (name "r-openland") - (version "1.0.2") - (source - (origin - (method url-fetch) - (uri (cran-uri "OpenLand" version)) - (sha256 - (base32 "02d1dflcbjvm9hgvsm5gpc3s0n0njf4w3224yqk9nc0i49nw01fi")))) - (properties `((upstream-name . "OpenLand"))) - (build-system r-build-system) - (propagated-inputs (list r-tidyr - r-raster - r-networkd3 - r-gridextra - r-ggplot2 - r-dplyr - r-circlize)) - (native-inputs (list r-knitr)) - (home-page "https://github.com/reginalexavier/OpenLand") - (synopsis "Quantitative Analysis and Visualization of LUCC") - (description - "This package provides tools for the analysis of land use and cover (LUC) time -series. It includes support for loading spatiotemporal raster data and -synthesized spatial plotting. Several LUC change (LUCC) metrics in regular or -irregular time intervals can be extracted and visualized through one- and -multistep sankey and chord diagrams. A complete intensity analysis according to -Aldwaik and Pontius (2012) is -implemented, including tools for the generation of standardized multilevel -output graphics.") - (license license:gpl3))) - (define-public r-openintro (package (name "r-openintro") @@ -7643,6 +7610,33 @@ custom decision criteria in early clinical trials during an ongoing trial. The inference is implemented using stan'.") (license license:asl2.0))) +(define-public r-oncofilterfast + (package + (name "r-oncofilterfast") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "Oncofilterfast" version)) + (sha256 + (base32 "1ns39r8ljzykpxy5cy4wvgsgiwqpdrida26641av7z3arr1f4kd1")))) + (properties `((upstream-name . "Oncofilterfast"))) + (build-system r-build-system) + (propagated-inputs (list r-survminer r-survival)) + (home-page "https://cran.r-project.org/package=Oncofilterfast") + (synopsis "Aids in the Analysis of Genes Influencing Cancer Survival") + (description + "Aids in the analysis of genes influencing cancer survival by including a +principal function, calculator(), which calculates the P-value for each provided +gene under the optimal cutoff in cancer survival studies. Grounded in +methodologies from significant works, this package references Therneau's +survival package (Therneau, 2024; ) +and the survival analysis extensions by Therneau and Grambsch (2000, ISBN +0-387-98784-3). It also integrates the survminer package by Kassambara et al. +(2021; ), enhancing survival curve +visualizations with ggplot2'.") + (license license:asl2.0))) + (define-public r-oncobayes2 (package (name "r-oncobayes2") @@ -9519,36 +9513,6 @@ Experimental Education. . (4) Champely, S. Available from .") (license license:gpl3))) -(define-public r-odpc - (package - (name "r-odpc") - (version "2.0.5") - (source - (origin - (method url-fetch) - (uri (cran-uri "odpc" version)) - (sha256 - (base32 "0cbkq8parb8br1j386xk5mgwz8gkmwvp79f9sjvzhs7z6wlbp0pv")))) - (properties `((upstream-name . "odpc"))) - (build-system r-build-system) - (propagated-inputs (list r-rcpparmadillo - r-rcpp - r-mass - r-forecast - r-foreach - r-doparallel)) - (home-page "https://cran.r-project.org/package=odpc") - (synopsis "One-Sided Dynamic Principal Components") - (description - "This package provides functions to compute the one-sided dynamic principal -components ('odpc') introduced in @code{Peña}, Smucler and Yohai (2019) -. odpc is a novel dimension reduction -technique for multivariate time series, that is useful for forecasting. These -dynamic principal components are defined as the linear combinations of the -present and past values of the series that minimize the reconstruction mean -squared error.") - (license license:gpl2+))) - (define-public r-odmeans (package (name "r-odmeans") @@ -10712,13 +10676,13 @@ distributions are implemented as described in O’Neill (2019) (define-public r-occumb (package (name "r-occumb") - (version "1.0.3") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "occumb" version)) (sha256 - (base32 "1gvcfhj3lhqj9y9qm3fh0f66bckv4wslpy9ri1dan96lp4qlqx2f")))) + (base32 "1rfaswipykflwkdiacq66ibbvf2hzzal2ffibsgrl8q1m6frj5k3")))) (properties `((upstream-name . "occumb"))) (build-system r-build-system) (inputs (list jags)) @@ -11453,3 +11417,32 @@ sets) (Löfstedt and Trygg, 2011 ; Löfstedt et al., 2 specific for each data set separately.") (license license:gpl3))) +(define-public r-o2geosocial + (package + (name "r-o2geosocial") + (version "1.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "o2geosocial" version)) + (sha256 + (base32 "0myzr25jjjvlszr0j5ay2nha1nrccwhgh0qd01p52xrlggfjhz1g")))) + (properties `((upstream-name . "o2geosocial"))) + (build-system r-build-system) + (propagated-inputs (list r-visnetwork + r-rcpp + r-outbreaker2 + r-ggplot2 + r-geosphere + r-data-table)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/alxsrobert/o2geosocial") + (synopsis "Reconstruction of Transmission Chains from Surveillance Data") + (description + "Bayesian reconstruction of who infected whom during past outbreaks using +routinely-collected surveillance data. Inference of transmission trees using +genotype, age specific social contacts, distance between cases and onset dates +of the reported cases. (Robert A, Kucharski AJ, Gastanaduy PA, Paul P, Funk S. +(2020) ).") + (license license:expat))) + diff --git a/guix-cran/packages/p.scm b/guix-cran/packages/p.scm index 2b499c1..2cade83 100644 --- a/guix-cran/packages/p.scm +++ b/guix-cran/packages/p.scm @@ -6806,31 +6806,6 @@ More details can be referred to Wei Liu, et al. (2023) .") (license license:gpl3))) -(define-public r-productplots - (package - (name "r-productplots") - (version "0.1.1") - (source - (origin - (method url-fetch) - (uri (cran-uri "productplots" version)) - (sha256 - (base32 "1igs6d0qwgsfk0z3vxabgv5kva9w2kpzi535gjfdrbx34j4pf3gx")))) - (properties `((upstream-name . "productplots"))) - (build-system r-build-system) - (propagated-inputs (list r-plyr r-ggplot2)) - (home-page "https://github.com/hadley/productplots") - (synopsis "Product Plots for R") - (description - "Framework for visualising tables of counts, proportions and probabilities. The -framework is called product plots, alluding to the computation of area as a -product of height and width, and the statistical concept of generating a joint -distribution from the product of conditional and marginal distributions. The -framework, with extensions, is sufficient to encompass over 20 visualisations -previously described in fields of statistical graphics and infovis', including -bar charts, mosaic plots, treemaps', equal area plots and fluctuation diagrams.") - (license license:gpl2))) - (define-public r-productivity (package (name "r-productivity") @@ -8487,13 +8462,13 @@ Data Warehouse (2020) }.") (define-public r-pricelevels (package (name "r-pricelevels") - (version "1.0.2") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "pricelevels" version)) (sha256 - (base32 "06997bxch7klpkibpszpwm2lr6kyl6fnxrphnw379hx3vac2p4zx")))) + (base32 "0g3ci22mr4faxhylyjca7bvqh6ikb0bqk0b0yl0fyv8cvhj5g3qs")))) (properties `((upstream-name . "pricelevels"))) (build-system r-build-system) (propagated-inputs (list r-minpack-lm r-data-table)) @@ -17122,6 +17097,27 @@ parsing, tabulating and plotting results generated by Perl-speaks-NONMEM pharmacometric models.") (license license:gpl3))) +(define-public r-pmxcv + (package + (name "r-pmxcv") + (version "0.0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "pmxcv" version)) + (sha256 + (base32 "0x74pjmj9335bnh2zbhidxwzq28f4a9281dhgnkbyllfq2kw2dsc")))) + (properties `((upstream-name . "pmxcv"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=pmxcv") + (synopsis "Integration-Based Coefficients of Variance") + (description + "Estimate coefficient of variance percent (CV%) for any arbitrary distribution, +including some built-in estimates for commonly-used transformations in +pharmacometrics. Methods are described in various sources, but applied here as +summarized in: Prybylski, (2024) .") + (license license:expat))) + (define-public r-pmxcode (package (name "r-pmxcode") @@ -20134,6 +20130,39 @@ in 2022 in Methods in Ecology and Evolution (Stears, et al., 2022) .") (license license:expat))) +(define-public r-plantphysior + (package + (name "r-plantphysior") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "plantphysioR" version)) + (sha256 + (base32 "15hp22b1h37dp0llbifz369rdaqzn0jl9dw07z4c4j0jnmr50h8h")))) + (properties `((upstream-name . "plantphysioR"))) + (build-system r-build-system) + (home-page "https://github.com/rameshram96/plantphysioR") + (synopsis "Fundamental Formulas for Plant Physiology") + (description + "This package provides functions tailored for scientific and student communities +involved in plant science research. Functionalities encompass estimation +chlorophyll content according to Arnon (1949) , +determination water potential of Polyethylene glycol(PEG)6000 as in Michel and +Kaufmann (1973) and functions related to estimation of +yield related indices like Abiotic tolerance index as given by Moosavi et +al.(2008), Geometric mean productivity (GMP) by +Fernandez (1992) , Golden Mean by Moradi et +al.(2012), HAM by Schneider et +al.(1997),MPI and TOL by Hossain +etal., (1990), RDI by Fischer et +al. (1979),SSI by Fisher et +al.(1978), STI by Fernandez +(1993),YSI by Bouslama & Schapaugh +(1984), Yield index by Gavuzzi et +al.(1997).") + (license license:gpl3+))) + (define-public r-plantecowrap (package (name "r-plantecowrap") diff --git a/guix-cran/packages/r.scm b/guix-cran/packages/r.scm index a8e33c8..0971615 100644 --- a/guix-cran/packages/r.scm +++ b/guix-cran/packages/r.scm @@ -1478,13 +1478,13 @@ performance.") (define-public r-rvmf (package (name "r-rvmf") - (version "0.0.8") + (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "rvMF" version)) (sha256 - (base32 "1386206s3i8a58fk3vsc7zg323hnmq5sc5p9yhcim6qbabsfnljc")))) + (base32 "0mlmkax5f86zpr1r81xvzcq874i18smh9af19jdkb70skg92jafs")))) (properties `((upstream-name . "rvMF"))) (build-system r-build-system) (propagated-inputs (list r-scmodels r-rfast r-rcpp r-bessel)) @@ -1496,7 +1496,8 @@ performance.") distribution on a sphere. This method is fast and efficient when generating a large number of pseudo-random vectors. Functions to generate random variates and compute density for the distribution of an inner product between von -Mises-Fisher random vector and its mean direction are also provided.") +Mises-Fisher random vector and its mean direction are also provided. Details +are in Kang and Oh (2024) .") (license license:gpl3+))) (define-public r-rvmethod @@ -4668,13 +4669,13 @@ summarizing model outputs. rsyncrosim requires @code{SyncroSim} 2.3.5 or higher (define-public r-rswipl (package (name "r-rswipl") - (version "9.3.3") + (version "9.3.3.1") (source (origin (method url-fetch) (uri (cran-uri "rswipl" version)) (sha256 - (base32 "1pjd6kzgzhd9rabcvp9d1qbmjrxwpp36bic48d4k0z5l8xj4qaw1")))) + (base32 "0f3p5rm33wc6vbxs3lv6p714b0jh4bb54d25cjyaq97zi38nczq5")))) (properties `((upstream-name . "rswipl"))) (build-system r-build-system) (arguments @@ -4938,24 +4939,24 @@ numbers from different sources.") (define-public r-rstrava (package (name "r-rstrava") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "rStrava" version)) (sha256 - (base32 "0k2nz17s4rlb86gmr0c4r56abw4j7dqshjk599kqy28jqmf2nkyy")))) + (base32 "1kn2x208iyz235zf64r2wz4jqgas5srzzjf6gpckqh8dkc6s234f")))) (properties `((upstream-name . "rStrava"))) (build-system r-build-system) (propagated-inputs (list r-xml2 r-xml + r-tidyterra r-tidyr r-tibble r-rvest r-rcurl r-purrr - r-prettymapr - r-plyr + r-maptiles r-magrittr r-httr r-googleway @@ -22948,13 +22949,13 @@ Reference Interval Estimation\". Clinical Chemistry (2022) (define-public r-ribd (package (name "r-ribd") - (version "1.6.1") + (version "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "ribd" version)) (sha256 - (base32 "1pzkbazm5mcr05ib2x0cs8aa7jk96k9nhkish96awjd2ihq6c019")))) + (base32 "1g378kpi6660176d64r84kw8zk662sai83r33ayjxbfn6w8s48xy")))) (properties `((upstream-name . "ribd"))) (build-system r-build-system) (propagated-inputs (list r-slam r-pedtools r-kinship2 r-glue)) @@ -22967,11 +22968,10 @@ coefficients are computed. Founders are allowed to be inbred, which enables construction of any given kappa coefficients, as described in Vigeland (2020) . In addition to the standard coefficients, ribd also computes a range of lesser-known coefficients, including generalised -kinship coefficients (Karigl (1981) ; -Weeks and Lange (1988) ), two-locus -coefficients (Thompson (1988) ) and multi-person -coefficients. Many features of ribd are available through the online app -@code{QuickPed} at ; see Vigeland (2022) +kinship coefficients, multi-person coefficients and two-locus coefficients +(Vigeland, 2023, ). Many features of ribd are +available through the online app @code{QuickPed} at +; see Vigeland (2022) .") (license license:gpl3))) @@ -27410,13 +27410,13 @@ large datasets.") (define-public r-restatapi (package (name "r-restatapi") - (version "0.22.5") + (version "0.23.1") (source (origin (method url-fetch) (uri (cran-uri "restatapi" version)) (sha256 - (base32 "1vaj20z45y3af1k38fqcxxkpn4fb8arwgm0q5jnf3shfq6ddnzyh")))) + (base32 "0sbyy35c7klwb9j99krmfr2hww16n51qmw1xdif32kmdq9sjiqdc")))) (properties `((upstream-name . "restatapi"))) (build-system r-build-system) (propagated-inputs (list r-xml2 r-rjson r-data-table)) @@ -29956,6 +29956,37 @@ in part by NSF IIS-0948893 and R21HG005912 from the National Human Genome Research Institute. Hahsler and Dunham (2010) .") (license license:gpl2))) +(define-public r-remla + (package + (name "r-remla") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "REMLA" version)) + (sha256 + (base32 "1s3ymb58nn8rci9dzdfwcl23h2fhnjv6531wv9vihdmyxn6vijjd")))) + (properties `((upstream-name . "REMLA"))) + (build-system r-build-system) + (propagated-inputs (list r-gparotation r-geex)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/knieser/REM") + (synopsis + "Robust Expectation-Maximization Estimation for Latent Variable Models") + (description + "Traditional latent variable models assume that the population is homogeneous, +meaning that all individuals in the population are assumed to have the same +latent structure. However, this assumption is often violated in practice given +that individuals may differ in their age, gender, socioeconomic status, and +other factors that can affect their latent structure. The robust expectation +maximization (REM) algorithm is a statistical method for estimating the +parameters of a latent variable model in the presence of population +heterogeneity as recommended by Nieser & Cochran (2023) +. The REM algorithm is based on the +expectation-maximization (EM) algorithm, but it allows for the case when all the +data are generated by the assumed data generating model.") + (license license:gpl3+))) + (define-public r-remiod (package (name "r-remiod") @@ -45311,6 +45342,38 @@ or full output is also available as well as a parameter to print Fit Statistics Parallel Analysis. Also weighted correlation matrices may be considered for PA.") (license license:gpl2+))) +(define-public r-random-cdisc-data + (package + (name "r-random-cdisc-data") + (version "0.3.15") + (source + (origin + (method url-fetch) + (uri (cran-uri "random.cdisc.data" version)) + (sha256 + (base32 "05hq7hvypc4nm72f879pjyf2iyvj9hgrr1gwjyvwj8by7pkyyw2y")))) + (properties `((upstream-name . "random.cdisc.data"))) + (build-system r-build-system) + (propagated-inputs (list r-yaml + r-tidyr + r-tibble + r-stringr + r-rlang + r-magrittr + r-lubridate + r-lifecycle + r-dplyr + r-checkmate)) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=random.cdisc.data") + (synopsis "Create Random ADaM Datasets") + (description + "This package provides a set of functions to create random Analysis Data Model +(A@code{DaM}) datasets and cached dataset. A@code{DaM} dataset specifications +are described by the Clinical Data Interchange Standards Consortium (CDISC) +Analysis Data Model Team.") + (license license:asl2.0))) + (define-public r-random (package (name "r-random") @@ -47309,52 +47372,6 @@ lost, the entire identity of the animal can be reconstructed. Thus, animal subjects are not confused and no ambiguity is introduced.") (license license:gpl3))) -(define-public r-rabhit - (package - (name "r-rabhit") - (version "0.2.5") - (source - (origin - (method url-fetch) - (uri (cran-uri "rabhit" version)) - (sha256 - (base32 "0c513sbldd85snww412k3c5rhmzd5k89s2wq4d713qsvzsh4v1xl")))) - (properties `((upstream-name . "rabhit"))) - (build-system r-build-system) - (propagated-inputs (list r-tigger - r-tidyr - r-stringi - r-splitstackshape - r-rlang - r-reshape2 - r-readr - r-rcolorbrewer - r-plyr - r-plotly - r-htmlwidgets - r-gtools - r-gtable - r-gridextra - r-ggplot2 - r-ggdendro - r-fastmatch - r-dplyr - r-dendextend - r-data-table - r-cowplot - r-alakazam)) - (native-inputs (list r-knitr)) - (home-page "https://yaarilab.bitbucket.io/RAbHIT/") - (synopsis "Inference Tool for Antibody Haplotype") - (description - "This package infers V-D-J haplotypes and gene deletions from AIRR-seq data for -Ig and TR chains, based on J, D, or V genes as anchor, by adapting a Bayesian -framework. It also calculates a Bayes factor, a number that indicates the -certainty level of the inference, for each haplotyped gene. Citation: Gidoni, -et al (2019) . Peres and Gidoni, et al (2019) -.") - (license license:cc-by-sa4.0))) - (define-public r-ra4bayesmeta (package (name "r-ra4bayesmeta") @@ -48572,13 +48589,13 @@ development and use of PACTA in R.") (define-public r-r2dii-analysis (package (name "r-r2dii-analysis") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "r2dii.analysis" version)) (sha256 - (base32 "11bhhwigybrcr8nbrdwbv6a9rk944la5apnn5y3ahvr457jqdjsv")))) + (base32 "02rawyr3z0zg2yhc04mdnjkwrczwwv2822vphwyv3vwwlayjy3fh")))) (properties `((upstream-name . "r2dii.analysis"))) (build-system r-build-system) (propagated-inputs (list r-zoo diff --git a/guix-cran/packages/s.scm b/guix-cran/packages/s.scm index 7f75b5f..307a148 100644 --- a/guix-cran/packages/s.scm +++ b/guix-cran/packages/s.scm @@ -2014,6 +2014,35 @@ formats as well as other swatch file formats can be found at .") (license license:expat))) +(define-public r-swarmverse + (package + (name "r-swarmverse") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "swaRmverse" version)) + (sha256 + (base32 "1z14ys2y42griwbwcjilk552haczlfbazjzwa5g6kvlxjibm1dq0")))) + (properties `((upstream-name . "swaRmverse"))) + (build-system r-build-system) + (propagated-inputs (list r-trackdf r-swarm r-rtsne r-pbapply r-geosphere)) + (native-inputs (list r-knitr)) + (home-page "https://marinapapa.github.io/swaRmverse/") + (synopsis "Swarm Space Creation") + (description + "This package provides a pipeline for the comparative analysis of collective +movement data (e.g. fish schools, bird flocks, baboon troops) by processing +2-dimensional positional data (x,y,t) from GPS trackers or computer vision +tracking systems, discretizing events of collective motion, calculating a set of +established metrics that characterize each event, and placing the events in a +multi-dimensional swarm space constructed from these metrics. The swarm space +concept, the metrics and data sets included are described in: Papadopoulou +Marina, Furtbauer Ines, O'Bryan Lisa R., Garnier Simon, Georgopoulou Dimitra G., +Bracken Anna M., Christensen Charlotte and King Andrew J. (2023) +.") + (license license:gpl3))) + (define-public r-swarm (package (name "r-swarm") @@ -17539,47 +17568,6 @@ discipline (Hankin, 2022, ). To cite the package in publications please use Hankin (2022) .") (license license:gpl2+))) -(define-public r-spqdep - (package - (name "r-spqdep") - (version "0.1.3.2") - (source - (origin - (method url-fetch) - (uri (cran-uri "spqdep" version)) - (sha256 - (base32 "03lzp368ylkf1hrnl00kndlkmp9lwma0j9w9b3hn5glzdljhalxl")))) - (properties `((upstream-name . "spqdep"))) - (build-system r-build-system) - (propagated-inputs (list r-tidyr - r-spdep - r-spatialreg - r-sp - r-sf - r-rsample - r-rgeoda - r-purrr - r-matrix - r-magrittr - r-lwgeom - r-igraph - r-gtools - r-gt - r-gridextra - r-ggplot2 - r-dplyr - r-broom)) - (native-inputs (list r-knitr)) - (home-page "https://f8l5h9.github.io/spqdep/") - (synopsis - "Testing for Spatial Independence of Qualitative Data in Cross Section") - (description - "Testing for Spatial Dependence of Qualitative Data in Cross Section. The list -of functions includes join-count tests, Q test, spatial scan test, similarity -test and spatial runs test. The methodology of these models can be found in - and .") - (license license:expat))) - (define-public r-sppop (package (name "r-sppop") @@ -17657,37 +17645,6 @@ potential outliers. Multiple groups can be compared in terms of centers and spreads as illustrated in the examples.") (license license:gpl3))) -(define-public r-spotsampling - (package - (name "r-spotsampling") - (version "0.1.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "SpotSampling" version)) - (sha256 - (base32 "0s47dvigzkcl9ynrdiwrjzwap18dpkb29jngi8ddvf9m4xywj4al")))) - (properties `((upstream-name . "SpotSampling"))) - (build-system r-build-system) - (propagated-inputs (list r-wavesampling r-sampling r-pracma r-mass - r-balancedsampling)) - (home-page "https://cran.r-project.org/package=SpotSampling") - (synopsis "SPatial and Optimally Temporal (SPOT) Sampling") - (description - "In spatial data, information of two neighboring units are generally very -similar. For spatial sampling, it is therefore more efficient to select samples -that are well spread out in space. Often, the interest lies not only in -estimating a measure at one point in time, but rather in estimating several -points in time to also study the evolution. Three new methods called Orfs -(Optimal Rotation with Fixed sample Size), Orsp (Optimal Rotation with Spread -sample), and Spot (Spatial and Optimally Temporal Sampling) are implemented in -this package. Orfs allows to select temporal samples with fixed size. Orsp -selects spatio-temporal samples with random size that are well spread out in -space at each point in time. And Spot generates spread sample with fixed sample -size at each wave. These methods provide an optimal time rotation of the -selected units using the systematic sampling.") - (license license:gpl2+))) - (define-public r-spotoroo (package (name "r-spotoroo") @@ -26477,13 +26434,13 @@ missing values and is delivered with a graphical user interface based on shiny'. (define-public r-somadataio (package (name "r-somadataio") - (version "6.0.0") + (version "6.1.0") (source (origin (method url-fetch) (uri (cran-uri "SomaDataIO" version)) (sha256 - (base32 "1ld0icylfj9nsdacm3dc7p4q6ysah393njcjxzj0zyp077k014nz")))) + (base32 "1r9hb804gjzqn0y91kyc4ays7x3pqxknsbz0b3gy2kkldkhb60c1")))) (properties `((upstream-name . "SomaDataIO"))) (build-system r-build-system) (propagated-inputs (list r-usethis @@ -26500,7 +26457,7 @@ missing values and is delivered with a graphical user interface based on shiny'. (synopsis "Input/Output 'SomaScan' Data") (description "Load and export @code{SomaScan} data via the @code{SomaLogic} Operating Co., -Inc. proprietary text file called an ADAT ('*.adat'). For file format see +Inc. structured text file called an ADAT ('*.adat'). For file format see }. The package also exports auxiliary functions for manipulating, wrangling, and extracting relevant information from an ADAT object once in memory.") @@ -45768,17 +45725,17 @@ Hypermutation; Biorxiv 2018 .") (define-public r-seqimpute (package (name "r-seqimpute") - (version "1.8") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "seqimpute" version)) (sha256 - (base32 "1vivs790zbwm8c7fwifz0nj0n9wzjmr8whz0f4pwp44gvcickxwn")))) + (base32 "1g60drnx12j6wzkisxlmhidvqzzgsrmmmmp8dljq94bb5iv8xjmz")))) (properties `((upstream-name . "seqimpute"))) (build-system r-build-system) - (propagated-inputs (list r-traminer - r-swfscmisc + (propagated-inputs (list r-traminerextras + r-traminer r-stringr r-rms r-ranger @@ -45793,12 +45750,13 @@ Hypermutation; Biorxiv 2018 .") r-dfidx r-cluster r-amelia)) + (native-inputs (list r-r-rsp)) (home-page "https://cran.r-project.org/package=seqimpute") (synopsis "Imputation of Missing Data in Sequence Analysis") (description "Multiple imputation of missing data present in a dataset through the prediction based on either a random forest or a multinomial regression model. Covariates -and time-dependant covariates can be included in the model. The prediction of +and time-dependent covariates can be included in the model. The prediction of the missing values is based on the method of Halpin (2012) .") (license license:gpl2))) @@ -48541,28 +48499,30 @@ evaluating the candidates in each stage.") (define-public r-selectionbias (package (name "r-selectionbias") - (version "1.0.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "SelectionBias" version)) (sha256 - (base32 "1lqpa5yyxipnx31r0gmja59dk85gmpg9j1rzpc9vh0lq3l87878b")))) + (base32 "00fk3ljm3x1slffni6g4j61s2766znlmamg16vmbkfjmrbb80nfy")))) (properties `((upstream-name . "SelectionBias"))) (build-system r-build-system) - (propagated-inputs (list r-arm)) + (propagated-inputs (list r-lifecycle r-arm)) (native-inputs (list r-knitr)) - (home-page "https://cran.r-project.org/package=SelectionBias") + (home-page "https://github.com/stizet/SelectionBias") (synopsis "Calculates Bounds for the Selection Bias for Binary Treatment and Outcome Variables") (description "Computes bounds and sensitivity parameters as part of sensitivity analysis for -selection bias. Two bounds are provided: the SV (Smith and @code{VanderWeele}) -bound and the AF (assumption-free) bound. The SV bound assumes an additional -dependence structure in form of a generalized M-structure whereas the AF bound -holds for general assumptions in the potential outcomes framework. See Smith -and @code{VanderWeele} (2019) and Zetterstrom -and Waernbaum (2022) .") +selection bias. Different bounds are provided: the SV (Smith and +@code{VanderWeele}), AF (assumption-free) bound, GAF (generalized AF), and CAF +(counterfactual AF) bounds. The calculation of the sensitivity parameters for +the SV and GAF bounds assume an additional dependence structure in form of a +generalized M-structure. The bounds can be calculated for any structure as long +as the necessary assumptions hold. See Smith and @code{VanderWeele} (2019) +, Zetterstrom and Waernbaum (2022) + and Zetterstrom (2024) .") (license license:expat))) (define-public r-selection-index @@ -55637,6 +55597,32 @@ complex survey option. In such cases, the model estimator in Mplus defaults to ML with robust standard errors.") (license license:expat))) +(define-public r-sbrl + (package + (name "r-sbrl") + (version "1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "sbrl" version)) + (sha256 + (base32 "0waq58bhbfs5g3p2gb888lcsq7h3r3h8llrs5zyhi6529g36y765")))) + (properties `((upstream-name . "sbrl"))) + (build-system r-build-system) + (inputs (list gsl gsl gmp)) + (propagated-inputs (list r-rcpp r-arules)) + (home-page "https://cran.r-project.org/package=sbrl") + (synopsis "Scalable Bayesian Rule Lists Model") + (description + "An efficient implementation of Scalable Bayesian Rule Lists Algorithm, a +competitor algorithm for decision tree algorithms; see Hongyu Yang, Cynthia +Rudin, Margo Seltzer (2017) . +It builds from pre-mined association rules and have a logical structure +identical to a decision list or one-sided decision tree. Fully optimized over +rule lists, this algorithm strikes practical balance between accuracy, +interpretability, and computational speed.") + (license license:gpl2+))) + (define-public r-sboost (package (name "r-sboost") @@ -56805,13 +56791,13 @@ Quarto Website.") (define-public r-sarima (package (name "r-sarima") - (version "0.9.2") + (version "0.9.3") (source (origin (method url-fetch) (uri (cran-uri "sarima" version)) (sha256 - (base32 "0zya0qpqvyiyq9lv8y2kcyd3v0hqw8n3chlqn2v24pyiq94h7kqg")))) + (base32 "0x6wndy7mdmnliabrbs9qbpm7ibf2h7s3m4d90pasna6hw11yg3d")))) (properties `((upstream-name . "sarima"))) (build-system r-build-system) (propagated-inputs (list r-rdpack @@ -56834,10 +56820,7 @@ documentation and vignettes for the current functionality. Function sarima() fits extended multiplicative seasonal ARIMA models with trends, exogenous variables and arbitrary roots on the unit circle, which can be fixed or estimated (for the algebraic basis for this see <@code{arXiv:2208.05055>}, a -paper on the methodology is being prepared). The suggested package -@code{FitARMA} can be installed with -remotes::install_github(\"cran/@code{FitARMA}\") if necessary but is no longer -needed in normal use.") +paper on the methodology is being prepared).") (license license:gpl2+))) (define-public r-sara4r diff --git a/guix-cran/packages/t.scm b/guix-cran/packages/t.scm index 0acfae7..bc9581e 100644 --- a/guix-cran/packages/t.scm +++ b/guix-cran/packages/t.scm @@ -7551,13 +7551,13 @@ running the vignette, install fwelnet from @code{GitHub} (define-public r-transport (package (name "r-transport") - (version "0.14-7") + (version "0.15-0") (source (origin (method url-fetch) (uri (cran-uri "transport" version)) (sha256 - (base32 "05l7slph5as2kzxv1s81v7pjc83w8ak7d8cxndc2pqny14sx07n0")))) + (base32 "0a9qych4qrdw6vcribsmzxbi2pd8pyqvagdbdzz8cma5xkddbaca")))) (properties `((upstream-name . "transport"))) (build-system r-build-system) (propagated-inputs (list r-rcppeigen r-rcpp r-data-table)) @@ -12425,13 +12425,13 @@ series, which are compatible with FAME frequencies.") (define-public r-tipsae (package (name "r-tipsae") - (version "0.0.18") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "tipsae" version)) (sha256 - (base32 "0w7ig4p23zgsn8q95cx6l031yz8kd1dk8jmzw5sf7b2b5snxlhvd")))) + (base32 "00m6frq9dkjazqh82zg5kh7snsd5gl705fk7v1idaxvm8d9gjli7")))) (properties `((upstream-name . "tipsae"))) (build-system r-build-system) (propagated-inputs (list r-stanheaders @@ -12458,7 +12458,8 @@ extensions (Janicki 2020 ). Such methods, developed within a Bayesian framework through Stan , come equipped with a set of diagnostics and complementary tools, visualizing and exporting functions. A Shiny application with a user-friendly interface can be -launched to further simplify the process.") +launched to further simplify the process. For further details, refer to De +@code{Nicolò} and Gardini (2024 ).") (license license:gpl3))) (define-public r-tips diff --git a/guix-cran/packages/v.scm b/guix-cran/packages/v.scm index 5ffa006..b97810d 100644 --- a/guix-cran/packages/v.scm +++ b/guix-cran/packages/v.scm @@ -14,11 +14,11 @@ #:use-module (gnu packages geo) #:use-module (gnu packages compression) #:use-module (gnu packages gcc) - #:use-module (gnu packages bioinformatics) - #:use-module (gnu packages perl) #:use-module (gnu packages curl) #:use-module (gnu packages ssh) #:use-module (gnu packages tls) + #:use-module (gnu packages bioinformatics) + #:use-module (gnu packages perl) #:use-module (gnu packages pcre) #:use-module (guix-cran packages z) #:use-module (guix-cran packages y) @@ -2112,33 +2112,6 @@ residue type, and potential changes to protein structures. Based on Stoeckle and Kerr (2012) .") (license license:gpl3+))) -(define-public r-vlda - (package - (name "r-vlda") - (version "1.1.5") - (source - (origin - (method url-fetch) - (uri (cran-uri "vlda" version)) - (sha256 - (base32 "17xn8qqh043dm05ib3h4l1qx07wxncf5d06x9l1wl6jbkvnsm2nq")))) - (properties `((upstream-name . "vlda"))) - (build-system r-build-system) - (propagated-inputs (list r-ggsci r-ggrepel r-ggplot2 r-ggiraph r-dplyr)) - (home-page "https://github.com/pnuwon/vlda") - (synopsis "Visualization of Multidimensional Longitudinal Data") - (description - "Assists in producing a plot that more effectively expresses changes over time -for two different types (long format and wide format) using a consistent calling -scheme for longitudinal data. It provides the ability to projection -supplementary information (supplementary objects and variables) that can often -occur in longitudinal data to graphs, as well as provides a new interactive -implementation to perform the additional interpretation, so it is also useful -for longitudinal data visuals analysis (see - -for more information).") - (license license:expat))) - (define-public r-vkr (package (name "r-vkr") @@ -5855,6 +5828,31 @@ requests in the same cassette use a cached HTTP response.") (description "Method to perform penalized variance component analysis.") (license license:gpl3+))) +(define-public r-vcpb + (package + (name "r-vcpb") + (version "1.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "vcPB" version)) + (sha256 + (base32 "11dn0l1w46shw4dqkwad5y91hfs9crkwrj6d1l4n9sc3f71b3zxq")))) + (properties `((upstream-name . "vcPB"))) + (build-system r-build-system) + (propagated-inputs (list r-rlist r-lme4 r-kernsmooth)) + (home-page "https://github.com/SangkyuStat/vcPB") + (synopsis "Longitudinal PB Varying-Coefficient Groupwise Disparity Model") + (description + "Estimating the disparity between two groups based on the extended model of the +Peters-Belson (PB) method. Our model is the first work on the longitudinal +data, and also can set a varying variable to find the complicated association +between other variables and the varying variable. Our work is an extension of +the Peters-Belson method which was originally published in Peters +(1941) and Belson +(1956).") + (license license:gpl3))) + (define-public r-vcov (package (name "r-vcov") @@ -5903,6 +5901,32 @@ meta-analysis methods. For details see: Statistical Methods for Psychologists, Volume 5, .") (license license:gpl3))) +(define-public r-vcfppr + (package + (name "r-vcfppr") + (version "0.4.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "vcfppR" version)) + (sha256 + (base32 "0j8z3njmwhdkyhj1h1zh6ckrcx3hiajd1rpqd9w2d26717qlgp2l")))) + (properties `((upstream-name . "vcfppR"))) + (build-system r-build-system) + (inputs (list zlib openssl openssh curl)) + (propagated-inputs (list r-rcpp)) + (native-inputs (list pkg-config)) + (home-page "https://github.com/Zilong-Li/vcfppR") + (synopsis "Rapid Manipulation of the Variant Call Format (VCF)") + (description + "The vcfpp.h () provides an easy-to-use C++ +API of htslib', offering full functionality for manipulating Variant Call Format +(VCF) files. The @code{vcfppR} package serves as the R bindings of the vcfpp.h +library, enabling rapid processing of both compressed and uncompressed VCF +files. Explore a range of powerful features for efficient VCF data +manipulation.") + (license license:expat))) + (define-public r-vcdextra (package (name "r-vcdextra")