{ "_id": "6ac23b46d743750d376d72d1", "Package": "BreedingExperiment", "Title": "Container and Relationship Matrices for Breeding and\nQuantitative Genomics", "Version": "0.99.4", "Authors@R": "person(\"Muhammad\", \"Farooqi\", email = \"mqfarooqi@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-4918-9791\"))", "Description": "Provides the BreedingExperiment class, a container that\nkeeps marker genotypes, phenotypes, pedigree and marker\ncoordinates together in one object, extending\nRangedSummarizedExperiment so that markers are addressable as\ngenomic ranges. Relationship matrices central to quantitative\ngenetics are computed as methods on the container: the pedigree\nnumerator relationship matrix of Henderson (1976)\n, the genomic relationship matrix of\nVanRaden (2008) , the dominance\nrelationship matrix of Vitezica, Varona and Legarra (2013)\n, and the single-step matrix\ncombining pedigree and genomic information of Legarra, Aguilar\nand Misztal (2009) and Christensen\nand Lund (2010) , which allows\ngenotyped and ungenotyped individuals to be analysed together\nas in Aguilar and others (2010) .\nMarker quality control, imputation, inbreeding coefficients and\nallele frequency summaries are included.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Language": "en-GB", "VignetteBuilder": "knitr", "biocViews": "Software, Genetics, SNP, GenomicVariation,\nDataRepresentation, Infrastructure, Regression, QualityControl", "URL": "https://github.com/mqfarooqi1/BreedingExperiment,\nhttps://mqfarooqi1.github.io/BreedingExperiment/", "BugReports": "https://github.com/mqfarooqi1/BreedingExperiment/issues", "Config/testthat/edition": "3", "Roxygen": "list(markdown = TRUE)", "Collate": "'AllClasses.R' 'AllGenerics.R' 'BreedingExperiment-package.R'\n'constructor.R' 'accessors.R' 'pedigree.R' 'relationship.R'\n'singlestep.R' 'qc.R' 'simulate.R' 'data.R' 'show.R'", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://mqfarooqi1.r-universe.dev", "Date/Publication": "2026-09-04 14:58:11 UTC", "RemoteUrl": "https://github.com/mqfarooqi1/BreedingExperiment", "RemoteRef": "HEAD", "RemoteSha": "c9e013ff73c2fe2b88ae22b5c0f6868393422a43", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-04 11:36:02 UTC", "User": "root" }, "Author": "Muhammad Farooqi [aut, cre] (ORCID:\n)", "Maintainer": "Muhammad Farooqi ", "_user": "mqfarooqi1", "_type": "src", "_file": "BreedingExperiment_0.99.4.tar.gz", "_fileid": 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of that section is kept and the heading renamed to Correctness, since\nwhat remains is a substantive claim about the package rather than about how it\nwas written: every method is an established published technique cited where it\nis implemented, and the relationship matrices are checked against values that\nfollow from theory rather than against a previous run.\n\nNothing about the built package changes beyond that heading: 81 tests pass, the\ntarball builds, it installs, and all 17 help pages are present.\n", "time": 1788533891 }, "_maintainer": { "name": "Muhammad Farooqi", "email": "mqfarooqi@gmail.com", "login": "mqfarooqi1", "linkedin": "in/muhammad-q-farooqi-609636120", "orcid": "0000-0003-4918-9791", "description": "", "uuid": 147016782 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "SummarizedExperiment", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": 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