{ "_id": "6a16a87cacfb0bcc41d8367a", "Package": "MoBPS", "Type": "Package", "Title": "Modular Breeding Program Simulator", "Version": "1.13.1", "Authors@R": "c(\nperson(given = \"Torsten\", family = \"Pook\", role = c(\"aut\", \"cre\"),\nemail = \"torsten.pook@wur.nl\", comment = c(ORCID = \"0000-0001-7874-8500\")),\nperson(given = \"Johannes\", family = \"Geibel\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7172-3263\")),\nperson(given = \"Azadeh\", family = \"Hassanpour\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1976-3457\")),\nperson(given = \"Tobias\", family = \"Niehoff\", role = \"ctb\", comment = c(ORCID = \"0000-0003-3046-6699\")))", "Maintainer": "Torsten Pook ", "Description": "Framework for the simulation framework for the simulation\nof complex breeding programs and compare their economic and\ngenetic impact. Associated publication: Pook et al. (2020)\n.", "License": "GPL (>= 3)", "LazyData": "TRUE", "SystemRequirements": "MiXBLUP (optional; used for multi-trait genomic\nevaluations); blupf90-family (optional; used for multi-trait\ngenomic evaluations)", "Additional_repositories": "https://tpook92.github.io/drat/", "RoxygenNote": "7.3.2", "Date": "2025-10-28", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-27 08:07:03 UTC", "User": "root" }, "Author": "Torsten Pook [aut, cre] (ORCID:\n), Johannes Geibel [ctb]\n(ORCID: ), Azadeh\nHassanpour [ctb] (ORCID:\n), Tobias Niehoff [ctb]\n(ORCID: )", "Repository": "https://tpook92.r-universe.dev", "Date/Publication": "2025-10-29 14:41:34 UTC", "RemoteUrl": "https://github.com/cran/MoBPS", "RemoteRef": "HEAD", "RemoteSha": "133a18bddfa50848ebd3a81b466bf314851dba69", "MD5sum": "6cb602afb31f32cd71cede237e117007", "_user": "tpook92", "_type": "src", "_file": "MoBPS_1.13.1.tar.gz", "_fileid": "817247384cb9897ecaa836eaec649be93ba4d14196368ecd08cf4031ee7ea255", "_filesize": 831863, "_sha256": "817247384cb9897ecaa836eaec649be93ba4d14196368ecd08cf4031ee7ea255", "_created": "2026-05-27T08:07:03.000Z", "_published": "2026-05-27T08:17:00.531Z", "_distro": "noble", "_jobs": [ { "job": 78034560377, "time": 453, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7235318180" }, { "job": 78034560298, "time": 473, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7235324321" }, { "job": 78034560362, "time": 406, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7235287954" }, { "job": 78034560398, "time": 328, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7235266765" }, { "job": 78033787621, "time": 290, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7235168672" }, { "job": 78034560282, "time": 325, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7235277681" }, { "job": 78034560357, "time": 443, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7235314820" }, { "job": 78034560321, "time": 383, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7235297516" }, { "job": 78034560280, "time": 383, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7235296682" } ], "_buildurl": "https://github.com/r-universe/tpook92/actions/runs/26498838583", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/MoBPS", "_commit": { "id": "133a18bddfa50848ebd3a81b466bf314851dba69", "author": "Torsten Pook ", "committer": "cran-robot ", "message": "version 1.13.1\n", "time": 1761748894 }, "_maintainer": { "name": "Torsten Pook", "email": "torsten.pook@wur.nl", "login": "tpook92", "orcid": "0000-0001-7874-8500", "description": "", "uuid": 38560663 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0", "role": "Depends" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "EMMREML", "role": "Suggests" }, { "package": "BGLR", "role": "Suggests" }, { "package": "MASS", "role": "Suggests" }, { "package": "doMPI", "role": "Suggests" }, { "package": "doRNG", "role": "Suggests" }, { "package": "compiler", "role": "Suggests" }, { "package": "foreach", "role": "Suggests" }, { "package": "sommer", "role": "Suggests" }, { "package": "vcfR", "role": "Suggests" }, { "package": "jsonlite", "role": "Suggests" }, { "package": "rrBLUP", "role": "Suggests" }, { "package": "biomaRt", "role": "Suggests" }, { "package": "Matrix", "role": "Suggests" }, { "package": "doParallel", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "optiSel", "role": "Suggests" }, { "package": "alstructure", "role": "Suggests" }, { "package": "NAM", "role": "Suggests" }, { "package": "gplots", "role": "Suggests" }, { "package": "phylogram", "role": "Suggests" }, { "package": "cPCG", "role": "Suggests" }, { "package": "VariantAnnotation", "role": "Suggests" }, { "package": "GenomicRanges", "role": "Suggests" }, { "package": "IRanges", "role": "Suggests" }, { "package": "MatrixGenerics", "role": "Suggests" }, { "package": "Rsamtools", "role": "Suggests" }, { "package": "visPedigree", "role": "Suggests" }, { "package": "data.table", "role": "Suggests" }, { "package": "methods", "role": "Suggests" }, { "package": "genio", "role": "Suggests" }, { "package": "miraculix", "version": ">= 0.9.10", "role": "Enhances" }, { "package": "RandomFieldsUtils", "version": ">= 0.5.9", "role": "Enhances" }, { "package": "MoBPSmaps", "role": "Enhances" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 1 } ], "_tags": [ { "name": "1.13.1", "date": "2025-10-29" } ], "_stars": 0, "_contributors": [ { "user": "tpook92", "count": 4, "uuid": 38560663 } ], "_userbio": { "uuid": 38560663, "type": "user", "name": "Torsten Pook" }, "_downloads": { "count": 233, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/MoBPS" }, "_mentions": 5, "_searchresults": 54, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MoBPS.html", "manual.pdf" ], "_realowner": "tpook92", "_cranurl": false, "_releases": [ { "version": "1.4.87", "date": "2020-03-28" }, { "version": "1.6.54", "date": "2021-08-23" }, { "version": "1.6.64", "date": "2021-11-09" }, { "version": "1.13.1", "date": "2025-10-29" } ], "_exports": [ "add.array", "add.combi", "add.diag", "add.diversity", "add.fixed.effects", "add.founder.kinship", "analyze.bv", "analyze.population", "breeding.diploid", "breeding.intern", "breeding.intern1", "breeding.intern2", "breeding.intern3", "breeding.intern4", "breeding.intern5", "breeding.intern6", "breeding.intern7", "breeding.intern8", "bv.development", "bv.development.box", "bv.standardization", "calculate.bv", "check.parents", "clean.up", "codeOriginsR", "combine.traits", "computing.costs", "computing.costs.cohorts", "computing.snps", "creating.diploid", "creating.phenotypic.transform", "creating.trait", "decodeOriginsR", "demiraculix", "derive.loop.elements", "diag.mobps", "effect.estimate.add", "exist.cohort", "founder.simulation", "get.admixture", "get.age.point", "get.allele.freq", "get.bv", "get.bve", "get.class", "get.cohorts", "get.cohorts.individual", "get.computing.time", "get.creating.type", "get.culling.time", "get.culling.type", "get.cullingtime", "get.database", "get.death.point", "get.dendrogram", "get.dendrogram.heatmap", "get.dendrogram.trait", "get.distance", "get.effect.freq", "get.effective.size", "get.fixed.effects.p", "get.geno", "get.geno.time", "get.genotyped", "get.genotyped.snp", "get.haplo", "get.id", "get.index", "get.infos", "get.is.first", "get.is.last", "get.litter", "get.litter.effect", "get.maf", "get.map", "get.ngen", "get.nindi", "get.npheno", "get.ntrait", "get.pca", "get.pedigree", "get.pedigree_old", "get.pedigree.visual", "get.pedigree2", "get.pedigree3", "get.pedmap", "get.pen", "get.pen.effect", "get.pheno", "get.pheno.off", "get.pheno.off.count", "get.pheno.single", "get.pheno.time", "get.phylogenetic.tree", "get.plink", "get.pool", "get.pool.founder", "get.qtl", "get.qtl.effects", "get.qtl.variance", "get.recombi", "get.reliability", "get.selectionbve", "get.selectionindex", "get.sex", "get.size", "get.snapshot", "get.snapshot.single", "get.time.point", "get.trafo.p", "get.trafo.p.single", "get.trait.name", "get.uhat", "get.variance", "get.variance.components", "get.vcf", "group.diff", "inbreeding.emp", "inbreeding.exp", "insert.bv", "insert.bve", "insert.pheno", "insert.pheno.single", "json.simulation", "kinship.development", "kinship.emp", "kinship.emp.fast", "kinship.emp.fast.between", "kinship.exp", "ld.decay", "matrix.posdef", "merging.cohorts", "merging.trait", "miraculix", "mutation.intro", "new.base.generation", "ogc.mobps", "optimize.cores", "pedigree.matrix", "pedigree.simulation", "recalculate.bv", "recalculate.manual", "recombination.function.haldane", "renaming.cohort", "rowMedian", "set.age.point", "set.class", "set.default", "set.mean.pool", "set.time.point", "sortd", "vlist" ], "_datasets": [ { "name": "cattle_chip", "title": "Cattle chip", "object": "cattle_chip", "class": [ "data.frame" ], "fields": [ "V1", "V2", "V3" ], "rows": 29, "table": true, "tojson": true }, { "name": "chicken_chip", "title": "chicken chip", "object": "chicken_chip", "class": [ "data.frame" ], "fields": [ "V1", "V2", "V3" ], "rows": 36, "table": true, "tojson": true }, { "name": "ex_json", "title": "ex_json", "object": "ex_json", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "ex_pop", "title": "ex_pop", "object": "ex_pop", "class": [ "population" ], "fields": [], "table": false, "tojson": false }, { "name": "maize_chip", "title": "maize chip", "object": "maize_chip", "class": [ "data.frame" ], "fields": [ "V1", "V2", "V3" ], "rows": 10, "table": true, "tojson": true }, { "name": "pig_chip", "title": "pig chip", "object": "pig_chip", "class": [ "data.frame" ], "fields": [ "V1", "V2", "V3" ], "rows": 18, "table": true, "tojson": true }, { "name": "sheep_chip", "title": "sheep chip", "object": "sheep_chip", "class": [ "data.frame" ], "fields": [ "V1", "V2", "V3" ], "rows": 26, "table": true, "tojson": true } ], "_help": [ { "page": "add.array", "title": "Add a genotyping array", "topics": [ "add.array" ] }, { "page": "add.combi", "title": "Add a trait as a linear combination of other traits", "topics": [ "add.combi" ] }, { "page": "add.diag", "title": "Add something to the diagonal", "topics": [ "add.diag" ] }, { "page": "add.diversity", "title": "Add additional diverse material to a population", "topics": [ "add.diversity" ] }, { "page": "add.fixed.effects", "title": "Add fixed effects to traits", "topics": [ "add.fixed.effects" ] }, { "page": "add.founder.kinship", "title": "Add a relationship matrix for founder individuals", "topics": [ "add.founder.kinship" ] }, { "page": "alpha_to_beta", "title": "Moore-Penrose-Transfomration", "topics": [ "alpha_to_beta" ] }, { "page": "analyze.bv", "title": "Analyze genomic values", "topics": [ "analyze.bv" ] }, { "page": "analyze.population", "title": "Analyze allele frequency of a single marker", "topics": [ "analyze.population" ] }, { "page": "bit.snps", "title": "Decoding of bitwise-storing in R", "topics": [ "bit.snps" ] }, { "page": "bit.storing", "title": "Bitwise-storing in R", "topics": [ "bit.storing" ] }, { "page": "breeding.diploid", "title": "Breeding function", "topics": [ "breeding.diploid" ] }, { "page": "breeding.intern", "title": "Internal function to simulate one meiosis", "topics": [ "breeding.intern" ] }, { "page": "breeding.intern1", "title": "Internal function to simulate one meiosis", "topics": [ "breeding.intern1" ] }, { "page": "breeding.intern2", "title": "Internal function to simulate one meiosis", "topics": [ "breeding.intern2" ] }, { "page": "breeding.intern3", "title": "Internal function to simulate one meiosis", "topics": [ "breeding.intern3" ] }, { "page": "breeding.intern4", "title": "Internal function to simulate one meiosis", "topics": [ "breeding.intern4" ] }, { "page": "breeding.intern5", "title": "Internal function to simulate one meiosis", "topics": [ "breeding.intern5" ] }, { "page": "breeding.intern6", "title": "Internal function to simulate one meiosis", "topics": [ "breeding.intern6" ] }, { "page": "breeding.intern7", "title": "Internal function to simulate one meiosis", "topics": [ "breeding.intern7" ] }, { "page": "breeding.intern8", "title": "Internal function to simulate one meiosis", "topics": [ "breeding.intern8" ] }, { "page": "bv.development", "title": "Development of genetic/breeding value", "topics": [ "bv.development" ] }, { "page": "bv.development.box", "title": "Development of genetic/breeding value using a boxplot", "topics": [ "bv.development.box" ] }, { "page": "bv.standardization", "title": "BV standardization", "topics": [ "bv.standardization" ] }, { "page": "calculate.bv", "title": "Calculate breeding values", "topics": [ "calculate.bv" ] }, { "page": "cattle_chip", "title": "Cattle chip", "topics": [ "cattle_chip" ] }, { "page": "check.parents", "title": "Relatedness check between two individuals", "topics": [ "check.parents" ] }, { "page": "chicken_chip", "title": "chicken chip", "topics": [ "chicken_chip" ] }, { "page": "clean.up", "title": "Clean-up recombination points", "topics": [ "clean.up" ] }, { "page": "codeOriginsR", "title": "Origins-coding(R)", "topics": [ "codeOriginsR" ] }, { "page": "combine.traits", "title": "Combine traits", "topics": [ "combine.traits" ] }, { "page": "computing.costs", "title": "Compute costs of a breeding program", "topics": [ "computing.costs" ] }, { "page": "computing.costs.cohorts", "title": "Compute costs of a breeding program by cohorts", "topics": [ "computing.costs.cohorts" ] }, { "page": "computing.snps", "title": "Compute genotype/haplotype", "topics": [ "computing.snps" ] }, { "page": "computing.snps_single", "title": "Compute genotype/haplotype in gene editing application", "topics": [ "computing.snps_single" ] }, { "page": "creating.diploid", "title": "Generation of the starting population", "topics": [ "creating.diploid" ] }, { "page": "creating.phenotypic.transform", "title": "Create a phenotypic transformation", "topics": [ "creating.phenotypic.transform" ] }, { "page": "creating.trait", "title": "Generation of genomic traits", "topics": [ "creating.trait" ] }, { "page": "decodeOriginsR", "title": "Origins-Decoding(R)", "topics": [ "decodeOriginsR" ] }, { "page": "demiraculix", "title": "Remove miraculix-coding for genotypes", "topics": [ "demiraculix" ] }, { "page": "derive.loop.elements", "title": "Derive loop elements", "topics": [ "derive.loop.elements" ] }, { "page": "diag.mobps", "title": "Diagonal matrix", "topics": [ "diag.mobps" ] }, { "page": "edges.fromto", "title": "Detection of parental/child nodes", "topics": [ "edges.fromto" ] }, { "page": "edit_animal", "title": "Internal gene editing function", "topics": [ "edit_animal" ] }, { "page": "effect.estimate.add", "title": "Estimation of marker effects", "topics": [ "effect.estimate.add" ] }, { "page": "effective.size", "title": "Estimate effective population size", "topics": [ "effective.size" ] }, { "page": "epi", "title": "Martini-Test function", "topics": [ "epi" ] }, { "page": "ex_json", "title": "ex_json", "topics": [ "ex_json" ] }, { "page": "ex_pop", "title": "ex_pop", "topics": [ "ex_pop" ] }, { "page": "exist.cohort", "title": "Function to extract if a cohort exists", "topics": [ "exist.cohort" ] }, { "page": "find.chromo", "title": "Position detection (chromosome)", "topics": [ "find.chromo" ] }, { "page": "find.snpbefore", "title": "Position detection (SNPs)", "topics": [ "find.snpbefore" ] }, { "page": "founder.simulation", "title": "Founder simulation", "topics": [ "founder.simulation" ] }, { "page": "generation.individual", "title": "Function to generate a new individual", "topics": [ "generation.individual" ] }, { "page": "get.admixture", "title": "Admixture Plot", "topics": [ "get.admixture" ] }, { "page": "get.age.point", "title": "Derive age point", "topics": [ "get.age.point" ] }, { "page": "get.allele.freq", "title": "Calculate allele frequencies", "topics": [ "get.allele.freq" ] }, { "page": "get.bv", "title": "Export underlying true breeding values", "topics": [ "get.bv" ] }, { "page": "get.bve", "title": "Export estimated breeding values", "topics": [ "get.bve" ] }, { "page": "get.class", "title": "Derive class", "topics": [ "get.class" ] }, { "page": "get.cohorts", "title": "Export Cohort-names", "topics": [ "get.cohorts" ] }, { "page": "get.cohorts.individual", "title": "Derive ID on an individual", "topics": [ "get.cohorts.individual" ] }, { "page": "get.computing.time", "title": "Derive computing time", "topics": [ "get.computing.time" ] }, { "page": "get.creating.type", "title": "Derive creating type", "topics": [ "get.creating.type" ] }, { "page": "get.culling.time", "title": "Derive culling time", "topics": [ "get.culling.time" ] }, { "page": "get.culling.type", "title": "Derive culling type", "topics": [ "get.culling.type" ] }, { "page": "get.cullingtime", "title": "Derive time of culling", "topics": [ "get.cullingtime" ] }, { "page": "get.database", "title": "gen/database/cohorts conversion", "topics": [ "get.database" ] }, { "page": "get.death.point", "title": "Derive death point", "topics": [ "get.death.point" ] }, { "page": "get.dendrogram", "title": "Dendrogram", "topics": [ "get.dendrogram" ] }, { "page": "get.dendrogram.heatmap", "title": "Dendrogram Heatmap", "topics": [ "get.dendrogram.heatmap" ] }, { "page": "get.dendrogram.trait", "title": "Dendrogram", "topics": [ "get.dendrogram.trait" ] }, { "page": "get.distance", "title": "Calculate Nei distance between two or more population", "topics": [ "get.distance" ] }, { "page": "get.effect.freq", "title": "Compute marker frequency in QTL-markers", "topics": [ "get.effect.freq" ] }, { "page": "get.effective.size", "title": "Estimate effective population size", "topics": [ "get.effective.size" ] }, { "page": "get.fixed.effects.p", "title": "Export parametrization of fixed effects", "topics": [ "get.fixed.effects.p" ] }, { "page": "get.geno", "title": "Derive genotypes of selected individuals", "topics": [ "get.geno" ] }, { "page": "get.geno.time", "title": "Derive genotyping timepoint", "topics": [ "get.geno.time" ] }, { "page": "get.genotyped", "title": "Derive genotyping status", "topics": [ "get.genotyped" ] }, { "page": "get.genotyped.snp", "title": "Derive which markers are genotyped of selected individuals", "topics": [ "get.genotyped.snp" ] }, { "page": "get.haplo", "title": "Derive haplotypes of selected individuals", "topics": [ "get.haplo" ] }, { "page": "get.id", "title": "Derive ID on an individual", "topics": [ "get.id" ] }, { "page": "get.index", "title": "Putting together indices for GxE / multi trait", "topics": [ "get.index" ] }, { "page": "get.infos", "title": "Extract bv/pheno/geno of selected individuals", "topics": [ "get.infos" ] }, { "page": "get.is.first", "title": "First copy", "topics": [ "get.is.first" ] }, { "page": "get.is.last", "title": "Last copy", "topics": [ "get.is.last" ] }, { "page": "get.litter", "title": "Export litter", "topics": [ "get.litter" ] }, { "page": "get.litter.effect", "title": "Export litter effect", "topics": [ "get.litter.effect" ] }, { "page": "get.maf", "title": "Calculate minor allele frequencies", "topics": [ "get.maf" ] }, { "page": "get.map", "title": "Map generation", "topics": [ "get.map" ] }, { "page": "get.ngen", "title": "Number of generations", "topics": [ "get.ngen" ] }, { "page": "get.nindi", "title": "Number of individuals", "topics": [ "get.nindi" ] }, { "page": "get.npheno", "title": "Export underlying number of observations per phenotype", "topics": [ "get.npheno" ] }, { "page": "get.ntrait", "title": "Number of traits", "topics": [ "get.ntrait" ] }, { "page": "get.pca", "title": "Principle components analysis", "topics": [ "get.pca" ] }, { "page": "get.pedigree", "title": "Derive pedigree", "topics": [ "get.pedigree" ] }, { "page": "get.pedigree_old", "title": "Derive pedigree", "topics": [ "get.pedigree_old" ] }, { "page": "get.pedigree.visual", "title": "Draw pedigree", "topics": [ "get.pedigree.visual" ] }, { "page": "get.pedigree2", "title": "Derive pedigree including grandparents", "topics": [ "get.pedigree2" ] }, { "page": "get.pedigree3", "title": "Derive pedigree parents and grandparents", "topics": [ "get.pedigree3" ] }, { "page": "get.pedmap", "title": "Generate plink-file (pedmap)", "topics": [ "get.pedmap" ] }, { "page": "get.pen", "title": "Export pen ID", "topics": [ "get.pen" ] }, { "page": "get.pen.effect", "title": "Export pen-effects", "topics": [ "get.pen.effect" ] }, { "page": "get.pheno", "title": "Export underlying phenotypes", "topics": [ "get.pheno" ] }, { "page": "get.pheno.off", "title": "Export underlying offspring phenotypes", "topics": [ "get.pheno.off" ] }, { "page": "get.pheno.off.count", "title": "Export underlying number of used offspring for offspring phenotypes", "topics": [ "get.pheno.off.count" ] }, { "page": "get.pheno.single", "title": "Export underlying phenotypes", "topics": [ "get.pheno.single" ] }, { "page": "get.pheno.time", "title": "Derive phenotyping time point", "topics": [ "get.pheno.time" ] }, { "page": "get.phylogenetic.tree", "title": "Phylogenetic Tree", "topics": [ "get.phylogenetic.tree" ] }, { "page": "get.plink", "title": "Generate binary plink-file", "topics": [ "get.plink" ] }, { "page": "get.pool", "title": "Export founder pool", "topics": [ "get.pool" ] }, { "page": "get.pool.founder", "title": "Derive founder pool", "topics": [ "get.pool.founder" ] }, { "page": "get.qtl", "title": "QTL extraction", "topics": [ "get.qtl" ] }, { "page": "get.qtl.effects", "title": "QTL effect extraction", "topics": [ "get.qtl.effects" ] }, { "page": "get.qtl.variance", "title": "QTL effect variance extraction", "topics": [ "get.qtl.variance" ] }, { "page": "get.recombi", "title": "Derive genetic origins", "topics": [ "get.recombi" ] }, { "page": "get.reliability", "title": "Export underlying reliabilities", "topics": [ "get.reliability" ] }, { "page": "get.selectionbve", "title": "Export derived breeding values based on the selection index", "topics": [ "get.selectionbve" ] }, { "page": "get.selectionindex", "title": "Export underlying last used selection index", "topics": [ "get.selectionindex" ] }, { "page": "get.sex", "title": "Extraction of individual sex", "topics": [ "get.sex" ] }, { "page": "get.size", "title": "Number of individuals in each generation", "topics": [ "get.size" ] }, { "page": "get.snapshot", "title": "Derive snapshot of selected individuals", "topics": [ "get.snapshot" ] }, { "page": "get.snapshot.single", "title": "Derive snapshot of selected individuals", "topics": [ "get.snapshot.single" ] }, { "page": "get.time.point", "title": "Derive time point of generation", "topics": [ "get.time.point" ] }, { "page": "get.trafo.p", "title": "Export parametrization of fixed effects", "topics": [ "get.trafo.p" ] }, { "page": "get.trafo.p.single", "title": "Export parametrization of fixed effects", "topics": [ "get.trafo.p.single" ] }, { "page": "get.trait.name", "title": "Name of traits", "topics": [ "get.trait.name" ] }, { "page": "get.uhat", "title": "Export estimated SNP effects", "topics": [ "get.uhat" ] }, { "page": "get.variance", "title": "Derive variances components (add/dom)", "topics": [ "get.variance" ] }, { "page": "get.variance.components", "title": "Derive variance components", "topics": [ "get.variance.components" ] }, { "page": "get.vcf", "title": "Generate vcf-file", "topics": [ "get.vcf" ] }, { "page": "group.diff", "title": "Exclude individuals from a database", "topics": [ "group.diff" ] }, { "page": "inbreeding.emp", "title": "Empirical kinship", "topics": [ "inbreeding.emp" ] }, { "page": "inbreeding.exp", "title": "Expected inbreeding", "topics": [ "inbreeding.exp" ] }, { "page": "insert.bv", "title": "Manually enter breeding values", "topics": [ "insert.bv" ] }, { "page": "insert.bve", "title": "Manually enter estimated breeding values", "topics": [ "insert.bve" ] }, { "page": "insert.pheno", "title": "Manually enter phenotypes", "topics": [ "insert.pheno" ] }, { "page": "insert.pheno.single", "title": "Manually enter phenotypes", "topics": [ "insert.pheno.single" ] }, { "page": "json.simulation", "title": "Simulation of a breeding program based on a JSON-file from MoBPSweb", "topics": [ "json.simulation" ] }, { "page": "kinship.development", "title": "Development of genetic/breeding value", "topics": [ "kinship.development" ] }, { "page": "kinship.emp", "title": "Empirical kinship", "topics": [ "kinship.emp" ] }, { "page": "kinship.emp.fast", "title": "Approximate empirical kinship", "topics": [ "kinship.emp.fast" ] }, { "page": "kinship.emp.fast.between", "title": "Approximate empirical kinship", "topics": [ "kinship.emp.fast.between" ] }, { "page": "kinship.exp", "title": "Derive expected kinship", "topics": [ "kinship.exp" ] }, { "page": "ld.decay", "title": "Generate LD plot", "topics": [ "ld.decay" ] }, { "page": "maize_chip", "title": "maize chip", "topics": [ "maize_chip" ] }, { "page": "matrix.posdef", "title": "Projection positive definite", "topics": [ "matrix.posdef" ] }, { "page": "merging.cohorts", "title": "Merging of cohorts", "topics": [ "merging.cohorts" ] }, { "page": "merging.trait", "title": "Generation of genomic traits", "topics": [ "merging.trait" ] }, { "page": "miesenberger.index", "title": "Miesenberger Index", "topics": [ "miesenberger.index" ] }, { "page": "miraculix", "title": "Add miraculix-coding for genotypes", "topics": [ "miraculix" ] }, { "page": "mutation.intro", "title": "Mutation intro", "topics": [ "mutation.intro" ] }, { "page": "new.base.generation", "title": "Set new base generation", "topics": [ "new.base.generation" ] }, { "page": "OGC", "title": "Optimal genetic contribution", "topics": [ "OGC" ] }, { "page": "ogc.mobps", "title": "Breeding function", "topics": [ "ogc.mobps" ] }, { "page": "optimize.cores", "title": "Optimize generation cores", "topics": [ "optimize.cores" ] }, { "page": "pedigree.matrix", "title": "Derive pedigree relationship matrix", "topics": [ "pedigree.matrix" ] }, { "page": "pedigree.simulation", "title": "Simulation of a given pedigree", "topics": [ "pedigree.simulation" ] }, { "page": "pedmap.to.phasedbeaglevcf", "title": "Internal function to perform imputing/phasing", "topics": [ "pedmap.to.phasedbeaglevcf" ] }, { "page": "pig_chip", "title": "pig chip", "topics": [ "pig_chip" ] }, { "page": "plot.population", "title": "Plot Population", "topics": [ "plot.population" ] }, { "page": "recalculate.bv", "title": "Recalculate genomic values", "topics": [ "recalculate.bv" ] }, { "page": "recalculate.manual", "title": "Recalculate genomic values", "topics": [ "recalculate.manual" ] }, { "page": "recombination.function.haldane", "title": "Haldane recombination function", "topics": [ "recombination.function.haldane" ] }, { "page": "renaming.cohort", "title": "Rename a cohort", "topics": [ "renaming.cohort" ] }, { "page": "rowMedian", "title": "Row-wise Median", "topics": [ "rowMedian" ] }, { "page": "scaling.relationship", "title": "scaling.relationship", "topics": [ "scaling.relationship" ] }, { "page": "set.age.point", "title": "Set age points", "topics": [ "set.age.point" ] }, { "page": "set.class", "title": "Set class", "topics": [ "set.class" ] }, { "page": "set.default", "title": "Set defaults", "topics": [ "set.default" ] }, { "page": "set.mean.pool", "title": "Set differences between founder pool", "topics": [ "set.mean.pool" ] }, { "page": "set.time.point", "title": "Set time point", "topics": [ "set.time.point" ] }, { "page": "sheep_chip", "title": "sheep chip", "topics": [ "sheep_chip" ] }, { "page": "sortd", "title": "Apply sort and unique", "topics": [ "sortd" ] }, { "page": "ssGBLUP", "title": "Single Step GBLUP", "topics": [ "ssGBLUP" ] }, { "page": "summary.population", "title": "Summary Population", "topics": [ "summary.population" ] }, { "page": "vlist", "title": "Generation of a sublist", "topics": [ "vlist" ] }, { "page": "write.pedigree", "title": "write.pedigree.mixblup", "topics": [ "write.pedigree" ] } ], "_rundeps": [], "_score": 2.4313637641589874, "_indexed": true, "_nocasepkg": "mobps", "_universes": [ "tpook92" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.13.1", "date": "2026-05-27T08:13:36.000Z", "distro": "noble", "commit": "133a18bddfa50848ebd3a81b466bf314851dba69", "fileid": "524d8cf50f39fb58b60063eb0603bdd7145b3995f2a3d35479283c73d7b3aab0", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/tpook92/actions/runs/26498838583" }, { "r": "4.6.0", "os": "linux", "version": "1.13.1", "date": "2026-05-27T08:13:58.000Z", "distro": "noble", "commit": "133a18bddfa50848ebd3a81b466bf314851dba69", "fileid": "1d68297b7d3600e027285103d1a504e57343e54cdab97e1f5dd82c20e4367c45", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/tpook92/actions/runs/26498838583" }, { "r": "4.5.3", "os": "mac", "version": "1.13.1", "date": "2026-05-27T08:12:36.000Z", "commit": "133a18bddfa50848ebd3a81b466bf314851dba69", "fileid": "d0e9580251b73026c0b77e65c1c05edbf26deca0b651cc901a891039da914427", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tpook92/actions/runs/26498838583" }, { "r": "4.6.0", "os": "mac", "version": "1.13.1", "date": "2026-05-27T08:11:39.000Z", "commit": "133a18bddfa50848ebd3a81b466bf314851dba69", "fileid": "b8e510f24656a541ccc68d8efa4fd2c20a5f78a8dced5a1f040bc7d9d6eab1cd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tpook92/actions/runs/26498838583" }, { "r": "4.6.0", "os": "wasm", "version": "1.13.1", "date": "2026-05-27T08:13:42.000Z", "commit": "133a18bddfa50848ebd3a81b466bf314851dba69", "fileid": "6c1ab8f0e75ad1525e87fc2a592c706fd97b0b242fb43507851416858f9dae23", "status": "success", "buildurl": "https://github.com/r-universe/tpook92/actions/runs/26498838583" }, { "r": "4.7.0", "os": "win", "version": "1.13.1", "date": "2026-05-27T08:13:28.000Z", "commit": "133a18bddfa50848ebd3a81b466bf314851dba69", "fileid": "a57b6b93c7984ffb0e153d6d4c0e2ca5d29a0aa6ced9a587689872d66e1aa32a", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/tpook92/actions/runs/26498838583" }, { "r": "4.5.3", "os": "win", "version": "1.13.1", "date": "2026-05-27T08:12:24.000Z", "commit": "133a18bddfa50848ebd3a81b466bf314851dba69", "fileid": "07fcfb52cad537bc3b33d4dcc59fe708c99f210d4c9e6e42cffba996ed65c6b8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tpook92/actions/runs/26498838583" }, { "r": "4.6.0", "os": "win", "version": "1.13.1", "date": "2026-05-27T08:12:36.000Z", "commit": "133a18bddfa50848ebd3a81b466bf314851dba69", "fileid": "550d9c9de1f31e938646cf6cc52140f894c3c3e6a08de09d643c455beaf1b98b", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/tpook92/actions/runs/26498838583" } ] }