{ "_id": "6ac925a0de46216d5edda20d", "Package": "SelectionTools", "Version": "26.5", "Date": "2026-09-20", "Title": "Simulation and Data Analysis for Plant Breeders", "Authors@R": "c(\nperson(\"Matthias\", \"Frisch\",\nemail = \"matthias.frisch@uni-giessen.de\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Hans Peter\", \"Maurer\", role = \"ctb\"),\nperson(\"Philipp\", \"Heilmann\", role = \"ctb\")\n)", "Description": "Provides tools for simulation of plant breeding programs\nas described, for example, by Melchinger and Frisch (2023)\n, prediction of segregation\nvariance (Osthushenrich, Frisch and Herzog (2017)\n), genomic prediction\n(Hofheinz and Frisch (2014) ),\nlinkage disequilibrium based haplotype construction, and\nplanning of marker assisted back crossing programs. It\nprovides an integrated framework for simulation and analysis of\nplant breeding programs.", "VignetteBuilder": "knitr", "License": "CC0", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-09 17:05:22 UTC", "User": "root" }, "Author": "Matthias Frisch [aut, cre], Hans Peter Maurer [ctb], Philipp\nHeilmann [ctb]", "Maintainer": "Matthias Frisch ", "Repository": "https://popgen-giessen.r-universe.dev", "Date/Publication": "2026-10-09 16:21:21 UTC", "RemoteUrl": "https://github.com/cran/SelectionTools", "RemoteRef": "HEAD", "RemoteSha": "459ed67694735ae1e9881c634d72cc4f4d55d6d1", "_user": "popgen-giessen", "_type": "src", "_file": "SelectionTools_26.5.tar.gz", "_fileid": "https://r2.ropensci.org/ea43ea617f162676c39d561bd66ec3bc10b2aea9c364032e052251169ccde71e", "_filesize": 3326686, "_sha256": "ea43ea617f162676c39d561bd66ec3bc10b2aea9c364032e052251169ccde71e", "_expires": "2027-01-17T17:34:22.000Z", "_created": "2026-10-09T17:05:22.000Z", "_published": "2026-10-09T17:34:24.821Z", "_buildurl": "https://github.com/r-universe/popgen-giessen/actions/runs/37963125529", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 113933161892, "time": 157, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11631899073" }, { "job": 113933162041, "time": 141, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11631724327" }, { "job": 113933161956, "time": 116, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11632318166" }, { "job": 113933162125, "time": 142, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11632268309" }, { "job": 113933161904, "time": 238, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11633786989" }, { "job": 113933161838, "time": 290, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11634346166" }, { "job": 113933161864, "time": 212, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11634230950" }, { "job": 113933162012, "time": 427, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11633747640" }, { "job": 113930893732, "time": 332, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11631658754" }, { "job": 113933161915, "time": 93, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11631504419" }, { "job": 113933161949, "time": 396, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11632298611" }, { "job": 113933161903, "time": 182, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11631504673" }, { "job": 113933161888, "time": 136, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11631584477" }, { "job": 113933162285, "time": 383, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11631849591" }, { "job": 113933161984, "time": 115, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11631539280" } ], "_upstream": "https://github.com/cran/SelectionTools", "_commit": { "id": "459ed67694735ae1e9881c634d72cc4f4d55d6d1", "author": "Matthias Frisch ", "committer": "cran-robot ", "message": "version 26.5\n", "time": 1791562881 }, "_maintainer": { "name": "Matthias Frisch", "email": "matthias.frisch@uni-giessen.de", "login": "popgen-giessen", "description": "", "uuid": 122392866 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-38", "n": 1 }, { "week": "2026-39", "n": 1 }, { "week": "2026-41", "n": 1 } ], "_tags": [ { "name": "26.3", "date": "2026-09-15" }, { "name": "26.4", "date": "2026-09-21" }, { "name": "26.5", "date": "2026-10-09" } ], "_stars": 0, "_contributors": [ { "user": "popgen-giessen", "count": 3, "uuid": 122392866 } ], "_userbio": { "uuid": 122392866, "type": "user", "name": "PopGen-Giessen", "followers": 0 }, "_downloads": { "count": 372, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SelectionTools" }, "_searchresults": 6, "_topics": [ "openblas", "openmp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/SelectionTools.html" ], "_realowner": "popgen-giessen", "_cranurl": false, "_releases": [ { "version": "26.3", "date": "2026-09-15" }, { "version": "26.4", "date": "2026-09-21" } ], "_exports": [ ".GS_ALLELE_MAX", ".GS_STVCF_MAX_ALT", "append.population", "be.quiet", "concat.population", "copy.population", "cross", "data.params", "define.effects", "define.effects.df", "define.genome", "define.map", "deprecated", "dh", "divide.population", "effect.weight.set.all", "effmap.remove", "effmap.remove.all", "evaluate.all.loci", "evaluate.allele", "evaluate.allele.freq", "evaluate.allele.freq2", "evaluate.allele2", "evaluate.genome", "evaluate.genotype", "evaluate.hap.calc", "evaluate.hap.calc.d", "evaluate.hap.free", "evaluate.hap.init", "evaluate.hap.return.genotype", "evaluate.hap.return.table", "evaluate.haplotype", "evaluate.ld", "evaluate.locus", "evaluate.mdp", "evaluate.population", "gd.allele.frequencies", "gd.allow.zero.frequencies", "gd.correct.missing", "gd.data.parameters", "gd.distance.similarity", "gd.genetic.distance", "gd.list.irregular", "gd.list.missing", "gd.mk.matr", "gd.pcoa", "gd.similarity.coefficient", "gd.splitdot", "gd.status.zero.frequencies", "generate.effect.file", "generate.map.file", "generate.population", "genome.contribution", "genome.parameter.get", "genome.parameter.set", "genome.segments", "genotype.population", "get.genome.par", "get.map", "get.mdp", "get.population", "get.population.gvalue", "get.population.info", "get.population.pvalue", "get.population.size", "get.score", "gs.build.esvs", "gs.build.tsps", "gs.build.V", "gs.build.Z", "gs.check.pvals", "gs.compare.effects", "gs.cross.eval.es", "gs.cross.eval.gd", "gs.cross.eval.gd.fct", "gs.cross.eval.ma", "gs.cross.eval.mi", "gs.cross.eval.mu", "gs.cross.eval.va", "gs.cross.info", "gs.cross.info.gd", "gs.cross.validation", "gs.esteff.lsq", "gs.esteff.rmla", "gs.esteff.rmlc", "gs.esteff.rmlr", "gs.esteff.rmlv", "gs.esteff.rr", "gs.estimate.gv", "gs.get.im", "gs.get.info.level", "gs.get.V", "gs.get.y", "gs.get.Z", "gs.info", "gs.lambda.aov", "gs.lambda.const", "gs.lambda.emstep", "gs.lambda.hsq", "gs.lambda.reg", "gs.lambda.rmla", "gs.lambda.rmla.02", "gs.lambda.rmlc", "gs.lambda.rmlr", "gs.lambda.rmlv", "gs.lambda.rrblup", "gs.mme.coeff", "gs.mme.invcoeff", "gs.mme.restcoeff", "gs.mme.restrhs", "gs.mme.rhs", "gs.mme.solve", "gs.mmet.coeff", "gs.mmet.coeff.3", "gs.mmet.rhs", "gs.mmet.solve", "gs.neg.effall", "gs.plot.effects", "gs.plot.model.fit", "gs.plot.validation", "gs.pos.effall", "gs.predict.genotypes", "gs.reset", "gs.restrict.marker.data.01", "gs.return.effects", "gs.return.pvals", "gs.set.all.info.levels", "gs.set.allele.codes", "gs.set.effects", "gs.set.info.level", "gs.set.lambda", "gs.set.num.threads", "gs.set.performance.data", "gs.single.marker.aov", "gs.single.marker.reg", "gs.start.timer", "gs.stop.timer", "gs.test.mp", "gs.testeff.lsq", "gs.testeff.rmlc", "gs.testeff.rmlv", "gs.vc.rrblup", "gs.w.aov", "gs.write.pseff", "homozygote", "il.eval.library", "il.eval.lines", "il.ideal.library", "il.overlapping.library", "info", "info.cat", "init.population", "linkage.drag", "linkage.map.get", "linkage.map.load", "linkage.map.save", "list.effects", "list.populations", "load.effmap", "load.internal.effmap", "load.linkage.map", "mab.compare", "mab.df", "mab.load.data", "mab.save.inds", "mab.simulate", "mab.tabulate", "optimize.population", "ph.linkage.map.create", "phenotype.population", "plabsim", "plabsim.init", "plabsim.R.date", "plabsim.R.version", "plabsim.version", "plant", "population.append", "population.concat", "population.copy", "population.divide", "population.exist", "population.individual.remove", "population.info.get", "population.info.set", "population.list", "population.matrix.load", "population.matrix.save", "population.name.swap", "population.optimize", "population.plabsim.load", "population.plabsim.save", "population.remove", "population.remove.all", "population.rename", "population.resize", "population.sample", "population.size.get", "population.sort", "population.swap.name", "population.transfer", "print.st.data.set.list", "print.st.switch.error", "read.vcf", "remove.all.populations", "remove.effmaps", "remove.evaluate.population", "remove.genotype.population", "remove.map", "remove.population", "rename.population", "reset.all", "reset.mdp", "resize.population", "resources", "return.population", "rng.choose", "rng.info", "rng.init", "rng.list", "sample.population", "save.linkage.map", "sdev", "sel.target.define", "select.all.best", "select.all.best.intern", "select.genotypes", "select.n.best", "select.n.best.segments", "set.co.freq", "set.eff.weight", "set.genome.par", "set.info.level", "set.mdp", "set.NoLociInit", "set.population.gvalue", "set.population.info", "show.phase", "single.cross", "sm.start.timer", "sm.stop.timer", "splitdt", "ssd.mating", "st_mixed", "st.calc.ld", "st.calc.ld.2", "st.calc.q", "st.calc.rf", "st.calculate.enrichment", "st.chrom.stats", "st.compact.data.set", "st.copy.marker.data", "st.data.set.list", "st.data.set.remove", "st.data.set.remove.all", "st.datadir", "st.dataframe.to.STvcf", "st.dd", "st.def.hblocks", "st.destroy.phase", "st.genetic.distances", "st.genetic.distances.02", "st.genetic.distances.fct", "st.get.info.level", "st.get.map", "st.get.num.threads", "st.get.simpop", "st.get.simpop.perfdata", "st.get.simpop2", "st.id", "st.indir", "st.info", "st.keep.intersection.markers", "st.LDheatmap", "st.LDplot.ld", "st.LDplot.map", "st.load.performance.data", "st.load.vcf.data", "st.mark.alleles", "st.marker.data.statistics", "st.markerdata.to.STvcf", "st.mxd", "st.od", "st.outdir", "st.phase", "st.phase.v1", "st.plot.corr", "st.plot.corr.l", "st.plot.gene.diversity", "st.plot.ggt", "st.plot.ggt.src", "st.read.map", "st.read.map.df", "st.read.marker.data", "st.read.marker.data.df", "st.read.performance.data", "st.recode.hbc", "st.recode.hil", "st.recode.ref", "st.recode.ref.2", "st.reset", "st.restrict.marker.data", "st.return.performance.data", "st.select.enrichment", "st.select.phen", "st.set.hblocks", "st.set.info.level", "st.set.matrix.ops", "st.set.num.threads", "st.set.openblas.threads", "st.set.sim.ef", "st.set.sim.gp", "st.set.sim.mp", "st.set.sim.pp", "st.set.simpop", "st.start.timer", "st.stop.timer", "st.STvcf.to.dataframe", "st.switch.error", "st.write.map", "st.write.marker.data", "summarize.gvalue", "swap.population.name", "talk.to.me", "write.vcf", "write.version.2" ], "_datasets": [ { "name": "DT_technow", "title": "Technow Hybrid Phenotype Data", "object": "DT_technow", "file": "DT_technow.rda", "class": [ "data.frame" ], "fields": [ "hybrid", "dent", "flint", "GY", "GM", "hy" ], "rows": 1254, "table": true, "tojson": true }, { "name": "gd.dummy.populations", "title": "Molecular marker data for several dummy populations", "object": "gd.dummy.populations", "file": "gd.dummy.populations.rda", "class": [ "data.frame" ], "fields": [ "p9.i1", "p10.i1", "p11.i1", "p1.i1", "p1.i2", "p1.i3", "p2.i1", "p2.i3", "p2.i2", "p3.i1", "p3.i2", "p4.1", "p5.1", "p6.1", "p6.2", "p7.i1", "p8.i1" ], "rows": 8, "table": true, "tojson": true }, { "name": "gd.maize.aflp", "title": "51 maize lines analyzed with 462 AFLP markers.", "object": "gd.maize.aflp", "file": "gd.maize.aflp.rda", "class": [ "data.frame" ], "fields": [ "l1.1", "l2.1", "l3.1", "l4.1", "l5.1", "l6.1", "l7.1", "l8.1", "l9.1", "l10.1", "l11.1", "l12.1", "l13.1", "l14.1", "l15.1", "l16.1", "l17.1", "l18.1", "l19.1", "l20.1", "l21.1", "l22.1", "l23.1", "l24.1", "l25.1", "l26.1", "l27.1", "l28.1", "l29.1", "l30.1", "l31.1", "l32.1", "l33.1", "l34.1", "l35.1", "l36.1", "l37.1", "l38.1", "l39.1", "l40.1", "l41.1", "l42.1", "l43.1", "l44.1", "l45.1", "l46.1", "l47.1", "l48.1", "l49.1", "l50.1", "l51.1" ], "rows": 462, "table": true, "tojson": true }, { "name": "gd.maize.lines", "title": "RFLP data from 50 maize lines", "object": "gd.maize.lines", "file": "gd.maize.lines.rda", "class": [ "data.frame" ], "fields": [ "CML15.1", "CML49.1", "CML78.1", "CML142.1", "CML176.1", "CML202.1", "CML216.1", "CML247.1", "CML287.1", "CML323.1", "CML343.1", "CML366.1", "CML206.1", "CML246.1", "CML254.1", "CML327.1", "CML373.1", "CML384.1", "CML258.1", "CML339.1", "CML341.1", "CML344.1", "CML279.1", "CML282.1", "CML291.1", "CML299.1", "CML310.1", "CML316.1", "CML324.1", "CML329.1", "CML334.1", "CML348.1", "CML354.1", "CML363.1", "LP1.1", "LP2.1", "LP3.1", "LP4.1", "LP5.1", "TS1.1", "TS2.1", "TS3.1", "TS4.1", "TS5.1", "CML249.1", "CML264.1", "CML268.1", "CML273.1", "CML274.1", "CML311.1", "CML321.1", "CML349.1", "P21.1", "P43.1", "P501.1", "P502.1", "SPLC7.1" ], "rows": 415, "table": true, "tojson": true }, { "name": "gd.maize.populations", "title": "SSR data from seven maize populations", "object": "gd.maize.populations", "file": "gd.maize.populations.rda", "class": [ "data.frame" ], "fields": [], "rows": 532, "table": true, "tojson": true }, { "name": "gd.salad.aflp", "title": "Jasminas 44 salads analyzed with 108 AFLP markers.", "object": "gd.salad.aflp", "file": "gd.salad.aflp.rda", "class": [ "data.frame" ], "fields": [ "l34.1", "l44.1", "l45.1", "l38.1", "l33.1", "l47.1", "l41.1", "l2.1", "l20.1", "l22.1", "l37.1", "l25.1", "l30.1", "l24.1", "l32.1", "l27.1", "l17.1", "l31.1", "l18.1", "l10.1", "l36.1", "l42.1", "l19.1", "l28.1", "l16.1", "l7.1", "l6.1", "l21.1", "l15.1", "l26.1", "l46.1", "l43.1", "l23.1", "l29.1", "l9.1", "l12.1", "l4.1", "l13.1", "l11.1", "l14.1", "l35.1", "l3.1", "l40.1", "l39.1" ], "rows": 108, "table": true, "tojson": true }, { "name": "lib00.map1", "title": "Linkage Map for Marker-Assisted Backcrossing Examples", "object": "lib00.map1", "file": "lib00.map1.rda", "class": [ "data.frame" ], "fields": [ "V1", "V2", "V3", "V4" ], "rows": 81, "table": true, "tojson": true }, { "name": "lib00.map1a", "title": "Reduced Linkage Map for Marker-Assisted Backcrossing Examples", "object": "lib00.map1a", "file": "lib00.map1a.rda", "class": [ "data.frame" ], "fields": [ "V1", "V2", "V3", "V4" ], "rows": 41, "table": true, "tojson": true }, { "name": "lib00.map2", "title": "Linkage Map for Three-Stage Marker-Assisted Backcrossing", "object": "lib00.map2", "file": "lib00.map2.rda", "class": [ "data.frame" ], "fields": [ "V1", "V2", "V3", "V4" ], "rows": 81, "table": true, "tojson": true }, { "name": "masbc.input", "title": "Input Files for Marker-Assisted Backcrossing Examples", "object": "masbc.input", "file": "masbc.input.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "Md_technow", "title": "Technow Dent Marker Data", "object": "Md_technow", "file": "Md_technow.rda", "class": [ "matrix", "array" ], "fields": [], "rows": 123, "table": false, "tojson": false }, { "name": "Mf_technow", "title": "Technow Flint Marker Data", "object": "Mf_technow", "file": "Mf_technow.rda", "class": [ "matrix", "array" ], "fields": [], "rows": 86, "table": false, "tojson": false }, { "name": "v.tropmaize.map", "title": "Genetic Map for Tropical Maize", "object": "v-tropmaize-map", "file": "v-tropmaize-map.rda", "class": [ "data.frame" ], "fields": [ "name", "chrom", "pos" ], "rows": 7140, "table": true, "tojson": true }, { "name": "v.tropmaize.phe", "title": "Phenotypic Data for Tropical Maize", "object": "v-tropmaize-phe", "file": "v-tropmaize-phe.rda", "class": [ "data.frame" ], "fields": [ "ii", "yy" ], "rows": 264, "table": true, "tojson": true }, { "name": "v.tropmaize.pop", "title": "Genotype Data for Tropical Maize", "object": "v-tropmaize-pop", "file": "v-tropmaize-pop.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "v.tropmaize.vcf", "title": "Compact STvcf Genotype and Genetic-Map Data for Tropical Maize", "object": "v-tropmaize-vcf", "file": "v-tropmaize-vcf.rda", "class": [ "STvcf" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "append.population", "title": "append.population()", "topics": [ "append.population" ] }, { "page": "be.quiet", "title": "Switch SelectionTools output to a quiet mode", "topics": [ "be.quiet" ] }, { "page": "concat.population", "title": "concat.population()", "topics": [ "concat.population" ] }, { "page": "copy.population", "title": "copy.population()", "topics": [ "copy.population" ] }, { "page": "cross", "title": "cross()", "topics": [ "cross" ] }, { "page": "data.params", "title": "Return or inspect parameters associated with a data object", "topics": [ "data.params" ] }, { "page": "define.effects", "title": "define.effects()", "topics": [ "define.effects" ] }, { "page": "define.effects.df", "title": "define.effects.df()", "topics": [ "define.effects.df" ] }, { "page": "define.genome", "title": "Define a genome from a linkage map and optional chromosome lengths", "topics": [ "define.genome" ] }, { "page": "define.map", "title": "define.map()", "topics": [ "define.map" ] }, { "page": "deprecated", "title": "Issue information for a deprecated function or object name", "topics": [ "deprecated" ] }, { "page": "dh", "title": "dh()", "topics": [ "dh" ] }, { "page": "divide.population", "title": "divide.population()", "topics": [ "divide.population" ] }, { "page": "DT_technow", "title": "Technow Hybrid Phenotype Data", "topics": [ "DT_technow" ] }, { "page": "effect.weight.set.all", "title": "Set effect weights for all effects", "topics": [ "effect.weight.set.all" ] }, { "page": "effmap.remove", "title": "Remove a stored effect map", "topics": [ "effmap.remove" ] }, { "page": "effmap.remove.all", "title": "Remove all stored effect maps", "topics": [ "effmap.remove.all" ] }, { "page": "evaluate.all.loci", "title": "Evaluate all loci in a population", "topics": [ "evaluate.all.loci" ] }, { "page": "evaluate.allele", "title": "evaluate.allele()", "topics": [ "evaluate.allele" ] }, { "page": "evaluate.allele.freq", "title": "Calculate or return allele frequencies for selected loci", "topics": [ "evaluate.allele.freq" ] }, { "page": "evaluate.allele.freq2", "title": "evaluate.allele.freq2()", "topics": [ "evaluate.allele.freq2" ] }, { "page": "evaluate.allele2", "title": "evaluate.allele2()", "topics": [ "evaluate.allele2" ] }, { "page": "evaluate.genome", "title": "evaluate.genome()", "topics": [ "evaluate.genome" ] }, { "page": "evaluate.genotype", "title": "evaluate.genotype()", "topics": [ "evaluate.genotype" ] }, { "page": "evaluate.hap.calc", "title": "Calculate haplotype information for a pair of loci", "topics": [ "evaluate.hap.calc" ] }, { "page": "evaluate.hap.calc.d", "title": "Calculate a haplotype statistic for a pair of loci", "topics": [ "evaluate.hap.calc.d" ] }, { "page": "evaluate.hap.free", "title": "Release or reset temporary haplotype-evaluation state", "topics": [ "evaluate.hap.free" ] }, { "page": "evaluate.hap.init", "title": "Initialize haplotype evaluation for a population", "topics": [ "evaluate.hap.init" ] }, { "page": "evaluate.hap.return.genotype", "title": "Return genotype results from the current haplotype evaluation", "topics": [ "evaluate.hap.return.genotype" ] }, { "page": "evaluate.hap.return.table", "title": "Return the table produced by the current haplotype evaluation", "topics": [ "evaluate.hap.return.table" ] }, { "page": "evaluate.haplotype", "title": "Evaluate haplotypes for selected loci in a population", "topics": [ "evaluate.haplotype" ] }, { "page": "evaluate.ld", "title": "Evaluate linkage disequilibrium for a population and genomic position", "topics": [ "evaluate.ld" ] }, { "page": "evaluate.locus", "title": "Evaluate selected loci in a population", "topics": [ "evaluate.locus" ] }, { "page": "evaluate.mdp", "title": "Evaluate marker-assisted donor-parent information for populations", "topics": [ "evaluate.mdp" ] }, { "page": "evaluate.population", "title": "Evaluate genetic values for simulation populations", "topics": [ "evaluate.population" ] }, { "page": "gd.allele.frequencies", "title": "gd.allele.frequencies()", "topics": [ "gd.allele.frequencies" ] }, { "page": "gd.allow.zero.frequencies", "title": "gd.allow.zero.frequencies()", "topics": [ "gd.allow.zero.frequencies" ] }, { "page": "gd.correct.missing", "title": "gd.correct.missing()", "topics": [ "gd.correct.missing" ] }, { "page": "gd.data.parameters", "title": "gd.data.parameters()", "topics": [ "gd.data.parameters" ] }, { "page": "gd.distance.similarity", "title": "Gd distance similarity", "topics": [ "gd.distance.similarity" ] }, { "page": "gd.dummy.populations", "title": "Molecular marker data for several dummy populations", "topics": [ "gd.dummy.populations" ] }, { "page": "gd.genetic.distance", "title": "gd.genetic.distance()", "topics": [ "gd.genetic.distance" ] }, { "page": "gd.list.irregular", "title": "gd.list.irregular()", "topics": [ "gd.list.irregular" ] }, { "page": "gd.list.missing", "title": "gd.list.missing()", "topics": [ "gd.list.missing" ] }, { "page": "gd.maize.aflp", "title": "51 maize lines analyzed with 462 AFLP markers.", "topics": [ "gd.maize.aflp", "maize.aflp" ] }, { "page": "gd.maize.lines", "title": "RFLP data from 50 maize lines", "topics": [ "gd.maize.lines" ] }, { "page": "gd.maize.populations", "title": "SSR data from seven maize populations", "topics": [ "gd.maize.populations" ] }, { "page": "gd.mk.matr", "title": "Construct a matrix from genetic-distance results", "topics": [ "gd.mk.matr" ] }, { "page": "gd.pcoa", "title": "gd.pcoa()", "topics": [ "gd.pcoa" ] }, { "page": "gd.salad.aflp", "title": "Jasminas 44 salads analyzed with 108 AFLP markers.", "topics": [ "gd.salad.aflp" ] }, { "page": "gd.similarity.coefficient", "title": "gd.similarity.coefficient()", "topics": [ "gd.similarity.coefficient" ] }, { "page": "gd.splitdot", "title": "Split or transform marker labels used by genetic-diversity routines", "topics": [ "gd.splitdot" ] }, { "page": "gd.status.zero.frequencies", "title": "Return status information concerning zero allele frequencies", "topics": [ "gd.status.zero.frequencies" ] }, { "page": "generate.effect.file", "title": "generate.effect.file()", "topics": [ "generate.effect.file" ] }, { "page": "generate.map.file", "title": "generate.map.file()", "topics": [ "generate.map.file" ] }, { "page": "generate.population", "title": "generate.population()", "topics": [ "generate.population" ] }, { "page": "genome.contribution", "title": "genome.contribution()", "topics": [ "genome.contribution" ] }, { "page": "genome.parameter.get", "title": "Return the current genome parameters", "topics": [ "genome.parameter.get" ] }, { "page": "genome.parameter.set", "title": "Set genome parameters used by the simulation code", "topics": [ "genome.parameter.set" ] }, { "page": "genome.segments", "title": "Extract or summarize genome segments for populations", "topics": [ "genome.segments" ] }, { "page": "genotype.population", "title": "genotype.population()", "topics": [ "genotype.population" ] }, { "page": "get.genome.par", "title": "get.genome.par()", "topics": [ "get.genome.par" ] }, { "page": "get.map", "title": "get.map()", "topics": [ "get.map" ] }, { "page": "get.mdp", "title": "Return the current marker-assisted donor-parent information", "topics": [ "get.mdp" ] }, { "page": "get.population", "title": "get.population()", "topics": [ "get.population" ] }, { "page": "get.population.gvalue", "title": "Get genetic values from a simulation population", "topics": [ "get.population.gvalue" ] }, { "page": "get.population.info", "title": "Return stored information for individuals in a population", "topics": [ "get.population.info" ] }, { "page": "get.population.pvalue", "title": "Get phenotypic values from a simulation population", "topics": [ "get.population.pvalue" ] }, { "page": "get.population.size", "title": "get.population.size()", "topics": [ "get.population.size" ] }, { "page": "get.score", "title": "get.score()", "topics": [ "get.score" ] }, { "page": "gs.build.esvs", "title": "Build estimation and validation subsets from a base data set", "topics": [ "gs.build.esvs" ] }, { "page": "gs.build.tsps", "title": "Build training and prediction subsets from a base data set", "topics": [ "gs.build.tsps" ] }, { "page": "gs.build.V", "title": "Build the genomic-selection variance or covariance matrix for a data set", "topics": [ "gs.build.V" ] }, { "page": "gs.build.z", "title": "gs.build.Z()", "topics": [ "gs.build.Z" ] }, { "page": "gs.check.pvals", "title": "Check whether p-values are available for a genomic-selection data set", "topics": [ "gs.check.pvals" ] }, { "page": "gs.compare.effects", "title": "gs.compare.effects()", "topics": [ "gs.compare.effects" ] }, { "page": "gs.cross.eval.es", "title": "Evaluate Crosses by Expected Superior Progeny Value", "topics": [ "gs.cross.eval.es" ] }, { "page": "gs.cross.eval.gd", "title": "Evaluate Crosses by Genetic Distance", "topics": [ "gs.cross.eval.gd" ] }, { "page": "gs.cross.eval.gd.fct", "title": "Evaluate crosses using genetic-distance function", "topics": [ "gs.cross.eval.gd.fct" ] }, { "page": "gs.cross.eval.ma", "title": "Evaluate Crosses by Maximum Marker-Effect Value", "topics": [ "gs.cross.eval.ma" ] }, { "page": "gs.cross.eval.mi", "title": "Evaluate Crosses by Minimum Marker-Effect Value", "topics": [ "gs.cross.eval.mi" ] }, { "page": "gs.cross.eval.mu", "title": "Evaluate Crosses by Expected Progeny Mean", "topics": [ "gs.cross.eval.mu" ] }, { "page": "gs.cross.eval.va", "title": "Evaluate Crosses by Segregation Variance", "topics": [ "gs.cross.eval.va" ] }, { "page": "gs.cross.info", "title": "Return or write information for evaluated crosses", "topics": [ "gs.cross.info" ] }, { "page": "gs.cross.info.gd", "title": "Return or write genetic-distance information for crosses", "topics": [ "gs.cross.info.gd" ] }, { "page": "gs.cross.validation", "title": "gs.cross.validation()", "topics": [ "gs.cross.validation" ] }, { "page": "gs.esteff.lsq", "title": "Estimate marker effects using the LSQ method", "topics": [ "gs.esteff.lsq" ] }, { "page": "gs.esteff.rmla", "title": "Estimate marker effects using the RMLA method", "topics": [ "gs.esteff.rmla" ] }, { "page": "gs.esteff.rmlc", "title": "gs.esteff.rmlc()", "topics": [ "gs.esteff.rmlc" ] }, { "page": "gs.esteff.rmlr", "title": "Estimate marker effects using the RMLR method", "topics": [ "gs.esteff.rmlr" ] }, { "page": "gs.esteff.rmlv", "title": "gs.esteff.rmlv()", "topics": [ "gs.esteff.rmlv" ] }, { "page": "gs.esteff.rr", "title": "Estimate Marker Effects by Ridge Regression", "topics": [ "gs.esteff.rr" ] }, { "page": "gs.estimate.gv", "title": "Estimate genomic values for an estimation or prediction data set", "topics": [ "gs.estimate.gv" ] }, { "page": "gs.get.im", "title": "Return the genomic-selection information matrix for a data set", "topics": [ "gs.get.im" ] }, { "page": "gs.get.info.level", "title": "Return the genomic-selection information level for a data set", "topics": [ "gs.get.info.level" ] }, { "page": "gs.get.V", "title": "Return the genomic-selection variance or covariance matrix for a data set", "topics": [ "gs.get.V" ] }, { "page": "gs.get.y", "title": "Return the genomic-selection response vector for a data set", "topics": [ "gs.get.y" ] }, { "page": "gs.get.Z", "title": "Return the genomic-selection marker or design matrix for a data set", "topics": [ "gs.get.Z" ] }, { "page": "gs.info", "title": "Print or handle a genomic-selection information message", "topics": [ "gs.info" ] }, { "page": "gs.lambda.aov", "title": "Estimate or set genomic-selection lambda values using the aov method", "topics": [ "gs.lambda.aov" ] }, { "page": "gs.lambda.const", "title": "Estimate or set genomic-selection lambda values using the const method", "topics": [ "gs.lambda.const" ] }, { "page": "gs.lambda.emstep", "title": "Estimate or set genomic-selection lambda values using the emstep method", "topics": [ "gs.lambda.emstep" ] }, { "page": "gs.lambda.hsq", "title": "Estimate or set genomic-selection lambda values using the hsq method", "topics": [ "gs.lambda.hsq" ] }, { "page": "gs.lambda.reg", "title": "Estimate or set genomic-selection lambda values using the reg method", "topics": [ "gs.lambda.reg" ] }, { "page": "gs.lambda.rmla", "title": "Estimate or set genomic-selection lambda values using the rmla method", "topics": [ "gs.lambda.rmla" ] }, { "page": "gs.lambda.rmla.02", "title": "Estimate or set genomic-selection lambda values using the rmla.02 method", "topics": [ "gs.lambda.rmla.02" ] }, { "page": "gs.lambda.rmlc", "title": "Estimate or set genomic-selection lambda values using the rmlc method", "topics": [ "gs.lambda.rmlc" ] }, { "page": "gs.lambda.rmlr", "title": "Estimate or set genomic-selection lambda values using the rmlr method", "topics": [ "gs.lambda.rmlr" ] }, { "page": "gs.lambda.rmlv", "title": "Estimate or set genomic-selection lambda values using the rmlv method", "topics": [ "gs.lambda.rmlv" ] }, { "page": "gs.lambda.rrblup", "title": "Estimate or set genomic-selection lambda values using the rrblup method", "topics": [ "gs.lambda.rrblup" ] }, { "page": "gs.mme.coeff", "title": "Gs mme coeff", "topics": [ "gs.mme.coeff" ] }, { "page": "gs.mme.invcoeff", "title": "Gs mme invcoeff", "topics": [ "gs.mme.invcoeff" ] }, { "page": "gs.mme.restcoeff", "title": "Gs mme restcoeff", "topics": [ "gs.mme.restcoeff" ] }, { "page": "gs.mme.restrhs", "title": "Gs mme restrhs", "topics": [ "gs.mme.restrhs" ] }, { "page": "gs.mme.rhs", "title": "Build or return the right-hand side for genomic-selection mixed-model equations", "topics": [ "gs.mme.rhs" ] }, { "page": "gs.mme.solve", "title": "Gs mme solve", "topics": [ "gs.mme.solve" ] }, { "page": "gs.mmet.coeff", "title": "Build or solve transformed mixed-model equations (coeff)", "topics": [ "gs.mmet.coeff" ] }, { "page": "gs.mmet.coeff.3", "title": "Build or solve transformed mixed-model equations (coeff.3)", "topics": [ "gs.mmet.coeff.3" ] }, { "page": "gs.mmet.rhs", "title": "Build or solve transformed mixed-model equations (rhs)", "topics": [ "gs.mmet.rhs" ] }, { "page": "gs.mmet.solve", "title": "Build or solve transformed mixed-model equations (solve)", "topics": [ "gs.mmet.solve" ] }, { "page": "gs.neg.effall", "title": "Set or process all marker effects using the negative-effect convention", "topics": [ "gs.neg.effall" ] }, { "page": "gs.plot.effects", "title": "gs.plot.effects()", "topics": [ "gs.plot.effects" ] }, { "page": "gs.plot.model.fit", "title": "Plot the Fit of a Genomic Prediction Model", "topics": [ "gs.plot.model.fit" ] }, { "page": "gs.plot.validation", "title": "gs.plot.validation()", "topics": [ "gs.plot.validation" ] }, { "page": "gs.pos.effall", "title": "Set or process all marker effects using the positive-effect convention", "topics": [ "gs.pos.effall" ] }, { "page": "gs.predict.genotypes", "title": "gs.predict.genotypes()", "topics": [ "gs.predict.genotypes" ] }, { "page": "gs.reset", "title": "Reset genomic-selection data and settings", "topics": [ "gs.reset" ] }, { "page": "gs.restrict.marker.data.01", "title": "Restrict marker data using the package genomic-selection interface", "topics": [ "gs.restrict.marker.data.01" ] }, { "page": "gs.return.effects", "title": "gs.return.effects()", "topics": [ "gs.return.effects" ] }, { "page": "gs.return.pvals", "title": "Return marker p-values for a genomic-selection data set", "topics": [ "gs.return.pvals" ] }, { "page": "gs.set.all.info.levels", "title": "Set all info levels used by the genomic-selection routines", "topics": [ "gs.set.all.info.levels" ] }, { "page": "gs.set.allele.codes", "title": "Set allele codes used by the genomic-selection routines", "topics": [ "gs.set.allele.codes" ] }, { "page": "gs.set.effects", "title": "Set effects used by the genomic-selection routines", "topics": [ "gs.set.effects" ] }, { "page": "gs.set.info.level", "title": "Set info level used by the genomic-selection routines", "topics": [ "gs.set.info.level" ] }, { "page": "gs.set.lambda", "title": "Set lambda used by the genomic-selection routines", "topics": [ "gs.set.lambda" ] }, { "page": "gs.set.num.threads", "title": "Set num threads used by the genomic-selection routines", "topics": [ "gs.set.num.threads" ] }, { "page": "gs.set.performance.data", "title": "Set performance data used by the genomic-selection routines", "topics": [ "gs.set.performance.data" ] }, { "page": "gs.single.marker.aov", "title": "Perform single-marker analysis for a genomic-selection data set", "topics": [ "gs.single.marker.aov" ] }, { "page": "gs.single.marker.reg", "title": "Perform single-marker analysis for a genomic-selection data set", "topics": [ "gs.single.marker.reg" ] }, { "page": "gs.start.timer", "title": "Start or stop the genomic-selection timing helper", "topics": [ "gs.start.timer" ] }, { "page": "gs.stop.timer", "title": "Start or stop the genomic-selection timing helper", "topics": [ "gs.stop.timer" ] }, { "page": "gs.test.mp", "title": "Test marker or model parameters used by genomic-selection routines", "topics": [ "gs.test.mp" ] }, { "page": "gs.testeff.lsq", "title": "Test estimated marker effects using the indicated method", "topics": [ "gs.testeff.lsq" ] }, { "page": "gs.testeff.rmlc", "title": "Test estimated marker effects using the indicated method", "topics": [ "gs.testeff.rmlc" ] }, { "page": "gs.testeff.rmlv", "title": "Test estimated marker effects using the indicated method", "topics": [ "gs.testeff.rmlv" ] }, { "page": "gs.vc.rrblup", "title": "Estimate variance components for ridge-regression BLUP", "topics": [ "gs.vc.rrblup" ] }, { "page": "gs.w.aov", "title": "Calculate weights or statistics used by the genomic-selection ANOVA method", "topics": [ "gs.w.aov" ] }, { "page": "gs.write.pseff", "title": "Write Marker Effects for the Simulation Backend", "topics": [ "gs.write.pseff" ] }, { "page": "homozygote", "title": "homozygote()", "topics": [ "homozygote" ] }, { "page": "il.eval.library", "title": "Construct or evaluate introgression-line libraries", "topics": [ "il.eval.library" ] }, { "page": "il.eval.lines", "title": "Construct or evaluate introgression-line libraries", "topics": [ "il.eval.lines" ] }, { "page": "il.ideal.library", "title": "Construct or evaluate introgression-line libraries", "topics": [ "il.ideal.library" ] }, { "page": "il.overlapping.library", "title": "Construct or evaluate introgression-line libraries", "topics": [ "il.overlapping.library" ] }, { "page": "info", "title": "Print or handle an information message", "topics": [ "info" ] }, { "page": "info.cat", "title": "Emit information-level-controlled status output", "topics": [ "info.cat" ] }, { "page": "init.population", "title": "init.population()", "topics": [ "init.population" ] }, { "page": "lib00.map1", "title": "Linkage Map for Marker-Assisted Backcrossing Examples", "topics": [ "lib00.map1" ] }, { "page": "lib00.map1a", "title": "Reduced Linkage Map for Marker-Assisted Backcrossing Examples", "topics": [ "lib00.map1a" ] }, { "page": "lib00.map2", "title": "Linkage Map for Three-Stage Marker-Assisted Backcrossing", "topics": [ "lib00.map2" ] }, { "page": "linkage.drag", "title": "Calculate or summarize linkage drag", "topics": [ "linkage.drag" ] }, { "page": "linkage.map.get", "title": "Get a linkage map used by the simulation routines", "topics": [ "linkage.map.get" ] }, { "page": "linkage.map.load", "title": "Load a linkage map used by the simulation routines", "topics": [ "linkage.map.load" ] }, { "page": "linkage.map.save", "title": "Save a linkage map used by the simulation routines", "topics": [ "linkage.map.save" ] }, { "page": "list.effects", "title": "list.effects()", "topics": [ "list.effects" ] }, { "page": "list.populations", "title": "list.populations", "topics": [ "list.populations" ] }, { "page": "load.effmap", "title": "load.effmap()", "topics": [ "load.effmap" ] }, { "page": "load.internal.effmap", "title": "Load an internal effect map", "topics": [ "load.internal.effmap" ] }, { "page": "load.linkage.map", "title": "load.linkage.map()", "topics": [ "load.linkage.map" ] }, { "page": "mab.compare", "title": "Run and Compare a Series of Marker-Assisted Backcrossing Simulations", "topics": [ "mab.compare" ] }, { "page": "mab.df", "title": "Helper used by the marker-assisted backcross simulation routines", "topics": [ "mab.df" ] }, { "page": "mab.Examples", "title": "mab.Examples", "topics": [ "mab.Examples" ] }, { "page": "mab.Input.files", "title": "Structure of input files for the optimize-mab routines.", "topics": [ "mab.Input.files" ] }, { "page": "mab.load.data", "title": "Loads the data of a simulation", "topics": [ "mab.load.data" ] }, { "page": "mab.save.inds", "title": "Helper used by the marker-assisted backcross simulation routines", "topics": [ "mab.save.inds" ] }, { "page": "mab.simulate", "title": "Simulates a marker-assisted backcrossing program", "topics": [ "mab.simulate" ] }, { "page": "mab.tabulate", "title": "Tabulate the results of a series of simulations", "topics": [ "mab.tabulate" ] }, { "page": "masbc.input", "title": "Input Files for Marker-Assisted Backcrossing Examples", "topics": [ "masbc.input" ] }, { "page": "Md_technow", "title": "Technow Dent Marker Data", "topics": [ "Md_technow" ] }, { "page": "Mf_technow", "title": "Technow Flint Marker Data", "topics": [ "Mf_technow" ] }, { "page": "optimize.population", "title": "Optimize a population using the package selection routines", "topics": [ "optimize.population" ] }, { "page": "ph.linkage.map.create", "title": "Create a linkage map for phenotype or simulation use", "topics": [ "ph.linkage.map.create" ] }, { "page": "phenotype.population", "title": "Generate phenotypic values for a simulation population", "topics": [ "phenotype.population" ] }, { "page": "plabsim", "title": "Perform the SelectionTools operation \"plabsim\"", "topics": [ "plabsim" ] }, { "page": "plabsim.init", "title": "Initialize the PLABSIM simulation state", "topics": [ "plabsim.init" ] }, { "page": "plabsim.R.date", "title": "Perform the SelectionTools operation \"plabsim R date\"", "topics": [ "plabsim.R.date" ] }, { "page": "plabsim.R.version", "title": "Perform the SelectionTools operation \"plabsim R version\"", "topics": [ "plabsim.R.version" ] }, { "page": "plabsim.version", "title": "Perform the SelectionTools operation \"plabsim version\"", "topics": [ "plabsim.version" ] }, { "page": "plant", "title": "Create or process a plant object in the simulation framework", "topics": [ "plant" ] }, { "page": "population.append", "title": "Append a copy of a simulation population", "topics": [ "population.append" ] }, { "page": "population.concat", "title": "Concatenate Simulation Populations", "topics": [ "population.concat" ] }, { "page": "population.copy", "title": "Copy a simulation population", "topics": [ "population.copy" ] }, { "page": "population.divide", "title": "Divide a simulation population", "topics": [ "population.divide" ] }, { "page": "population.exist", "title": "Check whether a simulation population exists", "topics": [ "population.exist" ] }, { "page": "population.individual.remove", "title": "Individual remove a population or population data", "topics": [ "population.individual.remove" ] }, { "page": "population.info.get", "title": "Return stored information for an individual", "topics": [ "population.info.get" ] }, { "page": "population.info.set", "title": "Set stored information for an individual", "topics": [ "population.info.set" ] }, { "page": "population.list", "title": "List a population or population data", "topics": [ "population.list" ] }, { "page": "population.matrix.load", "title": "Matrix load a population or population data", "topics": [ "population.matrix.load" ] }, { "page": "population.matrix.save", "title": "Matrix save a population or population data", "topics": [ "population.matrix.save" ] }, { "page": "population.name.swap", "title": "Swap the names of two simulation populations", "topics": [ "population.name.swap" ] }, { "page": "population.optimize", "title": "Optimize storage for simulation populations", "topics": [ "population.optimize" ] }, { "page": "population.plabsim.load", "title": "Load a population from PLABSIM-style data", "topics": [ "population.plabsim.load" ] }, { "page": "population.plabsim.save", "title": "Save a population in PLABSIM-style format", "topics": [ "population.plabsim.save" ] }, { "page": "population.remove", "title": "Remove a population or population data", "topics": [ "population.remove" ] }, { "page": "population.remove.all", "title": "Remove all a population or population data", "topics": [ "population.remove.all" ] }, { "page": "population.rename", "title": "Rename a simulation population", "topics": [ "population.rename" ] }, { "page": "population.resize", "title": "Resize a population or population data", "topics": [ "population.resize" ] }, { "page": "population.sample", "title": "Sample a simulation population", "topics": [ "population.sample" ] }, { "page": "population.size.get", "title": "Return the size and allocated capacity of a simulation population", "topics": [ "population.size.get" ] }, { "page": "population.sort", "title": "Sort a simulation population by genetic or phenotypic value", "topics": [ "population.sort" ] }, { "page": "population.swap.name", "title": "Swap simulation population names", "topics": [ "population.swap.name" ] }, { "page": "population.transfer", "title": "Transfer a population or population data", "topics": [ "population.transfer" ] }, { "page": "read.vcf", "title": "Read a Beagle-Oriented VCF into SelectionTools", "topics": [ "read.vcf" ] }, { "page": "remove.all.populations", "title": "remove.all.populations()", "topics": [ "remove.all.populations" ] }, { "page": "remove.effmaps", "title": "remove.effmaps()", "topics": [ "remove.effmaps" ] }, { "page": "remove.evaluate.population", "title": "Remove genetic and phenotypic evaluation values", "topics": [ "remove.evaluate.population" ] }, { "page": "remove.genotype.population", "title": "Remove cached genotype information from a population", "topics": [ "remove.genotype.population" ] }, { "page": "remove.map", "title": "Remove the linkage map from the simulation", "topics": [ "remove.map" ] }, { "page": "remove.population", "title": "remove.population()", "topics": [ "remove.population" ] }, { "page": "rename.population", "title": "rename.population()", "topics": [ "rename.population" ] }, { "page": "reset.all", "title": "reset.all()", "topics": [ "reset.all" ] }, { "page": "reset.mdp", "title": "Reset marker-assisted donor-parent information", "topics": [ "reset.mdp" ] }, { "page": "resize.population", "title": "Resize a population", "topics": [ "resize.population" ] }, { "page": "resources", "title": "Return or display resource information used by SelectionTools", "topics": [ "resources" ] }, { "page": "return.population", "title": "return.population()", "topics": [ "return.population" ] }, { "page": "rng.choose", "title": "Choose the simulation random-number generator state", "topics": [ "rng.choose" ] }, { "page": "rng.info", "title": "Info the simulation random-number generator state", "topics": [ "rng.info" ] }, { "page": "rng.init", "title": "Initialize the random-number generators", "topics": [ "rng.init" ] }, { "page": "rng.list", "title": "List the simulation random-number generator state", "topics": [ "rng.list" ] }, { "page": "sample.population", "title": "sample.population()", "topics": [ "sample.population" ] }, { "page": "save.linkage.map", "title": "Save a linkage map", "topics": [ "save.linkage.map" ] }, { "page": "sdev", "title": "Calculate a standard-deviation quantity used by the simulation code", "topics": [ "sdev" ] }, { "page": "sel.target.define", "title": "Define a selection target", "topics": [ "sel.target.define" ] }, { "page": "select.all.best", "title": "Select all individuals in the best value classes", "topics": [ "select.all.best" ] }, { "page": "select.all.best.intern", "title": "Determine the best value classes in a sorted population", "topics": [ "select.all.best.intern" ] }, { "page": "select.genotypes", "title": "Select specific allele combinations from populations", "topics": [ "select.genotypes" ] }, { "page": "select.n.best", "title": "Select a fixed number of best individuals", "topics": [ "select.n.best" ] }, { "page": "select.n.best.segments", "title": "Select the best genome segments according to the requested criterion", "topics": [ "select.n.best.segments" ] }, { "page": "set.co.freq", "title": "Set crossover-frequency information", "topics": [ "set.co.freq" ] }, { "page": "set.eff.weigth", "title": "set.eff.weight()", "topics": [ "set.eff.weight" ] }, { "page": "set.genome.par", "title": "set.genome.par()", "topics": [ "set.genome.par" ] }, { "page": "set.info.level", "title": "set.info.level()", "topics": [ "set.info.level" ] }, { "page": "set.mdp", "title": "Set marker-assisted donor-parent information", "topics": [ "set.mdp" ] }, { "page": "set.NoLociInit", "title": "Set the initial number of loci used by the simulation", "topics": [ "set.NoLociInit" ] }, { "page": "set.population.gvalue", "title": "Set genetic selection values for a simulation population", "topics": [ "set.population.gvalue" ] }, { "page": "set.population.info", "title": "Set population information used by the simulation routines", "topics": [ "set.population.info" ] }, { "page": "show.phase", "title": "Display a Compact Statistical Phasing Summary", "topics": [ "show.phase" ] }, { "page": "single.cross", "title": "Create or evaluate a single cross", "topics": [ "single.cross" ] }, { "page": "sm.start.timer", "title": "Start or stop the simulation timing helper", "topics": [ "sm.start.timer" ] }, { "page": "sm.stop.timer", "title": "Start or stop the simulation timing helper", "topics": [ "sm.stop.timer" ] }, { "page": "splitdt", "title": "Split a data object according to the package-specific convention", "topics": [ "splitdt" ] }, { "page": "ssd.mating", "title": "ssd.mating()", "topics": [ "ssd.mating" ] }, { "page": "st_mixed", "title": "Fit a mixed linear model", "topics": [ "st_mixed" ] }, { "page": "st.calc.ld", "title": "Calculate Linkage Disequilibrium from Marker Data", "topics": [ "st.calc.ld" ] }, { "page": "st.calc.ld.2", "title": "Calculate linkage disequilibrium from marker data", "topics": [ "st.calc.ld.2" ] }, { "page": "st.calc.q", "title": "Calculate the package-specific Q statistic or quantity", "topics": [ "st.calc.q" ] }, { "page": "st.calc.rf", "title": "Calculate recombination fractions", "topics": [ "st.calc.rf" ] }, { "page": "st.enrichment", "title": "Calculate Haplotype Enrichment and Select Donor Genotypes", "topics": [ "st.calculate.enrichment", "st.select.enrichment" ] }, { "page": "st.chrom.stats", "title": "Return chromosome statistics for a data set", "topics": [ "st.chrom.stats" ] }, { "page": "st.compact.data.set", "title": "Compact a SelectionTools Marker Data Set", "topics": [ "st.compact.data.set" ] }, { "page": "st.copy.marker.data", "title": "st.copy.marker.data()", "topics": [ "st.copy.marker.data" ] }, { "page": "st.data.set.list", "title": "List SelectionTools Marker Data Sets", "topics": [ "print.st.data.set.list", "st.data.set.list" ] }, { "page": "st.data.set.remove", "title": "Remove a SelectionTools Marker Data Set", "topics": [ "st.data.set.remove" ] }, { "page": "st.data.set.remove.all", "title": "Remove All SelectionTools Marker Data Sets", "topics": [ "st.data.set.remove.all" ] }, { "page": "st.datadir", "title": "Construct a path in the SelectionTools data directory", "topics": [ "st.datadir" ] }, { "page": "st.dataframe.to.STvcf", "title": "Convert a VCF-Like Data Frame to Compact STvcf Format", "topics": [ "st.dataframe.to.STvcf" ] }, { "page": "st.dd", "title": "Construct a path in the SelectionTools data directory", "topics": [ "st.dd" ] }, { "page": "st.def.hblocks", "title": "Define Haplotype Blocks", "topics": [ "st.def.hblocks" ] }, { "page": "st.destroy.phase", "title": "Randomize the Stored Phase of a Marker Data Set", "topics": [ "st.destroy.phase" ] }, { "page": "st.genetic.distances", "title": "st.genetic.distances()", "topics": [ "st.genetic.distances" ] }, { "page": "st.genetic.distances.02", "title": "Calculate genetic distances from SelectionTools marker data", "topics": [ "st.genetic.distances.02" ] }, { "page": "st.genetic.distances.fct", "title": "Calculate genetic distances from SelectionTools marker data", "topics": [ "st.genetic.distances.fct" ] }, { "page": "st.get.info.level", "title": "Return the current SelectionTools information level", "topics": [ "st.get.info.level" ] }, { "page": "st.get.map", "title": "Return the linkage map for a SelectionTools data set", "topics": [ "st.get.map" ] }, { "page": "st.get.num.threads", "title": "Return the configured number of computational threads", "topics": [ "st.get.num.threads" ] }, { "page": "st.get.simpop", "title": "Return Simulation-Population Data in SelectionTools Format", "topics": [ "st.get.simpop" ] }, { "page": "st.get.simpop.perfdata", "title": "Return simulation-population data in SelectionTools format", "topics": [ "st.get.simpop.perfdata" ] }, { "page": "st.get.simpop2", "title": "Return Simulation-Population Marker Data without a Linkage Map", "topics": [ "st.get.simpop2" ] }, { "page": "st.id", "title": "Construct a path in the SelectionTools input directory", "topics": [ "st.id" ] }, { "page": "st.indir", "title": "Construct a path in the SelectionTools input directory", "topics": [ "st.indir" ] }, { "page": "st.info", "title": "Print or handle a SelectionTools information message", "topics": [ "st.info" ] }, { "page": "st.keep.intersection.markers", "title": "Keep the Marker Intersection of Two SelectionTools Data Sets", "topics": [ "st.keep.intersection.markers" ] }, { "page": "st.LDheatmap", "title": "Plot a Linkage Disequilibrium Heat Map", "topics": [ "st.LDheatmap" ] }, { "page": "st.LDplot.ld", "title": "Prepare linkage-disequilibrium information for plotting", "topics": [ "st.LDplot.ld" ] }, { "page": "st.LDplot.map", "title": "Prepare linkage-disequilibrium information for plotting", "topics": [ "st.LDplot.map" ] }, { "page": "st.load.performance.data", "title": "Load Performance Data from an R Data Set", "topics": [ "st.load.performance.data" ] }, { "page": "st.load.vcf.data", "title": "Load Compact STvcf Marker and Linkage-Map Data", "topics": [ "st.load.vcf.data" ] }, { "page": "st.mark.alleles", "title": "Identify markers by effect and replace selected marker alleles in marker data", "topics": [ "st.mark.alleles" ] }, { "page": "st.marker.data.statistics", "title": "Summarize a SelectionTools Marker Data Set", "topics": [ "st.marker.data.statistics" ] }, { "page": "st.markerdata.to.STvcf", "title": "Convert a SelectionTools Marker Data Set to STvcf", "topics": [ "st.markerdata.to.STvcf" ] }, { "page": "st.mxd", "title": "Fit the package multi-kernel mixed-model routine", "topics": [ "st.mxd" ] }, { "page": "st.od", "title": "Construct a path in the SelectionTools output directory", "topics": [ "st.od" ] }, { "page": "st.outdir", "title": "Construct a path in the SelectionTools output directory", "topics": [ "st.outdir" ] }, { "page": "st.phase", "title": "Cohort and Reference-Assisted Phasing of Diploid Genotypes", "topics": [ "st.phase" ] }, { "page": "st.phase.v1", "title": "Statistical Phasing and Missing-Genotype Imputation of Diploid Marker Data", "topics": [ "st.phase.v1" ] }, { "page": "st.plot.corr", "title": "Plot correlation information from SelectionTools results", "topics": [ "st.plot.corr" ] }, { "page": "st.plot.corr.l", "title": "Plot correlation information from SelectionTools results", "topics": [ "st.plot.corr.l" ] }, { "page": "st.plot.gene.diversity", "title": "st.plot.gene.diversity()", "topics": [ "st.plot.gene.diversity" ] }, { "page": "st.plot.ggt", "title": "Plot Graphical Genotypes", "topics": [ "st.plot.ggt" ] }, { "page": "st.plot.ggt.src", "title": "Plot Graphical Genotypes from Map and Genotype Objects", "topics": [ "st.plot.ggt.src" ] }, { "page": "st.read.map", "title": "st.read.map()", "topics": [ "st.read.map" ] }, { "page": "st.read.map.df", "title": "Load a marker map from a data frame or matrix", "topics": [ "st.read.map.df" ] }, { "page": "st.read.marker.data", "title": "st.read.marker.data()", "topics": [ "st.read.marker.data" ] }, { "page": "st.read.marker.data.df", "title": "Load marker data from an R data frame or matrix", "topics": [ "st.read.marker.data.df" ] }, { "page": "st.read.performance.data", "title": "st.read.performance.data()", "topics": [ "st.read.performance.data" ] }, { "page": "st.recode.hbc", "title": "st.recode.hbc()", "topics": [ "st.recode.hbc" ] }, { "page": "st.recode.hil", "title": "Recode Defined Haplotype Blocks as Marker Loci", "topics": [ "st.recode.hil" ] }, { "page": "st.recode.ref", "title": "Recode Marker Alleles Relative to a Reference Individual", "topics": [ "st.recode.ref" ] }, { "page": "st.recode.ref.2", "title": "Recode reference-marker information using the package-specific convention", "topics": [ "st.recode.ref.2" ] }, { "page": "st.reset", "title": "Reset SelectionTools data and settings", "topics": [ "st.reset" ] }, { "page": "st.restrict.marker", "title": "st.restrict.marker.data()", "topics": [ "st.restrict.marker.data" ] }, { "page": "st.return.performance.data", "title": "Return performance data from a SelectionTools data set", "topics": [ "st.return.performance.data" ] }, { "page": "st.select.phen", "title": "Select individuals using phenotypic information", "topics": [ "st.select.phen" ] }, { "page": "st.set.hblocks", "title": "Set haplotype-block information", "topics": [ "st.set.hblocks" ] }, { "page": "st.set.info.level", "title": "Set info level used by SelectionTools", "topics": [ "st.set.info.level" ] }, { "page": "st.set.matrix.ops", "title": "Set matrix ops used by SelectionTools", "topics": [ "st.set.matrix.ops" ] }, { "page": "st.set.num.threads", "title": "Set num threads used by SelectionTools", "topics": [ "st.set.num.threads" ] }, { "page": "st.set.openblas.threads", "title": "Set openblas threads used by SelectionTools", "topics": [ "st.set.openblas.threads" ] }, { "page": "st.set.sim.ef", "title": "Transfer Marker Effects to the Simulation Backend", "topics": [ "st.set.sim.ef" ] }, { "page": "st.set.sim.gp", "title": "Set sim gp used by SelectionTools", "topics": [ "st.set.sim.gp" ] }, { "page": "st.set.sim.mp", "title": "Set sim mp used by SelectionTools", "topics": [ "st.set.sim.mp" ] }, { "page": "st.set.sim.pp", "title": "Transfer a Marker Population to the Simulation Backend", "topics": [ "st.set.sim.pp" ] }, { "page": "st.set.simpop", "title": "Initialize the Simulation Backend from a SelectionTools Data Set", "topics": [ "st.set.simpop" ] }, { "page": "st.start.timer", "title": "Start or stop the SelectionTools timing helper", "topics": [ "st.start.timer" ] }, { "page": "st.stop.timer", "title": "Start or stop the SelectionTools timing helper", "topics": [ "st.stop.timer" ] }, { "page": "st.STvcf.to.dataframe", "title": "Convert Compact STvcf Data to a VCF-Like Data Frame", "topics": [ "st.STvcf.to.dataframe" ] }, { "page": "st.switch.error", "title": "Calculate Switch Error against Known Phase", "topics": [ "print.st.switch.error", "st.switch.error" ] }, { "page": "st.write.map", "title": "Write linkage-map information for a SelectionTools data set", "topics": [ "st.write.map" ] }, { "page": "st.write.marker.data", "title": "st.write.marker.data()", "topics": [ "st.write.marker.data" ] }, { "page": "summarize.gvalue", "title": "summarize.gvalue()", "topics": [ "summarize.gvalue" ] }, { "page": "swap.population.name", "title": "Swap population names", "topics": [ "swap.population.name" ] }, { "page": "talk.to.me", "title": "Enable or control SelectionTools console output", "topics": [ "talk.to.me" ] }, { "page": "v-tropmaize-map", "title": "Genetic Map for Tropical Maize", "topics": [ "v-tropmaize-map", "v.tropmaize.map" ] }, { "page": "v-tropmaize-phe", "title": "Phenotypic Data for Tropical Maize", "topics": [ "v-tropmaize-phe", "v.tropmaize.phe" ] }, { "page": "v-tropmaize-pop", "title": "Genotype Data for Tropical Maize", "topics": [ "v-tropmaize-pop", "v.tropmaize.pop" ] }, { "page": "v-tropmaize-vcf", "title": "Compact STvcf Genotype and Genetic-Map Data for Tropical Maize", "topics": [ "v-tropmaize-vcf", "v.tropmaize.vcf" ] }, { "page": "write.vcf", "title": "Write SelectionTools Marker Data for Beagle", "topics": [ "write.vcf" ] }, { "page": "write.version.2", "title": "Write version information in the package-specific format", "topics": [ "write.version.2" ] } ], "_rundeps": [], "_sysdeps": [ { "shlib": "liblapack", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_vignettes": [ { "source": "v-hapld.Rnw", "filename": "v-hapld.pdf", "title": "Linkage disequilibrium based haplotype blocks", "engine": "utils::Sweave", "headings": [], "created": "2026-09-21 10:10:15", "modified": "2026-09-21 10:10:15", "commits": 1 }, { "source": "v-masbc.Rnw", "filename": "v-masbc.pdf", "title": "Marker-Assisted Backcrossing", "engine": "utils::Sweave", "headings": [], "created": "2026-10-09 16:21:21", "modified": "2026-10-09 16:21:21", "commits": 1 }, { "source": "v-cross.Rnw", "filename": "v-cross.pdf", "title": "Planing crosses", "engine": "utils::Sweave", "headings": [], "created": "2026-09-21 10:10:15", "modified": "2026-09-21 10:10:15", "commits": 1 }, { "source": "v-simbp.Rnw", "filename": "v-simbp.pdf", "title": "Simulating Breeding Programs", "engine": "utils::Sweave", "headings": [], "created": "2026-09-15 10:40:21", "modified": "2026-09-21 10:10:15", "commits": 2 }, { "source": "v-simmd.Rnw", "filename": "v-simmd.pdf", "title": "Simulating Mendel's Experiments", "engine": "utils::Sweave", "headings": [], "created": "2026-10-09 16:21:21", "modified": "2026-10-09 16:21:21", "commits": 1 }, { "source": "v-phase.Rnw", "filename": "v-phase.pdf", "title": "Statistical phasing with SelectionTools", "engine": "utils::Sweave", "headings": [], "created": "2026-09-21 10:10:15", "modified": "2026-10-09 16:21:21", "commits": 2 } ], "_score": 3.2552725051033065, "_indexed": true, "_nocasepkg": "selectiontools", "_universes": [ "popgen-giessen" ], "_previous": "26.4", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "26.5", "date": "2026-10-09T17:07:56.000Z", "distro": "resolute", "arch": "aarch64", "commit": "459ed67694735ae1e9881c634d72cc4f4d55d6d1", "fileid": "https://r2.ropensci.org/6776013778281ca918c1cb0995dfdb4fb037f936c419702d20756d98fdcdc142", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/popgen-giessen/actions/runs/37963125529" }, { "r": "4.7.0", "os": "linux", "version": "26.5", "date": "2026-10-09T17:07:29.000Z", "distro": "resolute", "arch": "x86_64", "commit": "459ed67694735ae1e9881c634d72cc4f4d55d6d1", "fileid": "https://r2.ropensci.org/3045800ce5f99d5dc97d13c945e061456e407243d4f09d657af0e319e221b39c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/popgen-giessen/actions/runs/37963125529" }, { "r": "4.6.1", "os": "linux", "version": "26.5", "date": "2026-10-09T17:07:19.000Z", "distro": "resolute", "arch": "aarch64", "commit": "459ed67694735ae1e9881c634d72cc4f4d55d6d1", "fileid": "https://r2.ropensci.org/483b8737a33b8ae0552eb519bf7919be631ee00dd3a5810b235bef1753300de2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/popgen-giessen/actions/runs/37963125529" }, { "r": "4.6.1", "os": "linux", "version": "26.5", "date": "2026-10-09T17:07:41.000Z", "distro": "resolute", "arch": "x86_64", "commit": "459ed67694735ae1e9881c634d72cc4f4d55d6d1", "fileid": "https://r2.ropensci.org/1565192444a42774159207eb0597c5dbbb6d80c210f4d82ea64157df9cf4b4f1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/popgen-giessen/actions/runs/37963125529" }, { "r": "4.5.3", "os": "mac", "version": "26.5", "date": "2026-10-09T17:27:56.000Z", "arch": "aarch64", "commit": "459ed67694735ae1e9881c634d72cc4f4d55d6d1", "fileid": "https://r2.ropensci.org/bd6271cbce1176b4c5a4b7d5d101dee349fb5d7d362e697659f8a7c8a2071c53", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/popgen-giessen/actions/runs/37963125529" }, { "r": "4.5.3", "os": "mac", "version": "26.5", "date": "2026-10-09T17:29:06.000Z", "arch": "x86_64", "commit": "459ed67694735ae1e9881c634d72cc4f4d55d6d1", "fileid": "https://r2.ropensci.org/fa1f3a4f8d6565a3c6a02732eff7036f8cd9da400a5b7f10907f0896ab3ce87c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/popgen-giessen/actions/runs/37963125529" }, { "r": "4.6.1", "os": "mac", "version": "26.5", "date": "2026-10-09T17:26:18.000Z", "arch": "aarch64", "commit": "459ed67694735ae1e9881c634d72cc4f4d55d6d1", "fileid": "https://r2.ropensci.org/943ffe47a6c092cd7fced0afcfafec85505e00aba9bb52d5c91902e7acc52761", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/popgen-giessen/actions/runs/37963125529" }, { "r": "4.6.1", "os": "mac", "version": "26.5", "date": "2026-10-09T17:31:30.000Z", "arch": "x86_64", "commit": "459ed67694735ae1e9881c634d72cc4f4d55d6d1", "fileid": "https://r2.ropensci.org/6d5cc713441fad80489b5c3e35325330c2bb0d7fb0dd29d0ee0a3784e5708bbf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/popgen-giessen/actions/runs/37963125529" }, { "r": "4.6.0", "os": "wasm", "version": "26.5", "date": "2026-10-09T17:07:32.000Z", "arch": "emscripten", "commit": "459ed67694735ae1e9881c634d72cc4f4d55d6d1", "fileid": "https://r2.ropensci.org/362a5f7a74de6a43f959c62eaa4a8be064a75443bbdc9a626179808a9072d50e", "status": "success", "buildurl": "https://github.com/r-universe/popgen-giessen/actions/runs/37963125529" }, { "r": "4.7.0", "os": "win", "version": "26.5", "date": "2026-10-09T17:11:06.000Z", "arch": "aarch64", "commit": "459ed67694735ae1e9881c634d72cc4f4d55d6d1", "fileid": "https://r2.ropensci.org/857d9055241f547d185994b21cf57cbd510a95567674a2af1200d106e4b8287f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/popgen-giessen/actions/runs/37963125529" }, { "r": "4.7.0", "os": "win", "version": "26.5", "date": "2026-10-09T17:07:01.000Z", "arch": "x86_64", "commit": "459ed67694735ae1e9881c634d72cc4f4d55d6d1", "fileid": "https://r2.ropensci.org/73061218f52544ceaab1966558a2fd32709c3ef2f20b9b19f794f8bd47ca894f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/popgen-giessen/actions/runs/37963125529" }, { "r": "4.5.3", "os": "win", "version": "26.5", "date": "2026-10-09T17:06:57.000Z", "arch": "x86_64", "commit": "459ed67694735ae1e9881c634d72cc4f4d55d6d1", "fileid": "https://r2.ropensci.org/ca1a7a64556c5eb428a6dfa4a8277b3d195a4c40d356bb0f94bda85f4ee86d54", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/popgen-giessen/actions/runs/37963125529" }, { "r": "4.6.1", "os": "win", "version": "26.5", "date": "2026-10-09T17:10:52.000Z", "arch": "aarch64", "commit": "459ed67694735ae1e9881c634d72cc4f4d55d6d1", "fileid": "https://r2.ropensci.org/470a427f89101d05362acb63d3396dce06b97233de93812689709b0acea7e260", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/popgen-giessen/actions/runs/37963125529" }, { "r": "4.6.1", "os": "win", "version": "26.5", "date": "2026-10-09T17:06:53.000Z", "arch": "x86_64", "commit": "459ed67694735ae1e9881c634d72cc4f4d55d6d1", "fileid": "https://r2.ropensci.org/71ef87817ee47642689b58c3d4ee906fe188c46b9ef238b9a27d0161da58fb10", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/popgen-giessen/actions/runs/37963125529" } ] }