{ "_id": "6a1165daacfb0bcc41cf04f7", "Package": "AlphaSimR", "Type": "Package", "Title": "Breeding Program Simulations", "Version": "2.1.0", "Date": "2025-11-08", "Authors@R": "c(person(\"Chris\", \"Gaynor\", email = \"gaynor.robert@hotmail.com\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-0558-6656\")),\nperson(\"Gregor\", \"Gorjanc\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0001-8008-2787\")),\nperson(\"John\", \"Hickey\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0001-5675-3974\")),\nperson(\"Daniel\", \"Money\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0001-5151-3648\")),\nperson(\"David\", \"Wilson\", role = \"ctb\"),\nperson(\"Thiago\", \"Oliveira\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-4555-2584\")),\nperson(\"Audrey\", \"Martin\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-2235-0098\")),\nperson(\"Philip\", \"Greenspoon\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0001-6284-7248\")),\nperson(\"Ros\", \"Craddock\", role = \"ctb\",\ncomment = c(ORCID = \"0009-0004-1578-1580\")),\nperson(\"Jana\", \"Obsteter\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-1511-3916\")))", "Description": "The successor to the 'AlphaSim' software for breeding\nprogram simulation [Faux et al. (2016)\n]. Used for stochastic\nsimulations of breeding programs to the level of DNA sequence\nfor every individual. Contained is a wide range of functions\nfor modeling common tasks in a breeding program, such as\nselection and crossing. These functions allow for constructing\nsimulations of highly complex plant and animal breeding\nprograms via scripting in the R software environment. Such\nsimulations can be used to evaluate overall breeding program\nperformance and conduct research into breeding program design,\nsuch as implementation of genomic selection. Included is the\n'Markovian Coalescent Simulator' ('MaCS') for fast simulation\nof biallelic sequences according to a population demographic\nhistory [Chen et al. (2009) ].", "License": "MIT + file LICENSE", "URL": "https://github.com/gaynorr/AlphaSimR,\nhttps://gaynorr.github.io/AlphaSimR/,\nhttps://www.edx.org/learn/animal-breeding/the-university-of-edinburgh-breeding-programme-modelling-with-alphasimr", "Encoding": "UTF-8", "RdMacros": "Rdpack", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "NeedsCompilation": "yes", "Repository": "https://gaynorr.r-universe.dev", "Date/Publication": "2025-11-24 15:52:35 UTC", "RemoteUrl": "https://github.com/gaynorr/alphasimr", "RemoteRef": "HEAD", "RemoteSha": "0a60280b8c9c65aaf8afcaee031e3498decd3b21", "Packaged": { "Date": "2026-05-23 08:15:39 UTC", "User": "root" }, "Author": "Chris Gaynor [aut, cre] (ORCID:\n),\nGregor Gorjanc [ctb] (ORCID: ),\nJohn Hickey [ctb] (ORCID: ),\nDaniel Money [ctb] (ORCID: ),\nDavid Wilson [ctb],\nThiago Oliveira [ctb] (ORCID: ),\nAudrey Martin [ctb] (ORCID: ),\nPhilip Greenspoon [ctb] (ORCID:\n),\nRos Craddock [ctb] (ORCID: ),\nJana Obsteter [ctb] (ORCID: )", 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"getGenMap", "title": "Get genetic map", "topics": [ "getGenMap" ] }, { "page": "getNumThreads", "title": "Number of available threads", "topics": [ "getNumThreads" ] }, { "page": "getPed", "title": "Get pedigree", "topics": [ "getPed" ] }, { "page": "getQtlMap", "title": "Get QTL genetic map", "topics": [ "getQtlMap" ] }, { "page": "getSnpMap", "title": "Get SNP genetic map", "topics": [ "getSnpMap" ] }, { "page": "gv", "title": "Genetic value", "topics": [ "gv" ] }, { "page": "hybridCross", "title": "Hybrid crossing", "topics": [ "hybridCross" ] }, { "page": "HybridPop-class", "title": "Hybrid population", "topics": [ "c,HybridPop-method", "HybridPop-class", "isHybridPop", "[,HybridPop-method" ] }, { "page": "importGenMap", "title": "Import genetic map", "topics": [ "importGenMap" ] }, { "page": "importHaplo", "title": "Import haplotypes", "topics": [ "importHaplo" ] }, { "page": "importInbredGeno", "title": "Import inbred, diploid genotypes", "topics": [ "importInbredGeno" ] }, { "page": "isFemale", "title": "Test if individuals of a population are female or male", "topics": [ "isFemale", "isMale" ] }, { "page": "isPop", "title": "Test if object is of a Population class", "topics": [ "isPop" ] }, { "page": "LociMap-class", "title": "Loci metadata", "topics": [ "LociMap-class" ] }, { "page": "makeCross", "title": "Make designed crosses", "topics": [ "makeCross" ] }, { "page": "makeCross2", "title": "Make designed crosses", "topics": [ "makeCross2" ] }, { "page": "makeDH", "title": "Generates DH lines", "topics": [ "makeDH" ] }, { "page": "MapPop-class", "title": "Raw population with genetic map", "topics": [ "c,MapPop-method", "isMapPop", "MapPop-class", "[,MapPop-method" ] }, { "page": "meanEBV", "title": "Mean estimated breeding values", "topics": [ "meanEBV" ] }, { "page": "meanG", "title": "Mean genetic values", "topics": [ "meanG" ] }, { "page": "meanP", "title": "Mean phenotypic values", "topics": [ "meanP" ] }, { "page": "mendelianSampling", "title": 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