{ "_id": "6a0f6abfacfb0bcc41c5e3b3", "Package": "SIMplyBee", "Type": "Package", "Title": "'AlphaSimR' Extension for Simulating Honeybee Populations and\nBreeding Programmes", "Version": "0.4.1", "Authors@R": "c(\nperson(\"Jana\", \"Obšteter\", email = \"obsteter.jana@gmail.com\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-1511-3916\")),\nperson(\"Laura\", \"Strachan\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-2569-0250\")),\nperson(\"Jernej\", \"Bubnič\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-1362-3736\")),\nperson(\"Gregor\", \"Gorjanc\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0001-8008-2787\")))", "Description": "An extension of the 'AlphaSimR' package\n() for stochastic\nsimulations of honeybee populations and breeding programmes.\n'SIMplyBee' enables simulation of individual bees that form a\ncolony, which includes a queen, fathers (drones the queen mated\nwith), virgin queens, workers, and drones. Multiple colony can\nbe merged into a population of colonies, such as an apiary or a\nwhole country of colonies. Functions enable operations on\ncastes, colony, or colonies, to ease 'R' scripting of whole\npopulations. All 'AlphaSimR' functionality with respect to\ngenomes and genetic and phenotype values is available and\nfurther extended for honeybees, including haplo-diploidy,\ncomplementary sex determiner locus, colony events (swarming,\nsupersedure, etc.), and colony phenotype values.", "URL": "https://github.com/HighlanderLab/SIMplyBee", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "Config/Needs/website": "tidyverse/tidytemplate", "VignetteBuilder": "knitr", "Repository": "https://highlanderlab.r-universe.dev", "Date/Publication": "2024-09-19 06:02:22 UTC", "RemoteUrl": "https://github.com/highlanderlab/SIMplyBee", "RemoteRef": "HEAD", "RemoteSha": "01a56eebb9efbb23e3e6113cbf9fdb3b99504bf9", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-21 08:38:47 UTC", "User": "root" }, "Author": "Jana Obšteter [aut, cre] (ORCID:\n),\nLaura Strachan [aut] (ORCID: ),\nJernej Bubnič [aut] (ORCID: ),\nGregor Gorjanc [aut] (ORCID: )", "Maintainer": "Jana Obšteter ", "MD5sum": "c6878d3617ade54ffbc564d964e8a156", "_user": "highlanderlab", "_type": "src", "_file": "SIMplyBee_0.4.1.tar.gz", "_fileid": "0ab868dfddcc20b3d0e36f53927100cacbaf81b163360387d1b9f6697bc84962", "_filesize": 5328064, "_sha256": "0ab868dfddcc20b3d0e36f53927100cacbaf81b163360387d1b9f6697bc84962", "_created": "2026-05-21T08:38:47.000Z", "_published": "2026-05-21T20:27:43.350Z", "_distro": "noble", "_jobs": [ { "job": 77262131525, "time": 175, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7131158098" }, { "job": 77262131650, "time": 182, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7131160396" }, { "job": 77262131829, "time": 162, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7131153089" }, { "job": 77262131782, "time": 177, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7131158636" }, { "job": 77262131808, "time": 152, "config": 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"methods", "role": "Imports" }, { "package": "R6", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "extraDistr", "version": ">= 1.9.1", "role": "Imports" }, { "package": "RANN", "role": "Imports" }, { "package": "Rcpp", "version": ">= 0.12.7", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "Matrix", "role": "Suggests" } ], "_owner": "highlanderlab", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 3, "_contributors": [ { "user": "gregorgorjanc", "count": 638, "uuid": 725834 }, { "user": "janaobsteter", "count": 333, "uuid": 18226551 }, { "user": "lstrachan", "count": 188, "uuid": 80959752 }, { "user": "jerbub", "count": 41, "uuid": 91527874 }, { "user": "gaynorr", "count": 3, "uuid": 10097653 } ], 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"addVirginQueens", "addWorkers", "areDronesPresent", "areFathersPresent", "areVirginQueensPresent", "areWorkersPresent", "buildUp", "calcBeeAlleleFreq", "calcBeeGRMIbd", "calcBeeGRMIbs", "calcColonyGv", "calcColonyPheno", "calcColonyValue", "calcInheritanceCriterion", "calcPerformanceCriterion", "calcQueensPHomBrood", "calcSelectionCriterion", "collapse", "combine", "createCastePop", "createColony", "createCrossPlan", "createDCA", "createDrones", "createMatingStationDCA", "createMultiColony", "createVirginQueens", "createWorkers", "cross", "downsize", "downsizePUnif", "getCaste", "getCasteId", "getCastePop", "getCasteSex", "getCsdAlleles", "getCsdGeno", "getDrones", "getDronesCsdAlleles", "getDronesCsdGeno", "getDronesGv", "getDronesIbdHaplo", "getDronesPheno", "getDronesQtlGeno", "getDronesQtlHaplo", "getDronesSegSiteGeno", "getDronesSegSiteHaplo", "getDronesSnpGeno", "getDronesSnpHaplo", "getEvents", "getFathers", "getFathersCsdAlleles", "getFathersCsdGeno", "getFathersGv", "getFathersIbdHaplo", "getFathersPheno", "getFathersQtlGeno", "getFathersQtlHaplo", "getFathersSegSiteGeno", "getFathersSegSiteHaplo", "getFathersSnpGeno", "getFathersSnpHaplo", "getGv", "getIbdHaplo", "getId", "getLocation", "getMisc", "getPheno", "getPooledGeno", "getQtlGeno", "getQtlHaplo", "getQueen", "getQueenAge", "getQueenCsdAlleles", "getQueenCsdGeno", "getQueenGv", "getQueenIbdHaplo", "getQueenPheno", "getQueenQtlGeno", "getQueenQtlHaplo", "getQueenSegSiteGeno", "getQueenSegSiteHaplo", "getQueenSnpGeno", "getQueenSnpHaplo", "getQueenYearOfBirth", "getSegSiteGeno", "getSegSiteHaplo", "getSnpGeno", "getSnpHaplo", "getVirginQueens", "getVirginQueensCsdAlleles", "getVirginQueensCsdGeno", "getVirginQueensGv", "getVirginQueensIbdHaplo", "getVirginQueensPheno", "getVirginQueensQtlGeno", "getVirginQueensQtlHaplo", "getVirginQueensSegSiteGeno", "getVirginQueensSegSiteHaplo", "getVirginQueensSnpGeno", "getVirginQueensSnpHaplo", "getWorkers", "getWorkersCsdAlleles", "getWorkersCsdGeno", "getWorkersGv", "getWorkersIbdHaplo", "getWorkersPheno", "getWorkersQtlGeno", "getWorkersQtlHaplo", "getWorkersSegSiteGeno", "getWorkersSegSiteHaplo", "getWorkersSnpGeno", "getWorkersSnpHaplo", "hasCollapsed", "hasSplit", "hasSuperseded", "hasSwarmed", "isCaste", "isColony", "isCsdActive", "isCsdHeterozygous", "isDrone", "isDronesPresent", "isEmpty", "isFather", "isFathersPresent", "isMultiColony", "isNULLColonies", "isProductive", "isQueen", "isQueenPresent", "isSimParamBee", "isVirginQueen", "isVirginQueenPresent", "isVirginQueens", "isVirginQueensPresent", "isWorker", "isWorkersPresent", "mapCasteToColonyGv", "mapCasteToColonyPheno", "mapCasteToColonyValue", "nCaste", "nColonies", "nCsdAlleles", "nDrones", "nDronesColonyPhenotype", "nDronesPoisson", "nDronesTruncPoisson", "nEmptyColonies", "nFathers", "nFathersPoisson", "nFathersTruncPoisson", "nHomBrood", "nNULLColonies", "nQueens", "nVirginQueens", "nVirginQueensColonyPhenotype", "nVirginQueensPoisson", "nVirginQueensTruncPoisson", "nWorkers", "nWorkersColonyPhenotype", "nWorkersPoisson", "nWorkersTruncPoisson", "pHomBrood", "pullCastePop", "pullColonies", "pullDroneGroupsFromDCA", "pullDrones", "pullInd", "pullQueen", "pullVirginQueens", "pullWorkers", "rcircle", "reduceDroneGeno", "reduceDroneHaplo", "removeCastePop", "removeColonies", "removeDrones", "removeQueen", "removeVirginQueens", "removeWorkers", "replaceCastePop", "replaceDrones", "replaceVirginQueens", "replaceWorkers", "reQueen", "resetEvents", "selectColonies", "setLocation", "setMisc", "setQueensYearOfBirth", "SimParamBee", "simulateHoneyBeeGenomes", "split", "splitPColonyStrength", "splitPUnif", "supersede", "swarm", "swarmPUnif" ], "_help": [ { "page": "addCastePop", "title": "Add caste individuals to the colony", "topics": [ "addCastePop", "addDrones", "addVirginQueens", "addWorkers" ] }, { "page": "buildUp", "title": "Build up Colony or MultiColony object by adding (raising) workers and drones", "topics": [ "buildUp" ] }, { "page": "combineNULLAndPop", "title": "Combine a NULL and AlphaSimR population", "topics": [ "c,NULLOrPop-method" ] }, { "page": "calcBeeGRMIbd", "title": "Calculate Genomic Relatedness Matrix (GRM) for honeybees from Identical By Descent genomic data", "topics": [ "calcBeeGRMIbd" ] }, { "page": "calcBeeGRMIbs", "title": "Calculate Genomic Relatedness Matrix (GRM) for honeybees from Identical By State genomic data", "topics": [ "calcBeeAlleleFreq", "calcBeeGRMIbs" ] }, { "page": "calcColonyValue", "title": "Calculate colony value(s)", "topics": [ "calcColonyAa", "calcColonyBv", "calcColonyDd", "calcColonyGv", "calcColonyPheno", "calcColonyValue" ] }, { "page": "calcInheritanceCriterion", "title": "Calculate the inheritance criterion", "topics": [ "calcInheritanceCriterion" ] }, { "page": "calcPerformanceCriterion", "title": "Calculate the performance criterion", "topics": [ "calcPerformanceCriterion" ] }, { "page": "calcQueensPHomBrood", "title": "The expected proportion and a realised number of csd homozygous brood", "topics": [ "calcQueensPHomBrood", "nHomBrood", "pHomBrood" ] }, { "page": "calcSelectionCriterion", "title": "Calculate the selection criterion", "topics": [ "calcSelectionCriterion" ] }, { "page": "collapse", "title": "Collapse", "topics": [ "collapse" ] }, { "page": "Colony-class", "title": "Honeybee colony", "topics": [ "c,ColonyOrNULL-method", "Colony-class", "isColony", "show,Colony-method" ] }, { "page": "combine", "title": "Combine two colony objects", "topics": [ "combine" ] }, { "page": "combineBeeGametes", "title": "Create diploid gametes from a mated queen", "topics": [ "combineBeeGametes" ] }, { "page": "combineBeeGametesHaploDiploid", "title": "Create diploid gametes from a mated queen", "topics": [ "combineBeeGametesHaploDiploid" ] }, { "page": "createCastePop", "title": "Creates caste population individuals from the colony", "topics": [ "createCastePop", "createDrones", "createVirginQueens", "createWorkers" ] }, { "page": "createColony", "title": "Create a new Colony", "topics": [ "createColony" ] }, { "page": "createCrossPlan", "title": "Create a plan for crossing virgin queens", "topics": [ "createCrossPlan" ] }, { "page": "createDCA", "title": "Create a drone congregation area (DCA)", "topics": [ "createDCA" ] }, { "page": "createMatingStationDCA", "title": "Create a DCA of drones at a mating stations", "topics": [ "createMatingStationDCA" ] }, { "page": "createMultiColony", "title": "Create MultiColony object", "topics": [ "createMultiColony" ] }, { "page": "cross", "title": "Cross (mate) virgin queen(s) as a population, of a colony, or of all given colonies", "topics": [ "cross" ] }, { "page": "downsize", "title": "Reduce number of workers and remove all drones and virgin queens from a Colony or MultiColony object", "topics": [ "downsize" ] }, { "page": "downsizePFun", "title": "Sample the downsize proportion - proportion of removed workers in downsizing", "topics": [ "downsizePUnif" ] }, { "page": "editCsdLocus", "title": "Edit the csd locus", "topics": [ "editCsdLocus" ] }, { "page": "getAa", "title": "Access epistasis values of individuals in a caste", "topics": [ "getAa", "getDronesAa", "getFathersAa", "getQueenAa", "getVirginQueensAa", "getWorkersAa" ] }, { "page": "getBv", "title": "Access breeding values of individuals in a caste", "topics": [ "getBv", "getDronesBv", "getFathersBv", "getQueenBv", "getVirginQueensBv", "getWorkersBv" ] }, { "page": "getCaste", "title": "Report caste of an individual", "topics": [ "getCaste" ] }, { "page": "getCasteId", "title": "Get IDs of individuals of a caste, or ID of all members of colony", "topics": [ "getCasteId" ] }, { "page": "getCastePop", "title": "Access individuals of a caste", "topics": [ "getCastePop", "getDrones", "getFathers", "getQueen", "getVirginQueens", "getWorkers" ] }, { "page": "getCasteSex", "title": "Get sex of individuals of a caste, or sex of all members of colony", "topics": [ "getCasteSex" ] }, { "page": "getCsdAlleles", "title": "Get csd alleles", "topics": [ "getCsdAlleles", "getDronesCsdAlleles", "getFathersCsdAlleles", "getQueenCsdAlleles", "getVirginQueensCsdAlleles", "getWorkersCsdAlleles" ] }, { "page": "getCsdGeno", "title": "Get genotypes from the csd locus", "topics": [ "getCsdGeno", "getDronesCsdGeno", "getFathersCsdGeno", "getQueenCsdGeno", "getVirginQueensCsdGeno", "getWorkersCsdGeno" ] }, { "page": "getDd", "title": "Access dominance values of individuals in a caste", "topics": [ "getDd", "getDronesDd", "getFathersDd", "getQueenDd", "getVirginQueensDd", "getWorkersDd" ] }, { "page": "getEvents", "title": "Report which colony events have occurred", "topics": [ "getEvents" ] }, { "page": "getGv", "title": "Access genetic values of individuals in a caste", "topics": [ "getDronesGv", "getFathersGv", "getGv", "getQueenGv", "getVirginQueensGv", "getWorkersGv" ] }, { "page": "getIbdHaplo", "title": "Access IBD haplotypes of individuals in a caste", "topics": [ "getDronesIbdHaplo", "getFathersIbdHaplo", "getIbdHaplo", "getQueenIbdHaplo", "getVirginQueensIbdHaplo", "getWorkersIbdHaplo" ] }, { "page": "getId", "title": "Get the colony ID", "topics": [ "getId" ] }, { "page": "getLocation", "title": "Get the colony location", "topics": [ "getLocation" ] }, { "page": "getMisc", "title": "Get miscellaneous information in a population", "topics": [ "getMisc" ] }, { "page": "getPheno", "title": "Access phenotype values of individuals in a caste", "topics": [ "getDronesPheno", "getFathersPheno", "getPheno", "getQueenPheno", "getVirginQueensPheno", "getWorkersPheno" ] }, { "page": "getPooledGeno", "title": "Get a pooled genotype from true genotypes", "topics": [ "getPooledGeno" ] }, { "page": "getQtlGeno", "title": "Access QTL genotypes of individuals in a caste", "topics": [ "getDronesQtlGeno", "getFathersQtlGeno", "getQtlGeno", "getQueenQtlGeno", "getVirginQueensQtlGeno", "getWorkersQtlGeno" ] }, { "page": "getQtlHaplo", "title": "Access QTL haplotypes of individuals in a caste", "topics": [ "getDronesQtlHaplo", "getFathersQtlHaplo", "getQtlHaplo", "getQueenQtlHaplo", "getVirginQueensQtlHaplo", "getWorkersQtlHaplo" ] }, { "page": "getQueenAge", "title": "Get (calculate) the queen's age", "topics": [ "getQueenAge" ] }, { "page": "getQueenYearOfBirth", "title": "Access the queen's year of birth", "topics": [ "getQueenYearOfBirth" ] }, { "page": "getSegSiteGeno", "title": "Access genotypes for all segregating sites of individuals in a caste", "topics": [ "getDronesSegSiteGeno", "getFathersSegSiteGeno", "getQueenSegSiteGeno", "getSegSiteGeno", "getVirginQueensSegSiteGeno", "getWorkersSegSiteGeno" ] }, { "page": "getSegSiteHaplo", "title": "Access haplotypes for all segregating sites of individuals in a caste", "topics": [ "getDronesSegSiteHaplo", "getFathersSegSiteHaplo", "getQueenSegSiteHaplo", "getSegSiteHaplo", "getVirginQueensSegSiteHaplo", "getWorkersSegSiteHaplo" ] }, { "page": "getSnpGeno", "title": "Access SNP array genotypes of individuals in a caste", "topics": [ "getDronesSnpGeno", "getFathersSnpGeno", "getQueenSnpGeno", "getSnpGeno", "getVirginQueensSnpGeno", "getWorkersSnpGeno" ] }, { "page": "getSnpHaplo", "title": "Access SNP array haplotypes of individuals in a caste", "topics": [ "getDronesSnpHaplo", "getFathersSnpHaplo", "getQueenSnpHaplo", "getSnpHaplo", "getVirginQueensSnpHaplo", "getWorkersSnpHaplo" ] }, { "page": "hasCollapsed", "title": "Test if colony has collapsed", "topics": [ "hasCollapsed" ] }, { "page": "hasSplit", "title": "Test if colony has split", "topics": [ "hasSplit" ] }, { "page": "hasSuperseded", "title": "Test if colony has superseded", "topics": [ "hasSuperseded" ] }, { "page": "hasSwarmed", "title": "Test if colony has swarmed", "topics": [ "hasSwarmed" ] }, { "page": "isCaste", "title": "Is individual a member of a specific caste", "topics": [ "isCaste", "isDrone", "isFather", "isQueen", "isVirginQueen", "isVirginQueens", "isWorker" ] }, { "page": "isCsdActive", "title": "Is csd locus activated", "topics": [ "isCsdActive" ] }, { "page": "isCsdHeterozygous", "title": "Test if individuals are heterozygous at the csd locus", "topics": [ "isCsdHeterozygous" ] }, { "page": "isDronesPresent", "title": "Are drones present", "topics": [ "isDronesPresent" ] }, { "page": "isEmpty", "title": "Check whether a population, colony or a multicolony object has no individuals within", "topics": [ "isEmpty" ] }, { "page": "isFathersPresent", "title": "Are fathers present (=queen mated)", "topics": [ "areFathersPresent", "isFathersPresent" ] }, { "page": "isGenoHeterozygous", "title": "Test if a multilocus genotype is heterozygous", "topics": [ "isGenoHeterozygous" ] }, { "page": "isNULLColonies", "title": "Check which of the colonies in a multicolony are NULL", "topics": [ "isNULLColonies" ] }, { "page": "isProductive", "title": "Test if colony is currently productive", "topics": [ "isProductive" ] }, { "page": "isQueenPresent", "title": "Is the queen present", "topics": [ "isQueenPresent" ] }, { "page": "isSimParamBee", "title": "Test if x is a SimParamBee class object", "topics": [ "isSimParamBee" ] }, { "page": "isVirginQueensPresent", "title": "Are virgin queen(s) present", "topics": [ "areVirginQueensPresent", "isVirginQueenPresent", "isVirginQueensPresent" ] }, { "page": "isWorkersPresent", "title": "Are workers present", "topics": [ "areDronesPresent", "areWorkersPresent", "isWorkersPresent" ] }, { "page": "mapCasteToColonyValue", "title": "Map caste member (individual) values to a colony value", "topics": [ "mapCasteToColonyAa", "mapCasteToColonyBv", "mapCasteToColonyDd", "mapCasteToColonyGv", "mapCasteToColonyPheno", "mapCasteToColonyValue" ] }, { "page": "mapLoci", "title": "Finds loci on a genetic map and return a list of positions", "topics": [ "mapLoci" ] }, { "page": "MultiColony-class", "title": "Honeybee multicolony object", "topics": [ "c,MultiColony-method", "c,MultiColonyOrNULL-method", "isMultiColony", "MultiColony-class", "show,MultiColony-method", "[,MultiColony,character-method", "[,MultiColony,integerOrNumericOrLogical-method", "[<-,MultiColony,integerOrNumericOrLogicalOrCharacter,ANY,MultiColony-method", "[[,MultiColony,character-method", "[[,MultiColony,integerOrNumericOrLogical-method", "[[<-,MultiColony,integerOrNumericOrLogicalOrCharacter,ANY,Colony-method" ] }, { "page": "nCaste", "title": "Level 0 function that returns the number of individuals of a caste in a colony", "topics": [ "nCaste", "nDrones", "nFathers", "nQueens", "nVirginQueens", "nWorkers" ] }, { "page": "nColonies", "title": "Number of colonies in a MultiColony object", "topics": [ "nColonies", "nEmptyColonies", "nNULLColonies" ] }, { "page": "nCsdAlleles", "title": "Report the number of distinct csd alleles", "topics": [ "nCsdAlleles" ] }, { "page": "nDronesFun", "title": "Sample a number of drones", "topics": [ "nDronesColonyPhenotype", "nDronesPoisson", "nDronesTruncPoisson" ] }, { "page": "nFathersFun", "title": "Sample a 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