Package: SIMplyBee 0.4.0

Jana Obšteter

SIMplyBee: 'AlphaSimR' Extension for Simulating Honeybee Populations and Breeding Programmes

An extension of the 'AlphaSimR' package (<https://cran.r-project.org/package=AlphaSimR>) for stochastic simulations of honeybee populations and breeding programmes. 'SIMplyBee' enables simulation of individual bees that form a colony, which includes a queen, fathers (drones the queen mated with), virgin queens, workers, and drones. Multiple colony can be merged into a population of colonies, such as an apiary or a whole country of colonies. Functions enable operations on castes, colony, or colonies, to ease 'R' scripting of whole populations. All 'AlphaSimR' functionality with respect to genomes and genetic and phenotype values is available and further extended for honeybees, including haplo-diploidy, complementary sex determiner locus, colony events (swarming, supersedure, etc.), and colony phenotype values.

Authors:Jana Obšteter [aut, cre], Laura Strachan [aut], Jernej Bubnič [aut], Gregor Gorjanc [aut]

SIMplyBee_0.4.0.tar.gz
SIMplyBee_0.4.0.zip(r-4.5)SIMplyBee_0.4.0.zip(r-4.4)SIMplyBee_0.4.0.zip(r-4.3)
SIMplyBee_0.4.0.tgz(r-4.4-x86_64)SIMplyBee_0.4.0.tgz(r-4.4-arm64)SIMplyBee_0.4.0.tgz(r-4.3-x86_64)SIMplyBee_0.4.0.tgz(r-4.3-arm64)
SIMplyBee_0.4.0.tar.gz(r-4.5-noble)SIMplyBee_0.4.0.tar.gz(r-4.4-noble)
SIMplyBee_0.4.0.tgz(r-4.4-emscripten)SIMplyBee_0.4.0.tgz(r-4.3-emscripten)
SIMplyBee.pdf |SIMplyBee.html✨
SIMplyBee/json (API)
NEWS

Peer review:

Bug tracker:https://github.com/highlanderlab/simplybee/issues

On CRAN:

201 exports 1.26 score 9 dependencies 18 scripts 256 downloads

Last updated 20 days agofrom:c018375d28. Checks:OK: 9. Indexed: yes.

Exports:addCastePopaddDronesaddVirginQueensaddWorkersareDronesPresentareFathersPresentareVirginQueensPresentareWorkersPresentbuildUpcalcBeeAlleleFreqcalcBeeGRMIbdcalcBeeGRMIbscalcColonyGvcalcColonyPhenocalcColonyValuecalcInheritanceCriterioncalcPerformanceCriterioncalcQueensPHomBroodcalcSelectionCriterioncollapsecombinecreateCastePopcreateColonycreateCrossPlancreateDCAcreateDronescreateMatingStationDCAcreateMultiColonycreateVirginQueenscreateWorkerscrossdownsizedownsizePUnifgetCastegetCasteIdgetCastePopgetCasteSexgetCsdAllelesgetCsdGenogetDronesgetDronesCsdAllelesgetDronesCsdGenogetDronesGvgetDronesIbdHaplogetDronesPhenogetDronesQtlGenogetDronesQtlHaplogetDronesSegSiteGenogetDronesSegSiteHaplogetDronesSnpGenogetDronesSnpHaplogetEventsgetFathersgetFathersCsdAllelesgetFathersCsdGenogetFathersGvgetFathersIbdHaplogetFathersPhenogetFathersQtlGenogetFathersQtlHaplogetFathersSegSiteGenogetFathersSegSiteHaplogetFathersSnpGenogetFathersSnpHaplogetGvgetIbdHaplogetIdgetLocationgetMiscgetPhenogetPooledGenogetQtlGenogetQtlHaplogetQueengetQueenAgegetQueenCsdAllelesgetQueenCsdGenogetQueenGvgetQueenIbdHaplogetQueenPhenogetQueenQtlGenogetQueenQtlHaplogetQueenSegSiteGenogetQueenSegSiteHaplogetQueenSnpGenogetQueenSnpHaplogetQueenYearOfBirthgetSegSiteGenogetSegSiteHaplogetSnpGenogetSnpHaplogetVirginQueensgetVirginQueensCsdAllelesgetVirginQueensCsdGenogetVirginQueensGvgetVirginQueensIbdHaplogetVirginQueensPhenogetVirginQueensQtlGenogetVirginQueensQtlHaplogetVirginQueensSegSiteGenogetVirginQueensSegSiteHaplogetVirginQueensSnpGenogetVirginQueensSnpHaplogetWorkersgetWorkersCsdAllelesgetWorkersCsdGenogetWorkersGvgetWorkersIbdHaplogetWorkersPhenogetWorkersQtlGenogetWorkersQtlHaplogetWorkersSegSiteGenogetWorkersSegSiteHaplogetWorkersSnpGenogetWorkersSnpHaplohasCollapsedhasSplithasSupersededhasSwarmedisCasteisColonyisCsdActiveisCsdHeterozygousisDroneisDronesPresentisEmptyisFatherisFathersPresentisMultiColonyisNULLColoniesisProductiveisQueenisQueenPresentisSimParamBeeisVirginQueenisVirginQueenPresentisVirginQueensisVirginQueensPresentisWorkerisWorkersPresentmapCasteToColonyGvmapCasteToColonyPhenomapCasteToColonyValuenCastenColoniesnCsdAllelesnDronesnDronesColonyPhenotypenDronesPoissonnDronesTruncPoissonnEmptyColoniesnFathersnFathersPoissonnFathersTruncPoissonnHomBroodnNULLColoniesnQueensnVirginQueensnVirginQueensColonyPhenotypenVirginQueensPoissonnVirginQueensTruncPoissonnWorkersnWorkersColonyPhenotypenWorkersPoissonnWorkersTruncPoissonpHomBroodpullCastePoppullColoniespullDroneGroupsFromDCApullDronespullIndpullQueenpullVirginQueenspullWorkersrcirclereduceDroneGenoreduceDroneHaploremoveCastePopremoveColoniesremoveDronesremoveQueenremoveVirginQueensremoveWorkersreplaceCastePopreplaceDronesreplaceVirginQueensreplaceWorkersreQueenresetEventsselectColoniessetLocationsetMiscsetQueensYearOfBirthSimParamBeesimulateHoneyBeeGenomessplitsplitPColonyStrengthsplitPUnifsupersedeswarmswarmPUnif

Dependencies:AlphaSimRBHextraDistrR6RANNrbibutilsRcppRcppArmadilloRdpack