Package: SIMplyBee 0.4.1

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_0.4.1.tar.gz
SIMplyBee_0.4.1.tar.gz(r-4.5-noble)SIMplyBee_0.4.1.tar.gz(r-4.4-noble)
SIMplyBee_0.4.1.tgz(r-4.4-emscripten)SIMplyBee_0.4.1.tgz(r-4.3-emscripten)
SIMplyBee.pdf |SIMplyBee.html✨
SIMplyBee/json (API)
NEWS

# Install 'SIMplyBee' in R:
install.packages('SIMplyBee', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

4.16 score 18 scripts 220 downloads 201 exports 9 dependencies

Last updated 3 months agofrom:e445fd722b. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-linux-x86_64OKNov 20 2024

Exports:addCastePopaddDronesaddVirginQueensaddWorkersareDronesPresentareFathersPresentareVirginQueensPresentareWorkersPresentbuildUpcalcBeeAlleleFreqcalcBeeGRMIbdcalcBeeGRMIbscalcColonyGvcalcColonyPhenocalcColonyValuecalcInheritanceCriterioncalcPerformanceCriterioncalcQueensPHomBroodcalcSelectionCriterioncollapsecombinecreateCastePopcreateColonycreateCrossPlancreateDCAcreateDronescreateMatingStationDCAcreateMultiColonycreateVirginQueenscreateWorkerscrossdownsizedownsizePUnifgetCastegetCasteIdgetCastePopgetCasteSexgetCsdAllelesgetCsdGenogetDronesgetDronesCsdAllelesgetDronesCsdGenogetDronesGvgetDronesIbdHaplogetDronesPhenogetDronesQtlGenogetDronesQtlHaplogetDronesSegSiteGenogetDronesSegSiteHaplogetDronesSnpGenogetDronesSnpHaplogetEventsgetFathersgetFathersCsdAllelesgetFathersCsdGenogetFathersGvgetFathersIbdHaplogetFathersPhenogetFathersQtlGenogetFathersQtlHaplogetFathersSegSiteGenogetFathersSegSiteHaplogetFathersSnpGenogetFathersSnpHaplogetGvgetIbdHaplogetIdgetLocationgetMiscgetPhenogetPooledGenogetQtlGenogetQtlHaplogetQueengetQueenAgegetQueenCsdAllelesgetQueenCsdGenogetQueenGvgetQueenIbdHaplogetQueenPhenogetQueenQtlGenogetQueenQtlHaplogetQueenSegSiteGenogetQueenSegSiteHaplogetQueenSnpGenogetQueenSnpHaplogetQueenYearOfBirthgetSegSiteGenogetSegSiteHaplogetSnpGenogetSnpHaplogetVirginQueensgetVirginQueensCsdAllelesgetVirginQueensCsdGenogetVirginQueensGvgetVirginQueensIbdHaplogetVirginQueensPhenogetVirginQueensQtlGenogetVirginQueensQtlHaplogetVirginQueensSegSiteGenogetVirginQueensSegSiteHaplogetVirginQueensSnpGenogetVirginQueensSnpHaplogetWorkersgetWorkersCsdAllelesgetWorkersCsdGenogetWorkersGvgetWorkersIbdHaplogetWorkersPhenogetWorkersQtlGenogetWorkersQtlHaplogetWorkersSegSiteGenogetWorkersSegSiteHaplogetWorkersSnpGenogetWorkersSnpHaplohasCollapsedhasSplithasSupersededhasSwarmedisCasteisColonyisCsdActiveisCsdHeterozygousisDroneisDronesPresentisEmptyisFatherisFathersPresentisMultiColonyisNULLColoniesisProductiveisQueenisQueenPresentisSimParamBeeisVirginQueenisVirginQueenPresentisVirginQueensisVirginQueensPresentisWorkerisWorkersPresentmapCasteToColonyGvmapCasteToColonyPhenomapCasteToColonyValuenCastenColoniesnCsdAllelesnDronesnDronesColonyPhenotypenDronesPoissonnDronesTruncPoissonnEmptyColoniesnFathersnFathersPoissonnFathersTruncPoissonnHomBroodnNULLColoniesnQueensnVirginQueensnVirginQueensColonyPhenotypenVirginQueensPoissonnVirginQueensTruncPoissonnWorkersnWorkersColonyPhenotypenWorkersPoissonnWorkersTruncPoissonpHomBroodpullCastePoppullColoniespullDroneGroupsFromDCApullDronespullIndpullQueenpullVirginQueenspullWorkersrcirclereduceDroneGenoreduceDroneHaploremoveCastePopremoveColoniesremoveDronesremoveQueenremoveVirginQueensremoveWorkersreplaceCastePopreplaceDronesreplaceVirginQueensreplaceWorkersreQueenresetEventsselectColoniessetLocationsetMiscsetQueensYearOfBirthSimParamBeesimulateHoneyBeeGenomessplitsplitPColonyStrengthsplitPUnifsupersedeswarmswarmPUnif

Dependencies:AlphaSimRBHextraDistrR6RANNrbibutilsRcppRcppArmadilloRdpack

Colony events

Rendered fromC_Colony_events.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2024-08-27
Started: 2022-12-15

Crossing

Rendered fromD_Crossing.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2024-09-21
Started: 2022-12-15

Frequently asked questions

Rendered fromZ_FAQ.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2024-08-27
Started: 2022-12-15

Genomics

Rendered fromE_Genomics.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2024-08-27
Started: 2022-12-15

Honeybee biology

Rendered fromA_Honeybee_biology.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2024-08-27
Started: 2022-12-15

Multiple colonies

Rendered fromB_Multiple_colonies.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2024-08-27
Started: 2022-12-15

Quantitative genetics

Rendered fromF_Quantitative_Genetics.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2024-08-27
Started: 2024-08-27

Sampling functions

Rendered fromG_Sampling_functions.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2024-08-27
Started: 2022-12-15

Readme and manuals

Help Manual

Help pageTopics
Add caste individuals to the colonyaddCastePop addDrones addVirginQueens addWorkers
Build up Colony or MultiColony object by adding (raising) workers and dronesbuildUp
Combine a NULL and AlphaSimR populationc,NULLOrPop-method
Calculate Genomic Relatedness Matrix (GRM) for honeybees from Identical By Descent genomic datacalcBeeGRMIbd
Calculate Genomic Relatedness Matrix (GRM) for honeybees from Identical By State genomic datacalcBeeAlleleFreq calcBeeGRMIbs
Calculate colony value(s)calcColonyAa calcColonyBv calcColonyDd calcColonyGv calcColonyPheno calcColonyValue
Calculate the inheritance criterioncalcInheritanceCriterion
Calculate the performance criterioncalcPerformanceCriterion
The expected proportion and a realised number of csd homozygous broodcalcQueensPHomBrood nHomBrood pHomBrood
Calculate the selection criterioncalcSelectionCriterion
Collapsecollapse
Honeybee colonyc,ColonyOrNULL-method Colony-class isColony show,Colony-method
Combine two colony objectscombine
Create diploid gametes from a mated queencombineBeeGametes
Create diploid gametes from a mated queencombineBeeGametesHaploDiploid
Creates caste population individuals from the colonycreateCastePop createDrones createVirginQueens createWorkers
Create a new ColonycreateColony
Create a plan for crossing virgin queenscreateCrossPlan
Create a drone congregation area (DCA)createDCA
Create a DCA of drones at a mating stationscreateMatingStationDCA
Create MultiColony objectcreateMultiColony
Cross (mate) virgin queen(s) as a population, of a colony, or of all given coloniescross
Reduce number of workers and remove all drones and virgin queens from a Colony or MultiColony objectdownsize
Sample the downsize proportion - proportion of removed workers in downsizingdownsizePUnif
Edit the csd locuseditCsdLocus
Access epistasis values of individuals in a castegetAa getDronesAa getFathersAa getQueenAa getVirginQueensAa getWorkersAa
Access breeding values of individuals in a castegetBv getDronesBv getFathersBv getQueenBv getVirginQueensBv getWorkersBv
Report caste of an individualgetCaste
Get IDs of individuals of a caste, or ID of all members of colonygetCasteId
Access individuals of a castegetCastePop getDrones getFathers getQueen getVirginQueens getWorkers
Get sex of individuals of a caste, or sex of all members of colonygetCasteSex
Get csd allelesgetCsdAlleles getDronesCsdAlleles getFathersCsdAlleles getQueenCsdAlleles getVirginQueensCsdAlleles getWorkersCsdAlleles
Get genotypes from the csd locusgetCsdGeno getDronesCsdGeno getFathersCsdGeno getQueenCsdGeno getVirginQueensCsdGeno getWorkersCsdGeno
Access dominance values of individuals in a castegetDd getDronesDd getFathersDd getQueenDd getVirginQueensDd getWorkersDd
Report which colony events have occurredgetEvents
Access genetic values of individuals in a castegetDronesGv getFathersGv getGv getQueenGv getVirginQueensGv getWorkersGv
Access IBD haplotypes of individuals in a castegetDronesIbdHaplo getFathersIbdHaplo getIbdHaplo getQueenIbdHaplo getVirginQueensIbdHaplo getWorkersIbdHaplo
Get the colony IDgetId
Get the colony locationgetLocation
Get miscellaneous information in a populationgetMisc
Access phenotype values of individuals in a castegetDronesPheno getFathersPheno getPheno getQueenPheno getVirginQueensPheno getWorkersPheno
Get a pooled genotype from true genotypesgetPooledGeno
Access QTL genotypes of individuals in a castegetDronesQtlGeno getFathersQtlGeno getQtlGeno getQueenQtlGeno getVirginQueensQtlGeno getWorkersQtlGeno
Access QTL haplotypes of individuals in a castegetDronesQtlHaplo getFathersQtlHaplo getQtlHaplo getQueenQtlHaplo getVirginQueensQtlHaplo getWorkersQtlHaplo
Get (calculate) the queen's agegetQueenAge
Access the queen's year of birthgetQueenYearOfBirth
Access genotypes for all segregating sites of individuals in a castegetDronesSegSiteGeno getFathersSegSiteGeno getQueenSegSiteGeno getSegSiteGeno getVirginQueensSegSiteGeno getWorkersSegSiteGeno
Access haplotypes for all segregating sites of individuals in a castegetDronesSegSiteHaplo getFathersSegSiteHaplo getQueenSegSiteHaplo getSegSiteHaplo getVirginQueensSegSiteHaplo getWorkersSegSiteHaplo
Access SNP array genotypes of individuals in a castegetDronesSnpGeno getFathersSnpGeno getQueenSnpGeno getSnpGeno getVirginQueensSnpGeno getWorkersSnpGeno
Access SNP array haplotypes of individuals in a castegetDronesSnpHaplo getFathersSnpHaplo getQueenSnpHaplo getSnpHaplo getVirginQueensSnpHaplo getWorkersSnpHaplo
Test if colony has collapsedhasCollapsed
Test if colony has splithasSplit
Test if colony has supersededhasSuperseded
Test if colony has swarmedhasSwarmed
Is individual a member of a specific casteisCaste isDrone isFather isQueen isVirginQueen isVirginQueens isWorker
Is csd locus activatedisCsdActive
Test if individuals are heterozygous at the csd locusisCsdHeterozygous
Are drones presentisDronesPresent
Check whether a population, colony or a multicolony object has no individuals withinisEmpty
Are fathers present (=queen mated)areFathersPresent isFathersPresent
Test if a multilocus genotype is heterozygousisGenoHeterozygous
Check which of the colonies in a multicolony are NULLisNULLColonies
Test if colony is currently productiveisProductive
Is the queen presentisQueenPresent
Test if x is a SimParamBee class objectisSimParamBee
Are virgin queen(s) presentareVirginQueensPresent isVirginQueenPresent isVirginQueensPresent
Are workers presentareDronesPresent areWorkersPresent isWorkersPresent
Map caste member (individual) values to a colony valuemapCasteToColonyAa mapCasteToColonyBv mapCasteToColonyDd mapCasteToColonyGv mapCasteToColonyPheno mapCasteToColonyValue
Finds loci on a genetic map and return a list of positionsmapLoci
Honeybee multicolony objectc,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
Level 0 function that returns the number of individuals of a caste in a colonynCaste nDrones nFathers nQueens nVirginQueens nWorkers
Number of colonies in a MultiColony objectnColonies nEmptyColonies nNULLColonies
Report the number of distinct csd allelesnCsdAlleles
Sample a number of dronesnDronesColonyPhenotype nDronesPoisson nDronesTruncPoisson
Sample a number of fathersnFathersPoisson nFathersTruncPoisson
Sample a number of virgin queensnVirginQueensColonyPhenotype nVirginQueensPoisson nVirginQueensTruncPoisson
Sample a number of workersnWorkersColonyPhenotype nWorkersPoisson nWorkersTruncPoisson
Pull individuals from a caste in a colonypullCastePop pullDrones pullQueen pullVirginQueens pullWorkers
Pull out some colonies from the MultiColony objectpullColonies
Pulls drone groups from a Drone Congregation Area (DCA)pullDroneGroupsFromDCA
Pull individuals from a populationpullInd
Sample random points within a circlercircle
Reduce drones' genotype to a single haplotypereduceDroneGeno
Reduce drone's double haplotypes to a single haplotypereduceDroneHaplo
Remove a proportion of caste individuals from a colonyremoveCastePop removeDrones removeQueen removeVirginQueens removeWorkers
Remove some colonies from the MultiColony objectremoveColonies
Replace a proportion of caste individuals with new onesreplaceCastePop replaceDrones replaceVirginQueens replaceWorkers
Re-queenreQueen
Reset colony eventsresetEvents
Select colonies from MultiColony objectselectColonies
Set colony locationsetLocation
Set miscellaneous information in a populationsetMisc
Set the queen's year of birthsetQueensYearOfBirth
Honeybee simulation parametersSimParamBee
Simulate the Honey bee genomesimulateHoneyBeeGenomes
Split colony in two MultiColonysplit
Sample the split proportion - proportion of removed workers in a managed splitsplitPColonyStrength splitPUnif
Supersedesupersede
Swarmswarm
Sample the swarm proportion - the proportion of workers that swarmswarmPUnif