Function reference • SIMplyBee

Class
`isColony()` `show(<Colony>)` `c(<ColonyOrNULL>)`	Honeybee colony
`isMultiColony()` `show(<MultiColony>)` `c(<MultiColony>)` `c(<MultiColonyOrNULL>)` `[`(<MultiColony>,<integerOrNumericOrLogical>) `[`(<MultiColony>,<character>) `[[`(<MultiColony>,<integerOrNumericOrLogical>) `[[`(<MultiColony>,<character>) `[<-`(<MultiColony>,<integerOrNumericOrLogicalOrCharacter>,<ANY>,<MultiColony>) `[[<-`(<MultiColony>,<integerOrNumericOrLogicalOrCharacter>,<ANY>,<Colony>)	Honeybee multicolony object
`SimParamBee`	Honeybee simulation parameters
`c(<NULLOrPop>)`	Combine a NULL and AlphaSimR population
Colony and MultiColony operations
Utility
`createColony()`	Create a new Colony
`setLocation()`	Set colony location
`createMultiColony()`	Create MultiColony object
`selectColonies()`	Select colonies from MultiColony object
`pullColonies()`	Pull out some colonies from the MultiColony object
`removeColonies()`	Remove some colonies from the MultiColony object
`getId()`	Get the colony ID
`rcircle()`	Sample random points within a circle
Events
`cross()`	Cross (mate) virgin queen(s) as a population, of a colony, or of all given colonies
`buildUp()`	Build up Colony or MultiColony object by adding (raising) workers and drones
`downsize()`	Reduce number of workers and remove all drones and virgin queens from a Colony or MultiColony object
`supersede()`	Supersede
`split()`	Split colony in two MultiColony
`swarm()`	Swarm
`collapse()`	Collapse
`combine()`	Combine two colony objects
`resetEvents()`	Reset colony events
Event information
`getEvents()`	Report which colony events have occurred
`hasCollapsed()`	Test if colony has collapsed
`hasSplit()`	Test if colony has split
`hasSuperseded()`	Test if colony has superseded
`hasSwarmed()`	Test if colony has swarmed
`isProductive()`	Test if colony is currently productive
Caste specific events - Add
`addCastePop()` `addWorkers()` `addDrones()` `addVirginQueens()`	Add caste individuals to the colony
Caste specific events - Replace
`reQueen()`	Re-queen
`replaceCastePop()` `replaceWorkers()` `replaceDrones()` `replaceVirginQueens()`	Replace a proportion of caste individuals with new ones
Caste specific events - Remove
`removeCastePop()` `removeQueen()` `removeWorkers()` `removeDrones()` `removeVirginQueens()`	Remove a proportion of caste individuals from a colony
Caste operations
Create (output is Population)
`createCastePop()` `createWorkers()` `createDrones()` `createVirginQueens()`	Creates caste population individuals from the colony
`createDCA()`	Create a drone congregation area (DCA)
Get (output is Population)
`getCastePop()` `getQueen()` `getFathers()` `getWorkers()` `getDrones()` `getVirginQueens()`	Access individuals of a caste
Pull (output is list of Populations)
`pullInd()`	Pull individuals from a population
`pullCastePop()` `pullQueen()` `pullWorkers()` `pullDrones()` `pullVirginQueens()`	Pull individuals from a caste in a colony
`pullDroneGroupsFromDCA()`	Pulls drone groups from a Drone Congregation Area (DCA)
Get information
`getCaste()`	Report caste of an individual
`getQueenAge()`	Get (calculate) the queen's age
`getCasteId()`	Get IDs of individuals of a caste, or ID of all members of colony
`getCasteSex()`	Get sex of individuals of a caste, or sex of all members of colony
`getLocation()`	Get the colony location
Queen’s birth
`setQueensYearOfBirth()`	Set the queen's year of birth
`getQueenYearOfBirth()`	Access the queen's year of birth
Is/are functions
Individuals
`isCaste()` `isQueen()` `isFather()` `isWorker()` `isDrone()` `isVirginQueens()` `isVirginQueen()`	Is individual a member of a specific caste
Is caste present
`isQueenPresent()`	Is the queen present
`isFathersPresent()` `areFathersPresent()`	Are fathers present (=queen mated)
`isWorkersPresent()` `areWorkersPresent()` `areDronesPresent()`	Are workers present
`isDronesPresent()`	Are drones present
`isVirginQueensPresent()` `isVirginQueenPresent()` `areVirginQueensPresent()`	Are virgin queen(s) present
Colony and MultiColony
`isColony()` `show(<Colony>)` `c(<ColonyOrNULL>)`	Honeybee colony
`isEmpty()`	Check whether a population, colony or a multicolony object has no individuals within
`isMultiColony()` `show(<MultiColony>)` `c(<MultiColony>)` `c(<MultiColonyOrNULL>)` `[`(<MultiColony>,<integerOrNumericOrLogical>) `[`(<MultiColony>,<character>) `[[`(<MultiColony>,<integerOrNumericOrLogical>) `[[`(<MultiColony>,<character>) `[<-`(<MultiColony>,<integerOrNumericOrLogicalOrCharacter>,<ANY>,<MultiColony>) `[[<-`(<MultiColony>,<integerOrNumericOrLogicalOrCharacter>,<ANY>,<Colony>)	Honeybee multicolony object
`isNULLColonies()`	Check which of the colonies in a multicolony are NULL
Other
`isSimParamBee()`	Test if x is a SimParamBee class object
Individuals
`nCaste()` `nQueens()` `nFathers()` `nWorkers()` `nDrones()` `nVirginQueens()`	Level 0 function that returns the number of individuals of a caste in a colony
`calcQueensPHomBrood()` `pHomBrood()` `nHomBrood()`	The expected proportion and a realised number of csd homozygous brood
Sampling individuals
`nFathersPoisson()` `nFathersTruncPoisson()`	Sample a number of fathers
`nWorkersPoisson()` `nWorkersTruncPoisson()` `nWorkersColonyPhenotype()`	Sample a number of workers
`nDronesPoisson()` `nDronesTruncPoisson()` `nDronesColonyPhenotype()`	Sample a number of drones
`nVirginQueensPoisson()` `nVirginQueensTruncPoisson()` `nVirginQueensColonyPhenotype()`	Sample a number of virgin queens
Colony and MultiColony
`nColonies()` `nNULLColonies()` `nEmptyColonies()`	Number of colonies in a MultiColony object
Proportion functions
`downsizePUnif()`	Sample the downsize proportion - proportion of removed workers in downsizing
`splitPUnif()` `splitPColonyStrength()`	Sample the split proportion - proportion of removed workers in a managed split
`swarmPUnif()`	Sample the swarm proportion - the proportion of workers that swarm
Genome
General
`simulateHoneyBeeGenomes()`	Simulate the Honey bee genome
`getPooledGeno()`	Get a pooled genotype from true genotypes
Csd
`isCsdActive()`	Is csd locus activated
`nCsdAlleles()`	Report the number of distinct csd alleles
`getCsdAlleles()` `getQueenCsdAlleles()` `getFathersCsdAlleles()` `getVirginQueensCsdAlleles()` `getWorkersCsdAlleles()` `getDronesCsdAlleles()`	Get csd alleles
`getCsdGeno()` `getQueenCsdGeno()` `getFathersCsdGeno()` `getVirginQueensCsdGeno()` `getWorkersCsdGeno()` `getDronesCsdGeno()`	Get genotypes from the csd locus
`isCsdHeterozygous()`	Test if individuals are heterozygous at the csd locus
`isGenoHeterozygous()`	Test if a multilocus genotype is heterozygous
`calcQueensPHomBrood()` `pHomBrood()` `nHomBrood()`	The expected proportion and a realised number of csd homozygous brood
`editCsdLocus()`	Edit the csd locus
Haploid drone genome
`reduceDroneHaplo()`	Reduce drone's double haplotypes to a single haplotype
`reduceDroneGeno()`	Reduce drones' genotype to a single haplotype
Get segregating sites’ haplotypes or genotypes
`getSegSiteHaplo()` `getQueenSegSiteHaplo()` `getFathersSegSiteHaplo()` `getVirginQueensSegSiteHaplo()` `getWorkersSegSiteHaplo()` `getDronesSegSiteHaplo()`	Access haplotypes for all segregating sites of individuals in a caste
`getSegSiteGeno()` `getQueenSegSiteGeno()` `getFathersSegSiteGeno()` `getVirginQueensSegSiteGeno()` `getWorkersSegSiteGeno()` `getDronesSegSiteGeno()`	Access genotypes for all segregating sites of individuals in a caste
Get QTL haplotypes or genotypes
`getQtlHaplo()` `getQueenQtlHaplo()` `getFathersQtlHaplo()` `getVirginQueensQtlHaplo()` `getWorkersQtlHaplo()` `getDronesQtlHaplo()`	Access QTL haplotypes of individuals in a caste
`getQtlGeno()` `getQueenQtlGeno()` `getFathersQtlGeno()` `getVirginQueensQtlGeno()` `getWorkersQtlGeno()` `getDronesQtlGeno()`	Access QTL genotypes of individuals in a caste
Get SNP haplotypes or genotypes
`getSnpHaplo()` `getQueenSnpHaplo()` `getFathersSnpHaplo()` `getVirginQueensSnpHaplo()` `getWorkersSnpHaplo()` `getDronesSnpHaplo()`	Access SNP array haplotypes of individuals in a caste
`getSnpGeno()` `getQueenSnpGeno()` `getFathersSnpGeno()` `getVirginQueensSnpGeno()` `getWorkersSnpGeno()` `getDronesSnpGeno()`	Access SNP array genotypes of individuals in a caste
Get IBD (Identity-By-Descent) haplotypes
`getIbdHaplo()` `getQueenIbdHaplo()` `getFathersIbdHaplo()` `getVirginQueensIbdHaplo()` `getWorkersIbdHaplo()` `getDronesIbdHaplo()`	Access IBD haplotypes of individuals in a caste
Calculate genomic information
`calcBeeGRMIbs()` `calcBeeAlleleFreq()`	Calculate Genomic Relatedness Matrix (GRM) for honeybees from Identical By State genomic data
`calcBeeGRMIbd()`	Calculate Genomic Relatedness Matrix (GRM) for honeybees from Identical By Descent genomic data
Calculate phenotypic information
`getPheno()` `getQueenPheno()` `getFathersPheno()` `getVirginQueensPheno()` `getWorkersPheno()` `getDronesPheno()`	Access phenotype values of individuals in a caste
Calculate criterion
`calcColonyValue()` `calcColonyPheno()` `calcColonyGv()` `calcColonyBv()` `calcColonyDd()` `calcColonyAa()`	Calculate colony value(s)
`calcInheritanceCriterion()`	Calculate the inheritance criterion
`calcPerformanceCriterion()`	Calculate the performance criterion
`calcSelectionCriterion()`	Calculate the selection criterion
Planned mating
`createMatingStationDCA()`	Create a DCA of drones at a mating stations
`createCrossPlan()`	Create a plan for crossing virgin queens
`mapCasteToColonyValue()` `mapCasteToColonyPheno()` `mapCasteToColonyGv()` `mapCasteToColonyBv()` `mapCasteToColonyDd()` `mapCasteToColonyAa()`	Map caste member (individual) values to a colony value
`cross()`	Cross (mate) virgin queen(s) as a population, of a colony, or of all given colonies
Quantitative Genetics
Genetic values
`getGv()` `getQueenGv()` `getFathersGv()` `getVirginQueensGv()` `getWorkersGv()` `getDronesGv()`	Access genetic values of individuals in a caste
Breeding values
`getBv()` `getQueenBv()` `getFathersBv()` `getVirginQueensBv()` `getWorkersBv()` `getDronesBv()`	Access breeding values of individuals in a caste
Dominance deviations
`getDd()` `getQueenDd()` `getFathersDd()` `getVirginQueensDd()` `getWorkersDd()` `getDronesDd()`	Access dominance values of individuals in a caste
Epistatic devaitions
`getAa()` `getQueenAa()` `getFathersAa()` `getVirginQueensAa()` `getWorkersAa()` `getDronesAa()`	Access epistasis values of individuals in a caste
Combine REMOVE EXPORT AND DELETE
`combineBeeGametesHaploDiploid()`	Create diploid gametes from a mated queen
`combineBeeGametes()`	Create diploid gametes from a mated queen

Reference

Class

Colony and MultiColony operations

Utility

Events

Event information

Caste specific events - Add

Caste specific events - Replace

Caste specific events - Remove

Caste operations

Create

Get

Pull

Get information

Queen’s birth

Is/are functions

Individuals

Is caste present

Colony and MultiColony

Other

Individuals

Sampling individuals

Colony and MultiColony

Proportion functions

Genome

General

Csd

Haploid drone genome

Get segregating sites’ haplotypes or genotypes

Get QTL haplotypes or genotypes

Get SNP haplotypes or genotypes

Get IBD (Identity-By-Descent) haplotypes

Calculate genomic information

Calculate phenotypic information

Calculate criterion

Planned mating

Quantitative Genetics

Genetic values

Breeding values

Dominance deviations

Epistatic devaitions

Combine REMOVE EXPORT AND DELETE