Colony-class            Honeybee colony
MultiColony-class       Honeybee multicolony object
SimParamBee             Honeybee simulation parameters
addCastePop             Add caste individuals to the colony
buildUp                 Build up Colony or MultiColony object by adding
                        (raising) workers and drones
c,NULLOrPop-method      Combine a NULL and AlphaSimR population
calcBeeGRMIbd           Calculate Genomic Relatedness Matrix (GRM) for
                        honeybees from Identical By Descent genomic
                        data
calcBeeGRMIbs           Calculate Genomic Relatedness Matrix (GRM) for
                        honeybees from Identical By State genomic data
calcColonyValue         Calculate colony value(s)
calcInheritanceCriterion
                        Calculate the inheritance criterion
calcPerformanceCriterion
                        Calculate the performance criterion
calcQueensPHomBrood     The expected proportion and a realised number
                        of csd homozygous brood
calcSelectionCriterion
                        Calculate the selection criterion
collapse                Collapse
combine                 Combine two colony objects
combineBeeGametes       Create diploid gametes from a mated queen
combineBeeGametesHaploDiploid
                        Create diploid gametes from a mated queen
createCastePop          Creates caste population individuals from the
                        colony
createColony            Create a new Colony
createDCA               Create a drone congregation area (DCA)
createMatingStationDCA
                        Create a DCA of drones at a mating stations
createMultiColony       Create MultiColony object
createRandomCrossPlan   Create a cross plan by randomly sampling drones
                        for each queen from a drone population
cross                   Cross (mate) virgin queen(s) as a population,
                        of a colony, or of all given colonies
downsize                Reduce number of workers and remove all drones
                        and virgin queens from a Colony or MultiColony
                        object
downsizePUnif           Sample the downsize proportion - proportion of
                        removed workers in downsizing
editCsdLocus            Edit the csd locus
getAa                   Access epistasis values of individuals in a
                        caste
getBv                   Access breeding values of individuals in a
                        caste
getCaste                Report caste of an individual
getCasteId              Get IDs of individuals of a caste, or ID of all
                        members of colony
getCastePop             Access individuals of a caste
getCasteSex             Get sex of individuals of a caste, or sex of
                        all members of colony
getCsdAlleles           Get csd alleles
getCsdGeno              Get genotypes from the csd locus
getDd                   Access dominance values of individuals in a
                        caste
getEvents               Report which colony events have occurred
getGv                   Access genetic values of individuals in a caste
getIbdHaplo             Access IBD haplotypes of individuals in a caste
getId                   Get the colony ID
getLocation             Get the colony location
getPheno                Access phenotype values of individuals in a
                        caste
getPooledGeno           Get a pooled genotype from true genotypes
getQtlGeno              Access QTL genotypes of individuals in a caste
getQtlHaplo             Access QTL haplotypes of individuals in a caste
getQueenAge             Get (calculate) the queen's age
getQueenYearOfBirth     Access the queen's year of birth
getSegSiteGeno          Access genotypes for all segregating sites of
                        individuals in a caste
getSegSiteHaplo         Access haplotypes for all segregating sites of
                        individuals in a caste
getSnpGeno              Access SNP array genotypes of individuals in a
                        caste
getSnpHaplo             Access SNP array haplotypes of individuals in a
                        caste
hasCollapsed            Test if colony has collapsed
hasSplit                Test if colony has split
hasSuperseded           Test if colony has superseded
hasSwarmed              Test if colony has swarmed
isCaste                 Is individual a member of a specific caste
isCsdActive             Is csd locus activated
isCsdHeterozygous       Test if individuals are heterozygous at the csd
                        locus
isDronesPresent         Are drones present
isEmpty                 Check whether a population, colony or a
                        multicolony object has no individuals within
isFathersPresent        Are fathers present (=queen mated)
isGenoHeterozygous      Test if a multilocus genotype is heterozygous
isNULLColonies          Check which of the colonies in a multicolony
                        are NULL
isProductive            Test if colony is currently productive
isQueenPresent          Is the queen present
isSimParamBee           Test if x is a SimParamBee class object
isVirginQueensPresent   Are virgin queen(s) present
isWorkersPresent        Are workers present
mapCasteToColonyValue   Map caste member (individual) values to a
                        colony value
nCaste                  Level 0 function that returns the number of
                        individuals of a caste in a colony
nColonies               Number of colonies in a MultiColony object
nCsdAlleles             Report the number of distinct csd alleles
nDronesPoisson          Sample a number of drones
nFathersPoisson         Sample a number of fathers
nVirginQueensPoisson    Sample a number of virgin queens
nWorkersPoisson         Sample a number of workers
pullCastePop            Pull individuals from a caste in a colony
pullColonies            Pull out some colonies from the MultiColony
                        object
pullDroneGroupsFromDCA
                        Pulls drone groups from a Drone Congregation
                        Area (DCA)
pullInd                 Pull individuals from a population
reQueen                 Re-queen
reduceDroneGeno         Reduce drones' genotype to a single haplotype
reduceDroneHaplo        Reduce drone's double haplotypes to a single
                        haplotype
removeCastePop          Remove a proportion of caste individuals from a
                        colony
removeColonies          Remove some colonies from the MultiColony
                        object
replaceCastePop         Replace a proportion of caste individuals with
                        new ones
resetEvents             Reset colony events
selectColonies          Select colonies from MultiColony object
setLocation             Set colony location
setQueensYearOfBirth    Set the queen's year of birth
simulateHoneyBeeGenomes
                        Simulate the Honey bee genome
split                   Split colony in two MultiColony
splitPUnif              Sample the split proportion - proportion of
                        removed workers in a managed split
supersede               Supersede
swarm                   Swarm
swarmPUnif              Sample the swarm proportion - the proportion of
                        workers that swarm
