SIMplyBee (version 0.4.1)

nCsdAlleles: Report the number of distinct csd alleles

Description

Level 0 function that returns the number of distinct csd alleles in input. See SimParamBee for more information about the csd locus.

Usage

nCsdAlleles(x, collapse = FALSE, simParamBee = NULL)

Value

integer representing the number of distinct csd alleles when x

is Pop-class (or ), list of integer when x is Colony-class (list nodes named by caste) and list of a list of integer when x is MultiColony-class, outer list is named by colony id when x is

MultiColony-class; the integer rep

Arguments

x

Pop-class, Colony-class, or MultiColony-class

collapse

logical, if TRUE, the function will return the number of distinct csd alleles in either the entire population, colony, or multicolony. Note this has nothing to do with the colony collapse. It's like paste(..., collapse = TRUE). Default is FALSE. See examples about this behaviour.Default is FALSE.

simParamBee

SimParamBee, global simulation parameters

Details

Queen has 2 distinct csd alleles, since she has to be heterozygous to be viable. The same holds for individual virgin queens and workers, but note that looking at csd genotypes of virgin queens or workers we are looking at a sample of 1 csd allele from the queen and 1 csd allele from their fathers, noting that homozygous genotypes are excluded. Therefore, nCsdAlleles() from virgin queens and workers is a noisy realisation of nCsdAlleles() from queens and fathers. For this reason, we also report nCsdAlleles() from queens and fathers combined (see the queenAndFathers list node) when x is Colony-class. This last measure is then the expected number of csd alleles in a colony as opposed to realised number of csd alleles in a sample of virgin queens and workers. Similarly as for virgin queens and workers, nCsdAlleles() from drones gives a noisy realisation of nCsdAlleles() from queens. The amount of noise will depend on the number of individuals, so in most cases with reasonable number of individuals there should be minimal amount of noise.

Examples

founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
SP <- SimParamBee$new(founderGenomes)
SP$nThreads = 1L
basePop <- createVirginQueens(founderGenomes)

drones <- createDrones(x = basePop[1], nInd = 1000)
droneGroups <- pullDroneGroupsFromDCA(drones, n = 10, nDrones = nFathersPoisson)

# Create a Colony and a MultiColony class
colony <- createColony(x = basePop[2])
colony <- cross(colony, drones = droneGroups[[1]])
colony <- buildUp(x = colony, nWorkers = 6, nDrones = 3)
colony <- addVirginQueens(x = colony, nInd = 4)

apiary <- createMultiColony(basePop[3:4], n = 2)
apiary <- cross(apiary, drones = droneGroups[c(2, 3)])
apiary <- buildUp(x = apiary, nWorkers = 6, nDrones = 3)
apiary <- addVirginQueens(x = apiary, nInd = 5)

nCsdAlleles(getQueen(colony))
nCsdAlleles(getWorkers(colony))

nCsdAlleles(colony)
nCsdAlleles(colony, collapse = TRUE)

nCsdAlleles(apiary)
nCsdAlleles(apiary, collapse = TRUE)