calcQueensPHomBrood: The expected proportion and a realised number of csd homozygous brood

Description

Level 0 functions that calculate or report the proportion of csd homozygous brood of a queen or a colony. The csd locus determines viability of fertilised eggs (brood) - homozygous brood is removed by workers. These functions 1) calculate the expected proportion of homozygous brood from the csd allele of the queen and fathers, 2) report the expected proportion of homozygous brood, or 3) report a realised number of homozygous brood due to inheritance process. See vignette(package = "SIMplyBee") for more details.

Usage

calcQueensPHomBrood(x, simParamBee = NULL)
pHomBrood(x, simParamBee = NULL)
nHomBrood(x, simParamBee = NULL)

Value

numeric, expected csd homozygosity named by colony id when x

is MultiColony-class

Arguments

x: Pop-class, Colony-class, or MultiColony-class
simParamBee: SimParamBee, global simulation parameters

Functions

pHomBrood(): Expected percentage of csd homozygous brood of a queen / colony
nHomBrood(): Realised number of csd homozygous brood produced by a queen

Examples

Run this code

# This is a bit long example - the key is at the end!
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 = 120, nDrones = 20)
colony <- addVirginQueens(x = colony, nInd = 1)

apiary <- createMultiColony(basePop[3:4], n = 2)
apiary <- cross(apiary, drones = droneGroups[c(2, 3)])
apiary <- buildUp(x = apiary, nWorkers = 100, nDrones = 10)

# Virgin queen
try(calcQueensPHomBrood(basePop[5]))

# Queens of colony
calcQueensPHomBrood(colony)

# Queens of apiary
calcQueensPHomBrood(apiary)

# Inbreed virgin queen with her brothers to generate csd homozygous brood
colony2 <- createColony(x = getVirginQueens(colony))
colony2 <- cross(x = colony2, drones = pullDrones(x = colony, nInd = nFathersPoisson())[[1]])

# Calculate the expected csd homozygosity
calcQueensPHomBrood(getQueen(colony2))
pHomBrood(colony2)

# Evaluate a realised csd homozygosity
nHomBrood(addWorkers(colony2, nInd = 100))
nHomBrood(addWorkers(colony2, nInd = 100))
# nHomBrood will vary between function calls due to inheritance process