The expected proportion and a realised number of csd homozygous brood

Source: R/Functions_L0_auxilary.R

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.

calcQueensPHomBrood(x)

pHomBrood(x)

nHomBrood(x)

Arguments

x

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

Value

numeric, expected csd homozygosity named by colony id when x

is MultiColony-class

Functions

  • pHomBrood(): Expected percentage of csd homozygous brood of a queen / colony

  • nHomBrood(): Realised number of csd homozygous brood produced by a queen

See also

Demo in the introductory vignette vignette("Honeybee_biology", package="SIMplyBee")

Examples

# This is a bit long example - the key is at the end!
founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
SP <- SimParamBee$new(founderGenomes)
basePop <- createVirginQueens(founderGenomes)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found

drones <- createDrones(x = basePop[1], nInd = 1000)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
droneGroups <- pullDroneGroupsFromDCA(drones, n = 10, nDrones = nFathersPoisson)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found

# Create a Colony and a MultiColony class
colony <- createColony(x = basePop[2])
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
colony <- cross(colony, drones = droneGroups[[1]])
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
colony <- buildUp(x = colony, nWorkers = 120, nDrones = 20)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
colony <- addVirginQueens(x = colony, nInd = 1)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found

apiary <- createMultiColony(basePop[3:4], n = 2)
#> Error in createMultiColony(basePop[3:4], n = 2): object 'basePop' not found
apiary <- cross(apiary, drones = droneGroups[c(2, 3)])
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
apiary <- buildUp(x = apiary, nWorkers = 100, nDrones = 10)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found

# Virgin queen
try(calcQueensPHomBrood(basePop[5]))
#> Error in is(x, class2 = "Pop") : object 'basePop' not found

# Queens of colony
calcQueensPHomBrood(colony)
#> Error in is(x, class2 = "Pop"): object 'colony' not found

# Queens of apiary
calcQueensPHomBrood(apiary)
#> Error in is(x, class2 = "Pop"): object 'apiary' not found

# Inbreed virgin queen with her brothers to generate csd homozygous brood
colony2 <- createColony(x = getVirginQueens(colony))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
colony2 <- cross(x = colony2, drones = pullDrones(x = colony, nInd = nFathersPoisson())[[1]])
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found

# Calculate the expected csd homozygosity
calcQueensPHomBrood(getQueen(colony2))
#> Error in is(x, class2 = "Colony"): object 'colony2' not found
pHomBrood(colony2)
#> Error in is(x, class2 = "Pop"): object 'colony2' not found

# Evaluate a realised csd homozygosity
nHomBrood(addWorkers(colony2, nInd = 100))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
nHomBrood(addWorkers(colony2, nInd = 100))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# nHomBrood will vary between function calls due to inheritance process