Level 0 function that calculates the inheritance criterion as the sum of the queen (maternal) and workers (direct) effect from the queen, as defined by Du et al. (2021). This can be seen as the expected value of drones from the queen or half the expected value of virgin queens from the queen.
calcInheritanceCriterion(x, queenTrait = 1, workersTrait = 2, use = "gv")Pop-class, Colony-class or
MultiColony-class
numeric (column position) or character (column name), trait
that represents queen's effect on the colony value; if NULL
then this effect is 0
numeric (column position) or character (column name), trait
that represents workers' effect on the colony value; if NULL
then this effect is 0
character, the measure to use for the calculation, being either "gv" (genetic value), "ebv" (estimated breeding value), or "pheno" (phenotypic value)
integer when x is
Colony-class and a named list when x is
MultiColony-class, where names are colony IDs
Du, M., et al. (2021) Short-term effects of controlled mating and selection on the genetic variance of honeybee populations. Heredity 126, 733–747. doi:/10.1038/s41437-021-00411-2
calcSelectionCriterion and
calcPerformanceCriterion and as well as
vignette(topic = "QuantitativeGenetics", package = "SIMplyBee")
founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
SP <- SimParamBee$new(founderGenomes)
meanA <- c(10, 10 / SP$nWorkers)
varA <- c(1, 1 / SP$nWorkers)
corA <- matrix(data = c( 1.0, -0.5,
-0.5, 1.0), nrow = 2, byrow = TRUE)
SP$addTraitA(nQtlPerChr = 100, mean = meanA, var = varA, corA = corA,
name = c("queenTrait", "workersTrait"))
varE <- c(3, 3 / SP$nWorkers)
corE <- matrix(data = c(1.0, 0.3,
0.3, 1.0), nrow = 2, byrow = TRUE)
SP$setVarE(varE = varE, corE = corE)
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
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
calcInheritanceCriterion(colony, queenTrait = 1, workersTrait = 2)
#> Error in is(x, class2 = "Pop"): object 'colony' not found
calcInheritanceCriterion(apiary, queenTrait = 1, workersTrait = 2)
#> Error in is(x, class2 = "Pop"): object 'apiary' not found
apiary[[2]] <- removeQueen(apiary[[2]])
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
calcInheritanceCriterion(apiary, queenTrait = 1, workersTrait = 2)
#> Error in is(x, class2 = "Pop"): object 'apiary' not found