getPheno {SIMplyBee}

Access phenotype values of individuals in a caste

Description

Level 0 function that returns phenotype values of individuals in a caste.

Usage

getPheno(x, caste = NULL, nInd = NULL, collapse = FALSE)

getQueenPheno(x, collapse = FALSE)

getFathersPheno(x, nInd = NULL, collapse = FALSE)

getVirginQueensPheno(x, nInd = NULL, collapse = FALSE)

getWorkersPheno(x, nInd = NULL, collapse = FALSE)

getDronesPheno(x, nInd = NULL, collapse = FALSE)

Arguments

x

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

caste

NULL or character, NULL when x is a Pop-class, and character when x is a Colony-class or MultiColony-class with the possible values of "queen", "fathers", "workers", "drones", "virginQueens", or "all"

nInd

numeric, number of individuals to access, if NULL all individuals are accessed, otherwise a random sample

collapse

logical, if the return value should be a single matrix with phenotypes of all the individuals

Value

vector of genetic values when x is Colony-class and list of vectors of genetic values when x is MultiColony-class, named by colony id when x is MultiColony-class

Functions

• getQueenPheno(): Access phenotype value of the queen

• getFathersPheno(): Access phenotype values of fathers

• getVirginQueensPheno(): Access phenotype values of virgin queens

• getWorkersPheno(): Access phenotype values of workers

• getDronesPheno(): Access phenotype values of drones

See Also

pheno and vignette(topic = "QuantitativeGenetics", package = "SIMplyBee")

Examples

founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
SP <- SimParamBee$new(founderGenomes)
SP$addTraitA(nQtlPerChr = 10, var = 1)
SP$setVarE(varE = 1)

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 = 5)

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)

# Input is a population
getPheno(x = getQueen(colony))
queens <- getQueen(apiary, collapse = TRUE)
getPheno(queens)

# Input is a colony
getPheno(colony, caste = "queen")
getQueenPheno(colony)

getPheno(colony, caste = "fathers")
getPheno(colony, caste = "fathers", nInd = 2)
getPheno(colony, caste = "fathers", nInd = 2) # random sample!
getFathersPheno(colony)
getFathersPheno(colony, nInd = 2)

getPheno(colony, caste = "workers")
getWorkersPheno(colony)
# Same aliases exist for all the castes!!!

# Get phenotypes for all individuals
getPheno(colony, caste = "all")
# Get all phenotypes in a single matrix
getPheno(colony, caste = "all", collapse = TRUE)

# Input is a MultiColony - same behaviour as for the Colony!
getPheno(apiary, caste = "queen")
getQueenPheno(apiary)

# Get the phenotypes of all individuals either by colony or in a single matrix
getPheno(apiary, caste = "all")
getPheno(apiary, caste = "all", collapse = TRUE)