SIMplyBee (version 0.4.1)

createCastePop: Creates caste population individuals from the colony

Description

Level 1 function that creates the specified number of caste individuals from the colony with a mated queens. If csd locus is active, it takes it into account and any csd homozygotes are removed and counted towards homozygous brood.

Usage

createCastePop(
  x,
  caste = NULL,
  nInd = NULL,
  exact = TRUE,
  year = NULL,
  editCsd = TRUE,
  csdAlleles = NULL,
  simParamBee = NULL,
  ...
)
createWorkers(x, nInd = NULL, exact = FALSE, simParamBee = NULL, ...)
createDrones(x, nInd = NULL, simParamBee = NULL, ...)
createVirginQueens(
  x,
  nInd = NULL,
  year = NULL,
  editCsd = TRUE,
  csdAlleles = NULL,
  simParamBee = NULL,
  ...
)

Value

when x is MapPop-class returns

virginQueens (a Pop-class); when x is Colony-class returns

virginQueens (a Pop-class); when x is MultiColony-class

return is a named list of virginQueens (a Pop-class); named by colony ID

Arguments

x

link[AlphaSimR]{MapPop-class} (only if caste is "virginQueens"), or Pop (only if caste is "drones") or Colony-class or MultiColony-class

caste

character, "workers", "drones", or "virginQueens"

nInd

numeric or function, number of caste individuals; if NULL then SimParamBee$nWorkers, SimParamBee$nDrones or SimParamBee$nVirginQueens is used depending on the caste; only used when x is Colony-class or MultiColony-class, when x is link[AlphaSimR]{MapPop-class} all individuals in x are converted into virgin queens

exact

logical, only relevant when creating workers, if the csd locus is active and exact is TRUE, create the exactly specified number of viable workers (heterozygous on the csd locus)

year

numeric, year of birth for virgin queens

editCsd

logical (only active when x is link[AlphaSimR]{MapPop-class}), whether the csd locus should be edited to ensure heterozygosity at the csd locus (to get viable virgin queens); see csdAlleles

csdAlleles

NULL or list (only active when x is link[AlphaSimR]{MapPop-class}); If NULL, then the function samples a heterozygous csd genotype for each virgin queen from all possible csd alleles. If not NULL, the user provides a list of length nInd with each node holding a matrix or a data.frame, each having two rows and n columns. Each row must hold one csd haplotype (allele) that will be assigned to a virgin queen. The n columns span the length of the csd locus as specified in SimParamBee. The two csd alleles must be different to ensure heterozygosity at the csd locus.

simParamBee

SimParamBee, global simulation parameters

...

additional arguments passed to nInd when this argument is a function

Functions

• createWorkers(): Create workers from a colony

• createDrones(): Create drones from a colony

• createVirginQueens(): Create virgin queens from a colony

Examples

founderGenomes <- quickHaplo(nInd = 4, nChr = 1, segSites = 50)
SP <- SimParamBee$new(founderGenomes)
SP$nThreads = 1L
SP$setTrackRec(TRUE)
SP$setTrackPed(isTrackPed = TRUE)

# Create virgin queens on a MapPop
basePop <- createCastePop(founderGenomes, caste = "virginQueens")
# Or alias
createVirginQueens(founderGenomes)
# Same aliases exist for all the castes!!!

# Create drones on a Pop
drones <- createDrones(x = basePop[1],  nInd = 200)
# Or create unequal number of drones from multiple virgin queens
drones <- createDrones(basePop[1:2], nInd = c(100, 200))
droneGroups <- pullDroneGroupsFromDCA(drones, n = 3, nDrones = nFathersPoisson)

# Create a Colony and a MultiColony class
colony <- createColony(x = basePop[2])
colony <- cross(colony, drones = droneGroups[[1]])
apiary <- createMultiColony(basePop[3:4], n = 2)
apiary <- cross(apiary, drones = droneGroups[c(2, 3)])

# Using default nInd in SP
colony@virginQueens <- createVirginQueens(colony)
colony@workers <- createWorkers(colony)$workers
colony@drones <- createDrones(colony)
# Usually, you would use functions buildUp() or addCastePop()

# These populations hold individual information
# Example on the virgin queens (same holds for all castes!)
virginQueens <- colony@virginQueens
virginQueens@id
virginQueens@sex
virginQueens@mother
virginQueens@father

# Specify own number
SP$nVirginQueens <- 15
SP$nWorkers <- 100
SP$nDrones <- 10
createVirginQueens(colony)
createVirginQueens(apiary)
# Or creating unequal numbers
createVirginQueens(apiary, nInd = c(5, 10))
# nVirginQueens will NOT vary between function calls when a constant is used

# Specify a function that will give a number
createVirginQueens(colony, nInd = nVirginQueensPoisson)
createVirginQueens(apiary, nInd = nVirginQueensPoisson)
# No. of individuals will vary between function calls when a function is used

# Store a function or a value in the SP object
SP$nVirginQueens <- nVirginQueensPoisson
createVirginQueens(colony)
createVirginQueens(colony)
createVirginQueens(apiary)
createVirginQueens(apiary)
# No. of individuals will vary between function calls when a function is used

# csd homozygosity - relevant when creating virgin queens
SP <- SimParamBee$new(founderGenomes, csdChr = 1, nCsdAlleles = 8)
SP$nThreads = 1L
basePop <- createVirginQueens(founderGenomes, editCsd = FALSE)
all(isCsdHeterozygous(basePop))

basePop <- createVirginQueens(founderGenomes, editCsd = TRUE)
all(isCsdHeterozygous(basePop))