SIMplyBee (version 0.4.1)

buildUp: Build up Colony or MultiColony object by adding (raising) workers and drones

Description

Level 2 function that builds up a Colony or MultiColony object by adding (raising) workers and drones usually in spring or after events such as split or swarming.

Usage

buildUp(
  x,
  nWorkers = NULL,
  nDrones = NULL,
  new = TRUE,
  exact = FALSE,
  resetEvents = FALSE,
  simParamBee = NULL,
  ...
)

Value

Colony-class or MultiColony-class with workers and drones replaced or added

Arguments

x

Colony-class or MultiColony-class

nWorkers

numeric or function, number of worker to add to the colony, but see new; if NULL then SimParamBee$nWorkers is used. If input is MultiColony-class, the input could also be a vector of the same length as the number of colonies. If a single value is provided, the same value will be applied to all the colonies.

nDrones

numeric or function, number of drones to add to the colony, but see new; if NULL then SimParamBee$nDrones is used. If input is MultiColony-class, the input could also be a vector of the same length as the number of colonies. If a single value is provided, the same value will be applied to all the colonies.

new

logical, should the number of workers and drones be added anew or should we only top-up the existing number of workers and drones to nWorkers and nDrones (see details)

exact

logical, if the csd locus is turned on and exact is TRUE, create the exact specified number of only viable workers (heterozygous on the csd locus)

resetEvents

logical, call resetEvents as part of the build up

simParamBee

SimParamBee, global simulation parameters

...

additional arguments passed to nWorkers or nDrones when these arguments are a function

Details

This function increases queen's nWorkers, nHomBrood, and nDrones counters. It also turns production on.

Argument new enables simulation of two common cases. First, if you are modelling year-to-year cycle, you will likely want new = TRUE, so that, say, in spring you will replace old (from last year) workers and drones with the new ones. This is the case that we are targeting and hence new = TRUE is default. Second, if you are modelling shorter period cycles, you will likely want new = FALSE to just top up the current workers and drones - you might also want to look at replaceWorkers and replaceDrones.

TODO: Discuss on how to model day-to-day variation with new = FALSE. We are not sure this is easy to achieve with current implementation just now, but could be expanded. https://github.com/HighlanderLab/SIMplyBee/issues/176

Examples

founderGenomes <- quickHaplo(nInd = 4, nChr = 1, segSites = 50)
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]])
isProductive(colony)
apiary <- createMultiColony(basePop[3:4], n = 2)
apiary <- cross(apiary, drones = droneGroups[c(2, 3)])
isProductive(apiary)

# Build up
# Using defaults in SP$nWorkers & SP$nDrones
(colony <- buildUp(colony))
isProductive(colony)
# Build-up a MultiColony class
(apiary <- buildUp(apiary))
isProductive(apiary)

# The user can also specify a function that will give a number
colony <- removeWorkers(colony) # Remove workers to start from fresh
colony <- removeDrones(colony) # Remove drones to start from fresh
buildUp(colony, nWorkers = nWorkersPoisson, nDrones = nDronesPoisson)
buildUp(colony, nWorkers = nWorkersPoisson, nDrones = nDronesPoisson)
# nWorkers and nDrones will vary between function calls when a function is used
# You can store these functions or a values in the SP object
SP$nWorkers <- nWorkersPoisson
SP$nDrones <- nDronesPoisson

# Specifying own number
colony <- buildUp(colony, nWorkers = 100)
# Build up a MultiColony class
apiary <- buildUp(apiary, nWorkers = 250)
# Build up with different numbers
apiary <- buildUp(apiary, nWorkers = c(1000, 2000), nDrones = c(100, 150))
nWorkers(apiary)
nDrones(apiary)

# Queen's counters
getMisc(getQueen(buildUp(colony)))