R/Functions_L2_Colony.R
buildUp.RdLevel 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.
buildUp(
x,
nWorkers = NULL,
nDrones = NULL,
new = TRUE,
exact = FALSE,
resetEvents = FALSE,
simParamBee = NULL,
...
)numeric or function, number of worker to add to the colony,
but see new; if NULL then SimParamBee$nWorkers
is used. If input is MultiColony-class,
the input could also be a vector of the same length as the number of colonies. If
a single value is provided, the same value will be applied to all the colonies.
numeric or function, number of drones to add to the colony,
but see new; if NULL then SimParamBee$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.
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)
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)
logical, call resetEvents as part of the
build up
SimParamBee, global simulation parameters
additional arguments passed to nWorkers or nDrones
when these arguments are a function
Colony-class or MultiColony-class with workers and
drones replaced or added
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
founderGenomes <- quickHaplo(nInd = 4, nChr = 1, segSites = 50)
SP <- SimParamBee$new(founderGenomes)
basePop <- createVirginQueens(founderGenomes)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
drones <- createDrones(x = basePop[1], nInd = 1000)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
droneGroups <- pullDroneGroupsFromDCA(drones, n = 10, nDrones = nFathersPoisson)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# Create a Colony and a MultiColony class
colony <- createColony(x = basePop[2])
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
colony <- cross(colony, drones = droneGroups[[1]])
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
isProductive(colony)
#> Error in is(x, class2 = "Colony"): object 'colony' not found
apiary <- createMultiColony(basePop[3:4], n = 2)
#> Error in createMultiColony(basePop[3:4], n = 2): object 'basePop' not found
apiary <- cross(apiary, drones = droneGroups[c(2, 3)])
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
isProductive(apiary)
#> Error in is(x, class2 = "Colony"): object 'apiary' not found
# Build up
# Using defaults in SP$nWorkers & SP$nDrones
(colony <- buildUp(colony))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
isProductive(colony)
#> Error in is(x, class2 = "Colony"): object 'colony' not found
# Build-up a MultiColony class
(apiary <- buildUp(apiary))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
isProductive(apiary)
#> Error in is(x, class2 = "Colony"): object 'apiary' not found
# The user can also specify a function that will give a number
colony <- removeWorkers(colony) # Remove workers to start from fresh
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
colony <- removeDrones(colony) # Remove drones to start from fresh
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
buildUp(colony, nWorkers = nWorkersPoisson, nDrones = nDronesPoisson)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
buildUp(colony, nWorkers = nWorkersPoisson, nDrones = nDronesPoisson)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# nWorkers and nDrones will vary between function calls when a function is used
# You can store these functions or a values in the SP object
SP$nWorkers <- nWorkersPoisson
SP$nDrones <- nDronesPoisson
# Specifying own number
colony <- buildUp(colony, nWorkers = 100)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# Build up a MultiColony class
apiary <- buildUp(apiary, nWorkers = 250)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# Build up with different numbers
apiary <- buildUp(apiary, nWorkers = c(1000, 2000), nDrones = c(100, 150))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
nWorkers(apiary)
#> Error in is(x, class2 = "Colony"): object 'apiary' not found
nDrones(apiary)
#> Error in is(x, class2 = "Colony"): object 'apiary' not found
# Queen's counters
getMisc(getQueen(buildUp(colony)))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found