R/Functions_L1_Pop.R
cross.RdLevel 1 function that crosses (mates) a virgin queen to a group
of drones. The virgin queen(s) could be within a population (Pop-class),
in a colony (Colony-class), or multi-colony (MultiColony-class).
This function does not create any progeny, it only stores the mated drones
(fathers) so we can later create progeny as needed. When input is a
(Colony-class) or (MultiColony-class), one
virgin queens is selected at random, mated, and promoted to the queen of
the colony. Other virgin queens are destroyed. Mated drones (fathers) are
stored for producing progeny at a later stage.
cross(x, drones, crossPlan = NULL, checkMating = "error", simParamBee = NULL)Pop-class or codeColony-class or MultiColony-class,
one or more virgin queens / colonies to be mated;
Pop-class or a list of Pop-class,
group(s) of drones that will be mated with virgin queen(s); if there is
more than one virgin queen, the user has to provide a list of drone
Pop-class. For this, the user can use pullDroneGroupsFromDCA
named list with names being virgin queen or colony IDs with
each list element holding the IDs of selected drones. Also see
createRandomCrossPlan. If cross plan is NULL, we cross
each virgin queen with the element-wise element of drones, which
should be the same length as the number of virgin queens If the cross plan
is provided, the drones argument must be a single Pop-class.
character, throw a warning (when checkMating = "warning"),
or stop error (when checkMating = "error") when some matings fail (see
Details)
SimParamBee, global simulation parameters
Pop-class with mated queen(s). The misc slot of the
queens contains additional information about the number of workers, drones,
and homozygous brood produced, and the expected percentage of csd homozygous
brood.
This function changes caste for the mated drones to fathers, and mated virgin queens to queens. See examples. This means that you can not use these individuals in matings any more!
If the supplied drone population is empty (has 0 individuals), which
can happen in edge cases or when nFathersPoisson is used
instead of nFathersTruncPoisson, then mating of a virgin
queen will fail and she will stay virgin. This can happen for just a few
of many virgin queens, which can be annoying to track down, but you can use
isQueen or isVirginQueen to find such virgin
queens. You can use checkMating to alert you about this situation.
Colony-class on how we store the fathers along the
queen.
For crossing virgin queens according to a cross plan, see
createRandomCrossPlan.
For crossing virgin queens on a mating stations, see
createMatingStationDCA
founderGenomes <- quickHaplo(nInd = 20, nChr = 1, segSites = 100)
SP <- SimParamBee$new(founderGenomes)
basePop <- createVirginQueens(founderGenomes)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
drones <- createDrones(x = basePop[1], nInd = 200)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
droneGroups <- pullDroneGroupsFromDCA(drones, n = 8, nDrones = nFathersPoisson)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# If input is a Pop class of virgin queen(s)
virginQueen1 <- basePop[2]
#> Error in eval(expr, envir, enclos): object 'basePop' not found
isQueen(virginQueen1)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
(matedQueen1 <- cross(
x = virginQueen1,
drones = droneGroups[[1]]
))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
isQueen(virginQueen1)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
isQueen(matedQueen1)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
nFathers(matedQueen1)
#> Error in is(x, class2 = "Pop"): object 'matedQueen1' not found
isDrone(getFathers(matedQueen1))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
isFather(getFathers(matedQueen1))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
virginQueen2 <- basePop[3]
#> Error in eval(expr, envir, enclos): object 'basePop' not found
(matedQueen2 <- cross(
x = virginQueen2,
drones = droneGroups[[2]]
))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
isQueen(virginQueen2)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
isQueen(matedQueen2)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
nFathers(matedQueen2)
#> Error in is(x, class2 = "Pop"): object 'matedQueen2' not found
matedQueens <- cross(
x = c(basePop[4], basePop[5]),
drones = droneGroups[c(3, 4)]
)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
isQueen(matedQueens)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
nFathers(matedQueens)
#> Error in is(x, class2 = "Pop"): object 'matedQueens' not found
getFathers(matedQueens)
#> Error in is(x, class2 = "Pop"): object 'matedQueens' not found
# Inbred mated queen (mated with her own sons)
matedQueen3 <- cross(
x = basePop[1],
drones = droneGroups[[5]]
)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# Check the expected csd homozygosity
pHomBrood(matedQueen3)
#> Error in is(x, class2 = "Pop"): object 'matedQueen3' not found
# If input is a Colony or MultiColony class
# Create Colony and MultiColony class
colony <- createColony(basePop[6])
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
isVirginQueen(getVirginQueens(colony))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
apiary <- createMultiColony(basePop[7:8], n = 2)
#> Error in createMultiColony(basePop[7:8], n = 2): object 'basePop' not found
all(isVirginQueen(mergePops(getVirginQueens(apiary))))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# Cross
colony <- cross(colony, drones = droneGroups[[6]])
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
isQueenPresent(colony)
#> Error in is(x, class2 = "Colony"): object 'colony' not found
apiary <- cross(apiary, drones = droneGroups[c(7, 8)])
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
all(isQueenPresent(apiary))
#> Error in is(x, class2 = "Colony"): object 'apiary' not found
nFathers(apiary)
#> Error in is(x, class2 = "Pop"): object 'apiary' not found
# Try mating with drones that were already used for mating
colony <- createColony(basePop[9])
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
try((matedColony <- cross(x = colony, drones = droneGroups[[1]])))
#> Error in get(x = "SP", envir = .GlobalEnv) : object 'SP' not found
# Create new drones and mate the colony with them
drones <- createDrones(x = basePop[1], nInd = 15)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
all(isDrone(drones))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
any(isFather(drones))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
(matedColony <- cross(x = colony, drones = drones))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
isQueenPresent(matedColony)
#> Error in is(x, class2 = "Colony"): object 'matedColony' not found