R/Functions_L3_Colonies.R
pullColonies.Rd
Level 3 function that pulls out some colonies from the MultiColony based on colony ID or random selection.
pullColonies(
multicolony,
ID = NULL,
n = NULL,
p = NULL,
by = NULL,
pullTop = TRUE
)
character or numeric, ID of a colony (one or more) to be pulled out
numeric, number of colonies to select
numeric, percentage of colonies pulled out (takes precedence
over n
)
matrix, matrix of values to select by with names being
colony IDs (can be obtained with calcColonyValue
.
If NULL, the colonies are pulled at random.
This parameter is used in combination
with n
or p
to determine the number of pulled colonies, and
pullTop
to determine whether to pull the best or the worst colonies.
logical, pull highest (lowest) values if TRUE
(FALSE
)
founderGenomes <- quickHaplo(nInd = 5, nChr = 1, segSites = 100)
SP <- SimParamBee$new(founderGenomes)
mean <- c(10, 10 / SP$nWorkers)
varA <- c(1, 1 / SP$nWorkers)
corA <- matrix(data = c(
1.0, -0.5,
-0.5, 1.0
), nrow = 2, byrow = TRUE)
varE <- c(3, 3 / SP$nWorkers)
varA / (varA + varE)
#> [1] 0.25 0.25
SP$addTraitADE(nQtlPerChr = 100,
mean = mean,
var = varA, corA = corA,
meanDD = 0.1, varDD = 0.2, corD = corA,
relAA = 0.1, corAA = corA)
SP$setVarE(varE = varE)
basePop <- createVirginQueens(founderGenomes)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
drones <- createDrones(x = basePop[1:4], nInd = 100)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
droneGroups <- pullDroneGroupsFromDCA(drones, n = 10, nDrones = 10)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
apiary <- createMultiColony(basePop[2:5], n = 4)
#> Error in createMultiColony(basePop[2:5], n = 4): object 'basePop' not found
apiary <- cross(apiary, drones = droneGroups[1:4])
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
apiary <- buildUp(apiary)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getId(apiary)
#> Error in getId(apiary): object 'apiary' not found
tmp <- pullColonies(apiary, ID = c(1, 2))
#> Error in is(x, class2 = "MultiColony"): object 'apiary' not found
getId(tmp$pulled)
#> Error in getId(tmp$pulled): object 'tmp' not found
getId(tmp$remnant)
#> Error in getId(tmp$remnant): object 'tmp' not found
tmp <- pullColonies(apiary, ID = c("3", "4"))
#> Error in is(x, class2 = "MultiColony"): object 'apiary' not found
getId(tmp$pulled)
#> Error in getId(tmp$pulled): object 'tmp' not found
getId(tmp$remnant)
#> Error in getId(tmp$remnant): object 'tmp' not found
tmp <- pullColonies(apiary, n = 2)
#> Error in is(x, class2 = "MultiColony"): object 'apiary' not found
getId(tmp$pulled)
#> Error in getId(tmp$pulled): object 'tmp' not found
getId(tmp$remnant)
#> Error in getId(tmp$remnant): object 'tmp' not found
tmp <- pullColonies(apiary, p = 0.75)
#> Error in is(x, class2 = "MultiColony"): object 'apiary' not found
getId(tmp$pulled)
#> Error in getId(tmp$pulled): object 'tmp' not found
getId(tmp$remnant)
#> Error in getId(tmp$remnant): object 'tmp' not found
# How to pull out colonies based on colony values?
colonyGv <- calcColonyGv(apiary)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
pullColonies(apiary, n = 1, by = colonyGv)
#> Error in is(x, class2 = "MultiColony"): object 'apiary' not found