Level 3 function that selects colonies from MultiColony object based on colony ID or random selection. Whilst user can provide all three arguments ID, p and n, there is a priority list: ID takes first priority. If no ID is provided, p takes precedence over n.
selectColonies(
multicolony,
ID = NULL,
n = NULL,
p = NULL,
by = NULL,
selectTop = TRUE
)
character or numeric, ID of a colony (one or more) to be selected
numeric, number of colonies to select
numeric, percentage of colonies selected (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 selected at random.
This parameter is used in combination
with n
or p
to determine the number of selected colonies, and
selectTop
to determine whether to select the best or the worst colonies.
logical, selects highest (lowest) values if TRUE
(FALSE
)
MultiColony-class
with selected colonies
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
getId(selectColonies(apiary, ID = 1))
#> Error in getId(multicolony): object 'apiary' not found
getId(selectColonies(apiary, ID = c("3", "4")))
#> Error in getId(multicolony): object 'apiary' not found
# ... alternative
getId(apiary[1])
#> Error in getId(apiary[1]): object 'apiary' not found
getId(apiary[["4"]])
#> Error in getId(apiary[["4"]]): object 'apiary' not found
# Select a random number of colonies
selectColonies(apiary, n = 3)
#> Error in "MultiColony" %in% class(multicolony): object 'apiary' not found
# Select a percentage of colonies
selectColonies(apiary, p = 0.2)
#> Error in is(x, class2 = "MultiColony"): object 'apiary' not found
# Since selection is random, you would get a different set of colonies with
# each function call
getId(selectColonies(apiary, p = 0.5))
#> Error in is(x, class2 = "MultiColony"): object 'apiary' not found
getId(selectColonies(apiary, p = 0.5))
#> Error in is(x, class2 = "MultiColony"): object 'apiary' not found
# How to select colonies based on colony values?
# Obtain colony phenotype
colonyPheno <- calcColonyPheno(apiary)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# Select the best colony
selectColonies(apiary, n = 1, by = colonyPheno)
#> Error in "MultiColony" %in% class(multicolony): object 'apiary' not found
# Select the worst 2 colonies
selectColonies(apiary, n = 2, by = colonyPheno, selectTop = FALSE)
#> Error in "MultiColony" %in% class(multicolony): object 'apiary' not found
# Select best colony based on queen's genetic value for trait 1
queenGv <- calcColonyGv(apiary, FUN = mapCasteToColonyGv, workersTrait = NULL)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
selectColonies(apiary, n = 1, by = queenGv)
#> Error in "MultiColony" %in% class(multicolony): object 'apiary' not found