SIMplyBee (version 0.4.1)

selectColonies: Select colonies from MultiColony object

Description

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.

Usage

selectColonies(
  multicolony,
  ID = NULL,
  n = NULL,
  p = NULL,
  by = NULL,
  selectTop = TRUE,
  simParamBee = NULL
)

Value

MultiColony-class with selected colonies

Arguments

multicolony

MultiColony-class

ID

character or numeric, ID of a colony (one or more) to be selected

n

numeric, number of colonies to select

p

numeric, percentage of colonies selected (takes precedence over n)

by

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.

selectTop

logical, selects highest (lowest) values if TRUE (FALSE)

simParamBee

SimParamBee, global simulation parameters

Examples

founderGenomes <- quickHaplo(nInd = 5, nChr = 1, segSites = 100)
SP <- SimParamBee$new(founderGenomes)
SP$nThreads = 1L
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$nWorkers)
varA / (varA + varE)
SP$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)

drones <- createDrones(x = basePop[1:4], nInd = 100)
droneGroups <- pullDroneGroupsFromDCA(drones, n = 10, nDrones = 10)
apiary <- createMultiColony(basePop[2:5], n = 4)
apiary <- cross(apiary, drones = droneGroups[1:4])
apiary <- buildUp(apiary)
getId(apiary)

getId(selectColonies(apiary, ID = 1))
getId(selectColonies(apiary, ID = c("3", "4")))
# ... alternative
getId(apiary[1])
getId(apiary[["4"]])

# Select a random number of colonies
selectColonies(apiary, n = 3)
# Select a percentage of colonies
selectColonies(apiary, p = 0.2)

# Since selection is random, you would get a different set of colonies with
# each function call
getId(selectColonies(apiary, p = 0.5))
getId(selectColonies(apiary, p = 0.5))

# How to select colonies based on colony values?
# Obtain colony phenotype
colonyPheno <- calcColonyPheno(apiary)
# Select the best colony
selectColonies(apiary, n = 1, by = colonyPheno)

# Select the worst 2 colonies
selectColonies(apiary, n = 2, by = colonyPheno, selectTop = FALSE)

# Select best colony based on queen's genetic value for trait 1
queenGv <- calcColonyGv(apiary, FUN = mapCasteToColonyGv, workersTrait = NULL)
selectColonies(apiary, n = 1, by = queenGv)