SIMplyBee (version 0.4.1)

pullColonies: Pull out some colonies from the MultiColony object

Description

Level 3 function that pulls out some colonies from the MultiColony based on colony ID or random selection.

Usage

pullColonies(
  multicolony,
  ID = NULL,
  n = NULL,
  p = NULL,
  by = NULL,
  pullTop = TRUE,
  simParamBee = NULL
)

Value

list with two MultiColony-class, the pulled

and the remnant

Arguments

multicolony

MultiColony-class

ID

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

n

numeric, number of colonies to select

p

numeric, percentage of colonies pulled out (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 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.

pullTop

logical, pull 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)

tmp <- pullColonies(apiary, ID = c(1, 2))
getId(tmp$pulled)
getId(tmp$remnant)

tmp <- pullColonies(apiary, ID = c("3", "4"))
getId(tmp$pulled)
getId(tmp$remnant)

tmp <- pullColonies(apiary, n = 2)
getId(tmp$pulled)
getId(tmp$remnant)

tmp <- pullColonies(apiary, p = 0.75)
getId(tmp$pulled)
getId(tmp$remnant)

# How to pull out colonies based on colony values?
colonyGv <- calcColonyGv(apiary)
pullColonies(apiary, n = 1, by = colonyGv)