SIMplyBee (version 0.4.1)

MultiColony-class: Honeybee multicolony object

Description

An object holding a collection of honeybee colonies. It behaves like a list.

Usage

isMultiColony(x)
# S4 method for MultiColony
show(object)
# S4 method for MultiColony
c(x, ...)
# S4 method for MultiColonyOrNULL
c(x, ...)
# S4 method for MultiColony,integerOrNumericOrLogical
[(x, i, j, drop)
# S4 method for MultiColony,character
[(x, i, j, drop)
# S4 method for MultiColony,integerOrNumericOrLogical
[[(x, i)
# S4 method for MultiColony,character
[[(x, i)
# S4 method for MultiColony,integerOrNumericOrLogicalOrCharacter,ANY,MultiColony
[(x, i, j) <- value
# S4 method for MultiColony,integerOrNumericOrLogicalOrCharacter,ANY,Colony
[[(x, i, j) <- value

Value

MultiColony-class or Colony-class

Arguments

x

MultiColony-class

object

MultiColony-class

...

NULL, Colony-class, or MultiColony-class

i

integer, numeric, logical, or character, index or ID to select a colony (see examples)

j

not used

drop

not used

value

Colony-class or MultiColony-class to assign into x based on colony index or name i

Functions

• isMultiColony(): Test if x is a MultiColony class object

• show(MultiColony): Show MultiColony object

• c(MultiColony): Combine multiple Colony and MultiColony objects

• c(MultiColonyOrNULL): Combine multiple Colony and MultiColony objects

• x[i: Extract a colony (one or more!) with an integer/numeric/logical index (position) (return MultiColony-class)

• x[i: Extract a colony (one or more!) with a character ID (name) (return MultiColony-class)

• x[[i: Extract a colony (just one!) with an integer/numeric/logical index (position) (return Colony-class)

• x[[i: Extract a colony (just one!) with a character ID (name) (return Colony-class)

• `[`(x = MultiColony, i = integerOrNumericOrLogicalOrCharacter, j = ANY) <- value: Assign colonies into MultiColony

• `[[`(x = MultiColony, i = integerOrNumericOrLogicalOrCharacter, j = ANY) <- value: Assign Colony into MultiColony

Slots

colonies

list, a collection of Colony-class objects

See Also

createMultiColony

Examples

founderGenomes <- quickHaplo(nInd = 10, nChr = 1, segSites = 100)
SP <- SimParamBee$new(founderGenomes)
SP$nThreads = 1L
basePop <- createVirginQueens(founderGenomes)

drones <- createDrones(x = basePop[1], nInd = 1000)
droneGroups <- pullDroneGroupsFromDCA(drones, n = 10, nDrones = nFathersPoisson)
apiary <- createMultiColony(basePop[1:6], n = 6)
apiary <- cross(apiary, drones = droneGroups[1:6])
apiary
show(apiary)
is(apiary)
isMultiColony(apiary)

getId(apiary)
apiary[1]
getId(apiary[1])
getId(apiary["2"])
getId(apiary[2])
getId(apiary[-1])
getId(apiary[5])

getId(apiary)
getId(apiary[c(1, 3)])
getId(apiary[c("2", "4")])
getId(apiary[c(TRUE, FALSE, TRUE, FALSE)])
getId(apiary[c(TRUE, FALSE)]) # beware of recycling!
getId(apiary[c(5, 6)])
getId(apiary[c("6", "7")])

apiary[[1]]
apiary[["2"]]
apiary[[3]]
apiary[["4"]]
try(apiary[[6]])
apiary[["7"]]

getId(c(apiary[c(1, 3)], apiary[2]))
getId(c(apiary[2], apiary[c(1, 3)]))

getId(c(apiary[2], apiary[0]))
getId(c(apiary[0], apiary[2]))

getId(c(apiary[2], NULL))
getId(c(NULL, apiary[2]))

apiary1 <- apiary[1:2]
apiary2 <- apiary[3:4]
getId(apiary1)
getId(apiary2)
apiary1[[1]] <- apiary2[[1]]
getId(apiary1)
try(apiary2[[1]] <- apiary2[[2]])

apiary1 <- apiary[1:2]
apiary2 <- apiary[3:5]
getId(apiary1)
getId(apiary2)
apiary2[1:2] <- apiary1
getId(apiary2)
try(apiary2[1] <- apiary1)
try(apiary2[1:3] <- apiary1)
try(apiary2[1:2] <- apiary1[[1]])

apiary2 <- apiary[3:5]
getId(apiary2)
try(apiary2[c("4", "5")] <- apiary1)
try(apiary2[c("4", "5")] <- apiary1)