setMetapopulation: Setting a metapopulation

In Ease: Simulating Explicit Population Genetics Models

Setting a metapopulation

Description

A metapopulation is a set of population(s) (from 1) that are simulated with potential migration between them. Only genotypes can migrate, i.e. adult individuals.

Usage

setMetapopulation(populations, migMat = matrix(1))

Arguments

populations	a list of Population objects
migMat	a migration matrix

Details

The construction of a Metapopulation object requires only two arguments (one optional). The first is a population(s) list, defined from the population class. The second is a migration matrix, which connects the populations together. This matrix is a probability matrix (square with the sum of the rows equal to 1, whose size is equal to the number of populations) where each value corresponds to the proportion of individuals (genotypes) that disperse from their source population (row) to their target population (column).

Value

a Metapopulation object

Author(s)

Ehouarn Le Faou

Examples

# Definition of a population in its simplest form:
DL <- list(dl = c("A", "a"))
HL <- list(hl = c("B", "b"))
mutations <- list(
  mutation(from = "A", to = "a", rate = 1e-3),
  mutation(from = "B", to = "b", rate = 1e-3)
)
genomeObj <- setGenome(listHapLoci = HL, listDipLoci = DL)
pop <- setPopulation(
  name = "A",
  size = 1000,
  dioecy = TRUE,
  genomeObj = genomeObj,
  selectionObj = setSelectNeutral(genomeObj),
  mutMatrixObj = setMutationMatrix(genomeObj, mutations = mutations)
)
metapop <- setMetapopulation(populations = list(pop))
metapop <- simulate(metapop, nsim = 10, seed = 123)
# Other examples available in the documentation of the package

Ease documentation built on Nov. 10, 2022, 5:54 p.m.