setPopulation: Setting a population

In Ease: Simulating Explicit Population Genetics Models

Setting a population

Description

Generation of a population by providing all the necessary ingredients for its definition, including a genome, a mutation matrix and a selection regime.

Usage

setPopulation(
  name,
  size,
  dioecy,
  genomeObj,
  mutMatrixObj,
  selectionObj,
  selfRate = 0,
  demography = F,
  growthRate = 0,
  initPopSize = NULL,
  initGenoFreq = NULL
)

Arguments

name	the name of the population
size	the population size
dioecy	logical indicating whether the simulated population is dioecious or hermaphroditic
genomeObj	a Genome object
mutMatrixObj	a MutationMatrix object
selectionObj	a Selection object
selfRate	the selfing rate
demography	a logic indicating whether the population should have a demography (stochasticity in the number of individuals present in the population + logistic growth with carrying capacity equal to the size parameter)
growthRate	a Genome object
initPopSize	the initial size of the population. It is necessarily equal to size if the population has no demography.
initGenoFreq	a vector of the size of the genotype number describing the initial allele frequencies common to all simulations

Details

A population is defined strictly by a name, a size, a sexual system (dioecy or hermaphodite), and the three objects defined previously: genome, mutation matrix and selection. In addition to that, it is possible to define - a selfing rate (by default equal to 0) - a vector of initial genotypic frequencies - a demography

Two demographic regimes are possible: no demography, i.e. a fixed population size, or demography, i.e. a population where the size fluctuates stochastically. The boolean argument 'demography' is used to define whether there should be stochasticity. For a fixed population size, it is therefore sufficient to define that 'demography = FALSE' (default) and to set the desired population size with the 'popSize' parameter.

For a fluctuating demography, 'demography' must be 'TRUE' and three other parameters are then needed: the initial population size ('initPopSize'), the population growth rate ('growthRate') and the carrying capacity of the population (the population size, 'popSize').

It is also possible to avoid defining a population size altogether, by setting off the genetic drift ('drift' parameter). This will allow the model to be simulated deterministically.

Value

a Population 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)
)

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