Metapopulation-class {Ease}

Metapopulation

Description

The class Metapopulation is used to centralise the information relating to the populations that we want to simulate, as well as to define the migration conditions between them if there are several. This class is thus defined by a list of objects Population and a migration matrix.

Slots

populations

list of objects Population

nbPop

number of populations

names

names of the populations

migMat

migration matrix between population (if there is more than one)

sizes

sizes of the populations

dioecies

sexual systems of the populations (they must all be the same)

selfRates

selfing rates of the populations

demographies

demography parameter of the populations

growthRates

growth rates of the populations

initPopSizes

initial population sizes of the populations

initGenoFreqs

initial genotypic frequencies of the populations

genome

a Genome object

genomeIDs

ID of the Genome object

mutMat

a MutationMatrix object

selection

a Selection object

recMat

recombination matrix

meiosisMat

a meiosis matrix

haploCrossMat

an haplotype crossing matrix

haploCrossMatNamed

an haplotype crossing matrix with names of genotypes instead of their indices

gametogenesisMat

a gametogenesis matrix

alleleFreqMat

a matrix for calculating allelic frequencies

rawOutputSimul

raw output of the simulation function, its refinement is done directly afterwards in the simulate method

stopCondition

list of stop conditions for the simulation (if required)

IDstopCondition

names of stop conditions. They are given an arbitrary name if none is given by the user.

results

data.frame.

records

list.

customOutput

list.

Author(s)

Ehouarn Le Faou