METAPOP_SIMULATION {Ease}

Simulation of a metapopulation

Description

Simulation of a metapopulation

Usage

METAPOP_SIMULATION(
  nbPop,
  ids,
  migMat,
  nsim,
  verbose,
  recording,
  recordGenGap,
  drift,
  nbHaplo,
  nbGeno,
  idGeno,
  nbAlleles,
  idAlleles,
  nbLoci,
  initGenoFreq,
  meiosisMat,
  gametogenesisMat,
  popSize,
  threshold,
  dioecy,
  selfRate,
  stopCondition,
  IDstopCondition,
  haploCrossMat,
  alleleFreqMat,
  gamFit,
  indFit,
  gamProdFit,
  demography,
  growthRate,
  initPopSize,
  nameOutFunct
)

Arguments

nbPop

number of populations in the metapopulation

ids

population IDs

migMat

migration matrix

nsim

number of simulations

verbose

boolean determining if the progress of the simulations should be displayed or not (useful in case of many simulations)

recording

a boolean indicating whether to record all mutations, i.e. to record allelic and genotypic frequencies along the simulations

recordGenGap

the number of generations between two records during simulation, if the record parameter is TRUE. Whatever the value of this parameter, both the first and the last generation will be included in the record

drift

a boolean indicating whether genetic drift should be considered (i.e. whether deterministic simulations are performed or not)

nbHaplo

number of haplotypes

nbGeno

number of genotypes

idGeno

genotypes ID

nbAlleles

number of alleles for each loci

idAlleles

alleles ID

nbLoci

number of loci

initGenoFreq

list of initial genotype frequencies in the populations

meiosisMat

meiosis matrix

gametogenesisMat

gametogenesis matrix

popSize

list population sizes

threshold

threshold for simulations

dioecy

whether the population(s) is dioecious or not (hermaphrodism)

selfRate

list of the selfing rate in populations (only for hermaphroditic population)

stopCondition

list of stop conditions

IDstopCondition

vector of stop condition ID

haploCrossMat

haplotypes crossing matrix

alleleFreqMat

matrix for calculating allelic frequencies

gamFit

fitness of gametes

indFit

fitness of individuals

gamProdFit

fitness for gamete production

demography

list of population demographies

growthRate

list of population growth rates

initPopSize

list of initial population

nameOutFunct

name of the custom output function

Author(s)

Ehouarn Le Faou