migration_settings {GenomeAdmixR}

Function to manage settings associated with migration

Description

creates a list with settings associated with migration.

Usage

migration_settings(
  migration_rate = NA,
  stop_at_critical_fst = FALSE,
  critical_fst = NA,
  population_size = c(100, 100),
  initial_frequencies = list(c(1, 0), c(0, 1)),
  generations_between_update = 10,
  sampled_individuals = 10,
  number_of_markers = 100,
  random_markers = TRUE
)

Arguments

migration_rate

Rate of migration between the two populations. Migration is implemented such that with probability m (migration rate) one of the two parents of a new offspring is from the other population, with probability 1-m both parents are of the focal population.

stop_at_critical_fst

option to stop at a critical FST value , default is FALSE

critical_fst

the critical fst value to stop, if stop_simulation_at_critical_fst is TRUE

population_size

vector of population sizes, one size for each population

initial_frequencies

A list describing the initial frequency of each ancestor in each population. Each entry in the list contains a vector with the frequencies for all ancestor. The length of the vector indicates the number of unique ancestors. If a vector not summing to 1 is provided, the vector is normalized.

generations_between_update

The number of generations after which the simulation has to check again whether the critical Fst value is exceeded

sampled_individuals

Number of individuals to be sampled at random from the population to estimate Fst

number_of_markers

Number of markers to be used to estimate Fst

random_markers

Are the markers to estimate Fst randomly distributed, or regularly distributed? Default is TRUE.

Value

list with migration associated settings. To be used to pass on migration settings to simulate_admixture.