simulate_admixture_until: Simulate admixture until reaching threshold divergence

In thijsjanzen/isoSIM: Simulate Linkage Disequilibrium Along Chromosomes in Isofemale Lines

Description

Individual based simulation of the breakdown of contiguous ancestry blocks, with or without selection. Two populations are simulated, and upon userdefined timepoints, genetic divergence between the populations is checked. If the divergence exceeds a certain threshold, simulation is stopped.

Usage

simulate_admixture_until(pop_size = 100,
                         number_of_founders = 2,
                         total_runtime = 100,
                         morgan = 1,
                         seed,
                         select_matrix = NA,
                         generations_between_update = 100,
                         critical_fst = 0.1,
                         sampled_individuals = 10,
                         number_of_markers = 100,
                         random_markers = TRUE,
                         overlap = 0,
                         multiplicative_selection = TRUE)

Arguments

pop_size	Number of individuals per population
number_of_founders	Number of unique ancestors
total_runtime	Maximum number of generations allowed to obtain level of genetic divergence
morgan	Length of the chromosome in Morgan (e.g. the number of crossovers during meiosis)
seed	Seed of the pseudo-random number generator
select_matrix	Selection matrix indicating the markers which are under selection. If not provided by the user, the simulation proceeds neutrally. If provided, each row in the matrix should contain five entries: location location of the marker under selection (in Morgan) fitness of wildtype (aa) fitness of heterozygote (aA) fitness of homozygote mutant (AA) Ancestral type that representes the mutant allele A
generations_between_update	Time interval used after which the FST is calculated again. Lower values increase accuracy, but also increase computation time
critical_fst	As long as the Fst between the two populations is lower than this fst, simulations continue
sampled_individuals	The number of individuals randomly sampled from the population to calculate the fst
number_of_markers	Number of markers used to calculate the Fst
random_markers	If TRUE, markers are randomly spaced along the chromosome, if FALSE, markers are equidistantly spaced along the chromosome.
overlap	Shared ancestry between the two populations. This is rounded to an integer, such that the number of shared ancestors is round(number_of_founders * overlap)
multiplicative_selection	Default: TRUE. If TRUE, fitness is calculated for multiple markers by multiplying fitness values for each marker. If FALSE, fitness is calculated by adding fitness values for each marker.

Value

A list with: Population_1 a population object containing all individuals in population 1,Population_2 a population object containing all individuals in population 2, Number_of_generations total number of generations required to obtain the cricital fst value, FST final FST value.

Author(s)

Thijs Janzen

thijsjanzen/isoSIM documentation built on May 29, 2019, 10:39 a.m.