simulate_sequence_migration: Individual based simulation of the breakdown of contiguous...

In thijsjanzen/GenomeAdmixR: Simulate Admixture of Genomes

Individual based simulation of the breakdown of contiguous ancestry blocks in two populations linked by migration

Description

Individual based simulation of the breakdown of contiguous ancestry blocks, with or without selection. Simulations can be started from scratch, or from a predefined input population. Two populations are simulated, connected by migration

Usage

simulate_sequence_migration(
  input_data_population_1 = NA,
  input_data_population_2 = NA,
  pop_size = c(100, 100),
  total_runtime = 100,
  morgan = 1,
  recombination_rate = NA,
  num_threads = 1,
  select_matrix = NA,
  markers = NA,
  verbose = FALSE,
  multiplicative_selection = TRUE,
  migration_rate = 0,
  stop_at_critical_fst = FALSE,
  critical_fst = NA,
  generations_between_update = 100,
  sampled_individuals = 10,
  number_of_markers = 100,
  random_markers = TRUE,
  mutation_rate = 0,
  substitution_matrix = matrix(1/4, 4, 4)
)

Arguments

input_data_population_1	Genomic data used as input, should be created by the function create_input_data or by the function combine_input_data
input_data_population_2	Genomic data used as input, should be created by thefunction create_input_data or by the function combine_input_data
pop_size	Vector containing the number of individuals in both populations.
total_runtime	Number of generations
morgan	Length of the chromosome in Morgan (e.g. the number of crossovers during meiosis)
recombination_rate	rate in cM / Mbp, used to map recombination to the markers. If the recombination_rate is not set, the value for morgan is used, assuming that the markers included span an entire chromosome.
num_threads	number of threads. Default is 1. Set to -1 to use all available threads
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
markers	A vector of locations of markers (relative locations in [0, 1]). If a vector is provided, ancestry at these marker positions is tracked for every generation.
verbose	Verbose output if TRUE. Default value is FALSE
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.
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
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.
mutation_rate	the per base probability of mutation. Default is 0.
substitution_matrix	a 4x4 matrix representing the probability of mutating to another base (where [1/2/3/4] = [a/c/t/g]), conditional on the event of a mutation happening. Default is the JC69 matrix, with equal probabilities for all transitions / transversions.

Value

A list with: population_1, population_2 two population objects, and three tibbles with allele frequencies (only contain values of a vector was provided to the argument markers: frequencies, initial_frequencies and final_frequencies. Each tibble contains five columns, time, location, ancestor, frequency and population, which indicates the number of generations, the location along the chromosome of the marker, the ancestral allele at that location in that generation, the frequency of that allele and the population in which it was recorded (1 or 2). If a critical fst value was used to terminate the simulation, and object FST with the final FST estimate is returned as well.

thijsjanzen/GenomeAdmixR documentation built on Feb. 16, 2024, 7:27 p.m.