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
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)
)Genomic data used as input, should be created
by the function create_input_data or by the function
combine_input_data
Genomic data used as input, should be created
by thefunction create_input_data or by the function
combine_input_data
Vector containing the number of individuals in both populations.
Number of generations
Length of the chromosome in Morgan (e.g. the number of crossovers during meiosis)
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.
number of threads. Default is 1. Set to -1 to use all available threads
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
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 output if TRUE. Default value is FALSE
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.
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.
option to stop at a critical FST value , default is FALSE
the critical fst value to stop, if
stop_simulation_at_critical_fst is TRUE
The number of generations after which the simulation has to check again whether the critical Fst value is exceeded
Number of individuals to be sampled at random from the population to estimate Fst
Number of markers to be used to estimate Fst
Are the markers to estimate Fst randomly distributed, or regularly distributed? Default is TRUE.
the per base probability of mutation. Default is 0.
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.
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.