creates a sequence module, which contains all relevant information in order to perform a simulation based on sequence data.
sequence_module(
molecular_data = NA,
initial_frequencies = NA,
morgan = 1,
recombination_rate = NA,
markers = NA,
mutation_rate = 0,
substitution_matrix = matrix(1/4, 4, 4)
)Genomic data used as input, should be of type genomeadmixr_data. Either a single dataset is provided, or a list of multiple genomeadmixr_data objects.
A vector describing the initial contribution of each provided input data set to the starting hybrid swarm. By default, equal frequencies are assumed. If a vector not summing to 1 is provided, the vector is normalized.
Length of the molecular sequence in Morgan (e.g. the number of crossovers during meiosis), alternatively, the recombination rate can be used, see below.
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.
A vector of locations of markers, these markers are tracked for every generation.
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.
sequence module object, used as starting point for simulate_admixture.