Getters for coalescent models
get_outgroup(model)get_outgroup_size(model, for_sim = FALSE)
get_sample_size(model, for_sim = FALSE)
get_features(model)
get_parameter_table(model)
get_parameter(model)
get_locus_length(model, locus = NULL, group = NULL, total = TRUE)
get_populations(model)
get_locus_length_matrix(model)
get_locus_number(model, group = NA, ignore_variation = FALSE)
get_population_individuals(model, pop, zero_indexed = FALSE, haploids = TRUE)
get_summary_statistics(model)
The coalescent model from which aspects are returned
If true, the sample size used internally for the simulation will be reported rather than the number of actual samples. The numbers can be unequal for the simulation of unphased data.
The number of the locus.
The group of loci.
If FALSE, the length of loci in a trio will be reported
individually. If TRUE the sum of the loci"s length will be reported.
This does not affect non-trio loci.
For internal use. Will likely be removed soon.
The population for which aspects are returned
If true, the names of the populations are started from 0 instead of from 1.
If TRUE, the function always returns all haploids
from the population, even if the model is polyploid.
get_outgroup(): Returns the population that is marked as outgroup
get_outgroup_size(): Returns the number of samples in the outgroup
get_sample_size(): Returns a vector containing the number of
haploids sampled per population. This is the default ordering of
individuals used by coala.
get_parameter_table(): Returns the ranged parameters of a model as a
data.frame
get_parameter(): Returns the ranged parameters of a model
get_locus_length(): Returns the length of the loci in a locus group
get_populations(): Returns a vector of populations in the model
get_locus_length_matrix(): Returns a matrix with detailed length
information about the loci in the model.
get_locus_number(): Returns the number of loci in a locus group
get_population_individuals(): Returns the index of the individuals of one
population. Ignores outgroups, so that it can be used for indexing
segregating sites.
get_summary_statistics(): Returns the summary statistics in the model
Paul Staab