View source: R/model_getters.R
get_outgroup | R Documentation |
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)
model |
The coalescent model from which aspects are returned |
for_sim |
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. |
locus |
The number of the locus. |
group |
The group of loci. |
total |
If |
ignore_variation |
For internal use. Will likely be removed soon. |
pop |
The population for which aspects are returned |
zero_indexed |
If true, the names of the populations are started from 0 instead of from 1. |
haploids |
If |
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
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