feat_recombination {coala}

Feature: Recombination

Description

This feature adds intra-locus recombination to a model. The rate is per locus for unlinked loci and per trio for linked locus trios. By default, the same recombination rate is used for all loci, but it is possible to change this with par_variation and par_zero_inflation. Coala assumes that recombination events can occur between all neighboring bases.

Usage

feat_recombination(rate, locus_group = "all")

Arguments

rate

The recombination rate. Can be a numeric or a parameter. The rate is equal to 4*N0*r, where r is the probability that a recombination event within the locus occurs in one generation.

locus_group

The loci for which this features is used. Can either be "all" (default), in which case the feature is used for simulating all loci, or a numeric vector. In the latter case, the feature is only used for the loci added in locus_ commands with the corresponding index starting from 1 in order in which the commands where added to the model. For example, if a model has locus_single(10) + locus_averaged(10, 11) + locus_single(12) and this argument is c(2, 3), than the feature is used for all but the first locus (that is locus 2 - 12).

Value

The feature, which can be added to a model using +.

The feature, which can be added to a model created with coal_model using +.

See Also

For creating a model: coal_model

For adding recombination: feat_mutation.

Other features: feat_growth(), feat_ignore_singletons(), feat_migration(), feat_mutation(), feat_outgroup(), feat_pop_merge(), feat_selection(), feat_size_change(), feat_unphased()

Examples

# Simulate a 1.5kb sequence for 10 individuals with recombination:
model <- coal_model(10, 2, 1500) +
  feat_recombination(1.5) +
  feat_mutation(5) +
  sumstat_sfs()
simulate(model)