R/model_examples.R

In statgenlmu/coala: A Framework for Coalescent Simulation

# Example models used in unittests

model_theta_tau <- function() {
  coal_model(c(10, 15), 10) +
    feat_pop_merge(par_range("tau", 0.01, 5), 2, 1) +
    feat_mutation(par_range("theta", 1, 10)) +
    sumstat_jsfs()
}


model_hky <- function() {
  coal_model(c(3, 3, 1), 2) +
    feat_pop_merge(par_range("tau", 0.01, 5), 2, 1) +
    feat_recombination(par_const(1)) +
    feat_pop_merge(par_expr("2*tau"), 3, 1) +
    feat_outgroup(3) +
    feat_mutation(par_range("theta", 1, 10), model = "HKY",
                  tstv_ratio = 2, base_frequencies = rep(.25, 4)) +
    sumstat_jsfs()
}


model_gtr <- function() {
  coal_model(c(3, 3, 2), 2) +
    feat_pop_merge(par_range("tau", 0.01, 5), 2, 1) +
    feat_pop_merge(par_expr("2*tau"), 3, 1) +
    feat_recombination(par_const(1)) +
    feat_outgroup(3) +
    feat_mutation(par_range("theta", 1, 10),
                  model = "GTR", gtr_rates = 1:6 / sum(1:6)) +
    sumstat_jsfs()
}


model_trios <- function() {
  coal_model(5) + feat_mutation(5) +
    locus_trio(locus_length = c(10, 20, 10), distance = c(5, 5)) +
    sumstat_seg_sites()
}