tracts.genetic_model

Bundles a demographic model together with the admixture and phase-type model configuration used to evaluate its likelihood.

This exists to avoid threading a long, repeated list of related parameters (ad_model_autosomes, ad_model_allosomes, rho_f, rho_m, TP, N_cores, plus the demographic model itself) through tracts.core’s optimization functions (_compute_objective(), optimize_cob_sex_biased_single_step(), optimize_cob_sex_biased_two_steps()) and their callers in tracts.driver.

Classes

GeneticModel(demographic_model[, ...])	Bundles a demographic model with the admixture and phase-type model configuration used to evaluate its likelihood against tract-length data.
LoglikBreakdown([autosomes, ...])	Log-likelihood contributions from each genome component included in a GeneticModel.loglik() evaluation.
PhaseTypeModelConfig([ad_model_autosomes, ...])	Configuration for the admixture and phase-type model used to compute the likelihood of a demographic model's migration matrices.