tracts.core

The optimization core: compute_objective() evaluates a demographic model’s log-likelihood for a given set of parameters, and optimize_cob_sex_biased_single_step()/ optimize_cob_sex_biased_two_steps() drive the actual optimization (in one step, or in two steps that first fit non-sex-bias parameters on autosomal data before fitting sex-bias parameters). Called by tracts.driver.

Functions

compute_objective(parameters, *, best_state, ...)	Evaluate the optimization objective (negative log-likelihood) for a given parameter vector.
optimize_cob_sex_biased_single_step(p0, ...)	Optimizes the log-likelihood over all parameters defined by the demographic model, given a specified pair of admixture models for autosomes and allosomes.
optimize_cob_sex_biased_two_steps(p0, ...[, ...])	Optimizes the log-likelihood over all parameters defined by the demographic model, for a specified admixture model applied to both autosomes and allosomes.