tracts.genetic_model.PhaseTypeModelConfig#

class PhaseTypeModelConfig(ad_model_autosomes='DC', ad_model_allosomes='DC', rho_f=1, rho_m=1, TP=2, N_cores=1)#

Bases: object

Configuration for the admixture and phase-type model used to compute the likelihood of a demographic model’s migration matrices.

Parameters:

  • ad_model_autosomes (str) – The admixture model used for autosomes. Must be one of 'DC' (Dioecious-Coarse), 'DF' (Dioecious-Fine), 'M' (Monoecious), 'H-DC' or 'H-DF' (the hybrid-pedigree refinements of DC and DF, respectively). Defaults to 'DC'.

  • ad_model_allosomes (str | None) – The admixture model used for allosomes. Must be one of 'DC', 'DF', 'H-DC', or 'H-DF'. If None, allosomal admixture is not modelled. Defaults to 'DC'.

  • rho_f (float) – The female-specific recombination rate. Defaults to 1.

  • rho_m (float) – The male-specific recombination rate. Defaults to 1.

  • TP (int) – The number of pedigree generations under the hybrid-pedigree refinements of the Dioecious models ('H-DC', 'H-DF'). Ignored otherwise. Defaults to 2.

  • N_cores (int) – The number of CPU cores to use for parallel processing under the hybrid-pedigree refinements. Ignored otherwise. Defaults to 1.

N_cores: int = 1#
TP: int = 2#
property models_allosomes: bool#

Whether allosomal admixture is modelled (ad_model_allosomes is not None).

rho_f: float = 1#
rho_m: float = 1#
property uses_hybrid_pedigree_allosomes: bool#

Whether the allosomal admixture model is a hybrid-pedigree refinement.

property uses_hybrid_pedigree_autosomes: bool#

Whether the autosomal admixture model is a hybrid-pedigree refinement.