tracts.core.optimize_cob_sex_biased_two_steps#

optimize_cob_sex_biased_two_steps(p0, population, model_func, parameter_handler, outofbounds_fun=None, verbose_log=0, verbose_screen=10, p_dict=None, exclude_tracts_below_cM=0, maxiter=None, reset_counter=True, ad_model_autosomes='DC', ad_model_allosomes='DC', npts=50)#

Optimizes the log-likelihood over all parameters defined by the demographic model, for a specified admixture model applied to both autosomes and allosomes. The procedure is carried out in two steps: first, the non–sex-bias parameters are estimated by maximizing the log-likelihood using autosomal data only. Second, the sex-bias parameters are estimated using both autosomal and allosomal data.

Parameters:

  • p0 (list) – An array of initial parameters to start the optimization.

  • population (Population) – A Population object containing the data to fit.

  • model_func (callable) – A function that takes a parameter array and returns a dictionary of migration matrices for each population.

  • parameter_handler (FixedParametersHandler) – An object that handles parameter transformations and fixed parameters.

  • outofbounds_fun (callable) – A function that takes a parameter array and returns a violation score indicating how much the parameters violate the bounds.

  • cutoff (int, default:0) – The number of bins to drop at the beginning of the array. This could be achieved with masks.

  • verbose_log (int) – If greater than zero, logs optimization status every verbose iterations.

  • verbose_screen (int) – If greater than zero, prints optimization status every verbose iterations.

  • p_dict (dict) – A dictionary mapping population labels to their corresponding indices in the model.

  • exclude_tracts_below_cM (float) – Minimum tract length in centimorgans to exclude from analysis. Default is 0.

  • maxiter (int) – Maximum iterations to run for.

  • reset_counter (bool) – Resets the iteration counter to zero. Set to False to continue iteration count (e.g., if optimization continues from previous point).

  • ad_model_autosomes (str) – The model to use for autosomal admixture. Must be one of ‘DC’, ‘DF’, ‘M’, ‘H-DC’ or ‘H-DF’. Default is ‘DC’.

  • ad_model_allosomes (str) – The model to use for allosomal admixture. Must be one of ‘DC’, ‘DF’, ‘H-DC’ or ‘H-DF’. Default is ‘DC’. If None, allosomal admixture will not be modeled.

  • npts (int) – Number of bins for the tract length histogram. Default is 50.

Returns:

A tuple containing the optimal parameters found and the corresponding likelihood.

Return type:

tuple[ndarray, float]