Index A | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V | X A ad_model_allosomes (InferenceConfig attribute) ad_model_autosomes (InferenceConfig attribute) all_possible_trees_as_arrays() (in module tracts.hybrid_pedigree) all_same_sign() (in module tracts.util) allosomes (SamplesConfig attribute) alpha_list (PhTMonoecious attribute) alpha_list_f (PhTDioecious attribute) alpha_list_m (PhTDioecious attribute) C Chrom (class in tracts.chromosome) (class in tracts.legacy) chromosomes (SamplesConfig attribute) chroms (Haploid attribute) Chropair (class in tracts.chromosome) (class in tracts.legacy) collect_pop() (in module tracts.population) CompositeDemographicModel (class in tracts.legacy) D DemographicModel (class in tracts.legacy) density_hybrid_pedigree() (in module tracts.hybrid_pedigree) directory (SamplesConfig attribute) E eprint() (in module tracts.legacy) (in module tracts.util) equilibrium_distribution (PhTMonoecious attribute) exclude_tracts_below_cm (InferenceConfig attribute) F filename_format (SamplesConfig attribute) fix_parameters_from_ancestry_proportions (InferenceConfig attribute) full_transition_matrix (PhTMonoecious attribute) full_transition_matrix_f (PhTDioecious attribute) full_transition_matrix_m (PhTDioecious attribute) G generate_trees() (in module tracts.hybrid_pedigree) get_current_func_info() (in module tracts.logs) get_pedigree() (in module tracts.hybrid_pedigree) get_survival_factors() (in module tracts.phase_type_distribution) get_time_scaled_model_bounds() (in module tracts.driver_utils) get_time_scaled_model_func() (in module tracts.driver_utils) H Haploid (class in tracts.haploid) (class in tracts.legacy) HP_loglik() (in module tracts.hybrid_pedigree) HP_tract_length_histogram_multi_windowed() (in module tracts.hybrid_pedigree) hybrid_pedigree_distribution() (in module tracts.hybrid_pedigree) I Indiv (class in tracts.indiv) (class in tracts.legacy) individual_names (SamplesConfig attribute) InferenceConfig (class in tracts.driver_utils) inverse_S0_list (PhTMonoecious attribute) inverse_S0_list_f (PhTDioecious attribute) inverse_S0_list_m (PhTDioecious attribute) L labels (SamplesConfig attribute) labs (Haploid attribute) load_driver_file() (in module tracts.driver_utils) load_model_from_driver() (in module tracts.driver_utils) load_population() (in module tracts.driver_utils) locate_file_path() (in module tracts.driver_utils) log_filename (InferenceConfig attribute) log_scale (InferenceConfig attribute) Ls (Haploid attribute) M male_names (SamplesConfig attribute) maximum_iterations (InferenceConfig attribute) migration_matrix (PhTMonoecious attribute) migration_matrix_f (PhTDioecious attribute) migration_matrix_m (PhTDioecious attribute) model_filename (InferenceConfig attribute) module tracts tracts.chromosome tracts.core tracts.demography tracts.doc_utils tracts.driver tracts.driver_utils tracts.haploid tracts.hybrid_pedigree tracts.indiv tracts.legacy tracts.legacy_models tracts.logs tracts.phase_type_distribution tracts.population tracts.tract tracts.util N name (Haploid attribute) npts (InferenceConfig attribute) num_generations (PhTDioecious attribute) (PhTMonoecious attribute) num_populations (PhTDioecious attribute) (PhTMonoecious attribute) O optimize() (in module tracts.core) (in module tracts.legacy) optimize_bfgs() (in module tracts.core) (in module tracts.legacy) optimize_brute_fracs2() (in module tracts.core) (in module tracts.legacy) optimize_brute_multifracs() (in module tracts.core) (in module tracts.legacy) optimize_cob() (in module tracts.core) (in module tracts.legacy) optimize_cob_fracs() (in module tracts.core) (in module tracts.legacy) optimize_cob_fracs2() (in module tracts.core) (in module tracts.legacy) optimize_cob_multifracs() (in module tracts.core) (in module tracts.legacy) optimize_cob_sex_biased() (in module tracts.core) optimize_cob_sex_biased_fixed_values() (in module tracts.core) optimize_slsqp() (in module tracts.core) (in module tracts.legacy) output_directory (InferenceConfig attribute) output_filename_format (InferenceConfig attribute) output_simulation_data_sex_biased() (in module tracts.driver_utils) P parse_chromosomes() (in module tracts.driver_utils) parse_individual_filenames() (in module tracts.driver_utils) parse_start_params() (in module tracts.driver_utils) PhaseTypeDistribution (class in tracts.phase_type_distribution) PhTDioecious (class in tracts.phase_type_distribution) PhTMonoecious (class in tracts.phase_type_distribution) plotmig() (in module tracts.core) (in module tracts.legacy) Population (class in tracts.legacy) (class in tracts.population) prepare_example_outputs_for_docs() (in module tracts.doc_utils) preprocess_color_dict() (in module tracts.population) prob_of_pop_setting() (in module tracts.hybrid_pedigree) R rate_to_optimizer_function() (in module tracts.core) rate_to_physical_function() (in module tracts.core) repetitions (InferenceConfig attribute) rho_f (PhTDioecious attribute) rho_m (PhTDioecious attribute) run_model() (in module tracts.driver) run_model_multi_init() (in module tracts.driver) run_model_sex_biased() (in module tracts.driver) run_tracts() (in module tracts.driver) S S0_list (PhTMonoecious attribute) S0_list_f (PhTDioecious attribute) S0_list_m (PhTDioecious attribute) samples (InferenceConfig attribute) SamplesConfig (class in tracts.driver_utils) scale_select_indices() (in module tracts.driver_utils) seed (InferenceConfig attribute) set_log_file() (in module tracts.logs) setup_logger() (in module tracts.logs) sex_bias_to_optimizer_function() (in module tracts.core) sex_bias_to_physical_function() (in module tracts.core) sex_model (PhTDioecious attribute) start_params (InferenceConfig attribute) StartParamsConfig (class in tracts.driver_utils) T t0_proportions (PhTMonoecious attribute) t0_proportions_f (PhTDioecious attribute) t0_proportions_m (PhTDioecious attribute) test_model_func() (in module tracts.legacy) time_to_optimizer_function() (in module tracts.core) time_to_physical_function() (in module tracts.core) Tract (class in tracts.legacy) (class in tracts.tract) tracts module tracts.chromosome module tracts.core module tracts.demography module tracts.doc_utils module tracts.driver module tracts.driver_utils module tracts.haploid module tracts.hybrid_pedigree module tracts.indiv module tracts.legacy module tracts.legacy_models module tracts.logs module tracts.phase_type_distribution module tracts.population module tracts.tract module tracts.util module transition_matrices (PhTMonoecious attribute) transition_matrices_f (PhTDioecious attribute) transition_matrices_m (PhTDioecious attribute) tree_to_array() (in module tracts.hybrid_pedigree) two_steps_optimization (InferenceConfig attribute) U unknown_labels_for_smoothing (InferenceConfig attribute) V verbose_log (InferenceConfig attribute) verbose_screen (InferenceConfig attribute) X X_chr (PhTDioecious attribute) X_chr_male (PhTDioecious attribute)