Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X _ __init__() (BaseFounderEvent method) (BaseMigrationEvent method) (BaseParametrizedDemography method) (Chrom method) (Chropair method) (ContinuousEvent method) (DependentParameter method) (FounderEvent method) (GeneticModel method) (Haploid method) (Indiv method) (Parameter method) (ParametrizedDemography method) (ParamType method) (PhaseTypeDistribution method) (PhTDioecious method) (PhTMonoecious method) (Population method) (PulseEvent method) (SexType method) (Tract method) _build_reoptimization_intro_message() (in module tracts.driver_utils) _build_step2_skip_message() (in module tracts.driver_utils) _compute_objective() (in module tracts.core) _default_param_bounds() (in module tracts.driver_utils) _flats (Population attribute) _get_display_param_indices() (in module tracts.driver_utils) _get_driver_for_reoptimization() (in module tracts.driver_utils) _get_founder_event_with_remainder() (in module tracts.driver_utils) _get_optimization_subtitle() (in module tracts.driver_utils) _get_params_for_newly_explicit_population() (in module tracts.driver_utils) _normalize_multi_init_result() (in module tracts.driver_utils) _plot_migration_matrices() (in module tracts.driver_utils) _print_and_log() (in module tracts.driver_utils) _print_optimal_values_and_likelihood() (in module tracts.driver_utils) _print_param_bounds_table() (in module tracts.driver_utils) _print_run_intro() (in module tracts.driver_utils) _print_step_header_block() (in module tracts.driver_utils) _reorder_ancestry_proportions() (in module tracts.driver_utils) _save_ancestry_proportions_table() (in module tracts.driver_utils) _select_full_data_likelihood() (in module tracts.driver_utils) _shared_time_param_admissibility_state (FixedParametersHandler attribute) _shared_time_param_non_admissible_warned (FixedParametersHandler attribute) _split_indivs() (in module tracts.population) _summarize_step_results() (in module tracts.driver_utils) _time_param_admissibility_state (FixedParametersHandler attribute) A ad_model_allosomes (ModelsConfig attribute) ad_model_autosomes (ModelsConfig attribute) add_continuous_migration() (ParametrizedDemography method) (ParametrizedDemographySexBiased method) add_dependent_parameter() (BaseParametrizedDemography method) add_fixed_parameters() (FixedParametersHandler method) add_founder_event() (ParametrizedDemography method) (ParametrizedDemographySexBiased method) add_parameter() (BaseParametrizedDemography method) add_population() (BaseParametrizedDemography method) add_pulse_migration() (ParametrizedDemography method) (ParametrizedDemographySexBiased method) all_possible_trees_as_arrays() (in module tracts.phase_type.hybrid_pedigree) all_same_sign() (in module tracts.util) allosome_bins (TractsData attribute), [1] allosome_label (ModelReloadContext attribute), [1] (ParametrizedDemographySexBiased attribute) allosome_labels (Population attribute) allosome_length (TractsData attribute), [1] allosome_lengths (Population attribute) allosome_proportions (ModelReloadContext attribute), [1] allosomes (Haploid attribute) (Indiv attribute) (SamplesConfig attribute) alpha_list (PhaseTypeDistribution attribute) (PhTMonoecious attribute) alpha_list_f (PhaseTypeDistribution attribute) (PhTDioecious attribute) alpha_list_m (PhaseTypeDistribution attribute) (PhTDioecious attribute) ancestry_at_pos() (Population method) ancestry_per_pos() (Population method) ancestryAmt() (Indiv method) ancestryProps() (Indiv method) ancestryPropsByChrom() (Indiv method) applychrom() (Chropair method) (Indiv method) (Population method) autosome_bins (TractsData attribute), [1] autosome_data_mapped (TractsData attribute), [1] autosome_proportions (ModelReloadContext attribute), [1] autosomes (LoglikBreakdown attribute), [1] B BaseFounderEvent (class in tracts.demography.base_parametrized_demography) BaseMigrationEvent (class in tracts.demography.base_parametrized_demography) BaseParametrizedDemography (class in tracts.demography.base_parametrized_demography) bootinds() (Population method) boundary_tol (OptimizationConfig attribute), [1] bounds (DependentParameter attribute) (InferenceConfig attribute), [1] (Parameter attribute) (ParamType attribute) bounds_proximity_tol (OptimizationConfig attribute), [1] build_boundary_reoptimization_model() (in module tracts.driver_utils) C calculate_allosome_lengths() (Population static method) calculate_allosome_proportions() (Population method) calculate_ancestry_proportions() (Population method) calculate_num_sexes() (Population static method) canv (Population attribute) check_bounds() (BaseParametrizedDemography method) check_constraints() (BaseParametrizedDemography method) check_final_parameters() (in module tracts.driver_utils) check_for_improper_constraint() (FixedParametersHandler method) check_for_unsolvable_proportions() (FixedParametersHandler method) check_optimal_params_near_bounds() (in module tracts.driver_utils) check_optimal_sex_bias_parameters_at_boundaries() (in module tracts.driver_utils) check_population_labels() (in module tracts.driver_utils) check_start_params() (in module tracts.driver_utils) chro_canvas (Population attribute) Chrom (class in tracts.chromosome) chromosomes (SamplesConfig attribute) chroms (Haploid attribute) (Indiv attribute) Chropair (class in tracts.chromosome) collapse_identical_start_params() (in module tracts.driver_utils) collect_pop() (in module tracts.population) colordict (Population attribute) compute_params_fixed_by_ancestry() (FixedParametersHandler method) compute_physical_start_params() (in module tracts.driver_utils) compute_remainder_params() (in module tracts.driver_utils) constant_params (BaseParametrizedDemography attribute) constraints (BaseParametrizedDemography attribute) ContinuousEvent (class in tracts.demography.parametrized_demography) convert_to_optimizer_params() (FixedParametersHandler method) convert_to_physical_params() (FixedParametersHandler method) copies (Chropair attribute) copy() (GeneticModel method) (Tract method) create_gamete() (Indiv method) currentplot (Population attribute) D demographic_model (GeneticModel attribute) demography (FixedParametersHandler attribute) density_hybrid_pedigree() (in module tracts.phase_type.hybrid_pedigree) dependent_params (BaseParametrizedDemography attribute) DependentParameter (class in tracts.demography.parameter) directory (SamplesConfig attribute) discrete_prob_DF() (PhTDioecious method) distribution_scaling_factor() (PhTMonoecious method) driver_path (ModelReloadContext attribute), [1] E enable_time_param_logging (FixedParametersHandler attribute) end (Chrom attribute) end_parameter (ContinuousEvent attribute) end_time (BaseFounderEvent attribute) (FounderEvent attribute) eprint() (in module tracts.util) equilibrium_distribution (PhTMonoecious attribute) events (BaseParametrizedDemography attribute) exclude_tracts_below_cm (OptimizationConfig attribute) execute() (ContinuousEvent method) (FounderEvent method) (PulseEvent method) execute_migration_events() (BaseParametrizedDemography method) (ParametrizedDemography method) expression (DependentParameter attribute) (SexType attribute) extend_parameters() (FixedParametersHandler method) extract() (Chrom method) F FEMALE (SexType attribute) female_allosomes (LoglikBreakdown attribute), [1] female_data_mapped (TractsData attribute), [1] filename_format (SamplesConfig attribute) finalize() (BaseParametrizedDemography method) finalized (BaseParametrizedDemography attribute) fix_parameters_by_value (OptimizationConfig attribute), [1] fix_parameters_from_ancestry_proportions (OptimizationConfig attribute) fixed_params (BaseParametrizedDemography attribute) FixedParametersHandler (class in tracts.demography.base_parametrized_demography) flat_imap() (Indiv method) flatpop() (Population method) found_time (BaseFounderEvent attribute) (FounderEvent attribute) founder_events (BaseParametrizedDemography attribute) FounderEvent (class in tracts.demography.base_parametrized_demography) from_file() (Haploid static method) from_files() (Indiv static method) from_haploids() (Indiv static method) from_population() (TractsData class method) full_CDF() (PhaseTypeDistribution method) full_params_objective_func() (FixedParametersHandler method) full_transition_matrix (PhTMonoecious attribute) full_transition_matrix_f (PhTDioecious attribute) full_transition_matrix_m (PhTDioecious attribute) G generate_trees() (in module tracts.phase_type.hybrid_pedigree) GeneticModel (class in tracts.genetic_model) get_admixture_models() (in module tracts.driver_utils) get_alternate_implicit_population() (in module tracts.driver_utils) get_ancestry_proportions() (in module tracts.driver_utils) get_equilibrium_distribution() (PhTMonoecious method) get_founding_time() (ParametrizedDemography method) get_global_allosome_tractlengths() (Population method) get_global_tractlength_table() (Population method) get_global_tractlengths() (Population method) get_index() (BaseParametrizedDemography method) get_label() (Tract method) get_mean_ancestry_proportions() (Population method) get_means() (Population method) get_meanvar() (Population method) get_migration_matrices() (GeneticModel method) (ParametrizedDemography method) get_param_names_by_type() (in module tracts.driver_utils) get_param_value() (BaseParametrizedDemography method) get_pedigree() (in module tracts.phase_type.hybrid_pedigree) get_predicted_ancestry_proportions() (in module tracts.driver_utils) get_random_parameters() (ParametrizedDemography method) get_sorted_indices() (FixedParametersHandler method) get_starting_ancestry_proportions() (in module tracts.driver_utils) get_survival_factors() (in module tracts.phase_type.base_phase_type) get_time_scaled_model_bounds() (in module tracts.driver_utils) get_time_scaled_model_func() (in module tracts.driver_utils) get_transition_matrix() (PhTMonoecious method) get_variance() (Population method) get_violation_score() (BaseParametrizedDemography method) getMeansByChrom() (Population method) goto() (Chrom method) H Haploid (class in tracts.haploid) has_allosome_data (TractsData property) has_been_fixed (BaseParametrizedDemography property) (FixedParametersHandler property) has_free_sex_bias_parameters() (in module tracts.driver_utils) HP_loglik() (in module tracts.phase_type.hybrid_pedigree) HP_tract_length_histogram_multi_windowed() (in module tracts.phase_type.hybrid_pedigree) hybrid_pedigree_distribution() (in module tracts.phase_type.hybrid_pedigree) I iflatten() (Indiv method) (Population method) implicit_population (ModelsConfig attribute), [1] include_allosomes (LikelihoodOptions attribute), [1] include_autosomes (LikelihoodOptions attribute), [1] index (DependentParameter attribute) (Parameter attribute) indices_to_labels() (FixedParametersHandler method) Indiv (class in tracts.indiv) individual_names (SamplesConfig attribute) indivs (Population attribute) InferenceConfig (class in tracts.driver_utils) initialize_CDF_values() (PhaseTypeDistribution static method) initialize_density_bins() (PhaseTypeDistribution static method) inner_CDF() (PhaseTypeDistribution method) insert_fixed_params() (FixedParametersHandler method) insert_params() (BaseParametrizedDemography method) insert_solved_params() (FixedParametersHandler method) inverse_S0_list (PhaseTypeDistribution attribute) (PhTMonoecious attribute) inverse_S0_list_f (PhaseTypeDistribution attribute) (PhTDioecious attribute) inverse_S0_list_m (PhaseTypeDistribution attribute) (PhTDioecious attribute) is_equal() (Chrom method) (Tract method) is_sex_biased (GeneticModel property) is_time_param() (BaseParametrizedDemography method) K known_ancestry_proportions (FixedParametersHandler attribute) L labels (SamplesConfig attribute) labs (Haploid attribute) len (Chrom attribute) (Chropair attribute) len() (Tract method) LikelihoodOptions (class in tracts.likelihood_options) list_chromosome() (Population method) load_demographic_model_from_driver() (in module tracts.driver_utils) load_driver_file() (in module tracts.driver_utils) load_from_YAML() (ParametrizedDemography static method) (ParametrizedDemographySexBiased static method) load_population() (in module tracts.driver_utils) locate_file_path() (in module tracts.driver_utils) log_filename (OutputConfig attribute) log_scale (OutputConfig attribute) logger (BaseFounderEvent attribute) (BaseMigrationEvent attribute) (BaseParametrizedDemography attribute) (FixedParametersHandler attribute) (FounderEvent attribute) (ParametrizedDemography attribute) (ParametrizedDemographySexBiased attribute) loglik() (GeneticModel method) (PhaseTypeDistribution method) LoglikBreakdown (class in tracts.genetic_model) Ls (Haploid attribute) (Indiv attribute) (Population attribute) M MALE (SexType attribute) male_allosomes (LoglikBreakdown attribute), [1] male_data_mapped (TractsData attribute), [1] male_female_sex_type_function() (SexType static method) male_list (Population attribute) male_names (SamplesConfig attribute) max_time (BaseParametrizedDemography attribute) (ParametrizedDemography attribute) (ParametrizedDemographySexBiased attribute) maximum_iterations (OptimizationConfig attribute) maxLen (PhaseTypeDistribution attribute) (Population attribute) merge_ancestries() (Chrom method) (Population method) migration_matrix (PhaseTypeDistribution attribute) (PhTMonoecious attribute) migration_matrix_f (PhaseTypeDistribution attribute) (PhTDioecious attribute) migration_matrix_m (PhaseTypeDistribution attribute) (PhTDioecious attribute) min_time (BaseParametrizedDemography attribute) (ParametrizedDemography attribute) (ParametrizedDemographySexBiased attribute) model_base_params (BaseParametrizedDemography attribute) (GeneticModel property) model_config (InferenceConfig attribute) (ModelsConfig attribute) (OptimizationConfig attribute) (OutputConfig attribute) (ParamBoundsConfig attribute) (SamplesConfig attribute) (StartParamsConfig attribute) model_filename (ModelsConfig attribute) model_func() (GeneticModel method) ModelReloadContext (class in tracts.driver_utils) models (InferenceConfig attribute), [1] models_allosomes (PhaseTypeModelConfig property) ModelsConfig (class in tracts.driver_utils) module tracts.chromosome tracts.core tracts.demography.base_parametrized_demography tracts.demography.parameter tracts.demography.parametrized_demography tracts.demography.parametrized_demography_sex_biased tracts.driver tracts.driver_utils tracts.genetic_model tracts.haploid tracts.indiv tracts.likelihood_options tracts.phase_type.base_phase_type tracts.phase_type.dioecious tracts.phase_type.hybrid_pedigree tracts.phase_type.monoecious tracts.population tracts.tract tracts.tracts_data tracts.util N N_cores (OptimizationConfig attribute), [1] (PhaseTypeModelConfig attribute) n_reoptimizations (OptimizationConfig attribute), [1] name (BaseParametrizedDemography attribute) (DependentParameter attribute) (Haploid attribute) (Indiv attribute) (Parameter attribute) (ParametrizedDemography attribute) (ParametrizedDemographySexBiased attribute) near_one (OptimizationConfig attribute), [1] new_indiv() (Population method) newgen() (Population method) nind (Population attribute) normalization_factor() (PhaseTypeDistribution method) npts (OptimizationConfig attribute) num_females (Population attribute) (TractsData attribute), [1] num_generations (PhTDioecious attribute) (PhTMonoecious attribute) num_males (Population attribute) (TractsData attribute), [1] num_populations (PhaseTypeDistribution attribute) (PhTDioecious attribute) (PhTMonoecious attribute) O optim (InferenceConfig attribute), [1] OptimizationConfig (class in tracts.driver_utils) optimize_cob_sex_biased_single_step() (in module tracts.core) optimize_cob_sex_biased_two_steps() (in module tracts.core) order_fixed_param_dict() (FixedParametersHandler method) outer_CDF() (PhaseTypeDistribution method) outofbounds_fun() (GeneticModel method) output (InferenceConfig attribute), [1] output_directory (OutputConfig attribute) output_filename_format (OutputConfig attribute) output_simulation_data_sex_biased() (in module tracts.driver_utils) OutputConfig (class in tracts.driver_utils) P ParamBoundsConfig (class in tracts.driver_utils) Parameter (class in tracts.demography.parameter) parameter_bounds (BaseParametrizedDemography property) parameter_handler (BaseParametrizedDemography attribute) (GeneticModel property) parametrized_populations (BaseParametrizedDemography attribute) ParametrizedDemography (class in tracts.demography.parametrized_demography) ParametrizedDemographySexBiased (class in tracts.demography.parametrized_demography_sex_biased) params_fixed_by_ancestry (BaseParametrizedDemography property) (FixedParametersHandler attribute) params_fixed_by_value (BaseParametrizedDemography property) params_not_fixed_by_ancestry (FixedParametersHandler attribute) ParamType (class in tracts.demography.parameter) parse_chromosomes() (in module tracts.driver_utils) parse_individual_filenames() (in module tracts.driver_utils) parse_param_bounds() (in module tracts.driver_utils) parse_proportions() (BaseParametrizedDemography static method) parse_start_params() (in module tracts.driver_utils) phase_type_config (GeneticModel attribute) PhaseTypeDistribution (class in tracts.phase_type.base_phase_type) PhaseTypeModelConfig (class in tracts.genetic_model) PhT_CDF() (PhTDioecious method) (PhTMonoecious method) PhT_CDF_windowed() (PhTDioecious method) (PhTMonoecious method) PhT_density() (PhTDioecious method) (PhTMonoecious method) PhT_density_windowed() (PhTDioecious method) (PhTMonoecious method) PhT_parameters_DC() (PhTDioecious method) PhT_parameters_DF() (PhTDioecious method) PhTDioecious (class in tracts.phase_type.dioecious) PhTMonoecious (class in tracts.phase_type.monoecious) plot() (Chrom method) (Chropair method) (Indiv method) (Population method) plot_admixture() (in module tracts.driver_utils) plot_all_ancestries() (Population method) plot_ancestries() (Population method) plot_chromosome() (Population method) plot_global_tractlengths() (Population method) plot_indiv() (Population method) plot_migration_matrices (OutputConfig attribute), [1] plot_next() (Population method) plot_previous() (Population method) populate_CDF_values() (PhaseTypeDistribution method) populate_density_bins() (PhaseTypeDistribution method) Population (class in tracts.population) population (TractsData attribute), [1] population_indices (BaseParametrizedDemography attribute) (GeneticModel property) preprocess_color_dict() (in module tracts.population) prob_of_pop_setting() (in module tracts.phase_type.hybrid_pedigree) proportions_from_matrices() (BaseParametrizedDemography method) (ParametrizedDemographySexBiased method) proportions_from_matrices_return_keys() (BaseParametrizedDemography method) (ParametrizedDemographySexBiased method) proportions_from_matrix() (BaseParametrizedDemography static method) PulseEvent (class in tracts.demography.parametrized_demography) R RATE (ParamType attribute) rate_param (BaseMigrationEvent attribute) rate_parameter (ContinuousEvent attribute) (PulseEvent attribute) rate_to_optimizer_function() (in module tracts.util) rate_to_physical_function() (in module tracts.util) recombine() (Chropair method) reduce_parameters() (FixedParametersHandler method) reduced_constraints (BaseParametrizedDemography attribute) (FixedParametersHandler attribute) release_fixed_parameters() (FixedParametersHandler method) remainder_population (BaseFounderEvent attribute) (FounderEvent attribute) reoptimization_likelihood_tolerance (OptimizationConfig attribute), [1] repetitions (OptimizationConfig attribute) repetitions_likelihood_tolerance (OptimizationConfig attribute), [1] rerun_optimization_on_boundaries (OptimizationConfig attribute), [1] rho_f (ModelsConfig attribute), [1] (PhaseTypeModelConfig attribute) (PhTDioecious attribute) rho_m (ModelsConfig attribute), [1] (PhaseTypeModelConfig attribute) (PhTDioecious attribute) run_boundary_reoptimization() (in module tracts.driver) run_model() (in module tracts.driver) run_model_multi_init() (in module tracts.driver) run_optimization() (in module tracts.driver) run_sex_bias_fixing_reoptimizations() (in module tracts.driver) run_tracts() (in module tracts.driver) S S0_list (PhaseTypeDistribution attribute) (PhTMonoecious attribute) S0_list_f (PhaseTypeDistribution attribute) (PhTDioecious attribute) S0_list_m (PhaseTypeDistribution attribute) (PhTDioecious attribute) S_matrix() (PhTDioecious method) samples (InferenceConfig attribute) SamplesConfig (class in tracts.driver_utils) save() (Population method) scale_select_indices() (in module tracts.driver_utils) script_dir (ModelReloadContext attribute), [1] seed (OptimizationConfig attribute) set_males() (Population method) set_up_fixed_parameters() (BaseParametrizedDemography method) (FixedParametersHandler method) (GeneticModel method) setup_fixed_parameters() (in module tracts.driver_utils) SEX_BIAS (ParamType attribute) sex_bias_to_optimizer_function() (in module tracts.util) sex_bias_to_physical_function() (in module tracts.util) sex_model (PhTDioecious attribute) SexType (class in tracts.demography.parametrized_demography_sex_biased) smooth_clip01() (in module tracts.demography.base_parametrized_demography) smooth_unknown() (Chrom method) smooth_unknowns() (Population method) softplus() (in module tracts.demography.base_parametrized_demography) source_population (BaseMigrationEvent attribute) (ContinuousEvent attribute) (PulseEvent attribute) source_populations (BaseFounderEvent attribute) (FounderEvent attribute) split_by_props() (Population method) start (Chrom attribute) start_parameter (ContinuousEvent attribute) start_params (InferenceConfig attribute) StartParamsConfig (class in tracts.driver_utils) submodel_probabilities() (PhTDioecious method) suffix (SexType attribute) T t0_proportions (PhaseTypeDistribution attribute) (PhTMonoecious attribute) t0_proportions_f (PhaseTypeDistribution attribute) (PhTDioecious attribute) t0_proportions_m (PhaseTypeDistribution attribute) (PhTDioecious attribute) TIME (ParamType attribute) time_parameter (PulseEvent attribute) time_to_optimizer_function() (in module tracts.util) time_to_physical_function() (in module tracts.util) to_optimizer_params_functions (FixedParametersHandler attribute) to_physical_params_functions (FixedParametersHandler attribute) total (LoglikBreakdown property) TP (ModelsConfig attribute), [1] (PhaseTypeModelConfig attribute) Tract (class in tracts.tract) tract_length_histogram_multi_windowed() (PhTDioecious method) (PhTMonoecious method) tractlength_histogram() (PhaseTypeDistribution method) (Population method) tractlength_histogram_windowed() (PhTDioecious method) (PhTMonoecious method) tractlengths() (Chrom method) tracts (Chrom attribute) tracts.chromosome module tracts.core module tracts.demography.base_parametrized_demography module tracts.demography.parameter module tracts.demography.parametrized_demography module tracts.demography.parametrized_demography_sex_biased module tracts.driver module tracts.driver_utils module tracts.genetic_model module tracts.haploid module tracts.indiv module tracts.likelihood_options module tracts.phase_type.base_phase_type module tracts.phase_type.dioecious module tracts.phase_type.hybrid_pedigree module tracts.phase_type.monoecious module tracts.population module tracts.tract module tracts.tracts_data module tracts.util module TractsData (class in tracts.tracts_data) transition_matrices (PhaseTypeDistribution attribute) (PhTMonoecious attribute) transition_matrices_f (PhaseTypeDistribution attribute) (PhTDioecious attribute) transition_matrices_m (PhaseTypeDistribution attribute) (PhTDioecious attribute) tree_to_array() (in module tracts.phase_type.hybrid_pedigree) two_steps_optimization (OptimizationConfig attribute) type (DependentParameter attribute) (Parameter attribute) U unknown_labels (Chrom attribute) unknown_labels_for_smoothing (OptimizationConfig attribute) unnamed_counter (Indiv attribute) unnormalized_prob_sex_vector() (PhTDioecious method) UNTYPED (ParamType attribute) use_autosomes_for_sex_bias (OptimizationConfig attribute), [1] user_params_fixed_by_value (FixedParametersHandler attribute) uses_hybrid_pedigree_allosomes (PhaseTypeModelConfig property) uses_hybrid_pedigree_autosomes (PhaseTypeModelConfig property) V verbose_log (LikelihoodOptions attribute) (OutputConfig attribute) verbose_screen (LikelihoodOptions attribute) (OutputConfig attribute) W win (Population attribute) with_overrides() (LikelihoodOptions method) X X_chr (PhaseTypeDistribution attribute) (PhTDioecious attribute) X_chr_male (PhaseTypeDistribution attribute) (PhTDioecious attribute)