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) (Haploid method) (Indiv method) (Parameter method) (ParametrizedDemography method) (ParamType method) (PhaseTypeDistribution method) (PhTDioecious method) (PhTMonoecious method) (Population method) (PulseEvent method) (SexType method) (Tract method) _flats (Population attribute) _split_indivs() (in module tracts.population) A ad_model_allosomes (InferenceConfig attribute) ad_model_autosomes (InferenceConfig 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_label (ParametrizedDemographySexBiased attribute) allosome_labels (Population attribute) allosome_lengths (Population attribute) 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) 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) bounds (DependentParameter attribute) (Parameter attribute) (ParamType attribute) 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_for_improper_constraint() (FixedParametersHandler method) check_for_unsolvable_proportions() (FixedParametersHandler method) chro_canvas (Population attribute) Chrom (class in tracts.chromosome) chromosomes (SamplesConfig attribute) chroms (Haploid attribute) (Indiv attribute) Chropair (class in tracts.chromosome) collect_pop() (in module tracts.population) colordict (Population attribute) compute_params_fixed_by_ancestry() (FixedParametersHandler method) 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() (Tract method) create_gamete() (Indiv method) currentplot (Population attribute) D 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) E 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 (InferenceConfig 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) filename_format (SamplesConfig attribute) finalize() (BaseParametrizedDemography method) finalized (BaseParametrizedDemography attribute) fix_parameters_from_ancestry_proportions (InferenceConfig 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) 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) 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() (ParametrizedDemography method) get_param_value() (BaseParametrizedDemography method) get_pedigree() (in module tracts.phase_type.hybrid_pedigree) get_random_parameters() (ParametrizedDemography method) get_sorted_indices() (FixedParametersHandler method) 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_been_fixed (BaseParametrizedDemography property) (FixedParametersHandler property) 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) 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_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) list_chromosome() (Population method) load_driver_file() (in module tracts.driver_utils) load_from_YAML() (ParametrizedDemography static method) (ParametrizedDemographySexBiased static method) 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) logger (BaseParametrizedDemography attribute) (FixedParametersHandler attribute) (ParametrizedDemography attribute) (ParametrizedDemographySexBiased attribute) loglik() (PhaseTypeDistribution method) Ls (Haploid attribute) (Indiv attribute) (Population attribute) M MALE (SexType attribute) 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 (InferenceConfig 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) model_config (InferenceConfig attribute) (SamplesConfig attribute) (StartParamsConfig attribute) model_filename (InferenceConfig attribute) 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.haploid tracts.indiv tracts.phase_type.base_phase_type tracts.phase_type.dioecious tracts.phase_type.hybrid_pedigree tracts.phase_type.monoecious tracts.population tracts.tract tracts.util N name (BaseParametrizedDemography attribute) (DependentParameter attribute) (Haploid attribute) (Indiv attribute) (Parameter attribute) (ParametrizedDemography attribute) (ParametrizedDemographySexBiased attribute) new_indiv() (Population method) newgen() (Population method) nind (Population attribute) normalization_factor() (PhaseTypeDistribution method) npts (InferenceConfig attribute) num_females (Population attribute) num_generations (PhTDioecious attribute) (PhTMonoecious attribute) num_males (Population attribute) num_populations (PhaseTypeDistribution attribute) (PhTDioecious attribute) (PhTMonoecious attribute) O 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) output_directory (InferenceConfig attribute) output_filename_format (InferenceConfig attribute) output_simulation_data_sex_biased() (in module tracts.driver_utils) P Parameter (class in tracts.demography.parameter) parameter_bounds (BaseParametrizedDemography property) parameter_handler (BaseParametrizedDemography attribute) 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_proportions() (BaseParametrizedDemography static method) parse_start_params() (in module tracts.driver_utils) PhaseTypeDistribution (class in tracts.phase_type.base_phase_type) 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_all_ancestries() (Population method) plot_ancestries() (Population method) plot_chromosome() (Population method) plot_global_tractlengths() (Population method) plot_indiv() (Population method) plot_next() (Population method) plot_previous() (Population method) populate_CDF_values() (PhaseTypeDistribution method) populate_density_bins() (PhaseTypeDistribution method) Population (class in tracts.population) population_indices (BaseParametrizedDemography attribute) 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) 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_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) seed (InferenceConfig attribute) set_males() (Population method) set_up_fixed_parameters() (BaseParametrizedDemography method) (FixedParametersHandler method) 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_unknown() (Chrom method) smooth_unknowns() (Population method) 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) 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.haploid module tracts.indiv 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.util module 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 (InferenceConfig attribute) type (DependentParameter attribute) (Parameter attribute) U unknown_labels (Chrom attribute) unknown_labels_for_smoothing (InferenceConfig attribute) unnamed_counter (Indiv attribute) unnormalized_prob_sex_vector() (PhTDioecious method) UNTYPED (ParamType attribute) user_params_fixed_by_value (FixedParametersHandler attribute) V verbose_log (InferenceConfig attribute) verbose_screen (InferenceConfig attribute) W win (Population attribute) X X_chr (PhaseTypeDistribution attribute) (PhTDioecious attribute) X_chr_male (PhaseTypeDistribution attribute) (PhTDioecious attribute)