Index

_

__init__() (tracts.chromosome.Chrom method) (tracts.chromosome.Chropair method) (tracts.demography.base_parametrized_demography.BaseFounderEvent method) (tracts.demography.base_parametrized_demography.BaseMigrationEvent method) (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.base_parametrized_demography.FixedParametersHandler method) (tracts.demography.base_parametrized_demography.FounderEvent method) (tracts.demography.composite_demographic_model.CompositeDemographicModel method) (tracts.demography.demographic_model.DemographicModel method) (tracts.demography.parameter.DependentParameter method) (tracts.demography.parameter.Parameter method) (tracts.demography.parameter.ParamType method) (tracts.demography.parametrized_demography.ContinuousEvent method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography.PulseEvent method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) (tracts.demography.parametrized_demography_sex_biased.SexType method) (tracts.driver.InferenceConfig method) (tracts.driver.SamplesConfig method) (tracts.driver.StartParamsConfig method) (tracts.haploid.Haploid method) (tracts.indiv.Indiv method) (tracts.legacy.Chrom method) (tracts.legacy.Chropair method) (tracts.legacy.CompositeDemographicModel method) (tracts.legacy.DemographicModel method) (tracts.legacy.Haploid method) (tracts.legacy.Indiv method) (tracts.legacy.Population method) (tracts.legacy.Tract method) (tracts.phase_type_distribution.PhaseTypeDistribution method) (tracts.phase_type_distribution.PhTDioecious method) (tracts.phase_type_distribution.PhTMonoecious method) (tracts.population.Population method) (tracts.tract.Tract method)

A

ad_model_allosomes (tracts.driver.InferenceConfig attribute) ad_model_autosomes (tracts.driver.InferenceConfig attribute) add_continuous_migration() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) add_dependent_parameter() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) add_fixed_parameters() (tracts.demography.base_parametrized_demography.FixedParametersHandler method) add_founder_event() (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) add_parameter() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) add_population() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) add_pulse_migration() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) all_possible_trees_as_arrays() (in module tracts.hybrid_pedigree)

all_same_sign() (in module tracts.util) allosomes (tracts.driver.SamplesConfig attribute) alpha_list (tracts.phase_type_distribution.PhTMonoecious attribute) alpha_list_f (tracts.phase_type_distribution.PhTDioecious attribute) alpha_list_m (tracts.phase_type_distribution.PhTDioecious attribute) ancestry_at_pos() (tracts.legacy.Population method) (tracts.population.Population method) ancestry_per_pos() (tracts.legacy.Population method) (tracts.population.Population method) ancestryAmt() (tracts.indiv.Indiv method) (tracts.legacy.Indiv method) ancestryProps() (tracts.indiv.Indiv method) (tracts.legacy.Indiv method) ancestryPropsByChrom() (tracts.indiv.Indiv method) (tracts.legacy.Indiv method) applychrom() (tracts.chromosome.Chropair method) (tracts.indiv.Indiv method) (tracts.legacy.Chropair method) (tracts.legacy.Indiv method) (tracts.legacy.Population method) (tracts.population.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() (tracts.legacy.Population method) (tracts.population.Population method)

C

calculate_allosome_lengths() (tracts.population.Population static method) calculate_allosome_proportions() (tracts.population.Population method) calculate_ancestry_proportions() (tracts.population.Population method) calculate_num_sexes() (tracts.population.Population static method) calculate_probabilities_at_population() (tracts.phase_type_distribution.PhTDioecious method) check_bounds() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) check_constraints() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) check_for_improper_constraint() (tracts.demography.base_parametrized_demography.FixedParametersHandler method) check_for_unsolvable_proportions() (tracts.demography.base_parametrized_demography.FixedParametersHandler method) Chrom (class in tracts.chromosome) (class in tracts.legacy) chromosomes (tracts.driver.SamplesConfig attribute) chroms (tracts.haploid.Haploid attribute) Chropair (class in tracts.chromosome) (class in tracts.legacy)

collect_pop() (in module tracts.population) collectpop() (tracts.legacy.Population method) CompositeDemographicModel (class in tracts.demography.composite_demographic_model) (class in tracts.legacy) compute_params_fixed_by_ancestry() (tracts.demography.base_parametrized_demography.FixedParametersHandler method) construct() (tracts.driver.InferenceConfig class method) (tracts.driver.SamplesConfig class method) (tracts.driver.StartParamsConfig class method) ContinuousEvent (class in tracts.demography.parametrized_demography) convert_to_optimizer_params() (tracts.demography.base_parametrized_demography.FixedParametersHandler method) convert_to_physical_params() (tracts.demography.base_parametrized_demography.FixedParametersHandler method) copy() (tracts.driver.InferenceConfig method) (tracts.driver.SamplesConfig method) (tracts.driver.StartParamsConfig method) (tracts.legacy.Tract method) (tracts.tract.Tract method) create_gamete() (tracts.indiv.Indiv method) (tracts.legacy.Indiv method)

D

DemographicModel (class in tracts.demography.demographic_model) (class in tracts.legacy) density_hybrid_pedigree() (in module tracts.hybrid_pedigree) DependentParameter (class in tracts.demography.parameter) dict() (tracts.driver.InferenceConfig method) (tracts.driver.SamplesConfig method) (tracts.driver.StartParamsConfig method)

directory (tracts.driver.SamplesConfig attribute) discrete_prob_DF() (tracts.phase_type_distribution.PhTDioecious method) distribution_scaling_factor() (tracts.phase_type_distribution.PhTMonoecious method)

E

eprint() (in module tracts.legacy) (in module tracts.util) equilibrium_distribution (tracts.phase_type_distribution.PhTMonoecious attribute) Erlang() (in module tracts.demography.demographic_model) (tracts.legacy.DemographicModel method) events (tracts.demography.parametrized_demography.ParametrizedDemography attribute) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased attribute) exclude_tracts_below_cm (tracts.driver.InferenceConfig attribute) execute() (tracts.demography.base_parametrized_demography.BaseFounderEvent method) (tracts.demography.base_parametrized_demography.BaseMigrationEvent method) (tracts.demography.base_parametrized_demography.FounderEvent method) (tracts.demography.parametrized_demography.ContinuousEvent method) (tracts.demography.parametrized_demography.PulseEvent method)

execute_migration_events() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) expectperbin() (tracts.demography.composite_demographic_model.CompositeDemographicModel method) (tracts.demography.demographic_model.DemographicModel method) (tracts.legacy.CompositeDemographicModel method) (tracts.legacy.DemographicModel method) extend_parameters() (tracts.demography.base_parametrized_demography.FixedParametersHandler method) extract() (tracts.chromosome.Chrom method) (tracts.legacy.Chrom method)

F

FEMALE (tracts.demography.parametrized_demography_sex_biased.SexType attribute) filename_format (tracts.driver.SamplesConfig attribute) finalize() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) fix_parameters_from_ancestry_proportions (tracts.driver.InferenceConfig attribute) fixed_params (tracts.demography.parametrized_demography.ParametrizedDemography attribute) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased attribute) FixedParametersHandler (class in tracts.demography.base_parametrized_demography) flat_imap() (tracts.indiv.Indiv method) (tracts.legacy.Indiv method) flatpop() (tracts.legacy.Population method) (tracts.population.Population method) founder_events (tracts.demography.parametrized_demography.ParametrizedDemography attribute) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased attribute) FounderEvent (class in tracts.demography.base_parametrized_demography) from_file() (tracts.haploid.Haploid static method) (tracts.legacy.Haploid static method)

from_files() (tracts.indiv.Indiv static method) (tracts.legacy.Indiv static method) from_haploids() (tracts.indiv.Indiv static method) (tracts.legacy.Indiv static method) from_orm() (tracts.driver.InferenceConfig class method) (tracts.driver.SamplesConfig class method) (tracts.driver.StartParamsConfig class method) full() (tracts.demography.demographic_model.DemographicModel method) (tracts.legacy.DemographicModel method) full_CDF() (tracts.phase_type_distribution.PhaseTypeDistribution method) (tracts.phase_type_distribution.PhTDioecious method) (tracts.phase_type_distribution.PhTMonoecious method) full_params_objective_func() (tracts.demography.base_parametrized_demography.FixedParametersHandler method) full_transition_matrix (tracts.phase_type_distribution.PhTMonoecious attribute) full_transition_matrix_f (tracts.phase_type_distribution.PhTDioecious attribute) full_transition_matrix_m (tracts.phase_type_distribution.PhTDioecious attribute)

G

gen_variance() (tracts.demography.demographic_model.DemographicModel method) (tracts.legacy.DemographicModel method) generate_trees() (in module tracts.hybrid_pedigree) get_current_func_info() (in module tracts.logs) get_discrete_transition_matrix() (tracts.phase_type_distribution.PhTMonoecious method) get_equilibrium_distribution() (tracts.phase_type_distribution.PhTMonoecious method) get_equilibrium_distribution_v2() (tracts.phase_type_distribution.PhTMonoecious method) get_founding_time() (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) get_global_allosome_tractlengths() (tracts.population.Population method) get_global_tractlength_table() (tracts.legacy.Population method) (tracts.population.Population method) get_global_tractlengths() (tracts.legacy.Population method) (tracts.population.Population method) get_index() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) get_label() (tracts.legacy.Tract method) (tracts.tract.Tract method) get_mean_ancestry_proportions() (tracts.legacy.Population method) (tracts.population.Population method) get_means() (tracts.legacy.Population method) (tracts.population.Population method) get_meanvar() (tracts.legacy.Population method) (tracts.population.Population method)

get_migration_matrices() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) get_param_value() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) get_pedigree() (in module tracts.hybrid_pedigree) get_random_parameters() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) get_sorted_indices() (tracts.demography.base_parametrized_demography.FixedParametersHandler method) get_survival_factors() (in module tracts.phase_type_distribution) get_time_scaled_model_bounds() (in module tracts.driver) get_time_scaled_model_func() (in module tracts.driver) get_time_transition_factor() (tracts.phase_type_distribution.PhTMonoecious method) get_TpopTau() (tracts.phase_type_distribution.PhTMonoecious method) get_transition_matrix() (tracts.phase_type_distribution.PhTMonoecious method) get_variance() (tracts.legacy.Population method) (tracts.population.Population method) get_violation_score() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) getMeansByChrom() (tracts.legacy.Population method) (tracts.population.Population method) goto() (tracts.chromosome.Chrom method) (tracts.legacy.Chrom method)

H

Haploid (class in tracts.haploid) (class in tracts.legacy) has_been_fixed (tracts.demography.base_parametrized_demography.BaseParametrizedDemography property) (tracts.demography.base_parametrized_demography.FixedParametersHandler property) (tracts.demography.parametrized_demography.ParametrizedDemography property) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased property)

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

iflatten() (tracts.indiv.Indiv method) (tracts.legacy.Indiv method) (tracts.legacy.Population method) (tracts.population.Population method) indices_to_labels() (tracts.demography.base_parametrized_demography.FixedParametersHandler method) Indiv (class in tracts.indiv) (class in tracts.legacy) individual_names (tracts.driver.SamplesConfig attribute) InferenceConfig (class in tracts.driver) init_list_tracts() (tracts.legacy.Chrom method) init_unif_tracts() (tracts.legacy.Chrom method) initialize_CDF_values() (tracts.phase_type_distribution.PhaseTypeDistribution static method) (tracts.phase_type_distribution.PhTDioecious static method) (tracts.phase_type_distribution.PhTMonoecious static method) initialize_density_bins() (tracts.phase_type_distribution.PhaseTypeDistribution static method) (tracts.phase_type_distribution.PhTDioecious static method) (tracts.phase_type_distribution.PhTMonoecious static method)

inner_CDF() (tracts.phase_type_distribution.PhaseTypeDistribution method) (tracts.phase_type_distribution.PhTDioecious method) (tracts.phase_type_distribution.PhTMonoecious method) inners() (tracts.demography.demographic_model.DemographicModel method) (tracts.legacy.DemographicModel method) insert_fixed_params() (tracts.demography.base_parametrized_demography.FixedParametersHandler method) insert_params() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) insert_solved_params() (tracts.demography.base_parametrized_demography.FixedParametersHandler method) inverse_S0_list (tracts.phase_type_distribution.PhTMonoecious attribute) inverse_S0_list_f (tracts.phase_type_distribution.PhTDioecious attribute) inverse_S0_list_m (tracts.phase_type_distribution.PhTDioecious attribute) is_equal() (tracts.chromosome.Chrom method) (tracts.tract.Tract method) is_time_param() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method)

J

json() (tracts.driver.InferenceConfig method) (tracts.driver.SamplesConfig method) (tracts.driver.StartParamsConfig method)

K

known_ancestry_proportions (tracts.demography.base_parametrized_demography.FixedParametersHandler attribute)

L

labels (tracts.driver.SamplesConfig attribute) labs (tracts.haploid.Haploid attribute) len() (tracts.chromosome.Chrom method) (tracts.legacy.Chrom method) (tracts.legacy.Tract method) (tracts.tract.Tract method) list_chromosome() (tracts.legacy.Population method) (tracts.population.Population method) list_parameters() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) load_driver_file() (in module tracts.driver) load_from_YAML() (tracts.demography.parametrized_demography.ParametrizedDemography static method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased static method) load_model_from_driver() (in module tracts.driver)

load_population() (in module tracts.driver) locate_file_path() (in module tracts.driver) logger (tracts.demography.base_parametrized_demography.BaseParametrizedDemography attribute) (tracts.demography.parametrized_demography.ParametrizedDemography attribute) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased attribute) loglik() (tracts.demography.composite_demographic_model.CompositeDemographicModel method) (tracts.demography.demographic_model.DemographicModel method) (tracts.legacy.CompositeDemographicModel method) (tracts.legacy.DemographicModel method) (tracts.phase_type_distribution.PhaseTypeDistribution method) (tracts.phase_type_distribution.PhTDioecious method) (tracts.phase_type_distribution.PhTMonoecious method) loglik_biascorrect() (tracts.demography.demographic_model.DemographicModel method) (tracts.legacy.DemographicModel method) Ls (tracts.haploid.Haploid attribute)

M

MALE (tracts.demography.parametrized_demography_sex_biased.SexType attribute) male_female_sex_type_function() (tracts.demography.parametrized_demography_sex_biased.SexType static method) male_names (tracts.driver.SamplesConfig attribute) maximum_iterations (tracts.driver.InferenceConfig attribute) merge_ancestries() (tracts.chromosome.Chrom method) (tracts.legacy.Chrom method) (tracts.legacy.Population method) (tracts.population.Population method) migration_matrix (tracts.phase_type_distribution.PhTMonoecious attribute) migration_matrix_f (tracts.phase_type_distribution.PhTDioecious attribute) migration_matrix_m (tracts.phase_type_distribution.PhTDioecious attribute) migs() (tracts.demography.composite_demographic_model.CompositeDemographicModel method) (tracts.legacy.CompositeDemographicModel method) model_base_params (tracts.demography.parametrized_demography.ParametrizedDemography attribute) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased attribute) model_computed_fields (tracts.driver.InferenceConfig attribute) (tracts.driver.SamplesConfig attribute) (tracts.driver.StartParamsConfig attribute) model_config (tracts.driver.InferenceConfig attribute) (tracts.driver.SamplesConfig attribute) (tracts.driver.StartParamsConfig attribute) model_construct() (tracts.driver.InferenceConfig class method) (tracts.driver.SamplesConfig class method) (tracts.driver.StartParamsConfig class method) model_copy() (tracts.driver.InferenceConfig method) (tracts.driver.SamplesConfig method) (tracts.driver.StartParamsConfig method) model_dump() (tracts.driver.InferenceConfig method) (tracts.driver.SamplesConfig method) (tracts.driver.StartParamsConfig method) model_dump_json() (tracts.driver.InferenceConfig method) (tracts.driver.SamplesConfig method) (tracts.driver.StartParamsConfig method) model_extra (tracts.driver.InferenceConfig property) (tracts.driver.SamplesConfig property) (tracts.driver.StartParamsConfig property) model_fields (tracts.driver.InferenceConfig attribute) (tracts.driver.SamplesConfig attribute) (tracts.driver.StartParamsConfig attribute) model_fields_set (tracts.driver.InferenceConfig property) (tracts.driver.SamplesConfig property) (tracts.driver.StartParamsConfig property) model_filename (tracts.driver.InferenceConfig attribute) model_json_schema() (tracts.driver.InferenceConfig class method) (tracts.driver.SamplesConfig class method) (tracts.driver.StartParamsConfig class method)

model_parametrized_name() (tracts.driver.InferenceConfig class method) (tracts.driver.SamplesConfig class method) (tracts.driver.StartParamsConfig class method) model_post_init() (tracts.driver.InferenceConfig method) (tracts.driver.SamplesConfig method) (tracts.driver.StartParamsConfig method) model_rebuild() (tracts.driver.InferenceConfig class method) (tracts.driver.SamplesConfig class method) (tracts.driver.StartParamsConfig class method) model_validate() (tracts.driver.InferenceConfig class method) (tracts.driver.SamplesConfig class method) (tracts.driver.StartParamsConfig class method) model_validate_json() (tracts.driver.InferenceConfig class method) (tracts.driver.SamplesConfig class method) (tracts.driver.StartParamsConfig class method) model_validate_strings() (tracts.driver.InferenceConfig class method) (tracts.driver.SamplesConfig class method) (tracts.driver.StartParamsConfig class method) module tracts tracts.chromosome tracts.core tracts.demography tracts.demography.base_parametrized_demography tracts.demography.composite_demographic_model tracts.demography.demographic_model tracts.demography.parameter tracts.demography.parametrized_demography tracts.demography.parametrized_demography_sex_biased tracts.driver tracts.haploid tracts.hybrid_pedigree tracts.indiv tracts.legacy tracts.legacy_models tracts.legacy_models.models_2pop tracts.legacy_models.models_3pop tracts.legacy_models.models_4pop tracts.logs tracts.phase_type_distribution tracts.population tracts.tract tracts.util

N

name (tracts.haploid.Haploid attribute) new_indiv() (tracts.legacy.Population method) (tracts.population.Population method) newgen() (tracts.legacy.Population method) (tracts.population.Population method) normalization_factor() (tracts.phase_type_distribution.PhaseTypeDistribution method) (tracts.phase_type_distribution.PhTDioecious method) (tracts.phase_type_distribution.PhTMonoecious method)

npts (tracts.driver.InferenceConfig attribute) num_generations (tracts.phase_type_distribution.PhTDioecious attribute) (tracts.phase_type_distribution.PhTMonoecious attribute) num_populations (tracts.phase_type_distribution.PhTDioecious attribute) (tracts.phase_type_distribution.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)

order_fixed_param_dict() (tracts.demography.base_parametrized_demography.FixedParametersHandler method) outer_CDF() (tracts.phase_type_distribution.PhaseTypeDistribution method) (tracts.phase_type_distribution.PhTDioecious method) (tracts.phase_type_distribution.PhTMonoecious method) outers() (tracts.demography.demographic_model.DemographicModel method) (tracts.legacy.DemographicModel method) outofbounds_pp() (in module tracts.legacy_models.models_2pop) outofbounds_pp_fix() (in module tracts.legacy_models.models_2pop) outofbounds_pp_px() (in module tracts.legacy_models.models_2pop) outofbounds_pp_px_fix() (in module tracts.legacy_models.models_2pop) outofbounds_pppp_pxxx_xpxx_xxpx() (in module tracts.legacy_models.models_4pop) outofbounds_pppp_pxxx_xpxx_xxpx_fix() (in module tracts.legacy_models.models_4pop) outofbounds_ppx_xxp() (in module tracts.legacy_models.models_3pop) outofbounds_ppx_xxp_fix() (in module tracts.legacy_models.models_3pop) output_directory (tracts.driver.InferenceConfig attribute) output_filename_format (tracts.driver.InferenceConfig attribute) output_simulation_data() (in module tracts.driver) output_simulation_data_sex_biased() (in module tracts.driver)

P

Parameter (class in tracts.demography.parameter) parameter_bounds (tracts.demography.base_parametrized_demography.BaseParametrizedDemography property) (tracts.demography.parametrized_demography.ParametrizedDemography property) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased property) ParametrizedDemography (class in tracts.demography.parametrized_demography) ParametrizedDemographySexBiased (class in tracts.demography.parametrized_demography_sex_biased) params_fixed_by_ancestry (tracts.demography.base_parametrized_demography.BaseParametrizedDemography property) (tracts.demography.parametrized_demography.ParametrizedDemography property) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased property) params_fixed_by_value (tracts.demography.base_parametrized_demography.BaseParametrizedDemography property) (tracts.demography.parametrized_demography.ParametrizedDemography property) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased property) ParamType (class in tracts.demography.parameter) parse_chromosomes() (in module tracts.driver) parse_file() (tracts.driver.InferenceConfig class method) (tracts.driver.SamplesConfig class method) (tracts.driver.StartParamsConfig class method) parse_individual_filenames() (in module tracts.driver) parse_obj() (tracts.driver.InferenceConfig class method) (tracts.driver.SamplesConfig class method) (tracts.driver.StartParamsConfig class method) parse_proportions() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography static method) (tracts.demography.parametrized_demography.ParametrizedDemography static method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased static method) parse_raw() (tracts.driver.InferenceConfig class method) (tracts.driver.SamplesConfig class method) (tracts.driver.StartParamsConfig class method) parse_start_params() (in module tracts.driver) PhaseTypeDistribution (class in tracts.phase_type_distribution) PhT_CDF() (tracts.phase_type_distribution.PhaseTypeDistribution method) (tracts.phase_type_distribution.PhTDioecious method) (tracts.phase_type_distribution.PhTMonoecious method) PhT_CDF_windowed() (tracts.phase_type_distribution.PhaseTypeDistribution method) (tracts.phase_type_distribution.PhTDioecious method) (tracts.phase_type_distribution.PhTMonoecious method) PhT_density() (tracts.phase_type_distribution.PhaseTypeDistribution method) (tracts.phase_type_distribution.PhTDioecious method) (tracts.phase_type_distribution.PhTMonoecious method) PhT_density_windowed() (tracts.phase_type_distribution.PhaseTypeDistribution method) (tracts.phase_type_distribution.PhTDioecious method) (tracts.phase_type_distribution.PhTMonoecious method) PhT_parameters_DC() (tracts.phase_type_distribution.PhTDioecious method) PhT_parameters_DF() (tracts.phase_type_distribution.PhTDioecious method) PhTDioecious (class in tracts.phase_type_distribution) PhTMonoecious (class in tracts.phase_type_distribution) plot() (tracts.chromosome.Chrom method) (tracts.chromosome.Chropair method) (tracts.indiv.Indiv method) (tracts.legacy.Chrom method) (tracts.legacy.Chropair method) (tracts.legacy.Indiv method) (tracts.legacy.Population method) (tracts.population.Population method)

plot_all_ancestries() (tracts.legacy.Population method) (tracts.population.Population method) plot_ancestries() (tracts.legacy.Population method) (tracts.population.Population method) plot_chromosome() (tracts.legacy.Population method) (tracts.population.Population method) plot_global_tractlengths() (tracts.legacy.Population method) (tracts.population.Population method) plot_indiv() (tracts.legacy.Population method) (tracts.population.Population method) plot_model_data() (tracts.demography.demographic_model.DemographicModel method) (tracts.legacy.DemographicModel method) plot_next() (tracts.legacy.Population method) (tracts.population.Population method) plot_previous() (tracts.legacy.Population method) (tracts.population.Population method) plotmig() (in module tracts.core) (in module tracts.legacy) popNdist() (tracts.demography.demographic_model.DemographicModel method) (tracts.legacy.DemographicModel method) populate_CDF_values() (tracts.phase_type_distribution.PhaseTypeDistribution method) (tracts.phase_type_distribution.PhTDioecious method) (tracts.phase_type_distribution.PhTMonoecious method) populate_density_bins() (tracts.phase_type_distribution.PhaseTypeDistribution method) (tracts.phase_type_distribution.PhTDioecious method) (tracts.phase_type_distribution.PhTMonoecious method) Population (class in tracts.legacy) (class in tracts.population) pp() (in module tracts.legacy_models.models_2pop) pp_fix() (in module tracts.legacy_models.models_2pop) pp_px() (in module tracts.legacy_models.models_2pop) pp_px_fix() (in module tracts.legacy_models.models_2pop) pppp_pxxx_xpxx_xxpx() (in module tracts.legacy_models.models_4pop) pppp_pxxx_xpxx_xxpx_fix() (in module tracts.legacy_models.models_4pop) ppx_xxp() (in module tracts.legacy_models.models_3pop) ppx_xxp_fix() (in module tracts.legacy_models.models_3pop) preprocess_color_dict() (in module tracts.population) prob_of_pop_setting() (in module tracts.hybrid_pedigree) propfrommig() (in module tracts.legacy_models.models_2pop) (in module tracts.legacy_models.models_3pop) (in module tracts.legacy_models.models_4pop) proportions_from_matrices() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) proportions_from_matrices_return_keys() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) proportions_from_matrix() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography static method) (tracts.demography.parametrized_demography.ParametrizedDemography static method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased static method) PulseEvent (class in tracts.demography.parametrized_demography)

R

random_realization() (tracts.demography.demographic_model.DemographicModel method) (tracts.legacy.DemographicModel method) randomize() (in module tracts.driver) RATE (tracts.demography.parameter.ParamType attribute) recombine() (tracts.chromosome.Chropair method) (tracts.legacy.Chropair method) reduce_parameters() (tracts.demography.base_parametrized_demography.FixedParametersHandler method)

release_fixed_parameters() (tracts.demography.base_parametrized_demography.FixedParametersHandler method) repetitions (tracts.driver.InferenceConfig attribute) rho_f (tracts.phase_type_distribution.PhTDioecious attribute) rho_m (tracts.phase_type_distribution.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 (tracts.phase_type_distribution.PhTMonoecious attribute) S0_list_f (tracts.phase_type_distribution.PhTDioecious attribute) S0_list_m (tracts.phase_type_distribution.PhTDioecious attribute) S_matrix() (tracts.phase_type_distribution.PhTDioecious method) samples (tracts.driver.InferenceConfig attribute) SamplesConfig (class in tracts.driver) save() (tracts.legacy.Population method) (tracts.population.Population method) scale_select_indices() (in module tracts.driver) schema() (tracts.driver.InferenceConfig class method) (tracts.driver.SamplesConfig class method) (tracts.driver.StartParamsConfig class method) schema_json() (tracts.driver.InferenceConfig class method) (tracts.driver.SamplesConfig class method) (tracts.driver.StartParamsConfig class method) seed (tracts.driver.InferenceConfig attribute) set_males() (tracts.population.Population method)

set_sex() (tracts.legacy.Chrom method) set_up_fixed_parameters() (tracts.demography.base_parametrized_demography.BaseParametrizedDemography method) (tracts.demography.base_parametrized_demography.FixedParametersHandler method) (tracts.demography.parametrized_demography.ParametrizedDemography method) (tracts.demography.parametrized_demography_sex_biased.ParametrizedDemographySexBiased method) SEX_BIAS (tracts.demography.parameter.ParamType attribute) sex_model (tracts.phase_type_distribution.PhTDioecious attribute) SexType (class in tracts.demography.parametrized_demography_sex_biased) show_INFO() (in module tracts.logs) smooth_unknown() (tracts.chromosome.Chrom method) smooth_unknowns() (tracts.population.Population method) split_by_props() (tracts.legacy.Population method) (tracts.population.Population method) start_params (tracts.driver.InferenceConfig attribute) StartParamsConfig (class in tracts.driver) switchdensity() (tracts.demography.demographic_model.DemographicModel method) (tracts.legacy.DemographicModel method)

T

t0_proportions (tracts.phase_type_distribution.PhTMonoecious attribute) t0_proportions_f (tracts.phase_type_distribution.PhTDioecious attribute) t0_proportions_m (tracts.phase_type_distribution.PhTDioecious attribute) test_model_func() (in module tracts.core) (in module tracts.legacy) TIME (tracts.demography.parameter.ParamType attribute) time_scaling_factor (tracts.driver.InferenceConfig attribute) Tract (class in tracts.legacy) (class in tracts.tract) tract_length_histogram_multi_windowed() (tracts.phase_type_distribution.PhaseTypeDistribution method) (tracts.phase_type_distribution.PhTDioecious method) (tracts.phase_type_distribution.PhTMonoecious method) tractlength_histogram() (tracts.phase_type_distribution.PhaseTypeDistribution method) (tracts.phase_type_distribution.PhTDioecious method) (tracts.phase_type_distribution.PhTMonoecious method) (tracts.population.Population method) tractlength_histogram_windowed() (tracts.phase_type_distribution.PhaseTypeDistribution method) (tracts.phase_type_distribution.PhTDioecious method) (tracts.phase_type_distribution.PhTMonoecious method) tractlengths() (tracts.chromosome.Chrom method) (tracts.legacy.Chrom method) tracts module tracts.chromosome module tracts.core module tracts.demography module tracts.demography.base_parametrized_demography module tracts.demography.composite_demographic_model module tracts.demography.demographic_model module tracts.demography.parameter module

tracts.demography.parametrized_demography module tracts.demography.parametrized_demography_sex_biased module tracts.driver module tracts.haploid module tracts.hybrid_pedigree module tracts.indiv module tracts.legacy module tracts.legacy_models module tracts.legacy_models.models_2pop module tracts.legacy_models.models_3pop module tracts.legacy_models.models_4pop module tracts.logs module tracts.phase_type_distribution module tracts.population module tracts.tract module tracts.util module transition_matrices (tracts.phase_type_distribution.PhTMonoecious attribute) transition_matrices_f (tracts.phase_type_distribution.PhTDioecious attribute) transition_matrices_m (tracts.phase_type_distribution.PhTDioecious attribute) tree_to_array() (in module tracts.hybrid_pedigree)

U

uniformizemat() (tracts.demography.demographic_model.DemographicModel method) (tracts.legacy.DemographicModel method) unknown_labels_for_smoothing (tracts.driver.InferenceConfig attribute) unnormalized_prob_sex_vector() (tracts.phase_type_distribution.PhTDioecious method)

UNTYPED (tracts.demography.parameter.ParamType attribute) update_forward_refs() (tracts.driver.InferenceConfig class method) (tracts.driver.SamplesConfig class method) (tracts.driver.StartParamsConfig class method)

V

validate() (tracts.driver.InferenceConfig class method) (tracts.driver.SamplesConfig class method) (tracts.driver.StartParamsConfig class method)

X

X_chr (tracts.phase_type_distribution.PhTDioecious attribute)

X_chr_male (tracts.phase_type_distribution.PhTDioecious attribute)

Z

Z() (tracts.demography.demographic_model.DemographicModel method) (tracts.legacy.DemographicModel method)