Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | X _ __init__() (AdaptivePolarizationPrior method) (Annotation method) (Annotator method) (BaseContextStratification method) (BaseInference method) (ChunkedStratification method) (CodingSequenceFiltration method) (Config method) (Covariate method) (DegeneracyAnnotation method) (DegeneracyStratification method) (DeviantOutgroupFiltration method) (DiscreteFractionalParametrization method) (DiscreteParametrization method) (ExistingOutgroupFiltration method) (Filterer method) (Filtration method) (JCSubstitutionModel method) (JointInference method) (K2SubstitutionModel method) (MaskedFiltration method) (MaximumLikelihoodAncestralAnnotation method) (MaximumParsimonyAncestralAnnotation method) (Parametrization method) (Parser method) (PolarizationPrior method) (SharedParams method) (SiteConfig method) (SiteInfo method) (Spectra method) (Spectrum method) (Stratification method) (SubstitutionModel method) (SynonymyAnnotation method) (TargetSiteCounter method) A AdaptivePolarizationPrior (class in fastdfe.annotation) all (Spectra property) AllFiltration (class in fastdfe.filtration) allow_divergence (PolarizationPrior attribute) alpha (BaseInference property) (JointInference property) AncestralAlleleAnnotation (class in fastdfe.annotation) AncestralBaseStratification (class in fastdfe.parser) annotate() (Annotator method) annotate_site() (Annotation method) (DegeneracyAnnotation method) (MaximumLikelihoodAncestralAnnotation method) (MaximumParsimonyAncestralAnnotation method) (SynonymyAnnotation method) Annotation (class in fastdfe.annotation) annotations (Annotator attribute) (Parser attribute) Annotator (class in fastdfe.annotation) apply() (Covariate method) apply_default() (Covariate method) B BaseContextStratification (class in fastdfe.parser) BaseInference (class in fastdfe.base_inference) BaseTransitionStratification (class in fastdfe.parser) BaseType (class in fastdfe.annotation) BiasedGCConversionFiltration (class in fastdfe.filtration) bootstrap() (BaseInference method) (JointInference method) bootstrap_if_required() (JointInference method) bootstrap_results (BaseInference attribute) (JointInference attribute) bootstraps (BaseInference attribute) (JointInference attribute) bounds (BaseInference attribute) (Covariate attribute) (DisplacedGammaParametrization attribute) (GammaDiscreteParametrization attribute) (GammaExpParametrization attribute) (JointInference attribute) (Parametrization attribute) (SubstitutionModel attribute) bounds_scale (Covariate attribute) C cache() (SubstitutionModel method) callback (Covariate attribute) cd (CodingSequenceFiltration attribute) check_fixed_params_exist() (BaseInference method) (JointInference method) check_no_shared_params_fixed() (JointInference method) check_shared_params() (JointInference method) chunk_sizes (ChunkedStratification attribute) ChunkedStratification (class in fastdfe.parser) CodingSequenceFiltration (class in fastdfe.filtration) combine() (Spectra method) compare_nested() (BaseInference method) (JointInference method) compare_nested_models() (BaseInference method) (JointInference method) compute_histogram() (Inference static method) confidence_threshold (MaximumLikelihoodAncestralAnnotation attribute) Config (class in fastdfe.config) configs (MaximumLikelihoodAncestralAnnotation attribute) contig (BaseContextStratification attribute) ContigStratification (class in fastdfe.parser) copy() (Spectra method) (Spectrum method) count() (TargetSiteCounter method) count_target_sites() (Annotation static method) counter (ChunkedStratification attribute) Covariate (class in fastdfe.optimization) covariates (JointInference attribute) create_config() (BaseInference method) (JointInference method) create_polydfe_init_file() (Config method) create_polydfe_sfs_config() (Config method) D DegeneracyAnnotation (class in fastdfe.annotation) DegeneracyStratification (class in fastdfe.parser) DeviantOutgroupFiltration (class in fastdfe.filtration) DiscreteFractionalParametrization (class in fastdfe.parametrization) DiscreteParametrization (class in fastdfe.parametrization) discretization (BaseInference attribute) (JointInference attribute) DisplacedGammaParametrization (class in fastdfe.parametrization) do_bootstrap (BaseInference attribute) (JointInference attribute) drop_empty() (Spectra method) drop_sparse() (Spectra method) drop_zero_entries() (Spectra method) E errors (DegeneracyAnnotation attribute) evaluate_likelihood() (BaseInference method) (JointInference method) (MaximumLikelihoodAncestralAnnotation method) exclude_samples (MaskedFiltration attribute) (Parser attribute) execution_time (BaseInference attribute) (JointInference attribute) ExistingOutgroupFiltration (class in fastdfe.filtration) F fastdfe.annotation module fastdfe.filtration module fastdfe.parametrization module fastdfe.parser module filter() (Filterer method) filter_site() (AllFiltration method) (BiasedGCConversionFiltration method) (CodingSequenceFiltration method) (DeviantOutgroupFiltration method) (ExistingOutgroupFiltration method) (Filtration method) (NoFiltration method) (PolyAllelicFiltration method) (SNPFiltration method) (SNVFiltration method) Filterer (class in fastdfe.filtration) Filtration (class in fastdfe.filtration) filtrations (Filterer attribute) (Parser attribute) first_node_ancestral (SiteInfo attribute) fixed_params (BaseInference attribute) (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) (JointInference attribute) (SubstitutionModel attribute) fold() (Spectra method) (Spectrum method) folded (BaseInference attribute) (JointInference attribute) from_config() (BaseInference class method) (JointInference class method) from_config_file() (BaseInference class method) (JointInference class method) from_data() (MaximumLikelihoodAncestralAnnotation class method) from_dataframe() (MaximumLikelihoodAncestralAnnotation class method) (Spectra static method) from_dict() (Config static method) (Spectra static method) from_est_sfs() (MaximumLikelihoodAncestralAnnotation class method) from_file() (BaseInference class method) (Config class method) (JointInference class method) (MaximumLikelihoodAncestralAnnotation class method) (Spectra class method) (Spectrum static method) from_json() (BaseInference class method) (Config static method) (JointInference class method) (MaximumLikelihoodAncestralAnnotation class method) from_list() (Spectra static method) (Spectrum static method) from_polydfe() (Spectrum static method) from_polymorphic() (Spectrum static method) from_spectra() (Spectra static method) from_spectrum() (Spectra static method) from_yaml() (Config static method) G GammaDiscreteParametrization (class in fastdfe.parametrization) GammaExpParametrization (class in fastdfe.parametrization) GenomePositionDependentStratification (class in fastdfe.parser) get_alpha() (BaseInference method) (JointInference method) get_bootstrap_param_names() (BaseInference method) (JointInference method) get_bootstrap_params() (BaseInference method) (JointInference method) get_bound() (JCSubstitutionModel method) get_bounds() (JCSubstitutionModel method) (K2SubstitutionModel method) (SubstitutionModel method) get_bounds_linear() (BaseInference method) (JointInference method) get_cdf() (DiscreteFractionalParametrization method) (DiscreteParametrization method) (DisplacedGammaParametrization static method) (GammaDiscreteParametrization static method) (GammaExpParametrization static method) (Parametrization method) get_cis_params_mle() (BaseInference method) (Inference static method) (JointInference method) get_counts() (BaseInference method) (JointInference method) get_degeneracy (DegeneracyStratification attribute) get_discretized() (BaseInference method) (Inference static method) (JointInference method) get_empty() (Spectra method) get_errors_discretized_dfe() (BaseInference method) (JointInference method) get_errors_params_mle() (Inference static method) get_fixed_param_names() (BaseInference method) (JointInference method) get_folded_spectra() (MaximumLikelihoodAncestralAnnotation method) get_inferences() (JointInference method) get_inferred_site_info() (MaximumLikelihoodAncestralAnnotation method) get_n_optimized() (BaseInference method) (JointInference method) get_optimized_param_names() (BaseInference method) (JointInference method) get_outgroup_divergence() (MaximumLikelihoodAncestralAnnotation method) get_p_config() (MaximumLikelihoodAncestralAnnotation class method) get_p_configs() (MaximumLikelihoodAncestralAnnotation class method) get_p_tree() (MaximumLikelihoodAncestralAnnotation static method) get_pdf() (DiscreteFractionalParametrization method) (DiscreteParametrization method) (DisplacedGammaParametrization static method) (GammaDiscreteParametrization static method) (GammaExpParametrization static method) (Parametrization method) get_polydfe_model() (Config method) get_residual() (BaseInference method) (JointInference method) get_scales_linear() (BaseInference method) (JointInference method) get_shared_param_names() (JointInference method) get_site_info() (MaximumLikelihoodAncestralAnnotation method) get_stats_discretized() (Inference static method) get_summary() (BaseInference method) (JointInference method) get_type() (AncestralBaseStratification method) (BaseContextStratification method) (BaseTransitionStratification method) (ChunkedStratification method) (ContigStratification method) (DegeneracyStratification method) (Stratification method) (SynonymyStratification method) (TransitionTransversionStratification method) (VEPStratification method) get_types() (AncestralBaseStratification method) (BaseContextStratification method) (BaseTransitionStratification method) (ChunkedStratification method) (ContigStratification method) (DegeneracyStratification method) (Stratification method) (SynonymyStratification method) (TransitionTransversionStratification method) (VEPStratification method) get_x0() (BaseInference method) (JointInference method) (SubstitutionModel static method) H has_div (Spectra property) (Spectrum property) has_dots() (Spectra method) I include_samples (MaskedFiltration attribute) (Parser attribute) infer() (MaximumLikelihoodAncestralAnnotation method) Inference (class in fastdfe.abstract_inference) info_tag (SnpEffStratification attribute) (VEPStratification attribute) ingroup_mask (DeviantOutgroupFiltration attribute) ingroups (DeviantOutgroupFiltration attribute) interval_sizes (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) intervals (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) is_filtered() (Filterer method) is_folded() (Spectra method) (Spectrum method) is_monotonic() (MaximumLikelihoodAncestralAnnotation method) is_synonymous() (SynonymyAnnotation static method) J JCSubstitutionModel (class in fastdfe.annotation) joint_inference_makes_sense() (JointInference method) joint_inferences (JointInference attribute) JointInference (class in fastdfe.joint_inference) K k (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) (Spectra property) K2SubstitutionModel (class in fastdfe.annotation) KingmanPolarizationPrior (class in fastdfe.annotation) L L2_residual (BaseInference attribute) (JointInference attribute) likelihood (BaseInference attribute) (JointInference attribute) (MaximumLikelihoodAncestralAnnotation attribute) likelihoods (BaseInference attribute) (JointInference attribute) (MaximumLikelihoodAncestralAnnotation attribute) locked (BaseInference attribute) (JointInference attribute) lrt() (BaseInference method) (JointInference method) M MAJOR (BaseType attribute) major_ancestral (SiteInfo attribute) major_base (SiteConfig attribute) (SiteInfo attribute) marginal_inferences (JointInference attribute) marginals_without_all() (JointInference method) MaskedFiltration (class in fastdfe.filtration) max_sites (MaximumLikelihoodAncestralAnnotation attribute) MaximumLikelihoodAncestralAnnotation (class in fastdfe.annotation) MaximumParsimonyAncestralAnnotation (class in fastdfe.annotation) merge_groups() (Spectra method) MINOR (BaseType attribute) minor_base (SiteConfig attribute) (SiteInfo attribute) mismatches (DegeneracyAnnotation attribute) model (BaseInference attribute) (JointInference attribute) (MaximumLikelihoodAncestralAnnotation attribute) module fastdfe.annotation fastdfe.filtration fastdfe.parametrization fastdfe.parser multiplicity (SiteConfig attribute) mutate() (SynonymyAnnotation static method) N n (BaseInference attribute) (JointInference attribute) (Parser attribute) (Spectra property) (Spectrum property) n_annotated (Annotation attribute) n_bootstrap_retries (BaseInference attribute) (JointInference attribute) n_bootstraps (BaseInference attribute) (JointInference attribute) n_chunks (ChunkedStratification attribute) n_div (Spectra property) (Spectrum property) n_filtered (Filterer attribute) (Filtration attribute) n_flanking (BaseContextStratification attribute) n_major (SiteConfig attribute) (SiteInfo attribute) n_monomorphic (Spectra property) (Spectrum property) n_no_ancestral (Parser attribute) n_polymorphic (Spectra property) (Spectrum property) n_processed (CodingSequenceFiltration attribute) n_runs (AdaptivePolarizationPrior attribute) (BaseInference attribute) (JointInference attribute) (MaximumLikelihoodAncestralAnnotation attribute) n_samples (TargetSiteCounter attribute) n_sites (MaximumLikelihoodAncestralAnnotation attribute) (Spectra property) (Spectrum property) n_skipped (DegeneracyAnnotation attribute) (Parser attribute) n_snpeff_comparisons (SynonymyAnnotation attribute) n_target_sites (MaximumLikelihoodAncestralAnnotation attribute) (TargetSiteCounter attribute) n_valid (Stratification attribute) n_vep_comparisons (SynonymyAnnotation attribute) NoFiltration (class in fastdfe.filtration) normalize() (Spectra method) (Spectrum method) O optimization (BaseInference attribute) (JointInference attribute) outgroup_bases (SiteConfig attribute) (SiteInfo attribute) outgroup_mask (DeviantOutgroupFiltration attribute) (ExistingOutgroupFiltration attribute) outgroups (DeviantOutgroupFiltration attribute) (ExistingOutgroupFiltration attribute) output (Annotator attribute) (Filterer attribute) P p_bases_first_node (SiteInfo attribute) p_bins (MaximumLikelihoodAncestralAnnotation attribute) p_first_node_ancestral (SiteInfo attribute) p_major (SiteConfig attribute) (SiteInfo attribute) p_major_ancestral (SiteInfo attribute) p_minor (SiteConfig attribute) (SiteInfo attribute) p_polarization (MaximumLikelihoodAncestralAnnotation property) parallelize (AdaptivePolarizationPrior attribute) (BaseInference attribute) (JointInference attribute) (MaximumLikelihoodAncestralAnnotation attribute) param (Covariate attribute) param_names (BaseInference property) (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) (JointInference property) (MaximumLikelihoodAncestralAnnotation attribute) (Parametrization attribute) Parametrization (class in fastdfe.parametrization) params (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) (SharedParams attribute) params_mle (BaseInference attribute) (JointInference attribute) (MaximumLikelihoodAncestralAnnotation attribute) params_mle_raw (JointInference attribute) parse() (Parser method) parse_polydfe_init_file() (Config method) parse_polydfe_sfs_config() (Config method) Parser (class in fastdfe.parser) parser (Stratification attribute) perform_lrt_covariates() (JointInference method) perform_lrt_shared() (JointInference method) plot() (Parametrization method) (PolarizationPrior method) (Spectra method) (Spectrum method) plot_all() (BaseInference method) (JointInference method) plot_bucket_sizes() (BaseInference method) (JointInference method) plot_continuous() (BaseInference method) (Inference static method) (JointInference method) plot_covariate() (JointInference method) plot_discretized() (BaseInference method) (Inference static method) (JointInference method) plot_inferred_parameters() (BaseInference method) (Inference static method) (JointInference method) plot_inferred_parameters_boxplot() (BaseInference method) (Inference static method) (JointInference method) plot_interval_density() (BaseInference method) (JointInference method) plot_likelihoods() (BaseInference method) (JointInference method) (MaximumLikelihoodAncestralAnnotation method) plot_nested_models() (BaseInference method) (JointInference method) plot_observed_sfs() (BaseInference method) (JointInference method) plot_sfs_comparison() (BaseInference method) (JointInference method) plot_tree() (SiteInfo method) PolarizationPrior (class in fastdfe.annotation) PolyAllelicFiltration (class in fastdfe.filtration) polymorphic (Spectra property) (Spectrum property) pool_branch_rates (SubstitutionModel attribute) prefix() (Spectra method) print() (Spectra method) prior (MaximumLikelihoodAncestralAnnotation attribute) probabilities (PolarizationPrior attribute) R raise_if_locked() (BaseInference method) (JointInference method) rate_params (SiteInfo attribute) rename() (Spectra method) reorder_levels() (Spectra method) replace_dots() (Spectra method) resample() (Spectrum method) result (BaseInference attribute) (JointInference attribute) (MaximumLikelihoodAncestralAnnotation attribute) retain_monomorphic (DeviantOutgroupFiltration attribute) rng (AdaptivePolarizationPrior attribute) (BaseInference attribute) (JointInference attribute) run() (BaseInference method) (JointInference method) run_if_required() (BaseInference method) (JointInference method) run_joint_without_covariates() (JointInference method) S samples (DeviantOutgroupFiltration attribute) (ExistingOutgroupFiltration attribute) (MaximumParsimonyAncestralAnnotation attribute) scales (BaseInference attribute) (DisplacedGammaParametrization attribute) (GammaDiscreteParametrization attribute) (GammaExpParametrization attribute) (JointInference attribute) (Parametrization attribute) seed (AdaptivePolarizationPrior attribute) (BaseInference attribute) (JointInference attribute) select() (Spectra method) set_mle_params() (MaximumLikelihoodAncestralAnnotation method) sfs (Parser attribute) sfs_mle (BaseInference attribute) (JointInference attribute) sfs_neut (BaseInference attribute) (JointInference attribute) sfs_sel (BaseInference attribute) (JointInference attribute) shared_params (JointInference attribute) SharedParams (class in fastdfe.optimization) SiteConfig (class in fastdfe.annotation) SiteInfo (class in fastdfe.annotation) sites (SiteConfig attribute) skip_non_polarized (Parser attribute) snpeff_mismatches (SynonymyAnnotation attribute) SnpEffStratification (class in fastdfe.parser) SNPFiltration (class in fastdfe.filtration) SNPStratification (class in fastdfe.parser) SNVFiltration (class in fastdfe.filtration) sort_types() (Spectra method) Spectra (class in fastdfe.spectrum) Spectrum (class in fastdfe.spectrum) standard_kingman() (Spectrum static method) Stratification (class in fastdfe.parser) stratifications (Parser attribute) strict_mode (DeviantOutgroupFiltration attribute) submodels (DisplacedGammaParametrization attribute) (GammaDiscreteParametrization attribute) (GammaExpParametrization attribute) (Parametrization attribute) subsample() (Spectra method) (Spectrum method) subsample_mode (Parser attribute) SubstitutionModel (class in fastdfe.annotation) SynonymyAnnotation (class in fastdfe.annotation) SynonymyStratification (class in fastdfe.parser) T target_site_counter (Parser attribute) TargetSiteCounter (class in fastdfe.parser) theta (BaseInference attribute) (JointInference attribute) (Spectrum property) to_dataframe() (Spectra method) to_dict() (Config method) (Spectra method) to_est_sfs() (MaximumLikelihoodAncestralAnnotation method) to_file() (BaseInference method) (Config method) (JointInference method) (MaximumLikelihoodAncestralAnnotation method) (Spectra method) (Spectrum method) to_fractional() (DiscreteFractionalParametrization method) to_json() (BaseInference method) (Config method) (JointInference method) (MaximumLikelihoodAncestralAnnotation method) to_list() (Spectra method) (Spectrum method) to_nominal() (DiscreteFractionalParametrization method) to_numpy() (Spectra method) (Spectrum method) to_spectra() (Spectra method) (Spectrum method) to_spectrum() (Spectra method) to_yaml() (Config method) TransitionTransversionStratification (class in fastdfe.parser) types (JointInference attribute) (SharedParams attribute) (Spectra property) U update() (Config method) use_parser (MaskedFiltration attribute) V validate_bounds() (SubstitutionModel static method) values (Covariate attribute) vep_mismatches (SynonymyAnnotation attribute) VEPStratification (class in fastdfe.parser) X x0 (BaseInference attribute) (Covariate attribute) (DisplacedGammaParametrization attribute) (GammaDiscreteParametrization attribute) (GammaExpParametrization attribute) (JointInference attribute) (Parametrization attribute)
