Index _ | A | B | C | D | E | F | G | I | J | K | L | M | N | O | P | R | S | T | U | V | X _ __init__() (BaseInference method) (Config method) (Covariate method) (DFE method) (DiscreteFractionalParametrization method) (DiscreteParametrization method) (DisplacedGammaParametrization method) (GammaDiscreteParametrization method) (GammaExpParametrization method) (InferenceResult method) (JointInference method) (Parametrization method) (SharedParams method) (Simulation method) A alpha (BaseInference property) (JointInference property) apply() (Covariate method) apply_default() (Covariate method) B BaseInference (class in fastdfe.base_inference) bootstrap() (BaseInference method) (JointInference method) bootstrap_if_required() (JointInference method) bootstrap_results (BaseInference attribute) (JointInference attribute) bootstraps (BaseInference attribute) (DFE attribute) (InferenceResult attribute) (JointInference attribute) bounds (BaseInference attribute) (Covariate attribute) (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) (DisplacedGammaParametrization attribute) (GammaDiscreteParametrization attribute) (GammaExpParametrization attribute) (JointInference attribute) (Parametrization attribute) bounds_scale (Covariate attribute) C callback (Covariate attribute) cdf() (DFE method) check_fixed_params_exist() (BaseInference method) (JointInference method) check_no_shared_params_fixed() (JointInference method) check_shared_params() (JointInference method) compare_nested() (BaseInference method) (JointInference method) compare_nested_models() (BaseInference method) (JointInference method) compute_histogram() (Inference static method) Config (class in fastdfe.config) config (InferenceResult 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 DFE (class in fastdfe.parametrization) dfe (InferenceResult attribute) (Simulation attribute) disable_pbar (Settings attribute) DiscreteFractionalParametrization (class in fastdfe.parametrization) DiscreteParametrization (class in fastdfe.parametrization) discretization (BaseInference attribute) (JointInference attribute) (Simulation attribute) discretize() (DFE method) DisplacedGammaParametrization (class in fastdfe.parametrization) do_bootstrap (BaseInference attribute) (JointInference attribute) E evaluate_likelihood() (BaseInference method) (JointInference method) execution_time (BaseInference attribute) (JointInference attribute) F fastdfe.parametrization module fixed_params (BaseInference attribute) (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) (JointInference attribute) folded (BaseInference attribute) (JointInference attribute) freeze() (DiscreteFractionalParametrization method) (DiscreteParametrization method) (DisplacedGammaParametrization method) (GammaDiscreteParametrization method) (GammaExpParametrization method) (Parametrization method) from_config() (BaseInference class method) (JointInference class method) from_config_file() (BaseInference class method) (JointInference class method) from_dict() (Config static method) from_file() (BaseInference class method) (Config class method) (DFE class method) (DiscreteFractionalParametrization class method) (DiscreteParametrization class method) (DisplacedGammaParametrization class method) (GammaDiscreteParametrization class method) (GammaExpParametrization class method) (InferenceResult class method) (JointInference class method) (Parametrization class method) from_json() (BaseInference class method) (Config static method) (DFE class method) (DiscreteFractionalParametrization class method) (DiscreteParametrization class method) (DisplacedGammaParametrization class method) (GammaDiscreteParametrization class method) (GammaExpParametrization class method) (InferenceResult class method) (JointInference class method) (Parametrization class method) from_yaml() (Config static method) G GammaDiscreteParametrization (class in fastdfe.parametrization) GammaExpParametrization (class in fastdfe.parametrization) get_alpha() (BaseInference method) (JointInference method) (Simulation method) get_bootstrap_dfes() (DFE method) get_bootstrap_param_names() (BaseInference method) (JointInference method) get_bootstrap_params() (BaseInference method) (JointInference 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_counts() (BaseInference method) (JointInference method) get_dfe() (BaseInference method) (JointInference method) get_discretized() (BaseInference method) (Inference static method) (JointInference method) get_errors_params_mle() (Inference static method) get_fixed_param_names() (BaseInference method) (JointInference method) get_inferences() (JointInference method) get_n_optimized() (BaseInference method) (JointInference method) get_neutral_sfs() (Simulation static method) get_omega() (BaseInference method) (JointInference method) (Simulation method) get_omega_a() (BaseInference method) (JointInference method) (Simulation method) get_optimized_param_names() (BaseInference method) (JointInference 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_spectra() (BaseInference method) (JointInference method) (Simulation method) get_stats_discretized() (BaseInference method) (Inference static method) (JointInference method) get_summary() (BaseInference method) (JointInference method) get_wright_fisher() (Simulation method) get_x0() (BaseInference method) (JointInference method) I include_divergence (BaseInference attribute) (JointInference attribute) Inference (class in fastdfe.abstract_inference) InferenceResult (class in fastdfe.base_inference) interval_sizes (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) intervals (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) J joint_inference_makes_sense() (JointInference method) joint_inferences (JointInference attribute) JointInference (class in fastdfe.joint_inference) K k (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) L L2_residual (BaseInference attribute) (JointInference attribute) likelihood (BaseInference attribute) (JointInference attribute) likelihoods (BaseInference attribute) (JointInference attribute) locked (BaseInference attribute) (JointInference attribute) lrt() (BaseInference method) (JointInference method) M marginal_inferences (JointInference attribute) marginals_without_all() (JointInference method) model (BaseInference attribute) (DFE attribute) (JointInference attribute) (Simulation attribute) module fastdfe.parametrization N n (BaseInference attribute) (JointInference attribute) (Simulation attribute) n_bootstrap_retries (BaseInference attribute) (JointInference attribute) n_bootstraps (BaseInference attribute) (JointInference attribute) n_runs (BaseInference attribute) (JointInference attribute) n_sites (Simulation attribute) n_sites_div (Simulation attribute) n_sites_div_neut (BaseInference attribute) (JointInference attribute) n_sites_div_sel (BaseInference attribute) (JointInference attribute) O omega (BaseInference property) (JointInference property) omega_a (BaseInference property) (JointInference property) optimization (BaseInference attribute) (JointInference attribute) P parallelize (BaseInference attribute) (JointInference attribute) (Settings attribute) param (Covariate attribute) param_names (BaseInference property) (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) (DisplacedGammaParametrization attribute) (GammaDiscreteParametrization attribute) (GammaExpParametrization attribute) (JointInference property) (Parametrization attribute) Parametrization (class in fastdfe.parametrization) params (DFE attribute) (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) (SharedParams attribute) (Simulation attribute) params_mle (BaseInference attribute) (JointInference attribute) params_mle_raw (JointInference attribute) parse_polydfe_init_file() (Config method) parse_polydfe_sfs_config() (Config method) pdf() (DFE method) perform_lrt_covariates() (JointInference method) perform_lrt_shared() (JointInference method) plot() (DFE method) (DiscreteFractionalParametrization method) (DiscreteParametrization method) (DisplacedGammaParametrization method) (GammaDiscreteParametrization method) (GammaExpParametrization method) (Parametrization 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) plot_many() (DFE static method) plot_nested_models() (BaseInference method) (JointInference method) plot_observed_sfs() (BaseInference method) (JointInference method) plot_sfs_comparison() (BaseInference method) (JointInference method) R raise_if_locked() (BaseInference method) (JointInference method) result (BaseInference attribute) (JointInference attribute) rng (BaseInference attribute) (JointInference attribute) run() (BaseInference method) (JointInference method) (Simulation method) run_if_required() (BaseInference method) (JointInference method) run_joint_without_covariates() (JointInference method) runs (BaseInference attribute) (InferenceResult attribute) (JointInference attribute) S scales (BaseInference attribute) (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) (DisplacedGammaParametrization attribute) (GammaDiscreteParametrization attribute) (GammaExpParametrization attribute) (JointInference attribute) (Parametrization attribute) seed (BaseInference attribute) (JointInference attribute) Settings (class in sfsutils.settings) sfs_mle (BaseInference attribute) (JointInference attribute) sfs_neut (BaseInference attribute) (JointInference attribute) (Simulation attribute) sfs_sel (BaseInference attribute) (JointInference attribute) (Simulation attribute) shared_params (JointInference attribute) SharedParams (class in fastdfe.optimization) Simulation (class in fastdfe.simulation) spectra (InferenceResult attribute) submodels (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) (DisplacedGammaParametrization attribute) (GammaDiscreteParametrization attribute) (GammaExpParametrization attribute) (Parametrization attribute) T theta (BaseInference attribute) (JointInference attribute) (Simulation attribute) to_dict() (Config method) to_file() (BaseInference method) (Config method) (DFE method) (DiscreteFractionalParametrization method) (DiscreteParametrization method) (DisplacedGammaParametrization method) (GammaDiscreteParametrization method) (GammaExpParametrization method) (InferenceResult method) (JointInference method) (Parametrization method) to_fractional() (DiscreteFractionalParametrization method) to_json() (BaseInference method) (Config method) (DFE method) (DiscreteFractionalParametrization method) (DiscreteParametrization method) (DisplacedGammaParametrization method) (GammaDiscreteParametrization method) (GammaExpParametrization method) (InferenceResult method) (JointInference method) (Parametrization method) to_nominal() (DiscreteFractionalParametrization method) to_yaml() (Config method) types (JointInference attribute) (SharedParams attribute) U update() (Config method) V values (Covariate attribute) X x0 (BaseInference attribute) (Covariate attribute) (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) (DisplacedGammaParametrization attribute) (GammaDiscreteParametrization attribute) (GammaExpParametrization attribute) (JointInference attribute) (Parametrization attribute)
