Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X _ __init__() (BetaCoalescent method) (BlockCountingStateSpace method) (Coalescent method) (CombinedReward method) (CustomReward method) (DemeReward method) (Demography method) (DiracCoalescent method) (DiscreteRateChanges method) (DiscretizedRateChange method) (DiscretizedRateChanges method) (Epoch method) (ExponentialPopSizeChanges method) (ExponentialRateChanges method) (FoldedSFSDistribution method) (Inference method) (JaxExpmBackend method) (JointBlockCountingStateSpace method) (JointSFS method) (JointSFSDistribution method) (JointSFSReward method) (L1Norm method) (L2Norm method) (LineageConfig method) (LineageCountingStateSpace method) (LineageReward method) (LInfNorm method) (LNorm method) (LocusConfig method) (LocusReward method) (MarginalDemeDistributions method) (MarginalLocusDistributions method) (MigrationRateChange method) (MigrationRateChanges method) (PhaseTypeDistribution method) (PopSizeChange method) (PopSizeChanges method) (PopulationSplit method) (SciPyExpmBackend method) (SFS method) (SFS2 method) (State method) (StateReward method) (StateSpace method) (SymmetricMigrationRateChanges method) (Transition method) (TreeHeightDistribution method) (TwoLocusBlockCountingStateSpace method) (TwoLocusSFS method) (TwoLocusSFSDistribution method) (TwoLocusSFSReward method) (UnfoldedSFSDistribution method) (WeightedLoss method) A accumulate() (Coalescent method) (FoldedSFSDistribution method) (JointSFSDistribution method) (PhaseTypeDistribution method) (TreeHeightDistribution method) (TwoLocusSFSDistribution method) (UnfoldedSFSDistribution method) add_bootstrap() (Inference method) add_bootstraps() (Inference method) add_event() (Demography method) add_events() (Demography method) add_run() (Inference method) add_runs() (Inference method) add_target() (Transition static method) alpha (BetaCoalescent attribute) (BlockCountingStateSpace property) (JointBlockCountingStateSpace property) (LineageCountingStateSpace property) (StateSpace property) (TwoLocusBlockCountingStateSpace property) ancestral (PopulationSplit attribute) average (WeightedLoss property) B backend (Backend attribute) Backend (class in phasegen.expm) BetaCoalescent (class in phasegen.coalescent_models) BLOCK (State attribute) block_configs (JointBlockCountingStateSpace property) (TwoLocusBlockCountingStateSpace property) block_counting_state_space (Coalescent property) block_index (JointBlockCountingStateSpace property) (TwoLocusBlockCountingStateSpace property) block_vectors (JointBlockCountingStateSpace property) (TwoLocusBlockCountingStateSpace property) BlockCountingReward (class in phasegen.rewards) BlockCountingStateSpace (class in phasegen.state_space) BlockCountingUnitReward (class in phasegen.rewards) bootstrap() (Inference method) bootstraps (Inference attribute) bounds (Inference attribute) C c (DiracCoalescent attribute) cache (Inference attribute) (WeightedLoss attribute) cache_epochs (Settings attribute) cdf() (TreeHeightDistribution method) coal (Inference attribute) coalesce() (Transition method) Coalescent (class in phasegen.distributions) CoalescentModel (class in phasegen.coalescent_models) combinations (CombinedReward attribute) CombinedReward (class in phasegen.rewards) compute() (JaxExpmBackend method) (L1Norm method) (L2Norm method) (Likelihood method) (LInfNorm method) (LNorm method) (MultinomialLikelihood method) (Norm method) (PoissonLikelihood method) (PyTorchExpmBackend method) (SciPyExpmBackend method) (TensorFlowExpmBackend method) (WeightedLoss method) copy() (JointSFS method) (SFS method) (SFS2 method) (State method) (TwoLocusSFS method) corr (FoldedSFSDistribution property) (MarginalDemeDistributions property) (MarginalLocusDistributions property) (UnfoldedSFSDistribution property) cov (FoldedSFSDistribution property) (JointSFSDistribution property) (MarginalDemeDistributions property) (MarginalLocusDistributions property) (UnfoldedSFSDistribution property) create_bootstrap() (Inference method) create_run() (Inference method) CustomReward (class in phasegen.rewards) D data (JointSFS attribute) (State attribute) default_opts (Inference attribute) DEME (State attribute) DemeReward (class in phasegen.rewards) demes (FoldedSFSDistribution property) (JointSFSDistribution property) (MarginalDemeDistributions property) (PhaseTypeDistribution property) (TreeHeightDistribution property) (TwoLocusSFSDistribution property) (UnfoldedSFSDistribution property) DemographicEvent (class in phasegen.demography) Demography (class in phasegen.demography) demography (Coalescent attribute) (FoldedSFSDistribution attribute) (JointSFSDistribution attribute) (PhaseTypeDistribution attribute) (TreeHeightDistribution attribute) (TwoLocusSFSDistribution attribute) (UnfoldedSFSDistribution attribute) derived (PopulationSplit attribute) dest_pop (DiscretizedRateChange attribute) DiracCoalescent (class in phasegen.coalescent_models) DiscreteDemographicEvent (class in phasegen.demography) DiscreteRateChanges (class in phasegen.demography) DiscretizedDemographicEvent (class in phasegen.demography) DiscretizedRateChange (class in phasegen.demography) DiscretizedRateChanges (class in phasegen.demography) dist_inferred (Inference attribute) do_bootstrap (Inference attribute) drop_cache() (BlockCountingStateSpace method) (Coalescent method) (JointBlockCountingStateSpace method) (LineageCountingStateSpace method) (StateSpace method) (TwoLocusBlockCountingStateSpace method) drop_S() (BlockCountingStateSpace method) (JointBlockCountingStateSpace method) (LineageCountingStateSpace method) (StateSpace method) (TwoLocusBlockCountingStateSpace method) E e (BlockCountingStateSpace property) (JointBlockCountingStateSpace property) (LineageCountingStateSpace property) (StateSpace property) (TwoLocusBlockCountingStateSpace property) end_time (Coalescent attribute) (DiscretizedRateChange attribute) (DiscretizedRateChanges attribute) (Epoch attribute) (ExponentialPopSizeChanges attribute) (ExponentialRateChanges attribute) (TreeHeightDistribution attribute) epoch (BlockCountingStateSpace attribute) Epoch (class in phasegen.demography) epoch (JointBlockCountingStateSpace attribute) (LineageCountingStateSpace attribute) (StateSpace attribute) (TwoLocusBlockCountingStateSpace attribute) epochs (Demography property) events (Demography attribute) (DiscretizedRateChanges attribute) (ExponentialPopSizeChanges attribute) (ExponentialRateChanges attribute) expm() (Backend class method) expm_action_min_dim (Settings attribute) expm_multiply() (Backend class method) ExponentialPopSizeChanges (class in phasegen.demography) ExponentialRateChanges (class in phasegen.demography) F f2() (Coalescent method) f3() (Coalescent method) f4() (Coalescent method) fill_monomorphic() (SFS2 method) (TwoLocusSFS method) flatten_block_counting (Settings attribute) fold() (SFS method) (SFS2 method) (TwoLocusSFS method) FoldedSFSDistribution (class in phasegen.distributions) FoldedSFSReward (class in phasegen.rewards) from_file() (Coalescent class method) (Inference class method) (JointSFS static method) (SFS static method) (SFS2 static method) (TwoLocusSFS static method) from_json() (Coalescent class method) (Inference class method) (JointSFS static method) (SFS2 static method) (TwoLocusSFS static method) from_list() (SFS static method) from_polydfe() (SFS static method) from_polymorphic() (SFS static method) fsfs (Coalescent property) fst (Coalescent property) func (CustomReward attribute) G generated_mass (FoldedSFSDistribution attribute) (UnfoldedSFSDistribution attribute) get() (MarginalDemeDistributions method) (MarginalLocusDistributions method) get_accumulation() (FoldedSFSDistribution method) (UnfoldedSFSDistribution method) get_coal() (Inference method) get_corr() (FoldedSFSDistribution method) (MarginalDemeDistributions method) (MarginalLocusDistributions method) (UnfoldedSFSDistribution method) get_cov() (FoldedSFSDistribution method) (JointSFSDistribution method) (MarginalDemeDistributions method) (MarginalLocusDistributions method) (UnfoldedSFSDistribution method) get_epoch() (Demography method) get_epochs() (Demography method) get_max_abs() (SFS2 method) (TwoLocusSFS method) get_mutation_config() (FoldedSFSDistribution method) (UnfoldedSFSDistribution method) get_mutation_configs() (FoldedSFSDistribution method) (UnfoldedSFSDistribution method) get_neutral() (SFS static method) get_sparsity() (BlockCountingStateSpace method) (JointBlockCountingStateSpace method) (LineageCountingStateSpace method) (StateSpace method) (TwoLocusBlockCountingStateSpace method) get_transitions() (BlockCountingStateSpace method) (JointBlockCountingStateSpace method) (LineageCountingStateSpace method) (StateSpace method) (TwoLocusBlockCountingStateSpace method) H has_div (SFS property) has_n_epochs() (Demography method) I Inference (class in phasegen.inference) is_absorbing() (State method) is_folded() (SFS method) (SFS2 method) (TwoLocusSFS method) items() (MarginalDemeDistributions method) (MarginalLocusDistributions method) J JaxExpmBackend (class in phasegen.expm) joint_block_counting_state_space (Coalescent property) JointBlockCountingReward (class in phasegen.rewards) JointBlockCountingStateSpace (class in phasegen.state_space) JointSFS (class in phasegen.spectrum) JointSFSDistribution (class in phasegen.distributions) JointSFSReward (class in phasegen.rewards) jsfs (Coalescent property) K k (BlockCountingStateSpace property) (JointBlockCountingStateSpace property) (LineageCountingStateSpace property) (StateSpace property) (TwoLocusBlockCountingStateSpace property) keys (WeightedLoss attribute) keys() (MarginalDemeDistributions method) (MarginalLocusDistributions method) L L1Norm (class in phasegen.norms) L2Norm (class in phasegen.norms) Likelihood (class in phasegen.norms) lineage_config (BlockCountingStateSpace attribute) (Coalescent attribute) (FoldedSFSDistribution attribute) (JointBlockCountingStateSpace attribute) (JointSFSDistribution attribute) (LineageCountingStateSpace attribute) (PhaseTypeDistribution attribute) (StateSpace attribute) (TreeHeightDistribution attribute) (TwoLocusBlockCountingStateSpace attribute) (TwoLocusSFSDistribution attribute) (UnfoldedSFSDistribution attribute) lineage_counting_state_space (Coalescent property) lineage_dict (LineageConfig property) LineageConfig (class in phasegen.lineage) LineageCountingReward (class in phasegen.rewards) LineageCountingStateSpace (class in phasegen.state_space) LineageReward (class in phasegen.rewards) lineages (BlockCountingStateSpace property) (JointBlockCountingStateSpace property) (LineageConfig attribute) (LineageCountingStateSpace property) (State property) (StateSpace property) (TwoLocusBlockCountingStateSpace property) LInfNorm (class in phasegen.norms) LINKAGE (State attribute) linked (BlockCountingStateSpace property) (JointBlockCountingStateSpace property) (LineageCountingStateSpace property) (State property) (StateSpace property) (TwoLocusBlockCountingStateSpace property) LNorm (class in phasegen.norms) loci (FoldedSFSDistribution property) (JointSFSDistribution property) (MarginalLocusDistributions property) (PhaseTypeDistribution property) (TreeHeightDistribution property) (TwoLocusSFSDistribution property) (UnfoldedSFSDistribution property) LOCUS (State attribute) locus_config (BlockCountingStateSpace attribute) (Coalescent attribute) (FoldedSFSDistribution attribute) (JointBlockCountingStateSpace attribute) (JointSFSDistribution attribute) (LineageCountingStateSpace attribute) (PhaseTypeDistribution attribute) (StateSpace attribute) (TreeHeightDistribution attribute) (TwoLocusBlockCountingStateSpace attribute) (TwoLocusSFSDistribution attribute) (UnfoldedSFSDistribution attribute) LocusConfig (class in phasegen.locus) LocusReward (class in phasegen.rewards) loss (Inference attribute) loss_inferred (Inference attribute) M m2 (FoldedSFSDistribution property) (JointSFSDistribution property) (PhaseTypeDistribution property) (TreeHeightDistribution property) (TwoLocusSFSDistribution property) (UnfoldedSFSDistribution property) MarginalDemeDistributions (class in phasegen.distributions) marginalize() (JointSFS method) MarginalLocusDistributions (class in phasegen.distributions) mask_diagonal() (SFS2 method) (TwoLocusSFS method) mask_upper() (SFS2 method) (TwoLocusSFS method) max_epochs (TreeHeightDistribution attribute) max_iter (TreeHeightDistribution attribute) max_squarings (JaxExpmBackend attribute) mean (FoldedSFSDistribution property) (JointSFSDistribution property) (PhaseTypeDistribution property) (TreeHeightDistribution property) (TwoLocusSFSDistribution property) (UnfoldedSFSDistribution property) method_mle (Inference attribute) migrate() (Transition method) migrate_linked() (Transition method) migrate_unlinked() (Transition method) migration_rates (DiscreteRateChanges attribute) (Epoch attribute) (MigrationRateChange attribute) (MigrationRateChanges attribute) (PopSizeChange attribute) (PopSizeChanges attribute) (SymmetricMigrationRateChanges attribute) MigrationRateChange (class in phasegen.demography) MigrationRateChanges (class in phasegen.demography) misidentify() (SFS method) model (BlockCountingStateSpace attribute) (Coalescent attribute) (JointBlockCountingStateSpace attribute) (LineageCountingStateSpace attribute) (StateSpace attribute) (TwoLocusBlockCountingStateSpace attribute) module phasegen.coalescent_models phasegen.demography phasegen.expm phasegen.inference phasegen.norms phasegen.rewards phasegen.settings phasegen.spectrum phasegen.state_space moment() (Coalescent method) (FoldedSFSDistribution method) (JointSFSDistribution method) (PhaseTypeDistribution method) (TreeHeightDistribution method) (TwoLocusSFSDistribution method) (UnfoldedSFSDistribution method) MultinomialLikelihood (class in phasegen.norms) multiplier (PopulationSplit attribute) N n (LineageConfig attribute) (LocusConfig attribute) (SFS property) n_blocks (JointBlockCountingStateSpace property) (State property) (TwoLocusBlockCountingStateSpace property) n_bootstraps (Inference attribute) n_demes (State property) n_div (SFS property) n_loci (State property) n_max (WeightedLoss attribute) n_monomorphic (SFS property) n_polymorphic (SFS property) n_pops (Demography attribute) (DiscreteRateChanges attribute) (Epoch attribute) (JointSFS property) (LineageConfig attribute) (MigrationRateChange attribute) (MigrationRateChanges attribute) (PopSizeChange attribute) (PopSizeChanges attribute) (SymmetricMigrationRateChanges attribute) n_runs (Inference attribute) n_sites (SFS property) n_unlinked (LocusConfig attribute) Norm (class in phasegen.norms) normalize() (SFS method) O observation (Inference attribute) opts (Inference attribute) P p (L1Norm attribute) (L2Norm attribute) (LInfNorm attribute) (LNorm attribute) p_absorption (TreeHeightDistribution attribute) parallelize (Inference attribute) (Settings attribute) param_names (Inference property) params_inferred (Inference attribute) pbar (Inference attribute) pdf() (TreeHeightDistribution method) phasegen.coalescent_models module phasegen.demography module phasegen.expm module phasegen.inference module phasegen.norms module phasegen.rewards module phasegen.settings module phasegen.spectrum module phasegen.state_space module PhaseTypeDistribution (class in phasegen.distributions) plot() (Demography method) (JointSFS method) (SFS method) (SFS2 method) (TwoLocusSFS method) plot_accumulation() (Coalescent method) (FoldedSFSDistribution method) (JointSFSDistribution method) (PhaseTypeDistribution method) (TreeHeightDistribution method) (TwoLocusSFSDistribution method) (UnfoldedSFSDistribution method) plot_bootstraps() (Inference method) plot_cdf() (TreeHeightDistribution method) plot_demography() (Inference method) plot_migration() (Demography method) (Inference method) plot_pdf() (TreeHeightDistribution method) plot_pop_sizes() (Demography method) (Inference method) plot_rates() (BlockCountingStateSpace method) (JointBlockCountingStateSpace method) (LineageCountingStateSpace method) (StateSpace method) (TwoLocusBlockCountingStateSpace method) plot_surface() (JointSFS method) (SFS2 method) (TwoLocusSFS method) PoissonLikelihood (class in phasegen.norms) polymorphic (SFS property) pop (DiscretizedRateChange attribute) pop_names (DemographicEvent attribute) (Demography attribute) (DiscreteDemographicEvent attribute) (DiscreteRateChanges attribute) (DiscretizedDemographicEvent attribute) (DiscretizedRateChange attribute) (DiscretizedRateChanges attribute) (Epoch attribute) (ExponentialPopSizeChanges attribute) (ExponentialRateChanges attribute) (LineageConfig attribute) (MigrationRateChange attribute) (MigrationRateChanges attribute) (PopSizeChange attribute) (PopSizeChanges attribute) (PopulationSplit attribute) (SymmetricMigrationRateChanges attribute) pop_sizes (DiscreteRateChanges attribute) (Epoch attribute) (MigrationRateChange attribute) (MigrationRateChanges attribute) (PopSizeChange attribute) (PopSizeChanges attribute) (SymmetricMigrationRateChanges attribute) PopSizeChange (class in phasegen.demography) PopSizeChanges (class in phasegen.demography) PopulationSplit (class in phasegen.demography) precision (SciPyExpmBackend attribute) prod() (Reward method) ProductReward (class in phasegen.rewards) psi (DiracCoalescent attribute) PyTorchExpmBackend (class in phasegen.expm) Q quantile() (TreeHeightDistribution method) R recombination_rate (LocusConfig attribute) recombine() (Transition method) register() (Backend class method) regularize (Settings attribute) requires_joint_state_space() (Reward static method) resample (Inference attribute) resample() (SFS method) result (Inference attribute) Reward (class in phasegen.rewards) reward (FoldedSFSDistribution attribute) (JointSFSDistribution attribute) (PhaseTypeDistribution attribute) (TreeHeightDistribution attribute) (TwoLocusSFSDistribution attribute) (UnfoldedSFSDistribution attribute) run() (Inference method) runs (Inference attribute) S S (BlockCountingStateSpace property) (JointBlockCountingStateSpace property) (LineageCountingStateSpace property) (StateSpace property) (TwoLocusBlockCountingStateSpace property) scale_theta() (SFS method) scale_time (BetaCoalescent attribute) (DiracCoalescent attribute) SciPyExpmBackend (class in phasegen.expm) seed (Inference attribute) set_pbar() (Settings static method) Settings (class in phasegen.settings) SFS (class in phasegen.spectrum) sfs (Coalescent property) SFS2 (class in phasegen.spectrum) sfs2 (Coalescent property) shape (JointSFS property) (JointSFSDistribution property) (TwoLocusSFSDistribution property) source_pop (DiscretizedRateChange attribute) standard_kingman() (SFS static method) StandardCoalescent (class in phasegen.coalescent_models) start_time (Coalescent attribute) (DemographicEvent attribute) (DiscreteDemographicEvent attribute) (DiscreteRateChanges attribute) (DiscretizedDemographicEvent attribute) (DiscretizedRateChange attribute) (DiscretizedRateChanges attribute) (Epoch attribute) (ExponentialPopSizeChanges attribute) (ExponentialRateChanges attribute) (MigrationRateChange attribute) (MigrationRateChanges attribute) (PopSizeChange attribute) (PopSizeChanges attribute) (PopulationSplit attribute) (SymmetricMigrationRateChanges attribute) (TreeHeightDistribution attribute) State (class in phasegen.state_space) state_space (FoldedSFSDistribution attribute) (JointSFSDistribution attribute) (PhaseTypeDistribution attribute) (Transition attribute) (TreeHeightDistribution attribute) (TwoLocusSFSDistribution attribute) (UnfoldedSFSDistribution attribute) StateReward (class in phasegen.rewards) states (BlockCountingStateSpace property) (JointBlockCountingStateSpace property) (LineageCountingStateSpace property) (StateSpace property) (TwoLocusBlockCountingStateSpace property) StateSpace (class in phasegen.state_space) std (FoldedSFSDistribution property) (JointSFSDistribution property) (PhaseTypeDistribution property) (TreeHeightDistribution property) (TwoLocusSFSDistribution property) (UnfoldedSFSDistribution property) step_size (DiscretizedRateChange attribute) subsample() (SFS method) sum() (Reward method) SumReward (class in phasegen.rewards) support() (Reward static method) supports() (CustomReward method) (Reward method) SymmetricMigrationRateChanges (class in phasegen.demography) symmetrize() (SFS2 method) (TwoLocusSFS method) T t_max (TreeHeightDistribution property) tajimas_d (UnfoldedSFSDistribution property) tau (Epoch property) TensorFlowExpmBackend (class in phasegen.expm) Theta (SFS property) theta (SFS property) theta_pi (UnfoldedSFSDistribution property) theta_w (UnfoldedSFSDistribution property) time (BlockCountingStateSpace attribute) (JointBlockCountingStateSpace attribute) (LineageCountingStateSpace attribute) (TwoLocusBlockCountingStateSpace attribute) times (DiscreteDemographicEvent attribute) (DiscreteRateChanges attribute) (MigrationRateChange attribute) (MigrationRateChanges attribute) (PopSizeChange attribute) (PopSizeChanges attribute) (PopulationSplit attribute) (SymmetricMigrationRateChanges attribute) to_file() (Coalescent method) (Inference method) (JointSFS method) (SFS method) (SFS2 method) (TwoLocusSFS method) to_json() (Coalescent method) (Inference method) (JointSFS method) (SFS2 method) (TwoLocusSFS method) to_list() (SFS method) to_msprime() (Coalescent method) (Demography method) to_numpy() (SFS method) to_spectra() (SFS method) to_string() (Epoch method) total_branch_length (Coalescent property) TotalBranchLengthLocusReward (class in phasegen.rewards) TotalBranchLengthReward (class in phasegen.rewards) TotalTreeHeightReward (class in phasegen.rewards) touch() (FoldedSFSDistribution method) (JointSFSDistribution method) (PhaseTypeDistribution method) (TreeHeightDistribution method) (TwoLocusSFSDistribution method) (UnfoldedSFSDistribution method) trajectory (DiscretizedRateChange attribute) transit() (Transition method) transition (BlockCountingStateSpace property) Transition (class in phasegen.state_space) transition (JointBlockCountingStateSpace property) (LineageCountingStateSpace property) (StateSpace property) (TwoLocusBlockCountingStateSpace property) tree_height (Coalescent property) (FoldedSFSDistribution attribute) (JointSFSDistribution attribute) (PhaseTypeDistribution attribute) (TreeHeightDistribution attribute) (TwoLocusSFSDistribution attribute) (UnfoldedSFSDistribution attribute) TreeHeightDistribution (class in phasegen.distributions) TreeHeightReward (class in phasegen.rewards) two_locus_block_counting_state_space (Coalescent property) TwoLocusBlockCountingReward (class in phasegen.rewards) TwoLocusBlockCountingStateSpace (class in phasegen.state_space) TwoLocusSFS (class in phasegen.spectrum) TwoLocusSFSDistribution (class in phasegen.distributions) TwoLocusSFSReward (class in phasegen.rewards) U UnfoldedSFSDistribution (class in phasegen.distributions) UnfoldedSFSReward (class in phasegen.rewards) UnitReward (class in phasegen.rewards) unlinked (BlockCountingStateSpace property) (JointBlockCountingStateSpace property) (LineageCountingStateSpace property) (State property) (StateSpace property) (TwoLocusBlockCountingStateSpace property) update_epoch() (BlockCountingStateSpace method) (JointBlockCountingStateSpace method) (LineageCountingStateSpace method) (StateSpace method) (TwoLocusBlockCountingStateSpace method) use_numba (Settings attribute) use_pbar (Settings attribute) V values() (MarginalDemeDistributions method) (MarginalLocusDistributions method) var (FoldedSFSDistribution property) (JointSFSDistribution property) (PhaseTypeDistribution property) (TreeHeightDistribution property) (TwoLocusSFSDistribution property) (UnfoldedSFSDistribution property) W warn_n_epochs (Demography attribute) WeightedLoss (class in phasegen.inference) weights (WeightedLoss attribute) X x0 (Inference property)
