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) (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) (UnfoldedSFSDistribution method) (WeightedLoss method) A accumulate() (Coalescent method) (FoldedSFSDistribution method) (PhaseTypeDistribution method) (TreeHeightDistribution 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) (LineageCountingStateSpace property) (StateSpace 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_counting_state_space (Coalescent 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() (SFS method) (SFS2 method) (State method) corr (FoldedSFSDistribution property) (MarginalDemeDistributions property) (MarginalLocusDistributions property) (UnfoldedSFSDistribution property) cov (FoldedSFSDistribution property) (MarginalDemeDistributions property) (MarginalLocusDistributions property) (UnfoldedSFSDistribution property) create_bootstrap() (Inference method) create_run() (Inference method) CustomReward (class in phasegen.rewards) D data (State attribute) default_opts (Inference attribute) DEME (State attribute) DemeReward (class in phasegen.rewards) demes (FoldedSFSDistribution property) (MarginalDemeDistributions property) (PhaseTypeDistribution property) (TreeHeightDistribution property) (UnfoldedSFSDistribution property) DemographicEvent (class in phasegen.demography) Demography (class in phasegen.demography) demography (Coalescent attribute) (FoldedSFSDistribution attribute) (PhaseTypeDistribution attribute) (TreeHeightDistribution 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) (LineageCountingStateSpace method) (StateSpace method) drop_S() (BlockCountingStateSpace method) (LineageCountingStateSpace method) (StateSpace method) E e (BlockCountingStateSpace property) (LineageCountingStateSpace property) (StateSpace 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 (LineageCountingStateSpace attribute) (StateSpace attribute) epochs (Demography property) events (Demography attribute) (DiscretizedRateChanges attribute) (ExponentialPopSizeChanges attribute) (ExponentialRateChanges attribute) expm() (Backend class method) ExponentialPopSizeChanges (class in phasegen.demography) ExponentialRateChanges (class in phasegen.demography) F fill_monomorphic() (SFS2 method) flatten_block_counting (Settings attribute) fold() (SFS method) (SFS2 method) FoldedSFSDistribution (class in phasegen.distributions) FoldedSFSReward (class in phasegen.rewards) from_file() (Coalescent class method) (Inference class method) (SFS static method) (SFS2 static method) from_json() (Coalescent class method) (Inference class method) (SFS2 static method) from_list() (SFS static method) from_polydfe() (SFS static method) from_polymorphic() (SFS static method) fsfs (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) (MarginalDemeDistributions method) (MarginalLocusDistributions method) (UnfoldedSFSDistribution method) get_epoch() (Demography method) get_epochs() (Demography method) get_max_abs() (SFS2 method) get_mutation_config() (FoldedSFSDistribution method) (UnfoldedSFSDistribution method) get_mutation_configs() (FoldedSFSDistribution method) (UnfoldedSFSDistribution method) get_sparsity() (BlockCountingStateSpace method) (LineageCountingStateSpace method) (StateSpace method) get_transitions() (BlockCountingStateSpace method) (LineageCountingStateSpace method) (StateSpace 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) items() (MarginalDemeDistributions method) (MarginalLocusDistributions method) J JaxExpmBackend (class in phasegen.expm) K k (BlockCountingStateSpace property) (LineageCountingStateSpace property) (StateSpace 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) (LineageCountingStateSpace attribute) (PhaseTypeDistribution attribute) (StateSpace attribute) (TreeHeightDistribution 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) (LineageConfig attribute) (LineageCountingStateSpace property) (State property) (StateSpace property) LInfNorm (class in phasegen.norms) LINKAGE (State attribute) linked (BlockCountingStateSpace property) (LineageCountingStateSpace property) (State property) (StateSpace property) LNorm (class in phasegen.norms) loci (FoldedSFSDistribution property) (MarginalLocusDistributions property) (PhaseTypeDistribution property) (TreeHeightDistribution property) (UnfoldedSFSDistribution property) LOCUS (State attribute) locus_config (BlockCountingStateSpace attribute) (Coalescent attribute) (FoldedSFSDistribution attribute) (LineageCountingStateSpace attribute) (PhaseTypeDistribution attribute) (StateSpace attribute) (TreeHeightDistribution attribute) (UnfoldedSFSDistribution attribute) LocusConfig (class in phasegen.locus) LocusReward (class in phasegen.rewards) loss (Inference attribute) loss_inferred (Inference attribute) M m2 (FoldedSFSDistribution property) (PhaseTypeDistribution property) (TreeHeightDistribution property) (UnfoldedSFSDistribution property) MarginalDemeDistributions (class in phasegen.distributions) MarginalLocusDistributions (class in phasegen.distributions) mask_diagonal() (SFS2 method) mask_upper() (SFS2 method) max_epochs (TreeHeightDistribution attribute) max_iter (TreeHeightDistribution attribute) max_squarings (JaxExpmBackend attribute) mean (FoldedSFSDistribution property) (PhaseTypeDistribution property) (TreeHeightDistribution 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) (LineageCountingStateSpace attribute) (StateSpace 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) (PhaseTypeDistribution method) (TreeHeightDistribution method) (UnfoldedSFSDistribution method) MultinomialLikelihood (class in phasegen.norms) multiplier (PopulationSplit attribute) N n (LineageConfig attribute) (LocusConfig attribute) (SFS property) n_blocks (State 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) (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) (SFS method) (SFS2 method) plot_accumulation() (Coalescent method) (FoldedSFSDistribution method) (PhaseTypeDistribution method) (TreeHeightDistribution 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) (LineageCountingStateSpace method) (StateSpace method) plot_surface() (SFS2 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) resample (Inference attribute) resample() (SFS method) result (Inference attribute) Reward (class in phasegen.rewards) reward (FoldedSFSDistribution attribute) (PhaseTypeDistribution attribute) (TreeHeightDistribution attribute) (UnfoldedSFSDistribution attribute) run() (Inference method) runs (Inference attribute) S S (BlockCountingStateSpace property) (LineageCountingStateSpace property) (StateSpace property) 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) 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) (PhaseTypeDistribution attribute) (Transition attribute) (TreeHeightDistribution attribute) (UnfoldedSFSDistribution attribute) StateReward (class in phasegen.rewards) states (BlockCountingStateSpace property) (LineageCountingStateSpace property) (StateSpace property) StateSpace (class in phasegen.state_space) std (FoldedSFSDistribution property) (PhaseTypeDistribution property) (TreeHeightDistribution 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) T t_max (TreeHeightDistribution property) tau (Epoch property) TensorFlowExpmBackend (class in phasegen.expm) Theta (SFS property) theta (SFS property) time (BlockCountingStateSpace attribute) (LineageCountingStateSpace attribute) times (DiscreteDemographicEvent attribute) (DiscreteRateChanges attribute) (MigrationRateChange attribute) (MigrationRateChanges attribute) (PopSizeChange attribute) (PopSizeChanges attribute) (PopulationSplit attribute) (SymmetricMigrationRateChanges attribute) to_file() (Coalescent method) (Inference method) (SFS method) (SFS2 method) to_json() (Coalescent method) (Inference method) (SFS2 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) (PhaseTypeDistribution method) (TreeHeightDistribution method) (UnfoldedSFSDistribution method) trajectory (DiscretizedRateChange attribute) transit() (Transition method) transition (BlockCountingStateSpace property) Transition (class in phasegen.state_space) transition (LineageCountingStateSpace property) (StateSpace property) tree_height (Coalescent property) (FoldedSFSDistribution attribute) (PhaseTypeDistribution attribute) (TreeHeightDistribution attribute) (UnfoldedSFSDistribution attribute) TreeHeightDistribution (class in phasegen.distributions) TreeHeightReward (class in phasegen.rewards) U UnfoldedSFSDistribution (class in phasegen.distributions) UnfoldedSFSReward (class in phasegen.rewards) UnitReward (class in phasegen.rewards) unlinked (BlockCountingStateSpace property) (LineageCountingStateSpace property) (State property) (StateSpace property) update_epoch() (BlockCountingStateSpace method) (LineageCountingStateSpace method) (StateSpace method) use_pbar (Settings attribute) V values() (MarginalDemeDistributions method) (MarginalLocusDistributions method) var (FoldedSFSDistribution property) (PhaseTypeDistribution property) (TreeHeightDistribution property) (UnfoldedSFSDistribution property) W warn_n_epochs (Demography attribute) WeightedLoss (class in phasegen.inference) weights (WeightedLoss attribute) X x0 (Inference property)
