Index Symbols | _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W Symbols "Quantitative genetic simulation" "Standard population genetic simulation" _ __init__ (fwdpy11.DataMatrixIterator attribute) (fwdpy11.GSLrng attribute) (fwdpy11.NoAncientSamples attribute) (fwdpy11.RecordNothing attribute) __init__() (fwdpy11.custom_genetic_value_decorators method) (fwdpy11.PyDiploidGeneticValue method) A add_mutation() (fwdpy11.DiploidPopulation method) Additive (class in fwdpy11) AdditivePleiotropy (class in fwdpy11) AddMutationFailure alive_nodes (fwdpy11.DiploidPopulation property) AlleleCount (class in fwdpy11.conditional_models) AlleleCountRange (class in fwdpy11.conditional_models) ancestral_state (fwdpy11.Site attribute) ancient_sample_genetic_values (fwdpy11.DiploidPopulation attribute) ancient_sample_metadata (fwdpy11.DiploidPopulation property) ancient_sample_nodes (fwdpy11.DiploidPopulation property) AncientSamplePolicy (class in fwdpy11.conditional_models) asblack() (fwdpy11.Additive method) (fwdpy11.AdditivePleiotropy method) (fwdpy11.DemographicModelDetails method) (fwdpy11.GaussianNoise method) (fwdpy11.GBR method) (fwdpy11.ModelParams method) (fwdpy11.Multiplicative method) (fwdpy11.MutationAndRecombinationRates method) (fwdpy11.Optimum method) (fwdpy11.PleiotropicOptima method) asdict() (fwdpy11.Additive method) (fwdpy11.AdditivePleiotropy method) (fwdpy11.conditional_models.EvolveOptions method) (fwdpy11.DemographicModelDetails method) (fwdpy11.ForwardDemesGraph method) (fwdpy11.GaussianNoise method) (fwdpy11.GBR method) (fwdpy11.ModelParams method) (fwdpy11.Multiplicative method) (fwdpy11.MutationAndRecombinationRates method) (fwdpy11.Optimum method) (fwdpy11.PleiotropicOptima method) B BinomialInterval (class in fwdpy11) BinomialIntervalMap (class in fwdpy11) BinomialPoint (class in fwdpy11) build_indexes() (fwdpy11.TableCollection method) built-in function fwdpy11.additive_effects() fwdpy11.custom_genetic_value_decorators.default_update() fwdpy11.custom_genetic_value_decorators.genetic_value_is_trait_default_clone() fwdpy11.custom_genetic_value_decorators.genetic_value_noise_default_clone() fwdpy11.gsl_ran_flat() fwdpy11.gsl_ran_gaussian_ziggurat() fwdpy11.gsl_ran_geometric() fwdpy11.gsl_ran_poisson() fwdpy11.gsl_rng_uniform() fwdpy11.strict_additive_effects() burnin_duration (fwdpy11.ForwardDemesGraph property) C calculate_gvalue() (fwdpy11.PyDiploidGeneticValue method) child (fwdpy11.Edge attribute) COMPLETION (fwdpy11.conditional_models.AncientSamplePolicy attribute) ConditionalModelOutput (class in fwdpy11.conditional_models) ConstantS (class in fwdpy11) Continue (fwdpy11.conditional_models.SimulationStatus attribute) count (fwdpy11.conditional_models.AlleleCount attribute) create_from_tskit() (fwdpy11.DiploidPopulation class method) D data (fwdpy11.conditional_models.NewMutationParameters attribute) data_matrix_from_tables() (in module fwdpy11) DataMatrix (class in fwdpy11) DataMatrixIterator (class in fwdpy11) decode_individual_metadata() (in module fwdpy11.tskit_tools) decode_mutation_metadata() (in module fwdpy11.tskit_tools) deme (fwdpy11.conditional_models.FocalDemeFixation attribute) (fwdpy11.conditional_models.NewMutationParameters attribute) (fwdpy11.DiploidMetadata property) (fwdpy11.Node attribute) deme_labels (fwdpy11.DemographicModelDetails property) (fwdpy11.ForwardDemesGraph property) deme_sizes() (fwdpy11.DiploidPopulation method) deme_time_intervals() (fwdpy11.ForwardDemesGraph method) demes_at_final_generation (fwdpy11.ForwardDemesGraph property) demes_graph (fwdpy11.ForwardDemesGraph property) DemographicModelCitation (class in fwdpy11) DemographicModelDetails (class in fwdpy11) DemographyDebugger (class in fwdpy11) derived_state (fwdpy11.MutationRecord attribute) diploid_metadata (fwdpy11.DiploidPopulation property) DiploidGeneticValue (class in fwdpy11) DiploidGenotype (class in fwdpy11) DiploidMetadata (class in fwdpy11) (class in fwdpy11.tskit_tools) DiploidMetadataVector (class in fwdpy11) DiploidPopulation (class in fwdpy11) diploids (fwdpy11.DiploidPopulation property) DiploidVector (class in fwdpy11) direct DiscreteDESD (class in fwdpy11) dump_tables_to_tskit() (fwdpy11.DiploidPopulation method) dump_to_file() (fwdpy11.DiploidPopulation method) DURATION (fwdpy11.conditional_models.AncientSamplePolicy attribute) E e (fwdpy11.DiploidMetadata property) Edge (class in fwdpy11) edges (fwdpy11.TableCollection property) EdgeTable (class in fwdpy11) epoch_time_intervals() (fwdpy11.ForwardDemesGraph method) esizes (fwdpy11.Mutation attribute) EvolveOptions (class in fwdpy11.conditional_models) evolvets() (in module fwdpy11) ExponentialDominance (class in fwdpy11) ExpS (class in fwdpy11) F final_generation (fwdpy11.ForwardDemesGraph property) first (fwdpy11.DiploidGenotype attribute) fitness fixation_index (fwdpy11.conditional_models.ConditionalModelOutput attribute) fixation_times (fwdpy11.DiploidPopulation attribute) fixations (fwdpy11.DiploidPopulation attribute) FixedCrossovers (class in fwdpy11) FixedDominance (class in fwdpy11) FocalDemeFixation (class in fwdpy11.conditional_models) ForwardDemesGraph (class in fwdpy11) ForwardTimeInterval (class in fwdpy11) frequency (fwdpy11.conditional_models.NewMutationParameters attribute) FrequencyRange (class in fwdpy11.conditional_models) from_demes() (fwdpy11.ForwardDemesGraph class method) fromdict() (fwdpy11.Additive class method) (fwdpy11.AdditivePleiotropy class method) (fwdpy11.conditional_models.EvolveOptions class method) (fwdpy11.DemographicModelDetails class method) (fwdpy11.ForwardDemesGraph class method) (fwdpy11.GaussianNoise class method) (fwdpy11.GBR class method) (fwdpy11.ModelParams class method) (fwdpy11.Multiplicative class method) (fwdpy11.MutationAndRecombinationRates class method) (fwdpy11.Optimum class method) (fwdpy11.PleiotropicOptima class method) fwdpy11.additive_effects() built-in function fwdpy11.conditional_models module fwdpy11.custom_genetic_value_decorators.default_update() built-in function fwdpy11.custom_genetic_value_decorators.genetic_value_is_trait_default_clone() built-in function fwdpy11.custom_genetic_value_decorators.genetic_value_noise_default_clone() built-in function fwdpy11.DiploidGeneticValueNoiseData (built-in class) fwdpy11.DiploidGeneticValueToFitnessData (built-in class) fwdpy11.gsl_ran_flat() built-in function fwdpy11.gsl_ran_gaussian_ziggurat() built-in function fwdpy11.gsl_ran_geometric() built-in function fwdpy11.gsl_ran_poisson() built-in function fwdpy11.gsl_rng_uniform() built-in function fwdpy11.PyDiploidGeneticValue (built-in class) fwdpy11.PyDiploidGeneticValueData (built-in class) fwdpy11.strict_additive_effects() built-in function fwdpy11.tskit_tools module fwdpy11.tskit_tools.INDIVIDUAL_IS_ALIVE (in module fwdpy11.tskit_tools) fwdpy11.tskit_tools.INDIVIDUAL_IS_FIRST_GENERATION (in module fwdpy11.tskit_tools) fwdpy11.tskit_tools.INDIVIDUAL_IS_PRESERVED (in module fwdpy11.tskit_tools) G g (fwdpy11.DiploidMetadata property) (fwdpy11.Mutation attribute) GammaS (class in fwdpy11) GaussianNoise (class in fwdpy11) GaussianS (class in fwdpy11) GaussianStabilizingSelection (class in fwdpy11) GBR (class in fwdpy11) generation (fwdpy11.DiploidPopulation attribute) genetic value genetic_value_to_fitness() (fwdpy11.PyDiploidGeneticValue method) genetic_values (fwdpy11.Additive property) (fwdpy11.AdditivePleiotropy property) (fwdpy11.DiploidGeneticValue property) (fwdpy11.DiploidPopulation attribute) (fwdpy11.GBR property) (fwdpy11.Multiplicative property) GeneticValueIsFitness (class in fwdpy11) GeneticValueIsTrait (class in fwdpy11) GeneticValueNoise (class in fwdpy11) GeneticValueToFitnessMap (class in fwdpy11) genome_length (fwdpy11.TableCollection property) genotypes (fwdpy11.VariantIterator property) geography (fwdpy11.DiploidMetadata property) get_toplevel_metadata() (in module fwdpy11.tskit_tools) GlobalFixation (class in fwdpy11.conditional_models) GSLrng (class in fwdpy11) H h (fwdpy11.Mutation attribute) haploid_genomes (fwdpy11.DiploidPopulation attribute) HaploidGenome (class in fwdpy11) HaploidGenomeVector (class in fwdpy11) heffects (fwdpy11.Mutation attribute) I indirect infinite_sites() (in module fwdpy11) initial_sizes (fwdpy11.ForwardDemesGraph property) initial_sizes_list (fwdpy11.DemographicModelDetails property) input_left (fwdpy11.TableCollection property) iterate_timepoints_with_individuals() (in module fwdpy11.tskit_tools) K key (fwdpy11.MutationRecord attribute) L label (fwdpy11.DiploidMetadata property) (fwdpy11.Mutation attribute) LargeEffectExponentiallyRecessive (class in fwdpy11) leaf_counts() (fwdpy11.TreeIterator method) left (fwdpy11.conditional_models.PositionRange attribute) (fwdpy11.Edge attribute) (fwdpy11.TreeIterator property) left_child() (fwdpy11.TreeIterator method) left_sib() (fwdpy11.TreeIterator method) load_from_file() (fwdpy11.DiploidPopulation class method) load_from_pickle_file() (fwdpy11.DiploidPopulation class method) LogNormalS (class in fwdpy11) M maps_to_fitness (fwdpy11.Additive property) (fwdpy11.AdditivePleiotropy property) (fwdpy11.DiploidGeneticValue property) (fwdpy11.GBR property) (fwdpy11.GeneticValueToFitnessMap property) (fwdpy11.Multiplicative property) maps_to_trait_value (fwdpy11.Additive property) (fwdpy11.AdditivePleiotropy property) (fwdpy11.DiploidGeneticValue property) (fwdpy11.GBR property) (fwdpy11.GeneticValueToFitnessMap property) (fwdpy11.Multiplicative property) maximum (fwdpy11.conditional_models.AlleleCountRange attribute) (fwdpy11.conditional_models.FrequencyRange attribute) merge() (fwdpy11.DataMatrix method) minimum (fwdpy11.conditional_models.AlleleCountRange attribute) (fwdpy11.conditional_models.FrequencyRange attribute) model_duration (fwdpy11.ForwardDemesGraph property) ModelParams (class in fwdpy11) module fwdpy11.conditional_models fwdpy11.tskit_tools Multiplicative (class in fwdpy11) MultivariateGaussianEffects (class in fwdpy11) Mutation (class in fwdpy11) mutation_index (fwdpy11.conditional_models.ConditionalModelOutput attribute) MutationAndRecombinationRates (class in fwdpy11) MutationDominance (class in fwdpy11) MutationRecord (class in fwdpy11) mutations (fwdpy11.DiploidPopulation attribute) (fwdpy11.HaploidGenome attribute) (fwdpy11.TableCollection property) mutations() (fwdpy11.TreeIterator method) MutationTable (class in fwdpy11) MutationVector (class in fwdpy11) mv() (fwdpy11.LogNormalS class method) mvDES (class in fwdpy11) N n (fwdpy11.HaploidGenome attribute) ncol (fwdpy11.DataMatrix property) neutral (fwdpy11.DataMatrix property) (fwdpy11.DataMatrixIterator attribute) (fwdpy11.MutationRecord attribute) neutral_keys (fwdpy11.DataMatrix property) (fwdpy11.DataMatrixIterator attribute) neutral_matrix() (fwdpy11.DataMatrix method) neutral_positions (fwdpy11.DataMatrixIterator attribute) NEVER (fwdpy11.conditional_models.AncientSamplePolicy attribute) NewMutationData (class in fwdpy11) NewMutationParameters (class in fwdpy11.conditional_models) NoAncientSamples (class in fwdpy11) Node (class in fwdpy11) node (fwdpy11.MutationRecord attribute) nodes (fwdpy11.DiploidMetadata property) (fwdpy11.TableCollection property) nodes() (fwdpy11.TreeIterator method) NodeTable (class in fwdpy11) NoNoise (class in fwdpy11) num_descendant_nodes (fwdpy11.conditional_models.ConditionalModelOutput attribute) O offspring_metadata (fwdpy11.DiploidGeneticValueNoiseData attribute) (fwdpy11.DiploidGeneticValueToFitnessData attribute) offspring_metadata_index (fwdpy11.DiploidGeneticValueNoiseData attribute) (fwdpy11.DiploidGeneticValueToFitnessData attribute) Optimum (class in fwdpy11) OutOfAttempts output_right (fwdpy11.TableCollection property) P params (fwdpy11.conditional_models.ConditionalModelOutput attribute) parent (fwdpy11.Edge attribute) parent() (fwdpy11.TreeIterator method) parent1_metadata (fwdpy11.DiploidGeneticValueNoiseData attribute) (fwdpy11.DiploidGeneticValueToFitnessData attribute) parent2_metadata (fwdpy11.DiploidGeneticValueNoiseData attribute) (fwdpy11.DiploidGeneticValueToFitnessData attribute) parents (fwdpy11.DiploidMetadata property) pickle_to_file() (fwdpy11.DiploidPopulation method) PleiotropicOptima (class in fwdpy11) pleiotropy() (fwdpy11.GaussianStabilizingSelection class method) PoissonInterval (class in fwdpy11) PoissonPoint (class in fwdpy11) pop (fwdpy11.conditional_models.ConditionalModelOutput attribute) pos (fwdpy11.Mutation attribute) position (fwdpy11.conditional_models.NewMutationParameters attribute) (fwdpy11.Site attribute) (fwdpy11.VariantIterator property) PositionRange (class in fwdpy11.conditional_models) positions (fwdpy11.StateMatrix property) preserve_first_generation (fwdpy11.conditional_models.EvolveOptions attribute) preserved_leaf_counts() (fwdpy11.TreeIterator method) preserved_nodes (fwdpy11.DiploidPopulation property) R RandomAncientSamples (class in fwdpy11) record_gvalue_matrix (fwdpy11.conditional_models.EvolveOptions attribute) RecordNothing (class in fwdpy11) records (fwdpy11.VariantIterator property) Region (class in fwdpy11) Restart (fwdpy11.conditional_models.SimulationStatus attribute) right (fwdpy11.conditional_models.PositionRange attribute) (fwdpy11.Edge attribute) (fwdpy11.TreeIterator property) right_child() (fwdpy11.TreeIterator method) right_sib() (fwdpy11.TreeIterator method) rng (fwdpy11.DiploidGeneticValueNoiseData attribute) roots (fwdpy11.TreeIterator property) S s (fwdpy11.Mutation attribute) sample_timepoints() (fwdpy11.DiploidPopulation method) SampleRecorder (class in fwdpy11) SampleRecorder.add_sample() (in module fwdpy11.SampleRecorder) SampleRecorder.assign() (in module fwdpy11.SampleRecorder) samples() (fwdpy11.TreeIterator method) samples_below() (fwdpy11.TreeIterator method) second (fwdpy11.DiploidGenotype attribute) selected (fwdpy11.DataMatrix property) (fwdpy11.DataMatrixIterator attribute) selected_keys (fwdpy11.DataMatrix property) (fwdpy11.DataMatrixIterator attribute) selected_matrix() (fwdpy11.DataMatrix method) selected_positions (fwdpy11.DataMatrixIterator attribute) selective_sweep() (in module fwdpy11.conditional_models) sex (fwdpy11.DiploidMetadata property) shape (fwdpy11.Additive property) (fwdpy11.AdditivePleiotropy property) (fwdpy11.DiploidGeneticValue property) (fwdpy11.GBR property) (fwdpy11.GeneticValueToFitnessMap property) (fwdpy11.Multiplicative property) (fwdpy11.StateMatrix property) simplification_interval (fwdpy11.conditional_models.EvolveOptions attribute) simplify_tables() (in module fwdpy11) SimulationStatus (class in fwdpy11.conditional_models) single_trait() (fwdpy11.GaussianStabilizingSelection class method) Site (class in fwdpy11) site (fwdpy11.MutationRecord attribute) (fwdpy11.VariantIterator property) sites (fwdpy11.TableCollection property) sites() (fwdpy11.TreeIterator method) SiteTable (class in fwdpy11) smutations (fwdpy11.HaploidGenome attribute) Sregion (class in fwdpy11) StateMatrix (class in fwdpy11) Success (fwdpy11.conditional_models.SimulationStatus attribute) suppress_table_indexing (fwdpy11.conditional_models.EvolveOptions attribute) T TableCollection (class in fwdpy11) tables (fwdpy11.DiploidPopulation property) (fwdpy11.TreeIterator property) time (fwdpy11.Node attribute) to_backwards_time() (fwdpy11.ForwardDemesGraph method) to_forwards_time() (fwdpy11.ForwardDemesGraph method) total_simulation_length (fwdpy11.DemographicModelDetails property) total_time() (fwdpy11.TreeIterator method) track_added_mutation() (in module fwdpy11.conditional_models) trait value TreeIterator (class in fwdpy11) tubes() (fwdpy11.ForwardDemesGraph class method) U UniformDominance (class in fwdpy11) UniformS (class in fwdpy11) update() (fwdpy11.PyDiploidGeneticValue method) V VariantIterator (class in fwdpy11) W w (fwdpy11.DiploidMetadata property)