Index

_

_array_type (xftsim.struct.XftAccessor attribute) _col_dim (xftsim.struct.XftAccessor attribute) _component_vars (xftsim.struct.XftAccessor attribute) _compute_component (xftsim.arch.ArchitectureComponent attribute) _fid (xftsim.ped.Pedigree attribute) _generation (xftsim.ped.Pedigree attribute)

_generational_depth (xftsim.ped.Pedigree attribute) _non_annotation_vars (xftsim.struct.XftAccessor attribute) _obj (xftsim.struct.XftAccessor attribute) _row_dim (xftsim.struct.XftAccessor attribute) _sample_vars (xftsim.struct.XftAccessor attribute) _variant_vars (xftsim.struct.XftAccessor attribute)

A

AdditiveEffects (class in xftsim.effect) AdditiveGeneticComponent (class in xftsim.arch) AdditiveNoiseComponent (class in xftsim.arch) AF (xftsim.effect.AdditiveEffects attribute) af (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) af_empirical (xftsim.struct.XftAccessor property) all_components (xftsim.struct.XftAccessor property) all_phenotypes (xftsim.struct.XftAccessor property) all_relatives (xftsim.struct.XftAccessor property) annotate() (xftsim.index.DiploidVariantIndex method) annotation (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property)

annotation_array (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) annotation_names (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) apply_filter() (xftsim.sim.Simulation method) apply_threshold_PGS() (in module xftsim.stats) apply_threshold_PGS_all() (in module xftsim.stats) Architecture (class in xftsim.arch) architecture (xftsim.sim.Simulation attribute) ArchitectureComponent (class in xftsim.arch) as_pd() (xftsim.struct.XftAccessor method) at_most() (xftsim.index.XftIndex method)

B

batch() (xftsim.mate.BatchedMatingRegime method), [1] BatchedMatingRegime (class in xftsim.mate) beta_raw_diploid (xftsim.effect.AdditiveEffects attribute) (xftsim.effect.AdditiveEffects property) beta_raw_haploid (xftsim.effect.AdditiveEffects attribute) (xftsim.effect.AdditiveEffects property) beta_scaled_standardized_diploid (xftsim.effect.AdditiveEffects attribute) beta_scaled_standardized_haploid (xftsim.effect.AdditiveEffects attribute) (xftsim.effect.AdditiveEffects property)

beta_scaled_unstandardized_diploid (xftsim.effect.AdditiveEffects attribute) beta_scaled_unstandardized_haploid (xftsim.effect.AdditiveEffects attribute) (xftsim.effect.AdditiveEffects property) beta_unscaled_standardized_diploid (xftsim.effect.AdditiveEffects attribute) beta_unscaled_standardized_haploid (xftsim.effect.AdditiveEffects attribute) (xftsim.effect.AdditiveEffects property) beta_unscaled_unstandardized_diploid (xftsim.effect.AdditiveEffects attribute) beta_unscaled_unstandardized_haploid (xftsim.effect.AdditiveEffects attribute) (xftsim.effect.AdditiveEffects property) BinarizingTransformation (class in xftsim.arch)

C

cartesian_product() (in module xftsim.utils) check_dependencies() (xftsim.arch.Architecture method) chrom (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) chroms (xftsim.struct.GeneticMap attribute) coefficient_matrix (xftsim.arch.LinearTransformationComponent attribute) (xftsim.arch.LinearVerticalComponent attribute) column_vars (xftsim.struct.XftAccessor attribute) (xftsim.struct.XftAccessor property) comp_type (xftsim.index.ComponentIndex property) component_index (xftsim.arch.GaussianFounderInitialization attribute) (xftsim.mate.GeneralAssortativeMatingRegime attribute) (xftsim.stats.GWAS_Estimator attribute) (xftsim.stats.HasemanElstonEstimator attribute) (xftsim.stats.HasemanElstonEstimatorSibship attribute) (xftsim.stats.Pop_GWAS_Estimator attribute) (xftsim.stats.SampleStatistics attribute) (xftsim.stats.Sib_GWAS_Estimator attribute) component_indexer (xftsim.effect.AdditiveEffects attribute) component_mindex (xftsim.struct.XftAccessor attribute) (xftsim.struct.XftAccessor property) component_name (xftsim.arch.ArchitectureComponent property) (xftsim.index.ComponentIndex attribute) (xftsim.index.ComponentIndex property) ComponentIndex (class in xftsim.index) components (xftsim.arch.Architecture attribute) compute_component() (xftsim.arch.AdditiveGeneticComponent method) (xftsim.arch.AdditiveNoiseComponent method) (xftsim.arch.ArchitectureComponent method) (xftsim.arch.BinarizingTransformation method) (xftsim.arch.CorrelatedNoiseComponent method) (xftsim.arch.LinearTransformationComponent method) (xftsim.arch.ProductComponent method) (xftsim.arch.SumAllTransformation method) (xftsim.arch.SumTransformation method)

compute_phenotypes() (xftsim.arch.Architecture method), [1] (xftsim.sim.Simulation method) constant_map_from_haplotypes() (xftsim.reproduce.RecombinationMap static method) ConstantCount (class in xftsim.utils) ConstantFounderInitialization (class in xftsim.arch) construct_cindexes() (xftsim.arch.BinarizingTransformation static method) (xftsim.arch.SumTransformation static method) construct_input_cindex() (xftsim.arch.BinarizingTransformation static method) (xftsim.arch.SumAllTransformation static method) (xftsim.arch.SumTransformation static method) construct_output_cindex() (xftsim.arch.BinarizingTransformation static method) (xftsim.arch.SumTransformation static method) control (xftsim.sim.Simulation attribute), [1] (xftsim.sim.Simulation property) coord_dict (xftsim.index.XftIndex property) coord_frame (xftsim.index.XftIndex property) coord_index (xftsim.index.XftIndex property) coord_mindex (xftsim.index.XftIndex property) coords (xftsim.index.XftIndex property) corr (xftsim.stats.SampleStatistics attribute) corr() (xftsim.effect.AdditiveEffects method) CorrelatedNoiseComponent (class in xftsim.arch) cov2cor() (in module xftsim.utils) cross_corr (xftsim.mate.GeneralAssortativeMatingRegime attribute) current_afs_empirical (xftsim.sim.Simulation attribute) (xftsim.sim.Simulation property) current_std_genotypes (xftsim.sim.Simulation attribute) (xftsim.sim.Simulation property) current_std_genotypes_filtered (xftsim.sim.Simulation property) current_std_phenotypes (xftsim.sim.Simulation attribute) (xftsim.sim.Simulation property) current_std_phenotypes_filtered (xftsim.sim.Simulation property)

D

dask (xftsim.stats.HasemanElstonEstimator attribute) (xftsim.stats.HasemanElstonEstimatorSibship attribute) data (xftsim.struct.XftAccessor attribute) (xftsim.struct.XftAccessor property) default_input_cindex() (xftsim.arch.ArchitectureComponent static method) default_output_cindex() (xftsim.arch.ArchitectureComponent static method) demo_routines (xftsim.sim.DemoSimulation attribute) DemoSimulation (class in xftsim.sim) dependency_graph (xftsim.arch.Architecture property) (xftsim.arch.ArchitectureComponent property) (xftsim.mate.MatingRegime property) (xftsim.sim.Simulation property) dependency_graph_edges (xftsim.arch.Architecture property) (xftsim.arch.ArchitectureComponent property) (xftsim.mate.MatingRegime property) (xftsim.sim.Simulation property)

depth (xftsim.arch.Architecture attribute) (xftsim.index.ComponentIndex attribute) (xftsim.index.ComponentIndex property) (xftsim.struct.XftAccessor property) diploid_chrom (xftsim.struct.XftAccessor property) diploid_vid (xftsim.struct.XftAccessor property) DiploidVariantIndex (class in xftsim.index) draw (xftsim.utils.ConstantCount attribute) (xftsim.utils.MixtureCount attribute) (xftsim.utils.NegativeBinomialCount attribute) (xftsim.utils.VariableCount attribute) (xftsim.utils.ZeroTruncatedPoissonCount attribute) draw_dependency_graph() (xftsim.arch.Architecture method) (xftsim.arch.ArchitectureComponent method) (xftsim.mate.MatingRegime method) (xftsim.sim.Simulation method)

E

effects (xftsim.arch.AdditiveGeneticComponent attribute) ensure2D() (in module xftsim.utils) enumerate_assignment() (xftsim.mate.MatingRegime method), [1] estimate() (xftsim.stats.Statistic method), [1] estimate_statistics() (xftsim.sim.Simulation method) estimator (xftsim.stats.Statistic attribute) estimator() (xftsim.stats.GWAS_Estimator method) (xftsim.stats.HasemanElstonEstimator method), [1] (xftsim.stats.HasemanElstonEstimatorSibship method), [1] (xftsim.stats.MatingStatistics method), [1] (xftsim.stats.Pop_GWAS_Estimator method) (xftsim.stats.SampleStatistics method), [1] (xftsim.stats.Sib_GWAS_Estimator method) exhaustive (xftsim.mate.MatingRegime attribute) exhaustive_enumerate() (in module xftsim.utils)

exhaustive_permutation() (in module xftsim.utils) expand_components (xftsim.arch.Architecture attribute) expectation (xftsim.utils.ConstantCount attribute) (xftsim.utils.MixtureCount attribute) (xftsim.utils.NegativeBinomialCount attribute) (xftsim.utils.PoissonCount attribute) (xftsim.utils.VariableCount attribute) (xftsim.utils.VariableCount property) (xftsim.utils.ZeroTruncatedPoissonCount attribute) expected_female_offspring_per_pair (xftsim.mate.MatingRegime attribute) (xftsim.mate.MatingRegime property) expected_mates_per_female (xftsim.mate.MatingRegime attribute) (xftsim.mate.MatingRegime property) expected_offspring_per_pair (xftsim.mate.MatingRegime attribute) (xftsim.mate.MatingRegime property)

F

female_offspring_per_pair (xftsim.mate.MatingRegime attribute) fid (xftsim.index.SampleIndex attribute) (xftsim.index.SampleIndex property) filter() (xftsim.index.SampleFilter method) filter_sample (xftsim.stats.Statistic attribute) FilteredMatingRegime (class in xftsim.mate) founder_haplotypes_from_AFs() (in module xftsim.founders) founder_haplotypes_from_plink_bfile() (in module xftsim.founders) founder_haplotypes_from_sgkit_dataset() (in module xftsim.founders) founder_haplotypes_uniform_AFs() (in module xftsim.founders) founder_initialization (xftsim.arch.ArchitectureComponent attribute) (xftsim.arch.SumAllTransformation attribute) (xftsim.arch.SumTransformation attribute)

founder_initializations (xftsim.arch.Architecture property) founder_initializations() (xftsim.arch.Architecture method) FounderInitialization (class in xftsim.arch) frame (xftsim.index.XftIndex property) (xftsim.struct.GeneticMap attribute) frame_copy() (xftsim.index.XftIndex method) from_arrays() (xftsim.index.ComponentIndex method) (xftsim.index.ComponentIndex static method) from_frame() (xftsim.index.ComponentIndex method) (xftsim.index.ComponentIndex static method) from_product() (xftsim.index.ComponentIndex method) (xftsim.index.ComponentIndex static method) (xftsim.struct.PhenotypeArray static method) from_pyrho_maps() (xftsim.struct.GeneticMap class method)

G

G (xftsim.ped.Pedigree attribute) GaussianFounderInitialization (class in xftsim.arch) GCTA_Architecture (class in xftsim.arch) GCTAEffects (class in xftsim.effect) GeneralAssortativeMatingRegime (class in xftsim.mate) generation (xftsim.sim.Simulation attribute) (xftsim.sim.Simulation property) (xftsim.struct.XftAccessor property) generation() (xftsim.ped.Pedigree method) generational_depth (xftsim.ped.Pedigree property) generations() (xftsim.ped.Pedigree method) genetic_correlation (xftsim.stats.HasemanElstonEstimator attribute) (xftsim.stats.HasemanElstonEstimatorSibship attribute) GeneticMap (class in xftsim.struct) genotypes_to_pseudo_haplotypes() (in module xftsim.io) get_annotation_dict() (xftsim.struct.XftAccessor method) get_column_indexer() (xftsim.struct.XftAccessor method)

get_comp_type() (xftsim.struct.XftAccessor method) get_component_indexer() (xftsim.struct.XftAccessor method) get_current_generation() (xftsim.ped.Pedigree method) get_intermediate_components() (xftsim.struct.XftAccessor method) get_k_rel() (xftsim.struct.XftAccessor method) get_mate_phenotypes() (xftsim.mate.MateAssignment method) get_mating_frame() (xftsim.mate.MateAssignment method) get_most_recent_K_generations() (xftsim.ped.Pedigree method) get_non_annotation_dict() (xftsim.struct.XftAccessor method) get_outcome_components() (xftsim.struct.XftAccessor method) get_potential_mates() (xftsim.mate.MatingRegime method), [1] get_recombination_map() (xftsim.reproduce.Meiosis method) get_reproduction_frame() (xftsim.mate.MateAssignment method) get_row_indexer() (xftsim.struct.XftAccessor method) get_sample_indexer() (xftsim.struct.XftAccessor method) get_variant_indexer() (xftsim.struct.XftAccessor method) grep_component_index() (xftsim.struct.XftAccessor method) GWAS_Estimator (class in xftsim.stats)

H

HaploidVariantIndex (class in xftsim.index) haplotype_store (xftsim.sim.Simulation attribute) HaplotypeArray (class in xftsim.struct) haplotypes (xftsim.sim.Simulation attribute) (xftsim.sim.Simulation property) haplotypes_filtered (xftsim.sim.Simulation property) haplotypes_from_sgkit_dataset() (in module xftsim.io)

haseman_elston() (in module xftsim.stats) HasemanElstonEstimator (class in xftsim.stats) HasemanElstonEstimatorSibship (class in xftsim.stats) hcopy (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) hierarchical_subsample() (in module xftsim.utils) HorizontalComponent (class in xftsim.arch)

I

ids_from_generation() (in module xftsim.utils) ids_from_generation_range() (in module xftsim.utils) ids_from_n_generation() (in module xftsim.utils) iid (xftsim.index.SampleIndex attribute) (xftsim.index.SampleIndex property) iloc() (xftsim.index.SampleIndex method) (xftsim.index.XftIndex method) increment_generation() (xftsim.sim.Simulation method) InfinitessimalArchitecture (class in xftsim.arch) initialize_component() (xftsim.arch.FounderInitialization method) initialize_founder_phenotype_array() (xftsim.arch.Architecture method), [1] initialize_phenotype_array() (xftsim.arch.Architecture method), [1]

input_cindex (xftsim.arch.ArchitectureComponent attribute) (xftsim.arch.SumAllTransformation attribute) (xftsim.arch.SumTransformation attribute) input_component_name (xftsim.arch.ArchitectureComponent property) input_haplotypes (xftsim.arch.ArchitectureComponent attribute) (xftsim.arch.SumAllTransformation attribute) (xftsim.arch.SumTransformation attribute) input_phenotype_name (xftsim.arch.ArchitectureComponent property) input_vorigin_relative (xftsim.arch.ArchitectureComponent property) interpolate_cM() (xftsim.struct.XftAccessor method) interpolate_cM_chrom() (xftsim.struct.GeneticMap method) is_constant_population (xftsim.mate.MateAssignment property)

K

k (xftsim.effect.AdditiveEffects attribute) K (xftsim.mate.GeneralAssortativeMatingRegime attribute) k_components (xftsim.index.ComponentIndex attribute) (xftsim.index.ComponentIndex property) (xftsim.struct.XftAccessor property) k_current (xftsim.struct.XftAccessor property) k_phenotypes (xftsim.index.ComponentIndex attribute) (xftsim.index.ComponentIndex property) (xftsim.struct.XftAccessor property)

k_relative (xftsim.index.ComponentIndex attribute) (xftsim.index.ComponentIndex property) (xftsim.struct.XftAccessor property) k_total (xftsim.index.ComponentIndex attribute) (xftsim.index.ComponentIndex property) (xftsim.struct.XftAccessor property)

L

LimitMemory (class in xftsim.proc) linear_transformation (xftsim.arch.LinearTransformationComponent property) LinearAssortativeMatingRegime (class in xftsim.mate)

LinearTransformationComponent (class in xftsim.arch) LinearVerticalComponent (class in xftsim.arch) load_haplotype_zarr() (in module xftsim.io)

M

m (xftsim.effect.AdditiveEffects attribute) (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) (xftsim.struct.XftAccessor property) m_causal (xftsim.effect.AdditiveEffects property) maf (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) maf_empirical (xftsim.struct.XftAccessor property) match() (in module xftsim.utils) matching_indices_conditional() (in module xftsim.utils) mate() (xftsim.mate.BatchedMatingRegime method), [1] (xftsim.mate.FilteredMatingRegime method) (xftsim.mate.GeneralAssortativeMatingRegime method), [1] (xftsim.mate.LinearAssortativeMatingRegime method) (xftsim.mate.MatingRegime method), [1] (xftsim.mate.RandomMatingRegime method) (xftsim.sim.Simulation method) MateAssignment (class in xftsim.mate) mateFunction (xftsim.mate.MatingRegime attribute) (xftsim.mate.MatingRegime property) maternal_integer_index (xftsim.mate.MateAssignment property) mates_per_female (xftsim.mate.MatingRegime attribute) mating (xftsim.sim.Simulation attribute) (xftsim.sim.Simulation property) mating_regime (xftsim.sim.Simulation attribute) mating_store (xftsim.sim.Simulation attribute) MatingRegime (class in xftsim.mate) MatingStatistics (class in xftsim.stats)

max_batch_size (xftsim.mate.BatchedMatingRegime attribute) means (xftsim.arch.GaussianFounderInitialization attribute) (xftsim.stats.SampleStatistics attribute) Meiosis (class in xftsim.reproduce) meiosis() (in module xftsim.reproduce) merge() (xftsim.index.XftIndex method) merge_duplicate_pairs() (in module xftsim.utils) merge_duplicates() (in module xftsim.utils) merged_component_indexer (xftsim.arch.Architecture property) merged_component_indexer() (xftsim.arch.Architecture method) merged_phenotype_indexer (xftsim.arch.ArchitectureComponent property) metadata (xftsim.arch.Architecture attribute) (xftsim.sim.Simulation attribute) (xftsim.stats.Statistic attribute) MixtureCount (class in xftsim.utils) module xftsim.arch xftsim.effect xftsim.founders xftsim.index xftsim.io xftsim.mate xftsim.ped xftsim.proc xftsim.reproduce xftsim.sim xftsim.stats xftsim.struct xftsim.utils move_forward() (xftsim.sim.Simulation method)

N

n (xftsim.index.SampleIndex attribute) (xftsim.index.SampleIndex property) (xftsim.struct.XftAccessor attribute) (xftsim.struct.XftAccessor property) n_annotations (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) n_chrom (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) n_fam (xftsim.index.SampleIndex attribute) (xftsim.index.SampleIndex property) n_female (xftsim.index.SampleIndex attribute) (xftsim.index.SampleIndex property) n_females (xftsim.mate.MateAssignment property) n_male (xftsim.index.SampleIndex attribute) (xftsim.index.SampleIndex property) n_males (xftsim.mate.MateAssignment property)

n_probe (xftsim.stats.HasemanElstonEstimator attribute) (xftsim.stats.HasemanElstonEstimatorSibship attribute) n_reproducing_pairs (xftsim.mate.MateAssignment property) n_total_offspring (xftsim.mate.MateAssignment property) name (xftsim.stats.Statistic attribute) NegativeBinomialCount (class in xftsim.utils) None() (xftsim.utils.VariableCount method) NonOverlappingEffects (class in xftsim.effect) nonzero_fraction (xftsim.utils.ConstantCount attribute) (xftsim.utils.MixtureCount attribute) (xftsim.utils.NegativeBinomialCount attribute) (xftsim.utils.PoissonCount attribute) (xftsim.utils.VariableCount attribute) (xftsim.utils.VariableCount property) (xftsim.utils.ZeroTruncatedPoissonCount attribute) normalize (xftsim.arch.LinearTransformationComponent attribute) (xftsim.arch.LinearVerticalComponent attribute) null_parser() (xftsim.stats.Statistic static method) NullFilter (class in xftsim.index)

O

offset (xftsim.effect.AdditiveEffects attribute) (xftsim.effect.AdditiveEffects property) offspring_fids (xftsim.mate.MateAssignment property) offspring_iids (xftsim.mate.MateAssignment property) offspring_per_pair (xftsim.mate.MatingRegime attribute) offspring_sample_index (xftsim.mate.MateAssignment property) offspring_sex (xftsim.mate.MateAssignment property) one_allele (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute)

output_cindex (xftsim.arch.ArchitectureComponent attribute) (xftsim.arch.SumAllTransformation attribute) (xftsim.arch.SumTransformation attribute) output_component_name (xftsim.arch.ArchitectureComponent property) output_phenotype_name (xftsim.arch.ArchitectureComponent property) output_vorigin_relative (xftsim.arch.ArchitectureComponent property)

P

p (xftsim.reproduce.Meiosis attribute) parent_haplotypes (xftsim.sim.Simulation attribute) (xftsim.sim.Simulation property) parent_mating (xftsim.sim.Simulation attribute) (xftsim.sim.Simulation property) parent_phenotypes (xftsim.sim.Simulation attribute) (xftsim.sim.Simulation property) parse_results() (xftsim.stats.Statistic method) paste() (in module xftsim.utils) paternal_integer_index (xftsim.mate.MateAssignment property) Pedigree (class in xftsim.ped) pedigree (xftsim.sim.Simulation attribute) phenotype_name (xftsim.arch.ArchitectureComponent property) (xftsim.index.ComponentIndex attribute) (xftsim.index.ComponentIndex property) phenotype_store (xftsim.sim.Simulation attribute) PhenotypeArray (class in xftsim.struct) phenotypes (xftsim.sim.Simulation attribute) (xftsim.sim.Simulation property) phenotypes_filtered (xftsim.sim.Simulation property) pickle_results() (xftsim.sim.Simulation method) plink1_sample_index() (in module xftsim.io) plink1_variant_index() (in module xftsim.io) ploidy (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) (xftsim.index.HaploidVariantIndex property)

PoissonCount (class in xftsim.utils) Pop_GWAS_Estimator (class in xftsim.stats) population_growth_factor (xftsim.mate.MatingRegime attribute) (xftsim.mate.MatingRegime property) pos_bp (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) pos_cM (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) post_processors (xftsim.sim.Simulation attribute) PostProcessor (class in xftsim.proc) prettify (xftsim.stats.HasemanElstonEstimator attribute) (xftsim.stats.HasemanElstonEstimatorSibship attribute) (xftsim.stats.SampleStatistics attribute) print_tree() (in module xftsim.utils) process() (xftsim.proc.PostProcessor method) (xftsim.sim.Simulation method) processor() (xftsim.proc.LimitMemory method) ProductComponent (class in xftsim.arch) profiled() (in module xftsim.utils) prune_generation() (xftsim.sim.Simulation method) prune_old_generations() (xftsim.sim.Simulation method)

R

randomized (xftsim.stats.HasemanElstonEstimator attribute) (xftsim.stats.HasemanElstonEstimatorSibship attribute) RandomMatingRegime (class in xftsim.mate) RandomSiblingFilter (class in xftsim.index) RandomSiblingSubsampleFilter (class in xftsim.index) RandomSubsampleFilter (class in xftsim.index) range_index() (xftsim.index.ComponentIndex method) (xftsim.index.ComponentIndex static method) read_plink1_as_pseudohaplotypes() (in module xftsim.io) recombination_map (xftsim.sim.Simulation attribute) RecombinationMap (class in xftsim.reproduce) recombinationMap (xftsim.reproduce.Meiosis attribute) reduce_merge() (xftsim.index.XftIndex static method) (xftsim.mate.MateAssignment static method)

regime (xftsim.mate.BatchedMatingRegime attribute) reindex_components() (xftsim.struct.XftAccessor method) reproduce() (xftsim.reproduce.Meiosis method) (xftsim.sim.Simulation method) reproducing_maternal_index (xftsim.mate.MateAssignment property) reproducing_paternal_index (xftsim.mate.MateAssignment property) reproduction_method (xftsim.sim.Simulation attribute) results (xftsim.sim.Simulation attribute) (xftsim.sim.Simulation property) results_store (xftsim.sim.Simulation attribute) row_vars (xftsim.struct.XftAccessor attribute) (xftsim.struct.XftAccessor property) run() (xftsim.sim.Simulation method) run_generation() (xftsim.sim.Simulation method)

S

sample_mindex (xftsim.struct.XftAccessor attribute) (xftsim.struct.XftAccessor property) SampleFilter (class in xftsim.index) SampleIndex (class in xftsim.index) sampleIndex_from_plink() (in module xftsim.index) sampleIndex_from_VCF() (in module xftsim.index) SampleStatistics (class in xftsim.stats) save_haplotype_zarr() (in module xftsim.io) sds (xftsim.arch.AdditiveNoiseComponent attribute) (xftsim.arch.GaussianFounderInitialization attribute) set_column_indexer() (xftsim.struct.XftAccessor method) set_row_indexer() (xftsim.struct.XftAccessor method) set_sample_indexer() (xftsim.struct.XftAccessor method) set_variant_indexer() (xftsim.struct.XftAccessor method) sex (xftsim.index.SampleIndex attribute) (xftsim.index.SampleIndex property) sex_aware (xftsim.mate.MatingRegime attribute) shape (xftsim.struct.XftAccessor attribute) (xftsim.struct.XftAccessor property)

Sib_GWAS_Estimator (class in xftsim.stats) SiblingPairFilter (class in xftsim.index) Simulation (class in xftsim.sim) sort_and_paste() (in module xftsim.utils) SpikeSlabArchitecture (class in xftsim.arch) split_by_component() (xftsim.struct.XftAccessor method) split_by_phenotype() (xftsim.struct.XftAccessor method) split_by_phenotype_vorigin() (xftsim.struct.XftAccessor method) split_by_vorigin() (xftsim.struct.XftAccessor method) stack() (xftsim.index.XftIndex method) standardize() (xftsim.struct.XftAccessor method) standardize_array() (in module xftsim.utils) standardize_array_hw() (in module xftsim.utils) Statistic (class in xftsim.stats) statistics (xftsim.sim.Simulation attribute) SumAllTransformation (class in xftsim.arch) SumTransformation (class in xftsim.arch)

T

threshold_PGS() (in module xftsim.stats) to_diploid() (xftsim.index.HaploidVariantIndex method), [1] (xftsim.struct.XftAccessor method) to_diploid_standardized() (xftsim.struct.XftAccessor method) to_haploid() (xftsim.index.DiploidVariantIndex method) to_proband() (xftsim.index.ComponentIndex method), [1]

to_proportions() (in module xftsim.utils) to_simplex() (in module xftsim.utils) to_vorigin() (xftsim.index.ComponentIndex method), [1] transmit_parental_phenotypes() (in module xftsim.reproduce) trio_view() (xftsim.mate.MateAssignment method) true_cov_beta (xftsim.arch.AdditiveGeneticComponent property) true_rho_beta (xftsim.arch.AdditiveGeneticComponent property)

U

unique_identifier (xftsim.index.ComponentIndex attribute) (xftsim.index.ComponentIndex property) (xftsim.index.SampleIndex property) (xftsim.index.XftIndex property)

unique_identifier() (in module xftsim.utils) update_pedigree() (xftsim.mate.MateAssignment method) (xftsim.sim.Simulation method) update_results() (xftsim.stats.Statistic method), [1] use_empirical_afs() (xftsim.struct.XftAccessor method)

V

v_input_dimension (xftsim.arch.LinearTransformationComponent attribute) (xftsim.arch.LinearVerticalComponent attribute) v_output_dimension (xftsim.arch.LinearTransformationComponent attribute) (xftsim.arch.LinearVerticalComponent attribute) validate() (xftsim.index.XftIndex method) variable_map_from_haplotypes_with_cM() (xftsim.reproduce.RecombinationMap static method) VariableCount (class in xftsim.utils) variance_components (xftsim.stats.SampleStatistics attribute) variances (xftsim.arch.AdditiveNoiseComponent attribute) (xftsim.stats.SampleStatistics attribute)

variant_indexer (xftsim.effect.AdditiveEffects attribute) variantIndex_from_plink() (in module xftsim.index) variantIndex_from_VCF() (in module xftsim.index) vcov (xftsim.stats.SampleStatistics attribute) VerticalComponent (in module xftsim.arch) vid (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute) vorigin_relative (xftsim.arch.ArchitectureComponent property) (xftsim.index.ComponentIndex attribute) (xftsim.index.ComponentIndex property)

W

write_to_plink1() (in module xftsim.io)

WriteToDisk (class in xftsim.proc)

X

XftAccessor (class in xftsim.struct) XftIndex (class in xftsim.index) xftsim.arch module xftsim.effect module xftsim.founders module xftsim.index module xftsim.io module xftsim.mate module

xftsim.ped module xftsim.proc module xftsim.reproduce module xftsim.sim module xftsim.stats module xftsim.struct module xftsim.utils module

Z

zero_allele (xftsim.index.DiploidVariantIndex attribute) (xftsim.index.DiploidVariantIndex property) (xftsim.index.HaploidVariantIndex attribute)

ZeroFounderInitialization (class in xftsim.arch) ZeroTruncatedPoissonCount (class in xftsim.utils)