Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W A added (dscat.diff.DiffResult attribute) adjusted_rand_index (analysis.stability.Comparison attribute) aggregate (analysis.stability.StabilitySummary attribute) align() (in module analysis.cli) align_to_named() (in module analysis.reference) Alignment (class in analysis.align) analysis.align module analysis.cache module analysis.checkpoint module analysis.cli module analysis.cohort module analysis.cohort.schema module analysis.cohort.spark module analysis.cohort.ssc module analysis.config module analysis.enrich module analysis.features module analysis.model module analysis.paths module analysis.progress module analysis.reference module analysis.replicate module analysis.requirements module analysis.run module analysis.selection module analysis.stability module analysis.strata module analysis.strata_data module anchors (analysis.reference.NamedAlignment attribute) anchors_hold (analysis.reference.NamedAlignment attribute) append() (analysis.checkpoint.CheckpointLog method) artefacts_dir() (in module analysis.paths) as_dict() (analysis.features.Typing method) assign() (analysis.strata.BinningPolicy method) (analysis.strata.FixedBands method) (analysis.strata.MaxEqualBins method) (analysis.strata.QuantileBins method) author_category_map() (in module analysis.config) author_feature_list() (in module analysis.config) awe() (in module analysis.selection) axes (analysis.strata_data.StrataData attribute) B benchmark (analysis.stability.NminResult attribute) BinningPolicy (class in analysis.strata) bootstrap_overall_correlation() (in module analysis.enrich) build() (in module docs_cli.cli) build_matrix() (in module analysis.cohort) build_milestone_disambiguator() (in module analysis.cohort.schema) build_strata_data() (in module analysis.strata_data) build_typing() (in module analysis.features) C cache_hit (analysis.run.RunContext attribute) cache_path() (in module dscat.docs) canonical_json() (in module analysis.cache) Catalogue (class in dscat.index) catalogue_dir() (in module dscat.paths) category_correlation (analysis.replicate.ReplicationResult attribute) (analysis.stability.Comparison attribute) category_signature() (in module analysis.enrich) changed (dscat.diff.DiffResult attribute) CheckpointLog (class in analysis.checkpoint) class_centroids() (in module analysis.model) class_overlap_matrix() (in module analysis.stability) clean() (in module docs_cli.cli) clear() (analysis.checkpoint.CheckpointLog method) clear_checkpoints() (in module analysis.checkpoint) clear_dataset() (dscat.index.Catalogue method) codes (analysis.strata.StratumAssignment attribute) cohens_d() (in module analysis.enrich) Cohort (class in analysis.cohort) cohort() (in module analysis.cli) CohortMatrix (class in analysis.cohort) columns (dscat.config.DatasetConfig attribute) commit() (dscat.index.Catalogue method) compare_to_reference() (in module analysis.stability) Comparison (class in analysis.stability) comparisons (analysis.stability.StabilitySummary attribute) compute_hash() (in module analysis.cache) container (dscat.config.DatasetConfig attribute) contributory_features() (in module analysis.enrich) convert_doc() (in module dscat.docs) correlation_ci (analysis.replicate.ReplicationResult attribute) correlations (analysis.align.Alignment attribute) (analysis.reference.NamedAlignment attribute) cost (analysis.align.Alignment attribute) (analysis.reference.NamedAlignment attribute) counts (analysis.features.Typing property) (analysis.requirements.PolicyReport attribute) (analysis.strata.StratumAssignment attribute) covariates (analysis.cohort.CohortMatrix attribute) csv (dscat.output.Format attribute) csv_columns() (in module analysis.cohort) D data_root() (in module dscat.paths) dataset (analysis.cohort.CohortMatrix attribute) (dscat.config.Version attribute) (dscat.diff.DiffResult attribute) (dscat.ingest.IngestSummary attribute) (dscat.model.FeatureRow attribute) (dscat.model.TableRow attribute) DatasetConfig (class in dscat.config) datasets() (dscat.index.Catalogue method) definition (dscat.model.FeatureRow attribute) degenerate (analysis.stability.Comparison attribute) demographics (analysis.requirements.PolicyReport attribute) (analysis.strata_data.StrataData attribute) derive_axes() (in module analysis.strata_data) describe() (in module dscat.queries) description (analysis.requirements.RequirementResult attribute) detail (analysis.requirements.RequirementResult attribute) diagnostics (analysis.strata_data.StrataData attribute) dictionary_glob (dscat.config.DatasetConfig attribute) dictionary_path (dscat.config.Version attribute) dictionary_typing() (in module analysis.features) diff_versions() (in module dscat.diff) DiffResult (class in dscat.diff) discover_docs() (in module dscat.docs) discover_versions() (in module dscat.config) display_hint (dscat.model.FeatureRow attribute) display_name (dscat.config.DatasetConfig attribute) display_title (dscat.model.FeatureRow attribute) (dscat.model.TableRow attribute) docs_cache_dir() (in module dscat.paths) docs_cli.cli module docs_figures_dir() (in module figures.paths) drift() (in module analysis.cli) E edge_perturbation (analysis.requirements.RequirementThresholds attribute) edges (analysis.strata.FixedBands attribute) (analysis.strata.StratumAssignment attribute) eligible (analysis.requirements.PolicyReport property) Engine (class in dscat.docs) environment_versions() (in module analysis.cache) estimate_floor() (in module analysis.stability) evaluate_policy() (in module analysis.requirements) expand_query() (in module dscat.queries) extract_sections() (in module dscat.docs) F feature_enrichment() (in module analysis.enrich) feature_names (analysis.cohort.CohortMatrix property) feature_sources() (in module dscat.queries) FeatureRow (class in dscat.model) features (analysis.cohort.CohortMatrix attribute) field_type (dscat.model.FeatureRow attribute) fieldid_row (dscat.config.DatasetConfig attribute) figure_stem() (in module figures.paths) figures.cli module figures.data module figures.nmin module figures.paths module figures.publish module figures.replication module figures.reproduction module figures.selection module figures.stability module figures.style module figures_dir() (in module figures.paths) FigureSpec (class in figures.publish) file_bytes (dscat.model.TableRow attribute) file_digest() (in module analysis.cache) file_glob (dscat.config.DatasetConfig attribute) file_name (figures.publish.FigureSpec attribute) file_path (dscat.model.TableRow attribute) find_documents() (in module dscat.queries) find_feature() (in module dscat.queries) find_repo_root() (in module analysis.paths) (in module dscat.paths) fit() (in module analysis.cli) fit_gfmm() (in module analysis.model) FitResult (class in analysis.model) fits (analysis.stability.StabilitySummary attribute) FixedBands (class in analysis.strata) flags (analysis.requirements.PolicyReport property) floor (analysis.stability.NminResult attribute) floor_ci (analysis.stability.NminResult attribute) Format (class in dscat.output) frame_digest() (in module analysis.cache) from_v (dscat.diff.DiffResult attribute) G get_cohort() (in module analysis.cohort) git_commit() (in module analysis.cache) greedy_overlap_align() (in module analysis.align) group_by (dscat.config.DatasetConfig attribute) H house_style() (in module figures.style) hungarian_align() (in module analysis.align) I index_path() (in module dscat.paths) infer_from_dictionary() (in module analysis.features) IngestSummary (class in dscat.ingest) init_schema() (dscat.index.Catalogue method) insert_documents() (dscat.index.Catalogue method) insert_features() (dscat.index.Catalogue method) insert_synonyms() (dscat.index.Catalogue method) insert_tables() (dscat.index.Catalogue method) instrument_years (analysis.strata_data.StrataData attribute) integrate() (analysis.cohort.Cohort method) (analysis.cohort.spark.SparkCohort method) (analysis.cohort.ssc.SscCohort method) J json (dscat.output.Format attribute) K k_values (analysis.selection.SelectionResult attribute) key (analysis.requirements.RequirementResult attribute) L labels (analysis.model.FitResult attribute) (analysis.strata.FixedBands attribute) (analysis.strata.StratumAssignment attribute) lag (analysis.strata_data.StrataData attribute) latest_version() (dscat.index.Catalogue method) latest_version_map() (in module dscat.queries) layout (dscat.config.DatasetConfig attribute) list_documents() (in module dscat.queries) list_tables() (in module dscat.queries) litman_typing_dir() (in module analysis.config) lmr_lrt_proxy() (in module analysis.selection) load() (analysis.checkpoint.CheckpointLog method) load_alignment() (in module figures.data) load_category_map() (in module analysis.features) load_configs() (in module dscat.config) load_feature_list() (in module analysis.cohort.schema) load_frame() (in module analysis.cache) load_json() (in module analysis.cache) load_model() (in module analysis.cache) load_nmin() (in module figures.data) load_pickle_typing() (in module analysis.features) load_replication() (in module figures.data) load_selection_summary() (in module figures.data) load_stability() (in module figures.data) load_synonyms() (in module dscat.synonyms) log (analysis.run.RunContext attribute) M main() (in module figures.cli) manifest_path() (in module analysis.paths) mapping (analysis.align.Alignment attribute) (analysis.reference.NamedAlignment attribute) markdown (dscat.output.Format attribute) marker (dscat.docs.Engine attribute) markitdown (dscat.docs.Engine attribute) max_bin_share (analysis.requirements.RequirementThresholds attribute) max_lag_correlation (analysis.requirements.RequirementThresholds attribute) max_reassigned_fraction (analysis.requirements.RequirementThresholds attribute) MaxEqualBins (class in analysis.strata) measurement_data (analysis.model.FitResult attribute) measurement_scale (dscat.model.FeatureRow attribute) metrics (analysis.model.FitResult attribute) (analysis.replicate.ReplicationResult attribute) (analysis.run.RunContext attribute) min_bin_size (analysis.requirements.RequirementThresholds attribute) (analysis.strata.MaxEqualBins attribute) min_coverage (analysis.requirements.RequirementThresholds attribute) min_n_bins (analysis.requirements.RequirementThresholds attribute) min_projected_smallest_class (analysis.requirements.RequirementThresholds attribute) model (analysis.model.FitResult attribute) module analysis.align analysis.cache analysis.checkpoint analysis.cli analysis.cohort analysis.cohort.schema analysis.cohort.spark analysis.cohort.ssc analysis.config analysis.enrich analysis.features analysis.model analysis.paths analysis.progress analysis.reference analysis.replicate analysis.requirements analysis.run analysis.selection analysis.stability analysis.strata analysis.strata_data docs_cli.cli figures.cli figures.data figures.nmin figures.paths figures.publish figures.replication figures.reproduction figures.selection figures.stability figures.style N n_assigned (analysis.requirements.PolicyReport attribute) n_cols (dscat.model.TableRow attribute) n_features (dscat.ingest.IngestSummary attribute) n_min (analysis.stability.NminResult attribute) n_missing (analysis.strata.StratumAssignment attribute) n_probands (analysis.cohort.CohortMatrix property) n_rows (dscat.model.TableRow attribute) n_tables (dscat.ingest.IngestSummary attribute) n_total (analysis.requirements.PolicyReport attribute) n_value_levels() (in module analysis.features) name (analysis.strata.FixedBands attribute) (analysis.strata.MaxEqualBins attribute) (analysis.strata.QuantileBins attribute) (dscat.config.DatasetConfig attribute) (dscat.model.FeatureRow attribute) (figures.publish.FigureSpec attribute) NamedAlignment (class in analysis.reference) nmin() (in module analysis.cli) (in module figures.cli) nmin_figure() (in module figures.nmin) NminResult (class in analysis.stability) notes (dscat.model.FeatureRow attribute) (dscat.model.TableRow attribute) null_overall (analysis.replicate.ReplicationResult attribute) O observed (analysis.requirements.RequirementResult attribute) observed_cardinality() (in module analysis.features) open() (dscat.index.Catalogue class method) open_catalogue() (in module analysis.cohort) overall_correlation (analysis.reference.NamedAlignment attribute) (analysis.replicate.ReplicationResult attribute) (analysis.stability.Comparison attribute) overlap (analysis.stability.Comparison attribute) overlap_mean (analysis.stability.StabilitySummary attribute) P p_value (analysis.replicate.ReplicationResult attribute) panel_title() (in module figures.style) params (analysis.run.RunContext attribute) parse() (in module dscat.adapters) parse_age_months() (in module analysis.cohort.schema) path() (analysis.run.RunContext method) per_fit (analysis.stability.NminResult attribute) per_fit_criteria() (in module analysis.selection) per_iteration (analysis.selection.SelectionResult attribute) PolicyReport (class in analysis.requirements) prepare_inputs() (in module analysis.model) profile_correlation() (in module analysis.enrich) publish() (in module figures.cli) publish_figure() (in module figures.publish) published_signature() (in module analysis.reference) Q q (analysis.strata.QuantileBins attribute) qualified_id (dscat.model.FeatureRow attribute) QuantileBins (class in analysis.strata) R read_columns() (in module analysis.cohort) read_manifest() (in module analysis.cache) read_sheet() (in module dscat.dictionary) rebuild_fts() (dscat.index.Catalogue method) reconcile() (in module analysis.features) removed (dscat.diff.DiffResult attribute) render() (in module dscat.output) replicate() (in module analysis.cli) (in module figures.cli) replication_figure() (in module figures.replication) ReplicationResult (class in analysis.replicate) report() (in module analysis.cli) reproduce() (in module figures.cli) reproduction_figure() (in module figures.reproduction) RequirementResult (class in analysis.requirements) RequirementThresholds (class in analysis.requirements) resolve_engine() (in module dscat.docs) resolve_run() (in module figures.data) results (analysis.requirements.PolicyReport attribute) role (dscat.model.TableRow attribute) roles (dscat.config.DatasetConfig attribute) roles_applicable (dscat.model.FeatureRow attribute) run_context() (in module analysis.run) run_dir (analysis.run.RunContext attribute) run_dir() (in module analysis.paths) run_hash (analysis.run.RunContext attribute) run_ingest() (in module dscat.ingest) run_multi_init_stability() (in module analysis.stability) run_nmin_sweep() (in module analysis.stability) run_replication() (in module analysis.replicate) run_selection() (in module analysis.selection) run_subsampling_stability() (in module analysis.stability) RunContext (class in analysis.run) S save_figure() (in module figures.style) save_frame() (in module analysis.cache) save_json() (in module analysis.cache) save_model() (in module analysis.cache) search() (in module dscat.queries) select() (in module analysis.cli) (in module figures.cli) selection_figure() (in module figures.selection) selection_metrics() (in module analysis.model) SelectionResult (class in analysis.selection) sensitivity() (in module analysis.cli) serve() (in module docs_cli.cli) shared_feature_set() (in module analysis.replicate) shared_features (analysis.replicate.ReplicationResult attribute) sheet (dscat.config.DatasetConfig attribute) sheet_names() (in module dscat.dictionary) ship_folder (dscat.config.Version attribute) short_hash() (in module analysis.cache) skip_sheets (dscat.config.DatasetConfig attribute) small_lag_years (analysis.requirements.RequirementThresholds attribute) smallest_class_fraction (analysis.requirements.RequirementThresholds attribute) smallest_class_proportion (analysis.stability.Comparison attribute) smd_flag (analysis.requirements.RequirementThresholds attribute) sort_key (dscat.config.Version property) source_csv() (in module analysis.cohort) source_sheet (dscat.model.FeatureRow attribute) source_stage (figures.publish.FigureSpec attribute) SparkCohort (class in analysis.cohort.spark) spec (analysis.requirements.PolicyReport attribute) (analysis.strata.StratumAssignment attribute) spec() (analysis.strata.BinningPolicy method) (analysis.strata.FixedBands method) (analysis.strata.MaxEqualBins method) (analysis.strata.QuantileBins method) SscCohort (class in analysis.cohort.ssc) stability() (in module analysis.cli) (in module figures.cli) stability_figure() (in module figures.stability) StabilitySummary (class in analysis.stability) stage (analysis.run.RunContext attribute) stage_dir() (in module analysis.paths) status (analysis.requirements.RequirementResult attribute) strata() (in module analysis.cli) strata_describe() (in module analysis.cli) StrataData (class in analysis.strata_data) stratify() (in module analysis.cli) StratumAssignment (class in analysis.strata) strip_version_suffix (dscat.config.DatasetConfig attribute) summarise() (in module analysis.strata_data) summary (analysis.selection.SelectionResult attribute) (analysis.stability.NminResult attribute) supports_timing() (analysis.cohort.Cohort method) (analysis.cohort.spark.SparkCohort method) (analysis.cohort.ssc.SscCohort method) T table (dscat.output.Format attribute) table_name (dscat.model.FeatureRow attribute) (dscat.model.TableRow attribute) TableRow (class in dscat.model) tables_added (dscat.diff.DiffResult attribute) tables_removed (dscat.diff.DiffResult attribute) task_bar() (in module analysis.progress) textutil (dscat.docs.Engine attribute) threshold (analysis.requirements.RequirementResult attribute) tier (analysis.requirements.RequirementResult attribute) to_frame() (analysis.requirements.PolicyReport method) to_v (dscat.diff.DiffResult attribute) total_cost (analysis.align.Alignment attribute) tsv (dscat.output.Format attribute) Typing (class in analysis.features) U upsert_dataset() (dscat.index.Catalogue method) upsert_version() (dscat.index.Catalogue method) V validation_log_likelihood() (in module analysis.selection) value_coding (dscat.model.FeatureRow attribute) version (analysis.cohort.CohortMatrix attribute) Version (class in dscat.config) version (dscat.config.Version attribute) (dscat.model.FeatureRow attribute) (dscat.model.TableRow attribute) version_dir (dscat.config.Version attribute) version_pattern (dscat.config.DatasetConfig attribute) version_sort_key() (in module dscat.config) versions (dscat.ingest.IngestSummary attribute) versions() (dscat.index.Catalogue method) (in module docs_cli.cli) W write_manifest() (in module analysis.cache)