Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | Y A additional_context (pysyrev.core.config.ReviewerConfig attribute) allow_abbrev (pysyrev.TopicModel attribute) api (pysyrev.core.config.OpenAlexSourceConfig attribute) (pysyrev.core.config.WosSourceConfig attribute) api_key (pysyrev.core.config.OpenAlexApiConfig attribute) (pysyrev.core.config.WosApiConfig attribute) api_pause (pysyrev.core.config.ReviewConfig attribute) (pysyrev.LLMReview attribute) author (pysyrev.core.config.ReportMetaConfig attribute) B backstory (pysyrev.core.config.ReviewerConfig attribute) batch_size (pysyrev.core.config.ReviewConfig attribute) (pysyrev.LLMReview attribute) berteley (pysyrev.core.config.TopicModelConfig attribute) bertopic (pysyrev.core.config.TopicModelConfig attribute) bertopic_model (pysyrev.TopicModel attribute) bertopic_results (pysyrev.TopicReport property) BertopicConfig (class in pysyrev.core.config) best_results (pysyrev.TopicReport property) bib (pysyrev.core.config.Config attribute) (pysyrev.Pipeline attribute) bib_network (pysyrev.core.config.Config attribute) (pysyrev.core.config.ReportSectionsConfig attribute) bib_network_config (pysyrev.TopicReport attribute) bib_network_graphs (pysyrev.core.config.Config attribute) BibConfig (class in pysyrev.core.config) BibDataset (class in pysyrev) BibExportConfig (class in pysyrev.core.config) BibNetwork (class in pysyrev) BibNetworkConfig (class in pysyrev.core.config) BibNetworkExportConfig (class in pysyrev.core.config) build_cocitation_network() (pysyrev.BibNetwork method) build_coupling_network() (pysyrev.BibNetwork method) C cache_dir (pysyrev.core.config.OpenAlexApiConfig attribute) (pysyrev.core.config.ReviewExportConfig attribute) (pysyrev.core.config.WosApiConfig attribute) calculate_probabilities (pysyrev.core.config.BertopicConfig attribute) citation_count (pysyrev.BibDataset property) clean (pysyrev.core.config.BibConfig attribute) clean_and_drop() (pysyrev.BibDataset method) CleanConfig (class in pysyrev.core.config) cluster_selection_method (pysyrev.core.config.HDBSCANConfig attribute) cocitation_graph (pysyrev.BibNetwork property) (pysyrev.core.config.BibNetworkExportConfig attribute) cocitation_network (pysyrev.core.config.BibNetworkConfig attribute) CocitationNetworkConfig (class in pysyrev.core.config) coherence_scorer (pysyrev.core.config.TopicModelConfig attribute) Config (class in pysyrev.core.config) config (pysyrev.Pipeline attribute) coupling_graph (pysyrev.BibNetwork property) (pysyrev.core.config.BibNetworkExportConfig attribute) coupling_network (pysyrev.core.config.BibNetworkConfig attribute) CouplingNetworkConfig (class in pysyrev.core.config) ctfidf (pysyrev.core.config.TopicModelConfig attribute) D dataset (pysyrev.BibDataset property) (pysyrev.core.config.BibExportConfig attribute) date_format (pysyrev.core.config.ReportMetaConfig attribute) decision_rule (pysyrev.core.config.ReviewConfig attribute) (pysyrev.LLMReview attribute) distance (pysyrev.core.config.TopicModelConfig attribute) (pysyrev.TopicModel attribute) doc_dataset (pysyrev.core.config.BibNetworkConfig attribute) (pysyrev.core.config.ReviewConfig attribute) (pysyrev.core.config.TopicModelConfig attribute) (pysyrev.LLMReview attribute) (pysyrev.TopicModel attribute) doi (pysyrev.BibDataset property) E email (pysyrev.core.config.OpenAlexApiConfig attribute) enabled (pysyrev.core.config.ResolveReferencesConfig attribute) env (pysyrev.core.config.Config attribute) exclude_doc_type (pysyrev.core.config.ExtractConfig attribute) exclusion_criteria (pysyrev.core.config.ReviewConfig attribute) export (pysyrev.core.config.BibConfig attribute) (pysyrev.core.config.BibNetworkConfig attribute) (pysyrev.core.config.ReviewConfig attribute) (pysyrev.core.config.TopicModelConfig attribute) (pysyrev.LLMReview attribute) export_dir (pysyrev.core.config.BibExportConfig attribute) (pysyrev.core.config.BibNetworkExportConfig attribute) (pysyrev.core.config.ReviewExportConfig attribute) (pysyrev.core.config.TopicExportConfig attribute) (pysyrev.TopicModel attribute) export_to (pysyrev.core.config.TopicReportConfig attribute) (pysyrev.TopicReport attribute) extra (pysyrev.core.config.ReportSectionsConfig attribute) extra_garbage_phrases (pysyrev.core.config.CleanConfig attribute) extract (pysyrev.core.config.BibConfig attribute) extract_documents() (pysyrev.BibDataset method) ExtractConfig (class in pysyrev.core.config) F fetch_abstracts() (pysyrev.BibDataset method) fetch_citations() (pysyrev.BibDataset method) file (pysyrev.core.config.OpenAlexSourceConfig attribute) (pysyrev.core.config.WosSourceConfig attribute) filters (pysyrev.core.config.OpenAlexApiConfig attribute) flag_shared_unresolved_references() (pysyrev.BibDataset method) flag_unresolved (pysyrev.core.config.ResolveReferencesConfig attribute) from_config() (pysyrev.BibDataset class method) (pysyrev.BibNetwork class method) (pysyrev.LLMReview class method) (pysyrev.OpenAlexDataset class method) (pysyrev.Pipeline class method) (pysyrev.TopicModel class method) (pysyrev.TopicReport class method) (pysyrev.WosDataset class method) fuzzy_score_cutoff (pysyrev.core.config.ResolveReferencesConfig attribute) G generate_bib() (pysyrev.BibDataset method) (pysyrev.OpenAlexDataset method) generate_report() (pysyrev.TopicReport method) H hdbscan (pysyrev.core.config.TopicModelConfig attribute) HDBSCANConfig (class in pysyrev.core.config) host (pysyrev.core.config.ReviewerConfig attribute) (pysyrev.core.config.TopicLabelerConfig attribute) I include_doc_type (pysyrev.core.config.ExtractConfig attribute) included_docs (pysyrev.core.config.ReviewExportConfig attribute) (pysyrev.LLMReview property) (pysyrev.ReviewedDataset attribute) inclusion_criteria (pysyrev.core.config.ReviewConfig attribute) items_per_call (pysyrev.core.config.ReviewConfig attribute) (pysyrev.core.config.ReviewerConfig attribute) K keep_n_results (pysyrev.core.config.TopicModelConfig attribute) (pysyrev.TopicModel attribute) L labeler_config (pysyrev.TopicReport attribute) language (pysyrev.core.config.BertopicConfig attribute) (pysyrev.core.config.ExtractConfig attribute) llm (pysyrev.core.config.Config attribute) LLMReview (class in pysyrev) load() (pysyrev.core.config.Config class method) low_memory (pysyrev.core.config.UMAPConfig attribute) M max_candidates (pysyrev.core.config.ResolveReferencesConfig attribute) max_candidates_per_row (pysyrev.core.config.MergeConfig attribute) max_concurrent_requests (pysyrev.core.config.ReviewConfig attribute) (pysyrev.core.config.ReviewerConfig attribute) (pysyrev.core.config.TopicLabelerConfig attribute) max_retries (pysyrev.core.config.ReviewConfig attribute) (pysyrev.core.config.ReviewerConfig attribute) (pysyrev.core.config.TopicLabelerConfig attribute) max_tokens (pysyrev.core.config.ReviewerConfig attribute) (pysyrev.core.config.TopicLabelerConfig attribute) merge (pysyrev.core.config.BibConfig attribute) merge() (pysyrev.BibDataset method) MergeConfig (class in pysyrev.core.config) meta (pysyrev.core.config.ReportConfig attribute) metric (pysyrev.core.config.HDBSCANConfig attribute) (pysyrev.core.config.UMAPConfig attribute) metrics (pysyrev.TopicReport property) min_cocitations (pysyrev.core.config.CocitationNetworkConfig attribute) min_dist (pysyrev.core.config.UMAPConfig attribute) min_sample_range (pysyrev.core.config.HDBSCANConfig attribute) (pysyrev.TopicModel attribute) min_sample_step (pysyrev.core.config.HDBSCANConfig attribute) (pysyrev.TopicModel attribute) min_shared (pysyrev.core.config.CouplingNetworkConfig attribute) min_signals_to_reject (pysyrev.core.config.CleanConfig attribute) min_topic_size_range (pysyrev.core.config.HDBSCANConfig attribute) (pysyrev.TopicModel attribute) model_id (pysyrev.core.config.ReviewerConfig attribute) (pysyrev.core.config.TopicLabelerConfig attribute) model_index (pysyrev.core.config.TopicReportConfig attribute) (pysyrev.TopicReport attribute) N n_cocitation_edges (pysyrev.BibNetwork property) n_cocitation_nodes (pysyrev.BibNetwork property) n_components (pysyrev.core.config.UMAPConfig attribute) (pysyrev.TopicModel attribute) n_coupling_edges (pysyrev.BibNetwork property) n_coupling_nodes (pysyrev.BibNetwork property) n_gram_range (pysyrev.core.config.BertopicConfig attribute) n_neighbors (pysyrev.core.config.UMAPConfig attribute) (pysyrev.TopicModel attribute) n_repr_docs_for_labeling (pysyrev.core.config.TopicLabelerConfig attribute) name (pysyrev.core.config.ReviewerConfig attribute) nb_citations (pysyrev.core.config.ExtractConfig attribute) nb_topics (pysyrev.TopicReport property) network (pysyrev.Pipeline attribute) ngram_size (pysyrev.core.config.MergeConfig attribute) (pysyrev.core.config.ResolveReferencesConfig attribute) nr_repr_docs (pysyrev.TopicModel attribute) O open_alex (pysyrev.core.config.BibConfig attribute) OpenAlexApiConfig (class in pysyrev.core.config) OpenAlexDataset (class in pysyrev) OpenAlexSourceConfig (class in pysyrev.core.config) overwrite (pysyrev.TopicModel attribute) P paper_selection (pysyrev.core.config.ReportSectionsConfig attribute) Pipeline (class in pysyrev) prediction_data (pysyrev.core.config.HDBSCANConfig attribute) provider (pysyrev.core.config.ReviewerConfig attribute) (pysyrev.core.config.TopicLabelerConfig attribute) pubmed (pysyrev.core.config.BibConfig attribute) PubmedDataset (class in pysyrev) purity_scorer (pysyrev.TopicModel attribute) Q query (pysyrev.core.config.OpenAlexApiConfig attribute) (pysyrev.core.config.WosApiConfig attribute) R random_state (pysyrev.core.config.UMAPConfig attribute) ranking_scorer (pysyrev.TopicModel attribute) reasoning (pysyrev.core.config.ReviewerConfig attribute) reasoning_effort (pysyrev.core.config.ReviewerConfig attribute) report (pysyrev.core.config.Config attribute) (pysyrev.Pipeline attribute) report_config (pysyrev.TopicReport attribute) ReportConfig (class in pysyrev.core.config) ReportMetaConfig (class in pysyrev.core.config) ReportSectionsConfig (class in pysyrev.core.config) resolve() (pysyrev.core.config.BibExportConfig method) (pysyrev.core.config.BibNetworkExportConfig method) (pysyrev.core.config.ReviewExportConfig method) resolve_references (pysyrev.core.config.BibConfig attribute) resolve_references() (pysyrev.BibDataset method) ResolveReferencesConfig (class in pysyrev.core.config) review (pysyrev.core.config.Config attribute) (pysyrev.Pipeline attribute) ReviewConfig (class in pysyrev.core.config) ReviewedDataset (class in pysyrev) ReviewerConfig (class in pysyrev.core.config) reviewers (pysyrev.core.config.ReviewConfig attribute) (pysyrev.LLMReview attribute) ReviewExportConfig (class in pysyrev.core.config) run() (pysyrev.BibNetwork method) (pysyrev.LLMReview method) (pysyrev.Pipeline method) (pysyrev.TopicModel method) run_dir (pysyrev.core.config.TopicReportConfig attribute) (pysyrev.TopicReport attribute) run_name (pysyrev.core.config.BibExportConfig attribute) (pysyrev.core.config.BibNetworkExportConfig attribute) (pysyrev.core.config.ReviewExportConfig attribute) (pysyrev.core.config.TopicExportConfig attribute) (pysyrev.TopicModel attribute) S sample() (pysyrev.BibDataset method) sample_size (pysyrev.core.config.ReviewConfig attribute) (pysyrev.LLMReview attribute) save() (pysyrev.BibNetwork method) (pysyrev.LLMReview method) scopus (pysyrev.core.config.BibConfig attribute) ScopusDataset (class in pysyrev) score_cutoff (pysyrev.core.config.ExtractConfig attribute) scorer (pysyrev.core.config.ExtractConfig attribute) (pysyrev.core.config.MergeConfig attribute) (pysyrev.core.config.ResolveReferencesConfig attribute) sections (pysyrev.core.config.ReportConfig attribute) selected_model_row (pysyrev.TopicReport property) source (pysyrev.core.config.OpenAlexSourceConfig attribute) (pysyrev.core.config.WosSourceConfig attribute) subtitle (pysyrev.core.config.ReportMetaConfig attribute) summary (pysyrev.core.config.ReportMetaConfig attribute) system_prompt (pysyrev.core.config.TopicLabelerConfig attribute) T temperature (pysyrev.core.config.ReviewerConfig attribute) (pysyrev.core.config.TopicLabelerConfig attribute) temporal (pysyrev.core.config.ReportSectionsConfig attribute) text_inputs (pysyrev.core.config.ReviewConfig attribute) (pysyrev.LLMReview attribute) title (pysyrev.core.config.ReportMetaConfig attribute) title_similarity (pysyrev.core.config.MergeConfig attribute) to_csv() (pysyrev.BibDataset method) topic (pysyrev.Pipeline attribute) topic_characteristics (pysyrev.core.config.ReportSectionsConfig attribute) topic_distribution (pysyrev.core.config.TopicModelConfig attribute) (pysyrev.TopicModel attribute) topic_info (pysyrev.TopicReport property) topic_model (pysyrev.core.config.Config attribute) topic_report (pysyrev.core.config.Config attribute) topic_similarity (pysyrev.core.config.ReportSectionsConfig attribute) topic_size_step (pysyrev.core.config.HDBSCANConfig attribute) (pysyrev.TopicModel attribute) TopicExportConfig (class in pysyrev.core.config) TopicLabelerConfig (class in pysyrev.core.config) TopicModel (class in pysyrev) TopicModelConfig (class in pysyrev.core.config) TopicReport (class in pysyrev) TopicReportConfig (class in pysyrev.core.config) topics (pysyrev.core.config.ReportSectionsConfig attribute) total_docs (pysyrev.core.config.ReviewExportConfig attribute) (pysyrev.ReviewedDataset attribute) transformer_model (pysyrev.core.config.BertopicConfig attribute) U umap (pysyrev.core.config.TopicModelConfig attribute) UMAPConfig (class in pysyrev.core.config) use_langdetect (pysyrev.core.config.CleanConfig attribute) use_resolved (pysyrev.core.config.CocitationNetworkConfig attribute) (pysyrev.core.config.CouplingNetworkConfig attribute) use_unresolved (pysyrev.core.config.CocitationNetworkConfig attribute) (pysyrev.core.config.CouplingNetworkConfig attribute) V version (pysyrev.core.config.ReportMetaConfig attribute) W workflow (pysyrev.core.config.ReviewConfig attribute) workflow_schema (pysyrev.LLMReview attribute) wos (pysyrev.core.config.BibConfig attribute) WosApiConfig (class in pysyrev.core.config) WosDataset (class in pysyrev) WosSourceConfig (class in pysyrev.core.config) Y year (pysyrev.core.config.ExtractConfig attribute)