Index

_

__init__() (pat2vec.main_pat2vec.main method), [1], [2] (pat2vec.pat2vec_search.cogstack_search_methods.CogStack method) (pat2vec.util.anonymisation_deid_documents.DeIdAnonymizer method) (pat2vec.util.config_pat2vec.config_class method) (pat2vec.util.current_pat_batch_path_methods.PathsClass method)

A

abstractEthnicity() (pat2vec.util.ethnicity_abstractor.EthnicityAbstractor static method) add_icd10 (pat2vec.util.config_pat2vec.config_class attribute) add_offset_column() (in module pat2vec.util.methods_get) add_opc4s (pat2vec.util.config_pat2vec.config_class attribute) aggregate_dataframe_mean() (in module pat2vec.util.post_processing) all_epr_patient_list_path (pat2vec.util.config_pat2vec.config_class attribute) all_paths (pat2vec.util.current_pat_batch_path_methods.PathsClass attribute) all_patient_list (pat2vec.main_pat2vec.main attribute), [1] analyze_client_codes() (in module pat2vec.pat2vec_pat_list.get_patient_treatment_list) annot_filter_options (pat2vec.util.config_pat2vec.config_class attribute) annot_pat_batch_docs() (in module pat2vec.util.methods_annotation) anonymization_log (pat2vec.util.anonymisation_deid_documents.DeIdAnonymizer attribute) anonymize_dataframe() (pat2vec.util.anonymisation_deid_documents.DeIdAnonymizer method)

anonymize_dataframe_quick() (in module pat2vec.util.anonymisation_deid_documents) anonymize_feature_names() (in module pat2vec.util.anonymisation_data_methods) anonymize_single_text() (in module pat2vec.util.anonymisation_deid_documents) anonymize_text() (pat2vec.util.anonymisation_deid_documents.DeIdAnonymizer method) anonymize_texts() (pat2vec.util.anonymisation_deid_documents.DeIdAnonymizer method) append_age_at_record_series() (in module pat2vec.pat2vec_search.data_helper_functions) append_regex_term_counts() (in module pat2vec.util.methods_annotation_regex) append_to_file() (in module pat2vec.util.compile_requirements) appendAge() (in module pat2vec.pat2vec_search.data_helper_functions) appendAgeAtRecord() (in module pat2vec.pat2vec_search.data_helper_functions) apply_bloods_data_type_filter() (in module pat2vec.util.filter_methods) apply_data_type_epr_docs_filters() (in module pat2vec.util.filter_methods) apply_data_type_mct_docs_filters() (in module pat2vec.util.filter_methods) appointments_time_field (pat2vec.util.config_pat2vec.config_class attribute)

B

batch_mode (pat2vec.util.config_pat2vec.config_class attribute) BatchConfig (class in pat2vec.patvec_get_batch_methods.get_prefetch_batches) bloods_time_field (pat2vec.util.config_pat2vec.config_class attribute) build_ipw_dataframe() (in module pat2vec.util.post_processing_build_ipw_dataframe) build_merged_bloods() (in module pat2vec.util.post_processing_build_methods)

build_merged_epr_mct_annot_df() (in module pat2vec.util.post_processing_build_methods) build_merged_epr_mct_doc_df() (in module pat2vec.util.post_processing_build_methods) build_patient_dict() (in module pat2vec.util.methods_get) bulk_str_extract() (in module pat2vec.pat2vec_search.search_helper_functions) bulk_str_extract_round_robin() (in module pat2vec.pat2vec_search.search_helper_functions) bulk_str_findall() (in module pat2vec.pat2vec_search.search_helper_functions)

C

calculate_age_append() (in module pat2vec.util.pre_processing) calculate_bmi_features() (in module pat2vec.pat2vec_get_methods.get_method_bmi) calculate_core_o2_features() (in module pat2vec.pat2vec_get_methods.get_method_core02) calculate_core_resus_features() (in module pat2vec.pat2vec_get_methods.get_method_core_resus) calculate_diagnostic_features() (in module pat2vec.pat2vec_get_methods.get_method_diagnostics) calculate_drug_features() (in module pat2vec.pat2vec_get_methods.get_method_drugs) calculate_hospital_site_features() (in module pat2vec.pat2vec_get_methods.get_method_hosp_site) calculate_interval() (in module pat2vec.util.calculate_interval) calculate_pretty_name_count_features() (in module pat2vec.util.methods_annotation) calculate_smoking_features() (in module pat2vec.pat2vec_get_methods.get_method_smoking) calculate_vectors (pat2vec.util.config_pat2vec.config_class attribute) calculate_vte_features() (in module pat2vec.pat2vec_get_methods.get_method_vte_status) cat (pat2vec.main_pat2vec.main attribute), [1] check_csv_files_in_directory() (in module pat2vec.util.methods_post_get) check_csv_integrity() (in module pat2vec.util.methods_post_get) check_list_presence() (in module pat2vec.util.post_processing) check_pat_document_annotation_complete() (in module pat2vec.util.methods_annotation) clean_observation_value() (in module pat2vec.pat2vec_get_methods.get_method_core02) client_idcode_term_name (pat2vec.util.config_pat2vec.config_class attribute) coerce_document_df_to_medcat_trainer_input() (in module pat2vec.util.post_processing_medcat) CogStack (class in pat2vec.pat2vec_search.cogstack_search_methods) cogstack2df() (pat2vec.pat2vec_search.cogstack_search_methods.CogStack method) cohort_searcher_no_terms() (in module pat2vec.pat2vec_search.cogstack_search_methods) cohort_searcher_no_terms_fuzzy() (in module pat2vec.pat2vec_search.cogstack_search_methods) cohort_searcher_with_terms_and_search() (in module pat2vec.pat2vec_search.cogstack_search_methods) cohort_searcher_with_terms_and_search_dummy() (in module pat2vec.util.get_dummy_data_cohort_searcher) cohort_searcher_with_terms_and_search_multi() (in module pat2vec.pat2vec_search.search_multiprocess) cohort_searcher_with_terms_no_search() (in module pat2vec.pat2vec_search.cogstack_search_methods) collapse_df_to_mean() (in module pat2vec.util.post_processing) compare_ipw_annotation_rows() (in module pat2vec.util.evaluation_methods)

compute_feature_stats() (in module pat2vec.pat2vec_get_methods.get_method_news) config_class (class in pat2vec.util.config_pat2vec) config_obj (pat2vec.main_pat2vec.main attribute), [1] control_list_path (pat2vec.util.config_pat2vec.config_class attribute) convert_date() (in module pat2vec.util.methods_get) convert_timestamp_to_tuple() (in module pat2vec.util.methods_get) convert_true_to_float() (in module pat2vec.util.post_processing) copy_files_and_dirs() (in module pat2vec.util.post_processing) copy_project_folders_with_substring_match() (in module pat2vec.util.methods_post_get) count_files() (in module pat2vec.util.post_processing) create_credentials_file() (in module pat2vec.pat2vec_search.cogstack_search_methods) create_diagnostic_features_dataframe() (in module pat2vec.pat2vec_get_methods.get_method_diagnostics) create_drug_features_dataframe() (in module pat2vec.pat2vec_get_methods.get_method_drugs) create_folders() (in module pat2vec.util.methods_get) create_folders_annot_csv_wrapper() (in module pat2vec.util.methods_get) create_folders_for_pat() (in module pat2vec.util.methods_get) create_local_folders() (in module pat2vec.util.methods_get) create_ner_results_dataframe() (in module pat2vec.util.medcat_misc_methods) create_powerpoint_from_images() (in module pat2vec.util.presentation_methods) create_powerpoint_from_images_group() (in module pat2vec.util.presentation_methods) create_powerpoint_slides() (in module pat2vec.util.presentation_methods) create_powerpoint_slides_client_idcode_groups() (in module pat2vec.util.presentation_methods) create_profile_reports() (pat2vec.util.evaluation_methods.CsvProfiler static method) create_random_date_from_globals() (in module pat2vec.util.get_dummy_data_cohort_searcher) create_remote_folders() (in module pat2vec.util.methods_get) credentials_path (pat2vec.util.config_pat2vec.config_class attribute) cs (pat2vec.main_pat2vec.main attribute), [1] CsvProfiler (class in pat2vec.util.evaluation_methods) current_pat_line_path (pat2vec.util.config_pat2vec.config_class attribute) current_pat_lines_path (pat2vec.util.config_pat2vec.config_class attribute)

D

data_type_filter_dict (pat2vec.util.config_pat2vec.config_class attribute) DataFrame() (pat2vec.pat2vec_search.cogstack_search_methods.CogStack method) dataframe_generator() (in module pat2vec.pat2vec_search.cogstack_search_methods) date_cleaner() (in module pat2vec.pat2vec_search.search_helper_functions) date_list (pat2vec.util.config_pat2vec.config_class attribute) days (pat2vec.util.config_pat2vec.config_class attribute) deanonymize_feature_names() (in module pat2vec.util.anonymisation_data_methods) DeIdAnonymizer (class in pat2vec.util.anonymisation_deid_documents) demo_to_latest() (in module pat2vec.util.pre_processing)

df_column_uniquify() (in module pat2vec.pat2vec_search.data_helper_functions) diagnostic_time_field (pat2vec.util.config_pat2vec.config_class attribute) draw_document_samples() (in module pat2vec.util.pre_processing) drop_columns_with_all_nan() (in module pat2vec.util.post_processing) dropna_doc_timestamps (pat2vec.util.config_pat2vec.config_class attribute) drug_time_field (pat2vec.util.config_pat2vec.config_class attribute) dummy_CAT (class in pat2vec.util.get_dummy_data_medcat_annotation) dummy_medcat_annotation_generator() (in module pat2vec.util.get_dummy_data_medcat_annotation) dump_results() (in module pat2vec.util.methods_get)

E

enabled_option (pat2vec.patvec_get_batch_methods.get_prefetch_batches.BatchConfig attribute), [1] enum_exact_target_date_vector() (in module pat2vec.util.methods_get) enum_target_date_vector() (in module pat2vec.util.methods_get) EthnicityAbstractor (class in pat2vec.util.ethnicity_abstractor) exist_check() (in module pat2vec.util.methods_get) extract_date_range() (in module pat2vec.util.get_dummy_data_cohort_searcher) extract_datetime_from_binary_columns() (in module pat2vec.util.post_processing)

extract_datetime_from_binary_columns_chunk_reader() (in module pat2vec.util.post_processing) extract_datetime_to_column() (in module pat2vec.util.post_processing) extract_labels_from_medcat_annotation_export() (in module pat2vec.util.medcat_misc_methods) extract_nhs_numbers() (in module pat2vec.util.helper_functions) extract_search_term_obscatalogmasteritem_displayname() (in module pat2vec.util.get_dummy_data_cohort_searcher) extract_treatment_id_list_from_docs() (in module pat2vec.pat2vec_pat_list.get_patient_treatment_list) extract_types_from_csv() (in module pat2vec.util.post_processing)

F

feature_engineering_arg_dict (pat2vec.util.config_pat2vec.config_class attribute) filter_and_select_rows() (in module pat2vec.util.post_processing) filter_and_update_csv() (in module pat2vec.util.post_processing) filter_annot_dataframe() (in module pat2vec.util.methods_annotation_filter_annot_dataframe) (in module pat2vec.util.post_processing_build_methods) filter_annot_dataframe2() (in module pat2vec.util.post_processing)

filter_dataframe_by_cui() (in module pat2vec.util.post_processing) filter_dataframe_by_fuzzy_terms() (in module pat2vec.util.filter_methods) filter_dataframe_by_timestamp() (in module pat2vec.util.filter_dataframe_by_timestamp) filter_dataframe_n_lists() (in module pat2vec.util.post_processing) filter_split_notes (pat2vec.util.config_pat2vec.config_class attribute) filter_stripped_list() (in module pat2vec.util.methods_get) find_date() (in module pat2vec.util.clinical_note_splitter)

G

generate_appointments_data() (in module pat2vec.util.get_dummy_data_cohort_searcher) generate_basic_observations_data() (in module pat2vec.util.get_dummy_data_cohort_searcher) generate_basic_observations_textual_obs_data() (in module pat2vec.util.get_dummy_data_cohort_searcher) generate_bmi_data() (in module pat2vec.util.get_dummy_data_cohort_searcher) generate_control_list() (in module pat2vec.pat2vec_pat_list.get_patient_treatment_list) generate_core_o2_data() (in module pat2vec.util.get_dummy_data_cohort_searcher) generate_core_resus_data() (in module pat2vec.util.get_dummy_data_cohort_searcher) generate_date_list() (in module pat2vec.util.generate_date_list) generate_diagnostic_orders_data() (in module pat2vec.util.get_dummy_data_cohort_searcher) generate_drug_orders_data() (in module pat2vec.util.get_dummy_data_cohort_searcher) generate_epr_documents_data() (in module pat2vec.util.get_dummy_data_cohort_searcher) generate_epr_documents_personal_data() (in module pat2vec.util.get_dummy_data_cohort_searcher) generate_hospital_site_data() (in module pat2vec.util.get_dummy_data_cohort_searcher) generate_observations_data() (in module pat2vec.util.get_dummy_data_cohort_searcher) generate_observations_MRC_text_data() (in module pat2vec.util.get_dummy_data_cohort_searcher) generate_observations_Reports_text_data() (in module pat2vec.util.get_dummy_data_cohort_searcher) generate_patient_timeline() (in module pat2vec.util.get_dummy_data_cohort_searcher) generate_patient_timeline_faker() (in module pat2vec.util.get_dummy_data_cohort_searcher) generate_pie_charts() (in module pat2vec.util.evaluation_methods_ploting) generate_report() (pat2vec.util.anonymisation_deid_documents.DeIdAnonymizer method) generate_uuid() (in module pat2vec.util.get_dummy_data_cohort_searcher) generate_uuid_list() (in module pat2vec.util.get_dummy_data_cohort_searcher) get_all_patients_list() (in module pat2vec.pat2vec_pat_list.get_patient_treatment_list) get_all_target_annots() (in module pat2vec.util.post_processing) get_annots_joined_to_docs() (in module pat2vec.util.post_processing_build_methods) get_appointments() (in module pat2vec.pat2vec_get_methods.get_method_appointments) get_bed() (in module pat2vec.pat2vec_get_methods.get_method_bed) get_bmi_features() (in module pat2vec.pat2vec_get_methods.get_method_bmi) get_cat() (in module pat2vec.util.methods_get_medcat) get_core_02() (in module pat2vec.pat2vec_get_methods.get_method_core02) get_core_resus() (in module pat2vec.pat2vec_get_methods.get_method_core_resus) get_current_pat_annotations() (in module pat2vec.pat2vec_get_methods.get_method_pat_annotations) get_current_pat_annotations_mrc_cs() (in module pat2vec.pat2vec_get_methods.get_method_current_pat_annotations_mrc_cs) get_current_pat_bloods() (in module pat2vec.pat2vec_get_methods.get_method_bloods) get_current_pat_diagnostics() (in module pat2vec.pat2vec_get_methods.get_method_diagnostics) get_current_pat_drugs() (in module pat2vec.pat2vec_get_methods.get_method_drugs) get_current_pat_report_annotations() (in module pat2vec.pat2vec_get_methods.get_method_report_annotations) get_current_pat_textual_obs_annotations() (in module pat2vec.pat2vec_get_methods.get_method_textual_obs_annotations) get_demo() (in module pat2vec.pat2vec_get_methods.get_method_demographics) get_demographics3() (in module pat2vec.pat2vec_get_methods.get_method_demo) get_demographics3_batch() (in module pat2vec.pat2vec_get_methods.get_method_demographics) get_docs_generator() (pat2vec.pat2vec_search.cogstack_search_methods.CogStack method) get_empty_date_vector() (in module pat2vec.util.methods_get) get_entities() (pat2vec.util.get_dummy_data_medcat_annotation.dummy_CAT method) get_entities_multi_texts() (pat2vec.util.get_dummy_data_medcat_annotation.dummy_CAT method) get_free_gpu() (in module pat2vec.util.methods_get) get_function (pat2vec.patvec_get_batch_methods.get_prefetch_batches.BatchConfig attribute), [1]

get_guess_datetime_column() (in module pat2vec.util.elasticsearch_methods) get_hosp_site() (in module pat2vec.pat2vec_get_methods.get_method_hosp_site) get_merged_pat_batch_appointments() (in module pat2vec.patvec_get_batch_methods.get_merged_batches) get_merged_pat_batch_bloods() (in module pat2vec.patvec_get_batch_methods.get_merged_batches) get_merged_pat_batch_bmi() (in module pat2vec.patvec_get_batch_methods.get_merged_batches) get_merged_pat_batch_demo() (in module pat2vec.patvec_get_batch_methods.get_merged_batches) get_merged_pat_batch_diagnostics() (in module pat2vec.patvec_get_batch_methods.get_merged_batches) get_merged_pat_batch_drugs() (in module pat2vec.patvec_get_batch_methods.get_merged_batches) get_merged_pat_batch_epr_docs() (in module pat2vec.patvec_get_batch_methods.get_merged_batches) get_merged_pat_batch_mct_docs() (in module pat2vec.patvec_get_batch_methods.get_merged_batches) get_merged_pat_batch_news() (in module pat2vec.patvec_get_batch_methods.get_merged_batches) get_merged_pat_batch_obs() (in module pat2vec.patvec_get_batch_methods.get_merged_batches) get_merged_pat_batch_reports() (in module pat2vec.patvec_get_batch_methods.get_merged_batches) get_merged_pat_batch_textual_obs_docs() (in module pat2vec.patvec_get_batch_methods.get_merged_batches) get_news() (in module pat2vec.pat2vec_get_methods.get_method_news) get_pat_batch_appointments() (in module pat2vec.patvec_get_batch_methods.main) get_pat_batch_bloods() (in module pat2vec.patvec_get_batch_methods.main) get_pat_batch_bmi() (in module pat2vec.patvec_get_batch_methods.main) get_pat_batch_demo() (in module pat2vec.patvec_get_batch_methods.main) get_pat_batch_diagnostics() (in module pat2vec.patvec_get_batch_methods.main) get_pat_batch_drugs() (in module pat2vec.patvec_get_batch_methods.main) get_pat_batch_epr_docs() (in module pat2vec.patvec_get_batch_methods.main) get_pat_batch_epr_docs_annotations() (in module pat2vec.patvec_get_batch_methods.main) get_pat_batch_mct_docs() (in module pat2vec.patvec_get_batch_methods.main) get_pat_batch_mct_docs_annotations() (in module pat2vec.patvec_get_batch_methods.main) get_pat_batch_news() (in module pat2vec.patvec_get_batch_methods.main) get_pat_batch_obs() (in module pat2vec.patvec_get_batch_methods.main) get_pat_batch_reports() (in module pat2vec.patvec_get_batch_methods.main) get_pat_batch_reports_docs_annotations() (in module pat2vec.patvec_get_batch_methods.main) get_pat_batch_textual_obs_annotation_batch() (in module pat2vec.util.methods_annotation_get_pat_document_annotation_batch) get_pat_batch_textual_obs_annotations() (in module pat2vec.patvec_get_batch_methods.main) get_pat_batch_textual_obs_docs() (in module pat2vec.patvec_get_batch_methods.main) get_pat_document_annotation_batch() (in module pat2vec.util.methods_annotation_get_pat_document_annotation_batch) get_pat_document_annotation_batch_mct() (in module pat2vec.util.methods_annotation_get_pat_document_annotation_batch) get_pat_document_annotation_batch_reports() (in module pat2vec.util.methods_annotation_get_pat_document_annotation_batch) get_pat_ipw_record() (in module pat2vec.util.post_processing_get_pat_ipw_record) get_patient_timeline_dummy() (in module pat2vec.util.get_dummy_data_cohort_searcher) get_search_client_idcode_list_from_nhs_number_list() (in module pat2vec.util.helper_functions) get_smoking() (in module pat2vec.pat2vec_get_methods.get_method_smoking) get_start_end_year_month() (in module pat2vec.util.get_start_end_year_month) get_structured_annotations() (pat2vec.util.anonymisation_deid_documents.DeIdAnonymizer method) get_treatment_docs_by_iterative_multi_term_cohort_searcher_no_terms_fuzzy() (in module pat2vec.util.pre_processing) get_treatment_records_by_drug_order_name() (in module pat2vec.util.pre_get_drug_treatment_docs) get_vte_status() (in module pat2vec.pat2vec_get_methods.get_method_vte_status) gpu_mem_threshold (pat2vec.util.config_pat2vec.config_class attribute) group_images_by_suffix() (in module pat2vec.util.presentation_methods) guess_datetime_columns() (in module pat2vec.util.elasticsearch_methods)

H

handle_inconsistent_dtypes() (in module pat2vec.util.elasticsearch_methods)

hostname (pat2vec.util.config_pat2vec.config_class attribute)

I

impute_dataframe() (in module pat2vec.util.post_processing) impute_datetime() (in module pat2vec.util.post_processing) individual_patient_id_column_name (pat2vec.util.config_pat2vec.config_class attribute) individual_patient_window (pat2vec.util.config_pat2vec.config_class attribute) individual_patient_window_controls_method (pat2vec.util.config_pat2vec.config_class attribute) individual_patient_window_df (pat2vec.util.config_pat2vec.config_class attribute) individual_patient_window_start_column_name (pat2vec.util.config_pat2vec.config_class attribute)

ingest_data_to_elasticsearch() (in module pat2vec.util.elasticsearch_methods) initialize_cogstack_client() (in module pat2vec.pat2vec_search.cogstack_search_methods) inspect_text() (pat2vec.util.anonymisation_deid_documents.DeIdAnonymizer method) is_loaded (pat2vec.util.anonymisation_deid_documents.DeIdAnonymizer attribute) iterative_drug_treatment_search() (in module pat2vec.util.pre_get_drug_treatment_docs) iterative_multi_term_cohort_searcher_no_terms_fuzzy() (in module pat2vec.pat2vec_search.cogstack_search_methods) iterative_multi_term_cohort_searcher_no_terms_fuzzy_mct() (in module pat2vec.pat2vec_search.cogstack_search_methods) iterative_multi_term_cohort_searcher_no_terms_fuzzy_textual_obs() (in module pat2vec.pat2vec_search.cogstack_search_methods)

J

join_docs_to_annots() (in module pat2vec.util.post_processing_build_methods) join_icd10_codes_to_annot() (in module pat2vec.util.post_processing)

join_icd10_OPC4S_codes_to_annot() (in module pat2vec.util.post_processing) json_to_dataframe() (in module pat2vec.util.methods_annotation_json_to_dataframe)

L

list_chunker() (in module pat2vec.pat2vec_search.cogstack_search_methods) list_dir_wrapper() (in module pat2vec.util.methods_get)

load_model() (pat2vec.util.anonymisation_deid_documents.DeIdAnonymizer method) logger (pat2vec.util.anonymisation_deid_documents.DeIdAnonymizer attribute) lookback (pat2vec.util.config_pat2vec.config_class attribute)

M

main (class in pat2vec.main_pat2vec), [1] main_batch() (in module pat2vec.pat2vec_main_methods.main_batch) main_options (pat2vec.util.config_pat2vec.config_class attribute) manually_label_annotation_df() (in module pat2vec.util.medcat_misc_methods) matcher() (in module pat2vec.pat2vec_search.matcher) maybe_nan() (in module pat2vec.util.get_dummy_data_cohort_searcher) mean_impute_dataframe() (in module pat2vec.util.impute_data_for_pipe) medcat (pat2vec.util.config_pat2vec.config_class attribute) medcat_trainer_export_to_df() (in module pat2vec.util.medcat_misc_methods) merge_appointments_csv() (in module pat2vec.util.post_processing_build_methods) merge_bmi_csv() (in module pat2vec.util.post_processing_build_methods) merge_demographics_csv() (in module pat2vec.util.post_processing_build_methods) merge_diagnostics_csv() (in module pat2vec.util.post_processing_build_methods) merge_drugs_csv() (in module pat2vec.util.post_processing_build_methods) merge_news_csv() (in module pat2vec.util.post_processing_build_methods) missing_percentage_df() (in module pat2vec.util.post_processing) model (pat2vec.util.anonymisation_deid_documents.DeIdAnonymizer attribute) model_path (pat2vec.util.anonymisation_deid_documents.DeIdAnonymizer attribute) module pat2vec.main_pat2vec pat2vec.pat2vec_get_methods pat2vec.pat2vec_get_methods.get_method_appointments pat2vec.pat2vec_get_methods.get_method_bed pat2vec.pat2vec_get_methods.get_method_bloods pat2vec.pat2vec_get_methods.get_method_bmi pat2vec.pat2vec_get_methods.get_method_core02 pat2vec.pat2vec_get_methods.get_method_core_resus pat2vec.pat2vec_get_methods.get_method_current_pat_annotations_mrc_cs pat2vec.pat2vec_get_methods.get_method_demo pat2vec.pat2vec_get_methods.get_method_demographics pat2vec.pat2vec_get_methods.get_method_diagnostics pat2vec.pat2vec_get_methods.get_method_drugs pat2vec.pat2vec_get_methods.get_method_hosp_site pat2vec.pat2vec_get_methods.get_method_news pat2vec.pat2vec_get_methods.get_method_pat_annotations pat2vec.pat2vec_get_methods.get_method_report_annotations pat2vec.pat2vec_get_methods.get_method_smoking pat2vec.pat2vec_get_methods.get_method_textual_obs_annotations pat2vec.pat2vec_get_methods.get_method_vte_status pat2vec.pat2vec_main_methods pat2vec.pat2vec_main_methods.main_batch pat2vec.pat2vec_pat_list pat2vec.pat2vec_pat_list.get_patient_treatment_list pat2vec.pat2vec_search pat2vec.pat2vec_search.cogstack_search_methods pat2vec.pat2vec_search.data_helper_functions pat2vec.pat2vec_search.matcher pat2vec.pat2vec_search.nearest pat2vec.pat2vec_search.search_helper_functions pat2vec.pat2vec_search.search_multiprocess pat2vec.patvec_get_batch_methods pat2vec.patvec_get_batch_methods.get_merged_batches pat2vec.patvec_get_batch_methods.get_prefetch_batches pat2vec.patvec_get_batch_methods.main pat2vec.util pat2vec.util.anonymisation_data_methods pat2vec.util.anonymisation_deid_documents pat2vec.util.calculate_interval pat2vec.util.clinical_note_splitter pat2vec.util.compile_requirements pat2vec.util.config_pat2vec pat2vec.util.credentials pat2vec.util.current_pat_batch_path_methods pat2vec.util.dummy_data_files pat2vec.util.dummy_data_files.dummy_lists pat2vec.util.elasticsearch_methods pat2vec.util.ethnicity_abstractor pat2vec.util.evaluation_methods pat2vec.util.evaluation_methods_ploting pat2vec.util.filter_dataframe_by_timestamp pat2vec.util.filter_methods pat2vec.util.generate_date_list pat2vec.util.get_best_gpu pat2vec.util.get_dummy_data_cohort_searcher pat2vec.util.get_dummy_data_medcat_annotation pat2vec.util.get_start_end_year_month pat2vec.util.helper_functions pat2vec.util.impute_data_for_pipe pat2vec.util.logger_setup pat2vec.util.medcat_misc_methods pat2vec.util.methods_annotation pat2vec.util.methods_annotation_filter_annot_dataframe pat2vec.util.methods_annotation_get_pat_document_annotation_batch pat2vec.util.methods_annotation_json_to_dataframe pat2vec.util.methods_annotation_multi_annots_to_df pat2vec.util.methods_annotation_regex pat2vec.util.methods_get pat2vec.util.methods_get_medcat pat2vec.util.methods_post_get pat2vec.util.parse_date pat2vec.util.post_processing pat2vec.util.post_processing_build_ipw_dataframe pat2vec.util.post_processing_build_methods pat2vec.util.post_processing_get_pat_ipw_record pat2vec.util.post_processing_medcat pat2vec.util.post_processing_process_csv_files pat2vec.util.pre_get_drug_treatment_docs pat2vec.util.pre_processing pat2vec.util.presentation_methods pat2vec.util.testing_helpers

months (pat2vec.util.config_pat2vec.config_class attribute) multi_annots_to_df() (in module pat2vec.util.methods_annotation_multi_annots_to_df) multi_annots_to_df_mct() (in module pat2vec.util.methods_annotation) multi_annots_to_df_reports() (in module pat2vec.util.methods_annotation) multi_annots_to_df_textual_obs() (in module pat2vec.util.methods_annotation) multi_process (pat2vec.util.config_pat2vec.config_class attribute)

N

n_pat_lines (pat2vec.util.config_pat2vec.config_class attribute) name (pat2vec.patvec_get_batch_methods.get_prefetch_batches.BatchConfig attribute), [1]

nearest() (in module pat2vec.pat2vec_search.nearest) negate_biochem (pat2vec.util.config_pat2vec.config_class attribute) negated_presence_annotations (pat2vec.util.config_pat2vec.config_class attribute)

O

output_folder (pat2vec.util.config_pat2vec.config_class attribute) output_folder_path (pat2vec.util.current_pat_batch_path_methods.PathsClass attribute)

override_medcat_model_path (pat2vec.util.config_pat2vec.config_class attribute) overwrite_stored_pat_docs (pat2vec.util.config_pat2vec.config_class attribute) overwrite_stored_pat_observations (pat2vec.util.config_pat2vec.config_class attribute)

P

parse_medcat_trainer_project_json() (in module pat2vec.util.medcat_misc_methods) parse_meta_anns() (in module pat2vec.util.methods_annotation_json_to_dataframe) password (pat2vec.util.config_pat2vec.config_class attribute) pat2vec.main_pat2vec module pat2vec.pat2vec_get_methods module pat2vec.pat2vec_get_methods.get_method_appointments module pat2vec.pat2vec_get_methods.get_method_bed module pat2vec.pat2vec_get_methods.get_method_bloods module pat2vec.pat2vec_get_methods.get_method_bmi module pat2vec.pat2vec_get_methods.get_method_core02 module pat2vec.pat2vec_get_methods.get_method_core_resus module pat2vec.pat2vec_get_methods.get_method_current_pat_annotations_mrc_cs module pat2vec.pat2vec_get_methods.get_method_demo module pat2vec.pat2vec_get_methods.get_method_demographics module pat2vec.pat2vec_get_methods.get_method_diagnostics module pat2vec.pat2vec_get_methods.get_method_drugs module pat2vec.pat2vec_get_methods.get_method_hosp_site module pat2vec.pat2vec_get_methods.get_method_news module pat2vec.pat2vec_get_methods.get_method_pat_annotations module pat2vec.pat2vec_get_methods.get_method_report_annotations module pat2vec.pat2vec_get_methods.get_method_smoking module pat2vec.pat2vec_get_methods.get_method_textual_obs_annotations module pat2vec.pat2vec_get_methods.get_method_vte_status module pat2vec.pat2vec_main_methods module pat2vec.pat2vec_main_methods.main_batch module pat2vec.pat2vec_pat_list module pat2vec.pat2vec_pat_list.get_patient_treatment_list module pat2vec.pat2vec_search module pat2vec.pat2vec_search.cogstack_search_methods module pat2vec.pat2vec_search.data_helper_functions module pat2vec.pat2vec_search.matcher module pat2vec.pat2vec_search.nearest module pat2vec.pat2vec_search.search_helper_functions module pat2vec.pat2vec_search.search_multiprocess module pat2vec.patvec_get_batch_methods module pat2vec.patvec_get_batch_methods.get_merged_batches module pat2vec.patvec_get_batch_methods.get_prefetch_batches module pat2vec.patvec_get_batch_methods.main module pat2vec.util module pat2vec.util.anonymisation_data_methods module pat2vec.util.anonymisation_deid_documents module pat2vec.util.calculate_interval module pat2vec.util.clinical_note_splitter module pat2vec.util.compile_requirements module pat2vec.util.config_pat2vec module pat2vec.util.credentials module pat2vec.util.current_pat_batch_path_methods module pat2vec.util.dummy_data_files module pat2vec.util.dummy_data_files.dummy_lists module pat2vec.util.elasticsearch_methods module pat2vec.util.ethnicity_abstractor module pat2vec.util.evaluation_methods module pat2vec.util.evaluation_methods_ploting module pat2vec.util.filter_dataframe_by_timestamp module

pat2vec.util.filter_methods module pat2vec.util.generate_date_list module pat2vec.util.get_best_gpu module pat2vec.util.get_dummy_data_cohort_searcher module pat2vec.util.get_dummy_data_medcat_annotation module pat2vec.util.get_start_end_year_month module pat2vec.util.helper_functions module pat2vec.util.impute_data_for_pipe module pat2vec.util.logger_setup module pat2vec.util.medcat_misc_methods module pat2vec.util.methods_annotation module pat2vec.util.methods_annotation_filter_annot_dataframe module pat2vec.util.methods_annotation_get_pat_document_annotation_batch module pat2vec.util.methods_annotation_json_to_dataframe module pat2vec.util.methods_annotation_multi_annots_to_df module pat2vec.util.methods_annotation_regex module pat2vec.util.methods_get module pat2vec.util.methods_get_medcat module pat2vec.util.methods_post_get module pat2vec.util.parse_date module pat2vec.util.post_processing module pat2vec.util.post_processing_build_ipw_dataframe module pat2vec.util.post_processing_build_methods module pat2vec.util.post_processing_get_pat_ipw_record module pat2vec.util.post_processing_medcat module pat2vec.util.post_processing_process_csv_files module pat2vec.util.pre_get_drug_treatment_docs module pat2vec.util.pre_processing module pat2vec.util.presentation_methods module pat2vec.util.testing_helpers module pat_maker() (pat2vec.main_pat2vec.main method), [1] PathsClass (class in pat2vec.util.current_pat_batch_path_methods) PathsClass_instance (pat2vec.util.config_pat2vec.config_class attribute) patient_id_column_name (pat2vec.util.config_pat2vec.config_class attribute) pii_labels (pat2vec.util.anonymisation_deid_documents.DeIdAnonymizer attribute) plot_missing_pattern_bloods() (in module pat2vec.util.post_processing) plot_ner_results() (in module pat2vec.util.medcat_misc_methods) pre_annotation_path (pat2vec.util.config_pat2vec.config_class attribute) pre_annotation_path_mrc (pat2vec.util.config_pat2vec.config_class attribute) pre_appointments_batch_path (pat2vec.util.config_pat2vec.config_class attribute) pre_bloods_batch_path (pat2vec.util.config_pat2vec.config_class attribute) pre_bmi_batch_path (pat2vec.util.config_pat2vec.config_class attribute) pre_demo_batch_path (pat2vec.util.config_pat2vec.config_class attribute) pre_diagnostics_batch_path (pat2vec.util.config_pat2vec.config_class attribute) pre_document_annotation_batch_path (pat2vec.util.config_pat2vec.config_class attribute) pre_document_annotation_batch_path_mct (pat2vec.util.config_pat2vec.config_class attribute) pre_document_batch_path (pat2vec.util.config_pat2vec.config_class attribute) pre_document_batch_path_mct (pat2vec.util.config_pat2vec.config_class attribute) pre_document_batch_path_reports (pat2vec.util.config_pat2vec.config_class attribute) pre_drugs_batch_path (pat2vec.util.config_pat2vec.config_class attribute) pre_merged_input_batches_path (pat2vec.util.config_pat2vec.config_class attribute) pre_misc_batch_path (pat2vec.util.config_pat2vec.config_class attribute) pre_news_batch_path (pat2vec.util.config_pat2vec.config_class attribute) pre_obs_batch_path (pat2vec.util.config_pat2vec.config_class attribute) pre_report_annotation_batch_path_report (pat2vec.util.config_pat2vec.config_class attribute) pre_report_batch_path (pat2vec.util.config_pat2vec.config_class attribute) pre_textual_obs_annotation_batch_path (pat2vec.util.config_pat2vec.config_class attribute) pre_textual_obs_document_batch_path (pat2vec.util.config_pat2vec.config_class attribute) prefetch_batches() (in module pat2vec.patvec_get_batch_methods.get_prefetch_batches) prefetch_pat_batches (pat2vec.util.config_pat2vec.config_class attribute) prepare_diagnostic_datetime() (in module pat2vec.pat2vec_get_methods.get_method_diagnostics) prepare_drug_datetime() (in module pat2vec.pat2vec_get_methods.get_method_drugs) prepare_hospital_site_data() (in module pat2vec.pat2vec_get_methods.get_method_hosp_site) prepare_smoking_data() (in module pat2vec.pat2vec_get_methods.get_method_smoking) prepare_vte_data() (in module pat2vec.pat2vec_get_methods.get_method_vte_status) process_chunk() (in module pat2vec.util.post_processing) process_csv_files() (in module pat2vec.util.post_processing_process_csv_files) process_csv_files_multi() (in module pat2vec.util.post_processing_process_csv_files) process_demographics_data() (in module pat2vec.pat2vec_get_methods.get_method_demo) process_requirements() (in module pat2vec.util.compile_requirements) produce_filtered_annotation_dataframe() (in module pat2vec.util.post_processing) proj_name (pat2vec.util.config_pat2vec.config_class attribute) pull_and_write() (in module pat2vec.pat2vec_search.search_multiprocess) pylist2searchlist() (in module pat2vec.pat2vec_search.search_helper_functions)

R

random_sample() (in module pat2vec.util.get_dummy_data_medcat_annotation) random_seed_val (pat2vec.util.config_pat2vec.config_class attribute) read_csv_wrapper() (in module pat2vec.util.methods_get) read_remote() (in module pat2vec.util.methods_get) read_test_data() (in module pat2vec.util.testing_helpers) recreate_json() (in module pat2vec.util.medcat_misc_methods) remote_dump (pat2vec.util.config_pat2vec.config_class attribute) remove_file_from_paths() (in module pat2vec.util.post_processing)

retrieve_pat_annotations() (in module pat2vec.util.methods_post_get) retrieve_pat_annots_mct_epr() (in module pat2vec.util.post_processing) retrieve_pat_bloods() (in module pat2vec.util.post_processing_build_methods) retrieve_pat_docs_mct_epr() (in module pat2vec.util.post_processing_build_methods) root_path (pat2vec.util.config_pat2vec.config_class attribute) (pat2vec.util.current_pat_batch_path_methods.PathsClass attribute) run_generate_patient_timeline_and_append() (in module pat2vec.util.get_dummy_data_cohort_searcher) run_pip_compile() (in module pat2vec.util.compile_requirements)

S

sample_by_terms() (in module pat2vec.util.post_processing_medcat) sample_treatment_docs (pat2vec.util.config_pat2vec.config_class attribute) sanitize_hospital_ids() (in module pat2vec.pat2vec_pat_list.get_patient_treatment_list) save_group() (in module pat2vec.patvec_get_batch_methods.get_merged_batches) save_log() (pat2vec.util.anonymisation_deid_documents.DeIdAnonymizer method) save_missing_percentage() (in module pat2vec.util.impute_data_for_pipe) save_missing_values_pickle() (in module pat2vec.util.post_processing) save_path_attr (pat2vec.patvec_get_batch_methods.get_prefetch_batches.BatchConfig attribute), [1] search_appointments() (in module pat2vec.pat2vec_get_methods.get_method_appointments) search_bed_data() (in module pat2vec.pat2vec_get_methods.get_method_bed) search_bloods_data() (in module pat2vec.pat2vec_get_methods.get_method_bloods) search_bmi_observations() (in module pat2vec.pat2vec_get_methods.get_method_bmi) search_cohort() (in module pat2vec.util.pre_processing) search_core_o2_observations() (in module pat2vec.pat2vec_get_methods.get_method_core02) search_core_resus_observations() (in module pat2vec.pat2vec_get_methods.get_method_core_resus) search_demographics() (in module pat2vec.pat2vec_get_methods.get_method_demo) search_diagnostic_orders() (in module pat2vec.pat2vec_get_methods.get_method_diagnostics) search_drug_orders() (in module pat2vec.pat2vec_get_methods.get_method_drugs) search_hospital_site() (in module pat2vec.pat2vec_get_methods.get_method_hosp_site) search_smoking() (in module pat2vec.pat2vec_get_methods.get_method_smoking) search_term (pat2vec.patvec_get_batch_methods.get_prefetch_batches.BatchConfig attribute), [1] search_vte() (in module pat2vec.pat2vec_get_methods.get_method_vte_status) set_best_gpu() (in module pat2vec.util.get_best_gpu) set_index_safe_wrapper() (in module pat2vec.pat2vec_search.cogstack_search_methods)

setup_logger() (in module pat2vec.util.logger_setup) sftp_client (pat2vec.util.config_pat2vec.config_class attribute) sftp_exists() (in module pat2vec.util.methods_get) share_sftp (pat2vec.util.config_pat2vec.config_class attribute) shuffle_pat_list (pat2vec.util.config_pat2vec.config_class attribute) skip_additional_listdir (pat2vec.util.config_pat2vec.config_class attribute) skipped_counter (pat2vec.util.config_pat2vec.config_class attribute) slow_execution_threshold_extreme (pat2vec.util.config_pat2vec.config_class attribute) slow_execution_threshold_high (pat2vec.util.config_pat2vec.config_class attribute) slow_execution_threshold_low (pat2vec.util.config_pat2vec.config_class attribute) split_and_append_chunks() (in module pat2vec.util.clinical_note_splitter) split_and_save_csv() (in module pat2vec.patvec_get_batch_methods.get_merged_batches) split_clinical_notes (pat2vec.util.config_pat2vec.config_class attribute) split_clinical_notes() (in module pat2vec.util.clinical_note_splitter) split_clinical_notes_mct() (in module pat2vec.util.clinical_note_splitter) start_date (pat2vec.util.config_pat2vec.config_class attribute) start_time (pat2vec.util.config_pat2vec.config_class attribute) store_annot (pat2vec.util.config_pat2vec.config_class attribute) store_pat_batch_docs (pat2vec.util.config_pat2vec.config_class attribute) store_pat_batch_observations (pat2vec.util.config_pat2vec.config_class attribute) stringlist2pylist() (in module pat2vec.pat2vec_search.search_helper_functions) stringlist2searchlist() (in module pat2vec.pat2vec_search.search_helper_functions) strip_list (pat2vec.util.config_pat2vec.config_class attribute) suffix (pat2vec.util.config_pat2vec.config_class attribute) (pat2vec.util.current_pat_batch_path_methods.PathsClass attribute)

T

t (pat2vec.main_pat2vec.main attribute), [1] temporary_file() (in module pat2vec.util.methods_annotation_multi_annots_to_df) test_data_path (pat2vec.util.config_pat2vec.config_class attribute) test_datetime_formats() (in module pat2vec.util.methods_get)

testing (pat2vec.util.config_pat2vec.config_class attribute) time_delta (pat2vec.util.config_pat2vec.config_class attribute) time_window_interval_delta (pat2vec.util.config_pat2vec.config_class attribute) treatment_control_ratio_n (pat2vec.util.config_pat2vec.config_class attribute) treatment_doc_filename (pat2vec.util.config_pat2vec.config_class attribute)

U

update_global_start_date() (in module pat2vec.util.config_pat2vec) update_pbar() (in module pat2vec.util.methods_get)

use_controls (pat2vec.util.config_pat2vec.config_class attribute) username (pat2vec.util.config_pat2vec.config_class attribute)

V

validate_and_fix_global_dates() (in module pat2vec.util.config_pat2vec) validate_input_dates() (in module pat2vec.util.parse_date)

verbosity (pat2vec.util.config_pat2vec.config_class attribute) verify_split_data_concatenated() (in module pat2vec.patvec_get_batch_methods.get_merged_batches) verify_split_data_individual() (in module pat2vec.patvec_get_batch_methods.get_merged_batches)

W

without_keys() (in module pat2vec.pat2vec_search.search_helper_functions)

write_csv_wrapper() (in module pat2vec.util.methods_get) write_remote() (in module pat2vec.util.methods_get)

Y

years (pat2vec.util.config_pat2vec.config_class attribute)