Man pages for patelm9/cartographR
| add_new_query_term | Add a new query term from the output of collect_query_terms... |
| append_staged_to_key | Adds PROGRESS_LIST$Staged to KEY |
| bulk_bucket_denovos | Bulk flags rows for denovo cui based on row numbers |
| bulk_edit_external_followup | Bulk flag rows for external followup |
| bulk_flag_rows_for_external_followup | Bulk flag rows for external followup |
| bulk_store_new_cui_in_local_key | Appends local key with new concept annotation using a... |
| bulk_timestamp_rows_for_completed_external_followup | Bulk changes PROGRESS_LIST$PARKED_FOR_EXTERNAL_FOLLOWUP and... |
| collect_query_terms | Interactively collect phrases that will be used in the WHERE... |
| create_new_table_of_contents | Creates a new table of contents from arguments in format:... |
| double_query_mrconso | Searching mrconso with 2 LIKE phrases |
| flag_rows_for_denovo_cui | Bulk flags rows for denovo cui based on row numbers |
| generate_next_id_number | Generate next ID number |
| get_first_possible_cui | Gets first possible cui for the input phrase in English and... |
| identity_from_csv | Gets IDENTITY data and cleans up based on parameters |
| identity_from_gs | Gets IDENTITY data and cleans up based on parameters |
| identity_from_xlsx | Gets IDENTITY data and cleans up based on parameters |
| interactive_double_term_search | Performs a double phrase search in MRCONSO rowwise in... |
| interactive_single_term_search | Performs a single phrase search in MRCONSO rowwise in... |
| jatpat_mrconso_coordinate | This function takes a column in a dataframe that contains... |
| join_progress_list | Takes IDENTITY and KEY and creates a PROGRESS LIST based on... |
| key_from_csv | Gets KEY data and cleans up based on parameters |
| key_from_gs | Gets KEY data and cleans up based on parameters |
| key_from_xlsx | Gets KEY data and cleans up based on parameters |
| lookup_native_attributes | Looks up native attributes from IDENTITY |
| observe_parked_for_denovo_to_bucket | Observe the PROGRES_LIST$PARKED_FOR_DENOVO to bucket these... |
| observe_parked_for_external_followup | Observe the PROGRES_LIST$PARKED_FOR_EXTERNAL_FOLLOWUP to map |
| observe_queue | Observe the PROGRES_LIST$QUEUE to map |
| progress_list | Fresh upload of IDENTITY and KEY to create a new... |
| progress_list_staged_to_key | Adds PROGRESS_LIST$Staged to KEY |
| qa_mrconso_net_glossary | This function will make sure that the GLOSSARY and list of... |
| qa_mrconso_net_glossary_2 | This function will deduplicate the GLOSSARY based on the... |
| query_mrconso_data_exact_limit_one | Queries MRCONSO UMLS table for the exact phrase and limit 1 |
| remove_record_from_glossary | Completely removes all traces of a query search |
| remove_source_concept_from_key | Completely removes all traces of a concept that didn't need... |
| report | Creates a REPORT that contains TABLE_OF_CONTENTS sourced from... |
| return_mrconso_net | Returns MRCONSO NETS that match the phrase |
| review_coordinates | Makes sure that the coordinate cui and its associated strings... |
| scavenge_na_concepts | Scavenges and assigns all NA concepts to the "C0027366" cui |
| set_paths | Sets the key location to iterate on when making updates |
| store_new_cui_in_local_key | Appends local key with new concept annotation |
| str_match_bw_parentheses | STR match splitting by parenthesis |
| str_match_with_rearrangement | Inverts concepts with a single dash to see if a string match... |
| view_progress_list_nrow | View the rownumber per status in progress_list |
| write_mrconso_coordinate | This function takes a column in a dataframe that contains... |
| write_mrconso_net | Writes a MRCONSO NET file if one does not exist for the given... |
