Man pages for niekverw/ukbpheno
Extraction and processing UK Biobank data to generate health outcome phenotypes
| add_child_nodes | Traverse hierarchical code dictionary |
| check_dfDefinitions_codes | Check if the illness/medication codes in definition table are... |
| CheckDuplicateTRAITS | Check if there is duplicates entries of phenotypes/traits in... |
| convert_cancerregister_to_episodedata | Convert illness codes from cancer register columns with... |
| convert_col_to_integer | Convert numbers in character to integer |
| convert_dataframelist_to_lst | Helper function to structure the processed definition |
| ConvertFactorsToStringReplaceNAInDf | Change factors to strings in a dataframe and assign NA to... |
| convert_nurseinterview_to_episodedata | Convert self-reported illness codes from verbal interview... |
| convert_touchscreen_to_episodedata | Convert self-reported illness codes from touchscreen with... |
| convert_year_to_date | Convert year in decimal unit to date of format yyyy-mm-dd |
| default_ukb_fields | Default_ukb_fields |
| dotplot_diseases_by_source | Dotplot by data sources |
| expand_dfDefinitions_processed | Expand the illness/medication codes in definition table to... |
| expand_dfDefinitions_processed2 | Expand the illness/medication codes in definition table to... |
| get_all_events | Get all episodes for a phenotype |
| get_allvarnames | Retrieve the required data fields in the ukb dataset... |
| get_case_count_by_source | Get case-control status (Any) by data sources |
| get_cases | Get case for a phenotype |
| get_cases_controls | Get case and controls for a phenotype |
| get_case_status_by_source | Get case-control status (Hx) by data sources used for upset... |
| get_incidence_prevalence | Get data for phenotype incidence and prevalence |
| get_lst_counts | Get summary counts on a list of data tables |
| get_stats_for_events | Summary statistics of events for single phenotype |
| harmonize_ukb_data | Prepare harmonized long format data from various data sources |
| isNullNaNan | Check if string variable is valid |
| lookup.codes | Helper function to look up the dependencies |
| make_upsetplot | Make upset plot |
| parse_gp_clinical_values | Parse the value columns of the Primary Care clinical records |
| parseIncludeExcludeCol | Helper function to parse the trait dependencies |
| pasteRemoveNA | Custom paste function with formatting step to remove... |
| plot_disease_timeline_by_source | data source trajectory over time |
| plot_individual_timeline | Get all episodes for a phenotype |
| PreProcessDfDefinitions | Preprocess the definition table |
| ProcessDfDefinitions | ProcessDfDefinitions |
| rand_col_vec | return random colors of specified length |
| read_death_data | Read Mortality data |
| read_definition_table | Process definition table |
| read_gp_clinical_data | Read Primary Care clinical event records |
| read_gp_script_data | Read Primary Care prescription records |
| read_hesin_data | Read Hospital Inpatient Data |
| read_ukb_metadata | Read the data dictionary for main dataset |
| read_ukb_tabdata | Read the main dataset |
| reexports | Objects exported from other packages |
| ReplaceNAWithNearestNonNAOnTheLeft | Replace NA With Nearest Non-NA On The Left |
