Function reference • codemapper

Setting up Build a local resource with lookup and mapping tables for various clinical coding systems.
`get_ukb_all_lkps_maps()`	Get UK Biobank resource 592 directly from UKB website
`read_all_lkps_maps()`	Read UK Biobank resource 592 into a named list
`build_all_lkps_maps()`	Build named list of clinical code look up and mapping tables
`all_lkps_maps_to_db()`	Build a SQLite database of clinical code look up and mapping tables
Clinical codes Functions for looking up clinical codes and mapping between different coding systems.
`lookup_codes()`	Look up descriptions for clinical codes
`codes_starting_with()`	Get codes that start with...
`code_descriptions_like()`	Search for codes that match a description
`map_codes()`	Map clinical codes from one coding system to another
`get_mapping_df()`	Get a 'from-to' mapping data frame
`reformat_icd10_codes()`	Reformat ICD-10 codes
`default_col_filters()`	Default filtering parameters for lookup and mapping tables.
`RunCodelistBuilder()`	Create a clinical codelist with R Shiny.
CALIBER Functions for reformatting CALIBER codelists to use with UK Biobank data
`download_caliber_repo()`	Download the caliber github repository
`read_caliber_raw()`	Import CALIBER code lists
`reformat_caliber_for_ukb()`	Reformat and map CALIBER codes for use with UK Biobank data
`default_overlapping_disease_categories_csv()`	CSV file for resolving overlapping disease categories in mapped CALIBER codes
`get_caliber_categories_mapping()`	Get a mapping table of CALIBER phenotypes/categories
Phecodes Functions for mapping UK Biobank data to Phecodes
`map_clinical_events_to_phecodes()`	Map UK Biobank clinical events to phecodes
`make_phecode_reverse_map()`	Reverse map from phecodes to Read and ICD 9
Dummy data Dummy data for tests.
`build_all_lkps_maps_dummy()`	Create a dummy all_lkps_maps
`read_all_lkps_maps_dummy()`	Read dummy UK Biobank resource 592 into R
`read_ukb_codings_dummy()`	Read dummy UK Biobank codings into R
`read_phecode_lkp_dummy()`	Read dummy Phecode definitions file into R
`read_icd10_phecode_map_dummy()`	Read dummy Phecode Map 1.2 with ICD-10 codes (beta) file into R
`dummy_clinical_events_tidy()`	Dummy UK Biobank clinical events, tidied
`codemapper_metadata()`	Metadata
`get_nhsbsa_snomed_bnf()`	Download and read the NHSBSA BNF_SNOMED mapping file
`get_ukb_self_report_med_to_atc_map()`	Download and read a UKB welf-reported medication code to ATC mapping file
`get_phecode_definitions()`	Download the Phecode 1.2 definitions file
`get_phecode_icd9_map()`	Download the Phecode 1.2 to ICD9 mapping file
`get_phecode_icd10_map()`	Download the Phecode 1.2 to ICD10 (beta) mapping file
`dummy_all_lkps_maps_path()`	Dummy UK Biobank resource 592 file path
`dummy_ukb_codings_path()`	Dummy UK Biobank codings file path
`dummy_phecode_lkp_path()`	Dummy Phecode definitions file path
`dummy_icd10_phecode_map_path()`	Dummy Phecode Map 1.2 with ICD-10 codes (beta) file path
`dummy_caliber_dir_path()`	Dummy CALIBER repository

Reference

Setting up

Clinical codes

CALIBER

Phecodes

Dummy data