map_codes: Map clinical codes from one coding system to another
In rmgpanw/codemapper: Functions for Mapping Between Clinical Coding Systems

map_codes

R Documentation

Map clinical codes from one coding system to another

Description

Uses the code mapping file provided by UK Biobank (resource 592).

Usage

map_codes(
  codes,
  from,
  to,
  all_lkps_maps = NULL,
  codes_only = FALSE,
  standardise_output = TRUE,
  unrecognised_codes = "error",
  preferred_description_only = NULL,
  reverse_mapping = "error",
  col_filters = default_col_filters()
)

Arguments

`codes`	A character vector of codes to be mapped.
`from`	Coding system that `codes` belong to.
`to`	Coding system to map `codes` to.
`all_lkps_maps`	Either a named list of lookup and mapping tables (either data frames or `tbl_dbi` objects), or the path to a SQLite database containing these tables (see also `build_all_lkps_maps()` and `all_lkps_maps_to_db()`). If `NULL`, will attempt to connect to an SQLite database named 'all_lkps_maps.db' in the current working directory, or to a a SQLite database specified by an environmental variable named 'ALL_LKPS_MAPS_DB' (see here for how to set environment variables using a `.Renviron` file). The latter method will be used in preference.
`codes_only`	bool. If `TRUE`, return a character vector of unique codes. If `FALSE` (default), return a data frame of all results including code descriptions (useful for manual validation).
`standardise_output`	bool. If `TRUE` (default), outputs a data frame with columns named 'code', 'description' and 'code_type'. Otherwise returns a data frame with all columns for the relevant lookup sheet from (UK Biobank resource 592).
`unrecognised_codes`	Either 'error' (default) or 'warning'. If any input `codes` are unrecognised for the coding system being mapped from, then either an error or warning will be raised.
`preferred_description_only`	If `TRUE`, return only preferred descriptions for clinical codes with synonyms. Can only be `TRUE` if `standardise_output` is also `TRUE`. Default value is `NULL`.
`reverse_mapping`	If 'error' (default), an error raised if attempting to map between coding systems for which a mapping table does not exist. If 'warning', will raise a warning and attempt to use an existing mapping table in the opposite direction (for example, a mapping from ICD10 to Read 3 would be attempted using the Read 3-to-ICD10 mapping table).
`col_filters`	A named list where each name in the list refers to the name of a lookup or mapping table. Each item is also a named list, where the names refer to column names in the corresponding table, and the items are vectors of values to filter for. For example, `⁠list(my_lookup_table = list(colA = c("A", "B"))⁠` will result in `my_lookup_table` being filtered for rows where `colA` is either 'A' or 'B'. Uses `default_col_filters()` by default. Set to `NULL` to remove all filters.

Details

The values for arguments from and to must be one of read2, read3, icd9, icd10, bnf, dmd, read2_drugs or opcs4.

Examples

# build dummy all_lkps_maps
all_lkps_maps_dummy <- build_all_lkps_maps_dummy()

# map codes from Read 2 to ICD10
map_codes(
  codes = "G20..",
  from = "read2",
  to = "icd10",
  all_lkps_maps = all_lkps_maps_dummy
)

rmgpanw/codemapper documentation built on Aug. 30, 2023, 4:07 p.m.