lookup_codes: Look up descriptions for clinical codes
In rmgpanw/codemapper: Functions for Mapping Between Clinical Coding Systems

lookup_codes

R Documentation

Look up descriptions for clinical codes

Description

Returns a data frame including descriptions for the codes of interest

Usage

lookup_codes(
  codes,
  code_type,
  all_lkps_maps = NULL,
  preferred_description_only = TRUE,
  standardise_output = TRUE,
  unrecognised_codes = "error",
  col_filters = default_col_filters(),
  .return_unrecognised_codes = FALSE
)

Arguments

`codes`	character. Vector of codes to lookup
`code_type`	character. The type of clinical code system to be searched. Must be one obnf, dmd, icd9, icd10, read2, read2_drugs, read3, opcs4, data_coding_3, data_coding_4, data_coding_5, data_coding_6, sct, or phecode)'.
`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.
`preferred_description_only`	bool. Return only preferred descriptions for clinical codes with synonyms. Default value is `TRUE`.
`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, then either an error or warning will be raised.
`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.
`.return_unrecognised_codes`	If `TRUE`, return a vector of unrecognised codes only.

Value

data frame

Examples

# build dummy all_lkps_maps
all_lkps_maps_dummy <- build_all_lkps_maps_dummy()

# look up ICD10 codes
lookup_codes(
  codes = c("E10", "E11"),
  code_type = "icd10",
  all_lkps_maps = all_lkps_maps_dummy
)

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