Get codes that start with...

This is case sensitive (important for read codes especially).

codes_starting_with(
  codes,
  code_type,
  all_lkps_maps = NULL,
  codes_only = FALSE,
  preferred_description_only = TRUE,
  standardise_output = TRUE,
  col_filters = default_col_filters()
)

Arguments

codes: character. A vector of code strings to search for matching codes.
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.
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).
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).
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.

Examples

# build dummy all_lkps_maps
all_lkps_maps_dummy <- build_all_lkps_maps_dummy()

# lookup codes
lookup_codes(
  codes = c("E10", "E11"),
  code_type = "icd10",
  all_lkps_maps = all_lkps_maps_dummy
)
#> # A tibble: 2 × 3
#>   code  description              code_type
#>   <chr> <chr>                    <chr>    
#> 1 E10   Type 1 diabetes mellitus icd10    
#> 2 E11   Type 2 diabetes mellitus icd10

Arguments

See also

Examples