Search for codes that match a description

Returns a data frame with clinical codes that match the provided description pattern.

Usage

DESCRIPTION(
  pattern,
  code_type = getOption("codeminer.code_type"),
  lookup_version = getOption("codeminer.lookup_version", default = "latest"),
  ignore_case = TRUE,
  codes_only = FALSE,
  preferred_description_only = TRUE
)

Arguments

pattern

The description to search for. See stringr::str_detect() for details.

code_type

character. Type of clinical code system to be searched. Depends on what is available in the lookup tables. See add_lookup_table() on how to add new lookup tables. This can also be configured through the codeminer.code_type option.

lookup_version

character. Version of the lookup table to use. Default: "latest". Can be configured through the codeminer.lookup_version option.

ignore_case

If TRUE (default), ignore case in description.

codes_only

logical. 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

logical. If TRUE, only returns the preferred description for each code. Default: FALSE.

Value

The result of CODES() for codes that match the description, or a character vector of codes if codes_only is TRUE.

Examples

# build dummy database
create_dummy_database()
#> Creating new database at /tmp/RtmpRK6Py7/file1bd37e537787.duckdb
#> Reading 17 selected tables from UKB Resource 592
#> 
#> Extending read_v2_drugs_bnf with BNF hierarchy and descriptions
#> Extending read_v2_icd10 by expanding ICD-10 code ranges
#> Adding tables to database
#> ✔ Lookup table BNF_UKB v4 added successfully.
#> ✔ Relationship table BNF_relationship_UKB v4 added successfully.
#> ✔ Lookup table DM+D_UKB v4 added successfully.
#> ✔ Lookup table ICD-9_UKB v4 added successfully.
#> ✔ Relationship table ICD-9_relationship_UKB v4 added successfully.
#> ✔ Lookup table ICD-10_UKB v4 added successfully.
#> ✔ Relationship table ICD-10_relationship_UKB v4 added successfully.
#> ✔ Mapping table ICD-9_ICD-10_UKB v4 added successfully.
#> ✔ Lookup table Read 2_UKB v4 added successfully.
#> ✔ Relationship table Read 2_relationship_UKB v4 added successfully.
#> ✔ Lookup table Read 2, drugs_UKB v4 added successfully.
#> ✔ Mapping table Read 2, drugs_BNF_UKB v4 added successfully.
#> ✔ Mapping table Read 2_ICD-9_UKB v4 added successfully.
#> ✔ Mapping table Read 2_ICD-10_UKB v4 added successfully.
#> ✔ Mapping table Read 2_OPCS4_UKB v4 added successfully.
#> ✔ Mapping table Read 2_Read 3_UKB v4 added successfully.
#> ✔ Lookup table Read 3_UKB v4 added successfully.
#> ✔ Mapping table Read 3_ICD-9_UKB v4 added successfully.
#> ✔ Mapping table Read 3_ICD-10_UKB v4 added successfully.
#> ✔ Mapping table Read 3_OPCS4_UKB v4 added successfully.
#> ✔ Mapping table Read 3_Read 2_UKB v4 added successfully.
#> ✔ Dummy database ready to use!

# lookup ICD10 code descriptions matching 'cyst'
DESCRIPTION("cyst", code_type = "ICD-10")
#> Warning: cannot open file '/home/runner/.local/share/codeminer/ontology.duckdb': No such file or directory
#> Error in file(con, "w"): cannot open the connection