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Look up descriptions for clinical codes

Source: R/codes.R
CODES.Rd

Returns a data frame including descriptions for the codes of interest

Usage

CODES(
  codes,
  code_type = getOption("codeminer.code_type"),
  lookup_version = getOption("codeminer.lookup_version", default = "latest"),
  preferred_description_only = TRUE
)

CODES_LIKE(
  pattern,
  code_type = getOption("codeminer.code_type"),
  lookup_version = getOption("codeminer.lookup_version", default = "latest"),
  preferred_description_only = TRUE
)

Arguments

codes

character. Vector of codes to lookup. If passing "all", returns all codes.

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.

preferred_description_only

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

pattern

a regular expression to search for

Value

A data.frame containing the codes and their descriptions

Details

CODES_LIKE searches for codes that match a given regular expression. The matching is case-insensitive.

See also

add_lookup_table() for adding new lookup tables to the database.

Other Clinical code lookups and mappings: MAP(), default_col_filters()

Examples

# Set up a temporary dummy database
temp_db <- tempfile(fileext = ".duckdb")
create_dummy_database(temp_db)
#> Creating new database at /tmp/RtmpRK6Py7/file1bd3b3c66ef.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!

# look up ICD10 codes
CODES(
  codes = c("E10", "E11"),
  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
CODES_LIKE("^E1", 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