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Look up descriptions for clinical codes

Source: R/codes.R
CODES.Rd

Returns a codelist with descriptions for the codes of interest. Supports flexible input: character vectors, || separated strings, or data frames.

Usage

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

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

Arguments

...

Codes to look up. Can be:

  • Character vectors: CODES("E10", "E11", type = "ICD-10")

  • || separated strings: CODES("E10 || E11", type = "ICD-10")

  • Data frame with code/description/code_type columns: CODES(my_df)

  • Mixed: CODES("E10", my_vector, "E13 || E14", type = "ICD-10")

Special values: "all" returns all codes; empty input returns empty codelist.

Comments can be added with << >> syntax: "E10 << Type 1 diabetes >>".

type

character. Type of clinical code system to be searched. Optional if input is a data frame with code_type column. 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.

col_filters

Column filters to apply. One of:

  • "default" (default): apply session-pinned or metadata-defined default filters

  • NULL: no filtering (return all rows)

  • A named list of column_name = c(values) pairs for explicit filtering

pattern

a regular expression to search for

Value

A codeminer_codelist object (tibble) 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(), get_lookup_table(), get_mapping_table(), get_relationship_table()

Examples

# Set up a temporary dummy database
temp_db <- tempfile(fileext = ".duckdb")
create_dummy_database(temp_db)
#> ✔ Dummy database ready to use!

# Multiple arguments
CODES("E10", "E11", type = "ICD-10")
#> ℹ Using 'UKB v4' as latest version
#> <codeminer_codelist>: 2 codes
#> Code type: "ICD-10"
#> 
#> # A tibble: 2 × 3
#>   code  description              code_type
#>   <chr> <chr>                    <chr>    
#> 1 E10   Type 1 diabetes mellitus ICD-10   
#> 2 E11   Type 2 diabetes mellitus ICD-10   

# With comments
CODES("E10 << Type 1 diabetes >>", type = "ICD-10")
#> <codeminer_codelist>: 1 code
#> Code type: "ICD-10"
#> 
#> # A tibble: 1 × 3
#>   code  description              code_type
#>   <chr> <chr>                    <chr>    
#> 1 E10   Type 1 diabetes mellitus ICD-10   

# || separated string
CODES("E10 || E11", type = "ICD-10")
#> <codeminer_codelist>: 2 codes
#> Code type: "ICD-10"
#> 
#> # A tibble: 2 × 3
#>   code  description              code_type
#>   <chr> <chr>                    <chr>    
#> 1 E10   Type 1 diabetes mellitus ICD-10   
#> 2 E11   Type 2 diabetes mellitus ICD-10   

# Splice operator
my_codes <- c("E10", "E11")
CODES(!!!my_codes, type = "ICD-10")
#> <codeminer_codelist>: 2 codes
#> Code type: "ICD-10"
#> 
#> # A tibble: 2 × 3
#>   code  description              code_type
#>   <chr> <chr>                    <chr>    
#> 1 E10   Type 1 diabetes mellitus ICD-10   
#> 2 E11   Type 2 diabetes mellitus ICD-10   

# Data frame input
df <- data.frame(
  code = c("E10", "E11"),
  description = c("Type 1", "Type 2"),
  code_type = c("ICD-10", "ICD-10")
)
CODES(df)
#> <codeminer_codelist>: 2 codes
#> Code type: "ICD-10"
#> 
#> # A tibble: 2 × 3
#>   code  description              code_type
#>   <chr> <chr>                    <chr>    
#> 1 E10   Type 1 diabetes mellitus ICD-10   
#> 2 E11   Type 2 diabetes mellitus ICD-10   
CODES_LIKE("^E1", type = "ICD-10")
#> <codeminer_codelist>: 55 codes
#> Code type: "ICD-10"
#> 
#> # A tibble: 55 × 3
#>    code  description                                                   code_type
#>    <chr> <chr>                                                         <chr>    
#>  1 E10   Type 1 diabetes mellitus                                      ICD-10   
#>  2 E100  Type 1 diabetes mellitus With coma                            ICD-10   
#>  3 E101  Type 1 diabetes mellitus With ketoacidosis                    ICD-10   
#>  4 E102  Type 1 diabetes mellitus With renal complications             ICD-10   
#>  5 E103  Type 1 diabetes mellitus With ophthalmic complications        ICD-10   
#>  6 E104  Type 1 diabetes mellitus With neurological complications      ICD-10   
#>  7 E105  Type 1 diabetes mellitus With peripheral circulatory complic… ICD-10   
#>  8 E106  Type 1 diabetes mellitus With other specified complications   ICD-10   
#>  9 E107  Type 1 diabetes mellitus With multiple complications          ICD-10   
#> 10 E108  Type 1 diabetes mellitus With unspecified complications       ICD-10   
#> # ℹ 45 more rows