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Map clinical codes from one coding system to another

Source: R/map.R
MAP.Rd

Map clinical codes from one coding system to another

Usage

MAP(
  ...,
  from = getOption("codeminer.map_from"),
  to = getOption("codeminer.map_to"),
  map_version = getOption("codeminer.map_version", default = "latest"),
  lookup_version = getOption("codeminer.lookup_version", default = "latest"),
  col_filters = "default"
)

Arguments

...

Codes to map. Supports flexible input like CODES(). Special value: "all" returns all mapped codes.

from

Coding system that ... codes belong to. Optional if input is a codelist with code_type.

to

Coding system to map codes to.

map_version

Version of the mapping table to use.

lookup_version

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

col_filters

Column filters to apply to the mapping table. 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

Note: this controls filtering of the mapping table, not the target lookup table (which uses its own default col_filters).

Value

A codeminer_codelist of the mapped codes with their descriptions.

If using codes = "all", returns the mapping table as a data.frame with columns:

  • from: the codes from the source code system

  • to: the mapped codes from the destination system

Details

If no mapping table matching the from -> to direction is found, but there is a table for to -> from, MAP() will return the reverse mapping with a warning. Note that this is not guaranteed to be correct, as most mapping tables only work one way.

See also

add_mapping_table() for adding new mapping tables to the codeminer database.

Other Clinical code lookups and mappings: CODES(), 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!
#> ℹ To reconnect to your previous database:
#>   `Sys.setenv(CODEMINER_DB_PATH = "/tmp/RtmpXyzdMY/file19d470a2a26a.duckdb")`
#>   `codeminer_connect()`

# Single code
MAP("X40J4", from = "Read 3", to = "ICD-10")
#> ℹ Using 'UKB v4' as latest version
#> ℹ Using 'UKB v4' as latest version
#> <codeminer_codelist>: 1 code
#> Code type: "ICD-10"
#> 
#> # A tibble: 1 × 3
#>   code  description                                    code_type
#>   <chr> <chr>                                          <chr>    
#> 1 E109  Type 1 diabetes mellitus Without complications ICD-10   

# Multiple codes
MAP("X40J4", "X40J5", from = "Read 3", to = "ICD-10")
#> Warning: ! The following codes were not found in the mapping table:
#> • `X40J5`
#> <codeminer_codelist>: 1 code
#> Code type: "ICD-10"
#> 
#> # A tibble: 1 × 3
#>   code  description                                    code_type
#>   <chr> <chr>                                          <chr>    
#> 1 E109  Type 1 diabetes mellitus Without complications ICD-10   

# || separated
MAP("X40J4 || X40J5", from = "Read 3", to = "ICD-10")
#> Warning: ! The following codes were not found in the mapping table:
#> • `X40J5`
#> <codeminer_codelist>: 1 code
#> Code type: "ICD-10"
#> 
#> # A tibble: 1 × 3
#>   code  description                                    code_type
#>   <chr> <chr>                                          <chr>    
#> 1 E109  Type 1 diabetes mellitus Without complications ICD-10   

# Data frame input (from is optional)
df <- data.frame(
  code = c("X40J4", "X40J5"),
  description = c("Desc 1", "Desc 2"),
  code_type = c("Read 3", "Read 3")
)
MAP(df, to = "ICD-10")
#> Warning: ! The following codes were not found in the mapping table:
#> • `X40J5`
#> <codeminer_codelist>: 1 code
#> Code type: "ICD-10"
#> 
#> # A tibble: 1 × 3
#>   code  description                                    code_type
#>   <chr> <chr>                                          <chr>    
#> 1 E109  Type 1 diabetes mellitus Without complications ICD-10   

# Return the mapping table itself
MAP("all", from = "Read 3", to = "ICD-10")
#> # A tibble: 5 × 8
#>   from  to    mapping_status refine_flag add_code_flag element_num block_num
#>   <chr> <chr> <chr>          <chr>       <chr>         <chr>       <chr>    
#> 1 X40J4 E109  D              C           P             0           0        
#> 2 C10.. E149  D              C           C             0           0        
#> 3 XaIP9 L721  D              C           C             0           0        
#> 4 XE0e0 N390  D              C           P             0           0        
#> 5 XE0Uc I10   D              C           C             0           0        
#> # ℹ 1 more variable: icd10_dagger_asterisk <chr>