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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(
  codes,
  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")
)

Arguments

codes

A character vector of codes to be mapped. If passing "all", all mapped codes will be returned.

from

Coding system that codes belong to.

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.

Value

A data.frame of the mapped codes with their descriptions, as returned by CODES().

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(), 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/file1bd3244e296e.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!

MAP("X40J4", from = "Read 3", to = "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

# Return the mapping table itself
MAP("all", from = "Read 3", to = "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