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Introduction to medicode

Chi Zhang

2023-02-27

Source: vignettes/medicode.Rmd
medicode.Rmd

Overview

medicode is a utility tool that contains metadata for medical classification and clinical coding.

The motivation is two-fold:

  • Standardization: in Norway, some systems (such as hospital electronic health record systems) have only Norwegian coding and abbreviations, which can be inconvenient to read for human researchers, and standardize in reports.
  • Reference: medicode provides a consistent way to extract corresponding code range, such as a list of causes of death.

List of code for Cause of death 

code_death <- medicode::cause_of_death
head(code_death)
#>    code                          description_en
#> 1:    0                All deaths from diseases
#> 2:    1       Infectious and parasitic diseases
#> 3:  1.1                            Tuberculosis
#> 4:  1.2                        AIDS HIV disease
#> 5:  1.3                         Viral hepatitis
#> 6:  1.4 Other infectious and parasitic diseases
#>                                 description_no
#> 1:                  Alle dødsfall av sykdommer
#> 2: Infeksiøse, inkludert parasittære sykdommer
#> 3:                                 Tuberkulose
#> 4:                       AIDS og HIV-infeksjon
#> 5:     Akutt hepatitt og kronisk virushepatitt
#> 6:   Andre infeksiøse og parasittære sykdommer
#>                                         code_icd10
#> 1:                                         A00-R99
#> 2:                                         A00-B99
#> 3:                                    A15-A19, B90
#> 4:                                         B20-B24
#> 5:                                  B15-B19, B94.2
#> 6: A00-A09, A20-B09, B25-B89, B91-B94.1, B94.8-B99

ICD-10 code

The English version (source)

head(medicode::icd10_en)
#>     Code                                     description_en
#> 1:  A000 Cholera due to Vibrio cholerae 01, biovar cholerae
#> 2:  A001    Cholera due to Vibrio cholerae 01, biovar eltor
#> 3:  A009                               Cholera, unspecified
#> 4: A0100                         Typhoid fever, unspecified
#> 5: A0101                                 Typhoid meningitis
#> 6: A0102               Typhoid fever with heart involvement

The Norwegian version (source)

head(medicode::icd10_no)
#>    Code                                         description_no
#> 1: A000 Kolera som skyldes Vibrio cholerae 01, biovar cholerae
#> 2: A001    Kolera som skyldes Vibrio cholerae 01, biovar eltor
#> 3: A009                                    Uspesifisert kolera
#> 4: A010                                            Tyfoidfeber
#> 5: A011                                      Paratyfoidfeber A
#> 6: A012                                      Paratyfoidfeber B