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Compute Comorbidity Index

comorbidity_index.Rd

This is a generic function that is wrapped by charlson_comorbidity_index() and elixhauser_comorbidity_index() and is not meant to be used directly. The function is an interface to comorbidity::comorbidity() for GEMINI data, providing options for outputting raw comorbidities or comorbidities at admission.

Usage

comorbidity_index(
  ipdiag,
  erdiag,
  map,
  weights,
  at_admission = TRUE,
  raw_comorbidities = FALSE
)

Arguments

ipdiag

(data.table or data.frame)
ipdiagnosis table as defined in the GEMINI Data Repository Dictionary.

erdiag

(data.table or data.frame)
erdiagnosis table as defined in the GEMINI Data Repository Dictionary. Typically, ER diagnoses should be included when deriving comorbidity in order to increase sensitivity. However, in certain scenarios, users may choose to only include IP diagnoses by specifying erdiag = NULL. This may be useful when comparing cohorts with different rates of ER admissions.

map

String denoting the mapping algorithm to be used (values are case-insensitive). Possible values are the Charlson score with either ICD-10 or ICD-9-CM codes (charlson_icd10_quan, charlson_icd9_quan) and the Elixhauser score, again using either ICD-10 or ICD-9-CM (elixhauser_icd10_quan, elixhauser_icd9_quan). These mapping are based on the paper by Quan et al. (2011). It is also possible to obtain a Swedish (charlson_icd10_se) or Australian (charlson_icd10_am) modification of the Charlson score using ICD-10 codes.

weights

A string denoting the weighting system to be used, which will depend on the mapping algorithm.

Possible values for the Charlson index are:

  • charlson, for the original weights by Charlson et al. (1987);

  • quan, for the revised weights by Quan et al. (2011).

Possible values for the Elixhauser score are:

  • vw, for the weights by van Walraven et al. (2009);

  • swiss, for the Swiss Elixhauser weights by Sharma et al. (2021).

Defaults to NULL, in which case an unweighted score will be used.

at_admission

(logical)
Whether to calculate the score for all comorbidities or for only pre-admit comorbidities.

raw_comorbidities

(logical)
Whether to output a data.table of raw comorbidities as opposed to pre-computed scores.

Value

(data.table)
By default, for each encounter, outputs the comorbidity score. If raw_comorbidities is TRUE, outputs a wide data.table with a column for each comorbidity for each encounter.

Details

A hierarchy of comorbidities is used when calculating the cormorbidity score, but not when outputting raw_comorbidites. This affects comorbidities present in a patient with different degrees of severity. See documentation for comorbidity::comorbidity() for details.