This function applies the updated Charlson Index to discharge abstract data set. The Charlson Index is used to weight the severity of comorbidities required for risk adjusting mortality ratio, readmissions, and other quality indicators. Codes and updated weights were taken from two Hude Quan articles referenced below.
a data.frame requiring between 1 and 25 ICD-10 diagnosis codes per row with naming convention diag_code_01 - diag_code_25 in that order If abstracts have varying number of diagnoses, those with fewer should populate columsn with blank or NA
if TRUE then abstract_data expected to have between 1 and 25 corresponding diagnoses types for each diagnosis code with naming convention diag_type_01 to diag_type25. Types are coded as per CIHI DAD standards and are used to include only certain diagnoses in Charlson Index.
There are 12 comorbidities with contribute to Charlson Index with the following weights:
Congestive heart failure - 2; Dementia - 2; Chronic pulmonary disease - 1; Rheamatologic disease - 1; Mild liver disease - 2; Diabetes with chronic complications - 1; Hemiplagia or paraplagia - 2; Renal disease - 1; Any malignancy, including leukemia and lymphoma - 2; Moderate or severe liver disease - 4; Metastatic solid tumour - 6; AIDS/HIV - 4
The maximum weight is 24. The following combinations are mutually exclusive: Mild liver disease & moderate/server liver disease; any malignancy & metastatic solid tumour
If diagnosis types used, only 1, W, Y, X are used in calculating Charlson Index.
A data.frame with all columns from abstract_data with with Charlson Index score appended, with values between 0 and 24 (0 is no comorbidities, 24 is all comorbidities)
Hude Quan. Coding algorithms for defining comorbidities in ICD-9-CM and ICD-10 administrative data. Med Care, 43(11):1130-9.
Hude Quan. Updated and Validating the Charlson Comorbidity Index and Score for Risk Adjustment in Hospital Discharge Using Data from 6 Countries. American Journal of Epidemiology. 2011.
Canadian Institute of Health Information (CIHI). DAD Abstracting Manual, 2015-2016 Edition.
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