dxComorbid: Code classification for Comorbidity

In DHLab-CGU/emr: An analysis tool for diagnosis and procedure records

Code classification for Comorbidity

Description

The comorbidities classification (AHRQ, Charlson ,and Elixhauser Comorbidity) for ICD diagnostic codes is a diagnostic categorization scheme that can employ in many types of projects analyzing data on diagnoses.

Usage

icdDxToComorbid(
  dxDataFile,
  idColName,
  icdColName,
  dateColName,
  icdVerColName = NULL,
  icd10usingDate = NULL,
  comorbidMethod,
  isDescription = FALSE
)

Arguments

dxDataFile	A data frame object of clinical diagnostic data with at least 3 columns: ID, ICD, and Date. As for date column, the data format should be YYYY/MM/DD or YYYY-MM-DD.
idColName	Column name of ID column in dxDataFile. Data type of this argumant should be string without quotation marks.
icdColName	Column name of ICD column in dxDataFile. Data type of this argumant should be string without quotation marks.
dateColName	Column name of date column in dxDataFile, and the type of date column should be a date format in R or a string format with date information in YYYY/MM/DD or YYYY-MM-DD. Data type of this argumant should be string without quotation marks.
icdVerColName	(Optional) Column name if there is a columns to record ICD-9/10 version used in dxDataFile. In this column, data format should be numeric 9L or 10L to indicate which ICD version is used for each cell. See examples below to get more information.
icd10usingDate	The date that ICD-10 was started to be used in dxDataFile dataset. The data format should be YYYY/MM/DD or YYYY-MM-DD. Necessary if icdVerColName is null.
comorbidMethod	Three comorbidity methods: AHRQ, Charlson and Elixhauser Comorbidity. Change it to any of the other possible variables (ahrq,charlson, and elix).
isDescription	Category name or category description of standard classification methods for ICD diagnostic codes. By default it is set to FALSE (Comorbidity categories).

Details

Collapse ICD codes into a smaller number of clinically meaningful categories that are more useful for presenting descriptive statistics than are individual ICD diagnostic codes.

Value

Three new data.tables. 1) groupedDT: Based on dxDataFile with two new columns for uniform format diagnostic codes and classified categories. 2) summarised_groupedDT: Summarized the groupedDT dataset and sorted by memberID. 3) Error: Potential error codes from standardization step: dxUniform ('icdDxShortToDecimal' and 'icdDxDecimalToShort').

See Also

Other code classification functions: dxPheWAS, dxCustom, DxCCS

Examples

# sample file for example

head(sampleDxFile)

# Group diagnostic codes into charlson comorbidity categories

icdDxToComorbid(sampleDxFile, ID, ICD, Date, icdVerColName = NULL, "2015-10-01", charlson)

DHLab-CGU/emr documentation built on Sept. 2, 2023, 9:16 p.m.