AHRQComorb: AHRQComorb: Convert diagnosis codes to table of comorbidities

In rplzzz/AHRQcomorb: Convert diagnosis codes to comorbidity lists

AHRQComorb: Convert diagnosis codes to table of comorbidities

Description

Convert ICD-10 diagnosis codes to tables of Elixhauser comorbidities using the comorbidity definitions from the US Agency for Healthcare Research and Quality (AHRQ), version 2021.1. This package is intended for use with the Standard Analytical Files (SAF) distributed by the Centers for Medicare and Medicaid Services (CMS); however, the interface is flexible enough that it should work with most other datasets containing similar data.

Basic functionality

The main function for converting diagnosis codes is comorb. It takes a long-format table of diagnosis codes, one code (and POA indicator) per row. For example:

id          diagnosis   poa
<chr>       <chr>     <dbl>
"15\u001f1" I2510         1
"15\u001f1" I959          1
"15\u001f1" J449          1
"15\u001f1" E119          1
"15\u001f1" R001          1

The diagnosis column must contain ICD-10 codes, and the poa column must be a numeric column consisting entirely of 1 (present on admission) and 0 (not present on admission) values. The id column indicates which rows belong to a single case (e.g., a patient, or an encounter). If this table were stored in dtbl, you would run:

comorb(dtbl, idcol='id')

The result would be a table with a row for each unique value of the id variable (just one, in this short example), and a series of columns, one for each of the 39 comorbidities. Ones in these columns indicate the presence of the comorbidities, while zeros indicate absence.

The R manual page for the comorb function contains further details about additional options and some notes on topics like groups of clinically similar comorbidities.

Additional functionality

Medical records, including the SAF, are often organized with cases in rows, and diagnoses and other information in columns. The claimpivot function pivots this wide-format data into long format, taking care to keep claims together with their corresponding POA indicators, and discarding unused columns.

A table of the 39 comorbidities tracked in the standard, along with an indicator for whether or not each one is required to be present on admission to be counted, is provided in the comorb_description table. The comorbidity column of this table contains the abbreviations for the various comorbidities, and is therefore useful for decoding the abbreviations, as well as for iterating over all of the possible comorbidities.

rplzzz/AHRQcomorb documentation built on Aug. 10, 2024, 8:12 a.m.