parseQuanDeyoSas: parse original SAS code defining Quan's update of Deyo comorbidities.

Description

As with parseAhrqSas, this function reads SAS code, and in, a very limited way, extracts definitions. In this case the code uses LET statements, with strings or lists of strings. This saves and invisibly returns a list with names corresponding to the comorbidities and values as a vector of 'short' form (i.e. non-decimal) ICD9 codes. Unlike parseAhrqSas, there are no ranges defined, so this interpretation is simpler.

With thanks to Dr. Quan, I have permission to distribute his SAS code. Previously, the SAS code would be downloaded from the University of Manitoba at http://mchp-appserv.cpe.umanitoba.ca/concept/ICD9_E_Charlson.sas.txt. There are structural differences between this version and the version directly from Dr. Quan, however, the parsing results in identical data.

Usage

parseQuanDeyoSas(sasPath = NULL, condense = FALSE, save = FALSE, path = "data")

Arguments

sasPath

single character string containing path or URL for some SAS code. The source SAS code is stored in extdata or at the location specified in URL. In development mode in devtools, this is actually inst/extdata. This function is internal, since it is used to generate data which ends up in the distributed package. However, the package user can verify that the code creates the distributed R data. Also, changes to the original SAS code can be used to regenerate the R data by the user, without waiting for a package release.

condense

logical whether to condense the result ranges to the minimal set of parent ICD-9 codes which exactly define the list. Defaults to FALSE so that the saved list will allow rapid look-up of codes without further processing. Small memory versus time trade-off.

save

logical whether to save the result in the source tree. Defaults to FALSE.

path

path to directory to save the data. This is typically the data folder in the devleopment source tree. Defaults to "~/icd9/data". Could possibly avoid hard-coding path with devtools functions.

Value

invisibly returns the list of vectors, where a co-morbidity name is associated with a character vector of ICD-9 codes.