icd9 (version 1.2)

icd9VanWalraven: Calculate van Walraven Elixhauser Score

Description

van Walraven Elixhauser score is calculated from the Quan revision of Elixhauser's ICD-9 mapping. This function allows for the hierarchical exlusion of less severe versions of comorbidities when their more severe version is also present via the applyHeirarchy argument. For the Elixhauser comorbidities, this is diabetes v. complex diabetes and solid tumor v. metastatic tumor

Usage

icd9VanWalraven(x, visitId = NULL, return.df = FALSE,
  stringsAsFactors = getOption("stringsAsFactors"), ...)
# S3 method for data.frame
icd9VanWalraven(x, visitId = NULL, return.df = FALSE,
  stringsAsFactors = getOption("stringsAsFactors"), ...)
icd9VanWalravenComorbid(x, visitId = NULL, applyHierarchy = FALSE)

Arguments

x

data frame containing a column of visit or patient identifiers, and a column of ICD-9 codes. It may have other columns which will be ignored. By default, the first column is the patient identifier and is not counted. If visitId is not specified, the first column is used.

visitId

The name of the column in the data frame which contains the patient or visit identifier. Typically this is the visit identifier, since patients come leave and enter hospital with different ICD-9 codes. It is a character vector of length one. If left empty, or NULL, then an attempt is made to guess which field has the ID for the patient encounter (not a patient ID, although this can of course be specified directly). The guesses proceed until a single match is made. Data frames may be wide with many matching fields, so to avoid false positives, anything but a single match is rejected. If there are no successful guesses, and visitId was not specified, then the first column of the data frame is used.

return.df

single logical value, if true, a two column data frame will be returned, with the first column named as in input data frame (i.e. visitId), containing all the visits, and the second column containing the Charlson Comorbidity Index.

stringsAsFactors

single logical, passed on when constructing data.frame if return.df is TRUE. If the input data frame x has a factor for the visitId, this is not changed, but a non-factor visitId may be converted or not converted according to your system default or this setting.

...

further arguments to pass on to icd9ComorbidQuanElix, e.g. icd9Field, applyHeirarchy

applyHierarchy

single logical value, default is FALSE. If TRUE, will drop DM if DMcx is present, etc.

Methods (by class)

• data.frame: van Walraven scores from data frame of visits and ICD-9 codes

References

van Walraven C, Austin PC, Jennings A, Quan H, Forster AJ. A Modification to the Elixhauser Comorbidity Measures Into a Point System for Hospital Death Using Administrative Data. Med Care. 2009; 47(6):626-633. http://www.ncbi.nlm.nih.gov/pubmed/19433995

Examples

# NOT RUN {
mydf <- data.frame(visitId = c("a", "b", "c"),
                   icd9 = c("412.93", "441", "044.9"))

print(
  cmb <- icd9ComorbidQuanElix(mydf, isShort = FALSE, applyHierarchy = TRUE, return.df=TRUE)
)
icd9VanWalravenComorbid(cmb)

icd9VanWalraven(mydf)
icd9VanWalraven(mydf, return.df = TRUE)
# }