icd9 (version 1.1)

icd9ComorbidShortCpp: find comorbidities from ICD-9 codes.

Description

RcppParallel approach with openmp and vector of integer strategy

This is the main function which extracts co-morbidities from a set of ICD-9 codes. This is when some trivial post-processing of the comorbidity data is done, e.g. renaming to human-friendly field names, and updating fields according to rules. The exact fields from the original mappings can be obtained using applyHierarchy = FALSE, but for comorbidity counting, Charlson Score, etc., the rules should be applied.

For Charlson/Deyo comorbidities, strictly speaking, there is no dropping of more e.g. uncomplicated DM if complicated DM exists, however, this is probaably useful, in general and is essential when calculating the Charlson score.

Usage

icd9ComorbidShortCpp(icd9df, icd9Mapping, visitId = "visitId",
  icd9Field = "icd9", threads = 8L, chunkSize = 256L, ompChunkSize = 1L,
  aggregate = TRUE)
icd9Comorbid(icd9df, icd9Mapping, visitId = "visitId", icd9Field = "icd9",
  isShort = icd9GuessIsShort(icd9df[[icd9Field]]),
  isShortMapping = icd9GuessIsShort(icd9Mapping), return.df = FALSE, ...)
icd9ComorbidShort(...)
icd9ComorbidAhrq(..., abbrevNames = TRUE, applyHierarchy = TRUE)
icd9ComorbidQuanDeyo(..., abbrevNames = TRUE, applyHierarchy = TRUE)
icd9ComorbidQuanElix(..., abbrevNames = TRUE, applyHierarchy = TRUE)
icd9ComorbidElix(..., abbrevNames = TRUE, applyHierarchy = TRUE)
icd9Comorbidities(...)
icd9ComorbiditiesAhrq(...)
icd9ComorbiditiesElixHauser(...)
icd9ComorbiditiesQuanDeyo(...)
icd9ComorbiditiesQuanElixhauser(...)

Arguments

icd9df

data frame containing columns for visitId (which is the feault name), icd9 (default for the icd9 code), and maybe also a POA flag.

icd9Mapping

list (or name of a list if character vector of length one is given as argument) of the comorbidities with each top-level list item containing a vector of decimal ICD9 codes. This is in the form of a list, with the names of the items corresponding to the comorbidities (e.g. "HTN", or "diabetes") and the contents of each list item being a character vector of short-form (no decimal place but ideally zero left-padded) ICD-9 codes. No default: user should prefer to use the derivative functions, e.g. icd9ComorbidAhrq, since these also provide appropriate naming for the fields, and squashing the hierarchy (see applyHierarchy below)

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. Defaults to "visitId"

icd9Field

The column in the data frame which contains the ICD-9 codes. This is a character vector of length one.

aggregate

single logical value, if /codeTRUE, then take (possible much) more time to aggregate out-of-sequence visit IDs in the icd9df data.frame. If this is FALSE, then each contiguous group of visit IDs will result in a row of comorbidities in the output data. If you know your visitIds are possible disordered, then use TRUE.

isShort

single logical value which determines whether the ICD-9 code provided is in short (TRUE) or decimal (FALSE) form. Where reasonable, this is guessed from the input data.

isShortMapping

Same as isShort, but applied to icd9Mapping instead of icd9df. All the codes in a mapping should be of the same type, i.e. short or decimal.

...

further arguments e.g. chunkSize and ompChunkSize pass to the C++ function

abbrevNames

single locical value that defaults to TRUE, in which case the ishorter human-readable names stored in e.g. ahrqComorbidNamesAbbrev are applied to the data frame column names.

applyHierarchy

single logical value that defaults to TRUE, in which case the hierarchy defined for the mapping is applied. E.g. in Elixhauser, you can't have uncomplicated and complicated diabetes both flagged.

...

arguments passed to the corresponding function from the alias. E.g. all the arguments passed to icd9ComorbiditiesAhrq are passed on to icd9ComorbidAhrq

Details

There is a change in behavior from previous versions. The visitId column is (implicitly) sorted by using std::set container. Previously, the visitId output order was whatever R's aggregate produced.

The threading of the C++ can be controlled using e.g. option(icd9.threads = 4). If it is not set, the number of cores in the machine is used.

Examples

# NOT RUN {
pts <- data.frame(visitId = c("2", "1", "2", "3", "3"),
                   icd9 = c("39891", "40110", "09322", "41514", "39891"))
   icd9ComorbidShort(pts, ahrqComorbid) # visitId is now sorted
# }