icd9 (version 1.3.1)

icd9LongToWide: convert ICD data from long to wide format

Description

This is more complicated than reshape or reshape2::dcast allows. This is a reasonably simple solution using built-in functions.

Usage

icd9LongToWide(icd9df, visitId = NULL, icd9Field = NULL, prefix = "icd_", min.width = 0, aggregate = TRUE, return.df = FALSE)

Arguments

icd9df

data.frame of long-form data, one column for visitId and one for ICD code

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.

icd9Field

The column in the data frame which contains the ICD codes. This is a character vector of length one. If it is NULL, icd9 will attempt to guess the column name, looking for progressively less likely possibilities until it matche a single column. Failing this, it will take the first column in the data frame. Specifying the column using this argument avoids the guesswork.

prefix

character, default "icd_" to prefix new columns

min.width,

single integer, if specified, writes out this many columns even if no patients have that many codes. Must be greater than or equal to the maximum number of codes per patient.

aggregate

single logical value, if TRUE (the default) will take more time to find out-of-order visitIds, and combine all the codes for each unique visitId. If FALSE, then out-of-order visitIds will result in a row in the output data per contiguous block of identical visitIds.

return.df

single logical value, if TRUE, return a data frame with a field for the visitId. This may be more convenient, but the default of FALSE gives the more natural return data of a matrix with rownames being the visitIds.

See Also

Other ICD-9 convert: icd9ChaptersToMap, icd9DropLeadingZeroes, icd9PartsToShort, icd9WideToLong

Examples

  longdf <- data.frame(visitId = c("a", "b", "b", "c"),
    icd9 = c("441", "4424", "443", "441"))
  icd9LongToWide(longdf)
  icd9LongToWide(longdf, prefix = "ICD10_")