icd9WideToLong: convert ICD data from wide to long format

In jackwasey/icd9: Tools for Working with ICD-9 Codes, and Finding Comorbidities

Description

This is different enough to dcast in reshape2 that it needs writing again specifically for ICD codes. This function packages the core reshape function. Empty strings and NA values will be dropped, and everything else kept. No validation of the ICD codes is done.

Usage

icd9WideToLong(x, visitId = NULL, icdLabels = NULL, icdName = "icdCode",
  icdRegex = c("icd", "diag", "dx_", "dx"), verbose = FALSE)

Arguments

x	data.frame in wide format, i.e. one row per patient, and multiple columns containing ICD codes, empty strings or NA.
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.
icdLabels	vector of column names in which codes are found. If NULL, all columns matching icd or ICD will be included.
icdName	character vector length one containing the new column name for the ICD codes, defaults to "icdCode"
icdRegex	vector of character strings containg a regex to identify ICD-9 diagnosis columns to try (case-insensitive) in order. Default is c("icd", "diag", "dx_", "dx")
verbose	single logical value, defaults to FALSE in most functions.

Value

data frame with visitId column named the same as input, and a column named by icd.name containing all the non-NA and non-empty codes found in the wide input data.

See Also

Other ICD-9 convert: icd9ChaptersToMap, icd9DropLeadingZeroes, icd9LongToWide, icd9PartsToShort

Examples

  widedf <- data.frame(visitId = c("a", "b", "c"),
    icd9_01 = c("441", "4424", "441"),
    icd9_02 = c(NA, "443", NA))
  icd9WideToLong(widedf)

jackwasey/icd9 documentation built on May 18, 2019, 7:57 a.m.