icd9Explain: explain ICD9 codes

Description

convert 'decimal' format (123.45 style) ICD9 codes into the name and description for human review there are official ICD9-CM data tables, not with conversion to decimal notation, but to the textual format.

Usage

icd9Explain(icd9, isShort = icd9GuessIsShort(icd9), doCondense = TRUE, brief = FALSE, warn = TRUE)
icd9ExplainShort(icd9Short, doCondense = TRUE, brief = FALSE, warn = TRUE)
icd9ExplainDecimal(icd9Decimal, doCondense = TRUE, brief = FALSE, warn = TRUE)
"icd9Explain"(icd9, isShort = icd9GuessIsShort(icd9), doCondense = TRUE, brief = FALSE, warn = TRUE)
"icd9Explain"(icd9, isShort = icd9GuessIsShort(icd9), doCondense = TRUE, brief = FALSE, warn = TRUE)
"icd9Explain"(icd9, isShort = icd9GuessIsShort(icd9), doCondense = TRUE, brief = FALSE, warn = TRUE)
"icd9Explain"(icd9, isShort = icd9GuessIsShort(icd9), doCondense = TRUE, brief = FALSE, warn = FALSE)

Arguments

icd9

is a character vector or factor of ICD-9 codes. If fewer than five characters is given in a code, then the digits are greedily assigned to hundreds, then tens, then units, before the decimal parts. E.g. "10" becomes "010", not "0010".

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.

doCondense

single logical value which indicates whether to condense the given set of ICD-9 codes by replacing subsets of codes with 'parent' codes which exactly encompass certain subsets. E.g. If all cholera diagnoses are provided, only '001 - Cholera' needs to be displayed, not all subtypes.

brief

single logical value, default is FALSE. If TRUE, the short description from the canonical CMS descriptions (included in extdata) will be used, otherwise the long description is used.

warn

single logical value, default is TRUE, meaning that codes which do not correspond to diagnoses, or to three-digit codes, will trigger a warning.

icd9Short

is a character vector of ICD-9 codes. If fewer than five characters is given in a code, then the digits are greedily assigned to hundreds, then tens, then units, before the decimal parts. E.g. "10" becomes "010", not "0010"

icd9Decimal

character vector of ICD-9 codes. If fewer than five characters is given in a code, then the digits are greedily assigned to hundreds, then tens, then units, before the decimal parts. E.g. "10" becomes "010", not "0010"

Value

data frame, or list of data frames, with fields for ICD9 code, name and description, derived from datamart lookup table

Methods (by class)

list: explain all ICD-9 codes in a list of vectors
factor: explain factor of ICD-9 codes
character: explain character vector of ICD-9 codes
numeric: explain numeric vector of ICD-9 codes, with warning. In general, this is not allowed because of the possible ambiguity of numeric decimal codes, but for convenience, this is allowed in this case to avoid typing many quotes.

Examples

Run this code

icd9ExplainShort(ahrqComorbid[[1]][1:3])
icd9Explain(ahrqComorbid[[1]][1:3], brief = TRUE)