icd (version 3.3)

simplify_map_lex: Internal function to simplify a comorbidity map by only including codes which are parents, or identical to, a given list of codes.

Description

Specifically, this is useful for ICD-10 codes where there are a huge number of possible codes, but we do not want to make a comorbidity map with such a large number of codes in it.

Usage

simplify_map_lex(pt_codes, map)

Arguments

map

named list containing vectors of ICD-9 codes. E.g. the AHRQ ICD-9 comorbidities, contains list(OBESE = c("2780", "27800", "27801", "27803", "V8554", "79391", "64910", "64911", "64912", "64913", "64914", "V8530", "V8531", "V8532", "V8533", "V8534", "V8535", "V8536", "V8537", "V8538", "V8539", "V8541", "V8542", "V8543", "V8544", "V8545" ), DEPRESS = c("3004", "30112", "3090", "3091", "311")) amongst other longer groups.

x

Character vector (not factor)

visit_name

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 visit_id was not specified, then the first column of the data frame is used.

icd_name

The name of 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 matches a single column. Failing this, it will take the first column in the data frame. Specifying the column using this argument avoids the guesswork.

See Also

https://github.com/s-u/fastmatch/blob/master/src/fastmatch.c

Examples

# NOT RUN {
# one exact match, next cmb parent code, next cmb child code
icd10 <- as.icd10(c("I0981", "A520", "I26019"))
pts <- data.frame(visit_id = c("a", "b", "c"), icd10)
simple_map <- icd:::simplify_map_lex(icd10, icd10_map_ahrq)
stopifnot(simple_map$CHF == "I0981")
stopifnot(simple_map$PHTN != character(0))
stopifnot(simple_map$PVD == "I26019")
umap <- icd:::simplify_map_lex(uranium_pathology$icd10, icd10_map_ahrq)
head(icd:::categorize_simple(uranium_pathology, icd10_map_ahrq,
                      id_name = "case", code_name = "icd10"))
head(icd:::categorize_simple(uranium_pathology, umap,
                             id_name = "case", code_name = "icd10"))
# }