GitHub - wtcooper/icdcoder: R package: ICD-9 and ICD-10 code utility functions and datasets (original) (raw)

icdcoder

ICD-9 and ICD-10 code utility functions and datasets

Overview

Utility functions to work with and between ICD-9 and ICD-10, along with datasets that provide the hierarchies for the ICD chapters, comorbidities, and CMS GEMs (for conversions). Includes functions to validate, get all codes within a range, all children of a code level, mappings to convert to/from icd9 and icd10 (CMS GEMs), and get comorbidities. Comorbidities (Elixhauser and Charlson from Quan et al. (2005), and Royal College of Surgeons Charlson) are based upon the comorbidities.icd10 package (https://github.com/gforge/comorbidities.icd10), and the dataset for the hierarchy of icd9 codes is taken directly from the icd9 package (https://github.com/jackwasey/icd9).

Installation

library(devtools) devtools::install_github("wtcooper/icdcoder")

Example Use

require(devtools) require(dplyr) require(data.table) require(icdcoder)

Set up example dataset

dat = data.table(patient=c(1,1,1,1,2,2,2,2), icdVer=c(9,9,9,10,9,9,10,10), code=c("042", "0703333", "140", "A520", "2038", "40403", "C008", "E1010"))

Check if codes are valid (2nd icd9 code not)

isValidICD((dat %>% filter(icdVer==9))$code, "icd9") isValidICD((dat %>% filter(icdVer==10))$code, "icd10")

Get a range of values...it's inclusive

getICDRange("001","002", "icd9") # return 001-002 getICDRange("001","001999999", "icd9") # eg non-inclusive endpoint getICDRange("A00","A03", "icd10") # icd10 codes in range

Get children under a hierarchy

getICDChildren("001", "icd9") # similar to range above but doesn't include 001 getICDChildren("A01", "icd10")

Convert codes using the GEMs

convICD("0011", "icd9") convICD("A001", "icd10")

note: parent codes don't convert so will return NAs for invalid or parent codes

convICD((dat %>% filter(icdVer==9))$code, "icd9") convICD((dat %>% filter(icdVer==10))$code, "icd10")

Get comorbidities

getComorbids((dat %>% filter(icdVer==9))$code, "icd9") getComorbids((dat %>% filter(icdVer==10))$code, "icd10")

roll out Elixhauser comorbidities to dummy codes

d = getComorbids((dat %>% filter(icdVer==9))$code, "icd9", type="Elixhauser") datComorbs = dat %>% filter(icdVer==9) %>% rename(icd9=code) %>% left_join(d, by="icd9") %>% filter(!is.na(Elixhauser))

datComorbs %>% group_by(patient) %>% select(Elixhauser) %>% table() %>% as.data.frame.matrix()