charlson: Calculate Charlson comorbidity score
In n8thangreen/HESmanip: Hospital length of stay data preprocessing and analysis

Description Usage Arguments Details Value Author(s) References Examples

Group patient records using ICD10 (or ICD9) codes and then take weighted sum to give a single comorbidity measure.

1	charlson(Patient, icd)

`Patient`	Patient ID could be Spell ID, Trust ID or HES ID for example
`icd`	vector of ICD codes

Three digit ICD codes (e.g. I50) can be matched as well as 4 digits (e.g. I500).

A matrix of unique patient ID by individual Charlson group counts and overall score.

N Green

V. Sundararajan et al. / Journal of Clinical Epidemiology 57 (2004) 1288–1294

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (Patient, icd) 
{
    d <- cbind.data.frame(Patient, icd)
    nobs <- nrow(d)
    d$code <- rep(NA, nobs)
    icd10 <- list()
    ICD3to4 <- function(x) union(unlist(sapply(x, function(y) if (nchar(y) == 
        3) {
        paste(y, 0:9, sep = "")
    })), x)
    icd10$codes$mi <- c("I21", "I22", "I252")
    icd10$codes$chf <- c("I50")
    icd10$codes$pvd <- c("I71", "I790", "I739", "R02", "Z958", 
        "Z959")
    icd10$codes$cvd <- c("I60", "I61", "I62", "I63", "I65", "I66", 
        "G450", "G451", "G452", "G458", "G459", "G46", "I64", 
        "G454", "I670", "I671", "I672", "I674", "I675", "I676", 
        "I677", "I678", "I679", "I681", "I682", "I688", "I69")
    icd10$codes$dem <- c("F00", "F01", "F02", "F051")
    icd10$codes$cpd <- c("J40", "J41", "J42", "J44", "J43", "J45", 
        "J46", "J47", "J67", "J44", "J60", "J61", "J62", "J63", 
        "J66", "J64", "J65")
    icd10$codes$rhm <- c("M32", "M34", "M332", "M053", "M058", 
        "M059", "M060", "M063", "M069", "M050", "M052", "M051", 
        "M353")
    icd10$codes$pep <- c("K25", "K26", "K27", "K28")
    icd10$codes$mld <- c("K702", "K703", "K73", "K717", "K740", 
        "K742", "K746", "K743", "K744", "K745")
    icd10$codes$dnc <- c("E109", "E119", "E139", "E149", "E101", 
        "E111", "E131", "E141", "E105", "E115", "E135", "E145")
    icd10$codes$dwc <- c("E102", "E112", "E132", "E142", "E103", 
        "E113", "E133", "E143", "E104", "E114", "E134", "E144")
    icd10$codes$ple <- c("G81", "G041", "G820", "G821", "G822")
    icd10$codes$ren <- c("N03", "N052", "N053", "N054", "N055", 
        "N056", "N072", "N073", "N074", "N01", "N18", "N19", 
        "N25")
    icd10$codes$can <- c("C0", "C1", "C2", "C3", "C40", "C41", 
        "C43", "C45", "C46", "C47", "C48", "C49", "C5", "C6", 
        "C70", "C71", "C72", "C73", "C74", "C75", "C76", "C80", 
        "C81", "C82", "C83", "C84", "C85", "C883", "C887", "C889", 
        "C900", "C901", "C91", "C92", "C93", "C940", "C941", 
        "C942", "C943", "C9451", "C947", "C95", "C96")
    icd10$codes$met <- c("C77", "C78", "C79", "C80")
    icd10$codes$liv <- c("K729", "K766", "K767", "K721")
    icd10$codes$hiv <- c("B20", "B21", "B22", "B23", "B24")
    icd10$weights <- split(c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 
        2, 2, 2, 3, 3, 6), names(icd10$codes))
    icd10$codes <- lapply(icd10$codes, ICD3to4)
    for (i in 1:nobs) {
        patientGroup <- unlist(lapply(icd10$codes, function(x) d[i, 
            "icd"] %in% x))
        d$code[i] <- ifelse(sum(patientGroup) == 0, NA, names(icd10$codes)[patientGroup])
    }
    mydata <- cast(d, value = "icd", Patient ~ code, fun.aggregate = length)
    chCols <- mydata[, -c(1, ncol(mydata))] > 0
    comorbidity.n <- rowSums(chCols)
    mydata$charlson <- apply((1 * chCols), 1, function(x) x %*% 
        unlist(icd10$weights)[colnames(chCols)])
    mydata$comorbidity.n <- comorbidity.n
    return(mydata)
  }