R/deyo.R

In gforge/comorbidities.icd10: Calculates Comorbidity Indices Based on ICD-9/10

#' Produces a Charlson Score based on the Deyo ICD-9-CM adaptation
#' 
#' This function take as input a data frame structured such that each row
#' contains a list of ICD-9-CM codes attributed to a single patient. The
#' function goes from row to row comparing the ICD-9-CM codes a patient has
#' with the Deyo comorbidity index diagnosis codes.  If a patient has a
#' diagnosis (as indicated by ICD-9-CM code) that belongs to one of the Deyo
#' diagnoses, then the patient is considered to have this diagnosis.
#' Regardless of how many different ICD-9-CM codes a patient has corresponding
#' to a particular comorbidity category, a comorbidity is only counted once.
#' 
#' The value returned consists of a vector and two data frames. The vector is
#' the total Charlson score.  In the first data frame returned each row in the
#' data frame is devoted to a particular patient, and each column is a
#' diagnosis.  The data frame codes a 0 if the patient does not have that
#' diagnosis and 1 if the patient does have that diagnosis.  The second data
#' frame, which codes the point value of that particular diagnosis in the
#' Charlson score rather than a 1.
#' 
#' The ICD-9-CM codes must be 5 characters long and have no decimal poinst.If
#' any codes are less than 5 digits, then they must be led by zeroes or
#' followed by the letter "X" to create a 5 character code.  No more than 2 "X"
#' ' s can be used at the tail end, or a meaningful ICD-9-CM code cannot be
#' derived.  If your ICD-9-CM codes contain decimals or some other filler
#' character, then they must be converted to the format above for this function
#' to work properly.
#' 
#' @section Warning:
#' This function is deprecated. We recommend you switch to the more general
#' \code{\link{cmrbdt.calc}} function instead.
#'
#' @param input.frame This is a data frame with 5 character ICD-9-CM codes
#' without decimal points.
#' @return A list of one vector and 2 data frames \item{CHARLSON.SCORE}{A
#' vector containing the Charlson score for each patient}
#' \item{COMORBIDITIES}{A data frame denoting which diagnoses each patient has
#' with a 1} \item{COMORBIDITIES.POINTS}{A data frame denoting which diagnoses
#' each patient has with the point value of that diagnosis}
#' @author Paul Gerrard, Max Gordon
#' @references Deyo RA, Cherkin DC, Ciol MA. (1992) Adapting a clinical
#' comorbidity index for use with ICD-9-CM administrative databases. J Clin
#' Epidemiol. 45(6):613-9.
#' @export
#' @examples
#' 
#' x <- matrix(NA, nrow = 3, ncol = 2)
#' x[1,] <- c("41000", "42800")
#' x[2,] <- c("57220", "1961X")
#' x[3,1] <- "042XX"
#' x <- as.data.frame(x)
#' deyo(x)
#' @keywords internal
deyo <- function(input.frame) {
  warning("This function is deprecated - use cmrbdt.calc instead")
  if(is.vector(input.frame)) input.frame <- data.frame(codes=input.frame)
  ret <- pr.deyo.comorbidities(input.frame)
  scores <- weight.Charlsons.org(ret)
  
  deyo.data <- list(CHARLSON.SCORE = rowSums(scores), 
                    COMORBIDITIES = ret, 
                    COMORBIDITIES.POINTS = scores)
  return(deyo.data)
}

#' Score points for Deyo Charlson's index
#' 
#' The following function develops a matrix with 
#' rows devoted to respondents and each column a comorbidity.
#' The number in each column is the point value of having the comorbidity.
#'  
#' @param input.frame This is a data frame with 5 digit ICD-9-CM codes as XXX.XX
#'  This can also be provided as a vector or matrix.
#' @return \code{matrix} Returns a matrix with the one column per 
#'  comorbidity. No comorbidity is indicated by 0 while 1 indicates 
#'  existing comorbidity.
#' @seealso \code{\link{deyo}}
#' @keywords internal
pr.deyo.comorbidities <- function(input.frame) {
  output.frame <- NULL
  for (i in 1:NROW(input.frame)){
    # The rbind() may be somewhat slower than setting up the 
    # the full matrix but I think the gain from separating the 
    # the identification function from the logic clearly outweighs 
    # this cost.
    output.frame <- rbind(output.frame,
                          cmrbdt.finder.numeric.charlson_Deyo1992(icd_codes = input.frame[i, ]))
  }
  
  output.frame <- hierarchy.charlson_Deyo1992(output.frame)  
  output.frame <- as.data.frame(output.frame)
  
  # Change the names to upper case as in original script
  colnames(output.frame) <- toupper(colnames(output.frame))
  return(output.frame)
}