R/med_calculate.R

In jonathanelee1993/clinicalresponsepackage: Seizure and Epileptic Medication Response Package

#' Med calculate
#'
#' This function will perform the calculations of the values for percent med free (on baseline days
#' and therapy days), med response (daily and for every 30 days), percent med
#' free response, med score, med number response (daily and for every 30 days),
#' and med number score
#' @param x Med load table
#' @param n Number that signifies which column number corresponse with the MED_NUMBER_DAY column
#' @param l Number that signifies which column number corresponds with the MED_LOAD_DAY column
#' @param baseline Subset of load table corresponding with baseline days
#' @param therapy Subset of load table corresponding with therapy days
#' @param patient Four-letter patient initials
#' @param mrnumber Medical record number object
#' @param type DAY_TYPE column object
#' @param number MED_NUMBER_DAY/MED_LOAD_DAY data frame object
#' @return med response/score calculations
#' @keywords med response

# Purpose - This script will perform the calculations of the values for percent med free (on baseline days
#           and therapy days), med response (daily and for every 30 days), percent med
#           free response, med score, med number response (daily and for every 30 days),
#           and med number score
# Parameters - x = med load table
#              n = number that signifies which column number corresponds with the MED_NUMBER_DAY column
#              l = number that signifies which column number corresponds with the MED_LOAD_DAY column
#              baseline = subset of load table corresponding with baseline days
#              therapy = subset of load table corresponding with therapy days
#              patient = four-letter patient initials
#              mrnumber = medical record number object
#              type = DAY_TYPE column object
#              number = MED_NUMBER_DAY/MED_LOAD_DAY data frame object
med_calculate <- function(x,n,l,baseline,therapy,patient,mrnumber,type,number) {

  ## percent free days during baseline
  base.free <- dim(baseline[baseline[,l]==0,])[1]
  free.base <- (base.free/dim(baseline)[1])*100
  print(paste("The percentage of baseline days with no meds is:",free.base,"%"))

  ## percent free days during therapy
  therapy.30.days <- split(therapy[,l],ceiling(seq_along(therapy[,l])/30))
  c <- c(1:dim(therapy)[1])
  r <- c[c[]/30 > 0 & c[]/30 <= 1]
  free.30.days <- data.frame(therapy$DATE[min(r)],
                             therapy$DATE[max(r)],
                             (length(therapy.30.days[[1]][therapy.30.days[[1]]==0])/(length(therapy.30.days[[1]])))*100)
  colnames(free.30.days)[1:2] <- c("FIRST_DATE","LAST_DATE")
  colnames(free.30.days)[3] <- "%_MED_FREE_DAYS"
  if (ceiling(dim(therapy)[1]/30) >= 2) {
    for (i in 2:(ceiling(dim(therapy)[1]/30))) {
      therapy.free <- (length(therapy.30.days[[i]][therapy.30.days[[i]]==0])/(length(therapy.30.days[[i]])))*100
      r <- c[c[]/30 > i-1 & c[]/30 <= i]
      newrow <- data.frame(therapy$DATE[min(r)],therapy$DATE[max(r)],therapy.free)
      colnames(newrow) <- colnames(free.30.days)
      free.30.days <- data.frame(rbind(free.30.days,newrow))
      colnames(free.30.days) <- colnames(newrow)
    }
  }

  baseline <- subset(baseline,baseline[,l]!=0)
  base.median <- median(baseline[,l])
  base.number.median <- median(baseline[,n])

  ## daily response calculation
  daily.response <- c((therapy[,l]/base.median)*100)
  daily.response <- data.frame(therapy$DATE,daily.response)
  colnames(daily.response)[1] <- "DATE"
  colnames(daily.response)[2] <- "MED_RESPONSE"

  ## daily number response calculation
  response <- c((therapy[,n]/base.number.median)*100)
  response <- data.frame(daily.response,response)

  t <- data.frame(type)
  ml <- data.frame(number[,1])
  mn <- data.frame(number[,2])
  response <- data.frame(rep(mrnumber,dim(response)[1]),response)
  response <- data.frame(response[,1:2],t,ml,mn,response[,3:4])
  colnames(response)[1] <- "MRNUMBER"
  colnames(response)[2] <- "DATE"
  colnames(response)[3] <- "DAY_TYPE"
  colnames(response)[4] <- "MED_LOAD_DAY"
  colnames(response)[5] <- "MED_NUMBER_DAY"
  colnames(response)[6] <- "MED_RESPONSE_DAY"
  colnames(response)[7] <- "MED_NUMBER_RESPONSE_DAY"

  ## 30 day response calculation
  period.response <- c()
  for (i in 1:(ceiling(dim(therapy)[1]/30))) {
    r <- c()
    period.median <- median(therapy.30.days[[i]][therapy.30.days[[i]]!=0])
    if (is.na(period.median) || period.median == 0) {
      r <- 0
    } else {
      r <- (period.median/base.median)*100
    }
    period.response <- c(period.response,r)
  }

  period.response <- data.frame(free.30.days[,1:2],period.response)
  colnames(period.response)[3] <- "MED_RESPONSE"

  ## 30 day number response calculation
  therapy.number.30.days <- split(therapy[,n],ceiling(seq_along(therapy[,n])/30))
  period.number.response <- c()
  for (i in 1:(ceiling(dim(therapy)[1]/30))) {
    period.number.median <- median(therapy.number.30.days[[i]][therapy.number.30.days[[i]]!=0])
    if (is.na(period.number.median) || period.number.median == 0) {
      r <- 0
    } else {
      r <- (period.number.median/base.number.median)*100
    }
    period.number.response <- c(period.number.response,r)
  }

  period.response <- data.frame(period.response,period.number.response)
  colnames(period.response)[4] <- "MED_NUMBER_RESPONSE"

  ## percent free response

  percent.free.response <- period.response
  percent.free.response[,3] <- 100 - (free.30.days[,3] - free.base)
  colnames(percent.free.response)[3] <- "%_MED_FREE_RESPONSE"

  ## score
  score.1 <- (((free.30.days[,3])/100) * ((percent.free.response[,3])/100)) * 100
  score.2 <- (((100-free.30.days[,3])/100) * ((period.response[,3])/100)) * 100
  score <- score.1 + score.2
  overall.score <- percent.free.response
  overall.score[,3] <- score
  colnames(overall.score)[3] <- "MED_SCORE"

  ## number score
  score.3 <- (((free.30.days[,3])/100) * ((percent.free.response[,3])/100)) * 100
  score.4 <- (((100-free.30.days[,3])/100) * ((period.response[,4])/100)) * 100
  score2 <- score.3 + score.4
  overall.number.score <- percent.free.response
  overall.number.score[,3] <- score2
  colnames(overall.number.score)[3] <- "MED_NUMBER_SCORE"

  results <- data.frame(overall.score[,1],
                        overall.score[,2],
                        cbind(free.30.days[,3],
                              period.response[,3],
                              period.response[,4],
                              percent.free.response[,3],
                              overall.score[,3],
                              overall.number.score[,3]))

  results <- data.frame(rep(mrnumber,dim(results)[1]),results)
  colnames(results)[1] <- "MRNUMBER"
  colnames(results)[2:3] <- c("FIRST_DATE","LAST_DATE")
  colnames(results)[4] <- "%_MED_FREE"
  colnames(results)[5] <- "MED_RESPONSE"
  colnames(results)[6] <- "MED_NUMBER_RESPONSE"
  colnames(results)[7] <- "% MED_FREE_RESPONSE"
  colnames(results)[8] <- "MED_SCORE"
  colnames(results)[9] <- "MED_NUMBER_SCORE"

  na <- rep(NA,dim(response)[1])
  outcome <- data.frame(response,a=na,b=na,c=na,d=na)
  colnames(outcome)[8] <- "%_MED_FREE_30_DAYS"
  colnames(outcome)[9] <- "MED_RESPONSE_30_DAYS"
  colnames(outcome)[10] <- "%_MED_FREE_RESPONSE_30_DAYS"
  colnames(outcome)[11] <- "MED_SCORE_30_DAYS"

  outcome[outcome$DATE %in% results$LAST_DATE,c(8:11)] <- results[,c(4,5,7,8)]
  return(outcome)
}