Calculation of time above MIC [R for BE/BA]

posted by Aceto81 – Belgium, 2008-06-30 15:50 (4906 d 10:31 ago) – Posting: # 1988
Views: 30,576

Hi HS,

the time above MIC was calculated during the Steady State, which goes from 12 hours to 120 hours. That's why the results differs. (I was struggling with this part as well :ponder: ).

Here the updated code:
time <- c(0.5, 1, 3, 5, 8, 12, 24, 36, 48, 60,
          72, 84, 96, 108, 120, 122, 124)
conc <- c(0.64, 0.7, 1.39, 1.35, 0.67, 1.48, 0.32, 2.08, 0.87, 0.93,
          1.09, 0.59, 1.01, 0.47, 0.99, 0.62, 0.13)
dat  <- data.frame(time, conc)

f <- function(dat, th) {
  under <- 0
  for (i in which(dat$conc < th)) {
      if (!is.na(dat$conc[i-1])) {
        y <- dat$conc[c(i-1,i)]
        x <- dat$time[c(i-1,i)]
        slope <- coef(lm(y~x))[2]
        under <- under + x[2]-x[1]-(th-y[1])/slope
      }
      if (!is.na(dat$conc[i+1])) {
        y <- dat$conc[c(i,i+1)]
        x <- dat$time[c(i,i+1)]
        slope <- coef(lm(y~x))[2]
        under <- under + (th-y[1])/slope
      }
    }
  return(under)
}

th    <- 0.517
first <- 12
last  <- 120
occupancy <- last-first - f(dat[dat$time >=first & dat$time <=last, ], th)
coverage  <- 100*occupancy/(last-first)
cat(" Time point interval:",first,"-",last,"\n",
    "Occupancy time:",occupancy,"\n",
    "Coverage:",coverage,"%\n")

Thanks for your valuable input

Ace

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