Bioequivalence and Bioavailability Forum • Time above MIC (R function)

Time above MIC (R function) [R for BE/BA]

posted by Aceto81 – Belgium, 2008-08-13 11:19 (4862 d 14:34 ago) – Posting: # 2176
Views: 30,103

Dear Helmut,

I changed the function radically, so here is version 2, with the data you provided (BLQ was changed to NA):

dat <- structure(list(time = c(0, 0.5167, 1, 1.5, 2, 2.5, 3, 3.5, 4, 

                               4.5, 5, 6, 9, 12.0333, 16.0167, 24.05),

                      conc = c(NA, NA, 1.144, 2.399, 3.226, 3.236, 2.943,

                               2.776, 3.393, 4.536, 3.934, 3.387, 1.643,

                               0.717, 0.231, NA)),

                      .Names = c("time", "conc"),

                      class = "data.frame", row.names = c(NA, -16L))

f2 <- function(dat,th,logarithmic=FALSE) {

  above = 0

  w <- dat$conc > th

  w[w == FALSE] <- 0

  w[w == TRUE] <- 1

  w2 <- which(abs(diff(w)) == 1)

  if (logarithmic == FALSE) {

    for (i in w2) {

      n1 <- diff(w)[i] * -1*(dat$time[i+1] + ((dat$time[i]-dat$time[i+1]) *

            (th-dat$conc[i+1])/(dat$conc[i]-dat$conc[i+1])))

      above <- above + n1

    }

  }

  if (logarithmic == TRUE) {

    for (i in w2) {

      if (diff(w)[i] == 1) {

        n1 <- (dat$time[i+1] + ((dat$time[i]-dat$time[i+1]) *

              (th-dat$conc[i+1])/(dat$conc[i]-dat$conc[i+1])))

        above <- above - n1

      }

      if (diff(w)[i] == -1) {

        n1 <- (dat$time[i+1] + ((dat$time[i]-dat$time[i+1]) *

              (log(th)-log(dat$conc[i+1]))/(log(dat$conc[i])-log(dat$conc[i+1]))))

        above <- above + n1

      }

    }

  }

  return(above)

}



f2(dat, th = 2.268, logarithmic = TRUE)

Best regards

Ace

Complete thread:

Calculation of time above MIC Aceto81 2008-06-26 16:31 [R for BE/BA]
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