R/pdfNCA.R

In pkr: Pharmacokinetics in R

pdfNCA = function(fileName="Temp-NCA.pdf", concData, colSubj="Subject", colTime="Time", colConc="conc", dose=0, adm="Extravascular", dur=0, doseUnit="mg", timeUnit="h", concUnit="ug/L", down="Linear", MW=0) 
{
  defPar = par(no.readonly=TRUE)
#  dev.off()

  PrepPDF(fileName)
  AddPage()
  Text1(1, 1, "Individual Noncompartmental Analysis Result", Cex=1.2)

  maxx = max(concData[,colTime])
  maxy = max(concData[,colConc])
  miny = min(concData[concData[,colConc] > 0,colConc])

  IDs = unique(concData[,colSubj])
  nID = length(IDs)
  Res = vector()
  for (i in 1:nID) {
    cID = IDs[i]
    x = concData[concData[,colSubj]==cID, colTime]
    y = concData[concData[,colSubj]==cID, colConc]
    tabRes = sNCA(x, y, dose=dose, adm=adm, dur=dur, doseUnit=doseUnit, timeUnit=timeUnit, concUnit=concUnit, down=down, MW=MW)
    tRes = txtNCA(x, y, dose=dose, adm=adm, dur=dur, doseUnit=doseUnit, timeUnit=timeUnit, concUnit=concUnit, down=down, MW=MW, returnNA=FALSE)
    Res = c(Res, tRes)

    AddPage(Header1=paste("Subject ID =", cID))
    TextM(tRes, StartRow=1, Header1=paste("Subject ID =", cID))

    scrnmat = matrix(0, 3, 4)
    scrnmat[1,] = c(0, 1, 0, 1)
    scrnmat[2,] = c(0.1, 0.9, 0.50, 0.95)
    scrnmat[3,] = c(0.1, 0.9, 0.05, 0.50)
    ScrNo = split.screen(scrnmat)

    screen(ScrNo[1])
    par(adj=0)
    Text1(1, 1, paste("Subject ID =", cID), Cex=1.0)

    screen(ScrNo[2])
    par(oma=c(1,1,1,1), mar=c(4,4,3,1), adj=0.5)
    plot(x, y, type="b", cex=0.7, xlim=c(0,maxx), ylim=c(0,maxy), xlab=paste0("Time (", timeUnit, ")"), ylab=paste0("Concentration (", concUnit, ")"))

    screen(ScrNo[3])
    par(oma=c(1,1,1,1), mar=c(4,4,3,1), adj=0.5)
    x0 = x[y > 0]
    y0 = y[y > 0]
    plot(x0, log10(y0), type="b", cex=0.7, xlim=c(0, maxx), ylim=c(log10(miny), log10(maxy)), yaxt="n", xlab=paste0("Time (", timeUnit, ")"), ylab=paste0("Concentration (log interval) (", concUnit, ")"))
    yticks = seq(round(min(log10(y0))), ceiling(max(log10(y0))))
    ylabels = sapply(yticks, function(i) as.expression(bquote(10^ .(i))))
    axis(2, at=yticks, labels=ylabels)
    x1 = tabRes["LAMZLL"]
    x2 = tabRes["LAMZUL"]
    deltaX = x1 * 0.05
    y1 = log10(2.718281828)*(tabRes["b0"] - tabRes["LAMZ"] * (x1 - deltaX))
    y2 = log10(2.718281828)*(tabRes["b0"] - tabRes["LAMZ"] * (x2 + deltaX))
    lines(c(x1 - deltaX, x2 + deltaX), c(y1, y2), lty=2, col="red")
    close.screen(all.screens=TRUE)
  }
  par(defPar)
  ClosePDF()
}