backfitRichards-package {backfitRichards}R Documentation

Backfitted independent values of Richards curves

Description

Backfitted values of the independent variable of Richards curves are computed and plotted.

Details

Package: backfitRichards
Type: Package
Version: 0.4.5
Date: 2008-09-01
License: GPL Version 2 or later

Author(s)

Jens Henrik Badsberg

Maintainer: Jens Henrik Badsberg <september2008richards@badsberg.eu>

References

Richards, F.J.: A flexible growth function for empirical use. J. Exp. Bot. 1959; 10:290-300.

Findlay JW, Dillard RF.: Appropriate calibration curve fitting in ligand binding assays. AAPS J. 2007 Jun 29;9(2).

Finney DJ.: Statistical methods in biological assay, 3rd ed. London: Griffin; 1978.

Finney DJ.: Response curves for radioimmunoassay. Clinical Chemistry 1983; 29:1562-1566.

Schofield T.: Assay Validation. In: Encyclopedia of Biopharmaceutical Statistics. New York: Marcel Dekker 2000; p. 21-30.

http://en.wikipedia.org/wiki/ELISA

Examples


## Not run: 

library(nlme)

data(ChickWeight)

ChickWeight <- cbind(ChickWeight, ExpTime = exp(ChickWeight[,"Time"]))

groupedChicks <- groupedData(weight ~ ExpTime | Diet / Chick, 
                             inner = ~ PR, data = ChickWeight)

listChicks <- split(groupedChicks, list(groupedChicks[,"Diet"],
                                        groupedChicks[,"Chick"]),
                    drop = TRUE)

fit.Fpl.BP <- function(X, start, lower, upper)
 {
  try(nls(weight ~ SSny1(ExpTime, a, d, b, x50),
          lower = lower, upper = upper, algorithm = "port",
          control = nls.control(warnOnly = TRUE), data = X))
 }

Start <- list(a =    25, d =  200, b =  10, x50 =    10, ny =  1)
Lower <- list(a = -2000, d =    5, b =   0, x50 =     1, ny =  0.01)
Upper <- list(a =    50, d = 1500, b =  50, x50 = 10^20, ny = 128)

myApplyFUN2X <- 
  function(X, FUN, start = Start, lower = Lower, upper = Upper,
              Report = print, ...) {
    if (dim(X)[1] > 0) {
      result <- FUN(X, start, lower, upper)
      if (is.null(result) | class(result) == "try-error")
        Report(X)
      return(result)
    }
  }

fits.Fpl.BP <- lamodified(listChicks, FUN = fit.Fpl.BP, n = 4,
                          applyFUN2X = myApplyFUN2X)

back.Fits <- backFits(listChicks, FUN = fit.Fpl.BP, ny = 1,
                      respName = "weight", indepName = "ExpTime",
                      applyFUN2X = myApplyFUN2X)

par(mfrow = c(2, 2))

Z.back <- backPlot(backFits = back.Fits, xt = function(x) x,
                   main = "Relative backfitted exp(time)", xlab = "Exp(Time)", 
                   ylim = c(0, 500), log = "x", pch = 1, col = "red")

Z.back <- backPlot(backFits = back.Fits, xt = function(x) log(x),
                   main = "Relative backfitted exp(time)", xlab = "Time", 
                   ylim = c(0, 500), pch = 1, col = "red")

Z.back <- backPlot(backFits = back.Fits, xt = function(x) log(x),
                   main = "Relative backfitted exp(time)", xlab = "Time", 
                   log = "y", ylim = c(1, 5000), pch = 1, col = "red")

Z.back <- backPlot(backFits = back.Fits, xt = function(x) log(x),
                   main = "Relative backfitted exp(time)", xlab = "Time", 
                   log = "y", ylim = c(10, 500), pch = 1, col = "red")

## End(Not run)


[Package backfitRichards version 0.5.0 Index]