backfitRichards-package {backfitRichards} | R Documentation |
Backfitted values of the independent variable of Richards curves are computed and plotted.
Package: | backfitRichards |
Type: | Package |
Version: | 0.4.5 |
Date: | 2008-09-01 |
License: | GPL Version 2 or later |
Jens Henrik Badsberg
Maintainer: Jens Henrik Badsberg <september2008richards@badsberg.eu>
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
## 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)