% File src/library/stats/man/plot.profile.nls.Rd
% Part of the R package, https://www.R-project.org
% Copyright 1995-2011 R Core Team
% Distributed under GPL 2 or later

\name{plot.profile.nls}
\alias{plot.profile.nls}
\title{Plot a \code{profile.nls} Object}
\description{
  Displays a series of plots of the profile t function and interpolated
  confidence intervals for the parameters in a nonlinear regression
  model that has been fit with \code{nls} and profiled with
  \code{profile.nls}.
}
\usage{
\method{plot}{profile.nls}(x, levels, conf = c(99, 95, 90, 80, 50)/100,
     absVal = TRUE, ylab = NULL, lty = 2, \dots)
}
\arguments{
  \item{x}{an object of class \code{"profile.nls"} }
  \item{levels}{levels, on the scale of the absolute value of a t
    statistic, at which to interpolate intervals.  Usually \code{conf}
    is used instead of giving \code{levels} explicitly.}
 \item{conf}{a numeric vector of confidence levels for profile-based
   confidence intervals on the parameters.
   Defaults to \code{c(0.99, 0.95, 0.90, 0.80, 0.50).}}
 \item{absVal}{a logical value indicating whether or not the plots
   should be on the scale of the absolute value of the profile t.
   Defaults to \code{TRUE}.}
 \item{lty}{the line type to be used for axis and dropped lines.}
 \item{ylab, \dots}{other arguments to the \code{\link{plot.default}}
   function can be passed here (but not \code{xlab}, \code{xlim},
   \code{ylim} nor \code{type}).}
}
\details{
  The plots are produced in a set of hard-coded colours, but as these
  are coded by number their effect can be changed by setting the
  \code{\link{palette}}.  Colour 1 is used for the axes and 4 for the
  profile itself.  Colours 3 and 6 are used for the axis line at zero and
  the horizontal/vertical lines dropping to the axes.
}
\references{
  Bates, D.M. and Watts, D.G. (1988),
  \emph{Nonlinear Regression Analysis and Its Applications},
  Wiley (chapter 6)
}
\author{Douglas M. Bates and Saikat DebRoy}
\seealso{
  \code{\link{nls}},
  \code{\link{profile}},
  \code{\link{profile.nls}}
}
\examples{
require(graphics)

# obtain the fitted object
fm1 <- nls(demand ~ SSasympOrig(Time, A, lrc), data = BOD)
# get the profile for the fitted model
pr1 <- profile(fm1, alphamax = 0.05)
opar <- par(mfrow = c(2,2), oma = c(1.1, 0, 1.1, 0), las = 1)
plot(pr1, conf = c(95, 90, 80, 50)/100)
plot(pr1, conf = c(95, 90, 80, 50)/100, absVal = FALSE)
mtext("Confidence intervals based on the profile sum of squares",
      side = 3, outer = TRUE)
mtext("BOD data - confidence levels of 50\%, 80\%, 90\% and 95\%",
      side = 1, outer = TRUE)
par(opar)
}
\keyword{nonlinear}
\keyword{regression}
\keyword{models}
