\name{profile.mle2-class}
\docType{class}
\alias{profile.mle2-class}
\alias{confint,profile.mle2-method}
\alias{confint.mle2}  %% bogus but good ref link
\alias{plot,profile.mle2-method}
\alias{plot,profile.mle2,missing-method}
\alias{show,profile.mle2-method}
\alias{plot.profile.mle2}
\title{Class "profile.mle2"; Profiling information for "mle2" object}
\description{Likelihood profiles along each parameter of likelihood function}
\section{Objects from the Class}{
Objects can be created by calls of the form \code{new("profile.mle2",
  ...)}, but most often by invoking \code{profile} on an "mle2" object.
}
\section{Slots}{
  \describe{
    \item{\code{profile}:}{Object of class \code{"list"}. List of
      profiles, one for each requested parameter. Each profile is a data
      frame with the first column called \code{z} being the signed square
      root of the deviance, and the others being the
      parameters with names prefixed by \code{par.vals.}}
    \item{\code{summary}:}{Object of class \code{"summary.mle2"}. Summary
      of object being profiled.}
  }
}
\section{Methods}{
  \describe{
    \item{confint}{\code{signature(object = "profile.mle2")}: Use profile
      to generate approximate confidence intervals for parameters.}
    \item{plot}{\code{signature(x = "profile.mle2", y = "missing")}: Plot
      profiles for each parameter.}
    \item{summary}{\code{signature(x = "profile.mle2")}: Plot
      profiles for each parameter.}
    \item{show}{\code{signature(object = "profile.mle2")}: Show object.}
  }
}
\usage{\S4method{plot}{profile.mle2}(x,
   levels, which=1:p, conf = c(99, 95, 90, 80, 50)/100,
   plot.confstr = TRUE,
   confstr = NULL, absVal = TRUE, add = FALSE,
   col.minval="green", lty.minval=2,
   col.conf="magenta", lty.conf=2,
   col.prof="blue", lty.prof=1,
   xlabs=nm, ylab="z",
   onepage=TRUE,
   ask=((prod(par("mfcol")) < length(which)) && dev.interactive() &&
               !onepage),
   show.points=FALSE,
   main, xlim, ylim, \dots)
}
\arguments{
  \item{x}{An object of class profile.mle2}
  \item{levels}{levels at which to plot likelihood cutoffs (set by conf
  by default)}
  \item{which}{(numeric or character) which parameter profiles to plot}
  \item{conf}{(1-alpha) levels at which to plot likelihood
    cutoffs/confidence intervals}
  \item{plot.confstr}{(logical) plot labels showing confidence levels?}
  \item{confstr}{(character) labels for confidence levels
    (by default, constructed from conf levels}
  \item{absVal}{(logical) plot absolute values of signed square
    root deviance difference ("V" plot rather than straight-line
    plot)?}
  \item{add}{(logical) add profile to existing graph?}
  \item{col.minval}{color for minimum line}
  \item{lty.minval}{line type for minimum line}
  \item{col.conf}{color for confidence intervals}
  \item{lty.conf}{line type for confidence intervals}
  \item{col.prof}{color for profile}
  \item{lty.prof}{line type for profile}
  \item{xlabs}{x labels}
  \item{ylab}{y label}
  \item{onepage}{(logical) plot all profiles on one page,
    adjusting par(mfcol) as necessary?}
  \item{ask}{(logical) pause for user input between plots?}
  \item{show.points}{(logical) show computed profile points
    as well as interpolated spline?}
  \item{main}{(logical) main title}
  \item{xlim}{x limits}
  \item{ylim}{y limits}
  \item{\dots}{other arguments}
}
\seealso{
  \code{\link{mle2}}, \code{\link{mle2-class}}, \code{\link{summary.mle2-class}} 
}
\examples{
x <- 0:10
y <- c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8)
d <- data.frame(x,y)
fit1 <- mle2(y~dpois(lambda=ymax/(1+x/xhalf)),start=list(ymax=1,xhalf=1),
   method="L-BFGS-B",lower=c(ymax=0.001,xhalf=0.001),data=d)
p1 <- profile(fit1)
plot(p1,main=c("first","second"),
     xlab=c(~y[max],~x[1/2]),ylab="Signed square root deviance")
}

\keyword{classes}