https://github.com/cran/bbmle
Tip revision: dac6dcfdd0a15c986353567773484d9e90d785de authored by Ben Bolker on 07 September 2011, 13:47:10 UTC
version 1.0.2
version 1.0.2
Tip revision: dac6dcf
profile.mle-class.Rd
\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}