\HeaderA{plot.Variogram}{Plot a Variogram Object}{plot.Variogram}
\keyword{models}{plot.Variogram}
\begin{Description}\relax
an \code{xyplot} of the semi-variogram versus the distances is
produced. If \code{smooth = TRUE}, a \code{loess} smoother is added to
the plot. If \code{showModel = TRUE} and \code{x} includes an
\code{"modelVariog"} attribute, the corresponding semi-variogram
is added to the plot.
\end{Description}
\begin{Usage}
\begin{verbatim}
## S3 method for class 'Variogram':
plot(x, smooth, showModel, sigma, span, xlab,
     ylab, type, ylim, grid, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] an object inheriting from class \code{Variogram},
consisting of a data frame with two columns named \code{variog} and
\code{dist}, representing the semi-variogram values and the corresponding
distances.

\item[\code{smooth}] an optional logical value controlling whether a
\code{loess} smoother should be added to the plot. Defaults to
\code{TRUE}, when \code{showModel} is \code{FALSE}.

\item[\code{showModel}] an optional logical value controlling whether the
semi-variogram corresponding to an \code{"modelVariog"} attribute of
\code{x}, if any is present, should be added to the
plot. Defaults to \code{TRUE}, when the \code{"modelVariog"}
attribute is present.

\item[\code{sigma}] an optional numeric value used as the height of a
horizontal line displayed in the plot. Can be used to represent the
process standard deviation. Default is \code{NULL}, implying that no
horizontal line is drawn. 

\item[\code{span}] an optional numeric value with the smoothing parameter for
the \code{loess} fit. Default is 0.6.

\item[\code{xlab,ylab}] optional character strings with the x- and y-axis
labels. Default respectively to \code{"Distance"} and
\code{"SemiVariogram"}. 

\item[\code{type}] an optional character indicating the type of plot. Defaults
to \code{"p"}.

\item[\code{ylim}] an optional numeric vector with the limits for the
y-axis. Defaults to \code{c(0, max(x\$variog))}.

\item[\code{grid}] an optional logical value indicating whether a grid should
be added to plot. Default is \code{FALSE}.
\item[\code{...}] optional arguments passed to the Trellis \code{xyplot} function.
\end{ldescription}
\end{Arguments}
\begin{Value}
an \code{xyplot} Trellis plot.
\end{Value}
\begin{Author}\relax
Jose Pinheiro \email{Jose.Pinheiro@pharma.novartis.com} and Douglas Bates \email{bates@stat.wisc.edu}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{Variogram}{Variogram}},
\code{\LinkA{xyplot}{xyplot}},
\code{\LinkA{loess}{loess}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
fm1 <- lme(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), Ovary)
plot(Variogram(fm1, form = ~ Time | Mare, maxDist = 0.7))
\end{ExampleCode}
\end{Examples}

