can be fitted by maximum likelihood (the default, Schluter et
al. 1997), least squares (\code{method = "pic"}, Felsenstein 1985), or
generalized least squares (\code{method = "GLS"}, Martins and Hansen
- 1997). In the latter case, the specification of \code{phy} and
- \code{model} are actually ignored: it is instead given through a
- correlation structure with the option \code{corStruct}.
+ 1997, Cunningham et al. 1998). In the latter case, the specification
+ of \code{phy} and \code{model} are actually ignored: it is instead
+ given through a correlation structure with the option \code{corStruct}.
For discrete characters (\code{type = "discrete"}), only maximum
likelihood estimation is available (Pagel 1994). The model is
\item{call}{the function call.}
}
\references{
+ Cunningham, C. W., Omland, K. E. and Oakley, T. H. (1998)
+ Reconstructing ancestral character states: a critical
+ reappraisal. \emph{Trends in Ecology & Evolution}, \bold{13},
+ 361--366.
+
Felsenstein, J. (1985) Phylogenies and the comparative
method. \emph{American Naturalist}, \bold{125}, 1--15.