\alias{pic}
\title{Phylogenetically Independent Contrasts}
\usage{
-pic(x, phy, scaled = TRUE, var.contrasts = FALSE)
+pic(x, phy, scaled = TRUE, var.contrasts = FALSE,
+ rescaled.tree = FALSE)
}
\arguments{
\item{x}{a numeric vector.}
\item{phy}{an object of class \code{"phylo"}.}
\item{scaled}{logical, indicates whether the contrasts should be
- scaled with their expected variance (default to \code{TRUE}).}
+ scaled with their expected variances (default to \code{TRUE}).}
\item{var.contrasts}{logical, indicates whether the expected
- variance of the contrasts should be returned (default to \code{FALSE}).}
+ variances of the contrasts should be returned (default to
+ \code{FALSE}).}
+ \item{rescaled.tree}{logical, if \code{TRUE} the rescaled tree is
+ returned together with the main results.}
}
\description{
Compute the phylogenetically independent contrasts using the method
than the tip labels of \code{phy}.
The user must be careful here since the function requires that both
- series of names perfectly match, so this operation may fail if there
- is a typing or syntax error. If both series of names do not match, the
- values in the \code{x} are taken to be in the same order than the tip
- labels of \code{phy}, and a warning message is issued.
+ series of names perfectly match. If both series of names do not match,
+ the values in the \code{x} are taken to be in the same order than the
+ tip labels of \code{phy}, and a warning message is issued.
}
\value{
either a vector of phylogenetically independent contrasts (if
\code{var.contrasts = FALSE}), or a two-column matrix with the
phylogenetically independent contrasts in the first column and their
- expected variance in the second column (if \code{var.contrasts = TRUE}).
+ expected variance in the second column (if \code{var.contrasts =
+ TRUE}). If the tree has node labels, these are used as labels of the
+ returned object.
+
+ If \code{rescaled.tree = TRUE}, a list is returned with two elements
+ named ``contr'' with the above results and ``rescaled.tree'' with the
+ tree and its rescaled branch lengths (see Felsenstein 1985).
}
\references{
Felsenstein, J. (1985) Phylogenies and the comparative method.
\emph{American Naturalist}, \bold{125}, 1--15.
}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
\seealso{
- \code{\link{read.tree}}, \code{\link{compar.gee}}, \code{\link{compar.lynch}}
+ \code{\link{read.tree}}, \code{\link{compar.gee}},
+ \code{\link{compar.lynch}}, \code{\link{pic.ortho}},
+ \code{\link{varCompPhylip}}
}
\examples{
### The example in Phylip 3.5c (originally from Lynch 1991)