last changes for ape 2.4-1

[ape.git] / man / vcv.phylo.Rd

diff --git a/man/vcv.phylo.Rd b/man/vcv.phylo.Rd
index 001bc68f94d179cc94d036d6ee158f27b98d58d8..7af6975cb1139a7dd3006ff904b092b1a37b023f 100644 (file)
--- a/man/vcv.phylo.Rd
+++ b/man/vcv.phylo.Rd
@@ -1,26 +1,31 @@
 \name{vcv.phylo}
+\alias{vcv}
 \alias{vcv.phylo}
+\alias{vcv.corPhyl}
 \title{Phylogenetic Variance-covariance or Correlation Matrix}
 \usage{
-vcv.phylo(phy, model = "Brownian", cor = FALSE)
+vcv(phy, ...)
+\method{vcv}{phylo}(phy, model = "Brownian", corr = FALSE, ...)
+\method{vcv}{corPhyl}(phy, corr = FALSE, ...)
 }
 \arguments{
-  \item{phy}{an object of class \code{"phylo"}.}
+  \item{phy}{an object of the correct class (see above).}
   \item{model}{a character giving the model used to compute the
-    variances and covariances of the phynotype; by default
-    \code{"Brownian"}. Currently only the Brownian model is available.}
-  \item{cor}{a logical indicating whether the correlation matrix should
+    variances and covariances; only \code{"Brownian"} is available.}
+  \item{corr}{a logical indicating whether the correlation matrix should
     be returned (\code{TRUE}); by default the variance-covariance matrix
     is returned (\code{FALSE}).}
+  \item{\dots}{further arguments to be passed to or from other methods.}
 }
 \description{
   This function computes the expected variances and covariances of a
-  continuous phenotype assuming it evolves under a given model
-  (currently only the model of Brownian motion is available).
+  continuous trait assuming it evolves under a given model.
+
+  This is a generic function with methods for objects of class
+  \code{"phylo"} and \code{"corPhyl"}.
 }
 \value{
-  a numeric matrix with the names of the tips (as given by the \code{tip.label}
-  of the argument \code{phy}) as colnames and rownames.
+  a numeric matrix with the names of the tips as colnames and rownames.
 }
 \references{
   Garland, T. Jr. and Ives, A. R. (2000) Using the past to predict the
@@ -28,9 +33,24 @@ vcv.phylo(phy, model = "Brownian", cor = FALSE)
   comparative methods. \emph{American Naturalist}, \bold{155}, 346--364.
 }
 
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
+\note{
+  Do not confuse this function with \code{\link[stats]{vcov}} which
+  computes the variance-covariance matrix among parameters of a fitted
+  model object.
+}
 \seealso{
-  \code{\link{read.tree}} to read tree files in Newick format
+  \code{\link{corBrownian}}, \code{\link{corMartins}},
+  \code{\link{corGrafen}}, \code{\link{corPagel}},
+  \code{\link{corBlomberg}}
+}
+\examples{
+tr <- rtree(5)
+## all are the same:
+vcv(tr)
+vcv(corBrownian(1, tr))
+vcv(corPagel(1, tr))
+vcv(corPagel(0, tr))
 }
 \keyword{manip}
 \keyword{multivariate}