The function needs three things:
+\itemize{
\item a phylogenetic tree which may contain multichotomies;
\item a formula which specifies the predictors of the model described
order than for the labels, then the values for the nodes sequentially
from the root to the most terminal nodes (i.e. in the order given by
\code{phy$edge}).
+}
- The user must obtain the values for the nodes separately.
+The user must obtain the values for the nodes separately.
- Note that the method in its present implementation assumes that the
- change in a species trait is more or less continuous between two nodes
- or between a node and a tip. Thus reconstructing the ancestral values
- with a Brownian motion model may be consistent with the present
- method. This can be done with the function \code{\link{pic}} but
- currently needs some hacking!
+Note that the method in its present implementation assumes that the
+change in a species trait is more or less continuous between two nodes
+or between a node and a tip. Thus reconstructing the ancestral values
+with a Brownian motion model may be consistent with the present
+method. This can be done with the function \code{\link{ace}}.
}
\value{
- A NULL value is returned, the results are simply printed.
+ A NULL value is returned, the results are simply printed. The output
+ includes the deviance of the null (intercept-only) model and a
+ likelihood-ratio test of the fitted model against the null model.
+ Note that the deviance of the null model is different from the one
+ returned by \code{\link{yule}} because of the different parametrizations.
}
\references{
Paradis, E. (2005) Statistical analysis of diversification with
species traits. \emph{Evolution}, \bold{59}, 1--12.
}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
\seealso{
\code{\link{branching.times}}, \code{\link{diversi.gof}},
\code{\link{diversi.time}}, \code{\link{ltt.plot}},
### the standard-error for x should be as large as
### the estimated parameter
yule.cov(bird.orders, ~ x)
-### compare with the simple Yule model, eventually
-### with a likelihood ratio test
-yule(bird.orders)
### another example with a tree that has a multichotomy
-### but we cannot run yule() because of this!
data(bird.families)
y <- rnorm(272) # 137 tips + 135 nodes
yule.cov(bird.families, ~ y)