\item a phylogenetic tree which may contain multichotomies;
\item a formula which specifies the predictors of the model described
- above: this is given as a standard R formula and has no response (no
+ above: this is given as a standard \R formula and has no response (no
left-hand side term), for instance: \code{~ x + y}, it can include
interactions (\code{~ x + a * b}) (see \code{\link[stats]{formula}}
for details);
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{ace}}.
+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
data(bird.families)
y <- rnorm(272) # 137 tips + 135 nodes
yule.cov(bird.families, ~ y)
-yule(multi2di(bird.families))
}
\keyword{models}