some news for ape 3.0-8

[ape.git] / man / yule.cov.Rd

diff --git a/man/yule.cov.Rd b/man/yule.cov.Rd
index ac6a749aa8dcd535576087c4fa11ab7d050ce3f3..9710a94d743e4a091bc60b6a5eb2cc410b4eeee0 100644 (file)
--- a/man/yule.cov.Rd
+++ b/man/yule.cov.Rd
@@ -39,10 +39,11 @@ yule.cov(phy, formula, data = NULL)
 
   The function needs three things:
 
 
   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
   \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);
   left-hand side term), for instance: \code{~ x + y}, it can include
   interactions (\code{~ x + a * b}) (see \code{\link[stats]{formula}}
   for details);


@@ -54,26 +55,30 @@ yule.cov(phy, formula, data = NULL)
   be equal to the number of tips of the tree + the number of nodes. The
   order is the following: first the values for the tips in the same
   order than for the labels, then the values for the nodes sequentially
   be equal to the number of tips of the tree + the number of nodes. The
   order is the following: first the values for the tips in the same
   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
+  from the root to the most terminal nodes (i.e., in the order given by

   \code{phy$edge}).
   \code{phy$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{
 }
 \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.
 }
 }
 \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}},
 \seealso{
   \code{\link{branching.times}}, \code{\link{diversi.gof}},
   \code{\link{diversi.time}}, \code{\link{ltt.plot}},


@@ -86,11 +91,7 @@ x <- rnorm(45) # the tree has 23 tips and 22 nodes
 ### the standard-error for x should be as large as
 ### the estimated parameter
 yule.cov(bird.orders, ~ x)
 ### 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
 ### 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)
 data(bird.families)
 y <- rnorm(272) # 137 tips + 135 nodes
 yule.cov(bird.families, ~ y)