new method = "REML" in ace() with continuous traits

[ape.git] / man / rTraitCont.Rd

diff --git a/man/rTraitCont.Rd b/man/rTraitCont.Rd
index 01d82e2bb60c936342b31872d53ba31101c8c487..f9ce291e73ceb823727bd837bae6b3e46be31382 100644 (file)
--- a/man/rTraitCont.Rd
+++ b/man/rTraitCont.Rd
@@ -2,8 +2,8 @@
 \alias{rTraitCont}
 \title{Continuous Character Simulation}
 \usage{
-rTraitCont(phy, model = "BM", sigma = 0.1, alpha = 1,
-           theta = 0, ancestor = FALSE, root.value = 0)
+rTraitCont(phy, model = "BM", sigma = 0.1, alpha = 1, theta = 0,
+           ancestor = FALSE, root.value = 0, ...)
 }
 \arguments{
   \item{phy}{an object of class \code{"phylo"}.}
@@ -20,6 +20,8 @@ rTraitCont(phy, model = "BM", sigma = 0.1, alpha = 1,
     values at the nodes as well (by default, only the values at the tips
     are returned).}
   \item{root.value}{a numeric giving the value at the root.}
+  \item{\dots}{further arguments passed to \code{model} if it is a
+    function.}
 }
 \description{
   This function simulates the evolution of a continuous character along a
@@ -40,31 +42,32 @@ rTraitCont(phy, model = "BM", sigma = 0.1, alpha = 1,
 
   \item{\code{"OU"}:}{an Ornstein-Uhlenbeck model is used. The above
   indexing rule is used for the three parameters \code{sigma},
-  \code{alpha}, and \code{theta}. This may be more interesting for the
-  last one to model varying phenotypic optima. Be careful that large
-  values of \code{alpha} may give unrealistic output.}
+  \code{alpha}, and \code{theta}. This may be interesting for the last
+  one to model varying phenotypic optima. The exact updating formula
+  from Gillespie (1996) are used which are reduced to BM formula if
+  \code{alpha = 0}.
 
   \item{A function:}{it must be of the form \code{foo(x, l)} where
   \code{x} is the trait of the ancestor and \code{l} is the branch
   length. It must return the value of the descendant. The arguments
   \code{sigma}, \code{alpha}, and \code{theta} are ignored.}
 }}
-\note{
-  Currently, the OU model is a bit difficult to tune. Hopefully, this
-  may be improved in the future.
-}
 \value{
   A numeric vector with names taken from the tip labels of
   \code{phy}. If \code{ancestor = TRUE}, the node labels are used if
   present, otherwise, ``Node1'', ``Node2'', etc.
 }
 \references{
+  Gillespie, D. T. (1996) Exact numerical simulation of the
+  Ornstein-Uhlenbeck process and its integral. \emph{Physical Review E},
+  \bold{54}, 2084--2091.
+
   Paradis, E. (2006) \emph{Analyses of Phylogenetics and Evolution with
     R.} New York: Springer.
 }
 \author{Emmanuel Paradis}
 \seealso{
-  \code{\link{rTraitDisc}}, \code{\link{ace}}
+  \code{\link{rTraitDisc}}, \code{\link{rTraitMult}}, \code{\link{ace}}
 }
 \examples{
 data(bird.orders)