X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2FrTraitCont.Rd;h=2251c8594bb5765ecd589c8103e31a4699d94204;hb=2014b83971be4b9cd1644d6127837df798e9335c;hp=01d82e2bb60c936342b31872d53ba31101c8c487;hpb=24fc6c03893f85a3f9ab3d088201b3731f3035b4;p=ape.git

diff --git a/man/rTraitCont.Rd b/man/rTraitCont.Rd
index 01d82e2..2251c85 100644
--- 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"}.}
@@ -20,11 +20,13 @@ 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
   phylogeny. The calculation is done recursively from the root. See
-  Paradis (2006, p. 151) for a brief introduction.
+  Paradis (2012, pp. 232 and 324) for an introduction.
 }
 \details{
   There are three possibilities to specify \code{model}:
@@ -40,37 +42,38 @@ 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{
-  Paradis, E. (2006) \emph{Analyses of Phylogenetics and Evolution with
-    R.} New York: Springer.
+  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. (2012) \emph{Analysis of Phylogenetics and Evolution with
+    R (Second Edition).} 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)
 rTraitCont(bird.orders) # BM with sigma = 0.1
 ### OU model with two optima:
-tr <- reorder(bird.orders, "p")
+tr <- reorder(bird.orders, "postorder")
 plot(tr)
 edgelabels()
 theta <- rep(0, Nedge(tr))