X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2FrTraitCont.Rd;h=2251c8594bb5765ecd589c8103e31a4699d94204;hb=c488b74490ee3d9d200de0e471881f002a18fe4f;hp=f9ce291e73ceb823727bd837bae6b3e46be31382;hpb=6ee9e0a4e1e6bbc09187382bfdef57fafe3844c7;p=ape.git

diff --git a/man/rTraitCont.Rd b/man/rTraitCont.Rd
index f9ce291..2251c85 100644
--- a/man/rTraitCont.Rd
+++ b/man/rTraitCont.Rd
@@ -26,7 +26,7 @@ rTraitCont(phy, model = "BM", sigma = 0.1, alpha = 1, theta = 0,
 \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}:
@@ -45,7 +45,7 @@ rTraitCont(phy, model = "BM", sigma = 0.1, alpha = 1, theta = 0,
   \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}.
+  \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
@@ -62,8 +62,8 @@ rTraitCont(phy, model = "BM", sigma = 0.1, alpha = 1, theta = 0,
   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.
+  Paradis, E. (2012) \emph{Analysis of Phylogenetics and Evolution with
+    R (Second Edition).} New York: Springer.
 }
 \author{Emmanuel Paradis}
 \seealso{
@@ -73,7 +73,7 @@ rTraitCont(phy, model = "BM", sigma = 0.1, alpha = 1, theta = 0,
 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))