final commit for ape 3.0

[ape.git] / man / rTraitDisc.Rd

diff --git a/man/rTraitDisc.Rd b/man/rTraitDisc.Rd
index ed1919d710de03821f7989b852c0f1bca6e72408..a800c465b032b7457f4344cb1055c07210d0b6be 100644 (file)
--- a/man/rTraitDisc.Rd
+++ b/man/rTraitDisc.Rd
@@ -4,7 +4,7 @@
 \usage{
 rTraitDisc(phy, model = "ER", k = if (is.matrix(model)) ncol(model) else 2,
            rate = 0.1, states = LETTERS[1:k], freq = rep(1/k, k),
-           ancestor = FALSE, root.value = 1)
+           ancestor = FALSE, root.value = 1, ...)
 }
 \arguments{
   \item{phy}{an object of class \code{"phylo"}.}
@@ -24,6 +24,8 @@ rTraitDisc(phy, model = "ER", k = if (is.matrix(model)) ncol(model) else 2,
   \item{root.value}{an integer giving the value at the root (by default,
     it's the first state). To have a random value, use \code{root.value
       = sample(k)}.}
+  \item{\dots}{further arguments passed to \code{model} if it is a
+    function.}
 }
 \description{
   This function simulates the evolution of a discrete character along a
@@ -63,15 +65,24 @@ rTraitDisc(phy, model = "ER", k = if (is.matrix(model)) ncol(model) else 2,
 }
 \author{Emmanuel Paradis}
 \seealso{
-  \code{\link{rTraitCont}}, \code{\link{ace}}
+  \code{\link{rTraitCont}}, \code{\link{rTraitMult}}, \code{\link{ace}}
 }
 \examples{
 data(bird.orders)
 ### the two followings are the same:
 rTraitDisc(bird.orders)
 rTraitDisc(bird.orders, model = matrix(c(0, 0.1, 0.1, 0), 2))
+
 ### two-state model with irreversibility:
 rTraitDisc(bird.orders, model = matrix(c(0, 0, 0.1, 0), 2))
+
+### simple two-state model:
+tr <- rcoal(n <- 40, br = runif)
+x <- rTraitDisc(tr, ancestor = TRUE)
+plot(tr, show.tip.label = FALSE)
+nodelabels(pch = 19, col = x[-(1:n)])
+tiplabels(pch = 19, col = x[1:n])
+
 ### an imaginary model with stasis 0.5 time unit after a node, then
 ### random evolution:
 foo <- function(x, l) {