fix bug in prop.clades

[ape.git] / man / boot.phylo.Rd

diff --git a/man/boot.phylo.Rd b/man/boot.phylo.Rd
index 6869f6724ced01aefe71cee3741b98f3f5463973..2e166656c4e858f6ccca93f7f57a49a854828eaf 100644 (file)
--- a/man/boot.phylo.Rd
+++ b/man/boot.phylo.Rd
@@ -8,9 +8,9 @@
 \title{Tree Bipartition and Bootstrapping Phylogenies}
 \usage{
 boot.phylo(phy, x, FUN, B = 100, block = 1,
-           trees = FALSE, quiet = FALSE)
+           trees = FALSE, quiet = FALSE, rooted = FALSE)
 prop.part(..., check.labels = TRUE)
-prop.clades(phy, ..., part = NULL)
+prop.clades(phy, ..., part = NULL, rooted = FALSE)
 \method{print}{prop.part}(x, ...)
 \method{summary}{prop.part}(object, ...)
 \method{plot}{prop.part}(x, barcol = "blue", leftmar = 4, ...)
@@ -27,6 +27,8 @@ prop.clades(phy, ..., part = NULL)
   \item{trees}{a logical specifying whether to return the bootstraped
     trees (\code{FALSE} by default).}
   \item{quiet}{a logical: a progress bar is displayed by default.}
+  \item{rooted}{a logical specifying whether the trees should be treated
+    as rooted or not (the default).}
   \item{\dots}{either (i) a single object of class \code{"phylo"}, (ii) a
     series of such objects separated by commas, or (iii) a list
     containing such objects. In the case of \code{plot} further
@@ -88,6 +90,10 @@ prop.clades(phy, ..., part = NULL)
   passed as \code{\dots} fulfills conditions (i) and (ii) above, then it
   might be faster to first call, e.g., \code{pp <- prop.part(...)}, then
   use the option \code{part}: \code{prop.clades(phy, part = pp)}.
+
+  You have to be careful that by default \code{prop.clades} considers
+  the trees as unrooted and this may result in spurious results if the
+  trees are rooted (see examples).
 }
 \value{
   \code{prop.part} returns an object of class \code{"prop.part"} which
@@ -127,15 +133,22 @@ tr <- f(woodmouse)
 for (i in 1:5)
   print(boot.phylo(tr, woodmouse, f, quiet = TRUE))
 ### How many partitions in 100 random trees of 10 labels?...
-TR <- replicate(100, rtree(10), FALSE)
+TR <- rmtree(100, 10)
 pp10 <- prop.part(TR)
 length(pp10)
 ### ... and in 100 random trees of 20 labels?
-TR <- replicate(100, rtree(20), FALSE)
+TR <- rmtree(100, 20)
 pp20 <- prop.part(TR)
 length(pp20)
 plot(pp10, pch = "x", col = 2)
 plot(pp20, pch = "x", col = 2)
+
+set.seed(1)
+tr <- rtree(10) # rooted by default
+prop.clades(tr, tr) # clearly wrong
+prop.clades(tr, tr, rooted = TRUE)
+tr <- rtree(10, rooted = FALSE)
+prop.clades(tr, tr) # correct
 }
 \keyword{manip}
 \keyword{htest}