new files for ape 3.0

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

diff --git a/man/boot.phylo.Rd b/man/boot.phylo.Rd
index 6869f6724ced01aefe71cee3741b98f3f5463973..fcbf1f3c4f5f7443ca35f7298b7186dc61202cc5 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