X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2Fboot.phylo.Rd;h=fcbf1f3c4f5f7443ca35f7298b7186dc61202cc5;hb=21426f51c5940cb37f3198a7853ef59743729b85;hp=448a4d8ac0a4ad4fe7a176114b819883451db71f;hpb=8fa54a671f763f10f68bfe660b6a5949123d3d41;p=ape.git

diff --git a/man/boot.phylo.Rd b/man/boot.phylo.Rd
index 448a4d8..fcbf1f3 100644
--- a/man/boot.phylo.Rd
+++ b/man/boot.phylo.Rd
@@ -7,9 +7,10 @@
 \alias{plot.prop.part}
 \title{Tree Bipartition and Bootstrapping Phylogenies}
 \usage{
-boot.phylo(phy, x, FUN, B = 100, block = 1, trees = FALSE)
+boot.phylo(phy, x, FUN, B = 100, block = 1,
+           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, ...)
@@ -25,6 +26,9 @@ prop.clades(phy, ..., part = NULL)
     together (see details).}
   \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
@@ -119,10 +123,11 @@ prop.clades(phy, ..., part = NULL)
 }
 \examples{
 data(woodmouse)
-tr <- nj(dist.dna(woodmouse))
+f <- function(x) nj(dist.dna(x))
+tr <- f(woodmouse)
 ### Are bootstrap values stable?
 for (i in 1:5)
-  print(boot.phylo(tr, woodmouse, function(xx) nj(dist.dna(xx))))
+  print(boot.phylo(tr, woodmouse, f, quiet = TRUE))
 ### How many partitions in 100 random trees of 10 labels?...
 TR <- replicate(100, rtree(10), FALSE)
 pp10 <- prop.part(TR)