various updates for ape 2.7-2 (fixed)

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

diff --git a/man/boot.phylo.Rd b/man/boot.phylo.Rd
index 5c05fd1f0bf41d799e572b7e941c5e5cd8364f02..6869f6724ced01aefe71cee3741b98f3f5463973 100644 (file)
--- a/man/boot.phylo.Rd
+++ b/man/boot.phylo.Rd
@@ -7,8 +7,9 @@
 \alias{plot.prop.part}
 \title{Tree Bipartition and Bootstrapping Phylogenies}
 \usage{
-boot.phylo(phy, x, FUN, B = 100, block = 1, trees = FALSE)
-prop.part(..., check.labels = FALSE)
+boot.phylo(phy, x, FUN, B = 100, block = 1,
+           trees = FALSE, quiet = FALSE)
+prop.part(..., check.labels = TRUE)
 prop.clades(phy, ..., part = NULL)
 \method{print}{prop.part}(x, ...)
 \method{summary}{prop.part}(object, ...)
@@ -25,14 +26,14 @@ 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{\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
     arguments for the plot (see details).}
   \item{check.labels}{a logical specifying whether to check the labels
-    of each tree. If \code{FALSE} (the default), it is assumed that all
-    trees have the same tip labels, and that they are in the same order
-    (see details).}
+    of each tree. If \code{FALSE}, it is assumed that all trees have the
+    same tip labels, and that they are in the same order (see details).}
   \item{part}{a list of partitions as returned by \code{prop.part}; if
     this is used then \code{\dots} is ignored.}
   \item{object}{an object of class \code{"prop.part"}.}
@@ -45,7 +46,9 @@ prop.clades(phy, ..., part = NULL)
   These functions analyse bipartitions found in a series of trees.
 
   \code{prop.part} counts the number of bipartitions found in a series
-  of trees given as \code{\dots}.
+  of trees given as \code{\dots}. If a single tree is passed, the
+  returned object is a list of vectors with the tips descending from
+  each node (i.e., clade compositions indexed by node number).
 
   \code{prop.clades} counts the number of times the bipartitions present
   in \code{phy} are present in a series of trees given as \code{\dots} or
@@ -63,11 +66,11 @@ prop.clades(phy, ..., part = NULL)
   be resampled altogether. For instance, if one wants to resample at the
   codon-level, then \code{block = 3} must be used.
 
-  Using (the default) \code{check.labels = FALSE} in \code{prop.part}
-  results in considerable decrease in computing times. This requires that
-  (i) all trees have the same tip labels, \emph{and} (ii) these labels
-  are ordered similarly in all trees (in other words, the element
-  \code{tip.label} are identical in all trees).
+  Using \code{check.labels = FALSE} in \code{prop.part} decreases
+  computing times. This requires that (i) all trees have the same tip
+  labels, \emph{and} (ii) these labels are ordered similarly in all
+  trees (in other words, the element \code{tip.label} are identical in
+  all trees).
 
   The plot function represents a contingency table of the different
   partitions (on the \emph{x}-axis) in the lower panel, and their observed
@@ -112,16 +115,17 @@ prop.clades(phy, ..., part = NULL)
   Felsenstein, J. (1985) Confidence limits on phylogenies: an approach
   using the bootstrap. \emph{Evolution}, \bold{39}, 783--791.
 }
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
 \seealso{
   \code{\link{dist.topo}}, \code{\link{consensus}}, \code{\link{nodelabels}}
 }
 \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)