X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2Fboot.phylo.Rd;h=2e166656c4e858f6ccca93f7f57a49a854828eaf;hb=5090ae602c33e1cd3bbdbd2429a43daa8188b8c3;hp=fa39eb7ce126a3c16913a3412d59cdbc843ca20c;hpb=c827059eeafc8cbe41c812b26979543ab287803e;p=ape.git

diff --git a/man/boot.phylo.Rd b/man/boot.phylo.Rd
index fa39eb7..2e16665 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)
-prop.part(..., check.labels = FALSE)
-prop.clades(phy, ..., part = NULL)
+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, rooted = FALSE)
 \method{print}{prop.part}(x, ...)
 \method{summary}{prop.part}(object, ...)
 \method{plot}{prop.part}(x, barcol = "blue", leftmar = 4, ...)
@@ -23,14 +24,18 @@ prop.clades(phy, ..., part = NULL)
   \item{B}{the number of bootstrap replicates.}
   \item{block}{the number of columns in \code{x} that will be resampled
     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
     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"}.}
@@ -43,7 +48,9 @@ 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
@@ -61,11 +68,11 @@ 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
@@ -83,6 +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
@@ -95,7 +106,10 @@ prop.clades(phy, ..., part = NULL)
 
   \code{prop.clades} and \code{boot.phylo} return a numeric vector
   which \emph{i}th element is the number associated to the \emph{i}th
-  node of \code{phy}.
+  node of \code{phy}. If \code{trees = TRUE}, \code{boot.phylo} returns
+  a list whose first element (named \code{"BP"}) is like before, and the
+  second element (\code{"trees"}) is a list with the bootstraped
+  trees.
 
   \code{summary} returns a numeric vector.
 }
@@ -107,26 +121,34 @@ 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)
+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}