various bug fixes

[ape.git] / man / consensus.Rd

diff --git a/man/consensus.Rd b/man/consensus.Rd
index 281eb4648e486d0b7399fc0aeee72d2d9d7d4267..2f7bdeb282018b18821a66d0958c90f8b1d59f37 100644 (file)
--- a/man/consensus.Rd
+++ b/man/consensus.Rd
@@ -2,14 +2,18 @@
 \alias{consensus}
 \title{Concensus Trees}
 \usage{
-consensus(..., p = 1)
+consensus(..., p = 1, check.labels = TRUE)
 }
 \arguments{
-  \item{...}{either (i) a single object of class \code{"phylo"}, (ii) a
+  \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.}
   \item{p}{a numeric value between 0.5 and 1 giving the proportion for a
     clade to be represented in the consensus tree.}
+  \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).}
 }
 \description{
   Given a series of trees, this function returns the consensus tree. By
@@ -17,10 +21,17 @@ consensus(..., p = 1)
   majority-rule consensus tree, use \code{p = 0.5}. Any value between
   0.5 and 1 can be used.
 }
+\details{
+  Using \code{check.labels = FALSE} results in
+  considerable decrease in computing times. This requires that all
+  trees have the same tip labels, \emph{and} these labels are
+  ordered similarly in all trees (in other words, the element
+  \code{tip.label} are identical in all trees).
+}
 \value{
   an object of class \code{"phylo"}.
 }
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
 \seealso{
   \code{\link{prop.part}}, \code{\link{dist.topo}}
 }