X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2Froot.Rd;h=05ef5935ba7237019b2b590ae2b4d75274491bc0;hb=b9e04a6e6af3beda74b916eda00b42ac38875563;hp=35295b893a94f1d61e42d2d285149fd9f169728e;hpb=1d0651b1374592d87400614a03b34b4e0cc63aae;p=ape.git

diff --git a/man/root.Rd b/man/root.Rd
index 35295b8..05ef593 100644
--- a/man/root.Rd
+++ b/man/root.Rd
@@ -4,7 +4,7 @@
 \alias{is.rooted}
 \title{Roots Phylogenetic Trees}
 \usage{
-root(phy, outgroup, node = NULL, resolve.root = FALSE)
+root(phy, outgroup, node = NULL, resolve.root = FALSE, interactive = FALSE)
 unroot(phy)
 is.rooted(phy)
 }
@@ -12,9 +12,12 @@ is.rooted(phy)
   \item{phy}{an object of class \code{"phylo"}.}
   \item{outgroup}{a vector of mode numeric or character specifying the
     new outgroup.}
-  \item{node}{alternatively, a node number where to root the tree.}
+  \item{node}{alternatively, a node number where to root the tree (this
+    should give the MRCA of the ingroup).}
   \item{resolve.root}{a logical specifying whether to resolve the new
     root as a bifurcating node.}
+  \item{interactive}{if \code{TRUE} the user is asked to select the node
+    by clicking on the tree which must be plotted.}
 }
 \description{
   \code{root} reroots a phylogenetic tree with respect to the specified
@@ -35,11 +38,11 @@ is.rooted(phy)
   tree is rerooted using the node below this tip as the new root.
 
   If \code{outgroup} is of length two or more, the most recent common
-  ancestor (MRCA) is used as the new root. Note that the tree is really
-  unrooted before being rerooted, so that if \code{outgroup} is already
-  the outgroup, then the returned tree is not the same than the original
-  one (see examples). If \code{outgroup} is not monophyletic, the
-  operation fails and an error message is issued.
+  ancestor (MRCA) \emph{of the ingroup} is used as the new root. Note
+  that the tree is unrooted before being rerooted, so that if
+  \code{outgroup} is already the outgroup, then the returned tree is not
+  the same than the original one (see examples). If \code{outgroup} is
+  not monophyletic, the operation fails and an error message is issued.
 
   If \code{resolve.root = TRUE}, \code{root} adds a zero-length branch
   below the MRCA of the ingroup.
@@ -52,7 +55,7 @@ is.rooted(phy)
   an object of class \code{"phylo"} for \code{root} and \code{unroot}; a
   single logical value for \code{is.rooted}.
 }
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
 \seealso{
   \code{\link{bind.tree}}, \code{\link{drop.tip}},
   \code{\link{nodelabels}}, \code{\link{identify.phylo}}