fixes in mantel.test() and extract.clade()

[ape.git] / man / root.Rd

diff --git a/man/root.Rd b/man/root.Rd
index d703745833a684f4d5f0a0e099454a07b23883ad..05ef5935ba7237019b2b590ae2b4d75274491bc0 100644 (file)
--- a/man/root.Rd
+++ b/man/root.Rd
@@ -4,7 +4,7 @@
 \alias{is.rooted}
 \title{Roots Phylogenetic Trees}
 \usage{
-root(phy, outgroup)
+root(phy, outgroup, node = NULL, resolve.root = FALSE, interactive = FALSE)
 unroot(phy)
 is.rooted(phy)
 }
@@ -12,10 +12,16 @@ 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 (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
-  outgroup.
+  outgroup or at the node specified in \code{node}.
 
   \code{unroot} unroots a phylogenetic tree, or returns it unchanged if
   it is already unrooted.
@@ -32,11 +38,14 @@ 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.
 
   A tree is considered rooted if either only two branches connect to the
   root, or if there is a \code{root.edge} element. In all other cases,
@@ -46,9 +55,10 @@ 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{bind.tree}}, \code{\link{drop.tip}},
+  \code{\link{nodelabels}}, \code{\link{identify.phylo}}
 }
 \examples{
 data(bird.orders)
@@ -61,8 +71,9 @@ is.rooted(tr)          # no!
 ### This is because the tree has been unrooted first before rerooting.
 ### You can delete the outgroup...
 is.rooted(drop.tip(tr, "Struthioniformes"))
-### ... or resolve the basal trichotomy:
+### ... or resolve the basal trichotomy in two ways:
 is.rooted(multi2di(tr))
+is.rooted(root(bird.orders, 1, r = TRUE))
 ### To keep the basal trichotomy but forcing the tree as rooted:
 tr$root.edge <- 0
 is.rooted(tr)