final fixes for ape 2.7-3

[ape.git] / man / root.Rd

diff --git a/man/root.Rd b/man/root.Rd
index 6559a690eaab39e7fd713c96886e8945a0969b84..05ef5935ba7237019b2b590ae2b4d75274491bc0 100644 (file)
--- a/man/root.Rd
+++ b/man/root.Rd
@@ -12,7 +12,8 @@ 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
@@ -37,11 +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.