[Adephylo-commits] r26 - pkg/man

[noreply at r-forge.r-project.org]

Author: jombart
Date: 2008-11-25 16:23:37 +0100 (Tue, 25 Nov 2008)
New Revision: 26

Added:
   pkg/man/sp.tips.Rd
Log:
Added doc for sp.tips.


Added: pkg/man/sp.tips.Rd
===================================================================
--- pkg/man/sp.tips.Rd	                        (rev 0)
+++ pkg/man/sp.tips.Rd	2008-11-25 15:23:37 UTC (rev 26)
@@ -0,0 +1,50 @@
+\name{sp.tips}
+\alias{sp.tips}
+\title{Find the shortest path between tips of a tree}
+\description{
+  The function \code{sp.tips} finds the shortest path between tips of a
+  tree, identified as \code{tip1} and \code{tip2}.
+  This function applies to trees with the class \code{\link[pkg:ape]{phylo}}, \linkS4class{phylo4} or
+  \linkS4class{phylo4d}. Several tips can be provided at a time.
+}
+\usage{
+sp.tips(x, tip1, tip2, useTipNames=FALSE, quiet=FALSE)
+}
+\arguments{
+  \item{x}{A tree of  class \code{\link[pkg:ape]{phylo}},
+    \linkS4class{phylo4} or \linkS4class{phylo4d}.}
+  \item{tip1}{A vector of integers identifying tips by their numbers, or
+    a vector of characters identifying tips by their names. Recycled if needed.}
+  \item{tip2}{A vector of integers identifying tips by their numbers, or
+    a vector of characters identifying tips by their names. Recycled if needed.}
+  \item{useTipNames}{a logical stating whether the output must be named
+    using tip names in all cases (TRUE), or not (FALSE). If not, names
+    of \code{tip1} and \code{tip2} will be used.}
+  \item{quiet}{a logical stating whether a warning must be issued when
+    tip1==tip2, or not (see details).}
+}
+\value{
+  A list whose components are vectors of named nodes forming the
+  shortest path between a couple of tips.
+}
+\details{
+  The function checks if there are cases where tip1 and tip2 are the
+  same. These cases are deleted when detected, issuing a warning (unless
+  \code{quiet} is set to TRUE).
+}
+\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\seealso{\code{\link[pkg:phylobase]{shortestPath}} which does the same
+  thing as \code{sp.tips}, for any node (internal or tip), but much more
+  slowly. \cr
+}
+\examples{
+if(require(ape) & require(phylobase)){
+## make a tree
+x <- as(rtree(20),"phylo4")
+plot(x,show.node=TRUE)
+## get shortest path between tip 1 and all other tips.
+sp.tips(x, "t1", "t2")
+sp.tips(x, 1, 2:20, TRUE)
+}
+}
+\keyword{manip}