[Ecopd-commits] r44 - in pkg: R man

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

Author: regetz
Date: 2009-10-22 01:49:23 +0200 (Thu, 22 Oct 2009)
New Revision: 44

Modified:
   pkg/R/utilities.R
   pkg/man/tipLength.Rd
Log:
enhanced tipLength to enable calculation of distance from root to tips


Modified: pkg/R/utilities.R
===================================================================
--- pkg/R/utilities.R	2009-10-21 22:22:30 UTC (rev 43)
+++ pkg/R/utilities.R	2009-10-21 23:49:23 UTC (rev 44)
@@ -55,10 +55,20 @@
 }
 
 # tip length extractor
-tipLength <- function(phy) {
-  tip.length <- edgeLength(phy, nodeId(phy, type="tip"))
-  names(tip.length) <- tipLabels(phy)
-  return(tip.length)
+tipLength <- function(phy, from=c("parent", "root")) {
+  from <- match.arg(from)
+  tips <- nodeId(phy, type="tip")
+  if (from=="parent") {
+    len <- edgeLength(phy, tips)
+  } else if (from=="root") {
+    root.node <- rootNode(phy)
+    anc <- ancestors(phy, tips, "ALL")
+    len <- sapply(anc, function(n) {
+      sumEdgeLength(phy, setdiff(n, root.node))
+    })
+  }
+  names(len) <- tipLabels(phy)
+  return(len)
 }
 
 # abundance extractor

Modified: pkg/man/tipLength.Rd
===================================================================
--- pkg/man/tipLength.Rd	2009-10-21 22:22:30 UTC (rev 43)
+++ pkg/man/tipLength.Rd	2009-10-21 23:49:23 UTC (rev 44)
@@ -1,25 +1,42 @@
 \name{tipLength}
 \alias{tipLength}
-\title{Extract terminal branch lengths}
+\title{Calculate distance to tips from ancestors}
 \description{
-  Returns the lengths of all tip edges of a phylogeny.
+  Returns the edge length between each tip and its parent, or
+  alternatively the total distance to each tip from the root node of the
+  phylogeny.
 }
 \usage{
-  tipLength(phy)
+  tipLength(phy, from=c("parent", "root"))
 }
 \arguments{
   \item{phy}{a \code{phylo4} object (or one that inherits from it)}
+  \item{from}{Should lengths represent distance from parents only (i.e.,
+    simply the lengths of terminal branches), or from the root node?}
 }
 \value{
   Numeric vector of lengths, with the associated tip node labels as
   names.
 }
+\note{
+  When calculating the distance from root, the length of the root edge
+  itself is \strong{not} included in the returned value. See examples
+  for a simple way to add this additional edge to the result.
+}
 \author{Jim Regetz (regetz at nceas.ucsb.edu)}
 \seealso{
-  This function is a simple wrapper of the
-  \code{\link[phylobase:phylo4-accessors]{edgeLength}} phylobase method.
+  Methods \code{\link[phylobase:phylo4-accessors]{edgeLength}} and
+  \code{\link[phylobase:phylo4-accessors]{sumEdgeLength}} in the
+  phylobase package.
 }
 \examples{
   data(weeds)
   tipLength(weeds$A)
+
+  # distance from the root node to each tip
+  tipLength(weeds$A, from="root")
+
+  # as above, but include root edge length
+  tipLength(weeds$A, from="root") + edgeLength(weeds$A,
+    rootNode(weeds$A))
 }