[Ecopd-commits] r83 - in branches/single-tree: R man

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

Author: regetz
Date: 2009-11-18 19:24:45 +0100 (Wed, 18 Nov 2009)
New Revision: 83

Modified:
   branches/single-tree/R/pd.R
   branches/single-tree/man/pd.Rd
Log:
added pd method for phylo4 trees, and updated documentation


Modified: branches/single-tree/R/pd.R
===================================================================
--- branches/single-tree/R/pd.R	2009-11-18 16:10:46 UTC (rev 82)
+++ branches/single-tree/R/pd.R	2009-11-18 18:24:45 UTC (rev 83)
@@ -6,6 +6,19 @@
     standardGeneric("pd")
 })
 
+setMethod("pd", signature(x="phylo4"),
+  function(x, method=c("traditional")) {
+    method <- match.arg(method)
+    if (isRooted(x)) {
+        nonroot.nodes <- setdiff(nodeId(x), rootNode(x))
+        tot.length <- sum(edgeLength(x, nonroot.nodes))
+    } else {
+        tot.length <- sum(edgeLength(x))
+    }
+    return(tot.length)
+  }
+)
+
 setMethod("pd", signature(x="phylo4d"), function(x,
   method=c("traditional", "polytomy", "yule"), ...) {
     phyc <- phylo4com(x, ...)

Modified: branches/single-tree/man/pd.Rd
===================================================================
--- branches/single-tree/man/pd.Rd	2009-11-18 16:10:46 UTC (rev 82)
+++ branches/single-tree/man/pd.Rd	2009-11-18 18:24:45 UTC (rev 83)
@@ -4,6 +4,7 @@
 \alias{pd-methods}
 \alias{pd,phylo4com-method}
 \alias{pd,phylo4d-method}
+\alias{pd,phylo4-method}
 \title{Calculate phylogenetic diversity}
 \description{
   Calculates PD (phylogenetic diversity) for a phylogeny
@@ -13,17 +14,23 @@
     "yule"))
   \S4method{pd}{phylo4d}(x, method = c("traditional", "polytomy",
     "yule"), \dots)
+  \S4method{pd}{phylo4}(x, method = c("traditional"))
 }
 \arguments{
-  \item{x}{A \code{phylo4com} or \code{phylo4d} object.}
+  \item{x}{A \code{phylo4com}, \code{phylo4d}, or \code{phylo4} object.}
   \item{method}{Method for calculating pd.}
   \item{\dots}{additional arguments to be passed to other methods}
 }
 \details{
   TODO
+
+  When applied to a \code{phylo4} tree, traditional PD is the only
+  option (because the object contains no abundance data in this case).
 }
 \value{
-  A numeric vector of length equal to the number of communities.
+  For \code{phylo4com} or \code{phylo4d}, a numeric vector of length
+  equal to the number of communities. For \code{phylo4}, a single
+  numeric value for the tree.
 }
 \references{
   TODO
@@ -31,7 +38,12 @@
 \author{Jim Regetz (regetz at nceas.ucsb.edu)}
 \examples{
   pd(weeds)
+
+  # traditional pd of the master tree
+  pd(phylo4(weeds))
+
 #  minTL(weeds$A) <- getMinTL(weeds$A, genera(weeds$A))
 #  pd(weeds$A, "polytomy")
 #  pd(weeds$A, "yule")
+
 }