[Ecopd-commits] r78 - branches/single-tree/man

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

Author: regetz
Date: 2009-11-18 01:08:14 +0100 (Wed, 18 Nov 2009)
New Revision: 78

Modified:
   branches/single-tree/man/pd.Rd
Log:
updated pd documentation to reflect its rewrite as a phylo4com method


Modified: branches/single-tree/man/pd.Rd
===================================================================
--- branches/single-tree/man/pd.Rd	2009-11-18 00:06:25 UTC (rev 77)
+++ branches/single-tree/man/pd.Rd	2009-11-18 00:08:14 UTC (rev 78)
@@ -1,31 +1,37 @@
 \name{pd}
+\docType{methods}
 \alias{pd}
+\alias{pd-methods}
+\alias{pd,phylo4com-method}
+\alias{pd,phylo4d-method}
 \title{Calculate phylogenetic diversity}
 \description{
   Calculates PD (phylogenetic diversity) for a phylogeny
 }
 \usage{
-  pd(phy, method=c("traditional", "polytomy", "yule"))
+  \S4method{pd}{phylo4com}(x, method = c("traditional", "polytomy",
+    "yule"))
+  \S4method{pd}{phylo4d}(x, method = c("traditional", "polytomy",
+    "yule"), \dots)
 }
 \arguments{
-  \item{phy}{A \code{phylo4d} object.}
+  \item{x}{A \code{phylo4com} or \code{phylo4d} object.}
   \item{method}{Method for calculating pd.}
+  \item{\dots}{additional arguments to be passed to other methods}
 }
 \details{
   TODO
 }
 \value{
-  A numeric vector of length 1.
+  A numeric vector of length equal to the number of communities.
 }
 \references{
   TODO
 }
 \author{Jim Regetz (regetz at nceas.ucsb.edu)}
 \examples{
-  data(weeds)
-  pd(weeds$A)
-
-  minTL(weeds$A) <- getMinTL(weeds$A, genera(weeds$A))
-  pd(weeds$A, "polytomy")
-  pd(weeds$A, "yule")
+  pd(weeds)
+#  minTL(weeds$A) <- getMinTL(weeds$A, genera(weeds$A))
+#  pd(weeds$A, "polytomy")
+#  pd(weeds$A, "yule")
 }