[Vegan-commits] r463 - in pkg: . R inst man

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

Author: jarioksa
Date: 2008-08-10 21:25:03 +0200 (Sun, 10 Aug 2008)
New Revision: 463

Added:
   pkg/R/treedive.R
   pkg/R/treeheight.R
   pkg/man/treedive.Rd
Modified:
   pkg/DESCRIPTION
   pkg/inst/ChangeLog
Log:
added functions for functional diversity a la Petchey & Gaston

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2008-08-10 19:15:57 UTC (rev 462)
+++ pkg/DESCRIPTION	2008-08-10 19:25:03 UTC (rev 463)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.14-8
-Date: July 30, 2008
+Version: 1.14-9
+Date: August 10, 2008
 Author: Jari Oksanen, Roeland Kindt, Pierre Legendre, Bob O'Hara, Gavin L. Simpson, 
    Peter Solymos, M. Henry H. Stevens, Helene Wagner  
 Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>

Added: pkg/R/treedive.R
===================================================================
--- pkg/R/treedive.R	                        (rev 0)
+++ pkg/R/treedive.R	2008-08-10 19:25:03 UTC (rev 463)
@@ -0,0 +1,17 @@
+`treedive` <-
+    function(comm, tree)
+{
+    if (!inherits(tree, "hclust"))
+        stop("'clus' must be an 'hclust' result object")
+    m <- as.matrix(cophenetic(tree))
+    ## Repeat for sites
+    div <- numeric(nrow(comm))
+    for (i in 1:nrow(comm)) {
+        k <- comm[i,] > 0
+        d <- as.dist(m[k,k])
+        cl <- update(tree, d = d)
+        div[i] <- treeheight(cl)
+    }
+    div
+}
+

Added: pkg/R/treeheight.R
===================================================================
--- pkg/R/treeheight.R	                        (rev 0)
+++ pkg/R/treeheight.R	2008-08-10 19:25:03 UTC (rev 463)
@@ -0,0 +1,18 @@
+`treeheight` <-
+    function(tree)
+{
+    tree <- as.hclust(tree)
+    m <- tree$merge
+    h <- tree$height
+    height <- 0
+    for (i in 1:nrow(m)) {
+        for (j in 1:2) {
+            if (m[i,j] < 0)
+                height <- height + h[i]
+            else
+                height <- height + h[i] - h[m[i,j]] 
+        }
+    }
+    height
+}
+

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2008-08-10 19:15:57 UTC (rev 462)
+++ pkg/inst/ChangeLog	2008-08-10 19:25:03 UTC (rev 463)
@@ -2,8 +2,14 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Versin 1.14-8 (opened July 30, 2008)
+Version 1.14-9 (open August 10, 2008)
 
+	* treedive: new functions for estimating functional diversity
+	defined as the height of a dendrogram of species properties for a
+	site (Petchey & Gaston). Still very preliminary.
+	
+Version 1.14-8 (closed August 10, 2008)
+
 	* wcmdscale: new function to perform metric scaling
 	(a.k.a. principal coordinates analysis) with weights for points.
 

Added: pkg/man/treedive.Rd
===================================================================
--- pkg/man/treedive.Rd	                        (rev 0)
+++ pkg/man/treedive.Rd	2008-08-10 19:25:03 UTC (rev 463)
@@ -0,0 +1,42 @@
+\name{treedive}
+\alias{treedive}
+\alias{treeheight}
+
+\title{ Functional Diversity estimated from Dendrogram Heights}
+\description{
+Functional diversity is defined as the total heights of connecting
+segments for a dendrogram of species properties for all species
+occurring in a site (Petchey and Gaston). 
+}
+\usage{
+treedive(comm, tree)
+treeheight(tree)
+}
+
+\arguments{
+  \item{comm}{Community data frame or matrix.}
+  \item{tree}{A dendrogram which for \code{treedive} must be for species.}
+}
+\details{
+\dots To come \dots
+}
+\value{
+Diversity values rows of \code{comm} (a vector).
+}
+\references{Petchey and Gaston}
+\author{Jari Oksanen}
+
+\seealso{ \code{\link{taxondive}} is something very similar from
+another world. }
+\examples{
+## There is no data set on species properties yet, and therefore
+## the example uses taxonomy 
+data(dune)
+data(dune.taxon)
+d <- taxa2dist(dune.taxon)
+cl <- hclust(d, "aver")
+treedive(dune, cl)
+}
+
+\keyword{ univar }
+