[Vegan-commits] r928 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2009-08-17 19:15:39 +0200 (Mon, 17 Aug 2009)
New Revision: 928

Added:
   pkg/vegan/R/treedist.R
Modified:
   pkg/vegan/R/treedive.R
   pkg/vegan/R/treeheight.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/treedive.Rd
Log:
treedist: dissimilarity based on species trees and other experimental changes that may be cancelled later

Added: pkg/vegan/R/treedist.R
===================================================================
--- pkg/vegan/R/treedist.R	                        (rev 0)
+++ pkg/vegan/R/treedist.R	2009-08-17 17:15:39 UTC (rev 928)
@@ -0,0 +1,21 @@
+`treedist` <-
+    function(x, tree, ...)
+{
+    n <- nrow(x)
+    ABJ <- matrix(0, n , n)
+    dmat <- as.matrix(cophenetic(tree))
+    for(j in 1:n)
+        for (k in j:n) {
+            jk <- x[j,] > 0 | x[k,] > 0
+            if (sum(jk) > 1)
+                ABJ[k, j] <- treeheight(update(tree, d = as.dist(dmat[jk, jk]))) 
+        }
+    A <- diag(ABJ)
+    AB <- as.dist(outer(A, A, "+"))
+    ABJ <- as.dist(ABJ)
+    out <- (2 * ABJ - AB)/ABJ
+    attr(out, "method") <- "treedist"
+    attr(out, "call") <- match.call()
+    attr(out, "Labels") <- row.names(x)
+    out
+}

Modified: pkg/vegan/R/treedive.R
===================================================================
--- pkg/vegan/R/treedive.R	2009-08-17 14:10:09 UTC (rev 927)
+++ pkg/vegan/R/treedive.R	2009-08-17 17:15:39 UTC (rev 928)
@@ -1,11 +1,11 @@
 `treedive` <-
     function(comm, tree, match.force = FALSE)
 {
-    if (!inherits(tree, "hclust"))
-        stop("'clus' must be an 'hclust' result object")
+    if (!inherits(tree, c("hclust", "spantree")))
+        stop("'clus' must be an 'hclust' or 'spantree' result object")
     m <- as.matrix(cophenetic(tree))
     ## Check tree/comm match by names
-    if (match.force || ncol(comm) != length(tree$order)) {
+    if (match.force || ncol(comm) != ncol(m)) {
         if (match.force)
             message("Forced matching of 'tree' labels and 'comm' names")
         else

Modified: pkg/vegan/R/treeheight.R
===================================================================
--- pkg/vegan/R/treeheight.R	2009-08-17 14:10:09 UTC (rev 927)
+++ pkg/vegan/R/treeheight.R	2009-08-17 17:15:39 UTC (rev 928)
@@ -1,6 +1,8 @@
 `treeheight` <-
     function(tree)
 {
+    if (inherits(tree, "spantree"))
+        return(sum(tree$dist))
     tree <- as.hclust(tree)
     m <- tree$merge
     h <- tree$height

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-08-17 14:10:09 UTC (rev 927)
+++ pkg/vegan/inst/ChangeLog	2009-08-17 17:15:39 UTC (rev 928)
@@ -6,6 +6,20 @@
 
 	* spantree: first argument 'd' like in hclust()instead of 'dis'.
 	Got a 'call' item so that update() works.
+
+	* treedive & treeheight: accept 'spantree' objects. EXPERIMENTAL
+	CHANGE THAT MAY BE CANCELLED.
+
+	* treedist: average distance of species trees for two
+	sites. Generalization of treedive(): builds a species tree of two
+	sites and sees how much of the tree is shared between two sites,
+	and how much is unique to the combination. The measure is similar
+	to Jaccard index: the proportion of unique (unshared) tree of the
+	combined tree. In principle, this is similar to UniFrac metric
+	(C. Lozupone & R. Knight, Appl. Environ. Microbiol. 71:8225-8235;
+	2005), but numerically and computationally different (and the
+	current implementation may specify a new unpublished method). AN
+	EXPERIMENTAL CHANGE THAT MAY BE CANCELLED.
 	
 Version 1.16-23 (closed August 17, 2009)
 

Modified: pkg/vegan/man/treedive.Rd
===================================================================
--- pkg/vegan/man/treedive.Rd	2009-08-17 14:10:09 UTC (rev 927)
+++ pkg/vegan/man/treedive.Rd	2009-08-17 17:15:39 UTC (rev 928)
@@ -1,6 +1,7 @@
 \name{treedive}
 \alias{treedive}
 \alias{treeheight}
+\alias{treedist}  ## Undocumented!! 
 
 \title{ Functional Diversity estimated from a Species Dendrogram}
 \description{