[Vegan-commits] r485 - in pkg: R inst man

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

Author: jarioksa
Date: 2008-08-25 18:39:58 +0200 (Mon, 25 Aug 2008)
New Revision: 485

Modified:
   pkg/R/treedive.R
   pkg/inst/ChangeLog
   pkg/man/treedive.Rd
Log:
treedive tries to match 'comm' and 'tree', docs tell to use oecosimu for testing

Modified: pkg/R/treedive.R
===================================================================
--- pkg/R/treedive.R	2008-08-25 07:29:25 UTC (rev 484)
+++ pkg/R/treedive.R	2008-08-25 16:39:58 UTC (rev 485)
@@ -1,9 +1,21 @@
 `treedive` <-
-    function(comm, tree)
+    function(comm, tree, match.force = FALSE)
 {
     if (!inherits(tree, "hclust"))
         stop("'clus' must be an 'hclust' result object")
     m <- as.matrix(cophenetic(tree))
+    ## Check tree/comm match by names
+    if (match.force || ncol(comm) != length(tree$order)) {
+        fnd <- colnames(comm) %in% tree$labels
+        if (!all(fnd)) {
+            warning("not all names of 'comm' found in 'tree'")
+            comm <- comm[, fnd]
+        }
+        fnd <- tree$labels %in% colnames(comm)
+        if (!all(fnd))
+            warning("not all names of 'tree' found in 'comm'")
+        comm <- comm[, tree$labels[fnd]]
+    }
     ## Repeat for sites
     div <- numeric(nrow(comm))
     for (i in 1:nrow(comm)) {
@@ -12,6 +24,7 @@
         cl <- update(tree, d = d)
         div[i] <- treeheight(cl)
     }
+    names(div) <- rownames(comm)
     div
 }
 

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2008-08-25 07:29:25 UTC (rev 484)
+++ pkg/inst/ChangeLog	2008-08-25 16:39:58 UTC (rev 485)
@@ -5,6 +5,10 @@
 
 Version 1.14-10 (opened August 21, 2008)
 
+	* treedive: tries to match 'comm' and 'tree' names if forced (by
+	an arg), or when sizes do not match. Output vector has names. Docs
+	discuss estimating signifcance using oecosimu().
+
 	* oecosimu: accepts now a vector of statistics and plain
 	statistics instead of the list item statistics. This means that
 	things like species richness for sites can be analysed with

Modified: pkg/man/treedive.Rd
===================================================================
--- pkg/man/treedive.Rd	2008-08-25 07:29:25 UTC (rev 484)
+++ pkg/man/treedive.Rd	2008-08-25 16:39:58 UTC (rev 485)
@@ -10,7 +10,7 @@
 }
 
 \usage{
-treedive(comm, tree)
+treedive(comm, tree, match.force = FALSE)
 treeheight(tree)
 }
 
@@ -18,6 +18,10 @@
   \item{comm}{Community data frame or matrix.}
   \item{tree}{A dendrogram which for \code{treedive} must be for species
     (columns).}
+  \item{match.force}{Force matching of column names in \code{comm} and
+    labels in \code{tree}. If \code{FALSE}, matching only happens when
+    dimensions differ, and in that case the species must be in identical
+    order in both.}
 }
 \details{
   Function \code{treeheight} finds the sum of lengths of connecting
@@ -43,6 +47,10 @@
   and usually the recommended clustering method is UPGMA (\code{method =
   "average"} in function \code{\link{hclust}}) (Podani and Schmera
   2006).
+
+  It is possible to analyse the non-randomness of functional diversity
+  using \code{\link{oecosimu}}. This provided specifying an adequate
+  Null model, and the results will change with this choice.
 }
 
 \value{
@@ -69,9 +77,12 @@
 ## the example uses taxonomy 
 data(dune)
 data(dune.taxon)
-d <- taxa2dist(dune.taxon)
+d <- taxa2dist(dune.taxon, varstep=TRUE)
 cl <- hclust(d, "aver")
 treedive(dune, cl)
+## Significance test using Null model communities.
+## The current choice fixes both species and site totals.
+oecosimu(dune, treedive, "quasiswap", tree = cl)
 }
 
 \keyword{ univar }