[Vegan-commits] r2392 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2013-01-28 15:09:13 +0100 (Mon, 28 Jan 2013)
New Revision: 2392

Modified:
   pkg/vegan/R/treedist.R
   pkg/vegan/R/treedive.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/treedive.Rd
Log:
fix (treedive) and add (treedist) matching of tree and data by names

Modified: pkg/vegan/R/treedist.R
===================================================================
--- pkg/vegan/R/treedist.R	2013-01-28 08:15:37 UTC (rev 2391)
+++ pkg/vegan/R/treedist.R	2013-01-28 14:09:13 UTC (rev 2392)
@@ -1,9 +1,16 @@
 `treedist` <-
-    function(x, tree, relative = TRUE,  ...)
+    function(x, tree, relative = TRUE,  match.force = FALSE, ...)
 {
     n <- nrow(x)
     ABJ <- matrix(0, n , n)
     dmat <- as.matrix(cophenetic(tree))
+    ## match names
+    if (ncol(x) != ncol(dmat) || match.force) {
+        if(!match.force)
+            warning("Dimensions do not match between 'x' and 'tree' - matching by names")
+        nm <- colnames(x)
+        dmat <- dmat[nm, nm]
+    }
     for(j in 1:n) {
         for (k in j:n) {
             jk <- x[j,] > 0 | x[k,] > 0

Modified: pkg/vegan/R/treedive.R
===================================================================
--- pkg/vegan/R/treedive.R	2013-01-28 08:15:37 UTC (rev 2391)
+++ pkg/vegan/R/treedive.R	2013-01-28 14:09:13 UTC (rev 2392)
@@ -19,6 +19,7 @@
         if (!all(fnd))
             warning("not all names of 'tree' found in 'comm'")
         comm <- comm[, tree$labels[fnd]]
+        m <- m[tree$labels[fnd], tree$labels[fnd]]
         if (length(unique(tree$labels)) != length(tree$labels))
             stop("names not unique in 'tree': match wrong")
         if (length(unique(colnames(comm))) != ncol(comm))

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2013-01-28 08:15:37 UTC (rev 2391)
+++ pkg/vegan/inst/ChangeLog	2013-01-28 14:09:13 UTC (rev 2392)
@@ -17,6 +17,12 @@
 	matrix. This should not influence the results, but one metaMDS()
 	trace result has a small difference in nearly-zero rmse (was
 	1.094382e-06, is 1.09439e-06) in my desktop.
+
+	* treedive, treedist: treedive() did not correctly match data and
+	tree when the tree contained species that did not occur in the
+	data. Function treedist() tries to match tree and data when their
+	sizes differ, and argument 'match.force' was added to force
+	matching even when sizes do not differ.
 	
 Version 2.1-23 (closed January 25, 2013)
 

Modified: pkg/vegan/man/treedive.Rd
===================================================================
--- pkg/vegan/man/treedive.Rd	2013-01-28 08:15:37 UTC (rev 2391)
+++ pkg/vegan/man/treedive.Rd	2013-01-28 14:09:13 UTC (rev 2392)
@@ -13,17 +13,18 @@
 \usage{
 treedive(comm, tree, match.force = FALSE)
 treeheight(tree)
-treedist(x, tree, relative = TRUE, ...)
+treedist(x, tree, relative = TRUE, match.force = FALSE, ...)
 }
 
 \arguments{
   \item{comm, x}{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.}
+  \item{match.force}{Force matching of column names in data
+    (\code{comm}, \code{x}) and labels in \code{tree}. If \code{FALSE},
+    matching only happens when dimensions differ (with a warning or
+    message). The order of data must match to the order in \code{tree}
+    if matching by names is not done.}
   \item{relative}{Use distances relative to the height of combined tree.}
   \item{\dots}{Other arguments passed to functions (ignored).}
 }
@@ -81,6 +82,15 @@
   can be used similarly.  
 }
 
+\seealso{
+  Function \code{treedive} is similar to the phylogenetic diversity
+  function \code{\link[picante]{pd}} in \pkg{picante}, but excludes tree
+  root if that is not needed to connect species. Function
+  \code{treedist} is similar to the phylogenetic similarity
+  \code{\link[picante]{phylosor}} in \pkg{picante}, but excludes
+  unneeded tree root and returns distances instead of similarities.  
+}
+
 \references{
   Lozupone, C. and Knight, R. 2005. UniFrac: a new phylogenetic method
   for comparing microbial communities. \emph{Applied and Environmental