[Vegan-commits] r2397 - in branches/2.0: R inst man

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

Author: jarioksa
Date: 2013-01-31 09:19:01 +0100 (Thu, 31 Jan 2013)
New Revision: 2397

Modified:
   branches/2.0/R/treedist.R
   branches/2.0/R/treedive.R
   branches/2.0/inst/ChangeLog
   branches/2.0/man/treedive.Rd
Log:
merge 2392,3: matching names in treedist() and treedive()

Modified: branches/2.0/R/treedist.R
===================================================================
--- branches/2.0/R/treedist.R	2013-01-30 16:56:45 UTC (rev 2396)
+++ branches/2.0/R/treedist.R	2013-01-31 08:19:01 UTC (rev 2397)
@@ -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: branches/2.0/R/treedive.R
===================================================================
--- branches/2.0/R/treedive.R	2013-01-30 16:56:45 UTC (rev 2396)
+++ branches/2.0/R/treedive.R	2013-01-31 08:19:01 UTC (rev 2397)
@@ -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: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2013-01-30 16:56:45 UTC (rev 2396)
+++ branches/2.0/inst/ChangeLog	2013-01-31 08:19:01 UTC (rev 2397)
@@ -7,6 +7,7 @@
 	* merge 2934 (partial, mc): oecosimu handles nestedfun() returning
 	data.frame. Not merged: checking length of statistic when setting
 	its name.
+	* merge 2932,3: matching names in treedive() and treedist().
 	* merge 2384: new FAQ entries.
 	* merge 2383: remove alias to print.wcmdscale.
 	* merge 2374,2376,2378,2382: orditorp gains argument select

Modified: branches/2.0/man/treedive.Rd
===================================================================
--- branches/2.0/man/treedive.Rd	2013-01-30 16:56:45 UTC (rev 2396)
+++ branches/2.0/man/treedive.Rd	2013-01-31 08:19:01 UTC (rev 2397)
@@ -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).}
 }
@@ -99,8 +100,17 @@
 
 \author{Jari Oksanen}
 
-\seealso{ \code{\link{taxondive}} is something very similar from
-another world. }
+\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.
+
+  \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