[Vegan-commits] r1090 - in branches/1.17: R inst man

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

Author: jarioksa
Date: 2010-01-02 16:25:06 +0100 (Sat, 02 Jan 2010)
New Revision: 1090

Removed:
   branches/1.17/R/treedist.R
Modified:
   branches/1.17/inst/ChangeLog
   branches/1.17/inst/NEWS
   branches/1.17/man/treedive.Rd
Log:
removed treedist() from branches/1.17

Deleted: branches/1.17/R/treedist.R
===================================================================
--- branches/1.17/R/treedist.R	2010-01-02 15:18:54 UTC (rev 1089)
+++ branches/1.17/R/treedist.R	2010-01-02 15:25:06 UTC (rev 1090)
@@ -1,21 +0,0 @@
-`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: branches/1.17/inst/ChangeLog
===================================================================
--- branches/1.17/inst/ChangeLog	2010-01-02 15:18:54 UTC (rev 1089)
+++ branches/1.17/inst/ChangeLog	2010-01-02 15:25:06 UTC (rev 1090)
@@ -1,8 +1,16 @@
 $Date$
 
+VEGAN RELEASE VERSIONS at http://cran.r-project.org/
+
+Version 1.17-0 (opened January 2, 2010)
+
+	* Copied from vegan/pkg/vegan version 1.16-34 (rev1087).
+
+	* removed treedist().
+
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.16-34 (opened December 13, 2009) -- (codename: Lucia)
+Version 1.16-34 (closed January 2, 2010) -- (codename: Lucia)
 
 	* twostagechao: deleted, because question regarding the
 	notation in the original article remained unanswered.

Modified: branches/1.17/inst/NEWS
===================================================================
--- branches/1.17/inst/NEWS	2010-01-02 15:18:54 UTC (rev 1089)
+++ branches/1.17/inst/NEWS	2010-01-02 15:25:06 UTC (rev 1090)
@@ -47,8 +47,6 @@
     - spandepth: a new function to find the depth of each node in the
       minimum spanning tree produced by spantree(). 
 
-    - treedist: undocumented (alias in treedive.Rd) --- REMOVE!
-
     - alias.cca: gained argument names.only.
 
     - betadisper: can use spatial medians which are the recommended

Modified: branches/1.17/man/treedive.Rd
===================================================================
--- branches/1.17/man/treedive.Rd	2010-01-02 15:18:54 UTC (rev 1089)
+++ branches/1.17/man/treedive.Rd	2010-01-02 15:25:06 UTC (rev 1090)
@@ -1,7 +1,6 @@
 \name{treedive}
 \alias{treedive}
 \alias{treeheight}
-\alias{treedist}  %% Undocumented!! 
 
 \title{ Functional Diversity estimated from a Species Dendrogram}
 \description{