[Vegan-commits] r2017 - branches/2.0/R branches/2.0/inst www

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

Author: jarioksa
Date: 2011-12-06 18:51:55 +0100 (Tue, 06 Dec 2011)
New Revision: 2017

Modified:
   branches/2.0/R/ordimedian.R
   branches/2.0/inst/ChangeLog
   branches/2.0/inst/NEWS.Rd
   www/NEWS.html
Log:
merge r2016: fix empty factor levels in betadisper

Modified: branches/2.0/R/ordimedian.R
===================================================================
--- branches/2.0/R/ordimedian.R	2011-11-30 15:53:07 UTC (rev 2016)
+++ branches/2.0/R/ordimedian.R	2011-12-06 17:51:55 UTC (rev 2017)
@@ -21,12 +21,13 @@
     #dmedfun <- NULL
     pts <- scores(ord, display = display, ...)
     inds <- names(table(groups))
-    medians <- matrix(0, nrow = length(inds), ncol = ncol(pts))
+    medians <- matrix(NA, nrow = length(inds), ncol = ncol(pts))
     rownames(medians) <- inds
     colnames(medians) <- colnames(pts)
     for (i in inds) {
         X <- pts[groups == i, , drop = FALSE]
-        medians[i, ] <- optim(apply(X, 2, median, na.rm = TRUE),
+        if (NROW(X) > 0)
+            medians[i, ] <- optim(apply(X, 2, median, na.rm = TRUE),
                               fn = medfun, gr = dmedfun,
                               ord = X, method = "BFGS")$par
         if(label)

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2011-11-30 15:53:07 UTC (rev 2016)
+++ branches/2.0/inst/ChangeLog	2011-12-06 17:51:55 UTC (rev 2017)
@@ -4,6 +4,8 @@
 
 Version 2.0-3 (opened November 13, 2011)
 
+	* merge r2016: empty factor levels in betadisper() fixed in
+	ordimedian(). 
 	* merge r2008,9,11,12: add rarecurve.
 	* merge r2007: FAQ update for arrow scaling.
 	* merge r2004: metaMDS(..., noshare=0) triggers stepacross(), but

Modified: branches/2.0/inst/NEWS.Rd
===================================================================
--- branches/2.0/inst/NEWS.Rd	2011-11-30 15:53:07 UTC (rev 2016)
+++ branches/2.0/inst/NEWS.Rd	2011-12-06 17:51:55 UTC (rev 2017)
@@ -15,6 +15,14 @@
     }
   } % end new functions
 
+  \subsection{BUG FIXES}{
+    \itemize{
+
+      \item \code{betadisper()} failed when the \code{groups} was a
+      factor with empty levels.
+
+    }
+  } % end bug fixes	
 		  
   \subsection{NEW FEATURES}{
      \itemize{

Modified: www/NEWS.html
===================================================================
--- www/NEWS.html	2011-11-30 15:53:07 UTC (rev 2016)
+++ www/NEWS.html	2011-12-06 17:51:55 UTC (rev 2017)
@@ -34,10 +34,27 @@
  
 </p>
 <p>
+
+
+<h4>BUG FIXES</h4>
+
+<p>
+
 </p>
 <p>
+<ul>
+<li> <code>betadisper()</code> failed when the <code>groups</code> was a
+factor with empty levels.
+</p>
+<p>
+</ul>
 
+</p>
+ 
+</p>
+<p>
 
+
 <h4>NEW FEATURES</h4>
 
 <p>