[Vegan-commits] r1491 - in branches/1.17: R inst

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

Author: jarioksa
Date: 2011-02-15 16:54:41 +0100 (Tue, 15 Feb 2011)
New Revision: 1491

Modified:
   branches/1.17/R/nestednodf.R
   branches/1.17/inst/ChangeLog
   branches/1.17/inst/NEWS
Log:
merge r1489: nestednodf with 'weighted = FALSE'

Modified: branches/1.17/R/nestednodf.R
===================================================================
--- branches/1.17/R/nestednodf.R	2011-02-15 08:40:50 UTC (rev 1490)
+++ branches/1.17/R/nestednodf.R	2011-02-15 15:54:41 UTC (rev 1491)
@@ -4,6 +4,8 @@
     bin.comm <- ifelse(comm > 0, 1, 0)
     rfill <- rowSums(bin.comm)
     cfill <- colSums(bin.comm)
+    if (!weighted)
+        comm <- bin.comm
     if (order) {
         if (weighted) {
             rgrad <- rowSums(comm)
@@ -13,7 +15,6 @@
         } else {
             rorder <- order(rfill, decreasing = TRUE)
             corder <- order(cfill, decreasing = TRUE)
-            comm <- bin.comm
         }
         comm <- comm[rorder, corder]
         rfill <- rfill[rorder]

Modified: branches/1.17/inst/ChangeLog
===================================================================
--- branches/1.17/inst/ChangeLog	2011-02-15 08:40:50 UTC (rev 1490)
+++ branches/1.17/inst/ChangeLog	2011-02-15 15:54:41 UTC (rev 1491)
@@ -4,8 +4,10 @@
 
 Version 1.17-7 (opened January 10, 2011)
 
-	* merged r1482,3: eigenvals for ade4 and labdsv.
+	* merged r1489: nestednodf with weighted = FALSE.
 
+	* merged r1482-4: eigenvals for ade4 and labdsv.
+
 	* merged r1476: zip data files.
 
 	* merged r1475: partially matched argunments in functions.

Modified: branches/1.17/inst/NEWS
===================================================================
--- branches/1.17/inst/NEWS	2011-02-15 08:40:50 UTC (rev 1490)
+++ branches/1.17/inst/NEWS	2011-02-15 15:54:41 UTC (rev 1491)
@@ -5,8 +5,8 @@
 
                        CHANGES IN VEGAN 1.17-7
 
-    - anova.cca: more robust when model are fitted without 'data'
-      argument, or when na.action or subset are used.
+    - anova.cca: more robust when model were fitted without 'data'
+      argument, or when na.action or subset was used.
 
     - capscale: implemented 'subset' in model definition. Additive
       constant with 'add = TRUE' is taken into account in predict()
@@ -16,6 +16,9 @@
     - eigenvals: can now extract eigenvalues of some ade4 and labdsv
       result objects. 
 
+    - nestenodf: did not use binary data when weighted = FALSE was
+      used together with order = FALSE. Reported by Daniel Spitale.
+
     - prestonfit: gained option to split tied frequencies (1, 2, 4, 8,
       etc.) between adjacent octaves.