[Vegan-commits] r2625 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2013-09-26 12:11:52 +0200 (Thu, 26 Sep 2013)
New Revision: 2625

Modified:
   pkg/vegan/R/oecosimu.R
   pkg/vegan/inst/ChangeLog
Log:
warn if oecosimu transforms quantitative to binary data

Modified: pkg/vegan/R/oecosimu.R
===================================================================
--- pkg/vegan/R/oecosimu.R	2013-09-25 09:11:49 UTC (rev 2624)
+++ pkg/vegan/R/oecosimu.R	2013-09-26 10:11:52 UTC (rev 2625)
@@ -34,8 +34,13 @@
             comm <- comm$data
         } else {
             nm <- nullmodel(comm, method)
-            if (nm$commsim$binary)
+            if (nm$commsim$binary) {
+                ## sometimes people do not realize that null model
+                ## makes their data binary
+                if (max(abs(comm - nm$data)) > 0.1)
+                    warning("nullmodel transformed 'comm' to binary data")
                 comm <- nm$data
+            }
         }
         method <- nm$commsim$method
     }

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2013-09-25 09:11:49 UTC (rev 2624)
+++ pkg/vegan/inst/ChangeLog	2013-09-26 10:11:52 UTC (rev 2625)
@@ -5,6 +5,10 @@
 Version 2.1-36 (opened September 25, 2013)
 
 	* opened with the release of vegan 2.0-9.
+
+	* oecosimu: warns user if the specified nullmodel 'method' changes
+	quantitative input data to binary data under cover. Some people
+	have not noticed this.
 	
 Version 2.1-35 (closed September 25, 2013)