[Vegan-commits] r2831 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2014-01-10 18:07:08 +0100 (Fri, 10 Jan 2014)
New Revision: 2831

Modified:
   pkg/vegan/R/cIndexKM.R
   pkg/vegan/inst/ChangeLog
Log:
Calinski criterion for one class is now NA instead of Inf, -Inf or NaN

Modified: pkg/vegan/R/cIndexKM.R
===================================================================
--- pkg/vegan/R/cIndexKM.R	2014-01-10 11:03:26 UTC (rev 2830)
+++ pkg/vegan/R/cIndexKM.R	2014-01-10 17:07:08 UTC (rev 2831)
@@ -26,7 +26,11 @@
     {
         n <- sum(clsize)
         k <- length(clsize)
-        zgss$bgss/(k - 1)/(zgss$wgss/(n - k))
+        ## undefined 0/0 for one class (or fewer in error cases)
+        if (k <= 1)
+            NA
+        else
+            zgss$bgss/(k - 1)/(zgss$wgss/(n - k))
     }
 ################################################
     ssi <- function(centers, clsize) 

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2014-01-10 11:03:26 UTC (rev 2830)
+++ pkg/vegan/inst/ChangeLog	2014-01-10 17:07:08 UTC (rev 2831)
@@ -11,6 +11,11 @@
 	be used in an incorrect context". The dots were added in r2765,
 	and now removed.
 
+	* cascadeKM: Calinski index for one group will now be NA instead
+	of randomly chosen Inf, -Inf or NaN which can cause confusion (see
+        http://stackoverflow.com/questions/21022848/r-produces-different-result-after-io-on-file
+	
+
 	* ordiellipse: failed if all points were on a line. Now handles
 	these cases by drawing a line trhough the points, and issuing a
 	warning from chol(): "the matrix is either rank-deficient or