[Vegan-commits] r1071 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2009-11-28 23:09:59 +0100 (Sat, 28 Nov 2009)
New Revision: 1071

Modified:
   pkg/vegan/R/bstick.cca.R
   pkg/vegan/inst/ChangeLog
Log:
bstick.cca refuses to handle capscale result with negative eigenvalues, because I have no clue how to do this

Modified: pkg/vegan/R/bstick.cca.R
===================================================================
--- pkg/vegan/R/bstick.cca.R	2009-11-18 16:34:26 UTC (rev 1070)
+++ pkg/vegan/R/bstick.cca.R	2009-11-28 22:09:59 UTC (rev 1071)
@@ -5,7 +5,11 @@
         stop("'n' not of class \"cca\" or \"rda\"")
     if(!is.null(n$CCA))
         stop("'bstick' only for unconstrained models.")
-    ## need to select appropriate total invertia
+    ## No idea how to define bstick for capscale with negative
+    ## eigenvalues
+    if (inherits(n, "capscale") && !is.null(n$CA$imaginary.rank))
+        stop("'bstick' cannot be used for 'capscale' with imaginary component") 
+    ## need to select appropriate total inertia
     tot.chi <- n$CA$tot.chi
     n.comp <- n$CA$rank
     res <- bstick.default(n.comp, tot.chi, ...)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-11-18 16:34:26 UTC (rev 1070)
+++ pkg/vegan/inst/ChangeLog	2009-11-28 22:09:59 UTC (rev 1071)
@@ -9,6 +9,10 @@
 	* spandepth: New function to find the depths of nodes in a
 	spanning tree from spantree() function. Per request of
 	W. E. Sharp. 
+
+	* bstick: refuses to analyse capscale() models with imaginary
+	components because I have no idea how to do it. Reported by
+	Richard Telford, Bergen.
 	
 Version 1.16-32 (closed November 13, 2009)