[Vegan-commits] r1321 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2010-09-27 08:04:44 +0200 (Mon, 27 Sep 2010)
New Revision: 1321

Modified:
   pkg/vegan/R/decorana.R
   pkg/vegan/inst/ChangeLog
Log:
revert r1318: decorana iterates on species scores and the true eigenvalues are for those

Modified: pkg/vegan/R/decorana.R
===================================================================
--- pkg/vegan/R/decorana.R	2010-09-26 17:06:09 UTC (rev 1320)
+++ pkg/vegan/R/decorana.R	2010-09-27 06:04:44 UTC (rev 1321)
@@ -141,7 +141,11 @@
     }
     else {
         evals.decorana <- evals
-        evals <- eigengrad(rproj, veg)
+        var.r <- cov.wt(rproj, aidot)
+        var.r <- diag(var.r$cov) * (1 - sum(var.r$wt^2))
+        var.c <- cov.wt(cproj, adotj)
+        var.c <- diag(var.c$cov) * (1 - sum(var.c$wt^2))
+        evals <- var.r/var.c
     }
     CA <- list(rproj = rproj, cproj = cproj, evals = evals, evals.decorana = evals.decorana, 
                origin = origin, v = v, fraction = v.fraction, adotj = adotj, 

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-09-26 17:06:09 UTC (rev 1320)
+++ pkg/vegan/inst/ChangeLog	2010-09-27 06:04:44 UTC (rev 1321)
@@ -4,10 +4,7 @@
 
 Version 1.18-13 (opened September 26, 2010)
 
-	* decorana: fixed true eigenvalues which were slightly off (too
-	low). Now uses eigengrad() which is more careful in calculations
-	(like in centring). Gives now warning if residual is bigger than
-	tolerance. 
+	* decorana: gives warning if residual is bigger than tolerance.
 	
 Version 1.18-12 (closed September 26, 2010)