[Vegan-commits] r405 - pkg/inst

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

Author: jarioksa
Date: 2008-06-09 06:39:11 +0200 (Mon, 09 Jun 2008)
New Revision: 405

Modified:
   pkg/inst/ChangeLog
Log:
updated ChangeLog: rda/cca rank issue should be no issue any more

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2008-06-09 04:34:32 UTC (rev 404)
+++ pkg/inst/ChangeLog	2008-06-09 04:39:11 UTC (rev 405)
@@ -4,24 +4,20 @@
 
 Version 1.14-3 (opened June 5, 2008)
 
-	* rda, cca, capscale: obviously do not handle correctly cases
-	where the rank of constraints + conditions is higher than the rank
-	of the dependent (community) data. Now issues a warning in
-	'print'. This is an ancient problem, but surfaced recently in
-	several places.
+        * rda.default, cca.default: vegan naively used only the rank of
+        the ordination, but indeed, there are three cases of ranks: rank
+        of the ordination or number of axes (returned as rank like
+        before), rank of the constraints after conditions (now returned as
+        qrank), rank of conditions + constraints (returned in QR$rank).
+        When only 'rank' was used, vegan for instance aliased terms beyond
+        rank of ordination axes, extractAIC did not get df right when
+        going beyond rank of ordination, anova(..., by="t") gave zero df
+        for constraints beyond rank of ordination, and calibrate.cca
+        ignored those extra variables (now stops). In addition predict.cca
+        and predict.rda(..., type="lc", newdata=somedata) gave wrong
+        results in partial model.  The following changes were made if
+        necessary to cca/rda support functions:
 
-	* rda, cca, capscale: constraints are not aliased any more if
-	their rank is higher than the rank of the community data.  Because
-	cca objects are handled by many other functions, this may cause
-	trouble in surprising places and the change is unstabilizing.
-
-	* rda.default, cca.default: vegan naively used only the rank of
-	the ordination, but indeed, there are three cases of ranks
-	(returned as rank): rank of the ordination or number of axes, rank
-	of the constraints after conditions (now returned as qrank), rank
-	of conditions + constraints (returned in QR$rank). The following
-	changes were made if necessary to cca/rda support functions: 
-
 	* alias.cca: QR$rank
 	* anova.ccabyaxis: OK 
 	* bstick.cca: OK