[Vegan-commits] r1614 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2011-05-29 16:07:49 +0200 (Sun, 29 May 2011)
New Revision: 1614

Modified:
   pkg/vegan/R/ordiR2step.R
   pkg/vegan/inst/ChangeLog
Log:
ordiR2step() is more informative for the reasons it refuses to build a model

Modified: pkg/vegan/R/ordiR2step.R
===================================================================
--- pkg/vegan/R/ordiR2step.R	2011-05-29 06:21:50 UTC (rev 1613)
+++ pkg/vegan/R/ordiR2step.R	2011-05-29 14:07:49 UTC (rev 1614)
@@ -23,10 +23,15 @@
         scope <- delete.response(formula(scope))
     if (!inherits(scope, "formula"))
         scope <- reformulate(scope)
-    R2.all <- RsquareAdj(update(object, scope))$adj.r.squared
+    R2.all <- RsquareAdj(update(object, scope))
     ## Check that the full model can be evaluated
-    if (is.na(R2.all))
-        stop("the upper scope cannot be fitted (too many terms?)")
+    if (is.na(R2.all$adj.r.squared)) {
+        if (R2.all$r.squared > 0.999)
+            stop("the upper scope cannot be fitted (too many terms?)")
+        else
+            stop("upper scope cannot be fitted (Condition() in scope?)")
+    }
+    R2.all <- R2.all$adj.r.squared
     ## Collect data to anotab returned as the 'anova' object
     anotab <-  list()
     ## Step forward and continue as long as R2.adj improves and R2.adj

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-05-29 06:21:50 UTC (rev 1613)
+++ pkg/vegan/inst/ChangeLog	2011-05-29 14:07:49 UTC (rev 1614)
@@ -4,6 +4,10 @@
 
 Version 1.18-31 (opened May 26, 2011)
 
+	* ordiR2step: more informative about rejecting 'scope': partial
+	models are not (currently) accepted due to the design of
+	RsquareAdj.rda().
+
 	* specnumber: gained argument 'groups' to find total richness
 	within each group. An example shows how to use this to find one
 	index that Whittaker suggested to estimate beta diversity.