[Vegan-commits] r1282 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2010-08-25 13:13:31 +0200 (Wed, 25 Aug 2010)
New Revision: 1282

Modified:
   pkg/vegan/R/ordiR2step.R
   pkg/vegan/inst/ChangeLog
Log:
ordiR2step was not able to add all variables of the scope

Modified: pkg/vegan/R/ordiR2step.R
===================================================================
--- pkg/vegan/R/ordiR2step.R	2010-08-25 09:37:03 UTC (rev 1281)
+++ pkg/vegan/R/ordiR2step.R	2010-08-25 11:13:31 UTC (rev 1282)
@@ -5,6 +5,8 @@
 `ordiR2step` <-
     function(object, scope, trace = TRUE)
 {
+    if (missing(scope))
+        stop("needs scope")
     ## Works only for rda(): cca() does not have (yet) R2.adjusted
     if (!inherits(object, "rda"))
         stop("can be used only with rda() or capscale()")
@@ -30,6 +32,9 @@
     R2.previous <- R2.0
     repeat {
         adds <- add.scope(object, scope)
+        ## Nothing to add, and we're done: break
+        if (length(adds) == 0)
+            break
         R2.adds <- numeric(length(adds))
         names(R2.adds) <- adds
         ## Loop over add scope

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-08-25 09:37:03 UTC (rev 1281)
+++ pkg/vegan/inst/ChangeLog	2010-08-25 11:13:31 UTC (rev 1282)
@@ -15,6 +15,9 @@
 
 	* biplot.CCorA: resets par that it sets.
 
+	* ordiR2step: can go to the end and include all variables of the
+	scope (and checks there is a scope).
+
 	* permutest.cca: defaults to 99 permutations instead of 100 (to
 	be consistent). Item 'call' now stores the call to permutest()
 	instead of the call of the ordination which is now saved in