[Vegan-commits] r312 - in pkg: R inst

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

Author: gsimpson
Date: 2008-04-10 18:25:42 +0200 (Thu, 10 Apr 2008)
New Revision: 312

Modified:
   pkg/R/adonis.R
   pkg/inst/ChangeLog
Log:
adonis was not dropping empty factor levels

Modified: pkg/R/adonis.R
===================================================================
--- pkg/R/adonis.R	2008-04-10 12:47:25 UTC (rev 311)
+++ pkg/R/adonis.R	2008-04-10 16:25:42 UTC (rev 312)
@@ -10,7 +10,7 @@
     lhs <- formula[[2]]
     lhs <- eval(lhs, data, parent.frame()) # to force evaluation 
     formula[[2]] <- NULL                # to remove the lhs
-    rhs.frame <- model.frame(formula, data) # to get the data frame of rhs
+    rhs.frame <- model.frame(formula, data, drop.unused.levels = TRUE) # to get the data frame of rhs
     op.c <- options()$contrasts
     options( contrasts=c(contr.unordered, contr.ordered) )
     rhs <- model.matrix(formula, rhs.frame) # and finally the model.matrix

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2008-04-10 12:47:25 UTC (rev 311)
+++ pkg/inst/ChangeLog	2008-04-10 16:25:42 UTC (rev 312)
@@ -21,6 +21,10 @@
 	* allPerms: Now accepts a vector from which number of observations 
 	can be deduced. This was the intended behaviour but allPerms failed
 	in such cases.
+
+	* adonis: Was not dropping empty levels of factors, which was 
+	leading to incorrect results (d.f. was inflated). Reported by
+	Tyler Smith.
 	
 Version 1.12-8 (closed April 6, 2008)