[Vegan-commits] r1044 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2009-10-14 15:46:05 +0200 (Wed, 14 Oct 2009)
New Revision: 1044

Modified:
   pkg/vegan/R/anova.ccabyaxis.R
   pkg/vegan/inst/ChangeLog
Log:
anova.ccabyaxis failed if fitted model had no data= statement

Modified: pkg/vegan/R/anova.ccabyaxis.R
===================================================================
--- pkg/vegan/R/anova.ccabyaxis.R	2009-10-14 07:16:23 UTC (rev 1043)
+++ pkg/vegan/R/anova.ccabyaxis.R	2009-10-14 13:46:05 UTC (rev 1044)
@@ -8,11 +8,15 @@
     if (is.null(object$terms)) 
         stop("Analysis is only possible for models fitted using formula")
     lc <- object$CCA$u
+    mf <- model.frame(object)
     ## Handle missing values in scores, both "omit" and "exclude" to
     ## match dims with data.
-    if (!is.null(object$na.action))
+    if (!is.null(object$na.action)) {
         lc <- stats:::napredict.exclude(object$na.action, lc)
-    newdata <- cbind(lc, eval(as.list(object$call)$data))
+        mf <- lapply(mf, function(x) stats:::napredict.exclude(object$na.action, x))
+        mf <- as.data.frame(mf)
+    }
+    newdata <- cbind(lc, mf)
     axnam <- colnames(lc)
     df <- c(rep(1, rnk), object$CA$rank)
     chi <- c(object$CCA$eig, Residual = object$CA$tot.chi)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-10-14 07:16:23 UTC (rev 1043)
+++ pkg/vegan/inst/ChangeLog	2009-10-14 13:46:05 UTC (rev 1044)
@@ -4,11 +4,12 @@
 
 Version 1.16-31 (opened October 3, 2009)
 
-	* constraind ordination (cca, rda, capscale) could not handle all
+	* constrained ordination (cca, rda, capscale) could not handle all
 	anova(.., by= "something") cases when the data were not in
-	data.frame but in working environment or attach'ed. Function
-	anova.ccabyaxis still fails, and all fail if the data was defined
-	using with(). 
+	data.frame but in working environment or defined using
+	with(data,...). Still failing: with(data, anova(..., by = "t"))
+	and attach'ed data frames which were detach'ed during anova (but
+	these work if attach'ed again).
 
 	* envfit: could drop data frame to a vector with na.action (broken
 	in 1.16-28).