[Vegan-commits] r2290 - in branches/2.0: R inst

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

Author: jarioksa
Date: 2012-09-18 19:27:31 +0200 (Tue, 18 Sep 2012)
New Revision: 2290

Modified:
   branches/2.0/R/anova.ccabyaxis.R
   branches/2.0/R/anova.ccabyterm.R
   branches/2.0/inst/ChangeLog
Log:
merge r2288,9: scoping issues that made anova.ccabyaxis, anova.ccabyterm fail in partial models

Modified: branches/2.0/R/anova.ccabyaxis.R
===================================================================
--- branches/2.0/R/anova.ccabyaxis.R	2012-09-16 15:42:12 UTC (rev 2289)
+++ branches/2.0/R/anova.ccabyaxis.R	2012-09-18 17:27:31 UTC (rev 2290)
@@ -1,8 +1,6 @@
 `anova.ccabyaxis` <-
     function (object, cutoff = 1,  ...) 
 {
-    if(inherits(object, "prc"))
-        stop("anova(..., by = 'axis') cannot be used for 'prc' results")
     cutoff <- cutoff + sqrt(.Machine$double.eps)
     rnk <- object$CCA$rank
     if (!max(rnk, 0)) 
@@ -51,8 +49,10 @@
     environment(object$terms) <- environment()
     fla <- paste(". ~ ", axnam[1], "+ Condition(",
                  paste(axnam[-1], collapse="+"),")")
-    if (!is.null(CondMat))
+    if (!is.null(CondMat)) {
         fla <- paste(fla, " + Condition(CondMat)")
+        lc$CondMat <- CondMat
+    }
     fla <- update(formula(object), fla)
     sol <- anova(update(object, fla, data=lc),  ...)
     out[c(1, rnk + 1), ] <- sol

Modified: branches/2.0/R/anova.ccabyterm.R
===================================================================
--- branches/2.0/R/anova.ccabyterm.R	2012-09-16 15:42:12 UTC (rev 2289)
+++ branches/2.0/R/anova.ccabyterm.R	2012-09-18 17:27:31 UTC (rev 2290)
@@ -28,7 +28,7 @@
     if (!is.null(object$call$data))
         modelframe <- ordiGetData(object$call, globalenv())
     else
-        modelframe <- NULL
+        modelframe <- model.frame(object)
     for (.ITRM in ntrm:2) {
         if (ntrm < 2) 
             break

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2012-09-16 15:42:12 UTC (rev 2289)
+++ branches/2.0/inst/ChangeLog	2012-09-18 17:27:31 UTC (rev 2290)
@@ -4,6 +4,7 @@
 
 Version 2.0-5 (opened June 18, 2012)
 
+	* merge r2288,9: scoping in anova.ccabyaxis and anova.ccabyterm.
 	* merge r2262, 2268:2270, and also r1950: mantel and
 	mantel.partial gained argument na.rm = FALSE. This needed hand
 	editing of merges, and also merging old r1950: beware and test.