[Vegan-commits] r1043 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2009-10-14 09:16:23 +0200 (Wed, 14 Oct 2009)
New Revision: 1043

Modified:
   pkg/vegan/R/ordiParseFormula.R
   pkg/vegan/inst/ChangeLog
Log:
anova.cca can handle some cases where data was not given as data= argument, but attached or found from the working environment

Modified: pkg/vegan/R/ordiParseFormula.R
===================================================================
--- pkg/vegan/R/ordiParseFormula.R	2009-10-12 20:17:56 UTC (rev 1042)
+++ pkg/vegan/R/ordiParseFormula.R	2009-10-14 07:16:23 UTC (rev 1043)
@@ -2,6 +2,8 @@
 function (formula, data, xlev = NULL, envdepth = 2, na.action = na.fail,
           subset = NULL) 
 {
+    if (missing(data))
+        data <- environment(formula)
     Terms <- terms(formula, "Condition", data = data)
     flapart <- fla <- formula <- formula(Terms, width.cutoff = 500)
     specdata <- formula[[2]]

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-10-12 20:17:56 UTC (rev 1042)
+++ pkg/vegan/inst/ChangeLog	2009-10-14 07:16:23 UTC (rev 1043)
@@ -4,6 +4,12 @@
 
 Version 1.16-31 (opened October 3, 2009)
 
+	* constraind 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(). 
+
 	* envfit: could drop data frame to a vector with na.action (broken
 	in 1.16-28).