[Vegan-commits] r1455 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2011-01-14 14:34:15 +0100 (Fri, 14 Jan 2011)
New Revision: 1455

Modified:
   pkg/vegan/R/anova.ccabyaxis.R
   pkg/vegan/R/anova.ccabyterm.R
   pkg/vegan/inst/ChangeLog
Log:
fix most open issues in anova.cca(..., by = "ax") and anova.cca(..., by = "term")

Modified: pkg/vegan/R/anova.ccabyaxis.R
===================================================================
--- pkg/vegan/R/anova.ccabyaxis.R	2011-01-13 07:41:37 UTC (rev 1454)
+++ pkg/vegan/R/anova.ccabyaxis.R	2011-01-14 13:34:15 UTC (rev 1455)
@@ -7,7 +7,7 @@
         stop("Needs a constrained ordination")
     if (is.null(object$terms)) 
         stop("Analysis is only possible for models fitted using formula")
-    lc <- object$CCA$u
+    lc<- as.data.frame(object$CCA$u)
     ## Handle missing values in scores, both "omit" and "exclude" to
     ## match dims with data.
     if (!is.null(object$na.action)) {
@@ -21,8 +21,10 @@
     Pval <- rep(NA, rnk+1)
     out <- data.frame(df, chi, Fval, nperm, Pval)
     environment(object$terms) <- environment()
-    fla <- update(formula(object), . ~ lc[,1] + Condition(lc[,-1]))
-    sol <- anova(update(object, fla),  ...)
+    fla <- paste(". ~ ", axnam[1], "+ Condition(",
+                 paste(axnam[-1], collapse="+"),")")
+    fla <- update(formula(object), fla)
+    sol <- anova(update(object, fla, data=lc),  ...)
     out[c(1, rnk + 1), ] <- sol
     seed <- attr(sol, "Random.seed")
     attr(out, "names") <- attr(sol, "names")
@@ -33,8 +35,10 @@
     bigperm <- out$N.Perm[1]
     if (rnk > 1) {
         for (.ITRM in 2:rnk) {
-            fla <- update(formula(object),  .~ lc[, .ITRM] + Condition(lc[,-(.ITRM)]) )
-            sol <- update(object, fla)
+            fla <- paste(".~", axnam[.ITRM], "+Condition(",
+                         paste(axnam[-(.ITRM)], collapse="+"),")")
+            fla <- update(formula(object),  fla) 
+            sol <- update(object, fla, data = lc)
             assign(".Random.seed", seed, envir = .GlobalEnv)
             out[.ITRM, ] <- as.matrix(anova(sol, ...))[1, 
                 ]

Modified: pkg/vegan/R/anova.ccabyterm.R
===================================================================
--- pkg/vegan/R/anova.ccabyterm.R	2011-01-13 07:41:37 UTC (rev 1454)
+++ pkg/vegan/R/anova.ccabyterm.R	2011-01-14 13:34:15 UTC (rev 1455)
@@ -25,7 +25,7 @@
     pchi[ntrm, ] <- sim$num
     df[ntrm:(ntrm + 1)] <- sim$df
     chi[ntrm:(ntrm + 1)] <- sim$chi
-    modelframe <- model.frame(object)
+    modelframe <- ordiGetData(object$call, NULL)
     environment(object$terms) <- environment()
     for (.ITRM in ntrm:2) {
         if (ntrm < 2) 

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-01-13 07:41:37 UTC (rev 1454)
+++ pkg/vegan/inst/ChangeLog	2011-01-14 13:34:15 UTC (rev 1455)
@@ -20,6 +20,13 @@
 	scale of input dissimilarities. The function uses only the real
 	axes, and imaginary dimensions are ignored.
 
+	* anova.cca: by = "term" and by = "axis" work now both with the
+	data= statement and with variables in the GlobalEnv both in
+	cca/rda and in capscale. A failing case is still anova(..., by =
+	"axis", subset=...) because subset is applied to the constraints,
+	but not to the response. Moreover, it seems that 'subset' is not
+	implemented for capscale(). 
+
 Version 1.18-20 (closed January 9, 2011)
 
 	* base of vegan release 1.17-6 (released on Jan 10, 2011).