[Vegan-commits] r1275 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2010-08-23 18:33:40 +0200 (Mon, 23 Aug 2010)
New Revision: 1275

Modified:
   pkg/vegan/R/permutest.cca.R
   pkg/vegan/R/print.permutest.cca.R
   pkg/vegan/inst/ChangeLog
Log:
permutest.cca saves its own 'call'

Modified: pkg/vegan/R/permutest.cca.R
===================================================================
--- pkg/vegan/R/permutest.cca.R	2010-08-23 14:46:53 UTC (rev 1274)
+++ pkg/vegan/R/permutest.cca.R	2010-08-23 16:33:40 UTC (rev 1275)
@@ -101,9 +101,10 @@
     ## numerical inaccuracy
     F.0 <- round(F.0, 12)
     F.perm <- round(F.perm, 12)
-    sol <- list(call = x$call, model = model, F.0 = F.0, F.perm = F.perm, 
-                chi = c(Chi.z, Chi.xz), num = num, den = den, df = c(q, 
-                                                              r), nperm = permutations, method = x$method, first = first,  Random.seed = seed)
+    sol <- list(call = match.call(), testcall = x$call, model = model,
+                F.0 = F.0, F.perm = F.perm,  chi = c(Chi.z, Chi.xz),
+                num = num, den = den, df = c(q, r), nperm = permutations,
+                method = x$method, first = first,  Random.seed = seed)
     if (!missing(strata)) {
         sol$strata <- deparse(substitute(strata))
         sol$stratum.values <- strata

Modified: pkg/vegan/R/print.permutest.cca.R
===================================================================
--- pkg/vegan/R/print.permutest.cca.R	2010-08-23 14:46:53 UTC (rev 1274)
+++ pkg/vegan/R/print.permutest.cca.R	2010-08-23 16:33:40 UTC (rev 1275)
@@ -2,14 +2,15 @@
     function (x, ...) 
 {
     cat("\nPermutation test for", x$method, "\n\n")
-    writeLines(strwrap(pasteCall(x$call)))
+    writeLines(strwrap(pasteCall(x$testcall)))
     Pval <- (sum(x$F.perm >= x$F.0) + 1)/(x$nperm + 1)
     cat("Permutation test for ")
     if (x$first)
         cat("first constrained eigenvalue\n")
     else
         cat("all constrained eigenvalues\n")
-    cat("Pseudo-F:\t", x$F.0, "\n")
+    cat("Pseudo-F:\t", x$F.0, "(with", paste(x$df, collapse = ", "),
+        "Degrees of Freedom)\n")
     cat("Significance:\t", format.pval(Pval), 
         "\n")
     cat("Based on", x$nperm, "permutations under", x$model, "model")

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-08-23 14:46:53 UTC (rev 1274)
+++ pkg/vegan/inst/ChangeLog	2010-08-23 16:33:40 UTC (rev 1275)
@@ -8,7 +8,9 @@
 	20, 2010.
 
 	* permutest.cca: defaults to 99 permutations instead of 100 (to
-	be consistent).
+	be consistent). Item 'call' no stores the call to permutest()
+	instead of the call of the ordination which is now saved in
+	'testcall'.  This means that update() works now.
 
 	* anova.ccalist: Started to work on the concept of permutation
 	test comparison of several cca/ rda/ capscale models. The first