[Vegan-commits] r491 - in pkg: R inst

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

Author: jarioksa
Date: 2008-09-01 16:45:07 +0200 (Mon, 01 Sep 2008)
New Revision: 491

Modified:
   pkg/R/permutest.cca.R
   pkg/R/print.permutest.cca.R
   pkg/inst/ChangeLog
Log:
permutest.cca tells if it analysed all eigenvalues or only the first

Modified: pkg/R/permutest.cca.R
===================================================================
--- pkg/R/permutest.cca.R	2008-08-31 17:04:27 UTC (rev 490)
+++ pkg/R/permutest.cca.R	2008-09-01 14:45:07 UTC (rev 491)
@@ -88,7 +88,7 @@
     }
     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, Random.seed = seed)
+                                                              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/R/print.permutest.cca.R
===================================================================
--- pkg/R/print.permutest.cca.R	2008-08-31 17:04:27 UTC (rev 490)
+++ pkg/R/print.permutest.cca.R	2008-09-01 14:45:07 UTC (rev 491)
@@ -4,7 +4,11 @@
     cat("\nPermutation test for", x$method, "\nCall:\n")
     cat(deparse(x$call), "\n\n")
     Pval <- sum(x$F.perm >= x$F.0)/x$nperm
-    cat("Test for significance of all constrained eigenvalues\n")
+    cat("Permutation test for ")
+    if (x$first)
+        cat("first constrained eigenvalue\n")
+    else
+        cat("all constrained eigenvalues\n")
     cat("Pseudo-F:\t", x$F.0, "\n")
     cat("Significance:\t", format.pval(Pval, eps = 1/x$nperm), 
         "\n")

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2008-08-31 17:04:27 UTC (rev 490)
+++ pkg/inst/ChangeLog	2008-09-01 14:45:07 UTC (rev 491)
@@ -29,10 +29,12 @@
 	needs evaluate the community within calling function. (The
 	environment() drives me absolutely crazy, says J.O.)
 
-	* specaccum: empy (all zeros) species removed from input
-	data. These confused sd estimation in method = "exact" which gave
-	all NA.
+	* specaccum: empty (all zeros) species removed from input
+	data. These confused method = "exact" which gave sd = NA.
 
+	* permutest.cca: tells whether the test was for all eigenvalues or
+	for the first (this is implicit in anova.cca).
+
 	* vegan-internal.Rd: brief documentation of internal functions for
 	developers with some guidelines of good practices.