[Vegan-commits] r841 - pkg/vegan/R

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

Author: jarioksa
Date: 2009-05-31 08:18:25 +0200 (Sun, 31 May 2009)
New Revision: 841

Modified:
   pkg/vegan/R/plot.anosim.R
   pkg/vegan/R/print.permutest.cca.R
   pkg/vegan/R/print.protest.R
Log:
final polishing of putting stat among permutations: remove 'eps' from format.pval()

Modified: pkg/vegan/R/plot.anosim.R
===================================================================
--- pkg/vegan/R/plot.anosim.R	2009-05-31 06:02:04 UTC (rev 840)
+++ pkg/vegan/R/plot.anosim.R	2009-05-31 06:18:25 UTC (rev 841)
@@ -5,7 +5,7 @@
            ...)
    title(title)
    if (x$permutations) {
-     pval <- format.pval(x$signif, eps=1/x$permutations)
+     pval <- format.pval(x$signif)
    } else {
      pval <- "not assessed"
    }

Modified: pkg/vegan/R/print.permutest.cca.R
===================================================================
--- pkg/vegan/R/print.permutest.cca.R	2009-05-31 06:02:04 UTC (rev 840)
+++ pkg/vegan/R/print.permutest.cca.R	2009-05-31 06:18:25 UTC (rev 841)
@@ -10,7 +10,7 @@
     else
         cat("all constrained eigenvalues\n")
     cat("Pseudo-F:\t", x$F.0, "\n")
-    cat("Significance:\t", format.pval(Pval, eps = 1/x$nperm), 
+    cat("Significance:\t", format.pval(Pval), 
         "\n")
     cat("Based on", x$nperm, "permutations under", x$model, "model")
     if (!is.null(x$strata)) 

Modified: pkg/vegan/R/print.protest.R
===================================================================
--- pkg/vegan/R/print.protest.R	2009-05-31 06:02:04 UTC (rev 840)
+++ pkg/vegan/R/print.protest.R	2009-05-31 06:18:25 UTC (rev 841)
@@ -6,7 +6,7 @@
   cat("Correlation in a symmetric Procrustes rotation:  ")
   cat(formatC(x$t0, digits = digits), "\n")
   cat("Significance:  ")
-  cat(format.pval(x$signif, eps = 1/x$permutations),"\n")
+  cat(format.pval(x$signif),"\n")
   cat("Based on", x$permutations, "permutations")
   if (!is.null(x$strata)) 
     cat(", stratified within", x$strata)