[Vegan-commits] r839 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2009-05-30 15:45:11 +0200 (Sat, 30 May 2009)
New Revision: 839

Modified:
   pkg/vegan/R/anosim.R
   pkg/vegan/R/print.anosim.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/anosim.Rd
Log:
anosim: test statistic is put among the permutations

Modified: pkg/vegan/R/anosim.R
===================================================================
--- pkg/vegan/R/anosim.R	2009-05-30 10:20:58 UTC (rev 838)
+++ pkg/vegan/R/anosim.R	2009-05-30 13:45:11 UTC (rev 839)
@@ -1,5 +1,5 @@
 "anosim" <-
-    function (dat, grouping, permutations = 1000,
+    function (dat, grouping, permutations = 999,
               distance = "bray", strata) 
 {
     if (inherits(dat, "dist")) 
@@ -28,6 +28,8 @@
     cl.vec[within] <- levels(grouping)[grouping[take]]
     cl.vec <- factor(cl.vec, levels = c("Between", levels(grouping)))
     if (permutations) {
+        if (permutations %% 100 == 0)
+            permutations <- permutations - 1
         perm <- rep(0, permutations)
         for (i in 1:permutations) {
             take <- permuted.index(N, strata)
@@ -36,7 +38,7 @@
             tmp.ave <- tapply(x.rank, tmp.within, mean)
             perm[i] <- -diff(tmp.ave)/div
         }
-        p.val <- sum(perm >= statistic)/permutations
+        p.val <- (1 + sum(perm >= statistic))/(1 + permutations)
         sol$signif <- p.val
         sol$perm <- perm
     }

Modified: pkg/vegan/R/print.anosim.R
===================================================================
--- pkg/vegan/R/print.anosim.R	2009-05-30 10:20:58 UTC (rev 838)
+++ pkg/vegan/R/print.anosim.R	2009-05-30 13:45:11 UTC (rev 839)
@@ -8,7 +8,7 @@
     cat(formatC(x$statistic, digits = digits), "\n")
     nperm <- x$permutations
     if (nperm) {
-        cat("      Significance:", format.pval(x$signif, eps = 1/nperm), 
+        cat("      Significance:", format.pval(x$signif), 
             "\n\n")
         cat("Based on ", nperm, " permutations")
     }

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-05-30 10:20:58 UTC (rev 838)
+++ pkg/vegan/inst/ChangeLog	2009-05-30 13:45:11 UTC (rev 839)
@@ -29,6 +29,9 @@
 	* mantel, mantel.partial: observed value of test statistic is now
 	considered as one of the permutations.
 
+	* anosim: observed value of test statistic is now considered as
+	one of the permutatons.
+
 Version 1.16-18 (closed May 14, 2009)
 
 	* tsallis: got new argument 'hill' similar to that of renyi.

Modified: pkg/vegan/man/anosim.Rd
===================================================================
--- pkg/vegan/man/anosim.Rd	2009-05-30 10:20:58 UTC (rev 838)
+++ pkg/vegan/man/anosim.Rd	2009-05-30 13:45:11 UTC (rev 839)
@@ -11,7 +11,7 @@
   of sampling units.
 }
 \usage{
-anosim(dat, grouping, permutations=1000, distance = "bray", strata)
+anosim(dat, grouping, permutations = 999, distance = "bray", strata)
 }
 
 \arguments{