[Vegan-commits] r659 - pkg/vegan/R

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

Author: hankstevens
Date: 2009-01-14 20:31:02 +0100 (Wed, 14 Jan 2009)
New Revision: 659

Modified:
   pkg/vegan/R/adonis.R
Log:
Changed the calculation of the P-value in adonis to add 1 to both the numerator and denominator

Modified: pkg/vegan/R/adonis.R
===================================================================
--- pkg/vegan/R/adonis.R	2009-01-14 14:08:14 UTC (rev 658)
+++ pkg/vegan/R/adonis.R	2009-01-14 19:31:02 UTC (rev 659)
@@ -92,7 +92,7 @@
                       MeanSqs = c(SS.Exp.each/df.Exp, SS.Res/df.Res, NA),
                       F.Model = c(F.Mod, NA,NA),
                       R2 = SumsOfSqs/SumsOfSqs[length(SumsOfSqs)],
-                      P = c(rowSums(t(f.perms) > F.Mod)/permutations, NA, NA))
+                      P = c((rowSums(t(f.perms)+1) > F.Mod)/(permutations+1), NA, NA))
     rownames(tab) <- c(attr(attr(rhs.frame, "terms"), "term.labels")[u.grps],
                        "Residuals", "Total")
     colnames(tab)[ncol(tab)] <- "Pr(>F)"