[Vegan-commits] r1081 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2009-12-14 19:25:35 +0100 (Mon, 14 Dec 2009)
New Revision: 1081

Modified:
   pkg/vegan/R/anova.ccabyterm.R
   pkg/vegan/R/permutest.cca.R
   pkg/vegan/inst/ChangeLog
Log:
avoid arbitrary ordering of tied order statistics by rounding to 12 decimal places

Modified: pkg/vegan/R/anova.ccabyterm.R
===================================================================
--- pkg/vegan/R/anova.ccabyterm.R	2009-12-14 17:42:13 UTC (rev 1080)
+++ pkg/vegan/R/anova.ccabyterm.R	2009-12-14 18:25:35 UTC (rev 1081)
@@ -51,8 +51,11 @@
     pchi <- sweep(pchi, 1, df, "/")
     pchi[-(ntrm + 1), ] <- sweep(pchi[-(ntrm + 1), , drop = FALSE], 
                                  2, pchi[ntrm + 1, , drop = FALSE], "/")
+    ## Round to avoid arbitrary P values due to numerical precision
+    pchi <- round(pchi, 12)
+    Fval <- round(Fval, 12)
     P <- rowSums(sweep(pchi[-(ntrm + 1), , drop = FALSE], 1, 
-                       Fval[-(ntrm + 1)], ">"))
+                       Fval[-(ntrm + 1)], ">="))
     P <- c((P + adj)/(step + adj), NA)
     out <- data.frame(df, chi, Fval, c(rep(step, ntrm), NA), 
                       P)

Modified: pkg/vegan/R/permutest.cca.R
===================================================================
--- pkg/vegan/R/permutest.cca.R	2009-12-14 17:42:13 UTC (rev 1080)
+++ pkg/vegan/R/permutest.cca.R	2009-12-14 18:25:35 UTC (rev 1081)
@@ -86,6 +86,10 @@
         den[i] <- ca.ev
         F.perm[i] <- (cca.ev/q)/(ca.ev/r)
     }
+    ## Round to avoid arbitrary ordering of statistics due to
+    ## 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)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-12-14 17:42:13 UTC (rev 1080)
+++ pkg/vegan/inst/ChangeLog	2009-12-14 18:25:35 UTC (rev 1081)
@@ -12,6 +12,12 @@
 	(r1051), but no R interface. Together with decostand(..., "log")
 	of r1052 this closes Feature Request #473 submitted by Etienne
 	Laliberte in R-Forge.
+
+	* anova.cca: tied values could be randomly broken due to
+	numerical precision, and this gave false P-values, for instance in
+	anova(cca(dune ~ Management, dune.env),
+	strata=dune.env$Management).  Now rounds statistics to 12 decimal
+	places in permutest.cca and in anova.ccabyterm.
 	
 Version 1.16-33 (closed December 13, 2009)