[Vegan-commits] r840 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2009-05-31 08:02:04 +0200 (Sun, 31 May 2009)
New Revision: 840

Modified:
   pkg/vegan/R/mrpp.R
   pkg/vegan/R/print.mrpp.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/mrpp.Rd
Log:
mrpp: better defaults for no. of permutations and print formatting

Modified: pkg/vegan/R/mrpp.R
===================================================================
--- pkg/vegan/R/mrpp.R	2009-05-30 13:45:11 UTC (rev 839)
+++ pkg/vegan/R/mrpp.R	2009-05-31 06:02:04 UTC (rev 840)
@@ -1,5 +1,5 @@
 "mrpp" <-
-function (dat, grouping, permutations = 1000, distance = "euclidean", 
+function (dat, grouping, permutations = 999, distance = "euclidean", 
     weight.type = 1, strata) 
 {
     classmean <- function(ind, dmat, indls) {

Modified: pkg/vegan/R/print.mrpp.R
===================================================================
--- pkg/vegan/R/print.mrpp.R	2009-05-30 13:45:11 UTC (rev 839)
+++ pkg/vegan/R/print.mrpp.R	2009-05-31 06:02:04 UTC (rev 840)
@@ -22,7 +22,7 @@
         formatC(x$E.delta),"\n\n")
     nperm <- x$permutations
     if (nperm) {
-        cat("Significance of delta:", format.pval(x$Pvalue, eps = 1/nperm), 
+        cat("Significance of delta:", format.pval(x$Pvalue), 
             "\n")
         cat("Based on ", nperm, " permutations")
     }

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-05-30 13:45:11 UTC (rev 839)
+++ pkg/vegan/inst/ChangeLog	2009-05-31 06:02:04 UTC (rev 840)
@@ -32,6 +32,9 @@
 	* anosim: observed value of test statistic is now considered as
 	one of the permutatons.
 
+	* mrpp: argument defaults and printing adated for having test
+	statistic among permutations (like the function always had).
+
 Version 1.16-18 (closed May 14, 2009)
 
 	* tsallis: got new argument 'hill' similar to that of renyi.

Modified: pkg/vegan/man/mrpp.Rd
===================================================================
--- pkg/vegan/man/mrpp.Rd	2009-05-30 13:45:11 UTC (rev 839)
+++ pkg/vegan/man/mrpp.Rd	2009-05-31 06:02:04 UTC (rev 840)
@@ -14,7 +14,7 @@
 groups of sampling units.  }
 
 \usage{
-mrpp(dat, grouping, permutations = 1000, distance = "euclidean",
+mrpp(dat, grouping, permutations = 999, distance = "euclidean",
      weight.type = 1, strata)
 meandist(dist, grouping, ...)
 \method{summary}{meandist}(object, ...)