[Vegan-commits] r663 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2009-01-16 07:38:44 +0100 (Fri, 16 Jan 2009)
New Revision: 663

Modified:
   pkg/vegan/R/adonis.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/adonis.Rd
Log:
adonis: default number of permutations increased from 5 to 999

Modified: pkg/vegan/R/adonis.R
===================================================================
--- pkg/vegan/R/adonis.R	2009-01-15 09:03:25 UTC (rev 662)
+++ pkg/vegan/R/adonis.R	2009-01-16 06:38:44 UTC (rev 663)
@@ -1,5 +1,5 @@
 `adonis` <-
-    function(formula, data=NULL, permutations=5, method="bray", strata=NULL,
+    function(formula, data=NULL, permutations=999, method="bray", strata=NULL,
              contr.unordered="contr.sum", contr.ordered="contr.poly",
              ...)
 {
@@ -8,7 +8,7 @@
     ## variables.  data is the data frame from which A, B, and C would
     ## be drawn.
     TOL <- 1e-7
-    ## Set no. of permutations to x-1 if x is an even hudred
+    ## Set no. of permutations to x-1 if x is an even hundred
     if (permutations %% 100 == 0) {
         permutations <- permutations - 1
         warning("Setting no. of permutations to ", permutations)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-01-15 09:03:25 UTC (rev 662)
+++ pkg/vegan/inst/ChangeLog	2009-01-16 06:38:44 UTC (rev 663)
@@ -10,7 +10,8 @@
 	2.9.0-ready. 
 
 	* adonis: uses now canonical (hits+1)/(tries+1) for P-values
-	instead of hits/tries.
+	instead of hits/tries. Default number of permutations increased
+	from 5 to 999.
 
 	* permatswap: new algorithm "swsh" is added to keep row/column
 	incidences (but not sums) constant. The name refers to the two

Modified: pkg/vegan/man/adonis.Rd
===================================================================
--- pkg/vegan/man/adonis.Rd	2009-01-15 09:03:25 UTC (rev 662)
+++ pkg/vegan/man/adonis.Rd	2009-01-16 06:38:44 UTC (rev 663)
@@ -11,7 +11,7 @@
   matrices; uses a permutation test with pseudo-F ratios.}
 
 \usage{
-adonis(formula, data, permutations = 5, method = "bray",
+adonis(formula, data, permutations = 999, method = "bray",
        strata = NULL, contr.unordered = "contr.sum",
        contr.ordered = "contr.poly", ...)
 }
@@ -158,7 +158,7 @@
 \examples{
 data(dune)
 data(dune.env)
-adonis(dune ~ Management*A1, data=dune.env, permutations=100)
+adonis(dune ~ Management*A1, data=dune.env, permutations=99)
 }
 
 \keyword{multivariate }