[Vegan-commits] r1186 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2010-05-05 16:27:40 +0200 (Wed, 05 May 2010)
New Revision: 1186

Modified:
   pkg/vegan/R/envfit.default.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/envfit.Rd
Log:
envfit defaults to 999 permutations instead of 0

Modified: pkg/vegan/R/envfit.default.R
===================================================================
--- pkg/vegan/R/envfit.default.R	2010-05-05 09:01:53 UTC (rev 1185)
+++ pkg/vegan/R/envfit.default.R	2010-05-05 14:27:40 UTC (rev 1186)
@@ -1,5 +1,5 @@
 "envfit.default" <-
-    function (ord, env, permutations = 0, strata, choices = c(1, 2), 
+    function (ord, env, permutations = 999, strata, choices = c(1, 2), 
              display = "sites", w = weights(ord), na.rm = FALSE, ...) 
 {
     weights.default <- function(object, ...) NULL

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-05-05 09:01:53 UTC (rev 1185)
+++ pkg/vegan/inst/ChangeLog	2010-05-05 14:27:40 UTC (rev 1186)
@@ -4,6 +4,9 @@
 
 Version 1.18-4 (opened April 15, 2010)
 
+	* envfit: defaults now to 999 permutations. Used to be 0 or no
+	permutations. 
+
 	* metaMDS: can handle NA values in dissimilarities (but I do not
 	know if isoMDS can handle them correctly).
 

Modified: pkg/vegan/man/envfit.Rd
===================================================================
--- pkg/vegan/man/envfit.Rd	2010-05-05 09:01:53 UTC (rev 1185)
+++ pkg/vegan/man/envfit.Rd	2010-05-05 14:27:40 UTC (rev 1186)
@@ -18,7 +18,7 @@
   the factors show the averages of factor levels.
 }
 \usage{
-\method{envfit}{default}(ord, env, permutations = 0, strata, choices=c(1,2), 
+\method{envfit}{default}(ord, env, permutations = 999, strata, choices=c(1,2), 
    display = "sites", w  = weights(ord), na.rm = FALSE, ...)
 \method{envfit}{formula}(formula, data, ...)
 \method{plot}{envfit}(x, choices = c(1,2), arrow.mul, at = c(0,0), axis = FALSE, 
@@ -40,7 +40,7 @@
     variable(s). These must be continuous for \code{vectorfit} and
     factors or characters for \code{factorfit}. }
   \item{permutations}{ Number of permutations for assessing significance
-    of vectors or factors.}
+    of vectors or factors. Set to \code{0} to skip permutations.}
   \item{formula, data}{Model  \code{\link{formula}} and data.  }
   \item{na.rm}{Remove points with missing values in ordination scores or 
     environmental variables}.