[Vegan-commits] r1222 - in branches/1.17: R inst man

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

Author: jarioksa
Date: 2010-06-07 08:52:35 +0200 (Mon, 07 Jun 2010)
New Revision: 1222

Modified:
   branches/1.17/R/envfit.default.R
   branches/1.17/inst/ChangeLog
   branches/1.17/man/envfit.Rd
Log:
merge r1186: use 999 permutations instead of 0 in envfit

Modified: branches/1.17/R/envfit.default.R
===================================================================
--- branches/1.17/R/envfit.default.R	2010-06-06 16:21:35 UTC (rev 1221)
+++ branches/1.17/R/envfit.default.R	2010-06-07 06:52:35 UTC (rev 1222)
@@ -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: branches/1.17/inst/ChangeLog
===================================================================
--- branches/1.17/inst/ChangeLog	2010-06-06 16:21:35 UTC (rev 1221)
+++ branches/1.17/inst/ChangeLog	2010-06-07 06:52:35 UTC (rev 1222)
@@ -20,6 +20,8 @@
 
 	* merge r1188: ordiresids de-weights *CA.
 
+	* merge r1186: envfit defaults to 999 permutations (was 0).
+
 	* merge r1185: metaMDS handles NA distances.
 
 	* merge r1182 (r1184 for Rd) r1187: mantel.correlog upgrades.

Modified: branches/1.17/man/envfit.Rd
===================================================================
--- branches/1.17/man/envfit.Rd	2010-06-06 16:21:35 UTC (rev 1221)
+++ branches/1.17/man/envfit.Rd	2010-06-07 06:52:35 UTC (rev 1222)
@@ -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}.