[Vegan-commits] r2112 - branches/2.0/R branches/2.0/inst branches/2.0/man www

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

Author: jarioksa
Date: 2012-03-01 14:59:55 +0100 (Thu, 01 Mar 2012)
New Revision: 2112

Modified:
   branches/2.0/R/simper.R
   branches/2.0/inst/NEWS.Rd
   branches/2.0/man/simper.Rd
   www/NEWS.html
Log:
deactive simper() permutation tests in the release version

Modified: branches/2.0/R/simper.R
===================================================================
--- branches/2.0/R/simper.R	2012-02-28 15:48:55 UTC (rev 2111)
+++ branches/2.0/R/simper.R	2012-03-01 13:59:55 UTC (rev 2112)
@@ -1,6 +1,8 @@
 `simper` <-
-    function(comm, group, permutations = 0, trace = FALSE,  ...)
+    function(comm, group, ...)
 {
+    permutations <- 0
+    trace <- FALSE
     comm <- as.matrix(comm)
     comp <- t(combn(unique(as.character(group)), 2))
     outlist <- NULL

Modified: branches/2.0/inst/NEWS.Rd
===================================================================
--- branches/2.0/inst/NEWS.Rd	2012-02-28 15:48:55 UTC (rev 2111)
+++ branches/2.0/inst/NEWS.Rd	2012-03-01 13:59:55 UTC (rev 2112)
@@ -23,9 +23,7 @@
       Journal of Ecology} 18, 117--143; 1993).  The method compares
       two or more groups and decomposes the average between-group
       Bray-Curtis dissimilarity index to contributions of individual
-      species.  The method also adds permutation tests as an
-      experimental feature: these tests may change or can be removed
-      in later releases.
+      species.  
 
     }
   } % end new functions

Modified: branches/2.0/man/simper.Rd
===================================================================
--- branches/2.0/man/simper.Rd	2012-02-28 15:48:55 UTC (rev 2111)
+++ branches/2.0/man/simper.Rd	2012-03-01 13:59:55 UTC (rev 2112)
@@ -10,7 +10,7 @@
 }
 
 \usage{
-  simper(comm, group, permutations = 0, trace = FALSE, ...)
+  simper(comm, group,  ...)
   
   \method{summary}{simper}(object, ordered = TRUE, 
      digits = max(3, getOption("digits") - 3), ...)
@@ -20,19 +20,11 @@
   \item{comm}{Community data matrix.}
   \item{group}{Factor describing the group structure. Must have at
     least 2 levels.}
-  \item{permutations}{Number of permutations or a permutation matrix
-    where each row gives a permuted index for assessing the
-    \dQuote{significance} of the average contribution. Default is set
-    to 0 (no permutation test), since computations may take long
-    time.}
-  \item{trace}{Trace permutations.}
   \item{object}{an object returned by \code{simper}.}
   \item{ordered}{Logical; Should the species be ordered by their
     average contribution?}
   \item{digits}{Number of digits in output.}
-  \item{...}{Parameters passed to other functions. In \code{simper} the
-    extra parameters are passed to \code{\link[permute]{shuffleSet}} if
-    permutations are used.}
+  \item{...}{Parameters passed to other functions.}
 }
 
 \details{ Similarity percentage, \code{simper} (Clarke 1993) is based
@@ -74,9 +66,6 @@
   \item{ord}{An index vector to order vectors by their contribution or
     order \code{cusum} back to the original data order.}
   \item{cusum}{Ordered cumulative per cent contribution.}
-  \item{p}{permutation \eqn{p}-value. Probability of getting a larger
-    or equal average contribution in random permutation of the group
-    factor.}
 }
 
 \examples{

Modified: www/NEWS.html
===================================================================
--- www/NEWS.html	2012-02-28 15:48:55 UTC (rev 2111)
+++ www/NEWS.html	2012-03-01 13:59:55 UTC (rev 2112)
@@ -36,9 +36,7 @@
 Journal of Ecology</EM> 18, 117–143; 1993).  The method compares
 two or more groups and decomposes the average between-group
 Bray-Curtis dissimilarity index to contributions of individual
-species.  The method also adds permutation tests as an
-experimental feature: these tests may change or can be removed
-in later releases.
+species.  
 </p>
 </ul>