[Vegan-commits] r280 - in pkg: inst man

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

Author: jarioksa
Date: 2008-03-24 07:43:08 +0100 (Mon, 24 Mar 2008)
New Revision: 280

Modified:
   pkg/inst/ChangeLog
   pkg/man/metaMDS.Rd
Log:
metaMDS uses now same transformations in WA scores for species as in ordination. This is an incompatible change, but you can re-establish the old behaviour with argument old.wa = T

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2008-03-24 06:26:17 UTC (rev 279)
+++ pkg/inst/ChangeLog	2008-03-24 06:43:08 UTC (rev 280)
@@ -2,8 +2,21 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.12-5 (opened Mar 20, 2008)
+Version 1.12-6 (opened Mar 24, 2008)
 
+	* metaMDS: WA scores for species are now based on the same
+	transformations and standardization (like wisconsin(sqrt())) as
+	the dissimilarities. They used to be based on the original data
+	even when the data were transformed for the ordination. The change
+	is minimal: data are evaluated similarly as in metaMDSdist if
+	wascores are requested. An alternative would have been to split
+	data manipulation function into an independent function from
+	metaMDSdist, but I try this first. For compatibility reasons, the
+	previous behaviour can be re-established using argument old.wa =
+	TRUE.
+	
+Version 1.12-5 (closed Mar 24, 2008)
+
 	* plot.procrustes: could fail if compared configurations were
 	numerically identical.
 

Modified: pkg/man/metaMDS.Rd
===================================================================
--- pkg/man/metaMDS.Rd	2008-03-24 06:26:17 UTC (rev 279)
+++ pkg/man/metaMDS.Rd	2008-03-24 06:43:08 UTC (rev 280)
@@ -25,7 +25,7 @@
 \usage{
 metaMDS(comm, distance = "bray", k = 2, trymax = 20, autotransform =TRUE,
         noshare = 0.1, wascores = TRUE, expand = TRUE, trace = 1,
-        plot = FALSE, previous.best, ...)
+        plot = FALSE, previous.best, old.wa = FALSE, ...)
 \method{plot}{metaMDS}(x, display = c("sites", "species"), choices = c(1, 2),
      type = "p", shrink = FALSE,  ...)
 \method{points}{metaMDS}(x, display = c("sites", "species"),
@@ -66,6 +66,11 @@
   \item{previous.best}{Start searches from a previous
     solutions. Otherwise use \code{\link[MASS]{isoMDS}} default for the
     starting solution.}
+  \item{old.wa}{Use the old way of calculating WA scores for species:
+    in vegan versions 1.12-5 and 1.11-2 WA scores were based on
+    untransformed data even when data were transformed in analysis, but
+    since then the similar transformation will be used in WA scores as
+    in ordination.}
   \item{x}{Dissimilarity matrix for \code{\link[MASS]{isoMDS}} or \code{plot}
     object.} 
   \item{choices}{Axes shown.}
@@ -236,7 +241,13 @@
   tries to reconstruct the used dissimilarities with original data
   transformation and possible \code{\link{stepacross}}.
 }
-
+\section{Warning}{
+  The calculation of \code{\link{wascores}} for species was changed in
+  \pkg{vegan} version 1.12-6. They are now based on the community data
+  transformed similarly as in the ordination. Previously the species
+  scores always were based on the original data. You can re-establish
+  the old behaviour with argument \code{old.wa = TRUE}.
+}
 \seealso{\code{\link[MASS]{isoMDS}}, \code{\link{decostand}},
   \code{\link{wisconsin}}, 
   \code{\link{vegdist}}, \code{\link{rankindex}}, \code{\link{stepacross}},