[Vegan-commits] r1673 - in pkg/vegan: . R inst man

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

Author: jarioksa
Date: 2011-07-03 13:25:12 +0200 (Sun, 03 Jul 2011)
New Revision: 1673

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/R/metaMDS.R
   pkg/vegan/R/print.metaMDS.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/metaMDS.Rd
Log:
remove backward compatibility arg 'old.wa' in metaMDS()

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2011-07-03 06:04:36 UTC (rev 1672)
+++ pkg/vegan/DESCRIPTION	2011-07-03 11:25:12 UTC (rev 1673)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.90-0
-Date: June 21, 2011
+Version: 1.90-1
+Date: July 3, 2011
 Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, 
    Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, 
    M. Henry H. Stevens, Helene Wagner  

Modified: pkg/vegan/R/metaMDS.R
===================================================================
--- pkg/vegan/R/metaMDS.R	2011-07-03 06:04:36 UTC (rev 1672)
+++ pkg/vegan/R/metaMDS.R	2011-07-03 11:25:12 UTC (rev 1673)
@@ -1,7 +1,7 @@
 `metaMDS` <-
     function (comm, distance = "bray", k = 2, trymax = 20, autotransform = TRUE, 
               noshare = 0.1, wascores = TRUE, expand = TRUE, trace = 1,
-              plot = FALSE, previous.best, old.wa = FALSE, ...) 
+              plot = FALSE, previous.best,  ...) 
 {
     commname <- deparse(substitute(comm))
     ## metaMDS was written for community data which should be all
@@ -37,10 +37,9 @@
     if (is.null(rownames(points))) 
         rownames(points) <- rownames(comm)
     if (wascores) {
-        if (!old.wa)
-            comm <- eval.parent(parse(text=attr(dis, "commname")))
+        ## transformed data
+        comm <- eval.parent(parse(text=attr(dis, "commname")))
         wa <- wascores(points, comm, expand = expand)
-        attr(wa, "old.wa") <- old.wa
     }
     else
         wa <- NA

Modified: pkg/vegan/R/print.metaMDS.R
===================================================================
--- pkg/vegan/R/print.metaMDS.R	2011-07-03 06:04:36 UTC (rev 1672)
+++ pkg/vegan/R/print.metaMDS.R	2011-07-03 11:25:12 UTC (rev 1673)
@@ -33,8 +33,6 @@
             cat("Species: non-expanded scores ")
         else
             cat("Species: expanded scores ")
-        if(attr(x$species, "old.wa"))
-            cat("based on untransformed data\n")
         else
             cat("based on", sQuote(x$data), "\n")
         

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-07-03 06:04:36 UTC (rev 1672)
+++ pkg/vegan/inst/ChangeLog	2011-07-03 11:25:12 UTC (rev 1673)
@@ -2,8 +2,15 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.90-0 (opened June 21, 2011)
+Version 1.90-1 (opened July 3, 2011)
 
+	* metaMDS: remove argument 'old.wa'. This was introduced in rev280
+	(24/3/08) for backward compatibility when calculating WA scores
+	started to use the same transformed data as the dissimilarities
+	analysed. 
+	
+Version 1.90-0 (closed July 3, 2011)
+
 	* vegan now depends on the permute package for new permutation
 	designs. This initially version strips out all the old "new"
 	permutation code from the R and Rd files, and patches up
@@ -21,7 +28,7 @@
 	updated for monoMDS. Stress type 2 is printed both in monoMDS and
 	metaMDS. stressplot() prints now R2 for monoMDS() results, and
 	docs tell that "linear fit" of stressplot() is related to "stress
-	2". 
+	2".
 
 Version 1.18-33 (closed June 21, 2011)
 

Modified: pkg/vegan/man/metaMDS.Rd
===================================================================
--- pkg/vegan/man/metaMDS.Rd	2011-07-03 06:04:36 UTC (rev 1672)
+++ pkg/vegan/man/metaMDS.Rd	2011-07-03 11:25:12 UTC (rev 1673)
@@ -26,7 +26,7 @@
 \usage{
 metaMDS(comm, distance = "bray", k = 2, trymax = 20, autotransform =TRUE,
         noshare = 0.1, wascores = TRUE, expand = TRUE, trace = 1,
-        plot = FALSE, previous.best, old.wa = FALSE, ...)
+        plot = FALSE, previous.best,  ...)
 \method{plot}{metaMDS}(x, display = c("sites", "species"), choices = c(1, 2),
      type = "p", shrink = FALSE,  ...)
 \method{points}{metaMDS}(x, display = c("sites", "species"),
@@ -71,11 +71,6 @@
   \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.}
@@ -268,12 +263,6 @@
   its NMDS engine till version 1.18-28, when this was replaced with
   the \code{\link{monoMDS}} function. You can set argument
   \code{engine} to select the old engine.
-
-  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{monoMDS}} (and \code{\link[MASS]{isoMDS}}), 
   \code{\link{decostand}},