[Vegan-commits] r788 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2009-04-05 08:39:40 +0200 (Sun, 05 Apr 2009)
New Revision: 788

Modified:
   pkg/vegan/R/decostand.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/decostand.Rd
Log:
stressplot(metaMDS(x, dist='gower', trymax=40)) failed due to decostand ...

Modified: pkg/vegan/R/decostand.R
===================================================================
--- pkg/vegan/R/decostand.R	2009-04-04 09:20:59 UTC (rev 787)
+++ pkg/vegan/R/decostand.R	2009-04-05 06:39:40 UTC (rev 788)
@@ -1,5 +1,5 @@
 "decostand" <-
-    function (x, method, MARGIN, range.global, na.rm = FALSE) 
+    function (x, method, MARGIN, range.global, na.rm = FALSE, ...) 
 {
     wasDataFrame <- is.data.frame(x)
     x <- as.matrix(x)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-04-04 09:20:59 UTC (rev 787)
+++ pkg/vegan/inst/ChangeLog	2009-04-05 06:39:40 UTC (rev 788)
@@ -15,7 +15,14 @@
 	* betadisper: Fix bug corrects the way distance to centroid is
 	computed when only one group is present in the data. betadisper 
 	can now also detect if 'd' is Euclidean, zapping zero Eigenvalues. 
-	Bug report and suggested improvements provided by Etienne Laliberté.
+	Bug report and suggested improvements provided by Etienne
+	Laliberté.
+
+	* decostand: added dots to the argument list to pass (ignored)
+	arguments to decostand(). This was done to to fix
+	stressplot(metaMDS(x, dist="gower", trymax=40)), which failed
+	because metaMDSdist/vegdist were passing 'trymax' to decostand()
+	while evaluating "gower" dissimilarity.
 	
 Version 1.16-16 (closed April 2, 2009)
 

Modified: pkg/vegan/man/decostand.Rd
===================================================================
--- pkg/vegan/man/decostand.Rd	2009-04-04 09:20:59 UTC (rev 787)
+++ pkg/vegan/man/decostand.Rd	2009-04-05 06:39:40 UTC (rev 788)
@@ -8,7 +8,7 @@
 methods for community ecologists.
 }
 \usage{
-decostand(x, method, MARGIN, range.global, na.rm=FALSE)
+decostand(x, method, MARGIN, range.global, na.rm=FALSE, ...)
 
 wisconsin(x)
 }
@@ -23,6 +23,7 @@
     subsets of data.  The dimensions of \code{MARGIN} must match with
     \code{x}. }
   \item{na.rm}{Ignore missing values in row or column standardizations.}
+  \item{\dots}{Other arguments to the function (ignored).}
 }
 \details{
   The function offers following standardization methods for community