[Vegan-commits] r2434 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2013-02-13 15:24:23 +0100 (Wed, 13 Feb 2013)
New Revision: 2434

Modified:
   pkg/vegan/R/wcmdscale.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/wcmdscale.Rd
Log:
return full wcmdscale object always with non-default arguments, including weights

Modified: pkg/vegan/R/wcmdscale.R
===================================================================
--- pkg/vegan/R/wcmdscale.R	2013-02-12 14:00:37 UTC (rev 2433)
+++ pkg/vegan/R/wcmdscale.R	2013-02-13 14:24:23 UTC (rev 2434)
@@ -8,6 +8,9 @@
     }
     if (add)
         .NotYetUsed("add")
+    ## Force eig=TRUE if add, x.ret or !missing(w)
+    if(add || x.ret || !missing(w))
+        eig <- TRUE
     ZERO <- sqrt(.Machine$double.eps)
     if (!inherits(d, "dist")) {
         op <- options(warn = 2)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2013-02-12 14:00:37 UTC (rev 2433)
+++ pkg/vegan/inst/ChangeLog	2013-02-13 14:24:23 UTC (rev 2434)
@@ -9,6 +9,12 @@
 
 	* tabasco: a sister function of vegemite() to display a compact
 	community table using heatmap(). 
+
+	* wcmdscale: return a full "wcmdscale" object if any argument is
+	set to non-default value. This also implies that if weights 'w'
+	are set, the result will be full "wcmdscale" object with a
+	"weights" item, instead of a simple matrix with no information
+	about weights used.
 	
 Version 2.1-25 (closed February 11, 2013)
 

Modified: pkg/vegan/man/wcmdscale.Rd
===================================================================
--- pkg/vegan/man/wcmdscale.Rd	2013-02-12 14:00:37 UTC (rev 2433)
+++ pkg/vegan/man/wcmdscale.Rd	2013-02-13 14:24:23 UTC (rev 2434)
@@ -49,10 +49,11 @@
 
   With default options, the function returns only a matrix of scores
   scaled by eigenvalues for all real axes. If the function is called
-  with \code{eig = TRUE} or \code{x.ret = TRUE}, the function returns an
-  object of class \code{"wcmdscale"} with \code{print}, \code{plot},
-  \code{scores}, \code{\link{eigenvals}} and \code{\link{stressplot}}
-  methods, and described in section Value.  }
+  with \code{eig = TRUE} or \code{x.ret = TRUE} or with weights
+  \code{w}, the function returns an object of class \code{"wcmdscale"}
+  with \code{print}, \code{plot}, \code{scores}, \code{\link{eigenvals}}
+  and \code{\link{stressplot}} methods, and described in section Value.
+  }
 
 \value{ If \code{eig = FALSE} and \code{x.ret = FALSE} (default), a
   matrix with \code{k} columns whose rows give the coordinates of the