[Vegan-commits] r2603 - in pkg/vegan: . inst man

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

Author: jarioksa
Date: 2013-09-05 12:01:18 +0200 (Thu, 05 Sep 2013)
New Revision: 2603

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/MDSrotate.Rd
Log:
Document MDSrotate changes and version to 2.1-35

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2013-09-05 10:00:25 UTC (rev 2602)
+++ pkg/vegan/DESCRIPTION	2013-09-05 10:01:18 UTC (rev 2603)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 2.1-34
-Date: August 28, 2013
+Version: 2.1-35
+Date: September 5, 2013
 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/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2013-09-05 10:00:25 UTC (rev 2602)
+++ pkg/vegan/inst/ChangeLog	2013-09-05 10:01:18 UTC (rev 2603)
@@ -2,8 +2,17 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 2.1-34 (opened August 28, 2013)
+Version 2.1-35 (opened September 5, 2013)
 
+	* MDSrotate: can now rotate a solution to more than one vector,
+	provided that the number of dimensions is higher than the number
+	of vectors. Because fitted vectors usually are correlated, only
+	the first vector is aligned to dimension 1, but second vector and
+	further are oblique to the corresponding axis. In any case they
+	will have zero correlation to all subsequent dimensions.
+
+Version 2.1-34 (closed September 5, 2013)
+
 	* DESCRIPTION: dependent on R >= 2.14.0.
 	
 	* DESCRIPTION, vignettes: R 3.0.2-to-be checks with --as-cran

Modified: pkg/vegan/man/MDSrotate.Rd
===================================================================
--- pkg/vegan/man/MDSrotate.Rd	2013-09-05 10:00:25 UTC (rev 2602)
+++ pkg/vegan/man/MDSrotate.Rd	2013-09-05 10:01:18 UTC (rev 2603)
@@ -19,8 +19,10 @@
  \item{object}{ A result object from \code{\link{metaMDS}} or
     \code{\link{monoMDS}}.}
 
-  \item{vec}{ A continuous environmental variable (vector of the same
-    length as the number of points).}
+  \item{vec}{ A continuous environmental variable or a matrix of such
+    variables. The number of variables must be lower than the number of
+    dimensions, and the solution is rotated to these variables in the
+    order they appear in the matrix.}
 
   \item{na.rm}{ Remove missing values from the continuous variable
     \code{vec}.}
@@ -29,14 +31,22 @@
 
 }
 
-\details{ The orientation and rotation are undefined in
-  multidimensional scaling.  Functions \code{\link{metaMDS}} and
-  \code{\link{metaMDS}} can rotate their solutions to principal
-  components so that the dispersion of the points is highest on the
-  first dimension. Sometimes a different rotation is more intuitive,
-  and \code{MDSrotate} allows rotation of the result so that the first
-  axis is parallel to a given external variable.  
-}
+\details{ The orientation and rotation are undefined in multidimensional
+  scaling.  Functions \code{\link{metaMDS}} and \code{\link{metaMDS}}
+  can rotate their solutions to principal components so that the
+  dispersion of the points is highest on the first dimension. Sometimes
+  a different rotation is more intuitive, and \code{MDSrotate} allows
+  rotation of the result so that the first axis is parallel to a given
+  external variable or two first variables are completely in a
+  two-dimensional plane etc. If several external variables are supplied,
+  they are applied in the order they are in the matrix. First axis is
+  rotated to the first supplied variable, and the second axis to the
+  second variable. Because variables are usually correlated, the second
+  variable is not usually aligned with the second axis, but it is
+  uncorrelated to later dimensions. There must be at least one free
+  dimension: the number of external variables must be lower than the
+  number of dimensions, and all used environmental variables are
+  uncorrelated with that free dimension.}
 
 \value{ Function returns the original ordination result, but with
   rotated scores (both site and species if available), and the