[Vegan-commits] r884 - in pkg/vegan: . R inst man

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

Author: jarioksa
Date: 2009-07-04 08:56:07 +0200 (Sat, 04 Jul 2009)
New Revision: 884

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/R/wcmdscale.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/wcmdscale.Rd
Log:
wcmdscale: returns scaled axes with negative eigenvalues

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2009-06-29 06:04:44 UTC (rev 883)
+++ pkg/vegan/DESCRIPTION	2009-07-04 06:56:07 UTC (rev 884)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.16-20
-Date: June 17, 2009
+Version: 1.16-21
+Date: July 4, 2009
 Author: Jari Oksanen, Roeland Kindt, Pierre Legendre, Bob O'Hara, Gavin L. Simpson, 
    Peter Solymos, M. Henry H. Stevens, Helene Wagner  
 Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>

Modified: pkg/vegan/R/wcmdscale.R
===================================================================
--- pkg/vegan/R/wcmdscale.R	2009-06-29 06:04:44 UTC (rev 883)
+++ pkg/vegan/R/wcmdscale.R	2009-07-04 06:56:07 UTC (rev 884)
@@ -27,16 +27,23 @@
     keep <- abs(e$values) > ZERO
     e$values <- e$values[keep]
     e$vectors <- e$vectors[, keep]
-    ## Get number of positive eigenvalues
-    if (missing(k))
+    ## Deweight and scale axes -- also negative
+    points <- sweep(e$vectors, 1, sqrt(w), "/")
+    points <- sweep(points, 2, sqrt(abs(e$values)), "*")
+    rownames(points) <- rownames(m)
+    ## If 'k' not given, find it as the number of positive
+    ## eigenvalues, and also save negative eigenvalues
+    negaxes <- NULL
+    if (missing(k) || k > sum(e$values > ZERO)) {
         k <- sum(e$values > ZERO)
-    ev <- e$values[1:k]
-    points <- sweep(e$vectors[, 1:k, drop=FALSE], 1, sqrt(w), "/")
-    points <- sweep(points, 2, sqrt(ev), "*")
-    rownames(points) <- rownames(m)
+        if (any(e$values < 0))
+            negaxes <- points[, e$values < 0, drop = FALSE]
+    }
+    points <- points[, 1:k, drop=FALSE]
     if (eig || x.ret || add) {
         out <- list(points = points, eig = if (eig) e$values,
-                    x = if (x.ret) m, ac = NA, GOF = NA, weights = w)
+                    x = if (x.ret) m, ac = NA, GOF = NA, weights = w,
+                    negaxes = negaxes)
         class(out) <- "wcmdscale"
     }
     else out <- points

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-06-29 06:04:44 UTC (rev 883)
+++ pkg/vegan/inst/ChangeLog	2009-07-04 06:56:07 UTC (rev 884)
@@ -2,8 +2,14 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Versin 1.16-20 (opened June 17, 2009)
+Version 1.16-21 (opened July 4, 2009)
 
+	* wcmdscale: returns negative eigevalues scaled by
+	sqrt(abs(eigenvalues)) if 'k' is not given or 'k' would include
+	any negative eigenvalue.
+	
+Version 1.16-20 (closed July 4, 2009)
+
 	* new version opened concurrently with the release of vegan 1.15-3
 	on June 17, 2009.
 

Modified: pkg/vegan/man/wcmdscale.Rd
===================================================================
--- pkg/vegan/man/wcmdscale.Rd	2009-06-29 06:04:44 UTC (rev 883)
+++ pkg/vegan/man/wcmdscale.Rd	2009-07-04 06:56:07 UTC (rev 884)
@@ -48,6 +48,9 @@
     \code{eig} is true.}
   \item{x}{the doubly centred and weighted distance matrix if \code{x.ret} is true.}
   \item{weights}{Weights.}
+  \item{negaxes}{A matrix of scores for axes with negative eigenvalues scaled 
+     by the absolute eigenvalues similarly as \code{points}. This is \code{NULL}
+     if there are no negative eigenvalues or \code{k} was specified, and would not     include negative eigenvalues.}
 }
 \references{
   Gower, J. C. (1966)