[Vegan-commits] r850 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2009-06-02 14:15:27 +0200 (Tue, 02 Jun 2009)
New Revision: 850

Modified:
   pkg/vegan/R/wcmdscale.R
   pkg/vegan/inst/ChangeLog
Log:
wcmdscale: remove zero eigenvalues, keep negative, do not assume that last is zero (bugfix)

Modified: pkg/vegan/R/wcmdscale.R
===================================================================
--- pkg/vegan/R/wcmdscale.R	2009-06-02 08:04:30 UTC (rev 849)
+++ pkg/vegan/R/wcmdscale.R	2009-06-02 12:15:27 UTC (rev 850)
@@ -23,6 +23,11 @@
     m <- t(weight.centre(t(m), w))
     m <- m * sqrt(w) %o% sqrt(w)
     e <- eigen(-m/2, symmetric = TRUE)
+    ## Remove zero eigenvalues, keep negative
+    keep <- abs(e$values) > ZERO
+    e$values <- e$values[keep]
+    e$vectors <- e$vectors[, keep]
+    ## Get number of positive eigenvalues
     if (missing(k))
         k <- sum(e$values > ZERO)
     ev <- e$values[1:k]
@@ -30,7 +35,7 @@
     points <- sweep(points, 2, sqrt(ev), "*")
     rownames(points) <- rownames(m)
     if (eig || x.ret || add) {
-        out <- list(points = points, eig = if (eig) e$values[-n],
+        out <- list(points = points, eig = if (eig) e$values,
                     x = if (x.ret) m, ac = NA, GOF = NA, weights = w)
         class(out) <- "wcmdscale"
     }

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-06-02 08:04:30 UTC (rev 849)
+++ pkg/vegan/inst/ChangeLog	2009-06-02 12:15:27 UTC (rev 850)
@@ -4,6 +4,9 @@
 
 Version 1.16-19 (opened May 14, 2009)
 
+	* wcmdscale: remove zero eigenvalues, keep negative, and do not
+	assume that the last eigenvalue is zero. 
+
 	* RsquareAdj.cca: returns R2, but no adjusted R2 (which is NA). 
 
 	* kendall.global: fixed a bug that caused incorrect counts of ties