[Vegan-commits] r1336 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2010-10-18 10:54:50 +0200 (Mon, 18 Oct 2010)
New Revision: 1336

Modified:
   pkg/vegan/R/isomap.R
   pkg/vegan/inst/ChangeLog
Log:
isomap returns only axes with positive eigenvalues

Modified: pkg/vegan/R/isomap.R
===================================================================
--- pkg/vegan/R/isomap.R	2010-10-16 05:24:54 UTC (rev 1335)
+++ pkg/vegan/R/isomap.R	2010-10-18 08:54:50 UTC (rev 1336)
@@ -3,6 +3,14 @@
 {
     dist <- isomapdist(dist, ...)
     out <- cmdscale(dist, k=ndim, eig=TRUE)
+    ## some versions of cmdscale may return NaN points corresponding
+    ## to negative eigenvalues
+    if (any(out$eig < 0)) {
+        out$eig <- out$eig[out$eig > 0]
+        out$points <- out$points[, seq_along(out$eig), drop = FALSE]
+        warning(gettextf("isomap returns only %d axes with positive eigenvalues",
+                         length(out$eig)))
+    }
     npoints <- nrow(out$points)
     net <- matrix(FALSE, nrow=npoints, ncol=npoints)
     net[lower.tri(net)][attr(dist, "net")] <- TRUE 

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-10-16 05:24:54 UTC (rev 1335)
+++ pkg/vegan/inst/ChangeLog	2010-10-18 08:54:50 UTC (rev 1336)
@@ -4,6 +4,8 @@
 
 Versin 1.18-14 (opened October 15, 2010)
 
+	* isomap: returns only axes associated with positive eigenvalues.
+
 	* wcmdscale: give two goodness of fit statistics for 'k' axes: one
 	is for the real part and based on the sum of positive eigenvalues,
 	and second is for all axes and based for the sum of absolute