[Vegan-commits] r2828 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2014-01-07 18:16:40 +0100 (Tue, 07 Jan 2014)
New Revision: 2828

Modified:
   pkg/vegan/R/ordiellipse.R
   pkg/vegan/R/veganCovEllipse.R
   pkg/vegan/inst/ChangeLog
Log:
ordiellipse handles two or more points strictly on line

Modified: pkg/vegan/R/ordiellipse.R
===================================================================
--- pkg/vegan/R/ordiellipse.R	2014-01-07 08:38:33 UTC (rev 2827)
+++ pkg/vegan/R/ordiellipse.R	2014-01-07 17:16:40 UTC (rev 2828)
@@ -37,7 +37,7 @@
     kk <- complete.cases(pts)
     for (is in inds) {
         gr <- out[groups == is & kk]
-        if (length(gr) > 2) {
+        if (length(gr) > 1) {
             X <- pts[gr, ]
             W <- w[gr]
             mat <- cov.wt(X, W)

Modified: pkg/vegan/R/veganCovEllipse.R
===================================================================
--- pkg/vegan/R/veganCovEllipse.R	2014-01-07 08:38:33 UTC (rev 2827)
+++ pkg/vegan/R/veganCovEllipse.R	2014-01-07 17:16:40 UTC (rev 2828)
@@ -5,5 +5,8 @@
     theta <- (0:npoints) * 2 * pi/npoints
     Circle <- cbind(cos(theta), sin(theta))
     ## scale, center and cov must be calculated separately
-    t(center + scale * t(Circle %*% chol(cov)))
+    Q <- chol(cov, pivot = TRUE)
+    ## pivot takes care of cases when points are on a line
+    o <- attr(Q, "pivot")
+    t(center + scale * t(Circle %*% Q[,o]))
 }

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2014-01-07 08:38:33 UTC (rev 2827)
+++ pkg/vegan/inst/ChangeLog	2014-01-07 17:16:40 UTC (rev 2828)
@@ -11,6 +11,15 @@
 	be used in an incorrect context". The dots were added in r2765,
 	and now removed.
 
+	* ordiellipse: failed if all points were on a line. Now handles
+	these cases by drawing a line trhough the points, and issuing a
+	warning from chol(): "the matrix is either rank-deficient or
+	indefinite". Earlier we required at least three points for an
+	ellipse, but these could still be on a line and fail. Now we
+	accept two points, and draw the line with a warning. The problem
+	with three points was reported by Paul Bacquet (Louvain,
+	Belgium). 
+
 	* BCI: names checked after http://www.theplantlist.org, but kept
 	the old (alphabetic) order of species. The changes are: Abarema
 	macradenium -> A. macradenia, Apeiba aspera -> A. glabra,