[Vegan-commits] r279 - in pkg: R inst

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

Author: jarioksa
Date: 2008-03-24 07:26:17 +0100 (Mon, 24 Mar 2008)
New Revision: 279

Modified:
   pkg/R/metaMDS.R
   pkg/inst/ChangeLog
Log:
plot.procrustes sometimes failed when two configurations are identical

Modified: pkg/R/metaMDS.R
===================================================================
--- pkg/R/metaMDS.R	2008-03-24 06:01:19 UTC (rev 278)
+++ pkg/R/metaMDS.R	2008-03-24 06:26:17 UTC (rev 279)
@@ -1,7 +1,7 @@
 `metaMDS` <-
     function (comm, distance = "bray", k = 2, trymax = 20, autotransform = TRUE, 
               noshare = 0.1, wascores = TRUE, expand = TRUE, trace = 1,
-              plot = FALSE, previous.best, ...) 
+              plot = FALSE, previous.best, old.wa = FALSE, ...) 
 {
     commname <- deparse(substitute(comm))
     if (inherits(comm, "dist"))
@@ -20,8 +20,11 @@
                       halfchange = (maxdis < 1.1), ...)
     if (is.null(rownames(points))) 
         rownames(points) <- rownames(comm)
-    if (wascores)
+    if (wascores) {
+        if (!old.wa)
+            comm <- eval.parent(parse(text=attr(dis, "commname")))
         wa <- wascores(points, comm, expand = expand)
+    }
     else
         wa <- NA
     out$points <- points

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2008-03-24 06:01:19 UTC (rev 278)
+++ pkg/inst/ChangeLog	2008-03-24 06:26:17 UTC (rev 279)
@@ -4,6 +4,9 @@
 
 Version 1.12-5 (opened Mar 20, 2008)
 
+	* plot.procrustes: could fail if compared configurations were
+	numerically identical.
+
 	* allPerms: New function to enumerate all possible permutations
 	for a given permutation scheme and number of samples. Has 'print'
 	and 'summary' methods.