[Vegan-commits] r535 - in branches/1.15: R inst

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

Author: jarioksa
Date: 2008-10-29 08:36:48 +0100 (Wed, 29 Oct 2008)
New Revision: 535

Modified:
   branches/1.15/R/nesteddisc.R
   branches/1.15/R/print.nesteddisc.R
   branches/1.15/R/wcmdscale.R
   branches/1.15/inst/ChangeLog
Log:
merged r526 (typo in wcmdscale rsult) and r533 (tie warning in nesteddisc) to branches/1.15

Modified: branches/1.15/R/nesteddisc.R
===================================================================
--- branches/1.15/R/nesteddisc.R	2008-10-27 13:54:18 UTC (rev 534)
+++ branches/1.15/R/nesteddisc.R	2008-10-29 07:36:48 UTC (rev 535)
@@ -2,11 +2,11 @@
 function(comm)
 {
     comm <- ifelse(comm > 0, 1, 0)
-    j <- rev(order(colSums(comm)))
+    rs <- colSums(comm)
+    j <- rev(order(rs))
     comm <- comm[, j] 
     Ad <- sum(comm[col(comm) <= rowSums(comm)] == 0)
-    out <- list(statistic=Ad)
+    out <- list(statistic=Ad, ties = length(unique(rs)) < length(rs))
     class(out) <- "nesteddisc"
     out
 }
-

Modified: branches/1.15/R/print.nesteddisc.R
===================================================================
--- branches/1.15/R/print.nesteddisc.R	2008-10-27 13:54:18 UTC (rev 534)
+++ branches/1.15/R/print.nesteddisc.R	2008-10-29 07:36:48 UTC (rev 535)
@@ -2,6 +2,7 @@
 function(x, ...)
 {
     cat("nestedness discrepancy:", x$statistic, "\n")
+    if(x$ties)
+        cat("There are tied column frequencies: result can depend on input order\n")
     invisible(x)
 }
-

Modified: branches/1.15/R/wcmdscale.R
===================================================================
--- branches/1.15/R/wcmdscale.R	2008-10-27 13:54:18 UTC (rev 534)
+++ branches/1.15/R/wcmdscale.R	2008-10-29 07:36:48 UTC (rev 535)
@@ -31,10 +31,9 @@
     rownames(points) <- rownames(m)
     if (eig || x.ret || add) {
         out <- list(points = points, eig = if (eig) e$values[-n],
-                    x = if (x.ret) m, ac = NA, GOF = NA, weigths = w)
+                    x = if (x.ret) m, ac = NA, GOF = NA, weights = w)
         class(out) <- "wcmdscale"
     }
     else out <- points
     out
 }
-

Modified: branches/1.15/inst/ChangeLog
===================================================================
--- branches/1.15/inst/ChangeLog	2008-10-27 13:54:18 UTC (rev 534)
+++ branches/1.15/inst/ChangeLog	2008-10-29 07:36:48 UTC (rev 535)
@@ -5,6 +5,10 @@
 
 Version 1.15-1 (opened October 10, 2008)
 
+	* merged r533: warning of ties in nesteddisc().
+
+	* merged r526: typo in wcmdscale() result object item.
+
 	* copied head/tail of summary.cca.
 
 	* merged r516, 519, 521: radfit fixes for 0..2 species