[Vegan-commits] r550 - in pkg: R inst

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

Author: jarioksa
Date: 2008-11-07 20:55:59 +0100 (Fri, 07 Nov 2008)
New Revision: 550

Modified:
   pkg/R/plot.cca.R
   pkg/inst/ChangeLog
Log:
plot.cca: neat plotting when input data has no row names

Modified: pkg/R/plot.cca.R
===================================================================
--- pkg/R/plot.cca.R	2008-11-02 20:38:00 UTC (rev 549)
+++ pkg/R/plot.cca.R	2008-11-07 19:55:59 UTC (rev 550)
@@ -6,6 +6,11 @@
     g <- scores(x, choices, display, scaling, const)
     if (!is.list(g)) 
         g <- list(default = g)
+    ## Take care that there are names
+    for (i in 1:length(g)) {
+        rownames(g[[i]]) <- rownames(g[[i]], do.NULL = FALSE,
+                                     prefix = substr(names(g)[i], 1, 3))
+    }
     if (!is.null(g$centroids)) {
         if (is.null(g$biplot)) 
             g$biplot <- scores(x, choices, "bp", scaling)

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2008-11-02 20:38:00 UTC (rev 549)
+++ pkg/inst/ChangeLog	2008-11-07 19:55:59 UTC (rev 550)
@@ -4,15 +4,19 @@
 
 Version 1.16-4 (opened November 1, 2008)
 
-    * permatwsap: quasiswap method is implemented for count data
-    based on the idea of Carsten Dormann in the swap.web::bipartite
-    function. This takes a random matrix first with same row and
-    column sums as the original (via r2dtable), and than restores
-    the original matrix fill through steps of swaping 2x2
-    submatrices. The current R code is slow.
+	* plot.cca: takes care that plotted items have non-NULL names that
+	plot neatly.  This was already take care of with formula
+	interface, but now it should work also in other cases in plots.
+	
+	* permatwsap: quasiswap method is implemented for count data based
+	on the idea of Carsten Dormann in the swap.web::bipartite
+	function. This takes a random matrix first with same row and
+	column sums as the original (via r2dtable), and than restores the
+	original matrix fill through steps of swaping 2x2 submatrices. The
+	current R code is slow.
 
-    * permatfull: when both cells and individuals are shuffled,
-    the matrix fill remains constant.
+	* permatfull: when both cells and individuals are shuffled, the
+	matrix fill remains constant.
 
 	* nesteddisc: replaced with a new function that orders tied
 	columns to minimize the discrepancy statistic. If there are <=7