[Vegan-commits] r2237 - in pkg/vegan: . R inst man

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

Author: jarioksa
Date: 2012-07-31 13:43:05 +0200 (Tue, 31 Jul 2012)
New Revision: 2237

Added:
   pkg/vegan/R/labels.envfit.R
Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/NAMESPACE
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/envfit.Rd
Log:
add labels.envfit()

The purpose is to allow setting names in plot.envfit(). The first
step is to add labels() function that shows the labels currently
in use. This is usually a list of two vector items, called "vectors"
and "factors", but now this is dropped to a vector if one of these
items is NULL.

This changes NAMESPACE and hence version number goes up.

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2012-07-30 18:56:59 UTC (rev 2236)
+++ pkg/vegan/DESCRIPTION	2012-07-31 11:43:05 UTC (rev 2237)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 2.1-17
-Date: June 18, 2012
+Version: 2.1-18
+Date: July 30, 2012
 Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, 
    Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, 
    M. Henry H. Stevens, Helene Wagner  

Modified: pkg/vegan/NAMESPACE
===================================================================
--- pkg/vegan/NAMESPACE	2012-07-30 18:56:59 UTC (rev 2236)
+++ pkg/vegan/NAMESPACE	2012-07-31 11:43:05 UTC (rev 2237)
@@ -177,6 +177,8 @@
 S3method(hiersimu, formula)
 # identify: graphics
 S3method(identify, ordiplot)
+# labels: base
+S3methods(labels, envfit)
 # lines: graphics
 S3method(lines, humpfit)
 S3method(lines, permat)

Added: pkg/vegan/R/labels.envfit.R
===================================================================
--- pkg/vegan/R/labels.envfit.R	                        (rev 0)
+++ pkg/vegan/R/labels.envfit.R	2012-07-31 11:43:05 UTC (rev 2237)
@@ -0,0 +1,9 @@
+`labels.envfit` <-
+    function(object, ...)
+{
+    out <- list("vectors" = rownames(object$vectors$arrows),
+                "factors" = rownames(object$factors$centroids))
+    if (is.null(out$vectors) || is.null(out$factors))
+        out <- unlist(out, use.names = FALSE)
+    out
+}

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2012-07-30 18:56:59 UTC (rev 2236)
+++ pkg/vegan/inst/ChangeLog	2012-07-31 11:43:05 UTC (rev 2237)
@@ -2,8 +2,13 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 2.1-17 (opened June 18, 2012)
+Version 2.1-18 (opened July 30, 2012)
 
+	* envift: got labels() method that returns the labels used in
+	plot().
+	
+Version 2.1-17 (closed July 30, 2012)
+
 	* New version opened with the CRAN release of vegan 2.0-4 on June
 	18, 2012.
 

Modified: pkg/vegan/man/envfit.Rd
===================================================================
--- pkg/vegan/man/envfit.Rd	2012-07-30 18:56:59 UTC (rev 2236)
+++ pkg/vegan/man/envfit.Rd	2012-07-31 11:43:05 UTC (rev 2237)
@@ -6,6 +6,7 @@
 \alias{factorfit}
 \alias{plot.envfit}
 \alias{scores.envfit}
+\alias{labels.envfit}
 
 \title{Fits an Environmental Vector or Factor onto an Ordination }
 \description{