[Vegan-commits] r1687 - in pkg/vegan: . R inst man

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

Author: jarioksa
Date: 2011-07-23 17:06:10 +0200 (Sat, 23 Jul 2011)
New Revision: 1687

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/R/ordilabel.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/ordilabel.Rd
Log:
ordilabel gained arg 'select'

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2011-07-22 19:05:34 UTC (rev 1686)
+++ pkg/vegan/DESCRIPTION	2011-07-23 15:06:10 UTC (rev 1687)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.90-1
-Date: July 3, 2011
+Version: 1.90-2
+Date: July 23, 2011
 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/R/ordilabel.R
===================================================================
--- pkg/vegan/R/ordilabel.R	2011-07-22 19:05:34 UTC (rev 1686)
+++ pkg/vegan/R/ordilabel.R	2011-07-23 15:06:10 UTC (rev 1687)
@@ -1,5 +1,5 @@
 `ordilabel` <-
-    function(x, display, labels, choices = c(1,2), priority,
+    function(x, display, labels, choices = c(1,2), priority, select,
              cex = 0.8, fill = "white", border = NULL, col = NULL,
              xpd = TRUE, ...)
 {
@@ -8,7 +8,13 @@
     x <- scores(x, choices = choices, display = display, ...)
     if (missing(labels))
         labels <- rownames(x)
+    if (!missing(select)) {
+        x <- x[select, , drop = FALSE]
+        labels <- labels[select]
+    }
     if (!missing(priority)) {
+        if (!missing(select))
+            priority <- priority[select]
         ord <- order(priority)
         x <- x[ord, ]
         labels <- labels[ord]

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-07-22 19:05:34 UTC (rev 1686)
+++ pkg/vegan/inst/ChangeLog	2011-07-23 15:06:10 UTC (rev 1687)
@@ -2,8 +2,12 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.90-1 (opened July 3, 2011)
+Version 1.90-2 (opened July 23, 2011)
 
+	* ordilabel: gained argument 'select'.
+	
+Version 1.90-1 (closed July 23, 2011)
+
 	* cca/rda/capscale support functions: cca/rda/capscale were
 	changed to return zero components instead of NULL for completely
 	aliased constraints (CCA) or saturated models (CA), but several

Modified: pkg/vegan/man/ordilabel.Rd
===================================================================
--- pkg/vegan/man/ordilabel.Rd	2011-07-22 19:05:34 UTC (rev 1686)
+++ pkg/vegan/man/ordilabel.Rd	2011-07-23 15:06:10 UTC (rev 1687)
@@ -10,8 +10,8 @@
   make the most important labels visible.  }
 
 \usage{
-ordilabel(x, display, labels, choices = c(1, 2), priority, cex = 0.8,
-    fill = "white", border = NULL, col = NULL, xpd = TRUE, ...)
+ordilabel(x, display, labels, choices = c(1, 2), priority, select, 
+    cex = 0.8, fill = "white", border = NULL, col = NULL, xpd = TRUE, ...)
 }
 
 \arguments{
@@ -20,10 +20,17 @@
   \item{display}{Kind of scores displayed (passed to
     \code{\link{scores}}). } 
   \item{labels}{Optional text used in plots. If this is not given, the
-    text is found from the ordination object.}
+     text is found from the ordination object.}
+  
   \item{choices}{Axes shown (passed to \code{\link{scores}}). }
-  \item{priority}{Vector of the same length as the number of labels. The
-    items with high priority will be plotted uppermost. }
+  
+  \item{priority}{Vector of the same length as the number of
+    labels. The items with high priority will be plotted uppermost.}
+  
+  \item{select}{Items to be displayed. This can either be a logical
+    vector which is \code{TRUE} for displayed items or a vector of
+    indices of displayed items.}
+  
   \item{cex}{ Character expansion for the text (passed to
     \code{\link{text}}). } 
   \item{fill}{ Background colour of the labels (the \code{col} argument