[Vegan-commits] r1246 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2010-07-22 14:47:27 +0200 (Thu, 22 Jul 2010)
New Revision: 1246

Modified:
   pkg/vegan/R/ordigrid.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/ordihull.Rd
Log:
ordigrid can use different lines for levels and replicates

Modified: pkg/vegan/R/ordigrid.R
===================================================================
--- pkg/vegan/R/ordigrid.R	2010-07-21 12:43:59 UTC (rev 1245)
+++ pkg/vegan/R/ordigrid.R	2010-07-22 12:47:27 UTC (rev 1246)
@@ -1,11 +1,14 @@
 "ordigrid" <-
-    function (ord, levels, replicates, display = "sites", ...) 
+    function (ord, levels, replicates, display = "sites", lty=c(1,1), col=c(1,1),
+              lwd = c(1,1), ...) 
 {
     pts <- scores(ord, display = display, ...)
     npoints <- nrow(pts)
     gr <- gl(levels, replicates, npoints)
-    ordisegments(pts, groups = gr, ...)
+    ordisegments(pts, groups = gr,  lty = lty[1], col = col[1],
+                 lwd = lwd[1], ...)
     gr <- gl(replicates, 1, npoints)
-    ordisegments(pts, groups = gr, ...)
+    ordisegments(pts, groups = gr, lty = lty[2], col = col[2],
+                 lwd = lwd[2], ...)
     invisible()
 }

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-07-21 12:43:59 UTC (rev 1245)
+++ pkg/vegan/inst/ChangeLog	2010-07-22 12:47:27 UTC (rev 1246)
@@ -4,7 +4,7 @@
 
 Version 1.18-8 (opened July 19, 2010)
 
-	* DEPENDENCE: does not suggest package 'ellipse'.
+	* DESCRIPTION: does not suggest package 'ellipse'.
 
 	* FAQ: new entry on negative or non-numeric data, and updates of
 	variance explained by ordination.
@@ -22,12 +22,15 @@
 	* decorana: change order of data checks so that non-numeric data
 	is detected (by rowSums()) before checking negative data entries.
 
+	* ordigrid: arguments lty, col and lwd to use different lines for
+	levels and replicate of the grid.
+
 Version 1.18-7 (closed July 19, 2010)
 
 	* new version opened with the release of vegan_1.17-3.
 
-	* veganCovEllipse: new internal for drawing covariance ellipses
-	(to be used both with ordiellipse() and plot.MOStest()).
+	* veganCovEllipse: new internal function for drawing covariance
+	ellipses (to be used both with ordiellipse() and plot.MOStest()).
 
 	* ordiellipse: uses veganCovEllipse.
 	

Modified: pkg/vegan/man/ordihull.Rd
===================================================================
--- pkg/vegan/man/ordihull.Rd	2010-07-21 12:43:59 UTC (rev 1245)
+++ pkg/vegan/man/ordihull.Rd	2010-07-22 12:47:27 UTC (rev 1246)
@@ -34,7 +34,8 @@
          show.groups, startmark, label = FALSE, ...)
 ordisegments(ord, groups, levels, replicates, display = "sites",
          show.groups, label = FALSE, ...)
-ordigrid(ord, levels, replicates, display = "sites",  ...)
+ordigrid(ord, levels, replicates, display = "sites",  lty = c(1,1), 
+         col = c(1,1), lwd = c(1,1), ...)
 ordicluster(ord, cluster, prune = 0, display = "sites",
          w = weights(ord, display), ...)
 }
@@ -82,6 +83,8 @@
     2df. }
   \item{cluster}{Result of hierarchic cluster analysis, such as
     \code{\link{hclust}} or \code{\link[cluster]{agnes}}.}
+  \item{lty, col, lwd}{Line type, line colour and line width used for 
+    \code{level}s and \code{replicate}s in \code{ordigrid}.}
   \item{prune}{Number of upper level hierarchies removed from the
     dendrogram. If \code{prune} \eqn{>0}, dendrogram will be
     disconnected.}