[Vegan-commits] r1671 - in pkg/vegan: R man

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

Author: jarioksa
Date: 2011-07-02 09:06:02 +0200 (Sat, 02 Jul 2011)
New Revision: 1671

Modified:
   pkg/vegan/R/stressplot.R
   pkg/vegan/man/goodness.metaMDS.Rd
Log:
narrower line for stressplot in LNMDS

Modified: pkg/vegan/R/stressplot.R
===================================================================
--- pkg/vegan/R/stressplot.R	2011-07-02 06:49:46 UTC (rev 1670)
+++ pkg/vegan/R/stressplot.R	2011-07-02 07:06:02 UTC (rev 1671)
@@ -5,8 +5,13 @@
 }
 
 `stressplot.monoMDS` <-
-    function(object, pch, p.col = "blue", l.col = "red", lwd = 2, ...)
+    function(object, pch, p.col = "blue", l.col = "red", lwd, ...)
 {
+    if (missing(lwd))
+        if (object$ngrp > 2)
+            lwd <- 1
+        else
+            lwd <- 2
     ## extract items to plot
     x <- object$diss
     y <- object$dist

Modified: pkg/vegan/man/goodness.metaMDS.Rd
===================================================================
--- pkg/vegan/man/goodness.metaMDS.Rd	2011-07-02 06:49:46 UTC (rev 1670)
+++ pkg/vegan/man/goodness.metaMDS.Rd	2011-07-02 07:06:02 UTC (rev 1671)
@@ -20,14 +20,16 @@
 \arguments{
   \item{object}{A result object from \code{\link{metaMDS}}, 
     \code{\link{monoMDS}} or \code{\link[MASS]{isoMDS}}. }
-  \item{dis}{Dissimilarities.  Rhis should  not used with
+  \item{dis}{Dissimilarities.  This should  not used with
     \code{\link{metaMDS}} or \code{\link{monoMDS}}, but must be used with
     \code{\link[MASS]{isoMDS}}.}
   \item{pch}{Plotting character for points.  Default is dependent on the
     number of points. }
   \item{p.col, l.col}{Point and line colours.}
-  \item{lwd}{Line width.}
-  \item{\dots}{Other parameters to functions, e.g. graphical parameters. }
+  \item{lwd}{Line width. For \code{\link{monoMDS} the default is
+    \code{lwd = 1} if more than two lines are drawn, and \code{lwd =
+    2} otherwise.}
+  \item{\dots}{Other parameters to functions, e.g. graphical parameters.}
 }
 \details{
   Function \code{goodness.metaMDS} finds a goodness of fit statistic for
@@ -54,8 +56,9 @@
   either case, the functions inspect that dissimilarities are
   consistent with current ordination, and refuse to analyse
   inconsistent dissimilarities.  Function \code{goodness.metaMDS} is
-  generic in \code{vegan}, but you must spell its name completely with
-  \code{\link[MASS]{isoMDS}} which has no class.  } 
+  generic in \pkg{vegan}, but you must spell its name completely with
+  \code{\link[MASS]{isoMDS}} which has no class.
+} 
 
 \value{ Function \code{goodness} returns a vector of values. Function
   \code{stressplot} returns invisibly an object with itmes for