[Vegan-commits] r2276 - in branches/2.0: inst man

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

Author: jarioksa
Date: 2012-09-10 10:39:28 +0200 (Mon, 10 Sep 2012)
New Revision: 2276

Modified:
   branches/2.0/inst/ChangeLog
   branches/2.0/man/decostand.Rd
   branches/2.0/man/varpart.Rd
Log:
mrege r2267,71: tweak documentation

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2012-09-10 08:28:57 UTC (rev 2275)
+++ branches/2.0/inst/ChangeLog	2012-09-10 08:39:28 UTC (rev 2276)
@@ -4,6 +4,8 @@
 
 Version 2.0-5 (opened June 18, 2012)
 
+	* merge r2271: tweak varpart.Rd. (plot coloured circles).
+	* merge r2267: tweak vegdist.Rd (ref to vegdist).
 	* merge r2260: streamline adonis (internal changes).
 	* merge r2258: protect betadisper against changes in R-devel API.
 	* merge r2254: stylistic in examples of Rd files.

Modified: branches/2.0/man/decostand.Rd
===================================================================
--- branches/2.0/man/decostand.Rd	2012-09-10 08:28:57 UTC (rev 2275)
+++ branches/2.0/man/decostand.Rd	2012-09-10 08:39:28 UTC (rev 2276)
@@ -61,9 +61,10 @@
      to presences, and \code{logbase = Inf} gives the presence/absence
      scaling. Please note this is \emph{not} \eqn{\log(x+1)}{log(x+1)}.
      Anderson et al. (2006) suggested this for their (strongly) modified
-     Gower distance, but the standardization can be used independently
-     of distance indices.
-   }
+     Gower distance (implemented as \code{method = "altGower"} in 
+     \code{\link{vegdist}}), but the standardization can be used 
+     independently of distance indices. 
+  }
   Standardization, as contrasted to transformation, means that the
   entries are transformed relative to other entries.
 

Modified: branches/2.0/man/varpart.Rd
===================================================================
--- branches/2.0/man/varpart.Rd	2012-09-10 08:28:57 UTC (rev 2275)
+++ branches/2.0/man/varpart.Rd	2012-09-10 08:39:28 UTC (rev 2276)
@@ -228,8 +228,12 @@
 # Formula shortcut "~ ." means: use all variables in 'data'.
 mod <- varpart(mite, ~ ., mite.pcnm, data=mite.env, transfo="hel")
 mod
-showvarparts(2)
-plot(mod)
+
+## argument 'bg' is passed to circle drawing, and the following
+## defines semitransparent colours
+col2 <- rgb(c(1,1),c(1,0), c(0,1), 0.3)
+showvarparts(2, bg = col2)
+plot(mod, bg = col2)
 # Alternative way of to conduct this partitioning
 # Change the data frame with factors into numeric model matrix
 mm <- model.matrix(~ SubsDens + WatrCont + Substrate + Shrub + Topo, mite.env)[,-1]