[Vegan-commits] r608 - in pkg/vegan: . R inst man

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

Author: jarioksa
Date: 2008-12-04 11:08:52 +0100 (Thu, 04 Dec 2008)
New Revision: 608

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/R/plot.rad.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/radfit.Rd
Log:
plot.rad gains argument log='y' so that log scales can be set on axes

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2008-12-04 05:35:37 UTC (rev 607)
+++ pkg/vegan/DESCRIPTION	2008-12-04 10:08:52 UTC (rev 608)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.16-5
-Date: November 25, 2008
+Version: 1.16-6
+Date: December 4, 2008
 Author: Jari Oksanen, Roeland Kindt, Pierre Legendre, Bob O'Hara, Gavin L. Simpson, 
    Peter Solymos, M. Henry H. Stevens, Helene Wagner  
 Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>

Modified: pkg/vegan/R/plot.rad.R
===================================================================
--- pkg/vegan/R/plot.rad.R	2008-12-04 05:35:37 UTC (rev 607)
+++ pkg/vegan/R/plot.rad.R	2008-12-04 10:08:52 UTC (rev 608)
@@ -1,8 +1,8 @@
 "plot.rad" <-
-    function(x, xlab="Rank", ylab="Abundance",  ...)
+    function(x, xlab="Rank", ylab="Abundance", log = "y", ...)
 {
     rnk <- seq(along=x)
-    plot(rnk, x, log="y", xlab=xlab, ylab=ylab, ...)
+    plot(rnk, x, log=log, xlab=xlab, ylab=ylab, ...)
     out <- list(species = cbind(rnk, x))
     class(out) <- "ordiplot"
     invisible(out)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2008-12-04 05:35:37 UTC (rev 607)
+++ pkg/vegan/inst/ChangeLog	2008-12-04 10:08:52 UTC (rev 608)
@@ -2,18 +2,24 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.16-5 (opened Nov 25, 2008)
+Version 1.16-6
 
-    * adipart: new implementation of adipart is now ready to be
-    released (needs some testing). Summary and plot methods have
-    been removed. The new implementation is based on oecosimu
-    and quantitative null model settings vis permat.conrol.
-    It contain only traditional diversity indices. More features
-    will be added later, gradually.
+	* plot.rad: gained argument log = "y", allowing log = "xy" so that
+	Zipf model is a straight line, or log = "" with arithmetic
+	scales.  Not (yet) implemented for Lattice alternatives.
+	
+Version 1.16-5 (closeed Dec 4, 2008)
 
-    * plot.nestedtemp: label argument accepts a vector of length 2
-    with elements for row and column labels, respectively.
+	* adipart: new implementation of adipart is now ready to be
+	released (needs some testing). Summary and plot methods have been
+	removed. The new implementation is based on oecosimu and
+	quantitative null model settings via permat.control.  It contains
+	only traditional diversity indices. More features will be added
+	later, gradually.
 
+	* plot.nestedtemp: label argument accepts a vector of length 2
+	with elements for row and column labels, respectively.
+
 	* mite.rda: Oribatid mites got species names (from Pierre
 	Legendre's web pages).
 

Modified: pkg/vegan/man/radfit.Rd
===================================================================
--- pkg/vegan/man/radfit.Rd	2008-12-04 05:35:37 UTC (rev 607)
+++ pkg/vegan/man/radfit.Rd	2008-12-04 10:08:52 UTC (rev 608)
@@ -45,7 +45,7 @@
 \method{lines}{radline}(x, ...)
 \method{points}{radline}(x, ...)
 as.rad(x)
-\method{plot}{rad}(x, xlab = "Rank", ylab = "Abundance", ...)
+\method{plot}{rad}(x, xlab = "Rank", ylab = "Abundance", log = "y", ...)
 }
 
 \arguments{
@@ -70,6 +70,11 @@
   \item{type}{Type of the plot, \code{"b"} for plotting both observed points
     and fitted lines, \code{"p"} for only points, \code{"l"} for only
     fitted lines, and \code{"n"} for only setting the frame. }
+  \item{log}{Use logarithmic scale for given axis. The default
+    \code{log =" y"} gives the traditional plot in community ecology
+    where the pre-emption model is a straight line, and with
+    \code{log = "xy"} Zipf model is a straight line. With
+    \code{log = ""} both axes are in the original arithmetic scale.}
   \item{\dots}{Other parameters to functions. }
 }
 \details{
@@ -224,7 +229,10 @@
 plot(mod)
 mod <- radfit(BCI[1,])
 ## Standard plot overlaid for all models
+## Pre-emption model is a line
 plot(mod)
+## log for both axes: Zipf model is a line
+plot(mod, log = "xy")
 ## Lattice graphics separately for each model
 radlattice(mod)
 # Take a subset of BCI to save time and nerves