[Vegan-commits] r608 - in pkg/vegan: . R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Dec 4 11:08:53 CET 2008
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
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