Dear Gavin and Jari:

Thank you both for your responses. I greatly appreciate it.

I have provided more information below, which I hope is helpful in making
what I am looking for clear. The gradient is a single variable and can be
conceptualized as continuous. Here are two examples of the "appearance" of
the plots I mean, i.e., figures that look like "ball and stick-like" plots
of abundance vs. a gradient.

a) Vellend, M. 2008. Oikos, 117: 1075 - 1085.

Figure 3. (top panels: page 1080). Ignore the genotype and
facilitation/competition dual niche axes parts. I am just interested in
plotting species versus a single environmental gradient, but with a similar
look to these figures. Notice the y-axis is final abundance, which is fine
(a  plot of relative or final abundance on the y-axis is fine).

b) Gravel et al. 2006. Ecology Letters, 9: 399-409.

Figure 4 (left panel: a through d). This shows species relative abundance
(positioned along x-axis by rank according to niche optima) versus niche
position along the environmental gradient. I was trying to describe this
figure earlier.

Thank you again for your time and consideration,
Laura



On Tue, Sep 14, 2010 at 1:40 AM, Jari Oksanen <jari.oksanen@oulu.fi> wrote:

> On 12/09/10 05:24 AM, "Laura S" <leslaura@gmail.com> wrote:
>
> > Dear all:
> >
> > I am interested in plotting species relative abundance versus niche
> position
> > along an environmental gradient. I would like the species' position along
> > the the x-axis (environment gradient position) to be ranked according to
> > each species' niche optima. I have seen this type of plot in
> publications,
> > but I am not sure how to make a nice plot in R.
> >
> Laura,
>
> Just like Gav, I don't know what you want to achieve. However, package
> gravy
> (that was intended to put some meat in vegan) contains functions
> boxgradient() and gaussgradient(), and there is a slim change this is what
> you wanted to have. The gravy package is experimental, and not yet
> released,
> but it is available from http://vegan.r-forge.r-project.org/. You can
> automatically install the package on the command line (provided you have
> privileges to install packages) using
>
> install.packages("gravy", repos="http://r-forge.r-project.org")
>
> or selecting the repository address in the GUI installer.
>
> The package is unreleased and experimental, and there may be rough edges.
> Proceed with care.
>
> Cheers, Jari Oksanen
>
>


-- 
" Genius is the summed production of the many with the names of the few
attached for easy recall, unfairly so to other scientists"

- E. O. Wilson (The Diversity of Life)

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