[R-sig-eco] NMS axis variance and legend

[Michael Denslow]

Hi Alida,

> Hello,
>
> I'm doing an NMS, and have decided to try out vegan and do everything
> in R.  In this attempt, I haven't been able to figure out how to get
> the variance explained by each axis, nor the total variation
> explained by the ordination.

It is my understanding that the concept of variance explained by an
axis does not make sense for NMS. In short, this is because an NMS
solution is the entire configuration so you can not look at one axis
alone. Despite this fact, variance explained by an axis is still
frequently reported in the literature and by many software packages.
Others please correct me if I am wrong here.
Measure of fit for NMS is often done with a shepard plot, see ?stressplot.

the other issue I have is how to get a
> legend, because I want to represent different sites in the
> ordination, but the sites are grouped by season in which they were
> sampled in order to look at differences in seasonality.  Therefore I
> would like to have a legend that represent each season by different
> symbols.  I've decided to start using R, so there are still some
> issues I have to figure out and learn the commands and functions to
> do what I need.

Maybe this example, will help with the legend.
library(vegan)
data(dune)
data(dune.env)
mod <- metaMDS(dune)
fig <- plot(mod, type = 'none')
points(fig, 'sites', pch = as.numeric(dune.env$Use))
legend('topleft', legend = c('Hayfield','Haypastu','Pasture'), pch = 1:3)

Also see additional comments by Gavin here.
http://n4.nabble.com/NMDS-Ordination-Graphics-Problem-td1751845.html#a1840305

Hope this helps,
Michael

>
> If you have any suggestions, please let me know,
>
> Thanks in advance,
> Alida
>
>
> ~~~
> Alida Mercado Cárdenas
>
> Ph.D. Candidate, Entomology-Neotropical Environment Option
> McGill University & Smithsonian Tropical Research Institute
>
> http://weevils-n-dreams.blogspot.com/
> ~~~
>
>
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>
>
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-- 
Michael Denslow

I.W. Carpenter Jr. Herbarium [BOON]
Department of Biology
Appalachian State University
Boone, North Carolina U.S.A.
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