[R] procrustes (vegan) plot of residual differences

[Peter Ehlers]

On 2012-05-23 08:19, Juan Antonio Balbuena wrote:
>
>     Hello
>     This is a simple question but I couldn't google an answer.
>     In   the   procrustes   function   of  the  vegan  package,  one  uses
>     plot(procrustes_object,  kind=2)  to  obtain  a  plot  of the residual
>     differences. For instance:
> data(varespec)
> vare.dist<- vegdist(wisconsin(varespec))
> library(MASS)
> mds.null<- isoMDS(vare.dist, tol=1e-7)
> mds.alt<- isoMDS(vare.dist, initMDS(vare.dist), maxit=200, tol=1e-7)
> vare.proc<- procrustes(mds.alt, mds.null)
> plot(vare.proc, kind=2)
>
>     In the resulting plot 3  horizontal lines (1 continuous and 2 dashed) are
>     displayed and I was wondering what they actually represent. (Perhaps mean
>     residual +/- 95% CI ?).
>     I would also like to know whether it is possible to customize the plot by,
>     for instance, removing the lines, changing their appearance, or making them
>     represent something else, such as mean +/- SD.
>     Thank you very much for your attention.
>     Juan Antonio Balbuena

If you take a look at the bottom of vegan:::plot.procrustes,
you will see that the lines represent the (type 7) quartiles
of the residuals of vare.proc and that these are plotted with
a single abline() call. To modify the plot, you could make
a (renamed) copy, comment out the abline() bit and then add
the lines of your choice. But, really, it's just a plot of
the residuals with type="h", so why not just create your
own plot?

Peter Ehlers

>
>     --
>
>     Dr. Juan A. Balbuena
>     Marine Zoology Unit
>     Cavanilles Institute of Biodiversity and Evolutionary Biology
>     University of
>     Valencia
>     [1]http://www.uv.es/~balbuena
>     P.O. Box 22085
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>     46071 Valencia, Spain
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>     e-mail: [4]j.a.balbuena at uv.es    tel. +34 963 543 658    fax +34 963 543 733
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> References
>
>     1. http://www.uv.es/%7Ebalbuena
>     2. http://www.uv.es/cavanilles/zoomarin/index.htm
>     3. http://cetus.uv.es/mullpardb/index.html
>     4. mailto:j.a.balbuena at uv.es
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