[R] procrustes (vegan) plot of residual differences
Peter Ehlers
ehlers at ucalgary.ca
Wed May 23 21:17:58 CEST 2012
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
> [2]http://www.uv.es/cavanilles/zoomarin/index.htm
> 46071 Valencia, Spain
> [3]http://cetus.uv.es/mullpardb/index.html
> 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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