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procrustes (vegan) plot of residual differences

2 messages · Juan Antonio Balbuena, Peter Ehlers

Juan Antonio Balbuena
# 
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

   --

   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
Peter Ehlers
#
On 2012-05-23 08:19, Juan Antonio Balbuena wrote:
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