R help - May 2012 - procrustes (vegan) plot of residual differences

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
   ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
   NOTE! For shipments by EXPRESS COURIER use the following street address:
   C/ Catedr??tico Jos?? Beltr??n 2, 46980 Paterna (Valencia), Spain.
   ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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

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
>     ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>     NOTE! For shipments by EXPRESS COURIER use the following street
address:
>     C/ Catedr??tico Jos?? Beltr??n 2, 46980 Paterna (Valencia), Spain.
>     ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> 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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