procrustes (vegan) plot of residual differences
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
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