[R-sig-eco] ordihull does not overlay hulls correctly

[cristabel.duran at waldbau.uni-freiburg.de]

On Wed, 15 Sep 2010 17:11:25 +0300
 Jari Oksanen <jari.oksanen at oulu.fi> wrote:
> On Wed, 2010-09-15 at 15:55 +0200,
> cristabel.duran at waldbau.uni-freiburg.de wrote:
> > Dear r-ecology members,
> > 
> > I am performing a NMDS ordination and I want to add
> hulls
> > with ordihull, to see which sites (vegetation plots)
> > belongs to a factor 
> > of my environmental variable. For that I used:
> > 
> > plot(metaf, display="sites", choices = c(1,2))
> > ordihull(metaf, env$clus, lty = 2, col = "blue",
> > label=TRUE)
> > # metaf is my ordination object.
> > # env$clus is the factor
> > 
> > The hulls vertices coincides with plots.
> > BUT... when plotting metaf chossing axis c(1,3) or
> c(2,3),
> > the vertices do not fit with the plots.
> > The ordination space is plotted with sites but with the
> > hulls corresponding to the ordination plot with axis 1
> and
> > 2.
> 
> Dear Cristabel,
> 
> Did you tell ordihull() about your choices? That is:
> 
> plot(metaf, display="sites", choices = c(1,3))
> ordihull(metaf, env$clus, lty = 2, col = "blue",
> label=TRUE,
> choices=c(1,3))
> 
> To avoid superfluous warnings, you can alternatively do:
> 
> pl <- plot(metaf, display="sites", choices = c(1,3))
> ordihull(pl, env$clus, lty = 2, col = "blue", label=TRUE)
> 
> Vegan ordination plot functions normally return invisibly
> an object of
> class "ordiplot" with plotted scores, and you can use
> this in subsequent
> comments where you add new items to plots. The invisible
> ordination
> object is practical when you have non-standard options in
> plots, like
> choices or scaling, and want to be sure that the same
> settings will be
> used subsequently.
> 
> The "invisible" object means that it is not printed, but
> once you catch
> and save the object, it is visible and usable. More
> details
> in ?invisible.
> 
> Cheers, Jari Oksanen

Cristabel Durán Rangel. PhD Student.
Institute of Silviculture. Faculty of Forest and
Environmental Sciences. University of Freiburg.
Germany
Telf: +49 (761) 203 8604 (ofc) 

„Man lernt die Physiognomie einer Landschaft desto besser
kennen, je genauer man die einzelnen Züge auffaßt, sie
untereinander vergleicht und so auf dem Wege der Analysis
den Quellen der Genüsse nachgeht, die uns das große
Naturgemälde bietet.“
				Alexander von Humboldt, 1799

Dear Jari,

thank you for your fast answer!
I specify in ordihull the choices,
it works! 
Thank you very much!

best regards,
Cristabel.