[R-sig-eco] different symbols to NMDS graph: it works PARTIALLY!??!?

cristabel.duran at waldbau.uni-freiburg.de cristabel.duran at waldbau.uni-freiburg.de
Thu Jan 13 11:13:38 CET 2011


Hi Jari abd Marcelino,

I'm embarrassed......(flushed face).
It was the missing blank!

Thanks a lot!
and have a nice day!
Cristabel.


 On Thu, 13 Jan 2011 11:51:42 +0200
 Jari Oksanen <jari.oksanen at oulu.fi> wrote:
> On 13/01/11 11:03 AM,
> "cristabel.duran at waldbau.uni-freiburg.de"
> <cristabel.duran at waldbau.uni-freiburg.de> wrote:
> 
> > Hola Marcelino,
> > 
> > I did now what you suggested,
> > the lengths of dim(ScoresNMDS) [1] and
> > length(pos$for_pos_anl) are the same.
> > and all the three categories exits in the vector...
> > I still do not find the solution for the problem.
> > 
> Cristabel,
> 
> Do not argue with computers: you'll lose. If the computer
> doesn't find an
> item, it doesn't exist. Computers are more pedantic than
> we humans, and they
> are correct. It may happen, for instance, that the name
> of your item is
> "forest " (note the blank), and then there is no "forest"
> (note the missing
> blank). It is rather easy to see what you get with
> 
> ScoresNMDS[pos$for_pos_anl=="forest",]
> 
> If those three cases you listed in your message are the
> only things that you
> should display, the following (or a variant of this)
> should work if 'metaf'
> is a metaMDS() result, and pos$for_pos_anl is a factor
> where levels are
> ordered as c("border", "gap", "forest"):
>  
> plot(metaf,type="none",choices = c(1,3))
> ## must be a factor
> indx <- as.numeric(pos$for_pos_anl)
> points(metaf,
> display="sites",choices = c(1,3),
>   pch=c(16,17,4)[indx], cex=0.8,
> 
>   col=c("green", "black", "red")[indx] )
> ## these use internal ordering of levels: check
> legend("topleft", levels(pos$for_pos_ani),
> pch=c(16,17,4), col =
> c("green","black", "red"))
> 
> All this is completely unchecked, and probably your
> factor levels are in
> different order and you must change the arguments
> correspondingly.
> 
> Cheers, Jari Oksanen
> 
> 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



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