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

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

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.

thank you for your fast answer! 
Cristabel.

On Thu, 13 Jan 2011 09:47:41 +0100
 Marcelino de la Cruz <marcelino.delacruz at upm.es> wrote:
> Cristabel:
> 
> check that the number of scores equals the length of your
> naming vector, i.e.,
> 
> dim(ScoresNMDS) [1]
> 
> shoud be equal to
> 
> length(pos$for_pos_anl)
> 
> And check also  that the mentioned categories are realy
> present in the vector, e.g.:
> 
> table(pos$for_pos_anl)
> 
> HTH,
> 
> Marcelino
> 
> 
> At 08:50 13/01/2011,
> cristabel.duran at waldbau.uni-freiburg.de wrote:
> >Dear list, I have a problem adding points with different
> symbols to my NMDS ordination graph. I performed a NMDS
> ordination with this vegan function (metaMSD) as follow:
>       metaf <- metaMDS(spp, distance = "bray", k = 3,
> trymax = 1000, wascores = T, autotrasform = F, shrink=T,
> noshare = 1) spp is my species matrix. Then, I want to
> assign different colors and symbols to my plots ("sites")
> according to three categories. These categories are in
> the vector called pos with the categories "gap", "border"
> and "forest". For that I am using the following functions
> and commands:      ScoresNMDS<-scores(metaf)
> plot(metaf,type="none",choices = c(1,3))
> points.metaMDS(ScoresNMDS[pos$for_pos_anl=="border",],
> display="sites",choices = c(1,3), pch=16, cex=0.8,
> col="green")
>
points.metaMDS(ScoresNMDS[pos$for_pos_anl=="gap",],display="sites",choices
> = c(1,3),pch=17, cex=0.8, col="black")
>
points.metaMDS(ScoresNMDS[pos$for_pos_anl=="forest",],display="sites",choices
> = c(1,3), pch=4,col="red",cex=0.8, bg="red") The problem:
> I get a empty ordination graph, were I am able to add the
> points corresponding to the first two categories
> ("border" and "gap"). The strange thing, is that it is
> impossible to add the third category, I get this error
> message:       Error in dimnames(x) <- dn :    length of
> 'dimnames' [1] not equal to array extent Already tried: -
> The length of my explanatory variable (pos) have the same
> length that the species matrix. - Changing the name from
> my open office spreadsheet, in the case there is a
> strange character. - Change colors and symbols. -
> etc...etc. What I also do not understand, is why it works
> for some categories of the same vector and why not for
> the last category. The same happens with ordiellipse and
> ordihull. I would appreciate your help! Thanks in advance
> and have a nice day! Cristabel. 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 Landschaaft 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
> _______________________________________________
> R-sig-ecology mailing list R-sig-ecology at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> 
> ____________________________________
> 
> Marcelino de la Cruz Rot
> Depto. Biologia Vegetal
> EUIT Agricola
> Universidad Politecnica de Madrid
> 
> tel: 34 + 913365435
> ____________________________________  

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