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@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 DurÃ¡n 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 
>ZÃ¼ge auffaÃŸt, sie untereinander vergleicht und 
>so auf dem Wege der Analysis den Quellen der 
>GenÃ¼sse nachgeht, die uns das groÃŸe 
>NaturgemÃ¤lde 
>bietet.â€œ 
>Alexander von Humboldt, 1799 
>_______________________________________________ 
>R-sig-ecology mailing list 
>R-sig-ecology@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
____________________________________  
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