Hi Elaine,

Maybe I'm missing something here.  So you would like each sample point in
the NMDS plot to be labeled by the 'site number', with the dune dataset
that is the rowname.  The code you posted does that.  I do not get the
number as (site number*site number)/2.  If that were the case site 20 would
be labeled (20*20)/2= '200', and I don't see that, I get '20'.  If you
wanted to be more explicit in the labels you could add something like.

text(NMDS, display = 'sites', labels=paste("site", rownames(dune), sep="_"))

Sorry if I misunderstood the issue. If you are getting different behavior
from the same code that's odd, perhaps check what version of R and vegan
you are using.

Cheers,
Alex


On Sun, Sep 8, 2013 at 3:00 AM, <r-sig-ecology-request@r-project.org> wrote:

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>    1. NMDS dot number=site number (vegan) (Elaine Kuo)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 7 Sep 2013 21:19:05 +0800
> From: Elaine Kuo <elaine.kuo.tw@gmail.com>
> To: "<r-sig-ecology@r-project.org>" <r-sig-ecology@r-project.org>
> Subject: [R-sig-eco] NMDS dot number=site number (vegan)
> Message-ID:
>         <CAGJhoDz8ZnG9BmxiZvuccWERJPyP4UCTTGDY=
> 4OVJGK4tep8Rg@mail.gmail.com>
> Content-Type: text/plain
>
> Dear list,
>
>
> This is Elaine, a postgraduate studying bird distributions in East Asia.
>
> I would like to ask how to generate NMDS graphs with the dot number
> equal to the site number, using R vegan.
>
> I read the vegan manual and copied the example code metaMDS.
> (The code is as below)
> However, the resulting NMDS graph has the dot number as
> (site number*site number)/2.
>
> Thank you in advance.
>
> Code
> library(MASS)
>   library(vegan)
>   NMDS  <-  metaMDS(dune,k=2, distfun  =  betadiver,  distance  =
>  "sim",trymax=100,zerodist="add")
>   plot(NMDS,  type  =  "n")
>
>   # species as symbols
>   points(NMDS, display = 'species', pch = '+', cex = 0.6)
>
>   # sites as text
>   text(NMDS, display = 'sites')
>
> Elaine
>
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>
>
>
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-- 
Alex Thomas

Temporary Employee
Knight Lab
University of Colorado, Boulder

Affiliate Researcher
Department of Ecology, Earth Sciences Division
Lawrence Berkeley National Laboratory

Independent Contractor
U.S. Geological Survey
Forest and Rangeland Ecosystem Science Center
Cascadia Field Station

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