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-requ...@r-project.org> wrote:
> Send R-sig-ecology mailing list submissions to
> r-sig-ecology@r-project.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> or, via email, send a message with subject or body 'help' to
> r-sig-ecology-requ...@r-project.org
>
> You can reach the person managing the list at
> r-sig-ecology-ow...@r-project.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of R-sig-ecology digest..."
>
>
> Today's Topics:
>
> 1. NMDS dot number=site number (vegan) (Elaine Kuo)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 7 Sep 2013 21:19:05 +0800
> From: Elaine Kuo <elaine.kuo...@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=
> 4ovjgk4tep...@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
>
> [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>
>
> End of R-sig-ecology Digest, Vol 66, Issue 2
> ********************************************
>
--
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
[[alternative HTML version deleted]]
_______________________________________________
R-sig-ecology mailing list
R-sig-ecology@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
