[R-sig-eco] predict NMS scores for new samples

[Dave Roberts]

Hi Jonathan,

    If you're using the metaMDS function in vegan with the monomds 
engine then it's possible.  I have posted a function (monomds)  at the 
bottom of

http://ecology.msu.montana.edu/labdsv/R/labs/lab9/lab9.html

that shows how to generate a labdsv:::nmds object from vegan's monomds 
function (courtesy of Peter Minchin).  You will have to have package 
vegan loaded to get the monomds FORTRAN code loaded.
Then you can use the function addpoints.nmds (also at the bottom of that 
page) to add points to an existing nmds.

    I'm not convinced that it's a good idea, but I worked with someone 
who needed it to fulfil contract obligations so I wrote it.

Dave

On 10/10/2014 11:07 AM, Jonathan Coop wrote:
> hi all,
>
> I'm wondering if anyone has developed code to predict NMS scores for new sample data, as the NMDS Scores Prediction algorithm functioned in PC-Ord.  I am looking at the effects of multiple fires (reburns) on vegetation composition.  I used an NMS ordination of pre-reburn vegetation samples to characterize vegetation, examine relationships between vegetation and subsequent fire severity, and stratify a re-sampling effort by key vegetation "types".  I'd love to go back now with the post-reburn vegetation samples and see where they fall out in the original ordination space.
>
> Any and all thoughts welcome!
>
> Thanks,
>
> Jonathan Coop
>
>
>
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-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
David W. Roberts                                     office 406-994-4548
Professor and Head                                      FAX 406-994-3190
Department of Ecology                         email droberts at montana.edu
Montana State University
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