Re: [R-sig-eco] predict NMS scores for new samples
Thanks to all for the useful suggestions -- I just wanted to report back on my experience using the code that Dave Roberts refers to below, on his web page. It worked beautifully. I imagine that the utility of this approach would depend on the compositional overlap of the new samples with the old. In the case of the research problem I am working on, there is quite a lot of overlap, and re-burning largely reinforces compositional shifts related to previous fires. Jonathan > From: jari.oksa...@oulu.fi > To: drobe...@montana.edu > Date: Sun, 12 Oct 2014 20:38:53 + > CC: r-sig-ecology@r-project.org > Subject: Re: [R-sig-eco] predict NMS scores for new samples > > > On 12/10/2014, at 23:13 PM, Dave Roberts wrote: > > > 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. > > > It looks like a very good idea to me. > > Cheers, Jari Oksanen > > ___ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] predict NMS scores for new samples
On 12/10/2014, at 23:13 PM, Dave Roberts wrote: > 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. > It looks like a very good idea to me. Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] predict NMS scores for new samples
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 [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- David W. Roberts office 406-994-4548 Professor and Head FAX 406-994-3190 Department of Ecology email drobe...@montana.edu Montana State University Bozeman, MT 59717-3460 ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] predict NMS scores for new samples
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 [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
