[R-sig-eco] adjusting for empty rows in metaMDS

[Tom_Philippi at nps.gov]

Tracy--

What, praytell, do you want dissimilarities involving empty plots to be?
Is the dissimilarity metric you are using even defined if one object has
zero species?  Does that make sense ecologically?

Then, I suspect that your actual computational problem is that you have
more than one plot with no species, so you have absolutely identical plots.
See fortunes::fortune(163), and possibly search the R-sig-eco archives for
that thread.

I hope that this points you in the right direction ...

Tom 2

-------------------------------------------
Tom Philippi, Ph.D.
Quantitative Ecologist
Inventory and Monitoring Program
National Park Service
c/o Cabrillo National Monument
1800 Cabrillo Memorial Dr
San Diego, CA 92106
(619) 523-4576
Tom_philippi at NPS.gov
http://science.nature.nps.gov/im/monitor
-------------------------------------------



                                                                           
             "Pinney, Tracy A"                                             
             <Tracy_Pinney at bay                                             
             lor.edu>                                                   To 
             Sent by:                  "r-sig-ecology at r-project.org"       
             r-sig-ecology-bou         <r-sig-ecology at r-project.org>       
             nces at r-project.or                                          cc 
             g                                                             
                                                                   Subject 
                                       [R-sig-eco] adjusting for empty     
             01/25/2012 03:07          rows in metaMDS                     
             PM CST                                                        
                                                                           
                                                                           
                                                                           
                                                                           
                                                                           




Hello,

   I am trying to use metaMDS (or isoMDS) for a community data set with 10
species.  However, I have several sites with no species present (empty
rows), and this seems to present a problem in the dissimilarity matrix in
the form of missing values.  Does anyone have suggestions on how to deal
with this?  Is it appropriate to create a dummy variable in the original
community matrix?  If so, what is the best way to do this?  Thanks for any
help.



Tracy Pinney



PhD candidate

Department of Biology

Baylor University

One Bear Place 97388-7388

Waco, TX  76798-7388


             [[alternative HTML version deleted]]

_______________________________________________
R-sig-ecology mailing list
R-sig-ecology at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology