Dear Tim,
I wrote a function to do a resampling/procrustes procedure to deal with a quite similar problem. See if the procedure is suitable for you:
Ferro, V. G. ; Melo, A. S. 2011. Diversity of tiger moths in a Neotropical hotspot: determinants of species composition and identification of biogeographic units. Journal of Insect Conservation 15:643-651.


In case so, please send me a private e-mail and I will prepare a more user-friendly version of the function.

Sincerely,
 
Adriano Sanches Melo
Departamento de Ecologia - ICB
Universidade Federal de Goiás - Brazil


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Enviadas: Sábado, 4 de Agosto de 2012 7:00
Assunto: R-sig-ecology Digest, Vol 53, Issue 3

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Today's Topics:

   1. NMDS with varying sampling effort (Tim Meehan)


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Message: 1
Date: Fri, 03 Aug 2012 18:18:40 -0500
From: Tim Meehan <tmeehan@wisc.edu>
To: r-sig-ecology@r-project.org
Subject: [R-sig-eco] NMDS with varying sampling effort
Message-ID: <7680f431145f38.501c1600@wiscmail.wisc.edu>
Content-Type: text/plain; CHARSET=US-ASCII

Hi all,



I am working with butterfly community data (rows=60 study sites, columns=120 species, cells=0 to 1500 individuals counted). I am using the metaMDS function from the vegan package to do NMDS, and then using the envfit function from vegan to link community structure to landscape covariates associated with each study site. 

One shortcoming of this dataset is that survey effort varies across sites, pretty dramatically. For example, the smallest total abundance for any site is 100 individual butterflies and the largest is 12,000. In order to reduce the influence of uneven sampling on the results, I divided the abundance recorded in each cell by the total abundance for the row (this, after a square-root transformation on all abundances to reduce the influence of abundant species). 



I'm not entirely satisfied with this approach for dealing with varying sampling effort, but do not know of another one. Is there a way to deal with this problem using resampling? If so, is there an R package/function already built to deal with this issue?



Thanks,

Tim



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