[R-sig-eco] NMDS with varying sampling effort

[Tim Meehan]

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