For an excellent head start on issues related to rarefaction, sampling curves and richness estimation, see these:
Colwell, R. K., and J. A. Coddington. 1994. Estimating terrestrial biodiversity through extrapolation. Philosophical Transactions of the Royal Society of London-B 345:101-118. Gotelli, N. J., and R. K. Colwell. 2001. Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecology Letters 4:379-391. Dan Gruner At 08:38 AM 1/4/2007, Gareth Russell wrote: >Bonnie, > >I am not sure you quite understand rarefaction. First, there are >individual-based and sample- >based versions. I'm guessing you mean individual based, as >sample-based version also take inter- >sample (i.e., usually spatial) heterogeneity into account. > >Individual-based rarefaction simply tells you the number of species >you would expect to get if you >took a real sample and extracted a smaller subsample at random. It >is used in the context of >uneven sample sizes, normally as a way to to standardize species >RICHNESS estimates to a >constant sample size. For example, if you have samples of 100, 150 >and 200 individuals from >each of three locations AND the difference is due to your sampling >effort, rather than to instrisic >differences in local abundance, you can't sensibly compare their raw >species richness counts, but >you can if you rarefy the '150' and '200' samples down to 100 >individuals. One might also want to >do this before comparing the sites using a DIVERSITY index, assuming >that the diversity index >takes into account overall species richness (as they mostly all do). > >So, rarefaction is a kind of 'pre-processing' step, rather than an >alternative, to a diversity index. > >Also, I can't think of a use for it in the context of equal sample >sizes, unless you are simply >interested the shapes of the rarefaction curves for the different >sites. But those shapes are >determined by the abundance distributions, so it would be more >straightforward to compare the >distributions directly. > >Hope this helps, > >Gareth Russell >NJIT/Rutgers > >On Tue, 2 Jan 2007 13:55:51 -0500, bonnie clark ><[EMAIL PROTECTED]> wrote: > > >Dear Colleagues, > >I'm considering using rarefaction as a measure of species diversity, since > >it takes both species richness and species abundance into account. There > >are several benefits of rarefaction over other indices like Shannon > >diversity. > > > >It is usually used when sample size is uneven. Would it be inappropriate to > >use it when sample sizes are even (equal)? > > > >Thank you, > >Bonnie > > > >_________________________________________________________________ > >Find sales, coupons, and free shipping, all in one place! MSN Shopping > >Sales & Deals > >http://shopping.msn.com/content/shp/?ctid=198,ptnrid=176,ptnrdata=200639 > >=========================================================== >==============
