Analytic Rarefaction

Fast individual-based rarefaction

Free

Version 2.0 - now even easier to use!

Requires OS X 10.7+

This new version brings numerous interface improvements to the reliable rarefaction engine. A click of a single button lets you choose your data file and run a rarefaction on it. You can now have data files with any name or location, and in many different formats; you can also save your file to whatever name and location you choose. Analytic Rarefaction works with you.

Rarefaction is used to estimate diversity and place confidence limits on diversity if sample size had been lower than it actually was. Rarefaction can't be used to estimate diversity for a greater sample size, or to estimate the total diversity in the entire community; for that, you need to use an extrapolation metric like Chao-1 or Chao-2. If that's what you want to do, check out Diversity.

Using Analytic Rarefaction

Analytic Rarefaction is easy to use. Save your list of species abundances in a .txt or .csv file; the abundances can be separated by spaces, tabs, commas, or returns - whichever you prefer. Click the button in Analytic Rarefaction, choose your file, and the rarefaction is completed quickly. The results show you the sample size, the expected number of species and its variance, as well as 95% and 99% confidence intervals. Save the output as a .txt file that you can open in Excel, R, and many other programs for plotting. For quick plotting of your data as well, try Diversity.

How Analytic Rarefaction works

Analytic Rarefaction uses the rarefaction equations for E given by Hurlbert (1971) and for Var given by Heck et al. (1975). These are the same equations used by Raup (1975) and Tipper (1979). In particular, this program uses the formulation of Tipper (1979), as his equations (1) and (2) are easy to program and avoid the overflow errors associated with the large combinatorials.