Rarefact is a program that performs rarefaction on species-abundance data. Given an input file of species counts from a single paleontological sample (x number of species of y counts each, z total counts), rarefact will estimate the species diversity (x') expected at smaller subsample sizes (z' total counts) and compute 95% confidence intervals around the estimates.
Download a self-extracting archive with Rarefact 1.0.
Two different methods of doing the analysis can be selected.
Bootstrap analysis: Given a particular subsample size (z'), this method repeatedly resamples the input file species-abundance distribution to generate a large number of subsamples of size z'. A diversity is calculated for each simulated subsample, generating a distribution of expected diversities at size z'. The observed diversity of an actual subsample is compared to the distribution of expected diversities to determine if observed diversity is greater than, less than, or equal to the expected diversity. The output from this analysis can be used to determine the level of statistical significance attributable to the comparison between expected and observed diversity.
Analytical analysis: This method calculates expected diversities and variances at subsample sizes from 1 to the size of the input file sample (z). Expected diversities are estimated using the hypergeometric distribution (sampling without replacement) and the multinomial distribution (sampling with replacement). The output from this program can be imported into a spreadsheet or graphing program to generate a rarefaction curve. Variances are converted and output as 95% confidence limits on the expected diversity values.
Three compiled versions of the program are included:
040 processor with FPU (floating point unit)
040 processor (no FPU)
A PowerMac version is not available, although the 040 (no FPU) version should run on PowerMacs.
The Fortran source code is included as 'Rarefact 1.0 text'.
I would appreciate hearing any questions or comments regarding this program. If you would like to suggest modifications and improvements to make it easier and better, or if you need to customize the output or calculations for a particular application, please contact me - I would be very happy to try to produce a version of the program that meets your needs!
J Bret Bennington GeoJBB@Hofstra.edu
This program is Freeware and may be distributed freely provided that no modifications are made to the original program.