Supplement 1. C source code containing the algorithms described in this paper, and a short description of the program and its options.

File List trialswap.c - C source code and extensions options.log - Input file governing the sampling method Sashegy.dat - Presence/absence matrix from the Sashegy Nature Reserve readme.txt - Description of the C source code trialswap.zip - All files at once DescriptionThe trialswap.c C program generates uniformly distributed random 0-1 matrices with given row and column totals using a Metropolis type Markov chain Monte Carlo method and different fast randomization methods for the initial seed of the Markov chain. Possible options are described in the readme.txt file. The main algorithms are described in the original paper; proofs of correctness of the methods can be read in Appendix A, Appendix B, and Appendix C.