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.