Testing sequential association: Estimating exact p values using sampled permutations

Assigning p values to all transitions in a matrix based on their z scores is problematic on 2 counts: The z scores may not be normally distributed,and transitions are interconnected. Permutation tests, which require fewer assumptions, are an attractive alternative to the standard asymptotic methods for assigning significance, Moreover, when asymptotic z scores are only somewhat above their critical value and sequences are short, often the exact probabilities of permutation tests are not less than .05. Log-linear and permutation methods may be used to winnow the set of transitions initially identified as significant even further. A computer program that program the performs these tests is available from the authors.