Seriation of an absence-presence (0/1) matrix using the algorithm described by Brower & Kile (1988). This method is typically applied to an association matrix with taxa (species) in the rows and samples in the columns. For constrained seriation (see below), columns should be ordered according to some criterion, normally stratigraphic level or position along a presumed faunal gradient.
The seriation routines attempt to reorganize the data matrix such that the presences are concentrated along the diagonal. There are two algorithms: Constrained and unconstrained optimization. In constrained optimization, only the rows (taxa) are free to move. Given an ordering of the columns, this procedure finds the 'optimal' ordering of rows, that is, the ordering of taxa which gives the prettiest range plot. Also, in the constrained mode, the program runs a 'Monte Carlo' simulation, generating and seriating 30 random matrices with the same number of occurences within each taxon, and compares these to the original matrix to see if it is more informative than a random one (this procedure is time-consuming for large data sets).
In the unconstrained mode, both rows and columns are free to move.
Missing data are treated as absences.
References
Brower, J.C. & K.M. Kile. 1988. Seriation of an original data matrix as applied to palaeoecology. Lethaia 21:79-93.