[R] transition matrices

Christos Hatzis christos at nuverabio.com
Wed Apr 4 18:16:24 CEST 2007

I think what you are looking for is also called seriation or ordination,
i.e. find the "best" enumeration order of a set of objects.

Take a look at the following link for more information and on criteria for
defining "best"


The link is for a windows application (PermutMatrix) that can perform
seriation on distance matrices used in hierarchical clustering, but might be
useful in your context as well.


Christos Hatzis, Ph.D.
Nuvera Biosciences, Inc.
400 West Cummings Park
Suite 5350
Woburn, MA 01801
Tel: 781-938-3830

> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch 
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Richard Rowe
> Sent: Wednesday, April 04, 2007 2:35 AM
> To: r-help at stat.math.ethz.ch
> Subject: [R] transition matrices
> I am working with transition matrices of sequences of animal 
> behaviours.  What I would like to do is parse the original 
> matrices, adjusting row/column order so that the matrix has 
> its main values in blocks surrounding the diagonal.  This 
> would cause behaviours involved in functional groupings (e.g. 
> grooming, resting, foraging etc) to appear as blocks.
> This can be done manually by applying subjective 'prior 
> knowledge' of sequences, however I would like to have an 
> algorithmic/objective method to generate at least a first cut ...
> Any suggestions or hints (even just thoughts) would be much 
> appreciated,
> Richard Rowe
> Dr Richard Rowe
> Zoology & Tropical Ecology
> School of Tropical Biology
> James Cook University
> Townsville 4811
> ph +61 7 47 81 4851
> fax +61 7 47 25 1570
> JCU has CRICOS Provider Code 00117J
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