Re: [R] transition matrices
On Wed, 4 Apr 2007 07:46:37 -0500 Ranjan Maitra <[EMAIL PROTECTED]> wrote: > Hi, > > It appears that you are trying to separate the states in the transition > matrix such that you have recurrent classes all next to each other. Sorry, I meant non-communicating classes. Btw, thinking about this some more, I think you can do this in a quick and dirty way: convert your transition probability matrix into 0 and 1 which is 0 if the entry is (+)ve. Then, make this into a distance matrix (using as.dist()), use hclust and single linkage and cut the tree at 1(?) to get the equivalence classes. The ordering of the tpm after this is easy. HTH, Ranjan > Here is an idea off the top of my head: make equivalence classes from your > statespace and then use that to create a block diagonal matrix. I did a > search on equivalence classes on RSiteSearch and came up with 17 articles> > You can take a look and see if any of these are useful. > > http://search.r-project.org/cgi-bin/namazu.cgi?query=equivalence+classes&max=20&result=normal&sort=score&idxname=Rhelp02a&idxname=functions&idxname=docs > > HTH, > Ranjan > > > On Wed, 04 Apr 2007 16:34:44 +1000 Richard Rowe <[EMAIL PROTECTED]> wrote: > > > 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 > > AUSTRALIA > > > > ph +61 7 47 81 4851 > > fax +61 7 47 25 1570 > > JCU has CRICOS Provider Code 00117J > > > > __ > > R-help@stat.math.ethz.ch mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] transition matrices
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" http://www.lirmm.fr/~caraux/PermutMatrix/EN/Seriation.htm 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 Christos Hatzis, Ph.D. Nuvera Biosciences, Inc. 400 West Cummings Park Suite 5350 Woburn, MA 01801 Tel: 781-938-3830 www.nuverabio.com > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Richard Rowe > Sent: Wednesday, April 04, 2007 2:35 AM > To: r-help@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 > AUSTRALIA > > ph +61 7 47 81 4851 > fax +61 7 47 25 1570 > JCU has CRICOS Provider Code 00117J > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] transition matrices
Hi Richard, You might want to have a look at Bertin's reorderable matrices, which seem to be solving a similar problem. Googling for bertin reorderable matrix gives a few automatic implementations. Hadley On 4/4/07, Richard Rowe <[EMAIL PROTECTED]> wrote: > 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 > AUSTRALIA > > ph +61 7 47 81 4851 > fax +61 7 47 25 1570 > JCU has CRICOS Provider Code 00117J > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] transition matrices
Hi, It appears that you are trying to separate the states in the transition matrix such that you have recurrent classes all next to each other. Here is an idea off the top of my head: make equivalence classes from your statespace and then use that to create a block diagonal matrix. I did a search on equivalence classes on RSiteSearch and came up with 17 articles> You can take a look and see if any of these are useful. http://search.r-project.org/cgi-bin/namazu.cgi?query=equivalence+classes&max=20&result=normal&sort=score&idxname=Rhelp02a&idxname=functions&idxname=docs HTH, Ranjan On Wed, 04 Apr 2007 16:34:44 +1000 Richard Rowe <[EMAIL PROTECTED]> wrote: > 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 > AUSTRALIA > > ph +61 7 47 81 4851 > fax +61 7 47 25 1570 > JCU has CRICOS Provider Code 00117J > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[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 AUSTRALIA ph +61 7 47 81 4851 fax +61 7 47 25 1570 JCU has CRICOS Provider Code 00117J __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
