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Bounty Ended with krkeane's answer chosen by Greg Markowsky
Added tag "transition-matrix" which is relevant here.
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User1865345
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I'm working on a time-dependent dataset, where basically I have two different populations and we're building Markov chains to describe their behaviors. What I'm trying to do is compare the transition matrices associated to the two populations, and decide whether the transition matrices are really different, or whether they could be due to chance. So my question is, is there a good way to compare two transition matrices in order to determine whether they are statistically different? Part of the problem we're running into is that both matrices have a lot of zeroes in them, but not always in the same places. Any suggestions are welcome.

Thank you, Greg

I'm working on a time-dependent dataset, where basically I have two different populations and we're building Markov chains to describe their behaviors. What I'm trying to do is compare the transition matrices associated to the two populations, and decide whether the transition matrices are really different, or whether they could be due to chance. So my question is, is there a good way to compare two transition matrices in order to determine whether they are statistically different? Part of the problem we're running into is that both matrices have a lot of zeroes in them, but not always in the same places. Any suggestions are welcome.

Thank you, Greg

I'm working on a time-dependent dataset, where basically I have two different populations and we're building Markov chains to describe their behaviors. What I'm trying to do is compare the transition matrices associated to the two populations, and decide whether the transition matrices are really different, or whether they could be due to chance. So my question is, is there a good way to compare two transition matrices in order to determine whether they are statistically different? Part of the problem we're running into is that both matrices have a lot of zeroes in them, but not always in the same places. Any suggestions are welcome.

Notice added Draw attention by Greg Markowsky
Bounty Started worth 100 reputation by Greg Markowsky
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statistical comparison of two markov chain transition matrices

I'm working on a time-dependent dataset, where basically I have two different populations and we're building Markov chains to describe their behaviors. What I'm trying to do is compare the transition matrices associated to the two populations, and decide whether the transition matrices are really different, or whether they could be due to chance. So my question is, is there a good way to compare two transition matrices in order to determine whether they are statistically different? Part of the problem we're running into is that both matrices have a lot of zeroes in them, but not always in the same places. Any suggestions are welcome.

Thank you, Greg