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I am working on some experimental data, which can be of types A, B and C. Now I observe this data for 5 time points, and I can see them move between A to B, B to C,... etc. I see such transitions for a number of independent data points, and I have the cumulative frequencies from all data.

For example, I have: $$ Period A B C \newline 1 4 4 2 2 1 2 7 3 0 1 9 4 10 0 0 5 8 1 1 $$

I DO know the transitions from one state to another, for example from A->B, B->C so on and so forth. For example I know that from Period 1, (all A's went to C. Among the missing B's one went to A, and rest to C.) I was thinking of what would be the best way to visually represent this time wise transitions from one state to another. I was thinking that there might be some better way than just having a transition matrix, maybe something that looks like a Markov Chain but which could accommodate all the 5 periods of transitions in a succinct way? I myself work on a statistical software called STATA, which has limited graphical applications. IS there something on other software packages (R maybe?) which can help me in this?

- Sorry for the hack representation of the data matrix.

1Is the first line correct or should that also add up to 10? And is my understanding correct that for example in line 3 you don't know where the singleton B came from? – Jan van der Vegt – 2016-04-19T07:42:24.450

1I'm not clear on your data, so its hard to suggest solution. I understand you have 5 "snapshots in time". So do you have, say 20 items that you are observing and from the first line, 4 are in state A, 4 are in state B, 3 are in state C? Then for period 2, only 1 is in state A, 2 are in state B and 7 in state C? If this is true, do you have more granular data? do you know the order that states change from and to, is the state transition matrix well established. – Marcus D – 2016-04-19T11:16:24.633

@JanvanderVegt Yes, I will edit to make it add up to 10. Also, I DO know what transitions where, so I know the flow from A->B, B->C etc – Juanito – 2016-04-19T18:43:25.137

@MarcusD I have edited the question to answer what you asked. I can track each data point, through the states for each point in time. There is no state transition matrix as such, as the probability from going from state A to B, is not fixed apriori. Let me know if that answers your questions. If not, direct me to where you would need more clarification, and I would be glad to do that. – Juanito – 2016-04-19T18:51:55.747

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This post I made in stack overflow some time ago may be of interest to you: http://stackoverflow.com/questions/32633507/r-need-help-on-multi-state-markov-and-block-bootstrap-please/32694008#32694008

– tguzella – 2016-04-19T21:14:09.3571What sort of analysis do you want to do in the end? I have an idea, but it could be completely off track, depending on what analysis you are doing. – Marcus D – 2016-04-19T21:15:45.773

I have the state transitions under 4 different treatments, and I am interested to see if the state transitions in different periods look different by treatments. (From just eyeballing the data, I think there is a difference. ) I am thinking of setting up the comparison exercise by first having a nice graph of chart of the period wise transitions by treatments. I have not thought of any statistical tests for significance yet, but I am guessing that comes later. Feel free to share what you have in mind. – Juanito – 2016-04-19T21:28:27.187