I am reading the comprehensive on-line documentation about msm.
The positive side is that it seems it has been designed for biomedical
statistics,
like Clinical Trials.
The bad side is that it does not seem to model observations sequences that
are not
independent but instead are autocorrelated, as it is my case. I did not find
any mention to
correlated observations therefore I assume the authors did not have to face
this problem.
Did I get it wrong ?

Since the breathing signals amplitude is an autocorrelated function of time
and phase, I would
greatly appreciate any comment about the possibility to use msm eventually
after carring out
some modifications  if the source code is available.

 Thank you in advance for your attention.
I am reading the comprehensive on-line documentation about msm.
The positive side is that it seems it has been designed for biomedical
statistics,
like Clinical Trials.
The bad side is that it does not seem to model observations sequences that
are not
independent but instead are autocorrelated, as it is my case. I did not find
any mention to
correlated observations therefore I assume the authors did not have to face
this problem.
Did I get it wrong ?

Since the breathing signals amplitude is an autocorrelated function of time
and phase, I would
greatly appreciate your comments about the possibility to use msm eventually
after carring out
some modifications  if the source code is available.

 Thank you in advance for your help.
-- 
Maura E.M

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