First of all you have to define all possible 6 events related to your problem like; 1S- first child is son, 1D- first child is Daughter . If you comfort with R, then make a data frame whose first column containing the first child of all patients, second column containing second child of all patient similarly third column. Convert all data set into the form of events defined above. The transition probability matrix will be 6X6 order matrix. Obtain the transition probabilities by following manner:

transition probability for 1S to 2S ; frequency of transition from event 1S to 2S divided by all transition from event 1S to all other state.

Rohit Patawa Thanks for the answer. Do you know got to calculate Emission probabilities for HMM. This is my code but its giving error saying "Undefined columns selected".

emix

Aymen Tasneem you have not described the whole problem and also about exam_seq. But as much as I am understanding your problem, you should read the example part of the article whose link I have given below.

https://rdrr.io/github/helske/seqHMM/man/build_hmm.html

Rohit Patawa Thank you so much for the link. I am following the same link to implement HMM for my dataset. and I am stuck while calculating emission matrix, the same code thats given in this link when I used it for my dataset (after modification) is giving errors "Undefined columns" or " incorrect number of subscripts on matrix", I checked my dataset and I have given the correct numbers of column in the matrix but its not reading it. As I am new to R so I dont know how to resolve this error. Do you know how to resolve this or do you know anyother way of calculating emission prob?