hidden_paths does not respect sequence length

[tbeason]

Perhaps I am missing something, but if I input sequence data where each sequence is a different length and estimate an HMM, running mpp <- hidden_paths(hmm$model) results in a "dense" matrix (all observations are assigned a state and no voids appear). Are there options to have it respect the void elements? Should I just set those to void ex post?

This is particularly problematic for me because I am then calling things like dur_output <- seqistatd(mpp) which of course gives nonsense results because the mpp sequences have these psuedo elements added relative to the original input data.

[helske]

The hidden_paths function computes the most probable states also for the missing values, which is how unequal sequence lengths are handled internally. But indeed, it makes often sense to set the tails to voids for visualization etc. I'll add an an option for this.

[tbeason]

In my case, and I suspect in many cases, they are not true "missing" observations. The sequences simply have different length. I will add a check in my code to reset these positions to void until you are able to add this option.

[helske]

Yes this makes sense. I just pushed an update, the hidden_paths function now has an argument respect_void (default is TRUE) which replaces the hidden states with voids according to the observed sequences. Let me know if you encounter problems, I didn't fully test this yet.

[tbeason]

Seems to be working fine. Thanks for the quick fix