Change CTMC default to probability matrix instead of rate matrix?

[volkm]

CTMCs models are the only model which store rates in the transition matrix instead of probabilities. Markov automata store probabilities and use the exit rates. CTMCs can also have exit rates but they are then redundant with the rate matrix.
I think rates for CTMCs can be confusing, because it is not consistent. I have also seen other people expecting different behavior and struggling with this.

My proposal would be to use a probability matrix as default for CTMCs to make it consistent with the other models. Uniformization changes the transition matrix anyway, so I feel that a potential overhead from converting rates to probabilities is fine. I also count 29 instances of using computeProbabilityMatrix so the probability matrix is used quite often.

@sjunges @tquatmann What is your view?

[sjunges]

I fully agree, it seems to be the easier/more logical representation in our context.

I tag @linusheck as this may eventually be relevant for stormvogel.

[tquatmann]

I also agree!