make named dy vector in rates_SEPAIHRD_str

[apascualgarcia]

The dy vectors monitor the transitions, it is of size N*M with N being the number of transitions and M the number of classes. Now it is filled with an integer but then the order appearing in the code should be exactly the same than the transitions generated in make_transitions.R, which is prone to errors and makes further modifications delicate.

Both scripts could be recoded (see issue #25) to be automatically created from the classes and the compartments to give labels to the transitions in make_transitions and then use these names in dy.

[apascualgarcia]

Now the number of transitions is hardcoded within the function to get the dimensions, this will not work as soon as the model changes.

[apascualgarcia]

The number of transitions is now given as a variable inspecting the transitions matrix