user selected time step

[slwu89]

Restructure model to accept user input dt (step size). All processes and event schedulers which need to compute transition probabilities have been rewritten to compute based on dt.

This PR should also address "3. State initialisation" in the google doc; the function setup_events in R/initialize.R (sorry about the z) schedules events for individuals starting in all states before the model run begins, so that it could be initialized with people in any states, not just S and E.

Currently I have not written a nice wrapper like run_simulation because I expect things will be changing a lot as we add vaccination.

Old files that are unneeded were put in R/deprecated.

Redoing the validation against squire with dt=0.1 the two models seem to be giving very similar results.

[codecov[bot]]

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