Fully rename parameters and decide hospitalization when symptoms appear

[atmyers]

This fully renames latent_period", infectious_period", and ``incubation_period" to have the same meanings as in the epi literature.

This also changes the point at which agents are hospitalized to be after symptoms develop (the end of the incubation_period)

[kcnguyen3191]

In the previous version, it only decides if the agent would be hospitalized once at the end of the latent_period_ptr. With this new change, will it decide the hospitalization everyday during the symptomatic period?

[atmyers]

Here are the infections and hospitalizations before and after these changes.

The hospitalization changes are reasonable given that the asymptomatic percentage was set to 40%.

[kcnguyen3191]

Thank you for making these changes. I think we can go ahead and merge this branch. However, there should be a period between the first day the agents start showing symptoms and the first day they got hospitalized.