Minor additions to how infections work

[xsaschako]

Motivation / Current Behaviour

No response

Enhancement description

TBD with others when going through changes @ infection in paper

Additional context

Differences i found:

We deleted the if -> else return 0 i think because that things in get_infectivity :-D

if (t >= m_viral_load.start_date && t <= m_viral_load.end_date) {
        if (t.days() <= m_viral_load.start_date.days() + m_viral_load.peak / m_viral_load.incline) {
            return m_viral_load.incline * (t - m_viral_load.start_date).days();
        }
        else {
            return m_viral_load.peak + m_viral_load.decline * (t.days() - m_viral_load.peak / m_viral_load.incline -
                                                               m_viral_load.start_date.days());
        }
    }
    else {
        return 0.;
    }

2. We switched forward and backwards drawing of infection state.

 TimePoint start_date = draw_infection_course_backward(rng, age, params, init_date, init_state);
    draw_infection_course_forward(rng, age, params, init_date, init_state, latest_protection);

got changed to:

TimePoint start_of_init_state = draw_infection_course_forward(rng, age, params, init_date, init_state, latest_protection);
    TimePoint start_date = draw_infection_course_backward(rng, age, params, start_of_init_state, init_state);

3. We added a rng to be in the middle of the initializing infection

// helper lambda for init_state
   auto determine_time_period = [&]() {
       if (!init_state) {
           // randomly initialize the infetion when it is not initialized at the time of transmission
           p = uniform_dist(rng); // a random amount of time that has passed since begin of the initial InfectionState
           auto time_draw      = time_in_state.get_distribution_instance()(rng, time_in_state.params);
           time_period         = days(p * time_draw);
           start_of_init_state = t - days((1 - p) * time_draw);
           init_state          = true;
       }
       else {
           time_period = days(time_in_state.get_distribution_instance()(rng, time_in_state.params));
       }
   };

Checklist

• Attached labels, especially loc:: or model:: labels.
• Linked to project