Add calculation of offspring per location per day

[averbraeck]

Offspring is the number of susceptible persons typically infected by an infectious person.

[averbraeck]

Offspring is not so easy to calculate, since medlabs typically uses an (extension of an) SEIR model. This means that persons in the models are exposed at the time when we know who causes the exposed state, but when the infectious state is reached, that relation is gone. Therefore, the changeDiseasePhase method in an implementation of DiseaseProgression interface separates the exposed stage into a separate exposed method that identifies the infecting persons (or a list of possible infecting persons from which one has to be chosen) for an exposed person. The exposed method returns a boolean indicating whether the exposure will lead in the end to an infection. The registration of an infection is then allocated to the day when the transmission of the disease took place.

[averbraeck]

DiseaseProgression implements the exposed methods as follows:

    public abstract boolean expose(Person exposedPerson, DiseasePhase exposurePhase);

    public void expose(final Person exposedPerson, final DiseasePhase exposurePhase, 
        final Person infectiousPerson)
    {
        if (expose(exposedPerson, exposurePhase))
        {
            getModel().getDiseaseMonitor().reportInfection(exposedPerson, infectiousPerson);
        }
    }

    public void expose(final Person exposedPerson, final DiseasePhase exposurePhase, 
        final TIntList infectiousPersonList)
    {
        if (infectiousPersonList.size() == 1)
        {
            expose(exposedPerson, exposurePhase, this.model.getPersonMap()
                    .get(infectiousPersonList.get(0)));
        }
        else if (infectiousPersonList.size() > 1)
        {
            expose(exposedPerson, exposurePhase, this.model.getPersonMap()
                    .get(infectiousPersonList.get(this.model.getRandomStream()
                    .nextInt(0, infectiousPersonList.size() - 1))));
        }
        else
        {
            expose(exposedPerson, exposurePhase);
        }
    }

[averbraeck]

The following changes are made:

• The class extending DiseaseProgression for an actual disease can decide how to implement the abstract exposed method.
• The DiseaseMonitor class can decide what to do with the reported infection.
• The class extending the DiseaseTransmission class calls the exposed method when exposure takes place, instead of calling changeDiseasePhase(person, DiseasePhase.exposed).
• the method DiseaseProgression.changeDiseasePhase(...) containing the SEIR state machine becomes protected rather than public since only expose is called externally, changeDiseasePhase calls itself using the simulation scheduler for successive stages of the disease.
• the method changePhase in Person is no longer needed (it always called DiseaseProgression.changeDiseasePhase(this, phase) and did nothing else), and will be removed.

[averbraeck]

Changes has been tested, and seem to work as intended.