Add more extensive offspring calculation

[averbraeck]

To do data mining on the offspring, more details are needed. Therefore, another file is added that details the infections and non-infections per location per infectious person. The name of the file will be offspringLocation.csv. The following columns will be added to the file, every time when a person leaves a location:

• Time(h) (simulation clock in hours)
• infectiousPersonId
• infectiousPersonType (class name)
• infectiousPersonAge
• infectiousPersonGender
• infectiousPersonDiseasePhase
• infectedPersonId (or -1 in case of no infections in this location)
• infectedPersonType (or "None" in case of no infections in this location)
• infectedPersonAge (or -1 in case of no infections in this location)
• infectedPersonGender (or "-" in case of no infections in this location)
• locationId
• subLocationIndex (the index of the sublocation, 0 if no sublocations)
• locationType
• timeInLocation(s) (this is the number of seconds spent by the infectious person in the (sub)location)
• areaLocation (area of the location in m2)
• areaSubLocation (area of the sublocation in m2)
• nrPersonsInLocation (this is the number of persons at the time when the infectious person leaves the location)
• nrPersonsInSubLocation (this is the number of persons at the time when the infectious person leaves the sublocation)

One line will be added per infection, so it can be multiple lines per infectious person. In case no infection takes place in the location, one line is added to the file as well, without information on the infected person(s).

[averbraeck]

Calculating the time in location can be difficult -- the contact time is dependent on the entering time and leaving time of both the infectious person(s) and the exposed person(s), Every time someone enters a location, calculateTransmissionEnter is called that looks at possible infections since the latest enter/leave. When someone leaves, calculateTransmissionLeave is called that does the same. Inbetween can be very small intervals that have nothing to do with either the time of the infectious person in the location, nor with the time the exposed person was in the room, nor the time of the overlap. Therefore, it's best to not output any times.

[averbraeck]

Offspring calculations have been built into the Medlabs library. The structure of the classes DiseaseTransmission and DiseaseProgression have changed as a result. The DiseaseTransmission class uses a cache of infectious persons who entered a location, and calculates the number of infections that that person has caused while being in the location. When the infectious person leaves the location, the count is sent to the DiseaseMonitor.reportOffspring method, which fires an OFFSPRING_EVENT for the ResultWriter class (and possibly graphs) to record the offspring results in a file. To properly calculate offspring, also results with 0 infections at a location are transmitted.

[averbraeck]

The results have been tested with the SEIR demo model, and look consistent and complete.

There is one small issue in the SEIR demo model that clearly shows in the infections.csv file and offspringLocation.csv files: The incubation time when to move from the exposed stage to the infected stage is drawn from a distribution. At the same time, the viral load is determined based on a triangular distribution that is based on a number of days since infection, where the starting point of the distribution is not the same as the exposed -> infected transition. This means that persons who have the disease status exposed can infect others. This is not an error in the offspring/infection statistics, but an inconsistency in the implementation of the SEIR model.

[averbraeck]

The calculation of the offspring looks correct. A new version of the medlabs and heros model will be tagged.