epi-sim

A library for simulating epidemics, with a focus on phylodynamics and observation models.

Available models

1. Birth-Death (see Epidemic.BirthDeath)
2. Birth-Death-Sampling (see Epidemic.BirthDeathSampling)
3. Birth-Death-Sampling-Occurrence (see Epidemic.BirthDeathSamplingOccurrence)
4. Birth-Death-Sampling-Catastrophe-Occurrence (see Epidemic.BirthDeathSamplingCatastropheOccurrence)
5. Birth-Death-Sampling-Catastrophe-Occurrence-Disaster (see Epidemic.BDSCOD)
6. Inhomogeneous Birth-Death (see Epidemic.InhomogeneousBD)
7. Inhomogeneous Birth-Death-Sampling (see Epidemic.InhomogeneousBDS)

Output

The output is a CSV with a header encoding which events occurred when and to whom: event,time,primaryPerson,secondaryPerson. The primary person is either the infecting person or the person who has been removed in some manner, the secondary person is the person who was infected, or this is a missing value. There are functions to assist in extracting observations from a full simulation: birthDeathSamplingOccurrenceObservedEvents. In the case of a catastrophe event where multiple individuals may be removed, they are represented as a colon separated list of identifiers in the primaryPerson field.