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epi-sim: A library for simulating epidemics as birth-death processes.

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

Available models

Output format

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.

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Properties

Versions 0.2.2.0, 0.2.2.0, 0.4.2, 0.7.0
Change log ChangeLog.md
Dependencies aeson (>=1.4.0 && <1.5), base (>=4.8.2 && <4.14), bytestring (>=0.10.6 && <0.11), cassava (>=0.5.2 && <0.6), hspec (>=2.7.4 && <2.8), mwc-random (>=0.14.0 && <0.15), primitive (>=0.6.1 && <0.8), statistics (>=0.15.0 && <0.16), trifecta (>=2.1 && <2.2), vector (>=0.11.0 && <0.13) [details]
License MIT
Copyright 2020 Alexander Zarebski
Author Alexander Zarebski
Maintainer aezarebski@gmail.com
Category Simulation
Home page https://github.com/aezarebski/epi-sim#readme
Bug tracker https://github.com/aezarebski/epi-sim/issues
Source repo head: git clone https://github.com/aezarebski/epi-sim
Uploaded by AlexanderZarebski at 2020-10-14T12:12:47Z

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Readme for epi-sim-0.2.2.0

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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.