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

This is a package candidate release! Here you can preview how this package release will appear once published to the main package index (which can be accomplished via the 'maintain' link below). Please note that once a package has been published to the main package index it cannot be undone! Please consult the package uploading documentation for more information.

[maintain] [Publish]

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.


[Skip to Readme]

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.*), 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

Modules

[Index]

Downloads

Maintainer's Corner

For package maintainers and hackage trustees


Readme for epi-sim-0.2.2.0

[back to package description]

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.