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epiverse-trace / epidemics

A library of published compartmental epidemic models, and classes to represent demographic structure, non-pharmaceutical interventions, and vaccination regimes, to compose epidemic scenarios.
https://epiverse-trace.github.io/epidemics/
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Initial implementation of the diphtheria model #146

Closed pratikunterwegs closed 8 months ago

pratikunterwegs commented 8 months ago

This PR adds an initial implementation of a diphtheria model, and fixes #141. See the issue for model features in this implementation.

This PR:

  1. Adds a C++ implementation of the ODE model using Boost odeint as the header inst/include/epidemic_diphtheria.h,
  2. Adds the internal Rcpp function .model_diphtheria_cpp(),
  3. Adds the user-facing function model_diphtheria_cpp() to run the diphtheria model, with some default parameters taken from Finger et al.; these could be updated,
  4. Adds very basic tests for the model running without errors, and having expected output types,
  5. Updates the Readme to add a reference to the model and Finger et al.

Note that:

  1. The model does not support a contact matrix and hence age-stratified contacts,
  2. The model does not support contacts interventions,
  3. The model does not support a vaccination regime,
  4. The model does not have an R implementation.
pratikunterwegs commented 8 months ago

Unfortunately this is being merged without review.