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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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Add hospitalised and funeral compartments to Ebola model #110

Closed pratikunterwegs closed 11 months ago

pratikunterwegs commented 11 months ago

This issue aims to fix #85 by adding a hospitalised and funeral compartment to the ebola model. These compartments have only been added to the R version. The C++ version has been made internal in this PR, and is not intended to be made available to users as it does not offer a speed boost.

The changes in this PR bring it in line with the model structure in Li et al. (2019). The main difference is that this model simplifies the transitions between the infectious, hospitalised, funeral, and removed compartments:

  1. Infectious individuals can move to the hospitalised compartment or the funeral compartment, but not to the removed compartment directly,
  2. Hospitalised individuals are expected to have Ebola-safe funerals, and only move to the removed compartment,
  3. Funerals lead to the removed compartment only.
  4. The hospitalised compartment has the same number of sub-compartments as the infectious compartment, and individuals who are hospitalised move to the same sub-compartment as they occupied in the infectious compartment.

This PR also allows rate interventions on the transmission rate $\beta$, but not on any other model rates. There is a good case for allowing interventions that increase rates such as the safety of treatment units, or of funerals, but this is open for discussion in #109.

pratikunterwegs commented 11 months ago

This PR is being merged, with time-dependence suggested to be added as issue #111, and with modifications to other parameters suggested to be added once interventions can have positive effects, see #109.