Add basic SIR model

[adamkucharski]

We would like to add a new model to epidemics. It will be a basic SIR model (i.e. no age structure) and will work with deSolve package. It will also use existing functionality from {epidemics} to allow interventions like vaccination.

(Note: this is a test issue with GitHub Copilot Workspace)

[pratikunterwegs]

Just to clarify for external viewers, this issue was added to explore Github Copilot + Workspaces for Epiverse, and the issue was taken as a reasonable domain-specific task for Copilot. @adamkucharski once you're back, would it be possible to actually make the Copilot-generated PR for future reference? Since Copilot allows comparing against existing codebase as well as its own previous solutions, it could be a good way to asses whether it's getting better at the task.

[adamkucharski]

✨✨ Here's an AI-assisted sketch of how you might approach this issue saved by @adamkucharski using Copilot Workspace v0.19

Topic

Does the SIR model without age structure, compatible with deSolve package and supporting interventions like vaccination, exist?

Before

• No, the SIR model without age structure, compatible with deSolve package and supporting interventions like vaccination, does not exist in the repository.
• The repository contains models with age structure and interventions, as seen in vignettes/design-principles.Rmd and vignettes/developer-walkthrough.Rmd, but not a basic SIR model as described.
• The issue description suggests adding a new model to the repository, indicating the absence of such a model currently.

After

• Yes, the SIR model without age structure, compatible with deSolve package and supporting interventions like vaccination, now exists in the repository.
• The model is implemented in a new file models/SIR_no_age_structure.R, utilizing the deSolve package for solving differential equations.
• The model supports interventions like vaccination through the existing functionality in the repository, as outlined in the vignettes vignettes/design-principles.Rmd and vignettes/developer-walkthrough.Rmd.

Plan

• models/SIR_no_age_structure.R (ADD)
  • Implement the SIR model equations using the deSolve package
  • Define parameters for the SIR model including transmission rate, recovery rate, and initial conditions
  • Include functionality to support interventions like vaccination
  • Write a function to simulate the SIR model over a specified time period
  • Document the function with examples of how to use it, including with interventions

Sketch of implementation

View the changes

Details

Code analyzed at f706261