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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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Corrections and code streamlining #145

Closed pratikunterwegs closed 8 months ago

pratikunterwegs commented 9 months ago

This PR makes a number of smaller edits to clean up and streamline the existing codebase prior to adding a diphtheria model.

  1. All references to infections have been removed unless appropriate, with variables renamed where necessary,
  2. All optional model inputs now use {checkmate}'s null.ok argument instead of an if-else ladder,
  3. All model checker functions now check whether optional arguments such as intervention are NULL, instead of missing (replacing missing() with is.null()),
  4. All model functions' documentation has been updated and compressed where possible,
  5. Internal C++ code for Vacamole has been modified to disallow rate interventions on derived parameters, and this is WIP #144,
  6. All helper functions now place required args before optional args,
  7. Helper functions return <data.frame> instead of <data.table> to improve interoperability, although {data.table} is still used internally,
  8. Helper functions' documentation has been updated,
  9. Vignettes have been corrected where required,
  10. Tests have been updated to account for data.frame output and renamed function arguments - a snapshot test for ebola has been updated to reflect data.frame output,
  11. Fixes #120 by correcting younger age group vaccination rates in vignette.