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Changelog

Source: NEWS.md

diseasy 0.0.0.9000

Features

  • DiseasyBaseModule: The baseline for all diseasy modules.

    Key features:

    • A caching system using cachem where computation can be stored in memory or on disk for persistence (#130).

  • DiseasyVariant: A functional module to implement scenarios for disease variants (#111).

  • DiseasyImmunity: A functional module to implement scenarios for waning immunity (#101). For examples of usage, see vignette("diseasy-immunity").

  • DiseasyModel: A base class for the model templates (#36).

    • Defines the interface for the models and empower the flexible configuration of models from the functional modules.

    • The model class has a system for model parameters (#116):

      • Parameters are easily overview via the $parameters binding.
      • Parameters are type-checked during setting.
      • Parameters can easily be adjusted during model initialisation.
      • Parameters are inherited from super classes as needed.

  • DiseasyModelOde: A base class for Ordinary Differential Equation (ODE) model templates (#142, #162).

    • Defines the interface for the ODE models.

  • DiseasyModelOdeSeir: A model template for SEIR-like models (#142, #162).

    • Dynamically allocated with configuration
      • Any number of E, I and R states.
      • Any number of age groups.
      • Any number of disease variants.
    • Methods for initialising from incidence data.

  • combineasy(): A utility to combine model templates into an ensemble (DiseasyEnsemble) (#166).

  • Standard generics for DiseasyEnsemble (#166):

    • print() - Simple console printing.
    • summary() - View of the composition of the ensemble.
    • predict() - Retrieve predictions from the ensemble.
    • plot() - Plot predictions from the ensemble.

  • A range of utility functions:

Documentation

  • The functions are fully documented.

  • Vignettes for the use of the package is included.