Package index • diseasy

Functional modules

The building blocks of diseasy.

DiseasyActivity(): Activity handler
DiseasyImmunity(): Diseasy' immunity handler
DiseasyObservables(): Diseasy' observables handler
DiseasySeason(): Diseasy' season handler
DiseasyVariant(): Diseasy' variant handler

Model templates

Templates that construct individual models.

Diseasy-BRM-models DiseasyModelBRM DiseasyModelB0 DiseasyModelB1: Meta module for the BRM class of models
Diseasy-GLM-models DiseasyModelGLM DiseasyModelG0 DiseasyModelG1: Meta module for the GLM class of models
DiseasyModelOdeSeir(): A flexible SEIR model template

Creating ensembles

Functions related to creating ensembles of models.

combineasy(): Easily combine modules and parameters to form a model ensemble
print(<DiseasyEnsemble>) summary(<DiseasyEnsemble>) predict(<DiseasyEnsemble>) plot(<DiseasyEnsemble>): Standard generics for DiseasyEnsemble objects

Helper functions

Functions that help with the construction of models.

plot(<DiseasyBaseModule>): Plotting method for diseasy modules
print(<DiseasyBaseModule>): Printing method for diseasy modules
diseasyoption(): Helper function to get options related to diseasy

Data sets

Data for the functional modules and model templates.

DiseasystoreSeirExample(): feature store handler for SEIR example data
contact_basis(): Contact basis
diseasy_immunity_optimiser_results(): diseasy_immunity_optimiser_results
dk_activity_units(): dk_activity_units
dk_reference_scenario(): dk_reference_scenario
seir_example_data(): seir_example_data

Helper functions

plot(<DiseasyBaseModule>): Plotting method for diseasy modules

Developer functions

Functions to create model templates and functional modules.

DiseasyBaseModule(): Base module for diseasy
DiseasyModel(): Base module for diseasy model templates
DiseasyModelOde(): Base module for the ODE class of models
DiseasyModelRegression(): Base module for the regression class of models
dhypo() phypo() qhypo() rhypo(): The hypoexponential distribution
hash_environment(): Holistic hashing of an environment