Package index • diseasy

Functional modules

The building blocks of diseasy.

DiseasyActivity(): Configure activity (contact) scenarios
DiseasyImmunity(): Configure (waning) immunity against different outcomes
DiseasyObservables(): Configure data-sources and observables
DiseasySeason(): Configure seasonality scenarios
DiseasyVariant(): Configure disease variants

Model templates

Templates that construct individual models.

Diseasy-BRM-models DiseasyModelBRM DiseasyModelB0 DiseasyModelB1: Simple bayesian regression models
Diseasy-GLM-models DiseasyModelGLM DiseasyModelG0 DiseasyModelG1: Simple generalized linear regression 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 for SEIR example data
contact_basis(): Contact basis
diseasy_immunity_optimiser_results(): Optimiser results for DiseasyImmunity
dk_activity_units(): Danish activity "units"
dk_reference_scenario(): Danish reference scenario (SARS-CoV-2 pandemic)
seir_example_data(): Synthetic epidemiological data

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