Package index • EpiStrainDynamics

Data

Datasets incorporated in the package for demonstration.

influenza: World Health Organisation Global Influenza Programme for Australia
sarscov2: United Kingdom Health Security Agency SARS-CoV-2 case data

Construct model functions

Functions for constructing model object.

p_spline(): Specify p_spline method
random_walk(): Specify random walk method
single(): Single pathogen structure
multiple(): Multiple pathogen structure
subtyped(): Subtyped pathogen structure
smoothing_structure(): Create Smoothing Structure Specification with Priors
dispersion_structure(): Create Dispersion Structure Specification
construct_model(): Construct model
print(<EpiStrainDynamics.model>): Print method for constructed EpiStrainDynamics models

Fit stan model

fit_model(): Generic Method for fitting model
diagnose_model(): Diagnose model convergence and fit

Post-modelling metrics calculations

Functions to calculate and plot metrics from fitted models.

Rt(): Generic Method for Rt Analysis
growth_rate(): Generic Method for Growth Rate Analysis
incidence(): Generic Method for Incidence Analysis
proportion(): Generic Method for proportion Analysis
plot(<incidence>) plot(<growth_rate>) plot(<Rt>) plot(<proportion>): Plot metrics calculation outputs