Package index • EpiStrainDynamics

Data

Datasets incorporated in the package for demonstration.

influenza: THIS NEEDS TO BE EDITED

sarscov2: United Kingdom Health Security Agency SARS-CoV-2 case data

Construct model functions

Functions for constructing model object.

construct_model(): Construct model

single(): Single pathogen structure

multiple(): Multiple pathogen structure

subtyped(): Subtyped pathogen structure

p_spline(): Specify p_spline method

random_walk(): Specify random walk method

Fit stan model

fit_model(): Generic Method for fitting model

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(): Generic Method for plotting metrics calculation outputs