Rsim: Simulate from a SEIR/SEIRS process using R (debug feature)

In grantbrown/ABSEIR: Posterior Approximation to Fully Bayesian Spatial SEIR Models Using Multithreaded C++

Description

Simulate from a SEIR/SEIRS process using R (debug feature)

Usage

Rsim(
  seed,
  params,
  exposure_model,
  reinfection_model,
  distance_model,
  transition_priors,
  initial_value_container
)

Arguments

seed	A random seed
params	Parameters needed for the simulation, a list including beta_SE, beta_RS, rho, gamma_EI, gamma_IR, and optionally path-specific parameters.
exposure_model	An exposure model object, which describes the spatial and temporal variability of the exposure/infection process. Valid exposure models are created using the ExposureModel function.
reinfection_model	A reinfection model object, which describes whether or not individuals are able to return from the Removed category to the Susceptible population. Valid reinfection models are created using the ReinfectionModel function.
distance_model	A distance model object which describes the underlying contact network, in addition to prior parameters which constrain the contact process. Valid distance models are created using DistanceModel
transition_priors	An object containing information about the E to I and I to R transition prior parameters. These are created using the TransitionPriors function, and involve either transition probabilities and corresponding effective sample sizes (amount of prior information), or manually specified probability distributions. .
initial_value_container	An object specifying the initial state of the epidemic for each spatial location, created by the InitialValueContainer function.

Details

This function is provided for testing and debugging purposes: it's not intended for the end user

Value

a list

Examples

## Not run: results = Rsim(seed, 
                                   beta_SE,
                                   beta_RS, 
                                   rho,
                                   exposure_model,
                                   reinfection_model,
                                   distance_model,
                                   transition_priors,
                                   initial_value_container)
## End(Not run)

grantbrown/ABSEIR documentation built on Oct. 14, 2021, 2:32 p.m.