run_particle_filter: Run particle filter

In mrc-ide/squire: SEIR transmission model of COVID-19

Run particle filter

Description

Create a model, and fit with the particle filter

Usage

run_particle_filter(
  data,
  squire_model,
  model_params,
  model_start_date = "2020-02-02",
  obs_params = list(phi_cases = 0.1, k_cases = 2, phi_death = 1, k_death = 2, exp_noise
    = 1e+06),
  n_particles = 1000,
  forecast_days = 0,
  save_particles = FALSE,
  full_output = FALSE,
  return = "full"
)

Arguments

data	to fit to.
squire_model	A squire model to use
model_params	Squire model parameters. Created from a call to one of the parameters_<type>_model functions.
model_start_date	Date to run model simulations from
obs_params	List of parameters used for comparing model to data in the particle filter t
n_particles	Number of particles
forecast_days	Days ahead to include in output
save_particles	Whether to save trajectories
full_output	Logical, indicating whether the full model output, including the state and the declared outputs are returned. Deafult = FALSE
return	Set return depending on what is needed. 'full' gives the entire particle filter output, 'll' gives the log-likelihood, 'sample' gives a sampled particle's trace, 'single' gives the final state

Value

Results from particle filter

mrc-ide/squire documentation built on Sept. 10, 2022, 1:11 a.m.