particle_filter: Run a particle filter

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

Run a particle filter

Description

Run a particle filter

Usage

particle_filter(
  data,
  model,
  compare,
  n_particles,
  forecast_days = 0,
  save_particles = FALSE,
  full_output = FALSE,
  save_sample_state = FALSE,
  save_end_states = FALSE
)

Arguments

data	Data to fit to. This must be constructed with particle_filter_data
model	An odin model, used to generate stochastic samples
compare	A function to generate log-weights
n_particles	Number of particles
forecast_days	Number of days to forecast forward from end states. Requires that save_particles is TRUE.
save_particles	Logical, indicating if we save full particle histories (this is slower).
full_output	Logical, indicating whether the full model output, including the state and the declared outputs are returned. Deafult = FALSE
save_sample_state	Logical, indicating whether we should save a single particle, chosen at random, at the final time point for which we have data
save_end_states	Logical, indicating whether we should save all particles at the final time point for which we have data

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