This function sets up and runs a particle MCMC that uses Dust, Odin and MCState
Usage
test_pf(
data_raw = NULL,
data_raw_pg = NULL,
data_raw_mg = NULL,
n_particles = 200,
proposal_matrix,
max_param = 1000,
max_steps = 1e+07,
atol = 1e-06,
rtol = 1e-06,
n_steps = 500,
n_threads = 4,
lag_rates = 10,
state_check = 0,
country = NULL,
admin_unit = NULL,
preyears = 2,
seasonality_on = 1,
seasonality_check = 0,
seed = 1L,
start_pf_time = 30,
stoch_param = c("EIR", "betaa"),
comparison = c("u5", "pgmg")
)Arguments
- data_raw
Time series data to fit model
- data_raw_pg
Time series of primigravidae ANC data to fit model
- data_raw_mg
Time series of multigravidae ANC data to fit model
- n_particles
Number of particles to be used in pMCMC (default = 200)
- proposal_matrix
Proposal matrix for MCMC parameters
- max_param
Ceiling for proposed stochastic parameter (either EIR or betaa) values (default = 1000)
- max_steps
Maximum steps for particle filter (default = 1e7)
- atol
atol for particle filter (default = 1e-3)
- rtol
rtol for particle filter (default = 1e-6)
- n_steps
Number of MCMC steps in a single chain (default = 500)
- n_threads
Number of processing threads (default = 4)
- lag_rates
Number of delay compartments (default = 10)
- state_check
Run equilibrium checks, if state_check = 1, returns expected deriv values which should equal 0 and sets stochastic model to have EIR constant at init_EIR If state_check = 1 and seasonality_on = 1, then the deterministic seasonal model is still run, but theta2 is forced to 1, forcing a constant seasonality profile If state_check = 0, no values are printed
- country
Name of country (needed if using seasonality model)
- admin_unit
Name of administrative unit (needed if using seasonality model)
- preyears
Length of time in years the deterministic seasonal model should run before Jan 1 of the year observations began (default = 2)
- seasonality_on
Toggle seasonality model run before observed time period (default = 1)
- seasonality_check
Toggle saving values of seasonality equilibrium (default = 1)
- seed
Allows user to specify a seed (default = 1L)
- start_pf_time
Number of days before first observation that particle filter will start (default = 30)
- stoch_param
Which parameter to test
- comparison
The comparison function to be used. Either 'u5' which equates the observed prevalence to prevalence under 5 years old in the model or 'pgmg' which calculates prevalence in primigravid and multigravid pregnant women for comparison with observed ANC data. c('u5','pg','sg','mg','pgmg','pgsg','ancall')