simulate_gillespie: Simulate a stochastic epidemic model path via Gillespie's...
In fintzij/stemr: Stochastic Epidemic Model Simulation and Estimation

simulate_gillespie

R Documentation

Simulate a stochastic epidemic model path via Gillespie's direct method and returns a matrix containing a simulated path from a stochastic epidemic model.

Description

Simulate a stochastic epidemic model path via Gillespie's direct method and returns a matrix containing a simulated path from a stochastic epidemic model.

Usage

simulate_gillespie(
  flow,
  parameters,
  constants,
  tcovar,
  t_max,
  init_states,
  rate_adjmat,
  tcovar_adjmat,
  tcovar_changemat,
  init_dims,
  forcing_inds,
  forcing_tcov_inds,
  forcings_out,
  forcing_transfers,
  rate_ptr
)

Arguments

`flow`	Flow matrix
`parameters`	Vector of parameters
`constants`	vector of constants
`tcovar`	matrix of time-varying covariates
`init_states`	vector of initial compartment counts
`rate_adjmat`	adjacency matrix for updating rates after each event
`tcovar_adjmat`	adjacency matrix for updating rates after each time a covariate changes
`tcovar_changemat`	indicator matrix identifying which covariates change at each time
`init_dims`	initial estimate for dimensions of the bookkeeping matrix, calculated as sum_strata(stratum size x number states x 3), rounded to the next greatest power of 2.
`forcing_inds`	logical vector of indicating at which times in the time-varying covariance matrix a forcing is applied.
`rate_ptr`	external function pointer to the lumped rate functions.
`forcing_matrix`	matrix containing the forcings.