Map parameters to the deterministic mean incidence increments for a stochastic epidemic model.

map_pars_2_ode(
  pathmat,
  ode_times,
  ode_pars,
  ode_param_vec,
  ode_param_inds,
  ode_tcovar_inds,
  init_start,
  param_update_inds,
  stoich_matrix,
  forcing_inds,
  forcing_tcov_inds,
  forcings_out,
  forcing_transfers,
  step_size,
  ode_pointer,
  set_pars_pointer
)

Arguments

pathmat: matrix where the ODE path should be stored
ode_times: vector of interval endpoint times
ode_pars: numeric matrix of parameters, constants, and time-varying covariates at each of the ode_times
init_start: index in the parameter vector where the initial compartment volumes start
param_update_inds: logical vector indicating at which of the times the ode parameters need to be updated.
stoich_matrix: stoichiometry matrix giving the changes to compartments from each reaction
forcing_inds: logical vector of indicating at which times in the time-varying covariance matrix a forcing is applied.
step_size: initial step size for the ODE solver (adapted internally, but too large of an initial step can lead to failure in stiff systems).
ode_pointer: external pointer to ode integration function.
set_pars_pointer: external pointer to the function for setting the ode parameters.
forcing_matrix: matrix containing the forcings.

Value

List containing the ODE incidence and prevalence paths.