census_latent_path: Construct a matrix containing the compartment counts and the...
In fintzij/stemr: Stochastic Epidemic Model Simulation and Estimation

census_latent_path

R Documentation

Construct a matrix containing the compartment counts and the incidence at a sequence of census times.

Description

Construct a matrix containing the compartment counts and the incidence at a sequence of census times.

Usage

census_latent_path(
  path,
  census_path,
  census_inds,
  event_inds,
  flow_matrix,
  do_prevalence,
  parmat,
  initdist_inds,
  forcing_inds,
  forcing_tcov_inds,
  forcings_out,
  forcing_transfers,
  row0 = 0L
)

Arguments

`path`	matrix containing the path to be censused (cumulative incidence).
`census_path`	matrix to be filled out with the path.
`census_inds`	vector of indices for census interval endpoints.
`event_inds`	vector of column indices in the path matrix for events that should be censused.
`flow_matrix`	matrix containing the flow matrix for the LNA (no incidence)
`do_prevalence`	should the prevalence be computed
`parmat`	matrix with parameters, constants, and time varying covariates and parameters.
`forcing_inds`	logical vector of indicating at which times in the time-varying covariance matrix a forcing is applied.
`init_state`	the initial compartment counts