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

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

Value

matrix containing the compartment counts at census times.