tparam_update: Sample a new LNA path via elliptical slice sampling.
In fintzij/stemr: Stochastic Epidemic Model Simulation and Estimation

tparam_update

R Documentation

Sample a new LNA path via elliptical slice sampling.

Description

Sample a new LNA path via elliptical slice sampling.

Usage

tparam_update(
  path,
  dat,
  iter,
  parmat,
  tparam,
  tparam_ess_control,
  pathmat_prop,
  censusmat,
  draws_prop,
  ess_draws_prop,
  emitmat,
  flow_matrix,
  stoich_matrix,
  census_times,
  forcing_inds,
  forcing_tcov_inds,
  forcings_out,
  forcing_transfers,
  param_vec,
  param_inds,
  const_inds,
  tcovar_inds,
  initdist_inds,
  param_update_inds,
  census_indices,
  event_inds,
  measproc_indmat,
  svd_d = NULL,
  svd_U = NULL,
  svd_V = NULL,
  proc_pointer,
  set_pars_pointer,
  d_meas_pointer,
  do_prevalence,
  step_size
)

Arguments

`path`	path list
`dat`	data matrix
`iter`	MCMC iteration
`tparam`	list of time-varying parameters
`pathmat_prop`	matrix for proposed paths
`censusmat`	census matrix
`emitmat`	emission matrix
`flow_matrix`	flow matrix
`stoich_matrix`	stoichiometry matrix
`forcing_inds`	forcing indices
`forcing_tcov_inds`	time varying covariate forcings
`forcings_out`	matrix with outflow from forcings
`forcing_transfers`	transfer matrix
`param_vec`	parameter vector for use in emission distribution
`initdist_inds`	indices of initial compartment counts
`census_indices`	indices where the path should be censused
`event_inds`	event indices
`measproc_indmat`	measurement process indices
`svd_d`	SVD objects for LNA, NULL if using the ODE approx
`svd_U`	SVD objects for LNA, NULL if using the ODE approx
`svd_V`	SVD objects for LNA, NULL if using the ODE approx
`proc_pointer`	C++ pointer for latent process
`d_meas_pointer`	C++ pointer for emission distribution
`do_prevalence`	should prevalence be computed
`step_size`	initial step size for ODE solvers