lna_update: Sample a new LNA path via elliptical slice sampling.

In fintzij/stemr: Stochastic Epidemic Model Simulation and Estimation

Sample a new LNA path via elliptical slice sampling.

Description

Sample a new LNA path via elliptical slice sampling.

Usage

lna_update(
  path,
  dat,
  iter,
  parmat,
  lna_ess_schedule,
  lna_ess_control,
  initdist_objects,
  tparam,
  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,
  svd_U,
  svd_V,
  proc_pointer,
  set_pars_pointer,
  d_meas_pointer,
  do_prevalence,
  joint_initdist_update,
  step_size
)

Arguments

path	path list
dat	data matrix
iter	MCMC iteration
lna_ess_schedule
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

Value

list with an updated LNA path along with its stochastic perturbations, the observed dat log-likelihood, and the lna log-likelihood, and a record of the number of elliptical slice sampling proposals

fintzij/stemr documentation built on March 25, 2022, 12:25 p.m.