initialize_lna: Initialize the LNA path

In fintzij/stemr: Stochastic Epidemic Model Simulation and Estimation

Initialize the LNA path

Description

Initialize the LNA path

Usage

initialize_lna(
  dat,
  parmat,
  param_blocks,
  tparam,
  censusmat,
  emitmat,
  stoich_matrix,
  proc_pointer,
  set_pars_pointer,
  census_times,
  param_vec,
  param_inds,
  const_inds,
  tcovar_inds,
  initdist_inds,
  param_update_inds,
  census_indices,
  event_inds,
  measproc_indmat,
  d_meas_pointer,
  do_prevalence,
  forcing_inds,
  forcing_tcov_inds,
  forcings_out,
  forcing_transfers,
  initialization_attempts,
  step_size,
  initdist_objects,
  ess_warmup
)

Arguments

parmat	matrix with parameters, contants, time-varying pars and covars
param_blocks	list of parameter blocks
tparam	list of time-varying parameters
censusmat	template matrix for the LNA path and incidence at the observation times
emitmat	matrix in which to store the log-emission probabilities
stoich_matrix	LNA stoichiometry matrix
proc_pointer	external LNA pointer
set_pars_pointer	pointer for setting the LNA parameters
census_times	times at which the LNA should be evaluated
param_vec	vector for storing lna parameters when evaluating the measurement process
param_inds	C++ column indices for parameters
const_inds	C++ column indices for constants
tcovar_inds	C++ column indices for time varying covariates
initdist_inds	C++ column indices in the LNA parameter matrix for the initial state
param_update_inds	logical vector indicating when to update the parameters
census_indices	C++ row indices of LNA times when the path is to be censused
event_inds	vector of column indices in the LNA path for which incidence will be computed.
measproc_indmat	logical matrix for evaluating the measuement process
d_meas_pointer	external pointer for the measurement process function
do_prevalence	should prevalence be computed?
forcing_inds	logical vector of indicating at which times in the time-varying covariance matrix a forcing is applied.
initialization_attempts	number of initialization attempts
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).
ess_warmup	number of elliptical slice sampling updates where likelihood is over indicators for monotonicity and non-negativity of LNA increments
data	matrix containing the dataset
par_init_fcn	function for initializing the parameter values

Value

LNA path along with its stochastic perturbations

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