Initialize the LNA path

Initialize the LNA path

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