View source: R/initialize_lna.R
initialize_lna | R Documentation |
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 )
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 |
LNA path along with its stochastic perturbations
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