R/calc_pop_likelihood.R

In fintzij/BDAepimodel: Fit Stochastic Epidemic Models in R via Bayesian Data Augmentation

#' Calculate likelihood for the population level trajectory
#'
#' @inheritParams simulate_epimodel
#' @param params optional vector of parameters if values other than the current
#'   values should be used (e.g. in a transition kernel)
#' @param log TRUE/FALSE for whether to return the log-likelihood or likelihood.
#'
#' @return vector with log-likelihood of the population level trajectory and
#'   measurement process log-likelihood.
#'
#' @export
#'

calc_pop_likelihood <- function(epimodel, log = TRUE) {

          pop_likelihood <-
                    populationLikelihood(
                              pop_mat             = epimodel$pop_mat,
                              irm                 = epimodel$irm,
                              initdist            = epimodel$initdist,
                              initdist_param_inds = epimodel$initdist_param_inds,
                              flow_inds           = epimodel$flow_inds,
                              keys                = epimodel$keys,
                              inds                = c(1, 
                                                      c(1:epimodel$ind_final_config)[-epimodel$obs_time_inds], 
                                                      epimodel$ind_final_config),
                              loglik = log
                    )
          
          return(pop_likelihood)
}