R/outbreaker_init_mcmc.R

In thibautjombart/outbreaker2: Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

## #' Initianilizes outputs for outbreaker
## #'
## #' This function creates initial outputs and parameter states for outbreaker.
## #'
## #' @author Thibaut Jombart (\email{thibautjombart@@gmail.com})
## #'
## #' @param param a list of data items as returned by \code{create_param}
## #'
## #' @param loglike a list of loglikelihood functions with enclosed data as returned by \code{custom_likelihood}
## #'
## #' @param priors a list of prior functions with enclosed parameters as returned by \code{custom_priors}
## #'
## #' @export
## #'
outbreaker_init_mcmc <- function(data, param_current, param_store, loglike, priors, config) {

    ## COMPUTE INITIAL LIKE/PRIOR/POST ##
    param_store$like[1] <- cpp_ll_all(data, param_current, NULL, loglike)
    param_store$prior[1] <- cpp_prior_all(param_current, config, priors)
    param_store$post[1] <- param_store$like[1] + param_store$prior[1]

    if(is.infinite(param_store$post[1])) {
        stop("Likelihood of initial parameter state is -Inf")
    }

    return(param_store)
}