R/pbla_gsem.R

In sdtemple/pblas: Pair-based Likelihood Approximations

#' PBLAs for General Stochastic Epidemic Model
#'
#' Run a pair-based likelihood approximation for a general stochastic epidemic model. Compatible with `pbla_prod`, `pbla_weak`, `pbla_std_gsem`, `pbla_sep_gsem`, `pbla_f_gsem`, and `pbla_ed_gsem`.
#'
#' @param rates numeric vector of rates
#' @param pbla function
#' @param r numeric vector of increasing removal times
#' @param N integer population size
#' @param etc other parameters to pass (e.g. lag)
#'
#' @return negative log likelihood
#'
#' @export
pbla_gsem = function(rates, pbla, r, N, etc = NULL){
  beta = rates[1]
  gamma = rates[2]
  if(is.null(etc)){ # use defaults
    return(do.call(pbla, list(r=r,beta=beta,gamma=gamma,N=N)))
  } else{ # pass in all parameters
    return(do.call(pbla, c(list(r=r,beta=beta,gamma=gamma,N=N), etc)))
  }
}