R/fn_ComputePrior.R

In a-henderson91/vectorbornefit: MCMC fit SEIR model of vetor borne transmission

##' Compute prior
##' 
##' @param iiH Numeric indicator of location given by location vector "locationtab[]"
##' @param thetaAlltab Current values of parameter set theta
##' @param thetaAllstar Proposed values of parameter set theta
##' @export
# thetaAlltab=thetaAlltab_current[iiH,];  thetaAllstar=thetaA_star; covartheta = cov_matrix_thetaA
ComputePrior <- function(iiH, thetaAlltab, thetaAllstar, covartheta){
  # Compute prior of proposed parameter set theta
  p_theta_star =  priorInf(1/thetaAllstar["Inf"])*
                  priorExp(1/thetaAllstar["Exp"])*
                  priorVEx(1/thetaAllstar["Vex"])*
                  priorMuV(1/thetaAllstar["MuV"])*
                  priorChi(thetaAllstar["chi"])*
                  priorBeta(thetaAllstar["beta_h"])*
                  priorBetaV(thetaAllstar["beta_v"])*
                  priorInitInf(thetaAllstar["intro_base"])*
                  priorInitWidth(thetaAllstar["intro_width"])*
                  priorIntro(thetaAllstar["intro_mid"])

  # If vector control is included in the model - include prior density of proposed 
  #   strength of control measure
  if(vector.control==T){
    #p_theta_star <- p_theta_star*prior_control(c(thetaAllstar["beta_base"], thetaAllstar["beta_mid"]))
    p_theta_star <- p_theta_star*prior_vectorcontrol(thetaAllstar["beta_base"])
  }
  # If seasonal transmission is estimated, include in prior
  if(seasonal.transmission==T){
    p_theta_star <- p_theta_star*                  
      priorBeta_amp(thetaAllstar["beta_v_amp"])*
      priorBeta_mid(thetaAllstar["beta_v_mid"])
  }
  
  # Compute prior of current parameter set theta
  p_theta = priorInf(1/thetaAlltab["Inf"])*
            priorExp(1/thetaAlltab["Exp"])*
            priorVEx(1/thetaAlltab["Vex"])*
            priorMuV(1/thetaAlltab["MuV"])*
            priorChi(thetaAlltab["chi"])*
            priorBeta(thetaAlltab["beta_h"])*
            priorBetaV(thetaAlltab["beta_v"])*
            priorInitInf(thetaAlltab["intro_base"])*
            priorInitWidth(thetaAlltab["intro_width"])*
            priorIntro(thetaAlltab["intro_mid"])
  
  # If vector control is included in the model - include prior density of proposed 
  #   strength of control measure
  if(vector.control==T){
    #p_theta <- p_theta*prior_control(c(thetaAlltab["beta_base"], thetaAlltab["beta_mid"]))
    p_theta <- p_theta*prior_vectorcontrol(thetaAlltab["beta_base"])
  }
  # If seasonal transmission is estimated, include in prior
  if(seasonal.transmission==T){
    p_theta <- p_theta*                  
      priorBeta_amp(thetaAlltab["beta_v_amp"])*
      priorBeta_mid(thetaAlltab["beta_v_mid"])
  }
  # formatting and replace NAs with 0 
  names(p_theta_star)=NULL;names(p_theta)=NULL
  if(is.na(p_theta_star)==T){p_theta_star=1}
  if(is.na(p_theta)==T){p_theta=1}
  return(list(prior.star=p_theta_star,prior=p_theta))
}