#include "model_ssm_nlg.h"

#include "filter_smoother.h"
#include "summary.h"

// [[Rcpp::export]]
Rcpp::List ekpf(const arma::mat& y, SEXP Z, SEXP H,
  SEXP T, SEXP R, SEXP Zg, SEXP Tg, SEXP a1, SEXP P1,
  const arma::vec& theta, SEXP log_prior_pdf, const arma::vec& known_params,
  const arma::mat& known_tv_params, const unsigned int n_states,
  const unsigned int n_etas,  const arma::uvec& time_varying,
  const unsigned int nsim, const unsigned int seed) {


  Rcpp::XPtr<nvec_fnPtr> xpfun_Z(Z);
  Rcpp::XPtr<nmat_fnPtr> xpfun_H(H);
  Rcpp::XPtr<nvec_fnPtr> xpfun_T(T);
  Rcpp::XPtr<nmat_fnPtr> xpfun_R(R);
  Rcpp::XPtr<nmat_fnPtr> xpfun_Zg(Zg);
  Rcpp::XPtr<nmat_fnPtr> xpfun_Tg(Tg);
  Rcpp::XPtr<a1_fnPtr> xpfun_a1(a1);
  Rcpp::XPtr<P1_fnPtr> xpfun_P1(P1);
  Rcpp::XPtr<prior_fnPtr> xpfun_prior(log_prior_pdf);

  ssm_nlg model(y, *xpfun_Z, *xpfun_H, *xpfun_T, *xpfun_R, *xpfun_Zg, *xpfun_Tg,
    *xpfun_a1, *xpfun_P1,  theta, *xpfun_prior, known_params, known_tv_params, n_states, n_etas,
    time_varying, seed);

  unsigned int m = model.m;
  unsigned n = model.n;

  arma::cube alpha(m, n+1, nsim, arma::fill::zeros);
  arma::mat weights(nsim, n+1, arma::fill::zeros);
  arma::umat indices(nsim, n, arma::fill::zeros);
  double loglik = model.ekf_filter(nsim, alpha, weights, indices);
  if (!std::isfinite(loglik)) 
    Rcpp::warning("Particle filtering stopped prematurely due to nonfinite log-likelihood.");
  

  arma::mat at(m, n + 1);
  arma::mat att(m, n + 1);
  arma::cube Pt(m, m, n + 1);
  arma::cube Ptt(m, m, n + 1);
  filter_summary(alpha, at, att, Pt, Ptt, weights);

  arma::inplace_trans(att);
  return Rcpp::List::create(
    Rcpp::Named("att") = att,
    Rcpp::Named("Ptt") = Ptt,
    Rcpp::Named("weights") = weights,
    Rcpp::Named("logLik") = loglik, Rcpp::Named("alpha") = alpha);
}

// [[Rcpp::export]]
Rcpp::List ekpf_smoother(const arma::mat& y, SEXP Z, SEXP H,
  SEXP T, SEXP R, SEXP Zg, SEXP Tg, SEXP a1, SEXP P1,
  const arma::vec& theta, SEXP log_prior_pdf, const arma::vec& known_params,
  const arma::mat& known_tv_params, const unsigned int n_states,
  const unsigned int n_etas,  const arma::uvec& time_varying,
  const unsigned int nsim, const unsigned int seed) {

  Rcpp::XPtr<nvec_fnPtr> xpfun_Z(Z);
  Rcpp::XPtr<nmat_fnPtr> xpfun_H(H);
  Rcpp::XPtr<nvec_fnPtr> xpfun_T(T);
  Rcpp::XPtr<nmat_fnPtr> xpfun_R(R);
  Rcpp::XPtr<nmat_fnPtr> xpfun_Zg(Zg);
  Rcpp::XPtr<nmat_fnPtr> xpfun_Tg(Tg);
  Rcpp::XPtr<a1_fnPtr> xpfun_a1(a1);
  Rcpp::XPtr<P1_fnPtr> xpfun_P1(P1);
  Rcpp::XPtr<prior_fnPtr> xpfun_prior(log_prior_pdf);

  ssm_nlg model(y, *xpfun_Z, *xpfun_H, *xpfun_T, *xpfun_R, *xpfun_Zg, *xpfun_Tg,
    *xpfun_a1, *xpfun_P1,  theta, *xpfun_prior, known_params, known_tv_params, n_states, n_etas,
    time_varying, seed);

  unsigned int m = model.m;
  unsigned n = model.n;

  arma::cube alpha(m, n + 1, nsim, arma::fill::zeros);
  arma::mat weights(nsim, n + 1, arma::fill::zeros);
  arma::umat indices(nsim, n, arma::fill::zeros);
  double loglik = model.ekf_filter(nsim, alpha, weights, indices);
  if (!std::isfinite(loglik)) 
    Rcpp::warning("Particle filtering stopped prematurely due to nonfinite log-likelihood.");
  

  arma::mat alphahat(model.m, model.n + 1);
  arma::cube Vt(model.m, model.m, model.n + 1);

  filter_smoother(alpha, indices);
  summary(alpha, alphahat, Vt);

  arma::inplace_trans(alphahat);

  return Rcpp::List::create(
    Rcpp::Named("alphahat") = alphahat, Rcpp::Named("Vt") = Vt,
    Rcpp::Named("weights") = weights,
    Rcpp::Named("logLik") = loglik, Rcpp::Named("alpha") = alpha);
  }