diff options
Diffstat (limited to 'src/nll_pcountOpen.cpp')
| -rw-r--r-- | src/nll_pcountOpen.cpp | 54 |
1 files changed, 15 insertions, 39 deletions
diff --git a/src/nll_pcountOpen.cpp b/src/nll_pcountOpen.cpp index 9d31e8e..235976c 100644 --- a/src/nll_pcountOpen.cpp +++ b/src/nll_pcountOpen.cpp @@ -1,44 +1,24 @@ -#include "nll_pcountOpen.h" -#include "tranprobs.h" +#include <RcppArmadillo.h> +#include <float.h> #include "distr.h" +#include "tranprobs.h" using namespace Rcpp ; +// [[Rcpp::export]] +double nll_pcountOpen(arma::imat ym, arma::mat Xlam, arma::mat Xgam, arma::mat Xom, + arma::mat Xp, arma::mat Xiota, arma::colvec beta_lam, arma::colvec beta_gam, + arma::colvec beta_om, arma::colvec beta_p, arma::colvec beta_iota, + double log_alpha, arma::colvec Xlam_offset, arma::colvec Xgam_offset, + arma::colvec Xom_offset, arma::colvec Xp_offset, arma::colvec Xiota_offset, + arma::imat ytna, arma::imat ynam, int lk, std::string mixture, + Rcpp::IntegerVector first, Rcpp::IntegerVector last, int M, int J, int T, + arma::imat delta, std::string dynamics, std::string fix, std::string go_dims, + bool immigration, arma::imat I, arma::imat I1, Rcpp::List Ib, Rcpp::List Ip) { -SEXP nll_pcountOpen( SEXP y_, SEXP Xlam_, SEXP Xgam_, SEXP Xom_, SEXP Xp_, SEXP Xiota_, SEXP beta_lam_, SEXP beta_gam_, SEXP beta_om_, SEXP beta_p_, SEXP beta_iota_, SEXP log_alpha_, SEXP Xlam_offset_, SEXP Xgam_offset_, SEXP Xom_offset_, SEXP Xp_offset_, SEXP Xiota_offset_, SEXP ytna_, SEXP yna_, SEXP lk_, SEXP mixture_, SEXP first_, SEXP last_, SEXP M_, SEXP J_, SEXP T_, SEXP delta_, SEXP dynamics_, SEXP fix_, SEXP go_dims_, SEXP immigration_, SEXP I_, SEXP I1_, SEXP Ib_, SEXP Ip_) { - int lk = as<int>(lk_); Rcpp::IntegerVector N = seq_len(lk)-1; - int M = as<int>(M_); - int J = as<int>(J_); - int T = as<int>(T_); - arma::imat ym = as<arma::imat>(y_); - arma::mat Xlam = as<arma::mat>(Xlam_); - arma::mat Xgam = as<arma::mat>(Xgam_); - arma::mat Xom = as<arma::mat>(Xom_); - arma::mat Xp = as<arma::mat>(Xp_); - arma::mat Xiota = as<arma::mat>(Xiota_); - arma::colvec beta_lam = as<arma::colvec>(beta_lam_); - arma::colvec beta_gam = as<arma::colvec>(beta_gam_); - arma::colvec beta_om = as<arma::colvec>(beta_om_); - arma::colvec beta_p = as<arma::colvec>(beta_p_); - arma::colvec beta_iota = as<arma::colvec>(beta_iota_); - double log_alpha = as<double>(log_alpha_); - arma::colvec Xlam_offset = as<arma::colvec>(Xlam_offset_); - arma::colvec Xgam_offset = as<arma::colvec>(Xgam_offset_); - arma::colvec Xom_offset = as<arma::colvec>(Xom_offset_); - arma::colvec Xp_offset = as<arma::colvec>(Xp_offset_); - arma::colvec Xiota_offset = as<arma::colvec>(Xiota_offset_); - std::string mixture = as<std::string>(mixture_); - std::string dynamics = as<std::string>(dynamics_); - std::string fix = as<std::string>(fix_); - std::string go_dims = as<std::string>(go_dims_); - bool immigration = as<bool>(immigration_); - arma::imat I = as<arma::imat>(I_); - arma::imat I1 = as<arma::imat>(I1_); - Rcpp::List Ib(Ib_); - Rcpp::List Ip(Ip_); int nrI = I.n_rows; int nrI1 = I1.n_rows; double alpha=0.0, psi=0.0; @@ -46,11 +26,7 @@ SEXP nll_pcountOpen( SEXP y_, SEXP Xlam_, SEXP Xgam_, SEXP Xom_, SEXP Xp_, SEXP alpha = exp(log_alpha); else if(mixture=="ZIP") psi = 1.0/(1.0+exp(-log_alpha)); - Rcpp::IntegerVector first(first_); - Rcpp::IntegerVector last(last_); - arma::imat ytna = as<arma::imat>(ytna_); // y[i,,t] are all NA - arma::imat ynam = as<arma::imat>(yna_); // y[i,j,t] is NA - arma::imat delta = as<arma::imat>(delta_); + // linear predictors arma::colvec lam = exp(Xlam*beta_lam + Xlam_offset); arma::mat omv = arma::ones<arma::colvec>(M*(T-1)); @@ -232,5 +208,5 @@ SEXP nll_pcountOpen( SEXP y_, SEXP Xlam_, SEXP Xgam_, SEXP Xom_, SEXP Xp_, SEXP } ll += log(ll_i + DBL_MIN); } - return wrap(-ll); + return -ll; } |