From 827508a5ef645e7bd3a0d76fd94acb4d9c3e3db4 Mon Sep 17 00:00:00 2001
From: Ken Kellner <ken@kenkellner.com>
Date: Sat, 2 Mar 2024 20:55:17 -0500
Subject: Refactor gdistsamp likelihood for stability

---
 R/RcppExports.R                 |  4 +--
 R/gdistsamp.R                   |  2 +-
 src/RcppExports.cpp             | 13 ++++------
 src/nll_gdistsamp.cpp           | 54 +++++++++++++++++++++++------------------
 tests/testthat/test_gdistsamp.R |  8 +++---
 5 files changed, 42 insertions(+), 39 deletions(-)

diff --git a/R/RcppExports.R b/R/RcppExports.R
index 70b57ac..7aba254 100644
--- a/R/RcppExports.R
+++ b/R/RcppExports.R
@@ -21,8 +21,8 @@ nll_gdistremoval <- function(beta, n_param, yDistance, yRemoval, ysum, mixture,
     .Call(`_unmarked_nll_gdistremoval`, beta, n_param, yDistance, yRemoval, ysum, mixture, keyfun, Xlam, A, Xphi, Xrem, Xdist, db, a, u, w, pl, K, Kmin, threads)
 }
 
-nll_gdistsamp <- function(beta, n_param, y, mixture, keyfun, survey, Xlam, Xlam_offset, A, Xphi, Xphi_offset, Xdet, Xdet_offset, db, a, u, w, k, lfac_k, lfac_kmyt, kmyt, Kmin, threads) {
-    .Call(`_unmarked_nll_gdistsamp`, beta, n_param, y, mixture, keyfun, survey, Xlam, Xlam_offset, A, Xphi, Xphi_offset, Xdet, Xdet_offset, db, a, u, w, k, lfac_k, lfac_kmyt, kmyt, Kmin, threads)
+nll_gdistsamp <- function(beta, n_param, y, mixture, keyfun, survey, Xlam, Xlam_offset, A, Xphi, Xphi_offset, Xdet, Xdet_offset, db, a, u, w, K, Kmin, threads) {
+    .Call(`_unmarked_nll_gdistsamp`, beta, n_param, y, mixture, keyfun, survey, Xlam, Xlam_offset, A, Xphi, Xphi_offset, Xdet, Xdet_offset, db, a, u, w, K, Kmin, threads)
 }
 
 nll_gmultmix <- function(beta, n_param, y, mixture, pi_fun, Xlam, Xlam_offset, Xphi, Xphi_offset, Xdet, Xdet_offset, k, lfac_k, lfac_kmyt, kmyt, Kmin, threads) {
diff --git a/R/gdistsamp.R b/R/gdistsamp.R
index c43076a..5342b8e 100644
--- a/R/gdistsamp.R
+++ b/R/gdistsamp.R
@@ -411,7 +411,7 @@ if(engine =="C"){
   nll <- function(params){
     nll_gdistsamp(params, n_param, y_long, mixture_code, keyfun, survey,
                   Xlam, Xlam.offset, A, Xphi, Xphi.offset, Xdet, Xdet.offset,
-                  db, a, t(u), w, k, lfac.k, lfac.kmyt, kmyt, Kmin, threads)
+                  db, a, t(u), w, K, Kmin, threads)
   }
 
 } else {
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
index 0fe45a8..69c817e 100644
--- a/src/RcppExports.cpp
+++ b/src/RcppExports.cpp
@@ -141,8 +141,8 @@ BEGIN_RCPP
 END_RCPP
 }
 // nll_gdistsamp
-double nll_gdistsamp(arma::vec beta, arma::uvec n_param, arma::vec y, int mixture, std::string keyfun, std::string survey, arma::mat Xlam, arma::vec Xlam_offset, arma::vec A, arma::mat Xphi, arma::vec Xphi_offset, arma::mat Xdet, arma::vec Xdet_offset, arma::vec db, arma::mat a, arma::mat u, arma::vec w, arma::vec k, arma::vec lfac_k, arma::cube lfac_kmyt, arma::cube kmyt, arma::uvec Kmin, int threads);
-RcppExport SEXP _unmarked_nll_gdistsamp(SEXP betaSEXP, SEXP n_paramSEXP, SEXP ySEXP, SEXP mixtureSEXP, SEXP keyfunSEXP, SEXP surveySEXP, SEXP XlamSEXP, SEXP Xlam_offsetSEXP, SEXP ASEXP, SEXP XphiSEXP, SEXP Xphi_offsetSEXP, SEXP XdetSEXP, SEXP Xdet_offsetSEXP, SEXP dbSEXP, SEXP aSEXP, SEXP uSEXP, SEXP wSEXP, SEXP kSEXP, SEXP lfac_kSEXP, SEXP lfac_kmytSEXP, SEXP kmytSEXP, SEXP KminSEXP, SEXP threadsSEXP) {
+double nll_gdistsamp(arma::vec beta, arma::uvec n_param, arma::vec y, int mixture, std::string keyfun, std::string survey, arma::mat Xlam, arma::vec Xlam_offset, arma::vec A, arma::mat Xphi, arma::vec Xphi_offset, arma::mat Xdet, arma::vec Xdet_offset, arma::vec db, arma::mat a, arma::mat u, arma::vec w, int K, arma::uvec Kmin, int threads);
+RcppExport SEXP _unmarked_nll_gdistsamp(SEXP betaSEXP, SEXP n_paramSEXP, SEXP ySEXP, SEXP mixtureSEXP, SEXP keyfunSEXP, SEXP surveySEXP, SEXP XlamSEXP, SEXP Xlam_offsetSEXP, SEXP ASEXP, SEXP XphiSEXP, SEXP Xphi_offsetSEXP, SEXP XdetSEXP, SEXP Xdet_offsetSEXP, SEXP dbSEXP, SEXP aSEXP, SEXP uSEXP, SEXP wSEXP, SEXP KSEXP, SEXP KminSEXP, SEXP threadsSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
@@ -163,13 +163,10 @@ BEGIN_RCPP
     Rcpp::traits::input_parameter< arma::mat >::type a(aSEXP);
     Rcpp::traits::input_parameter< arma::mat >::type u(uSEXP);
     Rcpp::traits::input_parameter< arma::vec >::type w(wSEXP);
-    Rcpp::traits::input_parameter< arma::vec >::type k(kSEXP);
-    Rcpp::traits::input_parameter< arma::vec >::type lfac_k(lfac_kSEXP);
-    Rcpp::traits::input_parameter< arma::cube >::type lfac_kmyt(lfac_kmytSEXP);
-    Rcpp::traits::input_parameter< arma::cube >::type kmyt(kmytSEXP);
+    Rcpp::traits::input_parameter< int >::type K(KSEXP);
     Rcpp::traits::input_parameter< arma::uvec >::type Kmin(KminSEXP);
     Rcpp::traits::input_parameter< int >::type threads(threadsSEXP);
-    rcpp_result_gen = Rcpp::wrap(nll_gdistsamp(beta, n_param, y, mixture, keyfun, survey, Xlam, Xlam_offset, A, Xphi, Xphi_offset, Xdet, Xdet_offset, db, a, u, w, k, lfac_k, lfac_kmyt, kmyt, Kmin, threads));
+    rcpp_result_gen = Rcpp::wrap(nll_gdistsamp(beta, n_param, y, mixture, keyfun, survey, Xlam, Xlam_offset, A, Xphi, Xphi_offset, Xdet, Xdet_offset, db, a, u, w, K, Kmin, threads));
     return rcpp_result_gen;
 END_RCPP
 }
@@ -573,7 +570,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_unmarked_nll_distsamp", (DL_FUNC) &_unmarked_nll_distsamp, 10},
     {"_unmarked_nll_distsampOpen", (DL_FUNC) &_unmarked_nll_distsampOpen, 42},
     {"_unmarked_nll_gdistremoval", (DL_FUNC) &_unmarked_nll_gdistremoval, 20},
-    {"_unmarked_nll_gdistsamp", (DL_FUNC) &_unmarked_nll_gdistsamp, 23},
+    {"_unmarked_nll_gdistsamp", (DL_FUNC) &_unmarked_nll_gdistsamp, 20},
     {"_unmarked_nll_gmultmix", (DL_FUNC) &_unmarked_nll_gmultmix, 17},
     {"_unmarked_nll_gpcount", (DL_FUNC) &_unmarked_nll_gpcount, 15},
     {"_unmarked_nll_multinomPois", (DL_FUNC) &_unmarked_nll_multinomPois, 10},
diff --git a/src/nll_gdistsamp.cpp b/src/nll_gdistsamp.cpp
index 80dc2d4..baed007 100644
--- a/src/nll_gdistsamp.cpp
+++ b/src/nll_gdistsamp.cpp
@@ -16,8 +16,7 @@ double nll_gdistsamp(arma::vec beta, arma::uvec n_param, arma::vec y,
     int mixture, std::string keyfun, std::string survey,
     arma::mat Xlam, arma::vec Xlam_offset, arma::vec A, arma::mat Xphi,
     arma::vec Xphi_offset, arma::mat Xdet, arma::vec Xdet_offset, arma::vec db,
-    arma::mat a, arma::mat u, arma::vec w, arma::vec k, arma::vec lfac_k,
-    arma::cube lfac_kmyt, arma::cube kmyt, arma::uvec Kmin, int threads){
+    arma::mat a, arma::mat u, arma::vec w, int K, arma::uvec Kmin, int threads){
 
   #ifdef _OPENMP
     omp_set_num_threads(threads);
@@ -25,9 +24,7 @@ double nll_gdistsamp(arma::vec beta, arma::uvec n_param, arma::vec y,
 
   int M = Xlam.n_rows;
   int T = Xphi.n_rows / M;
-  int R = y.size() / M;
-  unsigned J = R / T;
-  int K = k.size() - 1;
+  unsigned J = db.size() - 1;
 
   //Abundance
   const vec lambda = exp(Xlam * beta_sub(beta, n_param, 0) + Xlam_offset) % A;
@@ -51,43 +48,52 @@ double nll_gdistsamp(arma::vec beta, arma::uvec n_param, arma::vec y,
   #pragma omp parallel for reduction(+: loglik) if(threads > 1)
   for (int i=0; i<M; i++){
 
+    vec f = zeros(K+1); // should this be ones(K+1);
+    for (int k=Kmin(i); k<(K+1); k++){
+      f(k) = N_density(mixture, k, lambda(i), log_alpha);
+    }
+
     int t_ind = i * T;
     int y_ind = i * T * J;
 
     vec y_sub(J);
+    vec y_all(J+1);
+
+    vec cp(J);
+    vec cp_all(J+1);
+    double ptotal;
+
+    vec g = zeros(K+1);
 
-    mat mn = zeros(K+1, T);
     for(int t=0; t<T; t++){
       int y_stop = y_ind + J - 1;
       y_sub = y.subvec(y_ind, y_stop);
-      uvec not_missing = find_finite(y_sub);
+      y_all.subvec(0, (J-1)) = y_sub;
 
-      if(not_missing.size() == J){
+      uvec nm = find_finite(y_sub);
 
-        vec p1 = lfac_kmyt.subcube(span(i),span(t),span());
-        vec p = distprob(keyfun, det_param(t_ind), scale, survey, db,
-                          w, a.row(i));
-        vec p3 = p % u.col(i) * phi(t_ind);
-        //the following line causes a segfault only in R CMD check,
-        //when kmyt contains NA values
-        vec p4 = kmyt.subcube(span(i),span(t),span());
+      if((nm.size() == J)){
 
-        double p5 = 1 - sum(p3);
+        cp = distprob(keyfun, det_param(t_ind), scale, survey, db,
+                      w, a.row(i));
+        cp = cp % u.col(i) * phi(t_ind);
+        ptotal = sum(cp);
+
+        cp_all.subvec(0, (J-1)) = cp;
+        cp_all(J) = 1 - ptotal;
+
+        for (int k=Kmin(i); k<(K+1); k++){
+          y_all(J) = k - sum(y_sub);
+          g(k) += dmultinom(y_all, cp_all);
+        }
 
-        mn.col(t) = lfac_k - p1 + sum(y_sub % log(p3)) + p4 * log(p5);
       }
 
       t_ind += 1;
       y_ind += J;
     }
 
-    double site_lp = 0.0;
-    for (int j=Kmin(i); j<(K+1); j++){
-      site_lp += N_density(mixture, j, lambda(i), log_alpha) *
-        exp(sum(mn.row(j)));
-    }
-
-    loglik += log(site_lp + DBL_MIN);
+    loglik += log(sum(f % exp(g)));
 
   }
 
diff --git a/tests/testthat/test_gdistsamp.R b/tests/testthat/test_gdistsamp.R
index 1b232b2..e385566 100644
--- a/tests/testthat/test_gdistsamp.R
+++ b/tests/testthat/test_gdistsamp.R
@@ -351,7 +351,7 @@ test_that("gdistsamp with exp keyfunction works",{
                       keyfun="exp",engine="C", control=list(maxit=1))
     fm_R <- gdistsamp(~par1, ~par2, ~par3, umf, output="density", se=FALSE,
                       keyfun="exp",engine="R", control=list(maxit=1))
-    expect_equal(fm_C@AIC, fm_R@AIC)
+    expect_equal(coef(fm_C), coef(fm_R))
 
     #fm_R <- gdistsamp(~par1, ~par2, ~par3, umf, output="density", se=FALSE,
     #                  keyfun="exp",engine="R")
@@ -390,7 +390,7 @@ test_that("gdistsamp with exp keyfunction works",{
                       keyfun="exp",engine="C", se=F,control=list(maxit=1))
     fm_R <- gdistsamp(~elevation, ~1, ~chaparral, jayumf, output='density',
                       keyfun="exp",engine="R", se=F, control=list(maxit=1))
-    expect_equal(fm_C@AIC, fm_R@AIC, tol=1e-5)
+    expect_equal(coef(fm_C), coef(fm_R), tol=1e-5)
 
 })
 
@@ -439,7 +439,7 @@ test_that("gdistsamp with hazard keyfunction works",{
                       keyfun="hazard",engine="C", control=list(maxit=1))
     fm_R <- gdistsamp(~par1, ~par2, ~par3, umf, output="density", se=FALSE,
                       keyfun="hazard",engine="R", control=list(maxit=1))
-    expect_equal(fm_C@AIC, fm_R@AIC, tol=1e-5)
+    expect_equal(coef(fm_C), coef(fm_R), tol=1e-5)
 
     #fm_R <- gdistsamp(~par1, ~par2, ~par3, umf, output="density", se=FALSE,
     #                  keyfun="hazard",engine="R")
@@ -478,7 +478,7 @@ test_that("gdistsamp with hazard keyfunction works",{
                       keyfun="hazard",engine="C", se=F,control=list(maxit=1))
     fm_R <- gdistsamp(~elevation, ~1, ~chaparral, jayumf, output='density',
                       keyfun="hazard",engine="R", se=F, control=list(maxit=1))
-    expect_equal(fm_C@AIC, fm_R@AIC, tol=1e-3)
+    expect_equal(coef(fm_C), coef(fm_R), tol=1e-2) # why are these slightly different?
 })
 
 test_that("predict works for gdistsamp",{
-- 
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