Finish cpp updates and bump version. Fixes #258.

8 files changed, 106 insertions, 70 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 9800624..ba0d28e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: unmarked
-Version: 1.3.1.9001
+Version: 1.3.2
 Date: 2023-07-06
 Type: Package
 Title: Models for Data from Unmarked Animals
diff --git a/NEWS.md b/NEWS.md
index 8376684..3ef7115 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,8 @@
-# unmarked 1.3.1
+# unmarked 1.3.2
+
+* Modernize some Cpp code to pass new LTO checks
+
+#unmarked 1.3.1
 
 * Remove log.grad function to pass CRAN checks
 
diff --git a/R/RcppExports.R b/R/RcppExports.R
index c6aa6d2..79ab967 100644
--- a/R/RcppExports.R
+++ b/R/RcppExports.R
@@ -53,6 +53,14 @@ nll_occuMS <- function(beta, y, dm_state, dm_phi, dm_det, sind, pind, dind, prm,
     .Call(`_unmarked_nll_occuMS`, beta, y, dm_state, dm_phi, dm_det, sind, pind, dind, prm, S, T, J, N, naflag, guide)
 }
 
+nll_occuMulti_loglik <- function(fStart, fStop, dmF, dmOcc, beta, dmDet, dStart, dStop, y, yStart, yStop, Iy0, z, fixed0) {
+    .Call(`_unmarked_nll_occuMulti_loglik`, fStart, fStop, dmF, dmOcc, beta, dmDet, dStart, dStop, y, yStart, yStop, Iy0, z, fixed0)
+}
+
+nll_occuMulti <- function(fStart, fStop, dmF, dmOcc, beta, dmDet, dStart, dStop, y, yStart, yStop, Iy0, z, fixed0, penalty) {
+    .Call(`_unmarked_nll_occuMulti`, fStart, fStop, dmF, dmOcc, beta, dmDet, dStart, dStop, y, yStart, yStop, Iy0, z, fixed0, penalty)
+}
+
 nll_occuPEN <- function(y, X, V, beta_psi, beta_p, nd, knownOcc, navec, X_offset, V_offset, penalty) {
     .Call(`_unmarked_nll_occuPEN`, y, X, V, beta_psi, beta_p, nd, knownOcc, navec, X_offset, V_offset, penalty)
 }
diff --git a/R/occuMulti.R b/R/occuMulti.R
index 8b20dd1..7d31d47 100644
--- a/R/occuMulti.R
+++ b/R/occuMulti.R
@@ -88,10 +88,10 @@ occuMulti <- function(detformulas, stateformulas,  data, maxOrder,
 
   #Likelihood function in C----------------------------------------------------
   nll_C <- function(params) {
-    .Call("nll_occuMulti",
+    nll_occuMulti(
           fStart-1, fStop-1, t_dmF, dmOcc, params, dmDet, dStart-1, dStop-1,
-          y, yStart-1, yStop-1, Iy0, as.matrix(z), fixed0, penalty, 0,
-          PACKAGE = "unmarked")
+          y, yStart-1, yStop-1, Iy0, as.matrix(z), fixed0, penalty
+          )
   }
   #----------------------------------------------------------------------------
 
@@ -169,13 +169,11 @@ occuMultiLogLik <- function(fit, data){
   dmF <- Matrix::Matrix(dm$dmF, sparse=TRUE)
   t_dmF <- Matrix::t(dmF)
 
-  out <- .Call("nll_occuMulti",
+  out <- nll_occuMulti_loglik(
           dm$fStart-1, dm$fStop-1, t_dmF,
           dm$dmOcc, coef(fit), dm$dmDet, dm$dStart-1, dm$dStop-1, dm$y,
-          dm$yStart-1, dm$yStop-1, dm$Iy0, as.matrix(dm$z), dm$fixed0, 0,
-          #return site likelihoods
-          1,
-          PACKAGE = "unmarked")
+          dm$yStart-1, dm$yStop-1, dm$Iy0, as.matrix(dm$z), dm$fixed0
+          )
 
   as.vector(out)
 
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
index c69911a..6d89809 100644
--- a/src/RcppExports.cpp
+++ b/src/RcppExports.cpp
@@ -363,6 +363,55 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
+// nll_occuMulti_loglik
+arma::vec nll_occuMulti_loglik(Rcpp::IntegerVector fStart, Rcpp::IntegerVector fStop, arma::sp_mat dmF, Rcpp::List dmOcc, arma::colvec beta, Rcpp::List dmDet, Rcpp::IntegerVector dStart, Rcpp::IntegerVector dStop, arma::mat y, Rcpp::IntegerVector yStart, Rcpp::IntegerVector yStop, arma::mat Iy0, arma::mat z, Rcpp::LogicalVector fixed0);
+RcppExport SEXP _unmarked_nll_occuMulti_loglik(SEXP fStartSEXP, SEXP fStopSEXP, SEXP dmFSEXP, SEXP dmOccSEXP, SEXP betaSEXP, SEXP dmDetSEXP, SEXP dStartSEXP, SEXP dStopSEXP, SEXP ySEXP, SEXP yStartSEXP, SEXP yStopSEXP, SEXP Iy0SEXP, SEXP zSEXP, SEXP fixed0SEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::IntegerVector >::type fStart(fStartSEXP);
+    Rcpp::traits::input_parameter< Rcpp::IntegerVector >::type fStop(fStopSEXP);
+    Rcpp::traits::input_parameter< arma::sp_mat >::type dmF(dmFSEXP);
+    Rcpp::traits::input_parameter< Rcpp::List >::type dmOcc(dmOccSEXP);
+    Rcpp::traits::input_parameter< arma::colvec >::type beta(betaSEXP);
+    Rcpp::traits::input_parameter< Rcpp::List >::type dmDet(dmDetSEXP);
+    Rcpp::traits::input_parameter< Rcpp::IntegerVector >::type dStart(dStartSEXP);
+    Rcpp::traits::input_parameter< Rcpp::IntegerVector >::type dStop(dStopSEXP);
+    Rcpp::traits::input_parameter< arma::mat >::type y(ySEXP);
+    Rcpp::traits::input_parameter< Rcpp::IntegerVector >::type yStart(yStartSEXP);
+    Rcpp::traits::input_parameter< Rcpp::IntegerVector >::type yStop(yStopSEXP);
+    Rcpp::traits::input_parameter< arma::mat >::type Iy0(Iy0SEXP);
+    Rcpp::traits::input_parameter< arma::mat >::type z(zSEXP);
+    Rcpp::traits::input_parameter< Rcpp::LogicalVector >::type fixed0(fixed0SEXP);
+    rcpp_result_gen = Rcpp::wrap(nll_occuMulti_loglik(fStart, fStop, dmF, dmOcc, beta, dmDet, dStart, dStop, y, yStart, yStop, Iy0, z, fixed0));
+    return rcpp_result_gen;
+END_RCPP
+}
+// nll_occuMulti
+double nll_occuMulti(Rcpp::IntegerVector fStart, Rcpp::IntegerVector fStop, arma::sp_mat dmF, Rcpp::List dmOcc, arma::colvec beta, Rcpp::List dmDet, Rcpp::IntegerVector dStart, Rcpp::IntegerVector dStop, arma::mat y, Rcpp::IntegerVector yStart, Rcpp::IntegerVector yStop, arma::mat Iy0, arma::mat z, Rcpp::LogicalVector fixed0, double penalty);
+RcppExport SEXP _unmarked_nll_occuMulti(SEXP fStartSEXP, SEXP fStopSEXP, SEXP dmFSEXP, SEXP dmOccSEXP, SEXP betaSEXP, SEXP dmDetSEXP, SEXP dStartSEXP, SEXP dStopSEXP, SEXP ySEXP, SEXP yStartSEXP, SEXP yStopSEXP, SEXP Iy0SEXP, SEXP zSEXP, SEXP fixed0SEXP, SEXP penaltySEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Rcpp::IntegerVector >::type fStart(fStartSEXP);
+    Rcpp::traits::input_parameter< Rcpp::IntegerVector >::type fStop(fStopSEXP);
+    Rcpp::traits::input_parameter< arma::sp_mat >::type dmF(dmFSEXP);
+    Rcpp::traits::input_parameter< Rcpp::List >::type dmOcc(dmOccSEXP);
+    Rcpp::traits::input_parameter< arma::colvec >::type beta(betaSEXP);
+    Rcpp::traits::input_parameter< Rcpp::List >::type dmDet(dmDetSEXP);
+    Rcpp::traits::input_parameter< Rcpp::IntegerVector >::type dStart(dStartSEXP);
+    Rcpp::traits::input_parameter< Rcpp::IntegerVector >::type dStop(dStopSEXP);
+    Rcpp::traits::input_parameter< arma::mat >::type y(ySEXP);
+    Rcpp::traits::input_parameter< Rcpp::IntegerVector >::type yStart(yStartSEXP);
+    Rcpp::traits::input_parameter< Rcpp::IntegerVector >::type yStop(yStopSEXP);
+    Rcpp::traits::input_parameter< arma::mat >::type Iy0(Iy0SEXP);
+    Rcpp::traits::input_parameter< arma::mat >::type z(zSEXP);
+    Rcpp::traits::input_parameter< Rcpp::LogicalVector >::type fixed0(fixed0SEXP);
+    Rcpp::traits::input_parameter< double >::type penalty(penaltySEXP);
+    rcpp_result_gen = Rcpp::wrap(nll_occuMulti(fStart, fStop, dmF, dmOcc, beta, dmDet, dStart, dStop, y, yStart, yStop, Iy0, z, fixed0, penalty));
+    return rcpp_result_gen;
+END_RCPP
+}
 // nll_occuPEN
 double nll_occuPEN(arma::icolvec y, arma::mat X, arma::mat V, arma::colvec beta_psi, arma::colvec beta_p, Rcpp::IntegerVector nd, Rcpp::LogicalVector knownOcc, Rcpp::LogicalVector navec, arma::colvec X_offset, arma::colvec V_offset, double penalty);
 RcppExport SEXP _unmarked_nll_occuPEN(SEXP ySEXP, SEXP XSEXP, SEXP VSEXP, SEXP beta_psiSEXP, SEXP beta_pSEXP, SEXP ndSEXP, SEXP knownOccSEXP, SEXP navecSEXP, SEXP X_offsetSEXP, SEXP V_offsetSEXP, SEXP penaltySEXP) {
@@ -500,7 +549,6 @@ END_RCPP
 
 RcppExport SEXP getDetVecs(void *, void *, void *, void *, void *);
 RcppExport SEXP getSingleDetVec(void *, void *, void *);
-RcppExport SEXP nll_occuMulti(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
 
 static const R_CallMethodDef CallEntries[] = {
     {"_unmarked_get_lik_trans", (DL_FUNC) &_unmarked_get_lik_trans, 2},
@@ -516,14 +564,15 @@ static const R_CallMethodDef CallEntries[] = {
     {"_unmarked_nll_nmixTTD", (DL_FUNC) &_unmarked_nll_nmixTTD, 13},
     {"_unmarked_nll_occu", (DL_FUNC) &_unmarked_nll_occu, 11},
     {"_unmarked_nll_occuMS", (DL_FUNC) &_unmarked_nll_occuMS, 15},
+    {"_unmarked_nll_occuMulti_loglik", (DL_FUNC) &_unmarked_nll_occuMulti_loglik, 14},
+    {"_unmarked_nll_occuMulti", (DL_FUNC) &_unmarked_nll_occuMulti, 15},
     {"_unmarked_nll_occuPEN", (DL_FUNC) &_unmarked_nll_occuPEN, 11},
     {"_unmarked_nll_occuRN", (DL_FUNC) &_unmarked_nll_occuRN, 10},
     {"_unmarked_nll_occuTTD", (DL_FUNC) &_unmarked_nll_occuTTD, 17},
     {"_unmarked_nll_pcount", (DL_FUNC) &_unmarked_nll_pcount, 11},
     {"_unmarked_nll_pcountOpen", (DL_FUNC) &_unmarked_nll_pcountOpen, 35},
-    {"getDetVecs",      (DL_FUNC) &getDetVecs,       5},
-    {"getSingleDetVec", (DL_FUNC) &getSingleDetVec,  3},
-    {"nll_occuMulti",   (DL_FUNC) &nll_occuMulti,   16},
+    {"getDetVecs",      (DL_FUNC) &getDetVecs,      5},
+    {"getSingleDetVec", (DL_FUNC) &getSingleDetVec, 3},
     {NULL, NULL, 0}
 };
 
diff --git a/src/nll_occuMulti.cpp b/src/nll_occuMulti.cpp
index 3a44c7d..5310097 100644
--- a/src/nll_occuMulti.cpp
+++ b/src/nll_occuMulti.cpp
@@ -1,46 +1,21 @@
-#include "nll_occuMulti.h"
+#include <RcppArmadillo.h>
 
 using namespace Rcpp;
 using namespace arma;
 
-SEXP nll_occuMulti( SEXP fStartR, SEXP fStopR, SEXP dmFr, SEXP dmOccR, 
-    SEXP betaR, SEXP dmDetR, SEXP dStartR, SEXP dStopR, SEXP yR, SEXP yStartR, 
-    SEXP yStopR, SEXP Iy0r, SEXP zR, SEXP fixed0r, SEXP penaltyR,
-    SEXP returnLLr){
-  
-  //Inputs
-  IntegerVector fStart(fStartR);
-  IntegerVector fStop(fStopR);
-  
-  //if Matrix is a dependency
-  sp_mat dmF = as<sp_mat>(dmFr); //already transposed
-  
-  //if Matrix not a dependency
-  //sp_mat dmF( as<mat>(dmFr) );
-  
-  int nF = dmF.n_rows;
-  List dmOcc(dmOccR);
-
-  colvec beta = as<colvec>(betaR);
-  LogicalVector fixed0(fixed0r);
-  
-  List dmDet(dmDetR);
-  IntegerVector dStart(dStartR);
-  IntegerVector dStop(dStopR);
-  
-  mat y = as<mat>(yR);
+// [[Rcpp::export]]
+arma::vec nll_occuMulti_loglik(Rcpp::IntegerVector fStart, Rcpp::IntegerVector fStop,
+    arma::sp_mat dmF, Rcpp::List dmOcc,
+    arma::colvec beta, Rcpp::List dmDet,
+    Rcpp::IntegerVector dStart, Rcpp::IntegerVector dStop,
+    arma::mat y, Rcpp::IntegerVector yStart, Rcpp::IntegerVector yStop,
+    arma::mat Iy0, arma::mat z, Rcpp::LogicalVector fixed0){
+
+  int nF = dmF.n_rows; //dmF is already transposed
   int S = y.n_cols;
   int J = y.n_rows;
-  IntegerVector yStart(yStartR);
-  IntegerVector yStop(yStopR);
   int N = yStart.size();
-  mat Iy0 = as<mat>(Iy0r);
-
-  mat z = as<mat>(zR);
 
-  double penalty = as<double>(penaltyR);
-  int returnLL = as<int>(returnLLr);
-  
   //psi calculation
   int index = 0;
   mat f(N, nF);
@@ -54,7 +29,7 @@ SEXP nll_occuMulti( SEXP fStartR, SEXP fStopR, SEXP dmFr, SEXP dmOccR,
     }
   }
 
-  mat psi = exp( f * dmF ); 
+  mat psi = exp( f * dmF );
   for(unsigned int i = 0; i < psi.n_rows; i++){
     psi.row(i) = psi.row(i) / sum( psi.row(i) );
   }
@@ -72,15 +47,15 @@ SEXP nll_occuMulti( SEXP fStartR, SEXP fStopR, SEXP dmFr, SEXP dmOccR,
   vec logLik(N);
 
   for(int i = 0; i < N; i++){
-    
+
     mat ysub = y.rows(yStart[i], yStop[i]);
     mat psub = p.rows(yStart[i], yStop[i]);
     rowvec cdp(S);
     for(int j = 0; j < S; j++){
-     cdp(j) = exp( sum( ysub.col(j) % log(psub.col(j)) ) + 
+     cdp(j) = exp( sum( ysub.col(j) % log(psub.col(j)) ) +
                    sum( (1 - ysub.col(j)) % log( 1 - psub.col(j)) ) );
     }
-    
+
     rowvec prdProbY(M);
     for(int j = 0; j < M; j++){
       prdProbY(j) = prod( z.row(j) % cdp + (1 - z.row(j)) % Iy0.row(i) );
@@ -89,11 +64,21 @@ SEXP nll_occuMulti( SEXP fStartR, SEXP fStopR, SEXP dmFr, SEXP dmOccR,
     logLik(i) = log( sum( psi.row(i) % prdProbY ) );
 
   }
-  
-  if(returnLL){
-    return(wrap(logLik));
-  }
+
+  return logLik;
+}
+
+// [[Rcpp::export]]
+double nll_occuMulti(Rcpp::IntegerVector fStart, Rcpp::IntegerVector fStop,
+    arma::sp_mat dmF, Rcpp::List dmOcc,
+    arma::colvec beta, Rcpp::List dmDet,
+    Rcpp::IntegerVector dStart, Rcpp::IntegerVector dStop,
+    arma::mat y, Rcpp::IntegerVector yStart, Rcpp::IntegerVector yStop,
+    arma::mat Iy0, arma::mat z, Rcpp::LogicalVector fixed0, double penalty){
+
+  vec logLik = nll_occuMulti_loglik(fStart, fStop, dmF, dmOcc, beta, dmDet,
+      dStart, dStop, y, yStart, yStop, Iy0, z, fixed0);
 
   double pen = penalty * 0.5 * accu(pow(beta, 2));
-  return(wrap(-1.0 * (sum(logLik) - pen)));
+  return -1.0 * (sum(logLik) - pen);
 }
diff --git a/src/nll_occuMulti.h b/src/nll_occuMulti.h
deleted file mode 100644
index 47cb53e..0000000
--- a/src/nll_occuMulti.h
+++ /dev/null
@@ -1,11 +0,0 @@
-#ifndef _unmarked_NLL_OCCUMULTI_H
-#define _unmarked_NLL_OCCUMULTI_H
-
-#include <RcppArmadillo.h>
-
-RcppExport SEXP nll_occuMulti( SEXP fStartR, SEXP fStopR, SEXP dmFr, SEXP dmOccR, 
-    SEXP betaR, SEXP dmDetR, SEXP dStartR, SEXP dStopR, SEXP yR, SEXP yStartR, 
-    SEXP yStopR, SEXP Iy0r, SEXP zR, SEXP fixed0r, SEXP penaltyR,
-    SEXP returnLLr) ;
-
-#endif
diff --git a/tests/testthat/test_occuMulti.R b/tests/testthat/test_occuMulti.R
index d37cbc5..6ce7921 100644
--- a/tests/testthat/test_occuMulti.R
+++ b/tests/testthat/test_occuMulti.R
@@ -536,7 +536,10 @@ test_that("occuMulti penalized likelihood works",{
   set.seed(123)
   opt_fit  <- optimizePenalty(fm, penalties=c(0,1), boot=2)
   expect_equal(opt_fit@call$penalty, 1)
-
+  
+  ll <- unmarked:::occuMultiLogLik(fm, fm@data)
+  expect_equal(length(ll), numSites(fm@data))
+  expect_equal(-sum(ll), fm@negLogLike) 
   })