From 2614278006609bcc10549521b3528851c33aa89f Mon Sep 17 00:00:00 2001
From: Christine Stawitz - NOAA
 <47904621+ChristineStawitz-NOAA@users.noreply.github.com>
Date: Fri, 17 Nov 2023 12:41:55 -0800
Subject: [PATCH] special case last year of recdevs

---
 .../interface/rcpp/rcpp_objects/rcpp_recruitment.hpp       | 2 +-
 inst/include/population_dynamics/population/population.hpp | 7 +++++++
 tests/testthat/test-fims-estimation.R                      | 4 ++--
 3 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/inst/include/interface/rcpp/rcpp_objects/rcpp_recruitment.hpp b/inst/include/interface/rcpp/rcpp_objects/rcpp_recruitment.hpp
index 69d48e928..1b7fe205c 100644
--- a/inst/include/interface/rcpp/rcpp_objects/rcpp_recruitment.hpp
+++ b/inst/include/interface/rcpp/rcpp_objects/rcpp_recruitment.hpp
@@ -148,7 +148,7 @@ class BevertonHoltRecruitmentInterface : public RecruitmentInterfaceBase {
       }
     }
 
-    recruitment->log_recruit_devs.resize(this->log_devs.size()+1);
+    recruitment->log_recruit_devs.resize(this->log_devs.size());
     if (this->estimate_log_devs) {
       for (size_t i = 0; i < recruitment->log_recruit_devs.size(); i++) {
         recruitment->log_recruit_devs[i] = this->log_devs[i];
diff --git a/inst/include/population_dynamics/population/population.hpp b/inst/include/population_dynamics/population/population.hpp
index 2cb8abba2..fc6b48ff4 100644
--- a/inst/include/population_dynamics/population/population.hpp
+++ b/inst/include/population_dynamics/population/population.hpp
@@ -391,6 +391,12 @@ struct Population : public fims_model_object::FIMSObject<Type> {
                    << this->recruitment->evaluate(
                           this->spawning_biomass[year - 1], phi0)
                    << std::endl;
+    if(i_dev==this->nyears){
+          this->numbers_at_age[i_age_year] =
+        this->recruitment->evaluate(this->spawning_biomass[year - 1], phi0);
+        /*the final year of the time series has no data to inform recruitment devs,
+        so this value is set to the mean recruitment.*/
+    } else{
     this->numbers_at_age[i_age_year] =
         this->recruitment->evaluate(this->spawning_biomass[year - 1], phi0) *
         /*the log_recruit_dev vector does not include a value for year == 0
@@ -398,6 +404,7 @@ struct Population : public fims_model_object::FIMSObject<Type> {
         corresponds to the second year of the time series.*/
         fims_math::exp(this->recruitment->log_recruit_devs[i_dev-1]);
     this->expected_recruitment[year] = this->numbers_at_age[i_age_year];
+    }
     POPULATION_LOG << " numbers at age at index i_age_year " << i_age_year << " is "
                    << this->numbers_at_age[i_age_year] << std::endl;
   }
diff --git a/tests/testthat/test-fims-estimation.R b/tests/testthat/test-fims-estimation.R
index 2b42ab2fb..abe99c4a1 100644
--- a/tests/testthat/test-fims-estimation.R
+++ b/tests/testthat/test-fims-estimation.R
@@ -691,12 +691,12 @@ test_that("run FIMS in a for loop", {
     fims$CreateTMBModel()
     parameters <- list(p = fims$get_fixed())
     obj <- TMB::MakeADFun(data = list(), parameters, DLL = "FIMS")
-   
+
     opt <- with(obj, optim(par, fn, gr,
       method = "BFGS",
       control = list(maxit = 1000000, reltol = 1e-15)
     ))
-    
+
     report <- obj$report(obj$par)
     expect_false(is.null(report))