From 05e0816d04d1f118f38452f274476cc81424df4f Mon Sep 17 00:00:00 2001
From: Ron <ronald.klasky@noaa.gov>
Date: Tue, 21 Feb 2023 09:56:15 -0500
Subject: [PATCH] Mods for 1.6.1

---
 MSSPM_GuiEstimation/nmfEstimationTab02.cpp    | 15 ++--
 MSSPM_Main/nmfMainWindow.cpp                  |  7 +-
 .../NLopt_Estimator.cpp                       | 49 ++++++++----
 MSSPM_SimulatedData/nmfSimulatedData.cpp      | 78 +++++++++----------
 4 files changed, 86 insertions(+), 63 deletions(-)

diff --git a/MSSPM_GuiEstimation/nmfEstimationTab02.cpp b/MSSPM_GuiEstimation/nmfEstimationTab02.cpp
index e1c5c75..67c0b0f 100755
--- a/MSSPM_GuiEstimation/nmfEstimationTab02.cpp
+++ b/MSSPM_GuiEstimation/nmfEstimationTab02.cpp
@@ -904,7 +904,8 @@ nmfEstimation_Tab2::saveFitWeights(const bool& verbose)
     std::string tableName = nmfConstantsMSSPM::TableFitWeights;
     std::string cmd;
     std::string errorMsg = m_DatabasePtr->nmfUpdateDatabase(cmd);
-    QModelIndex indexBiomass,indexCatch;
+    std::string biomassStr = "";
+    std::string catchStr = "";
     QStringList SpeciesList;
     QStandardItemModel* smodel = qobject_cast<QStandardItemModel*>(Estimation_Tab2_WeightsFTCTV->model());
 
@@ -936,12 +937,16 @@ nmfEstimation_Tab2::saveFitWeights(const bool& verbose)
 
     cmd = "INSERT INTO " + tableName + " (ProjectName,ModelName,SpeName,Biomass,Catch) VALUES ";
     for (int i=0; i<smodel->rowCount(); ++i) {  // Species
-            indexBiomass = smodel->index(i,0);
-            indexCatch   = smodel->index(i,1);
+            biomassStr   = smodel->index(i,0).data().toString().toStdString();
+            catchStr     = smodel->index(i,1).data().toString().toStdString();
+            if (biomassStr.empty() || catchStr.empty()) {
+                biomassStr = "1.0";
+                catchStr   = "0.0";
+            }
             cmd += "('"  + m_ProjectName + "','" + m_ModelName +
                     "','" + SpeciesList[i].toStdString() +
-                    "', " + indexBiomass.data().toString().toStdString() +
-                    ", "  + indexCatch.data().toString().toStdString() + "),";
+                    "', " + biomassStr +
+                    ", "  + catchStr + "),";
     }
 
     cmd = cmd.substr(0,cmd.size()-1);
diff --git a/MSSPM_Main/nmfMainWindow.cpp b/MSSPM_Main/nmfMainWindow.cpp
index bc5278c..9dd0638 100755
--- a/MSSPM_Main/nmfMainWindow.cpp
+++ b/MSSPM_Main/nmfMainWindow.cpp
@@ -2161,7 +2161,7 @@ void
 nmfMainWindow::menu_about()
 {
     QString name    = "Multi-Species Surplus Production Model";
-    QString version = "MSSPM v1.6.0 ";
+    QString version = "MSSPM v1.6.1 ";
     QString specialAcknowledgement = "";
     QString cppVersion   = "C++??";
     QString mysqlVersion = "?";
@@ -6170,7 +6170,8 @@ nmfMainWindow::updateOutputBiomassTable(std::string& ForecastName,
                                                    EstCarryingCapacities[species],
                                                    EstCarryingCapacityCovariateCoeffs[species],
                                                    CarryingCapacitiesCovariate(timeMinus1,species));
-            HarvestTerm     = harvestFormPtr->evaluate(CovariateAlgorithmType,
+
+             HarvestTerm     = harvestFormPtr->evaluate(CovariateAlgorithmType,
                                                     timeMinus1,species,
                                                     EstBiomassTMinus1,
                                                     Catch,Effort,Exploitation,
@@ -11062,7 +11063,7 @@ nmfMainWindow::callback_RunEstimation(bool showDiagnosticsChart)
     QString multiRunSpeciesFilename;
     QString multiRunModelFilename;
     QString msg;
-qDebug() <<"isAMultiOrMohnsRhoRun: " << isAMultiRun;
+
     saveSettings();
     loadAllWidgets();
     readSettings();
diff --git a/MSSPM_ParameterEstimationNLoptAlgorithm/NLopt_Estimator.cpp b/MSSPM_ParameterEstimationNLoptAlgorithm/NLopt_Estimator.cpp
index feae89c..0c475e2 100755
--- a/MSSPM_ParameterEstimationNLoptAlgorithm/NLopt_Estimator.cpp
+++ b/MSSPM_ParameterEstimationNLoptAlgorithm/NLopt_Estimator.cpp
@@ -160,36 +160,45 @@ NLopt_Estimator::extractParameters(const nmfStructsQt::ModelDataStruct& NLoptDat
     }
     offset += NumSpeciesOrGuilds;
 
+    // Always extract growth rate covariates
+    for (int i=0; i<NumSpeciesOrGuilds; ++i) {
+        growthRateCovariateCoeffs.emplace_back(QString::number(EstParameters[offset+i],'f',6).toDouble());
+    }
+    offset += NumSpeciesOrGuilds;
+
     // Extract growth rate shape parameters if is logistic
     if (isLogistic) {
         for (int i=0; i<NumSpeciesOrGuilds; ++i) {
             growthRateShape.emplace_back(QString::number(EstParameters[offset+i],'f',6).toDouble());
         }
         offset += NumSpeciesOrGuilds;
+    } else {
+        for (int i=0; i<NumSpeciesOrGuilds; ++i) {
+            growthRateShape.emplace_back(0);
+        }
     }
 
-    // Always extract growth rate covariates
-    for (int i=0; i<NumSpeciesOrGuilds; ++i) {
-        growthRateCovariateCoeffs.emplace_back(QString::number(EstParameters[offset+i],'f',6).toDouble());
-    }
-    offset += NumSpeciesOrGuilds;
-
-    // Load the carrying capacity vector
-    for (int i=0; i<NumSpeciesOrGuilds; ++i) {
-        if (isLogistic) {
+    // Load the carrying capacity vector if it's logistic
+    if (isLogistic) {
+        for (int i=0; i<NumSpeciesOrGuilds; ++i) {
             carryingCapacity.emplace_back(QString::number(EstParameters[offset+i],'f',6).toDouble());
-        } else {
+        }
+        offset += NumSpeciesOrGuilds;
+    } else {
+        for (int i=0; i<NumSpeciesOrGuilds; ++i) {
             carryingCapacity.emplace_back(0);
         }
     }
-    offset += NumSpeciesOrGuilds;
 
     if (isLogistic) {
-//      offset += NumSpeciesOrGuilds;
         for (int i=0; i<NumSpeciesOrGuilds; ++i) {
             carryingCapacityCovariateCoeffs.emplace_back(QString::number(EstParameters[offset+i],'f',6).toDouble());
         }
         offset += NumSpeciesOrGuilds;
+    } else {
+        for (int i=0; i<NumSpeciesOrGuilds; ++i) {
+            carryingCapacityCovariateCoeffs.emplace_back(0);
+        }
     }
 
     if (isCatchability) {
@@ -201,9 +210,13 @@ NLopt_Estimator::extractParameters(const nmfStructsQt::ModelDataStruct& NLoptDat
             catchabilityCovariateCoeffs.emplace_back(QString::number(EstParameters[offset+i],'f',6).toDouble());
         }
         offset += NumSpeciesOrGuilds;
+    } else {
+        for (int i=0; i<NumSpeciesOrGuilds; ++i) {
+            catchability.emplace_back(0);
+            catchabilityCovariateCoeffs.emplace_back(0);
+        }
     }
 
-
     // Be sure to extract matrix data row by row which is for (row...) then for (col...)
 
     if (isAlpha) {
@@ -274,6 +287,10 @@ NLopt_Estimator::extractParameters(const nmfStructsQt::ModelDataStruct& NLoptDat
             exponent.emplace_back(EstParameters[offset+i]);
         }
         offset += NumSpeciesOrGuilds;
+    } else {
+        for (int i=0; i<NumSpeciesOrGuilds; ++i) {
+            exponent.emplace_back(0);
+        }
     }
 
     // Survey Q
@@ -286,7 +303,7 @@ NLopt_Estimator::extractParameters(const nmfStructsQt::ModelDataStruct& NLoptDat
         surveyQCovariateCoeffs.emplace_back(EstParameters[offset+i]);
     }
     offset += NumSpeciesOrGuilds;
-//qDebug() << "Num Parameters Extracted: " << offset;
+//qDebug() << "---> Num Parameters Extracted: " << offset;
 
     // Calculate MSY, BMSY, and FMSY values
     for (int i=0; i<NumSpeciesOrGuilds; ++i) {
@@ -1008,10 +1025,14 @@ NLopt_Estimator::setParameterBounds(nmfStructsQt::ModelDataStruct& NLoptStruct,
     std::vector<double> lowerBounds(NumEstParameters);
     std::vector<double> upperBounds(NumEstParameters);
 
+//qDebug() << "---> Num Parameter Bounds: " << NumEstParameters;
+
     // Set parameter bounds for all parameters
     for (int i=0; i<NumEstParameters; ++i) {
         lowerBounds[i] = ParameterRanges[i].first;
         upperBounds[i] = ParameterRanges[i].second;
+//qDebug() << "Setting parameter bounds: " << i << ", "
+//         << lowerBounds[i] << "," << upperBounds[i];
     }
     m_Optimizer.set_lower_bounds(lowerBounds);
     m_Optimizer.set_upper_bounds(upperBounds);
diff --git a/MSSPM_SimulatedData/nmfSimulatedData.cpp b/MSSPM_SimulatedData/nmfSimulatedData.cpp
index 87841f8..02a7570 100644
--- a/MSSPM_SimulatedData/nmfSimulatedData.cpp
+++ b/MSSPM_SimulatedData/nmfSimulatedData.cpp
@@ -224,47 +224,43 @@ nmfSimulatedData::createSimulatedBiomass(
             getGuildCarryingCapacity(isAggProd,species,SpeciesK,GuildNum,
                                      GuildSpecies,GuildCarryingCapacity);
 
-            GrowthTerm = SimGrowthForm.evaluate(
-                        covariateAlgorithmType,
-                        SimBiomassTMinus1,
-                        GrowthRate[species],
-                        GrowthRateShape[species],
-                        GrowthRateCovariateCoeffs[species],
-                        GrowthRateCovariate(timeMinus1,species),
-                        SpeciesK[species],
-                        SpeciesKCovariateCoeffs[species],
-                        SpeciesKCovariate(timeMinus1,species));
-            HarvestTerm = SimHarvestForm.evaluate(
-                        covariateAlgorithmType,
-                        timeMinus1,species,SimBiomassTMinus1,
-                        Catch,Effort,Exploitation,
-                        Catchability[species],
-                        CatchabilityCovariateCoeffs[species],
-                        CatchabilityCovariate(timeMinus1,species));
-            CompetitionTerm = SimCompetitionForm.evaluate(
-                        covariateAlgorithmType,
-                        timeMinus1,species,SimBiomassTMinus1,
-                        GrowthRate,
-                        GrowthRateCovariate,
-                        GuildCarryingCapacity,
-                        SystemCarryingCapacity,
-                        SimBiomassSpecies,
-                        SimulatedBiomassGuild,
-                        CompetitionAlpha,
-                        CompetitionAlphaCovariate,
-                        CompetitionBetaSpecies,
-                        CompetitionBetaSpeciesCovariate,
-                        CompetitionBetaGuild,
-                        CompetitionBetaGuildSpeciesCovariate,
-                        CompetitionBetaGuildGuild,
-                        CompetitionBetaGuildGuildCovariate);
-            PredationTerm = SimPredationForm.evaluate(
-                        covariateAlgorithmType,
-                        timeMinus1, species,
-                        SimBiomassSpecies,SimBiomassTMinus1,
-                        PredationRho,PredationRhoCovariate,
-                        PredationHandling,PredationHandlingCovariate,
-                        PredationExponent,PredationExponentCovariate);
+            GrowthTerm = SimGrowthForm.evaluate(covariateAlgorithmType,
+                                                SimBiomassTMinus1,
+                                                GrowthRate[species],
+                                                GrowthRateShape[species],
+                                                GrowthRateCovariateCoeffs[species],
+                                                GrowthRateCovariate(timeMinus1,species),
+                                                SpeciesK[species],
+                                                SpeciesKCovariateCoeffs[species],
+                                                SpeciesKCovariate(timeMinus1,species));
+            HarvestTerm = SimHarvestForm.evaluate(covariateAlgorithmType,
+                                                  timeMinus1,species,SimBiomassTMinus1,
+                                                  Catch,Effort,Exploitation,
+                                                  Catchability[species],
+                                                  CatchabilityCovariateCoeffs[species],
+                                                  CatchabilityCovariate(timeMinus1,species));
+            CompetitionTerm = SimCompetitionForm.evaluate(covariateAlgorithmType,
+                                                          timeMinus1,species,SimBiomassTMinus1,
+                                                          GrowthRate,
+                                                          GrowthRateCovariate,
+                                                          GuildCarryingCapacity,
+                                                          SystemCarryingCapacity,
+                                                          SimBiomassSpecies,
+                                                          SimulatedBiomassGuild,
+                                                          CompetitionAlpha,
+                                                          CompetitionAlphaCovariate,
+                                                          CompetitionBetaSpecies,
+                                                          CompetitionBetaSpeciesCovariate,
+                                                          CompetitionBetaGuild,
+                                                          CompetitionBetaGuildSpeciesCovariate,
+                                                          CompetitionBetaGuildGuild,
+                                                          CompetitionBetaGuildGuildCovariate);
+            PredationTerm = SimPredationForm.evaluate(covariateAlgorithmType,
+                                                      timeMinus1, species,
+                                                      SimBiomassSpecies,SimBiomassTMinus1,
+                                                      PredationRho,PredationRhoCovariate,
+                                                      PredationHandling,PredationHandlingCovariate,
+                                                      PredationExponent,PredationExponentCovariate);
 
             SimBiomassTMinus1 += GrowthTerm - HarvestTerm - CompetitionTerm - PredationTerm;