ADD fishing mortality process, plus improvements 202207

.gitignore

@@ -54,3 +54,217 @@ Documentation/UserManual/CASAL2_Age.synctex.gz
 Documentation/UserManual/CASAL2_Length.synctex.gz
 *.txss
 simCASAL2/simCASAL2.exe
+TestModels/SimAllObs/sim/sim_all_obs.1_01
+TestModels/SimAllObs/sim/sim_all_obs.1_02
+TestModels/SimAllObs/sim/sim_all_obs.1_03
+TestModels/SimAllObs/sim/sim_all_obs.1_04
+TestModels/SimAllObs/sim/sim_all_obs.1_05
+TestModels/SimAllObs/sim/sim_all_obs.1_06
+TestModels/SimAllObs/sim/sim_all_obs.1_07
+TestModels/SimAllObs/sim/sim_all_obs.1_08
+TestModels/SimAllObs/sim/sim_all_obs.1_09
+TestModels/SimAllObs/sim/sim_all_obs.1_10
+TestModels/SimAllObs/sim/sim_all_obs.2_01
+TestModels/SimAllObs/sim/sim_all_obs.2_02
+TestModels/SimAllObs/sim/sim_all_obs.2_03
+TestModels/SimAllObs/sim/sim_all_obs.2_04
+TestModels/SimAllObs/sim/sim_all_obs.2_05
+TestModels/SimAllObs/sim/sim_all_obs.2_06
+TestModels/SimAllObs/sim/sim_all_obs.2_07
+TestModels/SimAllObs/sim/sim_all_obs.2_08
+TestModels/SimAllObs/sim/sim_all_obs.2_09
+TestModels/SimAllObs/sim/sim_all_obs.2_10
+TestModels/SimAllObs/sim/sim_all_obs.3_01
+TestModels/SimAllObs/sim/sim_all_obs.3_02
+TestModels/SimAllObs/sim/sim_all_obs.3_03
+TestModels/SimAllObs/sim/sim_all_obs.3_04
+TestModels/SimAllObs/sim/sim_all_obs.3_05
+TestModels/SimAllObs/sim/sim_all_obs.3_06
+TestModels/SimAllObs/sim/sim_all_obs.3_07
+TestModels/SimAllObs/sim/sim_all_obs.3_08
+TestModels/SimAllObs/sim/sim_all_obs.3_09
+TestModels/SimAllObs/sim/sim_all_obs.3_10
+TestModels/SimAllObs/sim/sim_all_obs.4_01
+TestModels/SimAllObs/sim/sim_all_obs.4_02
+TestModels/SimAllObs/sim/sim_all_obs.4_03
+TestModels/SimAllObs/sim/sim_all_obs.4_04
+TestModels/SimAllObs/sim/sim_all_obs.4_05
+TestModels/SimAllObs/sim/sim_all_obs.4_06
+TestModels/SimAllObs/sim/sim_all_obs.4_07
+TestModels/SimAllObs/sim/sim_all_obs.4_08
+TestModels/SimAllObs/sim/sim_all_obs.4_09
+TestModels/SimAllObs/sim/sim_all_obs.4_10
+TestModels/SimAllObs/sim/sim_all_obs.5_01
+TestModels/SimAllObs/sim/sim_all_obs.5_02
+TestModels/SimAllObs/sim/sim_all_obs.5_03
+TestModels/SimAllObs/sim/sim_all_obs.5_04
+TestModels/SimAllObs/sim/sim_all_obs.5_05
+TestModels/SimAllObs/sim/sim_all_obs.5_06
+TestModels/SimAllObs/sim/sim_all_obs.5_07
+TestModels/SimAllObs/sim/sim_all_obs.5_08
+TestModels/SimAllObs/sim/sim_all_obs.5_09
+TestModels/SimAllObs/sim/sim_all_obs.5_10
+TestModels/SimAllObs/sim/sim_all_obs.6_01
+TestModels/SimAllObs/sim/sim_all_obs.6_02
+TestModels/SimAllObs/sim/sim_all_obs.6_03
+TestModels/SimAllObs/sim/sim_all_obs.6_04
+TestModels/SimAllObs/sim/sim_all_obs.6_05
+TestModels/SimAllObs/sim/sim_all_obs.6_06
+TestModels/SimAllObs/sim/sim_all_obs.6_07
+TestModels/SimAllObs/sim/sim_all_obs.6_08
+TestModels/SimAllObs/sim/sim_all_obs.6_09
+TestModels/SimAllObs/sim/sim_all_obs.6_10
+TestModels/SimAllObs/sim/sim_all_obs.7_01
+TestModels/SimAllObs/sim/sim_all_obs.7_02
+TestModels/SimAllObs/sim/sim_all_obs.7_03
+TestModels/SimAllObs/sim/sim_all_obs.7_04
+TestModels/SimAllObs/sim/sim_all_obs.7_05
+TestModels/SimAllObs/sim/sim_all_obs.7_06
+TestModels/SimAllObs/sim/sim_all_obs.7_07
+TestModels/SimAllObs/sim/sim_all_obs.7_08
+TestModels/SimAllObs/sim/sim_all_obs.7_09
+TestModels/SimAllObs/sim/sim_all_obs.7_10
+TestModels/SimAllObs/sim/sim_all_obs.8_01
+TestModels/SimAllObs/sim/sim_all_obs.8_02
+TestModels/SimAllObs/sim/sim_all_obs.8_03
+TestModels/SimAllObs/sim/sim_all_obs.8_04
+TestModels/SimAllObs/sim/sim_all_obs.8_05
+TestModels/SimAllObs/sim/sim_all_obs.8_06
+TestModels/SimAllObs/sim/sim_all_obs.8_07
+TestModels/SimAllObs/sim/sim_all_obs.8_08
+TestModels/SimAllObs/sim/sim_all_obs.8_09
+TestModels/SimAllObs/sim/sim_all_obs.8_10
+TestModels/SimAllObs/sim/sim_all_obs.9_01
+TestModels/SimAllObs/sim/sim_all_obs.9_02
+TestModels/SimAllObs/sim/sim_all_obs.9_03
+TestModels/SimAllObs/sim/sim_all_obs.9_04
+TestModels/SimAllObs/sim/sim_all_obs.9_05
+TestModels/SimAllObs/sim/sim_all_obs.9_06
+TestModels/SimAllObs/sim/sim_all_obs.9_07
+TestModels/SimAllObs/sim/sim_all_obs.9_08
+TestModels/SimAllObs/sim/sim_all_obs.9_09
+TestModels/SimAllObs/sim/sim_all_obs.9_10
+TestModels/additional_priors/run.err
+TestModels/agelength_cv_with_LF/run.err
+TestModels/agelength_cv_with_LF/run.log
+TestModels/agelengths_data/run.err
+TestModels/Complex/run.err
+TestModels/Complex/run.log
+TestModels/Complex_input/run.err
+TestModels/Complex_input/run.log
+TestModels/ComplexTag/estimate_betadiff.err
+TestModels/ComplexTag/estimate_betadiff.log
+TestModels/estimates_with_matching_bounds/run.err
+TestModels/LengthBasedNoPlusGroup/run.err
+TestModels/LengthBasedPlusGroup/run.err
+TestModels/mcmc_resume/mcmc.log
+TestModels/mcmc_resume/objectives.2
+TestModels/mcmc_resume/objectives.3
+TestModels/mcmc_resume/samples.2
+TestModels/mcmc_resume/samples.3
+TestModels/mcmc_start_mpd/esimate.err
+TestModels/mcmc_start_mpd/mcmc.err
+TestModels/mcmc_start_mpd/mcmc.log
+TestModels/mcmc_start_mpd/objectives.2
+TestModels/mcmc_start_mpd/objectives.3
+TestModels/mcmc_start_mpd/samples.2
+TestModels/mcmc_start_mpd/samples.3
+TestModels/mcmc_start_mpd_mcmc_fixed/esimate.err
+TestModels/mcmc_start_mpd_mcmc_fixed/mcmc.err
+TestModels/mcmc_start_mpd_mcmc_fixed/mcmc.log
+TestModels/mcmc_start_mpd_mcmc_fixed/objectives.1
+TestModels/mcmc_start_mpd_mcmc_fixed/samples.1
+TestModels/ORH3B/multi_sim.err
+TestModels/ORH3B/multi_sim.log
+TestModels/SBW/estimate_betadiff.err
+TestModels/SBW/estimate_betadiff.log
+TestModels/SexedLengthBased/estimate_adolc.err
+TestModels/SexedLengthBased/estimate_adolc.log
+TestModels/SexedLengthBased/estimate_gammadiff.err
+TestModels/SexedLengthBased/estimate_gammadiff.log
+TestModels/SimAllObs/multi_sim.err
+TestModels/SimAllObs/multi_sim.log
+TestModels/Simple/estimate_betadiff.err
+TestModels/Simple/estimate_betadiff.log
+TestModels/SimpleDirichletMultinomial/run.err
+TestModels/SingleSexTagByLength_input/run.err
+TestModels/SingleSexTagByLength_input/run.log
+TestModels/TwoSex_input/run.err
+TestModels/TwoSex_input/run.log
+TestModels/agelength_cv_with_LF/run.log
+TestModels/Complex/run.log
+TestModels/Complex_input/run.log
+TestModels/ComplexTag/estimate_betadiff.err
+TestModels/ComplexTag/estimate_betadiff.log
+TestModels/LengthBasedNoPlusGroup/run.err
+TestModels/mcmc_resume/mcmc.log
+TestModels/mcmc_resume/objectives.2
+TestModels/mcmc_resume/samples.2
+TestModels/mcmc_start_mpd/esimate.err
+TestModels/mcmc_start_mpd/mcmc.err
+TestModels/mcmc_start_mpd/mcmc.log
+TestModels/mcmc_start_mpd_mcmc_fixed/esimate.err
+TestModels/mcmc_start_mpd_mcmc_fixed/mcmc.err
+TestModels/mcmc_start_mpd_mcmc_fixed/mcmc.log
+TestModels/mcmc_start_mpd_mcmc_fixed/objectives.1
+TestModels/mcmc_start_mpd_mcmc_fixed/samples.1
+TestModels/ORH3B/multi_sim.err
+TestModels/ORH3B/multi_sim.log
+TestModels/SBW/estimate_betadiff.err
+TestModels/SBW/estimate_betadiff.log
+TestModels/SexedLengthBased/estimate_adolc.log
+TestModels/SexedLengthBased/estimate_betadiff.err
+TestModels/SexedLengthBased/estimate_betadiff.log
+TestModels/SexedLengthBased/estimate_gammadiff.log
+TestModels/SimAllObs/multi_sim.err
+TestModels/SimAllObs/multi_sim.log
+TestModels/SingleSexTagByLength_input/run.log
+TestModels/TwoSex_input/run.log
+TestModels/agelength_cv_with_LF/run.log
+TestModels/Complex/run.log
+TestModels/Complex_input/run.log
+TestModels/ComplexTag/estimate_betadiff.err
+TestModels/ComplexTag/estimate_betadiff.log
+TestModels/LengthBasedNoPlusGroup/run.err
+TestModels/mcmc_resume/mcmc.log
+TestModels/mcmc_resume/objectives.2
+TestModels/mcmc_resume/samples.2
+TestModels/mcmc_start_mpd/esimate.err
+TestModels/mcmc_start_mpd/mcmc.err
+TestModels/mcmc_start_mpd/mcmc.log
+TestModels/mcmc_start_mpd_mcmc_fixed/esimate.err
+TestModels/mcmc_start_mpd_mcmc_fixed/mcmc.err
+TestModels/mcmc_start_mpd_mcmc_fixed/mcmc.log
+TestModels/mcmc_start_mpd_mcmc_fixed/objectives.1
+TestModels/mcmc_start_mpd_mcmc_fixed/samples.1
+TestModels/ORH3B/multi_sim.err
+TestModels/ORH3B/multi_sim.log
+TestModels/SBW/estimate_betadiff.err
+TestModels/SBW/estimate_betadiff.log
+TestModels/SexedLengthBased/estimate_adolc.log
+TestModels/SexedLengthBased/estimate_betadiff.err
+TestModels/SexedLengthBased/estimate_betadiff.log
+TestModels/SexedLengthBased/estimate_gammadiff.log
+TestModels/SimAllObs/multi_sim.err
+TestModels/SimAllObs/multi_sim.log
+TestModels/Simple/estimate_gammadiff.err
+TestModels/Simple/estimate_gammadiff.log
+TestModels/SingleSexTagByLength_input/run.log
+TestModels/TwoSex/estimate_betadiff.err
+TestModels/TwoSex/estimate_betadiff.log
+TestModels/TwoSex_input/run.log
+TestModels/mcmc_start_mpd/objectives.1
+TestModels/mcmc_start_mpd/samples.1
+TestModels/mcmc_start_mpd_mcmc_fixed/mpd.log
+TestModels/TwoSex/estimate_gammadiff.log
+TestModels/TwoSex/estimate_gammadiff.err
+TestModels/TwoSex/estimate_adolc.log
+TestModels/TwoSex/estimate_adolc.err
+TestModels/Simple/estimate_adolc.log
+TestModels/Simple/estimate_adolc.err
+TestModels/SBW/estimate_gammadiff.log
+TestModels/SBW/estimate_gammadiff.err
+TestModels/SBW/estimate_adolc.log
+TestModels/SBW/estimate_adolc.err
+TestModels/mcmc_start_mpd_mcmc_fixed/samples.2
+TestModels/mcmc_start_mpd_mcmc_fixed/objectives.2

BuildSystem/Version.iss

@@ -1,2 +1,2 @@
 // WARNING: THIS FILE IS AUTOMATICALLY GENERATED BY doBuild version. DO NOT EDIT THIS FILE
-AppVersion='v22.08 (2022-08-04)'
+AppVersion='v22.08 (2022-08-23)'

BuildSystem/buildtools/classes/ModelRunner.py

@@ -30,9 +30,9 @@ def start(self):
     success_count = 0
     fail_count = 0
     ##estimation_dir_list = {"Simple", "SBW"}    # requires a config.csl2 file (uses whatever minimiser is defined)
-    estimation_betadiff_dir_list = {"TwoSex", "SBW", "Simple","ComplexTag", "SexedLengthBased"}  # requires a config-betadiff.csl2 file
-    estimation_gammadiff_dir_list = {"TwoSex", "SBW", "Simple", "SexedLengthBased"} # requires a config-gammadiff.csl2 file
-    estimation_adolc_dir_list = {"TwoSex", "SBW", "Simple", "SexedLengthBased"}     # requires a config-adolc.csl2 file
+    estimation_betadiff_dir_list = {"TwoSex", "TwoSexHybridMortality", "SBW", "Simple","ComplexTag", "SexedLengthBased"}  # requires a config-betadiff.csl2 file
+    estimation_gammadiff_dir_list = {"TwoSex", "TwoSexHybridMortality", "SBW", "Simple", "SexedLengthBased"} # requires a config-gammadiff.csl2 file
+    estimation_adolc_dir_list = {"TwoSex", "TwoSexHybridMortality", "SBW", "Simple", "SexedLengthBased"}     # requires a config-adolc.csl2 file
     simulate_dash_i_dir_list = {"ORH3B", "SimAllObs"} # if you change this you will need to formulate the report or python code below, not very general.
     run_dash_i_dir_list = {"Complex_input","TwoSex_input"}
     resume_mcmc_from_mpd_dir_list = {"mcmc_start_mpd_mcmc_fixed","mcmc_start_mpd"}

CASAL2/source/AddressableTransformations/AddressableTransformation.cpp

@@ -141,8 +141,8 @@ void AddressableTransformation::Validate() {
               LOG_FATAL_P(PARAM_PARAMETERS) << "parameter " << parameter_labels_[param_counter] << " could not be converted to an unsigned integer";
             if (u_index <= 0 || u_index > addressable_vectors_[param_counter]->size())
               LOG_FATAL_P(PARAM_PARAMETERS) << "parameter " << parameter_labels_[param_counter] << " index not in range for this parameter, please check the input";
-            vector_and_u_map_indicies_[param_counter].push_back(u_index);
-            init_values_.push_back((*addressable_vectors_[param_counter])[u_index]);
+            vector_and_u_map_indicies_[param_counter].push_back(u_index - 1);
+            init_values_.push_back((*addressable_vectors_[param_counter])[u_index - 1]);
             ++n_params_;
           }
         } else {
@@ -344,6 +344,8 @@ void AddressableTransformation::Verify(shared_ptr<Model> model) {
   for(unsigned i = 0; i < target_objects_.size(); ++i) {
     if(target_objects_[i]->IsAddressableUsedFor(parameter_lookup_for_verify_[i], addressable::kEstimate))
       LOG_FATAL_P(PARAM_PARAMETERS) << "There is an @estimate block for " << parameter_lookup_for_verify_[i] << " this is not allowed for parameters with a @parameter_transformation block";
+    if(target_objects_[i]->IsAddressableUsedFor(parameter_lookup_for_verify_[i], addressable::kProfile) & (model_->run_mode() == RunMode::kProfiling))
+      LOG_FATAL_P(PARAM_PARAMETERS) << "foung an @profile block for " << parameter_lookup_for_verify_[i] << ". You cannot have a @parameter_transformation and a @profile block for the same parameter.";
   }
 }
 

CASAL2/source/AddressableTransformations/Common/Logistic.cpp

@@ -41,6 +41,11 @@ void Logistic::DoValidate() {
     LOG_ERROR_P(PARAM_PARAMETERS) << "Logistic transformation only can transform 1 parameter at a time. You supplied " << parameter_labels_.size() << " parmaters" ;
   }
   restored_values_.resize(parameter_labels_.size(), 0.0);
+  if(init_values_[0] == lower_bound_)
+    LOG_ERROR_P(PARAM_PARAMETERS) << "initial value was equal to lower bound. This will cause an Inf and is not allowed. Change starting value";
+    if(init_values_[0] == upper_bound_)
+    LOG_ERROR_P(PARAM_PARAMETERS) << "initial value was equal to upper bound. This will cause an Inf and is not allowed. Change starting value";
+
   logistic_value_ = utilities::math::logit_bounds(init_values_[0], lower_bound_, upper_bound_); // this will get over-riden by load estimables
   restored_values_[0] = utilities::math::invlogit_bounds(logistic_value_, lower_bound_, upper_bound_);
   // Check the transformations are correct

CASAL2/source/AgeWeights/Age/Data.Test.cpp

@@ -326,7 +326,7 @@ end_table
 type process_removals_by_age
 likelihood multinomial
 time_step Annual
-mortality_instantaneous_process Instantaneous_Mortality
+mortality_process Instantaneous_Mortality
 categories Stock
 method_of_removal Fishery
 years 1986:2005

CASAL2/source/Catchabilities/Common/Nuisance.Test.cpp

@@ -256,7 +256,7 @@ time_step_proportion 1.0
 type process_removals_by_age
 likelihood multinomial
 time_step step1
-mortality_instantaneous_process instant_mort
+mortality_process instant_mort
 categories stock
 method_of_removal FishingWest
 ageing_error Ageing_error
@@ -314,7 +314,7 @@ type none
 type process_removals_by_age
 likelihood multinomial
 time_step step1
-mortality_instantaneous_process instant_mort
+mortality_process instant_mort
 categories stock
 ageing_error Ageing_error
 method_of_removal FishingEest

CASAL2/source/InitialisationPhases/Age/Cinitial.cpp

@@ -135,7 +135,7 @@ void Cinitial::DoBuild() {
 /**
  * Execute Cinitial - this code follows from the original CASAL algorithm
  */
-void Cinitial::Execute() {
+void Cinitial::DoExecute() {
   LOG_TRACE();
   map<string, vector<Double>> category_by_age_total;
   auto                        partition_iter = partition_->Begin();

CASAL2/source/InitialisationPhases/Age/Cinitial.h

@@ -37,13 +37,12 @@ class Cinitial : public niwa::InitialisationPhase {
   // methods
   explicit Cinitial(shared_ptr<Model> model);
   virtual ~Cinitial();
-  virtual void Execute() override final;
 
 protected:
   // methods
-  virtual void DoValidate() override final;
-  virtual void DoBuild() override final;
-
+  void DoValidate() override final;
+  void DoBuild() override final;
+  void DoExecute() override final;
 private:
   // members
   CombinedCategoriesPtr       partition_;

CASAL2/source/InitialisationPhases/Age/Derived.cpp

@@ -144,7 +144,7 @@ void Derived::DoBuild() {
 /**
  * Execute the Derived Initialisation phase
  */
-void Derived::Execute() {
+void Derived::DoExecute() {
   unsigned year_range = model_->age_spread();
 
   if (recruitment_)
@@ -232,14 +232,14 @@ void Derived::Execute() {
   // Check if we have B0 initialised or R0 initialised recruitment
   bool B0_initial_recruitment = false;
   for (auto recruitment_process : recruitment_process_) {
-    if (recruitment_process->b0_initialised()) {
+    if (recruitment_process->b0_initialised() & !recruitment_process->has_partition_been_scaled()) {
       LOG_FINEST() << PARAM_B0 << " has been defined for process labelled " << recruitment_process->label();
       recruitment_process->ScalePartition();
       B0_initial_recruitment = true;
     }
   }
   for (auto recruitment_process_with_devs : recruitment_process_with_devs_) {
-    if (recruitment_process_with_devs->b0_initialised()) {
+    if (recruitment_process_with_devs->b0_initialised()& !recruitment_process_with_devs->has_partition_been_scaled()) {
       LOG_FINEST() << PARAM_B0 << " has been defined for process labelled " << recruitment_process_with_devs->label();
       recruitment_process_with_devs->ScalePartition();
       B0_initial_recruitment = true;

CASAL2/source/InitialisationPhases/Age/Derived.h

@@ -4,7 +4,7 @@
  * @date 2/09/2014
  * @section LICENSE
  *
- * Copyright NIWA Science �2014 - www.niwa.co.nz
+ * Copyright NIWA Science �2014 - www.niwa.co.nz
  *
  * @section DESCRIPTION
  *
@@ -36,12 +36,12 @@ class Derived : public niwa::InitialisationPhase {
   // methods
   explicit Derived(shared_ptr<Model> model);
   virtual ~Derived() = default;
-  void Execute() override final;
 
 protected:
   // methods
   void DoValidate() override final;
   void DoBuild() override final;
+  void DoExecute() override final;
 
   // members
   unsigned                                       years_;