Recruitment ycs syntax change 202208

.github/workflows/Casal2_testsuite_modelrunner_archive.yml

@@ -10,11 +10,11 @@ on:
 ## for a release idea linux is fairly easy
 ## for windows look at this example https://github.com/freenet/wininstaller-innosetup/actions/runs/768471071/workflow
 jobs:
-  Compile-Casal2-linux:
+  Compile-Casal2-Linux:
   # should run on linux based operating system
   # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
     runs-on: ubuntu-20.04
-    timeout-minutes: 150
+    timeout-minutes: 180
     env:
       CC: gcc-10
       CXX: g++-10
@@ -114,7 +114,7 @@ jobs:
         continue-on-error: true
         uses: actions/[email protected]
         with:
-          name: Casal2-linux-modelrunner
+          name: Casal2-Linux-modelrunner
           path: TestModels/
 
       - name: Run Unit Tests from frontend build
@@ -126,10 +126,10 @@ jobs:
         continue-on-error: true
         uses: actions/[email protected]
         with:
-          name: Casal2-linux-unittest
+          name: Casal2-Linux-unittest
           path: BuildSystem/Casal2/unittests.log
   Base-R-Ubuntu:
-    needs: Compile-Casal2-linux
+    needs: Compile-Casal2-Linux
     runs-on: ubuntu-20.04
     steps:
       - uses: actions/checkout@v2
@@ -154,7 +154,7 @@ jobs:
         uses: actions/[email protected]
         with:
           # Artifact name
-          name: Casal2-linux-modelrunner # optional
+          name: Casal2-Linux-modelrunner # optional
           # Destination path
           path: CheckTestModels # optional
       ## now run an R script that will check R-library compatible with exe output
@@ -164,7 +164,7 @@ jobs:
     # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
     # https://github.com/actions/virtual-environments/blob/main/images/win/Windows2019-Readme.md
     runs-on: windows-2019
-    timeout-minutes: 150
+    timeout-minutes: 180
     steps:
       - uses: actions/checkout@v2
 

BuildSystem/Version.iss

@@ -1,2 +1,2 @@
 // WARNING: THIS FILE IS AUTOMATICALLY GENERATED BY doBuild version. DO NOT EDIT THIS FILE
-AppVersion='v22.08 (2022-08-24)'
+AppVersion='v22.08 (2022-08-30)'

BuildSystem/buildtools/classes/ModelRunner.py

@@ -30,7 +30,7 @@ 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", "TwoSexHybridMortality", "SBW", "Simple","ComplexTag", "SexedLengthBased"}  # requires a config-betadiff.csl2 file
+    estimation_betadiff_dir_list = {"TwoSex", "TwoSexHybridMortality", "SBW", "Simple","ComplexTag", "SexedLengthBased", "BCO_tc", "HAK_tc", "HOK_tc", "LIN_tc", "ORH_tc", "SBW_tc", "SCI_tc"}  # 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.
@@ -83,8 +83,10 @@ def start(self):
         print('[OK] - ' + folder + ' in ' + str(round(elapsed, 2)) + ' seconds')
         success_count += 1
       os.chdir(cwd)   
+
     # test -i functionality 
     for folder in run_dash_i_dir_list:
+      start = time.time()
       os.chdir("../TestModels/" + folder)
       if os.system(f"{exe_path} -r -i pars.out > run.log 2> run.err") != EX_OK:
         elapsed = time.time() - start
@@ -97,8 +99,10 @@ def start(self):
         print('[OK] - ' + folder + ' -i run in ' + str(round(elapsed, 2)) + ' seconds')
         success_count += 1
       os.chdir(cwd) 
+
     # test -I functionality 
     for folder in run_dash_I_dir_list:
+      start = time.time()
       os.chdir("../TestModels/" + folder)
       if os.system(f"{exe_path} -r -I pars.out > run.log 2> run.err") != EX_OK:
         elapsed = time.time() - start
@@ -111,16 +115,20 @@ def start(self):
         print('[OK] - ' + folder + ' -I run in ' + str(round(elapsed, 2)) + ' seconds')
         success_count += 1
       os.chdir(cwd) 
+
     # test -s functionality 
     for folder in simulate_dash_i_dir_list:
+      start = time.time()
       os.chdir("../TestModels/" + folder)
+
 	    # create sim directory casal will fail if this doesn't exist
       if not os.path.exists("sim"):
         os.mkdir("sim")	  
       ## first delete any previous simulated observations from previous model runners
       for filename in os.listdir('sim'):
         file_path = os.path.join('sim', filename)
         os.remove(file_path)
+
       if os.system(f"{exe_path} -s 10 -i samples.1  > multi_sim.log 2> multi_sim.err") != EX_OK:
         elapsed = time.time() - start
         print('[FAILED] - ' + folder + ' -s run in ' + str(round(elapsed, 2)) + ' seconds')
@@ -131,6 +139,7 @@ def start(self):
         elapsed = time.time() - start
         print('[OK] - ' + folder + ' -s run in ' + str(round(elapsed, 2)) + ' seconds')
         success_count += 1
+
       if folder == "ORH3B":
         # check the correct files were generated
         if not os.path.exists("sim/CPUEandes.1_01"):
@@ -151,8 +160,10 @@ def start(self):
           print('[FAILED] - ' + folder + ' -s run in ' + str(round(elapsed, 2)) + ' expected simulated file sim/sim_all_obs.1_10')
           fail_count += 1			
         os.chdir(cwd)
+
     # test -M mpd.log functionality 
     for folder in resume_mcmc_from_mpd_dir_list:
+      start = time.time()
       os.chdir("../TestModels/" + folder)
       if os.system(f"{exe_path} -E mpd.log > estimate.log 2> esimate.err") != EX_OK:
         elapsed = time.time() - start
@@ -164,6 +175,8 @@ def start(self):
         elapsed = time.time() - start
         print('[OK] - ' + folder + ' -E mpd.log run in ' + str(round(elapsed, 2)) + ' seconds')
         success_count += 1
+
+      start = time.time()
       if os.system(f"{exe_path} -M mpd.log > mcmc.log 2> mcmc.err ") != EX_OK:
         elapsed = time.time() - start
         print('[FAILED] - ' + folder + ' -M mpd.log run in ' + str(round(elapsed, 2)) + ' seconds')
@@ -175,8 +188,10 @@ def start(self):
         print('[OK] - ' + folder + ' -M mpd.log run in ' + str(round(elapsed, 2)) + ' seconds')
         success_count += 1
       os.chdir(cwd)
+
     # test -R mpd.log 
     for folder in resume_mcmc_dir_list:
+      start = time.time()
       os.chdir("../TestModels/" + folder)
       if os.system(f"{exe_path} -R mpd.log --objective-file objectives.1 --sample-file samples.1 > mcmc.log 2>&1") != EX_OK:
         elapsed = time.time() - start
@@ -189,8 +204,10 @@ def start(self):
         print('[OK] - ' + folder + ' -R run in ' + str(round(elapsed, 2)) + ' seconds')
         success_count += 1
       os.chdir(cwd)
+
     # test -e functionality
     for folder in estimation_betadiff_dir_list:
+      start = time.time()
       os.chdir("../TestModels/" + folder)
       if os.system(f"{exe_path} -e -g 20 -c config_betadiff.csl2 > estimate_betadiff.log 2> estimate_betadiff.err") != EX_OK:
         elapsed = time.time() - start
@@ -203,7 +220,9 @@ def start(self):
         print('[OK] - ' + folder + ' betadiff estimation in ' + str(round(elapsed, 2)) + ' seconds')
         success_count += 1
       os.chdir(cwd) 	  
+
     for folder in estimation_gammadiff_dir_list:
+      start = time.time()
       os.chdir("../TestModels/" + folder)
       if os.system(f"{exe_path} -e -g 20 -c config_gammadiff.csl2 > estimate_gammadiff.log 2> estimate_gammadiff.err") != EX_OK:
         elapsed = time.time() - start
@@ -216,7 +235,9 @@ def start(self):
         print('[OK] - ' + folder + ' gammadiff estimation in ' + str(round(elapsed, 2)) + ' seconds')
         success_count += 1
       os.chdir(cwd) 	  
+
     for folder in estimation_adolc_dir_list:
+      start = time.time()
       os.chdir("../TestModels/" + folder)
       if os.system(f"{exe_path} -e -g 20 --config config_adolc.csl2 > estimate_adolc.log 2> estimate_adolc.err") != EX_OK:
         elapsed = time.time() - start
@@ -229,6 +250,7 @@ def start(self):
         print('[OK] - ' + folder + ' adolc estimation in ' + str(round(elapsed, 2)) + ' seconds')
         success_count += 1
       os.chdir(cwd)  
+
     print('')
     print('Total Models: ' + str(success_count + fail_count))
     print('Failed Models: ' + str(fail_count))

CASAL2/source/AddressableTransformations/AddressableTransformation.Test.cpp

@@ -60,9 +60,8 @@ type recruitment_beverton_holt
 categories stock
 proportions 1
 b0 75000
-standardise_ycs_years 1975 1976 1977 
-ycs_values   	      1.00 1.02472	1.04658	
-ycs_years 1974:1976
+standardise_years 1976:1978
+recruitment_multipliers   	      1.00 1.02472	1.04658	
 steepness 0.9
 ssb biomass_t1
 age 1
@@ -145,7 +144,7 @@ b 3.288
 const std::string avg_diff_fail = R"(
   @parameter_transformation ycs_avg_diff
   type average_difference
-  parameters process[Recruitment].ycs_values{1975} process[Recruitment].ycs_values{1976}
+  parameters process[Recruitment].recruitment_multipliers{1976} process[Recruitment].recruitment_multipliers{1977}
 
   @estimate ycs_avg
   type uniform

CASAL2/source/AddressableTransformations/AddressableTransformation.h

@@ -59,12 +59,12 @@ class AddressableTransformation : public niwa::base::Object {
   void set_single_values_for_multiple_maps(vector<Double> values);
   void set_single_values_for_multiple_vectors(vector<Double> values);
   void set_single_values_for_multiple_string_maps(vector<Double> values);
-  // how is process[Recruit].ycs_values{2013} treated? is this a single value or a map?
+  // how is process[Recruit].recruitment_multipliers{2013} treated? is this a single value or a map?
   // and process[Instan_mort].m{male} treated? is this a single value or a map?
   // I want these to be single values is that easy?
 
   // These should only be used for special transformations which operate on an entire map/subset or vector/subset vector
-  // i.e only on process[Recruit].ycs_values or process[Recruit].ycs_values{1990:2013}
+  // i.e only on process[Recruit].recruitment_multipliers or process[Recruit].recruitment_multipliers{1990:2013}
   // or
   // selectivity[all_values_bounded].v or selectivity[all_values_bounded].v{1:5}
   // We can catch these from the above separate case as if we

CASAL2/source/AddressableTransformations/Common/Simplex.Test.cpp

@@ -155,8 +155,7 @@ type recruitment_beverton_holt
 categories stock
 proportions 1
 b0 75000
-ycs_values   1.3464 1.3797 1.4091 1.4315 1.4447 1.4468 1.4345 1.4047 1.3708 1.3502 0.5748 0.6419 0.7007 0.5146 0.7098 0.5994 0.9078 1.3517 1.0249 0.8798 0.7981 0.6579 0.4325 0.4085 0.2981 0.4483 0.2961 0.4426 1.2456 0.7079 0.5855 0.2521 0.4138 0.3496 0.3109 0.3503 4.0392 4.0392
-ycs_years 1974:2011
+recruitment_multipliers   1.3464 1.3797 1.4091 1.4315 1.4447 1.4468 1.4345 1.4047 1.3708 1.3502 0.5748 0.6419 0.7007 0.5146 0.7098 0.5994 0.9078 1.3517 1.0249 0.8798 0.7981 0.6579 0.4325 0.4085 0.2981 0.4483 0.2961 0.4426 1.2456 0.7079 0.5855 0.2521 0.4138 0.3496 0.3109 0.3503 4.0392 4.0392
 steepness 0.9
 ssb biomass_t1
 age 1
@@ -204,7 +203,7 @@ b 3.288
 
 @parameter_transformation simplex_ycs
 type simplex
-parameters process[Recruitment].ycs_values
+parameters process[Recruitment].recruitment_multipliers
 sum_to_one false
 prior_applies_to_restored_parameters true
 
@@ -225,7 +224,7 @@ TEST_F(InternalEmptyModel, AddressableTransformations_simplex_validate_simplex_c
   vector<Double>*  simplex = model_->objects().GetAddressableVector("parameter_transformation[simplex_ycs].simplex");
   vector<Double> result = {0.3068, 0.3422, 0.3759, 0.4059, 0.4308, 0.4493, 0.4587, 0.4562, 0.4506, 0.4552, -0.4109, -0.3105, -0.2308, -0.5567, -0.2442, -0.4285, -0.014, 0.4078, 0.1384, -0.0151, -0.1188, -0.3286, -0.7825, -0.8793, -1.2468, -0.8848, -1.3637, -1.0216, 0.0146, -0.6021, -0.8672, -1.8379, -1.48, -1.8324, -2.2012, -2.4449, 0};
   vector<Double> ycs_vals_in_config = {1.3464, 1.3797, 1.4091, 1.4315, 1.4447, 1.4468, 1.4345, 1.4047, 1.3708, 1.3502, 0.5748, 0.6419, 0.7007, 0.5146, 0.7098, 0.5994, 0.9078, 1.3517, 1.0249, 0.8798, 0.7981, 0.6579, 0.4325, 0.4085, 0.2981, 0.4483, 0.2961, 0.4426, 1.2456, 0.7079, 0.5855, 0.2521, 0.4138, 0.3496, 0.3109, 0.3503, 4.0392, 4.0392};
-  map<unsigned, Double>* restored_ycs_values = model_->objects().GetAddressableUMap("process[Recruitment].ycs_values");
+  map<unsigned, Double>* restored_recruitment_multipliers_values = model_->objects().GetAddressableUMap("process[Recruitment].recruitment_multipliers");
   // This result was generated against the following R-code
   // Assuming you copy the config about and run casal2 -r > run.out
   // With the added @reports
@@ -259,7 +258,7 @@ TEST_F(InternalEmptyModel, AddressableTransformations_simplex_validate_simplex_c
     EXPECT_NEAR(result[i], (*simplex)[i], 1e-3) << " with i = " << i + 1;
   }
   unsigned counter = 0;
-  for(auto ycs_val : (*restored_ycs_values)) {
+  for(auto ycs_val : (*restored_recruitment_multipliers_values)) {
     EXPECT_NEAR(ycs_vals_in_config[counter], ycs_val.second, 1e-3) << " year = " << ycs_val.first << " counter = " << counter;
     ++counter;
   }

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

@@ -76,10 +76,9 @@ proportions 0.5 0.5
 r0 5e6
 age 2
 steepness 0.9
-ycs_values 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
+recruitment_multipliers 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
 ssb ssb
-ycs_years 1973:2000
-standardise_ycs_years 1973:1999
+standardise_years 1975:2001
 
 @mortality halfm
 type constant_rate

CASAL2/source/AgeLengths/AgeLength.Test.cpp

@@ -59,9 +59,8 @@ type recruitment_beverton_holt
 categories stock
 proportions 1
 b0 5.18767e+008
-ycs_years 1974:1976
-standardise_ycs_years 1974:1976
-ycs_values          1.00 1.00 1.00 
+standardise_years 1975:1977
+recruitment_multipliers          1.00 1.00 1.00 
 steepness 0.9
 ssb biomass_t1
 age 1

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

@@ -74,17 +74,16 @@ type recruitment_beverton_holt_with_deviations
 categories Stock
 proportions 1.0
 b0 5973.9         
-last_year_with_no_bias 1986
-first_year_with_bias 1986
-last_year_with_bias 2005 
-first_recent_year_with_no_bias 2005
+last_year_with_no_bias 1987
+first_year_with_bias 1987
+last_year_with_bias 2006 
+first_recent_year_with_no_bias 2006
 b_max 1.0
 deviation_values 0.161055491247 0.0935823574532 -0.454148603651 -0.143755692424 -0.979662527968 1.70885246646 0.207878584523 -0.142998000652 0.448480496158 -1.25142717617 0.621050539438 0.0732265269830 0.0247523483886 0.137793954591 0.199439856167 -0.701101119095 0.613584736138 -0.103102553946 -0.101487357908 -0.412014325737
 steepness 0.5792984
 ssb SSB
 age 1     
 sigma_r 0.6
-deviation_years 1985:2004
 
 @process Ageing
 type ageing

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

@@ -67,12 +67,11 @@ type recruitment_beverton_holt
 categories stock
 proportions 1 
 b0 52583
-standardise_ycs_years 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009
-ycs_values          1.00 1.02472  1.04658 1.06324 1.07299 1.07458 1.06541 1.04328 1.01815 1.00285 0.426938  0.476756  0.520428  0.382199  0.527158  0.445187  0.67427 1.00397 0.761247  0.653433  0.592745  0.488619  0.321246  0.303421  0.221372  0.33299 0.219917  0.328752  0.925172  0.525766  0.434871  0.18722 0.307342  0.259689  0.230941  0.260211  3 3
+standardise_years 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010
+recruitment_multipliers          1.00 1.02472  1.04658 1.06324 1.07299 1.07458 1.06541 1.04328 1.01815 1.00285 0.426938  0.476756  0.520428  0.382199  0.527158  0.445187  0.67427 1.00397 0.761247  0.653433  0.592745  0.488619  0.321246  0.303421  0.221372  0.33299 0.219917  0.328752  0.925172  0.525766  0.434871  0.18722 0.307342  0.259689  0.230941  0.260211  3 3
 steepness 0.9
 ssb biomass_t1
 age 1
-ycs_years 1974:2011
 
 @process Ageing
 type ageing

CASAL2/source/Observations/Age/Abundance/Process.Test.cpp

@@ -4,7 +4,7 @@
  * @date 26/02/2014
  * @section LICENSE
  *
- * Copyright NIWA Science �2014 - www.niwa.co.nz
+ * Copyright NIWA Science �2014 - www.niwa.co.nz
  *
  */
 #ifdef TESTMODE
@@ -72,10 +72,9 @@ proportions 0.5 0.5
 r0 5e6
 age 2
 steepness 0.9
-ycs_values 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
+recruitment_multipliers 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
 ssb ssb
-ycs_years 1973:2000
-standardise_ycs_years 1973:1999
+standardise_years 1975:2001
 
 @mortality halfm
 type constant_rate