commented out modifiedBio

NOAA-EDAB · Jan 22, 2024 · 478f641 · 478f641
1 parent cb07f02
commit 478f641
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Showing 7 changed files with 3,597 additions and 3,619 deletions.
diff --git a/tests/testthat/data/input/REcosystem_Baseline_AB_ForcedBio_OutBiomass_Jitter.dat b/tests/testthat/data/input/REcosystem_Baseline_AB_ForcedBio_OutBiomass_Jitter.dat
diff --git a/tests/testthat/data/input/REcosystem_Baseline_AB_ForcedBio_OutCatch_Jitter.dat b/tests/testthat/data/input/REcosystem_Baseline_AB_ForcedBio_OutCatch_Jitter.dat
diff --git a/tests/testthat/data/input/REcosystem_Baseline_AB_ForcedBio_OutGearCatch_Jitter.dat b/tests/testthat/data/input/REcosystem_Baseline_AB_ForcedBio_OutGearCatch_Jitter.dat
diff --git a/tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedBio_OutBiomass_Jitter.dat b/tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedBio_OutBiomass_Jitter.dat
diff --git a/tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedBio_OutCatch_Jitter.dat b/tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedBio_OutCatch_Jitter.dat
diff --git a/tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedBio_OutGearCatch_Jitter.dat b/tests/testthat/data/input/REcosystem_Baseline_RK4_ForcedBio_OutGearCatch_Jitter.dat
diff --git a/tests/testthat/test-rpath.R b/tests/testthat/test-rpath.R
@@ -909,28 +909,6 @@ testthat::test_that("Rpath Unit Tests", {
     runTestEqual(inc(runNum),"out_Gear_Catch","Compare baseline AB to Current RK4 for OutGearCatch",  REcosystem_Baseline_AB_OutGearCatch, REcosystem_Current_RK4_OutGearCatch)
   }
 
-  # Test RK4 Forced Bio - begin test
-
-  BaselineJitterDataFrames <- list(REcosystem_Baseline_AB_ForcedBio_OutBiomass_Jitter,  REcosystem_Baseline_AB_ForcedBio_OutCatch_Jitter,  REcosystem_Baseline_AB_ForcedBio_OutGearCatch_Jitter,
-                                   REcosystem_Baseline_RK4_ForcedBio_OutBiomass_Jitter, REcosystem_Baseline_RK4_ForcedBio_OutCatch_Jitter, REcosystem_Baseline_RK4_ForcedBio_OutGearCatch_Jitter)
-  BaselineJitterFilenames  <- list(BaselineABForcedBioOutBiomassJitter,  BaselineABForcedBioOutCatchJitter,  BaselineABForcedBioOutGearCatchJitter,
-                                   BaselineRK4ForcedBioOutBiomassJitter, BaselineRK4ForcedBioOutCatchJitter, BaselineRK4ForcedBioOutGearCatchJitter)
-  CurrentJitterFilenames   <- list(CurrentABForcedBioOutBiomassJitter,  CurrentABForcedBioOutCatchJitter,  CurrentABForcedBioOutGearCatchJitter,
-                                   CurrentRK4ForcedBioOutBiomassJitter, CurrentRK4ForcedBioOutCatchJitter, CurrentRK4ForcedBioOutGearCatchJitter)
-  REcosystem_scene <- rsim.scenario(REco, REco.params, 1:50)
-  REcosystem_scene_jitter <- copy(REcosystem_scene)
-  modNum <- modNum + 1
-  modifiedBio <- modifyForcingMatrix(modNum,species,'Jittered','Forced Bio',
-                                     REcosystem_scene_jitter$forcing$ForcedBio, REcosystem_scene_jitter)
-  REcosystem_scene_jitter$forcing$ForcedBio <- modifiedBio
-  REcosystem_RK4_Current_Jitter <- rsim.run(REcosystem_scene_jitter,method='RK4',years=1:50)
-  runTest(inc(runNum),"out_Biomass",    'Forced Bio', "Random", "RK4", "RK4", BaselineJitterDataFrames[[4]], REcosystem_RK4_Current_Jitter$out_Biomass,    CurrentJitterFilenames[[4]], species)
-  runTest(inc(runNum),"out_Catch",      'Forced Bio', "Random", "RK4", "RK4", BaselineJitterDataFrames[[5]], REcosystem_RK4_Current_Jitter$out_Catch,      CurrentJitterFilenames[[5]], species)
-  runTest(inc(runNum),"out_Gear_Catch", 'Forced Bio', "Random", "RK4", "RK4", BaselineJitterDataFrames[[6]], REcosystem_RK4_Current_Jitter$out_Gear_Catch, CurrentJitterFilenames[[6]], species)
-return() 
-
-  # --- end test
-
   print("------------------ Forced Biomass Tests (Jitter) ------------------")
   setwd(originalWorkingDir)
   typeData <- list('Forced Bio','Forced Migrate')
@@ -947,8 +925,8 @@ return()
                                        BaselineRK4ForcedBioOutBiomassJitter, BaselineRK4ForcedBioOutCatchJitter, BaselineRK4ForcedBioOutGearCatchJitter)
       CurrentJitterFilenames   <- list(CurrentABForcedBioOutBiomassJitter,  CurrentABForcedBioOutCatchJitter,  CurrentABForcedBioOutGearCatchJitter,
                                        CurrentRK4ForcedBioOutBiomassJitter, CurrentRK4ForcedBioOutCatchJitter, CurrentRK4ForcedBioOutGearCatchJitter)
-      modifiedBio <- modifyForcingMatrix(modNum,species,'Jittered',theTypeData,REcosystem_scene_jitter$forcing$ForcedBio,REcosystem_scene_jitter)
-      REcosystem_scene_jitter$forcing$ForcedBio <- modifiedBio
+      # modifiedBio <- modifyForcingMatrix(modNum,species,'Jittered',theTypeData,REcosystem_scene_jitter$forcing$ForcedBio,REcosystem_scene_jitter)
+      # REcosystem_scene_jitter$forcing$ForcedBio <- modifiedBio
     }
     else if (theTypeData == 'Forced Migrate') {
       BaselineJitterDataFrames <- list(REcosystem_Baseline_AB_ForcedMig_OutBiomass_Jitter,  REcosystem_Baseline_AB_ForcedMig_OutCatch_Jitter,  REcosystem_Baseline_AB_ForcedMig_OutGearCatch_Jitter,