using jitter()

NOAA-EDAB · Jan 23, 2024 · 6e63a86 · 6e63a86
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commit 6e63a86
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Showing 7 changed files with 3,597 additions and 3,610 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
@@ -928,23 +928,10 @@ testthat::test_that("Rpath Unit Tests", {
 
       # Looks like this is causing the error...try re-writing it
       #
-print(paste0("Forced Bio is of type: ",class(REcosystem_scene_jitter$forcing$ForcedBio)))
-      # ForcedBio <- copy(REcosystem_scene_jitter$forcing$ForcedBio)
-      oldnames <- colnames(REcosystem_scene_jitter$forcing$ForcedBio)
-      ForcedBioMatrix = matrix(,nrow=nrow(REcosystem_scene_jitter$forcing$ForcedBio),
-                                ncol=ncol(REcosystem_scene_jitter$forcing$ForcedBio))
-      colnames(ForcedBioMatrix) <- oldnames
-# print(colnames(ForcedBio))
-      for (i in 1:length(species)) {
-        aSpecies <- species[[i]]
-        ForcedBioMatrix[,aSpecies] <- 10
-      }
-      REcosystem_scene_jitter$forcing$ForcedBio <- copy(ForcedBioMatrix)
+      REcosystem_scene_jitter$forcing$ForcedBio <- jitter(REcosystem_scene_jitter$forcing$ForcedBio,factor=5)
 
       # Refactoring these lines
-      # modifiedBio <- modifyForcingMatrix(modNum,species,'Jittered',theTypeData,REcosystem_scene_jitter$forcing$ForcedBio,REcosystem_scene_jitter)
-      # REcosystem_scene_jitter$forcing$ForcedBio <- modifiedBio
-
+      # REcosystem_scene_jitter$forcing$ForcedBio <- modifyForcingMatrix(modNum, species, 'Jittered', theTypeData, REcosystem_scene_jitter$forcing$ForcedBio, REcosystem_scene_jitter)
     }
     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,