Refreshed files to re-commit and check git action

tests/testthat/data/input/REcosystem_Baseline_AB.csv

@@ -1,27 +1,27 @@
 "","Group","StartBio","EndBio","BioES","StartCatch","EndCatch","CatchES"
 "Outside","Outside",1,1,1,0,0,NA
-"Seabirds","Seabirds",0.0149,0.0149000421028321,1.00000282569343,1e-05,1.00000282111217e-05,1.00000282111217
+"Seabirds","Seabirds",0.0149,0.0149000421028323,1.00000282569344,1e-05,1.00000282111218e-05,1.00000282111218
 "Whales","Whales",0.454,0.454000210323487,1.00000046326759,1e-07,1.00000046237396e-07,1.00000046237396
-"Seals","Seals",0.0249999999999718,0.0250002188221431,1.00000875288685,0.00200000000413891,0.00200001748905324,1.00000874245715
-"JuvRoundfish1","JuvRoundfish1",0.130430485118969,0.130433508003209,1.00002317620944,0.00300000000000001,0.00300006953210303,1.00002317736767
-"AduRoundfish1","AduRoundfish1",1.39,1.39005295588287,1.00003809775746,0.145000203632079,0.145005524262104,1.00003669394864
-"JuvRoundfish2","JuvRoundfish2",1.23260830921837,1.23259936869508,0.999992746663136,0.003,0.00299997823997374,0.999992746657912
-"AduRoundfish2","AduRoundfish2",5.553,5.55298124848838,0.999996623174568,0.389000250489473,0.388998687520254,0.999995982086857
-"JuvFlatfish1","JuvFlatfish1",0.0698844163992366,0.0698869780915876,1.00003665613141,0.002,0.00200007328635013,1.00003664317507
-"AduFlatfish1","AduFlatfish1",5.766,5.76631154105126,1.00005403070608,0.180000208050261,0.180009721333862,1.00005285151447
-"JuvFlatfish2","JuvFlatfish2",0.0962887696620608,0.0962884894227788,0.99999708959536,0.002,0.00199999420098711,0.999997100493556
-"AduFlatfish2","AduFlatfish2",0.739,0.739000130647141,1.00000017678909,0.0700000310249589,0.0700000137421647,0.99999975310305
-"OtherGroundfish","OtherGroundfish",7.4,7.39994608057505,0.999992713591223,0.379999997272581,0.379997231062138,0.999992720498784
-"Foragefish1","Foragefish1",5.1,5.09999811993401,0.999999631359611,0.350999998399263,0.350999870540216,0.999999635729209
-"Foragefish2","Foragefish2",4.7,4.70000128223243,1.00000027281541,0.0909999995496743,0.0910000247985853,1.00000027746056
-"OtherForagefish","OtherForagefish",5.1,5.09999705474722,0.999999422499456,0.0309999997462498,0.0309999820895145,0.99999943042789
-"Megabenthos","Megabenthos",19.7653839645524,19.7653695454297,0.999999270486083,0.189999999090599,0.189999861429518,0.999999275467992
-"Shellfish","Shellfish",7,7.00000501432483,1.00000071633212,0.509999999758437,0.51000036523584,1.00000071662236
-"Macrobenthos","Macrobenthos",17.4,17.3999776424532,0.99999871508352,9.99999987659067e-05,9.99998715476867e-05,0.999998727817784
+"Seals","Seals",0.0249999999999768,0.0250002188221547,1.00000875288712,0.00200000000413891,0.00200001748905377,1.00000874245741
+"JuvRoundfish1","JuvRoundfish1",0.130430485118969,0.130433508003186,1.00002317620926,0.003,0.00300006953210249,1.0000231773675
+"AduRoundfish1","AduRoundfish1",1.39,1.39005295588256,1.00003809775723,0.145000203632079,0.145005524262072,1.00003669394842
+"JuvRoundfish2","JuvRoundfish2",1.23260830921837,1.23259936869507,0.999992746663134,0.003,0.00299997823997373,0.999992746657911
+"AduRoundfish2","AduRoundfish2",5.553,5.55298124848836,0.999996623174565,0.389000250489473,0.388998687520253,0.999995982086855
+"JuvFlatfish1","JuvFlatfish1",0.0698844163992366,0.069886978091586,1.00003665613139,0.00199999999999999,0.00200007328635009,1.00003664317505
+"AduFlatfish1","AduFlatfish1",5.766,5.7663115410512,1.00005403070607,0.180000208050261,0.18000972133386,1.00005285151446
+"JuvFlatfish2","JuvFlatfish2",0.0962887696620608,0.0962884894227813,0.999997089595386,0.002,0.00199999420098716,0.999997100493582
+"AduFlatfish2","AduFlatfish2",0.739,0.739000130647185,1.00000017678915,0.0700000310249589,0.0700000137421689,0.99999975310311
+"OtherGroundfish","OtherGroundfish",7.4,7.39994608057543,0.999992713591274,0.379999997272581,0.379997231062158,0.999992720498835
+"Foragefish1","Foragefish1",5.1,5.09999811993404,0.999999631359616,0.350999998399263,0.350999870540218,0.999999635729215
+"Foragefish2","Foragefish2",4.7,4.70000128223247,1.00000027281542,0.0909999995496744,0.091000024798586,1.00000027746057
+"OtherForagefish","OtherForagefish",5.1,5.09999705474727,0.999999422499466,0.0309999997462498,0.0309999820895149,0.9999994304279
+"Megabenthos","Megabenthos",19.7653839645524,19.7653695454297,0.999999270486081,0.189999999090599,0.189999861429517,0.99999927546799
+"Shellfish","Shellfish",7,7.00000501432484,1.00000071633212,0.509999999758437,0.51000036523584,1.00000071662236
+"Macrobenthos","Macrobenthos",17.4,17.3999776424533,0.999998715083521,9.99999987659068e-05,9.99998715476867e-05,0.999998727817784
 "Zooplankton","Zooplankton",23,23.000000629589,1.00000002737344,0,0,NA
 "Phytoplankton","Phytoplankton",10,9.99999972809651,0.999999972809651,0,0,NA
 "Detritus","Detritus",3636.66711075279,3636.66738830137,1.00000007631949,0,0,NA
-"Discards","Discards",1.2182202,1.21823092208955,1.00000880143799,0,0,NA
+"Discards","Discards",1.2182202,1.21823092208953,1.00000880143798,0,0,NA
 "Trawlers","Trawlers",0,0,NA,0,0,NA
 "Midwater","Midwater",0,0,NA,0,0,NA
 "Dredgers","Dredgers",0,0,NA,0,0,NA

tests/testthat/data/input/REcosystem_Baseline_RK4.csv

@@ -1,27 +1,27 @@
 "","Group","StartBio","EndBio","BioES","StartCatch","EndCatch","CatchES"
 "Outside","Outside",1,1,1,0,0,NA
-"Seabirds","Seabirds",0.0149,0.0149000414705202,1.00000278325639,9.99999999999475e-06,1.00000277870872e-05,1.00000277870925
+"Seabirds","Seabirds",0.0149,0.0149000414705204,1.0000027832564,9.99999999999475e-06,1.00000277870874e-05,1.00000277870926
 "Whales","Whales",0.454,0.454000203549876,1.00000044834774,9.99999999999199e-08,1.00000044748892e-07,1.00000044748972
-"Seals","Seals",0.0249999999999718,0.0250002151253163,1.00000860501378,0.00200000000272358,0.00200001719370259,1.00000859548949
-"JuvRoundfish1","JuvRoundfish1",0.130430485118969,0.130433509907448,1.00002319080909,0.00299999999941579,0.00300006722470278,1.000022408429
-"AduRoundfish1","AduRoundfish1",1.39,1.3900529699139,1.00003810785173,0.145000201253226,0.145005476873034,1.00003638353438
-"JuvRoundfish2","JuvRoundfish2",1.23260830921836,1.23259937159164,0.999992749013086,0.00299999999971644,0.00299997893978356,0.99999298002237
-"AduRoundfish2","AduRoundfish2",5.553,5.55298128970033,0.999996630596134,0.389000247694946,0.388998687736761,0.999995989827272
-"JuvFlatfish1","JuvFlatfish1",0.0698844163992366,0.0698869785491005,1.00003666267812,0.00199999999751022,0.00200007140577223,1.00003570413105
-"AduFlatfish1","AduFlatfish1",5.766,5.76631158759197,1.00005403877766,0.180000206280042,0.180009663891873,1.00005254222774
-"JuvFlatfish2","JuvFlatfish2",0.0962887696620608,0.0962884904713711,0.999997100485439,0.00199999999817096,0.00199999422811603,0.999997114972532
-"AduFlatfish2","AduFlatfish2",0.739000000000001,0.739000142115137,1.00000019230736,0.0700000308235379,0.0700000121018634,0.999999732547625
-"OtherGroundfish","OtherGroundfish",7.4,7.39994606118236,0.999992710970589,0.37999999816591,0.379997230076909,0.999992715555226
-"Foragefish1","Foragefish1",5.1,5.09999812442392,0.999999632239984,0.3509999989451,0.350999870850301,0.999999635057553
-"Foragefish2","Foragefish2",4.7,4.700001283549,1.00000027309553,0.0909999997037419,0.0910000248242094,1.00000027604909
-"OtherForagefish","OtherForagefish",5.1,5.09999704663004,0.999999420907851,0.0309999998356158,0.0309999820405001,0.999999425964008
-"Megabenthos","Megabenthos",19.7653839645524,19.7653694849668,0.999999267427051,0.189999999383839,0.18999986084728,0.999999270860213
+"Seals","Seals",0.0249999999999768,0.0250002151253278,1.00000860501404,0.00200000000272359,0.00200001719370312,1.00000859548975
+"JuvRoundfish1","JuvRoundfish1",0.130430485118969,0.130433509907425,1.00002319080891,0.00299999999941577,0.00300006722470225,1.00002240842883
+"AduRoundfish1","AduRoundfish1",1.39,1.39005296991359,1.00003810785151,0.145000201253226,0.145005476873002,1.00003638353416
+"JuvRoundfish2","JuvRoundfish2",1.23260830921836,1.23259937159164,0.999992749013083,0.00299999999971644,0.00299997893978355,0.999992980022369
+"AduRoundfish2","AduRoundfish2",5.553,5.55298128970031,0.999996630596131,0.389000247694946,0.38899868773676,0.999995989827268
+"JuvFlatfish1","JuvFlatfish1",0.0698844163992366,0.0698869785490991,1.0000366626781,0.00199999999751021,0.00200007140577219,1.00003570413104
+"AduFlatfish1","AduFlatfish1",5.766,5.76631158759191,1.00005403877765,0.180000206280042,0.180009663891871,1.00005254222773
+"JuvFlatfish2","JuvFlatfish2",0.0962887696620608,0.0962884904713736,0.999997100485466,0.00199999999817096,0.00199999422811608,0.999997114972557
+"AduFlatfish2","AduFlatfish2",0.739000000000001,0.73900014211518,1.00000019230741,0.070000030823538,0.0700000121018677,0.999999732547685
+"OtherGroundfish","OtherGroundfish",7.4,7.39994606118274,0.999992710970641,0.37999999816591,0.379997230076929,0.999992715555277
+"Foragefish1","Foragefish1",5.1,5.09999812442395,0.999999632239989,0.3509999989451,0.350999870850303,0.999999635057559
+"Foragefish2","Foragefish2",4.7,4.70000128354904,1.00000027309554,0.0909999997037419,0.0910000248242102,1.0000002760491
+"OtherForagefish","OtherForagefish",5.1,5.09999704663009,0.999999420907861,0.0309999998356158,0.0309999820405005,0.999999425964018
+"Megabenthos","Megabenthos",19.7653839645524,19.7653694849667,0.99999926742705,0.189999999383839,0.189999860847279,0.999999270860211
 "Shellfish","Shellfish",7,7.00000502602804,1.00000071800401,0.509999999875786,0.510000366087145,1.00000071806149
-"Macrobenthos","Macrobenthos",17.4,17.3999776323994,0.999998714505715,9.99999992742293e-05,9.99998714891689e-05,0.999998722149387
+"Macrobenthos","Macrobenthos",17.4,17.3999776323995,0.999998714505716,9.99999992742293e-05,9.9999871489169e-05,0.999998722149387
 "Zooplankton","Zooplankton",23,23.000000626978,1.00000002725991,0,0,NA
-"Phytoplankton","Phytoplankton",10,9.99999972903496,0.999999972903496,0,0,NA
+"Phytoplankton","Phytoplankton",10,9.99999972903497,0.999999972903497,0,0,NA
 "Detritus","Detritus",3636.66711075279,3636.66738627725,1.0000000757629,0,0,NA
-"Discards","Discards",1.2182202,1.21823082510863,1.0000087218293,0,0,NA
+"Discards","Discards",1.2182202,1.21823082510862,1.00000872182929,0,0,NA
 "Trawlers","Trawlers",0,0,NA,0,0,NA
 "Midwater","Midwater",0,0,NA,0,0,NA
 "Dredgers","Dredgers",0,0,NA,0,0,NA

tests/testthat/test-rpath.R

@@ -146,7 +146,8 @@ runTestRDS <- function(runNum,tableName,forcedData,forcedType,baseAlg,currAlg,ba
     sumDiffTable <- sumDiffTable + abs(sumColsCurr[i]-sumColsBase[i])
   }
 #print(paste0("***sumDiffTable: ",sumDiffTable))
-#print(paste0("SUM of current,baselineDataFrame:  ", sum(currentDataFrame), ", ",sum(baselineDataFrame)))          # ok
+#print(paste0("SUM of currentDataFrame:  ", sum(currentDataFrame)))           # ok
+#print(paste0("SUM of baselineDataFrame: ", sum(baselineDataFrame)))          # ok
 #print("Comparing if sumDiffTable/sum(currentDataFrame) <= TOLERANCE_VALUE")
 #print(paste0("Is ",sumDiffTable,"/",sum(currentDataFrame)," <= ",TOLERANCE_VALUE," ?"))
 areIdentical <- (sumDiffTable/ sum(currentDataFrame) <= TOLERANCE_VALUE)
@@ -671,10 +672,8 @@ testthat::test_that("Rpath Unit Tests", {
       runTestRDS(inc(runNum),"out_Catch",      theTypeData, "Random", "AB",  "AB",  BaselineJitterDataFrames[[2]], CurrentJitterFilenames[[2]], species)
       runTestRDS(inc(runNum),"out_Gear_Catch", theTypeData, "Random", "AB",  "AB",  BaselineJitterDataFrames[[3]], CurrentJitterFilenames[[3]], species)
       runTestRDS(inc(runNum),"out_Biomass",    theTypeData, "Random", "RK4", "RK4", BaselineJitterDataFrames[[4]], CurrentJitterFilenames[[4]], species)
-      if (0) { # debug these 
       runTestRDS(inc(runNum),"out_Catch",      theTypeData, "Random", "RK4", "RK4", BaselineJitterDataFrames[[5]], CurrentJitterFilenames[[5]], species)
       runTestRDS(inc(runNum),"out_Gear_Catch", theTypeData, "Random", "RK4", "RK4", BaselineJitterDataFrames[[6]], CurrentJitterFilenames[[6]], species)
-      }
     }
   }
 
@@ -731,13 +730,11 @@ testthat::test_that("Rpath Unit Tests", {
       writeDataFile(REcosystem_RK4_Current_Stepped$out_Catch,      CurrentSteppedFiles[[5]])
       writeDataFile(REcosystem_RK4_Current_Stepped$out_Gear_Catch, CurrentSteppedFiles[[6]])
       runTestRDS(inc(runNum),"out_Biomass",    theTypeData, "Stepped", "AB", "AB", BaselineSteppedTables[[1]], CurrentSteppedFiles[[1]], species)
-      if (0) { # debug later
-        runTestRDS(inc(runNum),"out_Catch",      theTypeData, "Stepped", "AB", "AB", BaselineSteppedTables[[2]], CurrentSteppedFiles[[2]], species)
-        runTestRDS(inc(runNum),"out_Gear_Catch", theTypeData, "Stepped", "AB", "AB", BaselineSteppedTables[[3]], CurrentSteppedFiles[[3]], species)
-        runTestRDS(inc(runNum),"out_Biomass",    theTypeData, "Stepped", "RK4","RK4",BaselineSteppedTables[[4]], CurrentSteppedFiles[[4]], species)
-        runTestRDS(inc(runNum),"out_Catch",      theTypeData, "Stepped", "RK4","RK4",BaselineSteppedTables[[5]], CurrentSteppedFiles[[5]], species)
-        runTestRDS(inc(runNum),"out_Gear_Catch", theTypeData, "Stepped", "RK4","RK4",BaselineSteppedTables[[6]], CurrentSteppedFiles[[6]], species)
-      }
+      runTestRDS(inc(runNum),"out_Catch",      theTypeData, "Stepped", "AB", "AB", BaselineSteppedTables[[2]], CurrentSteppedFiles[[2]], species)
+      runTestRDS(inc(runNum),"out_Gear_Catch", theTypeData, "Stepped", "AB", "AB", BaselineSteppedTables[[3]], CurrentSteppedFiles[[3]], species)
+      runTestRDS(inc(runNum),"out_Biomass",    theTypeData, "Stepped", "RK4","RK4",BaselineSteppedTables[[4]], CurrentSteppedFiles[[4]], species)
+      runTestRDS(inc(runNum),"out_Catch",      theTypeData, "Stepped", "RK4","RK4",BaselineSteppedTables[[5]], CurrentSteppedFiles[[5]], species)
+      runTestRDS(inc(runNum),"out_Gear_Catch", theTypeData, "Stepped", "RK4","RK4",BaselineSteppedTables[[6]], CurrentSteppedFiles[[6]], species)
     }
   }
 
@@ -770,8 +767,6 @@ testthat::test_that("Rpath Unit Tests", {
       CurrentJitterFiles   <- list(CurrentABForcedFRaOutBiomassJitter,  CurrentABForcedFRaOutCatchJitter,  CurrentABForcedFRaOutGearCatchJitter,
                                    CurrentRK4ForcedFRaOutBiomassJitter, CurrentRK4ForcedFRaOutCatchJitter, CurrentRK4ForcedFRaOutGearCatchJitter)
     } else if (theTypeData == FORCED_CATCH) {
-      ForcedMatrix <- modifyFishingMatrix(modNum,species,fleets,theTypeData,fishingOriginalData[[i]],
-                                          REco.params$model,POSITIVE_ONLY)
       REcosystem_scenario_jitter$fishing$ForcedCatch  <- ForcedMatrix
       BaselineJitterTables <- list(REcosystem_Baseline_AB_ForcedCat_OutBiomass_Jitter, REcosystem_Baseline_AB_ForcedCat_OutCatch_Jitter, REcosystem_Baseline_AB_ForcedCat_OutGearCatch_Jitter,
                                 REcosystem_Baseline_RK4_ForcedCat_OutBiomass_Jitter,REcosystem_Baseline_RK4_ForcedCat_OutCatch_Jitter,REcosystem_Baseline_RK4_ForcedCat_OutGearCatch_Jitter) 
@@ -809,10 +804,8 @@ testthat::test_that("Rpath Unit Tests", {
   print("------------------ Forced Effort Tests (Stepped) ------------------")
   numMonths <- nrow(REcosystem_scenario$fishing$ForcedEffort)
   REcosystem_scenario_stepped <- REcosystem_scenario
-  fishingOriginalData <- list(REcosystem_scenario$fishing$ForcedEffort,
-                              REcosystem_scenario$fishing$ForcedFRate,
-                              REcosystem_scenario$fishing$ForcedCatch)
-  typeData <- list(FORCED_EFFORT,FORCED_FRATE,FORCED_CATCH)
+  fishingOriginalData  <- list(REcosystem_scenario$fishing$ForcedEffort, REcosystem_scenario$fishing$ForcedFRate, REcosystem_scenario$fishing$ForcedCatch)
+  typeData             <- list(FORCED_EFFORT,FORCED_FRATE,FORCED_CATCH)
   for (i in 1:length(fishingOriginalData)) {
     theTypeData  <- typeData[[i]]
     REcosystem_scenario_stepped <- REcosystem_scenario
@@ -825,7 +818,6 @@ testthat::test_that("Rpath Unit Tests", {
       CurrentSteppedFiles  <- list(CurrentABForcedEffOutBiomassStepped,  CurrentABForcedEffOutCatchStepped,  CurrentABForcedEffOutGearCatchStepped,
                                    CurrentRK4ForcedEffOutBiomassStepped, CurrentRK4ForcedEffOutCatchStepped, CurrentRK4ForcedEffOutGearCatchStepped)
     } else if (theTypeData == FORCED_FRATE) {
-
       REcosystem_scenario_stepped$fishing$ForcedFRate <- stepifyMatrix(fishingOriginalData[[i]],species,0.01)
       BaselineSteppedTables <- list(REcosystem_Baseline_AB_ForcedFRa_OutBiomass_Stepped,  REcosystem_Baseline_AB_ForcedFRa_OutCatch_Stepped,  REcosystem_Baseline_AB_ForcedFRa_OutGearCatch_Stepped,
                                     REcosystem_Baseline_RK4_ForcedFRa_OutBiomass_Stepped, REcosystem_Baseline_RK4_ForcedFRa_OutCatch_Stepped, REcosystem_Baseline_RK4_ForcedFRa_OutGearCatch_Stepped)
@@ -834,13 +826,7 @@ testthat::test_that("Rpath Unit Tests", {
       CurrentSteppedFiles  <- list(CurrentABForcedFRaOutBiomassStepped,  CurrentABForcedFRaOutCatchStepped,  CurrentABForcedFRaOutGearCatchStepped,
                                    CurrentRK4ForcedFRaOutBiomassStepped, CurrentRK4ForcedFRaOutCatchStepped, CurrentRK4ForcedFRaOutGearCatchStepped)      
     } else if (theTypeData == FORCED_CATCH) {
-      # print("Forced Catch data: ")
-      # print(fishingOriginalData[[i]])
-      # RSK - continue here
-      ForcedMatrix <- modifyFishingMatrix_constant(modNum,species,fleets,theTypeData,fishingOriginalData[[i]],
-                                          REco.params$model,POSITIVE_ONLY)
-      #REcosystem_scenario_stepped$fishing$ForcedCatch <- ForcedMatrix
-      REcosystem_scenario_stepped$fishing$ForcedCatch <- stepifyMatrix(ForcedMatrix,species,1)
+      REcosystem_scenario_stepped$fishing$ForcedCatch <- stepifyMatrix(fishingOriginalData[[i]],species,0.01)
       BaselineSteppedTables <- list(REcosystem_Baseline_AB_ForcedCat_OutBiomass_Stepped,  REcosystem_Baseline_AB_ForcedCat_OutCatch_Stepped,  REcosystem_Baseline_AB_ForcedCat_OutGearCatch_Stepped,
                                     REcosystem_Baseline_RK4_ForcedCat_OutBiomass_Stepped, REcosystem_Baseline_RK4_ForcedCat_OutCatch_Stepped, REcosystem_Baseline_RK4_ForcedCat_OutGearCatch_Stepped)
       BaselineSteppedFiles <- list(BaselineABForcedCatOutBiomassStepped, BaselineABForcedCatOutCatchStepped, BaselineABForcedCatOutGearCatchStepped,
@@ -864,14 +850,12 @@ testthat::test_that("Rpath Unit Tests", {
       writeDataFile(REcosystem_RK4_Current_Stepped$out_Biomass,    CurrentSteppedFiles[[4]])
       writeDataFile(REcosystem_RK4_Current_Stepped$out_Catch,      CurrentSteppedFiles[[5]])
       writeDataFile(REcosystem_RK4_Current_Stepped$out_Gear_Catch, CurrentSteppedFiles[[6]])
-      if (0) { # debug later
-        runTestRDS(inc(runNum),"out_Biomass",    theTypeData, "Stepped", "AB",  "AB",  BaselineSteppedTables[[1]], CurrentSteppedFiles[[1]], species)
-        runTestRDS(inc(runNum),"out_Catch",      theTypeData, "Stepped", "AB",  "AB",  BaselineSteppedTables[[2]], CurrentSteppedFiles[[2]], species)
-        runTestRDS(inc(runNum),"out_Gear_Catch", theTypeData, "Stepped", "AB",  "AB",  BaselineSteppedTables[[3]], CurrentSteppedFiles[[3]], species)
-        runTestRDS(inc(runNum),"out_Biomass",    theTypeData, "Stepped", "RK4", "RK4", BaselineSteppedTables[[4]], CurrentSteppedFiles[[4]], species)
-        runTestRDS(inc(runNum),"out_Catch",      theTypeData, "Stepped", "RK4", "RK4", BaselineSteppedTables[[5]], CurrentSteppedFiles[[5]], species)
-        runTestRDS(inc(runNum),"out_Gear_Catch", theTypeData, "Stepped", "RK4", "RK4", BaselineSteppedTables[[6]], CurrentSteppedFiles[[6]], species)
-      }
+      runTestRDS(inc(runNum),"out_Biomass",    theTypeData, "Stepped", "AB",  "AB",  BaselineSteppedTables[[1]], CurrentSteppedFiles[[1]], species)
+      runTestRDS(inc(runNum),"out_Catch",      theTypeData, "Stepped", "AB",  "AB",  BaselineSteppedTables[[2]], CurrentSteppedFiles[[2]], species)
+      runTestRDS(inc(runNum),"out_Gear_Catch", theTypeData, "Stepped", "AB",  "AB",  BaselineSteppedTables[[3]], CurrentSteppedFiles[[3]], species)
+      runTestRDS(inc(runNum),"out_Biomass",    theTypeData, "Stepped", "RK4", "RK4", BaselineSteppedTables[[4]], CurrentSteppedFiles[[4]], species)
+      runTestRDS(inc(runNum),"out_Catch",      theTypeData, "Stepped", "RK4", "RK4", BaselineSteppedTables[[5]], CurrentSteppedFiles[[5]], species)
+      runTestRDS(inc(runNum),"out_Gear_Catch", theTypeData, "Stepped", "RK4", "RK4", BaselineSteppedTables[[6]], CurrentSteppedFiles[[6]], species)
     }
   }