Merge branch 'UnitTests' into dev_merge_may2024

.gitignore

@@ -18,11 +18,12 @@ src/*.dll
 tests/testthat/data/output/*
 tests/testthat/data/bkup/*
 tests/testthat/data/input/REcosystem_Current_*.dat
+tests/testthat/data/input/REcosystem_Current_*.rds
 tests/testthat/data/input/REcosystem_Current_*.csv
 tests/testthat/old/*
 tests/testthat/bkup/*
 tests/testthat/old dat files/*
 docs
 doc
 Meta
-Rpath.Rproj
+Rpath.Rproj

DESCRIPTION

@@ -39,7 +39,7 @@ Suggests:
     generics,
     testthat (>= 3.0.0)
 VignetteBuilder: knitr
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 URL: https://github.com/NOAA-EDAB/Rpath
 BugReports: https://github.com/NOAA-EDAB/Rpath/issues
 Depends: 

src/ecosim.cpp

@@ -171,7 +171,7 @@ List rk4_run (List params, List instate, List forcing, List fishing, List stanza
 
         // If biomass goes crazy or hits NA, exit loop with crash signal.  Note it 
         // should still write the NA or INF values back to the output.
-        if ( any(is_na(cur_Biomass)) | any(is_infinite(cur_Biomass)) | any(is_nan(cur_Biomass)) )  {
+        if (bool(any(is_na(cur_Biomass))) || bool(any(is_infinite(cur_Biomass))) || bool(any(is_nan(cur_Biomass))))  {
           CRASH_YEAR = y; y = EndYear; m = STEPS_PER_YEAR;
         }
 
@@ -382,7 +382,7 @@ int y, m, dd;
     // should still write the NA or INF values back to the output.
     //NOJUV make sure crash tests work for juveniles.
 
-           if ( any(is_na(cur_Biomass)) | any(is_infinite(cur_Biomass)) | any(is_nan(cur_Biomass)) )  {
+           if (bool(any(is_na(cur_Biomass))) || bool(any(is_infinite(cur_Biomass))) || bool(any(is_nan(cur_Biomass))))  {
           CRASH_YEAR = y; y = EndYear; m = STEPS_PER_YEAR;
        }
 

tests/testthat/data/input/.gitignore

@@ -65,3 +65,4 @@ REcosystem_Current_RK4_ForcedCat_OutBiomass_Stepped.rds
 REcosystem_Current_RK4_ForcedCat_OutCatch_Jitter.rds
 REcosystem_Current_RK4_ForcedCat_OutCatch_Stepped.rds
 REcosystem_Current_RK4_ForcedCat_OutGearCatch_Jitter.rds
+REcosystem_Current_AB_ForcedBio_OutBiomass_Jitter.rds

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-constants.R

@@ -5,8 +5,7 @@ CREATE_BASELINE_FILES <- FALSE
 
 NUMBER_OF_STEPS <- 5 # should be an odd multiple of nrows=600 (i.e., 5,15,30)
 FACTOR_VALUE <- 5
-SEED_VALUE   <- 1 
-SEED_OFFSET <- 2000
+SEED_VALUE   <- 7 
 TOLERANCE_VALUE <- 1e-5
 RUN_QUIET <- TRUE
 YLIMIT_DIFFERENCE_PLOTS <- 0.05