.Rbuildignore
.gitattributes
.gitignore
.travis.yml
DESCRIPTION
DLMtool.Rproj
NAMESPACE
NEWS.md
R/Awatea2OM.R
R/Blow_funcs.R
R/DFO.R
R/DLMtool-package.R
R/Data2csv.R
R/Data_Functions.R
R/Data_Plotting.R
R/Data_make_update.R
R/DefineClasses.r
R/Fease_Functions.R
R/IOTC.R
R/MPs_Input.R
R/MPs_Mixed.R
R/MPs_Output.R
R/MPs_Reference.R
R/MPs_SupportingFunctions.R
R/MSC.R
R/MSE_Plotting.R
R/MSE_Plotting_PMs.R
R/MSE_functions.R
R/MSYplotDev.R
R/Misc_Exported.R
R/Misc_Internal.R
R/OM_Plotting.R
R/OM_functions.R
R/OM_init_doc.R
R/OMts_dev.R
R/PMobjects.R
R/PMtable.R
R/RcppExports.R
R/Roxy_DataObjects.r
R/SS2DLM.R
R/SampleOM.R
R/Sketch_Functions.R
R/StochasticSRA.R
R/Turing.R
R/aaImportFrom.R
R/data2OMfunctions.r
R/iSCAM2DLM.R
R/popdyn.R
R/popdynDEVELOP.R
R/runMSE.r
R/sysdata.rda
README.md
_pkgdown.yml
data/Albacore.RData
data/Atlantic_mackerel.RData
data/Blue_shark.RData
data/Bluefin_tuna.RData
data/Bluefin_tuna_WAtl.RData
data/Butterfish.RData
data/China_rockfish.RData
data/Cobia.RData
data/DataDescription.RData
data/DecE_Dom.RData
data/DecE_HDom.RData
data/DecE_NDom.RData
data/Example_datafile.RData
data/FlatE_Dom.RData
data/FlatE_HDom.RData
data/FlatE_NDom.RData
data/FleetDescription.RData
data/Generic_DecE.RData
data/Generic_FlatE.RData
data/Generic_IncE.RData
data/Generic_fleet.RData
data/Generic_obs.RData
data/Gulf_blue_tilefish.RData
data/Herring.RData
data/ImpDescription.RData
data/Imprecise_Biased.RData
data/Imprecise_Unbiased.RData
data/IncE_HDom.RData
data/IncE_NDom.RData
data/LHdatabase.RData
data/Low_Effort_Non_Target.RData
data/MSEDescription.RData
data/Mackerel.RData
data/OMDescription.RData
data/ObsDescription.RData
data/Overages.RData
data/Perfect_Imp.RData
data/Perfect_Info.RData
data/Porgy.RData
data/Precise_Biased.RData
data/Precise_Unbiased.RData
data/Red_snapper.RData
data/ReqData.RData
data/Rockfish.RData
data/SimulatedData.RData
data/Simulation_1.RData
data/Snapper.RData
data/Sole.RData
data/StockDescription.RData
data/Target_All_Fish.RData
data/Targeting_Small_Fish.RData
data/Toothfish.RData
data/ourReefFish.RData
data/testOM.RData
data/tiny.RData
docs/404.html
docs/BioEconomic/BioEco.Rmd
docs/BioEconomic/BioEco.html
docs/Bocinegro_MERA_MSC_Planning_Report.html
docs/Data/Data.Rmd
docs/Data/Data.html
docs/Data/Data.pdf
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docs/Data/Figures/CAA.PNG
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docs/Data/Figures/cal2.PNG
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docs/MERA/MERA_User_Guide_v6.html
docs/MERA/SRA_scope_vignette.html
docs/authors.html
docs/cheat_sheets/CheatSheets.html
docs/cheat_sheets/DLMtool_CheatSheets.pdf
docs/cheat_sheets/DLMtool_CheatSheets.pptx
docs/cheat_sheets/DLMtool_CheatSheets/Slide1.JPG
docs/cheat_sheets/DLMtool_CheatSheets/Slide2.JPG
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docs/cheat_sheets/old/Fleet.html
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docs/new_site/reference/Bluefin_tuna_WAtl.html
docs/new_site/reference/Butterfish.html
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docs/new_site/reference/DFO_proj.html
docs/new_site/reference/DLMDataDir.html
docs/new_site/reference/DLMextra.html
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docs/reference/LHdatabase.html
docs/reference/LSRA.html
docs/reference/LSRA2.html
docs/reference/LSRA_MCMC_sim.html
docs/reference/LSRA_opt.html
docs/reference/LSRA_opt_cpp.html
docs/reference/LW2OM.html
docs/reference/LinInterp.html
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docs/reference/Sense.html
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docs/reference/avail.html
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docs/reference/boxplot.Data.html
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docs/reference/index.html
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docs/reference/joinData.html
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docs/reference/makeMeanMP.html
docs/reference/makePerf.html
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docs/reference/movfit_Rcpp.html
docs/reference/optCPU.html
docs/reference/optMSY.html
docs/reference/optMSY_eq.html
docs/reference/optQ.html
docs/reference/plot-Fleet.html
docs/reference/plot-Imp.html
docs/reference/plot-OM.html
docs/reference/plot-Obs.html
docs/reference/plot.Data.html
docs/reference/plot.MSE.html
docs/reference/plot.Stock.html
docs/reference/plotFun.html
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docs/reference/plotM.html
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docs/reference/plotMPA.html
docs/reference/plotOFL.html
docs/reference/plotSelect.html
docs/reference/plotStock.html
docs/reference/popdynCPP.html
docs/reference/popdynOneTScpp.html
docs/reference/prob.class-class.html
docs/reference/replic8.html
docs/reference/runCOSEWIC.html
docs/reference/runInMP.html
docs/reference/runMP.html
docs/reference/runMSE.html
docs/reference/sample_steepness2.html
docs/reference/sampy.html
docs/reference/sdconv.html
docs/reference/setup.html
docs/reference/show-MSE.html
docs/reference/show-Rec.html
docs/reference/simCAA.html
docs/reference/simCAL.html
docs/reference/simYears.html
docs/reference/summary-Data.html
docs/reference/summary-MSE.html
docs/reference/testOM.html
docs/reference/tiny.html
docs/reference/tinyErr.html
docs/reference/trlnorm.html
docs/reference/userguide.html
docs/reference/validcpars.html
docs/reference/wormplot.html
docs/reference/writeCSV.html
docs/userguide/a-very-quick-demo.html
docs/userguide/acknowledgements.html
docs/userguide/applying-management-procedures.html
docs/userguide/assumptions-of-dlmtool.html
docs/userguide/averaging-mps.html
docs/userguide/changes.html
docs/userguide/checking-convergence.html
docs/userguide/creating-a-new-operating-model.html
docs/userguide/creating-your-own-data-object.html
docs/userguide/custom-parameters.html
docs/userguide/custom-performance-metrics.html
docs/userguide/customizing-the-operating-model.html
docs/userguide/determining-feasible-and-available-management-procedures.html
docs/userguide/developing-custom-management-procedures.html
docs/userguide/docs/ExampleData/China_rockfish.csv
docs/userguide/docs/ExampleData/MyData.md
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docs/userguide/running-the-mse.html
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docs/userguide/subsetting-the-mse-object.html
docs/userguide/the-fishery-data-object.html
docs/userguide/the-operating-model.html
docs/userguide/userguide.pdf
docs/userguide/userguide_files/figure-html/LH2OMexample1-1.png
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docs/userguide/userguide_files/figure-html/converge2-1.png
docs/userguide/userguide_files/figure-html/kobe-plot-1.png
docs/userguide/userguide_files/figure-html/optCPU-1.png
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docs/userguide/value-of-information.html
index.md
inst/Atlantic_mackerel.csv
inst/China_rockfish.csv
inst/Cobia.csv
inst/DFO_cosewic.Rmd
inst/DFO_generic.Rmd
inst/Data.csv
inst/Data.xlsx
inst/Data_Example.csv
inst/Data_Example.md
inst/Data_Example.xlsx
inst/Example_Chile_Hake.rmd
inst/Example_Chile_Hake.xlsx
inst/Example_datafile.csv
inst/Gulf_blue_tilefish.csv
inst/OM.rmd
inst/OM.xlsx
inst/PLimitTable.Rmd
inst/PLimitTable2.Rmd
inst/PObjTable.Rmd
inst/PObjTable2.Rmd
inst/Red_snapper.csv
inst/Rmd/Data/Data.md
inst/Rmd/Fleet/Catchability.Rmd
inst/Rmd/Fleet/Effort.Rmd
inst/Rmd/Fleet/Fleet.Rmd
inst/Rmd/Fleet/MPA.Rmd
inst/Rmd/Fleet/Selectivity.Rmd
inst/Rmd/Hist/Hist.Rmd
inst/Rmd/Imp/Imp.Rmd
inst/Rmd/OM/OM.Rmd
inst/Rmd/Obs/Obs.Rmd
inst/Rmd/Stock/Depletion.Rmd
inst/Rmd/Stock/Growth.Rmd
inst/Rmd/Stock/Maturity.Rmd
inst/Rmd/Stock/NaturalMortality.Rmd
inst/Rmd/Stock/Recruitment.Rmd
inst/Rmd/Stock/Spatial.Rmd
inst/Rmd/Stock/Stock.Rmd
inst/Simulation_1.csv
inst/ourReefFish.csv
logo.png
man-roxygen/Fleet_template.R
man-roxygen/Imp_template.R
man-roxygen/MPtemplate.R
man-roxygen/MPuses.R
man-roxygen/OM_desc.R
man-roxygen/Obs_desc.R
man-roxygen/Obs_template.R
man-roxygen/Stock_template.R
man-roxygen/userguide_link.R
man/AvC.Rd
man/AvC_MLL.Rd
man/BK.Rd
man/BlankSelPlot.Rd
man/Blow_opt.Rd
man/CALsimp.Rd
man/CC.Rd
man/CC1.Rd
man/CSRA.Rd
man/CSRAfunc.Rd
man/CalcMPDynamics.Rd
man/Can.Rd
man/CanMP.Rd
man/ChkObj.Rd
man/ChkYrs.Rd
man/Choose.Rd
man/CompSRA.Rd
man/CompSRA_.Rd
man/Converge.Rd
man/Cos_thresh_tab.Rd
man/Cplot.Rd
man/DBSRA.Rd
man/DBSRA_.Rd
man/DBSRAopt.Rd
man/DCAC.Rd
man/DCAC_.Rd
man/DD.Rd
man/DD_.Rd
man/DD_R.Rd
man/DDe.Rd
man/DFO_bar.Rd
man/DFO_hist.Rd
man/DFO_plot.Rd
man/DFO_plot2.Rd
man/DFO_proj.Rd
man/DFO_quant.Rd
man/DFO_report.Rd
man/DFO_spider.Rd
man/DFO_tab.Rd
man/DFO_tab_formatted.Rd
man/DLMDataDir.Rd
man/DLMenv.Rd
man/DLMextra.Rd
man/DLMtool-package.Rd
man/DTe40.Rd
man/Data-class-objects.Rd
man/Data-class.Rd
man/Data2csv.Rd
man/DataDescription.Rd
man/DataInit.Rd
man/Data_xl.Rd
man/Dom.Rd
man/DynF.Rd
man/EtargetLopt.Rd
man/FMSYref.Rd
man/Fadapt.Rd
man/Fdem.Rd
man/Fdem_.Rd
man/Fease.Rd
man/FilterSmooth.Rd
man/Fleet-class-objects.Rd
man/Fleet-class.Rd
man/FleetDescription.Rd
man/Fratio.Rd
man/Fratio_.Rd
man/GB_CC.Rd
man/GB_slope.Rd
man/GB_target.Rd
man/Gcontrol.Rd
man/Growth2OM.Rd
man/Hist-class.Rd
man/ICI.Rd
man/IOTC_plot.Rd
man/IT5.Rd
man/ITM.Rd
man/IT_.Rd
man/ITe5.Rd
man/Imp-class-objects.Rd
man/Imp-class.Rd
man/ImpDescription.Rd
man/Input.Rd
man/Iratio.Rd
man/Islope1.Rd
man/Islope_.Rd
man/Itarget1.Rd
man/Itarget1_MPA.Rd
man/ItargetE1.Rd
man/Itarget_.Rd
man/Itargeteff_.Rd
man/Kplot.Rd
man/L2A.Rd
man/LBSPR.Rd
man/LBSPR_.Rd
man/LBSPRgen.Rd
man/LH2OM.Rd
man/LHdatabase.Rd
man/LSRA.Rd
man/LSRA2.Rd
man/LSRA_MCMC_sim.Rd
man/LSRA_opt.Rd
man/LSRA_opt_cpp.Rd
man/LW2OM.Rd
man/LinInterp.Rd
man/Lratio_BHI.Rd
man/LstepCC1.Rd
man/LstepCE1.Rd
man/Ltarget1.Rd
man/LtargetE1.Rd
man/MCD.Rd
man/ML2D.Rd
man/MPStats.Rd
man/MPtype.Rd
man/MPurl.Rd
man/MRreal.Rd
man/MSE-class.Rd
man/MSEDescription.Rd
man/MSYCalcs.Rd
man/NAor0.Rd
man/NOAA_plot.Rd
man/OM-class.Rd
man/OMDescription.Rd
man/OMdoc.Rd
man/OMexample.Rd
man/OMinit.Rd
man/Obs-class-objects.Rd
man/Obs-class.Rd
man/ObsDescription.Rd
man/OneRep.Rd
man/PMLimit.Rd
man/PMobj-class.Rd
man/PWhisker.Rd
man/PerformanceMetric.Rd
man/Pplot.Rd
man/Pplot2.Rd
man/Range.Rd
man/Rcontrol.Rd
man/RealFease.Rd
man/Rec-class.Rd
man/Replace.Rd
man/Report.Rd
man/ReqData.Rd
man/Required.Rd
man/SBT1.Rd
man/SPMSY.Rd
man/SPSRA.Rd
man/SPSRA_.Rd
man/SPmod.Rd
man/SPslope.Rd
man/SRAcomp.Rd
man/SRAsim.Rd
man/SampleCpars.Rd
man/SampleFleetPars.Rd
man/SampleImpPars.Rd
man/SampleObsPars.Rd
man/SampleStockPars.Rd
man/Sense.Rd
man/SimulatedData.Rd
man/SketchFun.Rd
man/StochasticSRA.Rd
man/StochasticSRAcpp.Rd
man/Stock-class-objects.Rd
man/Stock-class.Rd
man/StockDescription.Rd
man/Sub.Rd
man/SubCpars.Rd
man/SubOM.Rd
man/TAC.Rd
man/TACfilter.Rd
man/Thresh_tab.Rd
man/Tplot.Rd
man/TradePlot.Rd
man/TradePlot_old.Rd
man/Turing.Rd
man/Uses.Rd
man/VOI.Rd
man/VOI2.Rd
man/VOIplot.Rd
man/VOIplot2.Rd
man/XL2Data.Rd
man/XL2OM.Rd
man/YPR.Rd
man/YPR_.Rd
man/alphaconv.Rd
man/applyMP.Rd
man/avail.Rd
man/barplot.MSE.Rd
man/boxplot.Data.Rd
man/calcMean.Rd
man/calcProb.Rd
man/char.log-class.Rd
man/cheatsheets.Rd
man/checkMSE.Rd
man/compplot.Rd
man/condmet.Rd
man/cparscheck.Rd
man/curE.Rd
man/cv.Rd
man/demographic2.Rd
man/dnormal.Rd
man/genSizeCompWrap.Rd
man/getAFC.Rd
man/getBlow.Rd
man/getEffhist.Rd
man/getFref3.Rd
man/getclass.Rd
man/getmov2.Rd
man/getq3.Rd
man/getr.Rd
man/getsel.Rd
man/gettempvar.Rd
man/hist2.Rd
man/iVB.Rd
man/initialize-methods.Rd
man/joinData.Rd
man/join_plots.Rd
man/label.class-class.Rd
man/makeMeanMP.Rd
man/makePerf.Rd
man/makeTransparent.Rd
man/matlenlim.Rd
man/movfit_Rcpp.Rd
man/optCPU.Rd
man/optMSY.Rd
man/optMSY_eq.Rd
man/optQ.Rd
man/plot-Fleet.Rd
man/plot-Imp.Rd
man/plot-OM.Rd
man/plot-Obs.Rd
man/plot.Data.Rd
man/plot.MSE.Rd
man/plot.Stock.Rd
man/plotFun.Rd
man/plotM.Rd
man/plotMPA.Rd
man/plotOFL.Rd
man/plotSelect.Rd
man/plotStock.Rd
man/popdynCPP.Rd
man/popdynOneTScpp.Rd
man/prob.class-class.Rd
man/replic8.Rd
man/runCOSEWIC.Rd
man/runInMP.Rd
man/runMP.Rd
man/runMSE.Rd
man/sample_steepness2.Rd
man/sampy.Rd
man/sdconv.Rd
man/setup.Rd
man/show-MSE.Rd
man/show-Rec.Rd
man/simCAA.Rd
man/simCAL.Rd
man/summary-Data.Rd
man/summary-MSE.Rd
man/testOM.Rd
man/tiny.Rd
man/tinyErr.Rd
man/trlnorm.Rd
man/userguide.Rd
man/validcpars.Rd
man/wormplot.Rd
man/writeCSV.Rd
src/LBSPR.cpp
src/LSRA_opt_cpp.cpp
src/RcppExports.cpp
src/bhnoneq_Rcpp.cpp
src/genLenComp.cpp
src/movefit_Rcpp.cpp
src/popddynCPP.cpp
tests/manual/2020-06-12DLMtool_V5.4.5.xml
tests/manual/Dockerfile
tests/manual/Test_Report.Rmd
tests/manual/coverage.R
tests/manual/old_stuff_delete_soon/run-coverage_code.R
tests/manual/old_stuff_delete_soon/runtests_long.R
tests/manual/old_stuff_delete_soon/test-Imp.R
tests/manual/old_stuff_delete_soon/test-discard.R
tests/manual/old_stuff_delete_soon/test_01_runMSE_testOM.R
tests/manual/old_stuff_delete_soon/test_02_runMSE_9_builtin_OMs.R
tests/manual/old_stuff_delete_soon/test_02a_runMSE_all_builtin_OMs.R
tests/manual/old_stuff_delete_soon/test_03a_testPlotting.R
tests/manual/old_stuff_delete_soon/test_04a_runMSE_allOM_allMP.R
tests/manual/old_stuff_delete_soon/test_05a_Can_Cant_allData.R
tests/manual/run-tests-code.R
tests/manual/run-tests-thorough.R
tests/manual/test-code/test-Data2csv.R
tests/manual/test-code/test-Data_Functions.R
tests/manual/test-code/test-Data_Plotting.R
tests/manual/test-code/test-Fease_Functions.R
tests/manual/test-code/test-Import_Data.R
tests/manual/test-code/test-MPs.R
tests/manual/test-code/test-MSE_Plotting.R
tests/manual/test-code/test-MSE_functions.R
tests/manual/test-code/test-OM_Plotting.R
tests/manual/test-code/test-OM_functions.R
tests/manual/test-code/test-OM_init_doc.R
tests/manual/test-code/test-PMobjects.R
tests/manual/test-code/test-RealIndices.R
tests/manual/test-code/test-checkPopdyn.R
tests/manual/test-code/test-cpars.R
tests/manual/test-code/test-runMSE.R
tests/manual/test-code/test-slotDescription.R
tests/manual/test.xml
tests/manual/test_dev/popdyn_tests.R