Files in Blue-Matter/MSEtool

Management Strategy Evaluation Toolkit

LICENSE.md NEWS.md R/ASAP2OM.R R/Awatea2OM.R R/BAM2OM.R R/B_Low_functions.R R/Class_definitions.R R/DFO.R R/Data2csv.R R/Data_Functions.R R/Data_Plotting.R R/Data_documentation.R R/Data_fit_index.R R/Data_make_update.R R/Empirical_MP.R R/Fease_Functions.R R/MICE_Rel.R R/MMSE_Object.r R/MMSE_plots.R R/MOM_import.R R/MOM_object.r R/MOM_plots.R R/MP_tuning.R R/MPs_Reference.R R/MSC.R R/MSE_Plotting.R R/MSE_Plotting_PMs.R R/MSE_functions.R R/Misc_Exported.R R/Misc_Internal.R R/Movement_calcs.R R/OM_Plotting.R R/OM_functions.R R/OM_import.R R/OM_init_doc.R R/OM_plots.R R/PMobjects.R R/PMtable.R R/RcppExports.R R/SAM2OM.R R/SS2Data.R R/SS2MOM.R R/SS2MOM_plots.R R/SS2OM.R R/SSinternal.R R/SampleOM.R R/Sketch_Functions.R R/Splot.R R/Turing.R R/VPA2OM.R R/WHAM2OM.R R/aaImportFrom.R R/applyMMP.R R/iSCAM2OM.R R/multiMSE.R R/multiMSE_internal.R R/multi_q_estimation.R R/popdyn.R R/popdyn_MICE.R R/runMSE.R R/spatial_targ_opt.R R/utils.R README.md README.rmd build_tools/Organize_Functions.R build_tools/RHub_CRAN_Test.R build_tools/build_data.R build_tools/local_cran_checks.R build_tools/write_class_definitions.R build_tools/write_readme.R cran-comments.md inst/Example_Chile_Hake.rmd inst/OM.rmd 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/SS/SS2MOM.Rmd inst/Rmd/SS/SS2OM.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 man-roxygen/Fleet_template.R man-roxygen/Imp_template.R man-roxygen/MPtemplate.R man-roxygen/MSE_template.R man-roxygen/Obs_template.R man-roxygen/Stock_template.R man/ASAP2OM.Rd man/Assess2MOM.Rd man/Assess2OM.Rd man/Awatea2OM.Rd man/BAM2MOM.Rd man/BlankSelPlot.Rd man/Blow_opt.Rd man/CALsimp.Rd man/CSRA.Rd man/CSRAfunc.Rd man/CalcAsymptoticDist.Rd man/CalcMPDynamics.Rd man/CalculateQ.Rd man/Can.Rd man/CheckDuplicate.Rd man/CheckMPs.Rd man/CheckOM.Rd man/ChkYrs.Rd man/Choose.Rd man/CombineMMP.Rd man/Converge.Rd man/Cos_thresh_tab.Rd man/Cplot.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/Data-class-objects.Rd man/Data-class.Rd man/Data2csv.Rd man/DataDescription.Rd man/DataDir.Rd man/DataInit.Rd man/DataSlots.Rd man/Data_xl.Rd man/Dom.Rd man/Emp.Rd man/FMSYref.Rd man/Fease.Rd man/Fleet-class-objects.Rd man/Fleet-class.Rd man/FleetDescription.Rd man/GenerateRandomWalk.Rd man/Herm-int.Rd man/Hist-class.Rd man/HistDescription.Rd man/HistMICE.Rd man/Imp-class-objects.Rd man/Imp-class.Rd man/ImpDescription.Rd man/Input.Rd man/Kplot.Rd man/L2A.Rd man/LH2OM.Rd man/LHdatabase.Rd man/Lag_Data.Rd man/LinInterp.Rd man/ML2D.Rd man/MMSE-class.Rd man/MOM-class-objects.Rd man/MOM-class.Rd man/MPCalcsNAs.Rd man/MPtype.Rd man/MPurl.Rd man/MSE-class.Rd man/MSEDescription.Rd man/MSEextra.Rd man/MSYCalcs.Rd man/NAor0.Rd man/NIL.Rd man/NOAA_plot.Rd man/OM-class-objects.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/RealFease.Rd man/Rec-class.Rd man/Replace.Rd man/Report.Rd man/ReqData.Rd man/Required.Rd man/ResFromRel.Rd man/SIL.Rd man/SS2Data.Rd man/SS2DataMOM.Rd man/SS2MOM.Rd man/SSBrefplot.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/Splot.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/TEG.Rd man/Taxa_Table.Rd man/Thresh_tab.Rd man/TradePlot.Rd man/Turing.Rd man/Uses.Rd man/VOI.Rd man/VOI2.Rd man/VOIplot.Rd man/WHAM2OM.Rd man/XL2Data.Rd man/XL2Fleet.Rd man/XL2OM.Rd man/XL2Stock.Rd man/alphaconv.Rd man/applyMMP.Rd man/applyMP.Rd man/avail.Rd man/boxplot.Data.Rd man/calcMean.Rd man/calcProb.Rd man/calcRefYield.Rd man/char.log-class.Rd man/checkMSE.Rd man/cparscheck.Rd man/cv.Rd man/dnormal.Rd man/doHCR.Rd man/doIfreq.Rd man/doRec.Rd man/genSizeCompWrap.Rd man/getAFC.Rd man/getBlow.Rd man/getDataList.Rd man/getEffhist.Rd man/getMP.Rd man/getclass.Rd man/getfirstlev.Rd man/getmov2.Rd man/getnIVs.Rd man/getq_multi_MICE.Rd man/getsel.Rd man/hconv.Rd man/hist2.Rd man/hrate.Rd man/iSCAM.Rd man/iSCAM2OM.Rd man/iSCAMcomps.Rd man/iSCAMinds.Rd man/initialize-methods.Rd man/joinData.Rd man/join_plots.Rd man/label.class-class.Rd man/ldim.Rd man/makeMOM.Rd man/makeRel.Rd man/makeTransparent.Rd man/makemov.Rd man/makemov2.Rd man/movestockCPP.Rd man/movfit_Rcpp.Rd man/multiData.Rd man/multiDataS.Rd man/multiMSE.Rd man/multidebug.Rd man/optCPU.Rd man/optMSY_eq.Rd man/optQ.Rd man/optYield.Rd man/plot.Data.Rd man/plot.MMSE.Rd man/plot.MOM.Rd man/plot.MSE.Rd man/plot.Stock.Rd man/plotFun.Rd man/plotOFL.Rd man/plotRel.Rd man/plotmulti.Rd man/plotquant.Rd man/popdynCPP.Rd man/popdynMICE.Rd man/popdynOneMICE.Rd man/popdynOneTScpp.Rd man/prob.class-class.Rd man/qestMICE.Rd man/quantile_plot.Rd man/replic8.Rd man/runCOSEWIC.Rd man/runInMP.Rd man/runMP.Rd man/runMSE.Rd man/sample_steepness2.Rd man/sdconv.Rd man/select_MP.Rd man/setup.Rd man/show-MSE.Rd man/show-MSEtool.Rd man/show-Rec.Rd man/simCAA.Rd man/simCAL.Rd man/simmov.Rd man/simmov2.Rd man/smoothy.Rd man/summary-Data.Rd man/summary-MMSE.Rd man/summary-MSE.Rd man/tinyErr.Rd man/trlnorm.Rd man/tune_MP.Rd man/validcpars.Rd man/wormplot.Rd man/writeCSV.Rd tests/manual/run-manual-tests.R tests/manual/test-code/test-Data-Conditioning.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-Data_indices.R tests/manual/test-code/test-Fease_Functions.R tests/manual/test-code/test-Import_Data.R tests/manual/test-code/test-MOM.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-ReferencePoints.R tests/manual/test-code/test-checkPopDynamics.R tests/manual/test-code/test-cpars_realdata.R tests/manual/test-code/test-runMSE.R tests/manual/test-code/test-slotDescription.R