Files in szuwalski/GeMS
Generic Management Strategy Evaluation
.Rbuildignore
.gitignore
DESCRIPTION
GeMS.Rproj
LICENSE
LICENSE.md
NAMESPACE
Paper/Figures/Fig1.tiff
Paper/Figures/Fig2.tiff
Paper/Figures/Fig3.tiff
Paper/Figures/Fig4.tiff
Paper/Figures/Fig5.tiff
Paper/Figures/Fig6.tiff
Paper/GEMS flowchart.pptx
Paper/Sup_GeMS.docx
R/AgeAssPlot.R
R/AgeStructureComp.R
R/BevHolt.R
R/CalculateBias.R
R/CalculateMohn.R
R/CheckGradient.R
R/CheckReferencePoints.R
R/CheckRetro.R
R/CleanInput.R
R/FindF35.R
R/FindFMSY.R
R/GeMS.R
R/GeMSplots.R
R/General_MSE_helpers.R
R/HarvestControlRule.R
R/MyBoxPlot.R
R/PlotLifeHistory.R
R/PlotParam.R
R/PolygonPlots.R
R/ProdMod.R
R/ProdModPlot.R
R/ProductionModelOutput.R
R/ProjPopDym.R
R/PullTimevary.R
R/PullTrueProj.R
R/ReadCTLfile.R
R/ReadPar.R
R/ReadRep.R
R/ReadTruDat.R
R/Recruitment.R
R/Ricker.R
R/SBPRfunc.R
R/StockRecCheck.R
R/StrLine.R
R/TakeOut.R
R/calcBHrec.R
R/calcREF.R
R/calcRICKrec.R
R/get_exec.R
R/initialN.R
R/plot_stuff_inside.R
R/run_GeMS.R
R/selAtAgeFunc.R
README.md
SimFish/server.R
SimFish/simfish/DESCRIPTION
SimFish/simfish/NAMESPACE
SimFish/simfish/R/BevHolt.R
SimFish/simfish/R/CleanInput.R
SimFish/simfish/R/HarvestControlRules.R
SimFish/simfish/R/Recruitment.R
SimFish/simfish/R/Ricker.R
SimFish/simfish/R/SBPRfunc.R
SimFish/simfish/R/StockRecCheck.R
SimFish/simfish/R/StrLine.R
SimFish/simfish/R/calcBHrec.R
SimFish/simfish/R/calcREF.R
SimFish/simfish/R/calcRickRec.R
SimFish/simfish/R/initialN.R
SimFish/simfish/R/simfish.R
SimFish/simfish/man/BevHolt.Rd
SimFish/simfish/man/CleanInput.Rd
SimFish/simfish/man/HarvestControlRule.Rd
SimFish/simfish/man/Recruitment.Rd
SimFish/simfish/man/Ricker.Rd
SimFish/simfish/man/SBPRfunc.Rd
SimFish/simfish/man/StockRecCheck.Rd
SimFish/simfish/man/StrLine.Rd
SimFish/simfish/man/calcBHrec.Rd
SimFish/simfish/man/calcREF.Rd
SimFish/simfish/man/calcRICKrec.Rd
SimFish/simfish/man/initialN.Rd
SimFish/simfish/man/simfish.Rd
SimFish/simfish/simfish.Rproj
SimFish/ui.R
SimFish/www/bigorb.png
SimFish/www/new_theme.css
SimFish/www/snap_logo.png
Wiki/CTLfile.png
Wiki/CTLfile1.png
Wiki/CTLfile2.png
Wiki/CTLfile3.png
Wiki/CTLfile4.png
Wiki/CTLfile5.png
Wiki/CTLfile6.png
Wiki/CTLfile7.png
Wiki/GEMS flowchart.png
Wiki/GEMS flowchart.pptx
Wiki/MSE figure.png
Wiki/SimpleExample.png
Wiki/dumb
inst/extdata/Cod_1_Production/Cod_Base_CTL.csv
inst/extdata/Cod_1_Production/Cod_Example.R
inst/extdata/Cod_1_Production/Cod_HighProd_CTL.csv
inst/extdata/Cod_1_Production/Cod_LowProd_CTL.csv
inst/extdata/Cod_1_Production/plots/LifeHistory_Cod_Base_CTL.png
inst/extdata/Cod_1_Production/plots/LifeHistory_Cod_HighProd_CTL.png
inst/extdata/Cod_1_Production/plots/LifeHistory_Cod_LowProd_CTL.png
inst/extdata/Cod_1_Production/plots/ProductionFits_Cod_Base_CTL.png
inst/extdata/Cod_1_Production/plots/ProductionFits_Cod_LowProd_CTLCod_Base_CTLCod_HighProd_CTL.png
inst/extdata/Cod_1_Production/plots/ProductionRefPoints_Cod_Base_CTL.png
inst/extdata/Cod_1_Production/plots/ProductionRefPoints_Cod_LowProd_CTLCod_Base_CTLCod_HighProd_CTL.png
inst/extdata/Cod_2_Selectivity/Cod_Example.R
inst/extdata/Cod_2_Selectivity/Cod_Selectivity_CTL.csv
inst/extdata/Cod_3_Movement/Cod_Example.R
inst/extdata/Cod_3_Movement/Cod_Movement_CTL.csv
inst/extdata/Cod_4_MPA/Cod_Example.R
inst/extdata/Cod_4_MPA/Cod_MPA_CTL.csv
inst/extdata/Cod_5_AgeStructure/Cod_AgeStructure_CTL.csv
inst/extdata/Cod_5_AgeStructure/Cod_Age_Mvary_CTL.csv
inst/extdata/Cod_5_AgeStructure/Cod_Age_Mvary_estM_CTL.csv
inst/extdata/Cod_5_AgeStructure/Cod_Example.R
inst/extdata/Cod_5_AgeStructure/plots/Catch_true_vs_estCod_AgeStructure_CTLCod_Age_Mvary_CTLCod_Age_Mvary_estM_CTL.png
inst/extdata/Cod_5_AgeStructure/plots/ComparePopulationProcess_Cod_AgeStructure_CTLCod_Age_Mvary_CTLCod_Age_Mvary_estM_CTL.png
inst/extdata/Cod_5_AgeStructure/plots/CompareRefPointsCod_AgeStructure_CTLCod_Age_Mvary_CTLCod_Age_Mvary_estM_CTL.png
inst/extdata/Cod_5_AgeStructure/plots/FitsToCatchLengths_Cod_AgeStructure_CTL.png
inst/extdata/Cod_5_AgeStructure/plots/FitsToDataAgeStruc_Cod_AgeStructure_CTL.png
inst/extdata/Cod_5_AgeStructure/plots/LifeHistory_Cod_AgeStructure_CTL.png
inst/extdata/Cod_5_AgeStructure/plots/Spbio_true_vs_estCod_AgeStructure_CTLCod_Age_Mvary_CTLCod_Age_Mvary_estM_CTL.png
inst/extdata/Cod_6_HCR_TimeVary/Cod_Base.csv
inst/extdata/Cod_6_HCR_TimeVary/Cod_EM.csv
inst/extdata/Cod_6_HCR_TimeVary/Cod_EM_LenComp.csv
inst/extdata/Cod_6_HCR_TimeVary/Cod_Example.R
inst/extdata/Cod_6_HCR_TimeVary/Cod_F35.csv
inst/extdata/Cod_6_HCR_TimeVary/Cod_F35_Slope.csv
inst/extdata/Cod_6_HCR_TimeVary/Cod_LenComp.csv
inst/extdata/Master_CTL.csv
inst/src/Check.Out
inst/src/SimAss
inst/src/SimAss.CTL
inst/src/SimAss.DAT
inst/src/SimAss.tpl
inst/src/TrueQuantities.DAT
inst/src/admodel.cov
inst/src/admodel.dep
inst/src/admodel.hes
inst/src/eigv.rpt
inst/src/eval.csv
inst/src/fmin.log
inst/src/simass.b01
inst/src/simass.bar
inst/src/simass.cor
inst/src/simass.cpp
inst/src/simass.eva
inst/src/simass.exe
inst/src/simass.htp
inst/src/simass.log
inst/src/simass.obj
inst/src/simass.p01
inst/src/simass.par
inst/src/simass.pin
inst/src/simass.r01
inst/src/simass.rep
inst/src/simass.std
inst/src/variance
man/AgeAssPlot.Rd
man/AgeStructureComp.Rd
man/BevHolt.Rd
man/CalculateBias.Rd
man/CalculateMohn.Rd
man/CheckGradient.Rd
man/CheckReferencePoints.Rd
man/CheckRetro.Rd
man/CleanInput.Rd
man/FindF35.Rd
man/FindFMSY.Rd
man/GeMS.Rd
man/GeMSplots.Rd
man/HarvestControlRule.Rd
man/MyBoxPlot.Rd
man/PlotLifeHistory.Rd
man/PlotParam.Rd
man/PolygonPlots.Rd
man/ProdMod.Rd
man/ProdModPlot.Rd
man/ProductionModelOutput.Rd
man/ProjPopDym.Rd
man/PullTimevary.Rd
man/PullTrueProj.Rd
man/ReadCTLfile.Rd
man/ReadPar.Rd
man/ReadRep.Rd
man/ReadTruDat.Rd
man/Recruitment.Rd
man/Ricker.Rd
man/SBPRfunc.Rd
man/StockRecCheck.Rd
man/StrLine.Rd
man/TakeOut.Rd
man/calcBHrec.Rd
man/calcREF.Rd
man/calcRICKrec.Rd
man/get_exec.Rd
man/initialN.Rd
man/plot_stuff_inside.Rd
man/run_GeMS.Rd
man/selAtAgeFunc.Rd
tests/testthat.R
tests/testthat/test-Master_CTL.R
tests/testthat/test-cod1works.R
tests/testthat/test-cod2works.R
tests/testthat/test-cod3works.R
tests/testthat/test-cod4works.R
tests/testthat/test-cod5works.R
