Files in tcarruth/MSEtool
Management Strategy Evaluation Toolkit
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
MSEtool.Rproj
NAMESPACE
NEWS.md
R/Ancillary_Indicators.R
R/Awatea2OM.R
R/CASAL2OM.R
R/HCRs.R
R/MMSE_Object.R
R/MMSE_plots.R
R/MOM_functions.R
R/MOM_object.R
R/MOM_plots.R
R/MSEtool-package.R
R/Misc_fun.R
R/Movement_calcs.R
R/SRA_scope.R
R/SRA_scope_data.R
R/SS2Data.R
R/SS2MOM.R
R/SS2OM.R
R/SSinternal.R
R/Single_stock_multi_q_REDUNDANT.R
R/VPA2OM.R
R/applyMMP.R
R/assess_DD.R
R/assess_SCA.R
R/assess_SCA2.R
R/assess_SCA_Pope.R
R/assess_SP.R
R/assess_SSS.R
R/assess_VPA.R
R/assess_cDD.R
R/define_S4_class_SRA.R
R/define_S4_class_assess.R
R/define_S4_class_profile.R
R/define_S4_class_project.R
R/define_S4_class_retro.R
R/define_S4_generic_SRA_scope.R
R/diagnostic_AM.R
R/document_data.R
R/iSCAM2OM.R
R/multiMSE.R
R/multiMSE_internal.R
R/multi_q_estimation.R
R/popdyn_MICE.R
R/report_DD_TMB.R
R/report_SCA.R
R/report_SCA_Pope.R
R/report_SP.R
R/report_SSS.R
R/report_VPA.R
R/report_auxiliary.R
R/report_cDD.R
R/report_spict.R
R/retrospective_AM.R
R/rmd_report.R
R/z_MPs.R
README.md
data-raw/Albacore_TwoFleet.R
data-raw/swordfish.R
data-raw/swordfish.csv
data/Albacore_TwoFleet.rda
data/swordfish.rda
inst/include/DD.hpp
inst/include/SCA.hpp
inst/include/SCA2.hpp
inst/include/SCA_Pope.hpp
inst/include/SP.hpp
inst/include/SRA_scope.hpp
inst/include/VPA.hpp
inst/include/cDD.hpp
inst/include/functions.hpp
inst/include/grav.hpp
inst/include/grav_Pbyarea.hpp
inst/include/ns/ns_SCA.hpp
inst/include/ns/ns_SP.hpp
inst/include/ns/ns_SRA_scope.hpp
inst/include/ns/ns_VPA.hpp
inst/include/ns/ns_cDD.hpp
inst/rmarkdown_templates/SS2OM.Rmd
man/Albacore_TwoFleet.Rd
man/Assessment-class.Rd
man/Awatea2OM.Rd
man/CASAL2OM.Rd
man/CASALpars.Rd
man/DD_TMB.Rd
man/HCR_FB.Rd
man/HCR_MSY.Rd
man/HCR_ramp.Rd
man/HCRlin.Rd
man/HistMICE.Rd
man/MMSE-class.Rd
man/MOM-class.Rd
man/MPCalcsNAs.Rd
man/MSEtool-package.Rd
man/Model-based-MP.Rd
man/NIL.Rd
man/PRBcalc.Rd
man/Probs.Rd
man/ResFromRel.Rd
man/SCA.Rd
man/SIL.Rd
man/SOL.Rd
man/SP.Rd
man/SP_production.Rd
man/SRA-class.Rd
man/SRA_scope.Rd
man/SS2Data.Rd
man/SS2MOM.Rd
man/SS2OM.Rd
man/SSS.Rd
man/TAC_MSY.Rd
man/TEG.Rd
man/VPA.Rd
man/VPA2OM.Rd
man/avail.Rd
man/cDD.Rd
man/compare_models.Rd
man/diagnostic_AM.Rd
man/expandHerm.Rd
man/fetch.file.names.Rd
man/getinds.Rd
man/getnIVs.Rd
man/getq_multi.Rd
man/getq_multi_MICE.Rd
man/hrate.Rd
man/iSCAM2Data.Rd
man/iSCAM2OM.Rd
man/iSCAMcomps.Rd
man/iSCAMinds.Rd
man/ldim.Rd
man/load.iscam.files.Rd
man/mahplot.Rd
man/make_MP.Rd
man/makemov.Rd
man/multiData.Rd
man/multiDataS.Rd
man/multiMSE.Rd
man/multidebug.Rd
man/optQ_multi.Rd
man/plot.Assessment.Rd
man/plot.MMSE.Rd
man/plot.MOM.Rd
man/plot.SRA.Rd
man/plot.prof.Rd
man/plot.retro.Rd
man/plotRel.Rd
man/plot_SR.Rd
man/plot_betavar.Rd
man/plot_composition.Rd
man/plot_crosscorr.Rd
man/plot_lognormalvar.Rd
man/plot_residuals.Rd
man/plot_steepness.Rd
man/plot_timeseries.Rd
man/plotmulti.Rd
man/plotquant.Rd
man/popdynMICE.Rd
man/popdynOneMICE.Rd
man/prelim_AM.Rd
man/prof-class.Rd
man/profile.Rd
man/project-class.Rd
man/projection.Rd
man/qestMICE.Rd
man/read.control.file.Rd
man/read.data.file.Rd
man/read.mcmc.Rd
man/read.par.file.Rd
man/read.projection.file.Rd
man/read.report.file.Rd
man/retro-class.Rd
man/retrospective.Rd
man/retrospective_AM.Rd
man/simmov.Rd
man/summary.Assessment.Rd
man/swordfish.Rd
man/tinyErr.Rd
man/userguide.Rd
src/MSEtool.cpp
tests/Data_files/Data_ORH7A.csv
tests/Data_files/GulfMenhaden_Data.csv
tests/Data_files/MERA_TokyoBayData.csv
tests/Data_files/Tiger_flathead_data.csv
tests/Data_files/Yellow_striped_MPerf.csv
tests/Data_files/dat.rda
tests/manual_tests.R
tests/test-DD_Assess.R
tests/test-Data2SRA.R
tests/test-Hist.R
tests/test-MSE.R
tests/test-SCA_Assess.R
tests/test-SP_Assess.R
tests/test-SRA_scope.R
tests/test-SS2Data.R
tests/test-SS2OM.R
tests/test-SS2OMa.R
tests/test-projection.R
vignettes/DLMtool_logo.png
vignettes/Delay_difference.Rmd
vignettes/MSEtool.Rmd
vignettes/SCA.Rmd
vignettes/SRA_scope.Rmd
vignettes/SRA_scope_eq.Rmd
vignettes/SRA_scope_sel.Rmd
vignettes/Surplus_production.Rmd
vignettes/VPA.Rmd
vignettes/fig_assess/DD_TAC.png
vignettes/fig_assess/DD_Tplot2.png
vignettes/fig_assess/DD_diagnostic_AM.png
vignettes/fig_assess/DD_profile.png
vignettes/fig_assess/DD_retrospective_AM.png
vignettes/fig_assess/DLMtool_design.png
vignettes/fig_assess/DLMtool_process.jpg
vignettes/fig_assess/MSEtool_design.png
vignettes/fig_multiMSE/MICE.png
vignettes/fig_multiMSE/MICE_F.png
vignettes/fig_multiMSE/MICE_sel.png
vignettes/fig_multiMSE/MICE_stock.png
vignettes/multiMSE.Rmd
