Files in flr/FLBEIA

Bio-Economic Impact Assessment of Management Strategies using FLR

.Rbuildignore

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.Rproj.user/840E831E/sdb/s-A135EF10/lock_file

.gitignore

.travis.yml

DESCRIPTION

Makefile

NAMESPACE

NEWS

R/Auxiliary_Functions_Calculations_exem.R R/Auxiliary_Functions_Checks.R R/Auxiliary_Functions_Data_Manipulation.R R/Auxiliary_Functions_Effort_Dynamics.R R/Auxiliary_Functions_Observation_Model.R R/Auxiliary_Functions_Population_Dynamics.R R/Auxiliary_Functions_biolfleets2flstock.R R/Auxiliary_Functions_remove_units.R R/Auxiliary_Functions_xtabs2.R R/Class_0a_FLlst-beia.R R/Class_0b_FLAccesors_beia.R R/Class_1_FLBDsim.R R/Class_2_FLSRsim.R R/Class_3_FLCatchExt.R R/Class_4_FLMetierExt.R R/Class_5_FLFleetExt.R R/Conditioning_1_CobbDouglasFit.R R/Conditioning_2_SelAtAge.R R/Conditioning_CtrlCreators_Observation.r R/Conditioning_CtrlCreators_advice.r R/Conditioning_CtrlCreators_assessment.r R/Conditioning_CtrlCreators_biols.R R/Conditioning_CtrlCreators_covars.r R/Conditioning_CtrlCreators_fleets.r R/Conditioning_InitialPop.R R/Conditioning_calculate.CDparam.R R/Conditioning_create.BDs.data.R R/Conditioning_create.SRs.data.R R/Conditioning_create.advice.data.R R/Conditioning_create.biol.arrays.R R/Conditioning_create.biols.data.R R/Conditioning_create.ecoData.arrays.R R/Conditioning_create.fleets.arrays.R R/Conditioning_create.fleets.data.R R/Conditioning_create.indices.data.R R/Conditioning_create.list.stks.flq.R R/Conditioning_create.list.stks.flqa.R R/Functions_Checks.R R/Functions_FLFleet.R R/Functions_FLFleets.R R/MAIN_Function.R R/MP_1_Observation.R R/MP_1a_Observation_Model.R R/MP_1b_Observation_Model_Functions.R R/MP_2_Assessment.R R/MP_2_Assessment_sca2flbeia.R R/MP_2_Assessment_spict2flbeia.R R/MP_3_Advice.R R/MP_3a_fwdBD.R R/MP_3a_fwdBDControl.R R/MP_3b_HCRs.R R/MP_3c_HCRE_ane.R R/MP_3c_HCR_BoBane.R R/MP_3c_HCR_BoBane_JD.R R/MP_3c_HCR_F2CatchHCR.R R/MP_3c_HCR_Froese.R R/MP_3c_HCR_ICES_MSY.R R/MP_3c_HCR_neaMAC_ltmp.R R/MP_3d_HCR_AnnexIV.R R/MP_3d_HCR_GHL.R R/MP_3d_HCR_ICES_Cat3.R R/MP_3d_HCR_ICES_Cat3_bsafe_hrcap.R R/MP_3e_HCR_SWWMAP.R R/MP_3f_CFP_MSY_HCR.R R/MP_3g_MultiStockHCR.R R/MP_3h_ModelFreeHCR.R R/Method_propagate_FLFleet.R R/OM_1_biol.om.R R/OM_1a1_Stock_Recruitment_functions.R R/OM_1a1_Stock_Recruitment_functions_segregmix.R R/OM_1a2_DensityDependent_weight_functions.R R/OM_1a_Population_Growth_Functions.R R/OM_2_fleet.om.R R/OM_2a1_Catch_Production_Functions.R R/OM_2a1_catchability2zero.R R/OM_2a_Effort_Dynamics.R R/OM_2a_Effort_Dynamics_Auxiliary.R R/OM_2a_Effort_Dynamics_LO_MaxProf.R R/OM_2a_Effort_Dynamics_LO_QuotaSwap_exem.R R/OM_2a_Effort_Dynamics_LO_functions_exem.R R/OM_2a_Effort_Dynamics_MaxProf.R R/OM_2a_Effort_Dynamics_SMFB.R R/OM_2a_Effort_Dynamics_SMFB_VarEffortShare.R R/OM_2b_EffDyn_TAC_OverS_Func.R R/OM_2b_Update_catch.R R/OM_2c_Price_Dynamics.R R/OM_2d_Fleet_Capital_Dynamics.R R/OM_2e_CapitalDyn_SCD.R R/OM_3_covars.om.R R/PlotEco.R R/PlotFLBiols.R R/PlotFLFleets.R R/PlotfltStkSum.R R/RcppExports.R R/Results_JoinIterations.R R/Results_Summary.R R/Results_SummaryPlots.R R/brps_seasonal.R R/data.R R/ecoSum_DAMARA_function.R R/genericMethods.R R/setPlusGroupFLBiol.R R/stf_correctSel.R README.md

_pkgdown.yml

appveyor.yml

data-raw/multi/data/fl1.met1.stk1_discards.n.csv

data-raw/multi/data/fl1.met1.stk1_landings.n.csv

data-raw/multi/data/fl1.met1.stk2_discards.n.csv

data-raw/multi/data/fl1.met1.stk2_landings.n.csv

data-raw/multi/data/fl1.met1_effshare.csv

data-raw/multi/data/fl1.met2.stk1_landings.n.csv

data-raw/multi/data/fl1.met2.stk2_landings.n.csv

data-raw/multi/data/fl1.met2_effshare.csv

data-raw/multi/data/fl1_capacity.csv

data-raw/multi/data/fl1_effort.csv

data-raw/multi/data/fl2.met1.stk1_discards.n.csv

data-raw/multi/data/fl2.met1.stk1_landings.n.csv

data-raw/multi/data/fl2.met1.stk2_discards.n.csv

data-raw/multi/data/fl2.met1.stk2_landings.n.csv

data-raw/multi/data/fl2.met1_effshare.csv

data-raw/multi/data/fl2.met1_vcost.csv

data-raw/multi/data/fl2.met2.stk1_discards.n.csv

data-raw/multi/data/fl2.met2.stk1_landings.n.csv

data-raw/multi/data/fl2.met2.stk2_discards.n.csv

data-raw/multi/data/fl2.met2.stk2_landings.n.csv

data-raw/multi/data/fl2.met2_effshare.csv

data-raw/multi/data/fl2.met2_vcost.csv

data-raw/multi/data/fl2_capacity.csv

data-raw/multi/data/fl2_effort.csv

data-raw/multi/data/fl2_fcost.csv

data-raw/multi/data/stk1.tac.csv

data-raw/multi/data/stk1_m.csv

data-raw/multi/data/stk1_mat.csv

data-raw/multi/data/stk1_n.csv

data-raw/multi/data/stk1_params.csv

data-raw/multi/data/stk1_proportion.csv

data-raw/multi/data/stk1_rec.csv

data-raw/multi/data/stk1_spwn.csv

data-raw/multi/data/stk1_ssb.csv

data-raw/multi/data/stk1_uncertainty.csv

data-raw/multi/data/stk1_wt.csv

data-raw/multi/data/stk2.tac.csv

data-raw/multi/data/stk2_biomass.csv

data-raw/multi/data/stk2_catch.csv

data-raw/multi/data/stk2_m.csv

data-raw/multi/data/stk2_mat.csv

data-raw/multi/data/stk2_n.csv

data-raw/multi/data/stk2_params.csv

data-raw/multi/data/stk2_spwn.csv

data-raw/multi/data/stk2_uncertainty.csv

data-raw/multi/data/stk2_wt.csv

data-raw/multi/multi.R data-raw/multistk/multistk.R

data-raw/mur/Biomass_IndexEvohe_BoB_CS.csv

data-raw/mur/mur.R

data-raw/mur/mur_catch.txt

data-raw/one/data/fl1.met1.stk1_discards.n.csv

data-raw/one/data/fl1.met1.stk1_landings.n.csv

data-raw/one/data/fl1.met1_effshare.csv

data-raw/one/data/fl1_capacity.csv

data-raw/one/data/fl1_crewshare.csv

data-raw/one/data/fl1_effort.csv

data-raw/one/data/fl1_fcost.csv

data-raw/one/data/stk1_advice.quota.share.csv

data-raw/one/data/stk1_advice.tac.csv

data-raw/one/data/stk1_fec.csv

data-raw/one/data/stk1_m.csv

data-raw/one/data/stk1_n.csv

data-raw/one/data/stk1_params.csv

data-raw/one/data/stk1_proportion.csv

data-raw/one/data/stk1_rec.csv

data-raw/one/data/stk1_spwn.csv

data-raw/one/data/stk1_ssb.csv

data-raw/one/data/stk1_uncertainty.csv

data-raw/one/data/stk1_wt.csv

data-raw/one/one.R

data-raw/oneIt/data/fl1.met1.stk1_discards.n.csv

data-raw/oneIt/data/fl1.met1.stk1_landings.n.csv

data-raw/oneIt/data/fl1.met1_effshare.csv

data-raw/oneIt/data/fl1_capacity.csv

data-raw/oneIt/data/fl1_crewshare.csv

data-raw/oneIt/data/fl1_effort.csv

data-raw/oneIt/data/fl1_fcost.csv

data-raw/oneIt/data/stk1_advice.quota.share.csv

data-raw/oneIt/data/stk1_advice.tac.csv

data-raw/oneIt/data/stk1_fec.csv

data-raw/oneIt/data/stk1_m.csv

data-raw/oneIt/data/stk1_n.csv

data-raw/oneIt/data/stk1_params.csv

data-raw/oneIt/data/stk1_proportion.csv

data-raw/oneIt/data/stk1_rec.csv

data-raw/oneIt/data/stk1_spwn.csv

data-raw/oneIt/data/stk1_ssb.csv

data-raw/oneIt/data/stk1_uncertainty.csv

data-raw/oneIt/data/stk1_wt.csv

data-raw/oneIt/oneIt.R data-raw/res_flbeia/res_flbeia.R

data/datalist

data/mixfish.RData

data/multi.RData

data/multistk.RData

data/mur.RData

data/one.RData

data/oneIt.RData

data/res_flbeia.RData

docs/404.html

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/FLBDsim.html

docs/reference/FLBEIA.html

docs/reference/FLCatchExt.html

docs/reference/FLCatchesExt.html

docs/reference/FLFleetExt.html

docs/reference/FLFleetsExt.html

docs/reference/FLMetierExt.html

docs/reference/FLMetiersExt.html

docs/reference/FLSRsim.html

docs/reference/SelAtAge.html

docs/reference/annualTAC.html

docs/reference/bioSum.html

docs/reference/biolfleets2flstock.html

docs/reference/calculate.q.sel.flrObjs.html

docs/reference/create.BDs.data.html

docs/reference/create.SRs.data.html

docs/reference/create.advice.ctrl.html

docs/reference/create.advice.data.html

docs/reference/create.assess.ctrl.html

docs/reference/create.biol.arrays.html

docs/reference/create.biols.ctrl.html

docs/reference/create.biols.data.html

docs/reference/create.covars.ctrl.html

docs/reference/create.ecoData.html

docs/reference/create.fleets.arrays.html

docs/reference/create.fleets.ctrl.html

docs/reference/create.fleets.data.html

docs/reference/create.indices.data.html

docs/reference/create.obs.ctrl.html

docs/reference/datasets.html

docs/reference/index.html

docs/reference/joinIter.html

docs/reference/landStock.f.html

docs/reference/plotEco.html

docs/reference/plotFLBiols.html

docs/reference/plotFLFleets.html

docs/reference/plotbioSum.html

docs/reference/plotfltStkSum.html

docs/reference/revenue_flbeia.html

docs/reference/setUnitsNA.html

docs/reference/stock.fleetInfo.html

docs/reference/summary_flbeia.html

docs/reference/unit2age.html

docs/reference/updateFLBiols.html

docs/reference/wtadStock.html

docs/reference/wtalStock.html

docs/reference/xtabs2.html

inst/CITATION

man/FLBDsim.Rd man/FLBEIA.Rd man/FLCatchExt.Rd man/FLCatchesExt.Rd man/FLFleetExt.Rd man/FLFleetsExt.Rd man/FLMetierExt.Rd man/FLMetiersExt.Rd man/FLSRsim.Rd man/SelAtAge.Rd man/annualTAC.Rd man/bioSum.Rd man/biolfleets2flstock.Rd man/brpsson.Rd man/calculate.q.sel.flrObjs.Rd man/checkFLBEIAData.Rd man/create.BDs.data.Rd man/create.SRs.data.Rd man/create.advice.ctrl.Rd man/create.advice.data.Rd man/create.assess.ctrl.Rd man/create.biol.arrays.Rd man/create.biols.ctrl.Rd man/create.biols.data.Rd man/create.covars.ctrl.Rd man/create.ecoData.Rd man/create.fleets.arrays.Rd man/create.fleets.ctrl.Rd man/create.fleets.data.Rd man/create.indices.data.Rd man/create.obs.ctrl.Rd man/datasets.Rd man/extractBRP.Rd

man/figures/flbeia.png

man/joinIter.Rd man/landStock.f.Rd man/plotBRPsson.Rd man/plotEco.Rd man/plotFLBiols.Rd man/plotFLFleets.Rd man/plotbioSum.Rd man/plotfltStkSum.Rd man/revenue_flbeia.Rd man/segremix.Rd man/setUnitsNA.Rd man/stock.fleetInfo.Rd man/summary_flbeia.Rd man/unit2age.Rd man/updateFLBiols.Rd man/wtadStock.Rd man/wtalStock.Rd

src/FLBEIA.dll

src/RcppExports.cpp

src/RcppExports.o

src/fun_fill_flcatches.cpp

src/fun_fill_flcatches.o

vignettes/00_MSE_Algorithm_Bibliography.bib

vignettes/01_Introduction.tex

vignettes/02_Concept_Of_FLBEIA.tex

vignettes/03_Running_FLBEIA.tex

vignettes/04_FLBEIA_FIRST_level_Func.tex

vignettes/05_FLBEIA_SECOND_level_Funcs.tex

vignettes/06_FLBEIA_THIRD_level_Funcs.tex

vignettes/07_FLBEIA_FOURTH_level_Funcs.tex

vignettes/08_FLBEIA_Smart_Conditioning.tex

vignettes/09_FLBEIA_Output_Summary.tex

vignettes/10_Acknowledgements.tex

vignettes/A1_New_Classes.tex

vignettes/A2_FLR_objects_Graphics.tex

vignettes/A3_Control_objects_tables.tex

vignettes/A4_SmartConditioning_tables.tex

vignettes/FLBDsim.jpg

vignettes/FLBEIA_manual-concordance.tex

vignettes/FLBEIA_manual.Rnw

vignettes/FLBEIA_manual.ltx

vignettes/FLBiol.jpg

vignettes/FLFleetExt.jpg

vignettes/FLIndex.jpg

vignettes/FLSRsim.jpg

vignettes/FLStock.jpg

vignettes/MP_scheme.JPG

vignettes/MSE_diagram.JPG

vignettes/OM_scheme.JPG

flr/FLBEIA documentation built on Feb. 22, 2024, 1:36 a.m.