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MSE code for testing catch-only fisheries models and related HCRs

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DLM-MSE

##Data-limited MSE R project
MSE code for testing catch-only fisheries models and related HCRs

#Developers: Jessica Walsh, Coilin Minto, Ernesto Jardim, Sean Anderson and co-authors on paper

Code for Paper: Walsh et al. Fish and Fisheries 2018
Title: Trade-offs for data-limited fisheries when using harvest strategies based on catch-only models
Developed as part of the Data Limited Fisheries Working Group funded by Conservation International and Gordon and Betty Moore Foundation.

#1 Simulations script - creates the simulated species 01-sim-setup.R

#2 Runs MSE using perfect informtion
02a-perfect-info-select-MSE-run.R #selects which scenario to run, and draws code from 02b_base code.
02b-pefect-info-MSE-base.R #contains base code for MSE
02c-perfect-info-performance

#3 Conduct assessment using catch only models - select scenarios to run assessment, and 05b is base code
03a-preassess-run.R
03b-dl-preassess-base.R

#4 Conduct MSE with COM assessments
04a-MSE-run.R
04b-MSE-base.R (run using 02a-MSE-run.R)

#5 Diagnostic plots to check simulations and MSE running
05a-plots-simulations.Rmd
05b_mse_diagnostic_all_sp.Rmd

#6 Performance metrics
06a-performance-metrics.Rmd
06b-performance-metrics-UR.R #with Underreporting

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