Assessment strategies in the app: rules with indicator species, species
complexes (pooled biomass or CPUE) and nominal assignment of stocks to
fleets, compared with the all-stocks rule; defaults from
ms_assessment_presets().
First version, ported from the dev-mmsy prototype in cpueTargeting and combined with the multispecies MSY app (mmsyapp).
Systems: ms_system() from four tables; habitat landscape for
catchability (ms_landscape()); Atlantic example and Gulf of Thailand
draft (atlantic_system(), got_system_draft()).
Calibration: ms_tune() (fleet composition at open access) and
ms_condition() (stock status, e.g. 2024 depletions).
Stocks: discrete Schaefer with exact F/Fmsy (harvest-rate ratio), F cap (persistence floor), JABBA-type process error scaled by r and depletion, and JABBA's floor in the process equation.
Equilibrium analyses: yield curves, shared-q comparison, safeguarded MMSY
(ms_optimise(); total yield, revenue, profit or the catch of one stock).
Harvest strategies: hcr_effort() with full effort at the MMSY days,
value-weighted or weakest-link status, triggers by segment, minimum
effort, phased annual changes, stock-triggered closures, indicator
species, complexes and nominal assignment; fixed metier closures
(ms_closure()); trigger tuning (ms_tune_hcr()).
Performance statistics in the mseviz format (ms_perf()), boxplots,
trade-offs and colour-coded decision tables (plot_quilt()).
Shiny app (run_app()) with a guide and a management-options tab.