Function reference • mmsyFM

Systems

Build, read and write a system; the example systems.

ms_system(): Build a multispecies fleet system from tables

read_ms_system(): Read a system from CSV tables

write_ms_system(): Write a system to CSV tables

ms_landscape(): Catchability from a habitat landscape

atlantic_system(): Atlantic example system

got_system_draft(): Gulf of Thailand system (draft)

got_species(): Gulf of Thailand species groups (mmsyapp input)

Calibration

ms_tune(): Tune daily costs so that a target fleet composition is an open-access equilibrium

ms_condition(): Condition stock status on target depletions

ms_open_access() ms_status_quo(): Open-access and status-quo equilibria

Simulation and equilibrium

ms_simulate(): Simulate the system forward

ms_summary(): Summaries over the kept years

ms_closure(): Fixed metier closures

ms_yield_curve(): Equilibrium yield curve over effort

ms_shared_q_curve(): Shared-q yield curve (the mmsyapp model)

ms_optimise(): Maximise an equilibrium objective over segment effort caps

allocate_effort(): Allocate segment effort to metiers

ffmsy(): F relative to Fmsy in the discrete Schaefer model

Harvest strategies

hcr_effort(): Segment effort rule with an optional choke-stock closure

ms_assessment_presets(): Default assessment strategies: indicator species, complexes and assignment

ms_tune_hcr(): Tune the triggers of hcr_effort() to a risk criterion

proc_sd_from_r(): Process SD by productivity: a power law in r through two anchors

relsig_jabba(): JABBA proc.dyn relative process SD

Performance statistics

ms_perf(): Performance statistics in the mseviz format

ms_statistics(): Definitions of the performance statistics

ms_perf_table(): Summary (decision) table of performance statistics

perf_rows() ms_performance(): Performance statistics of projection runs

Plots

plot_kobe(): Kobe plot of equilibrium states

plot_catchability(): Catchability heatmap

plot_landscape(): Plot a habitat landscape

plot_yield_curves(): Equilibrium yield curves

plot_projection(): Projections by stock: B/Bmsy, F/Fmsy or catch over time

plot_fleet(): Projections of days by segment and total yield

plot_bps(): Boxplots of performance statistics by management procedure

plot_tradeoffs(): Trade-off plots of performance statistics

plot_quilt(): Quilt plot: a colour-coded decision table

theme_ms() ms_cols ms_ink: Colours and theme of the package plots

App

run_app(): Launch the mmsyFM Shiny app