Package: mmsyFM 0.1.0

Henning Winker

mmsyFM: Multispecies MSY Fleet Model for Mixed-Fishery Harvest Strategies

Simulates mixed fisheries in which fleet segments (e.g. demersal, pelagic and mixed or small-scale) allocate their fishing days across metiers by expected profit, on top of Schaefer surplus-production stocks with seasonal availability and JABBA-type process error. Finds the multispecies maximum sustainable yield (MMSY) subject to a safeguard for every stock, tunes the fleet to an open-access status quo, and tunes and tests effort- and closure-based harvest strategies with assessment and implementation error, data lags, species complexes and nominal assignment of stocks to fleets.

Authors:Henning Winker [aut, cre], Ricardo Amoroso [aut], Maite Pons [aut], Rishi Sharma [aut]

mmsyFM_0.1.0.tar.gz
mmsyFM_0.1.0.zip(r-4.7-any)mmsyFM_0.1.0.zip(r-4.6-any)mmsyFM_0.1.0.zip(r-4.5-any)
mmsyFM_0.1.0.tgz(r-4.6-any)mmsyFM_0.1.0.tgz(r-4.5-any)
mmsyFM_0.1.0.tar.gz(r-4.7-any)mmsyFM_0.1.0.tar.gz(r-4.6-any)
mmsyFM_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mmsyFM/json (API)

# Install 'mmsyFM' in R:
install.packages('mmsyFM', repos = c('https://henning-winker.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/henning-winker/mmsyfm/issues

On CRAN:

Conda:

3.30 score 6 scripts 42 exports 18 dependencies

Last updated from:25bf4a0544. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK181
source / vignettesOK234
linux-releaseOK168
macos-releaseOK191
macos-oldrelOK268
windows-develOK164
windows-releaseOK134
windows-oldrelOK109
wasm-releaseOK96

Exports:allocate_effortatlantic_systemffmsygot_speciesgot_system_drafthcr_effortms_assessment_presetsms_closurems_colsms_conditionms_inkms_landscapems_open_accessms_optimisems_perfms_perf_tablems_performancems_shared_q_curvems_simulatems_statisticsms_status_quoms_summaryms_systemms_tunems_tune_hcrms_yield_curveperf_rowsplot_bpsplot_catchabilityplot_fleetplot_kobeplot_landscapeplot_projectionplot_quiltplot_tradeoffsplot_yield_curvesproc_sd_from_rread_ms_systemrelsig_jabbarun_apptheme_mswrite_ms_system

Dependencies:clicpp11data.tablefarverggplot2gluegtableisobandlabelinglifecycleR6RColorBrewerrlangS7scalesvctrsviridisLitewithr

Step by step: using mmsyFM
1. Load and inspect a system | 2. The status quo | 3. Equilibrium scenarios | 4. Yield curves | 5. Safeguarded MMSY | 6. Harvest strategies | 7. Performance statistics | 8. Projections | 9. Tuning triggers | 10. The app
Rendered frommmsyFM.Rmdusingknitr::rmarkdown

Last update: 2026-10-23
Started: 2026-10-22

Management options
Rendered frommanagement-options.Rmdusingknitr::rmarkdown

Last update: 2026-10-23
Started: 2026-10-23

Setting up the case studies: Atlantic and Gulf of Thailand
Part A: the Atlantic example | A1. Stocks | A2. Metiers and catchability: from a habitat landscape | A3. Fleet segments | A4. Tuning the status quo | Part B: the Gulf of Thailand draft | B1. The four tables | Species | Metiers and segments | B2. Catchability | Route A: an expert overlap matrix | Route B: a habitat landscape | B3. Fleet behaviour | B4. Calibrating the starting point | Checking the result | Part C: checklist for your own system | Next steps
Rendered fromscenario-setup.Rmdusingknitr::rmarkdown

Last update: 2026-10-23
Started: 2026-10-23

How mmsyFM works
Rendered fromhow-it-works.Rmdusingknitr::rmarkdown

Last update: 2026-10-23
Started: 2026-10-23

Readme and manuals

Help Manual

Help pageTopics
Atlantic example systematlantic_system
F relative to Fmsy in the discrete Schaefer modelffmsy
Gulf of Thailand species groups (mmsyapp input)got_species
Gulf of Thailand system (draft)got_system_draft
Segment effort rule with an optional choke-stock closurehcr_effort
Default assessment strategies: indicator species, complexes and assignmentms_assessment_presets
Fixed metier closuresms_closure
Condition stock status on target depletionsms_condition
Catchability from a habitat landscapems_landscape
Open-access and status-quo equilibriams_open_access ms_status_quo
Maximise an equilibrium objective over segment effort capsms_optimise
Performance statistics in the mseviz formatms_perf
Summary (decision) table of performance statisticsms_perf_table
Shared-q yield curve (the mmsyapp model)ms_shared_q_curve
Simulate the system forwardms_simulate
Definitions of the performance statisticsms_statistics
Summaries over the kept yearsms_summary
Build a multispecies fleet system from tablesms_system
Tune daily costs so that a target fleet composition is an open-access equilibriumms_tune
Tune the triggers of hcr_effort() to a risk criterionms_tune_hcr
Equilibrium yield curve over effortms_yield_curve
Performance statistics of projection runsms_performance perf_rows
Boxplots of performance statistics by management procedureplot_bps
Catchability heatmapplot_catchability
Projections of days by segment and total yieldplot_fleet
Kobe plot of equilibrium statesplot_kobe
Plot a habitat landscapeplot_landscape
Projections by stock: B/Bmsy, F/Fmsy or catch over timeplot_projection
Quilt plot: a colour-coded decision tableplot_quilt
Trade-off plots of performance statisticsplot_tradeoffs
Equilibrium yield curvesplot_yield_curves
Process SD by productivity: a power law in r through two anchorsproc_sd_from_r
Read a system from CSV tablesread_ms_system
JABBA 'proc.dyn' relative process SDrelsig_jabba
Launch the mmsyFM Shiny apprun_app
Colours and theme of the package plotsms_cols ms_ink theme_ms
Write a system to CSV tableswrite_ms_system