Package: FLOSS 0.5.8

FLOSS: FL Operating Model and Sampling Simulator

Builds multi-fleet, multi-species age-structured operating models from life-history parameters, fleet selectivity, relative catchability and a target MSY, driven by shared fleet effort (with optional effort creep), and generates the data such fisheries produce (catch, effort, CPUE, survey indices, length frequencies and biological samples). Designed for training and for trainers who need realistic example datasets with a known truth. Built on FLR ('FLCore', 'FLBRP', 'FLasher', 'FLife') and 'FLRef'.

Authors:Henning Winker [aut, cre]

FLOSS_0.5.8.tar.gz
FLOSS_0.5.8.zip(r-4.7-any)FLOSS_0.5.8.zip(r-4.6-any)FLOSS_0.5.8.zip(r-4.5-any)
FLOSS_0.5.8.tgz(r-4.6-any)
FLOSS_0.5.8.tar.gz(r-4.7-any)FLOSS_0.5.8.tar.gz(r-4.6-any)
FLOSS_0.5.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
FLOSS/json (API)

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

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

Pkgdown/docs site:https://henning-winker.github.io

On CRAN:

Conda:

3.62 score 14 scripts 85 exports 50 dependencies

Last updated from:c2c92c17ab. Checks:6 NOTE, 2 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develNOTE446
source / vignettesOK553
linux-releaseNOTE369
macos-releaseNOTE159
macos-oldrelFAIL99
windows-develNOTE152
windows-releaseNOTE141
windows-oldrelNOTE150
wasm-releaseOK345

Exports:alk_obsas_flrbuild_ombuild_omscaa_obscalibrate_msycatch_curvecatch_curve_lengthcatch_fleetcatch_tablecpue_checkdelete_specieseffort_simeffort_tableeffort_trendexport_dataexport_truthfisheryfishery_yearsfit_growthfit_lwfit_maturityfloss_gearsfloss_guidefloss_tipfloss.r4collength_indicatorslfd_aggregatelfd_annualload_fisheryload_speciesM_empiricalnominal_cpueoem_settingsone_gear_fisheryone_gear_speciesplanted_artefactsplot_aggregateplot_availabilityplot_bioplot_caaplot_effortplot_eqplot_eq_selectivityplot_fitplot_fleetsplot_indicatorsplot_kobeplot_length_indicatorsplot_lfdplot_obsplot_omplot_seasonsplot_srrplot_ssb_vbplot_treatmentplot_truthread_datasetread_specreef_fisheryreef_oemrun_apprun_treatmentsample_biosample_catchsample_cpuesample_datasample_effortsample_lfdsample_surveysave_speciesseason_designselectivitysimulate_fisheryspeciesspecies_lhparspecies_libraryspecies_selstatus_tablesurvey_settingstreatmenttrend_valuesvalidate_fisheryvalidate_specieswrite_spec

Dependencies:clicodetoolscowplotcpp11data.tabledoFuturefarverFLasherFLBRPFLCoreFLFisheryFLifeFLRefFLSRTMBforeachfuturefuture.applyggplot2ggplotFLggrepelglobalsgluegridExtragtableisobanditeratorslabelinglatticelifecyclelistenvMASSMatrixmsemvtnormparallellypatchworkplyrprogressrR6RColorBrewerRcppRcppEigenrlangS7scalesTMBvctrsviridisLitewithryaml

Appendix: methods and equations
Rendered fromfloss-05-methods.Rmdusingknitr::rmarkdown

Last update: 2026-11-04
Started: 2026-11-04

Training example: summed effort and nominal CPUE hide a shark decline
Rendered fromfloss-04-cpue-aggregation.Rmdusingknitr::rmarkdown

Last update: 2026-11-04
Started: 2026-11-04

FLOSS 1: a multi-fleet reef operating model from saved specs
Rendered fromfloss-01-reef-om.Rmdusingknitr::rmarkdown

Last update: 2026-11-03
Started: 2026-11-02

FLOSS teaching scenarios: predict the response, spot the warning flags
Rendered fromfloss-03-teaching.Rmdusingknitr::rmarkdown

Last update: 2026-11-03
Started: 2026-11-02

FLOSS user guide: four reef species, three fleets, from operating model to saved datasets
Rendered fromfloss-02-user-guide.Rmdusingknitr::rmarkdown

Last update: 2026-11-03
Started: 2026-11-02

How FLOSS works
Rendered fromfloss-00-how-it-works.Rmdusingknitr::rmarkdown

Last update: 2026-11-02
Started: 2026-11-02

Readme and manuals

Help Manual

Help pageTopics
Observed age-length keyalk_obs
FLR objects for JABBA3 and FLiccas_flr
Build a stochastic operating model for one speciesbuild_om
Build operating models for several species sharing one fisherybuild_oms
Catch-at-age from length samples and an age-length keycaa_obs
Equilibrium calibrated to a target MSYcalibrate_msy
Age-based catch curvecatch_curve
Length-converted catch curve and selectivitycatch_curve_length
True catch by fleetcatch_fleet
Catch, effort and nominal CPUE: by fleet or aggregatedcatch_table effort_table nominal_cpue
Check the CPUE assumptions against the truth (trainers)cpue_check
Simulate fleet efforteffort_sim
Effort trend for one fleeteffort_trend
Export datasets for traineesexport_data
Download the truth (trainers)export_truth
Define a fisheryfishery fishery_years validate_fishery
Fit von Bertalanffy growth to observed length-at-agefit_growth
Fit the length-weight relationshipfit_lw
Fit a logistic maturity ogivefit_maturity
FLRef gear objects for an operating modelfloss_gears
Copy, and optionally render, a FLOSS guidefloss_guide
Short explanations of FLOSS settingsfloss_tip
FLOSS colour palette (r4ss colours, as in JABBA)floss.r4col
Length-based indicators by year and sourcelength_indicators
Length samples: by fleet or pooled, as sampled or raised to the catchlfd_aggregate
Pool seasonal length samples into annual oneslfd_annual
Example fishery shipped with the packageload_fishery
Empirical natural mortality estimatorsM_empirical
Sampling settingsoem_settings
One-gear fishery with constant (or stepped) F/Fmsyone_gear_fishery
Adapt a species to a one-gear fisheryone_gear_species
Artefacts planted in the sampling settings and the fisheryplanted_artefacts
Plot catch, effort or nominal CPUE by fleet or aggregatedplot_aggregate
Plot which data exist for which yearsplot_availability
Plot biological samples (observations only)plot_bio
Plot catch-at-age from 'caa_obs()'plot_caa
Plot fleet effortplot_effort
Equilibrium curves with the realised trajectoryplot_eq
Equilibrium curves under alternative selectivitiesplot_eq_selectivity
Plot a basic fitplot_fit
Plot apical fishing mortality or catch by fleetplot_fleets
Indicator dashboardplot_indicators
Kobe plot of true statusplot_kobe
Plot length-based indicatorsplot_length_indicators
Plot length samplesplot_lfd
Plot observed catch, CPUE and survey indicesplot_obs
Plot stock status of an operating modelplot_om
Seasonal length sampling: sample sizes and mean length by seasonplot_seasons
Stock-recruitment curve with simulated pairsplot_srr
Spawning biomass versus vulnerable biomass by fleetplot_ssb_vb
Plot the response to treatmentsplot_treatment
Plot true status trajectoriesplot_truth
Read an exported datasetread_dataset
The three-fleet reef fishery used in the examplesreef_fishery
Sampling settings of the reef examplereef_oem
Start the FLOSS apprun_app
Run a baseline and treatments with common random numbersrun_treatment
Generate observed datasample_bio sample_catch sample_cpue sample_data sample_effort sample_lfd sample_survey
Seasonal sampling designseason_design
Selectivity-at-length for one fleetselectivity
Simulate a fishery and its data in one callsimulate_fishery
Define a speciesspecies validate_species
Life-history FLPar for FLifespecies_lhpar
Species librarydelete_species load_species save_species species_library
Selectivity-at-length and -at-age by fleetspecies_sel
True stock statusstatus_table
Survey settingssurvey_settings
Define a treatmenttreatment
Deterministic effort trend valuestrend_values
Write and read FLOSS specs as YAMLread_spec write_spec