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  "Description": "Builds multi-fleet, multi-species age-structured operating\nmodels from life-history parameters, fleet selectivity,\nrelative catchability and a target MSY, driven by shared fleet\neffort (with optional effort creep), and generates the data\nsuch fisheries produce (catch, effort, CPUE, survey indices,\nlength frequencies and biological samples). Designed for\ntraining and for trainers who need realistic example datasets\nwith a known truth. Built on FLR ('FLCore', 'FLBRP', 'FLasher',\n'FLife') and 'FLRef'.",
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  "_exports": [
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    "as_flr",
    "build_om",
    "build_oms",
    "caa_obs",
    "calibrate_msy",
    "catch_curve",
    "catch_curve_length",
    "catch_fleet",
    "catch_table",
    "cpue_check",
    "delete_species",
    "effort_sim",
    "effort_table",
    "effort_trend",
    "export_data",
    "export_truth",
    "fishery",
    "fishery_years",
    "fit_growth",
    "fit_lw",
    "fit_maturity",
    "floss_gears",
    "floss_guide",
    "floss_tip",
    "floss.r4col",
    "length_indicators",
    "lfd_aggregate",
    "lfd_annual",
    "load_fishery",
    "load_species",
    "M_empirical",
    "nominal_cpue",
    "oem_settings",
    "one_gear_fishery",
    "one_gear_species",
    "planted_artefacts",
    "plot_aggregate",
    "plot_availability",
    "plot_bio",
    "plot_caa",
    "plot_effort",
    "plot_eq",
    "plot_eq_selectivity",
    "plot_fit",
    "plot_fleets",
    "plot_indicators",
    "plot_kobe",
    "plot_length_indicators",
    "plot_lfd",
    "plot_obs",
    "plot_om",
    "plot_seasons",
    "plot_srr",
    "plot_ssb_vb",
    "plot_treatment",
    "plot_truth",
    "read_dataset",
    "read_spec",
    "reef_fishery",
    "reef_oem",
    "run_app",
    "run_treatment",
    "sample_bio",
    "sample_catch",
    "sample_cpue",
    "sample_data",
    "sample_effort",
    "sample_lfd",
    "sample_survey",
    "save_species",
    "season_design",
    "selectivity",
    "simulate_fishery",
    "species",
    "species_lhpar",
    "species_library",
    "species_sel",
    "status_table",
    "survey_settings",
    "treatment",
    "trend_values",
    "validate_fishery",
    "validate_species",
    "write_spec"
  ],
  "_help": [
    {
      "page": "alk_obs",
      "title": "Observed age-length key",
      "topics": [
        "alk_obs"
      ]
    },
    {
      "page": "as_flr",
      "title": "FLR objects for JABBA3 and FLicc",
      "topics": [
        "as_flr"
      ]
    },
    {
      "page": "build_om",
      "title": "Build a stochastic operating model for one species",
      "topics": [
        "build_om"
      ]
    },
    {
      "page": "build_oms",
      "title": "Build operating models for several species sharing one fishery",
      "topics": [
        "build_oms"
      ]
    },
    {
      "page": "caa_obs",
      "title": "Catch-at-age from length samples and an age-length key",
      "topics": [
        "caa_obs"
      ]
    },
    {
      "page": "calibrate_msy",
      "title": "Equilibrium calibrated to a target MSY",
      "topics": [
        "calibrate_msy"
      ]
    },
    {
      "page": "catch_curve",
      "title": "Age-based catch curve",
      "topics": [
        "catch_curve"
      ]
    },
    {
      "page": "catch_curve_length",
      "title": "Length-converted catch curve and selectivity",
      "topics": [
        "catch_curve_length"
      ]
    },
    {
      "page": "catch_fleet",
      "title": "True catch by fleet",
      "topics": [
        "catch_fleet"
      ]
    },
    {
      "page": "catch_table",
      "title": "Catch, effort and nominal CPUE: by fleet or aggregated",
      "topics": [
        "catch_table",
        "effort_table",
        "nominal_cpue"
      ]
    },
    {
      "page": "cpue_check",
      "title": "Check the CPUE assumptions against the truth (trainers)",
      "topics": [
        "cpue_check"
      ]
    },
    {
      "page": "effort_sim",
      "title": "Simulate fleet effort",
      "topics": [
        "effort_sim"
      ]
    },
    {
      "page": "effort_trend",
      "title": "Effort trend for one fleet",
      "topics": [
        "effort_trend"
      ]
    },
    {
      "page": "export_data",
      "title": "Export datasets for trainees",
      "topics": [
        "export_data"
      ]
    },
    {
      "page": "export_truth",
      "title": "Download the truth (trainers)",
      "topics": [
        "export_truth"
      ]
    },
    {
      "page": "fishery",
      "title": "Define a fishery",
      "topics": [
        "fishery",
        "fishery_years",
        "validate_fishery"
      ]
    },
    {
      "page": "fit_growth",
      "title": "Fit von Bertalanffy growth to observed length-at-age",
      "topics": [
        "fit_growth"
      ]
    },
    {
      "page": "fit_lw",
      "title": "Fit the length-weight relationship",
      "topics": [
        "fit_lw"
      ]
    },
    {
      "page": "fit_maturity",
      "title": "Fit a logistic maturity ogive",
      "topics": [
        "fit_maturity"
      ]
    },
    {
      "page": "floss_gears",
      "title": "FLRef gear objects for an operating model",
      "topics": [
        "floss_gears"
      ]
    },
    {
      "page": "floss_guide",
      "title": "Copy, and optionally render, a FLOSS guide",
      "topics": [
        "floss_guide"
      ]
    },
    {
      "page": "floss_tip",
      "title": "Short explanations of FLOSS settings",
      "topics": [
        "floss_tip"
      ]
    },
    {
      "page": "floss.r4col",
      "title": "FLOSS colour palette (r4ss colours, as in JABBA)",
      "topics": [
        "floss.r4col"
      ]
    },
    {
      "page": "length_indicators",
      "title": "Length-based indicators by year and source",
      "topics": [
        "length_indicators"
      ]
    },
    {
      "page": "lfd_aggregate",
      "title": "Length samples: by fleet or pooled, as sampled or raised to the catch",
      "topics": [
        "lfd_aggregate"
      ]
    },
    {
      "page": "lfd_annual",
      "title": "Pool seasonal length samples into annual ones",
      "topics": [
        "lfd_annual"
      ]
    },
    {
      "page": "load_fishery",
      "title": "Example fishery shipped with the package",
      "topics": [
        "load_fishery"
      ]
    },
    {
      "page": "M_empirical",
      "title": "Empirical natural mortality estimators",
      "topics": [
        "M_empirical"
      ]
    },
    {
      "page": "oem_settings",
      "title": "Sampling settings",
      "topics": [
        "oem_settings"
      ]
    },
    {
      "page": "one_gear_fishery",
      "title": "One-gear fishery with constant (or stepped) F/Fmsy",
      "topics": [
        "one_gear_fishery"
      ]
    },
    {
      "page": "one_gear_species",
      "title": "Adapt a species to a one-gear fishery",
      "topics": [
        "one_gear_species"
      ]
    },
    {
      "page": "planted_artefacts",
      "title": "Artefacts planted in the sampling settings and the fishery",
      "topics": [
        "planted_artefacts"
      ]
    },
    {
      "page": "plot_aggregate",
      "title": "Plot catch, effort or nominal CPUE by fleet or aggregated",
      "topics": [
        "plot_aggregate"
      ]
    },
    {
      "page": "plot_availability",
      "title": "Plot which data exist for which years",
      "topics": [
        "plot_availability"
      ]
    },
    {
      "page": "plot_bio",
      "title": "Plot biological samples (observations only)",
      "topics": [
        "plot_bio"
      ]
    },
    {
      "page": "plot_caa",
      "title": "Plot catch-at-age from 'caa_obs()'",
      "topics": [
        "plot_caa"
      ]
    },
    {
      "page": "plot_effort",
      "title": "Plot fleet effort",
      "topics": [
        "plot_effort"
      ]
    },
    {
      "page": "plot_eq",
      "title": "Equilibrium curves with the realised trajectory",
      "topics": [
        "plot_eq"
      ]
    },
    {
      "page": "plot_eq_selectivity",
      "title": "Equilibrium curves under alternative selectivities",
      "topics": [
        "plot_eq_selectivity"
      ]
    },
    {
      "page": "plot_fit",
      "title": "Plot a basic fit",
      "topics": [
        "plot_fit"
      ]
    },
    {
      "page": "plot_fleets",
      "title": "Plot apical fishing mortality or catch by fleet",
      "topics": [
        "plot_fleets"
      ]
    },
    {
      "page": "plot_indicators",
      "title": "Indicator dashboard",
      "topics": [
        "plot_indicators"
      ]
    },
    {
      "page": "plot_kobe",
      "title": "Kobe plot of true status",
      "topics": [
        "plot_kobe"
      ]
    },
    {
      "page": "plot_length_indicators",
      "title": "Plot length-based indicators",
      "topics": [
        "plot_length_indicators"
      ]
    },
    {
      "page": "plot_lfd",
      "title": "Plot length samples",
      "topics": [
        "plot_lfd"
      ]
    },
    {
      "page": "plot_obs",
      "title": "Plot observed catch, CPUE and survey indices",
      "topics": [
        "plot_obs"
      ]
    },
    {
      "page": "plot_om",
      "title": "Plot stock status of an operating model",
      "topics": [
        "plot_om"
      ]
    },
    {
      "page": "plot_seasons",
      "title": "Seasonal length sampling: sample sizes and mean length by season",
      "topics": [
        "plot_seasons"
      ]
    },
    {
      "page": "plot_srr",
      "title": "Stock-recruitment curve with simulated pairs",
      "topics": [
        "plot_srr"
      ]
    },
    {
      "page": "plot_ssb_vb",
      "title": "Spawning biomass versus vulnerable biomass by fleet",
      "topics": [
        "plot_ssb_vb"
      ]
    },
    {
      "page": "plot_treatment",
      "title": "Plot the response to treatments",
      "topics": [
        "plot_treatment"
      ]
    },
    {
      "page": "plot_truth",
      "title": "Plot true status trajectories",
      "topics": [
        "plot_truth"
      ]
    },
    {
      "page": "read_dataset",
      "title": "Read an exported dataset",
      "topics": [
        "read_dataset"
      ]
    },
    {
      "page": "reef_fishery",
      "title": "The three-fleet reef fishery used in the examples",
      "topics": [
        "reef_fishery"
      ]
    },
    {
      "page": "reef_oem",
      "title": "Sampling settings of the reef example",
      "topics": [
        "reef_oem"
      ]
    },
    {
      "page": "run_app",
      "title": "Start the FLOSS app",
      "topics": [
        "run_app"
      ]
    },
    {
      "page": "run_treatment",
      "title": "Run a baseline and treatments with common random numbers",
      "topics": [
        "run_treatment"
      ]
    },
    {
      "page": "sample_data",
      "title": "Generate observed data",
      "topics": [
        "sample_bio",
        "sample_catch",
        "sample_cpue",
        "sample_data",
        "sample_effort",
        "sample_lfd",
        "sample_survey"
      ]
    },
    {
      "page": "season_design",
      "title": "Seasonal sampling design",
      "topics": [
        "season_design"
      ]
    },
    {
      "page": "selectivity",
      "title": "Selectivity-at-length for one fleet",
      "topics": [
        "selectivity"
      ]
    },
    {
      "page": "simulate_fishery",
      "title": "Simulate a fishery and its data in one call",
      "topics": [
        "simulate_fishery"
      ]
    },
    {
      "page": "species",
      "title": "Define a species",
      "topics": [
        "species",
        "validate_species"
      ]
    },
    {
      "page": "species_lhpar",
      "title": "Life-history FLPar for FLife",
      "topics": [
        "species_lhpar"
      ]
    },
    {
      "page": "species_library",
      "title": "Species library",
      "topics": [
        "delete_species",
        "load_species",
        "save_species",
        "species_library"
      ]
    },
    {
      "page": "species_sel",
      "title": "Selectivity-at-length and -at-age by fleet",
      "topics": [
        "species_sel"
      ]
    },
    {
      "page": "status_table",
      "title": "True stock status",
      "topics": [
        "status_table"
      ]
    },
    {
      "page": "survey_settings",
      "title": "Survey settings",
      "topics": [
        "survey_settings"
      ]
    },
    {
      "page": "treatment",
      "title": "Define a treatment",
      "topics": [
        "treatment"
      ]
    },
    {
      "page": "trend_values",
      "title": "Deterministic effort trend values",
      "topics": [
        "trend_values"
      ]
    },
    {
      "page": "write_spec",
      "title": "Write and read FLOSS specs as YAML",
      "topics": [
        "read_spec",
        "write_spec"
      ]
    }
  ],
  "_readme": "https://github.com/Henning-Winker/FLOSS/raw/HEAD/README.md",
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