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  "Title": "Bayesian State-Space Surplus Production Models in 'RTMB'",
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  "Description": "The next generation of 'JABBA' (Just Another Bayesian\nBiomass Assessment), now with hyperdrive. Fits Bayesian\nstate-space surplus production models in 'RTMB' in well under a\nsecond, so you can spend less time waiting for chains to\nconverge and more time arguing about priors. Full posteriors\nare available through 'tmbstan' (NUTS) for those who still like\ntheir MCMC. Inputs and outputs follow 'FLR' conventions for use\nwith 'ggplotFL', 'FLRef' and 'mse', and helpers convert classic\n'JABBA' inputs so old scripts survive the jump to hyperspace.",
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  "Repository": "https://henning-winker.r-universe.dev",
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    "jabba3_info",
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    "jb3_bprior",
    "jb3_catchfill",
    "jb3_contraction",
    "jb3_convergence",
    "jb3_data",
    "jb3_data_jabba",
    "jb3_diags",
    "jb3_draws",
    "jb3_ensemble",
    "jb3_fill_table",
    "jb3_flpar",
    "jb3_flqs",
    "jb3_FLStockR",
    "jb3_fmsy2r",
    "jb3_fwd",
    "jb3_fwdtable",
    "jb3_hcr",
    "jb3_hindcast",
    "jb3_jointindex",
    "jb3_kobematrix",
    "jb3_kobematrix_gfcm",
    "jb3_kobematrix_ices",
    "jb3_kobematrix_iotc",
    "jb3_leslie",
    "jb3_model",
    "jb3_noise",
    "jb3_nuts_diags",
    "jb3_nuts_ess",
    "jb3_osa",
    "jb3_partable",
    "jb3_priors",
    "jb3_project",
    "jb3_projtable",
    "jb3_qtable",
    "jb3_r2fmsy",
    "jb3_retro",
    "jb3_rho_gt",
    "jb3_rho_table",
    "jb3_runs",
    "jb3_sel5",
    "jb3_selex",
    "jb3_splitindex",
    "jb3_tier1",
    "jb3_tier2",
    "jb3_trend",
    "jb3_tstable",
    "jb3_weights",
    "jb3_workflow",
    "jb3cols",
    "jbcatch2flq",
    "jbdat2flr",
    "jbidx2FLIndices",
    "jbinput2jabba3",
    "jbplot_advice",
    "jbplot_all",
    "jbplot_auxfits",
    "jbplot_biplot",
    "jbplot_bprior",
    "jbplot_catch",
    "jbplot_catcherror",
    "jbplot_catchfill",
    "jbplot_contraction",
    "jbplot_crisk",
    "jbplot_data",
    "jbplot_ebsb_status",
    "jbplot_energy",
    "jbplot_ensemble",
    "jbplot_fits",
    "jbplot_hcr",
    "jbplot_hcxval",
    "jbplot_indexcor",
    "jbplot_indices",
    "jbplot_jointindex",
    "jbplot_kobe",
    "jbplot_kobematrix",
    "jbplot_mcmcacf",
    "jbplot_mcmcdens",
    "jbplot_noise",
    "jbplot_nuts",
    "jbplot_nutsdiags",
    "jbplot_pairs",
    "jbplot_ppc",
    "jbplot_priorpost",
    "jbplot_priorpost_trj",
    "jbplot_procdev",
    "jbplot_production",
    "jbplot_projection",
    "jbplot_q",
    "jbplot_rank",
    "jbplot_residuals",
    "jbplot_retro",
    "jbplot_rhat",
    "jbplot_runs",
    "jbplot_selex",
    "jbplot_spdiags",
    "jbplot_spdyn",
    "jbplot_spphase",
    "jbplot_stdresiduals",
    "jbplot_steps",
    "jbplot_summary",
    "jbplot_trace",
    "jbplot_trend",
    "jbplot_trj",
    "scale_x_year",
    "spictinp2jabba3",
    "theme_jabba3"
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  "_datasets": [
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      "title": "Iccat example stocks (from JABBA)",
      "object": "iccat",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "jara_examples",
      "title": "Example data for the data-exploration (JARA) models",
      "object": "jara_examples",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "flr2jbdat",
      "title": "Convert FLR inputs back to classic JABBA data frames",
      "topics": [
        "flr2jbdat"
      ]
    },
    {
      "page": "iccat",
      "title": "Iccat example stocks (from JABBA)",
      "topics": [
        "iccat"
      ]
    },
    {
      "page": "jabba3",
      "title": "Fit a JABBA3 model",
      "topics": [
        "jabba3"
      ]
    },
    {
      "page": "jabba3_info",
      "title": "Engines and status of this JABBA3 installation",
      "topics": [
        "jabba3_info"
      ]
    },
    {
      "page": "jabbaplot3",
      "title": "JABBA3 summary plot with selectable panels",
      "topics": [
        "jabbaplot3",
        "plot.jabba3"
      ]
    },
    {
      "page": "jara_examples",
      "title": "Example data for the data-exploration (JARA) models",
      "topics": [
        "jara_examples"
      ]
    },
    {
      "page": "jb3_align",
      "title": "Alignment of the input series",
      "topics": [
        "jb3_align"
      ]
    },
    {
      "page": "jb3_bprior",
      "title": "Status priors (JABBA b.prior)",
      "topics": [
        "jb3_bprior"
      ]
    },
    {
      "page": "jb3_catchfill",
      "title": "Reconstruct catch series through missing years",
      "topics": [
        "jb3_catchfill"
      ]
    },
    {
      "page": "jb3_contraction",
      "title": "Prior-posterior contraction and shift",
      "topics": [
        "jb3_contraction"
      ]
    },
    {
      "page": "jb3_convergence",
      "title": "Convergence checks",
      "topics": [
        "jb3_convergence"
      ]
    },
    {
      "page": "jb3_data",
      "title": "Assessment data for JABBA3",
      "topics": [
        "jb3_data"
      ]
    },
    {
      "page": "jb3_data_jabba",
      "title": "Convert classic JABBA inputs",
      "topics": [
        "jb3_data_jabba"
      ]
    },
    {
      "page": "jb3_diags",
      "title": "Residual diagnostics: JABBA set + SPiCT set",
      "topics": [
        "jb3_diags"
      ]
    },
    {
      "page": "jb3_draws",
      "title": "Pseudo-posterior draws at the mode",
      "topics": [
        "jb3_draws"
      ]
    },
    {
      "page": "jb3_ensemble",
      "title": "Weighted ensemble of fits",
      "topics": [
        "jb3_ensemble"
      ]
    },
    {
      "page": "jb3_fill_table",
      "title": "Original series with missing values filled",
      "topics": [
        "jb3_fill_table"
      ]
    },
    {
      "page": "jb3_flqs",
      "title": "FLR outputs",
      "topics": [
        "jb3_flpar",
        "jb3_flqs"
      ]
    },
    {
      "page": "jb3_FLStockR",
      "title": "Convert a JABBA3 fit to an FLStockR",
      "topics": [
        "jb3_FLStockR"
      ]
    },
    {
      "page": "jb3_fmsy2r",
      "title": "Convert between Fmsy and the surplus production r for a given shape",
      "topics": [
        "jb3_fmsy2r",
        "jb3_r2fmsy"
      ]
    },
    {
      "page": "jb3_fwd",
      "title": "Forward projections with a forecast control (fwdctrl)",
      "topics": [
        "jb3_fwd"
      ]
    },
    {
      "page": "jb3_fwdtable",
      "title": "Fishing opportunities table",
      "topics": [
        "jb3_fwdtable"
      ]
    },
    {
      "page": "jb3_hcr",
      "title": "Hockey-stick harvest control rule",
      "topics": [
        "jb3_hcr"
      ]
    },
    {
      "page": "jb3_hindcast",
      "title": "Hindcast cross-validation",
      "topics": [
        "jb3_hindcast"
      ]
    },
    {
      "page": "jb3_jointindex",
      "title": "Joint index from a trend fit",
      "topics": [
        "jb3_jointindex"
      ]
    },
    {
      "page": "jb3_kobematrix",
      "title": "Kobe II strategy matrix",
      "topics": [
        "jb3_kobematrix"
      ]
    },
    {
      "page": "jb3_kobematrix_gfcm",
      "title": "Kobe II strategy matrix, GFCM format",
      "topics": [
        "jb3_kobematrix_gfcm",
        "jb3_kobematrix_ices"
      ]
    },
    {
      "page": "jb3_kobematrix_iotc",
      "title": "Kobe II strategy matrix, IOTC format",
      "topics": [
        "jb3_kobematrix_iotc"
      ]
    },
    {
      "page": "jb3_leslie",
      "title": "Intrinsic rate of increase and generation time from a Leslie matrix",
      "topics": [
        "jb3_leslie"
      ]
    },
    {
      "page": "jb3_model",
      "title": "Model structure for JABBA3",
      "topics": [
        "jb3_model"
      ]
    },
    {
      "page": "jb3_noise",
      "title": "Observation and process noise of indices",
      "topics": [
        "jb3_noise"
      ]
    },
    {
      "page": "jb3_nuts_diags",
      "title": "NUTS convergence summary",
      "topics": [
        "jb3_nuts_diags"
      ]
    },
    {
      "page": "jb3_nuts_ess",
      "title": "Effective sample size of the derived states",
      "topics": [
        "jb3_nuts_ess"
      ]
    },
    {
      "page": "jb3_osa",
      "title": "One-step-ahead residuals",
      "topics": [
        "jb3_osa"
      ]
    },
    {
      "page": "jb3_partable",
      "title": "Parameter and reference point table",
      "topics": [
        "jb3_partable"
      ]
    },
    {
      "page": "jb3_priors",
      "title": "Priors for JABBA3",
      "topics": [
        "jb3_priors"
      ]
    },
    {
      "page": "jb3_project",
      "title": "Projections",
      "topics": [
        "jb3_project"
      ]
    },
    {
      "page": "jb3_projtable",
      "title": "Projection tables",
      "topics": [
        "jb3_projtable"
      ]
    },
    {
      "page": "jb3_qtable",
      "title": "Catchability relative to the reference index",
      "topics": [
        "jb3_qtable"
      ]
    },
    {
      "page": "jb3_retro",
      "title": "Retrospective analysis",
      "topics": [
        "jb3_retro"
      ]
    },
    {
      "page": "jb3_rho_gt",
      "title": "Life-history guidance for the AR(1) persistence of process error",
      "topics": [
        "jb3_rho_gt",
        "jb3_rho_table"
      ]
    },
    {
      "page": "jb3_runs",
      "title": "Runs test with three-sigma control limits",
      "topics": [
        "jb3_runs"
      ]
    },
    {
      "page": "jb3_sel5",
      "title": "JABBA 5-parameter selectivity",
      "topics": [
        "jb3_sel5"
      ]
    },
    {
      "page": "jb3_selex",
      "title": "Selex inputs from length-based selectivity: EB/SB curves for the spawning-biomass state",
      "topics": [
        "jb3_selex"
      ]
    },
    {
      "page": "jb3_splitindex",
      "title": "Split an index at a change in vessel, gear or method",
      "topics": [
        "jb3_splitindex"
      ]
    },
    {
      "page": "jb3_trend",
      "title": "State-space trend models for abundance indices (JARA)",
      "topics": [
        "jb3_trend"
      ]
    },
    {
      "page": "jb3_tstable",
      "title": "Time series table of estimated quantities",
      "topics": [
        "jb3_tstable"
      ]
    },
    {
      "page": "jb3_weights",
      "title": "Ensemble weights from model diagnostics",
      "topics": [
        "jb3_weights"
      ]
    },
    {
      "page": "jb3_workflow",
      "title": "BioProcDyn workflows: Tier 1, Tier 2 and Selex",
      "topics": [
        "jb3_tier1",
        "jb3_tier2",
        "jb3_workflow"
      ]
    },
    {
      "page": "jb3cols",
      "title": "Colours for runs, scenarios or peels (r4ss rule, as JAGG and ss3diags)",
      "topics": [
        "jb3cols"
      ]
    },
    {
      "page": "jbdat2flr",
      "title": "Convert classic JABBA data frames to FLR objects",
      "topics": [
        "jbcatch2flq",
        "jbdat2flr",
        "jbidx2FLIndices"
      ]
    },
    {
      "page": "jbinput2jabba3",
      "title": "Convert a JABBA input object to JABBA3",
      "topics": [
        "jbinput2jabba3"
      ]
    },
    {
      "page": "jbplot_advice",
      "title": "Advice plot",
      "topics": [
        "jbplot_advice"
      ]
    },
    {
      "page": "jbplot_all",
      "title": "Save the standard plot set",
      "topics": [
        "jbplot_all"
      ]
    },
    {
      "page": "jbplot_auxfits",
      "title": "Fits to the auxiliary data",
      "topics": [
        "jbplot_auxfits"
      ]
    },
    {
      "page": "jbplot_biplot",
      "title": "Stock status biplot",
      "topics": [
        "jbplot_biplot"
      ]
    },
    {
      "page": "jbplot_bprior",
      "title": "Status priors: prior against posterior",
      "topics": [
        "jbplot_bprior"
      ]
    },
    {
      "page": "jbplot_catch",
      "title": "Catch: observed and estimated",
      "topics": [
        "jbplot_catch"
      ]
    },
    {
      "page": "jbplot_catcherror",
      "title": "Catch error: observed and estimated catch",
      "topics": [
        "jbplot_catcherror"
      ]
    },
    {
      "page": "jbplot_contraction",
      "title": "Plot prior-posterior contraction against shift",
      "topics": [
        "jbplot_contraction"
      ]
    },
    {
      "page": "jbplot_crisk",
      "title": "Catch risk curves",
      "topics": [
        "jbplot_crisk"
      ]
    },
    {
      "page": "jbplot_data",
      "title": "Data overview",
      "topics": [
        "jbplot_data"
      ]
    },
    {
      "page": "jbplot_ebsb_status",
      "title": "Selex: spawning and exploitable biomass status",
      "topics": [
        "jbplot_ebsb_status"
      ]
    },
    {
      "page": "jbplot_ensemble",
      "title": "Ensemble of fits",
      "topics": [
        "jbplot_ensemble"
      ]
    },
    {
      "page": "jbplot_fits",
      "title": "Fits to the abundance indices",
      "topics": [
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