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  "Title": "Fits the Multispecies Assessment Model (CEATTLE) Using TMB",
  "Version": "5.66.1",
  "Authors@R": "person(given = \"Grant\",\nfamily = \"Adams\",\nrole = c(\"aut\", \"cre\"),\nemail = \"grant.adams@noaa.gov\",\ncomment = c(ORCID = \"0000-0003-0297-8347\"))",
  "Description": "Implements the CEATTLE model using Template Model Builder\n('TMB'; Kristensen et al. 2015), which can be installed\nfollowing <https://github.com/kaskr/adcomp/wiki/Download>.\nStructured similar to the original manuscript in terms of\nmodularization. Separate functions estimate retrospective\ntemperature- and size-specific predator rations, prey\npreference, and weight-at-age. These are then used as inputs to\nthe CEATTLE model to evaluate how predation mortality,\nrecruitment, and survival of three target species change under\nhistorical climate conditions and harvest rates.",
  "URL": "https://afsc-assessments.github.io/Rceattle/,\nhttps://github.com/afsc-assessments/Rceattle",
  "BugReports": "https://github.com/afsc-assessments/Rceattle/issues",
  "License": "GPL (>= 2)",
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  "Roxygen": "list(markdown = TRUE)",
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  "Repository": "https://noaa-fisheries-integrated-toolbox.r-universe.dev",
  "Date/Publication": "2026-10-26 23:01:40 UTC",
  "RemoteUrl": "https://github.com/grantdadams/Rceattle",
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  "NeedsCompilation": "yes",
  "Packaged": {
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    "User": "root"
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  "Author": "Grant Adams [aut, cre] (ORCID: <https://orcid.org/0000-0003-0297-8347>)",
  "Maintainer": "Grant Adams <grant.adams@noaa.gov>",
  "_user": "noaa-fisheries-integrated-toolbox",
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  "_expires": "2027-02-04T00:02:42.000Z",
  "_created": "2026-10-26T23:36:40.000Z",
  "_published": "2026-10-27T00:02:45.564Z",
  "_upstream": "https://github.com/grantdadams/Rceattle",
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    "email": "grant.adams@noaa.gov",
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    "description": "I am a statistician at the NOAA Alaska Fisheries Science Center",
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    },
    {
      "page": "as.data.frame.Rceattle",
      "title": "Tidy long-format derived quantities from an Rceattle fit",
      "topics": [
        "as.data.frame.Rceattle"
      ]
    },
    {
      "page": "Atka2022",
      "title": "Data inputs for Atka mackerel CEATTLE model (2022)",
      "topics": [
        "Atka2022"
      ]
    },
    {
      "page": "BS2017MS",
      "title": "Data inputs for multispecies CEATTLE of the Bering Sea from 1979 to 2017",
      "topics": [
        "BS2017MS"
      ]
    },
    {
      "page": "BS2017SS",
      "title": "Data inputs for single species CEATTLE of the Bering Sea from 1979 to 2017",
      "topics": [
        "BS2017SS"
      ]
    },
    {
      "page": "build_bounds",
      "title": "Build parameter bounds",
      "topics": [
        "build_bounds"
      ]
    },
    {
      "page": "build_catchability",
      "title": "Catchability specification",
      "topics": [
        "build_catchability"
      ]
    },
    {
      "page": "build_composition",
      "title": "Composition-weighting specification",
      "topics": [
        "build_composition"
      ]
    },
    {
      "page": "build_data",
      "title": "Build an Rceattle data list in R",
      "topics": [
        "build_data"
      ]
    },
    {
      "page": "build_growth",
      "title": "Specify the growth model for Rceattle",
      "topics": [
        "build_growth"
      ]
    },
    {
      "page": "build_hcr",
      "title": "Specify the harvest control rule (HCR) used for Rceattle",
      "topics": [
        "build_hcr"
      ]
    },
    {
      "page": "build_hcr_map",
      "title": "Function to construct the TMB map argument for CEATTLE for projecting under alternative harvest control rules",
      "topics": [
        "build_hcr_map"
      ]
    },
    {
      "page": "build_M1",
      "title": "Specify the residual natural mortality (M1) model for Rceattle",
      "topics": [
        "build_M1"
      ]
    },
    {
      "page": "build_map",
      "title": "Main function to construct the TMB map argument for CEATTLE",
      "topics": [
        "build_map"
      ]
    },
    {
      "page": "build_map_catchability",
      "title": "Helper to set map for Catchability parameters",
      "topics": [
        "build_map_catchability"
      ]
    },
    {
      "page": "build_map_debug",
      "title": "Helper to set map for debug mode",
      "topics": [
        "build_map_debug"
      ]
    },
    {
      "page": "build_map_f_and_data_weights",
      "title": "Helper to set map for Fishing Mortality and Data Weights",
      "topics": [
        "build_map_f_and_data_weights"
      ]
    },
    {
      "page": "build_map_fixed_natage",
      "title": "Helper to set map for Fixed N-at-Age models",
      "topics": [
        "build_map_fixed_natage"
      ]
    },
    {
      "page": "build_map_growth",
      "title": "Helper to set map for growth parameters",
      "topics": [
        "build_map_growth"
      ]
    },
    {
      "page": "build_map_m1",
      "title": "Helper to set map for Natural Mortality (M1) parameters",
      "topics": [
        "build_map_m1"
      ]
    },
    {
      "page": "build_map_predation",
      "title": "Helper to set map for Predation Mortality (M2) parameters",
      "topics": [
        "build_map_predation"
      ]
    },
    {
      "page": "build_map_recruitment",
      "title": "Helper to set map for Recruitment parameters",
      "topics": [
        "build_map_recruitment"
      ]
    },
    {
      "page": "build_map_selectivity",
      "title": "Helper to set map for Selectivity parameters",
      "topics": [
        "build_map_selectivity"
      ]
    },
    {
      "page": "build_params",
      "title": "Build parameter list from cpp file",
      "topics": [
        "build_params"
      ]
    },
    {
      "page": "build_selectivity",
      "title": "Selectivity specification",
      "topics": [
        "build_selectivity"
      ]
    },
    {
      "page": "build_srr",
      "title": "Specify the stock-recruit relationship (SRR) for Rceattle",
      "topics": [
        "build_srr"
      ]
    },
    {
      "page": "check_mse",
      "title": "Check which saved MSE simulation files can be loaded",
      "topics": [
        "check_mse"
      ]
    },
    {
      "page": "clean_data",
      "title": "Default-fill and tidy a data list before fitting",
      "topics": [
        "clean_data"
      ]
    },
    {
      "page": "coef.Rceattle",
      "title": "Extract estimated parameters from an Rceattle fit",
      "topics": [
        "coef.Rceattle"
      ]
    },
    {
      "page": "combine_data",
      "title": "Combine two Rceattle data lists",
      "topics": [
        "combine_data"
      ]
    },
    {
      "page": "compare_sim",
      "title": "Evaluate simulation performance",
      "topics": [
        "compare_sim"
      ]
    },
    {
      "page": "convergence_diagnostics",
      "title": "Convergence diagnostics for a fitted Rceattle model",
      "topics": [
        "convergence_diagnostics"
      ]
    },
    {
      "page": "data_requirements",
      "title": "Report which data inputs a model configuration requires",
      "topics": [
        "data_requirements"
      ]
    },
    {
      "page": "EBS_ms_run",
      "title": "Fitted multispecies CEATTLE model for the Eastern Bering Sea",
      "topics": [
        "EBS_ms_run"
      ]
    },
    {
      "page": "EBS_ss_M_run",
      "title": "Fitted single-species CEATTLE model with estimated M for the Eastern Bering Sea",
      "topics": [
        "EBS_ss_M_run"
      ]
    },
    {
      "page": "EBS_ss_run",
      "title": "Fitted single-species CEATTLE model for the Eastern Bering Sea",
      "topics": [
        "EBS_ss_run"
      ]
    },
    {
      "page": "fit_control",
      "title": "Bundle the optimizer / sdreport / phasing controls for 'fit_mod()'",
      "topics": [
        "fit_control"
      ]
    },
    {
      "page": "fit_mod",
      "title": "Fit the CEATTLE assessment model",
      "topics": [
        "fit_mod"
      ]
    },
    {
      "page": "GeorgesBank3spp",
      "title": "Data inputs for a three-species Georges Bank CEATTLE model",
      "topics": [
        "GeorgesBank3spp"
      ]
    },
    {
      "page": "get_growth_matrix_r",
      "title": "Generate Length-at-Age Transition Matrix",
      "topics": [
        "get_growth_matrix_r"
      ]
    },
    {
      "page": "get_weight_at_age_r",
      "title": "Calculate Predicted Weight-at-Age",
      "topics": [
        "get_weight_at_age_r"
      ]
    },
    {
      "page": "GOA2018SS",
      "title": "Data inputs for a single-species Gulf of Alaska CEATTLE model (2018)",
      "topics": [
        "GOA2018SS"
      ]
    },
    {
      "page": "GOAatf",
      "title": "Data inputs for Gulf of Alaska arrowtooth flounder CEATTLE model",
      "topics": [
        "GOAatf"
      ]
    },
    {
      "page": "GOAatf2023",
      "title": "Data inputs for Gulf of Alaska arrowtooth flounder CEATTLE model (2023)",
      "topics": [
        "GOAatf2023"
      ]
    },
    {
      "page": "GOAcod",
      "title": "Data inputs for Gulf of Alaska Pacific cod CEATTLE model",
      "topics": [
        "GOAcod"
      ]
    },
    {
      "page": "GOApollock",
      "title": "Data inputs for Gulf of Alaska walleye pollock CEATTLE model",
      "topics": [
        "GOApollock"
      ]
    },
    {
      "page": "GOAsafe2018",
      "title": "Gulf of Alaska 2018 SAFE report reference values",
      "topics": [
        "GOAsafe2018"
      ]
    },
    {
      "page": "jitter",
      "title": "Jitter analysis",
      "topics": [
        "jitter"
      ]
    },
    {
      "page": "linkage_spec",
      "title": "Capture a linkage specification",
      "topics": [
        "linkage_spec"
      ]
    },
    {
      "page": "load_config",
      "title": "Load a model run configuration from a YAML file",
      "topics": [
        "load_config"
      ]
    },
    {
      "page": "load_mse",
      "title": "Load saved MSE simulation runs",
      "topics": [
        "load_mse"
      ]
    },
    {
      "page": "logLik.Rceattle",
      "title": "Log-likelihood of an Rceattle fit",
      "topics": [
        "logLik.Rceattle"
      ]
    },
    {
      "page": "model_average",
      "title": "Model average of derived quantities",
      "topics": [
        "model_average"
      ]
    },
    {
      "page": "model_config",
      "title": "Build a model-configuration slot for a data list",
      "topics": [
        "model_config"
      ]
    },
    {
      "page": "mse_summary",
      "title": "Management strategy evaluation performance metric summary",
      "topics": [
        "mse_summary"
      ]
    },
    {
      "page": "NorthernRockfish2022",
      "title": "Data inputs for Northern Rockfish CEATTLE model (2022)",
      "topics": [
        "NorthernRockfish2022"
      ]
    },
    {
      "page": "osa_diagnostics",
      "title": "Statistical diagnostics for OSA residuals",
      "topics": [
        "osa_diagnostics"
      ]
    },
    {
      "page": "osa_residuals",
      "title": "One-step-ahead (OSA) residuals for an Rceattle model",
      "topics": [
        "osa_residuals"
      ]
    },
    {
      "page": "parameter_dictionary",
      "title": "Look up what a CEATTLE parameter is",
      "topics": [
        "parameter_dictionary"
      ]
    },
    {
      "page": "parameter_index",
      "title": "Locate every estimated parameter in the model's own coordinates",
      "topics": [
        "parameter_index"
      ]
    },
    {
      "page": "plot_b_eaten",
      "title": "Plot biomass eaten by predation",
      "topics": [
        "plot_b_eaten"
      ]
    },
    {
      "page": "plot_b_eaten_prop",
      "title": "Plot biomass consumed of each prey species by predator",
      "topics": [
        "plot_b_eaten_prop"
      ]
    },
    {
      "page": "plot_biomass",
      "title": "Plot biomass",
      "topics": [
        "plot_biomass"
      ]
    },
    {
      "page": "plot_catch",
      "title": "Fishery catch fits",
      "topics": [
        "plot_catch"
      ]
    },
    {
      "page": "plot_catchability",
      "title": "Survey catchability over time",
      "topics": [
        "plot_catchability"
      ]
    },
    {
      "page": "plot_comp",
      "title": "Plot composition fits and residuals",
      "topics": [
        "plot_comp"
      ]
    },
    {
      "page": "plot_data",
      "title": "Timeline of data used in the model likelihoods",
      "topics": [
        "plot_data"
      ]
    },
    {
      "page": "plot_depletion",
      "title": "Plot biomass depletion",
      "topics": [
        "plot_depletion"
      ]
    },
    {
      "page": "plot_depletionSSB",
      "title": "Plot SSB depletion (deprecated name)",
      "topics": [
        "plot_depletionSSB"
      ]
    },
    {
      "page": "plot_diet_comp",
      "title": "Plot diet composition fits",
      "topics": [
        "plot_diet_comp"
      ]
    },
    {
      "page": "plot_diet_comp1",
      "title": "Plot diet composition fits (bubble/grid diagnostic)",
      "topics": [
        "plot_diet_comp1"
      ]
    },
    {
      "page": "plot_diet_comp2",
      "title": "Plot diet composition fits (aggregation-aware)",
      "topics": [
        "plot_diet_comp2"
      ]
    },
    {
      "page": "plot_exploitable_biomass",
      "title": "Plot exploitable biomass",
      "topics": [
        "plot_exploitable_biomass"
      ]
    },
    {
      "page": "plot_f",
      "title": "plot F",
      "topics": [
        "plot_f"
      ]
    },
    {
      "page": "plot_form",
      "title": "Plot functional form",
      "topics": [
        "plot_form"
      ]
    },
    {
      "page": "plot_index",
      "title": "Survey index fits",
      "topics": [
        "plot_index"
      ]
    },
    {
      "page": "plot_index_residual",
      "title": "Survey index residuals",
      "topics": [
        "plot_index_residual"
      ]
    },
    {
      "page": "plot_indexresidual",
      "title": "Plot survey index residuals (deprecated name)",
      "topics": [
        "plot_indexresidual"
      ]
    },
    {
      "page": "plot_m_at_age",
      "title": "Plot natural mortality by age",
      "topics": [
        "plot_m_at_age"
      ]
    },
    {
      "page": "plot_m2_at_age_prop",
      "title": "Plot predation mortality by age and predator",
      "topics": [
        "plot_m2_at_age_prop"
      ]
    },
    {
      "page": "plot_maturity",
      "title": "Plot maturity",
      "topics": [
        "plot_maturity"
      ]
    },
    {
      "page": "plot_mortality",
      "title": "Plot M1 or M2 at age",
      "topics": [
        "plot_mortality"
      ]
    },
    {
      "page": "plot_profile",
      "title": "Plot the likelihood components across a profile",
      "topics": [
        "plot_profile"
      ]
    },
    {
      "page": "plot_ration",
      "title": "Plot ration",
      "topics": [
        "plot_ration"
      ]
    },
    {
      "page": "plot_recruitment",
      "title": "Plot recruitment",
      "topics": [
        "plot_recruitment"
      ]
    },
    {
      "page": "plot_selectivity",
      "title": "Plot selectivity",
      "topics": [
        "plot_selectivity"
      ]
    },
    {
      "page": "plot_selectivity_vs_maturity",
      "title": "Plot fishery selectivity and maturity",
      "topics": [
        "plot_selectivity_vs_maturity"
      ]
    },
    {
      "page": "plot_ssb",
      "title": "Plot spawning stock biomass (SSB)",
      "topics": [
        "plot_ssb"
      ]
    },
    {
      "page": "plot_ssb_depletion",
      "title": "Plot SSB depletion",
      "topics": [
        "plot_ssb_depletion"
      ]
    },
    {
      "page": "plot_stock_recruit",
      "title": "Plot stock recruit function",
      "topics": [
        "plot_stock_recruit"
      ]
    },
    {
      "page": "plot_timeseries",
      "title": "Plot time-series",
      "topics": [
        "plot_timeseries"
      ]
    },
    {
      "page": "plot.Rceattle",
      "title": "Plot method for fitted Rceattle models",
      "topics": [
        "plot.Rceattle"
      ]
    },
    {
      "page": "plot.rceattle_osa",
      "title": "Plot one-step-ahead (OSA) residual diagnostics",
      "topics": [
        "plot.rceattle_osa"
      ]
    },
    {
      "page": "plot.Rceattle_profile",
      "title": "Plot method for a likelihood profile",
      "topics": [
        "plot.Rceattle_profile"
      ]
    },
    {
      "page": "print.Rceattle",
      "title": "Print method for fitted Rceattle models",
      "topics": [
        "print.Rceattle"
      ]
    },
    {
      "page": "print.Rceattle_data",
      "title": "Print method for an Rceattle data list",
      "topics": [
        "print.Rceattle_data",
        "summary.Rceattle_data"
      ]
    },
    {
      "page": "print.Rceattle_jitter",
      "title": "Print method for a jitter analysis",
      "topics": [
        "print.Rceattle_jitter"
      ]
    },
    {
      "page": "print.Rceattle_mse_summary",
      "title": "Print method for an MSE summary",
      "topics": [
        "print.Rceattle_mse_summary"
      ]
    },
    {
      "page": "print.Rceattle_profile",
      "title": "Print method for a likelihood profile",
      "topics": [
        "print.Rceattle_profile"
      ]
    },
    {
      "page": "print.rceattle_report",
      "title": "Print method for a set of assessment reporting tables",
      "topics": [
        "print.rceattle_report"
      ]
    },
    {
      "page": "print.Rceattle_retro",
      "title": "Print method for a retrospective analysis",
      "topics": [
        "print.Rceattle_retro"
      ]
    },
    {
      "page": "print.Rceattle_selftest",
      "title": "Print method for a self-test",
      "topics": [
        "print.Rceattle_selftest"
      ]
    },
    {
      "page": "print.summary.Rceattle",
      "title": "Print method for an Rceattle model summary",
      "topics": [
        "print.summary.Rceattle"
      ]
    },
    {
      "page": "prior_beta",
      "title": "Beta prior on a linkage coefficient",
      "topics": [
        "prior_beta"
      ]
    },
    {
      "page": "prior_gamma",
      "title": "Gamma prior on a linkage coefficient",
      "topics": [
        "prior_gamma"
      ]
    },
    {
      "page": "prior_lognormal",
      "title": "Lognormal prior on a linkage coefficient",
      "topics": [
        "prior_lognormal"
      ]
    },
    {
      "page": "prior_normal",
      "title": "Normal prior on a linkage coefficient",
      "topics": [
        "prior_normal"
      ]
    },
    {
      "page": "process_residuals",
      "title": "Process residuals for an Rceattle model's random-effect processes",
      "topics": [
        "process_residuals"
      ]
    },
    {
      "page": "profile_components",
      "title": "Likelihood components along a profile",
      "topics": [
        "profile_components"
      ]
    },
    {
      "page": "profile.Rceattle",
      "title": "Likelihood profile across one or more parameter cells",
      "topics": [
        "profile.Rceattle"
      ]
    },
    {
      "page": "quantity_dictionary",
      "title": "Look up what a CEATTLE reported quantity is",
      "topics": [
        "quantity_dictionary"
      ]
    },
    {
      "page": "rceattle-plot-args",
      "title": "Shared plotting arguments",
      "topics": [
        "rceattle-plot-args"
      ]
    },
    {
      "page": "rceattle-refit-args",
      "title": "Shared refit-diagnostic arguments",
      "topics": [
        "rceattle-refit-args"
      ]
    },
    {
      "page": "read_data",
      "title": "Read a CEATTLE excel data file",
      "topics": [
        "read_data"
      ]
    },
    {
      "page": "rearrange_data",
      "title": "Rearrange a data_list for TMB",
      "topics": [
        "rearrange_dat",
        "rearrange_data"
      ]
    },
    {
      "page": "remove_F",
      "title": "Rerun with F = 0.",
      "topics": [
        "remove_F"
      ]
    },
    {
      "page": "rename_output",
      "title": "Label the derived quantities reported by a CEATTLE fit",
      "topics": [
        "rename_output"
      ]
    },
    {
      "page": "report_tables",
      "title": "Assessment reporting tables from one or more Rceattle fits",
      "topics": [
        "report_tables"
      ]
    },
    {
      "page": "residuals.Rceattle",
      "title": "Residuals from an Rceattle fit",
      "topics": [
        "residuals.Rceattle"
      ]
    },
    {
      "page": "retrospective",
      "title": "Retrospective peels",
      "topics": [
        "retrospective"
      ]
    },
    {
      "page": "reweight_comps",
      "title": "Iteratively reweight composition data (McAllister-Ianelli)",
      "topics": [
        "reweight_comps"
      ]
    },
    {
      "page": "rich.colors.short",
      "title": "Make a vector of colors.",
      "topics": [
        "rich.colors.short"
      ]
    },
    {
      "page": "run_config",
      "title": "Extract the run configuration from a fit, data list, or config object",
      "topics": [
        "run_config"
      ]
    },
    {
      "page": "run_mse",
      "title": "Run a management strategy evaluation",
      "topics": [
        "run_mse"
      ]
    },
    {
      "page": "sample_rec",
      "title": "Sample historical recruitment deviations into the projection",
      "topics": [
        "sample_rec"
      ]
    },
    {
      "page": "save_config",
      "title": "Save a model run configuration to a documented YAML file",
      "topics": [
        "save_config"
      ]
    },
    {
      "page": "self_test",
      "title": "Self-test simulation analysis",
      "topics": [
        "self_test"
      ]
    },
    {
      "page": "set_phases",
      "title": "Default phasing order for CEATTLE parameters",
      "topics": [
        "set_phases"
      ]
    },
    {
      "page": "sim_mod",
      "title": "Simulate Rceattle data",
      "topics": [
        "sim_mod"
      ]
    },
    {
      "page": "simulate.Rceattle",
      "title": "Simulate data from a fitted Rceattle model",
      "topics": [
        "simulate.Rceattle"
      ]
    },
    {
      "page": "standard_output",
      "title": "Rceattle output in the NOAA standardized assessment format",
      "topics": [
        "standard_output"
      ]
    },
    {
      "page": "summary.Rceattle",
      "title": "Compact summary method for Rceattle fits",
      "topics": [
        "summary.Rceattle"
      ]
    },
    {
      "page": "switch_check",
      "title": "Function to check for missing switches for map and parameter functions",
      "topics": [
        "switch_check"
      ]
    },
    {
      "page": "TMBAIC",
      "title": "Calculate marginal AIC for a fitted model",
      "topics": [
        "TMBAIC"
      ]
    },
    {
      "page": "TMBphase",
      "title": "Run TMB with ADMB-style phased estimation",
      "topics": [
        "TMBphase"
      ]
    },
    {
      "page": "vcov.Rceattle",
      "title": "Variance-covariance matrix for an Rceattle fit",
      "topics": [
        "vcov.Rceattle"
      ]
    },
    {
      "page": "whamGrowthData",
      "title": "Data inputs for CEATTLE model with WHAM-estimated growth",
      "topics": [
        "whamGrowthData"
      ]
    },
    {
      "page": "write_data",
      "title": "Write a data list to a CEATTLE xlsx workbook",
      "topics": [
        "write_data"
      ]
    },
    {
      "page": "write_template",
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        "msmMode, single-species vs. multi-species",
        "initMode, initial age structure",
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        "estimateMode, what does fit_mod() actually do?",
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        "A snapshot-timed index on a fishery's selectivity",
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        "Age-to-length transition matrix",
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        "Fixed selectivity (optional)",
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        "10. Export back to Excel (optional)",
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