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  "Package": "cpueTargeting",
  "Title": "Simulators and Tools for CPUE Targeting and Standardization",
  "Version": "0.4.0",
  "Authors@R": "person(\"Henning\", \"Winker\", role = c(\"aut\", \"cre\"),\nemail = \"henning.winker@fao.org\")",
  "Description": "Multispecies operating models for exploring spatial and\nvertical targeting and catch-per-unit-effort standardization.\nIncludes the multi-habitat cluster example of Winker et al.\n(2014), the four-species bathymetric Run 22 model based on the\nspatial simulator of Thorson et al. (2017)\n<doi:10.1139/cjfas-2015-0598> and Ono et al. (2015)\n<doi:10.1016/j.fishres.2015.05.021>, and its extension to a\nlongline tuna fishery with species vertical distributions and\nhook depth by hooks-between-floats, following the habitat-based\napproach of Bigelow et al. (2002). Provides a step-by-step\ntoolbox for real catch and effort data: data formatting,\ncumulative species curves, fleet and catch composition\nexploration, habitat-based subsetting (Stephens and MacCall\n2004), and targeting covariates from the catch composition\n(principal components with the Optimal Coordinates test, and\nclustering into fishing tactics).",
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  "Repository": "https://henning-winker.r-universe.dev",
  "Date/Publication": "2026-10-14 12:05:18 UTC",
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  "Author": "Henning Winker [aut, cre]",
  "Maintainer": "Henning Winker <henning.winker@fao.org>",
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  "_exports": [
    "add_targeting",
    "as_set_data",
    "bathymetric_settings",
    "bind_comparisons",
    "cluster_tactics",
    "composition_pca",
    "compute_oc",
    "cpue_data",
    "cpue_diagnostics",
    "cpue_index",
    "cpue_matrix",
    "export_index",
    "fit_cpue",
    "influence_cpue",
    "logbook_settings",
    "logbook_truth",
    "nominal_cpue",
    "plot_availability",
    "plot_biplot",
    "plot_cluster_2014",
    "plot_clusters",
    "plot_composition",
    "plot_cpue_map",
    "plot_diagnostics",
    "plot_effects",
    "plot_fleet",
    "plot_index",
    "plot_indices",
    "plot_influence",
    "plot_logbook_om",
    "plot_nominal",
    "plot_oc",
    "plot_om",
    "plot_pcs",
    "plot_replicates",
    "plot_residuals",
    "plot_sections",
    "plot_species_curve",
    "plot_step",
    "plot_stephens_maccall",
    "plot_targeting",
    "plot_thermocline",
    "plot_thermocline_effect",
    "plot_tuna_vertical_distributions",
    "plot_vessel_effects",
    "plot_vessel_profile",
    "ppc_cpue",
    "read_replicates",
    "run_replicates",
    "select_models",
    "select_species",
    "select_tactics",
    "select_vessels",
    "simulate_bathymetric",
    "simulate_cluster",
    "simulate_logbook",
    "simulate_tuna",
    "species_curve",
    "standardize_cpue",
    "standardize_tuna_indices",
    "stephens_maccall",
    "tactic_table",
    "tuna_settings",
    "vessel_summary"
  ],
  "_help": [
    {
      "page": "add_targeting",
      "title": "Add targeting covariates: PC scores and fishing tactics",
      "topics": [
        "add_targeting"
      ]
    },
    {
      "page": "as_set_data",
      "title": "Reshape set-by-species records (long) to one row per set",
      "topics": [
        "as_set_data"
      ]
    },
    {
      "page": "bathymetric_settings",
      "title": "Default settings for the four-species bathymetric scenario (Run 22)",
      "topics": [
        "bathymetric_settings"
      ]
    },
    {
      "page": "bind_comparisons",
      "title": "Combine several standardisation results into one",
      "topics": [
        "bind_comparisons"
      ]
    },
    {
      "page": "cluster_tactics",
      "title": "Cluster operations into fishing tactics",
      "topics": [
        "cluster_tactics"
      ]
    },
    {
      "page": "composition_pca",
      "title": "Principal components of the catch composition",
      "topics": [
        "composition_pca"
      ]
    },
    {
      "page": "compute_oc",
      "title": "Optimal Coordinates test for the number of non-trivial components",
      "topics": [
        "compute_oc"
      ]
    },
    {
      "page": "cpue_data",
      "title": "Prepare catch and effort data for analysis",
      "topics": [
        "cpue_data"
      ]
    },
    {
      "page": "cpue_diagnostics",
      "title": "Compare fitted CPUE models",
      "topics": [
        "cpue_diagnostics"
      ]
    },
    {
      "page": "cpue_index",
      "title": "Standardised index table",
      "topics": [
        "cpue_index"
      ]
    },
    {
      "page": "cpue_matrix",
      "title": "CPUE of each operation",
      "topics": [
        "cpue_matrix"
      ]
    },
    {
      "page": "export_index",
      "title": "Write the standardised index to a CSV file",
      "topics": [
        "export_index"
      ]
    },
    {
      "page": "fit_cpue",
      "title": "Standardise CPUE for one species with mgcv",
      "topics": [
        "fit_cpue"
      ]
    },
    {
      "page": "influence_cpue",
      "title": "Influence of each model term on the index",
      "topics": [
        "influence_cpue"
      ]
    },
    {
      "page": "logbook_settings",
      "title": "Default settings for the logbook simulator",
      "topics": [
        "logbook_settings"
      ]
    },
    {
      "page": "logbook_truth",
      "title": "True relative biomass of one species from simulate_logbook()",
      "topics": [
        "logbook_truth"
      ]
    },
    {
      "page": "nominal_cpue",
      "title": "Nominal CPUE by year",
      "topics": [
        "nominal_cpue"
      ]
    },
    {
      "page": "plot_availability",
      "title": "Vertical availability by HBF over time",
      "topics": [
        "plot_availability"
      ]
    },
    {
      "page": "plot_biplot",
      "title": "PCA biplot of the catch composition",
      "topics": [
        "plot_biplot"
      ]
    },
    {
      "page": "plot_cluster_2014",
      "title": "Plot the 2014 cluster simulation",
      "topics": [
        "plot_cluster_2014"
      ]
    },
    {
      "page": "plot_clusters",
      "title": "What do the catch-composition clusters capture?",
      "topics": [
        "plot_clusters"
      ]
    },
    {
      "page": "plot_composition",
      "title": "Plot the catch composition over time",
      "topics": [
        "plot_composition"
      ]
    },
    {
      "page": "plot_cpue_map",
      "title": "Map of operations and CPUE",
      "topics": [
        "plot_cpue_map"
      ]
    },
    {
      "page": "plot_diagnostics",
      "title": "Compare the accuracy of standardised indices",
      "topics": [
        "plot_diagnostics"
      ]
    },
    {
      "page": "plot_effects",
      "title": "Partial effects of the covariates",
      "topics": [
        "plot_effects"
      ]
    },
    {
      "page": "plot_fleet",
      "title": "Overview of the fleet and the records",
      "topics": [
        "plot_fleet"
      ]
    },
    {
      "page": "plot_index",
      "title": "Plot standardised indices",
      "topics": [
        "plot_index"
      ]
    },
    {
      "page": "plot_indices",
      "title": "Plot standardised indices against the true biomass trend",
      "topics": [
        "plot_indices"
      ]
    },
    {
      "page": "plot_influence",
      "title": "Plot the influence of each model term",
      "topics": [
        "plot_influence"
      ]
    },
    {
      "page": "plot_logbook_om",
      "title": "Diagnostic plots of the logbook simulator",
      "topics": [
        "plot_logbook_om"
      ]
    },
    {
      "page": "plot_nominal",
      "title": "Plot nominal CPUE",
      "topics": [
        "plot_nominal"
      ]
    },
    {
      "page": "plot_oc",
      "title": "Plot the scree and the Optimal Coordinates test",
      "topics": [
        "plot_oc"
      ]
    },
    {
      "page": "plot_om",
      "title": "Diagnostic plots for an operating-model run",
      "topics": [
        "plot_om"
      ]
    },
    {
      "page": "plot_pcs",
      "title": "What do the principal components of the catch composition capture?",
      "topics": [
        "plot_pcs"
      ]
    },
    {
      "page": "plot_replicates",
      "title": "Accuracy of standardised indices across replicates",
      "topics": [
        "plot_replicates"
      ]
    },
    {
      "page": "plot_residuals",
      "title": "Residual diagnostics",
      "topics": [
        "plot_residuals"
      ]
    },
    {
      "page": "plot_sections",
      "title": "Species distributions in three dimensions: sections and depth layers",
      "topics": [
        "plot_sections"
      ]
    },
    {
      "page": "plot_species_curve",
      "title": "Plot the cumulative species curve",
      "topics": [
        "plot_species_curve"
      ]
    },
    {
      "page": "plot_step",
      "title": "Step plot of the standardisation",
      "topics": [
        "plot_step"
      ]
    },
    {
      "page": "plot_stephens_maccall",
      "title": "Diagnostic plots for Stephens and MacCall subsetting",
      "topics": [
        "plot_stephens_maccall"
      ]
    },
    {
      "page": "plot_targeting",
      "title": "What the targeting covariates capture",
      "topics": [
        "plot_targeting"
      ]
    },
    {
      "page": "plot_thermocline",
      "title": "Plot the thermocline anomaly",
      "topics": [
        "plot_thermocline"
      ]
    },
    {
      "page": "plot_thermocline_effect",
      "title": "Show how a thermocline shift moves species relative to the hooks",
      "topics": [
        "plot_thermocline_effect"
      ]
    },
    {
      "page": "plot_tuna_vertical_distributions",
      "title": "Plot species vertical profiles and hook-depth profiles by HBF",
      "topics": [
        "plot_tuna_vertical_distributions"
      ]
    },
    {
      "page": "plot_vessel_effects",
      "title": "Plot the random vessel effects",
      "topics": [
        "plot_vessel_effects"
      ]
    },
    {
      "page": "plot_vessel_profile",
      "title": "Catch profile of each vessel",
      "topics": [
        "plot_vessel_profile"
      ]
    },
    {
      "page": "ppc_cpue",
      "title": "Predictive check of the error distribution",
      "topics": [
        "ppc_cpue"
      ]
    },
    {
      "page": "read_replicates",
      "title": "Read replicate results saved one file per seed",
      "topics": [
        "read_replicates"
      ]
    },
    {
      "page": "run_replicates",
      "title": "Run scenarios over several seeds (replicates)",
      "topics": [
        "run_replicates"
      ]
    },
    {
      "page": "schaefer_update",
      "title": "The growth rate 'r' has one value per species and is applied by column. (The original code multiplied 'B' by 'r' directly, which recycles 'r' over cells rather than species.)",
      "topics": [
        "schaefer_update"
      ]
    },
    {
      "page": "select_models",
      "title": "Keep only some models of a standardisation result",
      "topics": [
        "select_models"
      ]
    },
    {
      "page": "select_species",
      "title": "Select the main species",
      "topics": [
        "select_species"
      ]
    },
    {
      "page": "select_tactics",
      "title": "Keep or drop fishing tactics and recompute the targeting covariates",
      "topics": [
        "select_tactics"
      ]
    },
    {
      "page": "select_vessels",
      "title": "Select core (indicator) vessels",
      "topics": [
        "select_vessels"
      ]
    },
    {
      "page": "simulate_bathymetric",
      "title": "Simulate the four-species bathymetric Run 22 scenario",
      "topics": [
        "simulate_bathymetric"
      ]
    },
    {
      "page": "simulate_cluster",
      "title": "Simulate the 2014 multi-habitat cluster scenario",
      "topics": [
        "simulate_cluster"
      ]
    },
    {
      "page": "simulate_logbook",
      "title": "Simulate a realistic multispecies logbook",
      "topics": [
        "simulate_logbook"
      ]
    },
    {
      "page": "simulate_tuna",
      "title": "Simulate a longline fishery for four tuna species with vertical targeting",
      "topics": [
        "simulate_tuna"
      ]
    },
    {
      "page": "species_curve",
      "title": "Cumulative species curve",
      "topics": [
        "species_curve"
      ]
    },
    {
      "page": "standardize_cpue",
      "title": "Standardise simulated CPUE with alternative targeting covariates",
      "topics": [
        "standardize_cpue",
        "standardize_tuna_indices"
      ]
    },
    {
      "page": "stephens_maccall",
      "title": "Select operations likely to have fished the habitat of a target species",
      "topics": [
        "stephens_maccall"
      ]
    },
    {
      "page": "subset.cpue_data",
      "title": "Keep a subset of operations",
      "topics": [
        "subset.cpue_data"
      ]
    },
    {
      "page": "tactic_table",
      "title": "Species composition of each fishing tactic",
      "topics": [
        "tactic_table"
      ]
    },
    {
      "page": "tuna_settings",
      "title": "Default settings for the longline tuna scenario",
      "topics": [
        "tuna_settings"
      ]
    },
    {
      "page": "vessel_summary",
      "title": "Summary of each vessel's activity and catches of target species",
      "topics": [
        "vessel_summary"
      ]
    }
  ],
  "_readme": "https://github.com/Henning-Winker/cpueTargeting/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "farver",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "R6",
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    "rlang",
    "S7",
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    {
      "source": "real-data-guide.Rmd",
      "filename": "real-data-guide.html",
      "title": "Analysing real catch and effort data: a step-by-step guide",
      "author": "Henning WinkerFAO Fisheries and Aquaculture Division, Assessment and Management Team (NFIFM)henning.winker@fao.org",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Example data",
        "Step 1. Format the data",
        "Step 2. Explore the fleet",
        "Step 3. Choose the species set",
        "Step 4. Nominal CPUE and catch composition",
        "Step 5. Habitat-based subsetting (optional)",
        "Step 6. Targeting covariates from the catch composition",
        "How many PCs?",
        "What do the PCs and clusters represent?",
        "Removing irrelevant tactics (optional)",
        "Step 7. Fit the standardisation models",
        "Step 8. Diagnostics",
        "Model comparison",
        "Indices and steps",
        "Influence",
        "Residuals, effects and vessels",
        "Predictive check of the error distribution",
        "Step 9. The final index",
        "Processing log",
        "Reporting checklist",
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      ],
      "created": "2026-10-13 23:42:55",
      "modified": "2026-10-14 12:00:38",
      "commits": 2
    },
    {
      "source": "logbook-om-guide.Rmd",
      "filename": "logbook-om-guide.html",
      "title": "Setting up the logbook simulator: a user guide",
      "author": "Henning WinkerFAO Fisheries and Aquaculture Division, Assessment and Management Team (NFIFM)henning.winker@fao.org",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1. Settings",
        "2. Environment",
        "3. Species and habitats",
        "4. Tactics",
        "5. Fleet: specialists, mixed vessels and loyalty",
        "6. Prices, closure and fleet changes",
        "7. Reporting: from sets to a logbook",
        "8. Basic mechanics: what the PCs and clusters capture",
        "PCs against tactic and habitat",
        "PCs against depth and the true position",
        "Mixed trips lie between the clusters",
        "Clusters against the true tactic",
        "Targeting over time",
        "Vessel profiles against the true vessel type",
        "Things to try",
        "References"
      ],
      "created": "2026-10-14 12:00:38",
      "modified": "2026-10-14 12:00:38",
      "commits": 1
    },
    {
      "source": "logbook-example.Rmd",
      "filename": "logbook-example.html",
      "title": "Standardising a realistic logbook: two worked examples",
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      "headings": [
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        "Step 2. Explore the fleet",
        "Step 3. Choose the species set",
        "Step 4. Nominal CPUE and catch composition",
        "Step 6. Targeting covariates for the whole fleet",
        "Part 2. Worked example: blackspot seabream",
        "Step 5. Remove the trips that could not catch seabream",
        "Step 6. Targeting covariates of the demersal trips",
        "Step 7. Fit the models",
        "Step 8. Diagnostics",
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        "Influence",
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        "Predictive check of the error distribution",
        "Effects and vessels",
        "Sensitivity to the data selection",
        "Step 9. The index",
        "Part 3. Worked example: dolphinfish",
        "Step 5. Keep the pelagic trips",
        "Step 6. Targeting covariates of the pelagic trips",
        "Influence and residuals",
        "Predictive check by month and by year",
        "Error distribution: Tweedie or delta-lognormal?",
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      "title": "Targeting along a continuous gradient: the bathymetric example",
      "author": "Henning WinkerFAO Fisheries and Aquaculture Division, Assessment and Management Team (NFIFM)henning.winker@fao.org",
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      "author": "Henning WinkerFAO Fisheries and Aquaculture Division, Assessment and Management Team (NFIFM)henning.winker@fao.org",
      "engine": "knitr::rmarkdown",
      "headings": [
        "The operating model in brief",
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        "Targeting through prices",
        "Species habitat",
        "Longline gear",
        "Environment",
        "Fleet and data",
        "Step 1: define the scenarios",
        "Step 2: simulate",
        "Step 3: the environment",
        "Step 4: why the thermocline matters for HBF",
        "Step 5: how the fishery responds",
        "Gear use",
        "Vertical availability by HBF",
        "Nominal CPUE versus true biomass",
        "Step 6: standardise",
        "Step 7: compare the indices with the truth",
        "Indices",
        "Accuracy",
        "What to look for",
        "Step 8: what do the principal components capture?",
        "Replicates: is the ranking robust?",
        "Optional: with or without space, and at what resolution",
        "Optional: interactions with year",
        "A note on habitat-based standardisation",
        "References"
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      "source": "tuna-flat-vs-contrast.Rmd",
      "filename": "tuna-flat-vs-contrast.html",
      "title": "Tuna longline targeting: flat versus contrasting true trends",
      "author": "Henning WinkerFAO Fisheries and Aquaculture Division, Assessment and Management Team (NFIFM)henning.winker@fao.org",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Settings",
        "Nominal CPUE versus the truth",
        "Standardised indices",
        "What do the PCs capture?",
        "What do the clusters capture?",
        "Replicates: flat versus contrasting trends",
        "What to take from this"
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