{
  "_id": "6a106986acfb0bcc41ca9a93",
  "Package": "fb4package",
  "Type": "Package",
  "Title": "'Fish Bioenergetics 4.0' Model Implementation with\nHigh-Performance 'TMB' Backend",
  "Version": "2.0.0",
  "Authors@R": "c(\nperson(\n\"Hans\", \"Ttito\",\nemail = \"kvttitos@gmail.com\",\nrole = c(\"aut\", \"cre\")\n)\n)",
  "Description": "An implementation of the 'Fish Bioenergetics 4.0'\nframework described in Deslauriers et al. (2017)\n<doi:10.1080/03632415.2017.1377558>. Provides automated\nparameter optimization, multi-prey diet modeling, and\ncomprehensive energy budget simulations for fisheries research\nand aquaculture applications. An optional 'TMB' (Template Model\nBuilder) backend delivers 10-50x speedup in maximum likelihood\nestimation while maintaining full backward compatibility.\nIncludes species-specific parameter databases and tools for\nmodeling fish growth, consumption, and metabolism under varying\nenvironmental conditions.",
  "URL": "https://hansttito.github.io/fb4package/,\nhttps://github.com/HansTtito/fb4package",
  "BugReports": "https://github.com/HansTtito/fb4package/issues",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "RoxygenNote": "7.3.2",
  "Language": "en-US",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-07 23:16:30 UTC",
    "User": "root"
  },
  "Author": "Hans Ttito [aut, cre]",
  "Maintainer": "Hans Ttito <kvttitos@gmail.com>",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-05-07 22:31:36 UTC",
  "RemoteUrl": "https://github.com/cran/fb4package",
  "RemoteRef": "HEAD",
  "RemoteSha": "213002fbe50b0c1e3e350f62936676b5ac2a87db",
  "MD5sum": "04c50365888e214724ec705b85af692c",
  "_user": "cran",
  "_type": "src",
  "_file": "fb4package_2.0.0.tar.gz",
  "_fileid": "dd3941a8dba395ca9014c80bff0c33dc6f0a31c2a2ad40775b99d3f2dba529ba",
  "_filesize": 2700074,
  "_sha256": "dd3941a8dba395ca9014c80bff0c33dc6f0a31c2a2ad40775b99d3f2dba529ba",
  "_created": "2026-05-07T23:16:30.000Z",
  "_published": "2026-05-22T14:34:46.844Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77401018437,
      "time": 225,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6868542158"
    },
    {
      "job": 77401018649,
      "time": 223,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6868542434"
    },
    {
      "job": 77401018506,
      "time": 213,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6868539628"
    },
    {
      "job": 77401018336,
      "time": 229,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6868543695"
    },
    {
      "job": 77401018031,
      "time": 445,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6868494854"
    },
    {
      "job": 77401017683,
      "time": 120,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7163085456"
    }
  ],
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/25526715835",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/fb4package",
  "_commit": {
    "id": "213002fbe50b0c1e3e350f62936676b5ac2a87db",
    "author": "Hans Ttito <kvttitos@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 2.0.0\n",
    "time": 1778193096
  },
  "_maintainer": {
    "name": "Hans Ttito",
    "email": "kvttitos@gmail.com",
    "login": "hansttito",
    "linkedin": "in/hansttito",
    "uuid": 120611082
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "TMB",
      "role": "LinkingTo"
    },
    {
      "package": "RcppEigen",
      "role": "LinkingTo"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "TMB",
      "version": ">= 1.7.0",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "pkgdown",
      "role": "Suggests"
    },
    {
      "package": "microbenchmark",
      "role": "Suggests"
    },
    {
      "package": "future",
      "role": "Suggests"
    },
    {
      "package": "furrr",
      "role": "Suggests"
    },
    {
      "package": "spelling",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-19",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "2.0.0",
      "date": "2026-05-07"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "hansttito",
      "count": 1,
      "uuid": 120611082
    }
  ],
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/fb4package"
  },
  "_devurl": "https://github.com/hansttito/fb4package",
  "_pkgdown": "https://hansttito.github.io/fb4package/",
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/fb4package.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_releases": [
    {
      "version": "2.0.0",
      "date": "2026-05-07"
    }
  ],
  "_exports": [
    "accumulate_validations",
    "analyze_composition_by_size",
    "analyze_composition_changes",
    "analyze_energy_budget",
    "analyze_feeding_performance",
    "analyze_growth_patterns",
    "analyze_growth_temperature_sensitivity",
    "analyze_population_variation",
    "assess_diet_quality",
    "Bioenergetic",
    "calculate_body_composition",
    "calculate_confidence_intervals",
    "calculate_consumption",
    "calculate_contaminant_accumulation",
    "calculate_egestion",
    "calculate_excretion",
    "calculate_final_weight_fb4",
    "calculate_mortality_reproduction",
    "calculate_np_ratios",
    "calculate_nutrient_balance",
    "calculate_nutrient_efficiencies",
    "calculate_predator_energy_density",
    "calculate_respiration",
    "calculate_stoichiometric_balance",
    "check_numeric_value",
    "clamp",
    "compare_individuals",
    "compare_scenarios",
    "compare_with_redfield",
    "comprehensive_nutritional_analysis",
    "create_empty_composition",
    "create_result_summary",
    "get_consumption_uncertainty",
    "get_efficiency_uncertainty",
    "get_energy_budget_uncertainty",
    "get_individual_results",
    "get_parameter_value",
    "get_population_results",
    "interpolate_time_series",
    "is.Bioenergetic",
    "is.fb4_result",
    "plot_distributions.fb4_result",
    "plot_growth_temperature_sensitivity",
    "plot_sensitivity.fb4_result",
    "plot_uncertainty.fb4_result",
    "predict_consumption_bootstrap",
    "predict_consumption_delta",
    "prepare_simulation_data",
    "process_bioenergetic_data",
    "process_composition_params",
    "process_consumption_params",
    "process_contaminant_params",
    "process_egestion_params",
    "process_excretion_params",
    "process_mortality_params",
    "process_nutrient_params",
    "process_predator_params",
    "process_respiration_params",
    "process_simulation_settings",
    "process_species_parameters",
    "run_fb4",
    "run_fb4_simulation",
    "safe_exp",
    "safe_sqrt",
    "set_diet",
    "set_environment",
    "set_parameter_value",
    "set_simulation_settings",
    "update_body_composition",
    "validate_basic_params",
    "validate_bioenergetic_for_simulation",
    "validate_body_composition",
    "validate_complete_simulation_data",
    "validate_contaminant_params",
    "validate_data_consistency",
    "validate_diet_consistency",
    "validate_equation_params",
    "validate_fb4_inputs",
    "validate_fb4_system",
    "validate_fitting_settings",
    "validate_fraction",
    "validate_individual_data",
    "validate_nutrient_concentrations",
    "validate_positive",
    "validate_predator_energy_params",
    "validate_species_equations",
    "validate_temperature",
    "validate_temporal_data",
    "validate_time_series_data",
    "validation_result"
  ],
  "_datasets": [
    {
      "name": "fish4_parameters",
      "title": "Fish Bioenergetics 4.0 Official Parameters Database",
      "object": "fish4_parameters",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "fish4_parameters_metadata",
      "title": "Fish Bioenergetics 4.0 Parameters Database Metadata",
      "object": "fish4_parameters",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "accumulate_validations",
      "title": "Accumulate multiple validation results",
      "topics": [
        "accumulate_validations"
      ]
    },
    {
      "page": "analysis-core",
      "title": "Core Analysis Functions for FB4 Results",
      "topics": [
        "analysis-core"
      ]
    },
    {
      "page": "analysis-extraction",
      "title": "Basic Analysis and Extraction Functions for FB4 Results",
      "topics": [
        "analysis-extraction"
      ]
    },
    {
      "page": "analysis-nutritional",
      "title": "Nutritional Analysis Functions for FB4 Results",
      "topics": [
        "analysis-nutritional"
      ]
    },
    {
      "page": "analysis-sensitivity",
      "title": "Sensitivity and Comparative Analysis Functions for FB4 Results",
      "topics": [
        "analysis-sensitivity"
      ]
    },
    {
      "page": "analyze_composition_by_size",
      "title": "Analyze body composition by size range",
      "topics": [
        "analyze_composition_by_size"
      ]
    },
    {
      "page": "analyze_composition_changes",
      "title": "Analyze composition changes with growth",
      "topics": [
        "analyze_composition_changes"
      ]
    },
    {
      "page": "analyze_energy_budget",
      "title": "Analyze energy budget from FB4 results",
      "topics": [
        "analyze_energy_budget"
      ]
    },
    {
      "page": "analyze_feeding_performance",
      "title": "Analyze feeding performance from FB4 results",
      "topics": [
        "analyze_feeding_performance"
      ]
    },
    {
      "page": "analyze_growth_patterns",
      "title": "Analyze growth patterns from FB4 results",
      "topics": [
        "analyze_growth_patterns"
      ]
    },
    {
      "page": "analyze_growth_temperature_sensitivity",
      "title": "Analyze growth rate sensitivity to temperature and feeding levels",
      "topics": [
        "analyze_growth_temperature_sensitivity"
      ]
    },
    {
      "page": "analyze_population_variation",
      "title": "Analyze population variation in hierarchical models",
      "topics": [
        "analyze_population_variation"
      ]
    },
    {
      "page": "assess_diet_quality",
      "title": "Assess nutritional quality of diet",
      "topics": [
        "assess_diet_quality"
      ]
    },
    {
      "page": "basic-validators",
      "title": "Basic Validation Functions for FB4",
      "topics": [
        "basic-validators"
      ]
    },
    {
      "page": "Bioenergetic",
      "title": "Constructor for Bioenergetic Objects",
      "topics": [
        "Bioenergetic"
      ]
    },
    {
      "page": "bioenergetic-classes",
      "title": "S3 Classes for FB4 Bioenergetic Model",
      "topics": [
        "bioenergetic-classes"
      ]
    },
    {
      "page": "bioenergetic-methods",
      "title": "Methods for FB4 Bioenergetic Model",
      "topics": [
        "bioenergetic-methods"
      ]
    },
    {
      "page": "body-composition",
      "title": "Body Composition Functions for FB4 Model",
      "topics": [
        "body-composition"
      ]
    },
    {
      "page": "calculate_body_composition",
      "title": "Calculate complete body composition (Mid-level - Main function)",
      "topics": [
        "calculate_body_composition"
      ]
    },
    {
      "page": "calculate_consumption",
      "title": "Calculate daily consumption (Mid-level - Main function)",
      "topics": [
        "calculate_consumption"
      ]
    },
    {
      "page": "calculate_contaminant_accumulation",
      "title": "Calculate contaminant accumulation (Mid-level - Main function)",
      "topics": [
        "calculate_contaminant_accumulation"
      ]
    },
    {
      "page": "calculate_egestion",
      "title": "Calculate daily egestion (Mid-level - Main function)",
      "topics": [
        "calculate_egestion"
      ]
    },
    {
      "page": "calculate_excretion",
      "title": "Calculate daily excretion (Mid-level - Main function)",
      "topics": [
        "calculate_excretion"
      ]
    },
    {
      "page": "calculate_final_weight_fb4",
      "title": "Calculate final weight using FB4 equations (Mid-level)",
      "topics": [
        "calculate_final_weight_fb4"
      ]
    },
    {
      "page": "calculate_mortality_reproduction",
      "title": "Calculate daily mortality and reproduction (Mid-level - Main function)",
      "topics": [
        "calculate_mortality_reproduction"
      ]
    },
    {
      "page": "calculate_np_ratios",
      "title": "Calculate N:P ratios for all processes",
      "topics": [
        "calculate_np_ratios"
      ]
    },
    {
      "page": "calculate_nutrient_balance",
      "title": "Calculate nutrient balance (Mid-level - Main function)",
      "topics": [
        "calculate_nutrient_balance"
      ]
    },
    {
      "page": "calculate_nutrient_efficiencies",
      "title": "Calculate nutrient retention efficiencies",
      "topics": [
        "calculate_nutrient_efficiencies"
      ]
    },
    {
      "page": "calculate_predator_energy_density",
      "title": "Calculate predator energy density (Mid-level - Main function)",
      "topics": [
        "calculate_predator_energy_density"
      ]
    },
    {
      "page": "calculate_respiration",
      "title": "Calculate daily respiration (Mid-level - Main function)",
      "topics": [
        "calculate_respiration"
      ]
    },
    {
      "page": "calculate_stoichiometric_balance",
      "title": "Calculate stoichiometric balance",
      "topics": [
        "calculate_stoichiometric_balance"
      ]
    },
    {
      "page": "check_numeric_value",
      "title": "Check Numeric Value",
      "topics": [
        "check_numeric_value"
      ]
    },
    {
      "page": "compare_individuals",
      "title": "Compare individuals from hierarchical models",
      "topics": [
        "compare_individuals"
      ]
    },
    {
      "page": "compare_scenarios",
      "title": "Compare multiple FB4 results",
      "topics": [
        "compare_scenarios"
      ]
    },
    {
      "page": "compare_with_redfield",
      "title": "Compare N:P ratios with Redfield ratios",
      "topics": [
        "compare_with_redfield"
      ]
    },
    {
      "page": "comprehensive_nutritional_analysis",
      "title": "Comprehensive nutritional analysis",
      "topics": [
        "comprehensive_nutritional_analysis"
      ]
    },
    {
      "page": "consumption-functions",
      "title": "Consumption Functions for FB4 Model",
      "topics": [
        "consumption-functions"
      ]
    },
    {
      "page": "contaminant-accumulation",
      "title": "Contaminant Accumulation Functions for FB4 Model",
      "topics": [
        "contaminant-accumulation"
      ]
    },
    {
      "page": "core-validators",
      "title": "Core Validation Functions for FB4",
      "topics": [
        "core-validators"
      ]
    },
    {
      "page": "create_empty_composition",
      "title": "Create empty composition for invalid inputs (Utility)",
      "topics": [
        "create_empty_composition"
      ]
    },
    {
      "page": "create_result_summary",
      "title": "Comprehensive post-simulation analysis summary",
      "topics": [
        "create_result_summary"
      ]
    },
    {
      "page": "data-processing",
      "title": "Data Processing Functions for FB4",
      "topics": [
        "data-processing"
      ]
    },
    {
      "page": "data-validators",
      "title": "Data Validation Functions for FB4",
      "topics": [
        "data-validators"
      ]
    },
    {
      "page": "egestion-excretion",
      "title": "Egestion and Excretion Functions for FB4 Model",
      "topics": [
        "egestion-excretion"
      ]
    },
    {
      "page": "fb4-analysis-plots",
      "title": "Analysis Plots for FB4 Results (Uncertainty and Sensitivity)",
      "topics": [
        "fb4-analysis-plots"
      ]
    },
    {
      "page": "fb4-bioenergetic-plots",
      "title": "Bioenergetic Object Plots for Setup Validation",
      "topics": [
        "fb4-bioenergetic-plots"
      ]
    },
    {
      "page": "fb4-daily-plots",
      "title": "Daily Simulation Plots for FB4 Results",
      "topics": [
        "fb4-daily-plots"
      ]
    },
    {
      "page": "fb4-plot-core",
      "title": "Core Plotting Functions for FB4 Results",
      "topics": [
        "fb4-plot-core"
      ]
    },
    {
      "page": "fb4-plots",
      "title": "FB4 Plotting Functions",
      "topics": [
        "fb4-plots"
      ]
    },
    {
      "page": "FB4-TMB-Shared",
      "title": "FB4 TMB Shared Functions",
      "topics": [
        "FB4-TMB-Shared"
      ]
    },
    {
      "page": "fish4_parameters",
      "title": "Fish Bioenergetics 4.0 Official Parameters Database",
      "topics": [
        "fish4_parameters"
      ]
    },
    {
      "page": "fish4_parameters_metadata",
      "title": "Fish Bioenergetics 4.0 Parameters Database Metadata",
      "topics": [
        "fish4_parameters_metadata"
      ]
    },
    {
      "page": "get_consumption_uncertainty",
      "title": "Get consumption results with uncertainty",
      "topics": [
        "get_consumption_uncertainty"
      ]
    },
    {
      "page": "get_efficiency_uncertainty",
      "title": "Get efficiency results with uncertainty",
      "topics": [
        "get_efficiency_uncertainty"
      ]
    },
    {
      "page": "get_energy_budget_uncertainty",
      "title": "Get energy budget components with uncertainty",
      "topics": [
        "get_energy_budget_uncertainty"
      ]
    },
    {
      "page": "get_individual_results",
      "title": "Get individual results from hierarchical models",
      "topics": [
        "get_individual_results"
      ]
    },
    {
      "page": "get_parameter_value",
      "title": "Get Parameter Value from Species Parameters",
      "topics": [
        "get_parameter_value"
      ]
    },
    {
      "page": "get_population_results",
      "title": "Get population results from hierarchical models",
      "topics": [
        "get_population_results"
      ]
    },
    {
      "page": "interpolate_time_series",
      "title": "Interpolate time series with error handling",
      "topics": [
        "interpolate_time_series"
      ]
    },
    {
      "page": "is.Bioenergetic",
      "title": "Test if Object is Bioenergetic",
      "topics": [
        "is.Bioenergetic"
      ]
    },
    {
      "page": "is.fb4_result",
      "title": "Test if Object is fb4_result",
      "topics": [
        "is.fb4_result"
      ]
    },
    {
      "page": "main-validators",
      "title": "Main Validation Functions for FB4",
      "topics": [
        "main-validators"
      ]
    },
    {
      "page": "mortality-reproduction",
      "title": "Mortality and Reproduction Functions for FB4 Model",
      "topics": [
        "mortality-reproduction"
      ]
    },
    {
      "page": "nutrient-regeneration",
      "title": "Nutrient Regeneration Functions for FB4 Model",
      "topics": [
        "nutrient-regeneration"
      ]
    },
    {
      "page": "parameter-processing",
      "title": "Parameter Processing Functions for FB4",
      "topics": [
        "parameter-processing"
      ]
    },
    {
      "page": "parameter-validators",
      "title": "Parameter Validation Functions for FB4",
      "topics": [
        "parameter-validators"
      ]
    },
    {
      "page": "plot_distributions.fb4_result",
      "title": "Plot parameter distributions for bootstrap and hierarchical methods",
      "topics": [
        "plot_distributions.fb4_result"
      ]
    },
    {
      "page": "plot_growth_temperature_sensitivity",
      "title": "Plot sensitivity analysis",
      "topics": [
        "plot_growth_temperature_sensitivity"
      ]
    },
    {
      "page": "plot_sensitivity.fb4_result",
      "title": "Plot temperature sensitivity analysis for a Bioenergetic object",
      "topics": [
        "plot_sensitivity.fb4_result"
      ]
    },
    {
      "page": "plot_uncertainty.fb4_result",
      "title": "Plot parameter uncertainty for probabilistic methods",
      "topics": [
        "plot_uncertainty.fb4_result"
      ]
    },
    {
      "page": "plot.Bioenergetic",
      "title": "Plot Bioenergetic object setup",
      "topics": [
        "plot.Bioenergetic"
      ]
    },
    {
      "page": "plot.fb4_result",
      "title": "Plot FB4 simulation results",
      "topics": [
        "plot.fb4_result"
      ]
    },
    {
      "page": "predator-energy-density",
      "title": "Predator Energy Density Functions for FB4 Model",
      "topics": [
        "predator-energy-density"
      ]
    },
    {
      "page": "predict_consumption_bootstrap",
      "title": "Bootstrap method for consumption uncertainty propagation",
      "topics": [
        "predict_consumption_bootstrap"
      ]
    },
    {
      "page": "predict_consumption_delta",
      "title": "Delta method for consumption uncertainty propagation",
      "topics": [
        "predict_consumption_delta"
      ]
    },
    {
      "page": "prepare_simulation_data",
      "title": "Prepare all simulation data",
      "topics": [
        "prepare_simulation_data"
      ]
    },
    {
      "page": "print.Bioenergetic",
      "title": "Print Method for Bioenergetic Objects",
      "topics": [
        "print.Bioenergetic"
      ]
    },
    {
      "page": "print.fb4_result",
      "title": "Print Method for fb4_result Objects",
      "topics": [
        "print.fb4_result"
      ]
    },
    {
      "page": "process_bioenergetic_data",
      "title": "Process Bioenergetic object temporal data for simulation",
      "topics": [
        "process_bioenergetic_data"
      ]
    },
    {
      "page": "process_composition_params",
      "title": "Process body composition parameters",
      "topics": [
        "process_composition_params"
      ]
    },
    {
      "page": "process_consumption_params",
      "title": "Process consumption parameters",
      "topics": [
        "process_consumption_params"
      ]
    },
    {
      "page": "process_contaminant_params",
      "title": "Process contaminant parameters",
      "topics": [
        "process_contaminant_params"
      ]
    },
    {
      "page": "process_egestion_params",
      "title": "Process egestion parameters",
      "topics": [
        "process_egestion_params"
      ]
    },
    {
      "page": "process_excretion_params",
      "title": "Process excretion parameters",
      "topics": [
        "process_excretion_params"
      ]
    },
    {
      "page": "process_mortality_params",
      "title": "Process mortality parameters",
      "topics": [
        "process_mortality_params"
      ]
    },
    {
      "page": "process_nutrient_params",
      "title": "Process nutrient parameters",
      "topics": [
        "process_nutrient_params"
      ]
    },
    {
      "page": "process_predator_params",
      "title": "Process predator energy density parameters",
      "topics": [
        "process_predator_params"
      ]
    },
    {
      "page": "process_respiration_params",
      "title": "Process respiration parameters",
      "topics": [
        "process_respiration_params"
      ]
    },
    {
      "page": "process_simulation_settings",
      "title": "Process simulation settings",
      "topics": [
        "process_simulation_settings"
      ]
    },
    {
      "page": "process_species_parameters",
      "title": "Process all species parameters for simulation",
      "topics": [
        "process_species_parameters"
      ]
    },
    {
      "page": "respiration-functions",
      "title": "Respiration Functions for FB4 Model",
      "topics": [
        "respiration-functions"
      ]
    },
    {
      "page": "result-builders-unified",
      "title": "Result Builders for FB4 Model",
      "topics": [
        "result-builders-unified"
      ]
    },
    {
      "page": "run_fb4",
      "title": "Run FB4 Simulation",
      "topics": [
        "run_fb4",
        "run_fb4.default"
      ]
    },
    {
      "page": "run_fb4_simulation",
      "title": "Run complete FB4 simulation (Mid-level - Main function)",
      "topics": [
        "run_fb4_simulation"
      ]
    },
    {
      "page": "run_fb4.Bioenergetic",
      "title": "Run FB4 simulation on Bioenergetic object",
      "topics": [
        "run_fb4.Bioenergetic"
      ]
    },
    {
      "page": "run-fb4-orchestrator",
      "title": "FB4 Main Orchestrator",
      "topics": [
        "run-fb4-orchestrator"
      ]
    },
    {
      "page": "set_diet",
      "title": "Set Diet Data for Bioenergetic Objects",
      "topics": [
        "set_diet"
      ]
    },
    {
      "page": "set_environment",
      "title": "Set Environmental Data for Bioenergetic Objects",
      "topics": [
        "set_environment"
      ]
    },
    {
      "page": "set_parameter_value",
      "title": "Set Parameter Value in Species Parameters",
      "topics": [
        "set_parameter_value"
      ]
    },
    {
      "page": "set_simulation_settings",
      "title": "Set Simulation Settings for Bioenergetic Objects",
      "topics": [
        "set_simulation_settings"
      ]
    },
    {
      "page": "simulation-engine",
      "title": "Simulation Engine for FB4 Model",
      "topics": [
        "simulation-engine"
      ]
    },
    {
      "page": "strategy-binary-search",
      "title": "Binary Search Strategy for FB4 Model",
      "topics": [
        "strategy-binary-search"
      ]
    },
    {
      "page": "strategy-bootstrap",
      "title": "Bootstrap Estimation Strategy for FB4 Model",
      "topics": [
        "strategy-bootstrap"
      ]
    },
    {
      "page": "strategy-commons",
      "title": "Strategy Commons for FB4 Model",
      "topics": [
        "strategy-commons"
      ]
    },
    {
      "page": "strategy-direct",
      "title": "Direct Strategies for FB4 Model",
      "topics": [
        "strategy-direct"
      ]
    },
    {
      "page": "strategy-hierarchical",
      "title": "Hierarchical Estimation Strategy for FB4 Model",
      "topics": [
        "strategy-hierarchical"
      ]
    },
    {
      "page": "strategy-interface",
      "title": "Strategy Interface and Factory for FB4 Model",
      "topics": [
        "strategy-interface"
      ]
    },
    {
      "page": "strategy-mle",
      "title": "Maximum Likelihood Estimation Strategy for FB4 Model",
      "topics": [
        "strategy-mle"
      ]
    },
    {
      "page": "strategy-optim",
      "title": "Optimisation Strategy for FB4 Model",
      "topics": [
        "strategy-optim"
      ]
    },
    {
      "page": "summary.Bioenergetic",
      "title": "Summary Method for Bioenergetic Objects",
      "topics": [
        "summary.Bioenergetic"
      ]
    },
    {
      "page": "summary.fb4_result",
      "title": "Summary Method for fb4_result Objects",
      "topics": [
        "summary.fb4_result"
      ]
    },
    {
      "page": "uncertainty-prediction",
      "title": "FB4 Uncertainty Propagation Functions",
      "topics": [
        "uncertainty-prediction"
      ]
    },
    {
      "page": "update_body_composition",
      "title": "Update body composition during simulation (Mid-level)",
      "topics": [
        "update_body_composition"
      ]
    },
    {
      "page": "utils",
      "title": "Utility Functions for fb4package",
      "topics": [
        "utils"
      ]
    },
    {
      "page": "validate_basic_params",
      "title": "Validate Basic Model Parameters",
      "topics": [
        "validate_basic_params"
      ]
    },
    {
      "page": "validate_bioenergetic_for_simulation",
      "title": "Comprehensive validation for Bioenergetic objects",
      "topics": [
        "validate_bioenergetic_for_simulation"
      ]
    },
    {
      "page": "validate_body_composition",
      "title": "Validate body composition",
      "topics": [
        "validate_body_composition"
      ]
    },
    {
      "page": "validate_contaminant_params",
      "title": "Validate contaminant parameters",
      "topics": [
        "validate_contaminant_params"
      ]
    },
    {
      "page": "validate_fb4_inputs",
      "title": "Validate inputs for FB4 simulation",
      "topics": [
        "validate_fb4_inputs"
      ]
    },
    {
      "page": "validate_fb4_system",
      "title": "Validate complete FB4 system ready for simulation",
      "topics": [
        "validate_fb4_system"
      ]
    },
    {
      "page": "validate_fraction",
      "title": "Validate fraction values (0-1 range)",
      "topics": [
        "validate_fraction"
      ]
    },
    {
      "page": "validate_individual_data",
      "title": "Validate individual data for hierarchical models",
      "topics": [
        "validate_individual_data"
      ]
    },
    {
      "page": "validate_nutrient_concentrations",
      "title": "Validate nutrient concentrations",
      "topics": [
        "validate_nutrient_concentrations"
      ]
    },
    {
      "page": "validate_positive",
      "title": "Validate positive values",
      "topics": [
        "validate_positive"
      ]
    },
    {
      "page": "validate_predator_energy_params",
      "title": "Validate predator energy density parameters",
      "topics": [
        "validate_predator_energy_params"
      ]
    },
    {
      "page": "validate_species_equations",
      "title": "Main function to validate all species equations",
      "topics": [
        "validate_species_equations"
      ]
    },
    {
      "page": "validate_temperature",
      "title": "Validate temperature values",
      "topics": [
        "validate_temperature"
      ]
    },
    {
      "page": "validate_time_series_data",
      "title": "Validate Time Series Data Structure (Basic Level)",
      "topics": [
        "validate_time_series_data"
      ]
    },
    {
      "page": "validation_result",
      "title": "Create standardized validation result",
      "topics": [
        "validation_result"
      ]
    }
  ],
  "_readme": "https://github.com/cran/fb4package/raw/HEAD/README.md",
  "_rundeps": [
    "lattice",
    "Matrix",
    "Rcpp",
    "RcppEigen",
    "TMB"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "fb4-case-study-chinook.Rmd",
      "filename": "fb4-case-study-chinook.html",
      "title": "Case Study: Chinook Salmon Bioenergetics",
      "author": "Hans Ttito",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "1. Species parameters",
        "2. Environmental data",
        "3. Diet composition",
        "4. Building the Bioenergetic object",
        "Setup visualisation",
        "5. Estimating consumption — binary search",
        "Growth trajectory",
        "Energy budget",
        "Full dashboard",
        "6. Consumption with a fixed feeding level",
        "7. Bootstrap uncertainty estimation",
        "8. Result analysis",
        "9. Ecological interpretation",
        "References"
      ],
      "created": "2026-05-07 22:31:36",
      "modified": "2026-05-07 22:31:36",
      "commits": 1
    },
    {
      "source": "fb4-species-database.Rmd",
      "filename": "fb4-species-database.html",
      "title": "Exploring the Species Parameter Database",
      "author": "Hans Ttito",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "1. Loading and inspecting the database",
        "2. Database structure",
        "3. Searching the database",
        "By scientific name (partial match)",
        "By common name",
        "4. Listing available life stages",
        "5. Comparing consumption parameters across species",
        "Temperature optima distribution",
        "6. Predator energy density equations",
        "7. Building a model directly from the database",
        "8. Adding a custom species",
        "References"
      ],
      "created": "2026-05-07 22:31:36",
      "modified": "2026-05-07 22:31:36",
      "commits": 1
    },
    {
      "source": "fb4-introduction.Rmd",
      "filename": "fb4-introduction.html",
      "title": "Introduction to fb4package",
      "author": "Hans Ttito",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "1. Species parameters",
        "2. Environmental and diet data",
        "3. Building a Bioenergetic object",
        "4. Running simulations",
        "4a. Direct simulation — fixed feeding level",
        "4b. Binary search — fit to a target final weight",
        "4c. MLE — uncertainty on p from observed weights",
        "4d. Bootstrap — non-parametric uncertainty",
        "5. Comparing strategies",
        "6. Analysing results",
        "7. Visualising results",
        "8. Temperature × p sensitivity",
        "9. Experimental features",
        "Contaminant bioaccumulation",
        "Nutrient regeneration",
        "Mortality rates",
        "References"
      ],
      "created": "2026-05-07 22:31:36",
      "modified": "2026-05-07 22:31:36",
      "commits": 1
    },
    {
      "source": "fb4-statistical-estimation.Rmd",
      "filename": "fb4-statistical-estimation.html",
      "title": "Statistical estimation strategies",
      "author": "Hans Ttito",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Shared setup",
        "Strategy 1 — Binary search",
        "Strategy 2 — Maximum Likelihood Estimation",
        "Strategy 3 — Bootstrap",
        "Strategy 4 — Hierarchical model (mark-recapture)",
        "Biological context",
        "Simulating a mark-recapture data set",
        "Running the hierarchical model",
        "Assumptions and limitations",
        "Comparing strategies",
        "Strategies 1–3: single-population estimates",
        "Strategy 4: population-level distribution",
        "References"
      ],
      "created": "2026-05-07 22:31:36",
      "modified": "2026-05-07 22:31:36",
      "commits": 1
    },
    {
      "source": "fb4-temperature-climate.Rmd",
      "filename": "fb4-temperature-climate.html",
      "title": "Temperature Sensitivity and Climate Change Scenarios",
      "author": "Hans Ttito",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "1. Base model — juvenile Chinook salmon",
        "2. Manual sensitivity analysis across temperature offsets",
        "3. Built-in sensitivity plot",
        "4. Climate change scenarios — projected growth",
        "5. Thermal performance window",
        "6. Management implications",
        "References"
      ],
      "created": "2026-05-07 22:31:36",
      "modified": "2026-05-07 22:31:36",
      "commits": 1
    }
  ],
  "_score": 3.3979400086720375,
  "_indexed": true,
  "_nocasepkg": "fb4package",
  "_universes": [
    "cran",
    "hansttito"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.0.0",
      "date": "2026-05-07T23:19:43.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "213002fbe50b0c1e3e350f62936676b5ac2a87db",
      "fileid": "03aa569de95b81060e9ffb48dfbf037896c992b0aafd3d5be2b25d9a0ae3b396",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25526715835"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.0.0",
      "date": "2026-05-07T23:19:41.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "213002fbe50b0c1e3e350f62936676b5ac2a87db",
      "fileid": "d99cb51e667a00b5e17b1044bb291d6e54cfd616d0db5998af97cb8011dafc3d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25526715835"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.0.0",
      "date": "2026-05-07T23:19:34.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "213002fbe50b0c1e3e350f62936676b5ac2a87db",
      "fileid": "56ab15571c2021e2c3577dae7326ae5b3c3f6482a944ee8a90f9135edc5db6e6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25526715835"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.0.0",
      "date": "2026-05-07T23:19:47.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "213002fbe50b0c1e3e350f62936676b5ac2a87db",
      "fileid": "6ea905e39e6202caa4a444f92cae386517a4e2fb6a18679f488ae6f6b0bdde58",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25526715835"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.0.0",
      "date": "2026-05-22T14:34:07.000Z",
      "arch": "emscripten",
      "commit": "213002fbe50b0c1e3e350f62936676b5ac2a87db",
      "fileid": "983b8b1fc360f7621446e40dc38539b93d6610a18614158b6e9b4a2d4f9f7a5b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25526715835"
    }
  ]
}