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  "Package": "rumenGP",
  "Title": "Rumen Gas Production Modeling, Comparison, and Visualization",
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  "Authors@R": "c(\nperson(\n\"Arlan\",\n\"Araujo Rodrigues\",\nemail = \"araujorodrig@wisc.edu\",\nrole = c(\"aut\", \"cre\")\n),\nperson(\n\"Hilario\",\n\"Cuquetto Mantovani\",\nemail = \"hcmantovani@wisc.edu\",\nrole = \"aut\"\n)\n)",
  "Description": "Provides tools for importing, processing, visualizing,\nfitting, comparing, and interpreting in vitro rumen gas\nproduction data. Supports ANKOM RF workflows, generic gas\nproduction datasets, and pressure-based measurements. Includes\nmultiple kinetic models, custom nonlinear models, model\ncomparison workflows, treatment-level ranking, diagnostic\ntools, and visualization functions for rumen fermentation\nstudies.",
  "License": "MIT + file LICENSE",
  "URL": "https://araujorodrig-lab.github.io/rumenGP/,\nhttps://github.com/araujorodrig-lab/rumenGP",
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  "Date/Publication": "2026-10-12 21:30:37 UTC",
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  "Maintainer": "Arlan Araujo Rodrigues <araujorodrig@wisc.edu>",
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  "_exports": [
    "as_rumen_gp",
    "best_model_by_treatment",
    "compare_models",
    "compare_models_by_treatment",
    "example_data",
    "exclude_heads",
    "fit_brody",
    "fit_burr_xii",
    "fit_custom",
    "fit_dual_logistic",
    "fit_exp0",
    "fit_expl",
    "fit_gompertz",
    "fit_groot",
    "fit_inverse_paralogistic",
    "fit_le0",
    "fit_lel",
    "fit_logistic",
    "fit_loglogistic",
    "fit_mitscherlich",
    "fit_mm",
    "fit_orskov",
    "flag_model",
    "model_win_frequency",
    "parse_ankom_time",
    "plot_all_fits",
    "plot_all_treatment_means",
    "plot_diagnostics",
    "plot_dual_pools",
    "plot_fit",
    "plot_gp",
    "plot_model_comparison",
    "plot_model_comparison_all",
    "plot_model_comparison_treatment",
    "plot_model_performance",
    "plot_model_rankings",
    "plot_residual_comparison",
    "plot_residuals",
    "plot_treatment_mean",
    "pressure_to_volume",
    "process_ankom",
    "rank_models",
    "rank_models_by_treatment",
    "read_ankom",
    "read_metadata",
    "validate_ankom",
    "validate_metadata"
  ],
  "_help": [
    {
      "page": "as_rumen_gp",
      "title": "Convert data to a rumen_gp object",
      "topics": [
        "as_rumen_gp"
      ]
    },
    {
      "page": "best_model_by_treatment",
      "title": "Identify the Best Model for Each Treatment",
      "topics": [
        "best_model_by_treatment"
      ]
    },
    {
      "page": "compare_models",
      "title": "Compare Fitted Kinetic Models",
      "topics": [
        "compare_models"
      ]
    },
    {
      "page": "compare_models_by_treatment",
      "title": "Compare Models by Treatment",
      "topics": [
        "compare_models_by_treatment"
      ]
    },
    {
      "page": "example_data",
      "title": "Example ANKOM Data",
      "topics": [
        "example_data"
      ]
    },
    {
      "page": "exclude_heads",
      "title": "Exclude Problematic ANKOM Heads",
      "topics": [
        "exclude_heads"
      ]
    },
    {
      "page": "fit_brody",
      "title": "Fit Brody model",
      "topics": [
        "fit_brody"
      ]
    },
    {
      "page": "fit_burr_xii",
      "title": "Fit Burr XII model",
      "topics": [
        "fit_burr_xii"
      ]
    },
    {
      "page": "fit_custom",
      "title": "Fit Custom Nonlinear Model",
      "topics": [
        "fit_custom"
      ]
    },
    {
      "page": "fit_dual_logistic",
      "title": "Fit dual-pool logistic model",
      "topics": [
        "fit_dual_logistic"
      ]
    },
    {
      "page": "fit_exp0",
      "title": "Fit exponential model without lag (EXP0)",
      "topics": [
        "fit_exp0"
      ]
    },
    {
      "page": "fit_expl",
      "title": "Fit exponential model with lag (EXPL)",
      "topics": [
        "fit_expl"
      ]
    },
    {
      "page": "fit_gompertz",
      "title": "Fit Gompertz model",
      "topics": [
        "fit_gompertz"
      ]
    },
    {
      "page": "fit_groot",
      "title": "Fit Groot model",
      "topics": [
        "fit_groot"
      ]
    },
    {
      "page": "fit_inverse_paralogistic",
      "title": "Fit Inverse Paralogistic model",
      "topics": [
        "fit_inverse_paralogistic"
      ]
    },
    {
      "page": "fit_le0",
      "title": "Fit Logistic-Exponential model (LE0)",
      "topics": [
        "fit_le0"
      ]
    },
    {
      "page": "fit_lel",
      "title": "Fit Logistic-Exponential model (LEL)",
      "topics": [
        "fit_lel"
      ]
    },
    {
      "page": "fit_logistic",
      "title": "Fit Logistic model",
      "topics": [
        "fit_logistic"
      ]
    },
    {
      "page": "fit_loglogistic",
      "title": "Fit Log-logistic model",
      "topics": [
        "fit_loglogistic"
      ]
    },
    {
      "page": "fit_mitscherlich",
      "title": "Fit Mitscherlich model",
      "topics": [
        "fit_mitscherlich"
      ]
    },
    {
      "page": "fit_mm",
      "title": "Fit Michaelis-Menten model",
      "topics": [
        "fit_mm"
      ]
    },
    {
      "page": "fit_orskov",
      "title": "Fit Orskov and McDonald model",
      "topics": [
        "fit_orskov"
      ]
    },
    {
      "page": "flag_model",
      "title": "Flag potentially problematic model fits",
      "topics": [
        "flag_model"
      ]
    },
    {
      "page": "model_win_frequency",
      "title": "Model Win Frequency",
      "topics": [
        "model_win_frequency"
      ]
    },
    {
      "page": "parse_ankom_time",
      "title": "Parse ANKOM Timestamps",
      "topics": [
        "parse_ankom_time"
      ]
    },
    {
      "page": "plot_all_fits",
      "title": "Plot All Fitted Curves",
      "topics": [
        "plot_all_fits"
      ]
    },
    {
      "page": "plot_all_treatment_means",
      "title": "Plot Treatment Means for All Treatments",
      "topics": [
        "plot_all_treatment_means"
      ]
    },
    {
      "page": "plot_diagnostics",
      "title": "Plot Diagnostic Summaries",
      "topics": [
        "plot_diagnostics"
      ]
    },
    {
      "page": "plot_dual_pools",
      "title": "Plot Dual-Pool Logistic Decomposition",
      "topics": [
        "plot_dual_pools"
      ]
    },
    {
      "page": "plot_fit",
      "title": "Plot Fitted Model",
      "topics": [
        "plot_fit"
      ]
    },
    {
      "page": "plot_gp",
      "title": "Plot Raw Gas Production Curve",
      "topics": [
        "plot_gp"
      ]
    },
    {
      "page": "plot_model_comparison",
      "title": "Compare Model Fits",
      "topics": [
        "plot_model_comparison"
      ]
    },
    {
      "page": "plot_model_comparison_all",
      "title": "Compare Models for All Bottles",
      "topics": [
        "plot_model_comparison_all"
      ]
    },
    {
      "page": "plot_model_comparison_treatment",
      "title": "Compare Models for a Treatment",
      "topics": [
        "plot_model_comparison_treatment"
      ]
    },
    {
      "page": "plot_model_performance",
      "title": "Plot Model Performance",
      "topics": [
        "plot_model_performance"
      ]
    },
    {
      "page": "plot_model_rankings",
      "title": "Plot Model Rankings",
      "topics": [
        "plot_model_rankings"
      ]
    },
    {
      "page": "plot_residual_comparison",
      "title": "Compare Residuals Across Models",
      "topics": [
        "plot_residual_comparison"
      ]
    },
    {
      "page": "plot_residuals",
      "title": "Plot Model Residuals",
      "topics": [
        "plot_residuals"
      ]
    },
    {
      "page": "plot_treatment_mean",
      "title": "Plot Treatment Means Across Models",
      "topics": [
        "plot_treatment_mean"
      ]
    },
    {
      "page": "pressure_to_volume",
      "title": "Convert Pressure to Gas Volume",
      "topics": [
        "pressure_to_volume"
      ]
    },
    {
      "page": "process_ankom",
      "title": "Process ANKOM RF Data",
      "topics": [
        "process_ankom"
      ]
    },
    {
      "page": "rank_models",
      "title": "Rank Models",
      "topics": [
        "rank_models"
      ]
    },
    {
      "page": "rank_models_by_treatment",
      "title": "Rank Models Within Each Treatment",
      "topics": [
        "rank_models_by_treatment"
      ]
    },
    {
      "page": "read_ankom",
      "title": "Import ANKOM RF Output",
      "topics": [
        "read_ankom"
      ]
    },
    {
      "page": "read_metadata",
      "title": "Import Metadata",
      "topics": [
        "read_metadata"
      ]
    },
    {
      "page": "summary.brody_fit",
      "title": "Summary of Brody Fits",
      "topics": [
        "summary.brody_fit"
      ]
    },
    {
      "page": "summary.burr_xii_fit",
      "title": "Summary of Burr XII Fits",
      "topics": [
        "summary.burr_xii_fit"
      ]
    },
    {
      "page": "summary.custom_fit",
      "title": "Summary of Custom Model Fits",
      "topics": [
        "summary.custom_fit"
      ]
    },
    {
      "page": "summary.dual_logistic_fit",
      "title": "Summary of Dual Logistic Fits",
      "topics": [
        "summary.dual_logistic_fit"
      ]
    },
    {
      "page": "summary.exp0_fit",
      "title": "Summary of EXP0 Fits",
      "topics": [
        "summary.exp0_fit"
      ]
    },
    {
      "page": "summary.expl_fit",
      "title": "Summary of EXPL Fits",
      "topics": [
        "summary.expl_fit"
      ]
    },
    {
      "page": "summary.gompertz_fit",
      "title": "Summary of Gompertz Fits",
      "topics": [
        "summary.gompertz_fit"
      ]
    },
    {
      "page": "summary.groot_fit",
      "title": "Summary of Groot Fits",
      "topics": [
        "summary.groot_fit"
      ]
    },
    {
      "page": "summary.inverse_paralogistic_fit",
      "title": "Summary of Inverse Paralogistic Fits",
      "topics": [
        "summary.inverse_paralogistic_fit"
      ]
    },
    {
      "page": "summary.le0_fit",
      "title": "Summary of LE0 Fits",
      "topics": [
        "summary.le0_fit"
      ]
    },
    {
      "page": "summary.lel_fit",
      "title": "Summary of LEL Fits",
      "topics": [
        "summary.lel_fit"
      ]
    },
    {
      "page": "summary.logistic_fit",
      "title": "Summary of Logistic Fits",
      "topics": [
        "summary.logistic_fit"
      ]
    },
    {
      "page": "summary.loglogistic_fit",
      "title": "Summary of Log-logistic Fits",
      "topics": [
        "summary.loglogistic_fit"
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    },
    {
      "page": "summary.mitscherlich_fit",
      "title": "Summary of Mitscherlich Fits",
      "topics": [
        "summary.mitscherlich_fit"
      ]
    },
    {
      "page": "summary.mm_fit",
      "title": "Summary of Michaelis-Menten Fits",
      "topics": [
        "summary.mm_fit"
      ]
    },
    {
      "page": "summary.orskov_fit",
      "title": "Summary of Orskov and McDonald Fits",
      "topics": [
        "summary.orskov_fit"
      ]
    },
    {
      "page": "validate_ankom",
      "title": "Validate Processed Rumen Gas Production Data",
      "topics": [
        "validate_ankom"
      ]
    },
    {
      "page": "validate_metadata",
      "title": "Validate Metadata",
      "topics": [
        "validate_metadata"
      ]
    }
  ],
  "_readme": "https://github.com/araujorodrig-lab/rumengp/raw/HEAD/README.md",
  "_rundeps": [
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    "cli",
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  "_vignettes": [
    {
      "source": "custom-models.Rmd",
      "filename": "custom-models.html",
      "title": "Building Custom Kinetic Models",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Example Dataset",
        "Example 1: Simple Exponential Model",
        "Example 2: Hyperbolic Model",
        "[Gas(t)",
        "Example 3: Richards Model",
        "Comparing Custom and Built-in Models",
        "Visualizing Custom Models",
        "Choosing Starting Values",
        "Using Bounds",
        "Best Practices",
        "Summary"
      ],
      "created": "2026-09-21 15:54:42",
      "modified": "2026-09-21 15:54:42",
      "commits": 1
    },
    {
      "source": "getting-started.Rmd",
      "filename": "getting-started.html",
      "title": "Getting Started with rumenGP",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Load Example Data",
        "Import ANKOM Data",
        "Validate Metadata",
        "Process ANKOM Data",
        "Validate Processed Data",
        "Visualize Raw Gas Production",
        "Fit Kinetic Models",
        "Summarize Model Fits",
        "Identify Potentially Problematic Bottles",
        "Plot Model Fits",
        "Plot Residuals",
        "Compare Models",
        "Rank Models",
        "Compare Models by Treatment",
        "Rank Models by Treatment",
        "Determine the Best Model per Treatment",
        "Model Win Frequency",
        "Quality Control Workflow",
        "Available Models",
        "Model Equivalence",
        "Groot and Generalized Michaelis-Menten",
        "Groot, Generalized Michaelis-Menten, and Log-logistic",
        "[V(t)",
        "Recommended Model Selection Workflow",
        "New Additions",
        "Burr XII",
        "VF\\left[1",
        "Inverse Paralogistic",
        "Next Steps",
        "Importing Manual Datasets",
        "Importing Pressure Data",
        "User-Defined Models",
        "Summary"
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