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  "Package": "PhotoGEA",
  "Version": "1.4.0",
  "Date": "2025-08-25",
  "Title": "Photosynthetic Gas Exchange Analysis",
  "Description": "Read, process, fit, and analyze photosynthetic gas\nexchange measurements. Documentation is provided by several\nvignettes; also see Lochocki, Salesse-Smith, & McGrath (2025)\n<doi:10.1111/pce.15501>.",
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  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
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  "Repository": "https://eloch216.r-universe.dev",
  "Date/Publication": "2025-08-28 20:09:03 UTC",
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    "bwplot_wrapper",
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    "calculate_c4_assimilation",
    "calculate_c4_assimilation_hyperbola",
    "calculate_gamma_star",
    "calculate_gas_properties",
    "calculate_gm_busch",
    "calculate_gm_ubierna",
    "calculate_isotope_discrimination",
    "calculate_jmax",
    "calculate_leakiness_ubierna",
    "calculate_peaked_gaussian",
    "calculate_temperature_response",
    "calculate_temperature_response_arrhenius",
    "calculate_temperature_response_gaussian",
    "calculate_temperature_response_johnson",
    "calculate_temperature_response_polynomial",
    "calculate_ternary_correction",
    "calculate_total_pressure",
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    "check_required_variables",
    "check_required_variables.data.frame",
    "check_required_variables.exdf",
    "check_response_curve_data",
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    "choose_input_licor_files",
    "choose_input_tdl_files",
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    "confidence_intervals_c3_variable_j",
    "confidence_intervals_c4_aci",
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    "consolidate.exdf",
    "dim.exdf",
    "dimnames.exdf",
    "dimnames<-.exdf",
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    "document_variables.data.frame",
    "document_variables.exdf",
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    "error_function_c3_variable_j",
    "error_function_c4_aci",
    "error_function_c4_aci_hyperbola",
    "estimate_licor_variance",
    "estimate_operating_point",
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    "exclude_outliers.data.frame",
    "exclude_outliers.exdf",
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    "factorize_id_column.character",
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    "identifier_columns.exdf",
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    "identify_common_columns.data.frame",
    "identify_common_columns.exdf",
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    "initial_guess_c3_variable_j",
    "initial_guess_c4_aci",
    "initial_guess_c4_aci_hyperbola",
    "is.exdf",
    "length.exdf",
    "multi_curve_colors",
    "multi_curve_line_colors",
    "multi_curve_point_colors",
    "optimizer_deoptim",
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    "optimizer_nlminb",
    "optimizer_nmkb",
    "optimizer_null",
    "organize_response_curve_data",
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    "plot_c3_aci_fit",
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    "process_tdl_cycle_polynomial",
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    "remove_points",
    "residual_stats",
    "set_variable",
    "smooth_tdl_data",
    "split.exdf",
    "str.exdf",
    "write.csv.exdf",
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      "object": "c3_temperature_param_bernacchi",
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      "table": false,
      "tojson": true
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      "fields": [],
      "table": false,
      "tojson": true
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      "object": "c3_temperature_param_sharkey",
      "class": [
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      "fields": [],
      "table": false,
      "tojson": true
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      "object": "c4_temperature_param_flat",
      "class": [
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      ],
      "fields": [],
      "table": true,
      "tojson": true
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      "title": "C4 temperature response parameters from von Caemmerer",
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      "table": false,
      "tojson": true
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      "object": "jmax_temperature_param_bernacchi",
      "class": [
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      "fields": [],
      "table": true,
      "tojson": true
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      "object": "jmax_temperature_param_flat",
      "class": [
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      ],
      "fields": [],
      "table": true,
      "tojson": true
    }
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  "_help": [
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      "title": "Calculate CO2 concentration in the chloroplast or mesophyll",
      "concept": [
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      "topics": [
        "apply_gm"
      ]
    },
    {
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      "concept": [
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      ],
      "topics": [
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      ]
    },
    {
      "page": "barchart_with_errorbars",
      "title": "Barcharts with error bars",
      "topics": [
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        "bwplot_wrapper"
      ]
    },
    {
      "page": "basic_stats",
      "title": "Calculate basic stats (mean and standard error)",
      "concept": [
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      ],
      "topics": [
        "basic_stats"
      ]
    },
    {
      "page": "by.exdf",
      "title": "Apply a function to an exdf object split by one or more factors",
      "concept": [
        "exdf"
      ],
      "topics": [
        "by.exdf"
      ]
    },
    {
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      "title": "C3 temperature response parameters from Bernacchi et al.",
      "concept": [
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      ],
      "topics": [
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    },
    {
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      "concept": [
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      "topics": [
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    },
    {
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      "title": "C3 temperature response parameters from Sharkey et al.",
      "concept": [
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      ],
      "topics": [
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      ]
    },
    {
      "page": "c4_temperature_param_flat",
      "title": "C4 temperature response parameters for a flat response",
      "concept": [
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      ],
      "topics": [
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      ]
    },
    {
      "page": "c4_temperature_param_vc",
      "title": "C4 temperature response parameters from von Caemmerer",
      "concept": [
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      "topics": [
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    },
    {
      "page": "calculate_ball_berry_index",
      "title": "Calculate the Ball-Berry index",
      "concept": [
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      ],
      "topics": [
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      ]
    },
    {
      "page": "calculate_c3_assimilation",
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      "concept": [
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      "topics": [
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    },
    {
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      "concept": [
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      ],
      "topics": [
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      ]
    },
    {
      "page": "calculate_c3_limitations_warren",
      "title": "Estimate the relative limiting factors to C3 photosynthesis",
      "concept": [
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      "topics": [
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    },
    {
      "page": "calculate_c3_variable_j",
      "title": "Calculate C3 variable J",
      "concept": [
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      ],
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      "concept": [
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      "topics": [
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    },
    {
      "page": "calculate_c4_assimilation_hyperbola",
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      "concept": [
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      "topics": [
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    },
    {
      "page": "calculate_gamma_star",
      "title": "Calculate Gamma_star from Rubisco specificity",
      "concept": [
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      ],
      "topics": [
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    },
    {
      "page": "calculate_gas_properties",
      "title": "Calculate gas properties that are typically not included in Licor files",
      "concept": [
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      "topics": [
        "calculate_gas_properties"
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    },
    {
      "page": "calculate_gm_busch",
      "title": "Calculate mesophyll conductance to CO2 diffusion",
      "concept": [
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      "topics": [
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    },
    {
      "page": "calculate_gm_ubierna",
      "title": "Calculate mesophyll conductance to CO2 diffusion",
      "concept": [
        "exdf"
      ],
      "topics": [
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      ]
    },
    {
      "page": "calculate_isotope_discrimination",
      "title": "Calculate photosynthetic isotope discrimination",
      "concept": [
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      ],
      "topics": [
        "calculate_isotope_discrimination"
      ]
    },
    {
      "page": "calculate_jmax",
      "title": "Calculate maximum electron transport rate",
      "concept": [
        "exdf"
      ],
      "topics": [
        "calculate_jmax"
      ]
    },
    {
      "page": "calculate_leakiness_ubierna",
      "title": "Calculate leakiness",
      "concept": [
        "exdf"
      ],
      "topics": [
        "calculate_leakiness_ubierna"
      ]
    },
    {
      "page": "calculate_temperature_response",
      "title": "Calculate temperature-dependent parameter values",
      "concept": [
        "exdf"
      ],
      "topics": [
        "calculate_temperature_response"
      ]
    },
    {
      "page": "calculate_temperature_response_arrhenius",
      "title": "Calculate temperature-dependent values using Arrhenius equations",
      "concept": [
        "exdf"
      ],
      "topics": [
        "calculate_temperature_response_arrhenius"
      ]
    },
    {
      "page": "calculate_temperature_response_gaussian",
      "title": "Calculate temperature-dependent values using Gaussian equations",
      "concept": [
        "exdf"
      ],
      "topics": [
        "calculate_temperature_response_gaussian"
      ]
    },
    {
      "page": "calculate_temperature_response_johnson",
      "title": "Calculate temperature-dependent values using Johnson-Eyring-Williams equations",
      "concept": [
        "exdf"
      ],
      "topics": [
        "calculate_temperature_response_johnson"
      ]
    },
    {
      "page": "calculate_temperature_response_polynomial",
      "title": "Calculate temperature-dependent values using polynomial equations",
      "concept": [
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      ],
      "topics": [
        "calculate_temperature_response_polynomial"
      ]
    },
    {
      "page": "calculate_ternary_correction",
      "title": "Calculate ternary correction factor",
      "concept": [
        "exdf"
      ],
      "topics": [
        "calculate_ternary_correction"
      ]
    },
    {
      "page": "calculate_total_pressure",
      "title": "Calculate the total pressure in bar",
      "concept": [
        "exdf"
      ],
      "topics": [
        "calculate_total_pressure"
      ]
    },
    {
      "page": "calculate_wue",
      "title": "Calculate intrinsic water use efficiency",
      "concept": [
        "exdf"
      ],
      "topics": [
        "calculate_wue"
      ]
    },
    {
      "page": "cbind.exdf",
      "title": "Combine exdf objects by columns or rows",
      "concept": [
        "exdf"
      ],
      "topics": [
        "cbind.exdf",
        "rbind.exdf"
      ]
    },
    {
      "page": "check_required_variables",
      "title": "Make sure required variables exist",
      "concept": [
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      "topics": [
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        "check_required_variables.data.frame",
        "check_required_variables.exdf"
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    },
    {
      "page": "check_response_curve_data",
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      "concept": [
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      "fileid": "https://r2.ropensci.org/b214579d59e8917f651c396a22007fc49de24239669fdde7902c3b17dd4b427d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eloch216/actions/runs/38546912562"
    }
  ]
}