{
  "_id": "6a140486acfb0bcc41d38eee",
  "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>.",
  "Authors@R": "c(\nperson(\"Edward B.\", \"Lochocki\", role = c('cre', 'aut'),\nemail = \"eloch@illinois.edu\",\ncomment = c(ORCID = \"0000-0002-4912-9783\")),\nperson(\"Coralie E.\", \"Salesse-Smith\", role = 'aut',\ncomment = c(ORCID = \"0000-0002-2856-4217\")),\nperson(\"Justin M.\", \"McGrath\", role = 'aut',\ncomment = c(ORCID = \"0000-0002-7025-3906\")),\nperson(\"PhotoGEA authors\", role = \"cph\")\n)",
  "VignetteBuilder": "knitr",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "URL": "https://github.com/eloch216/PhotoGEA,\nhttps://eloch216.github.io/PhotoGEA/",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://eloch216.r-universe.dev",
  "Date/Publication": "2025-08-28 20:09:03 UTC",
  "RemoteUrl": "https://github.com/eloch216/photogea",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
  "Packaged": {
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  "Author": "Edward B. Lochocki [cre, aut] (ORCID:\n<https://orcid.org/0000-0002-4912-9783>),\nCoralie E. Salesse-Smith [aut] (ORCID:\n<https://orcid.org/0000-0002-2856-4217>),\nJustin M. McGrath [aut] (ORCID:\n<https://orcid.org/0000-0002-7025-3906>),\nPhotoGEA authors [cph]",
  "Maintainer": "Edward B. Lochocki <eloch@illinois.edu>",
  "MD5sum": "16a9a3fc7d0639501cf837c887b67eb0",
  "_user": "eloch216",
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    "[<-.exdf",
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    "as.data.frame.exdf",
    "barchart_with_errorbars",
    "basic_stats",
    "bwplot_wrapper",
    "by.exdf",
    "calculate_arrhenius",
    "calculate_ball_berry_index",
    "calculate_c3_assimilation",
    "calculate_c3_limitations_grassi",
    "calculate_c3_limitations_warren",
    "calculate_c3_variable_j",
    "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",
    "calculate_wue",
    "cbind.exdf",
    "check_licor_data",
    "check_required_variables",
    "check_required_variables.data.frame",
    "check_required_variables.exdf",
    "check_response_curve_data",
    "choose_input_files",
    "choose_input_licor_files",
    "choose_input_tdl_files",
    "confidence_intervals_c3_aci",
    "confidence_intervals_c3_variable_j",
    "confidence_intervals_c4_aci",
    "confidence_intervals_c4_aci_hyperbola",
    "consolidate",
    "consolidate.data.frame",
    "consolidate.exdf",
    "dim.exdf",
    "dimnames.exdf",
    "dimnames<-.exdf",
    "document_variables",
    "document_variables.data.frame",
    "document_variables.exdf",
    "error_function_c3_aci",
    "error_function_c3_variable_j",
    "error_function_c4_aci",
    "error_function_c4_aci_hyperbola",
    "estimate_licor_variance",
    "estimate_operating_point",
    "exclude_outliers",
    "exclude_outliers.data.frame",
    "exclude_outliers.exdf",
    "exdf",
    "factorize_id_column",
    "factorize_id_column.character",
    "factorize_id_column.data.frame",
    "factorize_id_column.exdf",
    "fit_ball_berry",
    "fit_c3_aci",
    "fit_c3_variable_j",
    "fit_c4_aci",
    "fit_c4_aci_hyperbola",
    "fit_laisk",
    "fit_medlyn",
    "get_oxygen_from_preamble",
    "get_sample_valve_from_filename",
    "identifier_columns",
    "identifier_columns.data.frame",
    "identifier_columns.exdf",
    "identify_c3_limiting_processes",
    "identify_common_columns",
    "identify_common_columns.data.frame",
    "identify_common_columns.exdf",
    "identify_tdl_cycles",
    "initial_guess_c3_aci",
    "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",
    "optimizer_hjkb",
    "optimizer_nlminb",
    "optimizer_nmkb",
    "optimizer_null",
    "organize_response_curve_data",
    "pair_gasex_and_tdl",
    "pdf_print",
    "PhotoGEA_example_file_path",
    "plot_ball_berry_fit",
    "plot_c3_aci_fit",
    "plot_c4_aci_fit",
    "plot_c4_aci_hyperbola_fit",
    "plot_laisk_fit",
    "print.exdf",
    "process_tdl_cycle_erml",
    "process_tdl_cycle_polynomial",
    "rbind.exdf",
    "read_cr3000",
    "read_gasex_file",
    "read_licor_6800_Excel",
    "read_licor_6800_plaintext",
    "read_licor_file",
    "read_tdl_file",
    "read.csv.exdf",
    "remove_points",
    "residual_stats",
    "set_variable",
    "smooth_tdl_data",
    "split.exdf",
    "str.exdf",
    "write.csv.exdf",
    "xyplot_avg_rc"
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      "name": "c3_temperature_param_bernacchi",
      "title": "C3 temperature response parameters from Bernacchi et al.",
      "object": "c3_temperature_param_bernacchi",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "c3_temperature_param_flat",
      "title": "C3 temperature response parameters for a flat response",
      "object": "c3_temperature_param_flat",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "c3_temperature_param_sharkey",
      "title": "C3 temperature response parameters from Sharkey et al.",
      "object": "c3_temperature_param_sharkey",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "c4_temperature_param_flat",
      "title": "C4 temperature response parameters for a flat response",
      "object": "c4_temperature_param_flat",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "c4_temperature_param_vc",
      "title": "C4 temperature response parameters from von Caemmerer",
      "object": "c4_temperature_param_vc",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "jmax_temperature_param_bernacchi",
      "title": "Jmax-related temperature response parameters from Bernacchi et al.",
      "object": "jmax_temperature_param_bernacchi",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "jmax_temperature_param_flat",
      "title": "Jmax-related temperature response parameters from Bernacchi et al.",
      "object": "jmax_temperature_param_flat",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "apply_gm",
      "title": "Calculate CO2 concentration in the chloroplast or mesophyll",
      "concept": [
        "exdf"
      ],
      "topics": [
        "apply_gm"
      ]
    },
    {
      "page": "as.data.frame.exdf",
      "title": "Convert an exdf object to a data frame",
      "concept": [
        "exdf"
      ],
      "topics": [
        "as.data.frame.exdf"
      ]
    },
    {
      "page": "barchart_with_errorbars",
      "title": "Barcharts with error bars",
      "topics": [
        "barchart_with_errorbars",
        "bwplot_wrapper"
      ]
    },
    {
      "page": "basic_stats",
      "title": "Calculate basic stats (mean and standard error)",
      "concept": [
        "exdf"
      ],
      "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"
      ]
    },
    {
      "page": "c3_temperature_param_bernacchi",
      "title": "C3 temperature response parameters from Bernacchi et al.",
      "concept": [
        "temperature_response_parameters"
      ],
      "topics": [
        "c3_temperature_param_bernacchi"
      ]
    },
    {
      "page": "c3_temperature_param_flat",
      "title": "C3 temperature response parameters for a flat response",
      "concept": [
        "temperature_response_parameters"
      ],
      "topics": [
        "c3_temperature_param_flat"
      ]
    },
    {
      "page": "c3_temperature_param_sharkey",
      "title": "C3 temperature response parameters from Sharkey et al.",
      "concept": [
        "temperature_response_parameters"
      ],
      "topics": [
        "c3_temperature_param_sharkey"
      ]
    },
    {
      "page": "c4_temperature_param_flat",
      "title": "C4 temperature response parameters for a flat response",
      "concept": [
        "temperature_response_parameters"
      ],
      "topics": [
        "c4_temperature_param_flat"
      ]
    },
    {
      "page": "c4_temperature_param_vc",
      "title": "C4 temperature response parameters from von Caemmerer",
      "concept": [
        "temperature_response_parameters"
      ],
      "topics": [
        "c4_temperature_param_vc"
      ]
    },
    {
      "page": "calculate_ball_berry_index",
      "title": "Calculate the Ball-Berry index",
      "concept": [
        "exdf"
      ],
      "topics": [
        "calculate_ball_berry_index"
      ]
    },
    {
      "page": "calculate_c3_assimilation",
      "title": "Calculate C3 assimilation rates",
      "concept": [
        "exdf"
      ],
      "topics": [
        "calculate_c3_assimilation"
      ]
    },
    {
      "page": "calculate_c3_limitations_grassi",
      "title": "Estimate the relative limiting factors to C3 photosynthesis",
      "concept": [
        "exdf"
      ],
      "topics": [
        "calculate_c3_limitations_grassi"
      ]
    },
    {
      "page": "calculate_c3_limitations_warren",
      "title": "Estimate the relative limiting factors to C3 photosynthesis",
      "concept": [
        "exdf"
      ],
      "topics": [
        "calculate_c3_limitations_warren"
      ]
    },
    {
      "page": "calculate_c3_variable_j",
      "title": "Calculate C3 variable J",
      "concept": [
        "exdf"
      ],
      "topics": [
        "calculate_c3_variable_j"
      ]
    },
    {
      "page": "calculate_c4_assimilation",
      "title": "Calculate C4 assimilation rates",
      "concept": [
        "exdf"
      ],
      "topics": [
        "calculate_c4_assimilation"
      ]
    },
    {
      "page": "calculate_c4_assimilation_hyperbola",
      "title": "Calculate C4 assimilation rates using a hyperbola",
      "concept": [
        "exdf"
      ],
      "topics": [
        "calculate_c4_assimilation_hyperbola"
      ]
    },
    {
      "page": "calculate_gamma_star",
      "title": "Calculate Gamma_star from Rubisco specificity",
      "concept": [
        "exdf"
      ],
      "topics": [
        "calculate_gamma_star"
      ]
    },
    {
      "page": "calculate_gas_properties",
      "title": "Calculate gas properties that are typically not included in Licor files",
      "concept": [
        "exdf"
      ],
      "topics": [
        "calculate_gas_properties"
      ]
    },
    {
      "page": "calculate_gm_busch",
      "title": "Calculate mesophyll conductance to CO2 diffusion",
      "concept": [
        "exdf"
      ],
      "topics": [
        "calculate_gm_busch"
      ]
    },
    {
      "page": "calculate_gm_ubierna",
      "title": "Calculate mesophyll conductance to CO2 diffusion",
      "concept": [
        "exdf"
      ],
      "topics": [
        "calculate_gm_ubierna"
      ]
    },
    {
      "page": "calculate_isotope_discrimination",
      "title": "Calculate photosynthetic isotope discrimination",
      "concept": [
        "exdf"
      ],
      "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": [
        "exdf"
      ],
      "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"
      ]
    },
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      "version": "1.4.0",
      "date": "2026-05-25T08:08:52.000Z",
      "commit": "947709bed9fa1e6cd71cd9a91d771b5e47fd22c8",
      "fileid": "d08d971e5cf3c9f7e92d36c72a61107d1ec9569dc753ff470d2955770a4f8a8c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eloch216/actions/runs/26390255368"
    }
  ]
}