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  "Package": "aelab",
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  "Title": "Data Processing for Aquatic Ecology",
  "Version": "1.1.6",
  "Authors@R": "person(\"Zhao-Jun\", \"Yong\", role = c(\"cre\",\"aut\"), email = \"nuannuan0425@gmail.com\")",
  "Maintainer": "Zhao-Jun Yong <nuannuan0425@gmail.com>",
  "Description": "Facilitate the analysis of data related to aquatic\necology, specifically the establishment of carbon budget.\nCurrently, the package allows the below analysis. (i) the\ncalculation of greenhouse gas flux based on data obtained from\ntrace gas analyzer using the method described in Lin et al.\n(2024). (ii) the calculation of Dissolved Oxygen (DO)\nmetabolism based on data obtained from dissolved oxygen data\nlogger using the method described in Staehr et al. (2010). Yong\net al. (2024) <doi:10.5194/bg-21-5247-2024>. Staehr et al.\n(2010) <doi:10.4319/lom.2010.8.0628>.",
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  "Repository": "https://zhao-jun-yong.r-universe.dev",
  "Date/Publication": "2026-10-21 10:25:17 UTC",
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  "Author": "Zhao-Jun Yong [cre, aut]",
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  "_created": "2026-10-21T12:13:17.000Z",
  "_published": "2026-10-21T12:18:34.701Z",
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    "message": "docs(ghg_flux): describe AICc/Levy/below_mdf rules, cite journal pages\n\n- fit_type help, README and vignette no longer describe the old R2 > 0.01\n  rule or the MDF -> zero override\n- Maier et al. 2022 cited by journal page (p. 457)\n- g_factor_threshold help cites goFlux's g.limit and notes the different rule\n\nClaude-Session: https://claude.ai/code/session_01Fogtrf9QB15e5gBTCWdkMH\n",
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    "add_sun_times",
    "aelab_palettes",
    "aov_test",
    "calc_chla_trichromatic",
    "calculate_do",
    "calculate_ghg_flux",
    "calculate_MDF",
    "calculate_regression",
    "calculate_total_co2e",
    "combine_hobo",
    "combine_weather",
    "combine_weather_mh",
    "combine_weather_month",
    "convert_ghg_unit",
    "convert_time",
    "descriptive_statistic",
    "df_trans",
    "filter_complete_days",
    "find_outlier",
    "gantt_table",
    "gantt_text",
    "ks_test",
    "make_reference",
    "normality_test_aov",
    "normality_test_t",
    "plot_bar",
    "plot_box",
    "plot_ghg_flux",
    "plot_hobo",
    "plot_line",
    "plot_map_taiwan",
    "plot_point",
    "process_hobo",
    "process_info",
    "process_weather",
    "process_weather_mh",
    "process_weather_month",
    "scale_color_aelab_c",
    "scale_color_aelab_d",
    "scale_colour_aelab_c",
    "scale_colour_aelab_d",
    "scale_fill_aelab_c",
    "scale_fill_aelab_d",
    "sig_labels",
    "tidy_ghg_analyzer"
  ],
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      "name": "analyzer_precision",
      "title": "Instrument precision for supported trace gas analyzers",
      "object": "analyzer_precision",
      "class": [
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      ],
      "fields": [
        "model",
        "gas",
        "precision",
        "unit"
      ],
      "rows": 5,
      "table": true,
      "tojson": true
    },
    {
      "name": "hobo",
      "title": "Processed data from Onset HOBO Dissolved Oxygen Data Logger. A dataset containing 336 dissolved oxygen concentrations changed over time.",
      "object": "hobo",
      "class": [
        "data.frame"
      ],
      "fields": [
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        "pressure_hpa",
        "wind_ms",
        "do",
        "temp",
        "depth_m",
        "salinity",
        "start_date_time",
        "end_date_time",
        "sunrise",
        "sunset",
        "no_hobo",
        "site"
      ],
      "rows": 336,
      "table": true,
      "tojson": true
    },
    {
      "name": "n2o",
      "title": "Processed data from N2O LI-COR Trace Gas Analyzer. A dataset containing 567 N2O concentrations changed over time.",
      "object": "n2o",
      "class": [
        "data.frame"
      ],
      "fields": [
        "DATE",
        "TIME",
        "N2O",
        "date_time"
      ],
      "rows": 567,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "add_sun_times",
      "title": "add_sun_times",
      "topics": [
        "add_sun_times"
      ]
    },
    {
      "page": "aelab_palettes",
      "title": "aelab_palettes",
      "topics": [
        "aelab_palettes"
      ]
    },
    {
      "page": "analyzer_precision",
      "title": "Instrument precision for supported trace gas analyzers",
      "topics": [
        "analyzer_precision"
      ]
    },
    {
      "page": "aov_test",
      "title": "aov_test",
      "topics": [
        "aov_test"
      ]
    },
    {
      "page": "calc_chla_trichromatic",
      "title": "calc_chla_trichromatic",
      "topics": [
        "calc_chla_trichromatic"
      ]
    },
    {
      "page": "calculate_do",
      "title": "calculate_do",
      "topics": [
        "calculate_do"
      ]
    },
    {
      "page": "calculate_ghg_flux",
      "title": "calculate_ghg_flux",
      "topics": [
        "calculate_ghg_flux"
      ]
    },
    {
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      "title": "calculate_MDF",
      "topics": [
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      ]
    },
    {
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      "title": "calculate_regression",
      "topics": [
        "calculate_regression"
      ]
    },
    {
      "page": "calculate_total_co2e",
      "title": "calculate_total_co2e",
      "topics": [
        "calculate_total_co2e"
      ]
    },
    {
      "page": "combine_hobo",
      "title": "combine_hobo",
      "topics": [
        "combine_hobo"
      ]
    },
    {
      "page": "combine_weather",
      "title": "combine_weather",
      "topics": [
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      ]
    },
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      "title": "combine_weather_mh",
      "topics": [
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      ]
    },
    {
      "page": "combine_weather_month",
      "title": "combine_weather_month",
      "topics": [
        "combine_weather_month"
      ]
    },
    {
      "page": "convert_ghg_unit",
      "title": "convert_ghg_unit",
      "topics": [
        "convert_ghg_unit"
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    },
    {
      "page": "convert_time",
      "title": "convert_time",
      "topics": [
        "convert_time"
      ]
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      "page": "descriptive_statistic",
      "title": "descriptive_statistic",
      "topics": [
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      ]
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      "page": "df_trans",
      "title": "df_trans",
      "topics": [
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      ]
    },
    {
      "page": "filter_complete_days",
      "title": "filter_complete_days",
      "topics": [
        "filter_complete_days"
      ]
    },
    {
      "page": "find_outlier",
      "title": "find_outlier",
      "topics": [
        "find_outlier"
      ]
    },
    {
      "page": "gantt_table",
      "title": "Gantt-style coloured progress table",
      "topics": [
        "gantt_table"
      ]
    },
    {
      "page": "gantt_text",
      "title": "Plain-text Gantt for terminal and Neovim",
      "topics": [
        "gantt_text"
      ]
    },
    {
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      "title": "Processed data from Onset HOBO Dissolved Oxygen Data Logger. A dataset containing 336 dissolved oxygen concentrations changed over time.",
      "topics": [
        "hobo"
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    },
    {
      "page": "ks_test",
      "title": "ks_test",
      "topics": [
        "ks_test"
      ]
    },
    {
      "page": "make_reference",
      "title": "make_reference",
      "topics": [
        "make_reference"
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      "page": "n2o",
      "title": "Processed data from N2O LI-COR Trace Gas Analyzer. A dataset containing 567 N2O concentrations changed over time.",
      "topics": [
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      "page": "normality_test_aov",
      "title": "normality_test_aov",
      "topics": [
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    {
      "page": "normality_test_t",
      "title": "normality_test_t",
      "topics": [
        "normality_test_t"
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    {
      "page": "plot_bar",
      "title": "plot_bar",
      "topics": [
        "plot_bar"
      ]
    },
    {
      "page": "plot_box",
      "title": "plot_box",
      "topics": [
        "plot_box"
      ]
    },
    {
      "page": "plot_ghg_flux",
      "title": "plot_ghg_flux",
      "topics": [
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      "page": "plot_hobo",
      "title": "plot_hobo",
      "topics": [
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      "title": "plot_line",
      "topics": [
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      "page": "plot_map_taiwan",
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      "topics": [
        "plot_map_taiwan"
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      "page": "plot_point",
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      "topics": [
        "plot_point"
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      "page": "process_hobo",
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      "page": "process_info",
      "title": "process_info",
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      ]
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      "page": "process_weather",
      "title": "convert_time",
      "topics": [
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    },
    {
      "page": "process_weather_mh",
      "title": "process_weather_mh",
      "topics": [
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    },
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      "page": "process_weather_month",
      "title": "process_weather_month",
      "topics": [
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    },
    {
      "page": "scale_colour_aelab_c",
      "title": "scale_colour_aelab_c",
      "topics": [
        "scale_color_aelab_c",
        "scale_colour_aelab_c"
      ]
    },
    {
      "page": "scale_colour_aelab_d",
      "title": "scale_colour_aelab_d",
      "topics": [
        "scale_color_aelab_d",
        "scale_colour_aelab_d"
      ]
    },
    {
      "page": "scale_fill_aelab_c",
      "title": "scale_fill_aelab_c",
      "topics": [
        "scale_fill_aelab_c"
      ]
    },
    {
      "page": "scale_fill_aelab_d",
      "title": "scale_fill_aelab_d",
      "topics": [
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      "title": "sig_labels",
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      "title": "tidy_ghg_analyzer",
      "topics": [
        "tidy_ghg_analyzer"
      ]
    }
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      "filename": "aelab.html",
      "title": "aelab",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "GHG flux calculation",
        "Load and process the raw data file — tidy_ghg_analyzer()",
        "Calculate the slope — calculate_regression()",
        "Method 1: Load from excel",
        "Window type",
        "Per-row window overrides",
        "Model selection",
        "Quality flags",
        "Method 2: Type directly in R",
        "Method 3: Using make_reference()",
        "Calculate the flux — calculate_ghg_flux()",
        "Additional GHG tools",
        "convert_ghg_unit()",
        "calculate_MDF()",
        "calculate_total_co2e()",
        "NEM calculation",
        "Load and process the HOBO logger data — process_hobo()",
        "Batch processing with automated weather and sun times",
        "Combine logger files in a folder — combine_hobo()",
        "Keep only complete days — filter_complete_days()",
        "Sunrise and sunset from site coordinates — add_sun_times()",
        "Bulk weather import",
        "Putting it together",
        "Calculate GPP and ER — calculate_do()",
        "Statistical analysis",
        "Descriptive statistics — descriptive_statistic()",
        "Outlier detection — find_outlier()",
        "Normality testing",
        "Data transformation — df_trans()",
        "Parametric test — aov_test()",
        "Non-parametric test — ks_test()",
        "Faceted CLD annotation — sig_labels()",
        "Visualization",
        "References"
      ],
      "created": "2024-04-26 06:12:12",
      "modified": "2026-10-21 10:25:17",
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