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  "Title": "Read Stable Isotope Data Files",
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  "Description": "Interface to the raw data and metadata stored in the file\nformats commonly encountered in scientific disciplines that\nmake use of stable isotopes. Supports Isodat (.dxf, .cf, .did,\n.caf, .scn), IonOS (.iarc), LyticOS (.larc), Callisto (.bch),\nand Qtegra (.imexp) file formats. Provides a consistent data\nstructure together with tools to aggregate, convert signal\nunits, filter, and visualize the extracted data. The approach\nis described in Kopf et al. (2021) <doi:10.21105/joss.02878>.",
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    "ir_find_continuous_flow",
    "ir_find_dual_inlet",
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    "ir_find_scans",
    "ir_generate_cycles_tibble",
    "ir_generate_scans_tibble",
    "ir_generate_traces_tibble",
    "ir_get_aggregator",
    "ir_get_cycles",
    "ir_get_data",
    "ir_get_isoextract_version",
    "ir_get_metadata",
    "ir_get_option",
    "ir_get_options",
    "ir_get_problems",
    "ir_get_resistors",
    "ir_get_scans",
    "ir_get_supported_file_types",
    "ir_get_traces",
    "ir_get_vendor_data_table",
    "ir_join_metadata",
    "ir_load_aggregated_data",
    "ir_load_isofiles",
    "ir_mutate_metadata",
    "ir_options",
    "ir_plot_continuous_flow",
    "ir_plot_dual_inlet",
    "ir_plot_scans",
    "ir_plot_traces",
    "ir_read_isofiles",
    "ir_register_aggregator",
    "ir_save_aggregated_data",
    "ir_save_isofiles",
    "ir_show_problems",
    "ir_start_aggregator"
  ],
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      "page": "isoreader2-package",
      "title": "isoreader2: Read Stable Isotope Data Files",
      "topics": [
        "isoreader2-package",
        "isoreader2"
      ]
    },
    {
      "page": "auto",
      "title": "Automatic / default behavior",
      "topics": [
        "auto"
      ]
    },
    {
      "page": "c.ir_aggregated_data",
      "title": "Combine aggregated isofile data",
      "topics": [
        "c.ir_aggregated_data"
      ]
    },
    {
      "page": "c.ir_isofiles",
      "title": "Combine isofiles",
      "topics": [
        "c.ir_isofiles"
      ]
    },
    {
      "page": "ir_aggregate_isofiles",
      "title": "Aggregate data from isofiles",
      "topics": [
        "ir_aggregate_isofiles"
      ]
    },
    {
      "page": "ir_calculate_ratios",
      "title": "Calculate isotope ratios",
      "topics": [
        "ir_calculate_ratios"
      ]
    },
    {
      "page": "ir_check_isoextract",
      "title": "Check for the isoextract executables",
      "topics": [
        "ir_check_isoextract",
        "ir_check_isosolfs"
      ]
    },
    {
      "page": "ir_convert_intensity",
      "title": "Convert intensity between units",
      "topics": [
        "ir_convert_intensity"
      ]
    },
    {
      "page": "ir_default_theme",
      "title": "Default isoreader2 plotting theme",
      "topics": [
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    },
    {
      "page": "ir_examples_folder",
      "title": "Bundled example files",
      "topics": [
        "ir_copy_examples",
        "ir_examples_folder"
      ]
    },
    {
      "page": "ir_export_to_excel",
      "title": "Export data to Excel",
      "topics": [
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      ]
    },
    {
      "page": "ir_extract_isofiles",
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      "topics": [
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        "ir_get_isoextract_version"
      ]
    },
    {
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        "ir_filter_for_continuous_flow",
        "ir_filter_for_dual_inlet",
        "ir_filter_for_scans"
      ]
    },
    {
      "page": "ir_filter_masses",
      "title": "Filter isofiles by mass",
      "topics": [
        "ir_filter_masses"
      ]
    },
    {
      "page": "ir_find_isofiles",
      "title": "Find isodat files",
      "topics": [
        "ir_find_continuous_flow",
        "ir_find_dual_inlet",
        "ir_find_isofiles",
        "ir_find_scans"
      ]
    },
    {
      "page": "ir_generate_tibble",
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        "ir_generate_scans_tibble",
        "ir_generate_tibble",
        "ir_generate_traces_tibble"
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    },
    {
      "page": "ir_get_data",
      "title": "Get data frame from aggregated data",
      "topics": [
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        "ir_get_data",
        "ir_get_metadata",
        "ir_get_resistors",
        "ir_get_scans",
        "ir_get_traces",
        "ir_get_vendor_data_table"
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    },
    {
      "page": "problems",
      "title": "Retrieve parsing problems",
      "topics": [
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    },
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      "topics": [
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    },
    {
      "page": "ir_isofiles_storage",
      "title": "Save and load isofiles",
      "topics": [
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        "ir_load_isofiles",
        "ir_save_isofiles"
      ]
    },
    {
      "page": "ir_metadata",
      "title": "Filter, mutate, or join the metadata of isofiles",
      "topics": [
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        "ir_join_metadata",
        "ir_metadata",
        "ir_mutate_metadata"
      ]
    },
    {
      "page": "ir_options",
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      "topics": [
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        "ir_get_option",
        "ir_get_options",
        "ir_options"
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    },
    {
      "page": "ir_plot_dual_inlet",
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    },
    {
      "page": "ir_plot_scans",
      "title": "Plot scan data",
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    {
      "page": "ir_plot_traces",
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      "topics": [
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    },
    {
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      "title": "Read isotope data files",
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    {
      "page": "ir_aggregator",
      "title": "Dynamic data aggregator",
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        "ir_get_aggregator",
        "ir_register_aggregator",
        "ir_start_aggregator"
      ]
    },
    {
      "page": "ir_storage",
      "title": "Save and load aggregated isofile data",
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        "ir_save_aggregated_data",
        "ir_storage"
      ]
    }
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      "headings": [
        "Reading isotope files",
        "ir_find_isofiles() *",
        "ir_read_isofiles() *",
        "bonus: combine collections with c()",
        "bonus: ir_save_isofiles() / ir_load_isofiles()",
        "Aggregating data",
        "ir_aggregate_isofiles() *",
        "bonus: intensity units",
        "bonus: ir_get_aggregator()",
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        "bonus: ir_get_problems() / ir_show_problems()",
        "Accessing the data",
        "ir_get_data()",
        "shortcuts ir_get_metadata() / ir_get_traces() / ...",
        "bonus: ir_get_vendor_data_table()",
        "ir_filter_metadata() / ir_mutate_metadata() / ir_join_metadata()",
        "bonus: ir_filter_for_continuous_flow() / ir_filter_for_dual_inlet() / ir_filter_for_scans()",
        "ir_filter_masses()",
        "bonus: ir_save_aggregated_data() / ir_load_aggregated_data()",
        "Calculating ratios",
        "ir_calculate_ratios()",
        "bonus: base mass, additive offsets, and normalization",
        "Visualizing data",
        "ir_plot_traces()",
        "bonus: selecting masses and ratios",
        "bonus: ggplot modifications",
        "bonus ir_generate_traces_tibble() / ir_generate_cycles_tibble() / ir_generate_scans_tibble()",
        "ir_plot_dual_inlet()",
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        "Exporting data",
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        "Package options",
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      "created": "2026-06-09 19:34:04",
      "modified": "2026-08-14 12:39:40",
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