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  "Title": "Core Functions to Read and Fit 13c Time Series from Breath Tests",
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  "Description": "Reads several formats of 13C data (IRIS/Wagner, BreathID)\nand CSV.  Creates artificial sample data for testing.  Fits\nMaes/Ghoos, Bluck-Coward self-correcting formula using 'nls',\n'nlme'. Methods to fit breath test curves with Bayesian Stan\nmethods are refactored to package 'breathteststan'. For a Shiny\nGUI, see package 'dmenne/breathtestshiny' on github.",
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  "Author": "Dieter Menne [aut, cre],\nMenne Biomed Consulting Tuebingen [cph],\nBenjamin Misselwitz [fnd],\nMark Fox [fnd],\nAndreas Steingoetter [dtc],\nUniversity Hospital of Zurich, Dep. Gastroenterology [fnd, dtc]",
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    "breathtest_read_function",
    "btcore_file",
    "cleanup_data",
    "coef_by_group",
    "coef_diff_by_group",
    "cum_exp_beta",
    "dob_to_pdr",
    "exp_beta",
    "extract_id",
    "nlme_fit",
    "nls_fit",
    "null_fit",
    "read_any_breathtest",
    "read_breathid",
    "read_breathid_xml",
    "read_breathtest_excel",
    "read_iris",
    "read_iris_csv",
    "simulate_breathtest_data",
    "subsample_data",
    "t50_bluck_coward",
    "t50_maes_ghoos",
    "t50_maes_ghoos_scintigraphy",
    "tlag_bluck_coward",
    "tlag_maes_ghoos"
  ],
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      "name": "usz_13c",
      "title": "Zurich sample set of 13C breath test data",
      "object": "usz_13c",
      "file": "usz_13c.rda",
      "class": [
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        "tbl",
        "data.frame"
      ],
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        "patient_id",
        "group",
        "minute",
        "pdr"
      ],
      "rows": 10881,
      "table": true,
      "tojson": true
    },
    {
      "name": "usz_13c_a",
      "title": "Exotic 13C breath test data",
      "object": "usz_13c_a",
      "file": "usz_13c_a.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "patient_id",
        "group",
        "minute",
        "pdr"
      ],
      "rows": 986,
      "table": true,
      "tojson": true
    },
    {
      "name": "usz_13c_d",
      "title": "13C breath test data with MRI emptying for comparison",
      "object": "usz_13c_d",
      "file": "usz_13c_d.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "patient_id",
        "group",
        "minute",
        "pdr"
      ],
      "rows": 1176,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "AIC.breathtestnlmefit",
      "title": "S3 AIC method for breathtestnlmefit",
      "topics": [
        "AIC.breathtestnlmefit"
      ]
    },
    {
      "page": "augment.breathtestfit",
      "title": "Augmented prediction for breathtest fit",
      "topics": [
        "augment.breathtestfit"
      ]
    },
    {
      "page": "breathtest_data",
      "title": "Data structure with PDR data and descriptors for breath test records",
      "topics": [
        "breathtest_data"
      ]
    },
    {
      "page": "breathtest_read_function",
      "title": "Snoop method to read breath test file",
      "topics": [
        "breathtest_read_function"
      ]
    },
    {
      "page": "btcore_file",
      "title": "Path to example breath test data file",
      "topics": [
        "btcore_file"
      ]
    },
    {
      "page": "cleanup_data",
      "title": "Transforms 13C breath data into a clean format for fitting",
      "topics": [
        "cleanup_data"
      ]
    },
    {
      "page": "coef_by_group",
      "title": "Tabulates per-group breath test parameters",
      "topics": [
        "coef_by_group"
      ]
    },
    {
      "page": "coef_diff_by_group",
      "title": "Tabulates breath test parameter differences of groups",
      "topics": [
        "coef_diff_by_group"
      ]
    },
    {
      "page": "coef.breathtestfit",
      "title": "S3 coef and summary for breathtestfit",
      "topics": [
        "coef.breathtestfit"
      ]
    },
    {
      "page": "cum_exp_beta",
      "title": "Cumulative exponential beta function",
      "topics": [
        "cum_exp_beta"
      ]
    },
    {
      "page": "dob_to_pdr",
      "title": "Convert breath test DOB data to PDR data",
      "topics": [
        "dob_to_pdr"
      ]
    },
    {
      "page": "exp_beta",
      "title": "Exponential beta function for 13C breath data",
      "topics": [
        "exp_beta"
      ]
    },
    {
      "page": "extract_id",
      "title": "Extracts an ID from string IRIS CSV file",
      "topics": [
        "extract_id"
      ]
    },
    {
      "page": "nlme_fit",
      "title": "Mixed-model nlme fit to 13C Breath Data",
      "topics": [
        "nlme_fit"
      ]
    },
    {
      "page": "nls_fit",
      "title": "Individual curve fit with nls to 13C breath test data",
      "topics": [
        "nls_fit"
      ]
    },
    {
      "page": "null_fit",
      "title": "Convert data to class breathtestfit",
      "topics": [
        "null_fit"
      ]
    },
    {
      "page": "plot.breathtestfit",
      "title": "S3 plot method for breathtestfit",
      "topics": [
        "plot.breathtestfit"
      ]
    },
    {
      "page": "read_any_breathtest",
      "title": "Read breathtest files of any format",
      "topics": [
        "read_any_breathtest"
      ]
    },
    {
      "page": "read_breathid",
      "title": "Read BreathID file",
      "topics": [
        "read_breathid"
      ]
    },
    {
      "page": "read_breathid_xml",
      "title": "Read new BreathID/Examens XML file",
      "topics": [
        "read_breathid_xml"
      ]
    },
    {
      "page": "read_breathtest_excel",
      "title": "Reads breathtest data in Excel format",
      "topics": [
        "read_breathtest_excel"
      ]
    },
    {
      "page": "read_iris",
      "title": "Read 13C data from IRIS/Wagner Analysen",
      "topics": [
        "read_iris"
      ]
    },
    {
      "page": "read_iris_csv",
      "title": "Read 13C data from IRIS/Wagner Analysen in CSV Format",
      "topics": [
        "read_iris_csv"
      ]
    },
    {
      "page": "sigma.breathtestnlmefit",
      "title": "S3 method to extract the fit's residual standard deviation",
      "topics": [
        "sigma.breathtestnlmefit"
      ]
    },
    {
      "page": "simulate_breathtest_data",
      "title": "Simulate 13C breath time series data",
      "topics": [
        "simulate_breathtest_data"
      ]
    },
    {
      "page": "subsample_data",
      "title": "Decimate densely sampled 13C time series",
      "topics": [
        "subsample_data"
      ]
    },
    {
      "page": "t50_bluck_coward",
      "title": "Bluck-Coward self-corrected half-emptying time",
      "topics": [
        "t50_bluck_coward"
      ]
    },
    {
      "page": "t50_maes_ghoos",
      "title": "Half-emptying time by Maes/Ghoos method",
      "topics": [
        "t50_maes_ghoos"
      ]
    },
    {
      "page": "t50_maes_ghoos_scintigraphy",
      "title": "Half-emptying time t50 from Maes/Ghoos fit with scintigraphic correction",
      "topics": [
        "t50_maes_ghoos_scintigraphy"
      ]
    },
    {
      "page": "tidy.breathtestfit",
      "title": "Broom-style tidying methods for breathtestfit",
      "topics": [
        "tidy.breathtestfit"
      ]
    },
    {
      "page": "tlag_bluck_coward",
      "title": "Lag phase for Bluck-Coward self-correcting fit",
      "topics": [
        "tlag_bluck_coward"
      ]
    },
    {
      "page": "tlag_maes_ghoos",
      "title": "So-called lag time from Maes/Ghoos fit",
      "topics": [
        "tlag_maes_ghoos"
      ]
    },
    {
      "page": "usz_13c",
      "title": "Zurich sample set of 13C breath test data",
      "topics": [
        "usz_13c"
      ]
    },
    {
      "page": "usz_13c_a",
      "title": "Exotic 13C breath test data",
      "topics": [
        "usz_13c_a"
      ]
    },
    {
      "page": "usz_13c_d",
      "title": "13C breath test data with MRI emptying for comparison",
      "topics": [
        "usz_13c_d"
      ]
    }
  ],
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  "_vignettes": [
    {
      "source": "data_formats.Rmd",
      "filename": "data_formats.html",
      "title": "Data formats",
      "author": "Dieter Menne, dieter.menne@menne.biomed.de",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Concepts",
        "Automatic grouping",
        "Simulated data",
        "Built-in data sets",
        "Generic formats",
        "How to use the Excel data formats",
        "Two-column format",
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        "IRIS-Wagner composite data",
        "IRIS/Wagner CSV format",
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      "created": "2017-10-09 16:38:09",
      "modified": "2024-11-20 16:14:58",
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    {
      "source": "methods_and_concepts.Rmd",
      "filename": "methods_and_concepts.html",
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