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  "Title": "Chromatographic Data Analysis Toolkit",
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  "Authors@R": "c(\nperson(\"Ethan\", \"Bass\", , \"ethanbass@gmail.com\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-6175-6739\")),\nperson(c(\"Hans\",\"W\"), \"Borchers\", role = c(\"ctb\", \"cph\"),\ncomment = c(\"Author of savgol and pinv functions bundled from pracma\")),\nperson(\"Ron\", \"Wehrens\", role = c(\"ctb\", \"cph\"),\ncomment = c(\"Author of code adapted from alsace and ptw\"))\n)",
  "Maintainer": "Ethan Bass <ethanbass@gmail.com>",
  "Description": "Analyzes chromatographic data from high performance liquid\nchromatography with diode-array or ultraviolet detection\n(HPLC-DAD/UV), as well as other detectors, in a high-throughput\nand reproducible workflow. Provides functionality for\npreprocessing, alignment, peak detection, peak model fitting,\npeak table construction, and data visualization. Chromatogram\nalignment is available via parametric time warping (as\nimplemented in 'ptw') or variable penalty dynamic time warping\n(as implemented in 'VPdtw'). Peak detection is based on a\nfirst-derivative zero-crossing algorithm, and peak shapes are\nfitted using non-linear least squares. Underlying methodologies\nare described in: Wehrens et al. (2015)\n<doi:10.1007/s11306-014-0683-5> for preprocessing and peak\ntable construction; Eilers (2004) <doi:10.1021/ac034800e> and\nWehrens et al. (2015) <doi:10.1093/bioinformatics/btv299> for\nparametric time warping; Clifford & Stone (2012)\n<doi:10.18637/jss.v047.i08> for variable penalty dynamic time\nwarping; Tom O'Haver\n<https://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm>\nfor peak detection; Lan & Jorgenson (2001)\n<doi:10.1016/S0021-9673(01)00594-5> for exponential-Gaussian\nhybrid fitting; and Naish & Hartwell (1988)\n<doi:10.1007/BF02268168> for bi-exponentially modified Gaussian\nfitting.",
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  "Date/Publication": "2026-10-20 19:36:22 UTC",
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    "get_agilent_threshold",
    "get_baseline",
    "get_lambdas",
    "get_peaks",
    "get_peaktable",
    "get_purity",
    "get_spectra",
    "get_time_resolution",
    "get_times",
    "match_peaks",
    "merge_peaks",
    "mirror_plot",
    "normalize_data",
    "plot_all_spectra",
    "plot_baseline",
    "plot_chrom_contour",
    "plot_chroms",
    "plot_chroms_heatmap",
    "plot_spectrum",
    "plot_spectrum_inset",
    "preprocess",
    "read_chroms",
    "reshape_chroms",
    "reshape_peaktable",
    "scan_chrom",
    "subtract_blanks",
    "trim_peak",
    "write_peaktable"
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      "table": false,
      "tojson": true
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      "object": "Sa",
      "class": [
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      ],
      "fields": [],
      "table": true,
      "tojson": true
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      "title": "Preprocessed goldenrod root chromatograms",
      "object": "Sa_pr",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "Sa_warp",
      "title": "Warped goldenrod root chromatograms",
      "object": "Sa_warp",
      "class": [
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      "fields": [],
      "table": true,
      "tojson": true
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    {
      "page": "chromatographR-package",
      "title": "chromatographR: Chromatographic Data Analysis Toolkit",
      "topics": [
        "chromatographR-package",
        "chromatographR"
      ]
    },
    {
      "page": "sub-.matched_peak_list",
      "title": "Subset matched peak list",
      "topics": [
        "[.matched_peak_list"
      ]
    },
    {
      "page": "sub-.peak_list",
      "title": "Subset peak list",
      "topics": [
        "[.peak_list"
      ]
    },
    {
      "page": "sub-.peak_table",
      "title": "Subset peak table",
      "topics": [
        "[.peak_table"
      ]
    },
    {
      "page": "annotate_peaks",
      "title": "Annotate peaks on a chromatogram",
      "topics": [
        "annotate_peaks"
      ]
    },
    {
      "page": "attach_metadata",
      "title": "Attach sample metadata to a 'peak_table'",
      "topics": [
        "attach_metadata"
      ]
    },
    {
      "page": "attach_ref_spectra",
      "title": "Attach reference spectra to a 'peak_table' object",
      "topics": [
        "attach_ref_spectra"
      ]
    },
    {
      "page": "baseline_estimators",
      "title": "Baseline estimators",
      "topics": [
        "baseline_estimators"
      ]
    },
    {
      "page": "boxplot.peak_table",
      "title": "Make boxplot from peak table",
      "concept": [
        "visualization functions"
      ],
      "topics": [
        "boxplot.peak_table"
      ]
    },
    {
      "page": "cluster_spectra",
      "title": "Cluster spectra",
      "topics": [
        "cluster_spectra"
      ]
    },
    {
      "page": "combine_peaks",
      "title": "Combine duplicate peaks",
      "concept": [
        "utility functions"
      ],
      "topics": [
        "combine_peaks"
      ]
    },
    {
      "page": "correct_baseline",
      "title": "Correct baseline along the time axis",
      "concept": [
        "preprocessing functions"
      ],
      "topics": [
        "correct_baseline"
      ]
    },
    {
      "page": "correct_peaks",
      "title": "Correct peak positions according to a warping model",
      "topics": [
        "correct_peaks"
      ]
    },
    {
      "page": "correct_rt",
      "title": "Retention time alignment via time warping",
      "topics": [
        "correct_rt"
      ]
    },
    {
      "page": "correct_rt_group",
      "title": "Correct retention time with group-based warping",
      "topics": [
        "correct_rt_group"
      ]
    },
    {
      "page": "crop_chroms",
      "title": "Crop chromatograms",
      "concept": [
        "preprocessing functions"
      ],
      "topics": [
        "crop_chroms"
      ]
    },
    {
      "page": "filter_peaks",
      "title": "Filter peak lists",
      "topics": [
        "filter_peaks"
      ]
    },
    {
      "page": "filter_peaktable",
      "title": "Filter peak table",
      "topics": [
        "filter_peaktable"
      ]
    },
    {
      "page": "get_baseline",
      "title": "Retrieve estimated baseline",
      "concept": [
        "accessors"
      ],
      "topics": [
        "get_baseline"
      ]
    },
    {
      "page": "get_lambdas",
      "title": "Get lambdas",
      "concept": [
        "accessors"
      ],
      "topics": [
        "get_lambdas"
      ]
    },
    {
      "page": "get_peaks",
      "title": "Get peak list",
      "topics": [
        "get_peaks"
      ]
    },
    {
      "page": "get_peaktable",
      "title": "Convert peak lists into an aligned peak table",
      "topics": [
        "get_peaktable",
        "get_peaktable.default",
        "get_peaktable.matched_peak_list",
        "get_peaktable.matched_peak_list_set"
      ]
    },
    {
      "page": "get_spectra",
      "title": "Extract a spectrum from a chromatogram",
      "topics": [
        "get_spectra"
      ]
    },
    {
      "page": "get_time_resolution",
      "title": "Get time resolution",
      "concept": [
        "accessors"
      ],
      "topics": [
        "get_time_resolution"
      ]
    },
    {
      "page": "get_times",
      "title": "Get retention times",
      "concept": [
        "accessors"
      ],
      "topics": [
        "get_times"
      ]
    },
    {
      "page": "match_peaks",
      "title": "Match peaks across chromatograms",
      "topics": [
        "match_peaks"
      ]
    },
    {
      "page": "merge_peaks",
      "title": "Merge split peaks",
      "concept": [
        "utility functions"
      ],
      "topics": [
        "merge_peaks"
      ]
    },
    {
      "page": "mirror_plot",
      "title": "Make mirror plot from peak table",
      "concept": [
        "visualization functions"
      ],
      "topics": [
        "mirror_plot"
      ]
    },
    {
      "page": "normalize_data",
      "title": "Normalize peak table or chromatograms",
      "topics": [
        "normalize_data"
      ]
    },
    {
      "page": "peak_table-class",
      "title": "Peak Table Object",
      "topics": [
        "peak_table",
        "peak_table-class"
      ]
    },
    {
      "page": "pk_tab",
      "title": "Goldenrod peak table",
      "concept": [
        "data objects"
      ],
      "topics": [
        "pk_tab"
      ]
    },
    {
      "page": "plot_all_spectra",
      "title": "Plot all spectra for chosen peak",
      "concept": [
        "visualization functions"
      ],
      "topics": [
        "plot_all_spectra"
      ]
    },
    {
      "page": "plot_baseline",
      "title": "Plot an estimated baseline",
      "topics": [
        "plot_baseline"
      ]
    },
    {
      "page": "plot_chrom_contour",
      "title": "Plot a chromatogram as a contour plot",
      "concept": [
        "visualization functions"
      ],
      "topics": [
        "plot_chrom_contour"
      ]
    },
    {
      "page": "plot_chroms",
      "title": "Plot traces from list of chromatograms",
      "concept": [
        "visualization functions"
      ],
      "topics": [
        "plot_chroms"
      ]
    },
    {
      "page": "plot_chroms_heatmap",
      "title": "Plot chromatograms as heatmap",
      "concept": [
        "visualization functions"
      ],
      "topics": [
        "plot_chroms_heatmap"
      ]
    },
    {
      "page": "plot_spectrum",
      "title": "Plot spectrum from peak table",
      "concept": [
        "visualization functions"
      ],
      "topics": [
        "plot_spectrum"
      ]
    },
    {
      "page": "plot_spectrum_inset",
      "title": "Plot a chromatogram or chromatograms with an inset UV spectrum",
      "topics": [
        "plot_spectrum_inset"
      ]
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