{
  "_id": "6a211a1fcd65a98ecbd1d0f9",
  "Package": "alkahest",
  "Title": "Pre-Processing XY Data from Experimental Methods",
  "Version": "1.3.0.9000",
  "Authors@R": "c(\nperson(\"Nicolas\", \"Frerebeau\", , \"nicolas.frerebeau@u-bordeaux-montaigne.fr\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5759-4944\")),\nperson(\"Brice\", \"Lebrun\", role = \"art\",\ncomment = c(ORCID = \"0000-0001-7503-8685\", \"Logo designer\")),\nperson(\"Université Bordeaux Montaigne\", role = \"fnd\",\ncomment = c(ROR = \"03pbgwk21\")),\nperson(\"CNRS\", role = \"fnd\",\ncomment = c(ROR = \"02feahw73\"))\n)",
  "Maintainer": "Nicolas Frerebeau\n<nicolas.frerebeau@u-bordeaux-montaigne.fr>",
  "Description": "A lightweight, dependency-free toolbox for pre-processing\nXY data from experimental methods (i.e. any signal that can be\nmeasured along a continuous variable). This package provides\nmethods for baseline estimation and correction, smoothing,\nnormalization, integration and peaks detection. Baseline\ncorrection methods includes polynomial fitting as described in\nLieber and Mahadevan-Jansen (2003)\n<doi:10.1366/000370203322554518>, Rolling Ball algorithm after\nKneen and Annegarn (1996) <doi:10.1016/0168-583X(95)00908-6>,\nSNIP algorithm after Ryan et al. (1988)\n<doi:10.1016/0168-583X(88)90063-8>, 4S Peak Filling after\nLiland (2015) <doi:10.1016/j.mex.2015.02.009> and more.",
  "License": "GPL (>= 3)",
  "URL": "https://codeberg.org/tesselle/alkahest,\nhttps://tesselle.r-universe.dev/alkahest,\nhttps://packages.tesselle.org/alkahest/",
  "BugReports": "https://codeberg.org/tesselle/alkahest/issues",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "Collate": "'AllGenerics.R' 'alkahest-internal.R' 'alkahest-package.R'\n'baseline.R' 'data.R' 'integrate.R' 'peaks.R' 'replace.R'\n'resample.R' 'rescale.R' 'signal.R' 'smooth.R' 'windows.R'\n'xrd.R'",
  "Config/roxygen2/version": "8.0.0",
  "Repository": "https://tesselle.r-universe.dev",
  "Date/Publication": "2026-05-04 09:18:47 UTC",
  "RemoteUrl": "https://codeberg.org/tesselle/alkahest",
  "RemoteRef": "HEAD",
  "RemoteSha": "2bb8381d344f8f0710a2a1ce6f0ceb6e95753523",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-03 07:11:09 UTC",
    "User": "root"
  },
  "Author": "Nicolas Frerebeau [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-5759-4944>),\nBrice Lebrun [art] (ORCID: <https://orcid.org/0000-0001-7503-8685>,\nLogo designer),\nUniversité Bordeaux Montaigne [fnd] (ROR: <https://ror.org/03pbgwk21>),\nCNRS [fnd] (ROR: <https://ror.org/02feahw73>)",
  "MD5sum": "822ae8c49100f06fd770459cad0ad719",
  "_user": "tesselle",
  "_type": "src",
  "_file": "alkahest_1.3.0.9000.tar.gz",
  "_fileid": "dfcd6f4619a3bd72e1c9978e2efa8c723ffd796fa0f50535708899e90ecd3294",
  "_filesize": 2062555,
  "_sha256": "dfcd6f4619a3bd72e1c9978e2efa8c723ffd796fa0f50535708899e90ecd3294",
  "_created": "2026-06-03T07:11:09.000Z",
  "_published": "2026-06-04T06:24:31.406Z",
  "_distro": "noble",
  "_jobs": [
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  "_buildurl": "https://github.com/r-universe/tesselle/actions/runs/26869348436",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://codeberg.org/tesselle/alkahest",
  "_commit": {
    "id": "2bb8381d344f8f0710a2a1ce6f0ceb6e95753523",
    "author": "nfrerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>",
    "committer": "nfrerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>",
    "message": "Small fixes\n",
    "time": 1777886327
  },
  "_maintainer": {
    "name": "Nicolas Frerebeau",
    "email": "nicolas.frerebeau@u-bordeaux-montaigne.fr",
    "login": "nfrerebeau",
    "mastodon": "@nfrerebeau@archaeo.social",
    "orcid": "0000-0001-5759-4944",
    "description": "Archaeologist, research engineer at @crp2a",
    "uuid": 33983845
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
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    {
      "package": "markdown",
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    {
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      "role": "Suggests"
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      "package": "tinytest",
      "role": "Suggests"
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  "_owner": "codeberg-tesselle",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-23",
      "n": 1
    },
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  ],
  "_tags": [],
  "_topics": [
    "spectroscopy",
    "archaeometry"
  ],
  "_userbio": {
    "uuid": 78033555,
    "type": "organization",
    "name": "tesselle",
    "description": "A collection of R packages for archaeological research and teaching"
  },
  "_downloads": {
    "count": 205,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/alkahest"
  },
  "_devurl": "https://codeberg.org/tesselle/alkahest",
  "_pkgdown": "https://packages.tesselle.org/alkahest/",
  "_searchresults": 11,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/alkahest.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://codeberg.org/tesselle/alkahest",
  "_realowner": "nfrerebeau",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2022-09-15"
    },
    {
      "version": "1.1.0",
      "date": "2023-05-18"
    },
    {
      "version": "1.1.1",
      "date": "2023-06-13"
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      "date": "2024-07-26"
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  ],
  "_exports": [
    "baseline_asls",
    "baseline_linear",
    "baseline_peakfilling",
    "baseline_polynomial",
    "baseline_rollingball",
    "baseline_rubberband",
    "baseline_snip",
    "integrate_rectangle",
    "integrate_trapezoid",
    "ka2_strip_penalized",
    "peaks_find",
    "peaks_fwhm",
    "replace_negative",
    "replace_threshold",
    "resample_bin",
    "resample_down",
    "resample_interpolate",
    "rescale_area",
    "rescale_max",
    "rescale_min",
    "rescale_range",
    "rescale_snv",
    "rescale_total",
    "rescale_transform",
    "signal_bind",
    "signal_correct",
    "signal_drift",
    "signal_mean",
    "signal_select",
    "signal_shift",
    "signal_slice",
    "smooth_likelihood",
    "smooth_loess",
    "smooth_rectangular",
    "smooth_savitzky",
    "smooth_triangular",
    "smooth_whittaker",
    "window_sliding",
    "window_tumbling"
  ],
  "_datasets": [
    {
      "name": "BEGe",
      "title": "Gamma-Ray Spectrometry",
      "object": "BEGe",
      "class": [
        "data.frame"
      ],
      "fields": [
        "energy",
        "count"
      ],
      "rows": 8192,
      "table": true,
      "tojson": true
    },
    {
      "name": "LaBr",
      "title": "Gamma-Ray Spectrometry",
      "object": "LaBr",
      "class": [
        "data.frame"
      ],
      "fields": [
        "energy",
        "count"
      ],
      "rows": 1024,
      "table": true,
      "tojson": true
    },
    {
      "name": "Raman",
      "title": "Raman Spectroscopy",
      "object": "Raman",
      "class": [
        "data.frame"
      ],
      "fields": [
        "shift",
        "intensity"
      ],
      "rows": 1182,
      "table": true,
      "tojson": true
    },
    {
      "name": "XRD",
      "title": "Powder X-ray Diffraction",
      "object": "XRD",
      "class": [
        "data.frame"
      ],
      "fields": [
        "theta",
        "count"
      ],
      "rows": 2989,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "baseline_asls",
      "title": "Asymmetric Least Squares Smoothing",
      "concept": [
        "baseline estimation methods"
      ],
      "topics": [
        "baseline_asls",
        "baseline_asls,ANY,missing-method",
        "baseline_asls,numeric,numeric-method",
        "baseline_asls-method"
      ]
    },
    {
      "page": "baseline_linear",
      "title": "Linear Baseline Estimation",
      "concept": [
        "baseline estimation methods"
      ],
      "topics": [
        "baseline_linear",
        "baseline_linear,ANY,missing-method",
        "baseline_linear,numeric,numeric-method",
        "baseline_linear-method"
      ]
    },
    {
      "page": "baseline_peakfilling",
      "title": "4S Peak Filling",
      "concept": [
        "baseline estimation methods"
      ],
      "topics": [
        "baseline_peakfilling",
        "baseline_peakfilling,ANY,missing-method",
        "baseline_peakfilling,numeric,numeric-method",
        "baseline_peakfilling-method"
      ]
    },
    {
      "page": "baseline_polynomial",
      "title": "Polynomial Baseline Estimation",
      "concept": [
        "baseline estimation methods"
      ],
      "topics": [
        "baseline_polynomial",
        "baseline_polynomial,ANY,missing-method",
        "baseline_polynomial,numeric,numeric-method",
        "baseline_polynomial-method"
      ]
    },
    {
      "page": "baseline_rollingball",
      "title": "Rolling Ball Baseline Estimation",
      "concept": [
        "baseline estimation methods"
      ],
      "topics": [
        "baseline_rollingball",
        "baseline_rollingball,ANY,missing-method",
        "baseline_rollingball,numeric,numeric-method",
        "baseline_rollingball-method"
      ]
    },
    {
      "page": "baseline_rubberband",
      "title": "Rubberband Baseline Estimation",
      "concept": [
        "baseline estimation methods"
      ],
      "topics": [
        "baseline_rubberband",
        "baseline_rubberband,ANY,missing-method",
        "baseline_rubberband,numeric,numeric-method",
        "baseline_rubberband-method"
      ]
    },
    {
      "page": "baseline_snip",
      "title": "SNIP Baseline Estimation",
      "concept": [
        "baseline estimation methods"
      ],
      "topics": [
        "baseline_snip",
        "baseline_snip,ANY,missing-method",
        "baseline_snip,numeric,numeric-method",
        "baseline_snip-method"
      ]
    },
    {
      "page": "BEGe",
      "title": "Gamma-Ray Spectrometry",
      "concept": [
        "datasets"
      ],
      "topics": [
        "BEGe"
      ]
    },
    {
      "page": "integrate_rectangle",
      "title": "Rectangle Rule",
      "concept": [
        "integration methods"
      ],
      "topics": [
        "integrate_rectangle",
        "integrate_rectangle,ANY,missing-method",
        "integrate_rectangle,numeric,numeric-method",
        "integrate_rectangle-method"
      ]
    },
    {
      "page": "integrate_trapezoid",
      "title": "Trapezoidal Rule",
      "concept": [
        "integration methods"
      ],
      "topics": [
        "integrate_trapezoid",
        "integrate_trapezoid,ANY,missing-method",
        "integrate_trapezoid,numeric,numeric-method",
        "integrate_trapezoid-method"
      ]
    },
    {
      "page": "ka2_strip_penalized",
      "title": "Strip XRD ka2",
      "concept": [
        "specialized tools"
      ],
      "topics": [
        "ka2_strip_penalized",
        "ka2_strip_penalized,ANY,missing-method",
        "ka2_strip_penalized,numeric,numeric-method",
        "ka2_strip_penalized-method"
      ]
    },
    {
      "page": "LaBr",
      "title": "Gamma-Ray Spectrometry",
      "concept": [
        "datasets"
      ],
      "topics": [
        "LaBr"
      ]
    },
    {
      "page": "peaks_find",
      "title": "Find Peaks",
      "concept": [
        "peaks detection methods"
      ],
      "topics": [
        "peaks_find",
        "peaks_find,ANY,missing-method",
        "peaks_find,numeric,numeric-method",
        "peaks_find-method"
      ]
    },
    {
      "page": "peaks_fwhm",
      "title": "Half-Width at Half-Maximum",
      "concept": [
        "peaks detection methods"
      ],
      "topics": [
        "peaks_fwhm",
        "peaks_fwhm,ANY,missing-method",
        "peaks_fwhm,numeric,numeric-method",
        "peaks_fwhm-method"
      ]
    },
    {
      "page": "Raman",
      "title": "Raman Spectroscopy",
      "concept": [
        "datasets"
      ],
      "topics": [
        "Raman"
      ]
    },
    {
      "page": "replace_negative",
      "title": "Replace Negative Values",
      "concept": [
        "replacement methods"
      ],
      "topics": [
        "replace_negative",
        "replace_negative,ANY,missing-method",
        "replace_negative,numeric,numeric-method",
        "replace_negative-method"
      ]
    },
    {
      "page": "replace_threshold",
      "title": "Replace Values Below a Given Threshold",
      "concept": [
        "replacement methods"
      ],
      "topics": [
        "replace_threshold",
        "replace_threshold,ANY,missing,function-method",
        "replace_threshold,ANY,missing,numeric-method",
        "replace_threshold,numeric,numeric,function-method",
        "replace_threshold,numeric,numeric,numeric-method",
        "replace_threshold-method"
      ]
    },
    {
      "page": "resample_bin",
      "title": "Bin",
      "concept": [
        "resampling methods"
      ],
      "topics": [
        "resample_bin",
        "resample_bin,ANY,missing-method",
        "resample_bin,numeric,numeric-method",
        "resample_bin-method"
      ]
    },
    {
      "page": "resample_down",
      "title": "Downsample",
      "concept": [
        "resampling methods"
      ],
      "topics": [
        "resample_down",
        "resample_down,ANY,missing-method",
        "resample_down,numeric,numeric-method",
        "resample_down-method"
      ]
    },
    {
      "page": "resample_interpolate",
      "title": "Linearly Interpolate",
      "concept": [
        "resampling methods"
      ],
      "topics": [
        "resample_interpolate",
        "resample_interpolate,ANY,missing-method",
        "resample_interpolate,numeric,numeric-method",
        "resample_interpolate-method"
      ]
    },
    {
      "page": "rescale_area",
      "title": "Normalize intensities by AUC",
      "concept": [
        "normalization methods"
      ],
      "topics": [
        "rescale_area",
        "rescale_area,ANY,missing-method",
        "rescale_area,numeric,numeric-method",
        "rescale_area-method"
      ]
    },
    {
      "page": "rescale_range",
      "title": "Rescales intensities to have specified minimum and maximum",
      "concept": [
        "normalization methods"
      ],
      "topics": [
        "rescale_max",
        "rescale_max,ANY,missing-method",
        "rescale_max,numeric,numeric-method",
        "rescale_max-method",
        "rescale_min",
        "rescale_min,ANY,missing-method",
        "rescale_min,numeric,numeric-method",
        "rescale_min-method",
        "rescale_range",
        "rescale_range,ANY,missing-method",
        "rescale_range,numeric,numeric-method",
        "rescale_range-method"
      ]
    },
    {
      "page": "rescale_snv",
      "title": "Standard Normal Variate (SNV) Transformation",
      "concept": [
        "normalization methods"
      ],
      "topics": [
        "rescale_snv",
        "rescale_snv,ANY,missing-method",
        "rescale_snv,numeric,numeric-method",
        "rescale_snv-method"
      ]
    },
    {
      "page": "rescale_total",
      "title": "Rescale intensities to sum to a specified value",
      "concept": [
        "normalization methods"
      ],
      "topics": [
        "rescale_total",
        "rescale_total,ANY,missing-method",
        "rescale_total,numeric,numeric-method",
        "rescale_total-method"
      ]
    },
    {
      "page": "rescale_transform",
      "title": "Transform Intensities",
      "concept": [
        "normalization methods"
      ],
      "topics": [
        "rescale_transform",
        "rescale_transform,ANY,missing-method",
        "rescale_transform,numeric,numeric-method",
        "rescale_transform-method"
      ]
    },
    {
      "page": "signal_bind",
      "title": "Bind",
      "concept": [
        "signal processing methods"
      ],
      "topics": [
        "signal_bind",
        "signal_bind,ANY-method",
        "signal_bind-method"
      ]
    },
    {
      "page": "signal_correct",
      "title": "Baseline Correction",
      "concept": [
        "signal processing methods"
      ],
      "topics": [
        "signal_correct",
        "signal_correct,ANY,missing-method",
        "signal_correct,numeric,numeric-method",
        "signal_correct-method"
      ]
    },
    {
      "page": "signal_drift",
      "title": "Drift Intensities",
      "concept": [
        "signal processing methods"
      ],
      "topics": [
        "signal_drift",
        "signal_drift,ANY,missing,ANY-method",
        "signal_drift,numeric,numeric,numeric-method",
        "signal_drift-method"
      ]
    },
    {
      "page": "signal_mean",
      "title": "Mean Intensities",
      "concept": [
        "signal processing methods"
      ],
      "topics": [
        "signal_mean",
        "signal_mean,ANY-method",
        "signal_mean-method"
      ]
    },
    {
      "page": "signal_shift",
      "title": "Shift the X Scale",
      "concept": [
        "signal processing methods"
      ],
      "topics": [
        "signal_shift",
        "signal_shift,ANY,missing-method",
        "signal_shift,numeric,numeric-method",
        "signal_shift-method"
      ]
    },
    {
      "page": "smooth_likelihood",
      "title": "Penalized Likelihood Smoothing",
      "concept": [
        "smoothing methods"
      ],
      "topics": [
        "smooth_likelihood",
        "smooth_likelihood,ANY,missing-method",
        "smooth_likelihood,numeric,numeric-method",
        "smooth_likelihood-method"
      ]
    },
    {
      "page": "smooth_loess",
      "title": "Loess Smoothing",
      "concept": [
        "smoothing methods"
      ],
      "topics": [
        "smooth_loess",
        "smooth_loess,ANY,missing-method",
        "smooth_loess,numeric,numeric-method",
        "smooth_loess-method"
      ]
    },
    {
      "page": "smooth_rectangular",
      "title": "Rectangular Smoothing",
      "concept": [
        "smoothing methods"
      ],
      "topics": [
        "smooth_rectangular",
        "smooth_rectangular,ANY,missing-method",
        "smooth_rectangular,numeric,numeric-method",
        "smooth_rectangular-method"
      ]
    },
    {
      "page": "smooth_savitzky",
      "title": "Savitzky-Golay Filter",
      "concept": [
        "smoothing methods"
      ],
      "topics": [
        "smooth_savitzky",
        "smooth_savitzky,ANY,missing-method",
        "smooth_savitzky,numeric,numeric-method",
        "smooth_savitzky-method"
      ]
    },
    {
      "page": "smooth_triangular",
      "title": "Triangular Smoothing",
      "concept": [
        "smoothing methods"
      ],
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