{
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  "Package": "metabodecon",
  "Title": "Deconvolution and Alignment of 1d NMR Spectra",
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  "Authors@R": "c(\nperson(given = \"Tobias\",\nfamily = \"Schmidt\",\nrole = c(\"aut\", \"cre\", \"cph\"),\nemail = \"tobias.schmidt331@gmail.com\"),\nperson(given = \"Martina\",\nfamily = \"Haeckl\",\nrole = c(\"aut\", \"cph\"),\nemail = \"martina.haeckl@stud.uni-regensburg.de\"),\nperson(given = \"Yanren Linda\",\nfamily = \"Hu\",\nrole = c(\"ctb\"),\nemail = \"yanren-linda.hu@klinik.uni-regensburg.de\"),\nperson(given = \"Wolfram\",\nfamily = \"Gronwald\",\nrole = c(\"aut\", \"cph\"),\nemail = \"wolfram.gronwald@klinik.uni-regensburg.de\")\n)",
  "Author": "Tobias Schmidt [aut, cre, cph], Martina Haeckl [aut, cph],\nYanren Linda Hu [ctb], Wolfram Gronwald [aut, cph]",
  "Maintainer": "Tobias Schmidt <tobias.schmidt331@gmail.com>",
  "Description": "A framework for deconvolution, alignment and\npostprocessing of 1-dimensional (1d) nuclear magnetic resonance\n(NMR) spectra, resulting in a data matrix of aligned signal\nintegrals. The deconvolution part uses the algorithm described\nin Koh et al. (2009) <doi:10.1016/j.jmr.2009.09.003>. The\nalignment part is based on functions from the 'speaq' package,\ndescribed in Beirnaert et al. (2018)\n<doi:10.1371/journal.pcbi.1006018> and Vu et al. (2011)\n<doi:10.1186/1471-2105-12-405>. A detailed description and\nevaluation of an early version of the package, 'MetaboDecon1D\nv0.2.2', can be found in Haeckl et al. (2021)\n<doi:10.3390/metabo11070452>.",
  "License": "GPL (>= 3)",
  "URL": "https://github.com/spang-lab/metabodecon/,\nhttps://spang-lab.github.io/metabodecon/",
  "BugReports": "https://github.com/spang-lab/metabodecon/issues",
  "biocViews": "NMR, Deconvolution",
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  "Repository": "https://spang-lab.r-universe.dev",
  "Date/Publication": "2026-07-22 04:42:51 UTC",
  "RemoteUrl": "https://github.com/spang-lab/metabodecon",
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    "message": "CI: skip the align dependency-install test on Windows (#28)\n\nThe slow test \"align can install its dependencies\" unloads the compiled\nBioconductor packages impute/MassSpecWavelet, swaps .libPaths() and reloads\nthem from a fresh library. On Windows unloadNamespace() leaves the package DLL\nloaded and locked, so re-registering the native routines from the newly\ninstalled copy crashes the R session with an access violation (exit code\n-1073741819 / 0xC0000005) instead of failing an expectation.\n\nThis surfaced only after b3112d7 flipped the windows-latest release job from\n`fast` to `all`, which enabled RUN_SLOW_TESTS on Windows for the first time.\n\nThe auto-installation logic under test is OS-independent and stays covered by\nthe ubuntu and macOS runners.",
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  "_exports": [
    "aaa_Get_Started",
    "align",
    "as_decon0",
    "as_decon1",
    "as_decon2",
    "as_decons0",
    "as_decons1",
    "as_decons2",
    "as_spectra",
    "as_spectrum",
    "benchmark_mdm",
    "calculate_lorentz_curves",
    "check_mdrb",
    "check_mdrb_deps",
    "combine_peaks",
    "convert_pos",
    "convert_width",
    "cv_mdm",
    "datadir",
    "datadir_persistent",
    "datadir_temp",
    "decon_cachedir",
    "deconvolute",
    "dohCluster",
    "download_example_datasets",
    "draw_spectrum",
    "evalwith",
    "fit_mdm",
    "gen_feat_mat",
    "generate_lorentz_curves",
    "generate_lorentz_curves_sim",
    "get_data_dir",
    "get_names",
    "get_pgrid",
    "get_ppm_range",
    "get_si_mat",
    "get_started",
    "headtail",
    "install_mdrb",
    "is_align",
    "is_aligns",
    "is_decon0",
    "is_decon1",
    "is_decon2",
    "is_decons0",
    "is_decons1",
    "is_decons2",
    "is_spectra",
    "is_spectrum",
    "make_spectrum",
    "metabodecon_file",
    "MetaboDecon1D",
    "plot_lorentz_curves_save_as_png",
    "plot_spectra",
    "plot_spectrum",
    "plot_spectrum_superposition_save_as_png",
    "plot_triplets",
    "read_spectra",
    "read_spectrum",
    "simulate_spectrum",
    "speaq_align",
    "tmpdir",
    "transp",
    "tree",
    "tree_preview",
    "width"
  ],
  "_datasets": [
    {
      "name": "sap",
      "title": "The SAP Dataset",
      "object": "sap",
      "class": [
        "spectra"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sim",
      "title": "The Sim Dataset",
      "object": "sim",
      "class": [
        "spectra"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "aaa_Get_Started",
      "title": "Get URL of Metabodecon \"Get Started\" Page",
      "topics": [
        "aaa_Get_Started",
        "get_started"
      ]
    },
    {
      "page": "align",
      "title": "Align Spectra",
      "topics": [
        "align"
      ]
    },
    {
      "page": "as_metabodecon_class",
      "title": "Convert to a Metabodecon Object",
      "topics": [
        "as_decon0",
        "as_decon1",
        "as_decon2",
        "as_decons0",
        "as_decons1",
        "as_decons2",
        "as_metabodecon_class",
        "as_spectra",
        "as_spectrum"
      ]
    },
    {
      "page": "calculate_lorentz_curves",
      "title": "Calculate lorentz curves for each analyzed spectrum",
      "topics": [
        "calculate_lorentz_curves"
      ]
    },
    {
      "page": "check_mdrb",
      "title": "Check Rust Backend Requirements",
      "topics": [
        "check_mdrb",
        "check_mdrb_deps"
      ]
    },
    {
      "page": "combine_peaks",
      "title": "Combine Peaks",
      "topics": [
        "combine_peaks"
      ]
    },
    {
      "page": "convert_pos",
      "title": "Convert from unit A to unit B",
      "topics": [
        "convert_pos",
        "convert_width"
      ]
    },
    {
      "page": "datadir",
      "title": "Return path to metabodecon's data directory",
      "topics": [
        "datadir"
      ]
    },
    {
      "page": "datadir_persistent",
      "title": "Persistent Data Directory",
      "topics": [
        "datadir_persistent"
      ]
    },
    {
      "page": "datadir_temp",
      "title": "Temporary Data Directory",
      "topics": [
        "datadir_temp"
      ]
    },
    {
      "page": "decon_cachedir",
      "title": "Get Default Cache Directory for Deconvolution",
      "topics": [
        "decon_cachedir"
      ]
    },
    {
      "page": "deconvolute",
      "title": "Deconvolute one or more NMR spectra",
      "topics": [
        "deconvolute"
      ]
    },
    {
      "page": "dohCluster",
      "title": "Cluster Based Peak Alignment",
      "topics": [
        "dohCluster"
      ]
    },
    {
      "page": "download_example_datasets",
      "title": "Download metabodecon Example Datasets",
      "topics": [
        "download_example_datasets"
      ]
    },
    {
      "page": "draw_spectrum",
      "title": "Draw Spectrum",
      "topics": [
        "draw_spectrum"
      ]
    },
    {
      "page": "evalwith",
      "title": "Evaluate an expression with predefined global state",
      "topics": [
        "evalwith"
      ]
    },
    {
      "page": "gen_feat_mat",
      "title": "Generate Feature Matrix.",
      "topics": [
        "gen_feat_mat"
      ]
    },
    {
      "page": "generate_lorentz_curves",
      "title": "Deconvolute one or more NMR spectra",
      "topics": [
        "generate_lorentz_curves",
        "generate_lorentz_curves_sim"
      ]
    },
    {
      "page": "get_data_dir",
      "title": "Retrieve directory path of an example dataset",
      "topics": [
        "get_data_dir"
      ]
    },
    {
      "page": "get_names",
      "title": "Returns the names of a metabodecon collection object.",
      "topics": [
        "get_names"
      ]
    },
    {
      "page": "get_ppm_range",
      "title": "Get PPM Range covered by Spectra",
      "topics": [
        "get_ppm_range"
      ]
    },
    {
      "page": "get_si_mat",
      "title": "Extract Matrix of aligned Signal Intensities",
      "topics": [
        "get_si_mat"
      ]
    },
    {
      "page": "headtail",
      "title": "Show head and tail rows of a matrix-like object",
      "topics": [
        "headtail"
      ]
    },
    {
      "page": "install_mdrb",
      "title": "Install Rust Backend",
      "topics": [
        "install_mdrb"
      ]
    },
    {
      "page": "is_metabodecon_class",
      "title": "Is an Object from a Metabodecon Class?",
      "topics": [
        "is_align",
        "is_aligns",
        "is_decon0",
        "is_decon1",
        "is_decon2",
        "is_decons0",
        "is_decons1",
        "is_decons2",
        "is_metabodecon_class",
        "is_spectra",
        "is_spectrum"
      ]
    },
    {
      "page": "make_spectrum",
      "title": "Create a Spectrum Object",
      "topics": [
        "make_spectrum"
      ]
    },
    {
      "page": "mdm",
      "title": "Metabodecon Models",
      "topics": [
        "benchmark_mdm",
        "cv_mdm",
        "fit_mdm",
        "get_pgrid",
        "mdm"
      ]
    },
    {
      "page": "mdm_methods",
      "title": "S3 methods for mdm objects",
      "topics": [
        "coef.mdm",
        "mdm_methods",
        "plot.mdm",
        "predict.mdm",
        "print.mdm",
        "print.summary.mdm",
        "summary.mdm"
      ]
    },
    {
      "page": "metabodecon_file",
      "title": "Return Path to File or Directory in metabodecon Package",
      "topics": [
        "metabodecon_file"
      ]
    },
    {
      "page": "MetaboDecon1D",
      "title": "Deconvolute 1D NMR spectrum",
      "topics": [
        "MetaboDecon1D"
      ]
    },
    {
      "page": "plot_lorentz_curves_save_as_png",
      "title": "Plot lorentz curves for variable range",
      "topics": [
        "plot_lorentz_curves_save_as_png"
      ]
    },
    {
      "page": "plot_spectra",
      "title": "Plot Spectra",
      "topics": [
        "plot_spectra"
      ]
    },
    {
      "page": "plot_spectrum",
      "title": "Plot Spectrum",
      "topics": [
        "plot_spectrum"
      ]
    },
    {
      "page": "plot_spectrum_superposition_save_as_png",
      "title": "Plot spectrum approx for variable range",
      "topics": [
        "plot_spectrum_superposition_save_as_png"
      ]
    },
    {
      "page": "plot_triplets",
      "title": "Plot peak triplets for variable range",
      "topics": [
        "plot_triplets"
      ]
    },
    {
      "page": "print_methods",
      "title": "S3 Methods for Printing Metabodecon Objects",
      "topics": [
        "print.align",
        "print.aligns",
        "print.decon1",
        "print.decon2",
        "print.decons1",
        "print.decons2",
        "print.spectra",
        "print.spectrum",
        "print_methods"
      ]
    },
    {
      "page": "read_spectra",
      "title": "Read one or more spectra from Disk",
      "topics": [
        "read_spectra"
      ]
    },
    {
      "page": "read_spectrum",
      "title": "Read one or more spectra from Disk",
      "topics": [
        "read_spectrum"
      ]
    },
    {
      "page": "sap",
      "title": "The SAP Dataset",
      "topics": [
        "sap"
      ]
    },
    {
      "page": "sim",
      "title": "The Sim Dataset",
      "topics": [
        "sim"
      ]
    },
    {
      "page": "simulate_spectrum",
      "title": "Simulate a 1D NMR Spectrum",
      "topics": [
        "simulate_spectrum"
      ]
    },
    {
      "page": "speaq_align",
      "title": "Align Signals using 'speaq'",
      "topics": [
        "speaq_align"
      ]
    },
    {
      "page": "tmpdir",
      "title": "Temporary Session Directory",
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