{
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  "Title": "Exploratory Chemometrics for Spectroscopy",
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  "Date": "2025-09-08",
  "Authors@R": "c(\nperson(\"Bryan A.\", \"Hanson\",\nrole = c(\"aut\", \"cre\"), email =\n\"hanson@depauw.edu\",\ncomment = c(ORCID = \"0000-0003-3536-8246\")),\nperson(\"Mike\", \"Bostock\",\nrole = c(\"cph\", \"ctb\"),\ncomment = \"author of the d3.js library used by plotSpectraJS, http://d3js.org\"),\nperson(\"Matt\", \"Keinsley\",\nrole = \"ctb\",\ncomment = \"author of initial AOV-PCA code\"),\nperson(\"Tejasvi\", \"Gupta\",\nrole = \"ctb\",\ncomment = \"author of ggplot2 and plotly graphics interfaces\"))",
  "Description": "A collection of functions for top-down exploratory data\nanalysis of spectral data including nuclear magnetic resonance\n(NMR), infrared (IR), Raman, X-ray fluorescence (XRF) and other\nsimilar types of spectroscopy. Includes functions for plotting\nand inspecting spectra, peak alignment, hierarchical cluster\nanalysis (HCA), principal components analysis (PCA) and\nmodel-based clustering. Robust methods appropriate for this\ntype of high-dimensional data are available. ChemoSpec is\ndesigned for structured experiments, such as metabolomics\ninvestigations, where the samples fall into treatment and\ncontrol groups. Graphical output is formatted consistently for\npublication quality plots. ChemoSpec is intended to be very\nuser friendly and to help you get usable results quickly. A\nvignette covering typical operations is available.",
  "License": "GPL-3",
  "URL": "https://bryanhanson.github.io/ChemoSpec/",
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  "Repository": "https://bryanhanson.r-universe.dev",
  "Date/Publication": "2025-09-08 22:30:57 UTC",
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  "_exports": [
    ".chkReqPkgs",
    "aov_pcaSpectra",
    "aovPCAloadings",
    "aovPCAscores",
    "averageReplicates",
    "baselineSpectra",
    "binSpectra",
    "c_pcaSpectra",
    "check4Gaps",
    "chkGraphicsOpt",
    "chkSpectra",
    "clupaSpectra",
    "cv_pcaSpectra",
    "evalClusters",
    "files2SpectraObject",
    "hcaScores",
    "hcaSpectra",
    "hmapSpectra",
    "hypTestScores",
    "irlba_pcaSpectra",
    "matrix2SpectraObject",
    "mclust3dSpectra",
    "mclustSpectra",
    "normSpectra",
    "pcaDiag",
    "plot2Loadings",
    "plot3dScores",
    "plotLoadings",
    "plotScores",
    "plotScree",
    "plotSpectra",
    "plotSpectraDist",
    "plotSpectraJS",
    "r_pcaSpectra",
    "removeFreq",
    "removeGroup",
    "removeSample",
    "reviewAllSpectra",
    "rowDist",
    "s_pcaSpectra",
    "sampleDist",
    "sgfSpectra",
    "splitSpectraGroups",
    "sPlotSpectra",
    "sumGroups",
    "sumSpectra",
    "surveySpectra",
    "surveySpectra2"
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  "_datasets": [
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      "name": "alignMUD",
      "title": "Made Up NMR Data Sets",
      "object": "alignMUD",
      "file": "alignMUD.RData",
      "class": [
        "Spectra"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "metMUD1",
      "title": "Made Up NMR Data Sets",
      "object": "metMUD1",
      "file": "metMUD1.RData",
      "class": [
        "Spectra"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "metMUD2",
      "title": "Made Up NMR Data Sets",
      "object": "metMUD2",
      "file": "metMUD2.RData",
      "class": [
        "Spectra"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "SrE.IR",
      "title": "IR and NMR Spectra of Serenoa repens (Saw Palmetto) Oil Extracts and Reference Oils",
      "object": "SrE.IR",
      "file": "SrE.IR.RData",
      "class": [
        "Spectra"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "SrE.NMR",
      "title": "IR and NMR Spectra of Serenoa repens (Saw Palmetto) Oil Extracts and Reference Oils",
      "object": "SrE.NMR",
      "file": "SrE.NMR.RData",
      "class": [
        "Spectra"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "ChemoSpec-package",
      "title": "Exploratory Chemometrics for Spectroscopy",
      "topics": [
        "ChemoSpec-package",
        "ChemoSpec"
      ]
    },
    {
      "page": "aov_pcaSpectra",
      "title": "ANOVA-PCA Analysis of Spectra Data",
      "topics": [
        "aov_pcaSpectra"
      ]
    },
    {
      "page": "aovPCAloadings",
      "title": "Plot aovPCAscores Loadings of a Spectra Object",
      "topics": [
        "aovPCAloadings"
      ]
    },
    {
      "page": "aovPCAscores",
      "title": "Plot ANOVA-PCA Scores from a Spectra Object",
      "topics": [
        "aovPCAscores"
      ]
    },
    {
      "page": "averageReplicates",
      "title": "Average Replicates in a Spectra Object",
      "topics": [
        "averageReplicates"
      ]
    },
    {
      "page": "baselineSpectra",
      "title": "Baseline Correction of a Spectra Object",
      "topics": [
        "baselineSpectra"
      ]
    },
    {
      "page": "binSpectra",
      "title": "Bin or Bucket a Spectra Object",
      "topics": [
        "binSpectra"
      ]
    },
    {
      "page": "c_pcaSpectra",
      "title": "Classical PCA of Spectra Objects",
      "topics": [
        "c_pcaSpectra"
      ]
    },
    {
      "page": "check4Gaps",
      "title": "Check for Discontinuities (Gaps) in a Vector & Optionally Make a Plot",
      "topics": [
        "check4Gaps"
      ]
    },
    {
      "page": "chkGraphicsOpt",
      "title": "Check the Graphics Output Option/Mode",
      "topics": [
        "chkGraphicsOpt"
      ]
    },
    {
      "page": "chkSpectra",
      "title": "Verify the Integrity of a Spectra or Spectra2D Object",
      "topics": [
        "chkSpectra"
      ]
    },
    {
      "page": "clupaSpectra",
      "title": "Hierarchical Cluster-Based Peak Alignment on a Spectra Object",
      "topics": [
        "clupaSpectra"
      ]
    },
    {
      "page": "colorSymbol",
      "title": "Color and Symbols in ChemoSpec and ChemoSpec2D",
      "topics": [
        "colorSymbol"
      ]
    },
    {
      "page": "conColScheme",
      "title": "Change the Color Scheme of a Spectra or Spectra2D Object",
      "topics": [
        "conColScheme"
      ]
    },
    {
      "page": "cv_pcaSpectra",
      "title": "Cross-Validation of Classical PCA Results for a Spectra Object",
      "topics": [
        "cv_pcaSpectra"
      ]
    },
    {
      "page": "evalClusters",
      "title": "Evaluate or Compare the Quality of Clusters Quantitatively",
      "topics": [
        "evalClusters"
      ]
    },
    {
      "page": "files2SpectraObject",
      "title": "Import Data into a Spectra Object",
      "topics": [
        "files2SpectraObject",
        "matrix2SpectraObject"
      ]
    },
    {
      "page": "hcaScores",
      "title": "HCA on PCA/MIA/PARAFAC scores from a Spectra or Spectra2D Object",
      "topics": [
        "hcaScores"
      ]
    },
    {
      "page": "hcaSpectra",
      "title": "Plot HCA Results of a Spectra Object",
      "topics": [
        "hcaSpectra"
      ]
    },
    {
      "page": "hmapSpectra",
      "title": "Seriated Heat Map for a Spectra Object",
      "topics": [
        "hmapSpectra"
      ]
    },
    {
      "page": "hypTestScores",
      "title": "Conduct MANOVA using PCA Scores and Factors in a Spectra Object",
      "topics": [
        "hypTestScores"
      ]
    },
    {
      "page": "irlba_pcaSpectra",
      "title": "IRLBA PCA of Spectra Objects",
      "topics": [
        "irlba_pcaSpectra"
      ]
    },
    {
      "page": "mclust3dSpectra",
      "title": "mclust Analysis of a Spectra Object in 3D",
      "topics": [
        "mclust3dSpectra"
      ]
    },
    {
      "page": "mclustSpectra",
      "title": "mclust Analysis of a Spectra Object PCA Results",
      "topics": [
        "mclustSpectra"
      ]
    },
    {
      "page": "metMUD1",
      "title": "Made Up NMR Data Sets",
      "topics": [
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