{
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  "Package": "metabolyseR",
  "Title": "Methods for Pre-Treatment, Data Mining and Correlation Analyses\nof Metabolomics Data",
  "Version": "0.15.4",
  "Authors@R": "person(\"Jasen\", \"Finch\", email = \"jsf9@aber.ac.uk\", role = c(\"aut\", \"cre\"))",
  "Description": "A tool kit for pre-treatment, modelling, feature selection\nand correlation analyses of metabolomics data.",
  "URL": "https://jasenfinch.github.io/metabolyseR/",
  "BugReports": "https://github.com/jasenfinch/metabolyseR/issues",
  "biocViews": "Metabolomics",
  "License": "GPL (>= 3)",
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  "Collate": "all-classes.R analysis-accessors.R aggregate.R analysisData.R\ncorrection.R correlations.R impute.R info.R join.R keep.R mds.R\nmetabolyse.R metabolyseR.R modelling.R modelling-plots.R nlda.R\noccupancy.R parameters.R plotExplanatoryHeatmap.R plotFeature.R\nplotLDA.R plotOccupancy.R plotPCA.R plotRSD.R\nplotSupervisedRF.R plotTIC.R plotting.R plotUnsupervisedRF.R\npre-treatment.R predict.R QC.R reexports.R remove.R\nrandomForest-permute.R randomForest-classification.R\nrandomForest-regression.R randomForest-internals.R\nrandomForest-unsupervised.R randomForest.R rsd.R roc.R\nshow-method.R split.R transform.R tune.R univariate.R\nmodelling-accessors.R",
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  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev",
  "Repository": "https://aberhrml.r-universe.dev",
  "Date/Publication": "2023-09-12 15:01:48 UTC",
  "RemoteUrl": "https://github.com/aberHRML/metabolyseR",
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  "Packaged": {
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  "Author": "Jasen Finch [aut, cre]",
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    "aggregateMean",
    "aggregateMedian",
    "aggregateSum",
    "analysisData",
    "analysisElements",
    "analysisParameters",
    "analysisResults",
    "anova",
    "binaryComparisons",
    "bindRows",
    "changeParameter<-",
    "clsAdd",
    "clsArrange",
    "clsAvailable",
    "clsExtract",
    "clsRemove",
    "clsRename",
    "clsReplace",
    "correctionCenter",
    "correlations",
    "correlationsParameters",
    "dat",
    "dat<-",
    "explanatoryFeatures",
    "exportParameters",
    "features",
    "importance",
    "importanceMetrics",
    "imputeAll",
    "imputeClass",
    "keepClasses",
    "keepFeatures",
    "keepSamples",
    "linearRegression",
    "mds",
    "metabolyse",
    "metrics",
    "modellingMethods",
    "modellingParameters",
    "mtry",
    "nFeatures",
    "nSamples",
    "occupancy",
    "occupancyMaximum",
    "occupancyMinimum",
    "parameters",
    "parameters<-",
    "parseParameters",
    "plan",
    "plotExplanatoryHeatmap",
    "plotFeature",
    "plotImportance",
    "plotLDA",
    "plotMDS",
    "plotMetrics",
    "plotOccupancy",
    "plotPCA",
    "plotROC",
    "plotRSD",
    "plotSupervisedRF",
    "plotTIC",
    "plotUnsupervisedRF",
    "predict",
    "predictions",
    "preTreated",
    "preTreated<-",
    "preTreatmentElements",
    "preTreatmentMethods",
    "preTreatmentParameters",
    "proximity",
    "QCimpute",
    "QCoccupancy",
    "QCremove",
    "QCrsdFilter",
    "randomForest",
    "raw",
    "raw<-",
    "reAnalyse",
    "removeClasses",
    "removeFeatures",
    "removeSamples",
    "response",
    "roc",
    "rsd",
    "sinfo",
    "sinfo<-",
    "split",
    "transformArcSine",
    "transformAuto",
    "transformCenter",
    "transformLevel",
    "transformLn",
    "transformLog10",
    "transformPareto",
    "transformPercent",
    "transformRange",
    "transformSQRT",
    "transformTICnorm",
    "transformVast",
    "ttest",
    "tune",
    "type"
  ],
  "_help": [
    {
      "page": "aggregate",
      "title": "Sample aggregation",
      "topics": [
        "aggregateMean",
        "aggregateMean,AnalysisData-method",
        "aggregateMedian",
        "aggregateMedian,AnalysisData-method",
        "aggregateSum",
        "aggregateSum,AnalysisData-method"
      ]
    },
    {
      "page": "Analysis-class",
      "title": "Analysis S4 class",
      "topics": [
        "Analysis-class"
      ]
    },
    {
      "page": "analysisData",
      "title": "AnalysisData class constructor",
      "topics": [
        "analysisData"
      ]
    },
    {
      "page": "AnalysisData-class",
      "title": "AnalysisData S4 class",
      "topics": [
        "AnalysisData-class"
      ]
    },
    {
      "page": "analysisElements",
      "title": "Analysis elements",
      "topics": [
        "analysisElements"
      ]
    },
    {
      "page": "analysisParameters",
      "title": "Create an 'AnalysisParameters' S4 class object",
      "topics": [
        "analysisParameters"
      ]
    },
    {
      "page": "AnalysisParameters-class",
      "title": "AnalysisParameters S4 class",
      "topics": [
        "AnalysisParameters-class"
      ]
    },
    {
      "page": "anova",
      "title": "ANOVA",
      "topics": [
        "anova",
        "anova,AnalysisData-method"
      ]
    },
    {
      "page": "modelling-accessors",
      "title": "Modelling accessor methods",
      "topics": [
        "binaryComparisons",
        "binaryComparisons,AnalysisData-method",
        "explanatoryFeatures",
        "explanatoryFeatures,Analysis-method",
        "explanatoryFeatures,list-method",
        "explanatoryFeatures,RandomForest-method",
        "explanatoryFeatures,Univariate-method",
        "importance",
        "importance,Analysis-method",
        "importance,list-method",
        "importance,RandomForest-method",
        "importance,Univariate-method",
        "importanceMetrics",
        "importanceMetrics,RandomForest-method",
        "metrics",
        "metrics,Analysis-method",
        "metrics,list-method",
        "metrics,RandomForest-method",
        "mtry",
        "mtry,AnalysisData-method",
        "predictions",
        "predictions,Analysis-method",
        "predictions,list-method",
        "predictions,RandomForest-method",
        "proximity",
        "proximity,Analysis-method",
        "proximity,list-method",
        "proximity,RandomForest-method",
        "response",
        "response,RandomForest-method",
        "response,Univariate-method",
        "type",
        "type,RandomForest-method",
        "type,Univariate-method"
      ]
    },
    {
      "page": "bind",
      "title": "Bind 'AnalysisData' objects by row",
      "topics": [
        "bindRows",
        "bindRows,list-method"
      ]
    },
    {
      "page": "changeParameter",
      "title": "Change analysis parameters",
      "topics": [
        "changeParameter<-",
        "changeParameter<-,AnalysisParameters-method"
      ]
    },
    {
      "page": "cls",
      "title": "Sample meta information wrangling",
      "topics": [
        "clsAdd",
        "clsAdd,Analysis-method",
        "clsAdd,AnalysisData-method",
        "clsArrange",
        "clsArrange,Analysis-method",
        "clsArrange,AnalysisData-method",
        "clsAvailable",
        "clsAvailable,Analysis-method",
        "clsAvailable,AnalysisData-method",
        "clsExtract",
        "clsExtract,Analysis-method",
        "clsExtract,AnalysisData-method",
        "clsRemove",
        "clsRemove,Analysis-method",
        "clsRemove,AnalysisData-method",
        "clsRename",
        "clsRename,Analysis-method",
        "clsRename,AnalysisData-method",
        "clsReplace",
        "clsReplace,Analysis-method",
        "clsReplace,AnalysisData-method"
      ]
    },
    {
      "page": "correction",
      "title": "Batch/block correction",
      "topics": [
        "correctionCenter",
        "correctionCenter,AnalysisData-method"
      ]
    },
    {
      "page": "correlations",
      "title": "Feature correlation analysis",
      "topics": [
        "correlations",
        "correlations,Analysis-method",
        "correlations,AnalysisData-method"
      ]
    },
    {
      "page": "correlationsParameters",
      "title": "Correlations parameters",
      "topics": [
        "correlationsParameters"
      ]
    },
    {
      "page": "analysis-accessors",
      "title": "'AnalysisData' and 'Analysis' class accessors",
      "topics": [
        "analysisResults",
        "analysisResults,Analysis-method",
        "dat",
        "dat,Analysis-method",
        "dat,AnalysisData-method",
        "dat<-",
        "dat<-,Analysis-method",
        "dat<-,AnalysisData-method",
        "features",
        "features,Analysis-method",
        "features,AnalysisData-method",
        "nFeatures",
        "nFeatures,Analysis-method",
        "nFeatures,AnalysisData-method",
        "nSamples",
        "nSamples,Analysis-method",
        "nSamples,AnalysisData-method",
        "preTreated",
        "preTreated,Analysis-method",
        "preTreated<-",
        "preTreated<-,Analysis-method",
        "raw",
        "raw,Analysis-method",
        "raw<-",
        "raw<-,Analysis-method",
        "sinfo",
        "sinfo,Analysis-method",
        "sinfo,AnalysisData-method",
        "sinfo<-",
        "sinfo<-,Analysis-method",
        "sinfo<-,AnalysisData-method"
      ]
    },
    {
      "page": "impute",
      "title": "Missing data imputation",
      "topics": [
        "imputeAll",
        "imputeAll,AnalysisData-method",
        "imputeClass",
        "imputeClass,AnalysisData-method"
      ]
    },
    {
      "page": "keep",
      "title": "Keep samples, classes or features",
      "topics": [
        "keepClasses",
        "keepClasses,AnalysisData-method",
        "keepFeatures",
        "keepFeatures,AnalysisData-method",
        "keepSamples",
        "keepSamples,AnalysisData-method"
      ]
    },
    {
      "page": "linearRegression",
      "title": "Linear regression",
      "topics": [
        "linearRegression",
        "linearRegression,AnalysisData-method"
      ]
    },
    {
      "page": "mds",
      "title": "Multidimensional scaling (MDS)",
      "topics": [
        "mds",
        "mds,Analysis-method",
        "mds,list-method",
        "mds,RandomForest-method"
      ]
    },
    {
      "page": "metabolyse",
      "title": "Perform an analysis",
      "topics": [
        "metabolyse",
        "reAnalyse",
        "reAnalyse,Analysis-method"
      ]
    },
    {
      "page": "modelling-parameters",
      "title": "Modelling parameters",
      "topics": [
        "modellingMethods",
        "modellingParameters"
      ]
    },
    {
      "page": "occupancy",
      "title": "Calculate feature class occupancies",
      "topics": [
        "occupancy",
        "occupancy,AnalysisData-method"
      ]
    },
    {
      "page": "occupancyFilter",
      "title": "Feature occupancy filtering",
      "topics": [
        "occupancyMaximum",
        "occupancyMaximum,AnalysisData-method",
        "occupancyMinimum",
        "occupancyMinimum,AnalysisData-method"
      ]
    },
    {
      "page": "parameters",
      "title": "Get or set analysis parameters",
      "topics": [
        "parameters",
        "parameters,Analysis-method",
        "parameters,AnalysisParameters-method",
        "parameters<-",
        "parameters<-,Analysis-method",
        "parameters<-,AnalysisParameters-method"
      ]
    },
    {
      "page": "io-parameters",
      "title": "Parse/export analysis parameters",
      "topics": [
        "exportParameters",
        "exportParameters,Analysis-method",
        "exportParameters,AnalysisParameters-method",
        "parseParameters"
      ]
    },
    {
      "page": "plotExplanatoryHeatmap",
      "title": "Heatmap plot of explantory features",
      "topics": [
        "plotExplanatoryHeatmap",
        "plotExplanatoryHeatmap,Analysis-method",
        "plotExplanatoryHeatmap,list-method",
        "plotExplanatoryHeatmap,RandomForest-method",
        "plotExplanatoryHeatmap,Univariate-method"
      ]
    },
    {
      "page": "plotFeature",
      "title": "Plot a feature",
      "topics": [
        "plotFeature",
        "plotFeature,Analysis-method",
        "plotFeature,AnalysisData-method"
      ]
    },
    {
      "page": "plotImportance",
      "title": "Plot feature importance",
      "topics": [
        "plotImportance",
        "plotImportance,list-method",
        "plotImportance,RandomForest-method",
        "plotImportance,Univariate-method"
      ]
    },
    {
      "page": "plotLDA",
      "title": "Principle Component - Linear Discriminant Analysis plot",
      "topics": [
        "plotLDA",
        "plotLDA,Analysis-method",
        "plotLDA,AnalysisData-method"
      ]
    },
    {
      "page": "plotMDS",
      "title": "Multidimensional scaling (MDS) plot",
      "topics": [
        "plotMDS",
        "plotMDS,list-method",
        "plotMDS,RandomForest-method"
      ]
    },
    {
      "page": "plotMetrics",
      "title": "Plot model performance metrics",
      "topics": [
        "plotMetrics",
        "plotMetrics,list-method",
        "plotMetrics,RandomForest-method"
      ]
    },
    {
      "page": "plotOccupancy",
      "title": "Plot class occupancy distributions",
      "topics": [
        "plotOccupancy",
        "plotOccupancy,Analysis-method",
        "plotOccupancy,AnalysisData-method"
      ]
    },
    {
      "page": "plotPCA",
      "title": "Principle Component Analysis plot",
      "topics": [
        "plotPCA",
        "plotPCA,Analysis-method",
        "plotPCA,AnalysisData-method"
      ]
    },
    {
      "page": "plotROC",
      "title": "Plot receiver operator characteristic (ROC) curves",
      "topics": [
        "plotROC",
        "plotROC,list-method",
        "plotROC,RandomForest-method"
      ]
    },
    {
      "page": "plotRSD",
      "title": "Plot RSD distributions",
      "topics": [
        "plotRSD",
        "plotRSD,Analysis-method",
        "plotRSD,AnalysisData-method"
      ]
    },
    {
      "page": "plotSupervisedRF",
      "title": "Supervised random forest MDS plot",
      "topics": [
        "plotSupervisedRF",
        "plotSupervisedRF,Analysis-method",
        "plotSupervisedRF,AnalysisData-method"
      ]
    },
    {
      "page": "plotTIC",
      "title": "Plot sample total ion counts",
      "topics": [
        "plotTIC",
        "plotTIC,Analysis-method",
        "plotTIC,AnalysisData-method"
      ]
    },
    {
      "page": "plotUnsupervisedRF",
      "title": "Unsupervised random forest MDS plot",
      "topics": [
        "plotUnsupervisedRF",
        "plotUnsupervisedRF,Analysis-method",
        "plotUnsupervisedRF,AnalysisData-method"
      ]
    },
    {
      "page": "predict",
      "title": "Predict random forest model responses",
      "topics": [
        "predict",
        "predict,RandomForest,AnalysisData-method"
      ]
    },
    {
      "page": "pre-treatment-parameters",
      "title": "Pre-treatment parameters",
      "topics": [
        "preTreatmentElements",
        "preTreatmentMethods",
        "preTreatmentParameters"
      ]
    },
    {
      "page": "QC",
      "title": "Quality control (QC) sample treatments",
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