_pkgdown.yml

destination: ../peakPantheR.github.io/docs

reference:
  - title: Exported Functions
    desc: Functions exported by peakPantheR
    contents:
      - peakPantheR
      - peakPantheR_start_GUI
      - peakPantheR_singleFileSearch
      - peakPantheR_loadAnnotationParamsCSV
      - peakPantheR_parallelAnnotation
      - peakPantheR_plotEICFit
      - peakPantheR_plotPeakwidth
      - peakPantheR_ROIStatistics
      - peakPantheR_quickEIC
  - title: peakPantheRAnnotation object Accessors
    desc: Accessors
    contents:
      - peakPantheRAnnotation
      - cpdID
      - cpdName
      - ROI
      - uROI
      - FIR
      - filepath
      - cpdMetadata
      - spectraMetadata
      - acquisitionTime
      - uROIExist
      - useUROI
      - useFIR
      - TIC
      - peakTables
      - dataPoints
      - peakFit
      - isAnnotated
      - nbSamples
      - nbCompounds
      - annotationTable
      - EICs
      - filename
  - title: peakPantheRAnnotation object Methods
    desc: Methods
    contents:
      - matches("[[]")
      - annotationParamsDiagnostic
      - outputAnnotationParamsCSV
      - annotationDiagnosticPlots
      - outputAnnotationDiagnostic
      - outputAnnotationResult
      - resetAnnotation
      - resetFIR
      - retentionTimeCorrection
  - title: Internals
    desc: Internal functions and helpers
    contents:
      - extractSignalRawData
      - generateIonChromatogram
      - findTargetFeatures
      - fitCurve
      - is.peakPantheR_curveFit
      - annotationDiagnosticMultiplot
      - getAcquisitionDatemzML
      - getTargetFeatureStatistic
      - integrateFIR
      - plotEICDetectedPeakwidth
      - plotHistogram
      - predictCurve
      - saveSingleFileMultiEIC
      - prepare_advanced_target_parameters
      - prepare_basic_target_parameters
      - peakPantheR_applyRTCorrection
      - skewedGaussian_guess
      - skewedGaussian_minpack.lm
      - skewedGaussian_minpack.lm_objectiveFun
      - emgGaussian_guess
      - emgGaussian_minpack.lm
      - emgGaussian_minpack.lm_objectiveFun
      - gaussian_cerf
      - gaussian_erf
      - initialise_annotation_from_files_UI_helper
      - spectraPaths_and_metadata_UI_helper
      - load_annotation_from_file_UI_helper
      - annotation_showMethod_UI_helper
      - annotation_showText_UI_helper
      - annotation_diagnostic_multiplot_UI_helper
      - annotation_fit_summary_UI_helper
      - outputAnnotationSpectraMetadata_UI_helper
      - outputAnnotationFeatureMetadata_UI_helper
      - spectra_metadata_colourScheme_UI_helper