_pkgdown.yml

url: https://jasenfinch.github.io/metabolyseR/
template:
  bootstrap: 5

navbar:
  components:
    articles:
     text: Articles
     menu:
     - text: Metabolomics data pre-treatment
       href: articles/pre_treatment.html
     - text: Modelling and feature selection
       href: articles/modelling.html
       
reference:
  - title: Analysis S4 classes
    contents:
    - Analysis-class
    - AnalysisData-class
    - metabolyse
    - analysisData
    - dat
    - clsAdd
    
  - title: Analysis parameters
    contents:
    - AnalysisParameters-class
    - analysisElements
    - analysisParameters
    - parameters
    - changeParameter<-
    - exportParameters
    - parseParameters
    - preTreatmentElements
    - modellingMethods
    - correlationsParameters
    
  - title: Pre-treatment
    contents:
    - aggregateMean
    - correctionCenter
    - imputeAll
    - keepClasses
    - occupancyMaximum
    - QCimpute
    - removeSamples
    - transformCenter
    
  - title: Modelling
    contents:
    - RandomForest-class
    - Univariate-class
    - randomForest
    - anova
    - ttest
    - linearRegression
    - binaryComparisons
    - tune
    - mds
    - roc
    - predict

  - title: Correlations
    contents:
    - correlations

  - title: Plotting
    contents:
    - plotFeature
    - plotOccupancy
    - plotRSD
    - plotTIC
    - plotPCA
    - plotLDA
    - plotUnsupervisedRF
    - plotSupervisedRF
    - plotMDS
    - plotROC
    - plotMetrics
    - plotImportance
    - plotExplanatoryHeatmap
    
  - title: Miscellaneous
    contents:
    - bindRows
    - split
    - rsd
    - occupancy