_pkgdown.yml

url: https://agseifert.github.io/RFSurrogates
template:
  bootstrap: 5
reference:
  - title: Random Forest Surrogates
    desc: The basic object used in most further analysis functions.
    contents:
    - RandomForestSurrogates
  - title: Surrogate Minimal Depth
    desc: >
      Surrogate Minimal Depth (SMD) enables the identification of multiple
      features from the same metabolites and reveals meaningful biological
      relations, proving its high potential for the comprehensive utilization
      of high-dimensional metabolomics data.
      Reference:
      [10.3390/metabo12010005](https://doi.org/10.3390/metabo12010005)
    contents:
    - SurrogateMinimalDepth
    - MinimalDepth
    - MeanAdjustedAgreement
  - title: Mutual Impact of Features
    desc: >
      Mutual forest impact (MFI) is a relation parameter that evaluates the
      mutual association of the featurs to the outcome and, hence, goes beyond
      the analysis of correlation coefficients. Mutual impurity reduction (MIR)
      is an importance measure that combines this relation parameter with the
      importance of the individual features.
      Reference:
      [10.48550/ARXIV.2304.02490](https://doi.org/10.48550/ARXIV.2304.02490)
    contents:
    - MutualForestImpact
    - MFI
    - MutualImpurityReduction
    - MutualForestImpactVariableSelection
    - MutualImpurityReductionVariableSelection
  - title: Data
    desc: Example data sets shipped with this package.
    contents:
    - has_keyword("datasets")
  - title: "Version 0.3.x functions"
    desc: The original functions from prior versions remain available for backward compatability.
    contents:
    - var.relations
    - var.relations.mfi
    - var.select.md
    - var.select.smd
    - var.select.mir
  - title: Other functions
    desc: >
      Additional functions published as part of version 0.3.x and earlier versions.
      These will remain available for backward compatability.
    contents:
    - addLayer
    - addSurrogates
    - build.clusters
    - count.surrogates
    - getTreeranger
    - meanAdjAgree
    - mindep
    - reduce.surrogates
    - surrmindep