_pkgdown.yml

url: https://netcomi.de
template:
  bootstrap: 5
  light-switch: true
  bootswatch: simplex
  bslib:
    primary: "#a2bf48"

navbar:
  structure:
    left:  [intro, reference, articles, news]
    right: [search, github, lightswitch]
  bg: primary
    
home:
  links:
  - text: Orchestrating Microbiome Analysis
    href: https://microbiome.github.io/OMA/docs/devel/pages/network_learning.html
  - text: Development version
    href: https://github.com/stefpeschel/NetCoMi/tree/develop

articles:
- title: Main functionality
  navbar: ~
  contents:
  - net_comparison
  - diffnet
  - dissimilarity_networks
  - create_asso_perm

- title: More examples
  navbar: More examples
  contents:
  - plot_modifications
  - asso_as_input
  - cross_domain_networks
  - soil_example
  
reference:
- title: Main functions
  desc:  Main functions to follow the workflow of constructing, analyzing, and comparing microbiome networks.
- contents:
  - netConstruct
  - netAnalyze
  - netCompare
  - diffnet
  - installNetCoMiPacks
- title: Association estimation
  desc: Association estimation methods implemented in NetCoMi.
- contents:
  - cclasso
  - gcoda
- title: Helpers
  desc: A bunch of helpful functions that are mainly used by other functions.
- contents:
  - createAssoPerm
  - colToTransp
  - calcGCD
  - calcGCM
  - editLabels
  - multAdjust
  - plotHeat
  - renameTaxa
  - testGCM
- title: S3 methods
- contents:
  - plot.diffnet
  - plot.microNetProps
  - print.GCD
  - summary.microNetComp
  - summary.microNetProps
  
authors:
  Stefanie Peschel:
    href: https://stefpeschel.de/
  Christian L. Müller:
    href: https://www.statistik.uni-muenchen.de/personen/professuren/mueller/index.html
  Anne-Laure Boulesteix:
    href: https://www.en.ibe.med.uni-muenchen.de/mitarbeiter/professoren/boulesteix/index.html
  Erika von Mutius:
    href: https://www.helmholtz-munich.de/en/iap/pi/erika-von-mutius
  Martin Depner:
    href: https://www.helmholtz-munich.de/en/iap