_pkgdown.yml

url: https://pln-team.github.io/PLNmodels

# template:
#   params:
#     docsearch:
#       api_key: API_KEY
#       index_name: INDEX_NAME

navbar:
  structure:
    left:  [home, reference, slideshow, articles, news]
    right: [github]
  components:
    home: ~
    slideshow:
      text: "Slideshow on PLN"
      href: "https://pln-team.github.io/slideshow/slides"
    articles:
      text: "Vignettes"
      menu:
      - text: "The trichoptera data set"
        href: articles/Trichoptera.html
      - text: "Data importation in PLNmodels"
        href: articles/Import_data.html
      - text: "PLN: Multivariate Poisson regression"
        href: articles/PLN.html
      - text: "PLNPCA: Dimension Reduction"
        href: articles/PLNPCA.html
      - text: "PLNnetwork: sparse structure inference"
        href: articles/PLNnetwork.html
      - text: "PLNLDA: Discriminant Analysis"
        href: articles/PLNLDA.html
      - text: "PLNmixture: Model-based clustering for counts"
        href: articles/PLNmixture.html

reference:
- title: 'Top-level fitting functions'
  desc: >
    Set of functions to fit variants of the Poisson lognormal model
  contents:
    - '`PLNmodels`'
    - '`PLN`'
    - '`ZIPLN`'
    - '`PLNLDA`'
    - '`PLNPCA`'
    - '`PLNnetwork`'
    - '`ZIPLNnetwork`'
    - '`PLNmixture`'
- title: 'Poisson lognormal fit'
  desc: >
    Description of the PLNfit object and methods for its manipulation. Any PLN variant in the
    package inherits from this class (PLNPCAfit, PLNnetworkfit, PLNLDAfit).
  contents:
    - starts_with('PLNfit')
    - '`PLN_param`'
    - '`coef.PLNfit`'
    - '`vcov.PLNfit`'
    - '`sigma.PLNfit`'
    - '`predict.PLNfit`'
    - '`predict_cond.PLNfit`'
    - '`fitted.PLNfit`'
    - '`standard_error.PLNfit`'
- title: 'Zero Inflated Poisson lognormal fit'
  desc: >
    Description of the ZIPLNfit object and methods for its manipulation.
  contents:
    - starts_with('ZIPLNfit')
    - '`ZIPLN_param`'
    - '`coef.ZIPLNfit`'
    - '`sigma.ZIPLNfit`'
    - '`predict.ZIPLNfit`'
    - '`fitted.ZIPLNfit`'
    - '`plot.ZIPLNfit_sparse`'
- title: 'Linear discriminant analysis via a Poisson lognormal fit'
  desc: >
    Description of the PLNLDAfit object and methods for its manipulation.
  contents:
  - starts_with('PLNLDAfit')
  - '`PLNLDA_param`'
  - '`plot.PLNLDAfit`'
  - '`predict.PLNLDAfit`'
  - '`coef.PLNLDAfit`'
- title: 'Poisson Lognormal PCA fit'
  desc: >
    Description of the PLNPCAfit and PLNPCAfamily objects and methods for their manipulation.
  contents:
  - starts_with('PLNPCAfit')
  - '`PLNPCA_param`'
  - '`plot.PLNPCAfit`'
  - '`PLNPCAfamily`'
  - '`plot.PLNPCAfamily`'
  - '`getBestModel.PLNPCAfamily`'
  - '`getModel.PLNPCAfamily`'
- title: 'Mixture of Poisson Lognormal fits'
  desc: >
    Description of the PLNmixturefit and PLNmixturefamily objects and methods for their manipulation.
  contents:
  - starts_with('PLNmixturefit')
  - '`PLNmixture_param`'
  - '`plot.PLNmixturefit`'
  - '`PLNmixturefamily`'
  - '`plot.PLNmixturefamily`'
  - '`coef.PLNmixturefit`'
  - '`predict.PLNmixturefit`'
  - '`sigma.PLNmixturefit`'
  - '`fitted.PLNmixturefit`'
  - '`getBestModel.PLNmixturefamily`'
  - '`getModel.PLNmixturefamily`'
- title: 'Sparse Poisson lognormal fit and network, w/o Zero Inflated component'
  desc: >
    Description of the (ZI)PLNnetworkfit and (ZI)PLNnetworkfamily objects and methods for their manipulation.
  contents:
  - starts_with('PLNnetworkfit')
  - '`PLNnetwork_param`'
  - '`ZIPLNnetwork_param`'
  - '`plot.PLNnetworkfit`'
  - '`plot.ZIPLNfit_sparse`'
  - '`Networkfamily`'
  - '`ZIPLNnetworkfamily`'
  - '`PLNnetworkfamily`'
  - '`plot.PLNnetworkfamily`'
  - '`getBestModel.PLNnetworkfamily`'
  - '`getModel.PLNnetworkfamily`'
  - '`coefficient_path`'
  - '`stability_selection`'
  - '`extract_probs`'
- title: 'Other functions and objects'
  desc: ~
  contents:
    - '`prepare_data`'
    - '`compute_offset`'
    - '`PLNfamily`'
    - '`plot.PLNfamily`'
    - '`rPLN`'
    - '`compute_PLN_starting_point`'
- title: Data sets
  desc: ~
  contents:
    - '`trichoptera`'
    - '`oaks`'
    - '`barents`'
    - '`mollusk`'
    - '`scRNA`'