_pkgdown.yml

url: https://caravagnalab.github.io/rRACES/
template:
  bootstrap: 5

repo:
  url:
    home: https://github.com/caravagnalab/rRACES/
    source: https://github.com/caravagnalab/rRACES
    issue: https://github.com/caravagnalab/rRACES/issues
    user: https://github.com/caravagnalab

authors:
  Cancer Data Science Laboratory:
    href: https://www.caravagnalab.org/


articles:
- title: Introduction
  navbar: ~
  contents:
  - tissue_simulation
  - sampling
  - mutations
  - sequencing
- title: Advanced techniques
  contents:
  - growth_models
  - run_until
  - custom_engine
  - infinite_site_model
  - sample_partition
  - time_series
- title: Tests and Examples
  contents:
  - three_sampling
  - SCOUT

reference:
- title: "Spatial simulation interface"
  desc:  "Spatial simulation classes and methods"
  contents:
  - annotate_forest
  - bbox_sampler
  - load_samples_forest
  - starts_with("TissueRectangle")
  - starts_with("SamplesForest")
  - starts_with("SpatialSimulation")
  - plot_firings
  - plot_muller
  - plot_state
  - plot_timeseries
  - plot_tissue
  - recover_simulation
- title: "Mutation simulation interface"
  desc:  "Mutation simulation classes and methods"
  contents:
  - Amplification
  - starts_with("CNA")
  - Deletion
  - get_available_tumours_in
  - get_mutation_engine_codes
  - get_relevant_branches
  - load_phylogenetic_forest
  - starts_with("Mutation")
  - starts_with("MutationEngine")
  - starts_with("PhylogeneticForest")
  - plot_exposure_timeline
  - plot_forest
  - plot_sticks
  - SNV
  - WholeGenomeDoubling
- title: "Sequencing simulation interface"
  desc:  "Sequencing simulation methods"
  contents:
  - starts_with("BasicIlluminaSequencer")
  - starts_with("ErrorlessIlluminaSequencer")
  - label_mutations
  - plot_BAF
  - plot_DR
  - plot_VAF
  - plot_VAF_histogram
  - plot_VAF_marginals
  - starts_with("SampledCell")
  - simulate_seq
  - simulate_normal_seq
  - seq_to_long
- title: "Simulation Logics"
  desc:  "Simulation Logics"
  contents:
  - Expression
  - Formula
  - Variable