_pkgdown.yml

url: https://pawelqs.github.io/cevomod/
template:
  bootstrap: 5
  bootswatch: flatly
  bslib:
    pkgdown-nav-height: 100px

home:
  links:
  - text: Source Code
    href: https://github.com/pawelqs/cevomod
  - text: Bug Reports
    href: https://github.com/pawelqs/cevomod/issues


reference:
- title: cevodata
- contents:
  - as_cevo_snvs
  - init_cevodata
  - starts_with("add_")
  - starts_with("default_")
  - set_cancer_type
  - use_purity
- title: cevodata transformations
- contents:
  - filter.cevodata
  - split_by.cevodata
  - merge.cevodata
  - update.cevodata
- title: Other transformations
- contents:
  - annotate_mutation_contexts
  - unite_mutation_id
  - cut_f_intervals
  - filter_SNVs_by_regions
  - shuffle
- title: Data preparation
- contents:
  - annotate_normal_cn
  - calc_mutation_frequencies
  - intervalize_mutation_frequencies
  - prepare_SNVs
- title: Model fitting
- contents:
  - starts_with("fit_")
- title: Getters
- contents:
  - starts_with("get_")
  - active_models
  - SNVs_CNVs
- title: Evolutionary parameters
- contents:
  - get_mutation_rates
  - get_selection_coefficients
- title: Visualizations
- contents:
  - compare_models
  - geom_powerlaw
  - hide_facet_labels
  - hide_legend
  - starts_with("layer_")
  - has_keyword("palettes")
  - starts_with("plot")
  - rotate_x_labels
  - starts_with("scale_")
  - starts_with("stat_")
- title: Data
- contents:
  - driver_genes
  - test_data
  - test_data_fitted
- title: Other functions
- contents:
  - build_clip_container
  - fill_na
  - fix_powerlaw_N_mutations
  - generate_neutral_snvs
  - set_cevomod_verbosity
  - set_containers_dir
  - to_clip
  - "`%not in%`"
- title: internal
  contents:
    - count_mutation_types
    - count_mutations_by_component
    - tcga_brca_test
    - quick_save
    - print.cevo_palettes
    - run_browser
    - run_cevomod
    - variant_classification
    - variant_classification_filter



articles:
- title: Tutorials
  navbar: ~
  contents:
  - get_started
  - cevodata_class
  - fitting_models
  - visualizations