_pkgdown.yml

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

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

authors:
  Giulio Caravagna:
    href: https://sites.google.com/site/giuliocaravagna/

reference:
- title: Available data
  desc:  Data released with the package
  contents:
  - fit_example
  - LU4_lung_sample
  - LUFF76_lung_sample
  - cancer_genes_dnds

- title: Fitting functions
  desc:  Functions to cluster the data; density of a `mobster` fit and sampling functions.
  contents:
  - mobster_fit
  - choose_clusters
  - Clusters
  - Clusters_denovo
  - ddbpmm
  - rdbpmm
  - random_dataset
  - to_string

- title: S3 functions
  desc: The `mobster` S3 object.
  contents:
  - print.dbpmm
  - summary.dbpmm
  - plot.dbpmm

- title: Plotting functions
  desc:  These functions can be used to plot data and `mobster` fits.
  contents:
  - plot_NLL
  - plot_entropy
  - plot_fit_scores
  - plot_gofit
  - plot_init
  - plot_latent_variables
  - plot_mixing_proportions
  - plot_model_selection


- title: Bootstrap functions
  desc:  Bootstrap functions for `mobster` fits, and plotting functions.
  contents:
  - mobster_bootstrap
  - bootstrapped_statistics
  - plot_bootstrap_Beta
  - plot_bootstrap_coclustering
  - plot_bootstrap_mixing_proportions
  - plot_bootstrap_model_frequency
  - plot_bootstrap_tail


- title: Extra features
  desc:  Other analyses for `mobster` fits.
  contents:
  - dnds
  - evolutionary_parameters
  - get_clone_trees
  - load_vcf