_pkgdown.yml

reference:
- title: "Fit LDA models to data for specified K's"
- contents:
  - run_lda_models

- title: "Alignment function"
- contents:
  - align_topics

- title: "Visualization and diagnostics functions"
- contents:
  - plot_alignment
  - plot_beta
  - compute_number_of_paths
  - plot_number_of_paths

- title: "Alignment class and related functions"
- contents:
  - alignment-class
  - show,alignment-method
  - plot,alignment,missing-method
  - models,alignment-method
  - weights,alignment-method
  - topics,alignment-method
  - n_models,alignment-method
  - n_topics,alignment-method

- title: "Helper functions"
- contents:
  - align_graph
  - setup_edges
  - product_weights
  - transport_weights
  - trim_betas

- title: "Demo data"
- contents:
  - vm_data



articles:
- title: Demos
  navbar: Demos
  contents:
  - basic-alignment
  - microbiome-demo
- title: Simulations
  navbar: Simulations
  contents:
  - lda
  - background-noise
  - strain-switching
- title: Profiling
  navbar: Profiling
  contents:
  - timing