_pkgdown.yml

url: https://sbfnk.github.io/rbi

template:
  bootstrap: 5

reference:
  - title: "Run LibBi and analyse results"

  - subtitle: "LibBi operations"
    desc: "Functions for running LibBi."
    contents:
      - filter
      - generate_dataset
      - optimise
      - libbi
      - predict
      - run
      - sample
      - sample_obs
      - simulate

  - subtitle: "Read and write LibBi inputs/outputs"
    desc: "Functions for interacting with the NetCDF files used by LibBi."
    contents:
      - bi_contents
      - bi_file_summary
      - bi_read
      - bi_write

  - subtitle: "Analyse LibBi outputs"
    desc: "Functions for analysing LibBi results."
    contents:
      - extract_sample
      - get_traces
      - summary
      - logLik

  - subtitle: "Manipulate LibBi inputs/outputs"
    desc: "Functions for updating and saving LibBi objects."
    contents:
      - attach_data
      - join
      - read_libbi
      - save_libbi
      - update

  - title: "Construct, show and manipulate LibBi models"

  - subtitle: "Create a model"
    desc: "Function for creating a LibBi model."
    contents:
      - bi_model

  - subtitle: "Show models"
    desc: "Functions for getting information from LibBi models."
    contents:
      - get_block
      - get_const
      - get_dims
      - get_name
      - rewrite
      - var_names

  - subtitle: "Manipulate models"
    desc: "Functions for manipulating LibBi models."
    contents:
      - add_block
      - enable_outputs
      - fix
      - insert_lines
      - remove_lines
      - remove_vars
      - replace_all
      - set_name
      - write_model

  - subtitle: "Model operators"
    desc: "Operators for LibBi models"
    contents:
      - "`==.bi_model`"
      - "`[.bi_model`"
      - "`[<-.bi_model`"
      - "`!=.bi_model`"

  - title: "Other functions"

  - subtitle: "Utility functions"
    desc: "Useful additional functions."
    contents:
      - flatten
      - print_log

  - subtitle: "Deprecated functions"
    desc: "To be removed in the next version of rbi."
    contents:
      - bi_generate_dataset

articles:
  - title: Introduction
    navbar: ~
    contents:
      - rbi

  - title: Collection of SIR models for LibBi
    navbar: Examples
    contents:
      - idd_models