_pkgdown.yml

url: https://epiforecasts.io/EpiNow2/
template:
  bootstrap: 5
  opengraph:
    image:
      src: man/figures/unnamed-chunk-14-1.png
      alt: "Example estimates produced by EpiNow2 of the reproduction number, cases by date of infection and cases by date of report"
    twitter:
      creator: "@seabbs"
      site: "@epiforecasts"
      card: summary_large_image
  params:
    bootswatch: lumen
    docsearch:
      api_key: 43da981922253a06c4dfab7b53f2410e
      index_name: epinow2

development:
  mode: auto

authors:
  Sam Abbott:
    href: "https://www.samabbott.co.uk/"
  Sebastian Funk: 
    href: "https://www.lshtm.ac.uk/aboutus/people/funk.sebastian"
    
navbar:
  structure:
    left: [intro,metareference, modeldefs, usage, casestudies, news]
    right: [search, github]
  components:
    metareference:
      text: Reference
      menu:
      - text: R Reference
        href: reference/index.html
      - text: Stan Reference
        href: https://epiforecasts.io/EpiNow2/stan/
    modeldefs:
      text: Models
      menu:
      - text: Model overview
        href: articles/model_overview.html
      - text: Model features
        href: articles/model_features.html
      - text: "---"
      - text: estimate_infections()
        href: articles/estimate_infections.html
      - text: estimate_secondary()
        href: articles/estimate_secondary.html
      - text: estimate_truncation()
        href: articles/estimate_truncation.html
      - text: Gaussian Process implementation details
        href: articles/gaussian_process_implementation_details.html
    usage:
      text: Usage
      menu:
      - text: Workflow for Rt estimation and forecasting
        href: articles/estimate_infections_workflow.html
      - text: Prior choice and specification guide
        href: articles/prior_choice_guide.html
      - text: "Examples: estimate_infections()"
        href: articles/estimate_infections_options.html
      - text: Using epinow() for running in production mode
        href: articles/epinow.html
      - text: Fitting delay distributions
        href: articles/estimate-dist.html
      - text: Forecasting multiple data streams
        href: articles/forecasting_multiple_data_streams.html
    casestudies:
      text: Case studies
      menu:
      - text: External case studies and use in the literature
        href: articles/case-studies.html

articles:
- title: Start here
  navbar: ~
  contents:
  - EpiNow2
  - model_overview
  - model_features
- title: Model definitions
  navbar: Model definitions
  contents:
  - estimate_infections
  - estimate_secondary
  - estimate_truncation
  - estimate-dist
  - delays
  - gaussian_process_implementation_details
- title: Applied use
  navbar: Usage
  contents:
  - estimate_infections_workflow
  - estimate_infections_options
  - prior_choice_guide
  - epinow
  - forecasting_multiple_data_streams
- title: Case studies
  navbar: ~
  contents:
  - case-studies

figures:
  fig.width: 9
  fig.height: 9

reference:
- title: Estimation + Reporting
  desc: Functions that facilitate end-to-end analysis including imputing cases by infection, estimating Rt and reporting results.
  contents:
  - contains("epinow")

- title: Estimate, Simulate, and Forecast Parameters
  desc: Function to estimate, simulate and forecast parameters of interest.
  contents:
  - estimate_infections
  - forecast_infections
  - estimate_secondary
  - forecast_secondary
  - estimate_delay
  - estimate_dist
  - estimate_truncation

- title: Specify Arguments
  desc: Functions used by estimate_infections
  contents:
  - contains("_opts")
  - opts_list

- title: Preprocess Data
  desc: Functions used for preprocessing data
  contents:
  - fill_missing
  - add_breakpoints
  - filter_leading_zeros
  - apply_zero_threshold

- title: Regional Analysis
  desc: Functions used for summarising across regions (designed for use with regional_epinow)
  contents:
  - regional_summary
  - regional_runtimes
  - get_regional_results

- title: Summarise Results
  desc: Functions for summarising results
  contents:
  - contains("summary.")
  - contains("calc_")
  - make_conf
  - map_prob_change

- title: Plot Results
  desc: Plot generated results
  contents:
  - contains("plot")

- title: Report Results
  desc: Functions to report results
  contents:
  - report_plots
  - report_summary

- title: Distribution Functions
  desc: Functions to define and parameterise distributions
  contents:
  - Distributions
  - contains("dist_spec")
  - bound_dist
  - collapse
  - discretise
  - fix_parameters
  - get_parameters
  - get_pmf
  - get_distribution
  - is_constrained

- title: Fit Delay Distributions
  desc: Functions to fit delay distributions
  contents:
  - bootstrapped_dist_fit
  - dist_fit

- title: Simulation
  desc: Functions to help with simulating data or mapping to reported cases
  contents:
  - simulate_infections
  - simulate_secondary
  - convolve_and_scale

- title: Data
  desc: Package datasets that may be used to parameterise other functions or in examples
  contents:
  - example_generation_time
  - example_incubation_period
  - example_reporting_delay
  - example_confirmed
  - example_truncated

- title: Data Access
  desc: Functions for extracting data from objects or getting data from sources
  contents:
  - contains("get_")
  - contains("extract_")

- title: Data Cleaning
  desc: Functions for cleaning data
  contents:
  - contains("clean")

- title: Setup
  desc: Functions used for setting up functionality
  contents:
  - contains("setup_")

- title: Utilities
  desc: Utility functions
  contents:
  - run_region
  - expose_stan_fns
  - convert_to_logmean
  - convert_to_logsd
  - growth_to_R
  - R_to_growth
  - update_secondary_args

- title: Internal
  contents:
  - has_keyword("internal")