_pkgdown.yml

url: 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: [reference, modeldefs, casestudies, news]
    right: [search, github]
  components:
    modeldefs:
      text: Model definitions
      menu:
      - 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
    casestudies:
      text: Case studies
      menu:
      - text: External case studies and use in the literature
        href: articles/case-studies.html

figures:
  fig.width: 9
  fig.height: 9
  
reference:
  - title: Estimation + Reporting
    desc: Functions that faciliate 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
      - simulate_infections
      - estimate_secondary
      - forecast_secondary
      - estimate_delay
      - estimate_truncation
  - title: Internal epinow Functions
    desc: Functions used internally by epinow
    contents:
      - update_horizon
      - contains("save_")
      - estimates_by_report_date
      - copy_results_to_latest
      - construct_output
  - title: Internal estimate_infections Functions
    desc: Functions used by estimate_infections
    contents:
      - contains("_opts")
      - opts_list
      - contains("create_")
      - allocate_delays
      - allocate_empty
  - title: Model Fitting
    desc: Functions for model fitting
    contents:
      - contains("fit_")
      - init_cumulative_fit
  - title: Summarise Across Regions
    desc: Functions used for summarising across regions (designed for use with regional_epinow)
    contents:
      - regional_summary
      - regional_runtimes
  - title: Summarise results
    desc: Functions from summarising results
    contents:
      - contains("summary.")
      - contains("summarise")
      - contains("calc_")
      - contains("process_")
      - format_fit
      - 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_cases
      - report_plots
      - report_summary  
  - title: Define, Fit and Parameterise Distributions
    desc: Functions to define, fit and parameterise distributions
    contents:
      - contains("dist")
      - tune_inv_gamma
  - title: Simulate
    desc: Functions to help with simulating data or mapping to reported cases
    contents:
      - simulate_infections
      - simulate_secondary
      - adjust_infection_to_report
  - title: Data
    desc: Package datasets that may be used to parameterise other functions or in examples
    contents:
      - generation_times
      - incubation_periods
      - example_confirmed
  - title: Get/Extract Data
    desc: Functions for extracting data from objects or getting data from sources
    contents:
      - contains("get_")
      - contains("extract_")
  - title: Clean Data
    desc: Functions for cleaning data
    contents:
      - contains("clean")
  - title: Setup Utilities
    desc: Function used for setting up functionality
    contents:
      - contains("setup_")
  - title: Utilities
    desc: Utility functions
    contents:
      - match_output_arguments
      - run_region
      - expose_stan_fns
      - convert_to_logmean
      - convert_to_logsd
      - growth_to_R
      - R_to_growth
      - update_list
      - add_day_of_week
      - update_secondary_args