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_pkgdown.yml
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/
_pkgdown.yml
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url: epiforecasts.io/EpiNow2/
template:
opengraph:
image:
src: man/figures/unnamed-chunk-13-1.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: "@cmmid_lshtm"
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:
type: inverse
left:
- text: "Home"
href: index.html
- text: News
href: news/index.html
- icon: fa-file-code-o
text: "Functions"
href: reference/index.html
right:
- icon: fa-github
href: https://github.com/epiforecasts/EpiNow2
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 Parameters
desc: Function to estimate parameters of interest.
contents:
- estimate_infections
- forecast_infections
- estimate_delay
- estimate_truncation
- estimate_secondary
- forecast_secondary
- 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_cases
- 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: Map results
desc: Optional mapping functions (requires additional dependencies)
contents:
- global_map
- country_map
- theme_map
- 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