Package: EpiNow2 1.6.1

Sebastian Funk

EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters

Estimates the time-varying reproduction number, rate of spread, and doubling time using a range of open-source tools (Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1>), and current best practices (Gostic et al. (2020) <doi:10.1101/2020.06.18.20134858>). It aims to help users avoid some of the limitations of naive implementations in a framework that is informed by community feedback and is actively supported.

Authors:Sam Abbott [aut], Joel Hellewell [aut], Katharine Sherratt [aut], Katelyn Gostic [aut], Joe Hickson [aut], Hamada S. Badr [aut], Michael DeWitt [aut], James M. Azam [aut], Robin Thompson [ctb], Sophie Meakin [ctb], James Munday [ctb], Nikos Bosse [ctb], Paul Mee [ctb], Peter Ellis [ctb], Pietro Monticone [ctb], Lloyd Chapman [ctb], Andrew Johnson [ctb], Kaitlyn Johnson [ctb], EpiForecasts [aut], Sebastian Funk [aut, cre]

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EpiNow2.pdf |EpiNow2.html✨
EpiNow2/json (API)
NEWS

# Install 'EpiNow2' in R:

install.packages('EpiNow2', repos = c('https://epiforecasts.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/epiforecasts/epinow2/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

example_confirmed - Example Confirmed Case Data Set
example_generation_time - Example generation time
example_incubation_period - Example incubation period
example_reporting_delay - Example reporting delay
example_truncated - Example Case Data Set with Truncation
generation_times - Literature Estimates of Generation Times
incubation_periods - Literature Estimates of Incubation Periods

On CRAN:

backcalculation covid-19 gaussian-processes open-source reproduction-number stan

11.75 score 114 stars 209 scripts 977 downloads 7 mentions 86 exports 68 dependencies

Last updated 19 days agofrom:9b8cd4fcce (on v1.6.1). Checks:OK: 2 NOTE: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win-x86_64	NOTE	Oct 31 2024
R-4.5-linux-x86_64	OK	Oct 31 2024
R-4.4-win-x86_64	NOTE	Oct 31 2024
R-4.4-mac-x86_64	NOTE	Oct 31 2024
R-4.4-mac-aarch64	NOTE	Oct 31 2024
R-4.3-win-x86_64	NOTE	Oct 31 2024
R-4.3-mac-x86_64	NOTE	Oct 31 2024
R-4.3-mac-aarch64	NOTE	Oct 31 2024

Exports:adjust_infection_to_report apply_tolerance backcalc_opts bootstrapped_dist_fit bound_dist calc_CrI calc_CrIs calc_summary_measures calc_summary_stats clean_nowcasts collapse convert_to_logmean convert_to_logsd convolve_and_scale delay_opts discretise discretize dist_fit dist_skel epinow epinow2_cmdstan_model estimate_delay estimate_infections estimate_secondary estimate_truncation expose_stan_fns extract_CrIs extract_inits extract_samples extract_stan_param fix_dist fix_parameters Fixed forecast_infections forecast_secondary Gamma gamma_dist_def generation_time_opts get_dist get_distribution get_generation_time get_incubation_period get_parameters get_pmf get_regional_results gp_opts growth_to_R gt_opts is_constrained lognorm_dist_def LogNormal make_conf map_prob_change new_dist_spec NonParametric Normal obs_opts opts_list plot_estimates plot_summary R_to_growth regional_epinow regional_runtimes regional_summary report_cases report_plots report_summary rstan_opts rstan_sampling_opts rstan_vb_opts rt_opts sample_approx_dist secondary_opts set_dt_single_thread setup_default_logging setup_future setup_logging simulate_infections simulate_secondary stan_laplace_opts stan_opts stan_pathfinder_opts stan_sampling_opts stan_vb_opts trunc_opts update_secondary_args

Dependencies:abind backports BH callr checkmate cli colorspace cpp11 data.table desc distributional fansi farver formatR futile.logger futile.options generics ggplot2 glue gridExtra gtable inline isoband labeling lambda.r lattice lifecycle loo lubridate magrittr MASS Matrix matrixStats mgcv munsell nlme numDeriv patchwork pillar pkgbuild pkgconfig posterior processx ps purrr QuickJSR R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RcppEigen RcppParallel rlang rstan rstantools runner scales StanHeaders tensorA tibble timechange truncnorm utf8 vctrs viridisLite withr

Case studies and use in the literature

Rendered fromcase-studies.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2023-09-18
Started: 2022-10-17

Examples: estimate_infections()

Rendered fromestimate_infections_options.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-10-02
Started: 2023-10-03

Gaussian Process implementation details

Rendered fromgaussian_process_implementation_details.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-10-24
Started: 2023-04-27

Getting started with EpiNow2

Rendered fromEpiNow2.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-10-16
Started: 2024-01-09

Model definition: estimate_infections()

Rendered fromestimate_infections.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2023-10-16
Started: 2022-10-17

Model definition: estimate_secondary()

Rendered fromestimate_secondary.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2023-01-17
Started: 2022-10-17

Model definition: estimate_truncation()

Rendered fromestimate_truncation.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2023-10-16
Started: 2022-10-17

Using epinow() for running in production mode

Rendered fromepinow.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-10-02
Started: 2023-10-03

Workflow for Rt estimation and forecasting

Rendered fromestimate_infections_workflow.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-10-02
Started: 2023-10-03

Help page	Topics
Creates a delay distribution as the sum of two other delay distributions.	+.dist_spec
Back Calculation Options	backcalc_opts
Fit a Subsampled Bootstrap to Integer Values and Summarise Distribution Parameters	bootstrapped_dist_fit
Define bounds of a <dist_spec>	bound_dist
Combines multiple delay distributions for further processing	c.dist_spec
Calculate Credible Interval	calc_CrI
Calculate Credible Intervals	calc_CrIs
Calculate All Summary Measures	calc_summary_measures
Calculate Summary Statistics	calc_summary_stats
Clean Nowcasts for a Supplied Date	clean_nowcasts
Clean Regions	clean_regions
Collapse nonparametric distributions in a <dist_spec>	collapse collapse.dist_spec
Convert mean and sd to log mean for a log normal distribution	convert_to_logmean
Convert mean and sd to log standard deviation for a log normal distribution	convert_to_logsd
Convolve and scale a time series	convolve_and_scale
Delay Distribution Options	delay_opts
Discretise a <dist_spec>	discretise discretise.dist_spec discretize
Fit an Integer Adjusted Exponential, Gamma or Lognormal distributions	dist_fit
Probability distributions	Distributions Fixed Gamma LogNormal NonParametric Normal
Real-time Rt Estimation, Forecasting and Reporting	epinow
Load and compile an EpiNow2 cmdstanr model	epinow2_cmdstan_model
Estimate a Delay Distribution	estimate_delay
Estimate Infections, the Time-Varying Reproduction Number and the Rate of Growth	estimate_infections
Estimate a Secondary Observation from a Primary Observation	estimate_secondary
Estimate Truncation of Observed Data	estimate_truncation
Example Confirmed Case Data Set	example_confirmed
Example generation time	example_generation_time
Example incubation period	example_incubation_period
Example reporting delay	example_reporting_delay
Example Case Data Set with Truncation	example_truncated
Expose internal package stan functions in R	expose_stan_fns
Extract Credible Intervals Present	extract_CrIs
Generate initial conditions from a Stan fit	extract_inits
Extract all samples from a stan fit	extract_samples
Extract a Parameter Summary from a Stan Object	extract_stan_param
Filter Options for a Target Region	filter_opts
Fix the parameters of a <dist_spec>	fix_parameters fix_parameters.dist_spec
Forecast infections from a given fit and trajectory of the time-varying reproduction number	forecast_infections
Forecast Secondary Observations Given a Fit from estimate_secondary	forecast_secondary
Literature Estimates of Generation Times	generation_times
Get the distribution of a <dist_spec>	get_distribution
Get parameters of a parametric distribution	get_parameters
Get the probability mass function of a nonparametric distribution	get_pmf
Get Combined Regional Results	get_regional_results
Approximate Gaussian Process Settings	gp_opts
Convert Growth Rates to Reproduction numbers.	growth_to_R
Generation Time Distribution Options	generation_time_opts gt_opts
Literature Estimates of Incubation Periods	incubation_periods
Check if a <dist_spec> is constrained, i.e. has a finite maximum or nonzero CDF cutoff.	is_constrained is_constrained.dist_spec
Format Credible Intervals	make_conf
Categorise the Probability of Change for Rt	map_prob_change
Returns the maximum of one or more delay distribution	max.dist_spec
Returns the mean of one or more delay distribution	mean.dist_spec
Internal function for generating a 'dist_spec' given parameters and a distribution.	new_dist_spec
Observation Model Options	obs_opts
Return an _opts List per Region	opts_list
Plot EpiNow2 Credible Intervals	plot_CrIs
Plot Estimates	plot_estimates
Plot a Summary of the Latest Results	plot_summary
Plot PMF and CDF for a dist_spec object	plot.dist_spec
Plot method for epinow	plot.epinow
Plot method for estimate_infections	plot plot.estimate_infections
Plot method for estimate_secondary	plot.estimate_secondary
Plot method for estimate_truncation	plot.estimate_truncation
Prints the parameters of one or more delay distributions	print.dist_spec
Convert Reproduction Numbers to Growth Rates	R_to_growth
Real-time Rt Estimation, Forecasting and Reporting by Region	regional_epinow
Regional Summary Output	regional_summary
Report plots	report_plots
Provide Summary Statistics for Estimated Infections and Rt	report_summary
Rstan Options	rstan_opts
Rstan Sampling Options	rstan_sampling_opts
Rstan Variational Bayes Options	rstan_vb_opts
Time-Varying Reproduction Number Options	rt_opts
Run epinow with Regional Processing Code	run_region
Secondary Reports Options	secondary_opts
Setup Default Logging	setup_default_logging
Set up Future Backend	setup_future
Setup Logging	setup_logging
Simulate infections using the renewal equation	simulate_infections
Simulate secondary observations from primary observations	simulate_secondary
Stan Laplace algorithm Options	stan_laplace_opts
Stan Options	stan_opts
Stan pathfinder algorithm Options	stan_pathfinder_opts
Stan Sampling Options	stan_sampling_opts
Stan Variational Bayes Options	stan_vb_opts
Summary output from epinow	summary summary.epinow
Summary output from estimate_infections	summary.estimate_infections
Truncation Distribution Options	trunc_opts
Update estimate_secondary default priors	update_secondary_args

Package: EpiNow2 1.6.1

EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters

Case studies and use in the literature

Examples: estimate_infections()

Gaussian Process implementation details

Getting started with EpiNow2

Model definition: estimate_infections()

Model definition: estimate_secondary()

Model definition: estimate_truncation()

Using epinow() for running in production mode

Workflow for Rt estimation and forecasting

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)