Package: EpiNow2 1.5.2.9000

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], 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'))

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

backcalculationcovid-19gaussian-processesopen-sourcereproduction-numberstan

83 exports 105 stars 4.97 score 76 dependencies 1.5k downloads

Last updated 13 days agofrom:0b776fd1457c13cafd936d760e1eb045570cbd3e

Exports:adjust_infection_to_reportapply_tolerancebackcalc_optsbootstrapped_dist_fitcalc_CrIcalc_CrIscalc_summary_measurescalc_summary_statsclean_nowcastscollapseconvert_to_logmeanconvert_to_logsdconvolve_and_scaledelay_optsdiscretisediscretizedist_fitdist_skeldist_specepinowepinow2_cmdstan_modelestimate_delayestimate_infectionsestimate_secondaryestimate_truncationexpose_stan_fnsextract_CrIsextract_initsextract_samplesextract_stan_paramfix_distFixedforecast_infectionsforecast_secondaryGammagamma_dist_defgeneration_time_optsget_distget_distributionget_generation_timeget_incubation_periodget_parametersget_pmfget_regional_resultsgp_optsgrowth_to_Rlognorm_dist_defLogNormalmake_confmap_prob_changenew_dist_specNonParametricNormalobs_optsopts_listplot_estimatesplot_summaryR_to_growthregional_epinowregional_runtimesregional_summaryreport_casesreport_plotsreport_summaryrstan_optsrstan_sampling_optsrstan_vb_optsrt_optssample_approx_distsecondary_optsset_dt_single_threadsetup_default_loggingsetup_futuresetup_loggingsimulate_infectionssimulate_secondarystan_laplace_optsstan_optsstan_pathfinder_optsstan_sampling_optsstan_vb_optstrunc_optsupdate_secondary_args

Dependencies:abindbackportsBHcallrcheckmateclicodetoolscolorspacecpp11data.tabledescdigestdistributionalfansifarverformatRfutile.loggerfutile.optionsfuturefuture.applygenericsggplot2globalsgluegridExtragtableinlineisobandlabelinglambda.rlatticelifecyclelistenvloolubridatemagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivparallellypatchworkpillarpkgbuildpkgconfigposteriorprocessxprogressrpspurrrQuickJSRR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsrunnerscalesStanHeaderstensorAtibbletimechangetruncnormutf8vctrsviridisLitewithr

Case studies and use in the literature

Rendered fromcase-studies.Rmdusingknitr::rmarkdownon Jun 07 2024.

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

Examples: estimate_infections()

Rendered fromestimate_infections_options.Rmdusingknitr::rmarkdownon Jun 07 2024.

Last update: 2024-05-10
Started: 2023-10-03

Gaussian Process implementation details

Rendered fromgaussian_process_implementation_details.Rmdusingknitr::rmarkdownon Jun 07 2024.

Last update: 2023-04-27
Started: 2023-04-27

Getting started with EpiNow2

Rendered fromEpiNow2.Rmdusingknitr::rmarkdownon Jun 07 2024.

Last update: 2024-05-10
Started: 2024-01-09

Model definition: estimate_infections()

Rendered fromestimate_infections.Rmdusingknitr::rmarkdownon Jun 07 2024.

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

Model definition: estimate_secondary()

Rendered fromestimate_secondary.Rmdusingknitr::rmarkdownon Jun 07 2024.

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

Model definition: estimate_truncation()

Rendered fromestimate_truncation.Rmdusingknitr::rmarkdownon Jun 07 2024.

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

Using epinow() for running in production mode

Rendered fromepinow.Rmdusingknitr::rmarkdownon Jun 07 2024.

Last update: 2024-05-10
Started: 2023-10-03

Workflow for Rt estimation and forecasting

Rendered fromestimate_infections_workflow.Rmdusingknitr::rmarkdownon Jun 07 2024.

Last update: 2024-05-10
Started: 2023-10-03

Readme and manuals

Help Manual

Help pageTopics
Creates a delay distribution as the sum of two other delay distributions.+.dist_spec
Applies a threshold to all nonparametric distributions in a <dist_spec>apply_tolerance
Back Calculation Optionsbackcalc_opts
Fit a Subsampled Bootstrap to Integer Values and Summarise Distribution Parametersbootstrapped_dist_fit
Combines multiple delay distributions for further processingc.dist_spec
Calculate Credible Intervalcalc_CrI
Calculate Credible Intervalscalc_CrIs
Calculate All Summary Measurescalc_summary_measures
Calculate Summary Statisticscalc_summary_stats
Clean Nowcasts for a Supplied Dateclean_nowcasts
Clean Regionsclean_regions
Collapse nonparametric distributions in a <dist_spec>collapse
Convert mean and sd to log mean for a log normal distributionconvert_to_logmean
Convert mean and sd to log standard deviation for a log normal distributionconvert_to_logsd
Convolve and scale a time seriesconvolve_and_scale
Delay Distribution Optionsdelay_opts
Discretise a <dist_spec>discretise discretize
Fit an Integer Adjusted Exponential, Gamma or Lognormal distributionsdist_fit
Distribution Skeletondist_skel
Probability distributionsDistributions Fixed Gamma LogNormal NonParametric Normal
Real-time Rt Estimation, Forecasting and Reportingepinow
Load and compile an EpiNow2 cmdstanr modelepinow2_cmdstan_model
Estimate a Delay Distributionestimate_delay
Estimate Infections, the Time-Varying Reproduction Number and the Rate of Growthestimate_infections
Estimate a Secondary Observation from a Primary Observationestimate_secondary
Estimate Truncation of Observed Dataestimate_truncation
Example Confirmed Case Data Setexample_confirmed
Example generation timeexample_generation_time
Example incubation periodexample_incubation_period
Example reporting delayexample_reporting_delay
Example Case Data Set with Truncationexample_truncated
Expose internal package stan functions in Rexpose_stan_fns
Extract Credible Intervals Presentextract_CrIs
Generate initial conditions from a Stan fitextract_inits
Extract all samples from a stan fitextract_samples
Extract a Parameter Summary from a Stan Objectextract_stan_param
Filter Options for a Target Regionfilter_opts
Fix the parameters of a <dist_spec>fix_dist
Forecast infections from a given fit and trajectory of the time-varying reproduction numberforecast_infections
Forecast Secondary Observations Given a Fit from estimate_secondaryforecast_secondary
Generation Time Distribution Optionsgeneration_time_opts
Literature Estimates of Generation Timesgeneration_times
Get the distribution of a <dist_spec>get_distribution
Get parameters of a parametric distributionget_parameters
Get the probability mass function of a nonparametric distributionget_pmf
Get Combined Regional Resultsget_regional_results
Approximate Gaussian Process Settingsgp_opts
Convert Growth Rates to Reproduction numbers.growth_to_R
Literature Estimates of Incubation Periodsincubation_periods
Format Credible Intervalsmake_conf
Categorise the Probability of Change for Rtmap_prob_change
Returns the maximum of one or more delay distributionmax.dist_spec
Returns the mean of one or more delay distributionmean.dist_spec
Internal function for generating a 'dist_spec' given parameters and a distribution.new_dist_spec
Observation Model Optionsobs_opts
Return an _opts List per Regionopts_list
Plot EpiNow2 Credible Intervalsplot_CrIs
Plot Estimatesplot_estimates
Plot a Summary of the Latest Resultsplot_summary
Plot PMF and CDF for a dist_spec objectplot.dist_spec
Plot method for epinowplot.epinow
Plot method for estimate_infectionsplot plot.estimate_infections
Plot method for estimate_secondaryplot.estimate_secondary
Plot method for estimate_truncationplot.estimate_truncation
Prints the parameters of one or more delay distributionsprint.dist_spec
Convert Reproduction Numbers to Growth RatesR_to_growth
Real-time Rt Estimation, Forecasting and Reporting by Regionregional_epinow
Regional Summary Outputregional_summary
Report plotsreport_plots
Provide Summary Statistics for Estimated Infections and Rtreport_summary
Rstan Optionsrstan_opts
Rstan Sampling Optionsrstan_sampling_opts
Rstan Variational Bayes Optionsrstan_vb_opts
Time-Varying Reproduction Number Optionsrt_opts
Run epinow with Regional Processing Coderun_region
Secondary Reports Optionssecondary_opts
Setup Default Loggingsetup_default_logging
Set up Future Backendsetup_future
Setup Loggingsetup_logging
Simulate infections using the renewal equationsimulate_infections
Simulate secondary observations from primary observationssimulate_secondary
Stan Laplace algorithm Optionsstan_laplace_opts
Stan Optionsstan_opts
Stan pathfinder algorithm Optionsstan_pathfinder_opts
Stan Sampling Optionsstan_sampling_opts
Stan Variational Bayes Optionsstan_vb_opts
Summary output from epinowsummary summary.epinow
Summary output from estimate_infectionssummary.estimate_infections
Truncation Distribution Optionstrunc_opts
Update estimate_secondary default priorsupdate_secondary_args