Package: EpiNow2 1.6.0.9000
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:
EpiNow2_1.6.0.9000.tar.gz
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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
- 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
backcalculationcovid-19gaussian-processesopen-sourcereproduction-numberstan
Last updated 3 days agofrom:2e1aa86598. Checks:OK: 1 NOTE: 8. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 03 2024 |
R-4.5-win-x86_64 | NOTE | Oct 03 2024 |
R-4.5-linux-x86_64 | NOTE | Oct 03 2024 |
R-4.4-win-x86_64 | NOTE | Oct 03 2024 |
R-4.4-mac-x86_64 | NOTE | Oct 03 2024 |
R-4.4-mac-aarch64 | NOTE | Oct 03 2024 |
R-4.3-win-x86_64 | NOTE | Oct 03 2024 |
R-4.3-mac-x86_64 | NOTE | Oct 03 2024 |
R-4.3-mac-aarch64 | NOTE | Oct 03 2024 |
Exports:adjust_infection_to_reportapply_tolerancebackcalc_optsbootstrapped_dist_fitbound_distcalc_CrIcalc_CrIscalc_summary_measurescalc_summary_statsclean_nowcastscollapseconvert_to_logmeanconvert_to_logsdconvolve_and_scaledelay_optsdiscretisediscretizedist_fitdist_skelepinowepinow2_cmdstan_modelestimate_delayestimate_infectionsestimate_secondaryestimate_truncationexpose_stan_fnsextract_CrIsextract_initsextract_samplesextract_stan_paramfix_distfix_parametersFixedforecast_infectionsforecast_secondaryGammagamma_dist_defgeneration_time_optsget_distget_distributionget_generation_timeget_incubation_periodget_parametersget_pmfget_regional_resultsgp_optsgrowth_to_Rgt_optsis_constrainedlognorm_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:abindbackportsBHcallrcheckmateclicolorspacecpp11data.tabledescdistributionalfansifarverformatRfutile.loggerfutile.optionsgenericsggplot2gluegridExtragtableinlineisobandlabelinglambda.rlatticelifecycleloolubridatemagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivpatchworkpillarpkgbuildpkgconfigposteriorprocessxpspurrrQuickJSRR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsrunnerscalesStanHeaderstensorAtibbletimechangetruncnormutf8vctrsviridisLitewithr
Case studies and use in the literature
Rendered fromcase-studies.Rmd
usingknitr::rmarkdown
on Oct 03 2024.Last update: 2023-09-18
Started: 2022-10-17
Examples: estimate_infections()
Rendered fromestimate_infections_options.Rmd
usingknitr::rmarkdown
on Oct 03 2024.Last update: 2024-10-02
Started: 2023-10-03
Gaussian Process implementation details
Rendered fromgaussian_process_implementation_details.Rmd
usingknitr::rmarkdown
on Oct 03 2024.Last update: 2024-08-09
Started: 2023-04-27
Getting started with EpiNow2
Rendered fromEpiNow2.Rmd
usingknitr::rmarkdown
on Oct 03 2024.Last update: 2024-10-02
Started: 2024-01-09
Model definition: estimate_infections()
Rendered fromestimate_infections.Rmd
usingknitr::rmarkdown
on Oct 03 2024.Last update: 2023-10-16
Started: 2022-10-17
Model definition: estimate_secondary()
Rendered fromestimate_secondary.Rmd
usingknitr::rmarkdown
on Oct 03 2024.Last update: 2023-01-17
Started: 2022-10-17
Model definition: estimate_truncation()
Rendered fromestimate_truncation.Rmd
usingknitr::rmarkdown
on Oct 03 2024.Last update: 2023-10-16
Started: 2022-10-17
Using epinow() for running in production mode
Rendered fromepinow.Rmd
usingknitr::rmarkdown
on Oct 03 2024.Last update: 2024-10-02
Started: 2023-10-03
Workflow for Rt estimation and forecasting
Rendered fromestimate_infections_workflow.Rmd
usingknitr::rmarkdown
on Oct 03 2024.Last update: 2024-10-02
Started: 2023-10-03