Package: EpiEstim 2.4
EpiEstim: Estimate Time Varying Reproduction Numbers from Epidemic Curves
Tools to quantify transmissibility throughout an epidemic from the analysis of time series of incidence as described in Cori et al. (2013) <doi:10.1093/aje/kwt133> and Wallinga and Teunis (2004) <doi:10.1093/aje/kwh255>.
Authors:
EpiEstim_2.4.tar.gz
EpiEstim_2.4.zip(r-4.5)EpiEstim_2.4.zip(r-4.4)EpiEstim_2.4.zip(r-4.3)
EpiEstim_2.4.tgz(r-4.4-any)EpiEstim_2.4.tgz(r-4.3-any)
EpiEstim_2.4.tar.gz(r-4.5-noble)EpiEstim_2.4.tar.gz(r-4.4-noble)
EpiEstim_2.4.tgz(r-4.4-emscripten)EpiEstim_2.4.tgz(r-4.3-emscripten)
EpiEstim.pdf |EpiEstim.html✨
EpiEstim/json (API)
NEWS
# Install 'EpiEstim' in R: |
install.packages('EpiEstim', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mrc-ide/epiestim/issues
- Flu1918 - Data on the 1918 H1N1 influenza pandemic in Baltimore.
- Flu2009 - Data on the 2009 H1N1 influenza pandemic in a school in Pennsylvania.
- Measles1861 - Data on the 1861 measles epidemic in Hagelloch, Germany.
- MockRotavirus - Mock data on a rotavirus epidemic.
- SARS2003 - Data on the 2003 SARS epidemic in Hong Kong.
- Smallpox1972 - Data on the 1972 smallpox epidemic in Kosovo
- covid_deaths_2020_uk - Data on the 2020-2022 SARS-CoV-2 epidemic in the UK.
- flu_2009_NYC_school - Data on the 2009 H1N1 influenza pandemic in a school in New York city
- mers_2014_15 - Data on Middle East Respiratory Syndrome (MERS) in Saudi Arabia.
Last updated 9 days agofrom:238d43548d (on master). Checks:OK: 3 NOTE: 4. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 30 2024 |
R-4.5-win | NOTE | Aug 30 2024 |
R-4.5-linux | NOTE | Aug 30 2024 |
R-4.4-win | NOTE | Aug 30 2024 |
R-4.4-mac | NOTE | Aug 30 2024 |
R-4.3-win | OK | Aug 30 2024 |
R-4.3-mac | OK | Aug 30 2024 |
Exports:aggregate_incbackimpute_Icheck_cdt_samples_convergencecoarse2estimcompute_lambdacompute_si_cutoffcompute_t_mindefault_mcmc_controlsdefault_priorsdiscr_siDiscrSIdraw_epsilondraw_Restimate_advantageestimate_Restimate_R_aggestimate_R_plotsEstimateRfirst_nonzero_incidget_shape_epsilonget_shape_R_flatinit_mcmc_paramsmake_configmake_mcmc_controloverall_infectivityOverallInfectivityprocess_I_multivariantsample_posterior_Rwallinga_teunisWT
Dependencies:abindaweekclicoarseDataToolscodacolorspacecpp11distcretedplyrepitrixfansifarverfitdistrplusgenericsggplot2gluegridExtragtableincidenceisobandlabelinglatticelifecyclemagrittrMASSMatrixMatrixModelsmcmcMCMCpackmgcvmunsellnlmepatchworkpillarpkgconfigplyrpurrrquantregR6RColorBrewerRcppreshape2rlangscalessodiumSparseMstringistringrsurvivaltibbletidyrtidyselectutf8vctrsviridisLitewithr
Alternative software for estimating the reproduction number
Rendered fromalternative_software.Rmd
usingknitr::rmarkdown
on Aug 30 2024.Last update: 2023-04-20
Started: 2022-04-01
Dealing with missed generations of infections with EpiEstim
Rendered fromEpiEstim_backimputation.Rmd
usingknitr::rmarkdown
on Aug 30 2024.Last update: 2024-08-30
Started: 2024-08-30
EpiEstim: a demonstration
Rendered fromshort_demo.Rmd
usingknitr::rmarkdown
on Aug 30 2024.Last update: 2024-08-30
Started: 2021-04-09
EpiEstim for aggregated incidence data
Rendered fromEpiEstim_aggregated_data.Rmd
usingknitr::rmarkdown
on Aug 30 2024.Last update: 2023-07-03
Started: 2022-12-07
EpiEstim Vignette
Rendered fromfull_EpiEstim_vignette.Rmd
usingknitr::rmarkdown
on Aug 30 2024.Last update: 2024-08-30
Started: 2021-04-09
MV-EpiEstim
Rendered fromMV_EpiEstim_vignette.Rmd
usingknitr::rmarkdown
on Aug 30 2024.Last update: 2024-08-30
Started: 2021-11-26