Package: earlyR 0.0.5
Thibaut Jombart
earlyR: Estimation of Transmissibility in the Early Stages of a Disease Outbreak
Implements a simple, likelihood-based estimation of the reproduction number (R0) using a branching process with a Poisson likelihood. This model requires knowledge of the serial interval distribution, and dates of symptom onsets. Infectiousness is determined by weighting R0 by the probability mass function of the serial interval on the corresponding day. It is a simplified version of the model introduced by Cori et al. (2013) <doi:10.1093/aje/kwt133>.
Authors:
earlyR_0.0.5.tar.gz
earlyR_0.0.5.zip(r-4.5)earlyR_0.0.5.zip(r-4.4)earlyR_0.0.5.zip(r-4.3)
earlyR_0.0.5.tgz(r-4.4-any)earlyR_0.0.5.tgz(r-4.3-any)
earlyR_0.0.5.tar.gz(r-4.5-noble)earlyR_0.0.5.tar.gz(r-4.4-noble)
earlyR_0.0.5.tgz(r-4.4-emscripten)earlyR_0.0.5.tgz(r-4.3-emscripten)
earlyR.pdf |earlyR.html✨
earlyR/json (API)
NEWS
| # Install 'earlyR' in R: |
| install.packages('earlyR', repos = c('https://reconhub.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/reconhub/earlyr/issues
Pkgdown site:https://www.repidemicsconsortium.org
Last updated 4 years agofrom:61ee8bd091. Checks:3 OK, 4 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Dec 25 2024 |
| R-4.5-win | NOTE | Dec 25 2024 |
| R-4.5-linux | NOTE | Dec 25 2024 |
| R-4.4-win | NOTE | Dec 25 2024 |
| R-4.4-mac | NOTE | Dec 25 2024 |
| R-4.3-win | OK | Dec 25 2024 |
| R-4.3-mac | OK | Dec 25 2024 |
Dependencies:aweekclicoarseDataToolscodacolorspacecpp11distcretedplyrEpiEstimepitrixfansifarverfitdistrplusgenericsggplot2gluegridExtragtableincidenceisobandlabelinglatticelifecyclemagrittrMASSMatrixMatrixModelsmcmcMCMCpackmgcvmunsellnlmepillarpkgconfigplyrpurrrquantregR6RColorBrewerRcppreshape2rlangscalessodiumSparseMstringistringrsurvivaltibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Estimate the Reproduction Number | get_R get_R.default get_R.incidence get_R.integer get_R.numeric |
| Plot earlyR objects | plot.earlyR points.earlyR |
| Print method for earlyR objects | print.earlyR |
| Get a sample of plausible Reproduction Numbers | sample_R |
