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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>.
| Version: |
0.0.5 |
| Depends: |
R (≥ 3.3.0) |
| Imports: |
stats, distcrete, EpiEstim, epitrix, ggplot2 |
| Suggests: |
testthat, vdiffr, roxygen2, incidence, knitr, rmarkdown, projections, covr |
| Published: |
2020-10-27 |
| DOI: |
10.32614/CRAN.package.earlyR |
| Author: |
Thibaut Jombart [aut, cre],
Anne Cori [aut],
Pierre Nouvellet [aut],
Janetta Skarp [aut],
Zhian N. Kamvar [ctb],
Tim Taylor  [ctb] |
| Maintainer: |
Thibaut Jombart <thibautjombart at gmail.com> |
| BugReports: |
https://github.com/reconhub/earlyR/issues |
| License: |
MIT + file LICENSE |
| URL: |
https://www.repidemicsconsortium.org/earlyR/ |
| NeedsCompilation: |
no |
| Materials: |
NEWS |
| In views: |
Epidemiology |
| CRAN checks: |
earlyR results |
Documentation:
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.