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>.

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Description file content

Package
earlyR
Title
Estimation of Transmissibility in the Early Stages of a Disease Outbreak
Version
0.0.1
Description
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) .
Depends
R (>= 3.3.0)
License
MIT + file LICENSE
Encoding
UTF-8
LazyData
true
Imports
stats, distcrete, EpiEstim, epitrix
Suggests
testthat, vdiffr, roxygen2, incidence, knitr
RoxygenNote
6.0.1
URL
BugReports
https://github.com/reconhub/earlyR/issues
NeedsCompilation
no
Packaged
2017-12-05 23:00:54 UTC; thibaut
Author
Thibaut Jombart [aut, cre], Anne Cori [aut], Pierre Nouvellet [aut]
Maintainer
Thibaut Jombart
Repository
CRAN
Date/Publication
2017-12-06 15:50:22 UTC

install.packages('earlyR')

0.0.1

7 days ago

http://www.repidemicsconsortium.org/earlyR

Thibaut Jombart

MIT + file LICENSE

Depends on

R (>= 3.3.0)

Imports

stats, distcrete, EpiEstim, epitrix

Suggests

testthat, vdiffr, roxygen2, incidence, knitr

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