incidence: Compute, Handle, Plot and Model Incidence of Dated Events
Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. In addition, log-linear models can be fitted to 'incidence' objects using 'fit'. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
| Version: | 1.7.6 |
| Imports: | ggplot2 (≥ 3.3.2), aweek (≥ 0.2.0) |
| Suggests: | magrittr, outbreaks, testthat, vdiffr, knitr, rmarkdown, scales, cowplot |
| Published: | 2025-06-19 |
| DOI: | 10.32614/CRAN.package.incidence |
| Author: | Thibaut Jombart [aut],
Zhian N. Kamvar 
[aut],
Rich FitzJohn [aut],
Tim Taylor [cre],
Jun Cai [ctb],
Sangeeta Bhatia [ctb],
Jakob Schumacher [ctb],
Juliet R.C. Pulliam
[ctb] |
| Maintainer: | Tim Taylor <tim.taylor at hiddenelephants.co.uk> |
| BugReports: | https://github.com/reconhub/incidence/issues |
| License: | MIT + file LICENSE |
| URL: | https://www.repidemicsconsortium.org/incidence/ |
| NeedsCompilation: | no |
| Citation: | incidence citation info |
| Materials: | NEWS |
| In views: | Epidemiology |
| CRAN checks: | incidence results |
Documentation:
| Reference manual: | incidence.html , incidence.pdf |
| Vignettes: |
Conversions (source, R code) Customise graphics (source, R code) Incidence class (source, R code) Incidence fit class (source, R code) Overview (source, R code) |
Downloads:
| Package source: | incidence_1.7.6.tar.gz |
| Windows binaries: | r-devel: incidence_1.7.6.zip, r-release: incidence_1.7.6.zip, r-oldrel: incidence_1.7.6.zip |
| macOS binaries: | r-release (arm64): incidence_1.7.6.tgz, r-oldrel (arm64): incidence_1.7.6.tgz, r-release (x86_64): incidence_1.7.6.tgz, r-oldrel (x86_64): incidence_1.7.6.tgz |
| Old sources: | incidence archive |
Reverse dependencies:
| Reverse imports: | epiCo, EpiEstim, projections, ViroReportR |
| Reverse suggests: | earlyR, epitrix, outbreaks |
Linking:
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