doi:10.1093/aje/kwu209> for serial interval estimation and the retrospective method from Wallinga & Lipsitch (2007) <doi:10.1098/rspb.2006.3754> for reproduction number estimation. Originally developed for scabies transmission analysis but applicable to other infectious diseases including influenza, COVID-19, and emerging pathogens. Designed for epidemiologists, public health researchers, and infectious disease modelers working with outbreak surveillance data.">

mitey: Serial Interval and Case Reproduction Number Estimation (original) (raw)

Provides methods to estimate serial intervals and time-varying case reproduction numbers from infectious disease outbreak data. Serial intervals measure the time between symptom onset in linked transmission pairs, while case reproduction numbers quantify how many secondary cases each infected individual generates over time. These parameters are essential for understanding transmission dynamics, evaluating control measures, and informing public health responses. The package implements the maximum likelihood framework from Vink et al. (2014) <doi:10.1093/aje/kwu209> for serial interval estimation and the retrospective method from Wallinga & Lipsitch (2007) <doi:10.1098/rspb.2006.3754> for reproduction number estimation. Originally developed for scabies transmission analysis but applicable to other infectious diseases including influenza, COVID-19, and emerging pathogens. Designed for epidemiologists, public health researchers, and infectious disease modelers working with outbreak surveillance data.

Version: 0.2.0
Depends: R (≥ 3.5.0)
Imports: fdrtool, ggplot2, stats
Suggests: brms, broom, cowplot, dplyr, EpiLPS, flextable, forcats, ftExtra, ggridges, gt, here, ISOweek, knitr, lubridate, officer, openxlsx, outbreaks, purrr, rmarkdown, stringr, testthat (≥ 3.0.0), tidybayes, tidyr, viridis, zoo
Published: 2025-09-02
DOI: 10.32614/CRAN.package.mitey
Author: Kylie Ainslie ORCID iD [aut, cre, cph]
Maintainer: Kylie Ainslie <ainslie.kylie at gmail.com>
BugReports: https://github.com/kylieainslie/mitey/issues
License: EUPL-1.2
URL: https://github.com/kylieainslie/mitey,https://kylieainslie.github.io/mitey/
NeedsCompilation: no
Materials: README, NEWS
CRAN checks: mitey results

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