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mitey  

Serial Interval and Case Reproduction Number Estimation
View on CRAN: Click here


Download and install mitey package within the R console
Install from CRAN:
install.packages("mitey")

Install from Github:
library("remotes")
install_github("cran/mitey")

Install by package version:
library("remotes")
install_version("mitey", "0.2.0")



Attach the package and use:
library("mitey")
Maintained by
Kylie Ainslie
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2025-09-02
Latest Update: 2025-09-02
Description:
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.
How to cite:
Kylie Ainslie (2025). mitey: Serial Interval and Case Reproduction Number Estimation. R package version 0.2.0, https://cran.r-project.org/web/packages/mitey. Accessed 08 Mar. 2026.
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