Package: mitey
Title: Serial Interval and Case Reproduction Number Estimation
Version: 0.2.0
Authors@R: 
    person(given = "Kylie", 
           family = "Ainslie", 
           role = c("aut", "cre", "cph"), 
           email = "ainslie.kylie@gmail.com",
           comment = c(ORCID = "0000-0001-5419-7206"))
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.
Date: 2025-08-16
License: EUPL-1.2
Encoding: UTF-8
RoxygenNote: 7.3.2
Imports: fdrtool, ggplot2, stats
URL: https://github.com/kylieainslie/mitey,
        https://kylieainslie.github.io/mitey/
BugReports: https://github.com/kylieainslie/mitey/issues
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
Config/testthat/edition: 3
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2025-08-27 15:22:05 UTC; kylieainslie
Author: Kylie Ainslie [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0001-5419-7206>)
Maintainer: Kylie Ainslie <ainslie.kylie@gmail.com>
Repository: CRAN
Date/Publication: 2025-09-02 05:40:18 UTC
Built: R 4.5.3; ; 2026-06-10 03:05:52 UTC; windows
