mitey - mitey 0.2.0 - CRAN Release

mitey 0.2.0 - CRAN Release 🎉

We're excited to announce that mitey is now available on CRAN!

What is mitey?

A lightweight R package for estimating infectious disease dynamics parameters, originally developed as a companion to our scabies transmission research.

Key Features

• Serial interval estimation using maximum likelihood (Vink et al. 2014)
• Time-varying reproduction number estimation (Wallinga & Lipsitch 2007)
  
• Synthetic epidemic generation for testing and validation
• Comprehensive validation with real outbreak data

Installation

r install.packages("mitey")

Getting Started

• Quick start guide
• Reproduce Ainslie et al. results

Citation

If you use mitey in your research, please cite: Ainslie et al. 2025

- TeX
Published by kylieainslie 6 months ago

mitey - miteyv0.1.0

Initial release of mitey, a package for estimating infectious disease parameters!

Main features

si_estim() - Estimates the mean and standard deviation of serial interval distributions using the method by Vink et al. (2014) plot_si_fit() - Visualizes fitted mixture distributions used to estimate mean serial interval wallinga_lipsitch() - Calculates time-varying case reproduction numbers from incidence data using the Wallinga & Lipsitch (2007) method generate_synthetic_epidemic() - Creates simulated epidemic curves with specified parameters for testing methods

The package includes comprehensive documentation and vignettes demonstrating analyses both for scabies (with long serial intervals) and other infectious diseases.

This package was originally developed to accompany analyses in Ainslie et al. 2025 on scabies transmission, but the methods are applicable to epidemiological studies of various infectious diseases. For tutorials and examples, visit our package website.

- TeX
Published by kylieainslie 10 months ago