EpiTrans

An R package for estimating Epidemic Transmissibility in time and space

contributors: Chen-Hsuan Tu, Ta-Chou Ng, and Tzai-Hung Wen
contact: Tzai-Hung Wen, National Taiwan University
email: wenthung@ntu.edu.tw


Introduction

The package, EpiTrans, provides a new method for quantifying spatially adjusted (time-varying) reproductive numbers that reflects spatial heterogeneity in transmission potential among individuals. This method estimates individual-level effective reproductive numbers and a summarized indicator for population-level time-varying reproductive number.

Package Description

It provides several functions, including (1) plotting descriptive epidemic trends in time and space; (2) estimating reproductive numbers; (3) visualizing the graphics and animations of individual-level and aggregated-level reproductive numbers.

Installation

The package is available from Github. You can install the nightly build using the following R command:

> library(devtools)
> install_github("wenlab501/EpiTrans")

Tutorial

Click to see →

Functions and datasets

Click to see →

Reference:
Ng TC and Wen TH (2019), Spatially Adjusted Time-varying Reproductive Numbers: Understanding the Geographical Expansion of Urban Dengue Outbreaks, Scientific Reports 9: 19172.