This repository contains the code and data for the paper "Robust uncertainty quantification in popular estimators of the instantaneous reproduction number".
All source code is written in Julia. Example code in the form of Jupyter notebooks is also provided. Finally, R scripts are used to generate the figures in the paper.
Tutorials are included on the corresponding website Rt estimators in Julia, and in the correpsonding Jupyter notebooks in the this repository.
Other than a Julia installation, no external software is required to run this code. Simply clone this repository, open a Julia terminal in the main directory, and copy-paste the example code snippets. We recommend starting with EpiEstim here.
/data/: Contains the data used in the paper and example scripts./docs/: Files to host the correponding website. These can be ignored./paper/: Contains the code to generate and plot results in the paper and supplementary material./src/: Source code providing simple implementations of our methods, as well as helper functions to load data etc.EpiEstim.ipynb: Jupyter notebook with example code for fitting EpiEstim.EpiFilter.ipynb: Jupyter notebook with example code for fitting EpiFilter.
