This repository contains the code for the manuscript "Wastewater-based estimation of the effective reproductive number of SARS-CoV-2" by Huisman et al..
The scripts in this repository assume that the code of the Re estimation pipeline of Huisman, Scire et al. is available in a folder "covid-19-re-shiny-app" at the same level as this repository. The git-repo for the pipeline can be found here.
The code is split into 3 parts:
When run from within this repository, the code recreates the results and figures shown in the manuscript.
Includes case incidence data in Zurich and California. The wastewater data for Zurich is also deposited on the EAWAG open data portal, and for San Jose the data used here is a copy of the data included in the Stanford Digital repository.
The scan across SLD parameter pairs takes quite long to compute, so we have added the results (shown in the paper) to the folder "scan".
The folder "subsampling" contains the Rww estimates for the data that was subsampled by weekday/sampling regime (this takes less time to compute but is included for convenience).