Publication accepted at Science of the Total Environment
This repository contains the code required to reproduce the plots in the publication: Long-term wastewater monitoring of SARS-CoV-2 viral loads and variants at the major international passenger hub Amsterdam Schiphol Airport: a valuable addition to COVID-19 surveillance.
The code in this repository has been tested with R 4.2.2. with Tidyverse v2.0.0. Packages required are listed in scripts/supplementary_functions.R. The figures can be produced by running the run_analysis.R script, which automatically sources other scripts and gathers data from online databases and the Zenodo data set associated with the preprint, available under the Creative Commons Attribution 4.0 License.
A list of external data used for plotting is given below.
- https://data.rivm.nl/covid-19/COVID-19_varianten.csv: This data is made available by the Kiemsurveillance RIVM under the CC BY 4.0 Licence.
- https://data.rivm.nl/covid-19/COVID-19_rioolwaterdata_landelijk.csv: This data is made available by the Waterschappen, CBS & RIVM under the Public Domain Mark 1.0 Licence.
- https://raw.githubusercontent.com/cov-lineages/pango-designation/master/pango_designation/alias_key.json: This data part of the Pango-Designation GitHub repository made available under the CC BY-NC 4.0 Licence.
To include the hospitalization data in figure 3, please download the weekly hospital admission covid per million data from Our World in Data, and supply the .csv table to the figure_3.R script using the -a option. This data is made available by Our World in Data under the CC BY Licence.
Auke Haver & Anne-Merel van der Drift
- Anne-Merel van der Drift
- Auke Haver
- Astrid Kloosterman
- Ruud van der Beek
- Erwin Nagelkerke
- Dirk Eggink
- Jeroen Laros
- Consortium NRS
- Jaap van Dissel
- Ana Maria de Roda Husman
- Willemijn Lodder
This research was funded by the Dutch Ministry of Health, Welfare and Sport as part of the Dutch National Sewage Surveillance program.