covid-poops

This repository contains the code for cleaning, transforming and visualizing data from Environmental Services, whose researchers were monitoring COVID-19 prevalence in the metro area by analyzing SARS CoV-2 viral RNA load in Metro Plant wastewater.

Data update schedule

The Council generated daily wastewater data for the period of November 1, 2020 to September 27, 2023. It has transitioned to having all wastewater monitoring accomplished through the National Wastewater Surveillance System and the University of Minnesota Medical School Wastewater Project.

University of Minnesota Medical School Wastewater Project

National Wastewater Surveillance System

National Wastewater Surveillance System Dataset

Structure

All processing scripts for data and figures are in ./R. The prefix “d” indicates data processing, while the prefix “fig” indicates figure processing. 0_run_all.R runs all scripts and saves final data.

#> R
#> +-- 0_run_all.R
#> +-- covid-plot-theme.R
#> +-- d_copies_by_variant.R
#> +-- d_covid_cases.R
#> +-- d_load.R
#> +-- d_sewershed_map.R
#> +-- d_variants.R
#> +-- d_variants_umgc.R
#> +-- fig_cases_vs_load.R
#> +-- fig_copies_by_variant.R
#> +-- fig_copies_by_variant_stacked.R
#> +-- fig_plotly_cases_vs_load.R
#> +-- fig_plotly_variant_frequency.R
#> +-- fig_plotly_variant_load.R
#> +-- fig_variant_frequency.R
#> +-- map_sewershed_leaflet.R
#> \-- sharepointfilepath.R

The Shiny app is located in ./metc-wastewater-covid-monitor. /data contains relevant CSV data and /www contains CSS, HTML, and relevant font files the app needs upon running.

#> metc-wastewater-covid-monitor/
#> +-- data
#> +-- deploy.sh
#> +-- global.R
#> +-- server.R
#> +-- ui.R
#> \-- www

License

This project is shared freely under the MIT License. See LICENSE.md

Code of Conduct

Please note that the covid-poops project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Contributors

Special thanks to our community contributors!

@adamstener, @ashleyasmus, @eggsurplus, @ehesch, @enebo, @eroten, @JonathanEhrlichMC, @jpflanigan, @knumat, @Lex137, @lfletch0025, and @riggs.