HHD+Rice CDC Center of Excellence for Wastewater Epidemiology

https://hou-wastewater-epi.org

Rendered Tutorial Website: https://hou-wastewater-epi-org.github.io/online_trend_estimation/

Contact email: info@hou-wastewater-epi.org

Paper: "Online trend estimation and detection of trend deviations in sub-sewershed time series of SARS-CoV-2 RNA measured in wastewater ."

• Link to paper: https://www.nature.com/articles/s41598-024-56175-2
• To Cite:
  • Ensor, K.B., Schedler, J.C., Sun, T. et al. Online trend estimation and detection of trend deviations in sub-sewershed time series of SARS-CoV-2 RNA measured in wastewater. Sci Rep 14, 5575 (2024). https://doi.org/10.1038/s41598-024-56175-2

PI of Analytics Group: Dr. Katherine B. Ensor, Department of Statistics, Rice University

Lead Analyst for HHD: Rebecca Schneider, Houston Health Department

Lead Analyst for Rice: Julia Schedler, Department of Statistics, Rice University

Description

Tutorials detailing Algorithms 1 and 2 in "Online trend estimation and detection of trend deviations in sub-sewershed time series of SARS-CoV-2 RNA measured in wastewater ." are provided in a rendered format here:

Code

In addition to the code chunks in Algorithm1.qmd and Algorithm2.qmd, the following R files are included to produce the analyses used in the paper:

• KFAS_rolling_estimation.r applies KFAS_state_space_spline.r (wrappers for KFAS package functions)
• ww_ewma.r produces the EWMA control charts (a wrapper for qcc package functions)
• fplot.r, contains helper functions for producing nice plots.

Data

Synthetic example data in the file synthetic_ww_time_series.csvprovided in the Data folder to produce analysis and figures similar to those found in the paper.

Given the small populations associated with some of the lift stations, real data will be made available on a case-by-case basis by contacting the Houston Wastewater Epidemiology group and subsequent approval by Houston Health Department.

Licensing

Because code and intellectual work have different licensing needs, a separate LICENSE file is contained in each folder and applies to the files in that folder:

• Files in the Code folder are licensed under the GNU General Public License, Version 3 (GPL-3).

• Files in the Data folder are licensed under the Creative Commons NonCommercial ShareAlike (CC by-NC-SA) license.

We are happy to discuss the possibility of an alternate (dual) license for the files in either folder. If you encounter a situation where you are unable to use the work for desired purposes, for example, a license compatibility issue, please reach out to  info@hou-wastewater-epi.org.