SETr Analysis Tools and Workflow Guide

Tool Resource
May 2020

Surface Elevation Tables (SETs) are precise measurements of the height of a marsh surface and can be used to track whether a marsh is sinking or gaining elevation relative to sea level. Most sites within the network of 29 National Estuarine Research Reserves have been measuring SETs for several years.

A 2018 catalyst project developed tools for working with SET data, including a series of computer codes -  R scripts  - for processing, quality checking, analyzing and visualizing these complex datasets. The R-scripts for analyzing SET data are freely available through GitHub and are explained in a Guide to the SETr Workflow and two training webinars. The scripts have also been used to generate reserve-specific SET reports and a national synthesis report.

These tools are built in open-source software so the developed workflow and products can be shareable, reproducible, and useful well into the future, as additional years of data are generated. Input from technical and outreach-oriented working groups has ensured that these tools are appropriate and useful to a variety of end-users.

About these resources

The SETr GitHub Repository  -  SET analysis tools were developed with R, RStudio, and associated packages and are freely available through a GitHub Repository. The repository includes:

  • Data transformation scripts to re-format data into the SETr format (link to this content on GitHub)
  • Example SET datasets from Grand Bay NERR in Mississippi (link to this content on GitHub)
  • A QA/QC app to interact with graphs and tables of raw data and easily identify points that need inspection
  • Click-of-a-button report generation to produce basic analyses of rates of change and comparisons to sea level rise
  • Annotated visualizations that can be used to communicate results to both technical and non-technical audiences
  • Water level data and 19-year water level change calculation scripts (Link to this content on GitHub)

SETr Workflow Guide (PDF)  -  This guide is a thorough introduction to the SETr file directory and intended workflow. The workflow can be used for data entry, QA/QC, and repeating the team’s initial SET analyses, and is meant to useable for people with a range of familiarity with R software. The guide complements the zipped data file directories that were provided to participating reserves, and this section of the SETr GitHub Repository. 


Questions about these tools can be directed to: Kim Cressman, Grand Bay National Estuarine Research Reserve,