In afstarke/reSET: Gather and analyze SET-MH data to assess marsh elevation trends

knitr::opts_chunk$set(echo = TRUE)

reSET

reSET , while currently still under active development, intends to help collectors of marsh surface elevation tables and marker horizon (SET-MH) data with bringing their data into R for any number of QA, data visualization, analysis and report creation tasks that the user wishes. This package currently consists of some rather specific functions for interacting with the SET-MH database developed by the National Park Service (Marsh Elevation Monitoring Database v2.75) as referenced in Lynch et al (2015). It is my hope that as new database systems are developed to manage SET-MH data, functions can be enhanced to allow for more flexible database (or spreadsheets) inputs while yielding consistent outputs which can help create a reproducible workflow.

It is my hope that this somewhat narrowly focused package can be leveraged by other practitioners into something more robust that will promote the sharing of methods, analyses, and results so that we all can benefit from the work of so many using this technique of monitoring to answer some of our big questions relating to marsh resilience. With that as a goal, this code has been licensed under the GPL 3.0 which allows use of the code, provided any resulting products be licensed similarly so that we can all benefit from any development that builds from this or other similar efforts.

Installation

Currently this package is only available here on GitHub and can be installed using the remotes package.

# install.packages("remotes")

remotes::install_github("afstarke/reSET")

What reSET is NOT?

This package does not intend to be a push-button; get-answer type of tool. It can not substitute the need for careful and thoughtful approaches to data management, research questions being asked, statistical analysis etc. It is merely a tool to help in that process. View this as a disclaimer that there can be, and likely are, bugs in these functions that may result in error messages or erroneous results that users of this package should be on the look out for. Please file issues that you may encounter or contact me to help improve this work. Note too that this package is currently very specific to the Access database mentioned above. If there are other databases that users would like to see integrated into this package please reach out.

What's with the name?

reSET is actually a reboot of an effort begun several years ago under the SETr name. Between that time and resuming this current effort a very well crafted set of tools for working with and reporting SET data was developed by Kim Cressman as part of a larger national synthesis across NERR sites, which resulted in the creation of the SETr package. To avoid confusion (and competing branding issues when negotiating with corporate sponsors) moving forward this package was renamed to reSET but will always seek to interact well with the work that has gone into the SETr package. (see set_to_setr for example). I hope that the SET-MH community can both benefit and build from these two efforts.

Future Development

As mentioned this package is very far from what I envision as complete. You may find notes scattered within the code noting improvements needed or enhancements that would be nice to implement. These are all things that were added during development, some may be more important than others. If there are any glaring omissions or errors please feel free to reach out by filing an Issue through GitHub.

To date, the focus of this package was on simplifying the process of reading SET data into R for use in more typical R workflows. As I complete more of the documentation of what's currently in this package I hope to focus on the data visualization and statistical analysis side of the work flow.

Code of Conduct

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

References

James C. Lynch, Phillippe Hensel, and Donald R. Cahoon. "The Surface Elevation Table and Marker Horizon Technique: A Protocol for Monitoring Wetland Elevation Dynamics." Report. Natural Resource Report, 2015. USGS Publications Warehouse. http://pubs.er.usgs.gov/publication/70160049.

afstarke/reSET documentation built on July 16, 2025, 10:16 p.m.