Locations of Key Data, Code, and Protocols

This page provides an overview of where all datasets, metadata, code, methods, and other research resources are stored. Generally, code and data is stored in github repositories, spatial data (e.g., maps) on ArcGIS sites, and other all other documents in a Box folder (distribution within Duke and partners) or Dropbox folder (distribution within Bernhardt Lab/Duke Biology).

Please email J. Behrens directly to gain access. While most materials are restricted access until peer review and publish, I am always happy to discuss the feasibility of sharing preliminary materials, consistent with the policies of our funders and collaborators.

Data Portals and Storyboards

Below is a collection of websites containing our publicly available data and analysis.
Ellerbe Creek water chemistry data from Bass Team Projects (can be slow to load)
Includes data for sites nationally, including North Carolina

Site codes on StreamPULSE for each of our sites include:
  • Ellerbe Creek at Northgate Park: NC - Ellerbe Creek at Club Blvd
  • Ellerbe Creek near Glennstone Preserve: NC - Ellerbe Creek at Glenn Rd
  • Ellerbe Creek near Pearl Mill Preserve: NC - South Ellerbe Creek
  • New Hope Creek near Hollow Rock Preserve: NC - New Hope Creek
The following story maps provide an overview of analyses we conducted with some of the data provided in the data portals above. The storymaps were created by members of our Bass Connections Project, mentored by J. Behrens.

Water Synoptic Survey (Bass Project)

Synoptic survey water sampling data (non-spatial)
1. Raw and processed data, and associated code, is available in the Ellerbe-Creek-Bass-2022-23 Github repository
  • The repository includes merged sheets of all sampling from 2021-2023
  • Additional data from 2021-22, if needed, is available in the Ellerbe_Creek_Bass_2021-22 Github repository.
 2. All documents (e.g., protocols, guides, prep materials) are in the Field Work sub-folder of the 2022-23 Bass Box folder
  • Additional versions from 2021-22 are available in a sub-folder in that project's Box folder.

Spatial datasets
1. Spatial data produced as part of the Ellerbe Creek Bass projects are on the Ellerbe Creek Bass Project ArcGIS Group
  • Surveys for the synoptic surveys are collected through Survey123. Once a member of the group above, you will be able to see/access the surveys (to submit responses) via the Survey123 app/website.
2. Most code for spatial analyses are available in the Ellerbe_Creek_Bass_2021-22 Github repository. Some data is sensitive and thus not stored in Github but rather a protected Box folder. Contact J. Behrens for access to this Box folder.

Data Portal
1. Portal is publicly available here: https://dukerivercenter.shinyapps.io/EllerbeCreekWatershedData
2. Source available in the DataPlus2022-data Github repository.

Invertebrates Data, Keys, Resources (Bass Project and Dissertation)


Site Locations
1. This map provides the location of the 3 sites that are sampled on Ellerbe Creek and New Hope Creek, including parking locations.
2. Near real-time USGS gage data is available near the Ellerbe Creek sites at the following sites: Glennstone and Northgate
3. Flow/gage height data is available for NHC in the StreamPULSE data portal (Site: NC - New Hope Creek). This is not near real-time, unfortunately. However for a rough guess at real time conditions, there is a USGS gage on NHC downstream of our site. It isn't close, but is good for rough trends.

Benthic invertebrate larvae (ethanol preserved)
1. Spreadsheets are stored in the Ellerbe-Creek-Bass-2022-23 Github repository.
2. Photos are stored in the Bug and Friends Photos sub-folder of the 2022-23 Bass Box folder
3. Methods, guides, and software are stored in the Benthic-Larvae sub-folder of the 2022-23 Bass Box folder

Adult insects (sticky traps)
1. Spreadsheets, data, and code are stored in the in the Ellerbe-Creek-Bass-2022-23 Github repository.
2. Methods and guides are stored in the Adult-Insects_Sticky sub-folder of the 2022-23 Bass Box folder

Adult insects (frozen, from floating emergence traps)
1. Spreadsheets, data, and code are stored in the Ellerbe_Creek_JBehrens-Dissertation Github repository.
2. Methods and guides are stored in the Adult-Insects_Frozen sub-folder of the 2022-23 Bass Box folder

Spider Survey, Stream Morphology Survey
1. Spreadsheets, data, and code are stored in the Ellerbe_Creek_JBehrens-Dissertation Github repository.

Analytical Methods

Unless otherwise noted, all analytical methods are stored in various folders in the Bernhardt Laboratory Dropbox folder.
Water digestions for metals
  1. Digestion method for water samples
  2. Spreadsheet template for massing samples
Metals Quantification
  1. See methods from the Hsu Kim lab
E.coli and total coliforms
  1. Coliert/Quant Tray methods and tips
  2. Spreadsheet template for coliert/quant tray
  3. ("cheaper" but less accurate method) Bio 212L Methods for multi-tube fermentation
Nutrients and Major Ions (stored in Duke RC Box folder)
  1. Ion Chromatography for major ions (Duke River Center Method)
  2. Lachet for PO4 and NH3 (Duke River Center Method)
  3. TOC and TDN (Duke River Center Method)
Organic Contaminant Mixture Indicators
  1. Coming soon

Analytical and Other Methods

Unless otherwise noted, all analytical methods are stored in various folders in the Bernhardt Laboratory Dropbox folder.
Acid washing approach
  1. Specifically for trace metals/organics work (netting and bottles)
Miscellaneous
  1. General field protocol for all stream biological specimen collections

Favorite R Packages and Data Portals

These are NOT created by J. Behrens. Instead they are super useful resources that other incredible researchers and coders created.

Powerful R Packages

Data wrangling
Federal water quality and hydrology data
Stream ecosystem metabolism modeling
Hydrology models & watershed delineation
Water quality and streamflow analyses

Useful Data Portals

Chemistry, toxicity, and exposure data for contaminants
Download federal water quality and streamflow data
Durham, NC water quality data
Run & download hydrology models
Environmental spatial layers from NC DEQ