Evaluating Physical, Chemical, and Biological Impacts from the Savannah Harbor Expansion Project Cooperative Agreement Number W912HZ

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Evaluating Physical, Chemical, and Biological Impacts from the Savannah Harbor Expansion Project Cooperative Agreement Number W912HZ-13-2-0013 Annual Report FY 2017

1 Evaluating Physical, Chemical, and Biological Impacts from the Savannah Harbor Expansion Project Cooperative Agreement Number W912HZ Annual Report FY 2017 Submitted by Sergio Bernardes and Marguerite Madden Center for Geospatial Research (CGR) Department of Geography - University of Georgia Athens, Georgia

2 Evaluating Physical, Chemical, and Biological Impacts from the Savannah Harbor Expansion Project Cooperative Agreement Number W912HZ Annual Report FY 2017 (October 1, 2016 September 30, 2017) Submitted by Sergio Bernardes and Marguerite Madden Center for Geospatial Research (CGR) Department of Geography - University of Georgia Athens, Georgia Submitted to: U.S. Army Corps of Engineers (USACE) Planning Division 100 W. Oglethorpe Avenue Savannah, GA 31401

3 Evaluating Physical, Chemical, and Biological Impacts from the Savannah Harbor Expansion Project Center for Geospatial Research (CGR) Department of Geography - University of Georgia Contents Introduction... 4 Update and Maintenance of the Web Portal... 4 Update and Maintenance of GIS Database... 9 Mapping and Data Analysis... 9 Sturgeon Data... 9 Water Quality Vegetation/Marsh Avian Tissue Monitoring Data Access Other Activities Web Portal Analytics... 13

Introduction The following annual report covers FY 2017 (October 1, 2016 September 30, 2017) and summarizes progress made on objectives outlined in the Statement of Work for the project entitled

4 Introduction The following annual report covers FY 2017 (October 1, 2016 September 30, 2017) and summarizes progress made on objectives outlined in the Statement of Work for the project entitled Evaluating Physical, Chemical, and Biological Impacts from the Savannah Harbor Expansion Project (Cooperative Agreement Number W912HZ ). The objectives covered in this report are: 1. Update and maintain the web portal; 2. Update and maintain the GIS database; 3. Research and develop data analysis tools and standardized maps; and 4. Prepare quarterly progress reports and annual reports. Update and Maintenance of the Web Portal The GIS database and web portal are being continuously updated as information becomes available. The web portal is being maintained in a routine manner and substantial enhancements to the portal were implemented during this FY 2017, aiming to improve usability and data analysis. During this year we released a new version of the Mapping page of the SHEP Monitoring Program map portal ( The interface of the mapping tool has been improved and several new functionalities have been added to the system, including improved analysis tools. The new layout for the site, including new screen elements and toolbar, is presented by Figure 1. Figure 1: New layout for the SHEP Monitoring Program map portal, including new screen elements and toolbar.

5 A summary of changes to the web portal released in October 2016 is presented below: 1. Interface now contains toolbar with USACE's logo, link to SHEP's website and multiple new tools (i.e., Measurement, Draw, Info, Swipe, Time Slider, Chart, Print and About). 2. Scale bar (lower left corner) now presents scale using metric and English system. 3. Cursor coordinates (latitude/longitude) are now updated as user interacts with interface. Coordinates of a point can be retrieved by enabling "Click on maps" tool. 4. A pane at the bottom of the map can be opened to show data for individual layers. Using that pane, users can interact with the data and features displayed on the map: a. Displayed data records can be filtered by map extent. b. Specific features/data records can be zoomed into. c. Selecting data records selects the feature on the map. d. Data can be exported as csv files. e. Users can select what data columns (fields) to show. 5. Side panes (to the right) can be turned on and off. 6. The Layer List (Content pane) received new functionalities: a. Layers can be moved up and down controlling layer stacking and map layout. b. Attribute table with values for a specific layer can be opened and users can access data values when analyzing map. c. Users can disable pop-up windows (tooltips). 7. Users can use a drawing tool to add markers, lines, polygons and text to the map. a. Drawing tool allows for the selection of color, style, transparency, width for the features being drawn. Measurements can be retrieved from drawings. 8. An Info Summary tool allows for the display of a list of gages or stations (features) as they are presented by the map. a. Only features displayed are listed by the Info summary, so users can target specific features when conducting analyses. b. Clicking one instance of a feature locates that feature on the map and presents a tooltip with information on the feature. 9. Swipe tool allows for the selection of a layer for change in condition analysis. (e.g., change in bathymetry values). 10. Time slider tool: allows for the display of changes in layer values over time by selecting periods for data display or by enabling data animations. 11. Chart tool: allows for the creation of charts using data displayed by the map. 12. Printing maps: allows for creation of PDF versions of the map being displayed for printing or storage.

6 13. About tool: provides information on the map portal and on the Savannah Harbor Expansion Project. 14. USGS gage tooltip: clicking on a USGS gage opens a tooltip showing previews for graphs for dissolved oxygen and specific conductance based on data provided by USGS. a. Graphs are created for three time periods: 7 days, 30 days and 90 days. b. Clicking on graphs will take the user to the full resolution version of the graph. 15. Clicking on a feature opens a tooltip that allows users to pan to that feature and to open the attribute table to consult values for analyses. Changes to the website included a new water quality data flagging system. The system flags real time USGS gage data based on threshold values. A server at the Center for Geospatial Research periodically retrieves the most recent instantaneous value for any selected variable from USGS gage stations. Scripts using the Python language were written and tested to retrieve data using REST services from USGS ( Frequency of retrieval for dissolved oxygen and water conductance is pre-configured (currently every 15 minutes). The map portal has been programmed to continuously load the retrieved instantaneous data using a pre-configured refresh interval (5 minutes). Variables are symbolized using threshold values. For dissolved oxygen, values below 4 mg/l show as a flag positioned where the gage is located (Figure 2). Dissolved oxygen values above this threshold are not displayed. The figure below uses mock data to exemplify the use of the flag layer. Flags are displayed for gages and Figure 2: New water quality flagging system displays flags according to predefined water quality thresholds.

7 During FY 2017 we restructured the map portal's Reports page ( The more organized table-based layout uses a Year Time Unit (e.g., quarter, month, annual) organization scheme and helps users find specific reports. Figure 3 shows a section of the new Reports page and illustrates the organization of reports by quarter, month and year. Figure 3: Section of the Reports page re-structured in FY 2017 and illustrating the organization of reports by quarter, month and year. The augmented version of the SHEP Monitoring Program map portal brings multiple enhancements and increased data analysis capabilities. Because those extra capabilities increased map portal complexity, we implemented instructions on how to use the site. A new help page containing descriptions of interface elements was added to the site (Figure 4). The Help page can be accessed by clicking the About button on the menu bar of the map portal, and then clicking on the "map portal help" link. A direct link to the map portal help page is Descriptions of tools and functionalities were incorporated into the page.

8 Figure 4: Help page for the SHEP Monitoring Program map portal, describing interface elements.

9 We continue to monitor and incorporate user feedback into refinements to the web portal. We have been communicated by the Army Corps that the features of the Monitoring Portal introduced during FY17, including the water quality flagging system, were presented to resource agencies during a SHEP 401 WQC meeting in April 2017 and that site improvements have been well received. Update and Maintenance of GIS Database To guarantee continuous web site and database maintenance and to maximize uptime of the increasingly complex SHEP web portal we continued the training of additional CGR personnel to aid in maintaining the database and web portal. Standard Operating Procedures (SOP) for data reporting and handling were updated based on new and more complete datasets we received (e.g., sturgeon, vegetation/marsh data). We continue the refinement of data processing, visualization and display methods for the monitoring data, including sturgeon, water quality, and the vegetation/marsh datasets. The following sections represent some of the analysis and visualization methods incorporated into the website and map portal. Mapping and Data Analysis Sturgeon Data During FY17 we met with South Carolina Department of Natural Resources (SCDNR) and discussed strategies for sturgeon data processing, analysis and representation using the SHEP Monitoring Program web portal and the new mapping capabilities of the website. Following discussions, in April 2017, we received telemetry data for the sturgeon monitoring study in the Savannah River, including all receivers and dates for the past four years of acquisition. Strategies for data ingestion included the implementation of Visual Basic for Applications scripts to standardize data format and setting Structured Query Language statements for data check. A database of sturgeon data was created using the SQLite relational database. Database creation for sturgeon data used three tables (Detection, Transmitter and Receiver) and multiple fields, including a unique identifier (primary key) used when tables are joined. Details on those tables, including associated fields, are provided by the Third Quarterly Report submitted to USACE. During analysis of fish movement we considered sturgeons and other tagged species (i.e., Striped Bass and American Shad). Time-enabled data from the sturgeon monitoring stations were added to the map portal as individual layers, including sturgeon counts for shortnose and Atlantic (Figure 4), total sturgeon counts and manual tracking counts. We have received monthly reports for the sturgeon monitoring project for October to September FY 2017 and posted the reports to the SHEP monitoring website.

Figure 4: Savannah River spatial distribution of receivers and detection counts for shortnose and Atlantic sturgeon. Manual tracking and monitoring locations are also included.

10 Figure 4: Savannah River spatial distribution of receivers and detection counts for shortnose and Atlantic sturgeon. Manual tracking and monitoring locations are also included. Basemap (customizable) is Light Gray Canvas for increased contrast and to emphasize data content. Water Quality Water quality parameters are measured at 19 sites along the Savannah River pertaining to this project. These sites can monitor up to twelve different parameters, such as water temperature ( o C), dissolved oxygen (mg/l), ph, specific conductance ( S/cm), salinity, turbidity, and stream velocity (ft/s). However, not all the sites measure every parameter listed above. We incorporated the display of available parameters into the SHEP Monitoring Program website and have developed techniques to display water quality data in both real time and historically. The implemented functionality allows users to click on a gage to get real time data by accessing the USGS data portal. In addition, historical data can be queried for particular gage stations. Graphs showing temporal changes in water quality are presented to the user for three time periods (7, 30 and 90 days - Figure 5). The main objective of this visualization is to display how parameters are changing over time and space, including changes in dissolved oxygen following the activation of all the oxygen injection systems.

Figure 5: Gage station attribute window showing graphs for time series of water quality data. Top row shows graphs for dissolved oxygen and 7, 30 and 90 days.

11 Figure 5: Gage station attribute window showing graphs for time series of water quality data. Top row shows graphs for dissolved oxygen and 7, 30 and 90 days. Bottom row shows graphs for water conductance for 7, 30 and 90 days. Gage is (Back River at US 17 at Savannah, GA) Vegetation/Marsh Vegetation data, including marsh monitoring and hydrology data and GPS coordinates for the areas sampled, have been received for FY14, FY15 and FY16. Data processing included the identification of relevant variables, the identification/flagging of "no data", the assignment of a time stamp (time of acquisition) to each data point, the computation of statistics and the generation of GIS layers. Layers resulting from this processing are symbolized based on values for individual variables being represented and are associated with a time slider for temporal animation. All twelve monthly reports for FY 2017 as well as three quarterly reports (first,

12 second and third quarters), and an annual report have been posted to the SHEP Monitoring Program website. Avian Tissue Monitoring We received quarterly reports for collections and sampling efforts conducted in November and December 2016, as well as during February, March and May The quarterly reports have been posted to the SHEP monitoring website. We did not receive any new spreadsheets for the avian tissue monitoring project for FY Data Access Functionalities added to the Mapping page of the web portal allow users to download raw data from vector layers used in the portal. Users who need to access vector data are instructed to go to the Layer List pane, click the ellipsis ( ) associated with the layer to be downloaded and select View in Attribute Table. Users can then open the Attribute Table tab at the bottom of the map page (see for location of the tab), click the Options menu and select Export all to csv (if no feature is selected) or Export selected to csv. Other Activities In October 2016 our team presented the new mapping capabilities of the web portal during the Savannah Harbor Expansion Project interagency meeting. During the presentation, CGR demonstrated the SHEP Monitoring Program website, with emphasis on the implementation of the mapping portal and its potential uses for data analysis. Topics presented included: (a) the integration of multiple bathymetric datasets and their representation; (b) updates to the fish movement data and their representation, considering manual tracking and receivers for shortnose and Atlantic sturgeon; and (c) water quality stations displaying graphs of dissolved oxygen and water conductance. In particular, we demonstrated the flexibility of the web and map portal for data query using filters implemented into the enhanced version of the portal. During FY 2017, we presented our efforts to build and maintain the SHEP Monitoring Program information site at the ESRI User Conference in San Diego (July 10-14, 2017). The conference is an excellent venue to showcase the environmental monitoring and receive feedback, considering that in 2016 over 16,000 people from 138 countries attended the event. Mr. Brandon Adams, a GIS Specialist from the Center for Geospatial Research (CGR) at the University of Georgia attended the conference and presented the work. Participation at the conference was funded by CGR and Ms. Mary Richards and Mr. Nathan Dayan from USACE were co-authors of the work.

13 Web Portal Analytics Google Analytics were added to the website ( during the first year of the project to track user visits to the site. The line chart in Figure 6 below shows the daily number of page views for the website for FY Peak page views occurred in November 2016 and increased activity was observed for June-July The pie chart indicates that during this period, new users were 52.7% of the visitors to the site. The contact page for the website includes the option for visitors to sign up to receive alerts when new reports or data are added to the website. Figure 5: Pages views of during FY This document represents the FY 2017 Annual Report for this project and, following instructions from the Army Corps, it incorporates activities conducted during the 4 th Quarter of FY Quarterly reports (1 st, 2 nd and 3 rd Quarters) for FY 2017 have been submitted and posted to the SHEP Monitoring Program website.

14 Please feel free to contact either Sergio Bernardes or Marguerite Madden if you have questions or concerns regarding this report. Respectfully submitted, Sergio Bernardes, Ph.D. Associate Director, CGR Marguerite Madden, Ph.D. Professor and Director, CGR

Evaluating Physical, Chemical, and Biological Impacts from the Savannah Harbor Expansion Project Cooperative Agreement Number W912HZ

Evaluating Physical, Chemical, and Biological Impacts from the Savannah Harbor Expansion Project Cooperative Agreement Number W912HZ-13-2-0013 Annual Report FY 2018 Submitted by Sergio Bernardes and Marguerite