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 2018

1 Evaluating Physical, Chemical, and Biological Impacts from the Savannah Harbor Expansion Project Cooperative Agreement Number W912HZ Annual Report FY 2018 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 2018 (October 1, 2017 September 30, 2018) 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... 7 Mapping and Data Analysis... 8 Sturgeon Data... 8 Water Quality... 9 Vegetation/Marsh Avian Tissue Monitoring Bathymetric Data Data Access Web Portal Analytics... 11

4 Introduction The following annual report covers FY 2018 (October 1, 2017 September 30, 2018) and summarizes activities and 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 for the SHEP Monitoring Program are being continuously updated as information becomes available. Services related to the web portal, including web hosting and map services are being monitored and maintained in a routine manner to guarantee reduced downtime and service continuity. No downtime for the web portal and map services were observed during FY Improvements to usability and data analysis implemented during FY 2017 continued to be verified for availability, behavior, and performance. Data associated with environmental layers being served by the map portal ( continue to be available to users by using a pane at the bottom of the map. The pane can be opened to show data for individual layers and to interact with data and features displayed by the map. By using the pane, users can filter data records using the extent of the map; zoom into specific features/data records; select features on the map (by selecting the corresponding data record); export data as csv files and select what data columns (fields) are shown by the application. Enhancements to the web portal share functionalities with Geographic Information Systems and increase usability of datasets. Figure 1 presents these functionalities, including improved analysis tools and illustrates the use of the Attribute Table pane for data visualization, selection and download. The map portal uses near real time data streams provided by USGS and a checking system was configured to monitor connectivity and eventual broken links.

Figure 1: Layout for the SHEP Monitoring Program map portal, including multiple screen elements, multi-function toolbar and pane showing attributes for selected sturgeon dataset.

5 Figure 1: Layout for the SHEP Monitoring Program map portal, including multiple screen elements, multi-function toolbar and pane showing attributes for selected sturgeon dataset. During the 4 th Quarter of FY 2018 we explored changes to the web portal involving how datasets collected or created by the SHEP Monitoring Program are served. Changes involve modifications to the current layout used by the web portal and aim to increase the use of datasets in analyses and applications, by facilitating data access. The modified version of the web portal will allow users to directly download data stored following commonly used formats (spreadsheets, TIFF images, among others). These datasets could then be used for further analysis, including their incorporation into desktop-based data analysis packages and Geographic Information Systems. Server maintenance and updates were conducted at the Center for Geospatial Research to guarantee uninterrupted operation of the water quality data flagging system. The system flags real time USGS gage data based on threshold values and uses scripts developed in-house to use USGS REST services and periodically retrieve the most recent instantaneous value for selected

6 variables from USGS gage stations. Frequency of retrieval for dissolved oxygen and water conductance was kept at one retrieval every 15 minutes and the map portal loads the retrieved instantaneous data using a pre-configured refresh interval of 5 minutes. 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: Water quality flagging system displays flags according to predefined water quality thresholds. Reports continued to be added to the web portal using the restructured 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. The page also facilitates modifications, including the addition of new reports or new sections. Figure 3 shows a screen capture of part of the Reports page and illustrates the organization of reports by sections, quarter, month, year and type.

7 Figure 3: Section of the re-structured Reports page illustrating the organization of reports into sections, quarter, month, year and type of report. 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 conducted supervised hands-on activities of personnel at CGR, including database and web portal maintenance. Standard Operating Procedures (SOP) for data reporting and handling were reviewed for compliance with datasets. We continue to monitor recent developments in geospatial technologies aiming to refine data processing, visualization and display methods for the areas/variables being monitored, including sturgeon, water quality, vegetation/marsh, avian tissue and bathymetry. The following sections represent some of the analysis and visualization methods incorporated into the website and map portal.

8 Mapping and Data Analysis Sturgeon Data Sturgeon data continued to be received by using spreadsheets uploaded to an online folder shared with South Carolina Department of Natural Resources (SCDNR). These telemetry data, in Excel format, are imported into a relational database (SQLite) by CGR, as the total number of rows for all sheets of sturgeon data exceeds the allowed number of rows per sheet in Excel. Data manipulation involves data quality verification, including: 1. Use of Visual Basic for Applications scripts to standardize the format of date/time fields. 2. Use of pre-defined Structured Query Language statements for data check (check if all records/fields are populated, if format matches the data type, and if unique identifiers exist). The implemented standard relational database is being used for data assimilation, consisting in three database tables (Detection, Transmitter, Receiver). Descriptions of table contents are below: 1. Detection table: includes time stamp, transmitter and receiver. 2. Transmitter table: has transmitter ID, transmitter name, transmitter serial, species and life stage. 3. Receiver table: has receiver ID, station name, latitude and longitude. 4. These tables are linked (joined) by using unique identifiers/names/numbers. Based on the above, data analysis involves checking if all records/fields are populated, if format matches the data type and if those unique identifiers exist. Software developed in house is being used for data check. Figure 4 shows a representation of sturgeon data (manual tracking) including Shortnose and Atlantic sturgeon. Monitoring locations are also included. Monthly progress reports for October 2017 to June 2018 were posted to the web portal. The reports for July, August and September were incorporated into the 4 th Quarter report, which was also posted to the website. The Annual Report for FY 2018 has been posted as well.

Figure 4: Savannah River spatial distribution of manual tracking locations for Shortnose and Atlantic sturgeon. Monitoring locations are also included.

9 Figure 4: Savannah River spatial distribution of manual tracking locations for Shortnose and Atlantic sturgeon. 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.

Gage is 0219897945 (Back River at US 17 at Savannah, GA) Vegetation/Marsh All twelve monthly reports for FY 2018 as well as three quarterly reports (1 st, 2 nd and 3rd

10 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 All twelve monthly reports for FY 2018 as well as three quarterly reports (1 st, 2 nd and 3rd Quarters), and an annual report have been posted to the SHEP Monitoring Program website. Avian Tissue Monitoring Avian sampling spreadsheets received during this period have been ingested into SQLite databases and data field descriptions have been incorporated into the Standard Operating Procedures.

11 We received quarterly reports for avian tissue collections and sampling efforts for the 1 st, 2 nd and 3 rd Quarters of The quarterly reports and the Annual Report for FY 2018 have been posted to the SHEP monitoring website. We did not receive any new spreadsheets for the avian tissue monitoring project for FY Bathymetric Data Bathymetric data collected in the sediment basin were received and processed. Processing involved standardization for map portal integration and considered the original horizontal datum of Georgia State Plane and depth values referenced to Mean Lower Low Water. 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. Changes to the web portal involving the serving of datasets collected or created by the SHEP Monitoring Program are currently underway. Customizations applied to the current layout of the web portal should increase data usage by facilitating data access and direct download. Standardized and commonly-used file formats will be used for data sharing, including spreadsheets and TIFF images and should facilitate importing datasets into desktop-based data analysis packages and Geographic Information Systems. 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 During this period, there were 734 sessions (groups of interactions that may include one or more web page), through which a total of 470 users actively engaged with the website. Statistics include new and returning users. In total, there were 1,017 page views during the period, including repeated views of a single page. Peak page views occurred in November 2017, March 2018 and August During this period, new users were 13.7% of the visitors to the site. We continued to add visitor contact information to the new reports mailing list.

Figure 5: Pages views of www.shep.uga.edu during FY 2018.

th Quarter of FY 2018. Quarterly reports (1 st, 2 nd and 3 rd Quarters) for FY 2018 have been submitted and posted to the SHEP Monitoring Program website.

12 Figure 5: Pages views of during FY This document represents the FY 2018 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 2018 have been submitted and posted to the SHEP Monitoring Program website. 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 sbernard@uga.edu Marguerite Madden, Ph.D. Professor and Director, CGR mmadden@uga.edu

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 2017 Submitted by Sergio Bernardes and Marguerite