Updated Seagrass Retrieval in EDM

Estuary Data Mapper (EDM) now includes updated submerged aquatic vegetation (SAV) in estuaries of the conterminous United States. This page explains the technical aspects of the newly released data and strategies for accessing that data in EDM. 

On this page:

• Updated Submerged Aquatic Vegetation Data for Conterminous United States
• Strategy for Data Discovery, Visualization, and Download of SAV Data
• Example: Pacific Coast
• Example: Atlantic and Gulf Coast Retrievals
  • Table 1: Estuaries on Gulf and Florida coasts with available monitoring data for seagrass
  • Table 2. Estuaries on the Atlantic and Florida coasts with available seagrass monitoring data.
• Minimum Distance Filtering Added to Some Estuaries

---

Updated Submerged Aquatic Vegetation Data for Conterminous United States

A time series of monitoring data related to submerged aquatic vegetation (SAV) in estuaries (and some nearshore environments) of the conterminous United States has been updated recently and released for public use.  

The SAV data for the Pacific coast was reformatted slightly for EDM from a database published in 2018 by the Pacific Marine and Estuarine Fish Habitat Partnership (PMEP; www.pacificfishhabitat.org).  Subsequently EPA compiled SAV data from publicly available sources (generally states, Federal agencies, National Estuary Programs, or National Estuarine Research Reserve sites) for the Atlantic and Gulf coasts and formatted these datasets to be as similar to the Pacific coast as possible given the constraints of available metadata.  Attributes related to monitoring methods for the different sources are compiled into a table incorporated into the polygon coverage metadata as pipe-delimited records that can be extracted and parsed into a table in Excel or other open-source spreadsheet program. The data sources used by EDM can be viewed in   Seagrass Monitoring Data Sources (xlsx) (26.5 KB)

Geodatabase elements for SAV data have been exported as shapefiles for sharing via EDM. Static variables were retained in the shapefile, and time-varying attributes are provided in an associated csv file with common link (EelgrassUID) for matching.  (Note that the EelgrassUID variable name is a carryover from the Pacific Coast dataset which includes only Zostera species, while the full data set incorporating both Atlantic and Gulf Coast data includes other seagrass species as well.)  One significant difference between Pacific and other coastal databases is that the PMEP database recorded absence as well as presence data from surveys while the other surveys did not consistently record absence. Another significant difference is that the Pacific coast database is focused on Zostera (eelgrass), whereas species present in other coastal datasets are more diverse.  

In general, data were compiled by “unioning” SAV polygon coverages for a given estuary across different surveys so resultant polygons may represent one year or many years of record.  The latest year of record is recorded for each polygon to allow estimation of most recent recorded extent of SAV in any monitored estuary.  Maximum extent of seagrass across all years of record was also estimated.  The historic sequence is recorded so that users can analyze time series if desired. Time varying data are delivered in an accompanying csv file with the following fields: EelgrassUID :Unique ID for each eelgrass feature in the feature class and Year :Year in which data were collected. The EelgrassUID can be used to join with the polygon data so that users can extract data for any year of interest to evaluate time series.  In the process of simplifying polygon coverages to a common spatial resolution, some very small polygons were removed, converted to points, and saved with the original polygon attributes in a separate layer (Points2 in the menu).  This helps to speed up the visualization and download process for these fine-resolution datasets.

Due to the fine-scale resolution of SAV data and the extensive spatial and temporal coverage in some systems, we had to limit user access to one estuary (or subestuary for a few large systems) at a time for visualization and download of polygon data to prevent long delays in response or having the system “time-out” before full retrieval.  The full database for each coast is available from EPA on request for users needing to conduct more extensive analyses.  Thus, the retrieval strategy for SAV data is different from the standard protocol for data discovery, visualization, and downloads of other datasets in EDM.

Strategy for Data Discovery, Visualization, and Download of SAV Data

In general, gridded, Point, and Pac Point data are retrieved for the entire viewing area.  Polygon and Point2 data are retrieved for the selected ESTCODE shown in the adjacent menu and then the View automatically zooms to show the retrieved data.  For the Pacific coast, select either Eelgrass (Polygon) or Eelgrass (Pac Point).  For the Atlantic or Gulf coasts, select either Eelgrass(Polygon), Eelgrass(Point), or Eelgrass(Point2).  The Point2 dataset represents polygons too small to see (e.g., single pixel size).

Start by zooming to region of interest with any suitable background reference layers clicked on (state and estuary boundaries for Pacific coast in this example).  SAV results show up better against a light background, so we suggest you turn on Image and select “Roads” as the baselayer (Figure 1).

The Density(Gridded) option provides seagrass data from an earlier compilation, while the last four options provide access to the new dataset compilation.  

For gridded density data, the user can zoom to an area of interest and retrieve data using normal protocols but for the last four (new) options, a new set of rules apply.  For the Pacific coast, select either Eelgrass (Polygon) or Eelgrass (Pac Point).  

For the Atlantic or Gulf coasts, select either Eelgrass(Polygon), Eelgrass(Point), or Eelgrass(Point2).  The polygon layer represents areal coverage of seagrass, while the eelgrass Point or Pac Point coverages represent estuary centroids with associated summary statistics to describe results of most recent surveys (e.g., latest date of data collection, current acreage, etc.) and maximum extent.  

The remaining point layer (Point2) represents points associated with polygons in Atlantic and Gulf coast estuaries too small to be represented as polygons in these displays.  They are provided here as supplemental data for those doing system comparisons rather than for visualization.

Example: Pacific Coast

If you select Eelgrass(Pac Point) you can retrieve estuarine summaries for the entire dataset (all) for the Pacific coast for those estuaries for which SAV data exist.  When you click on the third (rightmost) variable menu, you can select one of the attributes for display, e.g., current (most recent) acreage (CURRENT_AC).  Then click on Retrieve and Show Selected Data.  Unlike for other time series data, you will not have to select a start date and time series duration as retrievals will always cover the range of years available (Figure 3).

However, if you are zoomed out to the entire region you will not be able to see the values effectively, so we suggest you zoom in either interactively (hold right mouse button down and drag diagonally) or go back to the Zoom tab, select state to zoom to (e.g., WA) and then an estuary to zoom to.  If you zoom in interactively, you can orient yourself by toggling between ESTUARY (Figure 4) and CURRENT_HA (Figure 5) on the Get Data tab.

 

Example: Atlantic and Gulf Coast Retrievals

When you retrieve estuarine summary data for the Atlantic or Gulf coast, you will start by zooming to the Atlantic or Gulf Region (Zoom tab), then turning on Seagrass – Eelgrass (Point) and clicking on Retrieve and Show Selected Data.  Note that there is a shorter list of attributes available for the Atlantic and Gulf coast data sets (Figure 6).

Seagrass monitoring data were not available for all estuaries in the Estuary Data Mapper dataset.  Those without recent seagrass data will have NA for Estuary (name) displayed.  Another way to determine which estuaries have data available is to switch to the CUR_YEAR variable (Figure 7). In this example, “-99” values for the current year indicate that there are no seagrass data available from publicly available surveys.  (In a few cases, older gridded data may be available for those systems, but vector data were not available to merge with the newer dataset.)
 

Table 1: Estuaries on Gulf and Florida coasts with available monitoring data for seagrass

ESTCODE	ESTUARY
APCA	Apalachicola Bay
APCE	Apalachee Bay
ARAN	Aransas Bay
BAFF	Baffin Bay
BISC	Biscayne Bay
BLAC	Blackwater Sound
BOGB	Boggy Bay
BRET	Breton/Chandeleur Sound
CHAH	Charlotte Harbor
CHOC	Choctawhatchee Bay
CLAY	Clay Creek
CLEA	Clearwater/ST JOSEPH SOUND
COCO	Cocohatchee River
CORP	Corpus Christi Bay
CRYS	Crystal River area
DEAD	Deadman Bay
ELEV	Eleven Prong Bay
ESTE	Estero Bay
FILL	Fillman Bayou
FIRS	First Bay & associated Bays
FISH	Fish Creek
FLOR	Coupon Bight
GALV	Galveston Bay
HORS	Horseshoe Cove
ICW4	Icw #4
INDB	Indian Bay
INDR	Indian River Lagoon
JOHN	Johnson Creek
LAGU	Icw(L-Madre-The Hole)
LLAG	Little Lagoon
LOWS	Lows Bay
LOXA	Loxahatchee River
LPIN	Little Pine 1 Bay
LROC	Little Rocky Creek
LWOR	Lake Boca Raton
MOBI	Mobile Bay
MORD	Matagorda Bay
MSND	Mississippi Sound
NAPL	Naples Bay
PENS	Pensacola Bay/Santa Rosa Sound
PERD	Perdido Bay
PITH	Pithlachascotee River
PONC	Ponce de Leon Inlet
ROC1	Rock 1 Bay
SAL2	Salt Creek
SALT	Blue Creek
SANA	Saluria Bayou
SARA	Sarasota Bay
SJB2	Saint Joseph Bay
STAN	Saint Andrew Bay
SUWA	Suwannee River
TAMP	Tampa Bay
TENT	Ten Thousand Islands/Marco Bay
WACC	Waccasassa River
WEEK	Weeki Wachee Bay
WITB	Withlacoochee Bay

Table 2. Estuaries on the Atlantic and Florida coasts with available seagrass monitoring data.

ESTCODE	ESTUARY
ESTCODE	ESTUARY
ALBE	Albemarle Sound
ANNI	Annisquam River/Blynman Canal
APCA	Apalachicola Bay
APCE	Apalachee Bay
ASSA	Assawoman Bay
BARN	Barnegat Bay
BISC	Biscayne Bay
BLAC	Blackwater Sound
BLUE	Blue Hill Bay
BOGB	Boggy Bay
BOGU	Bogue Sound/Core Sound
BOST	Boston Harbor
BRAV	Brave Boat Harbor
BROD	Broad Sound
BUSH	Bush River
BUZZ	Buzzards Bay
CAPE	Cape Fear River
CASC	Casco Bay
CBMN	Chesapeake Bay Mainstem
CHAH	Charlotte Harbor
CHAT	Pleasant Bay/Chatham Harbor
CHES	Chester River
CHIN	Chincoteague Bay
CHOC	Choctawhatchee Bay
CHOP	Choptank River
CLAY	Clay Creek
CLEA	Clearwater/ST JOSEPH SOUND
COBS	Cobscook
COCO	Cocohatchee River
CRYS	Crystal River area
CURR	Currituck Sound
DAMA	Booth Bay/Linekin Bay
DEAD	Deadman Bay
DELA	Delaware Bay
DUXB	Duxbury Bay/Plymouth Harbor
EAST	Eastern Bay
ELEV	Eleven Prong Bay
ELKR	Elk River
ESTE	Estero Bay
FILL	Fillman Bayou
FIRS	First Bay & associated Bays
FISH	Fish Creek
FLEE	Great Wilmico/Fleets Bay
FLOR	Coupon Bight
FREN	Frenchman's Bay
GARD	Gardiner Bay/Peconic Bay
GLOU	Glouchester Harbor
GOOS	Goosefare Bay
GOUL	Gouldsboro Bay
GREA	Great Bay
GSBY	Great South Bay
GUNP	Gunpowder River
HAYC	Haycock Harbor/Baileys Mistake
HONG	Honga River
HORS	Horseshoe Cove
HUDS	Hudson River
ICW4	Icw #4
INDB	Indian Bay
INDR	Indian Creek
JAME	James River
JOHN	Johnson Creek
KENN	Kennebec River Estuary
LKEN	Little Kennebec/Englishman Bay/Chandler Bay
LNAR	Little Narragansett Bay
LOCK	Lockwoods Folly River
LONG	Long Island Sound
LOWS	Lows Bay
LOXA	Loxahatchee River
LPIN	Little Pine 1 Bay
LROC	Little Rocky Creek
LWOR	Lake Boca Raton
MACH	Machias Bay
MADD	Maddaket Harbor
MAGO	Magothy River
MIDD	Middle and Back Rivers
MOJA	Mojack Bay
MUSC	Muscongus Bay
NANT	Nantucket Harbor
NAPL	Naples Bay
NARR	Narragansett Bay
NARS	Narraguagus Bay
NCIW	NC Intracoastal Waterway
NERI	Northeast River
NEWR	New River
OTTE	Otter Cove
PAML	Pamlico Sound
PASS	Passamaquoddy Bay/St. Croix River
PATA	Patapsco River
PATU	Patuxent River
PENO	Penobscot Bay
PENS	Pensacola Bay/Santa Rosa Sound
PIAN	Piankatank River
PITH	Pithlachascotee River
PLBY	Pleasant Bay
PONC	Ponce de Leon Inlet
POQU	Poquoson/Back Rivers
POTO	Potomac River
PROS	Prospect Harbor
QUOD	Quoddy Narrows
RAPP	Rappahannock River
ROC1	Rock 1 Bay
SACO	Saco Bay
SAL2	Salt Creek
SALE	Salem Sound
SALT	Blue Creek
SARA	Sarasota Bay
SASS	Sassafrass River
SCCP	Southern Cape Coastal Ponds
SENG	Sengekontacket Pond
SEVE	Severn River
SHEE	Sheepscot Bay
SHIN	Shinnecock Bay
SJB2	Saint Joseph Bay
SOME	Somes Sound/SW Bay
SOUT	South River
SRCP	Southern Coastal Ponds
STAN	Saint Andrew Bay
SUSQ	Susquehanna River
SUWA	Suwannee River
TAMP	Tampa Bay
TANG	Tangier & Pocomoke Sounds
TENA	Long Cove/Tenants Harbor
TENT	Ten Thousand Islands/Marco Bay
WACC	Waccasassa River
WEEK	Weeki Wachee Bay
WELL	Wells
WESB	Western Bay
WEST	West River
WITB	Withlacoochee Bay
YORH	York Harbor
YORK	York River

Selection of the Eelgrass (Polygon) or Eelgrass (Points2) layers requires that the user select an individual estuary for viewing (Figure 8).

After selection of CHAH followed by Retrieve and Show Selected Data, for example, EDM will automatically zoom into Charlotte Harbor.  Note that Charlotte Harbor takes a few minutes for retrieval as there are many small polygons present and multiple survey times available for this system.  Unlike for other attributes, the user does not need to select a starting date and time period of interest before retrieving data.  Different attributes can be displayed via selection using the third drop-down list. 
 

Minimum Distance Filtering Added to Some Estuaries

If you zoom in closely, you may notice that polygons for some systems have been rendered in EDM at a coarser resolution.  Across all three regions, the following estuaries have had minimum distance filtering added to EDM during polygon triangulation for interactive rendering. This increases the speed at which polygons are rendered in EDM but does not affect the spatial resolution of data that are actually downloaded.

• ARAN – Aransas Bay
• CHAH – Charlotte Harbor
• CLEA – Clearwater
• LAGU – Laguna Madre
• SARA – Sarasota Bay
• TAMP – Tampa Bay
• PUGE4 PUGE6 – Segments of Puget Sound
• DRAK – Drake Estero 
• MORR – Morro Bay
• SDIE – San Diego Bay
• SPED – San Pedro Bay
• YAQU – Yaquina Bay
• BOGU – Bogue Sound