Seafloor Elevation Change From 2004 to 2016 at Looe Key, Florida Keys

Step 1:The original 2016 NOAA NGS Topography Lidar DEM: Florida Keys Outer Reef Block 01 tagged image file format (TIFF) DEM was downloaded from https://inport.nmfs.noaa.gov/inport/item/48373 using the "Customized Download" capability of NOAA’s DigitalCoast website. The data were downloaded with the following parameters: UTM Zone: Zone 17 Range 084W-078W; Horizontal Datum: NAD83; Horizontal Units: Meters; Vertical Datum: NAVD88; Vertical Units: Meters; File Format: Tiff 32-bit Float; Bin Method: TIN; Bin Size: 1.0; Bin Units: Meters; Data Classification: Bathymetric Lidar Points; Data Returns: Any Points; Ancillary Data: No Ancillary Data; and Geoid Name: GEOID12B. Using VDatum version 3.9, a publicly available software from NOAA (https://vdatum.noaa.gov/), the lidar TIFF was transformed from the North American Horizontal Datum of 1983 (NAD83) Universal Transverse Mercator (UTM) Zone 17 North to NAD83 National Spatial Reference System (NSRS2007) horizontal datum, the vertical datum and geoid model were kept the same.

Step 2: The original Looe Key, Florida 2004 Lidar Coverage TIFF DEM was acquired (via file downloads from a secure server) directly from the U.S. Army Corps of Engineers. Horizontal coordinates (latitude and longitude, in decimal degrees) were provided in NAD83 and vertical positions were referenced to the NAD83 ellipsoid, in meters. Using VDatum version 3.9, the lidar TIFF was transformed from the NAD83 to the NAD83 (NSRS2007) horizontal datum, while the GEOID03 model was used to transform from ellipsoid to NAVD88 GEOID12B orthometric heights.

Step 3: Using Esri ArcGIS Desktop Advanced version 10.6, footprints of the original 2004 and 2016 lidar TIFF's were created with the "Reclassify (Spatial Analyst)" tool in ArcToolbox. To create each raster file, all old data values were replaced with 1 and the 'No Data' value with 0 to create the raster files. Then, the "Raster to Polygon (Conversion)" tool was used to create a footprint of the original lidar data by converting the raster files to polygon shape (SHP) files.

Step 4: Due to false returns, additional areas were removed from the 2016 lidar. Polygons encompassing the regions of error were created using Global Mapper 18.2 with the "Digitizer" tool and the 'Create Area/Polygon Features'. The polygons were exported as a single SHP file, see 2016_Lidar_EdgeEffects_Removed_Areas SHP file.

Step 5: A polygon SHP file of the geometric intersection between the two lidar surveys was created with the "Intersect (Analysis)" tool by adding the two lidar footprint SHP files (Step 3) as 'Input features'. Additional areas were deleted from the Intersect_footprint SHP file because of lidar edge effects using the "Erase (Analysis)" tool by specifying the Intersect_footprint SHP file as the 'Input features' and the 2016_Lidar_EdgeEffects_Removed_Areas SHP file as the 'Erase Features'. Then, the two lidar TIFF's (Step 1, 2) were clipped to the extent of the Intersect_footprint SHP file using the "Clip (Data Management)" tool by specifying one of the lidar TIFF’s as the 'Input Raster', the Intersect_footprint SHP file as the 'Output Extent', and box checked for 'Use Input Features for Clipping Geometry', creating the 2004_LooeKey_Lidar_Clip TIFF and the 2016_LooeKey_Lidar_Clip TIFF.

Step 6: A 2-m grid was created using the "Create Fishnet (Data Management)" tool with the following parameters: Template extent: Intersect_footprint SHP file (Step 5); Cell size width: 2; Cell size height: 2; Number of Rows: left blank, Number of Columns: left blank; Geometry type: POLYLINE and box checked for 'Create Label Points'. The 2-m grid label points SHP file was clipped to the extent of the Intersect_footprint SHP file using the "Clip (Analysis)" tool by specifying the 2-m grid label points SHP file as the 'Input features' and the Intersect_footprint SHP file as the 'Clip features.' XY coordinates were added to the 2-m grid SHP file using the "Add XY Coordinates (Data Management)" tool, to create the 2m_grid point SHP file.

Step 7: Values from the 2004_LooeKey_Lidar_Clip TIFF (Step 5) and 2016_LooeKey_Lidar_Clip TIFF (Step 5) were extracted at the location of the 2m_grid points using the "Extract Values to Points (Spatial Analyst)" tool by specifying the 2m_grid point SHP file as the 'Input point features' and the 2004_Lidar_Clip TIFF as the 'Input', creating the Lidar_Extract_Points SHP file. This step was repeated with the Lidar_Extract_Points SHP file as the 'Input point features' and the 2016_LooeKey_Lidar_Clip TIFF as the 'Input', creating the LooeKey_IntersectPoints SHP file.

Step 8: The elevation difference (Diff_m) between the 2016 lidar (RASTERVALU) and the 2004 lidar data (RASTERVA_1) were calculated by adding a field to the attribute table of the LooeKey_IntersectPoints SHP file using the "Field Calculator" and the expression Diff_m = [RASTERVALU] – [RASTERVA_1]. An additional point was removed from the LooeKey_IntersectPoints SHP file because it had a Diff_m value of 26.9, which was an outlier compared to the surrounding points.

Step 9: The original Unified Florida Reef Tract Map version 2.0 SHP file was downloaded from http://ocean.floridamarine.org/IntegratedReefMap/UnifiedReefTract.htm. Using Esri ArcGIS, the original habitat SHP file was modified using the "Clip (Analysis)" tool to clip the habitat SHP file to the extent of the Intersect_footprint SHP file (Step 5) by specifying the habitat SHP file as the 'Input Features' and the Intersect_footprint SHP file as the 'Clip Features', creating the LooeKey_Habitat_Clip. Using the "Select by Attribute" tool, individual habitat SHP files were created from the LooeKey_Habitat_Clip SHP file using the "Select by Attribute" tool to select one ClassLv2 habitat and exporting as a separate SHP file.

Step 10: Elevation change statistics were determined by habitat type using the XYZ points from the LooeKey_IntersectPoints SHP file. The "Select Layer by Location (Data Management)" tool was used to extract points within or on the boundary of a specific habitat type by using the following parameters: Input Feature Layer: LooeKey_IntersectPoints; Relationship: INTERSECT; Selecting Features: Habitat SHP file; Search Distance: left blank; and Selection type: NEW_SELECTION. An ArcMap model was created to automate the process, because these steps had to be repeated for 10 habitat types. Elevation change statistics from Looe Key were compiled by habitat type into a comma separated values (CSV) file using Microsoft Excel 2016, see LooeKey_Elevation_Statistics.csv. After analysis, no data values in the table were defined as "-".

Step 11: An elevation change surface model was created using the "Create TIN (3D Analyst)" tool by specifying the LooeKey_IntersectPoints SHP file (Step 7) as the 'Input Feature Class', Diff_m as the 'Height Field' and Mass_Points as the 'Type', creating the Intersect_TIN file. Then, the Intersect_TIN file was delineated using the "Delineate TIN Data Area (3D Analyst)" tool by specifying the Intersect_TIN as the 'Input TIN', a 'Maximum Edge Length' of 2.828428 (hypotenuse of a 2-m grid) and the 'Method' set to ALL. The delineated Intersect_TIN was clipped to the extent of the Intersect_footprint SHP file (Step 5) using the "Edit TIN (3D Analyst)" tool with the following parameters: Input TIN: Intersect_TIN; Input Features Class: Intersect_footprint SHP file; Height Field: None, Tag Field: None; and Type: Hard clip.

Step 12: In addition to elevation-change statistics, volume-change statistics per habitat type were calculated using the final TIN (Step 11). Surface volume changes were calculated for four cases using the "Surface Volume (3D Analyst)" tool. To calculate the net erosion lower limit (case 1) the 'Reference Plane' was set to BELOW and the 'Plane Height' set to -0.212 m. For the net erosion upper limit (case 2) the 'Reference Plane' was set to BELOW and the 'Plane Height' set to 0 m. For the net accretion lower limit (case 3) the 'Reference Plane' was set to ABOVE and the 'Plane Height' was set to 0.212 m. For the net accretion upper limit (case 4) the 'Reference Plane' was set to ABOVE and the 'Plane Height' was set to 0 m. A 0.212 m threshold was determined by vertical error analysis using the uncertainty for modern lidar (0.15 m) to calculate the Root Mean Square Error (RMSE) of 0.212 m. Minimum net volume was calculated by summing results from cases 1 and 3. Maximum net volume was calculated by summing results from cases 2 and 4. Area normalized volume change lower limit was calculated by dividing the minimum net volume change for each habitat by the habitat's total area. The area normalized volume change upper limit was calculated by diving the maximum net volume for each habitat by the habitat's total area. An ArcMap model was created to automate the process, because these steps had to be repeated for 10 habitat types. Volume change statistics from Looe Key were compiled by habitat type in CSV format using Microsoft Excel 2016, see LooeKey_Volume_Statistics.csv.

Added keywords section with USGS persistent identifier as theme keyword.