Seafloor Elevation Change From 2017 to 2018 at a Subsection of Crocker Reef, Florida Keys-Impacts from Hurricane Irma

Step 1: The original 2017 Crocker Reef multibeam dataset was downloaded from https://coastal.er.usgs.gov/data-release/doi-P9EASN2O and transformed from its native World Geodetic System of 1984 (WGS84) horizontal datum and ellipsoid heights to the North American Datum of 1983 NAD83(2007) horizontal datum, North American Vertical Datum of 1988 (NAVD88), and applied the GEOID12B model using a publicly available software package from the National Oceanic and Atmospheric Administration (NOAA), called VDatum version 3.9 (https://vdatum.noaa.gov/). The transformed XYZ points were loaded into Blue Marble Global Mapper version 18.2 and gridded using the "Create Elevation Grid from 2D Vector/Lidar Data" tool in the Analysis menu. Grid spacing was manually set to 1 meter (m) for the X- and Y-axes and the 'Elevation Grid No data Distance Criteria' was set to 3.0. The resultant digital elevation model (DEM) was exported as a tagged image file format (TIFF) with the following parameters: 32-bit floating point samples, Sample Spacing of 1 m for both X- and Y-axes, Always Generate Square Pixels, LZW Compression, Generate TFW (World) File, and Generate PRJ File. The original 2018 Crocker Reef multibeam dataset was downloaded from https://coastal.er.usgs.gov/data-release/doi-P93PPPHU and transformed using the same parameters.

Step 2: Using Esri ArcGIS Desktop Advanced version 10.6, footprints of the original 2017 and 2018 multibeam data were created using 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." Then, the "Raster to Polygon (Conversion)" tool was used to create a footprint of the original 2017 and 2018 multibeam data by converting their reclassified raster files to polygon shape (SHP) files.

Step 3: A polygon SHP file of the geometric intersection between the 2017 and 2018 multibeam files was created with the "Intersect (Analysis)" tool by adding the 2017 and 2018 multibeam footprint SHP files (Step 2) as 'Input features,' creating the intersect_footprint SHP file. Then, the 2017 and 2018 multibeam TIFF's (Step 1) were clipped to the extent of the intersect_footprint SHP file using the "Clip (Data Management)" tool by specifying the 2017 or 2018 multibeam TIFF as the 'Input features' and the intersection_footprint SHP file as the 'Clip Features,' creating the 2017_SubsectionCrockerReef_Multibeam_Clip TIFF and the 2018_SubsectionCrockerReef_Multibeam_Clip TIFF.

Step 4: A 2-m grid was created using the "Create Fishnet (Data Management)" tool with the following parameters: Template extent: intersect_footprint SHP file (Step 3); 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 2m_grid_label point SHP file was clipped to the extent of the intersect_footprint SHP file using the "Clip (Analysis)" tool by specifying the 2m_grid_label point SHP file as the 'Input point features' and the intersect_footprint SHP file as the 'Clip features.' XY coordinates were added to the 2m_grid_label point SHP file using the "Add XY Coordinates (Data Management)" tool.

Step 5: Values from the 2017_SubsectionCrockerReef_Multibeam_Clip TIFF (Step 3) and 2018_SubsectionCrockerReef_Multibeam_Clip TIFF (Step 3) were extracted at the location of the 2m_grid_label point SHP file using the "Extract Values to Points (Spatial Analyst)" tool by specifying the 2m_grid_label SHP file as the 'Input point features' and the 2017_SubsectionCrockerReef_Multibeam_Clip TIFF or the 2018_SubsectionCrockerReef_Multibeam_Clip TIFF as the 'Input,' creating the 17multibeam_extract SHP file and the 18multibeam_extract SHP file. Then, the 17multibeam_extract and 18multibeam_extract SHP files were spatially joined using the "Spatial Join (Analysis)" tool with the following parameters: Target features: 18multibeam_extract; Join features: 17multibeam_extract; Join Operation: ONE_TO_ONE; Match Option: Intersect and Distance field name: left blank creating the SubsectionCrockerReef_IntersectPoints point SHP file.

Step 6: Points with no data were removed from the SubsectionCrockerReef_IntersectPoints SHP file using the "Select by Attribute" tool to select points from the attribute table where the RASTERVALU (2018 multibeam) or the RASTERVA_1 (2017 multibeam) equaled 0. Then the "Editor Toolbox" was used to delete the points. The elevation difference (Diff_m) between the 2017 multibeam and 2018 multibeam data were calculated by adding a field to the attribute table of the SubsectionCrockerReef_IntersectPoints SHP file using the "Field Calculator" and the expression Diff_m = [RASTERVALU] - [RASTERVA_1].

Step 7: The original Unified Florida Reef Tract Map version 2.0 polygon SHP file was downloaded from http://ocean.floridamarine.org/IntegratedReefMap/UnifiedReefTract.htm. Using 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 (Step 3) by specifying the habitat SHP file as the 'Input Features' and the intersect_footprint SHP file as the 'Clip Features,' creating the SubsectionCrockerReef_Habitat_Clip SHP file. Using the "Union (Analysis)" tool the SubsectionCrockerReef_Habitat_Clip SHP file and intersect_footprint SHP file were merged under the following parameters, input features: SubsectionCrockerReef_Habitat_Clip and intersect_footprint; Join attributes: ALL; XY Tolerance: left blank, creating the SubsectionCrockerReef_Habitat_Clip SHP file. This creates an additional polygon in the file that includes the area of the multibeam DEM not covered by the Unified Florida Reef Tract Map. It was determined by visual analysis that the area this polygon encompasses is likely unconsolidated sediment and was labeled as such. Using the "Editing Toolbox," 'Likely Unconsolidated Sediment' was added to the attribute table of the SubsectionCrockerReef_Habitat_Clip SHP file as the Class Lv2 value of the newly created polygon. Using the "Select by Attribute" tool, individual habitat SHP files were created from the SubsectionCrockerReef_Habitat_Clip SHP file Using the "Select by Attribute" tool to select one ClassLv2 habitat and exporting it as a separate SHP file.

Step 8: Elevation change statistics were determined by habitat type using the XYZ points from the SubsectionCrockerReef_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: SubsectionCrockerReef_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 seven habitat types. Elevation change statistics from the Crocker Reef study site were compiled by habitat type into a comma separated values (CSV) table using Microsoft Excel 2016, see SubsectionCrockerReef_Elevation_Statistics.csv.

Step 9: An elevation change surface model was created using the "Create TIN (3D Analyst)' tool by specifying the SubsectionCrockerReef_IntersectPoints SHP file (Step 6) 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 was delineated using the "Delineate TIN Data Areas (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 4) using the "Edit TIN (3D Analyst)" tool with the following parameters: Input TIN: Intersect_TIN; Input Feature Class: intersect_footprint SHP file; Height Field: None; Tag Field: None; and Type: Hard clip.

Step 10: In addition to elevation-change statistics, volume-change statistics per habitat type were calculated. 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, and for the net accretion upper limit (case 4) the 'Reference Plane' was set to ABOVE and the 'Plane Height' was set to 0 m. The 0.212 m threshold was determined from vertical error analysis using the uncertainties reported in the metadata of the original lidar and multibeam products. Minimum net volume change was calculated by summing results of case 1 and case 3. Maximum net volume change was calculated by summing results of case 2 and case 4. Area normalized volume changes were calculated by dividing net volume changes for each study site by its total area. Because these steps had to be repeated for seven habitat types, an ArcMap model was created to automate the process. Volume change statistics from the Crocker Reef study site were compiled by habitat type into a CSV file using Microsoft Excel 2016, see SubsectionCrockerReef_Volume_Statistics.

Added keywords section with USGS persistent identifier as theme keyword.