Conceptual marsh units of eastern Long Island salt marsh complex, New York (ver. 3.0, May 2026)

Process Step 1. This process step and all subsequent process steps were performed by the same person, Robert Welk, in ArcMap (ver. 10.7.1) using tools from ArcToolbox, unless otherwise stated. For complex operations, names of specific tools used are given in CAPITAL letters (any critical parameters used are given in parentheses, separated by a semicolon, immediately after the tool name). The input and output file names are provided in [square brackets] when necessary. Units for length and area calculations are meters (m) and square meters (m2) unless otherwise stated.
Set the data frame coordinate system and projection to NAD 1983 UTM Zone 18N. Prepare elevation dataset to be clipped to the boundaries polygon. MOSAIC TO NEW RASTER(Pixel type= 32 bit float; Mosaic operator=Mean; Cellsize=1 m) the entire NED raster to a new raster dataset with 1 m resolution [elev_mosaic.tif].

Process Step 2. Prepare mask polygon to define analysis boundaries. In order to account for the possible influence of the surrounding terrain on the analysis, a mask area larger than the salt marsh extent is first created [UVVR_mask]. At the end of the analysis the results are clipped to the boundaries of the salt marsh area [MU_mask]. Both UVVR_mask and MU_mask are edited to determine which interior polygons are removed.
a) MERGE NWI wetland polygons with NYSDEC to obtain [NWI_DEC.shp].
b) EXPORT features from NWI_DEC.shp dataset after SELECT("ATTRIBUTE" LIKE 'E2%EM%' OR "ATTRIBUTE" LIKE 'E2AB3%' OR "ATTRIBUTE" LIKE 'E2EM%' OR "ATTRIBUTE" LIKE 'E2SS%' OR "ATTRIBUTE" LIKE 'E2US4%') to select from estuarine intertidal areas of 1) emergent wetland, 2) scrub-shrub area, 3) rooted vascular aquatic bed, 4) organic unconsolidated shore classes [NWI_exclusive_select.shp].
c) BUFFER(Input features=[NWI_exclusive_select.shp]; Linear unit=5 meters; Dissolve type=All) to obtain the mask polygon [buff5m.shp] and ELIMINATE POLYGON PART(Condition=Percentage; Percentage=99; Eliminate contained part only) to obtain [UVVR_mask01.shp]. Apply buffer with -5 meters to obtain [MU_mask01.shp].
d) EXPORT features from NWI dataset after SELECT("ATTRIBUTE" NOT LIKE 'E%' OR "ATTRIBUTE" LIKE '%FO') to obtain features that are not estuarine or are forested estuarine. MULTIPART TO SINGLEPART to separate individual polygons [NWI_inclusive_single.shp].
e) To exclude the voids in the NWI map during the analysis, these interior polygons need to be removed from the mask. Create a rectangular polygon that covers the domain [extent.shp]. ERASE [NWI_excusive_select.shp] from [extent.shp] and MULTIPART TO SINGLEPART to get [NWI_voids_single.shp].
f) SELECT BY LOCATION from [NWI_inclusive_single.shp] that are completely within the [MU_mask01.shp] and SELECT BY LOCATION from [NWI_voids_single.shp] that are completely within the [MU_mask01.shp]. If any of additional polygons need to be removed from the mask include them in a new feature layer [erase_mask_manual.shp]. Merge all three feature sets to get polygons to be excluded [erase_inside.shp] from the final masks.
g) ERASE [erase_inside.shp] from [MU_mask01.shp] and [UVVR_mask01.shp] to obtain [MU_mask.shp] and [UVVR_mask.shp], respectively.

Process Step 3. Revised in version 3. Although documented as part of the original work, this process step was not completed. In the original dataset, each marsh plain was not subdivided into smaller parcels ("marsh units"). For Version 3, these processing steps were completed, using ArcGIS Pro version 3.4.3, resulting in each marsh plain being properly subdivided into these smaller marsh units.
Define preliminary boundaries for marsh units by basin analysis:
a) EXTRACT BY MASK from mosaicked elevation dataset using [UVVR_mask.shp] polygon.
b) FILL(no Z limit) sinks in extracted elevation raster.
c) Calculate FLOW DIRECTION(do not force edge cells to flow outward) raster.
d) Calculate BASIN based on flow direction raster [basin_buff5m.tif].
e) Apply MAJORITY FILTER(Number of neighbors=8) to clean the raster and convert RASTER TO POLYGON. CLIP the polygon with 1-meter buffered marsh units mask [MU_mask_buff1m.shp]. This additional buffer is necessary to prevent any polygon smoothing algorithm from changing the exterior boundaries and will be removed by clipping to the [MU_mask.shp] later. MULTIPART TO SINGLEPART and ADD GEOMETRY ATTRIBUTES(Geometry properties=Area_geodesic; Area unit=Square_meters) to get [basin_single.shp].

Process Step 4. In the version 3 revision, this step was re-run (using ArcGIS Pro 3.4.3). This step merges the "orphan marsh units", units that are less than 5000 m2 in area, to the nearest to "parent marsh units", units that are larger than 5000 m2 to obtain the preliminary marsh units. A Python script that iteratively calls a list of ArcGIS tools to aggregate orphan units on parent units is used:
a) Create orphan marsh units features by exporting marsh units with an area less than 5000 m2 [lt5000.shp].
b) Create parent marsh units features by exporting marsh units with an area greater than or equal to 5000 m2 [ge5000.shp].
c) Run Python script (hydUnitloop.py). At each iteration step, the script uses NEAR tool to find orphan marsh units within 1 m of a parent marsh unit and merges them to the parent using UNION and DISSOLVE tools. The orphan units merged with a parent unit are removed from the orphan units dataset. Script will iterate until there is no change in the number of parent or orphan marsh units.
d) The remaining orphan marsh units are those that are more than 1 m away from any parent. DISSOLVE them to create larger orphan units by grouping the orphans attached together into larger units.
e) MULTIPART TO SINGLEPART to have single part polygons with unique identifiers.
f) UNION(with gaps) single part features with parent units to obtain preliminary marsh units [pMUopt1.shp].
g) SMOOTH POLYGON(Smoothing algorithm=PAEK; Smoothing tolerance=15 meters) to get the smoothed marsh units polygon [pMUopt1_smooth.shp].
h) CLIP the extra buffer around the smoothed marsh units using the marsh units mask, [MU_mask.shp]. If this results in any additional marsh units with an area less than 5000 m2, dissolve into the nearest parent units repeating the same steps above to obtain [pMUopt1_clip_final.shp]
i) Compute the final marsh units by removing any artefacts from [pMuOpt1_clip_final.shp] using ELIMINATE and REPAIR GEOMETRY tools. ELIMINATE(Expression="Area_geo" less than 900; Eliminating by border) polygon slivers smaller than 900 m2 by merging them to the main polygon. MULTIPART TO SINGLEPART to get conceptual marsh units [CMU.shp]. This only applies to polygons that are bordering other polygons. Polygons that are not bordering other polygons are not affected as those are more likely to be real features as opposed to geoprocessing artefacts.
j) DISSOLVE the conceptual marsh units to get the final outlines for the marsh complex [CMU_mask_final.shp].

Process Step 5. Determine the vegetated and unvegetated areas by image processing.
a) EXTRACT BY MASK from elevation raster [elev_mosaic.tif] using [UVVR_mask.shp] polygon. Rescale the elevation raster values to the same range with 8-bit NAIP imagery (0 to 255) using min-max scaling. Perform ISO CLUSTER UNSUPERVISED CLASSIFICATION with4-bands (Near Infrared, Blue, Green, and Red from the NAIP imagery and the rescaled elevation raster with 32 classes and a minimum class size of 5000 cells. RECLASSIFY the classified raster by visually comparing the NAIP imagery to obtain the unvegetated-vegetated raster [UVVc.tif]. For marsh units with invalid elevation data, the classification was processed with imagery bands only and later merged with the rest of the dataset.
b) Dissolve unvegetated regions smaller than a threshold value to the surrounding vegetated regions and vice versa to clean the UVV raster. For this purpose use the REGION(Number of neighbors=4; Zone grouping method=Within; Add Link field to output) to get the [UVV_region.tif], and TEST("Count" less than 9) to set a threshold value of 9 raster cells [UVV_test.tif]. Use RASTER CALCULATOR to toggle the value of the Link field in the region raster, where the test raster indicates regions with areas smaller than the threshold.
c) In the version 3 revision, this step was re-run (using ArcGIS Pro 3.4.3). RASTER TO POLYGON(Simplify polygons=False) and CLIP with the final marsh complex outline [CMU_mask_final.shp] to obtain [UVVc_filt_clip.shp].
d) In the version 3 revision, this step was re-run (using ArcGIS Pro 3.4.3). REPAIR GEOMETRY, ADD GEOMETRY ATTRIBUTES (Geometry properties=Area_geodesic; Area unit=Square_meters), CALCULATE FIELD (Python_9.3 expression; Field name=gridcode, Expression=filt(!gridcode!, !AREA_GEO!), Code Block= def filt(gridcode, AREA_GEO):/if gridcode== 0 and AREA_GEO < 9:/return 1/else:/return gridcode) and DISSOLVE (Dissolve field= grid code; Create multipart features=False) to get filtered, clipped and dissolved unvegetated-vegetated polygons [UVVc_filt_clip_diss.shp].
e) In the version 3 revision, this step was re-run (using ArcGIS Pro 3.4.3). INTERSECT the final conceptual marsh units [CMU.shp] with unvegetated-vegetated polygons [UVVc_filt_clip_diss.shp], REPAIR GEOMETRY, and calculate the area of unvegetated and vegetated polygons in each marsh unit. To do this ADD GEOMETRY ATTRIBUTES (Geometry properties=Area_geodesic; Area unit=Square_meters) to get [UVV_poly.shp], and DISSOLV (Input features=[UVV_poly.shp]; Dissolve fields=FID_CMU, gridcode; Statistics field=gridcode.MEAN) and REPAIR GEOMETRY to get [UVV_poly_diss.shp]. Add fields "TYP", "APGN_M2", and "ATOT_M2" for type of polygon indicating vegetated or unvegetated, surface area of the polygon, and total surface area of the marsh unit, respectively, and calculate "APGN_M2" and "ATOT_M2" areas.

Process Step 6. In the version 3 revision, this step was re-run (using ArcGIS Pro 3.4.3). Finalize the conceptual marsh units.
a) Add field "FLG" to flag anomalous marsh units based on absence of vegetation, elevation, surface area, and tidal range extrapolation. The flags are calculated in their respective shapefile (i.e., elevation flags are calculated in the elevation shapefile). Set FLG to: (-1) no vegetated area in the marsh unit; (-10) marsh unit elevation higher than the 99.8 percentile; (-100) marsh unit elevation less than the 0.2 percentile; (-200) greater than 25 percent of the marsh unit elevation is hydro-flattened; (-1000) marsh unit surface area less than 900 square meters; (-10000) mean tidal range of marsh unit is extrapolated; and (0) no flag. Combination of negative values indicates a combination of flags; for example, -1001 indicates no vegetated area and area less than 900 square meters.
b) Rearrange fields and change the projection for better performance of web services with online base maps. PROJECT (Output coordinate system=WGS 1984 Web Mercator Auxiliary Sphere) the feature dataset to obtain the final conceptual marsh units [CMU_ELI.shp].

Process Step 7. Added keywords section with USGS persistent identifier as theme keyword.

Process Step 8. Version 2 updates. Updates were performed in ArcGIS Pro 2.8.8. Duplicate marsh units were manually identified and compared to make sure the most appropriate duplicate marsh unit was deleted. Seventy-six duplicate marsh units were identified (out of 2828) in Mecox Bay, Sagaponack Pond and Georgica Pond and have been removed. After the duplicate marsh units were deleted, the elevation, hydroflattened percentage and elevation flag values were recalculated. Authorship was updated to include Kate Ackerman.

Process Step 9. Version 3 Updates. All updates were completed in ArcGIS Pro 3.4.3, using the version 2 of the dataset as the starting dataset. In the original dataset, each marsh plain was not subdivided into smaller parcels ("marsh units") because two processing steps were not completed. For Version 3, these processing steps were completed, resulting in each marsh plain being properly subdivided into these smaller marsh units. Using the new marsh units, UVVR and elevation values were recalculated. Tide range values were carried over from the original (larger) marsh plain polygons and applied to the new, smaller marsh units.
In this dataset (CMU_ELI), the calculations found in process steps 3-6 had to be re-run once the marsh units were created.
However, exposure potential (SCoRR) values and shoreline change values could not be recalculated at the marsh unit scale. They remain unchanged and still represent the larger marsh plain polygons. In the SCoRR and shoreline change datasets, the field FID_CMU has been renamed to MP to indicate that those polygons correspond to marsh plains, not the newly created marsh units. In the title of the data release for exposure potential and shoreline change, the words "marsh units" were changed to "marsh plains." Throughout the exposure potential and shoreline change metadata, the term 'marsh unit' is still used, but readers should understand that it actually refers to the marsh plain. Previous versions of the data can be obtained by contacting whsc_data_contact@usgs.gov.

Process Step 10. Removed the web services distribution formats in preparation for ScienceBase moving platforms and those services no longer being available.