Unvegetated to vegetated ratio of marsh units in Atlantic-facing New Jersey salt marshes

This process step and all subsequent process steps were performed by the same person, Kate Ackerman, in ArcGIS Pro (ver. 2.8.8), unless otherwise stated. For simple operations the name of the geoprocessing tool used is given in capital letters; for complex operations, the name of the geoprocessing tool used is given in capital letters and 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 unless otherwise stated.
a) Set the data frame coordinate system and projection to NAD 1983 UTM Zone 18N.
b) Establish marsh unit boundaries. Dissolve the vegetated and unvegetated classes in each marsh unit to have only one class for each marsh unit. DISSOLVE (Input features=[CMU_NJ_Atl.shp]; Dissolve field=FID_CMU; Statistics field=ATOT_M2 and FLG with Statistics type= First). PROJECT (Input coordinate system=WGS 1984 Web Mercator Auxiliary Sphere; Output coordinate system=NAD 1983 UTM Zone 18N) the feature dataset to obtain dissolved marsh units [mu_diss.shp].
c) Prepare elevation dataset. Combine all downloaded tiles into one raster, using MOSAIC TO NEW RASTER, and PROJECT RASTER to NAD 1983 UTM Zone 18N.
d) Create a polygon that covers the area of interest [extent.shp]. CLIP the mosaicked elevation dataset created in step (c) by [extent.shp] to create [elev_mosaic.tif].

This process step creates two mask polygons to define analysis boundaries over the area of interest. 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 created [UVVR_mask.shp]. This larger mask area is clipped to the boundaries of the salt marsh area to create [MU_mask.shp]. This process step explains how [UVVR_mask.shp] and [MU_mask.shp] are created and edited to determine which interior polygons are removed.
a) Create a shapefile of the salt marshes as defined by NWI. From the NWI dataset of all wetlands for the area (referred to as [NWI_entire.shp]), select estuarine intertidal areas of 1) emergent wetland, 2) scrub-shrub area, 3) rooted vascular aquatic bed, and 4) organic unconsolidated shore classes (SELECT (ATTRIBUTE LIKE 'E2%EM%' OR ATTRIBUTE LIKE 'E2AB3%' OR ATTRIBUTE LIKE 'E2EM%' OR ATTRIBUTE LIKE 'E2SS%' OR ATTRIBUTE LIKE 'E2US4%'). EXPORT features (in the same coordinate system as the data frame) to create [NWI_exclusive_select.shp]. In some areas, erroneous line features were eliminated or modified to allow the salt marsh extent to be consistent with imagery.
b) Create the preliminary masks that will be edited in the subsequent steps to make the final masks. BUFFER salt marsh classes (Input features=[NWI_exclusive_select.shp]; Linear unit=5 meters; Dissolve type=All) to obtain the mask polygon [buff5m.shp] and ELIMINATE POLYGON PART (Input features= [buff5m.shp]; Condition=Percentage; Percentage=99; Eliminate contained part only) to remove small interior polygons to obtain [UVVR_mask01.shp]. Apply BUFFER (Input features=[UVVR_mask01.shp]; Linear unit= -5 meters; Dissolve type= All) to obtain [MU_mask01.shp].
c) Create a shapefile of features that are not estuarine or are forested estuarine (SELECT (ATTRIBUTE NOT LIKE 'E%' OR ATTRIBUTE LIKE '%FO')) from the NWI dataset. EXPORT features to create [NWI_inclusive_select.shp]. MULTIPART TO SINGLEPART to separate individual polygons [NWI_inclusive_single.shp].
d) To exclude the voids in the NWI map during the analysis, these interior polygons need to be removed from the mask. ERASE [NWI_exclusive_select.shp] from [extent.shp] and MULTIPART TO SINGLEPART to get [NWI_exc_voids_single.shp].
To create the final mask shapefiles ([MU_mask.shp] and [UVVR_mask.shp]), areas that should not be included are removed (e.g., forest areas), and areas that should be included are incorporated (estuarine and marine wetland systems that are completely surrounded by salt marsh (e.g., interior ponds)):
e)SELECT BY LOCATION from [NWI_inclusive_single.shp] that are completely within the [MU_mask01.shp] and SELECT BY LOCATION from [NWI_exc_voids_single.shp] that are completely within the [MU_mask01.shp]. UNION all feature sets to get polygons to be excluded [erase_inside.shp] from the final masks.
f) Spatially join the [NWI_entire.shp] to [erase_inside.shp] in order to assign wetland attributes to the [erase_inside.shp] polygons. SPATIAL JOIN (target features= [erase_inside.shp]; join features= [NWI_entire.shp]; output feature class= [erase_inside_NWI_info.shp]; join operation= one to one; keep all target features; match option= intersect; search radius= -1 m).
g) Select the polygons that are marine or non-forested estuarine wetlands from [erase_inside_NWI_info.shp]: SELECT (ATTRIBUTE LIKE 'E1%' OR ATTRIBUTE LIKE 'E2AB%' OR ATTRIBUTE LIKE 'E2RF%' OR ATTRIBUTE LIKE 'E2SB%' OR ATTRIBUTE LIKE 'E2RS%' OR ATTRIBUTE LIKE 'E2US%' OR ATTRIBUTE LIKE 'E2EM%' OR ATTRIBUTE LIKE ‘E2SS%’ OR ATTRIBUTE LIKE ‘M1%’ OR ATTRIBUTE LIKE ‘M2%) to select all marine systems, estuarine subtidal systems, estuarine intertidal areas of aquatic bed, reef, streambed, rocky shore, unconsolidated shore, emergent, or scrub-shrub [erase_inside_keepIntPonds.shp].
h) Remove the polygons from [erase_inside_NWI_info.shp] that should be retained (these are the interior ponds): ERASE (input feature= [erase_inside_NWI_info.shp]; erase feature= [erase_inside_keepIntPonds.shp]; output feature= [erase_inside_final.shp]).
i) If any additional polygons need to be removed from the mask, include them in a new feature layer [erase_mask_manual.shp] and MERGE with [erase_inside_final.shp].
j) Remove any unwanted polygons from the original [MU_mask01.shp] to make the final [MU_Mask.shp]: ERASE (input feature= [MU_mask01.shp]; erase feature= [erase_inside_final.shp]; output feature= [MU_mask.shp]).
k) Use the NJ Wetlands tidal marsh boundaries to refine, and in some cases, replace polygons in [MU_mask.shp] that are not consistent with aerial imagery.
l) BUFFER [MU_mask.shp] by 5m (side type= full; end type= round; method: geodesic; dissolve type: single feature) to obtain [UVVR_mask.shp].

Compute vegetated and unvegetated areas by image processing.
a) MOSAIC TO NEW RASTER the NAIP tiles.
b) EXTRACT BY MASK from the elevation raster [elev_mosaic.tif] and the NAIP imagery raster using [UVVR_mask.shp] polygon and append “UVVR_mask” to the file name. Rescale the elevation raster values to the same range with 8-bit NAIP imagery (0 to 255) using min-max scaling in RASTER CALCULATOR (map algebra expression: (("elev_mosaic_UVVR_mask.tif"-(min value of the input raster))*(255-0)/(max value of the input raster)-( min value of the input raster)))+0). Perform ISO CLUSTER UNSUPERVISED CLASSIFICATION with 5 input bands: the Near Infrared, Blue, Green, and Red from the NAIP imagery and the rescaled elevation raster; with 32 classes and a minimum class size of 500 cells. RECLASSIFY (0= unvegetated, 1= vegetated) the classified raster by visually comparing the NAIP imagery to obtain the unvegetated-vegetated raster [UVVc.tif]. In some regions, a couple of the 32 classes are classified as vegetated in one area but unvegetated in another area. For these classes, the area can be split into separate sections to allow one section to be classified as vegetated and the other as unvegetated.
c) 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 GROUP (Number of neighbors=4; Zone grouping method=Within; Add Link field to output) to get the [UVV_region.tif], and TEST("Count" < 9) to set a threshold value of 9 raster cells [lt9.tif]. Use RASTER CALCULATOR to toggle the value of the Link field in the region raster [Map algebra expression=Con("%lt9.tif%", ~Lookup("%UVVc_region.tif%","LINK"),Lookup("%UVVc_region.tif%","LINK"))], where the test raster indicates regions with areas smaller than the threshold.
d) RASTER TO POLYGON (Simplify polygons=False) and CLIP with the final marsh complex outline [mu_diss.shp] to obtain [UVVc_filt_clip.shp].
e) 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].
f) INTERSECT the final conceptual marsh units [mu_diss.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 DISSOLVE (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.
g) Visually inspect and manually remove marsh units that are a result of geoprocessing artifacts (e.g., buffering).
h) Add field "UVVR" and calculate unvegetated to vegetated ratio based on "TYP", "APGN_M2" and "ATOT_M2" fields. If the vegetated area is zero for a marsh unit set the value of UVVR to -1.
i) DISSOLVE (Input features=[UVV_poly_diss.shp]; Dissolve fields=FID_CMU; Statistics field=UVVR, ATOT_M2 and FLG with Statistics type= First for all) to obtain [mu_UVVR_NJ_Atl.shp].
j) SELECT BY ATTRIBUTES FROM [CMU_NJ_Atl.shp] where "TYP"= 'vegetated,' and join field "APGN_M2" from [CMU_NJ_Atl.shp] to [mu_UVVR_NJ_Atl.shp] and rename this field "AVEG_M2."
k) 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.
l) 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 UVVR for each marsh unit [mu_UVVR_NJ_Atl.shp].