This project is a cooperative effort between the National Ocean Service, National Centers for Coastal Ocean Science, Center for Coastal Monitoring and Assessment, the United States Geological Survey, the National Park Service, and the National Geophysical Data Center, to produce benthic habitat maps and georeferenced imagery for Puerto Rico and the U.S. Virgin Islands. This project was conducted in support of the U.S. Coral Reef Task Force. Twenty-one distinct benthic habitat types within eight zones were mapped directly into a GIS system using visual interpretation of orthorectified aerial photographs. Benthic features were mapped that covered an area of 1600 km^2. In all, 49 km^2 of unconsolidated sediment, 721 km^2 of submerged vegetation, 73 km^2 of mangroves, and 756 km^2 of coral reef and colonized hardbottom were mapped.
The National Ocean Service is conducting research to digitally map biotic resources and coordinate a long-term monitoring program that can detect and predict change in U.S. coral reefs, and their associated habitats and biological communities.
Ground condition at date photos were taken (Feb, Mar, and Dec 1999). Maps reflect only the conditions at the time of the photos.
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Puerto Rico Department of Natural and Environmental Resources, University of Puerto Rico, the United States Geological Survey, the National Park Service, Virgin Islands Department of Planning and Natural Resources: Fish and Wildlife Division, University of Virgin Islands, Cons. Data Center, The Nature Conservancy, SeaGrant, and other local and regional experts for input and review.
The purpose of this study was to determine the relative accuracy of maps generated from on-screen digitizing using the ArcView Habitat Digitizer Extension, to those produced by digitizing directly from hard copy photos using a stereoplotter. Thematic accuracy of the Puerto Rico and U.S. Virgin Islands habitat maps was evaluated for the three most general habitat categories: unconsolidated sediment, submerged vegetation, and coral reef/hard bottom. Accuracy tests were conducted at two locations within the project area that included the full complement of habitat types, depth ranges, and water conditions representative of Puerto Rico and the U.S. Virgin Islands. For this reason, the accuracy of maps measured at these two locations is assumed to be representative of map accuracy elsewhere in the project area. This approach, which focused in two small areas, enabled a statistically robust evaluation of thematic accuracy to be conducted without the logical difficulty of collecting data for accuracy assessment over the entire project area. The two test sites chosen were located at Buck Island National Monument, St. Croix, and La Parguera, Puerto Rico. A stratified sampling protocol was used during which sample sites were pre-selected so that overall thematic accuracy of the three major habitat types across the range of depths and water conditions found in the field could be evaluated. Each preselected site was navigated to using a real time Differential Global Positioning System (DGPS) and habitat data was acquired. The Buck Island accuracy assessments tests showed that the ability to generate benthic habitat maps with an overall accuracy of 93.6 percent (Kappa 0.90) for on-screen digitizing and 87.8 percent (Kappa 0.82) for maps digitized directly from stereo pairs. Overall accuracy in the Parguera area was determined to be 93.6 percent (Kappa 0.93).
Individual color aerial photographs were georeferenced and mosaiced. During the digitizing process, image stretches and manipulating image contrast, brightness and color balance were performed in the ArcView Image Analysis Extension to enhance features in the processed imagery. Additional, collateral information including previously completed habitat maps, NOS nautical charts, and other descriptive references dealing with benthic and coastal habitats of Puerto Rico and the U.S. Virgin Islands was used to assist with image interpretation. GIS topologic quality was established by executing ArcView extension routines that check for: overlapping polygons, multipart polygons, sliver polygons and void polygons. Additionally, checks for adjacent polygons with the same habitat attributes were completed. All errors were identified and corrected. This file is believed to be logically consistent.
NOAA supplied georeferenced imagery to an independent contractor. Delineation of all habitat boundaries was conducted with the image scale at 1:6,000. Experimentation indicated that digitizing at this scale optimizes the tradeoff between positional accuracy of lines and time spent digitizing. All polygons were digitized at this scale except when subtle habitat boundaries were not easily discernable at 1:6000 and zooming out to a more broad scale was required to place boundaries correctly. In this case, digitizing generally took place at a scale of approximately 1:10000. Digitizing at a uniform scale ensures that the level of detail produced by the photointerpreter is consistent throughout the project. The Minimum Mapping Unit (MMU) for identifying habitats or features was 1 acre for visual photointerpretation. The software utilized in this project was designed to alert the photointerpreter each time a polygon was drawn smaller than the MMU. When this occurred the photointerpreter has the choice of whether to include the polygon in the data set or not.
The Minimum Mapping Unit (MMU) restriction was set to one acre when digitizing was conducted at 1:6000 scale. Polygons were digitized directly from georegistered orthophotos with spatial accuracy between 1 and 9 meters. These maps represent conditions at the time the aerial photographs were obtained. When considering horizontal map accuracy, it is important to keep in mind that the ocean floor is a dynamic environment. Physical factors such as water currents and hurricanes and biological factors such as seasonal growth and die-off, affect the distribution and stability of benthic habitats in this environment.
This document identifies the zone and habitat types attributed in this data set.
This ArcView extension was used to digitize and attribute benthic zones and habitats for Puerto Rico and the U.S. Virgin Islands.
Benthic features were interpreted and mapped from NGS aerial photos of Puerto Rico.
Benthic habitat maps were digitized by delineating habitat boundaries from georeferenced imagery loaded into ArcView 3.2 GIS software with the Image Analysis and NOAA Coral Reef Habitat Digitizing extensions both activated. On-screen digitizing was conducted with the minimum mapping unit (MMU) set to 1 acre and the image scale at 1:6000. During the digitizing process, image stretches and manipulating image contrast, brightness and color balance were performed in the ArcView Image Analysis Extension to enhance features in the processed imagery. Additional collateral information including previously completed habitat maps, NOS nautical charts, and other descriptive references dealing with benthic and coastal habitats of Puerto Rico and the U.S. Virgin Islands was used to assist with image interpretation. A first draft map was completed and features in the imagery where uncertainties existed, due to confusing or difficult to interpret signatures, were identified for future ground validation effort. An ArcView GIS point theme was generated with points positioned on the features of uncertain habitat type or along transects though gradients between habitat types. The GIS points were converted to GPS waypoints using Trimble Pathfinder Software and were navigated to in the field using a Trimble GeoExplorer 3 GPS data logger. A benthic habitat characterization was conducted at each site by snorkeling, free diving, or via observations from the surface where water depth and clarity permitted. GPS data were collected at each location and site ID, depth, habitat type, zone and the method used to make the assessment were recorded. The ground validation data were incorporated into the second draft of each map.
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Unique ID for each GIS Polygon
Software defined
Area of each polygon in acres
GIS software calculation
ID assigned to each detailed habitat type
Benthic Habitats of Puerto Rico and the U.S. Virgin Islands
Unconsolidated Sediments/Sand
User defined
Unconsolidated Sediments/Mud
Coral Reef and Hardbottom/Colonized Hardbottom/Linear Reef
Coral Reef and Hardbottom/Colonized Hardbottom/Spur and Groove
Coral Reef and Hardbottom/Colonized Hardbottom/Individual Patch Reef
Coral Reef and Hardbottom/Colonized Hardbottom/Aggregated Patch Reef
Coral Reef and Hardbottom/Colonized Hardbottom/Scattered Coral/Rock in Unconsolidated Sediment
Coral Reef and Hardbottom/Colonized Hardbottom/Colonized Pavement
User Defined
Coral Reef and Hardbottom/Colonized Hardbottom/Colonized Bedrock
Coral Reef and Hardbottom/Colonized Hardbottom/Colonized Pavement with Sand Channels
Coral Reef and Hardbottom/Uncolonized Hardbottom/Reef Rubble
Coral Reef and Hardbottom/Uncolonized Hardbottom/Uncolonized Pavement
Coral Reef and Hardbottom/Uncolonized Hardbottom/Uncolonized Bedrock
Coral Reef and Hardbottom/Uncolonized Hardbottom/Uncolonized Pavement with Channels
Other Delineations/Land
Other Delineations/Mangrove
Other Delineations/Artificial
Other Delineations/Unknown
Submerged Vegetation/Seagrass/Continuous Seagrass/90- less than 100%
Submerged Vegetation/Seagrass/Patchy/70- less than 90%
Submerged Vegetation/Seagrass/Patchy/50- less than 70%
Submerged Vegetation/Seagrass/Patchy/30- less than 50%
Submerged Vegetation/Seagrass/Patchy/10- less than 30%
Submerged Vegetation/Macroalgae/Patchy/50- less than 90%
Submerged Vegetation/Macroalgae/Patchy/10- less than 50%
Field containing concatenated habitat data
Name of benthic zone for each GIS polygon
Name of most general level benthic habitat for each GIS polygon
Subset of habitat
ArcView Habitat Digitizer Extension
Subset of type
Subset of Modifier1
Subset of Modifier2
Characteristic Species found in each GIS polygon
The National Oceanic and Atmospheric Administration (NOAA) National Centers for Coastal Ocean Science (NCCOS) produced this data CD-ROM. NCCOS Biogeography Program does not guarantee the accuracy of the geographic features or attributes. Please see the metadata records for each data set for complete information on the source, limitations, and proper use. Disclaimer- While every effort has been made to ensure that these data are accurate and reliable within the limits of the current state of the art, NOAA cannot assume liability for any damages caused by any errors or omissions in the data, nor as a result of the failure of the data to function on a particular system. NOAA makes no warranty, expressed or implied, nor does the fact of distribution constitute such a warranty.
