National Coral Reef Monitoring Program: Coral demographic data (adult and juvenile corals, species, colony length, condition, etc.) collected during Stratified Random Surveys (StRS) across the US Pacific since 2013 derived from in-situ diver surveys and structure-from-motion imagery (NCEI Accession 0298217)
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title: National Coral Reef Monitoring Program: Coral demographic data (adult and juvenile corals, species, colony length, condition, etc.) collected during Stratified Random Surveys (StRS) across the US Pacific since 2013 derived from in-situ diver surveys and structure-from-motion imagery (NCEI Accession 0298217)
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abstract: The data described here result from benthic coral demographic surveys within belt transects of specified length and width for two life stages (juveniles and adults) across the US Pacific since 2013. This data is collected as part of the NOAA Pacific Islands Fisheries Science Center (PIFSC) and Ecosystem Sciences Division (ESD; formerly the Coral Reef Ecosystem Division) led National Coral Reef Monitoring Program (NCRMP) missions around the Mariana Archipelago, American Samoa, Pacific Remote Island Areas, and the Hawaiian Archipelago since 2013. Originally coral demographic data was derived by in-situ diver surveys, and starting in 2023 the data collection transitioned to derivation from models generated with structure-from-motion imagery. The in-situ diver coral demographic surveys are part of the Rapid Ecological Assessment (REA) surveys for corals and fish conducted during ESD-led NCRMP missions. From 2013 to 2017, a two-stage stratified random sampling (StRS) design was used to survey the coral reef ecosystems across sub-island sectors and three depth strata (shallow: 0-6m, mid: 6-18m and deep: >18m). Starting in 2018 a one-stage StRS design was employed. These sites represent a broad range of depths (1-25 m), habitat types (aggregate reef, patch reef, pavement, rock and boulder and rubble), coral cover, and diving conditions. Allocation of sampling effort was proportional to strata area and variance in coral density. The StRS design effectively reduces estimate variance through stratification using environmental covariates and by sampling more sites rather than sampling more transects at a site. Therefore, site-level estimates and site to site comparisons should be used with caution. Starting in 2023 coral demographic data was also derived by the GIS analysis of benthic Structure from Motion (SfM) imagery. The source imagery was collected during in-water surveys conducted by divers, and is documented separately here: https://www.fisheries.noaa.gov/inport/item/63095. During each SfM survey, an 18m transect line was deployed along the isobath and photographed using underwater cameras while swimming in a back and forth swim pattern for later processing. At depths of 0-18m, SfM surveys were conducted over a 3 x 20m area and at depths >18m, a 3 x 13m area was surveyed, both with the transect running down the middle of the survey area. The photographs were processed using Agisoft Metashape software to generate orthomosaic images that were analyzed in ArcGIS for juvenile and adult coral colony demographic metrics. SfM imagery was not submitted as part of this archive package. The data provide information on adult coral colony counts, morphology, size, partial mortality (old and recent dead), presence and causation of disease and other compromised health conditions, including bleaching. Juvenile colony surveys include morphology and size. Taxonomic identification of adult colonies is to the lowest taxonomic level possible and genus level for juveniles. Some segment observations were repeated for internal quality control starting in 2019, and indicated with a repeat segment flag and transectnum = -999; use column OG_OR_RPT_SEG to filter for only original segments. Refer to data dictionaries for details on column conditions. The raw data also include individual observations of crustose coralline algae diseases and Alcyonarian disease type and lesion size as well as the presence of other Anthozoans, such as other cnidarians including Alcyonareans, Zoantharians, Corallimorpharians, and Antipatharians (does not apply to PMNM surveys conducted in 2014 and 2015 or surveys conducted after 2017).
purpose: The NOAA National Coral Reef Monitoring Program (NCRMP) details a long term approach to provide an ecosystem perspective via monitoring climate, fish, benthic, and socioeconomic variables in a consistent and integrated manner. The NCRMP coordinates various NOAA Coral Reef Conservation Program (CRCP) biological, physical, and human dimensions activities into a cohesive NOAA-wide effort. Through the implementation of the NCRMP, NOAA is able to clearly and concisely communicate results of national-scale monitoring to national, state, and territorial policy makers, resource managers, and the public on a periodic basis. NCRMP is a framework for conducting sustained observations of biological, climate, and socioeconomic indicators at 10 priority coral reefs across the U.S. and its territories. This integrated approach consolidates monitoring of coral reefs under a uniform method in the Pacific, Atlantic, Caribbean, and the Gulf of Mexico for the first time. NCRMP is funded by the CRCP and supported by NOAA Fisheries, NOAA National Centers for Coastal Ocean Science (NCCOS), and many other partners. The PIFSC Ecosystem Sciences Division (ESD) at NOAA Fisheries is leading biological monitoring in the U.S. Pacific Islands Region. The biological component of NCRMP in the Pacific provides a triennial ecological characterization at a broad spatial scale of general reef condition for reef fishes, corals and benthic habitat (i.e., fish species composition/density/size, benthic cover, and coral density/size/condition). Innovative analysis techniques are then used to develop products that give fellow scientists, managers, decision makers and the public a better understanding of a region’s resources and how they are changing over time.
credit: Funding Agency: US DOC; NOAA; NOS; Coral Reef Conservation Program
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topicCategory: (MD_TopicCategoryCode) environment
topicCategory: (MD_TopicCategoryCode) oceans
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beginPosition: 2013-08-02
endPosition: 2023-08-08
supplementalInformation: The Structure from Motion (SfM) imagery used to derive coral demographic data was not submitted as part of this archive package.
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description: Parameter or Variable: CORAL - COLONY SIZE (measured); Units: cm; Observation Category: in situ; Sampling Instrument: swimmer/diver; Sampling and Analyzing Method: At each site, benthic Rapid Ecological Assessment (REA) surveys were conducted within one 10 sq. meter belt transect, 18 meters in length. Adult coral colonies (>=5 cm) were surveyed within four (1.0 x 2.5 m) segments at 5 meter increments along the 18 meter transect in the following manner: 0-2.5 m (segment 0); 5.0-7.5 m (segment 5); 10-12.5 m (segment 10); and 15-17.5 m (segment 15). All colonies whose center fell within 0.5 m on either side of each transect line were measured for size (maximum diameter to nearest cm). In addition, partial mortality and condition of each colony was assessed. Partial mortality was estimated as percent of the colony in terms of old dead and recent dead. The cause of recent mortality was identified if possible. The condition of each colony including disease (not attributed to recent tissue loss) and bleaching was noted along with the extent (percent of colony affected) and level of severity (range from moderate to acute). Juvenile coral colonies (1 - 5 cm) were surveyed within the same segments of the transect. Juvenile colonies were distinguished in the field by a distinct tissue and skeletal boundary (not a fragment of larger colony). Each juvenile colony was measured for size by recording the maximum diameter to the nearest 5 mm.; Data Quality Method: Observations were made by experienced benthic survey personnel who have been trained, undergone a series of calibration surveys and coral taxon identification testing, and have met a set of minimum standards for colony assessment and taxon identification in each region..
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description: Parameter or Variable: CORAL - SPECIES IDENTIFICATION (measured); Units: unitless; Observation Category: in situ; Sampling Instrument: swimmer/diver; Sampling and Analyzing Method: At each site, benthic Rapid Ecological Assessment (REA) surveys were conducted within one 10 sq. meter belt transect, 18 meters in length. Adult coral colonies (>=5 cm) were surveyed within four (1.0 x 2.5 m) segments at 5 meter increments along the 18 meter transect in the following manner: 0-2.5 m (segment 0); 5.0-7.5 m (segment 5); 10-12.5 m (segment 10); and 15-17.5 m (segment 15). All colonies whose center fell within 0.5 m on either side of each transect line were identified to lowest taxonomic level possible (species or genus), and morphology was noted. The lowest taxonomic level of coral identification was genus except for a select number of species consistently identified to species by all divers conducting the surveys. The number of species may change for each survey year depending on the experience and training of the benthic divers conducting the surveys. The list of coral species is included for each survey year. Juvenile coral colonies (<5 cm) were surveyed segments along the same transect. Juvenile colonies were distinguished in the field by a distinct tissue and skeletal boundary (not a fragment of larger colony). Each juvenile colony was identified to genus level.; Data Quality Method: Observations were made by experienced benthic survey personnel who have been trained, undergone a series of calibration surveys and coral taxon identification testing, and have met a set of minimum standards for colony assessment and taxon identification in each region. The accuracy of species and genus level identification was high. The lowest taxonomic level of coral identification was genus except for a select number of species that were consistently identified to species by all divers conducting the surveys. The number of species may change for each survey year depending on the experience and training of the benthic divers. The list of coral species is included for each region and survey year. The total number of species was 54 coral species and 48 coral genera in 2022 in Guam and the Commonwealth of the Northern Marianas Islands. In other words, the individual records within each year may include many more species than encompassed by the region lists, however, these were not consistently identified across all surveys so these records should be assessed at the genus level..
processStep: (LE_ProcessStep)
description: Parameter or Variable: CORAL - CENSUS (measured); Units: unitless; Observation Category: in situ; Sampling Instrument: swimmer/diver; Sampling and Analyzing Method: Number of coral colonies of a specific taxon per survey area. Morphology, colony size, colony count, and species were identified for adult and juvenile corals along a given transect at a stratified-random site.; Data Quality Method: Internal review was performed by repeating observations, and preliminary data was analyzed to determine diver bias. Regular meetings were conducted during the field season to address and alleviate diver bias..
processStep: (LE_ProcessStep)
description: Parameter or Variable: CORAL - COLONY SIZE (calculated); Units: cm; Observation Category: laboratory analysis; Sampling Instrument: photo-identification techniques; Sampling and Analyzing Method: In ArcGIS, each site was set up for annotation by manually digitizing the transect and segments as a shapefile using the same sampling design as the PIFSC ESD-led in situ coral demography surveys, and setting up the attribute table in a geodatabase to mirror the in situ visual survey database (Swanson et al. 2018; Winston et al. 2019). To record and extract data from the orthomosaic, each coral colony was annotated following the in situ visual survey methods. Each colony was measured by digitizing a line across the maximum diameter of the colony. During annotation, the original JPEG imagery was viewed alongside the orthomosaic with the Viscore Image View feature to see fine scale colony details, observe colonies from multiple angles and locate colonies not visible in the orthomosaic (e.g. under ledges).; Data Quality Method: Prior to generating the 3D dense point clouds and 2D orthomosaics , the JPEG imagery was evaluated for image quality and images deemed unsatisfactory (e.g. overexposed, images of blue water or images of divers, or images not taken perpendicular to the reef) were removed from the image set. During annotation in ArcGIS, the original JPEG imagery was viewed alongside the orthomosaic using the Viscore Image View feature to see fine scale colony details, observe colonies from multiple angles and locate colonies not visible in the orthomosaic. Annotations created in ArcGIS were quality controlled using a multi-stage process. Data were first quality controlled in R with specific queries to identify and correct data entry errors (e.g. misspelled species names, missing segments, data in incorrect columns, partial mortality >100%). Then data were summarized to the segment-level by annotator to identify potential issues (e.g. anomalously high or low mean values for specific metrics relative to other annotators). If issues were identified for a given annotator, that annotator reviewed and corrected each site if they did find errors..
processStep: (LE_ProcessStep)
description: Parameter or Variable: CORAL - SPECIES IDENTIFICATION (calculated); Units: unitless; Observation Category: laboratory analysis; Sampling Instrument: photo-identification techniques; Sampling and Analyzing Method: In ArcGIS, each site was set up for annotation by manually digitizing the transect and segments as a shapefile using the same sampling design as the PIFSC ESD-led in situ coral demography surveys, and setting up the attribute table in a geodatabase to mirror the in situ visual survey database (Swanson et al. 2018; Winston et al. 2019).; Data Quality Method: Prior to generating the 3D dense point clouds and 2D orthomosaics , the JPEG imagery was evaluated for image quality and images deemed unsatisfactory (e.g. overexposed, images of blue water or images of divers, or images not taken perpendicular to the reef) were removed from the image set. During annotation in ArcGIS, the original JPEG imagery was viewed alongside the orthomosaic using the Viscore Image View feature to see fine scale colony details, observe colonies from multiple angles and locate colonies not visible in the orthomosaic. Annotations created in ArcGIS were quality controlled using a multi-stage process. Data were first quality controlled in R with specific queries to identify and correct data entry errors (e.g. misspelled species names, missing segments, data in incorrect columns, partial mortality >100%). Then data were summarized to the segment-level by annotator to identify potential issues (e.g. anomalously high or low mean values for specific metrics relative to other annotators). If issues were identified for a given annotator, that annotator reviewed and corrected each site if they did find errors..
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acquisitionInformation: (MI_AcquisitionInformation)
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code: photo-identification techniques
type: photo-identification techniques
description: A method of identifying species with persistent external patterns that can be used to identify unique individuals over the course of most of their adult life span. Examples include spots, anomalous pigmentation, and patterns on the trailing edges of marine mammal fins. https://gcmd.earthdata.nasa.gov/KeywordViewer/scheme/all/a9b6ed7f-2e26-4749-98f0-b3617451192b?gtm_keyword=Photo-Identification%20Techniques
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description: Title: NOAA Ship Flag: United States of America Vessel Type: Research Vessel (Hydrographic) DOB: Apr 1968 IMO: 6711003 Hull Classification: S 221
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