Data Management Plan

The data described here result from benthic photo-quadrat surveys conducted along transects at stratified random sites (StRS), as well as climate stations and permanent sites, surveyed across the Hawaiian Archipelago during the 2019 bleaching event. Benthic habitat imagery was quantitatively analyzed using the web-based annotation tool CoralNet (Beijbom et al. 2016) with the addition of codes for bleaching of hard coral. In general, images are analyzed to produce three functional group levels of benthic cover: Tier 1 (e.g., hard coral, soft coral, macroalgae, turf algae, etc.), Tier 2 (e.g., Hard Coral = massive, branching, foliose, encrusting, etc.; Macroalgae = upright macroalgae, encrusting macroalgae, bluegreen macroalgae, and Halimeda, etc.), and Tier 3 (e.g., Hard Coral = Astreopora sp, Favia sp, Pocillopora, etc.; Macroalgae = Caulerpa sp, Dictyosphaeria sp, Padina sp, etc.). For each category of hard coral, a bleached and non-bleached option existed during analysis to facilitate the collection of coral bleaching percent cover data.

In the Main Hawaiian Islands (MHI) and some sites in the Northwestern Hawaiian Islands (NWHI), a StRS design was employed to select random sites. The survey domain encompassed the majority of the mapped area of reef and hard bottom habitats in the 0-30 m depth range. The stratification scheme included island, reef zone, and depth in all regions, as well as habitat structure type in the Main Hawaiian Islands. Sampling effort was allocated based on strata area and sites were randomly located within strata. Sites were surveyed using photo-quadrats along transects to collect benthic imagery to ultimately produce estimates of relative abundance (percent cover), frequency of occurrence, benthic community taxonomic composition and relative generic richness.

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.

Surveys conducted in the Main Hawaiian Islands were conducted during shore-based missions and were all StRS, whereas surveys in the Northwestern Hawaiian Islands were performed opportunistically during the regularly scheduled NOAA National Coral Reef Monitoring Program (NCRMP) mission and encompassed StRS as well as fixed sites, which include climate stations and permanent sites

The data from the benthic cover surveys can be accessed online via the NOAA National Centers for Environmental Information (NCEI) Ocean Archive.

Main Hawaiian Islands (MHI), including Hawaii, Maui, Oahu, and Lanai, and the Northwestern Hawaiian Islands (NWHI), including French Frigate Shoals, Lisianski Island, Pearl & Hermes Reef, and Kure Atoll.

Lineage Statement:
The stratified random sampling (StRS) design and benthic photoquadrat survey methodology, employed by the NOAA Coral Reef Ecosystem Program (CREP) since 2013. Benthic imagery is collected at stratified random sites as well as at fixed sites which can be classified as climate stations or permanent sites. The imagery is analyzed using CoralNet to derive benthic cover values. A bleaching label set was produced to perform a bleaching analysis of benthic cover data.

Process Steps:

• A stratified random sampling (StRS) design was employed to conduct surveys during the 2019 bleaching event by the NOAA Ecosystem Sciences Division. The survey domain encompassed the majority of the mapped area of reef and hard bottom habitats. The stratification scheme included island, reef zone, and depth in all regions, as well as habitat structure type in the Main Hawaiian Islands. The habitat structure types included simple, complex, and coral-rich. Depth categories of shallow (0-6 m), mid (> 6-18m) and deep (>18-30 m) were also incorporated into the stratification scheme. Allocation of sampling effort was proportional to strata area. Sites were randomly selected within each stratum. A geographic information system (GIS) and digital spatial databases of benthic habitats (NOAA National Centers for Coastal Ocean Science NCCOS), reef zones (IKONOS satellite imagery, NDGC 1998) bathymetry (NDGC 1998, CREP benthic mapping data), and marine reserve boundaries (NOAA) were used to facilitate spatial delineation of the sampling survey domain, strata, and sample units. Map resolution was such that the survey domain could be overlain by a grid using a GIS with individual cells of size 50 m by 50 m in area. A two-stage sampling scheme following Cochran (1977) was employed to control for spatial variation in population parameters at scales smaller than the grid cell minimum mapping unit (2,500 m2). Grid cells containing hard-bottom reef habitats were designated as primary sample units (referred to as sites). NOAA Fisheries Ecosystem Sciences Division (ESD) conducted rapid visual assessments and photoquadrat assessments of coral bleaching using the methodology outlined by the NOAA Coral Bleaching standard operating procedure for 2019. Still photographs were collected to record the benthic community composition at predetermined points along the transect lines with a high-resolution digital camera. Overall, 30 photoquadrat images are collected at each site. Benthic substrate photos are taken at one meter intervals along the right hand side of the 30 m transect line. Raw data include 30 benthic photographs per survey site. Included in the archive package is a list of survey sites, including region, island, site, date (day, month, year), latitude (dd), longitude (dd), and depth (ft) where photoquads were collected and unique image name. The file naming convention for each photo/image is [SITE]_[YEAR]_[TRANSECT]_[PHOTO_NUMBER].JPG (for example: TUT-903_2012_A_01.JPG).
• The benthic photoquadrat imagery that are collected are analyzed by using the web-based annotation tool CoralNet (Beijbom et al. 2016) from 2015 to present. CoralNet assigns 10 random points per photo and the benthic elements falling directly underneath each point is identified to three functional group levels: Tier 1 (e.g. hard coral, soft coral, macroalgae, turf algae, etc.), Tier 2 (e.g. Hard coral by morphology = massive, branching, foliose, encrusting, etc.; Macroalgae = upright macroalgae, encrusting macroalgae, bluegreen macroalgae, and Halimeda, etc.), and Tier 3 (e.g. Hard coral by genus and morphology; Macroalgae by genus or grouped genera). A new label set was generated with CoralNet to include identifiers for bleached hard coral; the detailed list of each functional group level or tier is included in the benthic image analysis classification scheme.
• Raw survey data includes unique image name and individual point observations identified at three functional group levels of benthic cover with the corresponding physical data which reflect the description of the site. The physical data for all records includes the following: region, island, site, date (day, month, year), latitude (dd), longitude (dd), reef zone, habitat type, depth category, and depth.

Quality control is enforced by means of point-to-point, inter-observer calibration exercises that are conducted before each image analysis production series. Training modules and standard operating procedures have also been developed and documented to ensure improved performance and consistent imagery analysis results produced by multiple analysts.

Data can be accessed online via the NOAA National Centers for Environmental Information (NCEI) Ocean Archive.

NOAA IRC and NOAA Fisheries ITS resources and assets.