Data Sources
Data Sources
On this page
Reef Code integrates data from many sources to build transparent, reproducible analyses of U.S. Virgin Islands reefs. We do not own these data, and we claim no credit for collecting them. We do not host our collaborators’ raw data for download. This page names every source, links to where the raw data live, and gives the citation each source asks for.
To reproduce an analysis, obtain the raw data from the original source listed here, then run the code shown on the matching analysis page. Throughout the site we provide the analysis scripts and downloadable derived data products, the summaries our code builds from these sources. Reef Code is not a place to download the raw data. It is a place to see freely available data analyzed in the open.
How to read this page. Each analysis page links its datasets back to the matching entry below. An entry gives what the source covers, where to obtain the raw data, the citation, and how the data are accessed. Two sources are flagged: their raw data are not publicly downloadable, so we cite the model or paper and provide only the derived product.
Monitoring programs
Territorial Coral Reef Monitoring Program (TCRMP)
Covers: benthic cover, coral health, coral condition, bleaching and disease, fish, Diadema, and daily temperature at the TCRMP sites across St. Thomas, St. John, and St. Croix.
Obtain the raw data: vitcrmp.org (Data & Methods). Access requires a short request: email a brief intended use and a signed data-use agreement to the program (data contact listed on the site).
Citation: U.S. Virgin Islands Territorial Coral Reef Monitoring Program (TCRMP), University of the Virgin Islands, Center for Marine and Environmental Studies. Methods: Smith TB, Nemeth RS, Blondeau J, Calnan JM, Kadison E, Herzlieb S. 2008. Assessing coral reef health across onshore to offshore stress gradients in the US Virgin Islands. Marine Pollution Bulletin 56:1983–1991. Annual report: Krampitz NM, Kadison E, Ennis RS, Heidmann SL, Henderson LM, Warham M, Smith TB. 2022. The United States Virgin Islands Territorial Coral Reef Monitoring Program: 2022 Annual Report. University of the Virgin Islands, U.S. Virgin Islands.
Virgin Islands National Park Service (VINPS)
Covers: coral-cover video-transect data at VIIS (Virgin Islands National Park, St. John), BUIS (Buck Island Reef National Monument, St. Croix), and SARI (Salt River Bay), 1999–2024, plus the companion coral-disease, Diadema/colony-count, and reef temperature series.
Obtain the raw data: NPS Integrated Resource Management Applications (IRMA) DataStore, Reference 2310411 (SFCN Coral Reef Monitoring Data Package Version 2, 1999–2024). Public download.
Citation: National Park Service, South Florida / Caribbean Network. SFCN Coral Reef Monitoring Data Package Version 2 (1999–2024). NPS DataStore Reference 2310411. Protocol: Miller J, Rogers CS, Feeley MW, Atkinson AJ, Davis AD, Patterson ME, Waara RJ, Witcher BD, Patterson JM, Muller EM. 2017. Coral reef monitoring: protocol narrative, version 2.0. NPS/SFCN/NRR-2017/1464. National Park Service, Fort Collins, CO. https://irma.nps.gov/DataStore/Reference/Profile/2240837
California State University, Northridge (CSUN)
Covers: scleractinian percent cover at the fixed Yawzi and Tektite reefs and the random sites in Virgin Islands National Park, St. John, monitored since 1987 (Peter Edmunds lab, NSF LTREB), plus the associated Yawzi/Tektite temperature series and Diadema density.
Obtain the raw data: Environmental Data Initiative, doi:10.6073/pasta/eeda45f2f6521fc75092807d2e54b501 (percent cover, public, CC BY). Temperature: BCO-DMO 736809. Diadema: Dryad doi:10.5061/dryad.51c59zwcm.
Citation: California State University Northridge and P. Edmunds. 2025. Virgin Islands National Park: Coral Reef: Population Dynamics: Scleractinian corals, ver. 5. Environmental Data Initiative. Foundational studies: Edmunds PJ. 2013. Decadal-scale changes in the community structure of coral reefs of St. John, US Virgin Islands. Marine Ecology Progress Series 489:107–123. Edmunds PJ. 2024. Decadal-scale time series highlight the role of chronic disturbances in driving ecosystem collapse in the Anthropocene. Ecology 105:e4360.
Other data sources
Reef fish, NOAA NCRMP
Covers: reef-fish counts and diversity from the NOAA National Coral Reef Monitoring Program Reef Visual Census for St. Thomas/St. John and St. Croix, used on the NOAA fish-biodiversity page.
Obtain the raw data: NOAA SEFSC Reef Visual Census portal, grunt.sefsc.noaa.gov/rvc_analysis20 (public); archived subset at NOAA NCEI, doi:10.7289/v5f769mm.
Citation: NOAA National Centers for Coastal Ocean Science. National Coral Reef Monitoring Program: reef fish communities in the U.S. Virgin Islands. NOAA NCEI, doi:10.7289/v5f769mm. Data management: NOAA SEFSC Reef Visual Census program.
Coastline shapefile, USGS
Covers: the U.S. Virgin Islands / Puerto Rico coastline used to compute each site’s distance from shore.
Obtain the raw data: USGS Data Series 146, direct download pvishrpl.zip (public, no login).
Citation: Buczkowski BJ, Reid JA, Jenkins CJ, Reid JM, Williams SJ, Flocks JG. 2006. usSEABED: Gulf of Mexico and Caribbean (Puerto Rico and U.S. Virgin Islands) offshore surficial sediment data release. U.S. Geological Survey Data Series 146. Shoreline layer originated by NOAA National Ocean Service / National Geodetic Survey.
Marine managed areas, ProtectedSeas Navigator
Covers: marine managed-area boundaries and the level-of-fishing-protection attributes used to assign each site a management status.
Obtain the raw data: ProtectedSeas Navigator, navigatormap.org (free, CC BY 4.0); versioned release at Figshare doi:10.6084/m9.figshare.25970488.
Citation: Zetterlind V, Sletten J, Colegrove C, et al. 2025. Navigator: a global database of verified marine protected and managed area regulations and boundaries. Scientific Data 12:1212. Dataset: Vincent T. 2024. ProtectedSeas Navigator dataset. Figshare.
Ocean currents, USCROMS model
Raw data not publicly downloadable. These specific 2019 current time series were provided directly by the modeling team and are not archived at a public portal. Obtain them by contacting the modelers; the model itself is described in the citation below. Reef Code provides only the derived current summaries.
Covers: hourly zonal and meridional ocean currents at the reef sites for 2019, from the US Caribbean Regional Ocean Modeling System (USCROMS), provided by Ben Farmer (LSU) and Sonaljit Mukherjee (UVI) under VI EPSCoR.
Citation: Mukherjee S, Wilson D, Jobsis P, Habtes S. 2023. Numerical modeling of internal tides and submesoscale turbulence in the US Caribbean regional ocean. Scientific Reports 13:1091. doi:10.1038/s41598-023-27944-2.
Waves, CARICOOS SWAN
Exact slice no longer public. The SWAN wave model is public on the CARICOOS ERDDAP, but the exact 2015–2020 slice used here is gone: the cited endpoint is dead, and the live server now serves 2025 to present. Reef Code provides only the derived wave summaries.
Covers: significant wave height and period at the reef sites, 2015–2020, from the Caribbean Coastal Ocean Observing System (CARICOOS) nearshore SWAN model.
Obtain the current product: CARICOOS ERDDAP, dm3.caricoos.org/erddap/griddap/SWAN_HighRes_USVI.html.
Citation: CARICOOS (Caribbean Coastal Ocean Observing System). Nearshore Wave Model (SWAN) for Puerto Rico and the U.S. Virgin Islands. Implemented by M.F. Canals, University of Puerto Rico-Mayagüez.
Herbivory parameters (published)
Covers: the parrotfish bite-rate and bite-size parameters and grazing equations used in the herbivory analysis. These are published constants, not a downloaded dataset.
Citation: Mumby PJ. 2006. The impact of exploiting grazers (Scaridae) on the dynamics of Caribbean coral reefs. Ecological Applications 16:747–769. doi:10.1890/1051-0761(2006)016[0747:TIOEGS]2.0.CO;2. Bruggemann JH, van Kessel AM, van Rooij JM, Breeman AM. 1996. Bioerosion and sediment ingestion by the Caribbean parrotfish Scarus vetula and Sparisoma viride. Marine Ecology Progress Series 134:59–71. doi:10.3354/meps134059.
version 1.0.0 • in-review