Workflow to obtain the data from the HRI (AGRRA methodology) to use as input in the coral reef abundance prediction model.
Process data from HRI - Belize Summarize by year (2023, 2021, 2018)
Workflow to extract and summarize coral cover, fleshy algal cover, Commercial Fish Biomass, and Herbivorous Fish Biomass from from HRI data. Summarize by year (2023, 2021, 2018) and at the site level
For detailed methods see: https://oref.maps.arcgis.com/apps/dashboards/bdb35a48e40b49a6b12267e38633fd67
The code for each benthic group that is directly below 100 points marked at 10-cm intervals along the nominally 10-m benthic transects is recorded. Each benthic group is calculated as a proportion by summing the number of points for all its codes and dividing by the total number of available points in the transect length. The percentage cover for each group equals its proportion multiplied by 100. All transects for a given survey are averaged to give a final survey value.
Coral Cover: The percentage of the reef surface covered by live hard corals, indicating the reef's structural complexity and habitat availability. Values are summirized by Survey. A survey represent a site where several transects are deployed.
Fleshy Macro algae Cover: The proportion of the reef covered by fleshy macro algae, which can out compete corals and signify ecological imbalance when present in high amounts.
FISH ABUNDANCE
For the purposes of this work, only grouper, jacks, barracuda and snapper fish families were included in the commercial fish biomass calculation, and only fish species within the Parrotfish and Surgeon fish families were included in the herbivorous fish biomass calculation.
Fish biomass estimates from size class and length-weight formulas for each surveyed species are calculated by family. Biomass for each individual fish is calculated as a * (S * TL2FL)b, where a and b are the species biomass curve coefficients, S is the size (usually the size class midpoint for the AGRRA fishes), and TL2FL is a species total length to fork length conversion factor, if necessary, depending on the species coefficients provided in FishBase. The current data uses coefficient values collected for each species from FishBase in 2013 (values available upon request).
Summations are then used to calculate the total biomass of a species, group, or family. These summations are then normalized by dividing by the transect area and multiplying by 100 to produce biomass in grams per 100m2. All transect level values are averaged to give a final biomass value per survey.
COMMERICAL FISH BIOMASS
tLUTJ Snappers: Lutjanidae LANA Mutton Snapper: Lutjanus analis LAPO Schoolmaster: Lutjanus apodus LBUC Blackfin Snapper: Lutjanus buccanella LCYA Cubera Snapper: Lutjanus cyanopterus LGRI Gray Snapper: Lutjanus griseus LJOC Dog Snapper: Lutjanus jocu LMAH Mahogany Snapper: Lutjanus mahogoni LSYN Lane Snapper: Lutjanus synagris OCHR Yellowtail Snapper: Ocyurus chrysurus
tSERR Groupers: Epinephelidae CCRU Graysby: Cephalopholis cruentata CFUL Coney: Cephalopholis fulva EADS Rock Hind: Epinephelus adscensionis EGUT Red Hind: Epinephelus guttatus EITA Jewfish/Goliath Grouper: Epinephelus itajara EMOR Red Grouper: Epinephelus morio ESTR Nassau Grouper: Epinephelus striatus MACU Comb Grouper: Mycteroperca acutirostris MBON Black Grouper: Mycteroperca bonaci MINT Yellowmouth Grouper: Mycteroperca interstitialis MMIC Gag: Mycteroperca microlepis MPHE Scamp: Mycteroperca phenax MTIG Tiger Grouper: Mycteroperca tigris MVEN Yellowfin Grouper: Mycteroperca venenosa
tCARA Jacks: Carangidae CRUB Bar Jack: Caranx ruber TFAL Permit: Trachinotus falcatus
tSPHY Barracuda: Sphyraenidae SBAR Great Barracuda: Sphyraena barracuda
HERBIVOROUS FISH BIOMASS Parrotfish and Surgeon fish families were included in the herbivorous fish biomass calculation.
Surgeonfish: (tACAN) ACHI Doctorfish: Acanthurus chirurgus ACOE Blue Tang: Acanthurus coeruleus ATRA Ocean Surgeonfish: Acanthurus tractus
Parrotfish (tSCAR) CROS Bluelip Parrotfish: Cryptotomus roseus SATO Greenblotch Parrotfish: Sparisoma atomarium SAUR Redband Parrotfish: Sparisoma aurofrenatum SCEL Midnight Parrotfish: Scarus coelestinus SCER Blue Parrotfish: Scarus coeruleus SCHR Redtail Parrotfish: Sparisoma chrysopterum SGUA Rainbow Parrotfish: Scarus guacamaia SISE Striped Parrotfish: Scarus iseri SRAD Bucktooth Parrotfish: Sparisoma radians SRUB Yellowtail Parrotfish: Sparisoma rubripinne STAE Princess Parrotfish: Scarus taeniopterus SVET Queen Parrotfish: Scarus vetula SVIR Stoplight Parrotfish: Sparisoma viride