Area-normalized scaling of ReefBudget calcification, macrobioerosion, and microbioerosion rates for use with CoralNet Version 1.0

The following code generates area-normalized calcification, macrobioerosion, and microbioerosion rates from ReefBudget methodologies (http://geography.exeter.ac.uk/reefbudget/; Perry et al., 2018; Perry and Lange 2019) for use with CoralNet image identification labels to support the integration of estimated carbonate production rates with CoralNet, an automated benthic image analysis platform (https://coralnet.ucsd.edu/; Beijbom et al., 2015). The default rates include calcification, macrobioerosion, and microbioerosion to be consistent with ReefBudget methodologies, but the include_bioerosion argument can be set to FALSE at the beginning of the script to calculate the carbonate production rate data sheet without any sources of bioerosion. Because these rates have been adapted for CoralNet benthic image labels, the included estimates do not account for mobile sources of parrotfish or urchin bioerosion that are included in the complete ReefBudget methodologies. Calcification and bioerosion rates have been developed separately for the Indo-Pacific and Atlantic regions following the below methodologies and data sources.

Please cite the following data release for use of the area-normalized calcification and bioerosion rates as follows:

Courtney TA, Chan S, Lange ID, Perry CT, Kriegman DJ, Andersson AJ (2021) Area-normalized scaling of ReefBudget calcification, macrobioerosion, and microbioerosion rates for use with CoralNet Version 1.0 https://doi.org/10.5281/zenodo.5140477

References: Beijbom O, Edmunds PJ, Roelfsema C, Smith J, Kline DI, Neal BP, Dunlap MJ, Moriarty V, Fan T-Y, Tan C-J, Chan S, Treibitz T, Gamst A, Mitchell BG, Kriegman D (2015) Towards Automated Annotation of Benthic Survey Images: Variability of Human Experts and Operational Modes of Automation. PLoS ONE 10(7): e0130312.

Perry CT, Lange I, Januchowski-Hartley FA (2018) ReefBudget Indo Pacific: online resource and methodology. Retrieved from http://geography.exeter.ac.uk/reefbudget/

Perry CT and Lange ID (2019) ReefBudget Caribbean v2: online resource and methodology. Retrieved from http://geography.exeter.ac.uk/reefbudget/