reefbudgetR

This R package provides tools for working with ReefBudget carbonate budget data, with functions to process field-based and SfM-derived benthic, urchin, and parrotfish census data and calculate carbonate production and erosion.

For additional information on data analyses and methodological approaches, see:

Barkley, H.C., Halperin, A.A., Torres-Pulliza, D., Lamirand, M.S., Couch, C.S., Alagata, C.E., Weible, R.M., Smith, J.N., Oliver, T.A. and Perry, C.T., 2025. Estimating coral reef carbonate budgets using Structure-from-Motion photogrammetry. Coral Reefs, 44(3), pp.937-951.

Barkley HC, Weible RM, Halperin AA, Alagata CE, Kindinger TL, Torres-Pulliza D, Lamirand MS, Huntington BE, Couch CS, Amir CG, et al. 2023. Carbonate budget assessments in the U.S. Pacific Islands: report of methods comparison results and summary of standard operating procedures. U.S. Dept. of Commerce, NOAA Technical Memorandum NMFS-PIFSC-154, 7979 p. doi: 10.25923/g4hg-7686.

For additional metadata and downloadable data, see the NCRMP carbonate budgets InPort record.

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.

Installation

You can install the development version of reefbudgetR from GitHub with:

# install.packages("devtools")
devtools::install_github("hannahbarkley/reefbudgetR")

Example workflow for processing Hawaii data

Load benthic, urchin, and fish observation data sets:

library(reefbudgetR)

# Benthic observation data
benthic_data <- read.csv("ESD_NCRMP_CarbBudget_Benthic_HA_2024.csv", na = "", check.names = FALSE)

#Urchin observation data
urchin_data <- read.csv("ESD_NCRMP_CarbBudget_Urchin_HA_2024.csv", na = "", check.names = FALSE)

# Fish SPC data
fish_data <- read.csv("ESD_NCRMP_CarbBudget_Fish_HA_2024.csv", na = "", check.names = FALSE)

Process benthic data:

# Process benthic production data
prod <- process_prod(data = benthic_data)

# Summarize overall production data at site level
prod_site <- prod$summary_site

# Summarize overall production data at transect level
prod_transect <- prod$summary_transect

# Summarize production data at site level by coral group
prod_coral <- prod$summary_site_coral

# Summarize production data at site level by substrate group
prod_substrate <- prod$summary_site_substrateclass

# Return a summary of site metadata
sites_metadata <- prod$sites_metadata

Process urchin data:

 urch <- process_urchins(data = urchin_data)

# Summarize urchin erosion data at site level
 urch_site <- urch$site_erosion
 
 # Summarize urchin erosion data at transect level
 urch_transect <- urch$transect_erosion
 
 # Summarize urchin erosion data at transect level by taxon
 urch_taxon <- urch$transect_taxon

Process fish data:

# Process fish erosion data for all sites
fish_site <- process_fish(data = spc_data, method_type = "Fixed", fixed_metadata = sites_metadata) 

Calculate net production rates :

# Calculate net production at transect level
net_site <- process_net(prod = prod_transect, urch = urch_transect, fish = fish_site, sum_by = "transect")