Pacific NCRMP reefbudgetR

This R package provides tools for working with ReefBudget carbonate budget data collected by NOAA's National Coral Reef Monitoring Program (NCRMP) in the U.S. Pacific Islands, with functions to process benthic, urchin, and parrotfish census data and calculate carbonate production and erosion rates. Package tools and processes are translated to R based on Indo-Pacific ReefBudget methdology and materials (Perry et al. 2018) and modified for use with Pacific NCRMP data.

For additional information on data analyses and methodological approaches, see Barkley et al. (2023).

For additional information on ReefBudget, see Perry et al. (2018).

For additional metadata and downloadable data, see NOAA InPort. .

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.

References:

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: https://repository.library.noaa.gov/view/noaa/56372.

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

Installation

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

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

Example Workflow

Load benthic, urchin, and fish data sets:

library(reefbudgetR)

# Benthic observation data
benthic_data <- read.csv("ESD_CarbBudget_Benthic_OAHU_2021.csv", na = "", check.names = FALSE)

#Urchin observation data
urchin_data <- read.csv("ESD_CarbBudget_Urchins_OAHU_2021.csv", na = "", check.names = FALSE)

# Fish belt transect data
fish_data_belt <- read.csv("ESD_CarbBudget_Fixed_Belt_OAHU_2021.csv", na = "", check.names = FALSE)

# Fish fixed-site and stratified random stationary point count (SPC) data
fish_data_spc <- read.csv("ESD_CarbBudget_SPC_OAHU_2021.csv", na = "", check.names = FALSE)

Process benthic data by method type:

# Process Indo-Pacific ReefBudget (IPRB) benthic data
prod_iprb <- process_prod(
  data = benthic_data[benthic_data$CB_METHOD == "IPRB", ],
  method_name = "IPRB"
)

# Process NCRMP-intermediate (chords) benthic data
prod_chords <- process_prod(
  data = benthic_data[benthic_data$CB_METHOD == "Chords", ],
  method_name = "Chords"
)

# Process NCRMP-leveraged (Structure-from-Motion, SfM) benthic data
prod_sfm <- process_prod(
  data = benthic_data[benthic_data$CB_METHOD == "SfM", ],
  method_name = "SfM"
)

# Combine site-level production data
prod_site <- dplyr::bind_rows(
  prod_iprb$summary_site,
  prod_chords$summary_site,
  prod_sfm$summary_site
)

Process urchin data by method type:

# Process Indo-Pacific ReefBudget (IPRB) urchin data
urch_iprb <- process_urchins(
  data = urchin_data[urchin_data$CB_METHOD == "IPRB", ],
  method_name = "IPRB"
)

# Process NCRMP-intermediate (chords) urchin data
urch_chords <- process_urchins(
  data = urchin_data[urchin_data$CB_METHOD == "Chords", ],
  method_name = "Chords"
)

# Process NCRMP-leveraged (Structure-from-Motion, SfM) urchin data
urch_sfm <- process_urchins(
  data = urchin_data[urchin_data$CB_METHOD == "SfM", ],
  method_name = "SfM"
)

# Combine site-level urchin erosion data
urch_site <- dplyr::bind_rows(urch_iprb$site_erosion,
                              urch_chords$site_erosion,
                              urch_sfm$site_erosion)

Process fish data by method type:

# Process fish belt and stationary point count (SPC) data, open plot window to see strs shapefile plots
fish_site_ <- process_fish(spc_data = fish_data_spc,
                               dbase_type = "Kindinger",
                               belt_data = fish_data_belt,
                               subset_distance_m = 6000)
fish_site <- fish_site_$dat
fish_site_$assoc_site_count

Combine data and calculate net production rates by methodology:

# Calculate net production using IPRB methodology
net_site_iprb <- process_net(
  prod = prod_site[prod_site$CB_METHOD == "IPRB" ,],
  urch = urch_site[urch_site$CB_METHOD == "IPRB" ,],
  fish = fish_site[fish_site$CB_METHOD == "IPRB" ,],
  sum_by = "site"
)

net_site_iprb$METHOD <- "IPRB"

# Calculate net production using NCRMP-intermediate methodology
net_site_int <- process_net(
  prod = prod_site[prod_site$CB_METHOD == "Chords" ,],
  urch = urch_site[urch_site$CB_METHOD == "Chords" ,],
  fish = fish_site[fish_site$CB_METHOD == "Fixed SPC" ,],
  sum_by = "site"
)

net_site_int$METHOD <- "NCRMP-intermediate"

# Calculate net production using NCRMP-leveraged methodology
net_site_lev <- process_net(
  prod = prod_site[prod_site$CB_METHOD == "SfM" ,],
  urch = urch_site[urch_site$CB_METHOD == "SfM" ,],
  fish = fish_site[fish_site$CB_METHOD == "StRS SPC" ,],
  sum_by = "site"
)

net_site_lev$METHOD <- "NCRMP-leveraged"

# Calculate net production using NCRMP-proposed methodology
net_site_prop <- process_net(
  prod = prod_site[prod_site$CB_METHOD == "SfM" ,],
  urch = urch_site[urch_site$CB_METHOD == "Chords" ,],
  fish = fish_site[fish_site$CB_METHOD == "Fixed SPC" ,],
  sum_by = "site"
)

net_site_prop$METHOD <- "NCRMP-proposed"

# Combine net production data
net_site <- dplyr::bind_rows(net_site_iprb, net_site_int, net_site_lev, net_site_prop)