DOI: 10.5061/dryad.c866t1gcn
title: Coral reef benthic and fish monitoring data from Turneffe Atoll, Belize, 2010-2025

description: Coral reefs are crucial centres of biodiversity, sustaining diverse marine
 species and providing ecosystem services to coastal communities.
 Monitoring coral reefs allows us to assess how the reefs are changing over
 time, discerning the potential impact of environmental changes, human
 activities, and climate events on their health and
 biodiversity. Here, we present a collection of data obtained
 through methodologies from the Mesoamerican Barrier Reef Systems Synoptic
 Monitoring Program (MBRS SMP) and Atlantic and Gulf Rapid Reef Assessment
 (AGRRA) protocols, including data from benthic point-intercept and
 invertebrate surveys, coral recruit surveys, coral community
 characterizations, and reef fish surveys. The dataset encompasses
 observations spanning the years 2010 to 2025 within Turneffe Atoll Marine
 Reserve, Belize. By publishing this dataset, we aim to provide a resource
 for research endeavors related to coral reef dynamics and broader
 ecological trends. Use of this monitoring data supports the evolution of
 Turneffe Atoll Marine Reserve as a Marine Protected Area, contributing to
 informed decision-making and management strategies for the conservation of
 this vital ecosystem.
description: Our dataset consists of data collected for four surveys (benthic
 point-intercept-method (PIM), benthic invertebrates, coral community, and
 reef fish) carried out at the Turneffe Atoll Marine Reserve in Belize,
 annually between 2010-2018, and biennially between 2021-2025. For our
 annual surveys from 2010-2018, we followed the Mesoamerican Barrier Reef
 System Synoptic Monitoring Program (MBRS SMP)
 protocol<sup>1</sup>. For 2021, 2023, and 2025, our data
 collection followed the Atlantic and Gulf Rapid Reef Assessment (AGRRA)
 protocol<sup>2-6</sup>. The change in protocol between 2018
 and 2021 is due to the National adoption of the AGRRA protocol for coral
 reef monitoring in Belize<sup>7</sup>. The two protocols are
 very similar, as the MBRS SMP was based on AGRRA and Caribbean Coastal and
 Marine Productivity (CARICOMP)
 protocols<sup>1</sup>.  Between 2010-2021,
 we archived our collected data in Excel sheets, stored locally at the
 UB-ERI. Under UB-ERI guidance, volunteers digitized the data, entering it
 into tabular data format from waterproof data collection sheets used in
 the field. In 2023, we transformed the data format according to tidy data
 principles<sup>8</sup>, and FAIR data
 principles<sup>9</sup> using R Statistical
 Software<sup>10</sup>. We wrote custom validation rules in R,
 which allowed us to feed our data in and receive a report on any cell that
 violated a rule, such as a temperature measurement in Fahrenheit instead
 of Celsius. We then manually investigated each flagged cell to consider
 individually whether we should fix or exclude the measurement.
 Citations: Almada-Villela, P. C.,
 Sale, P. F., Gold-Bouchot, G., & Kjerfve, B. (2003). Manual of
 methods for the MBRS synoptic monitoring program: Selected methods for
 monitoring physical and biological parameters for use in the Mesoamerican
 region (Protocol 4; p. 155). Mesoamerican Barrier Reef Systems
 Project. https://rris.biopama.org/sites/default/files/2021-03/MBRS%20synoptic%20monitoring.pdf Lang, J., Marks, K., Kramer, P., Kramer, P., & Ginsburg, R. (2010). Agrra protocols version 5.4. ReVision A Journal of Consciousness and Transformation. Lang, J. C., Marks, K. W., Kramer, P. A., Kramer, P. R., & Ginsburg, R. N. (2016a). AGRRA Benthos Protocol. Summary Instructions. (Protocol Revision 2016-09-12; p. 3). Atlantic and Gulf Rapid Reef Assessment. https://www.agrra.org/wp-content/uploads/2016/06/AGRRA-Benthos-Protocol.pdf Lang, J. C., Marks, K. W., Kramer, P. A., Kramer, P. R., & Ginsburg, R. N. (2016b). AGGRA Detailed Fish Protocol. Instructions for Use, June 2016. (Revision 2016-09-12; p. 2). Atlantic and Gulf Rapid Reef Assessment. https://www.agrra.org/wp-content/uploads/2021/05/AGRRA-Fish-Protocol_June-2016.pdf AGRRA. (2021a). AGGRA Benthos Protocol. Summary Instructions, April 2021 Updated. (Revision 2021-04-12; p. 4). Ocean Research & Education. https://agrra.org/wp-content/uploads/2021/05/AGRRA-Benthos-Protocol-April_13_2021.pdf AGRRA. (2021b). AGGRA Coral Protocol. Summary Instructions, April 2021. (Revision 2021-04-12; p. 5). Ocean Research & Education. https://agrra.org/wp-content/uploads/2021/05/AGRRA-Coral-Protocol-April_13_2021.pdf McField, M., & Craig, N. (2018, February 28). Healthy Reefs letter to Belize Fisheries Department Wickham, H. (2014). Tidy Data. Journal of Statistical Software, 59(10). https://doi.org/10.18637/jss.v059.i10 Wilkinson, M. D., Dumontier, M., Aalbersberg, Ij. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., Da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., … Mons, B. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data, 3(1), 160018. https://doi.org/10.1038/sdata.2016.18 R Core Team. (2023). R: A Language and Environment for Statistical  Computing (version 4.3.1) [Computer software]. R Foundation for Statistical Computing. https://www.R-project.org
description: # Coral Reef Benthic and Fish Monitoring Data from Turneffe Atoll, Belize,
 2010-2025 [Access this dataset on Dryad](10.5061/dryad.c866t1gcn) Our
 dataset encompasses coral reef field data collected from Turneffe Atoll
 Marine Reserve, Belize, spanning the years 2010 to 2025. Using five
 distinct survey methods---benthic point intercept, benthic belt transect
 invertebrate, benthic coral recruits, coral community characterization,
 and reef fish belt transect---the data were gathered along transects or
 quadrats at various localities around the atoll, with individual sites
 targeting specific reef structures, including backreef, deep forereef, and
 shallow forereef. Data were validated with custom validation rules created
 in R Statistical Software. ## Description of the data and file structure
 Twelve total data files are included in this dataset. Five files contain
 survey data, and seven files contain supplementary information. Metadata
 for each file is provided below, including an explanation of each measured
 parameter, and in some cases, units of measurement and formatting rules. A
 thirteenth file, which contains an R script, provides the full code used
 to evaluate whether each measurement properly adheres to the rules of each
 column. Within the dataset, MISSING values are used to represent unknown
 or unavailable values. Some parameters were only measured in certain
 years, and some data were lost or unreadable, resulting in these missing
 values. NA values are used when a parameter is not applicable in certain
 cases, such as algae height not being applicable to a coral organism.
 **File #1: Reef Benthic PIM Survey** DataFileName =
 'Master_Benthic_PIM_2010-2025.csv'\ ProjectYears = 2010-2018,
 2021, 2023, 2025\ CollectionProtocol = Point-intercept method from MBRS
 Manual, pg. 27^1^, and AGRRA benthic protocol^2,3^ Each row of this file
 represents a single point along a unique transect. | **Parameter** |
 **Units** | **Description** | **Rules** | | :------------ | :-------- |
 :--------------------------------------------------------------------------------- | :---------------------------------------------------------------------------------------- | | Year | None | Year data were collected | Valid year (2010-2018, 2021, 2023, 2025) in format YYYY | | Date | None | Date data were collected | Format YYYY-MM-DD with the same year as Year | | Locality | None | Locality where data were collected | Valid locality for that site in Sites Turneffe data | | Site | None | Site where data were collected | From list of valid sites in Sites Turneffe data | | Transect | None | Transect at which data were collected at that Site during that Year | Integer from 1-6 | | Protocol | None | Protocol data were collected under | MBRS for Year 2010-2018, or AGRRA for Year 2021-2025 | | Start\_Time | None | Time at which data collection begins at that Site during that Year | Format must be 24-hour HH:MM | | Start\_Depth | m | Depth at start of the Transect | Integer from 1-60 | | End\_Depth | m | Depth at end of the Transect | Integer from 1-60 | | Temp | °C | Bottom temperature at Site during that Year | Integer from 25-35 | | Point | m | Point along the transect at which data were collected | Point must be a multiple of 0.25 for 2010-2018, multiple of 0.1 for 2021-2025 | | Organism | None | Organism found directly below transect tape at that specific Point | Must be an Organism from Organisms Benthic data | | Secondary | None | Second organism found directly below the transect tape at that specific Point | Must be an Organism from Organisms Benthic data | | Algae\_Height | cm | Height of algae Organism | Integer from 0-300 if the Organism of that row has Height = Yes in Organisms Benthic data | | Bleaching | None | Bleaching status of coral Organism; P for pale, BL for bleached, UB for unbleached | P, BL, or UB if the Organism of that row has Bleaching = Yes in Organisms Benthic data | | ND\_A | None | Whether an Organism is alive or newly dead; A for alive, ND for newly dead | ND or A if the Organism of that row has ND\_A = Yes in Organisms Benthic data | | Cloud\_Cover | None | Cloud cover at time of sampling | Integer from 0-8, where 0 is the least cover and 8 is the most | | Collector | None | Collector code that corresponds to field data collector of Observations | From list of valid collector codes in Collectors Turneffe data | | Notes | None | Any additional notes | Any string of text | **File #2: Reef Benthic Invertebrates Survey** DataFileName = 'Master_Benthic_Inverts_2010-2025.csv'\ ProjectYears = 2010-2015, 2017, 2018, 2021, 2023, 2025\ CollectionProtocol = Fish method, including *Diadema* urchin counts from the MBRS Manual, pg. 30^1^, and AGRRA benthic protocol^3^ This file is structured so that each unique transect is allocated a row for each of the six surveyed benthic invertebrate types. If a specific invertebrate is absent on a given transect, it is assigned an observation number, Num, of 0. If the invertebrate type was not being observed during a particular year, it is denoted with a Num of MISSING. | **Parameter** | **Units** | **Description** | **Rules** | | :------------ | :-------- | :---------------------------------------------------------------------- | :--------------------------------------------------------------------------------------- | | Year | None | Year data were collected | Valid year (2010-2015, 2017, 2018, 2021, or 2023) in format YYYY | | Date | None | Date data were collected | Format YYYY-MM-DD with the same year as Year | | Locality | None | Locality where data were collected | Valid locality for that site in Sites Turneffe data | | Site | None | Site where data were collected | From list of valid sites in Sites Turneffe data | | Transect | None | Transect at which data were collected at that Site during that Year | Integer from 1-8 | | Protocol | None | Protocol data were collected under | MBRS for Year 2010-2018, or AGRRA for Year 2021-2023 | | Start\_Time | None | Time at which data collection begins at that Site during that Year | Format must be 24-hour HH:MM | | Temp | °C | Bottom temperature at Site during that Year | Integer from 25-35 | | Species | None | Species of invertebrate that may be found on the transect | DiademaJuv, Diadema (adult *D. antillarum* ), OtherUrchins, Lobster, Conch, or Cucumbers | | Num | None | Number of that Species found on the transect | Integer from 0-100 | | Collector | None | Collector code that corresponds to field data collector of Observations | From list of valid collector codes in Collectors Turneffe data | | Notes | None | Any additional notes | Any string of text | **File #3: Coral Community Characterization** DataFileName = 'Master_Coral_Community_2010-2025.csv'\ ProjectYears = 2010-2018, 2021, 2025\ CollectionProtocol = Coral method from the MBRS Manual, pg. 27^1^, and AGRRA coral protocol^4^ This file is organized so that each row represents a single observed coral organism. | **Parameter** | **Units** | **Description** | **Rules** | | :---------------------- | :-------- | :--------------------------------------------------------------------------------------------------------- | :------------------------------------------------------------- | | Year | None | Year data were collected | Valid year (2010-2018, or 2021) in format YYYY | | Date | None | Date data were collected | Format YYYY-MM-DD with the same year as Year | | Locality | None | Locality where data were collected | Valid locality for that site in Sites Turneffe data | | Site | None | Site where data were collected | From list of valid sites in Sites Turneffe data | | Site\_Comments | None | Any additional notes about the site | Any string of text | | Transect | None | Transect at which data were collected at that Site during that Year | Integer from 1-5 | | Transect\_Comments | None | Any additional notes about the transect | Any string of text | | Area\_Surveyed | Meters | Length of transect line | Integer | | Protocol | None | Protocol data were collected under | MBRS for Year 2010-2018, or AGRRA for Year 2021 | | Start\_Time | None | Time at which data collection begins at that Site during that Year | Format must be 24-hour HH:MM | | End\_Time | None | Time at which data collection ends at that Site during that Year | Format must be 24-hour HH:MM | | Start\_Depth | m | Depth at start of the Transect | Integer from 1-60 | | End\_Depth | m | Depth at end of the Transect | Integer from 1-60 | | Temp | °C | Bottom temperature at Site during that Year | Integer from 25-35 | | Organism | None | Organism found directly below transect tape at that specific Point | Must be an Organism from Organisms Benthic data | | Isolates | None | FR for fragment, CL for clump, or number soft tissue isolates if colony/solitary | Must be FR, CL, or integer from 0-20 | | Depth\_Top | m | Water depth at the highest point of the coral | Numeric from 0.1-50 | | Max\_Diam | cm | Maximum projected diameter (live and dead areas) in plan view of the coral | Integer from 1-500 | | Max\_Length | cm | Maximum length perpendicular to the axis of growth of the coral | Integer from 1-500 | | Max\_Width | cm | Maximum width at right angles to the maximum length of the coral | Integer from 1-500 | | Max\_Height | cm | Maximum height parallel to the axis of growth of the coral | Numeric from 0.1-1, or integer from 1-500 | | OD | Percent | Percent of the coral that has old mortality | Integer from 0-100 | | TD | Percent | Percent of the coral that has transitional mortality | Integer from 0-100 | | RD | Percent | Percent of the coral that has recent mortality | Integer from 0-100 | | Disease | None | Code for a disease observed on the coral | Must be a Disease code from Disease Coral data | | Other\_Health\_Concerns | None | Any additional notes about health concerns for that coral | Any string of text | | Percent\_Pale | Percent | Percent of the coral that is pale | Integer from 0-100 | | Percent\_Bleach | Percent | Percent of the coral that is bleaching | Integer from 0-100 | | Bleaching | None | Discoloration; P for pale, PB for partly bleached, BL for bleached, UB for unbleached | Must be P, BL, PB, or UB | | Base | None | Whether there is a coral base beneath the coral being surveyed | Must be Y or N | | Base\_Coral | None | If there is a coral base beneath the coral being surveyed, the species of that base coral | Must be an Organism from Organisms Benthic data | | Clump\_L | None | If Isolates is CL (clump), tally of how many of the interval points are living | Integer from 0-100 | | Clump\_P | None | If Isolates is CL (clump), tally of how many of the interval points are pale | Integer from 0-100 | | Clump\_BL | None | If Isolates is CL (clump), tally of how many of the interval points are bleached | Integer from 0-100 | | Clump\_NM | None | If Isolates is CL (clump), tally of how many of the interval points are newly dead | Integer from 0-100 | | Clump\_TM | None | If Isolates is CL (clump), tally of how many of the interval points are in transitional mortality | Integer from 0-100 | | Clump\_OM | None | If Isolates is CL (clump), tally of how many of the interval points have old mortality | Integer from 0-100 | | Clump\_Other | None | If Isolates is CL (clump), tally of how many of the interval points are other than the existing categories | Integer from 0-100 | | Clump\_Interval | Cm | If Isolates is CL (clump), distance between intervals measured for the clump | Integer from 0-100 | | Collector | None | Collector code that corresponds to field data collector of Observations | From list of valid collector codes in Collectors Turneffe data | | Notes | None | Any additional notes | Any string of text | **File #4: Reef Fish Survey** DataFileName = 'Master_Fish_Survey_2010-2025.csv'\ ProjectYears = 2010-2015, 2017, 2018, 2021, 2023, 2025\ CollectionProtocol = Fish belt transect method from the MBRS Manual, pg. 30^1^, and AGRRA fish belt transect protocol^5^ The data in this file is systematically arranged, wherein each unique transect is allocated a designated row for every combination of fish species and size class under investigation that year. To illustrate, if a specific transect is targeted that year for the observation of lionfish in the 0-5cm size range, and none are identified during the survey, the corresponding row is retained with the observation count denoted as '0.' Detailed listings of the targeted fish species and associated years can be referenced in the Fish Species reference sheet. | **Parameter** | **Units** | **Description** | **Rules** | | :--------------- | :-------- | :--------------------------------------------------------------------------- | :---------------------------------------------------------------------------- | | Year | None | Year data were collected | Valid year (2010-2015, 2017, 2018, 2021, or 2023) in format YYYY | | Date | None | Date data were collected | Format YYYY-MM-DD with the same year as Year | | Locality | None | Locality where data were collected | Valid locality for that site in Sites Turneffe data | | Site | None | Site where data were collected | From list of valid sites in Sites Turneffe data | | Transect | None | Transect at which data were collected at that Site during that Year | Integer from 1-12 | | Protocol | None | Protocol data were collected under | MBRS for Year 2010-2018, or AGRRA for Year 2021-2023 | | Start\_Time | None | Time at which data collection begins at that Site during that Year | Format must be 24-hour HH:MM | | Start\_Depth | m | Depth at start of the Transect | Integer from 1-60 | | End\_Depth | m | Depth at end of the Transect | Integer from 1-60 | | Max\_Relief | cm | Terrain height variation in 1m radius circles at 5m intervals along Transect | Integer series, each integer a multiple of 5cm, integers separated by periods | | Temp | °C | Bottom temperature at Site during that Year | Integer from 25-35 | | Fish | None | Common name of fish | Must be a fish surveyed that Year, according to Fish Species data | | Fish\_Scientific | None | Scientific name of fish | Must be a Latin binomial for that Fish, according to Fish Species data | | Size\_Class | cm | Fish size grouping | Must be a valid Size\_Class from Ref\_Fish\_Sizes | | Observations | None | Number Fish observed of that Size\_Class at that Uniq\_Transect | Integer from 0-500 | | Cloud\_Cover | None | Cloud cover at time of sampling | Integer from 0-8, where 0 is the least cover and 8 is the most | | Sea\_Conditions | None | Sea conditions at time of sampling, either Calm, Moderate, or Choppy | Either Calm, Moderate, or Choppy | | Collector | None | Collector code that corresponds to field data collector of Observations | From list of valid collector codes in Collectors Turneffe data | | Notes | None | Any additional notes | Any string of text | **File #5: Reef Benthic Coral Recruitment Survey** DataFileName = 'Master_Benthic_Recruit_2023-2025.csv'\ ProjectYears = 2023, 2025\ CollectionProtocol = AGRRA benthic protocol^3^ Each coral recruit species found on a unique quadrat is assigned a row. When no recruits are found on a quadrat, NONE is listed for the organism. Every quadrat is classified as having a specific substrate, whether or not recruits are present. | **Parameter** | **Units** | **Description** | **Rules** | | :------------ | :-------- | :---------------------------------------------------------------------- | :-------------------------------------------------------------------------------------------------------------------------------------- | | Year | None | Year data were collected | Valid year (2010-2015, 2017, 2018, 2021, or 2023) in format YYYY | | Date | None | Date data were collected | Format YYYY-MM-DD with the same year as Year | | Locality | None | Locality where data were collected | Valid locality for that site in Sites Turneffe data | | Site | None | Site where data were collected | From list of valid sites in Sites Turneffe data | | Transect | None | Transect at which data were collected at that Site during that Year | Integer from 1-8 | | Temp | °C | Bottom temperature at Site during that Year | Integer from 25-35 | | Quadrat | None | Quadrat at which the data were recorded | Integer from 1-6 | | Protocol | None | Protocol data were collected under | MBRS for Year 2010-2018, or AGRRA for Year 2021-2023 | | Substratum | None | Primary substratum in the quadrat | Must be a Substratum from Ref\_Substrates\_Benthic; if two substrates are present, listed alphabetically and separated by an underscore | | Organism | None | The coral recruit species found on the quadrat | Must be an Organism from Organisms Benthic data | | Size | None | The size of the coral recruit species on the quadrat | Either SR for small recruit, or LR for large recruit | | Num | None | Number of that coral recruit Organism found on the transect | Integer from 0-100 | | Collector | None | Collector code that corresponds to field data collector of Observations | From list of valid collector codes in Collectors Turneffe data | | Notes | None | Any additional notes | Any string of text | **File #6: Collectors** DataFileName = 'Ref_Collectors_Turneffe.csv'\ ProjectYears = 2010-2018, 2021, 2023, 2025 | **Parameter:** | **Description:** | | :------------- | :------------------------------------------------------------------------------------------------------------------------------------- | | Collector | The code which references a specific collector, including the first 2 letters of the given name and the first 2 letters of the surname | | Name | The full name, if available, of the collector to which the code refers | **File #7: Coral Diseases** DataFileName = 'Ref_Diseases_Coral.csv'\ ProjectYears = 2010-2018, 2021, 2023, 2025 | **Parameter:** | **Description:** | | :------------- | :----------------------------------------------------------------------------------------- | | Disease | A code representing a specific kind of disease for coral | | Name | Name of the disease for that code | | Notes | Any notes about the disease code or disease by the data collector(s), compiler, or analyst | **File #8: Fish Species** DataFileName = 'Ref_Fish_Species.csv'\ ProjectYears = 2010-2018, 2021, 2023, 2025 | **Parameter:** | **Description:** | | :--------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------ | | Fish | The common English name of a fish species | | Fish\_Scientific | The scientific name of that fish species | | Fish\_Family | The taxonomic family within which the fish species belongs | | GBIF\_ID | The ID given to the fish species on the GBIF database; used to tie species to occurrence/distribution datasets worldwide, [GBIF](https://www.gbif.org/) | | List\_2010 | Whether the fish species was included in the list during the 2010 survey | | List\_2011 | Whether the fish species was included in the list during the 2011 survey | | … (cont.) | … (cont.) | | List\_2025 | Whether the fish species was included in the list during the 2025 survey | | Notes | Any notes about the fish by the data collector(s), compiler, or analyst | **File #9: Benthic Organism Codes** DataFileName = 'Ref_Organisms_Benthic.csv'\ ProjectYears = 2010-2018, 2021, 2023, 2025 | **Parameter:** | **Description:** | | :------------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Organism | The code corresponding to a particular organism or non-living substrate in the benthic zone, at the point directly below the transect | | Bucket | A bucket category used to classify the organism codes to standardize across years, collectors, and protocols | | Bucket\_Name | Description of organisms included in the bucket | | Bucket2 | An alternative bucket category used to classify the organism codes to standardize across years, collectors, and protocols | | Bucket2\_Name | Description of organisms included in the alternative bucket | | AGRRA\_Bucket | Bucket category used by AGRRA to classify the organism codes to standardize across years, collectors, and protocols | | AGRRA\_Code | The code typically used in the AGRRA protocol for that organism. May be found in raw or unprocessed data sheets. Codes used may vary by collector and year, however. | | MBRS\_Code | The code typically used in the MBRS protocol for that organism. May be found in raw or unprocessed data sheets. Codes used may vary by collector and year, however. | | Org\_Name | A description of the organism or non-living substrate | | Aphia\_ID | The AphiaID from the WoRMS database for that Organism, if applicable; used to tie taxonomic groups to specific literature and attributes, [WoRMS](htt%20p%20s://www.marinespecies.org/index.php) | | GBIF\_ID | The ID given to the taxonomic group on the GBIF database; used to tie species to occurrence/distribution datasets worldwide, [GBIF](https://www.gbif.org/) | | IUCN\_ID | The ID given to the taxonomic group on the IUCN database; used to tie species to redlist dataset, [IUCN](https://www.iucnredlist.org/en) | | Height? | Whether algae height should be recorded for this organism in benthic PIM methods | | Bleaching | Whether bleaching should be recorded for this organism in benthic PIM methods | | ND\_A | Whether ND\_A should be recorded for this organism in benthic PIM methods | **File #10: Sites** DataFileName = 'Ref_Sites_Turneffe.csv'\ ProjectYears = 2010-2018, 2021, 2023, 2025 | **Parameter:** | **Description:** | | :--------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Site | The site at which the data were collected, in a unique code format | | Locality | The locality to which the site belongs | | Reef\_Zone | The reef zone for that site, either Backreef, Deep\_Forereef, or Shallow\_Forereef. Backreef is leeward facing (&lt;3m), Deep\_Forereef is windward (&gt;10m), Shallow\_Forereef is windward (3-10m) | | Management\_Zone | The management zone in which the site is found, either Atoll, SpecialManagement, or Conservation | | Latitude | The latitude coordinate at which the site is found, in decimal format | | Longitude | The longitude coordinate at which the site is found, in decimal format | | Notes | Any additional notes by the data collector(s), compiler, or analyst | **File #11: Fish Size Ranges** DataFileName = 'Ref_Fish_Sizes.csv'\ ProjectYears = 2025 | **Parameter:** | **Description:** | | :------------- | :------------------------------------------------------------------ | | Size | Size of a fish found; the midpoint of a range of values | | Range | The corresponding range of fish sizes for that size midpoint | | Notes | Any additional notes by the data collector(s), compiler, or analyst | **File #12: Fish Size Ranges** DataFileName = 'Ref_Substrates_Benthic.csv'\ ProjectYears = 2025 | **Parameter:** | **Description:** | | :------------- | :-------------------------------------------------------------- | | Substratum | Substrate type or pair of substrate types in alphabetical order | | Description | A description of that substratum | **File #13: Validation Script** RScriptName = 'Validation.Rmd' ## References 1\. Almada-Villela, P. C., Sale, P. F., Gold-Bouchot, G. & Kjerfve, B. Manual of methods for the MBRS synoptic monitoring program: Selected methods for monitoring physical and biological parameters for use in the Mesoamerican region. [Link to Document](#0) (2003). 2\. Lang, J. C., Marks, K. W., Kramer, P. A., Kramer, P. R. & Ginsburg, R. N. AGRRA Benthos Protocol. Summary Instructions. [Link to Document](https://www.agrra.org/wp-content/uploads/2016/06/AGRRA-Benthos-Protocol.pdf) (2016). 3\. Atlantic and Gulf Rapid Reef Assessment. AGGRA Benthos Protocol. Summary Instructions, April 2021 Updated. [Link to Document](https://agrra.org/wp-content/uploads/2021/05/AGRRA-Benthos-Protocol-April_13_2021.pdf) (2021). 4\. Lang, J. C., Marks, K. W., Kramer, P. A., Kramer, P. R. & Ginsburg, R. N. AGGRA Detailed Fish Protocol. Instructions for Use, June 2016. [Link to Document](https://www.agrra.org/wp-content/uploads/2021/05/AGRRA-Fish-Protocol_June-2016.pdf) (2016). 5\. Atlantic and Gulf Rapid Reef Assessment. AGGRA Coral Protocol. Summary Instructions, April 2021. [Link to Document](https://agrra.org/wp-content/uploads/2021/05/AGRRA-Coral-Protocol-April_13_2021.pdf) (2021). ## Version Changes **Version 2: 7 Oct 2025** New Coauthors added * Noel McCord, UB-ERI * Wilbert Castillo, UB-ERI * Jeissen Mattu, TASA * Virginia Burns-Perez, TASA Documentation * Updated data validation software to reflect changes * Updated the readme file Fish * Remove the derivative column Uniq_Transect * Add columns Locality, Max_Relief * Add 2025 data Coral * Remove the derivative column Uniq_Transect * Add columns Locality, Site_Comments, Area_Surveyed, End_Time, Other_Health_Concerns, Transect_Comments, Base, Base_Coral, Clump_L, Clump_P, Clump_BL, Clump_NM, Clump_TM, Clump_OM, Clump_Other, Clump_Interval * Added 2021 clump type counts * Add 2025 data * Gave PDIG its own dedicated species code again to match AGRRA methods Benthic * Remove the derivative column Uniq_Transect * Add columns Locality, Secondary * Split dual benthic points so that secondary points are in the new Secondary column * Add 2025 data * Gave PDIG its own dedicated species code again to match AGRRA methods Invertebrates * Add 2025 data Recruits * Added new data on coral recruits * Add 2025 data Fish Species * Updated fish list to include 2025 fishes and a new column for the 2025 fish list * Changed fish size classes to midpoint numbers instead of ranges * Removed zero observation values from fish data, as this information can be later derived from the fish list, and it greatly impacts file size * Only do GBIF ID Benthic Species * Gave PDIG its own dedicated species code again to match AGRRA methods * Only do GBIF ID * Added new organism codes SABE, SERP, STA Collectors * Added new collector IDs for Noel McCord, Wilbert Castillo, and Jeissen Mattu Sites * Add new discontinued sites tags Size Ranges * Added a new reference sheet showing the corresponding size ranges to fish sizes Substrates * Added new reference sheet showing substrates