National Park Service 

U.S. Department of the Interior 

Natural Resource Program Center 

A Cooperative Multi-agency 

Reef Fish Monitoring Protocol for 

the Florida Keys Coral Reef Ecosystem 

Natural Resource Report NPS/SFCN/NRR—2009/150 
 

ON THE COVER 

Clockwise from top left: face of a French angelfish (Pomacanthus paru), school of Creole wrasse (Clepticus 

parrae) swimming over a Montastraea franksi coral, a rock beauty (Holacanthus tricolor), a red grouper 

(Epinephelus morio), a school of permit (Trachinotus falcatus). All photos taken in the Dry Tortugas by J. Luo. 
A Cooperative Multi-Agency 

Reef Fish Monitoring Protocol for 

the Florida Keys Coral Reef Ecosystem 

Natural Resource Report NPS/SFCN/NRR—2009/150 

Marilyn E. Brandt1,2, Natalia Zurcher1

, Alejandro Acosta3, Jerald S. Ault1, James A. 

Bohnsack4

, Michael W. Feeley3, Douglas E. Harper4, John H. Hunt3, Todd Kellison4, 

David B. McClellan4

, Matt E. Patterson2, Steven G. Smith1

1

University of Miami 

Rosenstiel School of Marine and Atmospheric Science 

4600 Rickenbacker Cswy 

Miami, FL 33149 

2

National Park Service 

South Florida / Caribbean Network 

18001 Old Cutler Rd., Suite 419 

Village of Palmetto Bay, FL 33157 

3

Florida Fish and Wildlife Conservation Commission 

Fish and Wildlife Research Institute 

South Florida Regional Lab 

2796 Overseas Hwy., Suite 119 

Marathon, FL 33050 

4

National Oceanic and Atmospheric Administration 

Southeast Fisheries Science Center 

75 Virginia Beach Drive 

Miami, FL 33149 

September 2009 

U.S. Department of the Interior 

National Park Service 

Natural Resource Program Center 

Fort Collins, Colorado 
 

 ii 

The National Park Service, Natural Resource Program Center publishes a range of 

reports that address natural resource topics of interest and applicability to a broad 

audience in the National Park Service and others in natural resource management, 

including scientists, conservation and environmental constituencies, and the public. 

The Natural Resource Report Series is used to disseminate high-priority, current 

natural resource management information with managerial application. The series 

targets a general, diverse audience, and may contain NPS policy considerations or 

address sensitive issues of management applicability. 

All manuscripts in the series receive the appropriate level of peer review to ensure 

that the information is scientifically credible, technically accurate, appropriately 

written for the intended audience, and designed and published in a professional 

manner. This report received formal peer review by subject-matter experts who were 

not directly involved in the collection, analysis, or reporting of the data, and whose 

background and expertise put them on par technically and scientifically with the 

authors of the information. 

Views, statements, findings, conclusions, recommendations, and data in this report 

are those of the author(s) and do not necessarily reflect views and policies of the 

National Park Service, U.S. Department of the Interior. Mention of trade names or 

commercial products does not constitute endorsement or recommendation for use 

by the National Park Service. 

This report is available from the South Florida / Caribbean Network website 

(http://science.nature.nps.gov/im/units/sfcn/) and the Natural Resource Publications 

Management website (http://www.nature.nps.gov/publications/NRPM). 

Please cite this publication as: 

Brandt, M. E., N. Zurcher, A. Acosta, J. S. Ault, J. A. Bohnsack, M. W. Feeley, D. E. 

Harper, J. H. Hunt, T. Kellison, D. B. McClellan, M. E. Patterson, and S. G. Smith. 

2009. A cooperative multi-agency reef fish monitoring protocol for the Florida Keys 

coral reef ecosystem. Natural Resource Report NPS/SFCN/NRR—2009/150. National 

Park Service, Fort Collins, Colorado. 

NPS 910/100304, September 2009 
 

 iii 

Contents 

Figures .....................................................................................................................vii 

Tables ........................................................................................................................ix 

Appendices .................................................................................................................x 

Executive Summary ...................................................................................................xi 

Acknowledgements .................................................................................................xiii 

Introduction ...............................................................................................................1 

Rationale behind this Document and Reef Fish Monitoring.............................1 

Fishing and Other Pressures on the Reef ..........................................................2 

Fishing Management ........................................................................................3 

Background and Objectives ........................................................................................5 

History .............................................................................................................5 

Measurable Objectives of Monitoring ..............................................................7 

Sampling Design...........................................................................................................................7 

Rationale for Selecting This Sampling Design over Others ...............................7 

Sampling Domain .............................................................................................9 

Sampling Frequency and Replication ...............................................................9 

Number and Location of Sampling Sites...........................................................9 

Frequency and Timing of Sampling ................................................................ 10 

Level of Change that can be Detected for Sampling Being Instituted .............. 10 

Field Methods........................................................................................................... 11 

Field Season Preparations and Equipment Setup............................................ 11 
 

 iv 

Sequence of Events during Field Season ......................................................... 11 

Details of Making Observations...................................................................... 11 

Post-collection Data Sheet and Logs Processing............................................. 12 

End-of-Season Procedures ............................................................................. 12 

Data Handling, Analysis and Reporting .................................................................... 12 

Data Entry, Verification and Editing .............................................................. 12 

Recommendations for Routine Data Summaries and Statistical Analyses....... 12 

Personnel Requirements and Training...................................................................... 13 

Roles and Responsibilities .............................................................................. 13 

Qualifications ................................................................................................. 13 

Training.......................................................................................................... 13 

Contacts.................................................................................................................... 14 

Standard Operating Procedure A: Statistical Sampling Design 

A.1 Introduction .............................................................................................. A-1 

A.2 Stratification............................................................................................... A-1 

A.3 Sample Allocation....................................................................................... A-5 

A.4 Sample Unit (Location) Selection ............................................................... A-7 

A.5 Example ..................................................................................................... A-8 

Standard Operating Procedure B: Participant Training 

B.1 Initial Participant Training ......................................................................... B-1 

B.2 Annual Refresher Training for Previous Participants ................................. B-2 

B.3 Data Entry and Proofing Training .............................................................. B-3 
 

 v 

Standard Operating Procedure C: Field Data Collection Methods 

C.1 Equipment..................................................................................................C-1 

C.2 Sequence of Events in the Field ..................................................................C-2 

C.2.i Locating and Assessing the Sample Site (Primary Unit) ....................C-2 

C.2.ii Diver Deployment, Descent, and Location of Survey Sites .............C-2 

C.3 Details of Observations Made in the Field ..................................................C-5 

C.3.i Field Forms ......................................................................................C-5 

C.3.ii Collecting Fish Data ........................................................................C-8 

C.3.iii Sample-Specific Data.................................................................... C-10 

C.3.iv Habitat Data ................................................................................. C-10 

C.4 Post-Collection Data Sheet and Logs Processing...................................... C-13 

Standard Operating Procedure D: Data Entry, Editing and Proofing 

D.1 Introduction ..............................................................................................D-1 

D.2 Data Entry..................................................................................................D-1 

D.2.i The RVC Data Entry Program..........................................................D-1 

D.2.ii Directions for Use of the RVC Data Entry Program ........................D-2 

D.3 Editing Saved Data .....................................................................................D-8 

D.4 Data Cataloguing........................................................................................D-9 

D.5 Data QA/QC and Verification ....................................................................D-9 

D.5.i Initial Diver Proofing .......................................................................D-9 

D.5.ii Participant-Level Proofing..............................................................D-9 

D.5.iii Agency-Level Proofing.................................................................D-12 
 

 vi 

D.5.iv Final Verification and Oracle Database ........................................D-13 

Standard Operating Procedure E: Data Analyses and Reporting 

E.1 Introduction ............................................................................................... E-1 

E.2 Descriptive Ecological Analysis .................................................................. E-1 

E.3 Fishery Assessment and Calculation of Fish Stock Status Indices ............... E-1 

E.3.i Mean Density.................................................................................... E-2 

E.3.ii Average Size in the Exploited Phase ................................................ E-3 

E.3.iii Assessing Changes to Reef Fish Metrics.......................................... E-4 

E.4 Multi-Species Fishery Stock Assessments ................................................... E-5 

E.5 Design Performance Analysis ..................................................................... E-5 

Literature Cited 

Appendices 
 

 vii 

Figures 

Figure 1.1 Designated management zoning of the Florida Keys coastal marine 

ecosystem, including the Florida Keys National Marine Sanctuary, Biscayne 

National Park and Dry Tortugas National Park ..........................................................4 

Figure A.1 Cross-shelf distribution of coral reef and hard-bottom habitat classes 

in the vicinity of Western Sambo NTMR overlain with the 200 m by 200 m 

primary unit sampling grid...................................................................................... A-2 

Figure A.2 Conceptual diagram of the sampling domain and sample units for a 

two-stage stratified random survey design .............................................................. A-3 

Figure A.3 Percent of all second-stage units sampled in the Florida Keys (2003- 

2007) which fell within different distances (m) from the primary unit center.......... A-8 

Figure A.4 Performance data for annual estimates of fish density for eight 

focal species and ten additional non-targeted species in Biscayne National 

Park during 2005-2007 ..................................................................................... A-11-14 

Figure C.1 The RVC All Purpose Tool (APT) used as a reference device for 

measuring habitat vertical relief, estimating fish lengths and the location of the 

center and outer edge of the sample cylinder ..........................................................C-1 

Figure C.2 Schematic representing location of counts along a deployed 

measuring tape........................................................................................................C-4 

Figure C.3 Field/Boat Log form...............................................................................C-6 

Figure C.4 Water Quality/Environmental Log form................................................C-7 

Figure C.5 Fish/Habitat Data Sheet.........................................................................C-8 

Figure C.6 Conceptual diagram of RVC diver within 7.5m-radius survey cylinder..C-9 

Figure C.7 Example photos of target habitats........................................................C-11 

Figure C.8 Diagram showing how to measure substrate slope, max vertical relief 

and surface relief coverage.................................................................................... C-14 

Figure D.1 The “Sample Data” window...................................................................D-4 

Figure D.2 The “Substrate data” window ................................................................D-6 
 

 viii 

Figure D.3 The “Species data” window ...................................................................D-8 

Figure D.4 Example proofing report sheet in common species names style ..........D-11 

Figure D.5 Example proofing report sheet in RVC species code style ...................D-12 

Figure D.6 Flow chart of verification procedures and production of oracle tables D-14 

Figure D.7 The Entity-Relationship diagram (ER diagram) of the schema with 

relationships between different tables in Oracle ...................................................D-22 
 

 ix 

Tables 

Table 1.1 Publications documenting the development or results of the multiagency reef fish sampling in the Florida Keys and Dry Tortugas ..............................6-7 

Table A.1 Total possible primary units (Nh) in statistical strata defined by subregion, cross-shelf zone, habitat class and depth, and management zone in 

surveys of the Florida Keys .................................................................................... A-4 

Table A.2 Total possible primary units (Nh) in statistical strata defined by subregion, habitat class, and management zone in the sampling surveys of the Dry 

Tortugas................................................................................................................. A-4 

Table A.3 Primary units (n) sampled by sub-region and year ................................. A-9 

Table A.4 Optimal primary unit sample number (n*) for comparisons of fish 

densities between years in Biscayne National Park .............................................. A-15 

Table D.1 Data management overview................................................................... D-1 

Table D.2 Variables in the sample output file (rvc_sample.xls) ............................ D-15 

Table D.3 Variables in the boat log output file (rvc_boatlog.xls) .......................... D-16 

Table D.4 Variables in the substrate output file (rvc_substrate.xls)...................... D-17 

Table D.5 Variables in the species output file (rvc_species.xls) ............................ D-18 

Table D.6 Variables in the verification file used (verify_2.xls).............................. D-18 

Table D.7 Variables in the map grid groundtrouthing file 

(mapgrid_groundtrouth.txt) used in verification ................................................. D-18 

Table D.8 Variables used in the Florida species master file 

(species_master_FL.xls) used in verification ........................................................ D-19 

Table D.9 Variables associated with the Oracle tables and their descriptions . D-19-21 
 

 x 

Appendices 

Appendix 1. Statistical Symbols and Computational Formulae ........................ App 1-i 

Appendix 2. Habitat Information Sheets........................................................... App 2-i 

Appendix 3. Printable Data Sheets .................................................................... App 3-i 

Appendix 4. FMRI 1998 – Benthic Habitats of the Florida Keys........................ App 4-i 
 

 xi 

Executive Summary 

Reef fish populations are conspicuous and essential components of coral reef 

ecosystems in the south Florida region. Recent precipitous declines in these 

populations are believed to be due to severe habitat degradation as well as significant 

increases in recreational and commercial fishing. The monitoring methodologies 

described in this document are necessary for understanding how natural and manmade stressors are changing reef fish populations and communities. These stressors 

will continue to increase, and understanding the responses of populations and 

communities will be critical for their sustainable management. 

This document provides the background behind and descriptions of the protocols 

developed for a collaborative, multi-agency effort to monitor reef fish populations in 

the Florida Keys and Dry Tortugas. Agencies involved include the National Oceanic 

and Atmospheric Administration Southeast Fisheries Science Center (NOAA 

Fisheries), Florida Fish and Wildlife Conservation Commission’s Florida Fish and 

Wildlife Research Institute (FWRI), the University of Miami’s Rosenstiel School of 

Marine and Atmospheric Science (UM-RSMAS), and the National Park Service 

(NPS). This collaborative effort is the culmination of nearly three decades of 

independent Florida Keys monitoring programs aimed at fish populations in the 

region. 

The Florida Keys reef tract extends some 370 km from Miami to the Dry Tortugas 

and encompasses a variety of benthic habitat types and management areas. In order 

to more efficiently sample within such a heterogeneous region, the sampling effort is 

optimized using a two-stage stratified random sampling design. Before sampling 

occurs, the Florida Keys and Dry Tortugas sampling domains are partitioned into 200 

x 200 m grid cells, or primary units, which are each assigned to a strata designation 

based on habitat type, geographic sub-region, management type (open vs. closed to 

extraction), and depth. The number of primary units to be sampled in each stratum 

type is based on a Neyman allocation scheme, which accounts for the stratum’s size 

and the strata standard deviations for eight focal fish species densities. Once the 

optimal number of primary units per stratum is chosen based on a target precision 

and the capabilities of the agencies, primary units to be sampled are randomly 

selected from a list of all possible primary units for each stratum. Within each 

selected primary unit, two smaller second-stage units are haphazardly selected. Each 

second-stage unit consists of a buddy pair of divers who each perform a Reef Visual 

Census (RVC) which is a 15 m diameter stationary point count. A stationary point 

count method was chosen as the in situ visual sampling method of choice because the 

complexity and spatial extent of Florida Keys habitats often precludes the use of 

linear transects and it has also been found to be a better estimator of exploited fish 

densities in the Florida Keys. The RVC method allows divers to simultaneously 

collect data on the density and size distributions of the entire fish community, as well 
 

 xii 

as information on benthic habitat features. Sampling occurs annually in the summer 

months throughout the Florida Keys reef tract and every even year in the Dry 

Tortugas. Qualified and trained personnel are represented from all participating 

agencies. 

This document first gives an overview of the objectives of the monitoring program, 

which are focused on tracking changes in the abundances, spatial distributions and 

size structures of exploited reef fish species and the reef fish community as a whole. 

These changes are evaluated each year with respect to the habitat features, the 

physical environment and potential management actions that may have affected the 

dynamics of the populations. 

The specifics of the methods used to accomplish monitoring objectives are detailed in 

five Standard Operating Procedures (SOPs). The SOPs are meant to be stand-alone 

documents that can be used at different stages of program implementation. These 

SOPs include A) Statistical Sampling Design, B) Participant Training, C) Field Data 

Collection Methods, D) Data Entry and Proofing, and E) Data Analyses and 

Reporting. This document also includes an appendix that is a glossary of statistical 

symbols and computational formulae used in the sample size calculations, an 

appendix of guides to habitat component identification that can be printed and used 

in the field for reference, an appendix of printable data sheets, and an appendix of 

the benthic habitats of the Florida Keys as defined by the Florida Department of 

Environmental Protection. 
 

 xiii 

Acknowledgements 

This document is the culmination of years of work by many people at each of the 

agencies involved. We’d like to extend special thanks to Andrea Atkinson and 

Benjamin Ruttenberg for their editorial contributions, as well as Alex Chester, Joe 

Kimmel, and Jim Tilmant for their critical review of the document and providing 

valuable comments and advice. We are also greatly indebted to Dr. Mei-Ling Shyu 

and her group at the Department of Electrical and Computer Engineering at the 

University of Miami for their work on the development of the data entry program, 

and Ashley McCrea-Strub for her initial documentation of data entry protocols. We 

also thank all of the participants of the 2008 field season for their patience and 

understanding during the first transitional year of this collaborative effort, and all 

past scientific divers for their important contributions to the collection and 

maintenance of data integrity and reliability. Funding for the development of this 

document and the 2008-2009 sampling season was provided by NOAA’s Coral Reef 

Conservation Program (Grant # NA080AR4320892 SB12) 17RJ12226 SB4, the 

National Park Service (Grant # H5000065040-J2117072985 and # H5000065040-

J5299061017), and NOAA’s Southeast Fisheries Science Center (SEFSC/NMFS Grant 

# NA17RJ12226 SB4). 

Development and application of these mapping and assessment methods over the last 

several years would not have been possible without the technical assistance of John 

Brock at USGS who provided LIDAR data for the Dry Tortugas. A thematic layer 

classification scheme modified by us was originally created by the Florida Marine 

Research Institute (FMRI 1998) from photogrammetric interpretation of aerial 

surveys performed between December 1991 and April 1992 (see Franklin et al. 2004 

for more information). The following funding sources in previous years contributed 

greatly to program development and/or application of these methodologies (in no 

particular order): U.S. Man and the Biosphere Program, National Undersea Research 

Program, Southeast Fisheries Science Center (SEFSC, NMFS), Department of the 

Interior and the National Park Service, Biscayne National Park, Everglades/Dry 

Tortugas National Park, Florida Keys National Marine Sanctuary, U.S. Army Corp of 

Engineers, NOAA Coastal Ocean Program, U.S. Environmental Protection Agency, 

National Fish and Wildlife Foundation, Florida Fish and Wildlife Conservation 

Commission, National Sea Grant College Program, NOAA Biogeography Program, 

Florida Fish and Wildlife Research Institute, the U.S. Fish and Wildlife Service, 

Federal Aid for Sportfish Restoration fisheries independent monitoring (F-43) and 

reef fish (F-7) projects, proceeds from the sale of Florida recreational fishing licenses, 

and NOAA’s Coral Reef Conservation Program.

Cooperative Coral Reef Fish Sampling & Assessment Protocol 

1 

Introduction 

Rationale behind this Document and Reef Fish Monitoring 

This document is meant as a reference and provides guidelines for survey design, 

training, sampling, data entry, data management, analysis and reporting for the 

annual fishery-independent monitoring of reef fish populations within the Florida 

Keys and Dry Tortugas reef ecosystems. This document conforms to the Oakley et al. 

(2003) formatting guidelines for NPS long-term monitoring protocols and is a more 

detailed and updated follow-up to a previously published guide for reef fish 

monitoring (Menza et al. 2006). A collaborative effort among government and 

university groups characterized the first instance of monitoring following these 

specific protocols in 2008, marking the culmination of nearly 30 years of fisheryindependent reef fish monitoring by multiple independent groups in the South 

Florida region.

Reef fish communities are a vital component of coral reef ecosystems, and have major 

economic and ecological importance throughout the world. Reef fish communities 

are the #2 vital sign (“vital sign”, as defined by NPS, being a subset of physical, 

chemical and biological elements and processes of park ecosystems that are selected 

to represent the overall health or condition of park resources or elements that have 

important human values) as ranked out of 69 considered by the seven National Parks 

within the South Florida / Caribbean Network of the National Park Service’s 

Inventory and Monitoring program. Their high ranking is due their significance to 

the functioning of coral reef ecosystems and because of their economic importance. 

These factors make coral reef fish communities a sensitive indicator of both 

ecosystem degradation and/or overexploitation, and they are therefore readily 

affected by management actions. 

Yet despite their significance, the abundance and diversity of reef fish communities 

throughout the Caribbean have seen unprecedented declines due to a combination of 

direct and indirect anthropogenic stressors, including overfishing (Hughes 1994, Ault 

et al. 1998, 2002, Mora 2008). Although the dynamics of reef communities have likely 

been altered for much longer (Jackson et al. 2001), recent increases in recreational 

and commercial fishing in the Florida Keys region have resulted in an overfished 

status for several economically important fish species (Ault et al. 2005a). Loss of 

spawning aggregations, declines in densities, and changes in size structures of 

exploitable fish populations have been documented and are indicators of 

overexploitation (Bohnsack et al. 1994, Ault et al. 1998). Once historically productive 

reef fisheries, such as groupers and snappers, have experienced major declines in 

catch estimates in recent times (Allen and Tashiro 1976, Bohnsack et al. 1994, Ault et 

al. 2005b). Extraction of key species has led to the alteration and/or shortening of 

marine food webs, which can result in a loss of ecosystem functioning and fishery 

resilience (Pauly et al. 2002). 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

2 

Changes in habitat structure and quality are also known to have quantifiable 

repercussions to associated reef fish abundances and diversity (McClanahan 1994, 

McClanahan et al. 1999, Wilson et al. 2006). Coastal development has increased 

sedimentation and has led to a degradation of water quality, with negative 

consequences to fish habitat. At regional-levels, events such as mass coral bleaching 

and disease epizootics have altered the structure and function of reefs by removing 

reef framework-building live coral (Gardner et al. 2003, Miller and Williams 2007) or 

causing coral community shifts such that topographic complexity is lost (Aronson 

and Precht 2001, Graham et al. 2007). Also, the complex life history strategies of 

many reef fish species can span multiple habitats and can include a large-scale 

dispersal phase. Fish assemblages can therefore be characteristic of specific habitats 

and the transport mechanisms among habitats and regions (Kimmel 1985, Chittaro et 

al. 2005). While changes in reef fish abundances and structure may indicate direct 

effects from overfishing, they can also be indicators of the status and trends of the 

system as a whole, and may be a reflection of one or a combination of changes in 

habitat quality, connectivity, fishing pressure and long-term ecosystem resilience. 

If coral reef ecosystems including reef fish abundance and diversity continue to 

decline, the many and diverse benefits provided by reef fish communities will be lost, 

with severe ecological and economic consequences. Monitoring programs, such as 

that described in this document, assess the temporal and spatial patterns of change in 

reef fish communities. Information from these monitoring programs can document 

and provide insight into ecosystem decline and its potential for recovery. 

Fishing and Other Pressures on the Reef 

Florida has been dubbed the “fishing capital of the world” by the Florida state 

legislature (FWC 2007) because its coral reefs support, in large part, the vital fisheries 

and tourism-based economy that generates an estimated $6 billion in economic 

activity per year (Johns et al. 2001). Fishing activities occurring in the waters of the 

Florida Keys are both commercial and recreational, though, in recent decades, 

recreational vessel registrations in South Florida have more than doubled and 

represent a significant portion of the overall fishing impact. Fishing has contributed 

significantly to the depletion of multiple reef fish stocks. Ault et al. (1998) found that 

13 of 16 groupers, 7 of 13 snappers, 1 wrasse (hogfish), and 2 of 5 grunts were 

overfished according to federal (NMFS) standards. In addition, fishing can negatively 

impact reef habitats by the direct removal of key species and non-target species as 

bycatch and by fishing-related habitat damage (Davis 1977, Clark 2006). Other 

impacts that have resulted in the degradation of Florida’s reef habitats and fish 

populations include hurricanes, coral bleaching events, and coastal development due 

to the exponential growth of Florida’s human population and a high volume of 

tourism. Additionally, over the past century activities managing water movement 

through the Everglades has lead to the massive alteration of land drainage patterns in 

the South Florida region. Although intensively managed, the Florida reef ecosystem 

is also considered one of the most stressed ecosystems in the nation (Porter et al. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

3 

1999). Clearly, reef fish populations represent one of the most valuable but also most 

threatened resources of the Florida Keys.

Fishing Management 

Numerous protected areas have been established within the South Florida region 

(Figure 1.1) for various purposes and with various levels of protection against 

resource use and extraction. As with all coastal regions in the state, the Florida Fish 

and Wildlife Conservation Commission and the Federal South Atlantic Fishery 

Management Council are responsible for specific fishery management regulations 

inside and outside of 3 miles of the coast, respectively. The largest designated area is 

the Florida Keys National Marine Sanctuary (FKNMS) which covers a total area of 

9,515 km2

 (3,673 mi2) extending from Miami to beyond the Dry Tortugas. Moving 

from east to west, other protected areas in the “Upper Keys” include Biscayne 

National Park (BNP), Key Largo National Marine Sanctuary, John Pennekamp Coral 

Reef State Park, Biscayne Bay and Card Sound Aquatic Preserve, and Lignumvitae 

Aquatic Preserve. In the Middle and Lower Keys, there are the National Key Deer 

Refuge, Coupon Bight Aquatic Preserve, Looe Key National Marine Sanctuary, the 

Great White Heron National Refuge, and the Key West Wildlife Refuge. To the west 

is the Dry Tortugas National Park (DTNP). In 1997, a network of 23 no take marine 

reserves (NTMRs) were implemented by FKNMS in various areas throughout the 

Keys. These are small areas, comprising a total area of 46 km2

, and they vary in level 

of protection, ranging from accessible only by special permit to the allowance of 

catch-and-release surface trolling. This network was expanded in 2001 in the Dry 

Tortugas with the addition of two NTMRs prohibiting anchoring and extraction: the 

Tortugas Ecological Reserve North and South, which cover approximately 566 km2. 

Most recently, in 2007, the National Park Service designated a 46 square mile area 

within Dry Tortugas National Park as a Research Natural Area, which also prohibits 

anchoring and extraction. 
4

Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Figure 1.1. Designated management zoning of the Florida Keys coastal marine ecosystem, including the Florida Keys National Marine Sanctuary, Biscayne National Park and Dry Tortugas National Park.
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

5 

Background and Objectives

History 

In 1979, the National Oceanic and Atmospheric Administration Southeast Fisheries 

Science Center (NOAA Fisheries) began monitoring reef fish populations at fixed 

sites along the Keys using a scuba-based Reef Fish Visual Census (RVC) approach 

(Bohnsack and Bannerot 1986). Through time the number and spatial distribution of 

these sites expanded. In 1997, the University of Miami’s Rosenstiel School of Marine 

and Atmospheric Science (UM-RSMAS) joined NOAA Fisheries as a partner and 

helped to design and implement a habitat-based stratified random survey design to 

locate RVC sample locations (Ault et al. 2001, 2002). In 1999, the first multi-agency 

high-intensity survey of the Dry Tortugas took place, and approximately 941 RVCs 

were completed using the habitat-based stratified random sampling design. Sampling 

has since continued as a collaborative effort between UM-RSMAS and NOAA 

Fisheries on an annual basis in the Florida Keys and every even year in the Dry 

Tortugas. Publications that documented or have resulted from these efforts are 

numerous and span multiple decades (Table 1.1). 

Meanwhile, in 1998, the Florida Fish and Wildlife Conservation Commission’s 

(FWC) Fisheries Independent Monitoring (FIM) program began a long-term 

monitoring effort of key reef fish populations in the Florida Keys National Marine 

Sanctuary. This effort was aimed at evaluating the relative abundance, size structure, 

and habitat utilization of specific reef fish species that are targeted by commercial and 

recreational fisheries. In 1999 and 2000, FWC did a formal comparison of the two 

most commonly used visual sampling techniques, the stationary point count method 

used by the NOAA/UM-RSMAS group (Bohnsack and Bannerot 1986) and the strip 

transect method (as reviewed in Sale 1997). This comparison determined that the 

stationary point count method was most successful at estimating fish densities, and 

was employed annually within FKNMS in the Florida Keys regions (Colvocoresses 

and Acosta 2007). 

In April 2007, FWC’s Fish and Wildlife Research Institute (FWRI) and the Florida 

Wildlife Legacy Initiative conducted a two day joint workshop to examine Reef Fish 

Visual Census techniques (RVC) for the assessment of population structure and 

biodiversity in waters of South Florida, U.S. The proposed outcome of the workshop 

was to establish a consensus on the most appropriate methodologies to use, and to 

standardize methodologies across the South Florida Region. The workshop goals 

included examining RVC techniques currently in use in South Florida, exploring 

alternative techniques and determining the types and magnitude of biotic change we 

want to detect. The final outcome from this workshop was an agreement between 

FWC-FWRI, NOAA Fisheries, and UM-RSMAS to collaborate on the design and 

conduct of annual coral reef fish monitoring and assessment efforts in the Florida 

Keys coral reef ecosystem. Early in 2008, the National Park Service Inventory and 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

6 

Monitoring Program South Florida and Caribbean Network Office (NPS) added their 

cooperative support. 

The protocols have been developed with the goal of determining trends in reef fish 

populations through time and across space, including determining the effect of 

various management zones on these trends. The protocols have been agreed upon by 

the representatives of the NOAA Fisheries, FWC-FWRI, UM-RSMAS, and NPS. 

These protocols are meant to guide cooperative monitoring efforts that began in 

2008. 

Table 1.1. Publications documenting the development or results of the multi-agency reef 

fish sampling in the Florida Keys and Dry Tortugas. 

Year Publication

1986

Bohnsack, J. A. and S. P. Bannerot. 

A stationary visual census technique for quantitatively assessing community structure of 

coral reef fishes. NOAA Tech. Report NMFS 41. 15 p.

1998

Ault, J. S., J. A. Bohnsack, and G. A. Meester. 

A retrospective (1979-1996) multispecies assessment of coral reef fish stocks in the Florida 

Keys. Fishery Bulletin 96:395-414.

1999

Ault, J.S., Diaz, G.A., Smith, S.G., Luo, J. and J.E. Serafy. 

An efficient sampling survey design to estimate pink shrimp population abundance in 

Biscayne Bay, Florida. North American Journal of Fisheries Management 19:696-712.

1999

Bohnsack, J.A., McClellan, D.B., Harper, D.E., Davenport, G.S., Konoval, G.J., Eklund, A., 

Contillo, J.P., Bolden, S.K., Fischel, P.C., Sandorf, G.S., Javech, J.C., White, M.W., Pickett, 

M.H., Hulsbeck, M.W., Tobias, J.L., Ault, J.S., Meester, G.A., Smith, S.G., and J. Luo. 

Baseline data for evaluating reef fish populations in the Florida Keys, 1979-1998. NOAA 

Technical Memorandum NMFS-SEFSC-427. 61p.

2001

Ault, J. S., S. G. Smith, G. A. Meester, J. Luo, and J. A. Bohnsack. 

Site characterization for Biscayne National Park: assessment of fisheries resources and 

habitats. NOAA Technical Memorandum NMFS-SEFSC-468. 185 p.

2002

Ault, J. S., S. G. Smith, J. Luo, G. A. Meester, J. A. Bohnsack, and S. L. Miller. 

Baseline multispecies coral reef fish stock assessment for the Dry Tortugas. NOAA 

Technical Memorandum NMFS-SEFSC-487. 117 p.

2002

Bohnsack, J. A., D. E. Harper, D. B. McClellan, D. L. Sutherland and M. White. 

Resource survey of fishes within Looe Key National Marine Sanctuary, 1983. NOAA 

Technical Memorandum NOS-NCCOS-CCMA-160 and NMFS-SERSC-478. 327 p.

2003

Ault, J. S., D. B. Smith, E. C. Franklin, J. Luo, and J. A. Bohnsack. 

Sampling design analysis for coral reef fish stock assessment in Dry Tortugas National Park. 

Final Report, National Park Service Contract No. H5000000494-0012. 87 p.

2003

Franklin, E. C., J. S. Ault, S. G. Smith, J. Luo, G. A. Meester, G. A. Diaz, M. Chiappone, D. 

W. Swanson, S. L. Miller, and J. A. Bohnsack. 

Benthic habitat mapping in the Tortugas region, Florida. Marine Geodesy 26:19-34.

2004

Bohnsack, J. A., J. S. Ault, and B. Causey. 

Why have no-take marine protected areas? Aquatic Protected Areas as Fisheries 

Management Tools 42:185-193.

2005

Ault, J. S., J. A. Bohnsack, S. G. Smith, and J. G. Luo. 

Towards sustainable multispecies fisheries in the Florida, USA, coral reef ecosystem. 

Bulletin of Marine Science 76:595-622.

cont’d 

 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

7 

 

2005

Ault, J. S., S. G. Smith, and J. A. Bohnsack. 

Evaluation of average length as an estimator of exploitation status for the Florida coral-reef 

fish community. Ices Journal of Marine Science 62:417-423.

2006

Ault, J. S., S. G. Smith, J. A. Bohnsack, J. G. Luo, D. E. Harper, and D. B. McClellan. 

Building sustainable fisheries in Florida's coral reef ecosystem: Positive signs in the Dry 

Tortugas. Bulletin of Marine Science 78:633-654.

2007

McClellan, D. B. and D. E. Harper (eds.). 

Compilation of selected unpublished RVC studies conducted by the Reef Resources Team, 

1985-2002. NOAA Technical Memorandum NMFS-SEFSC-561. 104 p. 

2008

Ault, J.S., Smith, S.G., Luo, J., Monaco, M.E., and R.S. Appeldoorn. 

Length-based assessment of sustainability benchmarks for coral reef fishes in Puerto Rico. 

Environmental Conservation 35(3):221-231.

2008

Bartholomew, A., J. A. Bohnsack, S. G. Smith, J. S. Ault, D. E. Harper, and D. B. McClellan. 

Influence of marine reserve size and boundary length on the initial response of exploited 

reef fishes in the Florida Keys National Marine Sanctuary, USA. Land. Ecology 23:55-65. 

Measurable Objectives of Monitoring 

The objective of the monitoring effort is to document reef fish community 

composition, abundance, and size structure and determine changes in these 

parameters over time within the Florida Keys region, specific sub-regions, and inside 

vs. outside different management zones. Special attention is also paid to specific 

exploited reef fish species. While each agency may have their own specific objectives 

that can vary by sampling year, this overall objective is agreed upon by all agencies 

and guides the monitoring effort. 

The sampling design is optimized with respect to eight focal species which are all 

important commercial and recreational fisheries in the South Florida region: white 

grunt (Haemulon plumieri), bluestriped grunt (H. sciurus), hogfish (Lachnolaimus 

maximus), mutton snapper (Lutjanus analis), gray snapper (L. griseus), yellowtail 

snapper (Ocyurus chrysurus), red grouper (Epinephelus morio), and black grouper 

(Mycteroperca bonaci). These species are the most prominent examples of overfished 

high-level predators in the Florida Keys (Ault et al. 1998). The sample design is 

optimized with respect to these species, but because all fish species are recorded, 

monitoring efforts also obtain important information about many other non-targeted 

species, the overall trophic structure, and form the scientific basis for effective 

management actions.

 

Sampling Design 

Rationale for Selecting This Sampling Design over Others 

There are many ways to select a sample from a population, but if information is 

known about a population, a selection method can be devised that provides more 

accurate and precise survey estimates. A simple random sampling design is 

appropriate for situations where there is no spatial structure in the variance of the 

investigated species or when little information is available upon which to logically 

stratify the sampling effort. But reef fish are typically heterogeneous with respect to 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

8 

geographic distribution and vary in space according to certain environmental 

covariates, such as depth and vertical relief. Knowing this, maps of environmental 

covariates can be used to effectively divide the sampled area into strata. Random 

samples can then be allocated into these strata based on each stratum’s proportional 

area and the variance structure of the population within that stratum. This type of 

stratified random sampling design is capable of more effectively and efficiently 

sampling a reef fish population than a simple random sampling design (Cochran 

1977). 

As documented in detail in SOP A, existing benthic habitat maps and data collected 

from previous reef fish sampling are used to optimize sampling according to this 

protocol. Site selection is based on a two-stage stratified random sampling design 

which uses the variance structure of collected data to select sites more efficiently 

from the sampling domain. Certain benthic habitat measures are strongly associated 

with principal reef fish population and community metrics. These measures include, 

depth, the degree of vertical relief (e.g., rugosity, complexity), and the degree of 

patchiness (e.g., amount of soft bottom substrate interspersed among reef structures) 

of the hardbottom substrate (Ault et al. 1999; Ault et al. 2002; Franklin et al. 2003; 

Ault et al. 2005a). The survey domain (i.e., the Florida Keys reef tract and the Dry 

Tortugas reef shelf) is partitioned into 200 x 200m grid cells called primary units, and 

each primary unit is defined by different strata including region, habitat, depth, and 

management level. The number of samples (primary units) allocated to these strata is 

based on the variance structure of fish species densities developed from previous 

sampling. Applying a stratified random method such as this instead of a simple 

random design has been shown to dramatically improve sampling efficiency (Ault et 

al. 1999; Ault et al. 2005a). A benefit of this sample design used here is that there is a 

clearly defined sample frame, with non-overlapping sample units that have a known 

chance of selection. This is essential for data analysis under sampling theory 

(Cochran 1977). These sample units are also updateable if the original designation is 

inaccurate, or as habitats change or better information becomes available. 

A stationary point count methodology was chosen as the fisheries-independent in situ 

visual sampling method versus other fishery-independent methods for several 

logistical reasons. Other methods include image-based methods (Risk and Risk 1997), 

aerial surveys (Sale and Sharp 1983), and in situ methods such as belt transects (Brock 

1954) and roving diver surveys (Pattengill-Semmens and Semmens 2003). For the 

purposes of this survey, stationary point counts are less costly than image-based 

analysis (Risk and Risk 1997) and provide more detailed and quantitative information 

than aerial or roving diver surveys. In comparison with belt transects, stationary 

point counts allow divers to simultaneously collect data on the density and size 

distributions of the entire fish community, with the exception of rare cryptic species 

(Bohnsack and Bannerot 1986). Most transect methods only target one or a limited 

number of specific fish groups and were found to be biased in their estimates of fish 

density and frequency of occurrence (Demartini and Roberts 1982; Sale and Sharp 

1983). Also, the Florida Keys reef tract encompasses a variety of habitat types, 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

9 

including some that are restricted in size, such as patch reefs, artificial reef structures, 

and areas that have been impacted by ship groundings. These habitats preclude the 

use of linear transects. Most recently, work in the Florida Keys by Colvocoresses and 

Acosta (2007) found higher, more accurate density estimates for the targeted fish 

groups using the point count versus belt transect method. 

Sampling Domain 

The Florida Keys reef tract consists of a system of reef habitats that extend 

approximately 370 km from Key Biscayne near Miami to the Dry Tortugas. The reef 

tract lies parallel to the Straits of Florida with the Florida current to the south and 

Florida Bay to the north. The reef tract encompasses a variety of habitats in addition 

to coral reefs, including mangrove stands, sea grass beds, lagoons, and freshwater 

marshes and estuaries. These diverse habitats are known to support more than 500 

species of fish (Stark 1968), many of which, including important commercial and 

recreational fisheries species such as snappers and groupers, utilize a range of 

habitats throughout their life history (Lindeman et al. 2000). However, 389 of the fish 

species are primarily associated with coral reef habitat (Stark 1968). Therefore, in 

order to increase efficiency and because the RVC methodology is optimized for reef 

habitat (Bohnsack and Bannerot 1986) the sampling domain for this protocol does 

not include the seagrass, mangrove, or other, non-reef habitats that lie within the 

region. Instead, the monitoring program for which this protocol was developed 

specifically targets reef fish populations and their primary associated coral reef 

habitats. Therefore, the sampling domain for reef fish monitoring in the Florida Keys 

and Dry Tortugas consists of all coral reef habitat stretching from Biscayne National 

Park to the lower Florida Keys as well as the shallow banks of the Dry Tortugas. 

Sampling Frequency and Replication 

Based on current funding allocation, sampling in the FKNMS and BNP will occur 

once annually and once in DTNP every other year. Optimally, sampling should occur 

in DTNP annually when funding permits. Available resources from each agency may 

vary extensively through time but the methodology does not require a fixed sample 

size. Therefore, the target sample size can be adjusted based on resources, goals, and 

participation, with the understanding that this will affect the precision of the 

sampling results. 

Number and Location of Sampling Sites 

Site locations are determined before each sampling season using a stratified random 

sampling design (rationale and details in SOP A). Stratification is based on 

geographic sub-region (e.g., upper Keys, middle Keys, lower Keys), management 

zone, depth, and habitat class. Digital layers for each of these components are 

contained within a geographic information system (GIS) and are used to delineate the 

survey domain, strata, and sample units. In order to control for spatial variation in 

population metrics, a two-stage sampling design following Cochran (1977) is used 

where 200 m by 200 m (40,000 m2

) grid cells serve as primary sample units, and two 

second-stage samples are randomly distributed within each primary unit. Each 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

10 

second-stage sample consists of a diver buddy team (typically two divers, sometimes 

more), with each diver executing a stationary point count. Therefore, at least four 

scientific dives are completed within each primary unit, but the average is taken of 

data for each buddy team, resulting in two samples per primary unit. The number of 

sites to be sampled in each stratum follows a Neyman allocation scheme, in which 

allocation is based on the proportional area of the stratum and the variance structure 

of the population metric (i.e., fish density) among strata. This analysis is performed 

using previous years’ data and under different levels of precision for the eight focal 

species (listed in Section 1.3). The final target number of primary sample units 

represents a balance between achieving an acceptable precision level in estimating 

abundances for each of the eight species as well as the capacities of the agencies to 

sample. 

The actual primary units and second-stage units are then selected for sampling based 

on a two-stage process (details in SOP A). The first stage of the sample selection 

process consists of randomly selecting primary units from the total possible primary 

units for each stratum. Then, two second-stage units are randomly selected from the 

list of total possible second-stage sample units within the selected primary unit. 

Frequency and Timing of Sampling 

After the list of sample sites is generated each year, representatives from the 

participating agencies will meet and assign responsibility for each specific sampling 

site to an agency. Thereafter, it is the responsibility of the agency to determine when 

each site will be surveyed. A list of alternate sites will also be generated and 

distributed in case sites are not accessible (e.g., outside safe diving limits). Surveying 

should occur sometime between May and September each sampling season. All sites 

should be surveyed during these summer months where minimum winds will not 

interfere with diving logistics and so that possible seasonal effects do not impact 

assessments of the status of the fish populations through time. 

Level of Change That Can Be Detected for Sampling Being Instituted 

The sampling design is targeted to allow statistically valid comparisons of population 

metrics through time and in space for selected economically and ecologically 

important reef fish species and their life stages (listed in Section 1.3). A second major 

goal is to be able to determine the efficacy of management zones in protecting and 

enhancing stocks of these species, therefore optimal sampling allocation distributes 

sites in protected and unprotected areas to allow for direct comparisons between 

them. Focal species include those targeted heavily by recreational and commercial 

fisheries. These species have seen significant declines in recent years and are 

currently considered overfished in South Florida (Ault et al. 2005a). The major 

population metric used for sampling optimization is mean stratum fish density (Dst), 

and the coefficient of variation (CV) of this metric for each species is used as a 

dominant performance measure (SOP A). Each year, the precision of sampling will 

change depending on the capacity of the agencies to perform the surveys, but 

typically a CV of <30% is achievable for the dominant species investigated. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

11 

Field Methods 

Field Season Preparations and Equipment Setup 

In preparation for each field season, agency groups will meet and determine the 

abilities and needs of each group for participation in field sampling. At this time, a 

schedule will be determined for all training activities (details in SOP B) that must take 

place prior to the start of sampling. All participants are personally responsible for 

ensuring their compliance with diving authorization requirements. Each agency will 

be responsible for verifying that their participants conform to the requirements and 

that they are equipped with all necessary sampling gear for that season. Equipment 

details can be found under the section “Equipment” in SOP C. Sample numbers, 

locations, and the agency/group responsible for each sample will be determined prior 

to the start of the field season (SOP A). 

Sequence of Events during Field Season 

At the start of the field season, each agency will be provided a list of sites which they 

will be responsible for sampling to the best of their abilities. Sampling schedules will 

likely vary by agency and due to considerations of weather and equipment. A list of 

alternate sites will also be provided that can be used in cases where sites are not 

accessible or if an agency has met their goal and is capable of additional sampling. As 

many sites as possible should be surveyed during a day: this goal should determine 

the assembly of sampling teams and location of sites that are in the same vicinity. 

Data that are collected are the responsibility of the participants and their respective 

agencies and should be entered and catalogued by the end of the field season 

following the methods detailed in SOP D. Preferably, data should be entered 

immediately upon return from the field (or within 1 day), as this tends to reduce error 

in data entry. However, all data must be entered at least by the end of the field 

season. Once all data are catalogued, each agency will follow proofing steps before 

submitting the data for final verification and entry into central database (SOP D). 

Details of Making Observations 

The RVC method used in these surveys is based on the stationary point count method 

of Bohnsack and Bannerot (1986), with some modifications and additions. The 

rationale and details of making observations in the field is covered in SOP C. In 

general, however, two sets of paired surveys take place per site, optimally separated 

by 20-60 m distance but within the same primary unit (200 x 200 m grid cell). Diver 

deployment can occur either by live boating or by anchoring. Live boating is 

preferred when 4-6 divers are aboard, while anchoring is best when the team consists 

of 3-4 members. Each buddy team will carry a reel with line attached to a surface 

buoy and surface GPS unit to record the location of the actual sample. For each site, 

three types of data are taken, including: 1) Field/Boat Log form data, which records 

where, when and by whom sites were sampled, 2) Water Quality/Environmental Log 

data, which are records of the water quality and environmental data associated with 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

12 

each set of paired surveys, and 3) fish/habitat data, which are the RVC-specific data 

recorded by each diver. 

Post-collection Data Sheet and Logs Processing 

Once data collection is completed and all divers are aboard, initial QA/QC should 

include discussions between buddy teams to ensure agreement on main variables 

(e.g., habitat characteristics, visibility, current). Data sheets should be maintained 

securely while on board, and once on land, copies of data sheets should be made and 

then distributed to data collectors for data entry. Data should then be entered 

according to the protocols detailed in SOP D. 

End-of-Season Procedures 

At the end of the season, each agency should follow their respective methods for 

cataloging and backing up data. All data should be proofed following methods in SOP 

D and then submitted to UM-RSMAS for final verification and use in future sample 

allocation (as described in SOP A). 

Data Handling, Analysis and Reporting 

Data Entry, Verification and Editing 

Data collected for each stationary point count should be entered via the RVC Data 

Entry Program following the methods outlined in SOP D. Data for the Field/Boat log 

and Water Quality/Environmental log should be kept on an agency-specific Excel 

spreadsheet. Initial data entry and proofing is the responsibility of the participants 

who collected the data in field. At the end of the field season, designated agencyspecific data managers will be responsible for assuring that all data collected have 

been entered and proofed (as described in SOP D). Each diver must maintain a 

minimum level of accuracy as described and defined in SOP D. Data managers will 

then distribute their agency’s data to the NOAA and UM-RSMAS data managers, who 

will be responsible for data verification, storage, and distribution following steps in 

SOP D. 

Recommendations for Routine Data Summaries and Statistical Analyses 

The range and types of statistical analyses that should be performed to assess the 

status and dynamics of reef fish populations and communities depends on the 

specific management questions and resource goals to be addressed. These questions 

and goals may change through time or vary by agency, but there are some 

fundamental metrics that should be generated after each sampling season which are 

outlined in SOP E. These analyses utilize a range of survey data types (abundance, 

size, taxonomic identification), and allow for the assessment of the status and trends 

of reef fish communities and populations over time and in relation to specific 

sustainability metrics. First, a basic descriptive ecological analysis, including species 

inventories and calculations of biodiversity indices, is recommended. For the eight 

focal species (Haemulon plumier, H. sciurus, Lachnolaimus maximus, Lutjanus analis, 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

13 

L. griseus, Ocyurus chrysurus, Epinephelus morio, and Mycteroperca bonaci) 

calculations of the fish stock status indices outlined in SOP E are also recommended, 

and details describing how to assess change in the these metrics provided in SOP E. 

Personnel Requirements and Training 

Roles and Responsibilities 

At the start of each field season, responsibilities for sampling will be delegated among 

the participating agencies. Each agency will provide participants, equipment, and 

facilities to the best of their ability depending on their budgeting constraints and 

responsibilities to other projects for that year. All agencies will designate a data 

manager, a chain of command, and points of contact for dealing with scheduling and 

logistical considerations, as well as for questions regarding procedures and policies. 

Points of contact should be clarified so that all participants, regardless of agency, are 

aware of who should be contacted in the event of a question or issue. 

Qualifications 

All participants must be trained in reef fish identification as well as in the ability to 

make the necessary observations (training requirements are covered in the 

subsequent section). All participants must also be certified to SCUBA dive in open 

water by a recognized and licensed organization (e.g., NAUI, PADI) and for work in 

the Dry Tortugas must also possess a certification to use enriched-oxygen (NITROX). 

Participants must be in compliance with their agency’s dive safety regulations. 

Depending on the agency in charge of the diving operations, reciprocity may need to 

be exchanged. In the Dry Tortugas, it is the responsibility of the agency in charge to 

confirm prior to operations that participating divers are cleared to dive. 

Training 

Training is a critical component of the RVC monitoring program, and should 

incorporate both initial and annual refresher training components. Participants 

should be capable of accurately identifying and estimating sizes of reef fish that are 

encountered on the Florida Keys reef tract. Participants should also be familiar with 

the habitat assessment techniques and benthic categories that are included in the 

method and detailed in SOP C. Annual out-of-water training meetings and in-water 

training activities will be held each year before sampling commences as detailed in 

SOP B. Out-of-water meetings will be held either jointly or independently depending 

on the needs of each agency and will consist of overviews of sampling design, 

logistics, RVC methods, habitat characteristics, and data entry and proofing. Inwater training will be organized and executed by each agency independently, 

although exchange of personnel among agencies is encouraged. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

14 

Contacts 

Contacts for questions regarding: 

Statistical design: 

 Jerald Ault (RSMAS-UM) 305-421-4884, jault@rsmas.miami.edu 

Steve Smith (RSMAS-UM) 305-421-4783, steve.smith@rsmas.miami.edu 

Training methods: 

Natalia Zurcher (RSMAS-UM) 305-421-4164, nzurcher@rsmas.miami.edu 

Data collection methods: 

 Fish: Natalia Zurcher (RSMAS-UM) 305-421-4164, nzurcher@rsmas.miami.edu 

Habitat: Marilyn Brandt (RSMAS-UM) 305-421-4736, 

mbrandt@rsmas.miami.edu

Data entry (RVC2.3.exe) and proofing: 

Natalia Zurcher (RSMAS-UM) 305-421-4164, nzurcher@rsmas.miami.edu 

Data analysis and reporting: 

Jerald Ault (RSMAS-UM) 305-421-4884, jault@rsmas.miami.edu 

Steve Smith (RSMAS-UM) 305-421-4783, steve.smith@rsmas.miami.edu 

Interagency collaboration: 

 Jerald Ault (RSMAS-UM) 305-421-4884, jault@rsmas.miami.edu 

James Bohnsack (NOAA-Fisheries) 305-361-4252, Jim.Bohnsack@noaa.gov 

John Hunt (FWC-FWRI) 305-289-2330, John.Hunt@MyFWC.com 

Matt Patterson (NPS) 305-252-0347, Matt_Patterson@nps.gov 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure A: Statistical Sampling Design 

A-1

Standard Operating Procedure A: 

Statistical Sampling Design 

(Version 1.0) 

Revision History Log 

Previous Revision 

No.

Revision Date Author Change 

Made

Reason for 

change

New Version 

No.

 

A.1 Introduction 

This SOP outlines a two-stage stratified random sampling allocation scheme that was 

been developed over the last decade and has been successfully applied in order to 

estimate important metrics for reef fish populations in the Florida Keys and Dry 

Tortugas (e.g., Ault et al. 1999, Ault et al. 2002, but see also Table 1.1). These methods 

are also useful for estimating population abundances in other regions (Ault et al. 

2008) and for other types of marine populations (Smith et al. in prep a). 

This sampling scheme includes stratifying the sample domain based on habitat, subregion, management zone, and depth and then follows a Neyman (or optimal) 

allocation in which sample units are allocated according to both stratum size and the 

strata standard deviations of specific fish species densities. This scheme increases the 

efficiency of sampling by allocating greater sampling effort to those strata that are 

larger and more variable while smaller, less variable strata receive less effort. 

A.2 Stratification 

The Florida Keys survey domain includes all mapped area of live coral habitat less 

than 33m depth between Miami and Key West. Similarly, the Dry Tortugas survey 

domain contains all mapped coral habitats shallower than 33 m but which are located 

on three distinct bank or atoll-like formations, including Dry Tortugas National 

Park, Tortugas Bank and Little Bank, and Riley’s Hump. To control for spatial 

variation in population abundance metrics, the survey domain is divided into strata 

based upon: (1) habitat characteristics and depth; (2) geographic sub-region; (3) 

management zone (see Figure 1.1 for management areas). The reef habitat 

classification scheme accounts for features that correlate with reef fish distributions, 

including topographic complexity (low-relief, mid-relief, high-relief), and the 

proportion of sand interspersed among hard-bottom structure (e.g., isolated reef, 

spur and groove, continuous reef). In the Florida Keys sampling, depth (shallow: 0-6 

m, mid-depth: 6-18 m, deep: 18-33 m) is also used to distinguish strata. The 

geographic sub-regional stratification variable (upper, middle, and lower Keys, and 

Dry Tortugas) and cross-shelf position in the Florida Keys (e.g., Hawk’s Channel 

inshore, Hawk’s Channel mid-channel; as described by FMRI 1998, included as 

Appendix 4) are used to account for oceanographic and geological features that 

influence the distribution, community dynamics, and biotic composition of reefs 

(Marszalek et al. 1977; Shinn et al. 1977). Management zones (i.e., no-take marine 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure A: Statistical Sampling Design 

A-2

reserves) are incorporated as a third stratification variable and delineate areas open 

or closed to consumptive activities. Strata defined for the Florida Keys and Dry 

Tortugas are listed in Tables A.1 and A.2. 

A geographic information system (GIS) containing digital layers for benthic habitat 

(FMRI 1998, included as Appendix 4), bathymetry (NGDC 1998), and no-take marine 

reserve boundaries (FKNMS, Marathon, Florida) is used to facilitate delineation of 

the sampling survey domain into strata. Map resolution is such that the survey 

domain (i.e., the entire Florida Keys reef tract and the three bank formations of the 

Dry Tortugas) is divided into a grid with individual cells of size 200 m by 200 m 

(40,000 m2), each cell designated as belonging to a specific stratum (e.g., Figure A.1). 

These grid cells are designated as primary sample units. Primary sample units are 

further subdivided into 15 m diameter visual census circular plots that can be 

sampled by divers which are the second-stage sample units. 

Figure A.1. Cross-shelf distribution of coral reef and hard-bottom habitat classes in the 

vicinity of Western Sambo NTMR overlain with the 200 m by 200 m primary unit sampling 

grid. 

The conceptual layout of this two-stage stratified random sampling (StRS) design is 

shown (Figure A.2), and survey design symbols and definitions are provided in 

Appendix 1. The survey domain A is divided into h strata. Each stratum is further 

subdivided into primary sample units i, and each primary unit is again subdivided 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure A: Statistical Sampling Design 

A-3

into second-stage sample units j. Note that each primary and second-stage sample 

unit contains a fixed amount of area; thus, the sum of second-stage sample units 

within primary units of all strata approximately equals the total area of the survey 

domain. The number of possible primary sample units (Nh) calculated for each 

stratum for the Florida Keys and Dry Tortugas survey domains are given in Tables 

A.1 and A.2. 

Figure A.2. Conceptual diagram of the sampling domain and sample units for a twostage stratified random survey design. Symbols are defined in Appendix 1. 
A-4

Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure A: Statistical Sampling Design Table A.1. Total possible primary units (

Nh) in statistical strata defined by sub-region (e.g., Lower Keys, Middle Keys), crossshelf zone, habitat class and depth, and management zone (“prot” = protected, “unprot” = unprotected) in the sampling 

surveys of the Florida Keys. 

Lower Keys Middle Keys Upper Keys Biscayne 

Stratum Cross-Shelf Zone Habitat Class (depth) prot unprot prot unprot prot unprot unprot 

1 Hawk's Channel, Inshore Mid-relief isolated reef (0-6 m) 30 114

0 31

0 76 166 

2 Hawk's Channel, Mid Channel Mid-relief isolated reef (0-6 m) 38 840

0 165 21 706 1366 

3 Hawk's Channel, Offshore Mid-relief isolated reef (0-6 m) 74 458

0 94 11 1025 144 

4 Hawk's Channel, Offshore High-relief spur and groove (0-6 m)

0

0

0

0 20 78 0 

5 Forereef Low-relief continuous reef (0-6 m)

0 71 27 176 46 775 276 

6 Forereef Low-relief continuous reef (6-18 m) 26 576

0 311 56 662 219 

7 Forereef High-relief spur and groove (0-6 m) 57 49 7 3 89 34 33 8 Forereef Low-relief spur and groove (6-18 m) 32 684 25 807 95 709 317 9 Forereef High-relief spur and groove (18-33 m) 53 535

0 74 27 468 315 

10 Forereef Low-relief isolated reef (0-6 m) 7 26 7 128 10 217 220 11 Forereef Low-relief rubble (0-6 m) 36 67

0 62 26 95 80 

Table A.2. Total possible primary units (

Nh) in statistical strata defined by sub-region (Tortugas Bank and Dry Tortugas 

National Park), habitat class, and management zone (“prot” = protected, “unprot” = unprotected) in the sampling surveys of the Dry Tortugas. 

Tortugas Bank Dry Tortugas National Park 

Stratum Habitat Class prot unprot prot unprot 

1 Low-relief continuous reef 1269 1111 1087 1301 2 Mid-relief continuous reef 23 12 56 164 3 High-relief continuous reef 255 26 31 15 4 Low-relief isolated reef 18 28 419 418 5 Mid-relief isolated reef 275 126 360 401 6 High-relief isolated reef 20

0 20 3 

7 Low-relief spur and groove

0

0 17 261 

8 High-relief spur and groove

0

0 22 86 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure A: Statistical Sampling Design 

A-5

A.3 Sample Allocation 

The two-stage stratified random design increases the efficiency of sampling by 

effectively stratifying the entire domain based on variables (e.g., habitat 

characteristics, depth, and management) that influence the variability of fish 

population densities. With this stratification scheme in place, the sample size 

necessary to achieve a specified level of precision can be calculated based on existing 

data. This type of allocation scheme is termed a Neyman (or optimum) allocation 

scheme (Cochran 1977) and it is used to determine the number of primary units to 

be sampled within each stratum. 

First the total number of primary units that would be required to achieve a specified 

variance under an optimal allocation scheme, n*, is calculated for each species. 

Derived from Cochran (1977), this optimal allocation of primary units for a given 

target variance, V, of fish density, Dst (individuals m-2), is calculated as: 

 

[ ] ∑

∑ ∑ ∑

+

⎟

⎟

⎠

⎞

⎜

⎜

⎝

⎛

+

=

h h

hh st

h h uhhh

hh

h

uhh uhh

N

sw DV

swm

sw

swsw

n 2

1

2

2

2

2

*

* (Eq. A-1) 

In Equation A-1: 

2

1h s is the sample variance among primary units i in stratum h and 22h s is the sample 

variance among second-stage units j in stratum h: 

1

)(

2

2

1 −

−

=

∑

h

i

hhi

h

n

DD

s (Eq. A-2) 

∑

∑

⎥

⎥

⎥

⎦

⎤

⎢

⎢

⎢

⎣

⎡

−

−

= i hi

i

hi hij

h

h

m

DD

n

s

1

)( 1

2

2

2 (Eq. A-3)

where Dhi is the mean density in primary unit i in stratum h, Dh is mean density in 

stratum h, Dhij is density in second-stage unit j in primary unit i in stratum h, and nh is 

the number of primary units sampled in stratum h. 

Also in Equation A-1, suh is the sample standard deviation in stratum h: 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure A: Statistical Sampling Design 

A-6

h

h

uh h M

s

ss

2

2 2

1 −= (Eq. A-4) 

and wh is the weighting factor for each stratum, calculated as its proportion of the 

overall survey domain (or sampling frame) where Nh is the total possible number of 

primary units in stratum h based on its total area, and Mh is the total possible number 

of second-stage units in a primary unit: 

∑

=

h

hh

hh

h MN

MN

w (Eq. A-5) 

Finally, in Equation A-1, m*h is the optimal number of second-stage units within a 

primary unit calculated as: 

uh

h

h

s

s

m

2

2 * = (Eq. A-6) 

The value of m*h has consistently been estimated as 2 by these monitoring efforts 

(Ault et al. 2002), and therefore this value is used in all calculations of n*. 

The target variance for a given species (V[ Dst ] in Eq. A-1) is calculated based on a 

target coefficient of variation (CV), which is an easily expressed standard measure of 

performance (Cochran 1977). The CV of a sample is actually the standard error 

expressed as a proportion (or percentage) of the mean: 

st

st

st y

ySE yCV ][ ][ = (Eq. A-7) 

Since the 95% confidence interval for a population metric is approximately two 

standard errors above and below the mean, the ability to statistically detect a 

difference translates to approximately ±2 times the CV. Therefore, if mean fish 

density in a sub-region has a CV of 50%, then a 100% change in the population, or a 

doubling of the population, can be detected. 

 In calculations of the target variance for fish density under this design, Dst is used as 

st y in Eq. A-7, which is mean fish density under a stratified design. Using a target CV, 

the target variance in Eq. A-1 is: 

2

⎟

⎠

⎞ ⎜

⎝

⎛ ⋅ ⎥⎦

⎤ ⎢⎣

⎡ = st DDCVV st (Eq. A-8) 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure A: Statistical Sampling Design 

A-7

The optimal number of primary units to sample in each stratum is then calculated as: 

* * h uh

h

h uh

h

w s

n n

w s

⎛ ⎞ ⎜ ⎟ = ⋅⎜ ⎟ ⎜ ⎟ ⎝ ⎠ ∑ (Eq. A-9) 

These calculations are made for multiple levels of desired variance for each species. 

They are then compared among species and also with the total capacity of the 

cooperative sampling group. A final target n* is chosen that will accomplish the best 

possible balance between achievable precision for the most number of exploited 

species and the capabilities of the agencies. 

All variable names and equations are also listed in Appendix 1. 

A.4 Sample Unit (Location) Selection 

Once the total number of primary units is determined, the actual selection of sites is 

carried out in two stages. First, the primary units i to be sampled per stratum are 

randomly selected from the complete list of Nh units within a stratum using a discrete 

uniform probability distribution, which assigns equal selection probability to each 

primary unit (Law 2007). Second, when in the field, two second-stage units j are 

haphazardly chosen from the total possible Mh units within a primary unit based on 

the distribution of target habitat within the primary unit and diving safety 

considerations. 

In concern for dive safety and because of possible spatial autocorrelation, each diver 

station (i.e., second-stage unit) consists of the average of combined stationary 

point count (RVC) estimates from the buddy pair for each metric recorded. 

Therefore, each diver station (i.e., second-stage unit) is sampled by two individual 

divers (i.e., a buddy pair), for a total of 4 scientific dives within each primary unit (2 

scientific dives per second-stage unit, two second-stage units sampled) under normal 

operations. The size of an individual primary sampling unit allows divers to swim to 

the location of any given second-stage sampling unit from a moored vessel. 

In theory, the selection of second-stage units within each primary unit should be 

random and not haphazard, but this is not practical in a field sampling situation. The 

authors have examined the distribution of secondary units within primary units using 

past field data and the distribution of second-stage units was biased towards the 

center point (Figure A.3). Therefore, the probability that a second-stage unit would 

be selected within a primary unit was not uniform across all second-stage units, and 

there was an increased probability of sampling secondary units near the center of the 

primary unit. This is likely due to a combination of the resolution of the grid and the 

distribution of habitat within primary units, and there is a possibility that spatial 

autocorrelation could affect the results. However, it is unlikely that this affects the 

overall results of sampling, but efforts are underway to evaluate its impact. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure A: Statistical Sampling Design 

A-8

Figure A.3. Percent of all second-stage units (adjusted for area) sampled in the Florida 

Keys (2003-2007) which fell within different distances (m) from the primary unit center. 

A.5 Example 

Reef fish populations are highly variable among species and within species among life 

history stages. Therefore, calculations should be made independently by species and 

life stage, and by taking into account the historical sampling design used to collect the 

data as well as the established and possible future goals of each targeted area in 

question. The n* calculated in this example is a baseline, but by no means should it 

be treated as a constant to be used for all future surveys. Optimal sampling 

allocation should be recalculated iteratively, and take into account acquired 

knowledge of the system, future data, and/or improved stratification methods. 

The suggested analyses focus on eight species of reef fish commonly targeted by 

commercial and recreational fisheries on Florida Keys reefs: white grunt (Haemulon 

plumieri), bluestriped grunt (H. sciurus), hogfish (Lachnolaimus maximus), mutton 

snapper (Lutjanus analis), gray snapper (Lutjanus griseus), yellowtail snapper 

(Ocyurus chrysurus), red grouper (Epinephelus morio), and black grouper 

(Mycteroperca bonaci). Because these species are known to exhibit habitat-specificity 

based on life stage which may influence their abundances across spatial gradients, 

each analysis is done separately by life stage (juveniles and adults). The current 

sampling allocation strategy is targeted towards these species because of their 

economic importance. However, these species are found in relatively low abundance 

throughout the Keys region and are considered overfished (Ault et al. 2005a). 

Therefore, if a sampling strategy is doing an adequate job of sampling for these lowabundance species, it is also likely doing an adequate job of sampling for other, more 

abundant, species such as the major herbivorous fish groups (e.g., parrotfishes, 

surgeonfishes) that may be important ecologically but not necessarily economically. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure A: Statistical Sampling Design 

A-9

To show this, the example has also calculated optimal sample numbers for an 

additional selection of non-targeted species. 

Below are the results of a performance analysis of reef fish sample data taken in 

Biscayne National Park (BISC), which is then used to calculate n*. The analysis 

focused on calculating n* for BISC with the goal of detecting differences in fish 

density for targeted species/life stages among years within BISC. To do this, 

sample data from Keys-wide annual sampling between 2005 and 2007 were analyzed 

using equations A-1 and A-9 with region as the stratum in calculations. Results are 

presented as tables with n* values for specified CV values, and CV versus n* graphs 

with actual sample sizes and CVs calculated from sampling in specific years. These 

calculations were compared with the number of primary units actually sampled in 

previous surveys (Table A.3). Also, a comparison was made of the CV achieved with 

current sampling and that which could be achieved with additional sampling. In 2008, 

68 primary units were sampled in BISC and approximately 6 samples were made per 

day. If an additional 10-11 days of sampling were assumed, this would approximately 

double the number of primary units sampled. Therefore the comparison of current 

CV achieved with potential CV attainable is based on a doubling of sampling effort to 

n = 136. 

Table A.3. Primary units (n) sampled by sub-region and year. 

Sub-region 2003 2004 2005 2006 2007 2008

Biscayne National Park 70 40 41 55 59 68

Upper Keys 96 70 88 110 84 103

Middle Keys 23 ND 49 62 72 86

Lower Keys 54 22 78 106 113 130

Total 243 132 256 335 328 387 

CV versus n* graphs were created for an additional ten non-targeted fish species that 

tended to be numerically more abundant. These species are important ecologically 

but not necessarily economically like the eight focal species. They included: ocean 

surgeonfish (Acanthurus bahianus), blue tang (A. coeruleus), foureye butterflyfish 

(Chaetodon capistratus), bluehead wrasse (Thalassia bifasciatum), spotted goatfish 

(Pseudopeneus maculatus), queen angelfish (Holocanthus ciliaris), gray angelfish 

(Pomacanthus arcuatus), bicolor damselfish (Stegastes partitus), striped parrotfish 

(Scarus iseri), and redband parrotfish (Sparisoma aurofrenatum). 

Example results: Examination of the CV vs. n* graphs for each species/life stage 

(Figure A.4) shows that for white grunt, gray snapper, hogfish, yellowtail snapper, 

and red grouper additional sampling will lead to negligible gains in precision (Figure 

A.4: a, b, g – n). Additional sampling would, however, increase precision for 

bluestriped grunt and mutton snapper adults (Figure A.4: c, d, e). Mutton snapper 

juveniles and black grouper were so sparse during sampling that a large amount of 

additional sampling would be required to accomplish any major gains in precision 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure A: Statistical Sampling Design 

A-10

(Figure A.4: f, o, p). In comparison, for non-targeted species, sampling either 

occurred where the curve leveled out or along the straight part of the curve for all 

species, indicating that these species were well sampled. 

Sampling in 2008 in BISC by the combined efforts of NOAA Fisheries, FWRI, and 

UM-RSMAS exceeded the calculated future optimal number necessary to detect 

differences in mean density of juveniles and adults of all eight targeted species at a CV 

level of 100%. In other words, current sampling exceeds that necessary to detect 3-

fold difference between years in BISC in a future survey (Table A.4). With the 

exception of black groupers and juvenile mutton snappers, current sampling is also 

greater than the future optimal number necessary to attain a CV of at least 50% 

(ability to detect a 100% difference) for all species/stage (Table A.4). By doubling the 

sampling effort of 2008 (adding approximately 10 extra sampling days), a predicted 

CV of 30% can be achieved for most species and 20 or 10% in some cases (Table A.4). 

Although current sampling is fairly precise, a doubling of effort would result in a large 

improvement in the precision of estimates of density for most species. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure A: Statistical Sampling Design 

A-11

Figure A.4. Performance data for annual estimates of fish density for eight focal species (a 

– p) and ten additional non-targeted species (q – z) in Biscayne National Park during 2005 – 

2007. Annual estimates (black squares) are compared to the relationship of CV versus n

for a stratified by benthic-habitat based survey design (red line).
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure A: Statistical Sampling Design 

A-12
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure A: Statistical Sampling Design 

A-13
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure A: Statistical Sampling Design 

A-14
A-15

Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure A: Statistical Sampling Design Table A.4. Optimal primary unit sample number (n*) for comparisons of fish densities between years in Biscayne National Park. 

Dst and CV[

Dst] are mean fish density and the CV of mean fish density, respectively, in BISC in 2007 (n = 59). Data from 

2005-2007 (n = 155) was used to make n* calculations. Dark gray boxes indicate where sample allocation in BISC in 2008 (n 

= 68) was >= the calculated n* for that level of CV. Yellow boxes indicate where doubling the 2008 allocation (to n = 136) would cause sampling to exceed or equal the calculated n* for that level of CV. 

Species

Life 

stage st D st CV D⎡ ⎤ ⎣ ⎦ n*, CV=10% n*, CV=20% n*, CV=30% n*, CV=40% n*, CV=50% n*, CV=70% n*, CV=100%

Adult 2.24 42% 757 221 101 58 37 19

9 white grunt 

(H. plumieri) Juvenile 6.41 15% 132 34 15

9

5

3 1

Adult 0.29 42% 1091 335 156 89 57 29 14 bluestriped grunt 

(H. sciurus) Juvenile 2.66 41% 548 155 71 40 26 13

6

Adult 0.42 16% 272 72 32 18 12

6

3 hogfish 

(L. maximus) Juvenile 0.73 20% 556 153 69 39 25 13

6

Adult 0.06 39% 584 173 80 45 29 15

7 mutton snapper 

(L. analis) Juvenile 0.24 41% 2051 667 314 180 116 60 30

Adult 0.51 29% 968 295 136 78 50 26 13 gray snapper 

(L. griseus) Juvenile 1.02 33% 528 153 70 40 26 13

6

Adult 0.68 26% 899 262 120 68 44 22 11 yellowtail snapper 

(O. chrysurus) Juvenile 1.30 16% 245 64 29 16 10

5

3

Adult 0.05 35% 1016 302 139 79 51 26 13 red grouper 

(E. morio) Juvenile 0.06 28% 834 233 106 60 39 20 10

Adult 0.01 53% 2684 1134 578 343 225 117 58 black grouper 

(M. bonaci) Juvenile 0.02 37% 1916 644 306 176 114 59 29 

Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure B: Participant Training

B-1

Standard Operating Procedure B: 

Participant Training 

(Version 1.0) 

Revision History Log 

Previous Revision 

No.

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Made

Reason for 

change

New Version 

No.

 

B.1 Initial Participant Training 

The following are guidelines for the training of new fish counters prior to 

participation. Failure to follow these guidelines may result in inaccurate and 

unusable data. 

Species identifications - All participants should be competent in the identification of 

reef fish to the species level before conducting in-water training. Participants should 

utilize resources including, but not limited to, the most recent edition of Humann and 

Deloach (2002), the Reef Fish ID: Florida, Caribbean, Bahamas – Interactive Edition 

CD/DVD field guide1, and the Reef Environmental Education Foundation on-line 

fish identification quizzes2. It is the responsibility of the program leaders for NOAA, 

FWRI, UM-RSMAS, and NPS to ensure that all participants from each respective 

agency or institution possess the necessary identification skills. 

Habitat characterization - All participants should be familiar with the habitat 

classification scheme used in the stratified survey design. They should be capable of 

distinguishing habitat types and classifying the different abiotic characteristics of the 

habitat that are measured. Participants should understand the metrics and terms 

used to assess major benthic groups and show familiarity with their identification. 

Guides for identification of major benthic groups and commonly misidentified 

organisms can be found in Appendix 2. It is suggested that these guides be printed 

and laminated and brought into the field as a reference. 

In-water Training - In-water training is intended to assess the accuracy of a diver’s 

estimates of fish size and distance from diver, as well as measure the ability of the 

diver to collect habitat data. Training should occur according to the following steps: 

a. Models of fish that are typically observed during RVC surveys (optimally, both 

fishery-targeted and non-targeted species) are prepared for deployment in the 

field. 

                                                           

1 Available from ReefNet Inc.: http://reefnet.ca/products/fishes/caribbean/ 

2 http://www.reef.org/resources/quizzes 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure B: Participant Training

B-2

b. A suitable test area is located (reef habitat, relatively shallow depth). Visibility 

must exceed 10 meters and the current should be minimal. 

c. A measuring tape transect (30m or longer) is extended in a straight line within 

the test area. Fish models (~20-30) are placed at varying distances (within the 

limits of visibility and at 0.5-m intervals) from the transect tape at 

predetermined and marked distances along the tape. 

d. For each fish model, a test administrator measures and records the (1) fish 

species, (2) model size (fork length to nearest cm) and (3) distance from the 

mark on the transect tape to the fish model (to nearest 0.5-m) for each model 

and (4) habitat data. 

e. Examinees enter the water with SCUBA gear, a reference measuring tool and 

clipboard. The reference measuring tool will be a marked t-stick/APT (see SOP 

C, Section C.1 for description of the APT). For each fish model, examinees 

estimate and record the (1) fork length (to nearest cm) and (2) distance from 

the center point (to nearest 0.5-m) and (3) complete the habitat data section of 

the fish/habitat data sheet. 

f. The estimated total length and distance from the transect tape for each model 

and habitat data are entered by each examinee into electronic format and 

compared with actual values to assess examinee-specific errors or consistent 

biases. This assessment may range from (1) an instructor or instructors 

assessing each examinee’s results, with subsequent reporting of results to, and 

discussion with, each examinee to (2) self-assessment by examinees, with 

subsequent group discussion of each examinee’s results. 

g. In all cases, additional training should be provided for examinees that exhibit 

consistent and considerable (> 20%) error, on average, in size or distance 

estimation, until error rates are less than 20%. Additional training should also 

be provided until the examinee has attained 100% accuracy in fish 

identifications. Habitat data should be examined by an instructor or 

instructors and determined if examinee needs more training. 

A new diver’s first RVC dives should occur with an experienced fish counter. The 

experienced fish counter should provide guidance, answer questions, and help the 

new diver with any fish identification skills. The new diver should also be calibrating 

their size estimates by comparing their size estimates to non-mobile reef components 

that can be measured exactly. Data taken during these first few dives and until the 

diver demonstrates competency with all necessary data taking skills should be 

marked as “Training – Observer” dives by selecting this from the “Sample Type” 

drop down list on the Sample Data screen upon entry into the RVC data entry 

program (SOP D.2.ii.a) . 

B.2 Annual Refresher Training for Previous Participants 

Each year, prior to the start of annual surveys, all fish counters, including those who 

have previously participated in surveys, should attend out-of-water training meetings 

that can be held either jointly or independently depending on the needs and abilities 

of the agencies. These out-of-water training meetings should cover the sampling 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure B: Participant Training

B-3

design, survey logistics, RVC methods, habitat characteristics, and data entry and 

proofing methods so that participants are familiar with all steps of the monitoring 

program. Presentations given at these training meetings will be posted online so that 

they are accessible to all participants throughout the field season. 

In-water training should be organized by each agency independently and focus on 

method execution, proper equipment handling, species identification and size 

estimation, and proper habitat characterization. Participants are also encouraged to 

independently use computer programs and books to practice species identification. 

B.3 Data Entry and Proofing Training 

Prior to surveying, all participants should be proficient in the use of the RVC data 

entry program (SOP D, Section D.2.i). Designated data managers from each agency 

should also be familiar with the steps involved in collating the data and producing 

proofing reports for individual divers to check their data (SOP D, Section D.5.iii) and 

for submitting final data files for data verification (SOP D, Section D.5.iv). This may 

require individual training when a new data manager is appointed and an 

experienced data manager from one of the agencies should be appointed to train the 

new data manager in the steps involved. 
 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure C: Field Data Collection Methods

C-1

Standard Operating Procedure C: 

Field Data Collection 

(Version 1.0) 

Revision History Log 

Previous Revision 

No.

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Made

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change

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C.1 Equipment 

Diver equipment – Each diver will be equipped with a data sheet and underwater slate, 

pencil(s), dive watch, and reference measuring tool (a marked PVC “t-stick” 

consisting of a 1m shaft marked at 10cm intervals and 30cm cross-piece marked at 

1cm intervals – Figure `C.1). The reference tool/t-stick is hereafter referred to as an 

All-Purpose Tool or APT. In addition to the APT divers may use tools such as a ruler 

affixed to a clipboard or slate, measuring tape, or gradations marked directly on a 

clipboard or slate. Preferably, divers will also be equipped with a digital camera for 

habitat documentation and to record images for subsequent verification or 

identification of fish or invertebrates, as necessary. 

Each dive team will be equipped with a reel and line. Attached to the line is a surface 

buoy/dive flag and GPS unit used to record the sampling location of the buddy pair. 

The time displayed on each diver’s watch should be set to within ±15 seconds of the 

local time as indicated on the GPS unit. One member of each dive team may also be 

equipped with a Secchi disc. The Secchi disc may be attached to the weighted reel 

connected to the surface dive flag. 

Figure C.1. The RVC All Purpose Tool (APT) used as a reference device for measuring

habitat vertical relief, estimating fish lengths and the location of the center and outer edge 

of the sample cylinder. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure C: Field Data Collection Methods

C-2

C.2 Sequence of Events in the Field 

Sampling teams should sample groups of sites within the same vicinity on the same 

sampling day to maximize sampling efficiency. Teams should also strive to sample 

sites across multiple habitat types each day to avoid temporal biases in fish-habitat 

characterizations that could arise by sampling multiple sites within 1-2 habitat types 

on a given day. 

C.2.i Locating and Assessing the Sample Site (Primary Unit) 

Sample sites are located using a vessel-mounted or hand-held GPS unit. Upon arrival 

at the sample site, divers should attempt to determine (e.g., via interpretation of 

depth finder display, battiscope, or snorkeling) whether the benthic habitat at the 

survey location is reef habitat. If the pre-assigned habitat type cannot be located, the 

sampling should proceed at the initial site coordinates, with divers recording the new 

habitat type on the Field/Boat Log. However, there are 3 cases when the divers 

should move around to actively locate the type of reef habitat indicated on the sample 

site list, (1) Contiguous reef structure: high relief spur and groove, (2) Isolated reef 

structure: Pinnacle, and (3) marine protected areas (MPAs). Once reef habitat is 

located, then the sampling should proceed, with divers noting whether or not they 

moved on the Field/Boat Log. 

If the benthic habitat is not reef habitat, the divers can do a short count and should 

note this on the Field/Boat Log. They should then prepare to dive the next site for 

that habitat on a list of alternate sites provided at the start of the field season. The 

alternate site does not need to be surveyed in the same day as the original site. 

C.2.ii Diver Deployment, Descent, and Location of Survey Sites 

At each sample site, two sets (replicates) of two paired surveys occur (each set is a 

replicate within the primary unit). Optimally, the two sets of surveys should be 

spatially separated by approximately 20 to 60m. Efforts should be made to deploy 

both sets of survey divers within the same primary unit. Spatially, a primary unit is 

equivalent to a square shaped area 200 meters on each side. The latitude-longitude 

site positions provided in the annual RVC survey plan mark the centers of the 

targeted primary units. The GPS unit used for vessel navigation should have 

waypoints stored for each RVC site listed in the annual plan. Vessel distance from a 

given stored waypoint can be used to determine that the sampling occurs within the 

targeted primary unit. The sampling would occur in the targeted primary unit if the 

distance from the waypoint is less than 100 meters (0.054 nautical mile) in a north, 

south, east, or west direction; or less than 141 meters (0.076 nautical mile) in a 

northeast, northwest, southeast or southwest direction. 

One of the following two approaches is utilized for diver deployment, descent, and 

location of diver-specific survey sites: 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure C: Field Data Collection Methods

C-3

C.2.ii.a Approach 1 – Live Boating: 

The field worker piloting the vessel will deploy two teams of two divers, with the 

teams separated by no less than ~30m and no more than ~75m. If necessary, during 

descent, divers will swim to appropriate habitat (e.g., if divers enter the water over 

sand, they will swim to nearby reef habitat for sampling). On reef habitat, each diver 

haphazardly chooses a sampling location such that each diver is within the distance 

of accepted “dive buddy” separation standards of his/her buddy. As described in 

Section C.1, each dive team will be equipped with a reel with line attached to a surface 

buoy and GPS unit. The reel can be secured to the bottom and serve as a starting 

point to measure the radius of the sampling cylinder using the APT (i.e., 7.5m or 5.0m 

depending on visibility), as a visual aid to measure visibility, as a point of reference 

(e.g., edge of cylinder) during data collection and as a point of return for both divers 

following data collection. 

Preferably, the live boating approach is utilized with 4-6 divers aboard the research 

vessel. When six divers are present; three teams of divers are formed for the days’ 

sampling, and two of the three teams are deployed at each sample site in a rotating 

format such that each team remains at the surface to pilot the research vessel every 

third sampling site. When five divers are present, divers rotate teams at each sample 

site in a format such that each diver remains at the surface at every fifth sample site. 

C.2.ii.b Approach 2 – Anchoring: 

The anchoring approach is typically utilized by a 3- or 4-member team. A dive team 

consists of two divers with the other team members remaining in the boat. Team 

members will deploy an anchor over nearby non-reef habitat so that current or wind 

guides the research vessel over or near the area to be sampled. As described in 

Section C.1, each dive team will be equipped with a reel with line attached to a surface 

buoy and GPS unit. Both divers descend to the bottom either following the anchor 

line or proceeding directly to the reef if it can be seen from the surface. 

On the bottom, the two divers determine the direction of the target habitat type. After 

a decision is made, the two divers swim to that habitat, secure the reel to the bottom, 

drop the weighted end of the tape next to the reel and begin to lay out the tape. If a 

distinct vertical reef edge is present, point counts should be conducted along the 

edge. If no distinct vertical edge is present, the divers should conduct the point count 

as completely within the predominant coral habitat in the area (i.e., low relief spur 

and groove, intermittent coral heads, hard bottom with soft coral, patchy encrusting 

coral, etc.) as possible. The first diver will lay out the tape across the habitat to be 

surveyed stopping at the 20m mark. The first diver then conducts a point count at the 

20m mark while the second diver conducts a point count at the 35m mark. At the 

completion of the first set of point counts, the divers reel in the tape then lay it out on 

suitable habitat in the opposite direction and conduct a second set of point counts at 

the 20m and 35m marks (Figure C.2). If the habitat is patchy and by stopping at a 

predetermined mark the point count will not include the characteristic habitat, then 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure C: Field Data Collection Methods

C-4

the center points can be adjusted accordingly. This approach will allow a minimum 

25 meters distance between samples. 

NOTE: Special consideration should be given to bottom times 

when sampling in deep waters (> 70’) using two divers to conduct 

all 4 point counts. Dives occurring at depths of 70’ or greater may 

take over 20 min to conduct and run the risk of putting divers 

breathing air into possible decompression status. We 

recommend having a minimum boat crew of four divers for 

sampling sites with depths of 70’ or greater. This will allow two 

separate dive teams to conduct the two sets of point counts and 

reduce the amount of time spent at depth. If a deep site is 

encountered and only three divers are onboard the boat, then 

only one set of point counts should be conducted at the site and a 

second visit to this site should be planned to complete the second 

count. Prior to each sampling season, representatives of FWRI 

and NOAA will determine which sites are better to be sampled by 

the 5-6 diver team (i.e., NOAA/RSMAS). 

Diver 1 and Diver 2

Starting 

point

20 meters

Diver 1 and Diver 2

42.5 m 35 m 27.5 m 20 m 12.5 m 12.5 m 20 m 27.5 m 35 m 42.5 m

7.5 m 15 m

20 meters

Diver 1 and Diver 2

Starting 

point

20 meters

Diver 1 and Diver 2

42.5 m 35 m 27.5 m 20 m 12.5 m 12.5 m 20 m 27.5 m 35 m 42.5 m

7.5 m 15 m

20 meters

Figure C.2. Schematic representing location of counts along deployed measuring tape. If 

visibility is low, the radius of each diver’s cylinder should be reduced to 5 m (10 m 

diameter). 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure C: Field Data Collection Methods

C-5

C.3 Details of Observations Made in the Field 

Data will be recorded on three data forms: (1) the Field/Boat Log, (2) the Water 

Quality/Environmental Log, and (3) the Fish/Habitat data sheet. Data for forms (1) 

and (2) are recorded at the surface by a surface support worker/diver. Data for form 

(3) are collected and recorded underwater at the sample site by divers. 

C.3.i Field Forms 

C.3.i.a Field/Boat Log 

This form (Figure C.3) serves as a record of where, when and by whom sites were 

sampled each day (a printable version of the form is included in Appendix 3). Two 

lines of data (one for each replicate pair of surveys) should be recorded for each 

sample site. The following information is recorded on the form: 

a. Dive of day: cumulative site number (e.g., 1, 2, 3...). This number will be the 

same for each of the two lines of data recorded at each site. 

b. Site ID: this is a three-character code listed on the sample site list. This 

number will be the same for each of the two lines of data recorded at each site. 

c. Estimated time: estimated time of beginning of dive. For divers using the 

anchoring method, the estimated time for the second set of paired surveys will 

be the time immediately preceding those surveys. 

d. Diver team: when the live boating method is used, this number corresponds to 

the first or second set of paired samples for a given sample site (i.e., divers 

performing the first set of paired samples are diver team 1; divers performing 

the second set of paired samples are diver team 2). When the anchoring 

method is used, only one diver team will be present. 

e. Latitude and longitude in degrees and minutes: position of surface vessel when 

divers enter the water. 

f. Habitat code: the diver’s consensus of the habitat type that was sampled; the 

suite of habitat codes is listed at the bottom of the Field / Boat log (Figure C.3); 

habitat types are defined in the Section C.3.iv. 

g. GPS #: when the live boating method is used, each dive team will have a GPS 

with number label; the GPS number is used to subsequently match GPS 

position with the data collected by each dive team. When only two divers are 

available for deployment at a given site, one GPS number would be used. 

h. Comments: any additional information judged to be important by the surface 

data collector (e.g., notation of a specific camera used by a diver). 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure C: Field Data Collection Methods

C-6

Reef Fish Visual Census (RVC) FIELD/BOAT LOG DATE

 Page of

Dive Site Est. Diver LATITUDE LONGITUDE Habitat

of Day ID Time Team Buddy Team (Diver A / Diver B) deg. minutes deg. minutes Code * GPS# Comments

* Habitat Codes

1 - Contiguous reef, Spur-Groove 5 - Sand-Seagrass-HB matrix

2 - Contiguous reef, Other 6 - Artifical reef

3 - Isolated reef structure(s) 0 - Sand

4 - Reef Rubble

Figure C.3. Field/Boat Log form. Printable version in Appendix 3. 

C.3.i.b Water Quality/Environmental Log 

This form (Figure C.4) serves as a record of water quality and environmental data 

associated with each set of paired surveys at each sample site (a printable version of 

the form is included in Appendix 3). The following information is collected by a 

surface support worker (either measured directly or communicated to the surface 

support worker by divers) and recorded on the form: 

a. Dive of Day: identical to dive of day column on Field / Boat Log; see preceding 

section. 

b. Site ID: identical to Site ID column on Field / Boat Log; see preceding section. 

c. Surface temperature (°C) *: water temperature measured in top 1m of water 

column. 

d. Surface salinity (ppt) *: water salinity measured in top 1m of water column. 

e. Bottom temperature (°C) *: water temperature measured 1-2m off the bottom. 

f. Bottom salinity (ppt) *: water salinity measured 1-2m off the bottom. 

g. Underwater visibility (ft or m): horizontal visibility, measured at depth by 

divers. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure C: Field Data Collection Methods

C-7

h. Wind direction (N, NE, E, SE, S, SW, W, or NW) and speed (mph): estimated 

by surface support worker(s). 

i. Percent cloud cover: estimated by surface support worker(s). 

j. Bottom current: estimated by divers for each paired survey; categories as 

follows: None (none), Mod. (diver is able to stay in same position with a gentle 

kick), High (diver struggles to stay in same position). 

k. Comments / notes: any additional information judged to be important by the 

surface data collector. 

*All measured from the research vessel using a salinity probe (e.g., YSI) with 

extension cable or refractometer or salinity probe and water retrieved from depth in 

a sample vial. 

Reef fish Visual Census (RVC) - Water Quality and Environmental Log

Date:

SurTemp Sur Sal BotTemp Bot Sal UW Visibility Clouds Current

Dive of Day SiteID ( o

 C ) (ppt) ( o C ) (ppt) ( ft ) or ( m ) dir mph (% cover) (N,M,H) Comments/Notes

WATER QUALITY DATA ENVIRONMENTAL DATA

Wind

Figure C.4. Water Quality/Environmental Log form. Printable version in Appendix 3. 

C.3.i.c Fish/Habitat Data Sheet 

Fish and habitat data are entered on the Fish/Habitat Data Sheet (Figure C.5; a 

printable version of the form is included in Appendix 3). Prior to each dive, divers 

should enter their name (name of observer / diver), name of dive buddy, and date on 

the data sheet. After entering the water, choosing a specific survey site, and 

recording dive and sample start times (time of beginning of dive and time of 

beginning of data collection, respectively; Figure C.5), each diver begins collection of 

fish, habitat, and sample-specific data as described in the following section. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure C: Field Data Collection Methods

C-8

Diver: ___________________ Date: Field Number:

Buddy: __________________ Sample Start Time: Habitat type: Underwater visibility: _____ ft m

Dive Start Time:___________ Sample End Time: 1. Contiguous S&G

Dive End Time: Max Dive Depth: ft 2. Cont. Not S&G

 Substrate Slope Station Depth: ft 3. Isolated

Max depth _____________ft Fishing Gear:

Min depth _____________ft Biotic Cover - Dominant Biological Cover %

 Max vertical Relief SAND HARDBOTTOM

Hard Relief ____________m "Bare"

Soft Relief ____________m Abiotic Footprint Algal Turf (<1cm) Algae (<1cm) 

 Surface Relief Coverage % SAND % Macro Algae Algae (>1cm) 

 Hard Avg. of Soft HARD-B % Sea grass Live Stony Coral 

 < 0.2 m % % RUBBLE % Sponge Octocoral 

0.2-0.5 m % % Total 100% ________ Other 1 Sponge 

0.5-1.0 m % % ________ Other 2 _________ Other 1 

1.0-1.5 m % % _________ Other 2 

 > 1.5 m % %

TOTAL 100% 100% TOTAL 100% 

Species N Avg Min Max Species N Avg Min Max

_ _ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _

_ _ _ _ _ _

Comments:

_ _ _ _ _ _

_ _ _ _ _ _

_ _ _ _ _ _

Presence of: A. palmata A. cervicornis Black Coral

_ _ _ _ _ _ Spiny Lobster # Conch # Diadema #

_ _ _

_ _ _

_ _ _

_ _ _

_ _ _

_ _ _

 0. (Sand) Current: None Mod. High

100%

 Crustose Algae 

_ _ _

_ _ _

_ _ _

 5. (Matrix) Radius of cylinder: 7.5m 5.0m

 4. Rubble Water temperature: _________ F

_ _ _

_ _ _

_ _ _

_ _ _

_ _ _

_ _ _

_ _ _

Figure C.5. Fish/Habitat Data Sheet. Printable version in Appendix 3. 

C.3.ii Collecting Fish Data 

The Reef fish Visual Census (RVC) methodology is modified from Bohnsack and 

Bannerot (1986), and occurs with the diver remaining at a fixed site. Fish are 

surveyed within an imaginary cylinder centered on the diver and extending from the 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure C: Field Data Collection Methods

C-9

reef substrate to the limits of vertical visibility, usually the surface (Figure C.6). If 

horizontal visibility is greater than or equal to 7.5m, then the radius of the cylinder 

will be 7.5m. If the horizontal visibility is less than 7.5m but greater than 5m, then the 

radius of the cylinder will be 5m. If the horizontal visibility is less than 5m, then 

further data collection will not occur. 

Figure C.6. Conceptual diagram of RVC diver within 7.5m-radius survey cylinder (from 

Rogers et al. 1994). 

Once horizontal visibility has been measured and the appropriate cylinder radius has 

been established, the RVC survey begins. Divers establish an imaginary fixed point 

on the bottom to serve as the center of the sample cylinder, and hover above the point 

(maintaining neutral buoyancy) to avoid damaging the benthic habitat. Divers record 

the sample start time on the Fish/Habitat Data Sheet and begin a timed count, using 

the stopwatch function on the diver’s watch to keep track of time. For a five-minute 

period, divers record all fish species observed. During this period, divers should 

rotate their position (while remaining above the imaginary fixed point) to ensure that 

all portions of the cylinder are surveyed. The diver should treat the survey as if they 

are taking a snapshot in time of all species and their associated densities and size 

distribution that they observe in the cylinder. 

After five minutes have elapsed, data are collected by each diver on the abundance 

(“N” column in Figure C.5) and sizes for each species. Individual fork lengths are 

recorded for the following species: all groupers (including graysbys, coneys and 

hinds), snappers, and hogfish (Lachnolaimus maximus). When 10 or less individuals 

of any of these species are present in a survey, individual lengths for all individuals 

will be recorded. When more than 10 individuals of any of these species are present, 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure C: Field Data Collection Methods

C-10

data are collected by each diver on the abundance (“N” column) and mean, minimum 

and maximum lengths (“Avg”, “Min” and “Max” columns in Figure C.5). For all 

other species, abundance (“N” column) and mean, minimum and maximum fork 

lengths (“Avg”, “Min” and “Max”) are recorded. 

For species with few individuals (e.g. angelfish, barracuda, hogfish) or for highly 

mobile species (e.g., sharks and Carangids), individuals are enumerated and their 

sizes are estimated when first observed. For enumeration and size estimation of 

other species (e.g. damselfish, wrasses, grunts, etc.), one 360-degree rotation is 

typically made for each species. 

Concurrent with the species enumeration and length estimation described above, 

new species that are observed after the initial five-minute observation period and 

until completion of all data collection are also recorded, as are estimates of their 

abundance and minimum, mean, and maximum lengths. These species are noted on 

the Fish/Habitat Data Sheet as having been observed “Between 5 and 10 minutes” or 

“After 10 minutes”, depending on the time elapsed at time of observation. If an 

individual or individuals of a species observed in the initial five-minute observation 

period is observed after data on the abundance, mean, minimum and maximum fork 

lengths for that species have been recorded, the diver should exclude these 

individuals from the count and continue recording only new species data. 

During the survey, the reference measurement tool (APT) is used to aid in measuring 

habitat vertical relief, estimation of fish lengths and the location of the center and 

outer edge of the sample cylinder. To the extent that conditions (e.g., current) permit, 

the diver should remain at the center of the survey cylinder for the entirety of the fish 

data collection portion of the survey. 

C.3.iii Sample-Specific Data 

Following fish data collection, the following sample-specific data are recorded on the 

Fish/Habitat data sheet: water temperature, current speed (None, Mod, or High), 

maximum dive depth, and station depth (bottom depth at the diver’s survey location). 

The horizontal visibility will have been measured and recorded prior to the RVC 

survey. 

C.3.iv Habitat Data 

Following the sample-specific data collection, habitat data are collected and recorded 

on the Fish/Habitat data sheet. The following variables are measured and recorded: 

Habitat type: chosen from the following categories (circle one on the Fish/Habitat 

data sheet). At the surface, the diver should discuss with their buddy and other 

team members and try to come to a consensus. If a consensus is not achieved, 

divers should note that in the Field/Boat Log. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure C: Field Data Collection Methods

C-11

Target habitats: 

• Isolated reef structure(s): E.g., patch reefs, rocky outcrops, pinnacle (Figure 

C.7-A) 

• Contiguous reef structure with distinct spur and groove formation: E.g., 

low or high relief spur and groove (Figure C.7-B) 

• Contiguous reef structure – Other: contiguous reef with no distinct 

formation; e.g., low relief hard bottom not spur and groove (Figure C.7-C) 

• Reef Rubble (Figure C.7-D) 

Isolated Reef Structure Contiguous Reef, Spur & Groove

Contiguous Reef, Other Reef Rubble

Figure C.7. Example photos of target habitats. 

Water temperature, Secchi visibility and Current: temperature and visibility at the 

bottom; water current estimated by divers for each paired survey; categories as 

follows: None (none), Mod. (diver is able to stay in same position with a gentle 

kick), High (diver struggles to stay in same position). 

Non-target habitats: if after diving for 5 minutes divers fail to find any of the target 

habitat types, divers should conduct a count in one of the non-target habitats 

noting the habitat type on the Field/Boat Log. 

• Sand 

• Sand-seagrass-hard-bottom matrix: mostly soft bottom, non-reef habitat 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure C: Field Data Collection Methods

C-12

• Artificial reef (e.g., wrecks) 

Substrate Slope: the maximum and minimum depths within the sample cylinder. 

These values refer to the maximum and minimum depths on the imaginary 

plane underlying the sample cylinder. If there is a slope these depths will be 

different (Figure C.8). 

Max Vertical Relief: the maximum vertical relief within the sample cylinder of both 

hard (e.g., coral structure, coralline spur, rocky outcrop) and soft (e.g., 

octocorals, sponges and macroalgae) substrate (Figure C.8). These values 

should not be zero. 

Surface Relief Coverage for Hard Vertical Relief (e.g., coral structure, coralline spur, 

rocky outcrop and sand): the estimated percentages of hard relief that fall into 

the following categories (all values in meters): < 0.2, 0.2-0.5, .05-1.0, 1.0-1.5, 

and >1.5. These values should sum to 100% (Figure C.8). 

Surface Relief Coverage for Soft Vertical Relief (e.g., octocorals, sponges and algae): 

the category (< 0.2, 0.2-0.5, .05-1.0, 1.0-1.5, and >1.5m) representing the 

average vertical relief of all soft relief should be indicated by writing “100%” by 

that category (Figure C.8). 

Abiotic Footprint: the percentage of the cylinder comprised of sand, hardbottom 

and rubble. These percentages should sum to 100%. Sand is defined as coarse 

biogenic or oolitic sand (grain sizes typically between 0.5-2 mm) and finer silt 

sized particles (< 0.2 mm). Sand is considered the substratum when sediment 

depth is usually 2-3 cm in depth or greater. It excludes a surface “dusting” of 

sediment particles overlying a consolidated substratum. Rubble ranges from 

coarse gravel (> 5 mm) to unconsolidated and moveable rocks (e.g. dislodged 

and moveable coral fragments). This category differs from consolidated hardbottom because of its loose and moveable nature. Consolidated hard-bottom 

includes solid, consolidated lithogenic or biogenic substratum, including living 

and dead coral, and non-coral hard-bottom. Areas covered by seagrass should 

be coded as sand, since the biotic “grass” is growing in the abiotic sand 

substrate. 

Biotic Cover - SAND: the percentage of the sand substrate that corresponds to the 

following categories: bare, under / supporting growth of macroalgae, under / 

supporting growth of seagrass, under / supporting growth of sponges, and 

other (e.g., Sargassum; see Appendix 2 for more examples). These values 

should sum to 100%. See preceding section for sand definition. 

Biotic Cover – HARDBOTTOM: While looking at an aerial, canopy view of the 

cylinder, the percentage of the hardbottom substrate covered with algae < 1 cm 

height (e.g., turf algae, Lobophora), macroalgae > 1 cm height (e.g., Halimeda, 

Dictyota), live coral, octocoral, sponge, and other (e.g., Palythoa, Cliona; see 

Appendix 2 for more examples). These values should sum to 100%. 

Comments: Under the “comments” section, divers should record information such 

as economically important species observed before or after the RVC survey 

(e.g., while descending or ascending), presence of Acropora palmata and/or 

Acropora cervicornis (if present circle), presence of black coral, number of 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure C: Field Data Collection Methods

C-13

Spiny Lobster, Conch and/or Diadema antillarum, and camera number used. 

If present, divers should also record the type and amount of fishing gear or 

debris (e.g., monofilament line, traps or trap debris including buoy line, etc.) 

within the cylinder in the “Fishing gear” section of the Fish/Habitat Data Sheet 

(see Figure C.5). Additionally, any comments relative to the sampling or 

conditions encountered should be recorded in the “Comments” section of the 

data sheet. 

Following fish and habitat data collection, sample end time is recorded and divers 

ensure that all sections on the Reef / Habitat data sheet are completed. Dive end time 

is recorded after all data have been collected and immediately prior to dive ascent. 

C.4 Post-Collection Data Sheet and Logs Processing 

Once all data collection has been completed underwater, divers deployed from an 

anchored vessel then return to the research vessel, while divers deployed from a live 

boating vessel ascend to the surface immediately adjacent to their surface dive flag 

and wait for the research vessel to approach. Immediately upon returning from a 

dive, initial QA/QC should include discussions between buddy teams to ensure 

agreement on variables such as habitat type, bottom current, and other variables of 

interest. Data sheets are maintained in a secure area aboard the research vessel. Once 

on land, data sheets are redistributed to data collectors for data entry. Copies 

(electronic or paper) of all data sheets should be made before redistribution to data 

collectors in case of loss of original data sheets. These copies should be maintained in 

a single storage location. 

Information recorded at-sea on the Boat/Field and Water Quality/Environmental 

logs should be entered into spreadsheet files customized for this data. LatitudeLongitude positions are entered into the Boat/Field log Spreadsheet file after surface 

buoy GPS unit tracklogs have been downloaded and sampling positions for each dive 

team determined. It is suggested that Latitude-Longitude positions be recorded in the 

form of degrees and minutes to three decimal places (dd° mm.mmm'). 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure C: Field Data Collection Methods

C-14

Figure C.8. Diagram showing how to measure substrate slope, max vertical relief and 

surface relief coverage. If there is NO slope then Max Depth = Min Depth (A). If there is a 

slope, then Max Depth > Min Depth (B). Soft Relief is measured from base of attachment 

to maximum height. Surface relief coverage (%) for the hard substrate components (e.g., 

coral structure, coralline spur, rocky outcrop and sand) is estimated by determining the 

percentages of the cylinder area that occupy the following vertical height categories (all 

values in meters): <0.2, 0.2-0.5, .05-1.0, 1.0-1.5, and >1.5. Average surface relief coverage 

(%) for soft substrate components (e.g., octocorals, sponges and algae) is estimated as the 

vertical height category within the cylinder representing the average vertical relief of all soft 

substrate components in the cylinder (including macroalgae). This should be indicated by 

writing “100%” in that vertical relief category. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-1

Standard Operating Procedure D: 

Data Entry and Proofing 

(Version 1.0) 

Revision History Log 

Previous Revision 

No.

Revision Date Author Change 

Made

Reason for 

change

New Version 

No.

 

D.1 Introduction 

Management of the data is an important and multi-level process. Steps that should be 

taken to manage the data once it has been collected include data entry, proofing and 

storage. The specific steps and those responsible for each step are outlined in Table 

D.1 and explained in detail in the following sections. 

Table D.1. Data management overview.

Steps Responsible 

person

Forms/Programs used

1) Field data collection Diver

1-Fish/Habitat data sheet 

2-Field/Boat log 

3-Water Quality/Environmental log

2) Enter/collate data Diver Fish/Habitat data entered into 

RVC2.3.exe Data Entry program

3) Check and merge data files Agency data 

manager Merge2.0.exe

4) Generate proofing reports Agency data 

manager SAS and Word Mail Merge

5) Proof and edit data Diver Visual comparison of original data 

sheets to proofing report

6) Create preliminary RVC 

Annual Master Excel file

Agency data 

manager

Excel

7) QA/QC and verification 

procedures

Statistician (UMRSMAS) SAS

8) Create final RVC Annual 

Master Excel file

Statistician (UMRSMAS) SAS

9) Storage of data in Oracle 

database

Statistician (UMRSMAS) Oracle 

D.2 Data entry 

D.2.i The RVC Data Entry Program 

Reef fish Visual Census (RVC) fish and habitat survey data are entered into an 

electronic database using the RVC Data Entry Program. This program was designed 

to standardize data entry and minimize the potential for error during the data entry 

process. Data are entered into the RVC program through three ‘window’ or data 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-2

entry screens, focusing on sample identifier information, habitat data, and fish and 

invertebrate species, size, and abundance data. 

The RVC Data Entry Program consists of one executable program (RVC2.3.exe) 

written in the C++ computer program language along with several, user modifiable, 

support files. Entered data are output as tilde (~) delimited ASCII files into one of 

three individual subfolders. The three subfolders are named “sample”, “substrate” 

and “species” and must be present on the computer hard drive in the same folder in 

which the RVC2.3.exe and support files are located. 

D.2.ii Directions for Use of the RVC Data Entry Program 

In order to properly use the RVC2.3.exe program for data entry, a folder containing 

the following files must be present on the user’s PC: 

RVC2.3.exe 

computerlist.noaa 

currentcomputer.noaa 

diverlist.noaa 

habitatlist.noaa 

otherspecieslist.noaa 

samplelist.noaa 

specieslist.noaa 

speciessizelist.noaa 

To open the RVC2.3.exe program and begin entering recorded data, double-click on 

the RVC2.3.exe filename or desktop icon. 

D.2.ii.a Entering Sample Data 

The first window in the program is titled “RVC Data Entry (Sample Data)” (Figure 

D.1). This is where general information about the diver’s sample is entered. The 

following directions should assist the user with data entry into the “Sample Data” 

window. 

• The data entry field labeled “Computer Name,” located in the top left 

corner of the window, should already contain the previously assigned name 

of the user’s pc. This name is listed in the “currentcomputer.noaa” file. 

• Enter the last name of the “Diver” and “Buddy” by clicking the drop-down 

arrow in each data field, and choose the appropriate name from the given 

list of divers. The “Diver” and “Buddy” data fields must not be left empty. 

• Choose the appropriate sampling method and habitat type using the dropdown arrows in both the “Sample Type” and “Habitat Type” entry fields. 

For RVC surveys, the sample type will be “Bohn-Bannerot Point”. If the 

diver is training, “Training – Observer” should be selected from the 

dropdown list instead. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-3

• Enter the date of the dive, the time when the dive started and ended, and 

the time when the sample started and ended in the appropriate entry fields. 

It is important that the date and times be entered in the proper, indicated 

format. The hour must be a number between 0 and 23, and the minutes 

must be a number between 0 and 59. The “Dive End Time” must be greater 

than the “Dive Start Time”, and the “Sample End Time” must be greater 

than the “Sample Start Time.” Additionally, the “Sample Start Time” and 

the “Sample End Time” must fall between the “Dive Start Time” and the 

“Dive End Time.” Warning windows will pop up when very early start 

times and very late end times for the dive are entered. 

• Enter the maximum depth of the dive and the depth of the sampling station 

(bottom depth at center of sampling cylinder) in the “Max Dive Depth” and 

“Station Depth” entry fields. These entries must be integers greater than 

zero. 

• The “Fishing Gear” entry field is a comment box where any fishing gear 

located within the sample area should be listed. Possible types of fishing 

gear include lobster traps, trap line, and monofilament fishing line. 

• The value of the “Field Number” will be provided by the diving coordinator 

/ data manager. 

• Enter the “Under Water Visibility” in measurement units of feet. This entry 

should be an integer greater than zero. 

• Enter any important remarks regarding the dive and/or sample into the 

“Comments” entry field. 

• Throughout the data entry process, dynamic evaluations of the data input 

into entry fields are performed by the program. Upon leaving an entry 

field, the program checks the validity of the data automatically. Prior to 

moving on to the next window, the information entered into the current 

window must be checked for errors once more by the program. This is 

accomplished by clicking on the “Check Data” icon. If no errors are 

detected, the program will generate the “Master Sample number”, and the 

second data entry window will open. The “Master Sample number” is the 

unique relational linking index with the Substrate data and Species data 

(see sections below).The “Master Sample Number” is composed of the 

following information: year+month+date+sample start time+diver number; 

The year, month, day, and sample start time are derived from entered data 

for a sample and the diver number is determined from the number (4 digit) 

assigned to each diver last name in the RVC data entry support file = 

diverlist.noaa. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-4

Figure D.1. The “Sample Data” window. 

D.2.ii.b Entering Habitat Data 

The second window of the RVC2.3.exe program is titled “RVC Data Entry (Substrate 

Data)” (Figure D.2). This is where the user enters information about the substrate of 

the sampled habitat. The generated “Master sample number” should now appear in 

the top right side of the window. The user has the option to either enter data into this 

window or to skip this window by clicking the “Skip” icon. As data is entered, the 

program evaluates the data dynamically in a manner similar to that of the first 

window. The following directions should assist the user with data entry into the 

“Substrate Data” window. 

• Enter the recorded “Max Depth” and “Min Depth” of the slope of the 

substrate in the respective entry fields. The maximum depth must be an 

integer greater than zero, and the minimum depth must be less than or 

equal to the maximum depth. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-5

• Enter the measured maximum vertical relief of the “Hard Substrate” and 

“Soft Substrate” in the respective entry fields. The relief of the hard and 

soft substrate must be greater than zero. 

• The estimated percent of the intervals of vertical relief that comprise the 

surface of the sample area must be entered into the “Surface Relief 

Coverage %” section. This section is divided into the intervals of “Hard” 

vertical relief and “Soft” vertical relief. The data entry fields that are 

activated depend on the values entered in the “Max vertical relief” section. 

For example, if the value of the maximum vertical relief of the soft substrate 

equals zero (i.e. no soft substrate was found in the sample area), then the 

entry fields for the “Soft” vertical relief in the “Surface Relief Coverage %” 

will not be activated. The total percent coverage of both “Hard” and “Soft” 

vertical relief must equal 100%. 

• The percent of sand, hard-bottom, and rubble that comprises the “Abiotic 

Footprint” of the sample area must be entered into the fields labeled 

“Sand”, “Hard-B”, and “Rubble” respectively. The values entered into 

these fields must add to 100%. If the percent of “Sand” in the “Abiotic 

Footprint” is not equal to zero, then the “Sand” portion of the “Biotic 

Cover” section will be activated. Likewise, if the percent of “Hard-B” in the 

“Abiotic Footprint” is not equal to zero, then the “Hardbottom” portion of 

the “Biotic Cover” section will be activated. Click the icon labeled “Input 

Data to Biotic Cover” to begin entering data into the “Biotic Cover” section. 

• Values for the estimated percent of various categories of biota covering 

both the “Sand” and “Hardbottom” must be entered into the “Biotic Cover 

– Dominant Biological Cover %” section. Any category that is not listed in 

this section, but was present in the sample area may be entered in one of the 

fields labeled “Other”. All values entered in the “Sand” portion of the 

section must add to 100%, and all values entered in the “Hardbottom” 

portion of the section must add to 100%. 

• As in the previous window, the information entered into the current 

window must be checked for errors by the program prior to moving on to 

the next data entry window. This is accomplished by clicking on the 

“Check Data” icon. If no errors are detected, the third and final data entry 

window will open. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-6

Figure D.2. The “Substrate data” window. 

D.2.ii.c Entering Fish Species Data 

The third window of the RVC2.3.exe program is titled “RVC Data Entry (Species 

data)” (Figure D.3). This is where data about the species observed and recorded in 

the sample area is entered. As in the previous two windows, dynamic data checking is 

also implemented by the program in this window. The following directions should 

assist the user with data entry into the “Species Data” window. 

In order to differentiate between species observed during the first five minutes of the 

sampling period and species observed during the 5-10 and > 10-minute periods, click 

the “Time period” icon in the top left corner of the window. Species observed after 

the first five minutes but before ten minutes have passed will be identified with the 

following notation “(**)”. The notation for species observed after ten minutes will be 

“(***)”. 

• Click the icon labeled “Species/Common” in the top left corner of the 

window in order to choose to enter the data according to either the species 

name or the common name. If the species name is selected, then the 

program will search for and provide the corresponding common name and 

vice versa. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-7

• By default, the program is automatically ready to enter “Reef fish” records 

into the data window. In order to input a species that is not a “Reef fish”, 

click on the icon labeled “Species type” at the top of the window, and select 

“Others.” “Others” includes lobster species, stone crab, urchins, conch, 

and various abiotic objects such as concrete, etc. 

• To begin entering records of observed species into the “Species data” 

window, click the drop-down arrow in the “Species” entry field or in the 

“Common” entry field, depending on the method of data entry chosen 

previously. Choose the appropriate species from the given list. Next, enter 

the observed number of individuals of that particular species in the field 

labeled “N.” If “N” is equal to one (i.e. only one or two individual(s) of that 

species were observed), for the estimated length is entered in the “Average” 

field. If “N” is equal to two, the estimated lengths are entered in the “Min” 

and “Max” fields. If “N” is equal to three or more, enter the average size of 

the individuals, and the minimum and maximum observed size in the 

“Average”, “Min”, and “Max” field, respectively. The “Average” value must 

be greater than the “Min” value and less than the “Max” value. 

• If a species is observed that is not on the species list, first check with the 

data manager to confirm that the species is not on the list and has not been 

seen in a previous RVC. If it is confirmed that the species has not been seen 

before, enter data for this species using “Other” from the species name 

drop down list or “New species” from the common name drop down list. 

Identify the species in the “Comments” entry field of the “Sample Data” 

window. It is possible, however extremely unlikely, to add up to three new 

species for a site. Therefore, confirmation with the UM-RSMAS data 

manager and statistician should always occur prior to adding a new species. 

• When the record for a particular species is complete, click the icon labeled 

“Add,” and the data record will appear in the box below the entry fields. 

Data for additional species may be added in the same manner. In order to 

delete a record, highlight the particular record and click the “Clear” icon. 

In order to edit a previously input species record, double-click on the 

record of interest. 

• The program is designed to allow the user to input multiple size classes 

within the same species. Therefore, multiple records for the same species 

may be created, but the “Min” and “Max” size values for each record must 

not overlap. 

• If it is necessary to go back and edit the “Substrate Data,” click the icon 

labeled “Back to Substrate Info.” Data must be re-checked “via the “check 

data” button when proceeding forward through data screens after moving 

back to previous screens. When all of the recorded data has been entered 

and no further editing is required, click the “Save” icon. This operation 

will save the entire data record. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-8

Figure D.3. The “Species data” window. 

D.3 Editing Saved Data 

The first window in the program provides an option to edit previously saved data 

records. The user must click the “Edit” icon on the top left corner of the “Sample 

Data” window and select “Edit.” When this function is chosen, the program opens 

the “Sample”, “Substrate”, and “Species” files corresponding to the specified “Diver” 

and the “Computer Name.” The user must scroll through the available records in 

order to find the record to be edited. When the user selects a particular record, the 

data in the “Sample,” “Substrate,” and “Species” files corresponding to that record 

will be deleted. At this point the user is able to change the previously entered data in 

each of the three windows. In order to move from the “Sample Data” window to the 

“Substrate Data” window, the user must click the “Check Data” icon. Likewise, in 

order to move from the “Substrate Data” window to the “Species Data” window, the 

user must again click the “Check” icon. When the editing is complete, the user must 

click the “Save” icon in order to save the record. If the user exits the program 

without saving, then the data in the edited record WILL BE LOST. 

• Entered data (sample, fish and environmental data) will be submitted for 

storage on the FWC FTP site, which can be accessed by FWC, NOAA, NPS, 

and UM-RSMAS staff. 

• All data entry should be completed by Dec. 1 each sampling year. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-9

• Subsequent to collation at NOAA, all raw data will be available to all 

agencies. 

• Data are made available to all agencies as soon as annual QA/QC is 

completed. 

• All groups agree on data release to outside data requests prior to actual 

release. 

D.4 Data Cataloguing 

All data should be catalogued and backups created such that several independent 

copies of the data are held in different physical locations but where they are 

accessible to all groups involved. These locations will include UM-RSMAS, NPS, 

NOAA, and FWRI. 

D.5 Data QA/QC and Verification 

Data proofing and verification are important steps in a monitoring program and there 

are a series of tasks that must be followed to accurately proof, correct, and verify the 

data before analysis. If errors are not caught during this phase they will likely go 

undetected, introducing error into the database. The most crucial data proofing is 

carried out by each diver immediately following each dive and at the time the diver 

enters his data in the RVC Data Entry Program. There is much more to proofing than 

simply verifying that the values for each variable were entered correctly. The proofers 

must be aware of the procedures and guidelines related to the data and recognize 

situations where the variables entered do not seem reasonable. 

D.5.i Initial Diver Proofing 

These are the most crucial proofing steps to ensure the accuracy of the data. Initial 

data proofing should be carried out by each diver immediately following each dive, 

and should involve reviewing the data sheet for errors and missing data, as well as 

discussing subjective data collection variables (e.g., habitat type and bottom current) 

with dive buddy. 

Following this, the diver is responsible for providing the agencies with the most 

correct data. The diver will make a conscious effort to enter the data into the RVC 

Data Entry Program as accurately as possible. This should include counting the 

number of species on the field data sheet and comparing it with what was entered 

into the program immediately after entering the data, as well as going back through 

the three windows and checking for any errors prior to saving the record. 

D.5.ii Participant-Level Proofing 

D.5.ii.a Data Proofing Criteria 

Each agency will be responsible for maintaining the integrity of data collected and 

entered by their participants. A minimum of 10% of the data collected by any 

participant and entered into the RVC database should be proofed after it is entered. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-10

This proofing shall consist of comparing data collected on underwater datasheets to 

that entered into the database which should be printed out as a proofing report. If 

there is any inconsistency between data recorded on the data sheet and that entered 

into the system, that sample should be recorded as an error. The number of samples 

recorded as an error divided by the number of samples proofed is the accuracy for 

that participant. A minimum accuracy level of 90% should be maintained for any 

participant. Each agency should follow their own steps to assure that all participants 

maintain this level of accuracy. 

D.5.ii.b Proofing Report Procedure 

Proofing reports can be created for a specific diver after data for that diver has been 

entered. The proofing report creation process involves the use of a SAS program to 

read the ASCII data entry files and output this data into an Excel file suitable for input 

into a Mail Merge template document created in Word. The SAS program can 

generate proofing reports in the common species name style (Figure D.4), or the RVC 

species code style (Figure D.5) depending on the diver’s recording of species on the 

underwater data sheet. After a proofing report has been printed, the information on 

the proofing report should be compared to the data on corresponding underwater 

data sheets as per the data proofing criteria described previously. Each agency should 

accomplish necessary corrections or changes discovered during the proofing report 

process using the “Edit” function of the RVC Data Entry Program. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-11

Figure D.4. Example proofing report sheet in common species names style. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-12

Figure D.5. Example proofing report sheet in RVC species code style. 

D.5.iii Agency-Level Proofing 

D.5.iii.a Data Merge and Verification 

After proofing of all diver entered data for an annual sampling cycle has been 

completed, the RVC Annual Master Spreadsheet file can be created. The data 

contained in this spreadsheet file includes: the ASCII sample, substrate and species 

data output from the RVC entry program along with entered data from the combined 

Boat/Field and Water Quality/Environmental log forms. Each of the four datasets 

becomes an individual worksheet in the RVC Annual Master Spreadsheet file. 

D.5.iii.b Merge of Diver-Entered ASCII Files 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-13

The Merge2.0.exe program is used to “merge” the numerous ASCII files created by 

the RVC Data Entry application into tilde (~) delimited files containing the sample, 

substrate, and species RVC data. These three files are imported as the first three 

worksheets of a Spreadsheet file. With the inclusion of the fourth dataset (combined 

Boat/Field and Water Quality/Environmental logs) the creation of the RVC Annual 

Master Spreadsheet file has been completed. 

D.5.iii.c Preliminary Annual Master Spreadsheet File Verification 

After the creation of the RVC Annual Master Spreadsheet file, verification that all 

RVC counts have been entered by divers can occur. This task is accomplished via a 

series of record checks of the sample diver entered data against the Boat/Field Log 

data. If missing diver samples are discovered during this check, divers will need to be 

contacted and resolution of missing data accomplished. The resolution may include a 

revision to Boat/Field Log or entry of missing RVC sample data. In addition to the 

missing data check, some preliminary checks of certain data elements such as Field 

Numbers, outliers in lengths or numbers of fishes, sampling dates, etc. is performed. 

The data proofing procedures described previously should reduce or eliminate 

occurrences of questionable data elements. However, should questionable data 

elements be discovered during this preliminary check, individual divers may need to 

be contacted for resolution. 

D.5.iv Final Verification and Oracle Database 

After the Preliminary Master Spreadsheet File Verifications has been completed, the 

RVC data undergoes a more rigorous software application program verification 

procedure(s) overseen by statisticians at UM-RSMAS. A detailed description of all 

procedures involved in this final verification, including SAS code can be found in 

Smith et al. (in prep b). This procedure systematically checks the data files created at 

the agency level and uses other files to produce Oracle database tables (Figure D.6). 

Variables associated with each file used in the verification process are listed in Tables 

D.2-D.8. The variables in the Oracle tables and their descriptions are listed in Table 

D.9. and a schema diagram for the Oracle database is also provided (Figure D.7). 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-14

Figure D.6. Flow chart of verification procedures and production of oracle tables from 

Excel files. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-15

Table D.2. Variables in the sample output file (rvc_sample.xls). 

variable # SAS/Excel name Oracle Name 

1 mastersampcd MASTER_SAMPLE_CD 

2 divnum DIVER_NR 

3 budnum BUDDY_NR 

4 samptype SAMPLE_TYPE_NR 

5 divhab

6 habname HABITAT_TYPE 

7 year YEAR 

8 month MONTH 

9 day DAY 

10 divbegh DIVE_START_TIME_HOURS 

11 divbegm DIVE_START_TIME_MINUTES 

12 divendh DIVE_END_TIME_HOURS 

13 divendm DIVE_END_TIME_MINUTES 

14 sampbegh SAMPLE_START_TIME_HOURS 

15 sampbegm SAMPLE_START_TIME_MINUTES 

16 sampendh SAMPLE_END_TIME_HOURS 

17 sampendm SAMPLE_END_TIME_MINUTES 

18 divdepth DIVE_DEPTH 

19 sampdepth SAMPLE_DEPTH 

20 fishgear FISHING_GEAR 

21 fieldid

22 vis UNDERWATER_VISIBILITY 

23 sampdescr SAMPLE_DESCR 

24 sppbeffive NR_OF_UNIQUE_SPECIES_BEFORE_FIVE 

25 sppaftfive NR_OF_UNIQUE_SPECIES_AFTER_FIVE 

26 sumbeffive SUM_OF_INDIVIDUAL_FISH_BEFORE_FIVE 

27 sumaftfive SUM_OF_INDIVIDUAL_FISH_AFTER_FIVE 

28 subswitch SUBSTRATE_SWITCH 

29 specswitch SPECIES_SWITCH 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-16

Table D.3. Variables in the boat log output file (rvc_boatlog.xls). 

variable # SAS/Excel name Oracle Name 

1 fieldid

2 year YEAR 

3 month MONTH 

4 day DAY 

5 diveofday

6 logbegh

7 logbegm

8 divnum DIVER_NR 

9 lat_deg

10 lat_min

11 long_deg

12 long_min

13 lat LAT_DEGREES 

14 lon LON_DEGREES 

15 temp_s SURFACE_TEMPERATURE 

16 sal_s SURFACE_SALINITY 

17 temp_b BOTTOM_TEMPERATURE 

18 sal_b BOTTOM_SALINITY 

19 comments LOG_COMMENTS 

20 mapgrid MAPGRID_CD 

21 maphab

22 depcat

23 region REGION_NR 

24 subreg SUBREGION_NR 

25 mpa MPA_NR 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-17

Table D.4. Variables in the substrate output file (rvc_substrate.xls). 

variable # SAS/Excel name Oracle Name 

1 mastersampcd MASTER_SAMPLE_CD 

2 submaxdep SUBSTRATE_MAX_DEPTH 

3 submindep SUBSTRATE_MIN_DEPTH 

4 vrel_h HARD_VERTICAL_RELIEF 

5 vrel_s SOFT_VERTICAL_RELIEF 

6 h_relcat_0 TYPE, INDEX, VALUE 

7 h_relcat_1 TYPE, INDEX, VALUE 

8 h_relcat_2 TYPE, INDEX, VALUE 

9 h_relcat_3 TYPE, INDEX, VALUE 

10 h_relcat_4 TYPE, INDEX, VALUE 

11 s_relcat_0 TYPE, INDEX, VALUE 

12 s_relcat_1 TYPE, INDEX, VALUE 

13 s_relcat_2 TYPE, INDEX, VALUE 

14 s_relcat_3 TYPE, INDEX, VALUE 

15 s_relcat_4 TYPE, INDEX, VALUE 

16 p_sand SAND_PERCENTAGE 

17 p_hb HARDB_PERCENTAGE 

18 p_rub RUBBLE_PERCENTAGE 

19 s_pcov_bare SAND_BARE 

20 s_pcov_algturf SAND_ALGAL_TURF 

21 s_pcov_macalg SAND_MACRO_ALGAE 

22 s_pcov_sg SAND_SEAGRASS 

23 s_pcov_sponge SAND_SPONGE 

24 s_pcov_oth1_lab TYPE, DESCRIPTION 

25 s_pcov_oth2_lab TYPE, DESCRIPTION 

26 s_pcov_oth1 TYPE, PERCENTAGE 

27 s_pcov_oth2 TYPE, PERCENTAGE 

28 h_pcov_crust HARDBOTTOM_CRUSTOSE_ALGAE 

29 h_pcov_algturf HARDBOTTOM_ALGAL_TURF 

30 h_pcov_macalg HARDBOTTOM_MACRO_ALGAE 

31 h_pcov_coral HARDBOTTOM_LIVE_CORAL 

32 h_pcov_octo HARDBOTTOM_OCTOCORAL 

33 h_pcov_sponge HARDBOTTOM_SPONGE 

34 h_pcov_oth1_lab TYPE, DESCRIPTION 

35 h_pcov_oth2_lab TYPE, DESCRIPTION 

36 h_pcov_oth1 TYPE, PERCENTAGE 

37 h_pcov_oth2 TYPE, PERCENTAGE 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-18

Table D.5. Variables in the species output file (rvc_species.xls). 

variable # SAS/Excel name Oracle Name 

1 mastersampcd MASTER_SAMPLE_CD 

2 species SPECIES_CD 

3 catch NUMBER_OF_INDIVIDUALS 

4 meanlen AVERAGE_LENGTH 

5 minlen MIN_LENGTH 

6 maxlen MAX_LENGTH 

7 time_seen TIME_SEEN 

8 instance_field

9 instance_key

Table D.6. Variables in the verification file used (verify_2.xls). 

variable # SAS/Excel name Oracle Name 

1 fieldid

2 stn STATION_CD 

3 rep REPLICATE_CD 

4 year YEAR 

5 month MONTH 

6 day DAY 

7 divnum DIVER_NR 

8 pr_num

9 pr_mod

10 hab HABITAT_NR 

11 divhab

12 maphab

13 sampdepth SAMPLE_DEPTH 

14 mapgrid MAPGRID_CD 

15 region REGION_NR 

16 subreg SUBREGION_NR 

17 mpa MPA_NR 

18 pr_unit PRIMARY_SAMPLE_UNIT 

 Table D.7. Variables in the map grid groundtrouthing file (mapgrid_groundtrouth.txt) 

used in verification. 

variable # SAS/Excel name Oracle Name 

1 mapgrid MAPGRID_CD 

2 year YEAR 

3 month MONTH 

4 day DAY 

5 maphab

6 obshab HABITAT_NR 

7 hab_chng

8 depcat

9 obsdepcat

10 dep_chng
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-19

Table D.8. Variables used in the Florida species master file (species_master_FL.xls) used in 

verification. 

variable # SAS/Excel name Oracle Name 

1 species SPECIES_CD 

2 latin SCIENTIFIC_NAME 

3 common COMMON_NAME 

4 family FAMILY_NAME 

5 com_fam COMMON_FAMILY 

6 specnum SPECIES_NR 

7 famnum FAMILY_NR 

8 max_size MAX_SIZE 

9 spectype SPECIES_TYPE 

10 bbtrawl

11 nps_creel

12 rvc_FL

Table D.9. Variables associated with the Oracle tables and their descriptions. 

Table Variable# Variable Name Description

1 MASTER_SAMPLE_CD VARCHAR(16) NOT NULL

2 DIVER_NR NUMBER(4) NOT NULL

3 BUDDY_NR NUMBER(4) NOT NULL

4 YEAR NUMBER(4) NOT NULL

5 MONTH NUMBER(2) NOT NULL

6 DAY NUMBER(2) NOT NULL

7 PRIMARY_SAMPLE_UNIT VARCHAR(4) NOT NULL

8 STATION_CD VARCHAR(1)

9 REPLICATE_CD VARCHAR(1)

10 DIVE_START_TIME_HOURS NUMBER(2) NOT NULL

11 DIVE_START_TIME_MINUTES NUMBER(2) NOT NULL

12 DIVE_END_TIME_HOURS NUMBER(2) NOT NULL

13 DIVE_END_TIME_MINUTES NUMBER(2) NOT NULL

14 SAMPLE_START_TIME_HOURS NUMBER(2) NOT NULL

15 SAMPLE_START_TIME_MINUTES NUMBER(2) NOT NULL

16 SAMPLE_END_TIME_HOURS NUMBER(2) NOT NULL

17 SAMPLE_END_TIME_MINUTES NUMBER(2) NOT NULL

18 DIVE_DEPTH NUMBER(6,2)

19 SAMPLE_DEPTH NUMBER(6,2)

20 FISHING_GEAR VARCHAR(50)

21 SAMPLE_TYPE_NR NUMBER(4) NOT NULL

22 SAMPLE_DESCR VARCHAR(150)

23 UNDERWATER_VISIBILITY NUMBER(6,2)

24 LOG_COMMENTS VARCHAR(100)

25 FISH_BEFORE_FIVE NUMBER(5)

26 FISH_AFTER_FIVE NUMBER(5)

27 SPECIES_BEFORE_FIVE NUMBER(3)

28 SPECIES_AFTER_FIVE NUMBER(3)

29 SUBSTRATE_SWITCH NUMBER(1)

SAMPLE

INFO

30 SPECIES_SWITCH NUMBER(1)

1 DIVER_NR NUMBER(4) NOT NULL DIVERS 2 DIVER_NAME VARCHAR(20) NOT NULL

1 SAMPLE_TYPE_NR NUMBER(4) NOT NULL

SAMPLE TYPES 2 SAMPLE_TYPE VARCHAR(20) NOT NULL

3 SAMPLE_TYPE_DESCRIPTION VARCHAR(100) NOT NULL

 

 

 

 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-20

Table D.9 cont’d 

Table Variable# Variable Name Description

1 YEAR NUMBER(4) NOT NULL

2 PRIMARY_SAMPLE_UNIT VARCHAR(4) NOT NULL

3 STATION_CD VARCHAR(1) NOT NULL

4 MAPGRID_CD VARCHAR(10)

5 LAT_DEGREES NUMBER(11,7)

6 LON_DEGREES NUMBER(11,7)

7 SURFACE_TEMPERATURE NUMBER(5,2)

8 BOTTOM_TEMPERATURE NUMBER(5,2)

9 SURFACE_SALINITY NUMBER(5,2)

BOAT LOG 

PHYSICAL

10 BOTTOM_SALINITY NUMBER(5,2)

1 MAPGRID_CD VARCHAR(10) NOT NULL

2 REGION_NR NUMBER(3)

3 SUBREGION_NR NUMBER(3)

MAPGRID 

DETAILS

4 MPA_NR NUMBER(3)

1 YEAR NUMBER(4) NOT NULL

2 PRIMARY_SAMPLE_UNIT VARCHAR(4) NOT NULL PRIMARY SAMPLE 

UNIT INFO 3 HABITAT_NR NUMBER(4) NOT NULL

1 HABITAT_NR NUMBER(4) NOT NULL HABITAT TYPES 2 HABITAT_TYPE VARCHAR(100) NOT NULL

1 MASTER_SAMPLE_CD VARCHAR(16) NOT NULL

2 SUBSTRATE_MAX_DEPTH NUMBER(6,2)

3 SUBSTRATE_MIN_DEPTH NUMBER(6,2)

4 HARD_VERTICAL_RELIEF NUMBER(5,2)

5 SOFT_VERTICAL_RELIEF NUMBER(5,2)

6 SAND_PERCENTAGE NUMBER(3) NOT NULL

7 HARDB_PERCENTAGE NUMBER(3)

8 RUBBLE_PERCENTAGE NUMBER(3)

9 SAND_BARE NUMBER(3)

10 SAND_ALGAL_TURF NUMBER(3)

11 SAND_MACRO_ALGAE NUMBER(3)

12 SAND_SEAGRASS NUMBER(3)

13 SAND_SPONGE NUMBER(3)

14 HARDBOTTOM_CRUSTOSE_ALGAE NUMBER(3)

15 HARDBOTTOM_ALGAL_TURF NUMBER(3)

16 HARDBOTTOM_MACRO_ALGAE NUMBER(3)

17 HARDBOTTOM_LIVE_CORAL NUMBER(3)

18 HARDBOTTOM_OCTOCORAL NUMBER(3)

SUBSTRATE INFO

19 HARDBOTTOM_SPONGE NUMBER(3)

1 MASTER_SAMPLE_CD VARCHAR(16) NOT NULL

2 TYPE NUMBER(2) NOT NULL

3 INDEX NUMBER(4) NOT NULL SURFACE RELIEF

4 VALUE NUMBER(3)

1 TYPE NUMBER(2) NOT NULL TYPE INDICES 2 NAME VARCHAR(20) NOT NULL

1 INDEX NUMBER(4) NOT NULL

2 LOWER_LIMIT NUMBER(5,2) NOT NULL

3 UPPER_LIMIT NUMBER(5,2) NOT NULL

4 ADDED_DATE DATE NOT NULL

SURFACE RELIEF 

MEASURING 

RANGES

5 DESCRIPTION VARCHAR(100)

1 MASTER_SAMPLE_CD VARCHAR(16) NOT NULL

2 TYPE NUMBER(2) NOT NULL

3 DESCRIPTION VARCHAR(25) NOT NULL

OTHER BIOTIC 

COVERS

4 PERCENTAGE NUMBER(3) NOT NULL

 

 

 

 

 

 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-21

Table D.9 cont’d 

Table Variable# Variable Name Description

1 MASTER_SAMPLE_CD VARCHAR(16) NOT NULL

2 SPECIES_NR NUMBER(4) NOT NULL

3 NUMBER_OF_INDIVIDUALS NUMBER(5)

4 AVERAGE_LENGTH NUMBER(5) NOT NULL

5 MIN_LENGTH NUMBER(5)

6 MAX_LENGTH NUMBER(5)

SPECIES

INFO

7 TIME_SEEN NUMBER(2)

1 SPECIES_NR NUMBER(4) NOT NULL

2 SPECIES_CD VARCHAR(8) NOT NULL

3 SCIENTIFIC_NAME VARCHAR(50)

4 COMMON_NAME VARCHAR(50)

5 FAMILY_NR NUMBER(4)

6 MAX_SIZE NUMBER(4)

SPECIES

7 SPECIES_TYPE NUMBER(2) NOT NULL

1 FAMILY_NR NUMBER(4) NOT NULL

SPECIES FAMILIES 2 FAMILY_NAME VARCHAR(30) NOT NULL

3 COMMON_FAMILY VARCHAR(50)

MASTER_SAMPLE_CD VARCHAR(16) NOT NULL

INDEX NUMBER(2) NOT NULL

IMAGES BLOB NOT NULL

IFS_LINK VARCHAR(50) NOT NULL

IMAGE_TYPE NUMBER(2)

SAMPLE IMAGES

PHOTOGRAPHER_NR NUMBER(4)
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure D: Data Entry and Proofing

D-22

Figure D.7. The Entity-Relationship diagram (ER diagram) of the schema with relationships 

between different tables in Oracle. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure E: Data Analyses and Reporting

E-1

Standard Operating Procedure E: 

Data Analyses and Reporting 

(Version 1.0) 

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E.1 Introduction 

The types of data analyses and reporting derived from the sample data will be specific 

to the types of management questions and resource goals that are being addressed. 

This section, however, describes some suggested analyses that should be applied to 

the data annually and before sampling commences in each subsequent season. 

E.2 Descriptive Ecological Analysis 

A basic descriptive ecological analysis should be completed annually based on that 

season’s data that includes a basic inventory and frequency of occurrence of all fish 

species observed as well as indices of fish biodiversity. The inventory of fish species 

and their frequency of occurrence should be specified by sub-region and 

management zone, and plotted spatially if warranted. Species composition should be 

assessed using the indices fish species richness and diversity. Richness is calculated 

simply as the number of species observed, but several types of diversity indices exist, 

including the Shannon index (Shannon and Wiener 1948), Simpson index (Simpson 

1949), and Pielou’s J (Pielou 1966). These indices integrate the numbers of species 

with their relative abundance, and are typically more complex measures of fish 

biodiversity. Both species richness and some measure of diversity (typically the 

Shannon index) should be calculated annually and considered by sub-region, 

management zone, and habitat type spatially across the sampling domain. 

E.3 Fishery Assessment and Calculation of Fish Stock Status Indices 

A primary motivation of the reef fish monitoring program is to evaluate changes in 

the population structures of commercially-important fish species. The eight focal 

species include: White grunt (Haemulon plumieri), Bluestriped Grunt (H. sciurus), 

Hogfish (Lachnolaimus maximus), Mutton Snapper (Lutjanus analis), Gray Snapper 

(L. griseus), Yellowtail Snapper (Ocyurus chrysurus), Red Grouper (Epinephelus 

morio), and Black Grouper (Mycteroperca bonaci). These fish species are 

ecologically and economically important, but their populations fluctuate in response 

to changes in the environment and/or fishing pressure. Therefore, a key component 

of annual data analysis should consist of calculating population measures for each of 

these species and comparing among management zones, and relative to sampling in 

years past. 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure E: Data Analyses and Reporting

E-2

Robust estimators of population “health” for the focal species above include the 

average density of species at different lifestages and the average length of the 

exploited phase individuals, L (Ault et al. 2001; Ault et al. 2005b). These two 

biological indicators should be calculated annually and compared to previous years, 

and between management zones with consideration to habitat. Mean density of 

lifestages and L should also be considered spatially across the domain. 

E.3.i Mean Density 

Mean fish density can be estimated for the entire domain (i.e., Florida Keys) or for a 

specified stratum of interest (i.e., habitat class, management zone, geographic subregion). Fish density, D, is the number of individuals observed per diver station (i.e., 

individuals observed/177m2

). However, because of dive safety considerations, the 

actual fish density for each diver station within a primary unit is actually the average 

density for the buddy team of divers (usually two, but sometimes three). There are 

typically two diver stations (second-stage units) sampled per primary unit. Therefore, 

the mean density within one primary unit i in stratum h is estimated as: 

= ∑

j

hij

hi

hi D

m

D 1 (Eq. E-1)

 

where mhi is the number of diver stations sampled in primary unit i and stratum h. 

Generally, this mhi is equal to 2, but there are occasions where a station is not sampled 

because one of the buddy teams must abort the dive. 

Mean fish density for an entire stratum h is then calculated as: 

= ∑

i

hi

h

h D

n

D 1 (Eq.E-2) 

Where nk is the number of primary units sampled in stratum h. 

To calculate the overall stratified mean density for the domain, stratum densities and 

a weighting factor are used: 

= ∑

h

hh st DwD (Eq.E-3) 

where wh is the stratum weighting factor. This weighting factor is calculated for each 

stratum as: 

∑

=

h

hh

hh

h MN

MN

w (Eq.E-4) 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure E: Data Analyses and Reporting

E-3

where Mh is the total possible number of diver stations within a primary unit and Nh is 

the total possible number of primary units in a stratum. The area of a stationary point 

count cylinder is approximately 177m2

 and the total area of a primary unit is 40,000m2 

(200 x 200m); therefore, the total possible number of diver stations within a primary 

unit, Mh, is equal to 226 for all strata. The total possible number of primary units in a 

stratum, Nh, is dependent on the area that the stratum extends over, and so values for 

Nh are derived directly from the GIS habitat maps. 

Overall stratified mean density and mean density for each stratum should be 

calculated separately for juvenile (size of first recruitment to the size of first maturity) 

and adult (size of first sexual maturity to maximum size) phases of each focal species, 

as these species are known to exhibit ontogenetic patterns among reef habitats 

through time. Calculations of mean densities should then be compared with 

consideration to changes through time and potential patterns in space. 

E.3.ii Average Size in the Exploited Phase ( L ) 

The average size of an animal (length or weight) in the exploited phase of the stock 

(Beverton and Holt 1957) is a physiologically-based indicator that is sensitive to 

direct and indirect stress on marine ecosystems (Ault et al. 2005b). It is highly 

correlated with average population size, and so reflects the rate of fishing mortality 

operating in the fishery. As fishing mortality rate increases, L decreases at a rate 

proportional to the population-dynamic tolerance of a stock (Ault et al. 2005b). L will 

decrease until it is nearly equal to the minimum size of first capture regulated by 

fishery management. By its definition, there also exists a value of L corresponding to 

a population size that produces maximum sustainable yields on a continuing basis. 

L at time t is defined as: 

∫

∫ = α

α

a

a

a

a

c

c

dataNtF

dataLtaNtF

tL

),()(

),(),()(

)( (Eq. E-5) 

where ac is the minimum age at first capture, aλ is the oldest age in the stock, N(a,t) is 

the abundance for age class a, L(a,t) is the length-at-age, and F(t) is the instantaneous 

fishing mortality rate at time t. 

E.3.iii Assessing Changes to Reef Fish Metrics 

An advantageous property of statistical sampling theory is that survey design 

estimates, such as stratum density and the variance of stratum density, do not require 

knowledge of the underlying probability distribution (e.g., normal, gamma, etc.) of 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure E: Data Analyses and Reporting

E-4

the respective population metric, (e.g., observations of stratum animal density, yhi) 

(Cochran 1977). A second property, based on large sample theory, is that survey 

design estimates (e.g., population means and totals) are normally distributed due to 

the central limit theorem if sample size is large. These properties facilitate the analysis 

of survey design estimates among times or areas (e.g., monitoring density over time, 

assessing MPA effectiveness). 

A simple, straightforward approach to performing statistical tests for differences 

among survey estimates for a particular time or area is via inspection of confidence 

intervals (CI). If the sample is relatively large (n > 100) and has a Normal distribution, 

the survey mean, st y , will lie within a CI bounded by: 

][ st ,/ dfk st ySEty ± α (Eq. E-6) 

With a probability of α, the Type I error rate, and where t is the critical value of 

Student’s t-distribution, and degrees of freedom d.f. = nh-1. Most commonly used reef 

metrics do not posses a Normal distribution which means the Type I error rate will 

not equal α. Cochran (1977) states α will be very close to what is expected if: 

 

 n > 25 2 G1

where 2 G1 is a Fisher’s measure of skewness. If a sample is too small and the 

population is heavily skewed, transforming the data (e.g., log[yst + 1], [yst]

2

) may help. 

With the cooperative effort of this program, this is typically not an issue. 

CIs can be used to test the hypothesis that samples were drawn from the same 

population, as is done to assess temporal change or determine MPA effectiveness. 

Cochran (1977), Sokal and Rohlf (2001), and Zar (1996) describe methods using CIs 

to test for differences among means. A comparison of multiple CIs (e.g., a time series) 

requires a Bonferoni adjustment to α. The Bonferoni adjustment is necessary because 

the true Type I error rate of simultaneous multiple tests is not α, as it should be for a 

single test. As the number of means (e.g. years) increases, however, a different 

adjustment may be more appropriate, for instance Tukey’s or SNK (Sokal and Rohlf 

2001). 

A useful relationship stemming from Equation E-6 is that the 95% CI for a population 

metric is approximately twice the CV, because the value of t for α = 0.05 and d.f. > 20 

is approximately 2. Thus, for example, a stratified random sampling survey that 

provides a domain-wide estimate of abundance with a CV of 15% would be able to 

statistically detect a minimum change of 30% in population abundance between 

survey time periods (with a Type I error rate = 0.05). 
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Standard Operating Procedure E: Data Analyses and Reporting

E-5

E.4 Multi-Species Fishery Stock Assessments 

Periodically, it is important to quantitatively assess stocks of the exploited reef 

species across the sampling domain and evaluate their status relative to established 

Federal and International benchmarks for sustainable management of fishery 

resources. Calculation of mean fish density by lifestage and L for each of the focal 

species is described above. Population dynamic parameters such as natural mortality 

rate, fishing mortality rate, spawning stock biomass, and spawning potential ratio 

may also be derived from the data set annually or when needed. Methodologies for 

computing these parameters from the data can be found in the scientific literature; 

for example, in Ault and Ehrhardt (1991), Ehrhardt and Ault (1992), and Ault and 

Olson (1996). 

E.5 Design Performance Analysis 

An analysis of the performance of the sampling allocation should be completed after 

each season. This analysis also aids in determining sampling allocation for the 

subsequent year as described in Section A.3 of SOP A. The performance of a 

sampling design is ultimately the result of trade-offs between the cost of surveying 

(usually measured by the number of samples) and the precision of population 

estimates. The performance measure that is typically used by this program is the 

coefficient of variation (CV), which is defined and discussed in detail in Section A.3 

of SOP A with an example detailed in Section A.5. 

Cooperative Coral Reef Fish Sampling & Assessment Protocol 

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Lit-i

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App 1-i

Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Appendix 1: Statistical Symbols and Computational Formulae Appendix 1: Glossary of Statistical Symbols and Computational Formulae Used In The Coral Reef Fish Sampling Survey. Symbol Definition Computational Formula Equation Number

h Stratum subscript 

i Primary sample unit subscript

j Second-stage sample unit subscript

hij T Area of 

jth second-stage unit in primary unit i in stratum 

h

hi

M Total possible number of second-stage units in primary unit i in stratum 

h

hi

a Area of ith primary unit in stratum 

h

∑=

=

hi M

j

hij hi Ta

1

h N Total possible number of primary units in stratum 

h

h A Area of stratum 

h

∑=

= h N

i

hi h aA

1

A Area of entire survey domain

∑

= h

h AA

hhMN Total possible number of second-stage units in stratum 

h

h w Stratum 

h weighting factor

∑

=

h

hh

hh

h MN

MN

w Eq A-5

hij F Number of individuals observed in second-stage unit 

j in 

primary unit i in stratum 

h

hij

D Density (individuals m-2) in second-stage unit 

j in primary 

unit i in stratum 

h

hij

hij

hij

F

D

T

=

hi

m

Number of second-stage units sampled in primary unit i in stratum 

h
App 1-ii

Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Appendix 1: Statistical Symbols and Computational Formulae hi

D Mean density in primary unit i in stratum 

h

∑

= j hij hi hi

D

m

D 1

h n Number of primary units sampled in stratum 

h

h D Mean density in stratum 

h

∑

= i hi

h

h D

n

D 1

2

1h s Sample variance among primary units i in stratum 

h ( )

1

2

2

1

−

−

=

∑

h

i

hhi

h n

DD

s Eq. A-2

2

2h s Sample variance among second-stage units 

j in stratum 

h

( )

∑

∑ ⎤

⎥⎥⎥⎦

⎡⎢⎢⎢⎣

−

−

= i hi

i

hi hij

h

h m

DD

n s 1

1

2

2

2 Eq. A-3

hhmn Number of second-stage units sampled in stratum 

h

st

D Domain-wide mean density for a stratified random survey

∑

= h hh st DwD

nm Number of second-stage units sampled in the survey domain

n Number of primary units sampled in the survey domain

][ st yCV Coefficient of variation of mean density

st

st

st

y

ySE yCV ][ ][

= Eq. A-7

suh Sample standard deviation in stratum 

h h

h

h uh

s

M

ss

2

2 2

1 −= Eq. A-4

m*h Optimum number of second-stage unit samples per primary unit in stratum 

h

uh

h

h s

s m

2

2 * = Eq. A-6

V Target variance for domain-wide mean density [ ] [ ] ( )

2

stst st DDCVDV ⋅= Eq. A-8
App 1-iii

Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Appendix 1: Statistical Symbols and Computational Formulae n* Number of primary unit samples required to achieve a specified variance [ ]

∑

∑ ∑ ∑

+

⎞⎟⎟⎠

⎛⎜⎜⎝

+

=

h h

hh

st

h h uhhh

hh

h

uhh uhh

N

sw DV

swm

sw

swsw

n 2

1

2

2

2

2

* *

Eq. A-1

n*h Optimal allocation of primary units among strata

⎞⎟⎟⎟⎠

⎛⎜⎜⎜⎝

=

∑h uhh

uhh

h

sw

sw *n*n Eq. A-9 

Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Appendix 2: Habitat Information Sheets

App 2-i

Appendix 2: Habitat Information Sheets 

The following pages are habitat information sheets formatted so that they can be 

printed directly onto sheets of underwater paper for use in the field. For this reason, 

no page numbers or headings are included. 

1st page: Stony Corals 

2nd page: Octocorals and Sponges 

3rd page: Macroalgae, Seagrasses, and Other 

4th page: Other (zooanthids), bottom of data sheet organisms, and living vs. bleached 

vs. recently dead coral identification 

Stony coral (scleractinia) morphotypes:

Massive:

All stony corals are

rigid and leave

behind reef

framework when

General coral anatomy:

STONY CORALS

M. B

framework when

they die. Polyps vary

in size and tentacles

are typically

retracted during the

day (exception is

pillar coral – bottom

right photo)

Polyp

A coral colony is made up

of genetically identical

polyps that are connected

b t/i k/ t di / i f / l i/

M. BrM. Br

Brandt

Branching: Small encrusting

colonies of A.

palmata. Note

the white

growing edges

and prominent

corallites

Acropora cervicornis Acropora palmata

**The presence/absence of either species should be noted

at the bottom of the data sheet**

www.sbg.ac.at/ipk/avstudio/pierofun/planci/

andtandt

M. Brandt

M. Brandt

corallites

M. Brandt

M. Brandt

Leafy, platey: Finger:

M. B

Fire corals

Other Black corals stony coral types: c.uk M. Brandt D. Schmitt

Brandt

M. Brandt

P. Human

P. Hu

Fire corals

http://coralpedia.bio.warwick.a

http://frank.itlab.us

n

umann

n

Unlike gorgonians, only tentacles come off of the

branches (left close‐up and diagram above), giving

colonies a pine tree‐like appearance. **Note the

presence of black coral at bottom of data sheet!**

Tend to be orange/tan in

appearance with white

tips/edges. Stinging polyps

look like sharp spines.

M. Brandt

P. Humann

J. Luo

Sheets assembled by M. Brandt (mbrandt@rsmas.miami.edu)
Octocoral morphotypes:

Sea fans:

Sea rods and plumes:

OCTOCORALS

P. H

M. Brandt

E ti i ft l k lik l Th t t

Humann

M. Brandt

J. Luo

Encrusting forms: Encrusting gorgonians often look like macroalgae. The two most common

species of encrusting gorgonians are Erythropodium caribaeorum (left) and

Briareum asbestinum (below). Erythropodium has brown tissue and long

tentacles that make it look “hairy”. Briareum has purple tissue with brown

tentacles that also make it look hairy or furry. When the tentacles are

retracted the ployps will often be apparent.

Briareum asbestinum

Erythropodium caribaeorum P. Humann

P. Humann

M. Brandt

Briareum asbestinum

Encrusting form is the purple  

and brown on the bases of the

colony. Top arrow indicates

where tentacles are extended,

b i di h

Upright form

encrusting form

n

bottom arrow indicates where

tentacles are retracted. Yellow

is live stony coral.

SPONGES

General sponge anatomy:

P. HumannP. Humann

M. BrandtM. BrandtM. Brandt

P. Humann

www.emc.maricopa.edu/faculty/farabee Live stony coral Sponge M. Brandt

M. Brandt

randt

Encrusting sponges include two species of

boring sponges, Cliona langue (left) and C.

delitrix (right). C. langue is brown and appears

smooth while C. delitrix is typically bright red

with conspicuous pores and osculums.

Live stony coral

Sponge

P. Humann

P. Humann

M. Br

Sheets assembled by M. Brandt (mbrandt@rsmas.miami.edu)
SEAGRASSES

www.igfa.org

Syringodium filiforme: Thalassia testudinum:

MACROALGAE

Macroalgae commonly found on hardbottom substrates:

Green calcareous 

(Halimeda opuntia) Green fleshy

N. Zurcher

www.utmsi.utexas.edu

Upright red calcareous

(Amphiroa rigida) 

f

P. Humann

Halophila baillonis:

M. Brand

M. Brandt

P. Humann

Brown fleshy (Dictyota sp.)

Brown fleshy 

(Turbinaria sp.)

Macroalgae commonly found on sand substrates:

Halimeda incrassata Caulerpa sertularioidesP. Humann P. Humann

M. Brandt t

Caulerpa cupressoides Penicillus pyriformis P. Humann

P. Humann

nn

Brown fleshy 

(Padina jamaicensis)

Crustose coralline algae (“algae <1cm”). Only found on hard 

substrates and is usually red or purple in color:

Brown fleshy 

(Sargassum sp.)

h

“OTHER” (1)

Anemones:

Stichodactyla helianthus

(Padina jamaicensis)

M. Brandt

Porolithon pachydermum

Humann & DeLoach

P. Humann

P. H

Peyssonnalia sp.

M. Brandt

Stichodactyla helianthus can occur in dense clusters and may 

look like stony coral. Look for flimsy edges of individuals.

Mat tunicate:

Trididemnum solidum

Can look like an 

encrusting sponge 

but it is a tunicate

Humann

www.izuzuki.com

P. Humann

P. Humann

but it is a tunicate. 

Appears as a 

green mat with slits 

that are the 

excurrent

openings.

Sheets assembled by M. Brandt (mbrandt@rsmas.miami.edu)
“OTHER” (2)

Palythoa caribaeorum (Order: Zooanthid): The polyps of the stony coral 

Montastraea cavernosa (below and 

right) and the zooanthid Palythoa 

caribaeorum (left) look very similar.

Montastraea cavernosa

Montastraea cavernosa

M. 

P. Humann

**Palythoa should 

be** classified as 

“other”

M. Brandt

Brandt

P. Humann

M

Montastraea faveolata (stony coral)

M.cavernosa

M. cavernosa: usually dark in color 

(unless bleaching). When polyps 

M

Montastraea faveolata (stony coral)

. Brandt

Palythoa

( g) p yp

are open, the mouths are a light 

color. When touched, the colony 

feels hard and slimy.

Palythoa caribaeorum (zooanthid)

A ii

Bottom of the data sheet Living vs. bleached vs. recently dead stony coral:

M

Palythoa: pale in color. When polyps are open, the mouths are 

hollow and deep. When touched, the colony feels soft and rubbery. M. Brandt

Acropora palmata 

(Elkhorn coral)

Acropora cervicornis 

(Staghorn coral)

BrandtBrandt

Living tissue: Corallites well defined, tentacles can 

sometimes be observed, no sediment on tissue.

Bleached coral: Tissue still present, algal symbionts absent 

or degraded giving colony a pale or bleached appearance.

Recently dead coral: Tissue absent. Sediment can settle 

and some algal colonization may have begun <1 day after 

death.

Old dead coral: Tissue absent, skeleton degraded, heavy 

M. Brandt

M. Brandt

M. BM. B

Normal living 

tissue

sediment and algal colonization. Dead coral can appear 

alive if corallite structure not degraded (e.g., brain corals 

and Montastraea cavernosa often retain their corallite

structure long after death). 

M. Brandt

J. Luo

Diadema antillarum 

(Long-spined sea urchin)

M. Brandt

S b i

Panulirus argus

(Spiny lobster)

Bleached 

tissue

Recently 

dead

NOAA

M. Brandt

Strombus gigas

(Queen Conch)

Sheets assembled by M. Brandt (mbrandt@rsmas.miami.edu)

M. BrandtM. Brandt
Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Appendix 3: Printable Data Sheets

App 3-i

Appendix 3: Printable Data Sheets

The following pages are data sheets formatted so that they can be printed directly 

onto sheets of underwater paper for use in the field. For this reason, no page 

numbers or headings are included. 

1st page: Field/Boat Log form 

2nd page: Water Quality/Environmental Log form 

3rd page: Fish/Habitat Data Sheet 

Reef Fish Visual Census (RVC) FIELD/BOAT LOG DATE

 Page of

Dive Site Est. Diver LATITUDE LONGITUDE Habitat

of Day ID Time Team Buddy Team (Diver A / Diver B) deg. minutes deg. minutes Code * GPS# Comments

* Habitat Codes

1 - Contiguous reef, Spur-Groove 5 - Sand-Seagrass-HB matrix

2 - Contiguous reef, Other 6 - Artifical reef3 - Isolated reef structure(s) 0 - Sand4 - Reef Rubble

Reef fish Visual Census (RVC) - Water Quality and Environmental Log

Date:

SurTemp Sur Sal BotTemp Bot Sal UW Visibility Clouds Curren

Dive of Day SiteID ( o C ) (ppt) ( o C ) (ppt) ( ft ) or ( m ) dir mph (% cover) (N,M,H

WATER QUALITY DATA ENVIRONMENTAL D

Wind

Diver: ___________________ Date: Field Number:

Buddy: __________________ Sample Start Time: Habitat type: Underwater visibility: _____ ft m

Dive Start Time:___________ Sample End Time: 1. Contiguous S&G

Dive End Time: Max Dive Depth: ft 2. Cont. Not S&G

 Substrate Slope Station Depth: ft 3. Isolated

Max depth _____________ft Fishing Gear:

Min depth _____________ft Biotic Cover - Dominant Biological Cover %

 Max vertical Relief SAND HARDBOTTOM

Hard Relief ____________m "Bare"

Soft Relief ____________m Abiotic Footprint Algal Turf (<1cm) Algae (<1cm) 

 Surface Relief Coverage % SAND % Macro Algae Algae (>1cm) 

 Hard Avg. of Soft HARD-B % Sea grass Live Stony Coral 

 < 0.2 m % % RUBBLE % Sponge Octocoral 

0.2-0.5 m %% Total 100% ________ Other 1 Sponge 

0.5-1.0 m % % ________ Other 2 _________ Other 1 

1.0-1.5 m % % _________ Other 2 

 > 1.5 m % %

TOTAL 100% 100% TOTAL 100% 

Species N Avg Min Max Species N Avg Min Max

_ _ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _

_ _ _ _ _ _ _ _

_ _ _ _ _ _

Comments:

_ _ _ _ _ _

_ _ _ _ _ _

_ _ _ _ _ _

Presence of: A. palmata A. cervicornis Black Coral

_ _ _ _ _ _ Spiny Lobster # Conch # Diadema #

_ _ _

_ _ _

_ _ _

_ _ _

 5. (Matrix) Radius of cylinder: 7.5m 5.0m

 4. Rubble Water temperature: _________ F

_ _ _

_ _ _

_ _ _

_ _ _

_ _ _

_ _ _

 0. (Sand) Current: None Mod. High

100%

 Crustose Algae 

_ _ _

_ _ _

_ _ _

_ _ _

_ _ _

_ _ _

Cooperative Coral Reef Fish Sampling & Assessment Protocol 

Appendix 4: FMRI 1998 – Benthic Habitats of the Florida Keys

App 4-i

Appendix 4: Benthic Habitats of the Florida Keys 

The following is the metadata directly obtained from NOAA’s website that 

accompanies the original thematic benthic habitat map layers of the South Florida 

region. These layers were developed by a cooperative effort between NOAA and the 

Florida Department of Environmental Protection and published as a Florida Marine 

Research Institute technical report (FMRI 1998). Further information can be found 

at: http://flkeysbenthicmaps.noaa.gov/welcome.html. 
Metadata for Florida Keys Benthic Habitats digital

geography

last updated July 1998

Digital geographies are in geographic coordinates, datum = NAD83, spheroid =

GRS1980.

GENERAL INFORMATION

Name: BENTHIC_G

Title: FLORIDA KEYS AND BISCAYNE BAY BENTHICS

Library: BENTHIC

Feature

Type: POLYGON

Geographic

Extent:

THE FURTHERMOST WESTERN BOUNDARY OF THE FLORIDA KEYS

NATIONAL MARINE SANCTUARY (DRY TORTUGAS)

NORTH TO WHERE 215TH STREET NORTHEAST IN

DADE COUNTY INTERSECTS BISCAYNE BAY

Creation

Date: UNKNOWN

Projection: GEOGRAPHIC COORDINATES, DECIMAL DEGREES, NAD83

Precision: SINGLE

Datum: NORTH AMERICAN DATUM OF 1983

Accuracy:

ACCURACY OF DISCRETE POINTS IS WITHIN TWO METERS. SHORELINE

AND REEF HABITATS HAVE AN ACCURACY OF FIVER METERS. SEAGRASSES

AND OTHER LESS RESISTANT HABITATS HAVE AN ACCURACY OF 10

METERS.

Purpose: TO VISUALLY REPRESENT GEOSPATIAL DATA.

Description

- Abstract:

POLYGON GEOGRAPHY TO VISUALLY REPRESENT THE BENTHIC HABITATS

GEOSPATIAL DATA OF SOUTH FLORIDA.

Report last

modified: 19980521

DATA SOURCE INFORMATION

Organization: FISH and WILDLIFE RESEARCH INSTITUTE

Contact: KATHLEEN O'KEIFE

Address: 100 8TH AVENUE S.E., ST. PETERSBURG, FL 33701-5095

Phone

Number: 727/8968626

Electronic

mail: Kathleen.OKeife@MyFWC.com

Scale: UNKNOWN

Benthic Habitats of the Florida Keys - Metadata http://flkeysbenthicmaps.noaa.gov/data/gis_files/benthic_habitats.html

1 of 8 3/16/2009 3:40 PM
Projection: GEOGRAPHIC COORDINATES, DECIMAL DEGREES, NAD83

Precision: SINGLE

Datum: NORTH AMERICAN DATUM OF 1983

Accuracy:

ACCURACY OF DISCRETE POINTS IS WITHIN TWO METERS. SHORELINE

AND REEF HABITATS HAVE AN ACCURACY OF FIVER METERS.

SEAGRASSES AND OTHER LESS RESISTANT HABITATS HAVE AN

ACCURACY OF 10 METERS.

Source

Format: UNKNOWN.

DISTRIBUTION INFORMATION

QA/QC

Status: COMPLETE

Distribution

Status: AVAILABLE

Data Format: ARC/INFO EXPORT FILE (.e00), ARCVIEW SHAPEFILE

FWRI

Contact: KATHLEEN O'KEIFE

FWRI

Address:

FLORIDA FISH AND WILDLIFE CONSERVATION COMMISSION, FISH AND

WILDLIFE RESEARCH INSTITUTE, 100 8TH AVENUE S.E., ST.

PETERSBURG, FL 33701-5095

FWRI Phone: 727/896-8626

Minimum mapping unit = 0.4 hectare (1 acre) for all habitat. Patch reefs may be <0.5

ha.

DATA DICTIONARY

Polygon attributes used in Benthic Habitat geography

01. Item:

A_CODE ALPHA CODE FOR THE BENTHIC HABITATS

 Type: Character

 Length: 5

 Decimals: 0

 Format: N/A

 Mandatory: N

Default Values: N/A

 Item Values:

 BM CARBONATE MUD

BMd CARBONATE MUD; DREDGED/EXCAVATED

 BO ORGANIC MUD

 BS CARBONATE SAND

BSb CARBONATE SAND; BANKS

BSd CARBONATE SAND; DREDGE/EXCAVATED

 BUd BOTTOM UNKNOWN; DREDGED/EXCAVATED

 CB BACK REEF

CPA AGGREGATED PATCH REEFS

CPB CORAL PATCHES IN BARE SAND

Benthic Habitats of the Florida Keys - Metadata http://flkeysbenthicmaps.noaa.gov/data/gis_files/benthic_habitats.html

2 of 8 3/16/2009 3:40 PM
 CPH HALO

 CPI INDIVIDUAL PATCH REEF

 CPIH INDIVIDUAL PATCH REEF AND HALO

 CPR REMNANT REEF

 CPSD REEF CONTAINING DROWNED SPUR AND GROOVE

 CPSS REEF CONTAINING SHALLOW SPUR AND GROOVE

 CR REEF RUBBLE

 h2o UNCLASSIFIED OCEANIC WATER

 HC SOFT CORAL,SPONGES,ALGAE

 HCb SOFT CORAL,SPONGES,ALGAE; BANKS

 HS HARDBOTTOM WITH PERCEPTIBLE SEAGRASS

 HSb HARDBOTTOM WITH PERCEPTIBLE SEAGRASS; BANKS

 HSd HARDBOTTOM WITH PERCEPTIBLE SEAGRASS;

DREDGRED/EXCAVATED

 InW UNCLASSIFIED INLAND WATER

 LAND LAND

 SD MODERATE TO DENSE, CONTINUOUS BEDS

 SDb MODERATE TO DENSE, CONTINUOUS BEDS; BANKS

 SDd MODERATE TO DENSE, CONTIUOUS BEDS; DREDGED/EXCAVATED

 SDdr MODERATE TO DENSE, CONTIUOUS BEDS;

DREDGED/EXCAVATED; RESTORATION

 SDr MODERATE TO DENSE, CONTIUOUS BEDS; RESTORATION

 SDB MODERATE TO DENSE, CONTIUOUS BEDS WITH BLOWOUTS

 SDBb MODERATE TO DENSE, CONTINUOUS BEDS WITH BLOWOUTS;

BANKS

 SDBd MODERATE TO DENSE, CONTIUOUS BEDS WITH BLOWOUTS;

DREDGED/EXCAVATED/RESTORATION

 SDBdr MODERATE TO DENSE, CONTIUOUS BEDS;

DREDGED/EXCAVATED; RESTORATION

 SDBr MODERATE TO DENSE, CONTIUOUS BEDS WITH BLOWOUTS;

RESTORATION

 SPA LARGELY MACROALGAL COVER WITH SCATTERED SEAGRASS

PATCHES

 SPAb LARGELY MACROALGAL COVER WITH SCATTERED SEAGRASS

PATCHES; BANKS

 SPH DENSE PATCHES OF SEAGRASS (>50%) IN A MATRIX OF

HARDBOTTOM

 SPHb DENSE PATCHES OF SEAGRASS (>50%) IN A MATRIX OF

HARDBOTTOM; BANKS

 SPHd DENSE PATCHES OF SEAGRASS (>50%) IN A MATRIX OF

HARDBOTTOM; DREDGED/EXCAVATED

 SPP DOMINANTLY SAND OR MUD WITH SMALL SCATTERED SEAGRASS

PATCHES (<50%)

 SPPb DOMINANTLY SAND OR MUD WITH SMALL SCATTERED SEAGRASS

PATCHES (<50%); BANKS

 SPPd DOMINANTLY SAND OR MUD WITH SMALL SCATTERED SEAGRASS

PATCHES (<50%); DREDGED/EXCAVATED

 SPS DENSE PATCHES OF SEAGRASS IN A MATRIX OF SPARSE

SEAGRASS

 SPSb DENSE PATCHES OF SEAGRASS IN A MATRIX OF SPARSE

SEAGRASS; BANKS

Benthic Habitats of the Florida Keys - Metadata http://flkeysbenthicmaps.noaa.gov/data/gis_files/benthic_habitats.html

3 of 8 3/16/2009 3:40 PM
SS SPARSE, CONTINUOUS BEDS

SSb SPARSE, CONTINUOUS BEDS; BANKS

 U UNMAPPABLE/UNKNOWN BOTTOM

 

02. Item:

AREA_METER AREA OF BENTHIC HABITAT IN SQUARE METERS

 Type: Integer

 Length: 16

 Decimals: 0

 Format: N/A

 Mandatory: N

Default Values: 0

 Item Values: N/A

ADDITIONAL METADATA - 1

Benthic Habitats of the Florida Keys Classification System (Data Dictionary)

Cross Reference Table of ARCINFO benthic_g geography and the ArcView Project files.

The benthic habitat types found in the ArcView project files are provided below. Listed in

parentheses with each benthic habitat type is the equivalent a_code(s) found in the

ARCINFO benthic habitat geography.

Within the ArcView project, benthic habitat modifiers (b - banks; d - dredged/excavated;

r - restoration) are provided as a separate thematic layer. As a result, they are not

included in this list.

Also within the ArcView project, land (LAND) is provided as a separate thematic layer.

As a result, it is not included in this list.

ArcView Shape File Polygon Type

A_CODE in the

BENTHIC_G ARCINFO

geography

Bare Substrate - Carbonate Mud BM

Bare Substrate - Carbonate Sand BS

Bare Substrate - Organic Mud BO

Continuous Seagrass - Dense Patches in a Matrix of Sparse

Seagrass (<50%) SPS

Continuous Seagrass - Moderate to Dense SD

Continuous Seagrass - Sparse SS

Hardbottom - Perceptible Seagrass (<50%) HS

Hardbottom - Soft Corals, Sponges, Algae HC

Inland Water InW

Patch Reefs - Aggregated CPA

Patch Reefs - Aggregated with Halo CPIH

Patch Reefs - Coral or Rock Patches with Bare Sand CPB

Patch Reefs - Halo CPH

Patch Reefs - Individual CPI

Patchy Seagrass - Dense Patches in a Matrix of Hardbottom SPH

Patchy Seagrass - Moderate to Dense with Blowouts SDB

Patchy Seagrass - Predominantly Microalgae Cover with

Scattered Seagrass Patches SPA

Patchy Seagrass - Predominantly Sand and-or Mud with Small,

Scattered Seagrass Patches (<50%) SPP

Benthic Habitats of the Florida Keys - Metadata http://flkeysbenthicmaps.noaa.gov/data/gis_files/benthic_habitats.html

4 of 8 3/16/2009 3:40 PM
Platform Margin Reefs - Back Reef CB

Platform Margin Reefs - Drowned Spur and Groove CPSD

Platform Margin Reefs - Reef Rubble CR

Platform Margin Reefs - Remnant - Low Profile CPR

Platform Margin Reefs - Shallow Spur and Groove CPSS

Unknown Bottom BU; U

More Metadata - 2

Descriptions of Benthic Habitats found in both the benthic_g ARCINFO geography and

the ArcView project files.

I. Coral Reefs

 A. Patch Reefs

 

Discrete coral communities, typically dome-shaped, usually outside of Hawk

Channel, with a few inshore. Can be linear features where several or a series

occurs. Mostly off Key Largo and Elliot Key (5,000) with a few off Big Pine, near

Key West, and at the Dry Tortugas. Usually composed of hard corals Montastraea

sp., Siderastrea sp., Diploria sp., and Colpophyllia sp.. Often surrounded by a

whitish appearing halo.

 1. Individual Patch (CPI)

 Isolated, barely visible on aerial photography, with or without a halo.

 2. Aggregated patch reefs (CPA)

 More than one, usually too close together to map individually or where halos

coalesce.

 3. Halo (CPH)

 

Barren, essentially unvegetated, variable, whitish zone around patch reef

resulting from grazing activity of urchins and fishes. Rubble from weathering

of patch reef may allow attachment sites for corals to expand the colony. Not

always present or large enough to be mapped.

 4. Individual Patch Reef and Halo (CPIH)

 Patch reef and halo combination too small to delineate directly on aerial

photography. Delineations of reef and halo performed during compilation.

 B. Platform Margin Reef

 

Generally, the "reef tract" or "barrier reef." Extends from northern boundary of

the Florida Keys National Marine Sanctuary to west of the Marquesas Keys and

also found at the Dry Tortugas. Diverse communities variable in morphology and

species composition. Both high and low relief. Includes all coral/hardbottom

features distinguishable from "patch reefs."

 1. Spur and Groove

 a. Shallow (e.g., Looe Key) (CPSS)

 

Well developed systems on "fore-reef" at major bank reefs on reef tract,

with vertical relief to about 4m. Actively growing upward and outward.

Distinctive signature on aerial photography due to shallow water (0 -

10m) and high vertical relief. Linear length to approximately 1000m or

more.

 b. Drowned (Transitional = older, drowned) (CPSD)

 

Older, not actively growing (probably eroding) features often being buried

by sand migration from shallower zone of reef tract. Nearly typical spur

and groove signature in aerial photographs, but sometimes with less

resolution or definition. Usually low profile, about 0.5 - 1.5m. Visible to

interpretable depth of photography (10m). Often greater linear length

than shallow spur and groove.

 2. Remnant - Low profile (CPR)

Benthic Habitats of the Florida Keys - Metadata http://flkeysbenthicmaps.noaa.gov/data/gis_files/benthic_habitats.html

5 of 8 3/16/2009 3:40 PM
 

Coral/hardbottom features not exhibiting distinctive signature of spur and

groove reefs. Usually parallel to line of reef tract, but may form transverse

features perpendicular to the reef tract. Relief from less than 0.5m - 1 or 2m.

 C. Coral Patches in Bare Sand (CPB)

 

Very sparse features that are similar in nature to patch reefs, but are on the

outer reef tract. These areas are dominantly sand or a veneer of sand over low

relief rock. Scattered throughout are small patches ranging from a single

gorgonian, sponge, or small coral head up to a low assemblage that may be a few

meters to 10m across. These patches make up a low percentage of the total

cover, yet are distinctive. This class is found mainly in the area from Big Pine

Shoal to Sombrero Light, and may be associated with the lack of a developed

forereef structure in this area.

 D. Back Reef (CB)

 

Shallow (<2m) platform landward of spur and groove features on bank reefs,

typically rubble zone colonized with numerous soft corals and pioneering

staghorn, fire and other hard corals. Corals here are widely spaced individuals on

a rubble platform.

 E. Reef Rubble (CR)

 

Zone landward of bank reefs and other high energy reef tract areas where

unstable rubble exists with little or no visible colonization. In relatively shallow

water (1 - 6m) often in association with Thallassia or Syringodium. Signature on

the aerial photographs is distinctive from other coral/hardbottom communities.

May form transverse features perpendicular to line of reef tract.

II. Hardbottom (Inshore only, stops at Hawk Channel for the Florida Keys National

Marine Sanctuary)

Solid, flat, low-relief substrate composed of Key Largo limestone (from west end of

the Newfound Harbor Keys off Big Pine to the north edge of the Florida Keys National

Marine Sanctuary) or Miami oolite (Big Pine Key and west). Depth ranges from

intertidal to approximately 7m in deep tidal channels and the inside edge of Hawk

Channel. May include a thin veneer of carbonate sand or mud, too thin and unstable

to support seagrass.

 A. Soft Coral, Hard Coral, Sponge, Algae (HC)

 

Benthic community (no perceptible seagrass) is variable and typically a function

of sediment, water, depth, and exposure to wind and current. May also include

solitary hard corals, Porites sp., Sideratrea sp., and Manicina sp.. Shallowest

zones (<1m) may include only attached or drift algae; soft corals are usually

more common in deeper zones.

 B. Hardbottom with perceptible seagrass (<50%) (HS)

 

Usually in patches, seagrasses occur in depressions and basins where adequate

sediment has accumulated, but constitute <50% bottom coverage. Hard bottom

may include solitary hard corals and soft corals, but most often sponges and

benthic algae (attached or in draft).

III. Bare Substrate

Open and essentially unvegetated, with no benthic community visible on

photographs, due to unstable nature of substrate. Can be large seagrass blowouts or

active erosional features. Largest areas are on reef tract, in the bottom of Hawk

Channel and west of the Marquesas Keys. May have sparse, ephemeral benthic algae

or diatom films that are not detectable on photography. Diatom films may develop in

a few days.

 A. Carbonate Sand (usually exposed locations) (BS)

 Sand-size carbonate sediments, usually in areas exposed to current and wind

energy that continually sort out and remove finer sediment fractions.

 B. Carbonate Mud (usually protected location) (BM)

 Fine carbonate sediments in deep water (Hawk Channel) or locations protected

from wind and wave energy. More depositional than erosional.

 C. Organic Mud (BO)

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On windward shorelines where drift seagrass and algae builds up in intertidal and

shallow water. Continual deposition and resuspension of organic matter limits

development of benthic community on natural as well as disturbed shorelines.

Especially common feature on windward shorelines of Big Pine, No Name, and

Little Pine Keys.

IV. Seagrass

 A. Moderate to Dense, continuous beds (SD)

 

Solid, continuous Thalassia, Syringodium, and Halodule, individually or in mixed

beds. Widespread in occurrence with range in depth from intertidal (bank) to

approximately 10m.

B. Moderate to Dense, nearly continuous beds (seagrass>50%), with blowouts

and/or sand or mud patches. (SDB)

 

Solid, continuous Thalassia or Syringodium, rarely Halodule, individually or in

mixed beds. Widespread in occurrence with range in depth from intertidal (bank)

to approximately 10m. Moderate to high energy regimes. Here, blowouts or

patches are dispersed as holes in otherwise continuous seagrass beds. Usually

found on reef tract and near entrances to tidal channels and passes. A common

habitat in back country of middle keys with large water movements between the

Gulf of Mexico and Atlantic Ocean.

 C. Sparse, continuous beds (SS)

 

Areas where seagrasses occur in low density (<50 shoots/m sq.). Typically in

shallow protected bays where physical conditions or substrate limits

development. May be hard to distinguish signature on aerial photographs from

barren bottom, requiring ground truthing.

 D. Patchy

 

Typically the result of depressional basins or creek-like features in seabed that

accumulate sediment or contain organic peat deposits from mangrove community

occurring during lower sea level. This greater depth of sediment allows seagrass

development in an area, or allows denser seagrasses compared to surrounding

areas. Widespread feature in inshore areas throughout the Florida Keys National

Marine Sanctuary and Biscayne Bay.

 1. Dense patches of seagrass (>50%) in a matrix of Hardbottom. (SPH)

 

One of the most common habitat types; patches occur in areas where a thin

sediment layer over flat natural rock precludes development of seagrasses.

Often numerous in number, highly visible on aerial photographs.

 2. Dense patches of seagrass in a matrix of sparse seagrass. (SPS)

 

Depressional features with deep sediment allow denser development of

seagrasses than on surrounding bottoms where only a thin layer may be

present. May be difficult to discern on aerial photographs from seagrass

patches in hardbottom. May occur more in deeper water or protected bays.

 3. Dominantly sand or mud with small scattered seagrass patches (<50%). (SPP)

 

Large sand features with recognizable seagrass patches. Similar location to

seagrass with blow-outs. Substrate may vary from sand to mud, and algae,

either fixed or drift, may be a significant component. Offshore features tend

to be more sandy, and inshore protected areas tend to be muddier in

composition.

 4. Largely MacroAlgal cover with scattered seagrass patches. (SPA)

 

Scattered seagrass patches are a significant habitat component, but dominant

is background of macroalgae. Algal cover is banks of Halimeda sp. or Pencillus

sp. May be difficult to delineate on aerial photographs without ground

truthing.

V. Special Modifiers

Special Modifiers are attached to a specific community type when applicable. Ex.

SDb; BSDBr

 A. Banks (Xb)

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Intertidal seagrass and some hardbottom communities, even if only intertidal at

spring low tides, often open water features or extending out from a shoreline.

Distinctive signature on aerial photographs compared to surrounding bottom.

Sometimes burned off patches are present on bank top. If these patches become

large enough, they are mapped as separate bare areas.

 B. Dredged/Excavation (Xd)

 Those locations where dredging or excavation has occurred for channels, rock

mines, or anchorages.

 C. Restoration (Xr)

 

Site of fill placement or backfilling of dredged area to restore original elevations

and intertidal or benthic community. Modifier applied to resulting benthic

community. Local knowledge of restoration sites necessary.

VI. Bottom Unknown, Unmappable, or Uninterpretable (BU; U)

This refers to those areas that are beyond the depth threshold of the aerial

photography (approximately 9m), and/or uninterpretable due to glare, or turbid

waters. Most narrow or deep access channels such as Key West Harbor, Hawk

Channel, or the deeper sides of the reef tract.

(top)

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