Hawaii Coral Reef Assessment and Monitoring Program (CRAMP): Benthic Data from 1999-2001 (NODC Accession 0000969)

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Frequently anticipated questions:

What does this data set describe?

Hawaii Coral Reef Assessment and Monitoring Program (CRAMP): Benthic Data from 1999-2001 (NODC Accession 0000969)
This dataset consists of CRAMP surveys taken in 1999-2001 and includes quantitative estimates of substrate type, species type, and percent coverage. Fish data are included in a separate submission. The types and coverages were derived objectively from photographic images using PointCount99, a software package which analyzes random points on images of coral reefs and substrate. This dataset does not include the images from video transects however these have been provided to NOAA separately. Photoquadrats are not included in this set. There are 32 survey sites, with 27 of these having both a shallow and deep transect. These sites are located on Kauai, Oahu, Maui, Kahoolawe, and Hawaii. Typically, one sampling date was made for each site per year. Annual surveys are scheduled at these sites and additional sites through at least 2002. This dataset replaces datasets previously given to NODC with NODC Accessions Numbers 0000757 and 0000513.
NOAASupplemental:Entry_ID: UnknownSensor_Name: SCUBA, Video cameraSource_Name: manualProject_Campaign: Hawaii Coral Reef Assessment and Monitoring Program (CRAMP)Originating_Center: Hawaii Institute of Marine Biology University of Hawaii at ManoaStorage_Medium: Excel, ASCIIOnline_size: 390 megabytes

Resource Description: NODC Accession Number 0000969

  1. How should this data set be cited?

    Jokiel, Dr. Paul , Hawaii Institute of Marine Biology, Oceanography, Department Of , School of Ocean and Earth Science and Technology, Hawaii, University Of , Brown, Mr. Eric , Hawaii Institute of Marine Biology, Oceanography, Department Of , School of Ocean and Earth Science and Technology, Hawaii, University Of , Friedlander, Dr. Alan , and Institute, The Oceanic , Unpublished material, Hawaii Coral Reef Assessment and Monitoring Program (CRAMP): Benthic Data from 1999-2001 (NODC Accession 0000969).

    Online Links:

    • https://accession.nodc.noaa.gov/969

  2. What geographic area does the data set cover?

    West_Bounding_Coordinate: -159.7273
    East_Bounding_Coordinate: -155.0171
    North_Bounding_Coordinate: 22.2109
    South_Bounding_Coordinate: 19.5118

  3. What does it look like?

  4. Does the data set describe conditions during a particular time period?

    Beginning_Date: 06-Jun-1999
    Beginning_Time: 0900
    Ending_Date: 01-Dec-2001
    Ending_Time: 1500
    Currentness_Reference: ground condition

  5. What is the general form of this data set?

  6. How does the data set represent geographic features?

    1. How are geographic features stored in the data set?

    2. What coordinate system is used to represent geographic features?

  7. How does the data set describe geographic features?

    Data organized by the following subdirectories:all_in_one/ and sites/The all_in_one/ directory has the original file as receivedfrom Eric Brown. The file contains all data for all stations.To make access easier, files were made for each site and eachyear, which can be found in the directory sites/.This dataset provides the results from PointCount99 for the videotransects only. It includes an ASCII text file dump from the MSAccess database of the PointCount output and an MS Excel97 code table,CRAMP99codesum.xls, discussed further down. Directories, files, andsizes are summarized:DIRECTORY FILE SIZE (BYTE)data/all_in_one ben99_00.txt 195929555data/sites ccccc_yyyyy.txt varieswhere ccccc is the site ID (see #SAMPLING STATIONS above,used the first 5 characters of column one), and yyyy is year.The CSV format has the following fields per record:YearIsland - 2 letter for each islandKa: Kauai; Oa: Oahu; Ma: Maui; Ke: KahoolaweSite - 3 letter code for each site within an islandDepth - metersSurveyDate - month/day/year and time (usually 0:00:00, not available)Latitude - degrees.minutes.decimal minutesLongitude - degrees.minutes.decimal minutesthe Status - conservation status (i.e. MLCD, NARS, KIR, blank(csv) means open access)Transect - transect #Frame - frame # on the transectAnalyInstitution - where the analysis was doneAnalyDate - Date of PointCount analysisFrameIder - person who did the PointCount analysisTotalPoint - number of points IDed on each frameType - substrate typeTaxonName - substrate identification for each pointTaxonID - PointCount # ID which is a subset of the Bishop Museum codes(see code explanation below)Point - Point number on the frameX - X coordinate on the image for each pointY - Y coordinate on the image for each pointIntensity - value for the pointRed - RGB value on the imageGreen - RGB value on the imageBlue - RGB value on the imageTaxa codes in PointCount output are provided in MS Excel97 file:CRAMP99codesum.xlsThe codes sheet was dumped into a CSV format in text file:taxacodes.csv
    Entity_and_Attribute_Detail_Citation: None

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)

  2. Who also contributed to the data set?

    Department of Commerce, National Oceanic and Atmospheric Administration Hawaii Coral Reef Initiative National Oceanic and Atmospheric Administration, National Ocean Service United States Geological Survey State of Hawaii, Department of Land and Natural Resources, Division of Aquatic Resources Kahoolawe Island Reserve Commission United States Fish and Wildlife Service, Coastal Program Limahuli National Botanical Garden Save Our Seas

  3. To whom should users address questions about the data?

    Dr. Paul Jokiel
    Hawaii Institute of Marine Biology University of Hawaii
    Principal Investigator
    P.O. Box 1346
    Kaneohe, Hawaii 96744

    808-236-7440 (voice)

Why was the data set created?

To understand the ecology of Hawaiian coral reefs in relation to other geographic areas and to monitor change at each given site. CRAMP experimental design allows detection of changes that can be attributed to various factors such as: overuse (over-fishing, anchor damage, aquarium trade collection, etc.), sedimentation, nutrient loading, catastrophic natural events (storm wave impact, lavaflows), coastal construction, urbanization, global warming (bleaching), introduced species, algal invasions, and fish and invertebrate diseases. The emphasis of the program is on the major problems facing Hawaiian coral reefs as listed by managers and reef scientists during workshops and meetingsheld in Hawaii (1997-1998). These are: over-fishing, sedimentation, eutrophication, and algal outbreaks. CRAMP experimental design gives priority to areas where baseline data relevant to these issues were previously collected. Transect dimensions, number of replicates, and methods of evaluation have been selected to detect changes with statistical confidence. Standard techniques include the establishment of permanent transects to quantify fish, coral, algae, and invertebrates at study sites. CRAMP researchers are quantifying changes that have occurred on coral reefs subjected to varying degrees of fishing pressure, sedimentation, eutrophication, and algal growth and are conducting experimental work in order to test hypotheses concerning the role of these environmental factors in the ecology of coral reefs. We are also in the process of resurveying, updating and integrating existing ecological information on an array of coral reefs that have been designated as areas of concern or, "hot spots," by managers and scientists.

How was the data set created?

  1. From what previous works were the data drawn?

    Brown and others, 1999 (source 1 of 5)
    Brown, E., Cox, E., Tissot, B., Rodgers, K., and Smith, W., 1999, Evaluation of benthic sampling methods considered for the Coral Reef Assessment and Monitoring Program (CRAMP) in Hawaii.

    International Conference on Scientific Aspects of Coral Reef Assessment, Monitoring, and Restoration. April 14-16, Ft. Lauderdale, FL.
    Type_of_Source_Media: paper
    Source_Contribution: benthic sampling methods

    Connell and others, 1997 (source 2 of 5)
    Connell, J. H. , Hughes, T. P. , and Wallace, C. C. , 1997, A 30-year study of coral abundance, recruitment, and disturbance at several scales in space and time: Ecol. Mono. 67(4): 461-488..

    Type_of_Source_Media: paper
    Source_Contribution: 30 year coral study

    Friedlander and Parrish, 1998 (source 3 of 5)
    Friedlander, Alan, and Parrish, James, 1998, Habitat characteristics affecting fish assemblages on a Hawaiian coral reef: Journal of Experimental Marine Biology and Ecology 224: 1-30..

    Type_of_Source_Media: paper
    Source_Contribution: Habitat characteristics

    Green and Smith, 1997 (source 4 of 5)
    Green, R. H. , and Smith, S. R. , 1997, Sample program design and environmental impact assessment on coral reef.: Proc 8th International Coral Reef Symposium 2: 1459-1464..

    Type_of_Source_Media: paper
    Source_Contribution: Sample program design

    McCormick, 1994 (source 5 of 5)
    McCormick, Mark, 1994, Comparison of field methods for measuring surfacetopography and their associations with a tropical reef fish assemblage: Marine Ecology Progress Series 112: 87-96.

    Type_of_Source_Media: paper
    Source_Contribution: Field methods comparison

  2. How were the data generated, processed, and modified?

    Date: Unknown (process 1 of 1)
    CRAMP Protocol One of the major objectives of the CRAMP program during the first year was to establish a sampling protocol that could detect change in coral cover over time with sufficient statistical power (P>0.8). The first step involved the evaluation of historical methods to determine if any of these procedures could be incorporated into the CRAMP protocol. After careful analysis it was determined that only the fixed photoquadrats utilized by Dr. Steve Coles at Bishop Museum had sufficient power. The method, which samples a relatively small area, is suitable to address small-scale questions on coral growth, recruitment and mortality, but inference on general reef condition is difficult across broader sections of reef.The second step involved soliciting input from colleagues conducting coral reef monitoring programs in the Florida Keys and the Great Barrier Reef. Their general recommendation was to use digital video to sample coral cover over large areas of the reef. Before we could implement their designs, however, we had to evaluate the appropriateness of these techniques for Hawai`i. The following parameters in the sampling design were determined in the third step: 1. Repeatability and appropriate length of the transects using different methods 2. Observer variation within different methods 3. Number of points per frame to analyze 4. Number of frames per transect to analyze 5. Number of transects per depth to sample 6. Random versus fixed transects 7. Time and monetary considerations to optimize sampling design. The results of this evaluation were presented at the National Coral Reef Institute Conference in Florida and are summarized by the CRAMP research team (Brown, et al. 1999). Repeatability and appropriate transect length weretested using photoquadrats on a transect line sampled over a short time interval. Shorter transects of 10m were found to have higher precision(Ability to replicate quadrats on a transect) than transects of 25m and 50m. Photoquadrats produced similar results to visual estimation techniques, regardless of observer, but neither method yielded satisfactory precision. Digital video was evaluated at Hanauma Bay, Oahu over 2 time intervals separated by 84 days. It was assumed that overall coral cover would not change dramatically during this time period. Power curves were constructed using methods described by Zar (1999) for detecting a 10% change in coral cover across 2 time periods (Figure 1). Number of frames was more important in increasing power than number of points though the difference was not substantial. This is primarily due to the fact that more frames sample a larger portion of the habitat, which incorporates more of the heterogeneity of the substrate. A sample size of 10 transects per site appeared to be adequate for characterizing the coral cover using a power value of 0.8 set as a convention by Cohen (1988).Fixed transects were chosen over random for several reasons. First, it is difficult to properly implement a randomized protocol for transect placement without a map of benthic habitats that is geo-referenced. At present this does not exist for the state of Hawai`i. Second, the majority of the historical data uses fixed transect locations so integrating the current protocol with previous work will be simpler. Third, after the initial random setup the fixed transects should be easier to resample, thus reducing preparation time and ultimately costs to generate the random grid for subsequent transect measurements (Green and Smith, 1997). Fourth, randomized sampling of transects will have difficulty in detecting change in coral cover if reefs change dramatically over time. This is because the random protocol measures inherent spatial variation at each sampling period, which adds variance associated with spatial heterogeneity of the reef rather than changes or patterns that are time-related (Green and Smith, 1997). Fifth, using a repeated measures ANOVA design with fixed transects can provide additional information on population and community structure that is difficult to obtain with random transects (Hughes, 1996; Connell et al.1997). Sixth, the time and cost complications with random transects are not worth the broader inference about reef "condition" especially if the fixed transects are representative of habitat variation (Andy Taylor, personal communication). Finally, interpreting results from fixed transects is much easier for the general public and resource managers to comprehend than using a randomized sampling design. Time and monetary constraints were examined to determine the optimum sampling protocol. The analysis revealed that digital video collected more data perunit time than visual estimation, planar point intercept and photoquadrats.It was the most expensive option considered at $5,500 for the system butsince field time underwater is the principal limiting factor then thequantity of field data collected outweighs the expense. In addition, digital video and photoquadrats also enable archiving of the data for laterre-analysis to address additional questions. Based on the results from the evaluation procedure we have selected 2 methods to address changes in overall coral cover and growth, recruitment andmortality of benthic organisms. Digital video will be used to measure changes in coral cover by initially selecting at random, ten permanent (fixed)transects at 2 depths (3m and 10m). Each transect will be 10m in length andanalyzed using 20 randomly selected video frames with 50 randomly selected points per frame. Frequency of sampling will be once a year at each site. This should be sufficient to detect a 10% change in coral cover over time with high statistical power across of variety of habitats in Hawai`i. The second method will employ fixed photoquadrats to examine trends of individual organisms with regards to growth, recruitment and mortality. Five haphazardly selected photoquadrats at each depth contour will be established with 4 pins at each corner to ensure accurate repositioning of the frame. The frame dimension will sample 0.33 m2 of the substrate at a height of 0.5m from the bottom. Images of sessile organisms will be traced and digitized for 2D estimates of aerial coverage. Sampling will be scheduled once a year at each site in concordance with the digital video surveys. Site Survey Protocol Two types of protocol are utilized by CRAMP: Monitoring Protocol and Assessment Protocol. This submission to NOAA only includes data taken using the Monitoring Protocol. The Assessment Protocol is simply an abbreviated version of the Monitoring Protocol. The Assessment Protocol is a rapid method that is most useful for describing spatial relationships. The Assessment Protocol lacks the statistical power of the Monitoring Protocol to detect change in the benthos. The Assessment Protocol is a more cost-effective method for answering certain questions on the status of coral reefs. Monitoring Protocol - General DescriptionInstalling the fixed monitoring sites is a process that was generally completed by a team of six divers during a single dive. All primary sites have been installed. The initial monitoring of a given site was generally initiated at some time after installation. More detail on installation is discussed under the section on Benthic Monitoring. Upon reaching an established monitoring site site a number of tasks must be performed. CRAMP generally surveys one site (3 m and 10 m transect locations at each site)per day with a team of 6 divers. The deeper site is surveyed in the morning, the shallow site in the afternoon after a proper surface interval. The beginning of the transect is located by visual lineups and/or GPS by skindivers and marked with a dive flag to alert boaters of our presence and enable quick location by the divers. Subsequent SCUBA teams entering the water take materials needed for the survey (spooled transect tapes, rugositychain, video camera, photo-quadrat apparatus, extra marker pins, etc) and deposit the material near the start of the transect for use by the teamsduring the dive. The first SCUBA team to enter the water consists of two divers: the person doing the fish survey and a back-up diver who stays within visual range and photographs the fixed photo-quadrats as the fish survey proceeds. Estimates of fish species richness, abundance, and biomass are taken before the benthic transect lines are laid out so as to sample a relatively undisturbed habitat. The standard CRAMP fish transect is taken along a depth contour within the CRAMP grid of benthic transects, and consists of four, 5x25mtransects that are separated by 5m. The scientist doing the fish survey counts fish while deploying a 25 m line behind him/her. As the survey proceeds, two more SCUBA divers enter the water. One of the pair starts video taping the replicate benthic transects while the second deploys the transect tapes and records species information on the corals/algae located along each transect for later reference. The third team of two divers follows the video transect team and measures rugosity under the replicatetransects. Upon completion of the fish transect, the first dive team completes the photo-quadrats. As other teams complete their work they return to the start of the transect and begin taking up the transect tapes. During the survey, various divers complete additional functions. These include taking sediment samples, stabilizing or replacing lose transect pins, routine photography of organisms, description of habitats, making algae collections or various activities. The same procedure is carried out at the shallow site during the afternoon. In addition, at various times of the day (depending on time availability)two members of the group will skin dive with a dive flag and water proof GPS unit while describing and recording habitat distribution throughout the study site for later mapping efforts. Benthic Monitoring - The basic unit for long term CRAMP monitoring is a 100 m x 3 m transect corridor that follows a depth contour. The transect is divided into a grid of 1 m intervals along its length by 0.5 m intervals along its width. Stainless steel pins are driven along the length of the central line or "spine" (shown in yellow on diagram below) to serve as the reference point for installation of the 10 transects and five photoquadrats. The spine pins are marked by slipping a short length of plastic tubing over the pin to identify the pin as a "spine" pin. In addition, the first spine pin (0 m)is marked with a single cable tie, the fifth pin (50 m) is marked with two cable ties and the tenth pin (100 m) is marked with three cable ties. Video Transect Method: 1. Field Recording Data are taken using a Sony DCR-TRV900 Mini DV camcorder enclosed in an Amphibico VHDB0900 Dive Buddy Housing. During early 2000 we added a Quest Aqua-Lite dual head U/W video light system. The videographer follows the following procedure: While on the surface, the diver videotapes the landmark "line-ups" used to locate the site. These serve to identify the tape if there is any question of proper labeling. Also, the images can be frame-grabbed and subsequently printed and laminated for use when relocating the site. In many cases the use of landmarks is faster and more convenient than using the GPS position to relocate the transect site. The diver then goes to the bottom and videotapes a full 360 degree panorama of the site as part of the permanent video record. The diver proceeds to the start of the first 10 mtransect and records the transect number on the video through use of hand signals in front of the camera (number of fingers representing transectno.). The videographer then moves slowly (4 min per transect) along the 10 mtransect while videotaping the bottom at a distance of 0.5 m. Initially a rod attached to the camera was used to insure proper distance from the bottom. This has been replaced with two small underwater lasers that cross at 0.5 m, allowing the videographer to hold the distance constant by keeping an overlap on the two red laser dots. Each of the 10 transects along the 100m spine line is recorded in this manner. One digital videotape (1 hour tape)is used to capture 10 transects.2. Laboratory Data AnalysisEach transect is 10 m in length. Twenty randomly selected, non-overlappingvideo frames are selected and processed using PointCount99 software todevelop estimates for coral and substrate types. The statistical dataanalysis includes a repeated measures ANOVA design with nesting of transects in depth where frames per transect are treated as sub-samples along a transect. The video tape is played back on a computer using PhotoShop with the plug-in Photo DV to grab frames. Each transect video consists of approximately 7500-9000 frames. Sequential overlapping frames that form a complete 10 m transect are captured onto the hard disk in JPEG file format.The 10 transects consisting of ~50-60 images per transect are written to a CD-ROM. Twenty randomly non-overlapping frames per transect are selected and analyzed with PointCount99. PointCount99 generates 50 randomly located points on the screen. The observer records the proper category under each ofthe 50 points. PointCount99 writes a Comma Separated Value (CSV) file thatis generic text and readily available for a variety of programs. This CSVfile is imported into MS-Excel for proofreading. After proofreading the CSVfile is imported into MS-Access for storage into the CRAMP database.PointCount99PointCount99 is a Win95/98 based PC program derived from PointCountfor Coral Reefs which was developed in support of the United StatesEnvironmental Protection Agency's Florida Keys Coral Reef MonitoringProject (US EPA CRMP). The software utilizes the random point countmethod for accurately estimating percent coverage of corals, sponges, and associated substrate from digitally frame-grabbed underwater video images. Unlike its predecessor, PointCount for Coral Reefs, which operated in conjunction with Media Cybernetics Image-Pro Plus graphics software, PointCount99 is a stand-alone Visual Basic program built on AccusoftsImage Gear platform. Funding for the development of PointCount99 wasprovided by the Jeanette and Lafayette Montgomery Foundation. PointCount99 makes image identification an efficient process. It calls up an image file and overlays a unique set of points supplied by an internal random number generator. PointCount99 is also able to use a unique set of random points (cd.dat) created for, and stored along with, a set of images. The user identifies each point and enters the data via a mouse driven graphic user interface. Species and substrate identifications require only a single mouseclick. Corrections and multiple selections are easy to make, and hot keys areavailable to expedite the process. PointCount?99 also makes identifications easier by allowing the user to zoom in and out on images and enhance image quality with buttons for brightness/contrast, sharpness, and color levels.

    Person who carried out this activity:

    Dr. Paul Jokiel
    Hawaii Institute of Marine Biology University of Hawaii
    Principal Investigator
    P.O. Box 1346
    Kaneohe, Hawaii 96744

    808-236-7440 (voice)

    Data sources used in this process:
    • Brown and others, 1999
    • Connell and others, 1997
    • Friedlander and Parrish, 1998
    • Green and Smith, 1997
    • McCormick, 1994

  3. What similar or related data should the user be aware of?

How reliable are the data; what problems remain in the data set?

  1. How well have the observations been checked?

  2. How accurate are the geographic locations?

  3. How accurate are the heights or depths?

  4. Where are the gaps in the data? What is missing?


  5. How consistent are the relationships among the observations, including topology?

    See Lineage - Process Step

How can someone get a copy of the data set?

Are there legal restrictions on access or use of the data?

Access_Constraints: None
NOAA and NODC would appreciate recognition as the resource from which these data were obtained in any publications and/or other representations of these data.

  1. Who distributes the data set? (Distributor 1 of 1)

    NOAA/NESDIS/National Oceanographic Data Center
    Attn: Data Access Group, User Services Team
    SSMC-3 Fourth Floor
    Silver Spring, MD 20910-3282

    301-713-3277 (voice)
    301-713-3302 (FAX)

    Hours_of_Service: 8am-5pm, Monday through Friday
  2. What's the catalog number I need to order this data set?

    Downloadable Data

  3. What legal disclaimers am I supposed to read?

    NOAA makes no warranty regarding these data, expressed or implied, nor does the fact of distribution constitute such a warranty. NOAA and NODC cannot assume liability for any damages caused by any errors or omissions in these data, nor as a result of the failure of these data to function on a particular system.

  4. How can I download or order the data?

Who wrote the metadata?

Last modified: 24-Jan-2017
Last Reviewed: 28-Jul-2005
To be reviewed: 01-Aug-2006
Metadata author:
Mr. Patrick C. Caldwell
Hawaii/US Pacific Liaison
1000 Pope Road, MSB 316
Honolulu, Hawaii 96822

(808)-956-4105 (voice)
(808) 956-2352 (FAX)

Hours_of_Service: 8 AM to 5 PM weekdays
Contact_Instructions: check services@nodc.noaa.gov if not available
Metadata standard:
FGDC Content Standard for Digital Geospatial Metadata (FGDC-STD-001-1998)

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