Hawaii Coral Reef Assessment and Monitoring Program (CRAMP): Benthic Data from 2002-2004 (NODC Accession 0002313)

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Frequently anticipated questions:

What does this data set describe?

Hawaii Coral Reef Assessment and Monitoring Program (CRAMP): Benthic Data from 2002-2004 (NODC Accession 0002313)
This dataset consists of CRAMP surveys taken in 2002-2004 and includes quantitative estimates of substrate and species type. From the data percent coverage of a given species can be estimated. The types and coverages were derived objectively from photographic images using PhotoGrid, a software package which analyzes random points on images of coral reefs and substrate. This dataset does not include the images from video transects or photoquadrats however these have been provided to NOAA separately. Fish transects were discontinued after 2002.

In 2002, there were 57 lines surveyed at 28 sites. Due to funding cuts, the number of surveys dropped in 2003 and 2004. There were 8 surveys provided to NODC for 2003 and 5 in 2004. A few more surveys during this time period could become available at a later date. Surveys typically consist of shallow (~3m) and deep (~10m) lines.

Sensor_Name digital camera Source_Name SCUBA Project_Campaign: Coral Reef Assessment and Monitoring Program (CRAMP) Originating_Center Hawaii Institute of Marine Biology Storage_Medium MS Excel and ASCII CSV Reference None Online_size: 110556 kilobytes
  1. How should this data set be cited?

    Jokiel, Dr. Paul , Rodgers, Dr. Kuulei , Brown, Mr. Eric , and Hawaii Institute of Marine Biology, Department Of Oceanography, School of Ocean and Earth Science and Technology, University Of Hawaii, Unknown, Hawaii Coral Reef Assessment and Monitoring Program (CRAMP): Benthic Data from 2002-2004 (NODC Accession 0002313).

    Online Links:

    • https://data.nodc.noaa.gov/accession/0002313

  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: 27-Mar-2002
    Ending_Date: 07-Sep-2004
    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?

    Directories separate for year 2002 and years 2003-2004 1. data/2002

    CSV (ASCII) output from the PhotoGrid for all surveyed lines.

    Filename template:


    where: yy: last two digits of year II: Island (Ka Kauai, Oa Oahu, Mo Molokai, Ma Maui, Ha Hawaii) S: site DD: depth m: always "m", meters yyyymmdd: survey date

    Fields in these files: Site Name - usually NA (not available) Station - usually NA Frame No - usually NA Image Date - usually NA, get survey (image) date from filename ID Name - equivalent to TaxonName in PointCount99, this is the species recorded but for some organisms if not identifiable to the species or even genus level then just to taxanomic level ID Code - usually NA

    The following are PhotoGrid parameters equivalent to PointCount parameters of the same name. Point - Point number on the frame X - X coordinate on the image for each point Y - Y coordinate on the image for each point Intensity - value for the point Red - RGB value on the image Green - RGB value on the image Blue - RGB value on the image

    Notes from Kuulei Rodgers concerning these parameters: "Point X and Y are the coordinates for each of the 50 points that are generated on an image. This way if you want to go back and check if it is correct or what someone called some organism it will regenerate the frame with the random points that were originally used. If for example you see Pavona maldivensis and want to see if that is correct because you don't think it is at that site and may have been interpreted, you can go back and look at point #7 to see what is under it. The program will use the coordinates to reconstruct the original random points on that frame. Red, Green and Blue are just the exact colors as the person who first did the analysis saw it. Since you can adjust the color balance and the contrast, the program saves the adjustments so it can be revisited if need be later."

    Filename - this is a critical parameter. It is the name of the image file. Convention is yyIISSSDDmTTFFF, yy : last two digits of year II : island SSS : site (see #STATIONS above) DDm : depth in meters TT : transect number FFF : frame number

    The remaining parameters can be ignored and are usually NA: Total Points,ID Date,Site ID,Site Code,Time Code,Institution,User Name,Habitat,WQS,Length,Depth

    Potential frequently asked question: -The CRAMP website lists available benthic data parameters: coral and substrate cover. Can these be derived from the PhotoGrid data given? How?

    Reply from Ku'ulei Rodgers: We use ACCESS, a relational database that calculates these for us but it can be done in EXCEL as well by sorting alphabetically and deriving a percent of the total for each substrate type. For example if you have 10 points that are Porites compressa and there are 20 frames with 50 points on each, this would be 10 out of 1000 points for the whole transect so 1% cover. This is then done for each substrate type. Then all the coral species percentages are added together for a total coral cover number.

    Within directory data/2002, there is a directory access/, which contains MS Excel spreadsheets that were made from various MS Access tables and queries. Redundant CSV files were made of each. Data are from 1999-2002. Files are:

    Filename Comments qryTaxonList.xls Taxon Name, Family, Species Code, synonym, Common Name, Hawaiian Name, Trophic, Endemic, mobility qryTaxonList.csv ASCII copy

    tblCoralSummary.xls Year, Site, Transect, Frame, Total of Taxon, Specific counts for taxa types, Total Coral tblCoralSummary.csv ASCII copy

    tblSite.xls SiteID, Island, Site, SiteName, Depth, Depth Code, Latitude, Longitude, Status, ReserveSize tblSite.csv ASCII copy

    tblSurvey.xls SurveyID, SiteID, Survey, Date, Year tblSurvey.csv ASCII copy

    tblTaxon.xls TaxonID, TaxonIDCode, Type, Family, SpeciesCode, TaxonName, synonym, Hawaiian Name, Common Name, Trophic, Endemic, Mobility tblTaxon.csv ASCII copy

    2. data/2003_4

    These are output from PhotoGrid as CSV files. Format same as described for the 2002 above.

    Files Comments 03OaAla03m.CSV Ala Wai, Oahu, 30 Nov 2003, 3m 03OaAla10m.csv same, 10m

    03OaHee02m.CSV Heeia, Oahu, 03 Oct 2003, 2m 03OaHee08m.CSV same, 8m

    03OaMok03m.CSV Moku o loe, Kaneohe Bay, Oahu, 23 Oct 2003, 3m 03OaMok08m.CSV same, 8m

    03OaWai02m.CSV Waiahole (Kaalaea), Kaneohe Bay, Oahu, 26 Sep 2003, 2m 03OaWai8m.CSV same, 8m

    04KaHan03m.CSV Hanalei, Kauai, 06 Sep 2004, 3m 04KaHan04m.CSV same, 4m 04KaHan08m.CSV same, 8m

    04KaLim.CSV Limahuli, Kauai, 07 Sep 2004, all depths

    04 Kamalo.CSV Kamalo, Molokai, 10 Mar 2004, all depths 04 Kamiloloa.CSV Kamiloloa, Molokai, 12 Mar 2004, all depths 04 Palaau.CSV Palaau, Molokai, 11 Mar 2004, all depths

    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 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 meetings held 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?

  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 were tested 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 per unit time than visual estimation, planar point intercept and photoquadrats. It was the most expensive option considered at $5,500 for the system but since field time underwater is the principal limiting factor then the quantity of field data collected outweighs the expense. In addition, digital video and photoquadrats also enable archiving of the data for later re-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 and mortality 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 and analyzed 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 Description

    Installing 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 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 skin divers 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, rugosity chain, video camera, photo-quadrat apparatus, extra marker pins, etc) and deposit the material near the start of the transect for use by the teams during 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, 5x25m transects 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 replicate transects. 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 and Digital Still Methods:

    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 m transect and records the transect number on the video through use of hand signals in front of the camera (number of fingers representing transect no.). The videographer then moves slowly (4 min per transect) along the 10 m transect 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 100 m spine line is recorded in this manner. One digital videotape (1 hour tape) is used to capture 10 transects.

    Digital stills replaced video transects in 2004. 20 images were taken per transect or 200 images per survey line.

    2. Laboratory Data Analysis

    PointCount99 was replaced with PhotoGrid starting in 2002. PhotoGrid was designed for CRAMP to output data in a PointCount format. They should be fully compatible except many of the categories are not applicable (N/A). The methodology of PhotoGrid software is similar to PointCount99.

    Each transect is 10 m in length. Twenty non-overlapping video frames or still images are selected and processed using Photogrid software to develop estimates for coral and substrate types. The statistical data analysis includes a repeated measures ANOVA design with nesting of transects in depth where frames per transect are treated as sub-samples along a transect.

    Brown, E, E Cox, B Tissot, K Rodgers, and W Smith (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.

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

    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.

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

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

    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)

  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?

    The 2002-2004 surveys were 100% complete

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

    see 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
Use_Constraints: Dataset credit required

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

    NOAA/NESDIS/NODC/NCDDC (National Coastal Data Development Center)
    National Coastal Data Development Center, Building 1100
    Stennis Space Center, MS 39529

    866-732-2382 (voice)
    228-688-2968 (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, NESDIS, NODC and NCDDC 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: 23-Mar-2009
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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