Long Term Monitoring

Rapid Assessment



Reference Site & Habitat Class Analogy
Reference Conditions
Classification of Habitats
Index of Biological Integrity
Hydrogeomorphic Model
Indicator Statistical Methods
Selection Criteria for Indicator Organisms
Indicator Results





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CRAMP Rapid Assessment. Indicator Statistical Methods

Ordination methods were used to highlight patterns in the data through spatial comparisons and habitat characterization. Ordination techniques can clarify habitat relationships and reveal trends and patterns with minimal expression of the noise typical of community data (Gauch 1982). Sample and species relationships are represented in a low-dimensional space with ordination techniques. Similar entities are placed close to each other while dissimilar species or samples are located far apart in ordination space allowing a visual representation of sample similarity.

Statistics were computed with Minitab 13.0. Explanatory variables were selected from among 23 environmental predictors. To avoid multicolinearity, variables that were highly correlated (>90%) were dropped from the analysis without loss of information (Clarke and Gorley 2001).

To determine which environmental variables best explain coral cover, species richness, fish biomass and fish numerical abundance, a general linear multiple regression models were used. A Best Subsets routine was used, applying Mallows Cp and R2 as the criteria in model selection. A lack of fit test was conducted to verify the model selection.

Although explored as a response variable, coral species richness may not be suitable since it is strongly dependent on sampling effort and observer variability, making it difficult to compare across sites. Richness values determined from coral cover data may miss some coral species in data collection.

Diversity was not used as a response variable since coral diversity is low in Hawai’i and may not be an appropriate indicator of environmental conditions in this region. Hawaiian communities are often dominated by a few primary species where diversity does not decline with decreasing latitude as in other regions (Grigg 1983). Due to geographic isolation, corals in Hawai’i are depauparate relative to the Indo-West Pacific. Only 16 genera containing 42 species have been documented from the Hawaiian Islands. Difficult field identification and detection of cryptic or deep species and low digital resolution may also reduce the predictive ability of diversity.

Multivariate statistical analyses were also conducted using Primer 5.0 and Multivariate Statistical Program version 3.0 (MVSP). These include the following statistical tools and techniques:

  • Correspondence analysis (CA)

  • A site similarity matrix was generated to evaluate species distributions.

  • A BIOENV procedure was used to link biological data to environmental data so that patterns in coral communities could be identified.

  • SIMPER was used to determine the contribution of each species to the dissimilarity between sites.

  • Discriminant analysis was used to determine if reference sites differed significantly from one another.


Clarke, K.R., and Gorley, R.N. 2001. PRIMER v5: user manual/Tutorial. PRIMER-E: Plymouth, United Kingdom. 91 pp.

Clarke, K.R., and Warwick, R.M. 2001. Change in marine communities: an approach to statistical analysis and interpretation. 2nd edition. PRIMER-E.: Plymouth, United Kingdom.

Gauch, H.G. Jr. 1982. Multivariate Analysis in Community Ecology. Press Syndicate of the University of Cambridge, New York, NY. 298 pp.

Grigg, R. W. 1983. Community structure, succession and development of coral reefs in Hawai‘i. Marine Ecology Progress Series 11: 1-14.


Last Update: 04/21/2008

By: Lea Hollingsworth

Hawai‘i Coral Reef Assessment & Monitoring Program

Hawai‘i Institute of Marine Biology

P.O. Box 1346

Kāne‘ohe, HI 96744

808-236-7440 phone

808-236-7443 fax