National Coral Reef Monitoring Program: Methodological Case Study for 'Downscaling Ecological Trends from the Spatially Randomized Datasets' in the Main Hawaiian Islands, 2005-07-14 to 2016-08-24 (NCEI Accession 0211127)
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title: National Coral Reef Monitoring Program: Methodological Case Study for 'Downscaling Ecological Trends from the Spatially Randomized Datasets' in the Main Hawaiian Islands, 2005-07-14 to 2016-08-24 (NCEI Accession 0211127)
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abstract: The data described here result from the application of a down-scaling method to NOAA National Coral Reef Monitoring Program (NCRMP) benthic cover data, in an attempt by the Pacific Islands Fisheries Science Center (PIFSC) Ecosystem Sciences Division (ESD) to make NCRMP data maximally useful to reef managers. ESD scientists took benthic cover data from the Main Hawaiian Islands from 2005-2016 and applied a statistical technique based on contiguous clustering and mixed model analysis to discover an optimal reporting sector for NCRMP data (Oliver et al. 2020). Specifically, clusters were identified based on NCRMP benthic cover data collected by ESD from 4 survey methods (towed diver, line point intercept, and photoquadrat surveys in which benthic images were analyzed either using CoralNet or CPCe) and then the optimal size and number of spatial sectors was assessed to generate reporting sector assignments that balanced minimal size against maximal ecological homogeneity and statistical power. These assignments are recorded in the dataset along with the source benthic cover observations, including live hard coral cover, soft coral cover, crustose coralline algae cover, macroalgal and turf algae cover, sediment cover, and all other categories are binned into "other".
purpose: To make NOAA National Coral Reef Monitoring Program (NCRMP) data maximally useful to managers, we explore the application of contiguous clustering and mixed model analysis to reduce the size of statistically robust reporting sectors. The NOAA National Coral Reef Monitoring Program (NCRMP) details a long-term approach to provide an ecosystem perspective via monitoring climate, fish, benthic, and socioeconomic variables in a consistent and integrated manner. The NCRMP coordinates various Coral Reef Conservation Coral Reef Program (CRCP) biological, physical, and human dimensions activities into a cohesive NOAA-wide effort. Through the implementation of the NCRMP, NOAA is able to clearly and concisely communicate results of national-scale monitoring to national, state, and territorial policy makers, resource managers, and the public on a periodic basis. NCRMP is a framework for conducting sustained observations of biological, climate, and socioeconomic indicators at 10 priority coral reefs areas across the U.S. and its territories. This integrated approach consolidates monitoring of coral reefs under a uniform method in the Pacific, Atlantic, Caribbean, and the Gulf of Mexico for the first time. NCRMP is funded by the CRCP and supported by NOAA Fisheries, NOAA National Centers for Coastal Ocean Science (NCCOS), and many other partners. The Ecosystem Sciences Division (ESD) at NOAA Fisheries is leading biological monitoring in the U.S. Pacific Islands Region. The biological component of NCRMP in the Pacific provides a triennial ecological characterization at a broad spatial scale of general reef condition for reef fishes, corals and benthic habitat (i.e., fish species composition/density/size, benthic cover, and coral density/size/condition). Innovative analysis techniques are then used to develop products that give fellow scientists, managers, decision makers and the public a better understanding of a region's resources and how they are changing over time.
credit: Related Funding Agency: NOAA Coral Reef Conservation Program
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title: Oliver, Thomas A.; Barkley, Hannah; Couch, Courtney S.; Kindinger, Tye; Williams, Ivor D. Downscaling Ecological Trends from the Spatially Randomized Datasets of the National Coral Reef Monitoring Program. NOAA technical memorandum NMFS-PIFSC; 106. 2020. https://doi.org/10.25923/2fef-8r42
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individualName: Oliver, Thomas A.
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Anchor: https://www.ncei.noaa.gov/archive/archive-management-system/OAS/bin/prd/jquery/institution/details/1670 US DOC; NOAA; OAR; OSS; NOAA Central Library
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name: NOAA technical memorandum NMFS-PIFSC ; 106
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beginPosition: 2005-07-14
endPosition: 2016-08-24
supplementalInformation: Submission Package ID: K15BKL
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fees: In most cases, electronic downloads of the data are free. However, fees may apply for custom orders, data certifications, copies of analog materials, and data distribution on physical media.
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description: Parameter or Variable: REEF AND/OR BOTTOM REGIME - PERCENT COVER (calculated); Units: percent; Observation Category: derived products; Sampling Instrument: Not applicable; Sampling and Analyzing Method: In the tech memo linked to and associated with this dataset, we present a statistical technique based on contiguous clustering and mixed model analysis to downscale the NCRMP Pacific Reef Assessment and Monitoring Program benthic cover data and apply it to a case study in the main Hawaiian Islands. Data Compilation: First, we summarize relevant data across methodologies and metrics. Data selected include benthic cover data from line-point intercept, benthic towed diver, and stratifed-random photoquadrat surveys (analyzed either in CPCe or CoralNet). A key step in this process is to thoughtfully, with an understanding of the respective methods, compile data into an analyzable dataset. Benthic categories selected for the analysis include hard live coral, soft coral, crustose coralline algae (CCA), macro and turf algae, sediment, and other. Hierarchical Contiguous Clustering: To perform the clustering, we first convert points to polygons using Voronoi tessellation, define a neighbor-joining network and assign branch lengths based on ecological distance across a number of benthic cover categories, and then prune the network into a minimum-spanning tree to set up for evaluating the quality of defined clusters. Select the Appropriate Number of Clusters: With the generation of a minimum spanning tree, we have a data structure that represents a hierarchically nested set of clusters, but we do not yet know the appropriate number of clusters. To assess the appropriate number of clusters to generate, we primarily balance the number/size of sectors against the statistical performance of the cluster set, as our other goals are inherently dealt with in the methodological approach. Mixed Model Analysis of Trends: Given a chosen level of clustering and the spatial polygons, we can define spatial sectors with which to run our analysis and apply hierarchical mixed models to evaluate long-term trends.; Data Quality Method: Accuracy of the sector-level estimates depend on sample size within the sector, and detailed descriptions of model fit are included in the technical memo associated with this dataset. The sectors presented here are defined by all benthic cover data available from NCRMP for the main Hawaiian Islands, 2005-2015. In analysis of trends, we also added the post-bleaching, 2016, data. This analysis was designed to as closely represent the conceptual vision given available data. The NOAA National Coral Reef Monitoring Program (NCRMP) runs thorough quality control procedures described in the original survey records. Our analysis was reviewed by all co-authors, their respective Division chiefs, and NOAA Fisheries technical and editorial review by the Pacific Islands Fisheries Science Center..
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