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Geomorphological metrics characterizing benthic habitats including slope, rugosity, curvature, and convexity were derived using best available bathymetry for each area. The fish assemblages and abundance data were collected during Rapid Ecological Assessment (REA) surveys from 2010 to 2016. These fish data were collected according to a stratified random survey design using depth as an environmental correlate. Based on the analysis for Tutuila, American Samoa, preliminary evidence was found that using both depth and convexity to define strata may result in more precise estimates of fish biomass. This analysis was expanded to the main Hawaiian Islands for the subsequent year of the project, and found that including several other metrics in CREP's sampling design can enhance the estimates of fish biomass.

Results and data from the analysis for Tutuila, American Samoa can be accessed online via the Pacific Islands Benthic Habitat Mapping Center website at http://www.soest.hawaii.edu/pibhmc/pibhmc_documentation.htm#other_pubs.

The PIFSC administrative report from the analysis for the main Hawaiian Islands is in review as of Aug 2017 and will be available on the  PIFSC website once published at https://www.pifsc.noaa.gov/library/staff_publications.php.</gco:CharacterString>
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                <gco:CharacterString>NODC OBSERVATION TYPES THESAURUS</gco:CharacterString>
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                <gco:CharacterString>CoRIS Place Thesaurus</gco:CharacterString>
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                <gmd:URL>ftp://ftp.soest.hawaii.edu/pibhmc/website/webdocs/documentation/LinkagesReport_FINAL.pdf</gmd:URL>
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                <gco:CharacterString>A report detailing the preliminary analysis to examine linkages between reef fish assemblages and benthic habitat characteristics in Tutuila, American Samoa.</gco:CharacterString>
              </gmd:description>
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                <gmd:CI_OnLineFunctionCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#CI_OnLineFunctionCode" codeListValue="download">download</gmd:CI_OnLineFunctionCode>
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                <gco:CharacterString>Archive_LinkagesRawData.zip</gco:CharacterString>
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              <gmd:description>
                <gco:CharacterString>The ReadMe.txt file describes the CSV files included in the ZIP file. The csv files include all the data used in the pilot analysis detailed in the report for Tutuila. The name of each file includes a geomorphology metric and a number (0, 30, 50, or 100), corresponding to the radius of the spatial averaging buffer (i.e., four different spatial scales) used to generate the metric. 

The data dictionary, or definition of each field included in the CSV files is included in the ReadMe.txt file.</gco:CharacterString>
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                <gmd:URL>ftp://ftp.soest.hawaii.edu/pibhmc/website/webdocs/documentation/linkages_project_methods_final.pdf</gmd:URL>
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                <gco:CharacterString>A report detailing the methods to derive benthic terrain metrics and to characterize the benthic landscape using bathymetric data using SAGA software.</gco:CharacterString>
              </gmd:description>
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                <gmd:CI_OnLineFunctionCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#CI_OnLineFunctionCode" codeListValue="download">download</gmd:CI_OnLineFunctionCode>
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      <gmd:scope>
        <gmd:DQ_Scope>
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            <gmd:MD_ScopeCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#MD_ScopeCode" codeListValue="dataset">dataset</gmd:MD_ScopeCode>
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            <gco:CharacterString>Representativeness</gco:CharacterString>
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          <gmd:evaluationMethodDescription>
            <gco:CharacterString>Two datasets collected by NOAA Coral Reef Ecosystem Program (CREP) were used for Tutuila, American Samoa. Gridded bathymetry compiled from multibeam data collected in 2004 and 2006 was used to derive geomorphological data including aspect, slope, rugosity, curvature, and convexity. The other dataset is in-situ fish demographic data collected under the Pacific Reef Assessment and Monitoring Program and the NOAA National Coral Reef Monitoring Program between 2010 and 2015. Gridded bathymetry and geomorphological data were then spatially correlated to the fish demographic data.
For the main Hawaiian Islands, LiDAR (Light Detection and Ranging) collected by U.S. Army Corps of Engineers (USACE), JALBTCX (Joint Airborne Lidar Bathymetry Technical Center of eXpertise) in 2013 were used to derive geomorphologic data. In addition to the metrics generated for Tutuila, slope of slope was also derived for the main Hawaiian Islands.  The in-situ fish demographic data were collected between 2010 and 2016.</gco:CharacterString>
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          <gmd:evaluationMethodDescription>
            <gco:CharacterString>Geomorphological data inherit the accuracy of the source gridded bathymetry. The attribute and positional accuracies of the gridded multibeam bathymetry for Tutuila, American Samoa are reported in the metadata which can be found at http://www.coris.noaa.gov/metadata/records/html/tutuila_5m.html.  The accuracies of the gridded LiDAR data can be found for each island in the main Hawaiian Islands at https://coast.noaa.gov/htdata/lidar1_z/geoid12a/data/. For the fish demographic data, researchers are trained to identify and estimate/measure the size of fish. Both classroom and field training and tests must be completed for all researchers before each round of surveys begins. This training ensures that the surveys are conducted consistently by all researchers within survey efforts and also across periodic survey efforts.</gco:CharacterString>
          </gmd:evaluationMethodDescription>
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            <gco:CharacterString>Comparability</gco:CharacterString>
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            <gco:CharacterString>Fish demographic data used for this analysis were collected in 2010, 2012, and 2015 for Tutuila, American Samoa, and 2010, 2012, 2013, 2015 and 2016 for the main Hawaiian Islands. The target precision for these surveys is large enough (e.g., Coefficient of Variation less than 20%) that inter-annual change would likely only be detectable on a decade timescale. Therefore, all survey years used in this analysis are likely comparable, but could easily be addressed by running the analysis separate for all years.</gco:CharacterString>
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          <gmd:result gco:nilReason="missing" />
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            <gco:CharacterString>Completeness Measure</gco:CharacterString>
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            <gco:CharacterString>For Tutuila, American Samoa, multibeam bathymetry data were not available for shallow areas where the NOAA Ship Hi'ialakai (a 218-foot research ship) or R/V Acoustic Habitat Investigator (a 25-foot survey launch) were not able to access. Bathymetry derived from multispectral IKONOS satellite imagery was investigated for shallow areas to fill gaps; however, bathymetry derived from IKONOS imagery was not included in the analysis due to uncertainty of the attribute accuracies. Therefore, the fish demographic data collected in areas where multibeam bathymetry data is not available (i.e., shallow areas generally less than 6 meter  depths) were omitted from the analysis.

For the main Hawaiian Islands, LiDAR data were not available for Niihau and Kahoolawe islands, and parts of Lanai and Big islands. The fish sites surveyed in the areas where there is no LiDAR data available were removed from the analysis.</gco:CharacterString>
          </gmd:evaluationMethodDescription>
          <gmd:result gco:nilReason="missing" />
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      <gmd:report>
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            <gco:CharacterString>Precision</gco:CharacterString>
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          <gmd:evaluationMethodDescription>
            <gco:CharacterString>The target Coefficient of Variation (CV) for fish demographic data reported at the island-level is 20%.</gco:CharacterString>
          </gmd:evaluationMethodDescription>
          <gmd:result gco:nilReason="missing" />
        </gmd:DQ_QuantitativeAttributeAccuracy>
      </gmd:report>
      <gmd:report>
        <gmd:DQ_CompletenessCommission>
          <gmd:nameOfMeasure>
            <gco:CharacterString>Completeness Report</gco:CharacterString>
          </gmd:nameOfMeasure>
          <gmd:evaluationMethodDescription>
            <gco:CharacterString>This is only a preliminary analysis of the relationship between geomorphological data and fish biomass. For Tutuila, American Samoa, Convexity was chosen for further analysis based on a qualitative assessment. Due to the incompleteness of the bathymetry data in Tutuila, American Samoa described in the “Completeness Measure” section, ideally the analyses should be conducted for a location where bathymetry data is available for shallow areas. For the main Hawaiian Islands, Rugosity, Slope, Slope of Slope and Profile Curvature were chosen for the further analysis.</gco:CharacterString>
          </gmd:evaluationMethodDescription>
          <gmd:result gco:nilReason="missing" />
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      </gmd:report>
      <gmd:lineage>
        <gmd:LI_Lineage>
          <gmd:statement>
            <gco:CharacterString>This project involves two primary analyses: one is to derive geomorphological data from gridded bathymetry, and the other is to examine the linkage between derived geomorphological data and fish demographic data from in-situ biological surveys. The analysis was performed for Tutuila, American Samoa during first year of the project, and then for Main Hawaiian Islands during the second year of the project.</gco:CharacterString>
          </gmd:statement>
          <gmd:processStep>
            <gmd:LI_ProcessStep>
              <gmd:description>
                <gco:CharacterString>Source gridded multibeam bathymetry data for Tutuila, American Samoa.</gco:CharacterString>
              </gmd:description>
              <gmd:processor>
                <gmd:CI_ResponsibleParty>
                  <gmd:organisationName>
                    <gco:CharacterString>Pacific Islands Fisheries Science Center</gco:CharacterString>
                  </gmd:organisationName>
                  <gmd:contactInfo>
                    <gmd:CI_Contact>
                      <gmd:phone>
                        <gmd:CI_Telephone>
                          <gmd:voice>
                            <gco:CharacterString>808-725-5360</gco:CharacterString>
                          </gmd:voice>
                        </gmd:CI_Telephone>
                      </gmd:phone>
                      <gmd:address>
                        <gmd:CI_Address>
                          <gmd:electronicMailAddress>
                            <gco:CharacterString>pifsc.info@noaa.gov</gco:CharacterString>
                          </gmd:electronicMailAddress>
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                      </gmd:address>
                    </gmd:CI_Contact>
                  </gmd:contactInfo>
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          </gmd:processStep>
          <gmd:processStep>
            <gmd:LI_ProcessStep>
              <gmd:description>
                <gco:CharacterString>The first step was to generate a series of geomorphology benthic variables from multibeam bathymetry for the nearshore environment of Tutuila, American Samoa using open source GIS software, System for Automated Geoscientific Analyses (SAGA) 2.1.4. Six geomorphology variables were derived for this study. Detailed descriptions of the tools used are available in Watkins (2015). 
Slope, aspect and profile curvature were derived from the multibeam bathymetry with the Slope, Aspect, Curvature tool in SAGA using the default option of the nine parameter 2nd order polynomial method. 
Real surface area was derived using the Real Surface Area tool in SAGA, which was then also used to calculate rugosity, a measure of roughness, derived by dividing real surface area by the geometric surface area. 
Terrain surface convexity is measured as the percentage of convex-upward cells within a constant radius of ten cells. The terrain surface convexity tool in SAGA was used to derive this variable.</gco:CharacterString>
              </gmd:description>
            </gmd:LI_ProcessStep>
          </gmd:processStep>
          <gmd:processStep>
            <gmd:LI_ProcessStep>
              <gmd:description>
                <gco:CharacterString>For each of the benthic geomorphology variables, site-specific values were extracted for each fish survey location in Tutuila using the Sample tool available in Esri's ArcToolbox. In addition, geomorphology values were averaged across all cells within the available data within a radius of 30, 50, and 100 meters from the fish survey site. The Buffer tool in Esri's ArcToolbox was used to create the zone shapefile with the radius of 30, 50, and 100 meters of each fish survey site. The Zonal Statistics tool in Esri's ArcToolbox was then used to generate the mean value for each geomorphology variable for each site.</gco:CharacterString>
              </gmd:description>
              <gmd:processor>
                <gmd:CI_ResponsibleParty>
                  <gmd:individualName>
                    <gco:CharacterString>Acoba, Tomoko S</gco:CharacterString>
                  </gmd:individualName>
                  <gmd:contactInfo>
                    <gmd:CI_Contact>
                      <gmd:phone>
                        <gmd:CI_Telephone>
                          <gmd:voice>
                            <gco:CharacterString>(808)725-5448</gco:CharacterString>
                          </gmd:voice>
                        </gmd:CI_Telephone>
                      </gmd:phone>
                      <gmd:address>
                        <gmd:CI_Address>
                          <gmd:electronicMailAddress>
                            <gco:CharacterString>tomoko.acoba@noaa.gov</gco:CharacterString>
                          </gmd:electronicMailAddress>
                        </gmd:CI_Address>
                      </gmd:address>
                    </gmd:CI_Contact>
                  </gmd:contactInfo>
                  <gmd:role>
                    <gmd:CI_RoleCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#gmd:CI_RoleCode" codeListValue="processor">processor</gmd:CI_RoleCode>
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                </gmd:CI_ResponsibleParty>
              </gmd:processor>
            </gmd:LI_ProcessStep>
          </gmd:processStep>
          <gmd:processStep>
            <gmd:LI_ProcessStep>
              <gmd:description>
                <gco:CharacterString>A total of nine fish biomass metrics were derived from NOAA Coral Reef Ecosystem Program Rapid Ecological Assessment (REA) fish surveys for each survey site. The metrics include four trophic groups (primary consumers, secondary consumers, planktivores, piscivores), three size classes (0-20 centimeters; 20-50 centimeters; and 50+ centimeters), as well as parrotfishes, and total fish biomass.</gco:CharacterString>
              </gmd:description>
              <gmd:processor>
                <gmd:CI_ResponsibleParty>
                  <gmd:organisationName>
                    <gco:CharacterString>Pacific Islands Fisheries Science Center</gco:CharacterString>
                  </gmd:organisationName>
                  <gmd:contactInfo>
                    <gmd:CI_Contact>
                      <gmd:phone>
                        <gmd:CI_Telephone>
                          <gmd:voice>
                            <gco:CharacterString>808-725-5360</gco:CharacterString>
                          </gmd:voice>
                        </gmd:CI_Telephone>
                      </gmd:phone>
                      <gmd:address>
                        <gmd:CI_Address>
                          <gmd:electronicMailAddress>
                            <gco:CharacterString>pifsc.info@noaa.gov</gco:CharacterString>
                          </gmd:electronicMailAddress>
                        </gmd:CI_Address>
                      </gmd:address>
                    </gmd:CI_Contact>
                  </gmd:contactInfo>
                  <gmd:role>
                    <gmd:CI_RoleCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#gmd:CI_RoleCode" codeListValue="processor">processor</gmd:CI_RoleCode>
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                </gmd:CI_ResponsibleParty>
              </gmd:processor>
            </gmd:LI_ProcessStep>
          </gmd:processStep>
          <gmd:processStep>
            <gmd:LI_ProcessStep>
              <gmd:description>
                <gco:CharacterString>Scatterplots and trend lines were created to reveal patterns between each fish biomass metric and each of the geomorphology metrics. Based on this, convexity was chosen as a promising geomorphology metric that could potentially be informative for surveying fish biomass. Using the scatterplots and trend lines as a guide, bin boundaries for high, moderate, and low convexity were selected.</gco:CharacterString>
              </gmd:description>
              <gmd:processor>
                <gmd:CI_ResponsibleParty>
                  <gmd:individualName>
                    <gco:CharacterString>Gorospe, Kelvin D</gco:CharacterString>
                  </gmd:individualName>
                  <gmd:contactInfo>
                    <gmd:CI_Contact>
                      <gmd:phone>
                        <gmd:CI_Telephone>
                          <gmd:voice>
                            <gco:CharacterString>(808)725-5488</gco:CharacterString>
                          </gmd:voice>
                        </gmd:CI_Telephone>
                      </gmd:phone>
                      <gmd:address>
                        <gmd:CI_Address>
                          <gmd:electronicMailAddress>
                            <gco:CharacterString>kelvin.gorospe@noaa.gov</gco:CharacterString>
                          </gmd:electronicMailAddress>
                        </gmd:CI_Address>
                      </gmd:address>
                    </gmd:CI_Contact>
                  </gmd:contactInfo>
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                    <gmd:CI_RoleCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#gmd:CI_RoleCode" codeListValue="processor">processor</gmd:CI_RoleCode>
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          </gmd:processStep>
          <gmd:processStep>
            <gmd:LI_ProcessStep>
              <gmd:description>
                <gco:CharacterString>By combining the current NOAA Coral Reef Ecosystem Program sampling design's depth strata (shallow 0-6 meter depth, moderate 6-18 meter depth, deep 18-30 meter depth) and the new convexity strata, total reef area for each strata combination (e.g., deep and low convexity, deep and moderate convexity, deep and high convexity, moderate depth and low convexity, etc.) was calculated using ArcGIS.</gco:CharacterString>
              </gmd:description>
              <gmd:processor>
                <gmd:CI_ResponsibleParty>
                  <gmd:individualName>
                    <gco:CharacterString>Acoba, Tomoko S</gco:CharacterString>
                  </gmd:individualName>
                  <gmd:contactInfo>
                    <gmd:CI_Contact>
                      <gmd:phone>
                        <gmd:CI_Telephone>
                          <gmd:voice>
                            <gco:CharacterString>(808)725-5448</gco:CharacterString>
                          </gmd:voice>
                        </gmd:CI_Telephone>
                      </gmd:phone>
                      <gmd:address>
                        <gmd:CI_Address>
                          <gmd:electronicMailAddress>
                            <gco:CharacterString>tomoko.acoba@noaa.gov</gco:CharacterString>
                          </gmd:electronicMailAddress>
                        </gmd:CI_Address>
                      </gmd:address>
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                    <gmd:CI_RoleCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#gmd:CI_RoleCode" codeListValue="processor">processor</gmd:CI_RoleCode>
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          <gmd:processStep>
            <gmd:LI_ProcessStep>
              <gmd:description>
                <gco:CharacterString>Sampling design performance was evaluated for each fish biomass metric, by calculating n* (i.e., the number of samples required to attain a target coefficient of variation). This was done for two sampling designs: (1) using depth as a covariate for stratification and (2) using a combination of depth and convexity as covariates for stratification.</gco:CharacterString>
              </gmd:description>
              <gmd:processor>
                <gmd:CI_ResponsibleParty>
                  <gmd:individualName>
                    <gco:CharacterString>Gorospe, Kelvin D</gco:CharacterString>
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                  <gmd:contactInfo>
                    <gmd:CI_Contact>
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                        <gmd:CI_Telephone>
                          <gmd:voice>
                            <gco:CharacterString>(808)725-5488</gco:CharacterString>
                          </gmd:voice>
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                      </gmd:phone>
                      <gmd:address>
                        <gmd:CI_Address>
                          <gmd:electronicMailAddress>
                            <gco:CharacterString>kelvin.gorospe@noaa.gov</gco:CharacterString>
                          </gmd:electronicMailAddress>
                        </gmd:CI_Address>
                      </gmd:address>
                    </gmd:CI_Contact>
                  </gmd:contactInfo>
                  <gmd:role>
                    <gmd:CI_RoleCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#gmd:CI_RoleCode" codeListValue="processor">processor</gmd:CI_RoleCode>
                  </gmd:role>
                </gmd:CI_ResponsibleParty>
              </gmd:processor>
            </gmd:LI_ProcessStep>
          </gmd:processStep>
          <gmd:processStep>
            <gmd:LI_ProcessStep>
              <gmd:description>
                <gco:CharacterString>Steps 1-3 were repeated for the main Hawaiian Islands with the LiDAR data acquired by U.S. Army Corps of Engineers (USACE), JALBTCX (Joint Airborne Lidar Bathymetry Technical Center of eXpertise). The gridded LiDAR data were downloaded from the NOAA Data Access Viewer (https://coast.noaa.gov/dataviewer/#/). In addition to the geomorphologic metrics derived for Tutuila, American Samoa, Slope of Slope was also derived for the main Hawaiian Islands. Due to the large file size of the LiDAR data, the method to calculate the mean and standard deviation values of the metrics for each site was modified by calculating focal mean and standard deviation using Focal Statistics tool in ArcToolbox at radius of 30m, 50m and 100m before assigning value to each site.</gco:CharacterString>
              </gmd:description>
            </gmd:LI_ProcessStep>
          </gmd:processStep>
          <gmd:processStep>
            <gmd:LI_ProcessStep>
              <gmd:description>
                <gco:CharacterString>Steps 4-5 were repeated for the fish demographic data collected for the main Hawaiian Islands between 2010-2016 with the associated geomorphologic metrics derived from LiDAR. It is found that the means of rugosity, slope, and slope of slope, and standard deviation of profile curvature has correlations with fish biomass metrics, and further analysed to derive n* described in Steps 6-7.</gco:CharacterString>
              </gmd:description>
            </gmd:LI_ProcessStep>
          </gmd:processStep>
          <gmd:processStep>
            <gmd:LI_ProcessStep>
              <gmd:description>
                <gco:CharacterString>To demonstrate the improvement of the sampling design efficiency with the geomorphological metrics derived from LiDAR, the n* was also calculated with the depth and its geomorphological information from the 50-m grid maps used in the current NCRMP sampling design.</gco:CharacterString>
              </gmd:description>
            </gmd:LI_ProcessStep>
          </gmd:processStep>
          <gmd:source>
            <gmd:LI_Source>
              <gmd:sourceCitation>
                <gmd:CI_Citation>
                  <gmd:title>
                    <gco:CharacterString>Gorospe KD, Acoba TS. 2017. A survey design performance analysis examining linkages between reef fish assemblages and benthic morphologies in the Main Hawaiian Islands. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-64, 35 p.</gco:CharacterString>
                  </gmd:title>
                  <gmd:date>
                    <gmd:CI_Date>
                      <gmd:date>
                        <gco:Date>2017-11-01</gco:Date>
                      </gmd:date>
                      <gmd:dateType>
                        <gmd:CI_DateTypeCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#CI_DateTypeCode" codeListValue="publication">publication</gmd:CI_DateTypeCode>
                      </gmd:dateType>
                    </gmd:CI_Date>
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                    <gmd:CI_ResponsibleParty>
                      <gmd:organisationName>
                        <gco:CharacterString>Pacific Islands Fisheries Science Center</gco:CharacterString>
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                        <gmd:CI_Contact>
                          <gmd:onlineResource>
                            <gmd:CI_OnlineResource>
                              <gmd:linkage>
                                <gmd:URL>https://doi.org/10.7289/V5/TM-PIFSC-64</gmd:URL>
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                                <gco:CharacterString>WWW:LINK-1.0-http--link</gco:CharacterString>
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                              <gmd:name>
                                <gco:CharacterString>NOAA Institutional Repository</gco:CharacterString>
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