Data Management Plan
Pacific Islands Fisheries Science Center
Data Set (DS) | Cat ID: 59172 | Published / External
Data Management Plan
DMP Template v2.0.1 (2015-01-01)Please provide the following information, and submit to the NOAA DM Plan Repository.
Reference to Master DM Plan (if applicable)
As stated in Section IV, Requirement 1.3, DM Plans may be hierarchical. If this DM Plan inherits provisions from a higher-level DM Plan already submitted to the Repository, then this more-specific Plan only needs to provide information that differs from what was provided in the Master DM Plan.
1. General Description of Data to be Managed
The benthic cover and fishing-net related data described in this dataset are derived from the GIS analysis of benthic orthophotos. The source imagery was collected using a Structure from Motion (SfM) approach during in-water marine debris swim surveys conducted by snorkelers in search of derelict fishing nets. Surveys were conducted by the NOAA Fisheries, Ecosystem Sciences Division (ESD) from September 24 to October 3, 2018 at Pearl and Hermes Atoll during an ESD-led marine debris mission to the Northwestern Hawaiian Islands (NWHI) aboard the NOAA Ship Oscar Elton Sette. The lagoon at Pearl and Hermes was surveyed equally across the spatial gradient, from locations where derelict fishing nets are common to locations where derelict fishing nets have never been observed.
During the 2018 mission, only a subset of marine debris surveys resulted in a SfM survey. Fishing nets were located during swim surveys and selected for SfM if the net was interacting with coral or hard substrate, the depth of the net was within ~1–4 m of the surface, and the area of the net fit within the 9 sq. meter SFM survey plot. During a SFM survey, a permanent 3 x 3 m plot was established around the center of the fishing net, and the net was photographed using a back and forth swim pattern (“before” photos) for later processing using a SfM approach. The net was then removed, the volume of net removed was estimated and recorded, and the same area was photographed again in the same way (“after” photos). A nearby (>50 m distant) paired control site was also photographed using the same method (“control” photos).
The photographs were processed using Agisoft Metashape software to generate orthomosaic images that were analyzed in ArcGIS for benthic cover using a random point approach. The number of points at net-impacted sites were constrained to the net coverage area and were scaled to the net area to ensure an equal point density among replicate net-impact sites. The same number of points were randomly assigned to the 3 × 3 m paired control site. Each point was classified into one of seven benthic categories: turf algae, macroalgae, sand, bare substrate, Porites compressa, sponge, or crustose coralline algae (CCA). The annotated points for each site were converted to percent cover for each benthic category. Fishing net size (sq m) and degree of fouling were also calculated from the orthophotos. Analyses were conducted to compare the benthic composition of net sites to control sites and to determine if fouling or net size contributed to these differences.
Notes: Only a maximum of 4000 characters will be included.
Notes: Data collection is considered ongoing if a time frame of type "Continuous" exists.
Notes: All time frames from all extent groups are included.
Geographic extent of marine debris structure from motion surveys conducted at Pearl and Hermes Atoll.
Notes: All geographic areas from all extent groups are included.
(e.g., digital numeric data, imagery, photographs, video, audio, database, tabular data, etc.)
(e.g., satellite, airplane, unmanned aerial system, radar, weather station, moored buoy, research vessel, autonomous underwater vehicle, animal tagging, manual surveys, enforcement activities, numerical model, etc.)
2. Point of Contact for this Data Management Plan (author or maintainer)
Notes: The name of the Person of the most recent Support Role of type "Metadata Contact" is used. The support role must be in effect.
Notes: The name of the Organization of the most recent Support Role of type "Metadata Contact" is used. This field is required if applicable.
3. Responsible Party for Data Management
Program Managers, or their designee, shall be responsible for assuring the proper management of the data produced by their Program. Please indicate the responsible party below.
Notes: The name of the Person of the most recent Support Role of type "Data Steward" is used. The support role must be in effect.
Programs must identify resources within their own budget for managing the data they produce.
5. Data Lineage and Quality
NOAA has issued Information Quality Guidelines for ensuring and maximizing the quality, objectivity, utility, and integrity of information which it disseminates.
(describe or provide URL of description):
Marine debris removal has been conducted by the Pacific Islands Fisheries Science Center's Ecosystem Sciences Division at the atolls, reefs and islands of Northwestern Hawaiian Islands since 1996. Standardized data collection has been implemented since 1999. Swim surveys are typically used in the comparatively high-relief and patchy lagoonal reef habitats. Survey areas are chosen based on regional reef morphology and past accumulation records. At each Structure from Motion (SfM) data collection site, a permanent 3 x 3 m plot was established around the center of the entangled fishing net. SfM images were taken underwater before and after net removal. The same method was also used at the paired control sites. We used Agisoft Metashape software to generate orthomosaic images from the photographs captured after the net was removed. The planar net area (square meters) was calculated by delineating the net boundary in ArcGIS. In addition, the degree of fouling was estimated for each net based on the percent of the net surface area that was covered by fouling organisms. Using the orthomosaics from the "after" and "control" sites, benthic cover was assessed using a random point approach within the boundary of the net and at the paired control site. Each point was classified into one of seven benthic categories. The annotated points for each site were converted to percent cover. Analyses were conducted to compare the benthic composition of net sites to control sites and to determine if fouling or net size contributed to these differences.
- The swim survey method was developed for surveys in lagoonal, reticulated reef areas. During swim surveys, two or more divers swim across reefs to search for debris while being directed by personnel in small boats to follow pre-planned routes and are coordinated for maximum visual area covered. Survey areas and routes are chosen based on regional reef morphology and past accumulation records. Based on this net prevalence information, five spatial zones were defined. A minimum of three nets in each of the five zones were surveyed using a Structure from Motion (SfM) approach if the net also fit within the additional selection criteria (≥ 75% hard substrate and within ~1-4 m depths). (Citation: Dameron, O. J., Parke, M., Albins, M. A., & Brainard, R. (2007). Marine debris accumulation in the Northwestern Hawaiian Islands: an examination of rates and processes. Marine Pollution Bulletin, 54(4), 423-433.)
- When a diver encounters debris larger than 0.012 cubic meters (size of small toolbox), descriptive data about the debris are recorded. At each site, a permanent 3 x 3 m plot was established around the center of the net by securing zip ties to the reef at each corner of the plot and taking a GPS location at the center. Depth measurements were recorded at each corner of the plot. Only nets that fit within the plot were selected for this study to allow rapid data collection of the Structure from Motion (SfM) imagery. SfM images were taken underwater before net removal to record the extent of the reef covered by net. Images were collected by snorkeling in a cross-hatch pattern over the plot at 1 m above the substrate to achieve image overlap of at least 60% (~580 images per site). JPEG images were collected using a Nikon SL2 digital camera in an underwater housing. (Citation: Suka R, Asbury M, Couch C, Gray A, Winston M, Oliver T. 2019. Processing Photomosaic Imagery of Coral Reefs Using Structure-from-Motion Standard Operating Procedures. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-93, 54 p. doi:10.25923/h2q8-jv47)
- Fishing nets were disentangled from the reef by hand or carefully cut using knives to free the net from the benthos in order to minimize impacts to the underlying habitat. Once removed and loaded into the cargo area of the small boat, the volume of each net removed from the reef was estimated and recorded. A second series of "after" images were collected in the same manner as the first series of "before" images (i.e., before the fishing net was removed from the reef). The volume of each fishing net removed from the reef was estimated when brought aboard the small boat. At the end of the marine debris survey, which could include one to several structure-from-motion surveys, or when the small boat reached its capacity, the small boat returned to the ship and the boat’s entire debris load was weighed and recorded. The estimated volume of each net was used to determine the percentage each net contributed to the boat's entire load, and weights for each net were calculated based on the percentage.
- A paired control site was selected for each net within the same zone (≥ 50 m away from net-impact site for independence). The same photogrammetry method was also used at the paired control sites (3 x 3 m plot).
- The Structure from Motion (SfM) approach produces an accurately scaled, two-dimensional (2D) orthomosaic model created from the overlapping imagery. We used Agisoft Metashape software (version 1.2.5 build 2735) to generate the orthomosaic following parameters published by Burns et al., 2015. (Citation: Burns J, Delparte D, Gates R, Takabayashi M. 2015. Integrating structure-from-motion photogrammetry with geospatial software as a novel technique for quantifying 3D ecological characteristics of coral reefs. PeerJ 3:e1077)
- From the pre-net removal ("before") orthomosaics, the planar net area (square meters) was calculated by delineating the net boundary with a polygon shapefile and using the Calculate Geometry tool in ArcMap v10.6.1. In addition, the degree of fouling was estimated for each net based on the percent of the net surface area that was covered by fouling organisms. Fouling scores ranged from 1 to 3, where 1 = Light: 1-40% of net surface area covered, 2 = Moderate: 41-75% of net surface area covered, and 3 = Heavy: >75% of net surface area covered (adapted from Donohue et al., 2001). Four nets were classified as fouling level 1, eight nets as fouling level 2, and eight nets as fouling level 3. (Citation: Donohue, M. J., Boland, R. C., Sramek, C. M., & Antonelis, G. A. (2001). Derelict fishing gear in the Northwestern Hawaiian Islands: diving surveys and debris removal in 1999 confirm threat to coral reef ecosystems. Marine pollution bulletin, 42(12), 1301-1312.)
- Using the post-net removal ("after") orthomosaic, benthic cover was assessed using a random point approach within the boundary of the net (based on the net boundary shapefile) in ArcMAP 10.6.1. The number of points at net-impacted sites was scaled to the net size to ensure an equal point density (mean point density = 10.9 points/m2 ± 0.40 SE) among replicate net-impact sites. Using the paired "control" orthomosaic, the same number of points were randomly assigned to the 3 x 3 m paired control site. Each point was classified into one of seven benthic categories: turf algae, macroalgae, sand, bare substrate, Porites compressa, sponge, and crustose coralline algae (CCA). The annotated points for each site were converted to percent cover (number of points for a given category/total number of points x 100) for each benthic category.
- To test whether derelict fishing nets impact benthic assemblages regardless of net size or level of fouling, all net-impact and control sites were compared using both multivariate and univariate techniques. Differences in the benthic assemblage between control and net-impact sites were visualized using an ordination plot generated from non-metric multi-dimensional scaling (nMDS) performed on Bray-Curtis distances using untransformed cover data. Assemblage differences indicated by the nMDS were tested for significance using a permutational analysis of variance (PERMANOVA) with treatment (net-impacts or control) as a fixed factor. PERMANOVA models used 999 permutations and the assumption of equal dispersion among the treatment groups was confirmed. To determine which specific categories drove the difference in the benthic assemblage between net-impact and control sites, we ran paired t-tests (or the non-parametric equivalent based on Shapiro-Wilk tests of normality) on the paired difference for each of the seven benthic cover categories.
- To test whether the impact of derelict nets on the benthos differed depending on the net size or level of fouling, a distance-based redundancy analysis (db-RDA) was performed. However, in this analysis control sites were excluded (as control sites have no associated derelict net) and only the net-impacted sites were analyzed (n=20). As with PERMANOVA, db-RDA is a method for carrying out constrained ordinations on data using non-Euclidean distance measures, such as Bray Curtis distance. The results of db-RDA can reveal whether a matrix of explanatory variables has some significant impact on the dissimilarities derived from the community composition data as a whole. The db-RDA model considered fouling level (ordinal) and net size (continuous) as explanatory variables. Although db-RDA does not make explicit assumptions about the distribution of the explanatory variables, net size and fouling level were evaluated for skew and co-linearity prior to executing the analysis. All data analyses were conducted in R Version 3.6.1. PERMANOVA and dbRDA analyses were conducted using the vegan package. Non-parametric paired t-test were carried out using the coin package.
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Size estimates of debris in water were verified against the more accurate volume estimates of the nets once removed from the shallow coral reef environments and hauled onto the small boats.
Each image set was evaluated for image quality. Images deemed unsatisfactory were removed from the image set.
The benthic category assigned to each random point across each mosaic were verified by an expert. Any points that fell onto an unidentifiable area (i.e., shadow) were re-generated.
6. Data Documentation
The EDMC Data Documentation Procedural Directive requires that NOAA data be well documented, specifies the use of ISO 19115 and related standards for documentation of new data, and provides links to resources and tools for metadata creation and validation.
- 1.7. Data collection method(s)
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7. Data Access
NAO 212-15 states that access to environmental data may only be restricted when distribution is explicitly limited by law, regulation, policy (such as those applicable to personally identifiable information or protected critical infrastructure information or proprietary trade information) or by security requirements. The EDMC Data Access Procedural Directive contains specific guidance, recommends the use of open-standard, interoperable, non-proprietary web services, provides information about resources and tools to enable data access, and includes a Waiver to be submitted to justify any approach other than full, unrestricted public access.
Notes: The name of the Organization of the most recent Support Role of type "Distributor" is used. The support role must be in effect. This information is not required if an approved access waiver exists for this data.
Notes: This field is required if a Distributor has not been specified.
Data can be accessed online via the NOAA National Centers for Environmental Information (NCEI) Ocean Archive.
Notes: This field is required if applicable.
8. Data Preservation and Protection
The NOAA Procedure for Scientific Records Appraisal and Archive Approval describes how to identify, appraise and decide what scientific records are to be preserved in a NOAA archive.
(Specify NCEI-MD, NCEI-CO, NCEI-NC, NCEI-MS, World Data Center (WDC) facility, Other, To Be Determined, Unable to Archive, or No Archiving Intended)
Notes: This field is required if archive location is World Data Center or Other.
Notes: This field is required if archive location is To Be Determined, Unable to Archive, or No Archiving Intended.
Notes: Physical Location Organization, City and State are required, or a Location Description is required.
Discuss data back-up, disaster recovery/contingency planning, and off-site data storage relevant to the data collection
NOAA IRC and NOAA Fisheries ITS resources and assets.
9. Additional Line Office or Staff Office Questions
Line and Staff Offices may extend this template by inserting additional questions in this section.