References

Allaire, JJ, Yihui Xie, Christophe Dervieux, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, et al. 2024. Rmarkdown: Dynamic Documents for r. https://github.com/rstudio/rmarkdown.

Barbier, Edward B. 2017. “Marine Ecosystem Services.” Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.03.020.

Benson, Abigail, Cassandra M. Brooks, Gabrielle Canonico, Emmett Duffy, Frank Muller-Karger, Heidi M. Sosik, Patricia Miloslavich, and Eduardo Klein. 2018. “Integrated Observations and Informatics Improve Understanding of Changing Marine Ecosystems.” Frontiers in Marine Science. Frontiers Media S.A. https://doi.org/10.3389/fmars.2018.00428.

Benson, Abigail, Diana LaScala-Gruenewald, Robert McGuinn, Erin Satterthwaite, Stace Beaulieu, Mathew Biddle, Lynn deWitt, et al. 2021. “Biological Observation Data Standardization - a Primer for Data Managers.” ESIP. https://doi.org/10.6084/m9.figshare.16806712.v1.

Benson, Abigail, Tylar Murray, Gabrielle Canonico, Enrique Montes, Frank Muller-Karger, Maria T. Kavanaugh, Joaquin Trinanes, and Lynn M. deWitt. 2021. “Data Management and Interactive Visualizations for the Evolving Marine Biodiversity Observation Network.” Oceanography. https://doi.org/10.5670/oceanog.2021.220.

Borer, Elizabeth T., Eric W. Seabloom, Matthew B. Jones, and Mark Schildhauer. 2009. “Some Simple Guidelines for Effective Data Management.” Bulletin of the Ecological Society of America 90 (April). https://doi.org/10.1890/0012-9623-90.2.205.

Canonico, Gabrielle, Pier Luigi Buttigieg, Enrique Montes, Frank E. Muller-Karger, Carol Stepien, Dawn Wright, Abigail Benson, et al. 2019. “Global Observational Needs and Resources for Marine Biodiversity.” Frontiers in Marine Science. Frontiers Media S.A. https://doi.org/10.3389/fmars.2019.00367.

Crystal-Ornelas, Robert, Charuleka Varadharajan, Ben Bond-Lamberty, Kristin Boye, Madison Burrus, Shreyas Cholia, Michael Crow, et al. 2021. “A Guide to Using GitHub for Developing and Versioning Data Standards and Reporting Formats.” Earth and Space Science, July, e2021EA001797. https://doi.org/10.1029/2021EA001797.

Davies, Neil, John Deck, Eric C Kansa, Sarah Whitcher Kansa, John Kunze, Christopher Meyer, Thomas Orrell, et al. 2021. “Internet of Samples (iSamples): Toward an Interdisciplinary Cyberinfrastructure for Material Samples.” GigaScience 10: 1–5. https://doi.org/10.1093/gigascience/giab028.

Djurhuus, Anni, Collin J. Closek, Ryan P. Kelly, Kathleen J. Pitz, Reiko P. Michisaki, Hilary A. Starks, Kristine R. Walz, et al. 2020. “Environmental DNA Reveals Seasonal Shifts and Potential Interactions in a Marine Community.” Nature Communications 11 (December): 1–9. https://doi.org/10.1038/s41467-019-14105-1.

Duffy, J. Emmett, Linda A. Amaral-Zettler, Daphne G. Fautin, Gustav Paulay, Tatiana A. Rynearson, Heidi M. Sosik, and John J. Stachowicz. 2013. “Envisioning a Marine Biodiversity Observation Network.” BioScience 63 (May): 350–61. https://doi.org/10.1525/bio.2013.63.5.8.

Fornwall, M, R Gisiner, S E Simmons, H Moustahfid, G Canonico, P Halpin, P Goldstein, et al. 2012. “Expanding Biological Data Standards Development Processes for US IOOS: Visual Line Transect Observing Community for Mammal, Bird, and Turtle Data.” IOOS. https://www.researchgate.net/publication/255681522.

Hardisty, Alex R., William K. Michener, Donat Agosti, Enrique Alonso García, Lucy Bastin, Lee Belbin, Anne Bowser, et al. 2019. “The Bari Manifesto: An Interoperability Framework for Essential Biodiversity Variables.” Ecological Informatics 49 (January): 22–31. https://doi.org/10.1016/j.ecoinf.2018.11.003.

Heberling, J Mason, Joseph T Miller, Daniel Noesgaard, Scott B Weingart C, Dmitry Schigel, and Douglas E Soltis. 2021. “Data Integration Enables Global Biodiversity Synthesis.” Proceedings of the National Academy of Sciences of the United States of America. https://doi.org/10.1073/pnas.2018093118/-/DCSupplemental.

Jonathan A. Hare, Mark W. Nelson, Wendy E. Morrison. n.d. “A Vulnerability Assessment of Fish and Invertebrates to Climate Change on the Northeast u.s. Continental Shelf.” PLoS ONE 11 (2): e0146756. https://doi.org/10.1371/journal.pone.0146756.

Jones, Matthew B., Mark P. Schildhauer, O. J. Reichman, and Shawn Bowers. 2006. “The New Bioinformatics: Integrating Ecological Data from the Gene to the Biosphere.” Annual Review of Ecology, Evolution, and Systematics. https://doi.org/10.1146/annurev.ecolsys.37.091305.110031.

Kavanaugh, Maria T., Matthew J. Oliver, Francisco P. Chavez, Ricardo M. Letelier, Frank E. Muller-Karger, and Scott C. Doney. 2016. “Seascapes as a New Vernacular for Pelagic Ocean Monitoring, Management and Conservation.” ICES Journal of Marine Science 73 (July): 1839–50. https://doi.org/10.1093/icesjms/fsw086.

Kot, Connie Y., Ei Fujioka, Lucie J. Hazen, Benjamin D. Best, Andrew J. Read, and Patrick N. Halpin. 2010. “Spatio-Temporal Gap Analysis of OBIS-SEAMAP Project Data: Assessment and Way Forward.” PLoS ONE 5 (September): 12990. https://doi.org/10.1371/journal.pone.0012990.

Lab, Malin Pinksy. n.d. “OceanAdapt.” GitHub. https://oceanadapt.rutgers.edu/.

Lamprecht, Anna-Lena, Leyla Garcia, Mateusz Kuzak, Carlos Martinez, Ricardo Arcila, Eva Martin Del Pico, Victoria Dominguez Del Angel, et al. 2019. “Towards FAIR Principles for Research Software.” Edited by Paul Groth. Data Science, 1–23. https://doi.org/10.3233/DS-190026.

Maria Dornelas, Brian McGill, Nicholas J. Gotelli. 2014. “Assemblage Time Series Reveal Biodiversity Change but Not Systematic Loss.” Science 344 (6181): 296–99. https://doi.org/10.1126/science.1248484.

McKenna, Megan F., Simone Baumann-Pickering, Annebelle C. M. Kok, William K. Oestreich, Jeffrey D. Adams, Jack Barkowski, Kurt M. Fristrup, et al. 2021. “Advancing the Interpretation of Shallow Water Marine Soundscapes.” Frontiers in Marine Science 0 (September): 1426. https://doi.org/10.3389/FMARS.2021.719258.

Miloslavich, Patricia, Nicholas J. Bax, Samantha E. Simmons, Eduardo Klein, Ward Appeltans, Octavio Aburto-Oropeza, Melissa Andersen Garcia, et al. 2018. “Essential Ocean Variables for Global Sustained Observations of Biodiversity and Ecosystem Changes.” Global Change Biology 24 (June): 2416–33. https://doi.org/10.1111/gcb.14108.

Montes, Enrique, Anni Djurhuus, Frank E. Muller-Karger, Daniel Otis, Christopher R. Kelble, and Maria T. Kavanaugh. 2020. “Dynamic Satellite Seascapes as a Biogeographic Framework for Understanding Phytoplankton Assemblages in the Florida Keys National Marine Sanctuary, United States.” Frontiers in Marine Science 7 (July): 575. https://doi.org/10.3389/fmars.2020.00575.

Moustahfid, Hassan, and Philip Goldstein. 2014. “IOOS Biological Data Services Enrollment Procedures.”

Moustahfid, Hassan, Jim Potemra, Philip Goldstein, Roy Mendelssohn, and Annette Desrochers. 2011. “Making United States Integrated Ocean Observing System (u.s. IOOS) Inclusive of Marine Biological Resources.” https://www.researchgate.net/publication/254013004.

Muller-Karger, Frank E., Erin Hestir, Christiana Ade, Kevin Turpie, Dar A. Roberts, David Siegel, Robert J. Miller, et al. 2018. “Satellite Sensor Requirements for Monitoring Essential Biodiversity Variables of Coastal Ecosystems.” Ecological Applications 28 (April): 749–60. https://doi.org/10.1002/eap.1682.

Muller-Karger, Frank E., Patricia Miloslavich, Nicholas J. Bax, Samantha Simmons, Mark J. Costello, Isabel Sousa Pinto, Gabrielle Canonico, et al. 2018. “Advancing Marine Biological Observations and Data Requirements of the Complementary Essential Ocean Variables (EOVs) and Essential Biodiversity Variables (EBVs) Frameworks.” Frontiers in Marine Science. Frontiers Media S.A. https://doi.org/10.3389/fmars.2018.00211.

Neeley, Aimee, Stace E. Beaulieu, Chris Proctor, Ivona Cetinić, Joe Futrelle, Inia Soto Ramos, Heidi M. Sosik, et al. 2021. “Standards and Practices for Reporting Plankton and Other Particle Observations from Images.” https://doi.org/10.1575/1912/27377.

O’Brien, Margaret, Colin A. Smith, Eric R. Sokol, Corinna Gries, Nina Lany, Sydne Record, and Max C. N. Castorani. 2021. “ecocomDP: A Flexible Data Design Pattern for Ecological Community Survey Data.” Ecological Informatics 64 (September): 101374. https://doi.org/10.1016/J.ECOINF.2021.101374.

Pooter, Daphnis De, Ward Appeltans, Nicolas Bailly, Sky Bristol, Klaas Deneudt, Menashè Eliezer, Ei Fujioka, et al. 2017. “Toward a New Data Standard for Combined Marine Biological and Environmental Datasets - Expanding OBIS Beyond Species Occurrences.” Biodiversity Data Journal 5 (January): 10989. https://doi.org/10.3897/BDJ.5.e10989.

Provoost, Pieter. n.d. “Iobis/Ebsa.” GitHub. https://github.com/iobis/ebsa.

R Core Team. 2024. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.

Rücknagel, J., P. Vierkant, R. Ulrich, G. Kloska, E. Schnepf, D. Fichtmüller, E. Reuter, et al. 2015. “Metadata Schema for the Description of Research Data Repositories. Version 3.0.” https://doi.org/10.2312/re3.008.

Rule, Adam, Amanda Birmingham, Cristal Zuniga, Ilkay Altintas, Shih-Cheng Huang, Rob Knight, Niema Moshiri, et al. 2019. “Ten Simple Rules for Writing and Sharing Computational Analyses in Jupyter Notebooks.” PLOS Computational Biology 15 (July): e1007007. https://doi.org/10.1371/JOURNAL.PCBI.1007007.

Santora, Jarrod A., Elliott L. Hazen, Isaac D. Schroeder, Steven J. Bograd, Keith M. Sakuma, and John C. Field. 2017. “Impacts of Ocean Climate Variability on Biodiversity of Pelagic Forage Species in an Upwelling Ecosystem.” Marine Ecology Progress Series 580 (September): 205–20. https://doi.org/10.3354/meps12278.

Schmid, Moritz S, Dominic Daprano, Kyler M Jacobson, Christopher Sullivan, Christian Briseño-Avena, Jessica Y Luo, and Robert K Cowen. 2021. A Convolutional Neural Network Based High-Throughput Image Classification Pipeline - Code and Documentation to Process Plankton Underwater Imagery Using Local HPC Infrastructure and NSF’s XSEDE. Zenodo. https://doi.org/10.5281/ZENODO.4641158.

Taylor, Gordon T., Frank E. Muller-Karger, Robert C. Thunell, Mary I. Scranton, Yrene Astor, Ramon Varela, Luis Troccoli Ghinaglia, et al. 2012. “Ecosystem Responses in the Southern Caribbean Sea to Global Climate Change.” Proceedings of the National Academy of Sciences of the United States of America 109 (November): 19315–20. https://doi.org/10.1073/pnas.1207514109.

Tittensor, Derek P, Camilo Mora, Walter Jetz, Heike K Lotze, Daniel Ricard, Edward Vanden Berghe, and Boris Worm. 2010. “Global Patterns and Predictors of Marine Biodiversity Across Taxa.” Nature 466 (7310): 1098.

Warren, R., J. Price, E. Graham, N. Forstenhaeusler, and J. VanDerWal. 2018. “The Projected Effect on Insects, Vertebrates, and Plants of Limiting Global Warming to 1.5°c Rather Than 2°c.” Science 360 (May): 791–95. https://doi.org/10.1126/science.aar3646.

Wieczorek, John, David Bloom, Robert Guralnick, Stan Blum, Markus Döring, Renato Giovanni, Tim Robertson, and David Vieglais. 2012. “Darwin Core: An Evolving Community-Developed Biodiversity Data Standard.” PLoS ONE 7 (January): 29715. https://doi.org/10.1371/journal.pone.0029715.

Wilkinson, Mark D., Michel Dumontier, IJsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, et al. 2016. “The FAIR Guiding Principles for Scientific Data Management and Stewardship.” Scientific Data 3 (March): 1–9. https://doi.org/10.1038/sdata.2016.18.

Xie, Yihui. 2014. “Knitr: A Comprehensive Tool for Reproducible Research in R.” In Implementing Reproducible Computational Research, edited by Victoria Stodden, Friedrich Leisch, and Roger D. Peng. Chapman; Hall/CRC.

———. 2015b. Dynamic Documents with R and Knitr. 2nd ed. Boca Raton, Florida: Chapman; Hall/CRC. http://yihui.name/knitr/.

———. 2015a. Dynamic Documents with R and Knitr. 2nd ed. Boca Raton, Florida: Chapman; Hall/CRC. https://yihui.org/knitr/.

———. 2016. Bookdown: Authoring Books and Technical Documents with R Markdown. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/bookdown.

———. 2024a. Bookdown: Authoring Books and Technical Documents with r Markdown. https://github.com/rstudio/bookdown.

———. 2024b. Knitr: A General-Purpose Package for Dynamic Report Generation in r. https://yihui.org/knitr/.

Xie, Yihui, J. J. Allaire, and Garrett Grolemund. 2018. R Markdown: The Definitive Guide. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown.

Xie, Yihui, Christophe Dervieux, and Emily Riederer. 2020. R Markdown Cookbook. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown-cookbook.