Spring haul-out behavior of seals in the Bering and Chukchi Seas: implications for abundance estimation

Josh M. London¹,✉, Paul B. Conn¹, Stacie M. Koslovsky¹, Erin L. Richmond¹, Jay M. Ver Hoef¹, Michael F. Cameron¹, Justin Crawford², Andrew L. Von Duyke³, Lori Quakenbush², and Peter L. Boveng¹

1. Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, USA
2. Arctic Marine Mammals Program, Alaska Department of Fish and Game, Fairbanks, Alaska, USA
3. Department of Wildlife Management, North Slope Borough, Utqiaġvik, Alaska, USA

✉ Correspondence: Josh M. London [email protected]

This repository serves as the research compendium in support of the above titled paper which has been accepted for publication at PeerJ

Spring haul-out behavior of seals in the Bering and Chukchi Seas: implications for abundance estimation

Major releases of the research compendium are published and archived with Zenodo https://doi.org/10.5281/zenodo.4638221

Contents

The analysis directory contains:

• 📁 paper: R Markdown source document for manuscript. Includes code to reproduce the figures and tables generated by the analysis. It also has a rendered PDF, London_HauloutBehavior.pdf, suitable for reading (the code is replaced by figures and tables in this file)
• 📁 figures: figures generated

The data directory contains

• 📁 data: data used for model fits and final model output
• :file: data_raw: data provided by partners from ADFG and NSB

{targets} and {renv} packages

This repository relies heavily on the {targets} and {renv} packages for management of analysis pipelines and reproducibility.

• 📁 R: pipeline functions developed in support of target pipeline
• 📄 _targets.R: target pipeline
• 📄 renv.lock: renv lockfile

Acknowledgements

We recognize that the species and ecosystems we studied are within the ancestral and present-day environs of the Inupiat and Yup'ik people who, through many uncredited contributions of traditional knowledge, provided early western naturalists and scientists with much of what gets described as the ‘basic biology’ of Arctic seals. The deployment of bio-logging devices used in this study were often done in collaboration with Alaska Native seal hunters and wiht the approval of their communities. We would like to especially acknowledge the Alaska communities of Kotzebue, Koyuk, Nome, Nuiqsut, Scammon Bay, St. Michael, Utqiaġvik, and Ulguniq (Wainwright) and the following individuals: James Adams, Jeff Barger, David Barr, Wendell Booth, Cyrus Harris, Nereus 'Doc' Harris, Grover Harris, Lee Harris, Tom Jones, Frank Garfield, Brenda Goodwin, Henry Goodwin, John Goodwin, Pearl Goodwin, Willie Goodwin, Brett Kirk, Noah Naylor, Virgil Naylor Jr., Virgil Naylor Sr., Dan Savetilik, Chuck Schaeffer, Ross Schaeffer, Allen Stone, and Randy Toshavik from Kotzebue; Merlin Henry from Koyuk; Tom Gray from Nome; Vernon Long and Richard Tukle from Nuiqsuit; Morgan Simon, River Simon, and Al Smith from Scammon Bay; Alex Niksik Jr. from St. Michael; Billy Adams, James Aiken, Tim Aiken, Howard Kittick, Gilbert Leavitt, Isaac Leavitt, J.R. Leavitt, Bobby Sarren, and Joe Skin from Utqiaġvik; Mary Ellen Ahmaogak, Enoch Oktollik, Shawn Oktollik, Stacey Osborn, and Fred Rexford from Ulguniq. We would also like to acknowledge the support of the Ice Seal Committee.

We are grateful for the assistance in catching and sampling seals by Ryan Adam, James Bailey, Michelle Barbieri, John Bengtson, Gavin Brady, Anna Bryan, Vladamir Burkanov, Cynthia Christman, Sarah Coburn, Shawn Dahle, Rob Delong, Stacy DiRocco, Deb Fauquier, Shannon Fitzgerald, Kathy Frost, Scott Gende, Craig George, Tracey Goldstein, Jeff Harris, Jason Herreman, Markus Horning, John Jansen, Shawn Johnson, Charles Littnan, Lloyd Lowry, Brett McClintock, Erin Moreland, Aaron Morris, Mark Nelson, Justin Olnes, Lorrie Rea, Bob Shears, Gay Sheffield, Kayla Scheimreif, Brent Stewart, Alexy Trukhin, Dave Withrow, and Heather Ziel. We also appreciate the commitment to science and safety by all officers and crew of the NOAA ship Oscar Dyson, the NOAA ship MacArthur II, the MV Tayfun, and the RV Thomas G. Thompson.

Telemetry data from the Alaska Department of Fish and Game (ADF&G) and the North Slope Borough Department of Wildlife Management (NSB) were important contributions to the findings presented here. Deployments in the western Bering Sea were done in collaboration with Russian colleagues and North Pacific Wildlife Consulting, LLC.

The findings and conclusions in the paper are those of the author(s) and do not necessarily represent the views of the National Marine Fisheries Service, NOAA. Any use of trade, product, or firm names does not imply an endorsement by the U.S. Government.

Funding for this study was provided by the U.S. National Oceanic and Atmospheric Administration. The field work was conducted under the authority of Marine Mammal Protection Act Research Permits Nos. 782-1676, 782-1765, 15126, and 19309 issued by the National Marine Fisheries Service, and Letters of Assurance of Compliance with Animal Welfare Act regulations, Nos. A/NW 2010-3 and A/NW 2016-1 from the Alaska Fisheries Science Center/Northwest Fisheries Science Center Institutional Animal Care and Use Committee (IACUC). ). Funding to ADF&G for tagging seals was provided by the Bureau of Ocean Energy Management (No. M13PC0015 for work in Kotzebue, Alaska in 2009) and the Office of Naval Research (No. N00014-16-1-3019). ADF&G and NSB field work was covered by Research Permits Nos. 358-1585, 358-1787, 15324, and 20466 and by ADF&G IACUC permits Nos. 06-16, 09-21, 2014-03, 2015-25, 2016-23, 0027-2017-27, 0027-2018-29, 0027-2019-041.

Inspiration

I would like to provide special acknowledgement to Ben Marwick and Carl Boetinger. This research compendium borrows heavily from Ben’s {rrtools} package. Carl’s example research compendiums (https://github.com/cboettig/noise-phenomena and https://github.com/cboettig/nonparametric-bayes) were also of great use when adapting the structure to meet my needs.