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
- Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, USA
- Arctic Marine Mammals Program, Alaska Department of Fish and Game, Fairbanks, Alaska, USA
- Department of Wildlife Management, North Slope Borough, Utqiaġvik, Alaska, USA
✉ Correspondence: Josh M. London josh.london@noaa.gov
This repository serves as the research compendium in support of the above titled paper. As the manuscript works its way through peer review and the publications process, additional reproducibility features (e.g. devcontainer) and documentation of key revisions and releases
Major releases of the research compendium are published and archived with Zenodo https://doi.org/10.5281/zenodo.4638221
Please note this manuscript is still in peer review and not final. Changes to results, code, and the manuscript are still possible and, until, final publication the latest pre-print at bioRxiv should be cited.
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
- 📁 templates: template files and scripts.
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
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
The dependency graph for our pipeline is shown below
We recognize that the species and ecosystems we studied are within the ancestral and present-day environs of the Inpuiat 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 the approval of their communities. We would like to especially acknowledge the 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, and Joe Skin from Utqiaġvik, Alaska; Mary Ellen Ahmaogak, Enoch Oktollik, Shawn Oktollik, Stacey Osborn, and Fred Rexford from Ulguniq.
We are grateful for the assistance in catching and sampling seals by Ryan Adam, James Bailey, Michelle Barbieri, John Bengtson, Gavin Brady, Vladamir Burkanov, Cynthia Christman, Sarah Coburn, Shawn Dahle, Rob Delong, Stacy DiRocco, Deb Fauquier, Shannon Fitzgerald, Kathy Frost, Scott Gende, Tracey Goldstein, Jeff Harris, Jason Herreman, Markus Horning, John Jansen, Shawn Johnson, Charles Littnan, Lloyd Lowry, Brett McClintock, Erin Moreland, Mark Nelson, Justin Olnes, Lorrie Rea, Bob Shears, Gay Sheffield, Brent Stewart, 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, 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.
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.
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.