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Expand Up @@ -16,8 +16,8 @@ knitr::opts_chunk$set(
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4638221.svg)](https://doi.org/10.5281/zenodo.4638221)
<!-- badges: end -->

## Haul-out behavior and aerial survey detectability of seals in the Bering and Chukchi seas
Josh M. London^1^,✉, Paul B. Conn^1^, Stacie K. Hardy^1^, Erin L. Richmond^1^, Jay M. Ver Hoef^1^, Michael F. Cameron^1^, Justin Crawford^2^, Andrew L. Von Duyke^3^, Lori T. Quakenbush^2^, and Peter L. Boveng^1^
## Spring haul-out behavior of seals in the Bering and Chukchi seas
Josh M. London^1^,✉, Paul B. Conn^1^, Stacie M. Koslovsky^1^, Erin L. Richmond^1^, Jay M. Ver Hoef^1^, Michael F. Cameron^1^, Justin Crawford^2^, Andrew L. Von Duyke^3^, Lori Quakenbush^2^, and Peter L. Boveng^1^

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
Expand All @@ -27,18 +27,16 @@ Josh M. London^1^,✉, Paul B. Conn^1^, Stacie K. Hardy^1^, Erin L. Richmond^1^,

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. Dockerfile, MyBinder.org) and
an R/Shiny application to explore results will be made developed and made available.
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](https://doi.org/10.5281/zenodo.4638221)

## Draft Manuscript Under Active Development

Please note this manuscript is still in draft form and under active development.
Changes to results, code, and the manuscript are likely and this **should not
be cited without author permission**. We plan to provide a preprint to
[bioRxiv](https://www.biorxiv.org/) once internal NOAA reviews and final
revisions are completed.
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.

## Contents

Expand All @@ -47,7 +45,7 @@ The **analysis** directory contains:
- [:file\_folder: paper](/analysis/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](https://github.com/jmlondon/berchukHaulout/blob/main/analysis/paper/London_HauloutBeahvior.pdf), suitable for reading (the code is replaced by figures
[London_HauloutBehavior.pdf](https://github.com/jmlondon/berchukHaulout/blob/main/analysis/paper/London_HauloutBehavior.pdf), suitable for reading (the code is replaced by figures
and tables in this file)
- [:file\_folder: figures](/analysis/figures): figures generated
- [:file\_folder: templates](/analysis/templates): template files and scripts.
Expand All @@ -73,25 +71,26 @@ The dependency graph for our pipeline is shown below
## 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
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 near
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, Alaska; Merlin Henry from Koyuk, Alaska; Tom
Gray from Nome; Vernon Long and Richard Tukle from Nuiqsuit, Alaska; Morgan
Simon, River Simon, and Al Smith from Scammon Bay, Alaska; Alex Niksik Jr. from
St. Michael, Alaska; Billy Adams, James Aiken, Tim Aiken, Howard Kittick,
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, Alaska.
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,
Expand All @@ -101,16 +100,31 @@ 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.
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 (ADFG) and the North
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. Both agencies collaborate closely
with Alaska Native communities and the contributions of local hunters to the
successful capture, deployment, and understanding of seal ecology are
invaluable. Deployments in the western Bering Sea were done in collaboration
with Russian colleagues and North Pacific Wildlife.
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.

## Inspiration

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Expand Up @@ -5,12 +5,12 @@
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4638221.svg)](https://doi.org/10.5281/zenodo.4638221)
<!-- badges: end -->

## Haul-out behavior and aerial survey detectability of seals in the Bering and Chukchi seas
## Spring haul-out behavior of seals in the Bering and Chukchi seas

Josh M. London<sup>1</sup>,✉, Paul B. Conn<sup>1</sup>, Stacie K.
Hardy<sup>1</sup>, Erin L. Richmond<sup>1</sup>, Jay M. Ver
Josh M. London<sup>1</sup>,✉, Paul B. Conn<sup>1</sup>, Stacie M.
Koslovsky<sup>1</sup>, Erin L. Richmond<sup>1</sup>, Jay M. Ver
Hoef<sup>1</sup>, Michael F. Cameron<sup>1</sup>, Justin
Crawford<sup>2</sup>, Andrew L. Von Duyke<sup>3</sup>, Lori T.
Crawford<sup>2</sup>, Andrew L. Von Duyke<sup>3</sup>, Lori
Quakenbush<sup>2</sup>, and Peter L. Boveng<sup>1</sup>

1. Marine Mammal Laboratory, Alaska Fisheries Science Center, National
Expand All @@ -25,50 +25,48 @@ Quakenbush<sup>2</sup>, and Peter L. Boveng<sup>1</sup>
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. Dockerfile, MyBinder.org) and an R/Shiny application to explore
results will be made developed and made available.
(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>

## Draft Manuscript Under Active Development

Please note this manuscript is still in draft form and under active
development. Changes to results, code, and the manuscript are likely and
this **should not be cited without author permission**. We plan to
provide a preprint to [bioRxiv](https://www.biorxiv.org/) once internal
NOAA reviews and final revisions are completed.
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.

## Contents

The **analysis** directory contains:

- [:file_folder: paper](/analysis/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](https://github.com/jmlondon/berchukHaulout/blob/main/analysis/paper/London_HauloutBeahvior.pdf),
suitable for reading (the code is replaced by figures and tables in
this file)
- [:file_folder: figures](/analysis/figures): figures generated
- [:file_folder: templates](/analysis/templates): template files and
scripts.
- [:file_folder: paper](/analysis/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](https://github.com/jmlondon/berchukHaulout/blob/main/analysis/paper/London_HauloutBehavior.pdf),
suitable for reading (the code is replaced by figures and tables in
this file)
- [:file_folder: figures](/analysis/figures): figures generated
- [:file_folder: templates](/analysis/templates): template files and
scripts.

The **data** directory contains

- [:file_folder: data](/data): data used for model fits and final
model output
- [:file: data_raw](/data_raw): data provided by partners from ADFG
and NSB
- [:file_folder: data](/data): data used for model fits and final model
output
- [:file: data_raw](/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.

- [:file_folder: R](/R): pipeline functions developed in support of
target pipeline
- [:page_facing_up: \_targets.R](/_targets.R): target pipeline
- [:page_facing_up: renv.lock](/renv.lock): renv lockfile
- [:file_folder: R](/R): pipeline functions developed in support of
target pipeline
- [:page_facing_up: \_targets.R](/_targets.R): target pipeline
- [:page_facing_up: renv.lock](/renv.lock): renv lockfile

The dependency graph for our pipeline is shown below

Expand All @@ -77,27 +75,26 @@ The dependency graph for our pipeline is shown below
## 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,
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 near 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, Alaska; Merlin
Henry from Koyuk, Alaska; Tom Gray from Nome; Vernon Long and Richard
Tukle from Nuiqsuit, Alaska; Morgan Simon, River Simon, and Al Smith
from Scammon Bay, Alaska; Alex Niksik Jr. from St. Michael, Alaska;
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, Alaska.
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,
Expand All @@ -108,17 +105,33 @@ 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.
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 (ADFG) and
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. Both agencies
collaborate closely with Alaska Native communities and the contributions
of local hunters to the successful capture, deployment, and
understanding of seal ecology are invaluable. Deployments in the western
Bering Sea were done in collaboration with Russian colleagues and North
Pacific Wildlife.
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.

## Inspiration

Expand Down
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Below, please find detailed responses to each of the reviewer comments. In
addition to this letter, the full suite of updates are all contained and
documented within a single pull request. We have also provided a pdf document
that indicates all changes between the revised manuscript and the submitted
manuscript.
documented within a single pull request (see
<https://github.com/noaa-afsc/berchukseals-haulout/pull/51>). We have also
provided a pdf document (*\[Compare Report\] London_HauloutBehavior.pdf\]*) that
indicates all changes between the compedium supporting this revised manuscript
and the compendium supporting the originally submitted manuscript.

Thank you, again, for your time and consideration. And, additionally, thank you
to the reviewers for their time. It is much appreciated and we feel the
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