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GAP-Production-Data-Documentation.tex
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\listoffigures
\listoftables
\mainmatter
\part{Welcome}
\begin{quote}
Report run date: Friday, October 18, 2024
\end{quote}
\section*{AFSC Bottom Trawl Surveys}\label{afsc-bottom-trawl-surveys}
\addcontentsline{toc}{section}{AFSC Bottom Trawl Surveys}
\markright{AFSC Bottom Trawl Surveys}
AFSC bottom trawl surveys are conducted by the AFSC's Groundfish
Assessment Program and Shellfish Assessment Program and are conducted in
the
\href{https://www.fisheries.noaa.gov/alaska/ecosystems/alaska-fish-research-surveys\#gulf-of-alaska-bottom-trawl-survey}{Gulf
of Alaska},
\href{https://www.fisheries.noaa.gov/alaska/ecosystems/alaska-fish-research-surveys\#aleutian-islands-bottom-trawl-survey}{Aleutian
Islands},
\href{https://www.fisheries.noaa.gov/alaska/ecosystems/alaska-fish-research-surveys\#eastern-bering-sea-upper-continental-slope-bottom-trawl-survey}{Eastern
Bering Sea Slope},
\href{https://www.fisheries.noaa.gov/alaska/ecosystems/alaska-fish-research-surveys\#eastern-bering-sea-shelf-bottom-trawl-survey}{Eastern
Bering Sea Shelf}, and
\href{https://www.fisheries.noaa.gov/alaska/ecosystems/alaska-fish-research-surveys\#northern-bering-sea-shelf-bottom-trawl-survey}{Northern
Bering Sea}. Each survey is a multispecies survey that collects data on
the distribution, abundance, and biological characteristics of fish,
crab, and other resources to inform groundfish stock assessment and
management. These fishery-independent surveys are conducted in the
summer aboard contracted commercial fishing vessels. Specifics regarding
each of the surveys can be found below.
\begin{figure}[H]
{\centering \includegraphics{index_files/mediabag/750x500-bottom-trawl.jpg}
}
\caption{Sorting and weighing fish on deck on the 2022 Bering Sea
groundfish survey aboard the F/V Alaska Knight. Credit: Emily
Markowitz/NOAA Fisheries.}
\end{figure}%
\section*{Documentation Objective}\label{documentation-objective}
\addcontentsline{toc}{section}{Documentation Objective}
\markright{Documentation Objective}
As part of our commitment to open science, reproducibility, and
transparency, we provide this metadata guide to compliment our
public-domain data.
\begin{quote}
Please consider this resource to be a \textbf{Living Document}. The code
in this repository is regularly being updated and improved. Please refer
to
\href{https://github.com/afsc-gap-products/gap_products/releases}{releases}
for finalized products and project milestones.
\end{quote}
\begin{quote}
At this time, these master
\href{https://afsc-gap-products.github.io/gap_products/content/product-intro.html}{production}
and
\href{https://afsc-gap-products.github.io/gap_products/content/akfin-intro.html}{AKFIN}
tables are \textbf{provisional and we are welcoming feedback before the
2024 survey season.} We look forward to hearing from you. Do not
hesitate to reach out (to us at either
\url{[email protected]} or
\href{https://github.com/afsc-gap-products/gap_products/issues}{GitHub
issues}, especially if you find discrepancies in the data or want to
suggest improvements to infrastructure. Thank you in advance for your
collaboration and partnership with us as we develop our future data
universe.
\end{quote}
\section*{User Resources}\label{user-resources}
\addcontentsline{toc}{section}{User Resources}
\markright{User Resources}
\begin{itemize}
\tightlist
\item
\href{https://www.fisheries.noaa.gov/alaska/science-data/groundfish-assessment-program-bottom-trawl-surveys}{Groundfish
Assessment Program Bottom Trawl Surveys}
\item
\href{https://www.fisheries.noaa.gov/about/resource-assessment-and-conservation-engineering-division}{AFSC's
Resource Assessment and Conservation Engineering Division}
\item
\href{https://www.fisheries.noaa.gov/alaska/ecosystems/alaska-fish-research-surveys}{All
AFSC Research Surveys}
\item
\href{https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual}{Survey
code books}
\item
\href{https://repository.library.noaa.gov/}{Publications and Data
Reports}
\item
\href{https://www.fisheries.noaa.gov/alaska/ecosystems/alaska-fish-research-surveys}{Research
Surveys conducted at AFSC}
\end{itemize}
\section*{Cite this data}\label{cite-this-data}
\addcontentsline{toc}{section}{Cite this data}
\markright{Cite this data}
Use the below
\href{https://github.com/afsc-gap-products/gap_products/blob/main/CITATION.bib}{bibtext
citations}, as cited in our group's
\href{https://github.com/afsc-gap-products/citations/blob/main/cite/bibliography.bib}{citation
repository} for citing the data created and maintained in this repo. Add
``note = \{Accessed: mm/dd/yyyy\}'' to append the day this data was
accessed. Included here are AFSC RACE Groundfish and Shellfish
Assessment Program's:
\begin{itemize}
\tightlist
\item
Design-Based Production Data (internal) (NOAA Fisheries Alaska
Fisheries Science Center, Goundfish Assessment Program, 2024).\\
\item
AFSC RACE Groundfish Data for AKFIN (Alaska Fisheries Information
Network (AKFIN), 2024).
\item
Public Data hosted on the Fisheries One Stop Shop (FOSS) Data Platform
(NOAA Fisheries Alaska Fisheries Science Center, 2024).
\end{itemize}
\begin{verbatim}
@misc{GAPProducts,
author = {{NOAA Fisheries Alaska Fisheries Science Center, Goundfish Assessment Program}},
year = {2023},
title = {AFSC Goundfish Assessment Program Design-Based Production Data},
howpublished = {https://www.fisheries.noaa.gov/alaska/science-data/groundfish-assessment-program-bottom-trawl-surveys},
publisher = {{U.S. Dep. Commer.}},
copyright = {Public Domain}
}
@misc{FOSSAFSCData,
author = {{NOAA Fisheries Alaska Fisheries Science Center}},
year = {2023},
title = {Fisheries One Stop Shop Public Data: RACE Division Bottom Trawl Survey Data Query},
howpublished = {https://www.fisheries.noaa.gov/foss},
publisher = {{U.S. Dep. Commer.}},
copyright = {Public Domain}
}
@misc{GAPakfin,
author = {{Alaska Fisheries Information Network (AKFIN)}},
institution = {{NOAA Fisheries Alaska Fisheries Science Center, Goundfish Assessment Program}},
year = {2023},
title = {AFSC Goundfish Assessment Program Design-Based Production Data},
howpublished = {https://www.psmfc.org/program/alaska-fisheries-information-network-akfin},
publisher = {{U.S. Dep. Commer.}},
copyright = {Public Domain}
}
\end{verbatim}
\section*{Access Constraints}\label{access-constraints}
\addcontentsline{toc}{section}{Access Constraints}
\markright{Access Constraints}
There are no legal restrictions on access to the data. They reside in
public domain and can be freely distributed.
\textbf{User Constraints:} Users must read and fully comprehend the
metadata and
\href{https://afsc-gap-products.github.io/gap_products/content/code-of-conduct.html}{code
of conduct} prior to use. Data should not be used beyond the limits of
the source scale. Acknowledgement of AFSC Groundfish Assessment Program,
as the source from which these data were obtained, in any publications
and/or other representations of these data, is suggested.
\section*{Suggestions and comments}\label{suggestions-and-comments}
\addcontentsline{toc}{section}{Suggestions and comments}
\markright{Suggestions and comments}
If the data or metadata can be improved, please create a pull request,
\href{https://github.com/afsc-gap-products/data-requests/issues}{submit
an issue to the GitHub organization} or
\href{https://github.com/afsc-gap-products/gap_products/issues}{submit
an issue to the code's repository}.
\section*{NOAA README}\label{noaa-readme}
\addcontentsline{toc}{section}{NOAA README}
\markright{NOAA README}
This repository is a scientific product and is not official
communication of the National Oceanic and Atmospheric Administration, or
the United States Department of Commerce. All NOAA GitHub project code
is provided on an `as is' basis and the user assumes responsibility for
its use. Any claims against the Department of Commerce or Department of
Commerce bureaus stemming from the use of this GitHub project will be
governed by all applicable Federal law. Any reference to specific
commercial products, processes, or services by service mark, trademark,
manufacturer, or otherwise, does not constitute or imply their
endorsement, recommendation or favoring by the Department of Commerce.
The Department of Commerce seal and logo, or the seal and logo of a DOC
bureau, shall not be used in any manner to imply endorsement of any
commercial product or activity by DOC or the United States Government.
\section*{NOAA License}\label{noaa-license}
\addcontentsline{toc}{section}{NOAA License}
\markright{NOAA License}
Software code created by U.S. Government employees is not subject to
copyright in the United States (17 U.S.C. §105). The United
States/Department of Commerce reserve all rights to seek and obtain
copyright protection in countries other than the United States for
Software authored in its entirety by the Department of Commerce. To this
end, the Department of Commerce hereby grants to Recipient a
royalty-free, nonexclusive license to use, copy, and create derivative
works of the Software outside of the United States.
\chapter{Survey Background}\label{survey-background}
\section{What we do}\label{what-we-do}
\section{Who is conducting the
research?}\label{who-is-conducting-the-research}
Scientists from the Alaska Fisheries Science Center's Groundfish
Assessment Program (GAP) conduct these bottom trawl surveys with
participation from the Alaska Department of Fish \& Game (ADF\&G), the
International Pacific Halibut Commission (IPHC), universities, and other
organizations. This research is conducted primarily on chartered fishing
vessels.
\section{What is the research
objective?}\label{what-is-the-research-objective}
Learn more about the
\href{https://www.fisheries.noaa.gov/alaska/science-data/groundfish-assessment-program-bottom-trawl-surveys}{program}.
The objectives of these surveys are to:
\begin{itemize}
\tightlist
\item
monitor the population and environmental trends in the marine
ecosystem of the Bering Sea, Aleutian Islands, and Gulf of Alaska,
\item
produce fishery-independent biomass (weight) and abundance (number)
estimates for commercially important fish and crab species, and
\item
collect other biological and environmental data for use in
ecosystem-based fishery management.
\end{itemize}
\section{Who is conducting the
research?}\label{who-is-conducting-the-research-1}
Scientists from the Alaska Fisheries Science Center conduct these bottom
trawl surveys with participation from the Alaska Department of Fish \&
Game (ADF\&G), the International Pacific Halibut Commission (IPHC), and
universities. This research is conducted on chartered fishing vessels.
\section{Bottom trawl surveys and
regions}\label{bottom-trawl-surveys-and-regions}
\begin{figure}[H]
{\centering \includegraphics[width=7in,height=\textheight]{content/../img/survey_plot_all.png}
}
\caption{Strata used in the all surveys.}
\end{figure}%
Each survey conducted by the
\href{https://www.fisheries.noaa.gov/alaska/population-assessments/north-pacific-groundfish-stock-assessments-and-fishery-evaluation}{Groundfish
Assessment Program} are multispecies bottom trawl surveys. We collect
environmental and biological data to assess how climate variability and
\href{https://www.fisheries.noaa.gov/alaska/ecosystems/habitat-and-ecological-processes-research-regarding-loss-sea-ice}{loss
of sea} ice are affecting bottom-dwelling marine life on the Bering Sea
shelf. We monitor trends in the distribution (location and movement
patterns) and abundance of groundfish and crab species as well as
oceanographic data (e.g., water temperature, depth). We collect
biological information such as organism weight, length, stomachs to
learn about diets, and
\href{https://www.fisheries.noaa.gov/alaska/science-data/alaska-age-and-growth-procedures-otolith-examination}{otoliths}
to
\href{https://www.fisheries.noaa.gov/alaska/science-data/fish-otolith-chronologies}{determine
fish ages}. We use this information in
\href{https://www.fisheries.noaa.gov/alaska/population-assessments/north-pacific-groundfish-stock-assessments-and-fishery-evaluation}{annual
stock assessments} and to assess the state of the ecosystem. This
research is conducted on fishing industry contract vessels.
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\subsection{\texorpdfstring{\textbf{Aleutian
Islands}}{Aleutian Islands}}\label{aleutian-islands}
Most recent data report: (Von Szalay et al., 2023)
\begin{itemize}
\tightlist
\item
Upper Continental Slope of the Aleutian Islands from Unimak Pass to
Stalemate Bank
\item
Triennial (1990s)/Biennial since 2000 in even years, since 1992
\item
Modified Index-Stratified Random of Successful Stations Survey Design
\item
Important commercial fish species include Atka mackerel,
\href{https://www.fisheries.noaa.gov/species/pacific-ocean-perch}{Pacific
ocean perch},
\href{https://www.fisheries.noaa.gov/species/alaska-pollock}{walleye
pollock},
\href{https://www.fisheries.noaa.gov/species/pacific-cod}{Pacific
cod},
\href{https://www.fisheries.noaa.gov/species/sablefish}{sablefish},
and other rockfish species.
\end{itemize}
\begin{figure}[H]
{\centering \includegraphics[width=7in,height=\textheight]{content/../img/survey_plot_ai.png}
}
\caption{Strata used in the Aleutian Islands bottom trawl survey.}
\end{figure}%
\subsection{\texorpdfstring{\textbf{Gulf of
Alaska}}{Gulf of Alaska}}\label{gulf-of-alaska}
Most recent data report: (Siple et al., 2024)
\begin{itemize}
\tightlist
\item
Continental Shelf and Upper Slope of the Gulf of Alaska extending from
the Islands of Four Mountains 2,300 km east to Dixon Entrance
\item
Triennial (1990s)/Biennial since 2001 in odd years, since 1991
\item
Stratified Random Survey Design
\item
Important commercial species in the Gulf of Alaska include
\href{https://www.fisheries.noaa.gov/species/pacific-ocean-perch}{Pacific
ocean perch},
\href{https://www.fisheries.noaa.gov/species/alaska-pollock}{walleye
pollock},
\href{https://www.fisheries.noaa.gov/species/pacific-cod}{Pacific
cod}, flatfish, and other rockfish species.
\end{itemize}
\begin{figure}[H]
{\centering \includegraphics[width=7in,height=\textheight]{content/../img/survey_plot_goa.png}
}
\caption{Strata used in the Gulf of Alaska bottom trawl survey.}
\end{figure}%
\subsection{\texorpdfstring{\textbf{Eastern Bering Sea
Shelf}}{Eastern Bering Sea Shelf}}\label{eastern-bering-sea-shelf}
Most recent data report: (Markowitz et al., 2024)
\begin{itemize}
\tightlist
\item
The continental shelf of the eastern Bering Sea from the Aleutian
Islands to the Bering Strait
\item
Conducted annually since 1982.
\item
Uses a stratified systematic sampling survey design with fixed
stations at center of 20 x 20 nm grid.