added new details to the FOSS platform how to use page

.quarto/xref/14aca4aa

@@ -1 +1 @@
-{"headings":["afsc-bottom-trawl-surveys","documentation-objective","user-resources","cite-this-data","access-constraints","suggestions-and-comments","noaa-readme","noaa-license"],"options":{"chapters":true},"entries":[]}
+{"entries":[],"options":{"chapters":true},"headings":["afsc-bottom-trawl-surveys","documentation-objective","user-resources","cite-this-data","access-constraints","suggestions-and-comments","noaa-readme","noaa-license"]}

GAP-Production-Data-Documentation.tex

@@ -519,7 +519,7 @@
 \setcounter{page}{1}
 \end{frontmatter}
 
-%%%%% end titlepage extension code\ifdefined\Shaded\renewenvironment{Shaded}{\begin{tcolorbox}[boxrule=0pt, interior hidden, breakable, enhanced, borderline west={3pt}{0pt}{shadecolor}, sharp corners, frame hidden]}{\end{tcolorbox}}\fi
+%%%%% end titlepage extension code\ifdefined\Shaded\renewenvironment{Shaded}{\begin{tcolorbox}[breakable, borderline west={3pt}{0pt}{shadecolor}, interior hidden, frame hidden, enhanced, sharp corners, boxrule=0pt]}{\end{tcolorbox}}\fi
 
 \renewcommand*\contentsname{Table of contents}
 {
@@ -7567,9 +7567,12 @@ \subsection{FOSS\_TAXON\_GROUP}\label{foss_taxon_group}}
 \hypertarget{using-the-foss-platform}{%
 \chapter{Using the FOSS platform}\label{using-the-foss-platform}}
 
+\hypertarget{select-and-filter}{%
+\section{Select and filter}\label{select-and-filter}}
+
 \begin{figure}
 
-{\centering \includegraphics[width=6.24in,height=\textheight]{content/../img/foss_1_interface.png}
+{\centering \includegraphics[width=2.87in,height=\textheight]{content/../img/foss_1_interface.png}
 
 }
 
@@ -7578,53 +7581,68 @@ \chapter{Using the FOSS platform}\label{using-the-foss-platform}}
 
 \end{figure}
 
-\hypertarget{select-and-filter}{%
-\section{Select and filter}\label{select-and-filter}}
-
-Select, filter, and package this and other NOAA Fisheries data from the
+Select, filter, and download this and other NOAA Fisheries data from the
 \href{https://www.fisheries.noaa.gov/foss}{Fisheries One Stop Shop
 (FOSS)} platform. A user guide for the FOSS platform can be found
 \href{https://www.fisheries.noaa.gov/foss/f?p=215:7:7542600605674:::::}{here}.
-To begin a report, select options from the boxes what you need data for.
+To begin a report, select the kind of data you need:
+\texttt{Haul\ and\ catch\ data}, \texttt{Haul\ data\ only},
+\texttt{All\ observed\ species}.
 
-For a given box, select one or a few options from the ``options box''
-(list on the left) to query by highlighting them. To select multiple
-options, hold down the CTRL key while clicking on the options of
-interest, or click and drag down the list. Once the options you wish to
-be included in your query are highlighted, click the right-pointing
-arrow (\texttt{\textgreater{}}) to move them into the ``selection box''
-(list on the right). If you accidentally select an option that you do
-not want to query, simply select the unwanted option from the selection
-box and click the left-pointing arrow (\texttt{\textless{}}).
+\begin{quote}
+In this example, we'll select for 2023 eastern Bering Sea Arctic cod
+data. Here, we used the \texttt{Search\ Species} box to search for
+species with the term ``cod'' in their common names and selected
+``Pacific cod'' from that shortened list.
+\end{quote}
 
-If you wish to select all options from the options box and send them to
-the selection box, simply click the double right-pointing arrow
-(\texttt{\textgreater{}\textgreater{}}). If you want to unselect all
-options from the selection box, use the double left-pointing arrow
-(\texttt{\textless{}\textless{}}) or the reset icon.
+\hypertarget{catch-and-haul}{%
+\subsection{Catch and haul}\label{catch-and-haul}}
 
-To find a specific species or group more quickly you can use the
-\texttt{Search\ Species} option to quickly narrow the options. Search
-for parts of species common names in the \texttt{Search\ Species} box by
-entering a term and clicking the \texttt{search} button. The platform
-will return a shorter list in the \texttt{Speices} options box of only
-species that contain a match to that search term.
+\begin{figure}
 
-Use the \texttt{Reset\ All\ Parameters} button to reset all parameters
-for entire form.
+{\centering \includegraphics[width=2.73in,height=\textheight]{content/../img/foss_1_interface_catch.png}
+
+}
+
+\caption{Catch data on the AFSC Groundfish and Crab Assessment Program
+Bottom Trawl Survey data interface on the Fisheries One Stop Shop
+platform.}
+
+\end{figure}
+
+\hypertarget{haul}{%
+\subsection{Haul}\label{haul}}
 
 \begin{figure}
 
-{\centering \includegraphics[width=6.67in,height=\textheight]{content/../img/foss_2_select.png}
+{\centering \includegraphics[width=3.61in,height=\textheight]{content/../img/foss_1_interface_haul.png}
 
 }
 
-\caption{Diagram of selection and search tools available on the FOSS
-platfrom.}
+\caption{Haul data on the AFSC Groundfish and Crab Assessment Program
+Bottom Trawl Survey data interface on the Fisheries One Stop Shop
+platform.}
+
+\end{figure}
+
+\hypertarget{species}{%
+\subsection{Species}\label{species}}
+
+\begin{figure}
+
+{\centering \includegraphics[width=3.12in,height=\textheight]{content/../img/foss_1_interface_species.png}
+
+}
+
+\caption{All species observed by survey on the AFSC Groundfish and Crab
+Assessment Program Bottom Trawl Survey data interface on the Fisheries
+One Stop Shop platform.}
 
 \end{figure}
 
-Filter options:
+The user must select a option in each of the three
+\texttt{option\ boxes}:
 
 \begin{itemize}
 \tightlist
@@ -7644,78 +7662,41 @@ \section{Select and filter}\label{select-and-filter}}
   code books}.
 \end{itemize}
 
-\begin{quote}
-In this example, we'll select for 2022 eastern Bering Sea Pacific cod
-data. Here, we used the \texttt{Search\ Species} box to search for
-species with the term ``cod'' in their common names and selected
-``Pacific cod'' from that shortened list.
-\end{quote}
-
-\begin{figure}
-
-{\centering \includegraphics[width=4.27in,height=\textheight]{content/../img/foss_3_selected.png}
-
-}
-
-\caption{Diagram of selection and search tools available on the FOSS
-platofrom.}
-
-\end{figure}
-
-\hypertarget{select-data-format}{%
-\section{Select data format}\label{select-data-format}}
+For a given box, select one or a few options from the
+\texttt{options\ box} (list on the left) to query. To select multiple
+options, hold down the \texttt{CTRL} key while clicking on the options
+of interest, or click and drag down the list. Once the options you wish
+to be included in your query are highlighted, click the right-pointing
+arrow (\texttt{\textgreater{}}) to move them into the ``selection box''
+(list on the right). This can also be achieved by double clicking the
+option item of interest. If you accidentally select an option that you
+do not want to query, simply select the unwanted option from the
+selection box and click the left-pointing arrow (\texttt{\textless{}}).
 
-Select from the below radio list of pre-designed output tables. Once you
-run the report, the user can further specify filter data and select
-columns of interest. The tables below will only include data from the
-selections made in the previous step.
+If you wish to select all options from the options box and send them to
+the selection box, simply click the double right-pointing arrow
+(\texttt{\textgreater{}\textgreater{}}). If you want to unselect all
+options from the selection box, use the double left-pointing arrow
+(\texttt{\textless{}\textless{}}) or the reset icon.
 
-\begin{itemize}
-\tightlist
-\item
-  \texttt{All\ Data\ Fields:\ Presence\ and\ Absence\ (zero-filled)}:
-  The most complete version of the data, including species, catch, haul,
-  and environmental data. This data will include catch data for where
-  species were caught and zeros for where the species were not caught.
-  This is important for calculating catch-per-unit-effort data,
-  preparing distribution plots (e.g.,
-  \href{https://github.com/afsc-gap-products/akgfmaps}{using the
-  akgfmaps R package}), and many statistical analyses.
-\item
-  \texttt{All\ Data\ Fields:\ Presence-only\ (non-zero)}: The second
-  most complete version of the data, including species, catch, haul, and
-  environmental data. However, this data only includes catch data for
-  where species were caught and does not include zeros for where the
-  species were not caught. This will return smaller, more focused data
-  and can be useful for quickly assessing how many species were caught
-  or how many stations species were caught at.
-\item
-  \texttt{Catch\ data:\ Presence\ and\ Absence\ (zero-filled)}: This
-  data set is similar to
-  \texttt{All\ Data\ Fields:\ Presence\ and\ Absence\ (zero-filled)},
-  but only includes catch and species data columns.
-\item
-  \texttt{Catch\ data:\ Presence-only\ (non-zero)}: This data set is
-  similar to \texttt{All\ Data\ Fields:\ Presence-only\ (non-zero)}, but
-  only includes catch and species data columns.
-\item
-  \texttt{Haul\ Data}: This data set only includes haul and
-  environmental data collected from the survey. This data will only
-  include one observation per haul event/station.
-\end{itemize}
+To find a specific species or group more quickly you can use the
+\texttt{Search\ Species} option to quickly narrow the options. Search
+for parts of species common names in the \texttt{Search\ Species} box by
+entering a term and clicking the \texttt{search} button. The platform
+will return a shorter list in the \texttt{Speices} options box of only
+species that contain a match to that search term.
 
-\begin{quote}
-In this example, we'll select
-\texttt{All\ Data\ Fields:\ Presence\ and\ Absence\ (zero-filled).}
-\end{quote}
+Use the \texttt{Reset\ All\ Parameters} button to reset all parameters
+for entire form.
 
 \begin{figure}
 
-{\centering \includegraphics[width=3.68in,height=\textheight]{content/../img/foss_4_data_format.png}
+{\centering \includegraphics[width=6.72in,height=\textheight]{content/../img/foss_2_catch_select_species.png}
 
 }
 
-\caption{Diagram of the pre-set data format options.}
+\caption{Diagram of selection and search tools available on the FOSS
+platfrom.}
 
 \end{figure}
 
@@ -7732,14 +7713,23 @@ \section{Run report}\label{run-report}}
 
 \begin{figure}
 
-{\centering \includegraphics[width=4.24in,height=\textheight]{content/../img/foss_5_run_report.png}
+{\centering \includegraphics[width=5.97in,height=\textheight]{content/../img/foss_3_run_report.png}
 
 }
 
 \caption{Example data returned from running the report.}
 
 \end{figure}
 
+\hypertarget{api}{%
+\section{API}\label{api}}
+
+APIs, or Application Programming Interfaces, allows users to pull data
+through a IDE, or integrated development environment, like RStudio or VS
+Code. Explore the API pages for each of the data pages
+(\texttt{Haul\ and\ catch\ data}, \texttt{Haul\ data\ only},
+\texttt{All\ observed\ species}).
+
 \hypertarget{access-via-api-and-r}{%
 \chapter{Access via API and R}\label{access-via-api-and-r}}