HowTo_get_survey_data.tex

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\hypersetup{
  pdftitle={Get and summarize AFSC survey data},
  pdfauthor={Kirstin Holsman, Alaska Fisheries Science Center},
  hidelinks,
  pdfcreator={LaTeX via pandoc}}

\title{Get and summarize AFSC survey data}
\author{Kirstin Holsman, Alaska Fisheries Science Center}
\date{}

\begin{document}
\maketitle

{
\setcounter{tocdepth}{2}
\tableofcontents
}
\begin{verbatim}
## Warning: package 'svMisc' was built under R version 4.1.3
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## Warning: package 'reshape2' was built under R version 4.1.3
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\hypertarget{afsc-survey-cpue-data-github.comkholsmanafsc_cpue}{%
\paragraph{\texorpdfstring{\href{https://github.com/kholsman/AFSC_CPUE}{\textbf{AFSC
Survey CPUE data:
github.com/kholsman/AFSC\_CPUE}}}{AFSC Survey CPUE data: github.com/kholsman/AFSC\_CPUE}}\label{afsc-survey-cpue-data-github.comkholsmanafsc_cpue}}

Repo maintained by:\\
Kirstin Holsman\\
Alaska Fisheries Science Center\\
NOAA Fisheries, Seattle WA\\
\textbf{\url{kirstin.holsman@noaa.gov}}\strut \\
\emph{Last updated: Oct 04, 2024}

\hypertarget{overview}{%
\section{Overview}\label{overview}}

The below scripts return a list object cpue\_data saved as a compressed
Rdata file with the naming `reg.srvy\#.spp.cpue\_data.Rdata' such as
``ebs.srvy98.plk.cpue\_data.Rdata''. Each cpue\_data list contains 8
data.frames:

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{load}\NormalTok{(}\FunctionTok{paste0}\NormalTok{(}\StringTok{"data/out/"}\NormalTok{,qrydate,}\StringTok{"/cpue/ebs/ebs.srvy98.plk.cpue\_data.Rdata"}\NormalTok{))}

\FunctionTok{names}\NormalTok{(cpue\_data)}
\end{Highlighting}
\end{Shaded}

There is a folder for each region ``ebs'', ``goa'', ``ai''. For the
``ebs'' (Bering Sea) there are two sets of cpue\_data, one that is
NEBS+SEBS combined (`ebs.srvy98.{[}sp{]}.cpue\_data.Rdata') and one that
is just SEBS survey areas (`sebs.srvy98.{[}sp{]}.cpue\_data.Rdata'). For
both the Gulf of Alaska (``goa'') and the Bering Sea, mean CPUE (Kg per
km2 or Number per km2) for each size bin at each strata was calculated
and then multiplied by the STRATA area to get total Biomass and
abundance. \textbf{Note:Since strata area estimates where not available
for the Aleutian Island (``ai'') or slope surveys (``slope'') these AREA
was set equal to 1 and the Total Biomass and abundance is actually the
sum of mean biomass. }

The data.frames within each cpue\_data object are:

\begin{enumerate}
\def\labelenumi{\arabic{enumi}.}
\tightlist
\item
  \textbf{totalB\_N}: Total biomass (kg) or abundance (\# of fish) for
  the species in each year\\
\item
  \textbf{mnCPUE\_strata\_yr} : Average survey CPUE (kg per Km2) or
  abundance (\# per Km2) for the species in each strata and year\\
\item
  \textbf{total\_bin\_B\_N}: Total biomass (kg) or abundance (\# of
  fish) for each bin (10 mm) for the species in each year\\
\item
  \textbf{mnCPUE\_strata\_bin\_yr} : Average survey CPUE (kg per Km2) or
  abundance (\# per Km2) for each size bin for the species in each
  strata and year
\item
  \textbf{CPUE\_station\_bin\_yr}: Station specific survey CPUE (kg per
  Km2) or abundance (\# per Km2) for each size bin for the species in
  each year\\
\item
  \textbf{CPUE\_station\_yr}: Station specific survey CPUE (kg per Km2)
  or abundance (\# per Km2) for the species in each year\\
\item
  \textbf{propByBin}: proportion of biomass in each size bin per species
  per year\\
\item
  \textbf{propByStrata}: proportion of biomass in each strata per
  species per year
\item
  \textbf{propByStrataBin}: proportion of biomass in each bin and strata
  per species per year
\end{enumerate}

\includegraphics{figs/Kearney_2023.jpg} To obtain population level
estimates of the biomass or abundance of fish by size bin \(l\), we used
a length weight regression to estimate the weight of each size fish
\(j\) measured (\(\hat{W}\)) to calculate the proportion by weight or
frequency at each station where \[\hat{W_j} = \alpha_s+L_j^{\beta_s} \]

where the species-specific (\(s\)) slope and intercept values
(\(\beta_s\) and \(\alpha_s\), respectively) were fit to all available
length and weight data from surveys from all years across the EBS, GOA,
and AI (rather than each basin separately).

The number and biomass (\(hat{W_j}\)) for each 1 (mm) length was summed
into 10 mm size bins \(l\) and expanded to include stations and bins
where CPUE = 0 (saved as the object
\texttt{cpue\_data\$CPUE\_station\_bin\_yr}). Bin-specific catch
\(\bar{CPUE}_{s,k,y,l}\) (kg per \(Km^2\) or number per \(Km^2\)) of all
stations \(i\) in strata \(k\) for size bin \(l\) (saved as the object
\texttt{cpue\_data\$mnCPUE\_strata\_bin\_yr})::
\[\bar{CPUE}^{B|N}_{s,k,y,l}=\frac{1}{n_k}\sum_{n_k}{CPUE^{B|N}_{s,k,y,l,i}}\]

and where \(CPUE^B_{s,k,y,l,i} = \sum_{n_l}\hat{W}_j\) and
\(CPUE^N_{s,k,y,l,i} = \sum_{n_l}1\) are the station specific CPUEs for
biomass and abundance of fish in size bin l (respectively). CPUE was
converted to total strata- and bin-specific biomass (\$B\_\{s,k,y,l\}
\$) by multiplying the strata average catch ( \(\bar{CPUE}_{s,k,y,l}\) )
for each species and bin by the strata area \(A_{k}\) ( \(Km2\); saved
as the object \texttt{cpue\_data\$total\_bin\_B\_N}):

\[B_{s,k,y,l} =  \bar{CPUE}^{B}_{s,k,y,l} \dot{}A_{k}\] and
\[N_{s,k,y,l} =  \bar{CPUE}^{N}_{s,k,y,l} \dot{}A_{k}\]

We then calculated the proportion of total annual abundance
(\(N_{s,y}= \sum_k{\sum_l{N_{s,k,y,l}}}\)) or biomass
(\(B_{s,y}= \sum_k{\sum_l{B_{s,k,y,l}}}\); saved as
\texttt{cpue\_data\$totalB\_N}) of each species and bin \(l\) in each
strata \(k\) as (saved as the object
\texttt{cpue\_data\$propByStrataBin}):

\[p^N_{s,k,y,l} = \frac{N_{s,k,y,l}}{ \sum_k{\sum_l{N_{s,k,y,l}}}}\] and
\[p^B_{s,k,y,l} = \frac{B_{s,k,y,l}}{ \sum_k{\sum_l{B_{s,k,y,l}}}}\] and
the proportion of total annual biomass (or abundance) of each species in
each strata as (saved as the object \texttt{cpue\_data\$propByStrata}):
\[p^B_{s,k,y} = \frac{\sum_l({B_{s,k,y,l}})}{ \sum_k{\sum_l{B_{s,k,y,l}}}}\]

and the proportion of total annual biomass of each species in each bin
l: (saved as the object \texttt{cpue\_data\$propByBin}):
\[p^B_{s,k,l} = \frac{\sum_k({B_{s,k,y,l}})}{ \sum_k{\sum_l{B_{s,k,y,l}}}}\]

\hypertarget{comparison-of-bering-sea-survey-biomass-indices}{%
\section{Comparison of Bering Sea survey biomass
indices}\label{comparison-of-bering-sea-survey-biomass-indices}}

\includegraphics{figs/plk_srvy.jpg}

\includegraphics{figs/pcod_srvy.jpg}

\begin{figure}
\centering
\includegraphics{figs/atf_srvy.jpg}
\caption{``arrowtooth''}
\end{figure}

\hypertarget{workflow-to-update-biomass-indices}{%
\section{Workflow to update biomass
indices}\label{workflow-to-update-biomass-indices}}

\hypertarget{step-1-2-set-up-the-r-workspace-update-lookups-and-lwa}{%
\subsection{Step 1 \& 2 : Set up the R workspace, update lookups and
LWA}\label{step-1-2-set-up-the-r-workspace-update-lookups-and-lwa}}

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{\# \#\# Step 0: Set up the R workspace}
\CommentTok{\# }
\CommentTok{\# The first step is to set up the switches for what files to update and create in the file \textasciigrave{}R/setup.R\textasciigrave{}. The code below then loads these settings as well as base data, functions, and packages. }
\CommentTok{\# }
\CommentTok{\# \#\# Step 1: Update SQL queries}
\CommentTok{\# This step must be run on a computer that has access to RACEBASE. The code below will generate the base files for steps 2 and 3 below,and will save them in the folder \textasciigrave{}r data.path \textasciigrave{} under subfolders for each region in \textasciigrave{}srvys$reg\textasciigrave{} and each species in \textasciigrave{}splist\textasciigrave{} (see \textasciigrave{}R/setup.R\textasciigrave{} to change these settings).}

\CommentTok{\# **IMPORTANT:**  }
\CommentTok{\#   }
\CommentTok{\#   * **This step  must be connected to the RACEBASE SQL database**}
\CommentTok{\# }
\CommentTok{\#   * **The code will connect to the SQL database using your password and username. Remember to update the \textasciigrave{}username\_path\textasciigrave{} in the first line of the \textasciigrave{}R/setup.R \textasciigrave{} file and corresponding \textasciigrave{}username\textasciigrave{} and \textasciigrave{}password\textasciigrave{} under \textasciigrave{}username\_password.R\textasciigrave{}. A template is available under \textasciigrave{}R/\textasciigrave{}.**}
\CommentTok{\# }
\CommentTok{\# \textless{}!{-}{-} ![Header of \textasciigrave{}setup.R\textasciigrave{} where \textasciigrave{}username\_path\textasciigrave{} can be adjusted. This file also is where species, regions, and bins are specified.](figs/setup.jpg)\{width=80\%\} {-}{-}\textgreater{}}
\CommentTok{\# }
 
  
  \CommentTok{\# get everything set up:}
  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
    \CommentTok{\# rm(list=ls())}
    \CommentTok{\# this uses the password saved in R/password.R}
\NormalTok{    update\_qrydate      }\OtherTok{\textless{}{-}}   \ConstantTok{TRUE}  \CommentTok{\# update the query date}
\NormalTok{    update\_LWdata       }\OtherTok{\textless{}{-}}   \ConstantTok{TRUE} \CommentTok{\# update LW regressions}
\NormalTok{    update\_lkups        }\OtherTok{\textless{}{-}}   \ConstantTok{TRUE} \CommentTok{\# update the lookuptables}
    \FunctionTok{suppressMessages}\NormalTok{(}\FunctionTok{source}\NormalTok{(}\StringTok{"R/make.R"}\NormalTok{))}

  \CommentTok{\# update the SQL queries for goa, ai, sebs and nebs}
  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}  }

  \FunctionTok{source}\NormalTok{(}\FunctionTok{file.path}\NormalTok{(code.path,}\StringTok{"R/sub\_scripts/runRACE\_qrys.R"}\NormalTok{))}

  \CommentTok{\# combine sebs and nebs into one region: ebs}
  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}  }
  \ControlFlowTok{if}\NormalTok{(}\FunctionTok{dir.exists}\NormalTok{(}\FunctionTok{file.path}\NormalTok{(data.path,}\StringTok{"ebs"}\NormalTok{)))}
      \FunctionTok{system}\NormalTok{(}\FunctionTok{paste}\NormalTok{(}\StringTok{"rm {-}r"}\NormalTok{,}\FunctionTok{file.path}\NormalTok{(data.path,}\StringTok{"ebs"}\NormalTok{)))}
    \FunctionTok{dir.create}\NormalTok{(}\FunctionTok{file.path}\NormalTok{(data.path,}\StringTok{"ebs"}\NormalTok{))}
  
  \CommentTok{\# combine files and rename survey area to all of EBS}
  \ControlFlowTok{for}\NormalTok{(sp }\ControlFlowTok{in} \FunctionTok{names}\NormalTok{(splist))\{}
    \ControlFlowTok{if}\NormalTok{(}\FunctionTok{dir.exists}\NormalTok{(}\FunctionTok{file.path}\NormalTok{(data.path,}\StringTok{"ebs"}\NormalTok{,sp)))}
      \FunctionTok{system}\NormalTok{(}\FunctionTok{paste}\NormalTok{(}\StringTok{"rm {-}r"}\NormalTok{,}\FunctionTok{file.path}\NormalTok{(data.path,}\StringTok{"ebs"}\NormalTok{,sp)))}
      \FunctionTok{dir.create}\NormalTok{(}\FunctionTok{file.path}\NormalTok{(data.path,}\StringTok{"ebs"}\NormalTok{,sp))}
    \CommentTok{\#"length.Rdata"         }
    \FunctionTok{load}\NormalTok{(}\FunctionTok{file.path}\NormalTok{(data.path,}\StringTok{"nebs"}\NormalTok{,sp,}\StringTok{"length.Rdata"}\NormalTok{))}
\NormalTok{    length\_nebs }\OtherTok{\textless{}{-}}\NormalTok{ length;}\FunctionTok{rm}\NormalTok{(length)}
    \FunctionTok{load}\NormalTok{(}\FunctionTok{file.path}\NormalTok{(data.path,}\StringTok{"sebs"}\NormalTok{,sp,}\StringTok{"length.Rdata"}\NormalTok{))}
\NormalTok{    length\_sebs }\OtherTok{\textless{}{-}}\NormalTok{ length;}\FunctionTok{rm}\NormalTok{(length)}
\NormalTok{    length}\OtherTok{\textless{}{-}} \FunctionTok{rbind}\NormalTok{(length\_nebs}\SpecialCharTok{\%\textgreater{}\%}
      \FunctionTok{mutate}\NormalTok{(}\AttributeTok{SURVEY\_DEFINITION\_ID\_aka =}\NormalTok{SURVEY\_DEFINITION\_ID,}\AttributeTok{SURVEY\_DEFINITION\_ID =}\DecValTok{98}\NormalTok{),}
\NormalTok{     length\_sebs}\SpecialCharTok{\%\textgreater{}\%}
      \FunctionTok{mutate}\NormalTok{(}\AttributeTok{SURVEY\_DEFINITION\_ID\_aka =}\NormalTok{SURVEY\_DEFINITION\_ID,}\AttributeTok{SURVEY\_DEFINITION\_ID =}\DecValTok{98}\NormalTok{))}
    
    \FunctionTok{save}\NormalTok{(length,}\AttributeTok{file =} \FunctionTok{file.path}\NormalTok{(data.path,}\StringTok{"ebs"}\NormalTok{,sp,}\StringTok{"length.Rdata"}\NormalTok{))}
    \FunctionTok{rm}\NormalTok{(length)}
    
    \CommentTok{\#"location.Rdata"        }
    \FunctionTok{load}\NormalTok{(}\FunctionTok{file.path}\NormalTok{(data.path,}\StringTok{"nebs"}\NormalTok{,sp,}\StringTok{"location.Rdata"}\NormalTok{))}
\NormalTok{    location\_nebs }\OtherTok{\textless{}{-}}\NormalTok{ location;}\FunctionTok{rm}\NormalTok{(location)}
    \FunctionTok{load}\NormalTok{(}\FunctionTok{file.path}\NormalTok{(data.path,}\StringTok{"sebs"}\NormalTok{,sp,}\StringTok{"location.Rdata"}\NormalTok{))}
\NormalTok{    location\_sebs }\OtherTok{\textless{}{-}}\NormalTok{ location;}\FunctionTok{rm}\NormalTok{(location)}
\NormalTok{    location      }\OtherTok{\textless{}{-}} \FunctionTok{rbind}\NormalTok{(location\_nebs, location\_sebs)}
    
    \FunctionTok{save}\NormalTok{(location,}\AttributeTok{file =} \FunctionTok{file.path}\NormalTok{(data.path,}\StringTok{"ebs"}\NormalTok{,sp,}\StringTok{"location.Rdata"}\NormalTok{))}
    
    
    \CommentTok{\#"location\_catch.Rdata"}
    \FunctionTok{load}\NormalTok{(}\FunctionTok{file.path}\NormalTok{(data.path,}\StringTok{"nebs"}\NormalTok{,sp,}\StringTok{"location\_catch.Rdata"}\NormalTok{))}
\NormalTok{    location\_catch\_nebs }\OtherTok{\textless{}{-}}\NormalTok{ location\_catch;}\FunctionTok{rm}\NormalTok{(location\_catch)}
    \FunctionTok{load}\NormalTok{(}\FunctionTok{file.path}\NormalTok{(data.path,}\StringTok{"sebs"}\NormalTok{,sp,}\StringTok{"location\_catch.Rdata"}\NormalTok{))}
\NormalTok{    location\_catch\_sebs }\OtherTok{\textless{}{-}}\NormalTok{ location\_catch;}\FunctionTok{rm}\NormalTok{(location\_catch)}
\NormalTok{    location\_catch      }\OtherTok{\textless{}{-}} \FunctionTok{rbind}\NormalTok{(location\_catch\_nebs}\SpecialCharTok{\%\textgreater{}\%}
      \FunctionTok{mutate}\NormalTok{(}\AttributeTok{SURVEY\_DEFINITION\_ID\_aka =}\NormalTok{SURVEY\_DEFINITION\_ID,}\AttributeTok{SURVEY\_DEFINITION\_ID =}\DecValTok{98}\NormalTok{),}
\NormalTok{     location\_catch\_sebs}\SpecialCharTok{\%\textgreater{}\%}
      \FunctionTok{mutate}\NormalTok{(}\AttributeTok{SURVEY\_DEFINITION\_ID\_aka =}\NormalTok{SURVEY\_DEFINITION\_ID,}\AttributeTok{SURVEY\_DEFINITION\_ID =}\DecValTok{98}\NormalTok{))}
    
    \FunctionTok{save}\NormalTok{(location\_catch,}\AttributeTok{file =} \FunctionTok{file.path}\NormalTok{(data.path,}\StringTok{"ebs"}\NormalTok{,sp,}\StringTok{"location\_catch.Rdata"}\NormalTok{))}
    
\NormalTok{  \}}

    
\CommentTok{\#\textasciigrave{}\textasciigrave{}\textasciigrave{}}


\DocumentationTok{\#\# Step 2: Update the LWA regressions}

\CommentTok{\# The default code for RACEBASE uses set LW relationships, however we prefer to update the LW regressions using glms. Depending on how many observations exist the LW relationships can be region specific or use data across all regions.The default below is all regions combined. This code generates two outputs in \textasciigrave{}r data.out\textasciigrave{}, \textasciigrave{}r LWname\textasciigrave{} and \textasciigrave{}LW\_SmryTable.Rdata\textasciigrave{}. It also updates the \textasciigrave{}species\_lkup$LW\_a\textasciigrave{} and species\_lkup$LW\_b\textasciigrave{} parms used in Step 3.}
\CommentTok{\# }
\CommentTok{\# \#\textasciigrave{}\textasciigrave{}\textasciigrave{}\{r updateLWglms, echo=TRUE, eval=FALSE\}    }

  \CommentTok{\# GAP\_PRODUCTS.AKFIN\_LENGTHS}
  \CommentTok{\# update the LW regressions }
  \CommentTok{\#{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}  }

  \ControlFlowTok{if}\NormalTok{(update\_LWdata)\{    }
     \FunctionTok{source}\NormalTok{(}\FunctionTok{file.path}\NormalTok{(code.path,}\StringTok{"R/sub\_scripts/updateLW.R"}\NormalTok{))}
     \CommentTok{\# reload with updated data:}
     \FunctionTok{source}\NormalTok{(}\FunctionTok{file.path}\NormalTok{(code.path,}\StringTok{"R/load\_data.R"}\NormalTok{))}
\NormalTok{  \}}
\NormalTok{  species\_lkup}
\end{Highlighting}
\end{Shaded}

\hypertarget{step-3-get-cpue-data-from-the-surveys}{%
\subsection{Step 3: Get CPUE data from the
surveys}\label{step-3-get-cpue-data-from-the-surveys}}

This code is the core script for generating the CPUE\_NUMKM2 and
CPUE\_BIOMKM2 values by size bin, region, and species.

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{  STRATA\_AREA}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{filter}\NormalTok{(REGION}\SpecialCharTok{==}\StringTok{"BS"}\NormalTok{)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{group\_by}\NormalTok{(YEAR)}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{summarise}\NormalTok{(}\AttributeTok{mnAREA  =} \FunctionTok{mean}\NormalTok{(AREA, }\AttributeTok{na.rm=}\NormalTok{T),}
                               \AttributeTok{sumAREA =} \FunctionTok{sum}\NormalTok{(AREA, }\AttributeTok{na.rm=}\NormalTok{T),}
                               \AttributeTok{cnt =} \FunctionTok{length}\NormalTok{(}\FunctionTok{unique}\NormalTok{(STRATUM)))}
  
\NormalTok{   STRATA\_AREA}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{filter}\NormalTok{(REGION}\SpecialCharTok{==}\StringTok{"GOA"}\NormalTok{)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{group\_by}\NormalTok{(YEAR)}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{summarise}\NormalTok{(}\AttributeTok{mnAREA  =} \FunctionTok{mean}\NormalTok{(AREA, }\AttributeTok{na.rm=}\NormalTok{T),}
                               \AttributeTok{sumAREA =} \FunctionTok{sum}\NormalTok{(AREA, }\AttributeTok{na.rm=}\NormalTok{T),}
                               \AttributeTok{cnt =} \FunctionTok{length}\NormalTok{(}\FunctionTok{unique}\NormalTok{(STRATUM)))}
  
\NormalTok{   STRATA\_AREA}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{filter}\NormalTok{(REGION}\SpecialCharTok{==}\StringTok{"BS"}\NormalTok{,YEAR}\SpecialCharTok{==}\DecValTok{2022}\NormalTok{)}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{select}\NormalTok{(STRATUM)}

   \CommentTok{\# overwrite the NEBS frame from setup for the next set of code (ebs = sebs+nebs now forward)}
   \CommentTok{\# up above I combine the NEBS+SEBS into the ebs folder and rename the rest NEBS or SEBS accordingly }
   \CommentTok{\# {-} so even though the survey number is 98 it;s actually 98 \& 143.}
\NormalTok{  srvys }\OtherTok{\textless{}{-}} \FunctionTok{data.frame}\NormalTok{(}\AttributeTok{reg=}\FunctionTok{c}\NormalTok{(}\StringTok{"ebs"}\NormalTok{,}\StringTok{"goa"}\NormalTok{,}\StringTok{"ai"}\NormalTok{,}\StringTok{"slope"}\NormalTok{),}\AttributeTok{RGN =} \FunctionTok{c}\NormalTok{(}\StringTok{"BS"}\NormalTok{,}\StringTok{"GOA"}\NormalTok{,}\StringTok{"AI"}\NormalTok{,}\StringTok{"SLOPE"}\NormalTok{), }\AttributeTok{num=}\FunctionTok{c}\NormalTok{(}\DecValTok{98}\NormalTok{,}\DecValTok{47}\NormalTok{,}\DecValTok{52}\NormalTok{,}\DecValTok{78}\NormalTok{)  )}
  \CommentTok{\# srvys \textless{}{-} data.frame(reg=c("ebs","goa","ai"),RGN = c("BS","GOA","AI"), num=c(98,47,52)  )}
\NormalTok{  nreg }\OtherTok{\textless{}{-}} \FunctionTok{length}\NormalTok{(srvys}\SpecialCharTok{$}\NormalTok{reg)}
\NormalTok{  nspp }\OtherTok{\textless{}{-}} \FunctionTok{length}\NormalTok{(species\_lkup}\SpecialCharTok{$}\NormalTok{sp)}
  
  \ControlFlowTok{for}\NormalTok{ (r }\ControlFlowTok{in} \DecValTok{1}\SpecialCharTok{:}\NormalTok{nreg)\{}
    \ControlFlowTok{for}\NormalTok{(s }\ControlFlowTok{in} \DecValTok{1}\SpecialCharTok{:}\NormalTok{nspp)\{}
      
      \ControlFlowTok{if}\NormalTok{(srvys[r,]}\SpecialCharTok{$}\NormalTok{reg }\SpecialCharTok{==}\StringTok{"ebs"}\NormalTok{)\{}
        \CommentTok{\# first SEBS only:}
        \CommentTok{\# {-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
\NormalTok{        STRATA\_AREAUSE }\OtherTok{\textless{}{-}}\NormalTok{ STRATA\_AREA}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{filter}\NormalTok{(REGION}\SpecialCharTok{==}\NormalTok{srvys}\SpecialCharTok{$}\NormalTok{RGN[r])}
\NormalTok{        maxyr          }\OtherTok{\textless{}{-}} \FunctionTok{max}\NormalTok{(STRATA\_AREAUSE}\SpecialCharTok{$}\NormalTok{YEAR)}
\NormalTok{        STRATA\_AREAUSE }\OtherTok{\textless{}{-}}\NormalTok{ STRATA\_AREAUSE}\SpecialCharTok{\%\textgreater{}\%}
          \FunctionTok{filter}\NormalTok{(YEAR}\SpecialCharTok{==}\DecValTok{2022}\NormalTok{)}\SpecialCharTok{\%\textgreater{}\%}
          \FunctionTok{group\_by}\NormalTok{(REGION,STRATUM)}\SpecialCharTok{\%\textgreater{}\%}
          \FunctionTok{summarize}\NormalTok{(}\AttributeTok{AREA =} \FunctionTok{mean}\NormalTok{(AREA, }\AttributeTok{na.rm=}\NormalTok{T))}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{ungroup}\NormalTok{()}
        
        \CommentTok{\# label "sebs"}
\NormalTok{         flnm }\OtherTok{\textless{}{-}} \FunctionTok{paste0}\NormalTok{(}\StringTok{"s"}\NormalTok{,srvys[r,]}\SpecialCharTok{$}\NormalTok{reg,}\StringTok{".srvy"}\NormalTok{,}
\NormalTok{                     srvys[r,]}\SpecialCharTok{$}\NormalTok{num,}\StringTok{"."}\NormalTok{,}
\NormalTok{                     species\_lkup[s,]}\SpecialCharTok{$}\NormalTok{sp)}
        \FunctionTok{cat}\NormalTok{(}\StringTok{"now getting data for: "}\NormalTok{,flnm,}\StringTok{"}\SpecialCharTok{\textbackslash{}n}\StringTok{"}\NormalTok{)}
\NormalTok{        cpue\_data }\OtherTok{\textless{}{-}} \FunctionTok{suppressMessages}\NormalTok{(}
          \FunctionTok{get\_CPUE\_DATA}\NormalTok{(}
          \AttributeTok{datapath   =}\NormalTok{ data.path,}
          \AttributeTok{out\_dir    =} \FunctionTok{file.path}\NormalTok{(data.out),}
          \AttributeTok{STRATA\_AREAIN =}\NormalTok{ STRATA\_AREAUSE,}
          \AttributeTok{flnm       =}\NormalTok{ flnm,}
          \AttributeTok{species    =}\NormalTok{ species\_lkup[s,]}\SpecialCharTok{$}\NormalTok{SPECIES\_CODE,}
          \AttributeTok{survey     =}\NormalTok{ srvys[r,]}\SpecialCharTok{$}\NormalTok{num,}
          \AttributeTok{includeNBS =} \ConstantTok{FALSE}\NormalTok{,}
          \AttributeTok{NEBSStrataIN =}\NormalTok{ NEBS\_strata ,}
          \AttributeTok{saveit     =}\NormalTok{ T,}
          \AttributeTok{bins       =}\NormalTok{ sp\_bins[[ species\_lkup[s,]}\SpecialCharTok{$}\NormalTok{sp ]]))}
        
        \FunctionTok{rm}\NormalTok{(cpue\_data)}
        
        \CommentTok{\# Now NESB + SEBS}
        \CommentTok{\# {-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
\NormalTok{        flnm }\OtherTok{\textless{}{-}} \FunctionTok{paste0}\NormalTok{(srvys[r,]}\SpecialCharTok{$}\NormalTok{reg,}\StringTok{".srvy"}\NormalTok{,}
\NormalTok{                     srvys[r,]}\SpecialCharTok{$}\NormalTok{num,}\StringTok{"."}\NormalTok{,}
\NormalTok{                     species\_lkup[s,]}\SpecialCharTok{$}\NormalTok{sp)}
        \FunctionTok{cat}\NormalTok{(}\StringTok{"now getting data for: "}\NormalTok{,flnm,}\StringTok{"}\SpecialCharTok{\textbackslash{}n}\StringTok{"}\NormalTok{)}
\NormalTok{        cpue\_data }\OtherTok{\textless{}{-}} \FunctionTok{suppressMessages}\NormalTok{(}
          \FunctionTok{get\_CPUE\_DATA}\NormalTok{(}
          \AttributeTok{datapath   =}\NormalTok{ data.path,}
          \AttributeTok{out\_dir    =} \FunctionTok{file.path}\NormalTok{(data.out),}
          \AttributeTok{STRATA\_AREAIN =}\NormalTok{ STRATA\_AREAUSE,}
          \AttributeTok{flnm       =}\NormalTok{ flnm,}
          \AttributeTok{species    =}\NormalTok{ species\_lkup[s,]}\SpecialCharTok{$}\NormalTok{SPECIES\_CODE,}
          \AttributeTok{survey     =}\NormalTok{ srvys[r,]}\SpecialCharTok{$}\NormalTok{num,  }\CommentTok{\#? shouldn\textquotesingle{}t this be 98\&143? No, I see, up above I combine the NEBS+SEBS into the ebs folder and rename the rest NEBS or SEBS accordingly {-} so even though the survey number is 98 it;s actually 98 \& 143.}
          \AttributeTok{includeNBS   =} \ConstantTok{TRUE}\NormalTok{,}
          \AttributeTok{NEBSStrataIN =}\NormalTok{ NEBS\_strata ,}
          \AttributeTok{saveit     =}\NormalTok{ T,}
          \AttributeTok{bins       =}\NormalTok{ sp\_bins[[ species\_lkup[s,]}\SpecialCharTok{$}\NormalTok{sp ]]))}
        
\NormalTok{      \}}
      \ControlFlowTok{if}\NormalTok{(srvys[r,]}\SpecialCharTok{$}\NormalTok{reg }\SpecialCharTok{==}\StringTok{"goa"}\NormalTok{)\{}
\NormalTok{        STRATA\_AREAUSE }\OtherTok{\textless{}{-}}\NormalTok{ STRATA\_AREA}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{filter}\NormalTok{(REGION}\SpecialCharTok{==}\NormalTok{srvys}\SpecialCharTok{$}\NormalTok{RGN[r])}
\NormalTok{        maxyr }\OtherTok{\textless{}{-}} \FunctionTok{max}\NormalTok{(STRATA\_AREAUSE}\SpecialCharTok{$}\NormalTok{YEAR)}
\NormalTok{        STRATA\_AREAUSE }\OtherTok{\textless{}{-}}\NormalTok{ STRATA\_AREAUSE}\SpecialCharTok{\%\textgreater{}\%}
          \FunctionTok{filter}\NormalTok{(YEAR}\SpecialCharTok{==}\DecValTok{1993}\NormalTok{)}\SpecialCharTok{\%\textgreater{}\%}
          \FunctionTok{group\_by}\NormalTok{(REGION,STRATUM)}\SpecialCharTok{\%\textgreater{}\%}
          \FunctionTok{summarize}\NormalTok{(}\AttributeTok{AREA =} \FunctionTok{mean}\NormalTok{(AREA, }\AttributeTok{na.rm=}\NormalTok{T))}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{ungroup}\NormalTok{()}
        
\NormalTok{        flnm }\OtherTok{\textless{}{-}} \FunctionTok{paste0}\NormalTok{(srvys[r,]}\SpecialCharTok{$}\NormalTok{reg,}\StringTok{".srvy"}\NormalTok{,}
\NormalTok{                     srvys[r,]}\SpecialCharTok{$}\NormalTok{num,}\StringTok{"."}\NormalTok{,}
\NormalTok{                     species\_lkup[s,]}\SpecialCharTok{$}\NormalTok{sp)}
        \FunctionTok{cat}\NormalTok{(}\StringTok{"now getting data for: "}\NormalTok{,flnm,}\StringTok{"}\SpecialCharTok{\textbackslash{}n}\StringTok{"}\NormalTok{)}
\NormalTok{        cpue\_data }\OtherTok{\textless{}{-}} \FunctionTok{suppressMessages}\NormalTok{(}
          \FunctionTok{get\_CPUE\_DATA}\NormalTok{(}
          \AttributeTok{datapath   =}\NormalTok{ data.path,}
          \AttributeTok{out\_dir    =} \FunctionTok{file.path}\NormalTok{(data.out),}
          \AttributeTok{STRATA\_AREAIN =}\NormalTok{ STRATA\_AREAUSE,}
          \AttributeTok{flnm       =}\NormalTok{ flnm,}
          \AttributeTok{species    =}\NormalTok{ species\_lkup[s,]}\SpecialCharTok{$}\NormalTok{SPECIES\_CODE,}
          \AttributeTok{survey     =}\NormalTok{ srvys[r,]}\SpecialCharTok{$}\NormalTok{num,}
          \AttributeTok{includeNBS =} \ConstantTok{FALSE}\NormalTok{,}
          \AttributeTok{NEBSStrataIN =}\NormalTok{ NEBS\_strata ,}
          \AttributeTok{saveit     =}\NormalTok{ T,}
          \AttributeTok{bins       =}\NormalTok{ sp\_bins[[ species\_lkup[s,]}\SpecialCharTok{$}\NormalTok{sp ]]))}
        
\NormalTok{      \}}
      \ControlFlowTok{if}\NormalTok{(}\SpecialCharTok{!}\NormalTok{srvys[r,]}\SpecialCharTok{$}\NormalTok{reg}\SpecialCharTok{\%in\%}\FunctionTok{c}\NormalTok{(}\StringTok{"ebs"}\NormalTok{,}\StringTok{"goa"}\NormalTok{))\{}
        \ControlFlowTok{if}\NormalTok{(species\_lkup[s,]}\SpecialCharTok{$}\NormalTok{sp}\SpecialCharTok{==}\StringTok{"yfs"}\SpecialCharTok{\&}\NormalTok{srvys[r,]}\SpecialCharTok{$}\NormalTok{reg}\SpecialCharTok{==}\StringTok{"slope"}\NormalTok{)\{}
          \CommentTok{\#skip}
\NormalTok{        \}}\ControlFlowTok{else}\NormalTok{\{}
\NormalTok{          flnm }\OtherTok{\textless{}{-}} \FunctionTok{paste0}\NormalTok{(srvys[r,]}\SpecialCharTok{$}\NormalTok{reg,}\StringTok{".srvy"}\NormalTok{,}
\NormalTok{                       srvys[r,]}\SpecialCharTok{$}\NormalTok{num,}\StringTok{"."}\NormalTok{,}
\NormalTok{                       species\_lkup[s,]}\SpecialCharTok{$}\NormalTok{sp)}
          \FunctionTok{cat}\NormalTok{(}\StringTok{"now getting data for: "}\NormalTok{,flnm,}\StringTok{"}\SpecialCharTok{\textbackslash{}n}\StringTok{"}\NormalTok{)}
\NormalTok{          cpue\_data }\OtherTok{\textless{}{-}} \FunctionTok{suppressMessages}\NormalTok{(}
            \FunctionTok{get\_CPUE\_DATA}\NormalTok{(}
            \AttributeTok{datapath   =}\NormalTok{ data.path,}
            \AttributeTok{out\_dir    =} \FunctionTok{file.path}\NormalTok{(data.out),}
            \AttributeTok{STRATA\_AREAIN =} \ConstantTok{NULL}\NormalTok{,}
            \AttributeTok{flnm       =}\NormalTok{ flnm,}
            \AttributeTok{species    =}\NormalTok{ species\_lkup[s,]}\SpecialCharTok{$}\NormalTok{SPECIES\_CODE,}
            \AttributeTok{survey     =}\NormalTok{ srvys[r,]}\SpecialCharTok{$}\NormalTok{num,}
            \AttributeTok{includeNBS =} \ConstantTok{FALSE}\NormalTok{,}
            \AttributeTok{NEBSStrataIN =}\NormalTok{ NEBS\_strata ,}
            \AttributeTok{saveit     =}\NormalTok{ T,}
            \AttributeTok{bins       =}\NormalTok{ sp\_bins[[ species\_lkup[s,]}\SpecialCharTok{$}\NormalTok{sp ]]))}
\NormalTok{        \}}

\NormalTok{      \}}
     
      \CommentTok{\# \# check the data :}
      \ControlFlowTok{if}\NormalTok{(}\DecValTok{1}\SpecialCharTok{==}\DecValTok{10}\NormalTok{)\{}
\NormalTok{        tt }\OtherTok{\textless{}{-}}\NormalTok{ cpue\_data}\SpecialCharTok{\%\textgreater{}\%}
              \FunctionTok{group\_by}\NormalTok{(YEAR,REGION,STATIONID,SN)}\SpecialCharTok{\%\textgreater{}\%}
              \FunctionTok{filter}\NormalTok{(BIN }\SpecialCharTok{==}\DecValTok{400}\NormalTok{)}\SpecialCharTok{\%\textgreater{}\%}
              \FunctionTok{summarize}\NormalTok{(}\AttributeTok{cnt =}\FunctionTok{length}\NormalTok{(STATIONID))}
         \FunctionTok{max}\NormalTok{(tt}\SpecialCharTok{$}\NormalTok{cnt)  }\CommentTok{\#Should be 1}
        \CommentTok{\#this looks to be a duplicate sampling...}
        \CommentTok{\#mis{-}entry or code error ?}
\NormalTok{         cpue\_data}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{filter}\NormalTok{(YEAR}\SpecialCharTok{==}\DecValTok{1988}\NormalTok{,STATIONID}\SpecialCharTok{==}\StringTok{"J{-}13"}\NormalTok{)}
\NormalTok{      \}}
       \FunctionTok{rm}\NormalTok{(cpue\_data)}

\NormalTok{    \}}
\NormalTok{  \}}
  
\CommentTok{\# Now make BT and SST files for strata, station and all basin}
  

  \CommentTok{\# srvys \textless{}{-} data.frame(reg=c("ebs","goa","ai"),RGN = c("BS","GOA","AI"), num=c(98,47,52)  )}
\NormalTok{  nreg }\OtherTok{\textless{}{-}} \FunctionTok{length}\NormalTok{(srvys}\SpecialCharTok{$}\NormalTok{reg)}

\NormalTok{  na.length }\OtherTok{\textless{}{-}} \ControlFlowTok{function}\NormalTok{(x,}\AttributeTok{na.rm=}\NormalTok{F)\{}
    \ControlFlowTok{if}\NormalTok{(na.rm }\SpecialCharTok{==}\NormalTok{ T)}
       \ControlFlowTok{if}\NormalTok{(}\FunctionTok{any}\NormalTok{(}\FunctionTok{is.na}\NormalTok{(x)))}
\NormalTok{         x }\OtherTok{\textless{}{-}}\NormalTok{ x[}\SpecialCharTok{!}\FunctionTok{is.na}\NormalTok{(x)]}
   \FunctionTok{return}\NormalTok{( }\FunctionTok{length}\NormalTok{(x))}
\NormalTok{  \}}
\NormalTok{  i }\OtherTok{\textless{}{-}}\DecValTok{0}
  \ControlFlowTok{for}\NormalTok{(regfl }\ControlFlowTok{in}\NormalTok{ srvys[,}\DecValTok{1}\NormalTok{] )\{}
    \ControlFlowTok{if}\NormalTok{(regfl}\SpecialCharTok{!=}\StringTok{"slope"}\NormalTok{)\{}
\NormalTok{    i }\OtherTok{\textless{}{-}}\NormalTok{ i }\SpecialCharTok{+}\DecValTok{1}
    \FunctionTok{load}\NormalTok{(}\FunctionTok{file.path}\NormalTok{(data.path,regfl,}\StringTok{"plk/location.Rdata"}\NormalTok{))}
    
\NormalTok{    tmp}\OtherTok{\textless{}{-}}\NormalTok{location}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{group\_by}\NormalTok{(YEAR,STRATUM,STATIONID)}\SpecialCharTok{\%\textgreater{}\%}
      \FunctionTok{summarize}\NormalTok{(}
        \AttributeTok{TEMP=}\FunctionTok{mean}\NormalTok{(TEMP,}\AttributeTok{na.rm=}\NormalTok{T),}
       \CommentTok{\# sdTEMP = sd(TEMP,na.rm=T),}
        \AttributeTok{num=} \FunctionTok{na.length}\NormalTok{(TEMP,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{SST =} \FunctionTok{mean}\NormalTok{(SST,}\AttributeTok{na.rm=}\NormalTok{T),}
       \CommentTok{\# sdSST = sd(SST,na.rm=T),}
        \AttributeTok{LAT=}\FunctionTok{mean}\NormalTok{(LAT,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{LON =} \FunctionTok{mean}\NormalTok{ (LON,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{MONTH =} \FunctionTok{mean}\NormalTok{(MONTH,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{DAY =} \FunctionTok{mean}\NormalTok{ (DAY,}\AttributeTok{na.rm=}\NormalTok{T))}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{mutate}\NormalTok{(}\AttributeTok{region =}\NormalTok{ regfl)}
    
    \ControlFlowTok{if}\NormalTok{(i }\SpecialCharTok{==}\DecValTok{1}\NormalTok{)}
\NormalTok{      TEMP }\OtherTok{\textless{}{-}}\NormalTok{ tmp}
    \ControlFlowTok{else}
\NormalTok{      TEMP }\OtherTok{\textless{}{-}} \FunctionTok{rbind}\NormalTok{(TEMP,tmp)}
    \FunctionTok{rm}\NormalTok{(tmp)}
\NormalTok{\}}
\NormalTok{  \}}
\NormalTok{  TEMP\_station }\OtherTok{\textless{}{-}}\NormalTok{ TEMP}
\NormalTok{  TEMP\_yk }\OtherTok{\textless{}{-}}\NormalTok{ TEMP}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{group\_by}\NormalTok{(YEAR,STRATUM,region)}\SpecialCharTok{\%\textgreater{}\%}
      \FunctionTok{summarize}\NormalTok{(}
        \AttributeTok{mnTEMP=}\FunctionTok{mean}\NormalTok{(TEMP,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{sdTEMP =} \FunctionTok{sd}\NormalTok{(TEMP,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{num=} \FunctionTok{na.length}\NormalTok{(TEMP,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{mnSST =} \FunctionTok{mean}\NormalTok{(SST,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{sdSST =} \FunctionTok{sd}\NormalTok{(SST,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{LAT=}\FunctionTok{mean}\NormalTok{(LAT,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{LON =} \FunctionTok{mean}\NormalTok{ (LON,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{MONTH =} \FunctionTok{mean}\NormalTok{(MONTH,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{DAY =} \FunctionTok{mean}\NormalTok{ (DAY,}\AttributeTok{na.rm=}\NormalTok{T))}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{ungroup}\NormalTok{()}
  
  \CommentTok{\# Now just for EBS and GOA}
  
  \CommentTok{\# {-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}{-}}
\NormalTok{        STRATA\_AREAUSE }\OtherTok{\textless{}{-}}\NormalTok{ STRATA\_AREA}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{filter}\NormalTok{(REGION}\SpecialCharTok{==}\StringTok{"BS"}\NormalTok{)}
\NormalTok{        STRATA\_AREAUSE }\OtherTok{\textless{}{-}}\NormalTok{ STRATA\_AREAUSE}\SpecialCharTok{\%\textgreater{}\%}
          \FunctionTok{filter}\NormalTok{(YEAR}\SpecialCharTok{==}\DecValTok{2022}\NormalTok{)}\SpecialCharTok{\%\textgreater{}\%}  \CommentTok{\# updated with revised projection datum. Use 2022}
          \FunctionTok{group\_by}\NormalTok{(REGION,STRATUM)}\SpecialCharTok{\%\textgreater{}\%}
          \FunctionTok{summarize}\NormalTok{(}\AttributeTok{AREA =} \FunctionTok{mean}\NormalTok{(AREA, }\AttributeTok{na.rm=}\NormalTok{T))}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{ungroup}\NormalTok{()}
  
\NormalTok{  sub}\OtherTok{\textless{}{-}}\NormalTok{ TEMP\_yk}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{group\_by}\NormalTok{(YEAR,STRATUM,region)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{filter}\NormalTok{(region }\SpecialCharTok{\%in\%} \FunctionTok{c}\NormalTok{(}\StringTok{"nebs"}\NormalTok{,}\StringTok{"sebs"}\NormalTok{))}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{mutate}\NormalTok{(}\AttributeTok{REGION =} \StringTok{"BS"}\NormalTok{)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{left\_join}\NormalTok{(STRATA\_AREAUSE)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{ungroup}\NormalTok{()}
  
\NormalTok{  sub}\OtherTok{\textless{}{-}}\NormalTok{ sub}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{left\_join}\NormalTok{(}
\NormalTok{      sub}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{group\_by}\NormalTok{(YEAR,STRATUM,REGION)}\SpecialCharTok{\%\textgreater{}\%}
        \FunctionTok{summarize}\NormalTok{(}\AttributeTok{AREA =} \FunctionTok{unique}\NormalTok{(AREA))}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{ungroup}\NormalTok{()}\SpecialCharTok{\%\textgreater{}\%}
        \FunctionTok{group\_by}\NormalTok{(YEAR,REGION)}\SpecialCharTok{\%\textgreater{}\%}
        \FunctionTok{summarize}\NormalTok{(}\AttributeTok{sumAREA=}\FunctionTok{sum}\NormalTok{(AREA,}\AttributeTok{na.rm=}\NormalTok{T)))}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{mutate}\NormalTok{(}\AttributeTok{propA =}\NormalTok{ AREA}\SpecialCharTok{/}\NormalTok{sumAREA)}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{ungroup}\NormalTok{()}
    
  
\NormalTok{  sub}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{group\_by}\NormalTok{(YEAR,REGION)}\SpecialCharTok{\%\textgreater{}\%}
        \FunctionTok{summarize}\NormalTok{(}\FunctionTok{sum}\NormalTok{(propA,}\AttributeTok{na.rm=}\NormalTok{T))}
  
  
\NormalTok{  SEBS\_NEBS\_TEMP\_y }\OtherTok{\textless{}{-}}\NormalTok{ sub}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{group\_by}\NormalTok{(YEAR,REGION)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{summarize}\NormalTok{(}
        \AttributeTok{mnTEMP =} \FunctionTok{sum}\NormalTok{(mnTEMP}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{sdTEMP =} \FunctionTok{sum}\NormalTok{(sdTEMP}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{mnSST  =} \FunctionTok{sum}\NormalTok{(mnSST}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{sdSST  =} \FunctionTok{sum}\NormalTok{(sdSST}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{num    =} \FunctionTok{sum}\NormalTok{(num,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{MONTH  =} \FunctionTok{sum}\NormalTok{(MONTH}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{DAY    =} \FunctionTok{sum}\NormalTok{ (DAY}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T))}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{ungroup}\NormalTok{()}
  
  \CommentTok{\# now just the NEBS:}
\NormalTok{  sub}\OtherTok{\textless{}{-}}\NormalTok{ TEMP\_yk}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{group\_by}\NormalTok{(YEAR,STRATUM,region)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{filter}\NormalTok{(region }\SpecialCharTok{\%in\%} \FunctionTok{c}\NormalTok{(}\StringTok{"nebs"}\NormalTok{))}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{mutate}\NormalTok{(}\AttributeTok{REGION =} \StringTok{"BS"}\NormalTok{)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{left\_join}\NormalTok{(STRATA\_AREAUSE)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{ungroup}\NormalTok{()}
  
\NormalTok{  sub}\OtherTok{\textless{}{-}}\NormalTok{ sub}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{left\_join}\NormalTok{(}
\NormalTok{      sub}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{group\_by}\NormalTok{(YEAR,STRATUM,REGION)}\SpecialCharTok{\%\textgreater{}\%}
        \FunctionTok{summarize}\NormalTok{(}\AttributeTok{AREA =} \FunctionTok{unique}\NormalTok{(AREA))}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{ungroup}\NormalTok{()}\SpecialCharTok{\%\textgreater{}\%}
        \FunctionTok{group\_by}\NormalTok{(YEAR,REGION)}\SpecialCharTok{\%\textgreater{}\%}
        \FunctionTok{summarize}\NormalTok{(}\AttributeTok{sumAREA=}\FunctionTok{sum}\NormalTok{(AREA,}\AttributeTok{na.rm=}\NormalTok{T)))}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{mutate}\NormalTok{(}\AttributeTok{propA =}\NormalTok{ AREA}\SpecialCharTok{/}\NormalTok{sumAREA)}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{ungroup}\NormalTok{()}
  
\NormalTok{  sub}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{group\_by}\NormalTok{(YEAR,REGION)}\SpecialCharTok{\%\textgreater{}\%}
        \FunctionTok{summarize}\NormalTok{(}\FunctionTok{sum}\NormalTok{(propA,}\AttributeTok{na.rm=}\NormalTok{T))}
  
  
\NormalTok{  NEBS\_TEMP\_y }\OtherTok{\textless{}{-}}\NormalTok{ sub}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{group\_by}\NormalTok{(YEAR,REGION)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{summarize}\NormalTok{(}
        \AttributeTok{mnTEMP =} \FunctionTok{sum}\NormalTok{(mnTEMP}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{sdTEMP =} \FunctionTok{sum}\NormalTok{(sdTEMP}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{mnSST  =} \FunctionTok{sum}\NormalTok{(mnSST}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{sdSST  =} \FunctionTok{sum}\NormalTok{(sdSST}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{num    =} \FunctionTok{sum}\NormalTok{(num,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{MONTH  =} \FunctionTok{sum}\NormalTok{(MONTH}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{DAY    =} \FunctionTok{sum}\NormalTok{ (DAY}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T))}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{ungroup}\NormalTok{()}
  
   \CommentTok{\# now just the NEBS:}
\NormalTok{  sub}\OtherTok{\textless{}{-}}\NormalTok{ TEMP\_yk}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{group\_by}\NormalTok{(YEAR,STRATUM,region)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{filter}\NormalTok{(region }\SpecialCharTok{\%in\%} \FunctionTok{c}\NormalTok{(}\StringTok{"sebs"}\NormalTok{))}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{mutate}\NormalTok{(}\AttributeTok{REGION =} \StringTok{"BS"}\NormalTok{)}\SpecialCharTok{\%\textgreater{}\%}
   \FunctionTok{left\_join}\NormalTok{(STRATA\_AREAUSE)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{ungroup}\NormalTok{()}
  
\NormalTok{  sub}\OtherTok{\textless{}{-}}\NormalTok{ sub}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{left\_join}\NormalTok{(}
\NormalTok{      sub}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{group\_by}\NormalTok{(YEAR,STRATUM,REGION)}\SpecialCharTok{\%\textgreater{}\%}
        \FunctionTok{summarize}\NormalTok{(}\AttributeTok{AREA =} \FunctionTok{unique}\NormalTok{(AREA))}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{ungroup}\NormalTok{()}\SpecialCharTok{\%\textgreater{}\%}
        \FunctionTok{group\_by}\NormalTok{(YEAR,REGION)}\SpecialCharTok{\%\textgreater{}\%}
        \FunctionTok{summarize}\NormalTok{(}\AttributeTok{sumAREA=}\FunctionTok{sum}\NormalTok{(AREA,}\AttributeTok{na.rm=}\NormalTok{T)))}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{mutate}\NormalTok{(}\AttributeTok{propA =}\NormalTok{ AREA}\SpecialCharTok{/}\NormalTok{sumAREA)}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{ungroup}\NormalTok{()}
    
  
\NormalTok{  sub}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{group\_by}\NormalTok{(YEAR,REGION)}\SpecialCharTok{\%\textgreater{}\%}
        \FunctionTok{summarize}\NormalTok{(}\FunctionTok{sum}\NormalTok{(propA,}\AttributeTok{na.rm=}\NormalTok{T))}
  
  
\NormalTok{  SEBS\_TEMP\_y }\OtherTok{\textless{}{-}}\NormalTok{ sub}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{group\_by}\NormalTok{(YEAR,REGION)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{summarize}\NormalTok{(}
        \AttributeTok{mnTEMP =} \FunctionTok{sum}\NormalTok{(mnTEMP}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{sdTEMP =} \FunctionTok{sum}\NormalTok{(sdTEMP}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{mnSST  =} \FunctionTok{sum}\NormalTok{(mnSST}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{sdSST  =} \FunctionTok{sum}\NormalTok{(sdSST}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{num    =} \FunctionTok{sum}\NormalTok{(num,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{MONTH  =} \FunctionTok{sum}\NormalTok{(MONTH}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{DAY    =} \FunctionTok{sum}\NormalTok{ (DAY}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T))}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{ungroup}\NormalTok{()}
  
  
  \CommentTok{\# now for GOA}
  
\NormalTok{  STRATA\_AREAUSE }\OtherTok{\textless{}{-}}\NormalTok{ STRATA\_AREA}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{filter}\NormalTok{(REGION}\SpecialCharTok{==}\StringTok{"GOA"}\NormalTok{)}
\NormalTok{       STRATA\_AREAUSE }\OtherTok{\textless{}{-}}\NormalTok{ STRATA\_AREAUSE}\SpecialCharTok{\%\textgreater{}\%}
          \FunctionTok{filter}\NormalTok{(YEAR}\SpecialCharTok{==}\DecValTok{1993}\NormalTok{)}\SpecialCharTok{\%\textgreater{}\%}
          \FunctionTok{group\_by}\NormalTok{(REGION,STRATUM)}\SpecialCharTok{\%\textgreater{}\%}
          \FunctionTok{summarize}\NormalTok{(}\AttributeTok{AREA =} \FunctionTok{mean}\NormalTok{(AREA, }\AttributeTok{na.rm=}\NormalTok{T))}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{ungroup}\NormalTok{()}
        
\NormalTok{  sub}\OtherTok{\textless{}{-}}\NormalTok{ TEMP\_yk}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{group\_by}\NormalTok{(YEAR,STRATUM,region)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{filter}\NormalTok{(region }\SpecialCharTok{\%in\%} \FunctionTok{c}\NormalTok{(}\StringTok{"goa"}\NormalTok{))}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{mutate}\NormalTok{(}\AttributeTok{REGION =} \StringTok{"GOA"}\NormalTok{)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{left\_join}\NormalTok{(STRATA\_AREAUSE)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{ungroup}\NormalTok{()}
  
\NormalTok{  sub}\OtherTok{\textless{}{-}}\NormalTok{ sub}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{left\_join}\NormalTok{(}
\NormalTok{      sub}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{group\_by}\NormalTok{(YEAR,STRATUM,REGION)}\SpecialCharTok{\%\textgreater{}\%}
        \FunctionTok{summarize}\NormalTok{(}\AttributeTok{AREA =} \FunctionTok{unique}\NormalTok{(AREA))}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{ungroup}\NormalTok{()}\SpecialCharTok{\%\textgreater{}\%}
        \FunctionTok{group\_by}\NormalTok{(YEAR,REGION)}\SpecialCharTok{\%\textgreater{}\%}
        \FunctionTok{summarize}\NormalTok{(}\AttributeTok{sumAREA=}\FunctionTok{sum}\NormalTok{(AREA,}\AttributeTok{na.rm=}\NormalTok{T)))}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{mutate}\NormalTok{(}\AttributeTok{propA =}\NormalTok{ AREA}\SpecialCharTok{/}\NormalTok{sumAREA)}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{ungroup}\NormalTok{()}
    
  
\NormalTok{  sub}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{group\_by}\NormalTok{(YEAR,REGION)}\SpecialCharTok{\%\textgreater{}\%}
        \FunctionTok{summarize}\NormalTok{(}\FunctionTok{sum}\NormalTok{(propA,}\AttributeTok{na.rm=}\NormalTok{T))}
  
  
\NormalTok{  GOA\_TEMP\_y }\OtherTok{\textless{}{-}}\NormalTok{ sub}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{group\_by}\NormalTok{(YEAR,REGION)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{summarize}\NormalTok{(}
        \AttributeTok{mnTEMP =} \FunctionTok{sum}\NormalTok{(mnTEMP}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{sdTEMP =} \FunctionTok{sum}\NormalTok{(sdTEMP}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{mnSST  =} \FunctionTok{sum}\NormalTok{(mnSST}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{sdSST  =} \FunctionTok{sum}\NormalTok{(sdSST}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{num    =} \FunctionTok{sum}\NormalTok{(num,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{MONTH  =} \FunctionTok{sum}\NormalTok{(MONTH}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T),}
        \AttributeTok{DAY    =} \FunctionTok{sum}\NormalTok{ (DAY}\SpecialCharTok{*}\NormalTok{propA,}\AttributeTok{na.rm=}\NormalTok{T))}\SpecialCharTok{\%\textgreater{}\%}\FunctionTok{ungroup}\NormalTok{()}
  
  
  \ControlFlowTok{if}\NormalTok{(}\SpecialCharTok{!}\FunctionTok{dir.exists}\NormalTok{(}\FunctionTok{file.path}\NormalTok{(data.out,}\StringTok{"Temp"}\NormalTok{)))}
    \FunctionTok{dir.create}\NormalTok{(}\FunctionTok{file.path}\NormalTok{(data.out,}\StringTok{"Temp"}\NormalTok{))}
  \FunctionTok{save}\NormalTok{(GOA\_TEMP\_y,}\AttributeTok{file =} \FunctionTok{file.path}\NormalTok{(data.out,}\StringTok{"Temp/GOA\_TEMP\_y.Rdata"}\NormalTok{))}
  \FunctionTok{save}\NormalTok{(SEBS\_TEMP\_y,}\AttributeTok{file =} \FunctionTok{file.path}\NormalTok{(data.out,}\StringTok{"Temp/SEBS\_TEMP\_y.Rdata"}\NormalTok{))}
  \FunctionTok{save}\NormalTok{(NEBS\_TEMP\_y,}\AttributeTok{file =} \FunctionTok{file.path}\NormalTok{(data.out,}\StringTok{"Temp/NEBS\_TEMP\_y.Rdata"}\NormalTok{))}
  \FunctionTok{save}\NormalTok{(SEBS\_NEBS\_TEMP\_y,}\AttributeTok{file =} \FunctionTok{file.path}\NormalTok{(data.out,}\StringTok{"Temp/SEBS\_NEBS\_TEMP\_y.Rdata"}\NormalTok{))}
  \FunctionTok{save}\NormalTok{(TEMP\_station,}\AttributeTok{file =} \FunctionTok{file.path}\NormalTok{(data.out,}\StringTok{"Temp/TEMP\_station.Rdata"}\NormalTok{))}
  \FunctionTok{save}\NormalTok{(TEMP\_yk,}\AttributeTok{file =} \FunctionTok{file.path}\NormalTok{(data.out,}\StringTok{"Temp/TEMP\_yk.Rdata"}\NormalTok{))}
  
  \FunctionTok{cat}\NormalTok{(}\StringTok{"The cpue files are now saved in the directory "}\NormalTok{,}\FunctionTok{file.path}\NormalTok{(data.out,}\StringTok{"../"}\NormalTok{))}
\CommentTok{\#}
\CommentTok{\# \textasciigrave{}\textasciigrave{}\textasciigrave{}}
\CommentTok{\# }
\CommentTok{\# *The cpue files are now saved in the directory \textasciigrave{}r file.path(data.out,"../")\textasciigrave{}*}
\CommentTok{\# }
\CommentTok{\# \textasciigrave{}\textasciigrave{}\textasciigrave{}\{r viewcpue\_data, echo=TRUE, eval=FALSE\} }
  \CommentTok{\# this uses the password saved in R/password.R}
  \CommentTok{\#  suppressMessages(source("R/make.R"))}
\FunctionTok{load}\NormalTok{(}\FunctionTok{file.path}\NormalTok{(data.out,}\StringTok{"cpue/ebs/ebs.srvy98.pcod.cpue\_data.Rdata"}\NormalTok{))}

\FunctionTok{names}\NormalTok{(cpue\_data)}

\FunctionTok{library}\NormalTok{(dplyr)}

\NormalTok{checkit }\OtherTok{\textless{}{-}}\ControlFlowTok{function}\NormalTok{(x)\{}
   \ControlFlowTok{if}\NormalTok{(}\FunctionTok{round}\NormalTok{(}\FunctionTok{max}\NormalTok{(x ),}\DecValTok{1}\NormalTok{)}\SpecialCharTok{!=}\DecValTok{1}\NormalTok{) \{}
     \FunctionTok{warning}\NormalTok{(}\StringTok{"ERROR! propB \textgreater{} 1 "}\NormalTok{)}
     \FunctionTok{print}\NormalTok{(x)\}}
  
\NormalTok{\}}

  \CommentTok{\#double check the results}
\NormalTok{  cnt\_ByStrataBin }\OtherTok{\textless{}{-}}\NormalTok{ cpue\_data}\SpecialCharTok{$}\NormalTok{propByStrataBin}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{select}\NormalTok{(}\StringTok{"REGION"}\NormalTok{,}\StringTok{"YEAR"}\NormalTok{,}\StringTok{"STRATUM"}\NormalTok{,BIN,BIN\_mm,}
\NormalTok{           SPECIES\_CODE,CN,SN,sp,num,}
           \StringTok{"propB\_ykl"}\NormalTok{,}\StringTok{"propN\_ykl"}\NormalTok{)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{group\_by}\NormalTok{(YEAR,REGION,SN,CN)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{summarise}\NormalTok{(}\AttributeTok{sum\_propB\_ykl=}\FunctionTok{sum}\NormalTok{(propB\_ykl,}\AttributeTok{na.rm=}\NormalTok{T),}
              \AttributeTok{sum\_propN\_ykl=}\FunctionTok{sum}\NormalTok{(propN\_ykl,}\AttributeTok{na.rm=}\NormalTok{T))}
  
\NormalTok{  cnt\_ByStrata }\OtherTok{\textless{}{-}}\NormalTok{ cpue\_data}\SpecialCharTok{$}\NormalTok{propByStrata}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{select}\NormalTok{(}\StringTok{"REGION"}\NormalTok{,}\StringTok{"YEAR"}\NormalTok{,}\StringTok{"STRATUM"}\NormalTok{,}
\NormalTok{           SPECIES\_CODE,CN,SN,sp,num,}
           \StringTok{"propB\_yk"}\NormalTok{,}\StringTok{"propN\_yk"}\NormalTok{)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{group\_by}\NormalTok{(YEAR,REGION,SN,CN)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{summarise}\NormalTok{(}\AttributeTok{sum\_propB\_yk=}\FunctionTok{sum}\NormalTok{(propB\_yk,}\AttributeTok{na.rm=}\NormalTok{T),}
              \AttributeTok{sum\_propN\_yk=}\FunctionTok{sum}\NormalTok{(propN\_yk,}\AttributeTok{na.rm=}\NormalTok{T))}
    
\NormalTok{  cnt\_ByBin }\OtherTok{\textless{}{-}}\NormalTok{ cpue\_data}\SpecialCharTok{$}\NormalTok{propByBin}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{select}\NormalTok{(}\StringTok{"REGION"}\NormalTok{,}\StringTok{"YEAR"}\NormalTok{,BIN,BIN\_mm,num,}
\NormalTok{           SPECIES\_CODE,CN,SN,sp,}
           \StringTok{"propB\_yl"}\NormalTok{,}\StringTok{"propN\_yl"}\NormalTok{)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{group\_by}\NormalTok{(YEAR,REGION,SN,CN)}\SpecialCharTok{\%\textgreater{}\%}
    \FunctionTok{summarise}\NormalTok{(}\AttributeTok{sum\_propB\_yl=}\FunctionTok{sum}\NormalTok{(propB\_yl ,}\AttributeTok{na.rm=}\NormalTok{T),}
              \AttributeTok{sum\_propN\_yl=}\FunctionTok{sum}\NormalTok{(propN\_yl ,}\AttributeTok{na.rm=}\NormalTok{T))}
  
  \FunctionTok{checkit}\NormalTok{(cnt\_ByStrataBin}\SpecialCharTok{$}\NormalTok{sum\_propB\_ykl)}
  \FunctionTok{checkit}\NormalTok{(cnt\_ByStrata}\SpecialCharTok{$}\NormalTok{sum\_propB\_yk)}
  \FunctionTok{checkit}\NormalTok{(cnt\_ByBin}\SpecialCharTok{$}\NormalTok{sum\_propB\_yl)}
  
  
  \CommentTok{\# Step 4 Create Assessment files}
  \ControlFlowTok{if}\NormalTok{(}\DecValTok{1}\SpecialCharTok{==}\DecValTok{10}\NormalTok{)\{}
\NormalTok{    thisYr }\OtherTok{\textless{}{-}} \FunctionTok{format}\NormalTok{(}\FunctionTok{Sys.time}\NormalTok{(), }\StringTok{"\%Y"}\NormalTok{)}
\NormalTok{    today  }\OtherTok{\textless{}{-}} \FunctionTok{format}\NormalTok{(}\FunctionTok{Sys.time}\NormalTok{(), }\StringTok{"\%b \%d, \%Y)}
\StringTok{      source("}\NormalTok{R}\SpecialCharTok{/}\NormalTok{make.R}\StringTok{")}
\StringTok{    \}}
\StringTok{    }
\StringTok{ }
\StringTok{   source("}\NormalTok{R}\SpecialCharTok{/}\NormalTok{sub\_scripts}\SpecialCharTok{/}\NormalTok{make\_assessment\_files.R}\StringTok{")}
\StringTok{  }
\StringTok{\# }
\end{Highlighting}
\end{Shaded}

\hypertarget{step-4-make-some-plots}{%
\subsection{Step 4: make some plots}\label{step-4-make-some-plots}}

\hypertarget{appendix-1-rsetup.rprimary-setup-script}{%
\subsection{\texorpdfstring{Appendix 1: \texttt{R/setup.R}primary setup
script}{Appendix 1: R/setup.Rprimary setup script}}\label{appendix-1-rsetup.rprimary-setup-script}}

\end{document}